Integrated Microfluidic Lectin Barcode Platform for High-Performance Focused Glycomic Profiling

PubMed Central

Shang, Yuqin; Zeng, Yun; Zeng, Yong

2016-01-01

Protein glycosylation is one of the key processes that play essential roles in biological functions and dysfunctions. However, progress in glycomics has considerably lagged behind genomics and proteomics, due in part to the enormous challenges in analysis of glycans. Here we present a new integrated and automated microfluidic lectin barcode platform to substantially improve the performance of lectin array for focused glycomic profiling. The chip design and flow control were optimized to promote the lectin-glycan binding kinetics and speed of lectin microarray. Moreover, we established an on-chip lectin assay which employs a very simple blocking method to effectively suppress the undesired background due to lectin binding of antibodies. Using this technology, we demonstrated focused differential profiling of tissue-specific glycosylation changes of a biomarker, CA125 protein purified from ovarian cancer cell line and different tissues from ovarian cancer patients in a fast, reproducible, and high-throughput fashion. Highly sensitive CA125 detection was also demonstrated with a detection limit much lower than the clinical cutoff value for cancer diagnosis. This microfluidic platform holds the potential to integrate with sample preparation functions to construct a fully integrated “sample-to-answer” microsystem for focused differential glycomic analysis. Thus, our technology should present a powerful tool in support of rapid advance in glycobiology and glyco-biomarker development. PMID:26831207

Analyzing machine noise for real time maintenance

NASA Astrophysics Data System (ADS)

Yamato, Yoji; Fukumoto, Yoshifumi; Kumazaki, Hiroki

2017-02-01

Recently, IoT technologies have been progressed and applications of maintenance area are expected. However, IoT maintenance applications are not spread in Japan yet because of one-off solution of sensing and analyzing for each case, high cost to collect sensing data and insufficient maintenance automation. This paper proposes a maintenance platform which analyzes sound data in edges, analyzes only anomaly data in cloud and orders maintenance automatically to resolve existing technology problems. We also implement a sample application and compare related work.

Determinants of health: a progressive political platform.

PubMed

Terris, M

1994-01-01

This paper is based on the statement in the Ottawa Charter for Health Promotion that "The fundamental conditions and resources for health are peace, shelter, education, food, income, a stable eco-system, sustainable resources, social justice and equity. Improvement in health requires a secure foundation in these basic prerequisites." It attempts to formulate a progressive political platform for a number of these prerequisites, offering a series of recommendations regarding education, employment, income, and housing, and urging that the proposed programs be funded by progressive taxation and major reductions in the military budget.

Cloud computing and validation of expandable in silico livers.

PubMed

Ropella, Glen E P; Hunt, C Anthony

2010-12-03

In Silico Livers (ISLs) are works in progress. They are used to challenge multilevel, multi-attribute, mechanistic hypotheses about the hepatic disposition of xenobiotics coupled with hepatic responses. To enhance ISL-to-liver mappings, we added discrete time metabolism, biliary elimination, and bolus dosing features to a previously validated ISL and initiated re-validated experiments that required scaling experiments to use more simulated lobules than previously, more than could be achieved using the local cluster technology. Rather than dramatically increasing the size of our local cluster we undertook the re-validation experiments using the Amazon EC2 cloud platform. So doing required demonstrating the efficacy of scaling a simulation to use more cluster nodes and assessing the scientific equivalence of local cluster validation experiments with those executed using the cloud platform. The local cluster technology was duplicated in the Amazon EC2 cloud platform. Synthetic modeling protocols were followed to identify a successful parameterization. Experiment sample sizes (number of simulated lobules) on both platforms were 49, 70, 84, and 152 (cloud only). Experimental indistinguishability was demonstrated for ISL outflow profiles of diltiazem using both platforms for experiments consisting of 84 or more samples. The process was analogous to demonstration of results equivalency from two different wet-labs. The results provide additional evidence that disposition simulations using ISLs can cover the behavior space of liver experiments in distinct experimental contexts (there is in silico-to-wet-lab phenotype similarity). The scientific value of experimenting with multiscale biomedical models has been limited to research groups with access to computer clusters. The availability of cloud technology coupled with the evidence of scientific equivalency has lowered the barrier and will greatly facilitate model sharing as well as provide straightforward tools for scaling simulations to encompass greater detail with no extra investment in hardware.

Inhibition of Breast Cancer Progression by Blocking Heterocellular Contact Between Epithelial Cells and Fibroblasts

DTIC Science & Technology

2013-04-01

by employing a microfluidic -based compartmentalized 3D co-culture platform enabling both contact-free and contact-associated co-cultures. 15...SUBJECT TERMS Heterocellular contact between cancer cells and stromal fibroblasts, Microfluidics , 3D 16. SECURITY CLASSIFICATION OF: 17. LIMITATION...and human mammary fibroblasts (HMFs) in breast cancer progression by employing a microfluidic - based compartmentalized 3D co-culture platform

Computer-assisted upper extremity training using interactive biking exercise (iBikE) platform.

PubMed

Jeong, In Cheol; Finkelstein, Joseph

2012-01-01

Upper extremity exercise training has been shown to improve clinical outcomes in different chronic health conditions. Arm-operated bicycles are frequently used to facilitate upper extremity training however effective use of these devices at patient homes is hampered by lack of remote connectivity with clinical rehabilitation team, inability to monitor exercise progress in real time using simple graphical representation, and absence of an alert system which would prevent exertion levels exceeding those approved by the clinical rehabilitation team. We developed an interactive biking exercise (iBikE) platform aimed at addressing these limitations. The platform uses a miniature wireless 3-axis accelerometer mounted on a patient wrist that transmits the cycling acceleration data to a laptop. The laptop screen presents an exercise dashboard to the patient in real time allowing easy graphical visualization of exercise progress and presentation of exercise parameters in relation to prescribed targets. The iBikE platform is programmed to alert the patient when exercise intensity exceeds the levels recommended by the patient care provider. The iBikE platform has been tested in 7 healthy volunteers (age range: 26-50 years) and shown to reliably reflect exercise progress and to generate alerts at pre-setup levels. Implementation of remote connectivity with patient rehabilitation team is warranted for future extension and evaluation efforts.

Fully integrated multiplexed lab-on-a-card assay for enteric pathogens

NASA Astrophysics Data System (ADS)

Weigl, B. H.; Gerdes, J.; Tarr, P.; Yager, P.; Dillman, L.; Peck, R.; Ramachandran, S.; Lemba, M.; Kokoris, M.; Nabavi, M.; Battrell, F.; Hoekstra, D.; Klein, E. J.; Denno, D. M.

2006-01-01

Under this NIH-funded project, we are developing a lab-on-a-card platform to identify enteric bacterial pathogens in patients presenting with acute diarrhea, with special reference to infections that might be encountered in developing countries. Component functions that are integrated on this platform include on-chip immunocapture of live or whole pathogens, multiplexed nucleic acid amplification and on-chip detection, sample processing to support direct use of clinical specimens, and dry reagent storage and handling. All microfluidic functions are contained on the lab card. This new diagnostic test will be able to rapidly identify and differentiate Shigella dysenteriae serotype 1, Shigella toxin-producing Escherichia coli, E. coli 0157, Campylobacter jejuni, and Salmonella and Shigella species. This presentation will report on progress to date on sample and bacteria processing methodologies, identification and validation of capture antibodies and strategy for organism immunocapture, identification and validation of specific polymerase chain reaction (PCR) primer sequences for over 200 clinical isolates of enteric pathogens, and implementation of on-chip nucleic acid extraction for a subset of those pathogens.

Generic HPLC platform for automated enzyme reaction monitoring: Advancing the assay toolbox for transaminases and other PLP-dependent enzymes.

PubMed

Börner, Tim; Grey, Carl; Adlercreutz, Patrick

2016-08-01

Methods for rapid and direct quantification of enzyme kinetics independent of the substrate stand in high demand for both fundamental research and bioprocess development. This study addresses the need for a generic method by developing an automated, standardizable HPLC platform monitoring reaction progress in near real-time. The method was applied to amine transaminase (ATA) catalyzed reactions intensifying process development for chiral amine synthesis. Autosampler-assisted pipetting facilitates integrated mixing and sampling under controlled temperature. Crude enzyme formulations in high and low substrate concentrations can be employed. Sequential, small (1 µL) sample injections and immediate detection after separation permits fast reaction monitoring with excellent sensitivity, accuracy and reproducibility. Due to its modular design, different chromatographic techniques, e.g. reverse phase and size exclusion chromatography (SEC) can be employed. A novel assay for pyridoxal 5'-phosphate-dependent enzymes is presented using SEC for direct monitoring of enzyme-bound and free reaction intermediates. Time-resolved changes of the different cofactor states, e.g. pyridoxal 5'-phosphate, pyridoxamine 5'-phosphate and the internal aldimine were traced in both half reactions. The combination of the automated HPLC platform with SEC offers a method for substrate-independent screening, which renders a missing piece in the assay and screening toolbox for ATAs and other PLP-dependent enzymes. Copyright © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Material platforms for spin-based photonic quantum technologies

NASA Astrophysics Data System (ADS)

Atatüre, Mete; Englund, Dirk; Vamivakas, Nick; Lee, Sang-Yun; Wrachtrup, Joerg

2018-05-01

A central goal in quantum optics and quantum information science is the development of quantum networks to generate entanglement between distributed quantum memories. Experimental progress relies on the quality and efficiency of the light-matter quantum interface connecting the quantum states of photons to internal states of quantum emitters. Quantum emitters in solids, which have properties resembling those of atoms and ions, offer an opportunity for realizing light-matter quantum interfaces in scalable and compact hardware. These quantum emitters require a material platform that enables stable spin and optical properties, as well as a robust manufacturing of quantum photonic circuits. Because no emitter system is yet perfect and different applications may require different properties, several light-matter quantum interfaces are being developed in various platforms. This Review highlights the progress in three leading material platforms: diamond, silicon carbide and atomically thin semiconductors.

A Novel Microfluidic Device for Isolation of Circulating Tumor Cells from Pancreatic Cancer Blood Samples.

PubMed

Varillas, Jose I; Chen, Kangfu; Zhang, Jinling; George, Thomas J; Hugh Fan, Z

2017-01-01

Enumeration of circulating tumor cells (CTCs) can provide valuable prognostic information to guide cancer treatment as well as help monitor disease progression. Analysis of these rare malignant cells has the potential to further our understanding of cancer metastasis by gaining insights into CTC characteristics and properties. Microfluidics presents a unique platform to isolate and study CTCs. In this chapter, we describe the detailed procedures for the fabrication and use of a microfluidic device to detect CTCs from the blood of pancreatic cancer patients.

What does Beijing Plus Five equal?

PubMed

Farmer, A

2000-01-01

In June 2000, the UN will conduct a review of the Beijing+5 (B+5) platform for action to assess the progress women have made since the Fourth World Conference on Women in 1995. This review is regarded by many women's rights advocates as an opportunity to advance the platform. Following the platform's 1995 recommendations, many countries began initiating new laws and policies addressing women's reproductive and sexual health needs as shown in the case of Brazil, France, Egypt, Japan, Cambodia and even the US. However, the B+5 platform is constantly challenged by concerted opposition and delaying tactics of the Vatican and a small group of Islamic and Catholic countries. Despite the progress made by the B+5 platform in the last 5 years, there are still some areas that need to be addressed particularly on the reproductive health needs of adolescents and young adults. Thus, it is hoped that the B+5 review will inspire women to continue to fight for freedom in exercising their reproductive rights.

Floating sample-collection platform with stage-activated automatic water sampler for streams with large variation in stage

USGS Publications Warehouse

Tarte, Stephen R.; Schmidt, A.R.; Sullivan, Daniel J.

1992-01-01

A floating sample-collection platform is described for stream sites where the vertical or horizontal distance between the stream-sampling point and a safe location for the sampler exceed the suction head of the sampler. The platform allows continuous water sampling over the entire storm-runoff hydrogrpah. The platform was developed for a site in southern Illinois.

Deregulation of MiR-34b/Sox2 Predicts Prostate Cancer Progression.

PubMed

Forno, Irene; Ferrero, Stefano; Russo, Maria Veronica; Gazzano, Giacomo; Giangiobbe, Sara; Montanari, Emanuele; Del Nero, Alberto; Rocco, Bernardo; Albo, Giancarlo; Languino, Lucia R; Altieri, Dario C; Vaira, Valentina; Bosari, Silvano

2015-01-01

Most men diagnosed with prostate cancer will have an indolent and curable disease, whereas approximately 15% of these patients will rapidly progress to a castrate-resistant and metastatic stage with high morbidity and mortality. Therefore, the identification of molecular signature(s) that detect men at risk of progressing disease remains a pressing and still unmet need for these patients. Here, we used an integrated discovery platform combining prostate cancer cell lines, a Transgenic Adenocarcinoma of the Mouse Prostate (TRAMP) model and clinically-annotated human tissue samples to identify loss of expression of microRNA-34b as consistently associated with prostate cancer relapse. Mechanistically, this was associated with epigenetics silencing of the MIR34B/C locus and increased DNA copy number loss, selectively in androgen-dependent prostate cancer. In turn, loss of miR-34b resulted in downstream deregulation and overexpression of the "stemness" marker, Sox2. These findings identify loss of miR-34b as a robust biomarker for prostate cancer progression in androgen-sensitive tumors, and anticipate a potential role of progenitor/stem cell signaling in this stage of disease.

Building and Testing a Superconductivity Measurement Platform for a Helium Cryostat

NASA Astrophysics Data System (ADS)

Rose, Heath; Ostrander, Joshua; Wu, Jim; Ramos, Roberto

2013-03-01

Superconductivity experiments using Josephson junctions are an excellent environment to study quantum mechanics and materials science. A standard electrical transport technique uses filtered four wire measurement of these superconducting devices. We report our experience as undergraduates in a liberal arts college in building and testing an experimental platform anchored on the cold-finger of a helium cryostat and designed for performing differential conductance measurements in Josephson junctions. To filter out RF, we design, build and test cryogenic filters using ceramic capacitors and inductors and thermocoax cables. We also use fixed attenuators for thermal anchoring and use miniature connectors to connect wires and coax to a sample box. We report on progress in our diagnostic measurements as well as low-temperature tunneling experiments to probe the structure of the energy gap in both single- and multi-gapped superconductors. We acknowledge the support of the National Science Foundation through NSF Grant DMR-1206561.

Recent progress on gas sensor based on quantum cascade lasers and hollow fiber waveguides

NASA Astrophysics Data System (ADS)

Liu, Ningwu; Sun, Juan; Deng, Hao; Ding, Junya; Zhang, Lei; Li, Jingsong

2017-02-01

Mid-infrared laser spectroscopy provides an ideal platform for trace gas sensing applications. Despite this potential, early MIR sensing applications were limited due to the size of the involved optical components, e.g. light sources and sample cells. A potential solution to this demand is the integration of hollow fiber waveguide with novelty quantum cascade lasers.Recently QCLs had great improvements in power, efficiency and wavelength range, which made the miniaturized platforms for gas sensing maintaining or even enhancing the achievable sensitivity conceivable. So that the miniaturization of QCLs and HWGs can be evolved into a mini sensor, which may be tailored to a variety of real-time and in situ applications ranging from environmental monitoring to workplace safety surveillance. In this article, we introduce QCLs and HWGs, display the applications of HWG based on QCL gas sensing and discuss future strategies for hollow fiber coupled quantum cascade laser gas sensor technology.

Fluidics platform and method for sample preparation and analysis

DOEpatents

Benner, W. Henry; Dzenitis, John M.; Bennet, William J.; Baker, Brian R.

2014-08-19

Herein provided are fluidics platform and method for sample preparation and analysis. The fluidics platform is capable of analyzing DNA from blood samples using amplification assays such as polymerase-chain-reaction assays and loop-mediated-isothermal-amplification assays. The fluidics platform can also be used for other types of assays and analyzes. In some embodiments, a sample in a sealed tube can be inserted directly. The following isolation, detection, and analyzes can be performed without a user's intervention. The disclosed platform may also comprises a sample preparation system with a magnetic actuator, a heater, and an air-drying mechanism, and fluid manipulation processes for extraction, washing, elution, assay assembly, assay detection, and cleaning after reactions and between samples.

Recent Progress in Optical Biosensors Based on Smartphone Platforms

PubMed Central

Geng, Zhaoxin; Zhang, Xiong; Fan, Zhiyuan; Lv, Xiaoqing; Su, Yue; Chen, Hongda

2017-01-01

With a rapid improvement of smartphone hardware and software, especially complementary metal oxide semiconductor (CMOS) cameras, many optical biosensors based on smartphone platforms have been presented, which have pushed the development of the point-of-care testing (POCT). Imaging-based and spectrometry-based detection techniques have been widely explored via different approaches. Combined with the smartphone, imaging-based and spectrometry-based methods are currently used to investigate a wide range of molecular properties in chemical and biological science for biosensing and diagnostics. Imaging techniques based on smartphone-based microscopes are utilized to capture microscale analysts, while spectrometry-based techniques are used to probe reactions or changes of molecules. Here, we critically review the most recent progress in imaging-based and spectrometry-based smartphone-integrated platforms that have been developed for chemical experiments and biological diagnosis. We focus on the analytical performance and the complexity for implementation of the platforms. PMID:29068375

Progress in standoff surface contaminant detector platform

NASA Astrophysics Data System (ADS)

Dupuis, Julia R.; Giblin, Jay; Dixon, John; Hensley, Joel; Mansur, David; Marinelli, William J.

2017-05-01

Progress towards the development of a longwave infrared quantum cascade laser (QLC) based standoff surface contaminant detection platform is presented. The detection platform utilizes reflectance spectroscopy with application to optically thick and thin materials including solid and liquid phase chemical warfare agents, toxic industrial chemicals and materials, and explosives. The platform employs an ensemble of broadband QCLs with a spectrally selective detector to interrogate target surfaces at 10s of m standoff. A version of the Adaptive Cosine Estimator (ACE) featuring class based screening is used for detection and discrimination in high clutter environments. Detection limits approaching 0.1 μg/cm2 are projected through speckle reduction methods enabling detector noise limited performance. The design, build, and validation of a breadboard version of the QCL-based surface contaminant detector are discussed. Functional test results specific to the QCL illuminator are presented with specific emphasis on speckle reduction.

Recent Progress in Optical Biosensors Based on Smartphone Platforms.

PubMed

Geng, Zhaoxin; Zhang, Xiong; Fan, Zhiyuan; Lv, Xiaoqing; Su, Yue; Chen, Hongda

2017-10-25

With a rapid improvement of smartphone hardware and software, especially complementary metal oxide semiconductor (CMOS) cameras, many optical biosensors based on smartphone platforms have been presented, which have pushed the development of the point-of-care testing (POCT). Imaging-based and spectrometry-based detection techniques have been widely explored via different approaches. Combined with the smartphone, imaging-based and spectrometry-based methods are currently used to investigate a wide range of molecular properties in chemical and biological science for biosensing and diagnostics. Imaging techniques based on smartphone-based microscopes are utilized to capture microscale analysts, while spectrometry-based techniques are used to probe reactions or changes of molecules. Here, we critically review the most recent progress in imaging-based and spectrometry-based smartphone-integrated platforms that have been developed for chemical experiments and biological diagnosis. We focus on the analytical performance and the complexity for implementation of the platforms.

Advancing the speed, sensitivity and accuracy of biomolecular detection using multi-length-scale engineering

PubMed Central

Kelley, Shana O.; Mirkin, Chad A.; Walt, David R.; Ismagilov, Rustem F.; Toner, Mehmet; Sargent, Edward H.

2015-01-01

Rapid progress in identifying disease biomarkers has increased the importance of creating high-performance detection technologies. Over the last decade, the design of many detection platforms has focused on either the nano or micro length scale. Here, we review recent strategies that combine nano- and microscale materials and devices to produce large improvements in detection sensitivity, speed and accuracy, allowing previously undetectable biomarkers to be identified in clinical samples. Microsensors that incorporate nanoscale features can now rapidly detect disease-related nucleic acids expressed in patient samples. New microdevices that separate large clinical samples into nanocompartments allow precise quantitation of analytes, and microfluidic systems that utilize nanoscale binding events can detect rare cancer cells in the bloodstream more accurately than before. These advances will lead to faster and more reliable clinical diagnostic devices. PMID:25466541

Advancing the speed, sensitivity and accuracy of biomolecular detection using multi-length-scale engineering

NASA Astrophysics Data System (ADS)

Kelley, Shana O.; Mirkin, Chad A.; Walt, David R.; Ismagilov, Rustem F.; Toner, Mehmet; Sargent, Edward H.

2014-12-01

Rapid progress in identifying disease biomarkers has increased the importance of creating high-performance detection technologies. Over the last decade, the design of many detection platforms has focused on either the nano or micro length scale. Here, we review recent strategies that combine nano- and microscale materials and devices to produce large improvements in detection sensitivity, speed and accuracy, allowing previously undetectable biomarkers to be identified in clinical samples. Microsensors that incorporate nanoscale features can now rapidly detect disease-related nucleic acids expressed in patient samples. New microdevices that separate large clinical samples into nanocompartments allow precise quantitation of analytes, and microfluidic systems that utilize nanoscale binding events can detect rare cancer cells in the bloodstream more accurately than before. These advances will lead to faster and more reliable clinical diagnostic devices.

SERS diagnostic platforms, methods and systems microarrays, biosensors and biochips

DOEpatents

Vo-Dinh, Tuan [Knoxville, TN

2007-09-11

A Raman integrated sensor system for the detection of targets including biotargets includes at least one sampling platform, at least one receptor probe disposed on the sampling platform, and an integrated circuit detector system communicably connected to the receptor. The sampling platform is preferably a Raman active surface-enhanced scattering (SERS) platform, wherein the Raman sensor is a SERS sensor. The receptors can include at least one protein receptor and at least one nucleic acid receptor.

The DIAN-TU Next Generation Alzheimer’s prevention trial: adaptive design and disease progression model

PubMed Central

Bateman, Randall J.; Benzinger, Tammie L.; Berry, Scott; Clifford, David B.; Duggan, Cynthia; Fagan, Anne M.; Fanning, Kathleen; Farlow, Martin R.; Hassenstab, Jason; McDade, Eric M.; Mills, Susan; Paumier, Katrina; Quintana, Melanie; Salloway, Stephen P.; Santacruz, Anna; Schneider, Lon S.; Wang, Guoqiao; Xiong, Chengjie

2016-01-01

INTRODUCTION The Dominantly Inherited Alzheimer Network Trials Unit (DIAN-TU) trial is an adaptive platform trial testing multiple drugs to slow or prevent the progression of Alzheimer’s disease in autosomal dominant Alzheimer’s disease (ADAD) families. With completion of enrollment of the first two drug arms, the DIAN-TU now plans to add new drugs to the platform, designated as the Next Generation Prevention Trial (NexGen). METHODS In collaboration with ADAD families, philanthropic organizations, academic leaders, the DIAN-TU Pharma Consortium, the NIH, and regulatory colleagues, the DIAN-TU developed innovative clinical study designs for the DIAN-TU NexGen trial. RESULTS Our expanded trials toolbox consists of a Disease Progression Model for ADAD, primary endpoint DIAN-TU cognitive performance composite, biomarker development, self-administered cognitive assessments, adaptive dose adjustments, and blinded data collection through the last participant completion. CONCLUSION These steps represent elements to improve efficacy of the adaptive platform trial and a continued effort to optimize prevention and treatment trials in ADAD. PMID:27583651

Carbonate Platform Development and Stromatolite Morphogenesis: Constraints on Environmental and Biological Evolution

NASA Technical Reports Server (NTRS)

Grotzinger, John P.

2003-01-01

Work has been completed on the digital mapping of a terminal Proterozoic reef complex in Namibia. This complex formed an isolated carbonate platform developed downdip on a carbonate ramp of the Nama Group. The stratigraphic evolution of the platform was digitally reconstructed from an extensive dataset that was compiled by using digital surveying technologies. The platform comprises three accommodation cycles in which each subsequent cycle experienced progressively greater influence of a long-term accommodation increase. Aggradation and progradation during the first cycle resulted in a flat, uniform, sheet-like platform. The coarsening and shallowing-upward sequence representing the first cycle is dominated by columnar stromatolitic thrombolites and massive dolostones with interbedded mudstone-grainstone at the base of the sequence grading into cross-bedded dolostones. The second cycle features aggradation, formation of a distinct margin containing thrombolite mounds and domes, and the development of a bucket geometry. Columnar stromatolitic thrombolites dominate the platform interior. The final stage of platform development shows a deepening trend with initial aggradation and formation of well-bedded, thin deposits in the interior and mound development at the margins. While the interior drowned, the platform margin kept up with rising sea level and a complex pinnacle reef formed containing fused and coalesced thrombolite mounds flanked by bioclastic grainstones (containing Cloudina and Namacalathus fossils) and collapse breccias. A set of isolated large thrombolite mounds flanked by shales indicate the final stage of the carbonate platform. During a progressive increase in accommodation, a flat-topped isolated carbonate platform becomes aerially less extensive by either backstepping or formation of smaller pinnacles or a combination of both. The overall geometric evolution of the studied platform from flat-topped to bucket with elevated margins is recorded in many Proterozoic and Phanerozoic isolated carbonate platforms with similar dimensions. The terminal Proterozoic, microbial-dominated, isolated carbonate platform of this study clearly illustrates that the answer to accommodation changes was already familiar among carbonate platforms before the dawn of metazoan-dominated platforms.

Cloud computing and validation of expandable in silico livers

PubMed Central

2010-01-01

Background In Silico Livers (ISLs) are works in progress. They are used to challenge multilevel, multi-attribute, mechanistic hypotheses about the hepatic disposition of xenobiotics coupled with hepatic responses. To enhance ISL-to-liver mappings, we added discrete time metabolism, biliary elimination, and bolus dosing features to a previously validated ISL and initiated re-validated experiments that required scaling experiments to use more simulated lobules than previously, more than could be achieved using the local cluster technology. Rather than dramatically increasing the size of our local cluster we undertook the re-validation experiments using the Amazon EC2 cloud platform. So doing required demonstrating the efficacy of scaling a simulation to use more cluster nodes and assessing the scientific equivalence of local cluster validation experiments with those executed using the cloud platform. Results The local cluster technology was duplicated in the Amazon EC2 cloud platform. Synthetic modeling protocols were followed to identify a successful parameterization. Experiment sample sizes (number of simulated lobules) on both platforms were 49, 70, 84, and 152 (cloud only). Experimental indistinguishability was demonstrated for ISL outflow profiles of diltiazem using both platforms for experiments consisting of 84 or more samples. The process was analogous to demonstration of results equivalency from two different wet-labs. Conclusions The results provide additional evidence that disposition simulations using ISLs can cover the behavior space of liver experiments in distinct experimental contexts (there is in silico-to-wet-lab phenotype similarity). The scientific value of experimenting with multiscale biomedical models has been limited to research groups with access to computer clusters. The availability of cloud technology coupled with the evidence of scientific equivalency has lowered the barrier and will greatly facilitate model sharing as well as provide straightforward tools for scaling simulations to encompass greater detail with no extra investment in hardware. PMID:21129207

Molecularly imprinted polymers for sample preparation and biosensing in food analysis: Progress and perspectives.

PubMed

Ashley, Jon; Shahbazi, Mohammad-Ali; Kant, Krishna; Chidambara, Vinayaka Aaydha; Wolff, Anders; Bang, Dang Duong; Sun, Yi

2017-05-15

Molecularly imprinted polymers (MIPs) are biomimetics which can selectively bind to analytes of interest. One of the most interesting areas where MIPs have shown the biggest potential is food analysis. MIPs have found use as sorbents in sample preparation attributed to the high selectivity and high loading capacity. MIPs have been intensively employed in classical solid-phase extraction and solid-phase microextraction. More recently, MIPs have been combined with magnetic bead extraction, which greatly simplifies sample handling procedures. Studies have consistently shown that MIPs can effectively minimize complex food matrix effects, and improve recoveries and detection limits. In addition to sample preparation, MIPs have also been viewed as promising alternatives to bio-receptors due to the inherent molecular recognition abilities and the high stability in harsh chemical and physical conditions. MIPs have been utilized as receptors in biosensing platforms such as electrochemical, optical and mass biosensors to detect various analytes in food. In this review, we will discuss the current state-of-the-art of MIP synthesis and applications in the context of food analysis. We will highlight the imprinting methods which are applicable for imprinting food templates, summarize the recent progress in using MIPs for preparing and analysing food samples, and discuss the current limitations in the commercialisation of MIPs technology. Finally, future perspectives will be given. Copyright © 2017 Elsevier B.V. All rights reserved.

A New Size-based Platform for Circulating Tumor Cell Detection in Colorectal Cancer Patients.

PubMed

Oh, Bo Young; Kim, Jhingook; Lee, Woo Yong; Kim, Hee Cheol

2017-09-01

Circulating tumor cells (CTCs) might play a significant role in cancer progression and metastasis. However, the ability to detect CTCs is limited, especially in cells undergoing epithelial-mesenchymal transition. In this study, we evaluated a new size-based CTC detection platform and its clinical efficacy in colorectal cancer. Blood samples were obtained from 76 patients with colorectal cancer and 20 healthy control subjects for CTC analysis. CTCs were enriched using a high-density microporous chip filter and were detected using a 4-color staining protocol including 4',6-diamidino-2-phenylindole (DAPI) for nucleated cells, CD45 monoclonal antibody (mAb) as a leukocyte marker, and epithelial cell adhesion molecule (EpCAM) mAb or cytokeratin (CK) mAb as an epithelial cell marker. CTC positivity was defined as DAPI-positive (DAPI + )/CD45 - /EpCAM + or CK + cells and clinical outcomes of patients were analyzed according to CTC counts. CTCs were detected in 50 patients using this size-based filtration platform. CTC + patients were more frequently identified with a high level of carcinoembryonic antigen and advanced stage cancer (P = .038 and P = .017, respectively). CTC counts for patients with stage IV cancer (12.47 ± 24.00) were significantly higher than those for patients with cancers that were stage I to III (2.84 ± 5.29; P = .005) and healthy control subjects (0.25 ± 0.55; P < .001). In addition, progression-free survival tended to be lower in CTC + patients compared with CTC - patients (P = .092). In patients with stage I to III cancer, recurrence occurred only in CTC + patients. CTC positivity was found to correlate with clinical features of colorectal cancer patients. Our results suggest that this new size-based platform has potential for determining prognosis and therapeutic response in colorectal cancer patients. Copyright © 2017 Elsevier Inc. All rights reserved.

Space transportation, satellite services, and space platforms

NASA Technical Reports Server (NTRS)

Disher, J. H.

1979-01-01

The paper takes a preview of the progressive development of vehicles for space transportation, satellite services, and orbital platforms. A low-thrust upper stage of either the ion engine or chemical type will be developed to transport large spacecraft and space platforms to and from GEO. The multimission spacecraft, space telescope, and other scientific platforms will require orbital serves going beyond that provided by the Shuttle's remote manipulator system, and plans call for extravehicular activity tools, improved remote manipulators, and a remote manned work station (the cherry picker).

Affinity proteomics within rare diseases: a BIO-NMD study for blood biomarkers of muscular dystrophies

PubMed Central

Ayoglu, Burcu; Chaouch, Amina; Lochmüller, Hanns; Politano, Luisa; Bertini, Enrico; Spitali, Pietro; Hiller, Monika; Niks, Eric H; Gualandi, Francesca; Pontén, Fredrik; Bushby, Kate; Aartsma-Rus, Annemieke; Schwartz, Elena; Le Priol, Yannick; Straub, Volker; Uhlén, Mathias; Cirak, Sebahattin; ‘t Hoen, Peter A C; Muntoni, Francesco; Ferlini, Alessandra; Schwenk, Jochen M; Nilsson, Peter; Al-Khalili Szigyarto, Cristina

2014-01-01

Despite the recent progress in the broad-scaled analysis of proteins in body fluids, there is still a lack in protein profiling approaches for biomarkers of rare diseases. Scarcity of samples is the main obstacle hindering attempts to apply discovery driven protein profiling in rare diseases. We addressed this challenge by combining samples collected within the BIO-NMD consortium from four geographically dispersed clinical sites to identify protein markers associated with muscular dystrophy using an antibody bead array platform with 384 antibodies. Based on concordance in statistical significance and confirmatory results obtained from analysis of both serum and plasma, we identified eleven proteins associated with muscular dystrophy, among which four proteins were elevated in blood from muscular dystrophy patients: carbonic anhydrase III (CA3) and myosin light chain 3 (MYL3), both specifically expressed in slow-twitch muscle fibers and mitochondrial malate dehydrogenase 2 (MDH2) and electron transfer flavoprotein A (ETFA). Using age-matched sub-cohorts, 9 protein profiles correlating with disease progression and severity were identified, which hold promise for the development of new clinical tools for management of dystrophinopathies. PMID:24920607

Automation Improvements for Synchrotron Based Small Angle Scattering Using an Inexpensive Robotics Platform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quintana, John P.

This paper reports on the progress toward creating semi-autonomous motion control platforms for beamline applications using the iRobot Create registered platform. The goal is to create beamline research instrumentation where the motion paths are based on the local environment rather than position commanded from a control system, have low integration costs and also be scalable and easily maintainable.

A new European small platform: Proteus and prospected optical application missions

NASA Astrophysics Data System (ADS)

Dubois, J.-B.; Paoli, F.

2018-04-01

Progress in technology in recent years and new industrial approaches now make it possible to design valuable optical missions using a small-class satellite, like the PROTEUS multi mission platform. Some future space optical missions using existing or planned instruments, combined with the PROTEUS platform, have been assessed by AEROSPATIALE / SPACE and DEFENSE and/or the CNES (French National Space Agency).

Cosmogenic nuclides application on French Mediterranean shore platform development

NASA Astrophysics Data System (ADS)

Giuliano, Jérémy; Lebourg, Thomas; Godard, Vincent; Dewez, Thomas; Braucher, Régis; Bourlès, Didier; Marçot, Nathalie

2014-05-01

Rocky shorelines are among the most common elements of the world's littoral zone, and the potential effects of rising sea level on the ever increasing populations require a better understanding of their dynamics. The sinuosity and heterogeneity of the shoreline morphology at large and intermediate wavelengths (1-100 km) results from their constant evolution under the combined influence of marine and continental forcings. This macro-scale organization is the expression of the action of elementary erosion processes acting at shorter wavelengths (<1 km) which lead to the development of shore platforms by landward retreat of cliff edges. Modern analytical techniques (laser-scaning, micro-erosion meters, aerial surveys) constitute appropriate methods to identify and quantify processes of cliff retreat to 1-100 yrs time-scales. But over this time frame, shore platform development appears imperceptible. Precise knowledge of long-term erosion rates are needed to understand rocky shore evolution, and develop quantitative modeling of platform development. Rocky coasts constitute a Quaternary sea level evolution archive that is partly preserved and progressively destroyed. One major challenges is to determine the degree to which coast morphologies are (i) contemporary, (ii) or ancient features inherited, (iii) or partly inherited from Quaternary interglacial stages. In order to fill the lack of long term coast morphodynamic data, we use cosmogenic nuclides (36Cl) to study abrasion surfaces carved in carbonates lithologies along the French Mediterranean coast, in a microtidal environment (Côte Bleue, West of Marseille). 36Cl concentration heritage influences strongly our interpretations in terms of age and denudation of the surfaces. We propose to constrain heritage in sampling oldest relic marine surfaces at 10m of altitude, and along recent cliff scarp. 36Cl concentrations show that the lowest platforms near sea level are contemporary and the highest ones (8-14 m above sea level) marine surfaces are associated to MIS 5.5. A total of 50 samples allows to investigate the variations through time in relative sea level, climate and tectonic activity. Key words: cosmogenic, shore platform, rocky coast, Mediterranean, erosion rate.

A review of digital microfluidics as portable platforms for lab-on a-chip applications.

PubMed

Samiei, Ehsan; Tabrizian, Maryam; Hoorfar, Mina

2016-07-07

Following the development of microfluidic systems, there has been a high tendency towards developing lab-on-a-chip devices for biochemical applications. A great deal of effort has been devoted to improve and advance these devices with the goal of performing complete sets of biochemical assays on the device and possibly developing portable platforms for point of care applications. Among the different microfluidic systems used for such a purpose, digital microfluidics (DMF) shows high flexibility and capability of performing multiplex and parallel biochemical operations, and hence, has been considered as a suitable candidate for lab-on-a-chip applications. In this review, we discuss the most recent advances in the DMF platforms, and evaluate the feasibility of developing multifunctional packages for performing complete sets of processes of biochemical assays, particularly for point-of-care applications. The progress in the development of DMF systems is reviewed from eight different aspects, including device fabrication, basic fluidic operations, automation, manipulation of biological samples, advanced operations, detection, biological applications, and finally, packaging and portability of the DMF devices. Success in developing the lab-on-a-chip DMF devices will be concluded based on the advances achieved in each of these aspects.

Latent feature decompositions for integrative analysis of multi-platform genomic data

PubMed Central

Gregory, Karl B.; Momin, Amin A.; Coombes, Kevin R.; Baladandayuthapani, Veerabhadran

2015-01-01

Increased availability of multi-platform genomics data on matched samples has sparked research efforts to discover how diverse molecular features interact both within and between platforms. In addition, simultaneous measurements of genetic and epigenetic characteristics illuminate the roles their complex relationships play in disease progression and outcomes. However, integrative methods for diverse genomics data are faced with the challenges of ultra-high dimensionality and the existence of complex interactions both within and between platforms. We propose a novel modeling framework for integrative analysis based on decompositions of the large number of platform-specific features into a smaller number of latent features. Subsequently we build a predictive model for clinical outcomes accounting for both within- and between-platform interactions based on Bayesian model averaging procedures. Principal components, partial least squares and non-negative matrix factorization as well as sparse counterparts of each are used to define the latent features, and the performance of these decompositions is compared both on real and simulated data. The latent feature interactions are shown to preserve interactions between the original features and not only aid prediction but also allow explicit selection of outcome-related features. The methods are motivated by and applied to, a glioblastoma multiforme dataset from The Cancer Genome Atlas to predict patient survival times integrating gene expression, microRNA, copy number and methylation data. For the glioblastoma data, we find a high concordance between our selected prognostic genes and genes with known associations with glioblastoma. In addition, our model discovers several relevant cross-platform interactions such as copy number variation associated gene dosing and epigenetic regulation through promoter methylation. On simulated data, we show that our proposed method successfully incorporates interactions within and between genomic platforms to aid accurate prediction and variable selection. Our methods perform best when principal components are used to define the latent features. PMID:26146492

Suspension arrays based on nanoparticle-encoded microspheres for high-throughput multiplexed detection

PubMed Central

Leng, Yuankui

2017-01-01

Spectrometrically or optically encoded microsphere based suspension array technology (SAT) is applicable to the high-throughput, simultaneous detection of multiple analytes within a small, single sample volume. Thanks to the rapid development of nanotechnology, tremendous progress has been made in the multiplexed detecting capability, sensitivity, and photostability of suspension arrays. In this review, we first focus on the current stock of nanoparticle-based barcodes as well as the manufacturing technologies required for their production. We then move on to discuss all existing barcode-based bioanalysis patterns, including the various labels used in suspension arrays, label-free platforms, signal amplification methods, and fluorescence resonance energy transfer (FRET)-based platforms. We then introduce automatic platforms for suspension arrays that use superparamagnetic nanoparticle-based microspheres. Finally, we summarize the current challenges and their proposed solutions, which are centered on improving encoding capacities, alternative probe possibilities, nonspecificity suppression, directional immobilization, and “point of care” platforms. Throughout this review, we aim to provide a comprehensive guide for the design of suspension arrays, with the goal of improving their performance in areas such as multiplexing capacity, throughput, sensitivity, and cost effectiveness. We hope that our summary on the state-of-the-art development of these arrays, our commentary on future challenges, and some proposed avenues for further advances will help drive the development of suspension array technology and its related fields. PMID:26021602

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Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-23

...; 30-day Comment Request: National Cancer Institute (NCI) Cancer Nanotechnology Platform Partnership...: Dorothy Farrell, Center for Strategic Scientific Initiatives, Office of Cancer Nanotechnology Research... Cancer Institute (NCI) Alliance for Nanotechnology in Cancer Platform Partnership Scientific Progress...

MEASUREMENTS OF NON-METHANE VOLATILE ORGANIC COMPOUNDS IN THE LOWER TROPOSPHERE FROM TETHERED BALLOON AND KITE SAMPLING PLATFORMS BY INTERNAL STANDARD CALIBRATION USING AMBIENT CFC REFERENCE COMPOUNDS

EPA Science Inventory

A new analytical approach for the sampling and analysis of volatile organic compounds (VOCs) from sampling platforms used in the vertical profiling of the lower troposphere, such as kites, balloons, and remotely piloted vehicles will be developed. These sampling platforms a...

Small unmanned aircraft systems for remote sensing and Earth science research

NASA Astrophysics Data System (ADS)

Hugenholtz, Chris H.; Moorman, Brian J.; Riddell, Kevin; Whitehead, Ken

2012-06-01

To understand and predict Earth-surface dynamics, scientists often rely on access to the latest remote sensing data. Over the past several decades, considerable progress has been made in the development of specialized Earth observation sensors for measuring a wide range of processes and features. Comparatively little progress has been made, however, in the development of new platforms upon which these sensors can be deployed. Conventional platforms are still almost exclusively restricted to piloted aircraft and satellites. For many Earth science research questions and applications these platforms do not yet have the resolution or operational flexibility to provide answers affordably. The most effective remote sensing data match the spatiotemporal scale of the process or feature of interest. An emerging technology comprising unmanned aircraft systems (UAS), also known as unmanned aerial vehicles (UAV), is poised to offer a viable alternative to conventional platforms for acquiring high-resolution remote sensing data with increased operational flexibility, lower cost, and greater versatility (Figure 1).

Recommendations for Benchmarking Preclinical Studies of Nanomedicines.

PubMed

Dawidczyk, Charlene M; Russell, Luisa M; Searson, Peter C

2015-10-01

Nanoparticle-based delivery systems provide new opportunities to overcome the limitations associated with traditional small-molecule drug therapy for cancer and to achieve both therapeutic and diagnostic functions in the same platform. Preclinical trials are generally designed to assess therapeutic potential and not to optimize the design of the delivery platform. Consequently, progress in developing design rules for cancer nanomedicines has been slow, hindering progress in the field. Despite the large number of preclinical trials, several factors restrict comparison and benchmarking of different platforms, including variability in experimental design, reporting of results, and the lack of quantitative data. To solve this problem, we review the variables involved in the design of preclinical trials and propose a protocol for benchmarking that we recommend be included in in vivo preclinical studies of drug-delivery platforms for cancer therapy. This strategy will contribute to building the scientific knowledge base that enables development of design rules and accelerates the translation of new technologies. ©2015 American Association for Cancer Research.

Perspective: Recommendations for benchmarking pre-clinical studies of nanomedicines

PubMed Central

Dawidczyk, Charlene M.; Russell, Luisa M.; Searson, Peter C.

2015-01-01

Nanoparticle-based delivery systems provide new opportunities to overcome the limitations associated with traditional small molecule drug therapy for cancer, and to achieve both therapeutic and diagnostic functions in the same platform. Pre-clinical trials are generally designed to assess therapeutic potential and not to optimize the design of the delivery platform. Consequently, progress in developing design rules for cancer nanomedicines has been slow, hindering progress in the field. Despite the large number of pre-clinical trials, several factors restrict comparison and benchmarking of different platforms, including variability in experimental design, reporting of results, and the lack of quantitative data. To solve this problem, we review the variables involved in the design of pre-clinical trials and propose a protocol for benchmarking that we recommend be included in in vivo pre-clinical studies of drug delivery platforms for cancer therapy. This strategy will contribute to building the scientific knowledge base that enables development of design rules and accelerates the translation of new technologies. PMID:26249177

Assessing the Quality, Feasibility, and Efficacy of Electronic Patient Platforms Designed to Support Adolescents and Young Adults With Cancer: A Systematic Review Protocol

PubMed Central

McCann, Lisa

2017-01-01

Background A range of innovative websites, mobile technologies, eHealth and mHealth platforms have emerged to support adolescents and young adults (AYAs) with cancer. Previous reviews have identified these various applications and solutions, but no review has summarized the quality, feasibility, and efficacy of existing patient platforms (inclusive of websites, mobile technologies, mHealth and eHealth platforms) developed specifically for young people with cancer. Objective This paper describes the design of a protocol to conduct a review of published studies or reports which describe or report on an existing platform designed specifically for AYAs who have had a cancer diagnosis. Methods A search string was developed using a variety of key words and Medical Subject Heading and applied to bibliographic databases. General data (sample characteristics, patient platform development, design and, if applicable, pilot testing outcomes) will be extracted from reports and studies. Drawing on a previously developed coding schematic, the identified patient platforms will be coded for mode of delivery into (1) automated functions, (2) communicative functions, and (3) use of supplementary modes. An adapted version of the Mobile App Rating Scale (MARS) will be used to assess the of quality of each identified patient platform. The methodological quality of included studies will be assessed using the Quality Assessment Criteria for Evaluating Primary Research Papers from a Variety of Fields (QualSyst). Both authors will independently screen eligible studies for final inclusion and will both be responsible for data extraction and appraisal. Data will be synthesized narratively to provide an overview of identified patient platforms. Results The review began in October 2016 and is currently in progress. The review paper will be submitted for peer-review and publication in the summer of 2017. Conclusions This review will be unique in its focus on assessing, where possible, the quality and efficacy of patient platforms for adolescents and young adults diagnosed with cancer. Results generated from this review will provide an invaluable insight into the utility of modern technology in supporting young people with cancer. PMID:28096067

Deregulation of MiR-34b/Sox2 Predicts Prostate Cancer Progression

PubMed Central

Russo, Maria Veronica; Gazzano, Giacomo; Giangiobbe, Sara; Montanari, Emanuele; Del Nero, Alberto; Rocco, Bernardo; Albo, Giancarlo; Languino, Lucia R.; Altieri, Dario C.; Vaira, Valentina; Bosari, Silvano

2015-01-01

Most men diagnosed with prostate cancer will have an indolent and curable disease, whereas approximately 15% of these patients will rapidly progress to a castrate-resistant and metastatic stage with high morbidity and mortality. Therefore, the identification of molecular signature(s) that detect men at risk of progressing disease remains a pressing and still unmet need for these patients. Here, we used an integrated discovery platform combining prostate cancer cell lines, a Transgenic Adenocarcinoma of the Mouse Prostate (TRAMP) model and clinically-annotated human tissue samples to identify loss of expression of microRNA-34b as consistently associated with prostate cancer relapse. Mechanistically, this was associated with epigenetics silencing of the MIR34B/C locus and increased DNA copy number loss, selectively in androgen-dependent prostate cancer. In turn, loss of miR-34b resulted in downstream deregulation and overexpression of the “stemness” marker, Sox2. These findings identify loss of miR-34b as a robust biomarker for prostate cancer progression in androgen-sensitive tumors, and anticipate a potential role of progenitor/stem cell signaling in this stage of disease. PMID:26107383

Electrochemical imaging of cells and tissues

PubMed Central

Lin, Tzu-En; Rapino, Stefania; Girault, Hubert H.

2018-01-01

The technological and experimental progress in electrochemical imaging of biological specimens is discussed with a view on potential applications for skin cancer diagnostics, reproductive medicine and microbial testing. The electrochemical analysis of single cell activity inside cell cultures, 3D cellular aggregates and microtissues is based on the selective detection of electroactive species involved in biological functions. Electrochemical imaging strategies, based on nano/micrometric probes scanning over the sample and sensor array chips, respectively, can be made sensitive and selective without being affected by optical interference as many other microscopy techniques. The recent developments in microfabrication, electronics and cell culturing/tissue engineering have evolved in affordable and fast-sampling electrochemical imaging platforms. We believe that the topics discussed herein demonstrate the applicability of electrochemical imaging devices in many areas related to cellular functions. PMID:29899947

Societal costs of multiple sclerosis in Ireland.

PubMed

Carney, Peter; O'Boyle, Derek; Larkin, Aidan; McGuigan, Christopher; O'Rourke, Killian

2018-05-01

This paper evaluates the impact of multiple sclerosis (MS) in Ireland, and estimates the associated direct, indirect, and intangible costs to society based on a large nationally representative sample. A questionnaire was developed to capture the demographics, disease characteristics, healthcare use, informal care, employment, and wellbeing. Referencing international studies, standardized survey instruments were included (e.g. CSRI, MFIS-5, EQ-5D) or adapted (EDSS) for inclusion in an online survey platform. Recruitment was directed at people with MS via the MS Society mailing list and social media platforms, as well as in traditional media. The economic costing was primarily conducted using a 'bottom-up' methodology, and national estimates were achieved using 'prevalence-based' extrapolation. A total of 594 people completed the survey in full. The sample had geographic, disease, and demographic characteristics indicating good representativeness. At an individual level, average societal cost was estimated at €47,683; the average annual costs for those with mild, moderate, and severe MS were calculated as €34,942, €57,857, and €100,554, respectively. For a total Irish MS population of 9,000, the total societal costs of MS amounted to €429m. Direct costs accounted for just 30% of the total societal costs, indirect costs amounted to 50% of the total, and intangible or QoL costs represented 20%. The societal cost associated with a relapse in the sample is estimated as €2,438. The findings highlight that up to 70% of the total costs associated with MS are not routinely counted. These "hidden" costs are higher in Ireland than the rest of Europe, due in part to significantly lower levels of workforce participation, a higher likelihood of permanent workforce withdrawal, and higher levels of informal care needs. The relationship between disease progression and costs emphasize the societal importance of managing and slowing the progression of the illness.

Text Stream Trend Analysis using Multiscale Visual Analytics with Applications to Social Media Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steed, Chad A; Beaver, Justin M; BogenII, Paul L.

In this paper, we introduce a new visual analytics system, called Matisse, that allows exploration of global trends in textual information streams with specific application to social media platforms. Despite the potential for real-time situational awareness using these services, interactive analysis of such semi-structured textual information is a challenge due to the high-throughput and high-velocity properties. Matisse addresses these challenges through the following contributions: (1) robust stream data management, (2) automated sen- timent/emotion analytics, (3) inferential temporal, geospatial, and term-frequency visualizations, and (4) a flexible drill-down interaction scheme that progresses from macroscale to microscale views. In addition to describing thesemore » contributions, our work-in-progress paper concludes with a practical case study focused on the analysis of Twitter 1% sample stream information captured during the week of the Boston Marathon bombings.« less

A novel nano-immunoassay method for quantification of proteins from CD138-purified myeloma cells: biological and clinical utility

PubMed Central

Misiewicz-Krzeminska, Irena; Corchete, Luis Antonio; Rojas, Elizabeta A.; Martínez-López, Joaquín; García-Sanz, Ramón; Oriol, Albert; Bladé, Joan; Lahuerta, Juan-José; Miguel, Jesús San; Mateos, María-Victoria; Gutiérrez, Norma C.

2018-01-01

Protein analysis in bone marrow samples from patients with multiple myeloma has been limited by the low concentration of proteins obtained after CD138+ cell selection. A novel approach based on capillary nano-immunoassay could make it possible to quantify dozens of proteins from each myeloma sample in an automated manner. Here we present a method for the accurate and robust quantification of the expression of multiple proteins extracted from CD138-purified multiple myeloma samples frozen in RLT Plus buffer, which is commonly used for nucleic acid preservation and isolation. Additionally, the biological and clinical value of this analysis for a panel of 12 proteins essential to the pathogenesis of multiple myeloma was evaluated in 63 patients with newly diagnosed multiple myeloma. The analysis of the prognostic impact of CRBN/Cereblon and IKZF1/Ikaros mRNA/protein showed that only the protein levels were able to predict progression-free survival of patients; mRNA levels were not associated with prognosis. Interestingly, high levels of Cereblon and Ikaros proteins were associated with longer progression-free survival only in patients who received immunomodulatory drugs and not in those treated with other drugs. In conclusion, the capillary nano-immunoassay platform provides a novel opportunity for automated quantification of the expression of more than 20 proteins in CD138+ primary multiple myeloma samples. PMID:29545347

A novel nano-immunoassay method for quantification of proteins from CD138-purified myeloma cells: biological and clinical utility.

PubMed

Misiewicz-Krzeminska, Irena; Corchete, Luis Antonio; Rojas, Elizabeta A; Martínez-López, Joaquín; García-Sanz, Ramón; Oriol, Albert; Bladé, Joan; Lahuerta, Juan-José; Miguel, Jesús San; Mateos, María-Victoria; Gutiérrez, Norma C

2018-05-01

Protein analysis in bone marrow samples from patients with multiple myeloma has been limited by the low concentration of proteins obtained after CD138 + cell selection. A novel approach based on capillary nano-immunoassay could make it possible to quantify dozens of proteins from each myeloma sample in an automated manner. Here we present a method for the accurate and robust quantification of the expression of multiple proteins extracted from CD138-purified multiple myeloma samples frozen in RLT Plus buffer, which is commonly used for nucleic acid preservation and isolation. Additionally, the biological and clinical value of this analysis for a panel of 12 proteins essential to the pathogenesis of multiple myeloma was evaluated in 63 patients with newly diagnosed multiple myeloma. The analysis of the prognostic impact of CRBN /Cereblon and IKZF1 /Ikaros mRNA/protein showed that only the protein levels were able to predict progression-free survival of patients; mRNA levels were not associated with prognosis. Interestingly, high levels of Cereblon and Ikaros proteins were associated with longer progression-free survival only in patients who received immunomodulatory drugs and not in those treated with other drugs. In conclusion, the capillary nano-immunoassay platform provides a novel opportunity for automated quantification of the expression of more than 20 proteins in CD138 + primary multiple myeloma samples. Copyright © 2018 Ferrata Storti Foundation.

The DIAN-TU Next Generation Alzheimer's prevention trial: Adaptive design and disease progression model.

PubMed

Bateman, Randall J; Benzinger, Tammie L; Berry, Scott; Clifford, David B; Duggan, Cynthia; Fagan, Anne M; Fanning, Kathleen; Farlow, Martin R; Hassenstab, Jason; McDade, Eric M; Mills, Susan; Paumier, Katrina; Quintana, Melanie; Salloway, Stephen P; Santacruz, Anna; Schneider, Lon S; Wang, Guoqiao; Xiong, Chengjie

2017-01-01

The Dominantly Inherited Alzheimer Network Trials Unit (DIAN-TU) trial is an adaptive platform trial testing multiple drugs to slow or prevent the progression of Alzheimer's disease in autosomal dominant Alzheimer's disease (ADAD) families. With completion of enrollment of the first two drug arms, the DIAN-TU now plans to add new drugs to the platform, designated as the Next Generation (NexGen) prevention trial. In collaboration with ADAD families, philanthropic organizations, academic leaders, the DIAN-TU Pharma Consortium, the National Institutes of Health, and regulatory colleagues, the DIAN-TU developed innovative clinical study designs for the DIAN-TU NexGen prevention trial. Our expanded trial toolbox consists of a disease progression model for ADAD, primary end point DIAN-TU cognitive performance composite, biomarker development, self-administered cognitive assessments, adaptive dose adjustments, and blinded data collection through the last participant completion. These steps represent elements to improve efficacy of the adaptive platform trial and a continued effort to optimize prevention and treatment trials in ADAD. Copyright © 2016 the Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

Fluidics platform and method for sample preparation

DOEpatents

Benner, Henry W.; Dzenitis, John M.

2016-06-21

Provided herein are fluidics platforms and related methods for performing integrated sample collection and solid-phase extraction of a target component of the sample all in one tube. The fluidics platform comprises a pump, particles for solid-phase extraction and a particle-holding means. The method comprises contacting the sample with one or more reagents in a pump, coupling a particle-holding means to the pump and expelling the waste out of the pump while the particle-holding means retains the particles inside the pump. The fluidics platform and methods herein described allow solid-phase extraction without pipetting and centrifugation.

A rapid, maskless 3D prototyping for fabrication of capillary circuits: Toward urinary protein detection.

PubMed

Yan, Sheng; Zhu, Yuanqing; Tang, Shi-Yang; Li, Yuxing; Zhao, Qianbin; Yuan, Dan; Yun, Guolin; Zhang, Jun; Zhang, Shiwu; Li, Weihua

2018-04-01

Proteinuria is an established risk marker for progressive renal function loss and patients would significantly benefit from a point-of-care testing. Although extensive work has been done to develop the microfluidic devices for the detection of urinary protein, they need the complicated operation and bulky peripherals. Here, we present a rapid, maskless 3D prototyping for fabrication of capillary fluidic circuits using laser engraving. The capillary circuits can be fabricated in a short amount of time (<10 min) without the requirements of clean-room facilities and photomasks. The advanced capillary components (e.g., trigger valves, retention valves and retention bursting valves) were fabricated, enabling the sequential liquid delivery and sample-reagent mixing. With the integration of smartphone-based detection platform, the microfluidic device can quantify the urinary protein via a colorimetric analysis. By eliminating the bulky and expensive equipment, this smartphone-based detection platform is portable for on-site quantitative detection. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

78 FR 27974 - Proposed Collection; 60-Day Comment Request: National Cancer Institute (NCI) Alliance for...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-13

... Comment Request: National Cancer Institute (NCI) Alliance for Nanotechnology in Cancer Platform... Nanotechnology Research, National Cancer Institute, 31 Center Drive, Bldg. 31 A, Rm. 10A52, Bethesda, MD 20892 or... Institute (NCI) Alliance for Nanotechnology in Cancer Platform Partnership Scientific Progress Reports, 0925...

A novel rotating experimental platform in a superconducting magnet.

PubMed

Chen, Da; Cao, Hui-Ling; Ye, Ya-Jing; Dong, Chen; Liu, Yong-Ming; Shang, Peng; Yin, Da-Chuan

2016-08-01

This paper introduces a novel platform designed to be used in a strong static magnetic field (in a superconducting magnet). The platform is a sample holder that rotates in the strong magnetic field. Any samples placed in the platform will rotate due to the rotation of the sample holder. With this platform, a number of experiments such as material processing, culture of biological systems, chemical reactions, or other processes can be carried out. In this report, we present some preliminary experiments (protein crystallization, cell culture, and seed germination) conducted using this platform. The experimental results showed that the platform can affect the processes, indicating that it provides a novel environment that has not been investigated before and that the effects of such an environment on many different physical, chemical, or biological processes can be potentially useful for applications in many fields.

A lectin-coupled, targeted proteomic mass spectrometry (MRM MS) platform for identification of multiple liver cancer biomarkers in human plasma.

PubMed

Ahn, Yeong Hee; Shin, Park Min; Oh, Na Ree; Park, Gun Wook; Kim, Hoguen; Yoo, Jong Shin

2012-09-18

Aberrantly glycosylated proteins related to liver cancer progression were captured with specific lectin and identified from human plasma by multiple reaction monitoring (MRM) mass spectrometry as multiple biomarkers for hepatocellular carcinoma (HCC). The lectin fractionation for fucosylated protein glycoforms in human plasma was conducted with a fucose-specific aleuria aurantia lectin (AAL). Following tryptic digestion of the lectin-captured fraction, plasma samples from 30 control cases (including 10 healthy, 10 hepatitis B virus [HBV], and 10 cirrhosis cases) and 10 HCC cases were quantitatively analyzed by MRM to identify which glycoproteins are viable HCC biomarkers. A1AG1, AACT, A1AT, and CERU were found to be potent biomarkers to differentiate HCC plasma from control plasmas. The AUROC generated independently from these four biomarker candidates ranged from 0.73 to 0.92. However, the lectin-coupled MRM assay with multiple combinations of biomarker candidates is superior statistically to those generated from the individual candidates with AUROC more than 0.95, which can be an alternative to the immunoassay inevitably requiring tedious development of multiple antibodies against biomarker candidates to be verified. Eventually the lectin-coupled, targeted proteomic mass spectrometry (MRM MS) platform was found to be efficient to identify multiple biomarkers from human plasma according to cancer progression. Copyright © 2012 Elsevier B.V. All rights reserved.

High-speed multiple sequence alignment on a reconfigurable platform.

PubMed

Oliver, Tim; Schmidt, Bertil; Maskell, Douglas; Nathan, Darran; Clemens, Ralf

2006-01-01

Progressive alignment is a widely used approach to compute multiple sequence alignments (MSAs). However, aligning several hundred sequences by popular progressive alignment tools requires hours on sequential computers. Due to the rapid growth of sequence databases biologists have to compute MSAs in a far shorter time. In this paper we present a new approach to MSA on reconfigurable hardware platforms to gain high performance at low cost. We have constructed a linear systolic array to perform pairwise sequence distance computations using dynamic programming. This results in an implementation with significant runtime savings on a standard FPGA.

Platform for combined analysis of functional and biomolecular phenotypes of the same cell.

PubMed

Kelbauskas, L; Ashili, S; Zeng, J; Rezaie, A; Lee, K; Derkach, D; Ueberroth, B; Gao, W; Paulson, T; Wang, H; Tian, Y; Smith, D; Reid, B; Meldrum, Deirdre R

2017-03-16

Functional and molecular cell-to-cell variability is pivotal at the cellular, tissue and whole-organism levels. Yet, the ultimate goal of directly correlating the function of the individual cell with its biomolecular profile remains elusive. We present a platform for integrated analysis of functional and transcriptional phenotypes in the same single cells. We investigated changes in the cellular respiration and gene expression diversity resulting from adaptation to repeated episodes of acute hypoxia in a premalignant progression model. We find differential, progression stage-specific alterations in phenotypic heterogeneity and identify cells with aberrant phenotypes. To our knowledge, this study is the first demonstration of an integrated approach to elucidate how heterogeneity at the transcriptional level manifests in the physiologic profile of individual cells in the context of disease progression.

Enabling screening in 3D microenvironments: probing matrix and stromal effects on the morphology and proliferation of T47D breast carcinoma cells.

PubMed

Montanez-Sauri, Sara I; Sung, Kyung Eun; Berthier, Erwin; Beebe, David J

2013-03-01

During breast carcinoma progression, the three-dimensional (3D) microenvironment is continuously remodeled, and changes in the composition of the extracellular matrix (ECM) occur. High throughput screening platforms have been used to decipher the complexity of the microenvironment and to identify ECM components responsible for cancer progression. However, traditional screening platforms are typically limited to two-dimensional (2D) cultures, and often exclude the influence of ECM and stromal components. In this work, a system that integrates 3-dimensional cell culture techniques with an automated microfluidic platform was used to create a new ECM screening platform that cultures cells in more physiologically relevant 3D in vitro microenvironments containing stromal cells and different ECM molecules. This new ECM screening platform was used to culture T47D breast carcinoma cells in mono- and co-culture with human mammary fibroblasts (HMF) with seven combinations of three different ECM proteins (collagen, fibronectin, laminin). Differences in the morphology of T47D clusters, and the proliferation of T47D cells were found in ECM compositions rich in fibronectin or laminin. In addition, an MMP enzyme activity inhibition screening showed the capabilities of the platform for small molecule screening. The platform presented in this work enables screening for the effects of matrix and stromal compositions and show promises for providing new insights in the identification of key ECM components involved in breast cancer.

Defining the Canary Islands Oceanic Platform (PLOCAN) Observing System mission

NASA Astrophysics Data System (ADS)

Delory, Eric; Hernández-Brito, Joaquín.; Llínas, Octavio

2010-05-01

A permanent multidisciplinary ocean observing system is planned as both a technological and scientific infrastructure for the Canary Islands Oceanic Platform (PLOCAN). The first component of its two-fold mission is to respond to systems and processes' in-situ environmental testing, certification and benchmarking requirements. This will generally take place in dedicated oceanic experimental areas, from the vicinity of the platform to the deep ocean. While these areas and related infrastructures still are at definition stage, an anticipated prerequisite is that testbed observing assets will have to provide a broad range of measurements in agreement with, as well as in contribution to, current and upcoming environmental and technical standards. The second component is to contribute to the global effort towards continuous and real-time multidisciplinary ocean observations. Related activities will encompass climate change parameters characterization as well as important regional specificities like the preservation and study of the region's unique marine biodiversity and sparsely explored seabed. Continuous sampling is planned to progressively expand from the platform vicinity down to the end of the continental slope - to about 3000m depth, the surrounding seabed and water column, then scale up to the region, through mobile systems and fixed open-ocean stations. Such a large and diverse spectrum of observing activities stems from the fact that the PLOCAN observing system is at the center of a long-term strategy, thus granting the opportunity to plan its mission by way of an ambitious set of ocean measurement methods and technologies.

E-SMART system for in-situ detection of environmental contaminants. Quarterly technical progress report, July--September 1996

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1996-10-01

General Atomics (GA) leads a team of industrial, academic, and government organizations to develop the Environmental Systems Management, Analysis and Reporting neTwork (E-SMART) for the Defense Advanced Research Project Agency (DARPA), by way of this Technology Reinvestment Project (TRP). E-SMART defines a standard by which networks of smart sensing, sampling, and control devices can interoperate. E-SMART is intended to be an open standard, available to any equipment manufacturer. The user will be provided a standard platform on which a site-specific monitoring plan can be implemented using sensors and actuators from various manufacturers and upgraded as new monitoring devices become commerciallymore » available. This project will further develop and advance the E-SMART standardized network protocol to include new sensors, sampling systems, and graphical user interfaces.« less

Microfluidics for genome-wide studies involving next generation sequencing

PubMed Central

Murphy, Travis W.; Lu, Chang

2017-01-01

Next-generation sequencing (NGS) has revolutionized how molecular biology studies are conducted. Its decreasing cost and increasing throughput permit profiling of genomic, transcriptomic, and epigenomic features for a wide range of applications. Microfluidics has been proven to be highly complementary to NGS technology with its unique capabilities for handling small volumes of samples and providing platforms for automation, integration, and multiplexing. In this article, we review recent progress on applying microfluidics to facilitate genome-wide studies. We emphasize on several technical aspects of NGS and how they benefit from coupling with microfluidic technology. We also summarize recent efforts on developing microfluidic technology for genomic, transcriptomic, and epigenomic studies, with emphasis on single cell analysis. We envision rapid growth in these directions, driven by the needs for testing scarce primary cell samples from patients in the context of precision medicine. PMID:28396707

A New Approach to Standardize Multicenter Studies: Mobile Lab Technology for the German Environmental Specimen Bank

PubMed Central

Lermen, Dominik; Schmitt, Daniel; Bartel-Steinbach, Martina; Schröter-Kermani, Christa; Kolossa-Gehring, Marike; von Briesen, Hagen; Zimmermann, Heiko

2014-01-01

Technical progress has simplified tasks in lab diagnosis and improved quality of test results. Errors occurring during the pre-analytical phase have more negative impact on the quality of test results than errors encountered during the total analytical process. Different infrastructures of sampling sites can highly influence the quality of samples and therewith of analytical results. Annually the German Environmental Specimen Bank (ESB) collects, characterizes, and stores blood, plasma, and urine samples of 120–150 volunteers each on four different sampling sites in Germany. Overarching goal is to investigate the exposure to environmental pollutants of non-occupational exposed young adults combining human biomonitoring with questionnaire data. We investigated the requirements of the study and the possibility to realize a highly standardized sampling procedure on a mobile platform in order to increase the required quality of the pre-analytical phase. The results lead to the development of a mobile epidemiologic laboratory (epiLab) in the project “Labor der Zukunft” (future’s lab technology). This laboratory includes a 14.7 m2 reception area to record medical history and exposure-relevant behavior, a 21.1 m2 examination room to record dental fillings and for blood withdrawal, a 15.5 m2 biological safety level 2 laboratory to process and analyze samples on site including a 2.8 m2 personnel lock and a 3.6 m2 cryofacility to immediately freeze samples. Frozen samples can be transferred to their final destination within the vehicle without breaking the cold chain. To our knowledge, we herewith describe for the first time the implementation of a biological safety laboratory (BSL) 2 lab and an epidemiologic unit on a single mobile platform. Since 2013 we have been collecting up to 15.000 individual human samples annually under highly standardized conditions using the mobile laboratory. Characterized and free of alterations they are kept ready for retrospective analyses in their final archive, the German ESB. PMID:25141120

A new approach to standardize multicenter studies: mobile lab technology for the German Environmental Specimen Bank.

PubMed

Lermen, Dominik; Schmitt, Daniel; Bartel-Steinbach, Martina; Schröter-Kermani, Christa; Kolossa-Gehring, Marike; von Briesen, Hagen; Zimmermann, Heiko

2014-01-01

Technical progress has simplified tasks in lab diagnosis and improved quality of test results. Errors occurring during the pre-analytical phase have more negative impact on the quality of test results than errors encountered during the total analytical process. Different infrastructures of sampling sites can highly influence the quality of samples and therewith of analytical results. Annually the German Environmental Specimen Bank (ESB) collects, characterizes, and stores blood, plasma, and urine samples of 120-150 volunteers each on four different sampling sites in Germany. Overarching goal is to investigate the exposure to environmental pollutants of non-occupational exposed young adults combining human biomonitoring with questionnaire data. We investigated the requirements of the study and the possibility to realize a highly standardized sampling procedure on a mobile platform in order to increase the required quality of the pre-analytical phase. The results lead to the development of a mobile epidemiologic laboratory (epiLab) in the project "Labor der Zukunft" (future's lab technology). This laboratory includes a 14.7 m(2) reception area to record medical history and exposure-relevant behavior, a 21.1 m(2) examination room to record dental fillings and for blood withdrawal, a 15.5 m(2) biological safety level 2 laboratory to process and analyze samples on site including a 2.8 m(2) personnel lock and a 3.6 m2 cryofacility to immediately freeze samples. Frozen samples can be transferred to their final destination within the vehicle without breaking the cold chain. To our knowledge, we herewith describe for the first time the implementation of a biological safety laboratory (BSL) 2 lab and an epidemiologic unit on a single mobile platform. Since 2013 we have been collecting up to 15.000 individual human samples annually under highly standardized conditions using the mobile laboratory. Characterized and free of alterations they are kept ready for retrospective analyses in their final archive, the German ESB.

Across-Platform Imputation of DNA Methylation Levels Incorporating Nonlocal Information Using Penalized Functional Regression.

PubMed

Zhang, Guosheng; Huang, Kuan-Chieh; Xu, Zheng; Tzeng, Jung-Ying; Conneely, Karen N; Guan, Weihua; Kang, Jian; Li, Yun

2016-05-01

DNA methylation is a key epigenetic mark involved in both normal development and disease progression. Recent advances in high-throughput technologies have enabled genome-wide profiling of DNA methylation. However, DNA methylation profiling often employs different designs and platforms with varying resolution, which hinders joint analysis of methylation data from multiple platforms. In this study, we propose a penalized functional regression model to impute missing methylation data. By incorporating functional predictors, our model utilizes information from nonlocal probes to improve imputation quality. Here, we compared the performance of our functional model to linear regression and the best single probe surrogate in real data and via simulations. Specifically, we applied different imputation approaches to an acute myeloid leukemia dataset consisting of 194 samples and our method showed higher imputation accuracy, manifested, for example, by a 94% relative increase in information content and up to 86% more CpG sites passing post-imputation filtering. Our simulated association study further demonstrated that our method substantially improves the statistical power to identify trait-associated methylation loci. These findings indicate that the penalized functional regression model is a convenient and valuable imputation tool for methylation data, and it can boost statistical power in downstream epigenome-wide association study (EWAS). © 2016 WILEY PERIODICALS, INC.

A lightweight, inexpensive robotic system for insect vision.

PubMed

Sabo, Chelsea; Chisholm, Robert; Petterson, Adam; Cope, Alex

2017-09-01

Designing hardware for miniaturized robotics which mimics the capabilities of flying insects is of interest, because they share similar constraints (i.e. small size, low weight, and low energy consumption). Research in this area aims to enable robots with similarly efficient flight and cognitive abilities. Visual processing is important to flying insects' impressive flight capabilities, but currently, embodiment of insect-like visual systems is limited by the hardware systems available. Suitable hardware is either prohibitively expensive, difficult to reproduce, cannot accurately simulate insect vision characteristics, and/or is too heavy for small robotic platforms. These limitations hamper the development of platforms for embodiment which in turn hampers the progress on understanding of how biological systems fundamentally work. To address this gap, this paper proposes an inexpensive, lightweight robotic system for modelling insect vision. The system is mounted and tested on a robotic platform for mobile applications, and then the camera and insect vision models are evaluated. We analyse the potential of the system for use in embodiment of higher-level visual processes (i.e. motion detection) and also for development of navigation based on vision for robotics in general. Optic flow from sample camera data is calculated and compared to a perfect, simulated bee world showing an excellent resemblance. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Platform for combined analysis of functional and biomolecular phenotypes of the same cell

PubMed Central

Kelbauskas, L.; Ashili, S.; Zeng, J.; Rezaie, A.; Lee, K.; Derkach, D.; Ueberroth, B.; Gao, W.; Paulson, T.; Wang, H.; Tian, Y.; Smith, D.; Reid, B.; Meldrum, Deirdre R.

2017-01-01

Functional and molecular cell-to-cell variability is pivotal at the cellular, tissue and whole-organism levels. Yet, the ultimate goal of directly correlating the function of the individual cell with its biomolecular profile remains elusive. We present a platform for integrated analysis of functional and transcriptional phenotypes in the same single cells. We investigated changes in the cellular respiration and gene expression diversity resulting from adaptation to repeated episodes of acute hypoxia in a premalignant progression model. We find differential, progression stage-specific alterations in phenotypic heterogeneity and identify cells with aberrant phenotypes. To our knowledge, this study is the first demonstration of an integrated approach to elucidate how heterogeneity at the transcriptional level manifests in the physiologic profile of individual cells in the context of disease progression. PMID:28300162

A Perspective on Implementing a Quantitative Systems Pharmacology Platform for Drug Discovery and the Advancement of Personalized Medicine

PubMed Central

Stern, Andrew M.; Schurdak, Mark E.; Bahar, Ivet; Berg, Jeremy M.; Taylor, D. Lansing

2016-01-01

Drug candidates exhibiting well-defined pharmacokinetic and pharmacodynamic profiles that are otherwise safe often fail to demonstrate proof-of-concept in phase II and III trials. Innovation in drug discovery and development has been identified as a critical need for improving the efficiency of drug discovery, especially through collaborations between academia, government agencies, and industry. To address the innovation challenge, we describe a comprehensive, unbiased, integrated, and iterative quantitative systems pharmacology (QSP)–driven drug discovery and development strategy and platform that we have implemented at the University of Pittsburgh Drug Discovery Institute. Intrinsic to QSP is its integrated use of multiscale experimental and computational methods to identify mechanisms of disease progression and to test predicted therapeutic strategies likely to achieve clinical validation for appropriate subpopulations of patients. The QSP platform can address biological heterogeneity and anticipate the evolution of resistance mechanisms, which are major challenges for drug development. The implementation of this platform is dedicated to gaining an understanding of mechanism(s) of disease progression to enable the identification of novel therapeutic strategies as well as repurposing drugs. The QSP platform will help promote the paradigm shift from reactive population-based medicine to proactive personalized medicine by focusing on the patient as the starting and the end point. PMID:26962875

Chemical Characterisation of the Coarse and Fine Particulate Matter in the Environment of an Underground Railway System: Cytotoxic Effects and Oxidative Stress—A Preliminary Study

PubMed Central

Spagnolo, Anna Maria; Ottria, Gianluca; Perdelli, Fernanda; Cristina, Maria Luisa

2015-01-01

Background: Exposure to the particulate matter produced in underground railway systems is arousing increasing scientific interest because of its health effects. The aim of our study was to evaluate the airborne concentrations of PM10 and three sub-fractions of PM2.5 in an underground railway system environment in proximity to platforms and in underground commercial areas within the system, and to compare these with the outdoor airborne concentrations. We also evaluated the metal components, the cytotoxic properties of the various fractions of particulate matter (PM) and their capacity to induce oxidative stress. Method: We collected the coarse fraction (5–10 µm) and the fine fractions (1–2.5 µm; 0.5–1 µm; 0.25–0.5 µm). Chemical characterisation was determined by means of spectrometry. Cytotoxicity and oxidative stress were evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and Reactive Oxygen Species (ROS) assessment. Results: The concentrations of both PM10 and PM2.5 proved to be similar at the three sampling sites. Iron and other transition metals displayed a greater concentration at the subway platform than at the other two sites. The 2.5–10 µm and 1–2.5 µm fractions of PM from all three sampling sites determined a greater increase in ROS; the intensity of oxidative stress progressively declined as particle diameter diminished. Moreover, ROS concentrations were correlated with the concentrations of some transition metals, namely Mn, Cr, Ti, Fe, Cu, Zn, Ni and Mo. All particulate matter fractions displayed lower or similar ROS values between platform level and the outdoor air. Conclusions: The present study revealed that the underground railway environment at platform level, although containing higher concentrations of some particularly reactive metallic species, did not display higher cytotoxicity and oxidative stress levels than the outdoor air. PMID:25872016

Chemical characterisation of the coarse and fine particulate matter in the environment of an underground railway system: cytotoxic effects and oxidative stress-a preliminary study.

PubMed

Spagnolo, Anna Maria; Ottria, Gianluca; Perdelli, Fernanda; Cristina, Maria Luisa

2015-04-13

Exposure to the particulate matter produced in underground railway systems is arousing increasing scientific interest because of its health effects. The aim of our study was to evaluate the airborne concentrations of PM10 and three sub-fractions of PM2.5 in an underground railway system environment in proximity to platforms and in underground commercial areas within the system, and to compare these with the outdoor airborne concentrations. We also evaluated the metal components, the cytotoxic properties of the various fractions of particulate matter (PM) and their capacity to induce oxidative stress. We collected the coarse fraction (5-10 µm) and the fine fractions (1-2.5 µm; 0.5-1 µm; 0.25-0.5 µm). Chemical characterisation was determined by means of spectrometry. Cytotoxicity and oxidative stress were evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and Reactive Oxygen Species (ROS) assessment. The concentrations of both PM10 and PM2.5 proved to be similar at the three sampling sites. Iron and other transition metals displayed a greater concentration at the subway platform than at the other two sites. The 2.5-10 µm and 1-2.5 µm fractions of PM from all three sampling sites determined a greater increase in ROS; the intensity of oxidative stress progressively declined as particle diameter diminished. Moreover, ROS concentrations were correlated with the concentrations of some transition metals, namely Mn, Cr, Ti, Fe, Cu, Zn, Ni and Mo. All particulate matter fractions displayed lower or similar ROS values between platform level and the outdoor air. The present study revealed that the underground railway environment at platform level, although containing higher concentrations of some particularly reactive metallic species, did not display higher cytotoxicity and oxidative stress levels than the outdoor air.

Variants in human papillomavirus receptor and associated genes are associated with type-specific HPV infection and lesion progression of the cervix

PubMed Central

Chen, Tingting; Yang, Shizhou; Huang, Yongjie; Hong, Die; Li, Yang; Chen, Xiaojing; Wang, Xinyu; Cheng, Xiaodong; Lu, Weiguo; Xie, Xing

2016-01-01

Human papillomavirus (HPV) infects cervical epithelial cells through cellular membrane receptors, and then induces the initiation and progression of cervical cancer. Single nucleotide polymorphisms (SNPs) may impact the susceptibility and outcome of diseases, but it's still unknown whether variant in HPV receptor and associated genes is associated with type-specific HPV infection and cervical lesion progression. We examined 96 SNPs in 8 genes which may participate in the HPV infection process in 875 samples with HPV negative or single HPV16, 18, 52, 58 positive from 3299 cervical exfoliated cell samples, by Illumina BeadXpress VeraCode platform, and analyzed the correlation between the SNPs and type-specific HPV infection and cervical lesions progression. We found rs28384376 in EGFR and rs12034979 in HSPG2 significantly correlated to HPV16 infection; rs2575738, rs2575712, rs2575735 in SDC2 and rs6697265 in HSPG2 significantly correlated to HPV18 infection; rs10510097 in FGFR2, rs12718946 in EGFR significantly correlated to HPV52 infection; rs4947972 in EGFR, rs2981451 in FGFR2, rs2575735 in SDC2 significantly correlated to HPV58 infection. And rs3135772, rs1047057 and rs2556537 in FGFR2, rs12034979 in HSPG2, rs16894821 in SDC2 significantly correlated to cervical lesion progression induced by HPV16 infection; rs6697265 and rs6680566 in HSPG2, rs16860426 in ITGA6 by HPV18 infection; rs878949 in HSPG2, rs12718946 and rs12668175 in EGFR by HPV52 infection; no SNP by HPV58 infection. Our findings suggest that HPV receptor and associated gene variants may influence the susceptibilities to HPV type-specific infection and cervical lesion progression, which might have a potential application value in cervical cancer screening and therapy. PMID:27223085

Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

PubMed Central

Lasitschka, Bärbel; Jones, David; Northcott, Paul; Hutter, Barbara; Jäger, Natalie; Kool, Marcel; Taylor, Michael; Lichter, Peter; Pfister, Stefan; Wolf, Stephan; Brors, Benedikt; Eils, Roland

2013-01-01

The emergence of high-throughput, next-generation sequencing technologies has dramatically altered the way we assess genomes in population genetics and in cancer genomics. Currently, there are four commonly used whole-genome sequencing platforms on the market: Illumina’s HiSeq2000, Life Technologies’ SOLiD 4 and its completely redesigned 5500xl SOLiD, and Complete Genomics’ technology. A number of earlier studies have compared a subset of those sequencing platforms or compared those platforms with Sanger sequencing, which is prohibitively expensive for whole genome studies. Here we present a detailed comparison of the performance of all currently available whole genome sequencing platforms, especially regarding their ability to call SNVs and to evenly cover the genome and specific genomic regions. Unlike earlier studies, we base our comparison on four different samples, allowing us to assess the between-sample variation of the platforms. We find a pronounced GC bias in GC-rich regions for Life Technologies’ platforms, with Complete Genomics performing best here, while we see the least bias in GC-poor regions for HiSeq2000 and 5500xl. HiSeq2000 gives the most uniform coverage and displays the least sample-to-sample variation. In contrast, Complete Genomics exhibits by far the smallest fraction of bases not covered, while the SOLiD platforms reveal remarkable shortcomings, especially in covering CpG islands. When comparing the performance of the four platforms for calling SNPs, HiSeq2000 and Complete Genomics achieve the highest sensitivity, while the SOLiD platforms show the lowest false positive rate. Finally, we find that integrating sequencing data from different platforms offers the potential to combine the strengths of different technologies. In summary, our results detail the strengths and weaknesses of all four whole-genome sequencing platforms. It indicates application areas that call for a specific sequencing platform and disallow other platforms. This helps to identify the proper sequencing platform for whole genome studies with different application scopes. PMID:23776689

Bridging the Faraoni and Selli oceanic anoxic events: late Hauterivian to early Aptian dysaerobic to anaerobic phases in the Tethys

NASA Astrophysics Data System (ADS)

Föllmi, K. B.; Bôle, M.; Jammet, N.; Froidevaux, P.; Godet, A.; Bodin, S.; Adatte, T.; Matera, V.; Fleitmann, D.; Spangenberg, J. E.

2012-01-01

A detailed geochemical analysis was performed on the upper part of the Maiolica Formation in the Breggia (southern Switzerland) and Capriolo sections (northern Italy). The analysed sediments consist of well-bedded, partly siliceous, pelagic carbonate, which lodges numerous thin, dark and organic-rich layers. Stable-isotope, phosphorus, organic-carbon and a suite of redox-sensitive trace-element contents (RSTE: Mo, U, Co, V and As) were measured. The RSTE pattern and Corg:Ptot ratios indicate that most organic-rich layers were deposited under dysaerobic rather than anaerobic conditions and that latter conditions were likely restricted to short intervals in the latest Hauterivian, the early Barremian and the pre-Selli early Aptian. Correlations are both possible with organic-rich intervals in central Italy (the Gorgo a Cerbara section) and the Boreal Lower Saxony Basin, as well as with the facies and drowning pattern in the Helvetic segment of the northern Tethyan carbonate platform. Our data and correlations suggest that the latest Hauterivian witnessed the progressive installation of dysaerobic conditions in the Tethys, which went along with the onset in sediment condensation, phosphogenesis and platform drowning on the northern Tethyan margin, and which culminated in the Faraoni anoxic episode. This episode is followed by further episodes of dysaerobic conditions in the Tethys and the Lower Saxony Basin, which became more frequent and progressively stronger in the late early Barremian. Platform drowning persisted and did not halt before the latest early Barremian. The late Barremian witnessed diminishing frequencies and intensities in dysaerobic conditions, which went along with the progressive installation of the Urgonian carbonate platform. Near the Barremian-Aptian boundary, the increasing density in dysaerobic episodes in the Tethyan and Lower Saxony Basins is paralleled by a change towards heterozoan carbonate production on the northern Tethyan shelf. The following return to more oxygenated conditions is correlated with the second phase of Urgonian platform growth and the period immediately preceding and corresponding to the Selli anoxic episode is characterised by renewed platform drowning and the change to heterozoan carbonate production. Changes towards more humid climate conditions were the likely cause for the repetitive installation of dys- to anaerobic conditions in the Tethyan and Boreal basins and the accompanying changes in the evolution of the carbonate platform towards heterozoan carbonate-producing ecosystems and platform drowning.

Evaluation of high throughput gene expression platforms using a genomic biomarker signature for prediction of skin sensitization.

PubMed

Forreryd, Andy; Johansson, Henrik; Albrekt, Ann-Sofie; Lindstedt, Malin

2014-05-16

Allergic contact dermatitis (ACD) develops upon exposure to certain chemical compounds termed skin sensitizers. To reduce the occurrence of skin sensitizers, chemicals are regularly screened for their capacity to induce sensitization. The recently developed Genomic Allergen Rapid Detection (GARD) assay is an in vitro alternative to animal testing for identification of skin sensitizers, classifying chemicals by evaluating transcriptional levels of a genomic biomarker signature. During assay development and biomarker identification, genome-wide expression analysis was applied using microarrays covering approximately 30,000 transcripts. However, the microarray platform suffers from drawbacks in terms of low sample throughput, high cost per sample and time consuming protocols and is a limiting factor for adaption of GARD into a routine assay for screening of potential sensitizers. With the purpose to simplify assay procedures, improve technical parameters and increase sample throughput, we assessed the performance of three high throughput gene expression platforms--nCounter®, BioMark HD™ and OpenArray®--and correlated their performance metrics against our previously generated microarray data. We measured the levels of 30 transcripts from the GARD biomarker signature across 48 samples. Detection sensitivity, reproducibility, correlations and overall structure of gene expression measurements were compared across platforms. Gene expression data from all of the evaluated platforms could be used to classify most of the sensitizers from non-sensitizers in the GARD assay. Results also showed high data quality and acceptable reproducibility for all platforms but only medium to poor correlations of expression measurements across platforms. In addition, evaluated platforms were superior to the microarray platform in terms of cost efficiency, simplicity of protocols and sample throughput. We evaluated the performance of three non-array based platforms using a limited set of transcripts from the GARD biomarker signature. We demonstrated that it was possible to achieve acceptable discriminatory power in terms of separation between sensitizers and non-sensitizers in the GARD assay while reducing assay costs, simplify assay procedures and increase sample throughput by using an alternative platform, providing a first step towards the goal to prepare GARD for formal validation and adaption of the assay for industrial screening of potential sensitizers.

RNA-Targeted Therapeutics.

PubMed

Crooke, Stanley T; Witztum, Joseph L; Bennett, C Frank; Baker, Brenda F

2018-04-03

RNA-targeted therapies represent a platform for drug discovery involving chemically modified oligonucleotides, a wide range of cellular RNAs, and a novel target-binding motif, Watson-Crick base pairing. Numerous hurdles considered by many to be impassable have been overcome. Today, four RNA-targeted therapies are approved for commercial use for indications as diverse as Spinal Muscular Atrophy (SMA) and reduction of low-density lipoprotein cholesterol (LDL-C) and by routes of administration including subcutaneous, intravitreal, and intrathecal delivery. The technology is efficient and supports approaching "undruggable" targets. Three additional agents are progressing through registration, and more are in clinical development, representing several chemical and structural classes. Moreover, progress in understanding the molecular mechanisms by which these drugs work has led to steadily better clinical performance and a wide range of mechanisms that may be exploited for therapeutic purposes. Here we summarize the progress, future challenges, and opportunities for this drug discovery platform. Copyright © 2018 Elsevier Inc. All rights reserved.

Epigenetics and Proteomics Join Transcriptomics in the Quest for Tuberculosis Biomarkers

PubMed Central

Esterhuyse, Maria M.; Weiner, January; Caron, Etienne; Loxton, Andre G.; Iannaccone, Marco; Wagman, Chandre; Saikali, Philippe; Stanley, Kim; Wolski, Witold E.; Mollenkopf, Hans-Joachim; Schick, Matthias; Aebersold, Ruedi; Linhart, Heinz; Walzl, Gerhard

2015-01-01

ABSTRACT An estimated one-third of the world’s population is currently latently infected with Mycobacterium tuberculosis. Latent M. tuberculosis infection (LTBI) progresses into active tuberculosis (TB) disease in ~5 to 10% of infected individuals. Diagnostic and prognostic biomarkers to monitor disease progression are urgently needed to ensure better care for TB patients and to decrease the spread of TB. Biomarker development is primarily based on transcriptomics. Our understanding of biology combined with evolving technical advances in high-throughput techniques led us to investigate the possibility of additional platforms (epigenetics and proteomics) in the quest to (i) understand the biology of the TB host response and (ii) search for multiplatform biosignatures in TB. We engaged in a pilot study to interrogate the DNA methylome, transcriptome, and proteome in selected monocytes and granulocytes from TB patients and healthy LTBI participants. Our study provides first insights into the levels and sources of diversity in the epigenome and proteome among TB patients and LTBI controls, despite limitations due to small sample size. Functionally the differences between the infection phenotypes (LTBI versus active TB) observed in the different platforms were congruent, thereby suggesting regulation of function not only at the transcriptional level but also by DNA methylation and microRNA. Thus, our data argue for the development of a large-scale study of the DNA methylome, with particular attention to study design in accounting for variation based on gender, age, and cell type. PMID:26374119

Nanoconfinement platform for nanostructure quantification via grazing-transmission X-ray scattering

DOEpatents

Black, Charles T.; Yager, Kevin G.

2017-01-31

A nano-confinement platform that may allow improved quantification of the structural order of nanometer-scale systems. Sample-holder `chips` are designed for the GTSAXS experimental geometry. The platform involves fabricated nanostructured sample holders on and in one or more corners of a substrate support where the sample material of interest is positioned at the corner of the substrate support. In an embodiment, the substrate material making up the substrate support beneath the sample-holding area is removed. A scattering x-ray sample platform includes a substrate support arranged in a parallelepiped form, having a substantially flat base and a substantially flat top surface, the top surface being substantially parallel with the base, the parallelepiped having a plurality of corners. At least one corner of the substrate support has a sample holding area formed in the top surface of the substrate support and within a predetermined distance from the corner. The sample holding area includes a regular array of nano-wells formed in the top surface of the substrate support.

A remark on copy number variation detection methods.

PubMed

Li, Shuo; Dou, Xialiang; Gao, Ruiqi; Ge, Xinzhou; Qian, Minping; Wan, Lin

2018-01-01

Copy number variations (CNVs) are gain and loss of DNA sequence of a genome. High throughput platforms such as microarrays and next generation sequencing technologies (NGS) have been applied for genome wide copy number losses. Although progress has been made in both approaches, the accuracy and consistency of CNV calling from the two platforms remain in dispute. In this study, we perform a deep analysis on copy number losses on 254 human DNA samples, which have both SNP microarray data and NGS data publicly available from Hapmap Project and 1000 Genomes Project respectively. We show that the copy number losses reported from Hapmap Project and 1000 Genome Project only have < 30% overlap, while these reports are required to have cross-platform (e.g. PCR, microarray and high-throughput sequencing) experimental supporting by their corresponding projects, even though state-of-art calling methods were employed. On the other hand, copy number losses are found directly from HapMap microarray data by an accurate algorithm, i.e. CNVhac, almost all of which have lower read mapping depth in NGS data; furthermore, 88% of which can be supported by the sequences with breakpoint in NGS data. Our results suggest the ability of microarray calling CNVs and the possible introduction of false negatives from the unessential requirement of the additional cross-platform supporting. The inconsistency of CNV reports from Hapmap Project and 1000 Genomes Project might result from the inadequate information containing in microarray data, the inconsistent detection criteria, or the filtration effect of cross-platform supporting. The statistical test on CNVs called from CNVhac show that the microarray data can offer reliable CNV reports, and majority of CNV candidates can be confirmed by raw sequences. Therefore, the CNV candidates given by a good caller could be highly reliable without cross-platform supporting, so additional experimental information should be applied in need instead of necessarily.

Outpatient Tinnitus Clinic, Self-Help Web Platform, or Mobile Application to Recruit Tinnitus Study Samples?

PubMed Central

Probst, Thomas; Pryss, Rüdiger C.; Langguth, Berthold; Spiliopoulou, Myra; Landgrebe, Michael; Vesala, Markku; Harrison, Stephen; Schobel, Johannes; Reichert, Manfred; Stach, Michael; Schlee, Winfried

2017-01-01

For understanding the heterogeneity of tinnitus, large samples are required. However, investigations on how samples recruited by different methods differ from each other are lacking. In the present study, three large samples each recruited by different means were compared: N = 5017 individuals registered at a self-help web platform for tinnitus (crowdsourcing platform Tinnitus Talk), N = 867 users of a smart mobile application for tinnitus (crowdsensing platform TrackYourTinnitus), and N = 3786 patients contacting an outpatient tinnitus clinic (Tinnitus Center of the University Hospital Regensburg). The three samples were compared regarding age, gender, and duration of tinnitus (month or years perceiving tinnitus; subjective report) using chi-squared tests. The three samples significantly differed from each other in age, gender and tinnitus duration (p < 0.05). Users of the TrackYourTinnitus crowdsensing platform were younger, users of the Tinnitus Talk crowdsourcing platform had more often female gender, and users of both newer technologies (crowdsourcing and crowdsensing) had more frequently acute/subacute tinnitus (<3 months and 4–6 months) as well as a very long tinnitus duration (>20 years). The implications of these findings for clinical research are that newer technologies such as crowdsourcing and crowdsensing platforms offer the possibility to reach individuals hard to get in contact with at an outpatient tinnitus clinic. Depending on the aims and the inclusion/exclusion criteria of a given study, different recruiting strategies (clinic and/or newer technologies) offer different advantages and disadvantages. In general, the representativeness of study results might be increased when tinnitus study samples are recruited in the clinic as well as via crowdsourcing and crowdsensing. PMID:28484389

Outpatient Tinnitus Clinic, Self-Help Web Platform, or Mobile Application to Recruit Tinnitus Study Samples?

PubMed

Probst, Thomas; Pryss, Rüdiger C; Langguth, Berthold; Spiliopoulou, Myra; Landgrebe, Michael; Vesala, Markku; Harrison, Stephen; Schobel, Johannes; Reichert, Manfred; Stach, Michael; Schlee, Winfried

2017-01-01

For understanding the heterogeneity of tinnitus, large samples are required. However, investigations on how samples recruited by different methods differ from each other are lacking. In the present study, three large samples each recruited by different means were compared: N = 5017 individuals registered at a self-help web platform for tinnitus (crowdsourcing platform Tinnitus Talk), N = 867 users of a smart mobile application for tinnitus (crowdsensing platform TrackYourTinnitus), and N = 3786 patients contacting an outpatient tinnitus clinic (Tinnitus Center of the University Hospital Regensburg). The three samples were compared regarding age, gender, and duration of tinnitus (month or years perceiving tinnitus; subjective report) using chi-squared tests. The three samples significantly differed from each other in age, gender and tinnitus duration ( p < 0.05). Users of the TrackYourTinnitus crowdsensing platform were younger, users of the Tinnitus Talk crowdsourcing platform had more often female gender, and users of both newer technologies (crowdsourcing and crowdsensing) had more frequently acute/subacute tinnitus (<3 months and 4-6 months) as well as a very long tinnitus duration (>20 years). The implications of these findings for clinical research are that newer technologies such as crowdsourcing and crowdsensing platforms offer the possibility to reach individuals hard to get in contact with at an outpatient tinnitus clinic. Depending on the aims and the inclusion/exclusion criteria of a given study, different recruiting strategies (clinic and/or newer technologies) offer different advantages and disadvantages. In general, the representativeness of study results might be increased when tinnitus study samples are recruited in the clinic as well as via crowdsourcing and crowdsensing.

Progress at Standard Space Platforms Corporation

NASA Astrophysics Data System (ADS)

Perkins, Frederick W.

1992-08-01

An account is given of a simple program structure with low costs and short schedules for the space R&D community operating outside mission-oriented, government-funded programs. In addition to furnishing launch services into orbit, the program structure furnishes engineering services through its ground station, control room, and 3-year duration 'MMSB' platform. Flights may begin as little as a year after contract signature.

Optofluidic cellular immunofunctional analysis by localized surface plasmon resonance

NASA Astrophysics Data System (ADS)

Kurabayashi, Katsuo; Oh, Bo-Ram

2014-08-01

Cytokine secretion assays provide the means to quantify intercellular-signaling proteins secreted by blood immune cells. These assays allow researchers and clinicians to obtain valuable information on the immune status of the donor. Previous studies have demonstrated that localized surface plasmon resonance (LSPR) effects enable label-free, real-time biosensing on a nanostructured metallic surface with simple optics and sensing tunability. However, limited sensitivity coupled with a lack of sample handling capability makes it challenging to implement LSPR biosensing in cellular functional immunoanalysis based on cytokine secretion assay. This paper describes our recent progress towards full development of a label-free LSPR biosensing technique to detect cell-secreted tumor necrosis factor (TNF)-α cytokines in clinical blood samples. We integrate LSPR bionanosensors in an optofluidic platform capable of handling target immune cells in a microfluidic chamber while readily permitting optical access for cytokine detection.

E-SMART system for in-situ detection of environmental contaminants. Quarterly technical progress report, April--June 1997

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1997-08-01

General Atomics (GA) leads a team of industrial, academic, and government organizations in the development of the Environmental Systems Management, Analysis and Reporting neTwork (E-SMART) for the Defense Advanced Research Project Agency (DARPA), by way of this Technology Reinvestment Project (TRP). E-SMART defines a standard by which networks of smart sensing, sampling, and control devices can interoperate. E-SMART is intended to be an open standard, available to any equipment manufacturer. The user will be provided a standard platform on which a site-specific monitoring plan can be implemented using sensors and actuators from various manufacturers and upgraded as new monitoring devicesmore » become commercially available. This project will further develop and advance the E-SMART standardized network protocol to include new sensors, sampling systems, and graphical user interfaces.« less

Rapid bacterial diagnostics via surface enhanced Raman microscopy.

PubMed

Premasiri, W R; Sauer-Budge, A F; Lee, J C; Klapperich, C M; Ziegler, L D

2012-06-01

There is a continuing need to develop new techniques for the rapid and specific identification of bacterial pathogens in human body fluids especially given the increasing prevalence of drug resistant strains. Efforts to develop a surface enhanced Raman spectroscopy (SERS) based approach, which encompasses sample preparation, SERS substrates, portable Raman microscopy instrumentation and novel identification software, are described. The progress made in each of these areas in our laboratory is summarized and illustrated by a spiked infectious sample for urinary tract infection (UTI) diagnostics. SERS bacterial spectra exhibit both enhanced sensitivity and specificity allowing the development of an easy to use, portable, optical platform for pathogen detection and identification. SERS of bacterial cells is shown to offer not only reproducible molecular spectroscopic signatures for analytical applications in clinical diagnostics, but also is a new tool for studying biochemical activity in real time at the outer layers of these organisms.

Evolutionary space platform concept study. Volume 2, part A: SASP special emphasis trade studies

NASA Technical Reports Server (NTRS)

1982-01-01

Efforts are in progress to define an approach to provide a simple and cost effective solution to the problem of long duration space flight. This approach involves a Space Platform in low Earth orbit, which can be tended by the Space Shuttle and which will provide, for extended periods of time, stability, utilities and access for a variety of replaceable payloads. The feasibility of an evolutionary space system which would cost effectively support unmanned payloads in groups, using a Space Platform which provides centralized basic subsystems is addressed.

Chemistry and mineralogy of pyrite-enriched sediments at a passive margin sulfide brine seep: abyssal Gulf of Mexico

USGS Publications Warehouse

Commeau, R.F.; Paull, C.K.; Commeau, J.A.; Poppe, L.J.

1987-01-01

Pyrite is rapidly accumulating at the contact between the Cretaceous limestones of the Florida Platform and the hemipelagic sediments of the abyssal Gulf of Mexico. Sediments sampled with the submersible "Alvin" in 3266 m of water are associated with a dense community of organisms that depend on chemosynthetic primary production as a food source. Analysis of the chemistry, mineralogy, and textural composition of these sediments indicate that iron sulfide mineralization is occurring at the seafloor within an anoxic micro-habitat sustained by the advection of hydrogen sulfide-charged saline brines from the adjacent platform. The chemosynthetic bacteria that directly overlie the sediments oxidize hydrogen sulfide for energy and provide elemental sulfur that reacts with iron monosulfide to form some of the pyrite. The sediments are mixtures of pyrite (??? 30 wt.%), BaSr sulfates (??? 4 wt.%), clays, and locally derived biogenic carbonates and are progressively being cemented by iron sulfides. Oxidation of hydrogen sulfide produces locally acidic conditions that corrode the adjacent limestones. Potential sources of S, H2S, Fe, Ba, and Sr are discussed. ?? 1987.

Flexible and Stretchable Physical Sensor Integrated Platforms for Wearable Human-Activity Monitoringand Personal Healthcare.

PubMed

Trung, Tran Quang; Lee, Nae-Eung

2016-06-01

Flexible and stretchable physical sensors that can measure and quantify electrical signals generated by human activities are attracting a great deal of attention as they have unique characteristics, such as ultrathinness, low modulus, light weight, high flexibility, and stretchability. These flexible and stretchable physical sensors conformally attached on the surface of organs or skin can provide a new opportunity for human-activity monitoring and personal healthcare. Consequently, in recent years there has been considerable research effort devoted to the development of flexible and stretchable physical sensors to fulfill the requirements of future technology, and much progress has been achieved. Here, the most recent developments of flexible and stretchable physical sensors are described, including temperature, pressure, and strain sensors, and flexible and stretchable sensor-integrated platforms. The latest successful examples of flexible and stretchable physical sensors for the detection of temperature, pressure, and strain, as well as their novel structures, technological innovations, and challenges, are reviewed first. In the next section, recent progress regarding sensor-integrated wearable platforms is overviewed in detail. Some of the latest achievements regarding self-powered sensor-integrated wearable platform technologies are also reviewed. Further research direction and challenges are also proposed to develop a fully sensor-integrated wearable platform for monitoring human activity and personal healthcare in the near future. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Perspective on Implementing a Quantitative Systems Pharmacology Platform for Drug Discovery and the Advancement of Personalized Medicine.

PubMed

Stern, Andrew M; Schurdak, Mark E; Bahar, Ivet; Berg, Jeremy M; Taylor, D Lansing

2016-07-01

Drug candidates exhibiting well-defined pharmacokinetic and pharmacodynamic profiles that are otherwise safe often fail to demonstrate proof-of-concept in phase II and III trials. Innovation in drug discovery and development has been identified as a critical need for improving the efficiency of drug discovery, especially through collaborations between academia, government agencies, and industry. To address the innovation challenge, we describe a comprehensive, unbiased, integrated, and iterative quantitative systems pharmacology (QSP)-driven drug discovery and development strategy and platform that we have implemented at the University of Pittsburgh Drug Discovery Institute. Intrinsic to QSP is its integrated use of multiscale experimental and computational methods to identify mechanisms of disease progression and to test predicted therapeutic strategies likely to achieve clinical validation for appropriate subpopulations of patients. The QSP platform can address biological heterogeneity and anticipate the evolution of resistance mechanisms, which are major challenges for drug development. The implementation of this platform is dedicated to gaining an understanding of mechanism(s) of disease progression to enable the identification of novel therapeutic strategies as well as repurposing drugs. The QSP platform will help promote the paradigm shift from reactive population-based medicine to proactive personalized medicine by focusing on the patient as the starting and the end point. © 2016 Society for Laboratory Automation and Screening.

A measure of the signal-to-noise ratio of microarray samples and studies using gene correlations.

PubMed

Venet, David; Detours, Vincent; Bersini, Hugues

2012-01-01

The quality of gene expression data can vary dramatically from platform to platform, study to study, and sample to sample. As reliable statistical analysis rests on reliable data, determining such quality is of the utmost importance. Quality measures to spot problematic samples exist, but they are platform-specific, and cannot be used to compare studies. As a proxy for quality, we propose a signal-to-noise ratio for microarray data, the "Signal-to-Noise Applied to Gene Expression Experiments", or SNAGEE. SNAGEE is based on the consistency of gene-gene correlations. We applied SNAGEE to a compendium of 80 large datasets on 37 platforms, for a total of 24,380 samples, and assessed the signal-to-noise ratio of studies and samples. This allowed us to discover serious issues with three studies. We show that signal-to-noise ratios of both studies and samples are linked to the statistical significance of the biological results. We showed that SNAGEE is an effective way to measure data quality for most types of gene expression studies, and that it often outperforms existing techniques. Furthermore, SNAGEE is platform-independent and does not require raw data files. The SNAGEE R package is available in BioConductor.

New Data, Old Tensions: Big Data, Personalized Learning, and the Challenges of Progressive Education

ERIC Educational Resources Information Center

Dishon, Gideon

2017-01-01

Personalized learning has become the most notable application of big data in primary and secondary schools in the United States. The combination of big data and adaptive technological platforms is heralded as a revolution that could transform education, overcoming the outdated classroom model, and realizing the progressive vision of…

Approaches to a global quantum key distribution network

NASA Astrophysics Data System (ADS)

Islam, Tanvirul; Bedington, Robert; Ling, Alexander

2017-10-01

Progress in realising quantum computers threatens to weaken existing public key encryption infrastructure. A global quantum key distribution (QKD) network can play a role in computational attack-resistant encryption. Such a network could use a constellation of high altitude platforms such as airships and satellites as trusted nodes to facilitate QKD between any two points on the globe on demand. This requires both space-to-ground and inter-platform links. However, the prohibitive cost of traditional satellite based development limits the experimental work demonstrating relevant technologies. To accelerate progress towards a global network, we use an emerging class of shoe-box sized spacecraft known as CubeSats. We have designed a polarization entangled photon pair source that can operate on board CubeSats. The robustness and miniature form factor of our entanglement source makes it especially suitable for performing pathfinder missions that studies QKD between two high altitude platforms. The technological outcomes of such mission would be the essential building blocks for a global QKD network.

Biphasic Finite Element Modeling Reconciles Mechanical Properties of Tissue-Engineered Cartilage Constructs Across Testing Platforms.

PubMed

Meloni, Gregory R; Fisher, Matthew B; Stoeckl, Brendan D; Dodge, George R; Mauck, Robert L

2017-07-01

Cartilage tissue engineering is emerging as a promising treatment for osteoarthritis, and the field has progressed toward utilizing large animal models for proof of concept and preclinical studies. Mechanical testing of the regenerative tissue is an essential outcome for functional evaluation. However, testing modalities and constitutive frameworks used to evaluate in vitro grown samples differ substantially from those used to evaluate in vivo derived samples. To address this, we developed finite element (FE) models (using FEBio) of unconfined compression and indentation testing, modalities commonly used for such samples. We determined the model sensitivity to tissue radius and subchondral bone modulus, as well as its ability to estimate material parameters using the built-in parameter optimization tool in FEBio. We then sequentially tested agarose gels of 4%, 6%, 8%, and 10% weight/weight using a custom indentation platform, followed by unconfined compression. Similarly, we evaluated the ability of the model to generate material parameters for living constructs by evaluating engineered cartilage. Juvenile bovine mesenchymal stem cells were seeded (2 × 10 7 cells/mL) in 1% weight/volume hyaluronic acid hydrogels and cultured in a chondrogenic medium for 3, 6, and 9 weeks. Samples were planed and tested sequentially in indentation and unconfined compression. The model successfully completed parameter optimization routines for each testing modality for both acellular and cell-based constructs. Traditional outcome measures and the FE-derived outcomes showed significant changes in material properties during the maturation of engineered cartilage tissue, capturing dynamic changes in functional tissue mechanics. These outcomes were significantly correlated with one another, establishing this FE modeling approach as a singular method for the evaluation of functional engineered and native tissue regeneration, both in vitro and in vivo.

Quantification of NS1 dengue biomarker in serum via optomagnetic nanocluster detection

NASA Astrophysics Data System (ADS)

Antunes, Paula; Watterson, Daniel; Parmvi, Mattias; Burger, Robert; Boisen, Anja; Young, Paul; Cooper, Matthew A.; Hansen, Mikkel F.; Ranzoni, Andrea; Donolato, Marco

2015-11-01

Dengue is a tropical vector-borne disease without cure or vaccine that progressively spreads into regions with temperate climates. Diagnostic tools amenable to resource-limited settings would be highly valuable for epidemiologic control and containment during outbreaks. Here, we present a novel low-cost automated biosensing platform for detection of dengue fever biomarker NS1 and demonstrate it on NS1 spiked in human serum. Magnetic nanoparticles (MNPs) are coated with high-affinity monoclonal antibodies against NS1 via bio-orthogonal Cu-free ‘click’ chemistry on an anti-fouling surface molecular architecture. The presence of the target antigen NS1 triggers MNP agglutination and the formation of nanoclusters with rapid kinetics enhanced by external magnetic actuation. The amount and size of the nanoclusters correlate with the target concentration and can be quantified using an optomagnetic readout method. The resulting automated dengue fever assay takes just 8 minutes, requires 6 μL of serum sample and shows a limit of detection of 25 ng/mL with an upper detection range of 20000 ng/mL. The technology holds a great potential to be applied to NS1 detection in patient samples. As the assay is implemented on a low-cost microfluidic disc the platform is suited for further expansion to multiplexed detection of a wide panel of biomarkers.

Slope failures and timing of turbidity flows north of Puerto Rico

USGS Publications Warehouse

ten Brink, Uri S.; Chaytor, Jason D.

2014-01-01

The submerged carbonate platform north of Puerto Rico terminates in a high (3,000–4,000 m) and in places steep (>45°) slope characterized by numerous landslide scarps including two 30–50 km-wide amphitheater-shaped features. The origin of the steep platform edge and the amphitheaters has been attributed to: (1) catastrophic failure, or (2) localized failures and progressive erosion. Determining which of the two mechanisms has shaped the platform edge is critically important in understanding landslide-generated tsunami hazards in the region. Multibeam bathymetry, seismic reflection profiles, and a suite sediment cores from the Puerto Rico Trench and the slope between the trench and the platform edge were used to test these two hypotheses. Deposits within trench axis and at the base of the slope are predominantly composed of sandy carbonate turbidites and pelagic sediment with inter-fingering of chaotic debris units. Regionally-correlated turbidites within the upper 10 m of the trench sediments were dated between ∼25 and 22 kyrs and ∼18–19 kyrs for the penultimate and most recent events, respectively. Deposits on the slope are laterally discontinuous and vary from thin layers of fragmented carbonate platform material to thick pelagic layers. Large debris blocks or lobes are absent within the near-surface deposits at the trench axis and the base of slope basins. Progressive small-scale scalloping and self-erosion of the carbonate platform and underlying stratigraphy appears to be the most likely mechanism for recent development of the amphitheaters. These smaller scale failures may lead to the generation of tsunamis with local, rather than regional, impact.

Toward Precision Medicine: A Cancer Molecular Subtyping Nano-Strategy for RNA Biomarkers in Tumor and Urine.

PubMed

Koo, Kevin M; Wee, Eugene J H; Mainwaring, Paul N; Wang, Yuling; Trau, Matt

2016-12-01

Cancer is a heterogeneous disease which manifests as different molecular subtypes due to the complex nature of tumor initiation, progression, and metastasis. The concept of precision medicine aims to exploit this cancer heterogeneity by incorporating diagnostic technology to characterize each cancer patient's molecular subtype for tailored treatments. To characterize cancer molecular subtypes accurately, a suite of multiplexed bioassays have currently been developed to detect multiple oncogenic biomarkers. Despite the reliability of current multiplexed detection techniques, novel strategies are still needed to resolve limitations such as long assay time, complex protocols, and difficulty in interpreting broad overlapping spectral peaks of conventional fluorescence readouts. Herein a rapid (80 min) multiplexed platform strategy for subtyping prostate cancer tumor and urine samples based on their RNA biomarker profiles is presented. This is achieved by combining rapid multiplexed isothermal reverse transcription-recombinase polymerase amplification (RT-RPA) of target RNA biomarkers with surface-enhanced Raman spectroscopy (SERS) nanotags for "one-pot" readout. This is the first translational application of a RT-RPA/SERS-based platform for multiplexed cancer biomarker detection to address a clinical need. With excellent sensitivity of 200 zmol (100 copies) and specificity, we believed that this platform methodology could be a useful tool for rapid multiplexed subtyping of cancers. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

ToxCast Profiling in a Human Stem Cell Assay for ...

EPA Pesticide Factsheets

Standard practice for assessing disruptions in embryogenesis involves testing pregnant animals of two species, typically rats and rabbits, exposed during major organogenesis and evaluated just prior to term. Under this design the major manifestations of developmental toxicity are observed as one or more apical endpoints including intrauterine death, fetal growth retardation, structural malformations and variations. Alternative approaches to traditional developmental toxicity testing have been proposed in the form of in vitro data (e.g., embryonic stem cells, zebrafish embryos, HTS assays) and in silico models (e.g., computational toxicology). To increase the diversity of assays used to assess developmental toxicity in EPA’s ToxCast program, we tested the chemicals in Stemina’s metabolomics-based platform that utilizes the commecrially available H9 human embryonic stem cell line. The devTOXqP dataset for ToxCast of high-quality based on replicate samples and model performance (82% balanced accuracy, 0.71 sensitivity and 1.00 specificity). To date, 136 ToxCast chemicals (12.8% of 1065 tested) were positive in this platform; 48 triggered the biomarker signal without any change in hESC viability and 88 triggered activity concurrent with effects on cell viability. Work is in progress to complete the STM dataset entry into the TCPL, compare data with results from zFish and mESC platforms, profile bioactivity (ToxCastDB), endpoints (ToxRefDB), chemotypes (DSSTox)

Floating Ocean Platform

DTIC Science & Technology

2003-08-15

floating structures create novel habitats for subtidal epibiota?, MARINE ECOLOGY -PROGRESS SERIES, 43-52 Mar. Ecol.- Prog. Ser., 2002 Vegueria, SFJ Godoy... ECOLOGICAL APPLICATIONS, 350-366 Ecol. Appl., 2000 Niedzwecki, JM van de Lindt, JW Gage, JH Teigen, PS, Design estimates of surface wave interaction with...The ecological effects beyond the offshore platform, Coastal Zone: Proceedings of the Symposium on Coastal and Ocean Management, v 2, n pt2, 1989, p

Validation of a multiplex electrochemiluminescent immunoassay platform in human and mouse samples

PubMed Central

Bastarache, J.A.; Koyama, T.; Wickersham, N.E; Ware, L.B.

2014-01-01

Despite the widespread use of multiplex immunoassays, there are very few scientific reports that test the accuracy and reliability of a platform prior to publication of experimental data. Our laboratory has previously demonstrated the need for new assay platform validation prior to use of biologic samples from large studies in order to optimize sample handling and assay performance. In this study, our goal was to test the accuracy and reproducibility of an electrochemiluminescent multiplex immunoassay platform (Meso Scale Discovery, MSD®) and compare this platform to validated, singleplex immunoassays (R&D Systems®) using actual study subject (human plasma and mouse bronchoalveolar lavage fluid (BALF) and plasma) samples. We found that the MSD platform performed well on intra- and inter-assay comparisons, spike and recovery and cross-platform comparisons. The mean intra-assay CV% and range for MSD was 3.49 (0.0-10.4) for IL-6 and 2.04 (0.1-7.9) for IL-8. The correlation between values for identical samples measured on both MSD and R&D was R=0.97 for both analytes. The mouse MSD assay had a broader range of CV% with means ranging from 9.5-28.5 depending on the analyte. The range of mean CV% was similar for single plex ELISAs at 4.3-23.7 depending on the analyte. Regardless of species or sample type, CV% was more variable at lower protein concentrations. In conclusion, we validated a multiplex electrochemiluminscent assay system and found that it has superior test characteristics in human plasma compared to mouse BALF and plasma. Both human and MSD assays compared favorably to well-validated singleplex ELISA's PMID:24768796

Universal Solid-phase Reversible Sample-Prep for Concurrent Proteome and N-glycome Characterization

PubMed Central

Zhou, Hui; Morley, Samantha; Kostel, Stephen; Freeman, Michael R.; Joshi, Vivek; Brewster, David; Lee, Richard S.

2017-01-01

SUMMARY We describe a novel Solid-phase Reversible Sample-Prep (SRS) platform, which enables rapid sample preparation for concurrent proteome and N-glycome characterization by mass spectrometry. SRS utilizes a uniquely functionalized, silica-based bead that has strong affinity toward proteins with minimal-to-no affinity for peptides and other small molecules. By leveraging the inherent size difference between, SRS permits high-capacity binding of proteins, rapid removal of small molecules (detergents, metabolites, salts, etc.), extensive manipulation including enzymatic and chemical treatments on beads-bound proteins, and easy recovery of N-glycans and peptides. The efficacy of SRS was evaluated in a wide range of biological samples including single glycoprotein, whole cell lysate, murine tissues, and human urine. To further demonstrate the SRS platform, we coupled a quantitative strategy to SRS to investigate the differences between DU145 prostate cancer cells and its DIAPH3-silenced counterpart. Our previous studies suggested that DIAPH3 silencing in DU145 prostate cancer cells induced transition to an amoeboid phenotype that correlated with tumor progression and metastasis. In this analysis we identified distinct proteomic and N-glycomic alterations between the two cells. Intriguingly, a metastasis-associated tyrosine kinase receptor ephrin-type-A receptor (EPHA2) was highly upregulated in DIAPH3-silenced cells, indicating underling connection between EPHA2 and DIAPH3. Moreover, distinct alterations in the N-glycome were identified, suggesting a cross-link between DIAPH3 and glycosyltransferase networks. Overall, SRS is an enabling universal sample preparation strategy that is not size limited and has the capability to efficiently prepare and clean peptides and N-glycans concurrently from nearly all sample types. Conceptually, SRS can be utilized for the analysis of other posttranslational modifications, and the unique surface chemistry can be further transformed for high-throughput automation. The technical simplicity, robustness, and modularity of SRS make it a highly promising technology with great potential in proteomic-based research. PMID:26791391

Cross-platform comparison for the detection of RAS mutations in cfDNA (ddPCR Biorad detection assay, BEAMing assay, and NGS strategy).

PubMed

Garcia, Jessica; Forestier, Julien; Dusserre, Eric; Wozny, Anne-Sophie; Geiguer, Florence; Merle, Patrick; Tissot, Claire; Ferraro-Peyret, Carole; Jones, Frederick S; Edelstein, Daniel L; Cheynet, Valérie; Bardel, Claire; Vilchez, Gaelle; Xu, Zhenyu; Bringuier, Pierre Paul; Barritault, Marc; Brengle-Pesce, Karen; Guillet, Marielle; Chauvenet, Marion; Manship, Brigitte; Brevet, Marie; Rodriguez-Lafrasse, Claire; Hervieu, Valérie; Couraud, Sébastien; Walter, Thomas; Payen, Léa

2018-04-20

CfDNA samples from colon (mCRC) and non-small cell lung cancers (NSCLC) (CIRCAN cohort) were compared using three platforms: droplet digital PCR (ddPCR, Biorad); BEAMing/OncoBEAM™-RAS-CRC (Sysmex Inostics); next-generation sequencing (NGS, Illumina), utilizing the 56G oncology panel (Swift Biosciences). Tissue biopsy and time matched cfDNA samples were collected at diagnosis in the mCRC cohort and during 1st progression in the NSCLC cohort. Excellent matches between cfDNA/FFPE mutation profiles were observed. Detection thresholds were between 0.5-1% for cfDNA samples examined using ddPCR and NGS, and 0.03% with BEAMing. This high level of sensitivity enabled the detection of KRAS mutations in 5/19 CRC patients with negative FFPE profiles. In the mCRC cohort, comparison of mutation results obtained by testing FFPE to those obtained by testing cfDNA by ddPCR resulted in 47% sensitivity, 77% specificity, 70% positive predictive value (PPV) and 55% negative predictive value (NPV). For BEAMing, we observed 93% sensitivity, 69% specificity, 78% PPV and 90% NPV. Finally, sensitivity of NGS was 73%, specificity was 77%, PPV 79% and NPV 71%. Our study highlights the complementarity of different diagnostic approaches and variability of results between OncoBEAM™-RAS-CRC and NGS assays. While the NGS assay provided a larger breadth of coverage of the major targetable alterations of 56 genes in one run, its performance for specific alterations was frequently confirmed by ddPCR results.

Cross-platform comparison for the detection of RAS mutations in cfDNA (ddPCR Biorad detection assay, BEAMing assay, and NGS strategy)

PubMed Central

Garcia, Jessica; Forestier, Julien; Dusserre, Eric; Wozny, Anne-Sophie; Geiguer, Florence; Merle, Patrick; Tissot, Claire; Ferraro-Peyret, Carole; Jones, Frederick S.; Edelstein, Daniel L.; Cheynet, Valérie; Bardel, Claire; Vilchez, Gaelle; Xu, Zhenyu; Bringuier, Pierre Paul; Barritault, Marc; Brengle-Pesce, Karen; Guillet, Marielle; Chauvenet, Marion; Manship, Brigitte; Brevet, Marie; Rodriguez-Lafrasse, Claire; Hervieu, Valérie; Couraud, Sébastien; Walter, Thomas; Payen, Léa

2018-01-01

CfDNA samples from colon (mCRC) and non-small cell lung cancers (NSCLC) (CIRCAN cohort) were compared using three platforms: droplet digital PCR (ddPCR, Biorad); BEAMing/OncoBEAM™-RAS-CRC (Sysmex Inostics); next-generation sequencing (NGS, Illumina), utilizing the 56G oncology panel (Swift Biosciences). Tissue biopsy and time matched cfDNA samples were collected at diagnosis in the mCRC cohort and during 1st progression in the NSCLC cohort. Excellent matches between cfDNA/FFPE mutation profiles were observed. Detection thresholds were between 0.5–1% for cfDNA samples examined using ddPCR and NGS, and 0.03% with BEAMing. This high level of sensitivity enabled the detection of KRAS mutations in 5/19 CRC patients with negative FFPE profiles. In the mCRC cohort, comparison of mutation results obtained by testing FFPE to those obtained by testing cfDNA by ddPCR resulted in 47% sensitivity, 77% specificity, 70% positive predictive value (PPV) and 55% negative predictive value (NPV). For BEAMing, we observed 93% sensitivity, 69% specificity, 78% PPV and 90% NPV. Finally, sensitivity of NGS was 73%, specificity was 77%, PPV 79% and NPV 71%. Our study highlights the complementarity of different diagnostic approaches and variability of results between OncoBEAM™-RAS-CRC and NGS assays. While the NGS assay provided a larger breadth of coverage of the major targetable alterations of 56 genes in one run, its performance for specific alterations was frequently confirmed by ddPCR results. PMID:29765524

Liquid chromatography-mass spectrometry platform for both small neurotransmitters and neuropeptides in blood, with automatic and robust solid phase extraction

NASA Astrophysics Data System (ADS)

Johnsen, Elin; Leknes, Siri; Wilson, Steven Ray; Lundanes, Elsa

2015-03-01

Neurons communicate via chemical signals called neurotransmitters (NTs). The numerous identified NTs can have very different physiochemical properties (solubility, charge, size etc.), so quantification of the various NT classes traditionally requires several analytical platforms/methodologies. We here report that a diverse range of NTs, e.g. peptides oxytocin and vasopressin, monoamines adrenaline and serotonin, and amino acid GABA, can be simultaneously identified/measured in small samples, using an analytical platform based on liquid chromatography and high-resolution mass spectrometry (LC-MS). The automated platform is cost-efficient as manual sample preparation steps and one-time-use equipment are kept to a minimum. Zwitter-ionic HILIC stationary phases were used for both on-line solid phase extraction (SPE) and liquid chromatography (capillary format, cLC). This approach enabled compounds from all NT classes to elute in small volumes producing sharp and symmetric signals, and allowing precise quantifications of small samples, demonstrated with whole blood (100 microliters per sample). An additional robustness-enhancing feature is automatic filtration/filter back-flushing (AFFL), allowing hundreds of samples to be analyzed without any parts needing replacement. The platform can be installed by simple modification of a conventional LC-MS system.

An alpha-synuclein MRM assay with diagnostic potential for Parkinson's disease and monitoring disease progression.

PubMed

Yang, Li; Stewart, Tessandra; Shi, Min; Pottiez, Gwenael; Dator, Romel; Wu, Rui; Aro, Patrick; Schuster, Robert J; Ginghina, Carmen; Pan, Catherine; Gao, Yuqian; Qian, Weijun; Zabetian, Cyrus P; Hu, Shu-Ching; Quinn, Joseph F; Zhang, Jing

2017-07-01

The alpha-synuclein (α-syn) level in human cerebrospinal fluid (CSF), as measured by immunoassays, is promising as a Parkinson's disease (PD) biomarker. However, the levels of total α-syn are inconsistent among studies with large cohorts and different measurement platforms. Total α-syn level also does not correlate with disease severity or progression. Here, the authors developed a highly sensitive MRM method to measure absolute CSF α-syn peptide concentrations without prior enrichment or fractionation, aiming to discover new candidate biomarkers. Six peptides covering 73% of protein sequence were reliably identified, and two were consistently quantified in cross-sectional and longitudinal cohorts. Absolute concentration of α-syn in human CSF was determined to be 2.1 ng/mL. A unique α-syn peptide, TVEGAGSIAAATGFVK (81-96), displayed excellent correlation with previous immunoassay results in two independent PD cohorts (p < 0.001), correlated with disease severity, and its changes significantly tracked the disease progression longitudinally. An MRM assay to quantify human CSF α-syn was developed and optimized. Sixty clinical samples from cross-sectional and longitudinal PD cohorts were analyzed with this approach. Although further larger scale validation is needed, the results suggest that α-syn peptide could serve as a promising biomarker in PD diagnosis and progression. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An alpha-synuclein MRM assay with diagnostic potential for Parkinson's disease and monitoring disease progression

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Li; Stewart, Tessandra; Shi, Min

Aim: The alpha-synuclein (α-syn) level in human cerebrospinal fluid (CSF), as measured by immunoassays, is promising as a Parkinson’s disease (PD) biomarker. However, the levels of total α-syn are inconsistent among studies with large cohorts and different measurement platforms. Total α-syn level also does not correlate with disease severity or progression. Here, we developed a highly sensitive Multiple Reaction Monitoring (MRM) method to measure absolute CSF α-syn peptide concentrations without prior enrichment or fractionation, aiming to discover new candidate biomarkers. Results: Six peptides covering 73% of protein sequence were reliably identified, and two were consistently quantified in cross-sectional and longitudinalmore » cohorts. Absolute concentration of α-syn in human CSF was determined to be 2.1ng/mL. A unique α-syn peptide, TVEGAGSIAAATGFVK (81-96), displayed excellent correlation with previous immunoassay results in two independent PD cohorts (p < 0.001), correlated with disease severity, and its changes significantly tracked the disease progression longitudinally. Conclusions: An MRM assay to quantify human CSF α-syn was developed and optimized. Sixty clinical samples from cross-sectional and longitudinal PD cohorts were analyzed with this approach. Although further larger-scale validation is needed, the results suggest that α-syn peptide could serve as a promising biomarker in PD diagnosis and progression.« less

Vaccines for Viral Hemorrhagic Fevers – Progress and Shortcomings

PubMed Central

Falzarano, Darryl; Feldmann, Heinz

2013-01-01

With a few exceptions, vaccines for viruses that cause hemorrhagic fever remain unavailable or lack well-documented efficacy. In the past decade this has not been due to a lack of the ability to develop vaccine platforms against highly pathogenic viruses, but rather the lack of will/interest to invest in platforms that have the potential to become successful vaccines. The two exceptions to this are vaccines against Dengue virus and Rift Valley Fever virus, which recently have seen significant progress in putting forward new and improved vaccines, respectively. Experimental vaccines for filoviruses and Lassa virus do exist but are hindered by a lack of financial interest and only partially or ill-defined correlates/mechanisms of protection that could be assessed in clinical trials. PMID:23773330

Observing the ocean with different platforms/methods. Advantages, disadvantages and lessons learnt

NASA Astrophysics Data System (ADS)

Petihakis, George; Potiris, Manolis; Ntoumas, Manolis; Frangoulis, Kostas; Tsiaras, Kostas; Triantafyllou, George; Pollani, Annika

2015-04-01

Methods for observing/measuring the ocean, present remarkable diversity. In situ sampling or remote sensing, automated or not measurements with sensing probes, utilize different measuring principles, sample different parts of the system, are characterized by different accuracy/precision and sample over a large range of spatial and temporal scales with variable resolution. Measurements, quite often are dependent on the platform design and the platform interaction with the highly variable ambient environment. To add to the aforementioned issues that render the combination of data from different sources challenging from a scientific perspective, there are also a number of technical and data issues. These are important for the good operational status of the platforms, the smooth data flow and the collection of appropriate meta-data. Finally the raw data files need to be processed into a user friendly output format so the operator will be able to identify as early as possible sensor drift and failures. In this work, data from different observation platforms/sensors is analysed and compared, while mechanisms and processes responsible for differences are identified. More detailed, temperature, salinity and chlorophyll data from four fixed observing stations, one Ferry Box, satellites and a monthly in situ sampling program, is used. Main results indicate that a) regular calibration according to expected parameter range and well-defined, consistent deployment plan of proven sensors is sufficient for acquiring high quality data in the long term. Better knowledge of site specific response of new instrumentation is required for producing consistent long term data b) duplicate sensors on one platform considerably improve data flow and data quality c) if an area is sampled by multiple platforms, then platform dependent errors can be quantified d) fixed point observatories are efficient tools for assessing regional performance of satellite products. Higher vertical and temporal sampling rate of the upper 20m of the water column increase inter-comparability between the two platforms e) delayed mode, lower processing level data/meta-data should be archived and disseminated in addition to standard formatted files due to analysis artifacts and loss of information during transmission and processing.

Formal Learning Sequences and Progression in the Studio: A Framework for Digital Design Education

ERIC Educational Resources Information Center

Wärnestål, Pontus

2016-01-01

This paper examines how to leverage the design studio learning environment throughout long-term Digital Design education in order to support students to progress from tactical, well-defined, device-centric routine design, to confidently design sustainable solutions for strategic, complex, problems for a wide range of devices and platforms in the…

RNase One Gene Isolation, Expression, and Affinity Purification Models Research Experimental Progression and Culminates with Guided Inquiry-Based Experiments

ERIC Educational Resources Information Center

Bailey, Cheryl P.

2009-01-01

This new biochemistry laboratory course moves through a progression of experiments that generates a platform for guided inquiry-based experiments. RNase One gene is isolated from prokaryotic genomic DNA, expressed as a tagged protein, affinity purified, and tested for activity and substrate specificity. Student pairs present detailed explanations…

RDT&E Progress and Plansfor Hexavalent Chromium (Cr6+)

DTIC Science & Technology

2011-05-12

RDT&E Progress and Plans for Hexavalent Chromium (Cr6+) Bruce Sartwell Weapons Systems and Platforms Program Manager E2S2 Conference May 12, 2011...2011 2. REPORT TYPE 3. DATES COVERED 00-00-2011 to 00-00-2011 4. TITLE AND SUBTITLE RDT&E Progress and Plansfor Hexavalent Chromium (Cr6+) 5a...Tasks/Projects Surface treatments and soluble inhibitors: 1. Fundamental studies of the Trivalent Chrome Process (TCP) 2. Mechanisms of selected

Comparison of Online Survey Recruitment Platforms for Hard-to-Reach Pregnant Smoking Populations: Feasibility Study

PubMed Central

Agas, Jessica Marie; Lee, Melissa; Pan, Julia Lily; Buttenheim, Alison Meredith

2018-01-01

Background Recruiting hard-to-reach populations for health research is challenging. Web-based platforms offer one way to recruit specific samples for research purposes, but little is known about the feasibility of online recruitment and the representativeness and comparability of samples recruited through different Web-based platforms. Objective The objectives of this study were to determine the feasibility of recruiting a hard-to-reach population (pregnant smokers) using 4 different Web-based platforms and to compare participants recruited through each platform. Methods A screener and survey were distributed online through Qualtrics Panel, Soapbox Sample, Reddit, and Amazon Mechanical Turk (mTurk). Descriptive statistics were used to summarize results of each recruitment platform, including eligibility yield, quality yield, income, race, age, and gestational age. Results Of the 3847 participants screened for eligibility across all 4 Web-based platforms, 535 were eligible and 308 completed the survey. Amazon mTurk yielded the fewest completed responses (n=9), 100% (9/9) of which passed several quality metrics verifying pregnancy and smoking status. Qualtrics Panel yielded 14 completed responses, 86% (12/14) of which passed the quality screening. Soapbox Sample produced 107 completed surveys, 67% (72/107) of which were found to be quality responses. Advertising through Reddit produced the highest completion rate (n=178), but only 29.2% (52/178) of those surveys passed the quality metrics. We found significant differences in eligibility yield, quality yield, age, number of previous pregnancies, age of smoking initiation, current smokers, race, education, and income (P<.001). Conclusions Although each platform successfully recruited pregnant smokers, results varied in quality, cost, and percentage of complete responses. Moving forward, investigators should pay careful attention to the percentage yield and cost of online recruitment platforms to maximize internal and external validity. PMID:29661751

Development and Validation of a Novel Platform-Independent Metastasis Signature in Human Breast Cancer

PubMed Central

Speers, Corey; Liu, Meilan; Wilder-Romans, Kari; Lawrence, Theodore S.; Pierce, Lori J.; Feng, Felix Y.

2015-01-01

Purpose The molecular drivers of metastasis in breast cancer are not well understood. Therefore, we sought to identify the biological processes underlying distant progression and define a prognostic signature for metastatic potential in breast cancer. Experimental design In vivo screening for metastases was performed using Chick Chorioallantoic Membrane assays in 21 preclinical breast cancer models. Expressed genes associated with metastatic potential were identified using high-throughput analysis. Correlations with biological function were determined using the Database for Annotation, Visualization and Integrated Discovery. Results We identified a broad range of metastatic potential that was independent of intrinsic breast cancer subtypes. 146 genes were significantly associated with metastasis progression and were linked to cancer-related biological functions, including cell migration/adhesion, Jak-STAT, TGF-beta, and Wnt signaling. These genes were used to develop a platform-independent gene expression signature (M-Sig), which was trained and subsequently validated on 5 independent cohorts totaling nearly 1800 breast cancer patients with all p-values < 0.005 and hazard ratios ranging from approximately 2.5 to 3. On multivariate analysis accounting for standard clinicopathologic prognostic variables, M-Sig remained the strongest prognostic factor for metastatic progression, with p-values < 0.001 and hazard ratios > 2 in three different cohorts. Conclusion M-Sig is strongly prognostic for metastatic progression, and may provide clinical utility in combination with treatment prediction tools to better guide patient care. In addition, the platform-independent nature of the signature makes it an excellent research tool as it can be directly applied onto existing, and future, datasets. PMID:25974184

Towards a “Sample-In, Answer-Out” Point-of-Care Platform for Nucleic Acid Extraction and Amplification: Using an HPV E6/E7 mRNA Model System

PubMed Central

Gulliksen, Anja; Keegan, Helen; Martin, Cara; O'Leary, John; Solli, Lars A.; Falang, Inger Marie; Grønn, Petter; Karlgård, Aina; Mielnik, Michal M.; Johansen, Ib-Rune; Tofteberg, Terje R.; Baier, Tobias; Gransee, Rainer; Drese, Klaus; Hansen-Hagge, Thomas; Riegger, Lutz; Koltay, Peter; Zengerle, Roland; Karlsen, Frank; Ausen, Dag; Furuberg, Liv

2012-01-01

The paper presents the development of a “proof-of-principle” hands-free and self-contained diagnostic platform for detection of human papillomavirus (HPV) E6/E7 mRNA in clinical specimens. The automated platform performs chip-based sample preconcentration, nucleic acid extraction, amplification, and real-time fluorescent detection with minimal user interfacing. It consists of two modular prototypes, one for sample preparation and one for amplification and detection; however, a common interface is available to facilitate later integration into one single module. Nucleic acid extracts (n = 28) from cervical cytology specimens extracted on the sample preparation chip were tested using the PreTect HPV-Proofer and achieved an overall detection rate for HPV across all dilutions of 50%–85.7%. A subset of 6 clinical samples extracted on the sample preparation chip module was chosen for complete validation on the NASBA chip module. For 4 of the samples, a 100% amplification for HPV 16 or 33 was obtained at the 1 : 10 dilution for microfluidic channels that filled correctly. The modules of a “sample-in, answer-out” diagnostic platform have been demonstrated from clinical sample input through sample preparation, amplification and final detection. PMID:22235204

Defense.gov - Special Report - Progress Report: Department of Defense

Science.gov Websites

the need to re-shape and re-balance the direction of the Department and an increasingly challenging capabilities, requirements, risks and needs for the purpose of shifting the Department toward a different , the Landing Platform Dock ship and Mobile Landing Platform ship; and Completing production of the C-17

Use of Sequence-independent, single-primer amplification (SISPA) with NGS platform for detection of RNA viruses in clinical samples

USDA-ARS?s Scientific Manuscript database

Current technologies for next generation sequencing (NGS) have revolutionized metagenomics analysis of clinical samples. One advantage of the NGS platform is the possibility to sequence the genetic material in samples without any prior knowledge of the sequence contained within. Sequence-Independent...

Multiparametric, Longitudinal Optical Coherence Tomography Imaging Reveals Acute Injury and Chronic Recovery in Experimental Ischemic Stroke

PubMed Central

Srinivasan, Vivek J.; Mandeville, Emiri T.; Can, Anil; Blasi, Francesco; Climov, Mihail; Daneshmand, Ali; Lee, Jeong Hyun; Yu, Esther; Radhakrishnan, Harsha; Lo, Eng H.; Sakadžić, Sava; Eikermann-Haerter, Katharina; Ayata, Cenk

2013-01-01

Progress in experimental stroke and translational medicine could be accelerated by high-resolution in vivo imaging of disease progression in the mouse cortex. Here, we introduce optical microscopic methods that monitor brain injury progression using intrinsic optical scattering properties of cortical tissue. A multi-parametric Optical Coherence Tomography (OCT) platform for longitudinal imaging of ischemic stroke in mice, through thinned-skull, reinforced cranial window surgical preparations, is described. In the acute stages, the spatiotemporal interplay between hemodynamics and cell viability, a key determinant of pathogenesis, was imaged. In acute stroke, microscopic biomarkers for eventual infarction, including capillary non-perfusion, cerebral blood flow deficiency, altered cellular scattering, and impaired autoregulation of cerebral blood flow, were quantified and correlated with histology. Additionally, longitudinal microscopy revealed remodeling and flow recovery after one week of chronic stroke. Intrinsic scattering properties serve as reporters of acute cellular and vascular injury and recovery in experimental stroke. Multi-parametric OCT represents a robust in vivo imaging platform to comprehensively investigate these properties. PMID:23940761

Characteristics of produced water discharged to the Gulf of Mexico hypoxiczone.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Veil, J. A.; Kimmell, T. A.; Rechner, A. C.

2005-08-24

Each summer, an area of low dissolved oxygen (the hypoxic zone) forms in the shallow nearshore Gulf of Mexico waters from the Mississippi River Delta westward to near the Texas/Louisiana border. Most scientists believe that the leading contributor to the hypoxic zone is input of nutrients (primarily nitrogen and phosphorus compounds) from the Mississippi and Atchafalaya Rivers. The nutrients stimulate growth of phytoplankton. As the phytoplankton subsequently die, they fall to the bottom waters where they are decomposed by microorganisms. The decomposition process consumes oxygen in the bottom waters to create hypoxic conditions. Sources other than the two rivers mentionedmore » above may also contribute significant quantities of oxygen-demanding pollutants. One very visible potential source is the hundreds of offshore oil and gas platforms located within or near the hypoxic zone. Many of these platforms discharge varying volumes of produced water. However, only limited data characterizing oxygen demand and nutrient concentration and loading from offshore produced water discharges have been collected. No comprehensive and coordinated oxygen demand data exist for produced water discharges in the Gulf of Mexico. This report describes the results of a program to sample 50 offshore oil and gas platforms located within the Gulf of Mexico hypoxic zone. The program was conducted in response to a requirement in the U.S. Environmental Protection Agency (EPA) general National Pollutant Discharge Elimination System (NPDES) permit for offshore oil and gas discharges. EPA requested information on the amount of oxygen-demanding substances contained in the produced water discharges. This information is needed as inputs to several water quality models that EPA intends to run to estimate the relative contributions of the produced water discharges to the occurrence of the hypoxic zone. Sixteen platforms were sampled 3 times each at approximately one-month intervals to give an estimate of temporal variability. An additional 34 platforms were sampled one time. The 50 sampled platforms were scattered throughout the hypoxic zone to give an estimate of spatial variability. Each platform was sampled for biochemical oxygen demand (BOD), total organic carbon (TOC), nitrogen (ammonia, nitrate, nitrite, and total Kjeldahl nitrogen [TKN]), and phosphorus (total phosphorus and orthophosphate). In addition to these parameters, each sample was monitored for pH, conductivity, salinity, and temperature. The sampling provided average platform concentrations for each parameter. Table ES-1 shows the mean, median, maximum, and minimum for the sampled parameters. For some of the parameters, the mean is considerably larger than the median, suggesting that one or a few data points are much higher than the rest of the points (outliers). Chapter 4 contains an extensive discussion of outliers and shows how the sample results change if outliers are deleted from consideration. A primary goal of this study is to estimate the mass loading (lb/day) of each of the oxygen-demanding pollutants from the 50 platforms sampled in the study. Loading is calculated by multiplying concentrations by the discharge volume and then by a conversion factor to allow units to match. The loadings calculated in this study of 50 platforms represent a produced water discharge volume of about 176,000 bbl/day. The total amount of produced water generated in the hypoxic zone during the year 2003 was estimated as 508,000 bbl/day. This volume is based on reports by operators to the Minerals Management Service each year. It reflects the volume of produced water that is generated from each lease, not the volume that is discharged from each platform. The mass loadings from offshore oil and gas discharges to the entire hypoxic zone were estimated by multiplying the 50-platform loadings by the ratio of total water generated to 50-platform discharge volume. The loadings estimated for the 50 platforms and for the entire hypoxic zone are shown in Table ES-2. These estimates and the sampling data from 50 platforms represent the most complete and comprehensive effort ever undertaken to characterize the amount and potential sources of the oxygen demand in offshore oil and gas produced water discharges.« less

Ubiquitous Stereo Vision for Controlling Safety on Platforms in Railroad Station

NASA Astrophysics Data System (ADS)

Yoda, Ikushi; Hosotani, Daisuke; Sakaue, Katushiko

Dozens of people are killed every year when they fall off of train platforms, making this an urgent issue to be addressed by the railroads, especially in the major cities. This concern prompted the present work that is now in progress to develop a Ubiquitous Stereo Vision based system for safety management at the edge of rail station platforms. In this approach, a series of stereo cameras are installed in a row on the ceiling that are pointed downward at the edge of the platform to monitor the disposition of people waiting for the train. The purpose of the system is to determine automatically and in real-time whether anyone or anything is in the danger zone at the very edge of the platform, whether anyone has actually fallen off the platform, or whether there is any sign of these things happening. The system could be configured to automatically switch over to a surveillance monitor or automatically connect to an emergency brake system in the event of trouble.

Apprenticeship and Progression in the Healthcare Sector: Can Labour Market Theory Illuminate Barriers and Opportunities in Contrasting Occupations?

ERIC Educational Resources Information Center

Turbin, Jill; Fuller, Alison; Wintrup, Julie

2014-01-01

There is growing research and policy interest in the extent to which government supported Apprenticeship in England provides a platform for educational and career progression in different occupational sectors. This paper makes a contribution to this debate by presenting research on the healthcare sector undertaken in a regional health authority in…

Comparison of three multiplex gastrointestinal platforms for the detection of gastroenteritis viruses

PubMed Central

Chhabra, Preeti; Gregoricus, Nicole; Weinberg, Geoffrey A.; Halasa, Natasha; Chappell, James; Hassan, Ferdaus; Selvarangan, Rangaraj; Mijatovic-Rustempasic, Slavica; Ward, M. Leanne; Bowen, Michael; Payne, Daniel C.; Vinjé, Jan

2018-01-01

Background Viruses are major etiological agents of childhood gastroenteritis. In recent years, several molecular platforms for the detection of viral enteric pathogens have become available. Objective/study design We evaluated the performance of three multiplex platforms including Biofire’s Gastrointestinal Panel (FilmArray), Luminex xTAG® Gastrointestinal Pathogen Panel (GPP), and the TaqMan Array Card (TAC) for the detection of five gastroenteritis viruses using a coded panel of 300 archived stool samples. Results The FilmArray detected a virus in 199 (96.1%) and the TAC in 172 (83.1%) of the 207 samples (187 samples positive for a single virus and 20 samples positive for more than one virus) whereas the GPP detected a virus in 100 (78.7%) of the 127 (97 positive for one virus and three positive for more than one virus) samples. Overall the clinical accuracy was highest for the FilmArray (98%) followed by TAC (97.2%) and GPP (96.9%). The sensitivity of the FilmArray, GPP and TAC platforms was highest for rotavirus (100%, 95.8%, and 89.6%, respectively) and lowest for adenovirus type 40/41 (97.4%, 57.9% and 68.4%). The specificity of the three platforms ranged from 95.6% (rotavirus) to 99.6% (norovirus/sapovirus) for the FilmArray, 99.6% (norovirus) to 100% (rotavirus/adenovirus) for GPP, and 98.9% (astrovirus) to 100% (rotavirus/sapovirus) for TAC. Conclusion The FilmArray demonstrated the best analytical performance followed by TAC. In recent years, the availability of multi-enteric molecular testing platforms has increased significantly and our data highlight the strengths and weaknesses of these platforms. PMID:28889082

Plug-and-actuate on demand: multimodal individual addressability of microarray plates using modular hybrid acoustic wave technology.

PubMed

Rezk, Amgad R; Ramesan, Shwathy; Yeo, Leslie Y

2018-01-30

The microarray titre plate remains a fundamental workhorse in genomic, proteomic and cellomic analyses that underpin the drug discovery process. Nevertheless, liquid handling technologies for sample dispensing, processing and transfer have not progressed significantly beyond conventional robotic micropipetting techniques, which are not only at their fundamental sample size limit, but are also prone to mechanical failure and contamination. This is because alternative technologies to date suffer from a number of constraints, mainly their limitation to carry out only a single liquid operation such as dispensing or mixing at a given time, and their inability to address individual wells, particularly at high throughput. Here, we demonstrate the possibility for true sequential or simultaneous single- and multi-well addressability in a 96-well plate using a reconfigurable modular platform from which MHz-order hybrid surface and bulk acoustic waves can be coupled to drive a variety of microfluidic modes including mixing, sample preconcentration and droplet jetting/ejection in individual or multiple wells on demand, thus constituting a highly versatile yet simple setup capable of improving the functionality of existing laboratory protocols and processes.

Technologies for Assessment of Motor Disorders in Parkinson’s Disease: A Review

PubMed Central

Oung, Qi Wei; Muthusamy, Hariharan; Lee, Hoi Leong; Basah, Shafriza Nisha; Yaacob, Sazali; Sarillee, Mohamed; Lee, Chia Hau

2015-01-01

Parkinson’s Disease (PD) is characterized as the commonest neurodegenerative illness that gradually degenerates the central nervous system. The goal of this review is to come out with a summary of the recent progress of numerous forms of sensors and systems that are related to diagnosis of PD in the past decades. The paper reviews the substantial researches on the application of technological tools (objective techniques) in the PD field applying different types of sensors proposed by previous researchers. In addition, this also includes the use of clinical tools (subjective techniques) for PD assessments, for instance, patient self-reports, patient diaries and the international gold standard reference scale, Unified Parkinson Disease Rating Scale (UPDRS). Comparative studies and critical descriptions of these approaches have been highlighted in this paper, giving an insight on the current state of the art. It is followed by explaining the merits of the multiple sensor fusion platform compared to single sensor platform for better monitoring progression of PD, and ends with thoughts about the future direction towards the need of multimodal sensor integration platform for the assessment of PD. PMID:26404288

The Effect of Lithospheric Discontinuities on the Composition of Lavas From the Northern Galápagos Platform Extension

NASA Astrophysics Data System (ADS)

Schlitzer, W.; Harpp, K. S.; Mittelstaedt, E. L.; Kurz, M. D.; Geist, D.

2011-12-01

The platform supporting the Galápagos Archipelago extends ~50 km NW toward the Galápagos Spreading Center (GSC) into the Northern Galapagos Volcanic Province (NGVP), where it underlies Pinta, Marchena, and Genovesa Islands. Approximately 45 km north of Pinta is the southern termination of a ~100-km long transform fault, at 90o50'W. The seafloor surrounding the NGVP was surveyed and dredged during the 2010 MV1007 and 2001 DRIFT04 cruises. All the large volcanoes, including the islands, have elongate bathymetric footprints with extensive submarine ridges. Lavas from this small region (<150 km in diameter) exhibit isotopic and trace element signatures that span the compositional range of the entire Galápagos Archipelago. Pinta and its submarine extension have the most enriched signatures, whereas at the eastern end of the platform extension, Genovesa is indistinguishable from normal MORB. Samples dredged around Pinta and Marchena have intermediate compositions. In contrast, lavas from the adjacent transform fault are more depleted than those from Genovesa and anywhere along the GSC for hundreds of km in both directions. Lavas from this region exhibit a range of 3He/4He (6.5-9.5 Ra), significantly lower than the high 3He/4He signature of material erupted by the plume-rich western Galápagos shield volcanoes (>25 Ra). Whereas the compositions of lavas erupted on the Nazca Plate in the NGVP require 3 or more distinct mantle endmembers to explain their compositions, our data indicate that the platform extension region only requires components previously described for the Galápagos Islands. In addition, Sm/Yb decreases abruptly along an E-W transect from Pinta to Genovesa. Gibson and Geist (2010) concluded that Sm/Yb ratios reflect variations in surface wave velocities (Villagomez et al., 2007), enabling them to predict lithospheric thickness. We apply the relationship defined by Gibson and Geist to map lithospheric thickness across our study area. Our results suggest that the lithosphere (and thus minimum melt generation depth) gets progressively shallower from Pinta to Genovesa; this phenomenon may explain unexpected Holocene volcanism in the NGVP. The wide range in Sm/Yb further suggests a complex lithospheric structure underlying the platform extension, which we propose reflects formation of the adjacent GSC transform fault within the last ~3 Ma, possibly through a series of ridge jumps as suggested by modeling of new magnetic data. We propose a model in which heterogeneous plume material with enriched and depleted components (Ito and Mahoney, 2005) is migrating toward the GSC along the base of the lithosphere, having previously lost its primordial helium signature during deep melting near the western shield volcanoes. As the material crosses the complex lithospheric thickness variations in the NGVP, melt generation becomes progressively shallower. The enriched compositions at Pinta thus result from limited, deep melting of enriched compositions owing to a thick lithospheric cap. East of Pinta, the plume melts more extensively and to shallower depths, producing progressively depleted signatures toward Genovesa.

Evaluation of Multiple Immunoassay Technology Platforms to Select the Anti-Drug Antibody Assay Exhibiting the Most Appropriate Drug and Target Tolerance

PubMed Central

Collet-Brose, Justine

2016-01-01

The aim of this study was, at the assay development stage and thus with an appropriate degree of rigor, to select the most appropriate technology platform and sample pretreatment procedure for a clinical ADA assay. Thus, ELISA, MSD, Gyrolab, and AlphaLISA immunoassay platforms were evaluated in association with target depletion and acid dissociation sample pretreatment steps. An acid dissociation step successfully improved the drug tolerance for all 4 technology platforms and the required drug tolerance was achieved with the Gyrolab and MSD platforms. The target tolerance was shown to be better for the ELISA format, where an acid dissociation treatment step alone was sufficient to achieve the desired target tolerance. However, inclusion of a target depletion step in conjunction with the acid treatment raised the target tolerance to the desired level for all of the technologies. A higher sensitivity was observed for the MSD and Gyrolab assays and the ELISA, MSD, and Gyrolab all displayed acceptable interdonor variability. This study highlights the usefulness of evaluating the performance of different assay platforms at an early stage in the assay development process to aid in the selection of the best fit-for-purpose technology platform and sample pretreatment steps. PMID:27243038

Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges.

PubMed

Yin, Zekun; Lan, Haidong; Tan, Guangming; Lu, Mian; Vasilakos, Athanasios V; Liu, Weiguo

2017-01-01

The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the challenge of gaining a profound insight into the deepest biological functions from big biological data. This in turn requires massive computational resources. Therefore, high performance computing (HPC) platforms are highly needed as well as efficient and scalable algorithms that can take advantage of these platforms. In this paper, we survey the state-of-the-art HPC platforms for big biological data analytics. We first list the characteristics of big biological data and popular computing platforms. Then we provide a taxonomy of different biological data analysis applications and a survey of the way they have been mapped onto various computing platforms. After that, we present a case study to compare the efficiency of different computing platforms for handling the classical biological sequence alignment problem. At last we discuss the open issues in big biological data analytics.

Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing.

PubMed

Fang, Chao; Zhong, Huanzi; Lin, Yuxiang; Chen, Bing; Han, Mo; Ren, Huahui; Lu, Haorong; Luber, Jacob M; Xia, Min; Li, Wangsheng; Stein, Shayna; Xu, Xun; Zhang, Wenwei; Drmanac, Radoje; Wang, Jian; Yang, Huanming; Hammarström, Lennart; Kostic, Aleksandar D; Kristiansen, Karsten; Li, Junhua

2018-03-01

More extensive use of metagenomic shotgun sequencing in microbiome research relies on the development of high-throughput, cost-effective sequencing. Here we present a comprehensive evaluation of the performance of the new high-throughput sequencing platform BGISEQ-500 for metagenomic shotgun sequencing and compare its performance with that of 2 Illumina platforms. Using fecal samples from 20 healthy individuals, we evaluated the intra-platform reproducibility for metagenomic sequencing on the BGISEQ-500 platform in a setup comprising 8 library replicates and 8 sequencing replicates. Cross-platform consistency was evaluated by comparing 20 pairwise replicates on the BGISEQ-500 platform vs the Illumina HiSeq 2000 platform and the Illumina HiSeq 4000 platform. In addition, we compared the performance of the 2 Illumina platforms against each other. By a newly developed overall accuracy quality control method, an average of 82.45 million high-quality reads (96.06% of raw reads) per sample, with 90.56% of bases scoring Q30 and above, was obtained using the BGISEQ-500 platform. Quantitative analyses revealed extremely high reproducibility between BGISEQ-500 intra-platform replicates. Cross-platform replicates differed slightly more than intra-platform replicates, yet a high consistency was observed. Only a low percentage (2.02%-3.25%) of genes exhibited significant differences in relative abundance comparing the BGISEQ-500 and HiSeq platforms, with a bias toward genes with higher GC content being enriched on the HiSeq platforms. Our study provides the first set of performance metrics for human gut metagenomic sequencing data using BGISEQ-500. The high accuracy and technical reproducibility confirm the applicability of the new platform for metagenomic studies, though caution is still warranted when combining metagenomic data from different platforms.

Dielectrophoresis-based microfluidic platforms for cancer diagnostics.

PubMed

Chan, Jun Yuan; Ahmad Kayani, Aminuddin Bin; Md Ali, Mohd Anuar; Kok, Chee Kuang; Yeop Majlis, Burhanuddin; Hoe, Susan Ling Ling; Marzuki, Marini; Khoo, Alan Soo-Beng; Ostrikov, Kostya Ken; Ataur Rahman, Md; Sriram, Sharath

2018-01-01

The recent advancement of dielectrophoresis (DEP)-enabled microfluidic platforms is opening new opportunities for potential use in cancer disease diagnostics. DEP is advantageous because of its specificity, low cost, small sample volume requirement, and tuneable property for microfluidic platforms. These intrinsic advantages have made it especially suitable for developing microfluidic cancer diagnostic platforms. This review focuses on a comprehensive analysis of the recent developments of DEP enabled microfluidic platforms sorted according to the target cancer cell. Each study is critically analyzed, and the features of each platform, the performance, added functionality for clinical use, and the types of samples, used are discussed. We address the novelty of the techniques, strategies, and design configuration used in improving on existing technologies or previous studies. A summary of comparing the developmental extent of each study is made, and we conclude with a treatment of future trends and a brief summary.

Age progressive volcanism opposite Nazca plate motion: Insights from seamounts on the northeastern margin of the Galapagos Platform

NASA Astrophysics Data System (ADS)

Sinton, Christopher W.; Hauff, Folkmar; Hoernle, Kaj; Werner, Reinhard

2018-06-01

We present new geochemical and 40Ar/39Ar analyses from seven seamounts located off the northeastern margin of the shallow Galápagos Platform. Initial volcanism at 5.2 Ma created a small island (Pico) over the current location of the hotspot with geochemically enriched lavas. There is no further record of magmatism in the study area until 3.8 to 2.5 Ma, during which four roughly conical volcanoes (Sunray, Grande, Fitzroy, and Beagle) formed through eruption of lavas derived from a depleted mantle source. Sunray, Fitzroy, and Grande were islands that existed for 3 m.y. ending with the submergence of Fitzroy at 0.5 Ma. The youngest seamounts, Largo and Iguana, do not appear to have been subaerial and were active at 1.3 Ma and 0.5 Ma, respectively, with the style of edifice changing from the previous large cones to E-W elongate, composite structures. The progression of magmatism suggests that Pico erupted near 91.5°W near the location of the Galápagos plume while the others formed well east of the plume center. If the locations of initial volcanism are calculated using the eastward velocity of the Nazca plate, there appears to be a progression of younger volcanism toward the east, opposite what would be expected from a fixed mantle plume source. The rate that initial volcanism moves eastward is close to the plate velocity. A combination of higher temperature and geochemical enrichment of the thickened lithosphere of the Galápagos platform could have provided a viscosity gradient at the boundary between the thick lithosphere and the thinner oceanic lithosphere to the northeast. As this boundary moved eastward with the Nazca plate, it progressively triggered shear-driven mantle upwelling and volcanism.

Monitoring sepsis using electrical cell profiling.

PubMed

Prieto, Javier L; Su, Hao-Wei; Hou, Han Wei; Vera, Miguel Pinilla; Levy, Bruce D; Baron, Rebecca M; Han, Jongyoon; Voldman, Joel

2016-11-01

Sepsis is a potentially lethal condition that may be ameliorated through early monitoring of circulating activated leukocytes for faster stratification of severity of illness and improved administration of targeted treatment. Characterization of the intrinsic electrical properties of leukocytes is label-free and can provide a quick way to quantify the number of activated cells as sepsis progresses. Iso-dielectric separation (IDS) uses dielectrophoresis (DEP) to characterize the electrical signatures of cells. Here, we use IDS to show that activated and non-activated leukocytes have different electrical properties. We then present a double-sided version of the IDS platform to increase throughput to characterize thousands of cells. This new platform is less prone to cell fouling and allows faster characterization. Using peripheral blood samples from a cecal ligation and puncture (CLP) model of polymicrobial sepsis in mice, we estimate the number of activated leukocytes by looking into differences in the electrical properties of cells. We show for the first time using animal models that electrical cell profiling correlates with flow cytometry (FC) results and that IDS is therefore a good candidate for providing rapid monitoring of sepsis by quantifying the number of circulating activated leukocytes.

Development of an impairment-based individualized treatment workflow using an iPad-based software platform.

PubMed

Kiran, Swathi; Des Roches, Carrie; Balachandran, Isabel; Ascenso, Elsa

2014-02-01

Individuals with language and cognitive deficits following brain damage likely require long-term rehabilitation. Consequently, it is a huge practical problem to provide the continued communication therapy that these individuals require. The present project describes the development of an impairment-based individualized treatment workflow using a software platform called Constant Therapy. This article is organized into two sections. We will first describe the general methods of the treatment workflow for patients involved in this study. There are four steps in this process: (1) the patient's impairment is assessed using standardized tests, (2) the patient is assigned a specific and individualized treatment plan, (3) the patient practices the therapy at home and at the clinic, and (4) the clinician and the patient can analyze the results of the patient's performance remotely and monitor and alter the treatment plan accordingly. The second section provides four case studies that provide a representative sample of participants progressing through their individualized treatment plan. The preliminary results of the patient treatment provide encouraging evidence for the feasibility of a rehabilitation program for individuals with brain damage based on the iPad (Apple Inc., Cupertino, CA). Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Implementation of a Multiplex and Quantitative Proteomics Platform for Assessing Protein Lysates Using DNA-Barcoded Antibodies.

PubMed

Lee, Jinho; Geiss, Gary K; Demirkan, Gokhan; Vellano, Christopher P; Filanoski, Brian; Lu, Yiling; Ju, Zhenlin; Yu, Shuangxing; Guo, Huifang; Bogatzki, Lisa Y; Carter, Warren; Meredith, Rhonda K; Krishnamurthy, Savitri; Ding, Zhiyong; Beechem, Joseph M; Mills, Gordon B

2018-06-01

Molecular analysis of tumors forms the basis for personalized cancer medicine and increasingly guides patient selection for targeted therapy. Future opportunities for personalized medicine are highlighted by the measurement of protein expression levels via immunohistochemistry, protein arrays, and other approaches; however, sample type, sample quantity, batch effects, and "time to result" are limiting factors for clinical application. Here, we present a development pipeline for a novel multiplexed DNA-labeled antibody platform which digitally quantifies protein expression from lysate samples. We implemented a rigorous validation process for each antibody and show that the platform is amenable to multiple protocols covering nitrocellulose and plate-based methods. Results are highly reproducible across technical and biological replicates, and there are no observed "batch effects" which are common for most multiplex molecular assays. Tests from basal and perturbed cancer cell lines indicate that this platform is comparable to orthogonal proteomic assays such as Reverse-Phase Protein Array, and applicable to measuring the pharmacodynamic effects of clinically-relevant cancer therapeutics. Furthermore, we demonstrate the potential clinical utility of the platform with protein profiling from breast cancer patient samples to identify molecular subtypes. Together, these findings highlight the potential of this platform for enhancing our understanding of cancer biology in a clinical translation setting. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Bridging the Faraoni and Selli oceanic anoxic events: short and repetitive dys- and anaerobic episodes during the late Hauterivian to early Aptian in the central Tethys

NASA Astrophysics Data System (ADS)

Föllmi, K. B.; Bôle, M.; Jammet, N.; Froidevaux, P.; Godet, A.; Bodin, S.; Adatte, T.; Matera, V.; Fleitmann, D.; Spangenberg, J. E.

2011-06-01

A detailed stratigraphical and geochemical analysis was performed on the upper part of the Maiolica Formation outcropping in the Breggia (southern Switzerland) and Capriolo sections (northern Italy). In these localities, the Maiolica Formation consists of well-bedded, partly siliceous, pelagic, micritic carbonate, which lodges numerous thin, dark and organic-rich layers. Stable-isotope, phosphorus, organic-carbon and a suite of redox-sensitive trace-metal contents (RSTE: Mo, U, Co, V and As) were measured. Higher densities of organic-rich layers were identified in the uppermost Hauterivian, lower Barremian and the Barremian-Aptian boundary intervals, whereas the upper Barremian interval and the interval immediately following the Barremian-Aptian boundary interval are characterized by lower densities of organic-rich layers. TOC contents, RSTE pattern and Corg:Ptot ratios indicate that most layers were deposited under dysaerobic rather than anaerobic conditions and that latter conditions were likely restricted to short intervals in the latest Hauterivian, the early Barremian and the pre-Selli early Aptian. Correlations are possible with organic-rich intervals in central Italy (the Gorgo a Cerbara section) and the Boreal northwest German Basin, and with the facies and drowning pattern in the evolution of the Helvetic segment of the northern Tethyan carbonate platform. Our data and correlations suggest that the latest Hauterivian witnessed the progressive installation of dysaerobic conditions in the Tethys, which went along with the onset in sediment condensation, phosphogenesis and platform drowning on the northern Tethyan margin, and which culminated in the Faraoni anoxic episode. This brief episode is followed by further episodes of dysaerobic conditions in the Tethys and the northwest German Basin, which became more frequent and progressively stronger in the late early Barremian. Platform drowning persisted and did not halt before the latest early Barremian. The late Barremian witnessed diminishing frequencies and intensities in dysaerobic conditions, which went along with the progressive installation of the Urgonian carbonate platform. Near the Barremian-Aptian boundary, the increasing density in dysaerobic episodes in the Tethyan and northwest German Basins is paralleled by a change towards heterozoan carbonate production on the northern Tethyan shelf. The following return to more oxygenated conditions is correlated with the second phase of Urgonian platform growth and the period immediately preceding and corresponding to the Selli anoxic episode is characterized by renewed platform drowning and the change to heterozoan carbonate production. Changes towards more humid climate conditions were likely the cause for the repetitive installation of dys- to anaerobic conditions in the Tethyan and Boreal basins and the accompanying changes in the evolution of the carbonate platform towards heterozoan carbonate-producing ecosystems and platform drowning.

Comparison of reverse transcription-quantitative polymerase chain reaction methods and platforms for single cell gene expression analysis.

PubMed

Fox, Bridget C; Devonshire, Alison S; Baradez, Marc-Olivier; Marshall, Damian; Foy, Carole A

2012-08-15

Single cell gene expression analysis can provide insights into development and disease progression by profiling individual cellular responses as opposed to reporting the global average of a population. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the "gold standard" for the quantification of gene expression levels; however, the technical performance of kits and platforms aimed at single cell analysis has not been fully defined in terms of sensitivity and assay comparability. We compared three kits using purification columns (PicoPure) or direct lysis (CellsDirect and Cells-to-CT) combined with a one- or two-step RT-qPCR approach using dilutions of cells and RNA standards to the single cell level. Single cell-level messenger RNA (mRNA) analysis was possible using all three methods, although the precision, linearity, and effect of lysis buffer and cell background differed depending on the approach used. The impact of using a microfluidic qPCR platform versus a standard instrument was investigated for potential variability introduced by preamplification of template or scaling down of the qPCR to nanoliter volumes using laser-dissected single cell samples. The two approaches were found to be comparable. These studies show that accurate gene expression analysis is achievable at the single cell level and highlight the importance of well-validated experimental procedures for low-level mRNA analysis. Copyright © 2012 Elsevier Inc. All rights reserved.

A Paper-Based Device for Performing Loop-Mediated Isothermal Amplification with Real-Time Simultaneous Detection of Multiple DNA Targets.

PubMed

Seok, Youngung; Joung, Hyou-Arm; Byun, Ju-Young; Jeon, Hyo-Sung; Shin, Su Jeong; Kim, Sanghyo; Shin, Young-Beom; Han, Hyung Soo; Kim, Min-Gon

2017-01-01

Paper-based diagnostic devices have many advantages as a one of the multiple diagnostic test platforms for point-of-care (POC) testing because they have simplicity, portability, and cost-effectiveness. However, despite high sensitivity and specificity of nucleic acid testing (NAT), the development of NAT based on a paper platform has not progressed as much as the others because various specific conditions for nucleic acid amplification reactions such as pH, buffer components, and temperature, inhibitions from technical differences of paper-based device. Here, we propose a paper-based device for performing loop-mediated isothermal amplification (LAMP) with real-time simultaneous detection of multiple DNA targets. We determined the optimal chemical components to enable dry conditions for the LAMP reaction without lyophilization or other techniques. We also devised the simple paper device structure by sequentially stacking functional layers, and employed a newly discovered property of hydroxynaphthol blue fluorescence to analyze real-time LAMP signals in the paper device. This proposed platform allowed analysis of three different meningitis DNA samples in a single device with single-step operation. This LAMP-based multiple diagnostic device has potential for real-time analysis with quantitative detection of 10 2 -10 5 copies of genomic DNA. Furthermore, we propose the transformation of DNA amplification devices to a simple and affordable paper system approach with great potential for realizing a paper-based NAT system for POC testing.

A Paper-Based Device for Performing Loop-Mediated Isothermal Amplification with Real-Time Simultaneous Detection of Multiple DNA Targets

PubMed Central

Seok, Youngung; Joung, Hyou-Arm; Byun, Ju-Young; Jeon, Hyo-Sung; Shin, Su Jeong; Kim, Sanghyo; Shin, Young-Beom; Han, Hyung Soo; Kim, Min-Gon

2017-01-01

Paper-based diagnostic devices have many advantages as a one of the multiple diagnostic test platforms for point-of-care (POC) testing because they have simplicity, portability, and cost-effectiveness. However, despite high sensitivity and specificity of nucleic acid testing (NAT), the development of NAT based on a paper platform has not progressed as much as the others because various specific conditions for nucleic acid amplification reactions such as pH, buffer components, and temperature, inhibitions from technical differences of paper-based device. Here, we propose a paper-based device for performing loop-mediated isothermal amplification (LAMP) with real-time simultaneous detection of multiple DNA targets. We determined the optimal chemical components to enable dry conditions for the LAMP reaction without lyophilization or other techniques. We also devised the simple paper device structure by sequentially stacking functional layers, and employed a newly discovered property of hydroxynaphthol blue fluorescence to analyze real-time LAMP signals in the paper device. This proposed platform allowed analysis of three different meningitis DNA samples in a single device with single-step operation. This LAMP-based multiple diagnostic device has potential for real-time analysis with quantitative detection of 102-105 copies of genomic DNA. Furthermore, we propose the transformation of DNA amplification devices to a simple and affordable paper system approach with great potential for realizing a paper-based NAT system for POC testing. PMID:28740546

Comparison of Online Survey Recruitment Platforms for Hard-to-Reach Pregnant Smoking Populations: Feasibility Study.

PubMed

Ibarra, Jose Luis; Agas, Jessica Marie; Lee, Melissa; Pan, Julia Lily; Buttenheim, Alison Meredith

2018-04-16

Recruiting hard-to-reach populations for health research is challenging. Web-based platforms offer one way to recruit specific samples for research purposes, but little is known about the feasibility of online recruitment and the representativeness and comparability of samples recruited through different Web-based platforms. The objectives of this study were to determine the feasibility of recruiting a hard-to-reach population (pregnant smokers) using 4 different Web-based platforms and to compare participants recruited through each platform. A screener and survey were distributed online through Qualtrics Panel, Soapbox Sample, Reddit, and Amazon Mechanical Turk (mTurk). Descriptive statistics were used to summarize results of each recruitment platform, including eligibility yield, quality yield, income, race, age, and gestational age. Of the 3847 participants screened for eligibility across all 4 Web-based platforms, 535 were eligible and 308 completed the survey. Amazon mTurk yielded the fewest completed responses (n=9), 100% (9/9) of which passed several quality metrics verifying pregnancy and smoking status. Qualtrics Panel yielded 14 completed responses, 86% (12/14) of which passed the quality screening. Soapbox Sample produced 107 completed surveys, 67% (72/107) of which were found to be quality responses. Advertising through Reddit produced the highest completion rate (n=178), but only 29.2% (52/178) of those surveys passed the quality metrics. We found significant differences in eligibility yield, quality yield, age, number of previous pregnancies, age of smoking initiation, current smokers, race, education, and income (P<.001). Although each platform successfully recruited pregnant smokers, results varied in quality, cost, and percentage of complete responses. Moving forward, investigators should pay careful attention to the percentage yield and cost of online recruitment platforms to maximize internal and external validity. ©Jose Luis Ibarra, Jessica Marie Agas, Melissa Lee, Julia Lily Pan, Alison Meredith Buttenheim. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 16.04.2018.

An automated synthesis-purification-sample-management platform for the accelerated generation of pharmaceutical candidates.

PubMed

Sutherland, J David; Tu, Noah P; Nemcek, Thomas A; Searle, Philip A; Hochlowski, Jill E; Djuric, Stevan W; Pan, Jeffrey Y

2014-04-01

A flexible and integrated flow-chemistry-synthesis-purification compound-generation and sample-management platform has been developed to accelerate the production of small-molecule organic-compound drug candidates in pharmaceutical research. Central to the integrated system is a Mitsubishi robot, which hands off samples throughout the process to the next station, including synthesis and purification, sample dispensing for purity and quantification analysis, dry-down, and aliquot generation.

Data-intensive computing on numerically-insensitive supercomputers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahrens, James P; Fasel, Patricia K; Habib, Salman

2010-12-03

With the advent of the era of petascale supercomputing, via the delivery of the Roadrunner supercomputing platform at Los Alamos National Laboratory, there is a pressing need to address the problem of visualizing massive petascale-sized results. In this presentation, I discuss progress on a number of approaches including in-situ analysis, multi-resolution out-of-core streaming and interactive rendering on the supercomputing platform. These approaches are placed in context by the emerging area of data-intensive supercomputing.

DNA extraction for streamlined metagenomics of diverse environmental samples.

PubMed

Marotz, Clarisse; Amir, Amnon; Humphrey, Greg; Gaffney, James; Gogul, Grant; Knight, Rob

2017-06-01

A major bottleneck for metagenomic sequencing is rapid and efficient DNA extraction. Here, we compare the extraction efficiencies of three magnetic bead-based platforms (KingFisher, epMotion, and Tecan) to a standardized column-based extraction platform across a variety of sample types, including feces, oral, skin, soil, and water. Replicate sample plates were extracted and prepared for 16S rRNA gene amplicon sequencing in parallel to assess extraction bias and DNA quality. The data demonstrate that any effect of extraction method on sequencing results was small compared with the variability across samples; however, the KingFisher platform produced the largest number of high-quality reads in the shortest amount of time. Based on these results, we have identified an extraction pipeline that dramatically reduces sample processing time without sacrificing bacterial taxonomic or abundance information.

Portable fiber-optic taper coupled optical microscopy platform

NASA Astrophysics Data System (ADS)

Wang, Weiming; Yu, Yan; Huang, Hui; Ou, Jinping

2017-04-01

The optical fiber taper coupled with CMOS has advantages of high sensitivity, compact structure and low distortion in the imaging platform. So it is widely used in low light, high speed and X-ray imaging systems. In the meanwhile, the peculiarity of the coupled structure can meet the needs of the demand in microscopy imaging. Toward this end, we developed a microscopic imaging platform based on the coupling of cellphone camera module and fiber optic taper for the measurement of the human blood samples and ascaris lumbricoides. The platform, weighing 70 grams, is based on the existing camera module of the smartphone and a fiber-optic array which providing a magnification factor of 6x.The top facet of the taper, on which samples are placed, serves as an irregular sampling grid for contact imaging. The magnified images of the sample, located on the bottom facet of the fiber, are then projected onto the CMOS sensor. This paper introduces the portable medical imaging system based on the optical fiber coupling with CMOS, and theoretically analyzes the feasibility of the system. The image data and process results either can be stored on the memory or transmitted to the remote medical institutions for the telemedicine. We validate the performance of this cell-phone based microscopy platform using human blood samples and test target, achieving comparable results to a standard bench-top microscope.

Quantifying EGFR alterations in the lung cancer genome with nanofluidic digital PCR arrays.

PubMed

Wang, Jun; Ramakrishnan, Ramesh; Tang, Zhe; Fan, Weiwen; Kluge, Amy; Dowlati, Afshin; Jones, Robert C; Ma, Patrick C

2010-04-01

The EGFR [epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)] gene is known to harbor genomic alterations in advanced lung cancer involving gene amplification and kinase mutations that predict the clinical response to EGFR-targeted inhibitors. Methods for detecting such molecular changes in lung cancer tumors are desirable. We used a nanofluidic digital PCR array platform and 16 cell lines and 20 samples of genomic DNA from resected tumors (stages I-III) to quantify the relative numbers of copies of the EGFR gene and to detect mutated EGFR alleles in lung cancer. We assessed the relative number of EGFR gene copies by calculating the ratio of the number of EGFR molecules (measured with a 6-carboxyfluorescein-labeled Scorpion assay) to the number of molecules of the single-copy gene RPP30 (ribonuclease P/MRP 30kDa subunit) (measured with a 6-carboxy-X-rhodamine-labeled TaqMan assay) in each panel. To assay for the EGFR L858R (exon 21) mutation and exon 19 in-frame deletions, we used the ARMS and Scorpion technologies in a DxS/Qiagen EGFR29 Mutation Test Kit for the digital PCR array. The digital array detected and quantified rare gefitinib/erlotinib-sensitizing EGFR mutations (0.02%-9.26% abundance) that were present in formalin-fixed, paraffin-embedded samples of early-stage resectable lung tumors without an associated increase in gene copy number. Our results also demonstrated the presence of intratumor molecular heterogeneity for the clinically relevant EGFR mutated alleles in these early-stage lung tumors. The digital PCR array platform allows characterization and quantification of oncogenes, such as EGFR, at the single-molecule level. Use of this nanofluidics platform may provide deeper insight into the specific roles of clinically relevant kinase mutations during different stages of lung tumor progression and may be useful in predicting the clinical response to EGFR-targeted inhibitors.

Recent Advances in Laser-Ablative Synthesis of Bare Au and Si Nanoparticles and Assessment of Their Prospects for Tissue Engineering Applications.

PubMed

Al-Kattan, Ahmed; Nirwan, Viraj P; Popov, Anton; Ryabchikov, Yury V; Tselikov, Gleb; Sentis, Marc; Fahmi, Amir; Kabashin, Andrei V

2018-05-24

Driven by surface cleanness and unique physical, optical and chemical properties, bare (ligand-free) laser-synthesized nanoparticles (NPs) are now in the focus of interest as promising materials for the development of advanced biomedical platforms related to biosensing, bioimaging and therapeutic drug delivery. We recently achieved significant progress in the synthesis of bare gold (Au) and silicon (Si) NPs and their testing in biomedical tasks, including cancer imaging and therapy, biofuel cells, etc. We also showed that these nanomaterials can be excellent candidates for tissue engineering applications. This review is aimed at the description of our recent progress in laser synthesis of bare Si and Au NPs and their testing as functional modules (additives) in innovative scaffold platforms intended for tissue engineering tasks.

Gamification and service marketing.

PubMed

Conaway, Roger; Garay, Mario Cortés

2014-01-01

Our paper addresses the development of the gamification concept with business applications. We report on our survey of customers and managers seeking to participate in gamification on their websites. We examined both customer and manager perspectives and compare survey results in terms of service marketing and characteristics of consumers who engage with gamification platforms. Our data supported a design theory delineating four key characteristics in gamification platforms that attract consumers toward an enterprise's website. Those features attract individuals through (1) Progress Paths, (2) Feedback and Reward, (3) Social Connection, and (4) Attractiveness of the site. Results from the managers' survey reflected key characteristics that must exist for implementation of a gamification platform. The data revealed a particular demographic profile of a gamification individual drawn to a website. These findings may help company managers who wish to adopt a gamification platform in the future.

Research on digital city geographic information common services platform

NASA Astrophysics Data System (ADS)

Chen, Dequan; Wu, Qunyong; Wang, Qinmin

2008-10-01

Traditional GIS (Geographic Information System) software development mode exposes many defects that will largely slow down the city informational progress. It is urgent need to build a common application infrastructure for informational project to speed up the development pace of digital city. The advent of service-oriented architecture (SOA) has motivated the adoption of GIS functionality portals that can be executed in distributed computing environment. According to the SOA principle, we bring forward and design a digital city geographic information common services platform which provides application development service interfaces for field users that can be further extended relevant business application. In the end, a public-oriented Web GIS is developed based on the platform for helping public users to query geographic information in their daily life. It indicates that our platform have the capacity that can be integrated by other applications conveniently.

Comprehensive Assessments of RNA-seq by the SEQC Consortium: FDA-Led Efforts Advance Precision Medicine.

PubMed

Xu, Joshua; Gong, Binsheng; Wu, Leihong; Thakkar, Shraddha; Hong, Huixiao; Tong, Weida

2016-03-15

Studies on gene expression in response to therapy have led to the discovery of pharmacogenomics biomarkers and advances in precision medicine. Whole transcriptome sequencing (RNA-seq) is an emerging tool for profiling gene expression and has received wide adoption in the biomedical research community. However, its value in regulatory decision making requires rigorous assessment and consensus between various stakeholders, including the research community, regulatory agencies, and industry. The FDA-led SEquencing Quality Control (SEQC) consortium has made considerable progress in this direction, and is the subject of this review. Specifically, three RNA-seq platforms (Illumina HiSeq, Life Technologies SOLiD, and Roche 454) were extensively evaluated at multiple sites to assess cross-site and cross-platform reproducibility. The results demonstrated that relative gene expression measurements were consistently comparable across labs and platforms, but not so for the measurement of absolute expression levels. As part of the quality evaluation several studies were included to evaluate the utility of RNA-seq in clinical settings and safety assessment. The neuroblastoma study profiled tumor samples from 498 pediatric neuroblastoma patients by both microarray and RNA-seq. RNA-seq offers more utilities than microarray in determining the transcriptomic characteristics of cancer. However, RNA-seq and microarray-based models were comparable in clinical endpoint prediction, even when including additional features unique to RNA-seq beyond gene expression. The toxicogenomics study compared microarray and RNA-seq profiles of the liver samples from rats exposed to 27 different chemicals representing multiple toxicity modes of action. Cross-platform concordance was dependent on chemical treatment and transcript abundance. Though both RNA-seq and microarray are suitable for developing gene expression based predictive models with comparable prediction performance, RNA-seq offers advantages over microarray in profiling genes with low expression. The rat BodyMap study provided a comprehensive rat transcriptomic body map by performing RNA-Seq on 320 samples from 11 organs in either sex of juvenile, adolescent, adult and aged Fischer 344 rats. Lastly, the transferability study demonstrated that signature genes of predictive models are reciprocally transferable between microarray and RNA-seq data for model development using a comprehensive approach with two large clinical data sets. This result suggests continued usefulness of legacy microarray data in the coming RNA-seq era. In conclusion, the SEQC project enhances our understanding of RNA-seq and provides valuable guidelines for RNA-seq based clinical application and safety evaluation to advance precision medicine.

A mechanical cell disruption microfluidic platform based on an on-chip micropump.

PubMed

Cheng, Yinuo; Wang, Yue; Wang, Zhiyuan; Huang, Liang; Bi, Mingzhao; Xu, Wenxiao; Wang, Wenhui; Ye, Xiongying

2017-03-01

Cell disruption plays a vital role in detection of intracellular components which contain information about genetic and disease characteristics. In this paper, we demonstrate a novel microfluidic platform based on an on-chip micropump for mechanical cell disruption and sample transport. A 50  μ l cell sample can be effectively lysed through on-chip multi-disruption in 36 s without introducing any chemical agent and suffering from clogging by cellular debris. After 30 cycles of circulating disruption, 80.6% and 90.5% cell disruption rates were achieved for the HEK293 cell sample and human natural killer cell sample, respectively. Profiting from the feature of pump-on-chip, the highly integrated platform enables more convenient and cost-effective cell disruption for the analysis of intracellular components.

A mechanical cell disruption microfluidic platform based on an on-chip micropump

PubMed Central

Cheng, Yinuo; Wang, Yue; Wang, Zhiyuan; Bi, Mingzhao; Xu, Wenxiao; Ye, Xiongying

2017-01-01

Cell disruption plays a vital role in detection of intracellular components which contain information about genetic and disease characteristics. In this paper, we demonstrate a novel microfluidic platform based on an on-chip micropump for mechanical cell disruption and sample transport. A 50 μl cell sample can be effectively lysed through on-chip multi-disruption in 36 s without introducing any chemical agent and suffering from clogging by cellular debris. After 30 cycles of circulating disruption, 80.6% and 90.5% cell disruption rates were achieved for the HEK293 cell sample and human natural killer cell sample, respectively. Profiting from the feature of pump-on-chip, the highly integrated platform enables more convenient and cost-effective cell disruption for the analysis of intracellular components. PMID:28798848

GridAPPS-D Conceptual Design v1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Melton, Ronald B.; Schneider, Kevin P.; McDermott, Thomas E.

2017-05-31

The purpose of this document is to provide a conceptual design of the distribution system application development platform being developed for the U.S. Department of Energy’s Advanced Distribution Management System (ADMS) Program by the Grid Modernization Laboratory Consortium project GM0063. The platform will be referred to as GridAPPS-D. This document provides a high level, conceptual view of the platform and provides related background and contextual information. This document is intended to both educate readers about the technical work of the project and to serve as a point of reference for the project team. The document will be updated as themore » project progresses.« less

Optofluidic platforms based on surface-enhanced Raman scattering.

PubMed

Lim, Chaesung; Hong, Jongin; Chung, Bong Geun; deMello, Andrew J; Choo, Jaebum

2010-05-01

We report recent progress in the development of surface-enhanced Raman scattering (SERS)-based optofluidic platforms for the fast and sensitive detection of chemical and biological analytes. In the current context, a SERS-based optofluidic platform is defined as an integrated analytical device composed of a microfluidic element and a sensitive Raman spectrometer. Optofluidic devices for SERS detection normally involve nanocolloid-based microfluidic systems or metal nanostructure-embedded microfluidic systems. In the current review, recent advances in both approaches are surveyed and assessed. Additionally, integrated real-time sensing systems that combine portable Raman spectrometers with microfluidic devices are also reviewed. Such real-time sensing systems have significant utility in environmental monitoring, forensic science and homeland defense applications.

Real-Time PCR Assay To Detect Smallpox Virus

PubMed Central

Sofi Ibrahim, M.; Kulesh, David A.; Saleh, Sharron S.; Damon, Inger K.; Esposito, Joseph J.; Schmaljohn, Alan L.; Jahrling, Peter B.

2003-01-01

We developed a highly sensitive and specific assay for the rapid detection of smallpox virus DNA on both the Smart Cycler and LightCycler platforms. The assay is based on TaqMan chemistry with the orthopoxvirus hemagglutinin gene used as the target sequence. With genomic DNA purified from variola virus Bangladesh 1975, the limit of detection was estimated to be approximately 25 copies on both machines. The assay was evaluated in a blinded study with 322 coded samples that included genomic DNA from 48 different isolates of variola virus; 25 different strains and isolates of camelpox, cowpox, ectromelia, gerbilpox, herpes, monkeypox, myxoma, rabbitpox, raccoonpox, skunkpox, vaccinia, and varicella-zoster viruses; and two rickettsial species at concentrations mostly ranging from 100 fg/μl to 1 ng/μl. Contained within those 322 samples were variola virus DNA, obtained from purified viral preparations, at concentrations of 1 fg/μl to 1 ng/μl. On the Smart Cycler platform, 2 samples with false-positive results were detected among the 116 samples not containing variola virus tested; i.e., the overall specificity of the assay was 98.3%. On the LightCycler platform, five samples with false-positive results were detected (overall specificity, 95.7%). Of the 206 samples that contained variola virus DNA ranging in concentrations from 100 fg/μl to 1 ng/μl, 8 samples were considered negative on the Smart Cycler platform and 1 sample was considered negative on the LightCycler platform. Thus, the clinical sensitivities were 96.1% for the Smart Cycler instrument and 99.5% for the LightCycler instrument. The vast majority of these samples were derived from virus-infected cell cultures and variola virus-infected tissues; thus, the DNA material contained both viral DNA and cellular DNA. Of the 43 samples that contained purified variola virus DNA ranging in concentration from 1 fg/μl to 1 ng/μl, the assay correctly detected the virus in all 43 samples on both the Smart Cycler and the LightCycler platforms. The assay may be useful for the early detection of smallpox virus infections should such infections occur as a result of a deliberate or an accidental recurrence. PMID:12904397

Application of a Smartphone Metabolomics Platform to the Authentication of Schisandra sinensis.

PubMed

Kwon, Hyuk Nam; Phan, Hong-Duc; Xu, Wen Jun; Ko, Yoon-Joo; Park, Sunghyouk

2016-05-01

Herbal medicines have been used for a long time all around the world. Since the quality of herbal preparations depends on the source of herbal materials, there has been a strong need to develop methods to correctly identify the origin of materials. To develop a smartphone metabolomics platform as a simpler and low-cost alternative for the identification of herbal material source. Schisandra sinensis extracts from Korea and China were prepared. The visible spectra of all samples were measured by a smartphone spectrometer platform. This platform included all the necessary measures built-in for the metabolomics research: data acquisition, processing, chemometric analysis and visualisation of the results. The result of the smartphone metabolomics platform was compared to that of NMR-based metabolomics, suggesting the feasibility of smartphone platform in metabolomics research. The smartphone metabolomics platform gave similar results to the NMR method, showing good separation between Korean and Chinese materials and correct predictability for all test samples. With its accuracy and advantages of affordability, user-friendliness, and portability, the smartphone metabolomics platform could be applied to the authentication of other medicinal plants. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

An Interactive Platform to Visualize Data-Driven Clinical Pathways for the Management of Multiple Chronic Conditions.

PubMed

Zhang, Yiye; Padman, Rema

2017-01-01

Patients with multiple chronic conditions (MCC) pose an increasingly complex health management challenge worldwide, particularly due to the significant gap in our understanding of how to provide coordinated care. Drawing on our prior research on learning data-driven clinical pathways from actual practice data, this paper describes a prototype, interactive platform for visualizing the pathways of MCC to support shared decision making. Created using Python web framework, JavaScript library and our clinical pathway learning algorithm, the visualization platform allows clinicians and patients to learn the dominant patterns of co-progression of multiple clinical events from their own data, and interactively explore and interpret the pathways. We demonstrate functionalities of the platform using a cluster of 36 patients, identified from a dataset of 1,084 patients, who are diagnosed with at least chronic kidney disease, hypertension, and diabetes. Future evaluation studies will explore the use of this platform to better understand and manage MCC.

Green factory: plants as bioproduction platforms for recombinant proteins.

PubMed

Xu, Jianfeng; Dolan, Maureen C; Medrano, Giuliana; Cramer, Carole L; Weathers, Pamela J

2012-01-01

Molecular farming, long considered a promising strategy to produce valuable recombinant proteins not only for human and veterinary medicine, but also for agriculture and industry, now has some commercially available products. Various plant-based production platforms including whole-plants, aquatic plants, plant cell suspensions, and plant tissues (hairy roots) have been compared in terms of their advantages and limits. Effective recombinant strategies are summarized along with descriptions of scalable culture systems and examples of commercial progress and success. Copyright © 2011 Elsevier Inc. All rights reserved.

[Strategic thinking of the construction of national schistosomiasis laboratory network in China].

PubMed

Qin, Zhi-Qiang; Xu, Jing; Feng, Ting; Zhu, Hong-Qing; Li, Shi-Zhu; Xiao, Ning; Zhou, Xiao-Nong

2013-08-01

A schistosomiasis laboratory network and its quality assurance system have been built and will be more and more perfect in China. This paper introduces the present situation of schistosomiasis diagnosis in China and expounds the basic ideas and the progress in the construction of schistosomiasis network platform. Furthermore, the face of schistosomiasis diagnosis network platform construction and operation of the challenge and the future work will be put forward in the latter part of this paper.

Rugged large volume injection for sensitive capillary LC-MS environmental monitoring

NASA Astrophysics Data System (ADS)

Roberg-Larsen, Hanne; Abele, Silvija; Demir, Deniz; Dzabijeva, Diana; Amundsen, Sunniva F.; Wilson, Steven R.; Bartkevics, Vadims; Lundanes, Elsa

2017-08-01

A rugged and high throughput capillary column (cLC) LC-MS switching platform using large volume injection and on-line automatic filtration and filter back-flush (AFFL) solid phase extraction (SPE) for analysis of environmental water samples with minimal sample preparation is presented. Although narrow columns and on-line sample preparation are used in the platform, high ruggedness is achieved e.g. injection of 100 non-filtrated water samples would did not result in a pressure rise/clogging of the SPE/capillary columns (inner diameter 300 µm). In addition, satisfactory retention time stability and chromatographic resolution were also features of the system. The potential of the platform for environmental water samples was demonstrated with various pharmaceutical products, which had detection limits (LOD) in the 0.05 - 12.5 ng/L range. Between-day and within-day repeatability of selected analytes were < 20% RSD.

The European Microkelvin Platform

NASA Astrophysics Data System (ADS)

Pickett, George; Enss, Christian

2018-03-01

The growing demands of quantum materials, engineering and technology make access to microkelvin temperatures ever more essential. Experience in Europe suggests that new working methods, encouraged by an imaginative funding atmosphere, can accelerate progress in this frontier field.

Quantifying environmental DNA signals for aquatic invasive species across multiple detection platforms.

PubMed

Nathan, Lucas M; Simmons, Megan; Wegleitner, Benjamin J; Jerde, Christopher L; Mahon, Andrew R

2014-11-04

The use of molecular surveillance techniques has become popular among aquatic researchers and managers due to the improved sensitivity and efficiency compared to traditional sampling methods. Rapid expansion in the use of environmental DNA (eDNA), paired with the advancement of molecular technologies, has resulted in new detection platforms and techniques. In this study we present a comparison of three eDNA surveillance platforms: traditional polymerase chain reaction (PCR), quantitative PCR (qPCR), and digital droplet PCR (ddPCR) in which water samples were collected over a 24 h time period from mesocosm experiments containing a population gradient of invasive species densities. All platforms reliably detected the presence of DNA, even at low target organism densities within the first hour. The two quantitative platforms (qPCR and ddPCR) produced similar estimates of DNA concentrations. The analyses completed with ddPCR was faster from sample collection through analyses and cost approximately half the expenditure of qPCR. Although a new platform for eDNA surveillance of aquatic species, ddPCR was consistent with more commonly used qPCR and a cost-effective means of estimating DNA concentrations. Use of ddPCR by researchers and managers should be considered in future eDNA surveillance applications.

[Willingness to accept an Internet-based mobility platform in different age cohorts. Empiric results of the project S-Mobil 100].

PubMed

Beil, J; Cihlar, V; Kruse, A

2015-02-01

The aim of the project S-Mobil 100 is to develop and implement a prototype of an internet-based, generation-appropriate mobility platform in the model region Siegen-Wittgenstein. In the context of an empirical preliminary study, use of technology, experience with technology, general attitudes towards technology, general technology commitment, and the willingness to accept the mobility platform were investigated in different age cohorts. The investigation was carried out using a written survey based on a standardized questionnaire. The sample of 358 persons aged 40-90 years was divided in four age cohorts (40-54, 55-64, 65-74, and 75 + years). Our results show a high willingness to accept the mobility platform in the overall sample. Age, residence, income, and general technology commitment were significant predictors for the judgment of the platform. Although there were group differences in accepting the mobility platform, the older cohorts are also open-minded towards this new technology.

Recent Progress and Future Plans for Fusion Plasma Synthetic Diagnostics Platform

NASA Astrophysics Data System (ADS)

Shi, Lei; Kramer, Gerrit; Tang, William; Tobias, Benjamin; Valeo, Ernest; Churchill, Randy; Hausammann, Loic

2015-11-01

The Fusion Plasma Synthetic Diagnostics Platform (FPSDP) is a Python package developed at the Princeton Plasma Physics Laboratory. It is dedicated to providing an integrated programmable environment for applying a modern ensemble of synthetic diagnostics to the experimental validation of fusion plasma simulation codes. The FPSDP will allow physicists to directly compare key laboratory measurements to simulation results. This enables deeper understanding of experimental data, more realistic validation of simulation codes, quantitative assessment of existing diagnostics, and new capabilities for the design and optimization of future diagnostics. The Fusion Plasma Synthetic Diagnostics Platform now has data interfaces for the GTS and XGC-1 global particle-in-cell simulation codes with synthetic diagnostic modules including: (i) 2D and 3D Reflectometry; (ii) Beam Emission Spectroscopy; and (iii) 1D Electron Cyclotron Emission. Results will be reported on the delivery of interfaces for the global electromagnetic PIC code GTC, the extended MHD M3D-C1 code, and the electromagnetic hybrid NOVAK eigenmode code. Progress toward development of a more comprehensive 2D Electron Cyclotron Emission module will also be discussed. This work is supported by DOE contract #DEAC02-09CH11466.

PD_Manager: an mHealth platform for Parkinson's disease patient management.

PubMed

Tsiouris, Kostas M; Gatsios, Dimitrios; Rigas, George; Miljkovic, Dragana; Koroušić Seljak, Barbara; Bohanec, Marko; Arredondo, Maria T; Antonini, Angelo; Konitsiotis, Spyros; Koutsouris, Dimitrios D; Fotiadis, Dimitrios I

2017-06-01

PD_Manager is a mobile health platform designed to cover most of the aspects regarding the management of Parkinson's disease (PD) in a holistic approach. Patients are unobtrusively monitored using commercial wrist and insole sensors paired with a smartphone, to automatically estimate the severity of most of the PD motor symptoms. Besides motor symptoms monitoring, the patient's mobile application also provides various non-motor self-evaluation tests for assessing cognition, mood and nutrition to motivate them in becoming more active in managing their disease. All data from the mobile application and the sensors is transferred to a cloud infrastructure to allow easy access for clinicians and further processing. Clinicians can access this information using a separate mobile application that is specifically designed for their respective needs to provide faster and more accurate assessment of PD symptoms that facilitate patient evaluation. Machine learning techniques are used to estimate symptoms and disease progression trends to further enhance the provided information. The platform is also complemented with a decision support system (DSS) that notifies clinicians for the detection of new symptoms or the worsening of existing ones. As patient's symptoms are progressing, the DSS can also provide specific suggestions regarding appropriate medication changes.

PD_Manager: an mHealth platform for Parkinson's disease patient management

PubMed Central

Gatsios, Dimitrios; Rigas, George; Miljkovic, Dragana; Koroušić Seljak, Barbara; Bohanec, Marko; Arredondo, Maria T.; Antonini, Angelo; Konitsiotis, Spyros; Koutsouris, Dimitrios D.

2017-01-01

PD_Manager is a mobile health platform designed to cover most of the aspects regarding the management of Parkinson's disease (PD) in a holistic approach. Patients are unobtrusively monitored using commercial wrist and insole sensors paired with a smartphone, to automatically estimate the severity of most of the PD motor symptoms. Besides motor symptoms monitoring, the patient's mobile application also provides various non-motor self-evaluation tests for assessing cognition, mood and nutrition to motivate them in becoming more active in managing their disease. All data from the mobile application and the sensors is transferred to a cloud infrastructure to allow easy access for clinicians and further processing. Clinicians can access this information using a separate mobile application that is specifically designed for their respective needs to provide faster and more accurate assessment of PD symptoms that facilitate patient evaluation. Machine learning techniques are used to estimate symptoms and disease progression trends to further enhance the provided information. The platform is also complemented with a decision support system (DSS) that notifies clinicians for the detection of new symptoms or the worsening of existing ones. As patient's symptoms are progressing, the DSS can also provide specific suggestions regarding appropriate medication changes. PMID:28706727

Carbon nanostructures as immobilization platform for DNA: A review on current progress in electrochemical DNA sensors.

PubMed

Rasheed, P Abdul; Sandhyarani, N

2017-11-15

Development of a sensitive, specific and cost-effective DNA detection method is motivated by increasing demand for the early stage diagnosis of genetic diseases. Recent developments in the design and fabrication of efficient sensor platforms based on nanostructures make the highly sensitive sensors which could indicate very low detection limit to the level of few molecules, a realistic possibility. Electrochemical detection methods are widely used in DNA diagnostics as it provide simple, accurate and inexpensive platform for DNA detection. In addition, the electrochemical DNA sensors provide direct electronic signal without the use of expensive signal transduction equipment and facilitates the immobilization of single stranded DNA (ssDNA) probe sequences on a wide variety of electrode substrates. It has been found that a range of nanomaterials such as metal nanoparticles (MNPs), carbon based nanomaterials, quantum dots (QDs), magnetic nanoparticles and polymeric NPs have been introduced in the sensor design to enhance the sensing performance of electrochemical DNA sensor. In this review, we discuss recent progress in the design and fabrication of efficient electrochemical genosensors based on carbon nanostructures such as carbon nanotubes, graphene, graphene oxide and nanodiamonds. Copyright © 2017 Elsevier B.V. All rights reserved.

Design and development of synthetic microbial platform cells for bioenergy

PubMed Central

Lee, Sang Jun; Lee, Sang-Jae; Lee, Dong-Woo

2013-01-01

The finite reservation of fossil fuels accelerates the necessity of development of renewable energy sources. Recent advances in synthetic biology encompassing systems biology and metabolic engineering enable us to engineer and/or create tailor made microorganisms to produce alternative biofuels for the future bio-era. For the efficient transformation of biomass to bioenergy, microbial cells need to be designed and engineered to maximize the performance of cellular metabolisms for the production of biofuels during energy flow. Toward this end, two different conceptual approaches have been applied for the development of platform cell factories: forward minimization and reverse engineering. From the context of naturally minimized genomes,non-essential energy-consuming pathways and/or related gene clusters could be progressively deleted to optimize cellular energy status for bioenergy production. Alternatively, incorporation of non-indigenous parts and/or modules including biomass-degrading enzymes, carbon uptake transporters, photosynthesis, CO2 fixation, and etc. into chassis microorganisms allows the platform cells to gain novel metabolic functions for bioenergy. This review focuses on the current progress in synthetic biology-aided pathway engineering in microbial cells and discusses its impact on the production of sustainable bioenergy. PMID:23626588

Multipurpose floating platform for hyperspectral imaging, sampling and sensing of surface water sources used in irrigation and recreation

USDA-ARS?s Scientific Manuscript database

The objective of this work was to design, construct, and test the self-propelled aquatic platform for imaging, multi-tier water sampling, water quality sensing, and depth profiling to document microbial content and environmental covariates in the interior of irrigation ponds and reservoirs. The plat...

Adaptation of Laser Microdissection Technique for the Study of a Spontaneous Metastatic Mammary Carcinoma Mouse Model by NanoString Technologies

PubMed Central

Saylor, Karen L.; Anver, Miriam R.; Salomon, David S.; Golubeva, Yelena G.

2016-01-01

Laser capture microdissection (LCM) of tissue is an established tool in medical research for collection of distinguished cell populations under direct microscopic visualization for molecular analysis. LCM samples have been successfully analyzed in a number of genomic and proteomic downstream molecular applications. However, LCM sample collection and preparation procedure has to be adapted to each downstream analysis platform. In this present manuscript we describe in detail the adaptation of LCM methodology for the collection and preparation of fresh frozen samples for NanoString analysis based on a study of a model of mouse mammary gland carcinoma and its lung metastasis. Our adaptation of LCM sample preparation and workflow to the requirements of the NanoString platform allowed acquiring samples with high RNA quality. The NanoString analysis of such samples provided sensitive detection of genes of interest and their associated molecular pathways. NanoString is a reliable gene expression analysis platform that can be effectively coupled with LCM. PMID:27077656

A Centrifugal Microfluidic Platform That Separates Whole Blood Samples into Multiple Removable Fractions Due to Several Discrete but Continuous Density Gradient Sections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moen, Scott T.; Hatcher, Christopher L.; Singh, Anup K.

We present a miniaturized centrifugal platform that uses density centrifugation for separation and analysis of biological components in small volume samples (~5 μL). We demonstrate the ability to enrich leukocytes for on-disk visualization via microscopy, as well as recovery of viable cells from each of the gradient partitions. In addition, we simplified the traditional Modified Wright-Giemsa staining by decreasing the time, volume, and expertise involved in the procedure. From a whole blood sample, we were able to extract 95.15% of leukocytes while excluding 99.8% of red blood cells. Furthermore, this platform has great potential in both medical diagnostics and researchmore » applications as it offers a simpler, automated, and inexpensive method for biological sample separation, analysis, and downstream culturing.« less

A Centrifugal Microfluidic Platform That Separates Whole Blood Samples into Multiple Removable Fractions Due to Several Discrete but Continuous Density Gradient Sections

DOE PAGES

Moen, Scott T.; Hatcher, Christopher L.; Singh, Anup K.

2016-04-07

We present a miniaturized centrifugal platform that uses density centrifugation for separation and analysis of biological components in small volume samples (~5 μL). We demonstrate the ability to enrich leukocytes for on-disk visualization via microscopy, as well as recovery of viable cells from each of the gradient partitions. In addition, we simplified the traditional Modified Wright-Giemsa staining by decreasing the time, volume, and expertise involved in the procedure. From a whole blood sample, we were able to extract 95.15% of leukocytes while excluding 99.8% of red blood cells. Furthermore, this platform has great potential in both medical diagnostics and researchmore » applications as it offers a simpler, automated, and inexpensive method for biological sample separation, analysis, and downstream culturing.« less

20180312 - US EPA-Unilever Collaborative Partnership: Accomplishments and Next Steps (SOT)

EPA Science Inventory

Reiterating the goals of the partnership, this summarizes the accomplishments and progress made so far in the collaboration, and announces a two phase extension focused on further development of high-throughput transcriptomic platform

Early Rockets

NASA Image and Video Library

1940-03-21

Goddard rocket in launching tower at Roswell, New Mexico, March 21, 1940. Fuel was injected by pumps from the fueling platform at left. From 1930 to 1941, Dr. Goddard made substantial progress in the development of progressively larger rockets, which attained altitudes of 2400 meters, and refined his equipment for guidance and control, his techniques of welding, and his insulation, pumps, and other associated equipment. In many respects, Dr. Goddard laid the essential foundations of practical rocket technology

Energy Tracking Software Platform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryan Davis; Nathan Bird; Rebecca Birx

2011-04-04

Acceleration has created an interactive energy tracking and visualization platform that supports decreasing electric, water, and gas usage. Homeowners have access to tools that allow them to gauge their use and track progress toward a smaller energy footprint. Real estate agents have access to consumption data, allowing for sharing a comparison with potential home buyers. Home builders have the opportunity to compare their neighborhood's energy efficiency with competitors. Home energy raters have a tool for gauging the progress of their clients after efficiency changes. And, social groups are able to help encourage members to reduce their energy bills and helpmore » their environment. EnergyIT.com is the business umbrella for all energy tracking solutions and is designed to provide information about our energy tracking software and promote sales. CompareAndConserve.com (Gainesville-Green.com) helps homeowners conserve energy through education and competition. ToolsForTenants.com helps renters factor energy usage into their housing decisions.« less

GOLIAH: A Gaming Platform for Home-Based Intervention in Autism – Principles and Design

PubMed Central

Bono, Valentina; Narzisi, Antonio; Jouen, Anne-Lise; Tilmont, Elodie; Hommel, Stephane; Jamal, Wasifa; Xavier, Jean; Billeci, Lucia; Maharatna, Koushik; Wald, Mike; Chetouani, Mohamed; Cohen, David; Muratori, Filippo

2016-01-01

Children with Autism need intensive intervention and this is challenging in terms of manpower, costs, and time. Advances in Information Communication Technology and computer gaming may help in this respect by creating a nomadically deployable closed-loop intervention system involving the child and active participation of parents and therapists. An automated serious gaming platform enabling intensive intervention in nomadic settings has been developed by mapping two pivotal skills in autism spectrum disorder: Imitation and Joint Attention (JA). Eleven games – seven Imitations and four JA – were derived from the Early Start Denver Model. The games involved application of visual and audio stimuli with multiple difficulty levels and a wide variety of tasks and actions pertaining to the Imitation and JA. The platform runs on mobile devices and allows the therapist to (1) characterize the child’s initial difficulties/strengths, ensuring tailored and adapted intervention by choosing appropriate games and (2) investigate and track the temporal evolution of the child’s progress through a set of automatically extracted quantitative performance metrics. The platform allows the therapist to change the game or its difficulty levels during the intervention depending on the child’s progress. Performance of the platform was assessed in a 3-month open trial with 10 children with autism (Trial ID: NCT02560415, Clinicaltrials.gov). The children and the parents participated in 80% of the sessions both at home (77.5%) and at the hospital (90%). All children went through all the games but, given the diversity of the games and the heterogeneity of children profiles and abilities, for a given game the number of sessions dedicated to the game varied and could be tailored through automatic scoring. Parents (N = 10) highlighted enhancement in the child’s concentration, flexibility, and self-esteem in 78, 89, and 44% of the cases, respectively, and 56% observed an enhanced parents–child relationship. This pilot study shows the feasibility of using the developed gaming platform for home-based intensive intervention. However, the overall capability of the platform in delivering intervention needs to be assessed in a bigger open trial. PMID:27199777

GOLIAH: A Gaming Platform for Home-Based Intervention in Autism - Principles and Design.

PubMed

Bono, Valentina; Narzisi, Antonio; Jouen, Anne-Lise; Tilmont, Elodie; Hommel, Stephane; Jamal, Wasifa; Xavier, Jean; Billeci, Lucia; Maharatna, Koushik; Wald, Mike; Chetouani, Mohamed; Cohen, David; Muratori, Filippo

2016-01-01

Children with Autism need intensive intervention and this is challenging in terms of manpower, costs, and time. Advances in Information Communication Technology and computer gaming may help in this respect by creating a nomadically deployable closed-loop intervention system involving the child and active participation of parents and therapists. An automated serious gaming platform enabling intensive intervention in nomadic settings has been developed by mapping two pivotal skills in autism spectrum disorder: Imitation and Joint Attention (JA). Eleven games - seven Imitations and four JA - were derived from the Early Start Denver Model. The games involved application of visual and audio stimuli with multiple difficulty levels and a wide variety of tasks and actions pertaining to the Imitation and JA. The platform runs on mobile devices and allows the therapist to (1) characterize the child's initial difficulties/strengths, ensuring tailored and adapted intervention by choosing appropriate games and (2) investigate and track the temporal evolution of the child's progress through a set of automatically extracted quantitative performance metrics. The platform allows the therapist to change the game or its difficulty levels during the intervention depending on the child's progress. Performance of the platform was assessed in a 3-month open trial with 10 children with autism (Trial ID: NCT02560415, Clinicaltrials.gov). The children and the parents participated in 80% of the sessions both at home (77.5%) and at the hospital (90%). All children went through all the games but, given the diversity of the games and the heterogeneity of children profiles and abilities, for a given game the number of sessions dedicated to the game varied and could be tailored through automatic scoring. Parents (N = 10) highlighted enhancement in the child's concentration, flexibility, and self-esteem in 78, 89, and 44% of the cases, respectively, and 56% observed an enhanced parents-child relationship. This pilot study shows the feasibility of using the developed gaming platform for home-based intensive intervention. However, the overall capability of the platform in delivering intervention needs to be assessed in a bigger open trial.

Electrochemical pesticide detection with AutoDip--a portable platform for automation of crude sample analyses.

PubMed

Drechsel, Lisa; Schulz, Martin; von Stetten, Felix; Moldovan, Carmen; Zengerle, Roland; Paust, Nils

2015-02-07

Lab-on-a-chip devices hold promise for automation of complex workflows from sample to answer with minimal consumption of reagents in portable devices. However, complex, inhomogeneous samples as they occur in environmental or food analysis may block microchannels and thus often cause malfunction of the system. Here we present the novel AutoDip platform which is based on the movement of a solid phase through the reagents and sample instead of transporting a sequence of reagents through a fixed solid phase. A ball-pen mechanism operated by an external actuator automates unit operations such as incubation and washing by consecutively dipping the solid phase into the corresponding liquids. The platform is applied to electrochemical detection of organophosphorus pesticides in real food samples using an acetylcholinesterase (AChE) biosensor. Minimal sample preparation and an integrated reagent pre-storage module hold promise for easy handling of the assay. Detection of the pesticide chlorpyrifos-oxon (CPO) spiked into apple samples at concentrations of 10(-7) M has been demonstrated. This concentration is below the maximum residue level for chlorpyrifos in apples defined by the European Commission.

Design and Proof-of-Concept Use of a Circular PMMA Platform with 16-Well Sample Capacity for Microwave-Accelerated Bioassays.

PubMed

Mohammed, Muzaffer; Aslan, Kadir

2013-01-01

We demonstrate the design and the proof-of-concept use of a new, circular poly(methyl methacrylate)-based bioassay platform (PMMA platform), which affords for the rapid processing of 16 samples at once. The circular PMMA platform (5 cm in diameter) was coated with a silver nanoparticle film to accelerate the bioassay steps by microwave heating. A model colorimetric bioassay for biotinylated albumin (using streptavidin-labeled horse radish peroxidase) was performed on the PMMA platform coated with and without silver nanoparticles (a control experiment), and at room temperature and using microwave heating. It was shown that the simulated temperature profile of the PMMA platform during microwave heating were comparable to the real-time temperature profile during actual microwave heating of the constructed PMMA platform in a commercial microwave oven. The model colorimetric bioassay for biotinylated albumin was successfully completed in ~2 min (total assay time) using microwave heating, as compared to 90 min at room temperature (total assay time), which indicates a ~45-fold decrease in assay time. Our PMMA platform design afforded for significant reduction in non-specific interactions and low background signal as compared to non-silvered PMMA surfaces when employed in a microwave-accelerated bioassay carried out in a conventional microwave cavity.

Assessing the impacts of canopy openness and flight parameters on detecting a sub-canopy tropical invasive plant using a small unmanned aerial system

NASA Astrophysics Data System (ADS)

Perroy, Ryan L.; Sullivan, Timo; Stephenson, Nathan

2017-03-01

Small unmanned aerial systems (sUAS) have great potential to facilitate the early detection and management of invasive plants. Here we show how very high-resolution optical imagery, collected from small consumer-grade multirotor UAS platform at altitudes of 30-120 m above ground level (agl), can be used to detect individual miconia (Miconia calvescens) plants in a highly invaded tropical rainforest environment on the island of Hawai'i. The central aim of this research was to determine how overstory vegetation cover, imagery resolution, and camera look-angle impact the aerial detection of known individual miconia plants. For our finest resolution imagery (1.37 cm ground sampling distance collected at 30 m agl), we obtained a 100% detection rate for sub-canopy plants with above-crown openness values >40% and a 69% detection rate for those with >20% openness. We were unable to detect any plants with <10% above crown openness. Detection rates progressively declined with coarser spatial resolution imagery, ending in a 0% detection rate for the 120 m agl flights (ground sampling distance of 5.31 cm). The addition of forward-looking oblique imagery improved detection rates for plants below overstory vegetation, though this effect decreased with increasing flight altitude. While dense overstory canopy cover, limited flight times, and visual line of sight regulations present formidable obstacles for detecting miconia and other invasive plant species, we show that sUAS platforms carrying optical sensors can be an effective component of an integrated management plan within challenging subcanopy forest environments.

Orbital Observatory for Planetary Science on Low Cost Autonomous Platform

NASA Astrophysics Data System (ADS)

Tavrov, Alexander; Bisikalo, Dmitry; Vedenkin, Nikolay; Korablev, Oleg; Markov, Alexander; Kiselev, Alexander; Kokorich, Mikhail

The Space Research Institute of Russian Academy of Science (IKI RAS) and Dauria Aerospace are currently developing the middle class space telescope project aiming to observe Solar system planets by a long term spectroscopy and polarimetry monitoring, as well aiming to extra solar planets (exoplanets) engineering and scientific goals. The spacecraft is scheduled to be launched in 2017. It is planned first to be delivered on board of the ISS by the Progress spacecraft, then it will be released to the desired orbit approx. 550 km by the Progress in the way to its final destination. The “Planetary monitoring” telescope has a 0.6 meter primary mirror diameter Telescope currently includes 5 science instruments: NIR: 1000..4000 nm high-resolution spectrometer with the spectral resolution of R>10000; Visible Field camera with filters wheel; UV-VIS field resolved Fourier spectrometer; UV-VIS spectropolarimeter; Stellar coronagraph linked with a low-resolution spectrometer. The scientific goals of the “Planetary monitoring” telescope are devoted to explore not yet well studied questions on Mars (methane, ozone, dust and clouds, isotope ratio of HDO/H2O), on Venus (UV absorber, night glow, atmosphere dynamics), icy and gaseous Solar system planets, Jovian moons, Lunar exosphere, comets, meteorites. This telescope aims also for engineering development of exoplanet study by stellar coronagraphy linked with a low-resolution spectrometry. This Orbital Observatory mission uses the first low cost small satellite platform developed by the Dauria Aerospace® - Russian private company and reuses the Progress to elevate the observatory orbit. The Progress launches four times per year to provide supplies and scientific instruments to the ISS. The Progress is capable of raising the height of the orbit for the piggyback scientific missions; therefore, the implementation of the Orbital Observatory mission is considered not just as a development of a successful science mission so it is most importantly developing an affordable and frequent flight opportunities for space sciences research in Russia and worldwide. The paper describes the scientific objectives and corresponding instruments, and introduces the low cost satellite platform and launch opportunities.

A hybrid approach to device integration on a genetic analysis platform

NASA Astrophysics Data System (ADS)

Brennan, Des; Jary, Dorothee; Kurg, Ants; Berik, Evgeny; Justice, John; Aherne, Margaret; Macek, Milan; Galvin, Paul

2012-10-01

Point-of-care (POC) systems require significant component integration to implement biochemical protocols associated with molecular diagnostic assays. Hybrid platforms where discrete components are combined in a single platform are a suitable approach to integration, where combining multiple device fabrication steps on a single substrate is not possible due to incompatible or costly fabrication steps. We integrate three devices each with a specific system functionality: (i) a silicon electro-wetting-on-dielectric (EWOD) device to move and mix sample and reagent droplets in an oil phase, (ii) a polymer microfluidic chip containing channels and reservoirs and (iii) an aqueous phase glass microarray for fluorescence microarray hybridization detection. The EWOD device offers the possibility of fully integrating on-chip sample preparation using nanolitre sample and reagent volumes. A key challenge is sample transfer from the oil phase EWOD device to the aqueous phase microarray for hybridization detection. The EWOD device, waveguide performance and functionality are maintained during the integration process. An on-chip biochemical protocol for arrayed primer extension (APEX) was implemented for single nucleotide polymorphism (SNiP) analysis. The prepared sample is aspirated from the EWOD oil phase to the aqueous phase microarray for hybridization. A bench-top instrumentation system was also developed around the integrated platform to drive the EWOD electrodes, implement APEX sample heating and image the microarray after hybridization.

Told through the wine: A liquid chromatography-mass spectrometry interplatform comparison reveals the influence of the global approach on the final annotated metabolites in non-targeted metabolomics.

PubMed

Díaz, Ramon; Gallart-Ayala, Hector; Sancho, Juan V; Nuñez, Oscar; Zamora, Tatiana; Martins, Claudia P B; Hernández, Félix; Hernández-Cassou, Santiago; Saurina, Javier; Checa, Antonio

2016-02-12

This work focuses on the influence of the selected LC-HRMS platform on the final annotated compounds in non-targeted metabolomics. Two platforms that differed in columns, mobile phases, gradients, chromatographs, mass spectrometers (Orbitrap [Platform#1] and Q-TOF [Platform#2]), data processing and marker selection protocols were compared. A total of 42 wines samples from three different protected denomination of origin (PDO) were analyzed. At the feature level, good (O)PLS-DA models were obtained for both platforms (Q(2)[Platform#1]=0.89, 0.83 and 0.72; Q(2)[Platform#2]=0.86, 0.86 and 0.77 for Penedes, Ribera del Duero and Rioja wines respectively) with 100% correctly classified samples in all cases. At the annotated metabolite level, platforms proposed 9 and 8 annotated metabolites respectively which were identified by matching standards or the MS/MS spectra of the compounds. At this stage, there was no coincidence among platforms regarding the suggested metabolites. When screened on the raw data, 6 and 5 of these compounds were detected on the other platform with a similar trend. Some of the detected metabolites showed complimentary information when integrated on biological pathways. Through the use of some examples at the annotated metabolite level, possible explanations of this initial divergence on the results are presented. This work shows the complications that may arise on the comparison of non-targeted metabolomics platforms even when metabolite focused approaches are used in the identification. Copyright © 2016 Elsevier B.V. All rights reserved.

MULTIFUNCTION ENERGY PLATFORM (MFP) PILOT

EPA Science Inventory

• Multi-sector Baseline Survey:  A five-sector survey (agriculture, energy, water, health, and general - demogr...

• HEP data analysis using jHepWork and Java.

  DOE Office of Scientific and Technical Information (OSTI.GOV)

  Chekanov, S.; High Energy Physics

  2009-03-23

  A role of Java in high-energy physics (HEP) and recent progress in development of a platform-independent data-analysis framework, jHepWork, is discussed. The framework produces professional graphics and has many libraries for data manipulation.

• Comparative Performance of Reagents and Platforms for Quantitation of Cytomegalovirus DNA by Digital PCR

  PubMed Central

  Gu, Z.; Sam, S. S.; Sun, Y.; Tang, L.; Pounds, S.; Caliendo, A. M.

  2016-01-01

  A potential benefit of digital PCR is a reduction in result variability across assays and platforms. Three sets of PCR reagents were tested on two digital PCR systems (Bio-Rad and RainDance), using three different sets of PCR reagents for quantitation of cytomegalovirus (CMV). Both commercial quantitative viral standards and 16 patient samples (n = 16) were tested. Quantitative accuracy (compared to nominal values) and variability were determined based on viral standard testing results. Quantitative correlation and variability were assessed with pairwise comparisons across all reagent-platform combinations for clinical plasma sample results. The three reagent sets, when used to assay quantitative standards on the Bio-Rad system, all showed a high degree of accuracy, low variability, and close agreement with one another. When used on the RainDance system, one of the three reagent sets appeared to have a much better correlation to nominal values than did the other two. Quantitative results for patient samples showed good correlation in most pairwise comparisons, with some showing poorer correlations when testing samples with low viral loads. Digital PCR is a robust method for measuring CMV viral load. Some degree of result variation may be seen, depending on platform and reagents used; this variation appears to be greater in samples with low viral load values. PMID:27535685

• Communicating climate change adaptation information using web-based platforms

  NASA Astrophysics Data System (ADS)

  Karali, Eleni; Mattern, Kati

  2017-07-01

  To facilitate progress in climate change adaptation policy and practice, it is important not only to ensure the production of accurate, comprehensive and relevant information, but also the easy, timely and affordable access to it. This can contribute to better-informed decisions and improve the design and implementation of adaptation policies and other relevant initiatives. Web-based platforms can play an important role in communicating and distributing data, information and knowledge that become constantly available, reaching out to a large group of potential users. Indeed in the last decade there has been an extensive increase in the number of platforms developed for this purpose in many fields including climate change adaptation. This short paper concentrates on the web-based adaptation platforms developed in Europe. It provides an overview of the recently emerged landscape, examines the basic characteristics of a set of platforms that operate at national, transnational and European level, and discusses some of the key challenges related to their development, maintenance and overall management. Findings presented in this short paper are discussed in greater detailed in the Technical Report of the European Environment Agency Overview of climate change adaptation platforms in Europe.

• Operation of Lanzhou all permanent electron cyclotron resonance ion source No. 2 on 320 kV platform with highly charged ions.

  PubMed

  Lu, W; Li, J Y; Kang, L; Liu, H P; Li, H; Li, J D; Sun, L T; Ma, X W

  2014-02-01

  The 320 kV platform for multi-discipline research with highly charged ions is a heavy ion beam acceleration instrument developed by Institute of Modern Physics, which is dedicated to basic scientific researches such as plasma, atom, material physics, and astrophysics, etc. The platform has delivered ion beams of 400 species for 36,000 h. The average operation time is around 5000 h/year. With the beams provided by the platform, lots of outstanding progresses were made in various research fields. The ion source of the platform is an all-permanent magnet electron cyclotron resonance ion source, LAPECR2 (Lanzhou All Permanent ECR ion source No. 2). The maximum axial magnetic fields are 1.28 T at injection and 1.07 T at extraction, and the radial magnetic field is up to 1.21 T at the inner wall of the plasma chamber. The ion source is capable to produce low, medium, and high charge state gaseous and metallic ion beams, such as H(+), (40)Ar(8+), (129)Xe(30+), (209)Bi(33+), etc. This paper will present the latest result of LAPECR2 and the routine operation status for the high voltage platform.

• Ex-vivo sensitivity profiling to guide clinical decision making in acute myeloid leukemia: A pilot study.

  PubMed

  Swords, Ronan T; Azzam, Diana; Al-Ali, Hassan; Lohse, Ines; Volmar, Claude-Henry; Watts, Justin M; Perez, Aymee; Rodriguez, Ana; Vargas, Fernando; Elias, Roy; Vega, Francisco; Zelent, Arthur; Brothers, Shaun P; Abbasi, Taher; Trent, Jonathan; Rangwala, Shaukat; Deutsch, Yehuda; Conneally, Eibhlin; Drusbosky, Leylah; Cogle, Christopher R; Wahlestedt, Claes

  2018-01-01

  A precision medicine approach is appealing for use in AML due to ease of access to tumor samples and the significant variability in the patients' response to treatment. Attempts to establish a precision medicine platform for AML, however, have been unsuccessful, at least in part due to the use of small compound panels and having relatively slow turn over rates, which restricts the scope of treatment and delays its onset. For this pilot study, we evaluated a cohort of 12 patients with refractory AML using an ex vivo drug sensitivity testing (DST) platform. Purified AML blasts were screened with a panel of 215 FDA-approved compounds and treatment response was evaluated after 72h of exposure. Drug sensitivity scoring was reported to the treating physician, and patients were then treated with either DST- or non-DST guided therapy. We observed survival benefit of DST-guided therapy as compared to the survival of patients treated according to physician recommendation. Three out of four DST-treated patients displayed treatment response, while all of the non-DST-guided patients progressed during treatment. DST rapidly and effectively provides personalized treatment recommendations for patients with refractory AML. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Development of a standardized differential-reflective bioassay for microbial pathogens

NASA Astrophysics Data System (ADS)

Wilhelm, Jay; Auld, J. R. X.; Smith, James E.

2008-04-01

This research examines standardizing a method for the rapid/semi-automated identification of microbial contaminates. It introduces a method suited to test for food/water contamination, serology, urinalysis and saliva testing for any >1 micron sized molecule that can be effectively bound to an identifying marker with exclusivity. This optical biosensor method seeks to integrate the semi-manual distribution of a collected sample onto a "transparent" substrate array of binding sites that will then be applied to a standard optical data disk and run for analysis. The detection of most microbe species is possible in this platform because the relative scale is greater than the resolution of the standard-scale digital information on a standard CD or DVD. This paper explains the critical first stage in the advance of this detection concept. This work has concentrated on developing the necessary software component needed to perform highly sensitive small-scale recognition using the standard optical disk as a detection platform. Physical testing has made significant progress in demonstrating the ability to utilize a standard optical drive for the purposes of micro-scale detection through the exploitation of CIRC error correction. Testing has also shown a definable trend in the optimum scale and geometry of micro-arrayed attachment sites for the technology's concept to reach achievement.

Constructing temporary sampling platforms for hydrologic studies

Treesearch

Manuel H. Martinez; Sandra E. Ryan

2000-01-01

This paper presents instructions for constructing platforms that span the width of stream channels to accommodate the measurement of hydrologic parameters over a wide range of discharges. The platforms provide a stable, safe, noninvasive, easily constructed, and relatively inexpensive means for permitting data collection without wading in the flow. We have used the...

Visible and infrared polarization ratio spectroreflectometer

NASA Technical Reports Server (NTRS)

Batten, C. E. (Inventor)

1980-01-01

The instrument assists in determining the refractive index and absorption index, at different spectral frequencies, of a solid sample by illuminating the sample at various angles in incidence and measuring the corresponding reflected intensities at various spectral frequencies and polarization angles. The ratio of the intensity of the reflected light for parallel polarized light to that for perpendicular polarized light at two different angles of incidence can be used to determine the optical constants of the sample. The invention involves an apparatus for facilitating the utilization of a wide variety of angles of incidence. The light source and polarizing element are positioned on an outer platform; the sample is positioned on an inner platform. The two platforms rotate about a common axis and cooperate in their rotation such that the sample is rotated one degree for every two degrees of rotation of the light source. This maintains the impingement of the reflected light upon the detector for any angle of incidence without moving or adjusting the detector which allows a continuous change in the angle of incidence.

Tectonic control of Middle Devonian reef building in the Mechra ben Abbou (northern Rehamna, Morocco)Contrôle tectonique de l'édification des récifs Dévonien moyen de Mechra ben Abbou (Rehamna, Maroc)

NASA Astrophysics Data System (ADS)

El Kamel, Fouad; El Hassani, Ahmed; Mohsine, Assia; Remmal, Toufik

2000-01-01

In the carbonated platform of Upper Emsian to Givetian age, the reef edification is previous to, and contemporaneous with, a tilted block tectonic that has favoured the bioconstruction in its upper part. The tectonic expression is illustrated by several instability marks, such as tension faults, progressive unconformity and the resulting landslide, observed in both the reef development zone and the external platform.

Thermotropic Liquid Crystal-Assisted Chemical and Biological Sensors

PubMed Central

Honaker, Lawrence W.; Usol’tseva, Nadezhda; Mann, Elizabeth K.

2017-01-01

In this review article, we analyze recent progress in the application of liquid crystal-assisted advanced functional materials for sensing biological and chemical analytes. Multiple research groups demonstrate substantial interest in liquid crystal (LC) sensing platforms, generating an increasing number of scientific articles. We review trends in implementing LC sensing techniques and identify common problems related to the stability and reliability of the sensing materials as well as to experimental set-ups. Finally, we suggest possible means of bridging scientific findings to viable and attractive LC sensor platforms. PMID:29295530

Technology platforms for remote monitoring of vital signs in the new era of telemedicine.

PubMed

Zhao, Fang; Li, Meng; Tsien, Joe Z

2015-07-01

Driven by healthcare cost and home healthcare need, the development of remote monitoring technologies is poised to improve and revolutionize healthcare delivery and accessibility. This paper reviews the recent progress in the field of remote monitoring technologies that may have the potential to become the basic platforms for telemedicine. In particular, key techniques and devices for monitoring cardiorespiratory activity, blood pressure and blood glucose concentration are summarized and discussed. In addition, the US FDA approved remote vital signs monitoring devices currently available on the market are presented.

Long-Term Global Morphology of Gravity Wave Activity Using UARS Data

NASA Technical Reports Server (NTRS)

Eckermann, Stephen D.; Bacmeister, Julio T.; Wu, Dong L.

1998-01-01

Progress in research into the global morphology of gravity wave activity using UARS data is described for the period March-June, 1998. Highlights this quarter include further progress in the analysis and interpretation of CRISTA temperature variances; model-generated climatologies of mesospheric gravity wave activity using the HWM-93 wind and temperature model; and modeling of gravity wave detection from space-based platforms. Preliminary interpretations and recommended avenues for further analysis are also described.

Dr. Robert H. Goddard and His Rocket

NASA Technical Reports Server (NTRS)

1940-01-01

Goddard rocket in launching tower at Roswell, New Mexico, March 21, 1940. Fuel was injected by pumps from the fueling platform at left. From 1930 to 1941, Dr. Goddard made substantial progress in the development of progressively larger rockets, which attained altitudes of 2400 meters, and refined his equipment for guidance and control, his techniques of welding, and his insulation, pumps, and other associated equipment. In many respects, Dr. Goddard laid the essential foundations of practical rocket technology

Team Oriented Robotic Exploration Task on Scorpion and K9 Platforms

NASA Technical Reports Server (NTRS)

Kirchner, Frank

2003-01-01

This final report describes the achievements that have been made in the project over the complete period of performance. The technical progress highlights the different areas of work in terms of Progress in Mechatronics, Sensor integration, Software Development. User Interfaces, Behavior Development and Experimental Results and System Testing. The different areas are: Mechatronics, Sensor integration, Software development, Experimental results and Basic System Testing, Behaviors Development and Advanced System Testing, User Interface and Wireless Communication.

Metaproteomics as a Complementary Approach to Gut Microbiota in Health and Disease

NASA Astrophysics Data System (ADS)

Petriz, Bernardo A.; Franco, Octávio L.

2017-01-01

Classic studies on phylotype profiling are limited to the identification of microbial constituents, where information is lacking about the molecular interaction of these bacterial communities with the host genome and the possible outcomes in host biology. A range of OMICs approaches have provided great progress linking the microbiota to health and disease. However, the investigation of this context through proteomic mass spectrometry-based tools is still being improved. Therefore, metaproteomics or community proteogenomics has emerged as a complementary approach to metagenomic data, as a field in proteomics aiming to perform large-scale characterization of proteins from environmental microbiota such as the human gut. The advances in molecular separation methods coupled with mass spectrometry (e.g. LC-MS/MS) and proteome bioinformatics have been fundamental in these novel large-scale metaproteomic studies, which have further been performed in a wide range of samples including soil, plant and human environments. Metaproteomic studies will make major progress if a comprehensive database covering the genes and expresses proteins from all gut microbial species is developed. To this end, we here present some of the main limitations of metaproteomic studies in complex microbiota environments such as the gut, also addressing the up-to-date pipelines in sample preparation prior to fractionation/separation and mass spectrometry analysis. In addition, a novel approach to the limitations of metagenomic databases is also discussed. Finally, prospects are addressed regarding the application of metaproteomic analysis using a unified host-microbiome gene database and other meta-OMICs platforms.

An X-ray transparent microfluidic platform for screening of the phase behavior of lipidic mesophases

PubMed Central

Khvostichenko, Daria S.; Kondrashkina, Elena; Perry, Sarah L.; Pawate, Ashtamurthy S.; Brister, Keith

2013-01-01

Lipidic mesophases are a class of highly ordered soft materials that form when certain lipids are mixed with water. Understanding the relationship between the composition and the microstructure of mesophases is necessary for fundamental studies of self-assembly in amphiphilic systems and for applications, such as crystallization of membrane proteins. However, the laborious formulation protocol for highly viscous mesophases and the large amounts of material required for sample formulation are significant obstacles in such studies. Here we report a microfluidic platform that facilitates investigations of the phase behavior of mesophases by reducing sample consumption, and automating and parallelizing sample formulation. The mesophases were formulated on-chip using less than 40 nL of material per sample and their microstructure was analyzed in situ using small-angle X-ray scattering (SAXS). The 220 μm-thick X-ray compatible platform was comprised of thin polydimethylsiloxane (PDMS) layers sandwiched between cyclic olefin copolymer (COC) sheets. Uniform mesophases were prepared using an active on-chip mixing strategy coupled with periodic cooling of the sample to reduce the viscosity. We validated the platform by preparing and analyzing mesophases of lipid monoolein (MO) mixed with aqueous solutions of different concentrations of β-octylglucoside (βOG), a detergent frequently used in membrane protein crystallization. Four samples were prepared in parallel on chip, by first metering and automatically diluting βOG to obtain detergent solutions of different concentration, then metering MO, and finally mixing by actuation of pneumatic valves. Integration of detergent dilution and subsequent mixing significantly reduced the number of manual steps needed for sample preparation. Three different types of mesophases typical for monoolein were successfully identified in SAXS data from on-chip samples. Microstructural parameters of identical samples formulated in different chips showed excellent agreement. Phase behavior observed on-chip corresponded well with that of samples prepared via the traditional coupled-syringe method (“off-chip”) using 300-fold larger amount of material, further validating the utility of the microfluidic platform for on-chip characterization of mesophase behavior. PMID:23882463

Progress and challenges in TB vaccine development

PubMed Central

Voss, Gerald; Casimiro, Danilo; Neyrolles, Olivier; Williams, Ann; Kaufmann, Stefan H.E.; McShane, Helen; Hatherill, Mark; Fletcher, Helen A

2018-01-01

The Bacille Calmette Guerin (BCG) vaccine can provide decades of protection against tuberculosis (TB) disease, and although imperfect, BCG is proof that vaccine mediated protection against TB is a possibility. A new TB vaccine is, therefore, an inevitability; the question is how long will it take us to get there? We have made substantial progress in the development of vaccine platforms, in the identification of antigens and of immune correlates of risk of TB disease. We have also standardized animal models to enable head-to-head comparison and selection of candidate TB vaccines for further development.  To extend our understanding of the safety and immunogenicity of TB vaccines we have performed experimental medicine studies to explore route of administration and have begun to develop controlled human infection models. Driven by a desire to reduce the length and cost of human efficacy trials we have applied novel approaches to later stage clinical development, exploring alternative clinical endpoints to prevention of disease outcomes. Here, global leaders in TB vaccine development discuss the progress made and the challenges that remain. What emerges is that, despite scientific progress, few vaccine candidates have entered clinical trials in the last 5 years and few vaccines in clinical trials have progressed to efficacy trials. Crucially, we have undervalued the knowledge gained from our “failed” trials and fostered a culture of risk aversion that has limited new funding for clinical TB vaccine development. The unintended consequence of this abundance of caution is lack of diversity of new TB vaccine candidates and stagnation of the clinical pipeline. We have a variety of new vaccine platform technologies, mycobacterial antigens and animal and human models.  However, we will not encourage progression of vaccine candidates into clinical trials unless we evaluate and embrace risk in pursuit of vaccine development. PMID:29568497

Progress and challenges in TB vaccine development.

PubMed

Voss, Gerald; Casimiro, Danilo; Neyrolles, Olivier; Williams, Ann; Kaufmann, Stefan H E; McShane, Helen; Hatherill, Mark; Fletcher, Helen A

2018-01-01

The Bacille Calmette Guerin (BCG) vaccine can provide decades of protection against tuberculosis (TB) disease, and although imperfect, BCG is proof that vaccine mediated protection against TB is a possibility. A new TB vaccine is, therefore, an inevitability; the question is how long will it take us to get there? We have made substantial progress in the development of vaccine platforms, in the identification of antigens and of immune correlates of risk of TB disease. We have also standardized animal models to enable head-to-head comparison and selection of candidate TB vaccines for further development.  To extend our understanding of the safety and immunogenicity of TB vaccines we have performed experimental medicine studies to explore route of administration and have begun to develop controlled human infection models. Driven by a desire to reduce the length and cost of human efficacy trials we have applied novel approaches to later stage clinical development, exploring alternative clinical endpoints to prevention of disease outcomes. Here, global leaders in TB vaccine development discuss the progress made and the challenges that remain. What emerges is that, despite scientific progress, few vaccine candidates have entered clinical trials in the last 5 years and few vaccines in clinical trials have progressed to efficacy trials. Crucially, we have undervalued the knowledge gained from our "failed" trials and fostered a culture of risk aversion that has limited new funding for clinical TB vaccine development. The unintended consequence of this abundance of caution is lack of diversity of new TB vaccine candidates and stagnation of the clinical pipeline. We have a variety of new vaccine platform technologies, mycobacterial antigens and animal and human models.  However, we will not encourage progression of vaccine candidates into clinical trials unless we evaluate and embrace risk in pursuit of vaccine development.

Multi-function microfluidic platform for sensor integration.

PubMed

Fernandes, Ana C; Semenova, Daria; Panjan, Peter; Sesay, Adama M; Gernaey, Krist V; Krühne, Ulrich

2018-03-06

The limited availability of metabolite-specific sensors for continuous sampling and monitoring is one of the main bottlenecks contributing to failures in bioprocess development. Furthermore, only a limited number of approaches exist to connect currently available measurement systems with high throughput reactor units. This is especially relevant in the biocatalyst screening and characterization stage of process development. In this work, a strategy for sensor integration in microfluidic platforms is demonstrated, to address the need for rapid, cost-effective and high-throughput screening in bioprocesses. This platform is compatible with different sensor formats by enabling their replacement and was built in order to be highly flexible and thus suitable for a wide range of applications. Moreover, this re-usable platform can easily be connected to analytical equipment, such as HPLC, laboratory scale reactors or other microfluidic chips through the use of standardized fittings. In addition, the developed platform includes a two-sensor system interspersed with a mixing channel, which allows the detection of samples that might be outside the first sensor's range of detection, through dilution of the sample solution up to 10 times. In order to highlight the features of the proposed platform, inline monitoring of glucose levels is presented and discussed. Glucose was chosen due to its importance in biotechnology as a relevant substrate. The platform demonstrated continuous measurement of substrate solutions for up to 12 h. Furthermore, the influence of the fluid velocity on substrate diffusion was observed, indicating the need for in-flow calibration to achieve a good quantitative output. Copyright © 2018 Elsevier B.V. All rights reserved.

Integrating clinical and biological information in a shanghai biobank: an introduction to the sample repository and information sharing platform project.

PubMed

Cui, Wenbin; Zheng, Peiyong; Yang, Jiahong; Zhao, Rong; Gao, Jiechun; Yu, Guangjun

2015-02-01

Biobanks are important resources and central tools for translational medicine, which brings scientific research outcomes to clinical practice. The key purpose of biobanking in translational medicine and other medical research is to provide biological samples that are integrated with clinical information. In 2008, the Shanghai Municipal Government launched the "Shanghai Tissue Bank" in an effort to promote research in translational medicine. Now a sharing service platform has been constructed to integrate clinical practice and biological information that can be used in diverse medical and pharmaceutical research studies. The platform collects two kinds of data: sample data and clinical data. The sample data are obtained from the hospital biobank management system, and mainly include the donors' age, gender, marital status, sample source, sample type, collection time, deposit time, and storage method. The clinical data are collected from the "Hospital-Link" system (a medical information sharing system that connects 23 tertiary hospitals in Shanghai). The main contents include donors' corresponding medication information, test reports, inspection reports, and hospital information. As of the end of September 2014, the project has a collection of 16,020 donors and 148,282 samples, which were obtained from 12 medical institutions, and automatically acquired donors' corresponding clinical data from the "Hospital-Link" system for 6830 occurrences. This project will contribute to scientific research at medical institutions in Shanghai, and will also support the development of the biopharmaceutical industry. In this article, we will describe the significance, the construction phases, the application prospects, and benefits of the sample repository and information sharing service platform.

A Sustainable Architecture for Lunar Resource Prospecting from an EML-based Exploration Platform

NASA Astrophysics Data System (ADS)

Klaus, K.; Post, K.; Lawrence, S. J.

2012-12-01

Introduction - We present a point of departure architecture for prospecting for Lunar Resources from an Exploration Platform at the Earth - Moon Lagrange points. Included in our study are launch vehicle, cis-lunar transportation architecture, habitat requirements and utilization, lander/rover concepts and sample return. Different transfer design techniques can be explored by mission designers, testing various propulsive systems, maneuvers, rendezvous, and other in-space and surface operations. Understanding the availability of high and low energy trajectory transfer options opens up the possibility of exploring the human and logistics support mission design space and deriving solutions never before contemplated. For sample return missions from the lunar surface, low-energy transfers could be utilized between EML platform and the surface as well as return of samples to EML-based spacecraft. Human Habitation at the Exploration Platform - Telerobotic and telepresence capabilities are considered by the agency to be "grand challenges" for space technology. While human visits to the lunar surface provide optimal opportunities for field geologic exploration, on-orbit telerobotics may provide attractive early opportunities for geologic exploration, resource prospecting, and other precursor activities in advance of human exploration campaigns and ISRU processing. The Exploration Platform provides a perfect port for a small lander which could be refueled and used for multiple missions including sample return. The EVA and robotic capabilities of the EML Exploration Platform allow the lander to be serviced both internally and externally, based on operational requirements. The placement of the platform at an EML point allows the lander to access any site on the lunar surface, thus providing the global lunar surface access that is commonly understood to be required in order to enable a robust lunar exploration program. Designing the sample return lander for low-energy trajectories would reduce the overall mass and potentially increase the sample return mass. The Initial Lunar Mission -Building upon Apollo sample investigations, the recent results of the LRO/LCROSS, international missions such as Chandrayaan-1, and legacy missions including Lunar Prospector, and Clementine, among the most important science and exploration goals is surface prospecting for lunar resources and to provide ground truth for orbital observations. Being able to constrain resource production potential will allow us to estimate the prospect for reducing the size of payloads launched from Earth required for Solar System exploration. Flight opportunities for something like the NASA RESOLVE instrument suite to areas of high science and exploration interest could be used to refine and improve future Exploration architectures, reducing the outlays required for cis-lunar operations. Summary - EML points are excellent for placement of a semi-permanent human-tended Exploration Platform both in the near term, while providing important infrastructure and deep-space experience that will be built upon to gradually increase long-term operational capabilities.

Adaptive Observatories for Observing Moving Marine Organisms (Invited)

NASA Astrophysics Data System (ADS)

Bellingham, J. G.; Scholin, C.; Zhang, Y.; Godin, M. A.; Hobson, B.; Frolov, S.

2010-12-01

The ability to characterize the response of small marine organisms to each other, and to their environment, is a demanding observational challenge. Small organisms live in a water reference frame, while existing cable or mooring-based observatories operate in an Earth reference frame. Thus repeated observations from a fixed system observe different populations as currents sweep organisms by the sensors. In contrast, mobile systems are typically optimized for spatial coverage rather than repeated observations of the same water volume. Lagrangian drifters track water mass, but are unable to find or reposition themselves relative to ocean features. We are developing a system capable of finding, following and observing discrete populations of marine organisms over time, leveraging a decade and a half investment in the Autonomous Ocean Sampling Network (AOSN) program. AOSN undertook the development of platforms to enable multi-platform coordinated measurement of ocean properties in the late 1990s, leading to the development of a variety of autonomous underwater vehicles (AUVs) and associated technologies, notably several glider systems, now in common use. Efforts by a number of research groups have focused on methods to employ these networked systems to observe and predict dynamic physical ocean phenomena. For example, periodic large scale field programs in Monterey Bay have progressively integrated these systems with data systems, predictive models, and web-based collaborative portals. We are adapting these approaches to follow and observe the dynamics of marine organisms. Compared to physical processes, the temporal and spatial variability of small marine organisms, particularly micro-organisms, is typical greater. Consequently, while multi-platform observations of physical processes can be coordinated via intermittent communications links from shore, biological observations require a higher degree of adaptability of the observation system in situ. This talk will describe the platform capabilities developed for such observations, the onboard intelligence for finding and observing discrete populations, and the cyberinfrastructure employed to understand and coordinate observations from shore.

Evidence that molecular changes in cells occur before morphological alterations during the progression of breast ductal carcinoma

PubMed Central

Castro, Nadia P; Osório, Cynthia ABT; Torres, César; Bastos, Elen P; Mourão-Neto, Mário; Soares, Fernando A; Brentani, Helena P; Carraro, Dirce M

2008-01-01

Introduction Ductal carcinoma in situ (DCIS) of the breast includes a heterogeneous group of preinvasive tumors with uncertain evolution. Definition of the molecular factors necessary for progression to invasive disease is crucial to determining which lesions are likely to become invasive. To obtain insight into the molecular basis of DCIS, we compared the gene expression pattern of cells from the following samples: non-neoplastic, pure DCIS, in situ component of lesions with co-existing invasive ductal carcinoma, and invasive ductal carcinoma. Methods Forty-one samples were evaluated: four non-neoplastic, five pure DCIS, 22 in situ component of lesions with co-existing invasive ductal carcinoma, and 10 invasive ductal carcinoma. Pure cell populations were isolated using laser microdissection. Total RNA was purified, DNase treated, and amplified using the T7-based method. Microarray analysis was conducted using a customized cDNA platform. The concept of molecular divergence was applied to classify the sample groups using analysis of variance followed by Tukey's test. Results Among the tumor sample groups, cells from pure DCIS exhibited the most divergent molecular profile, consequently identifying cells from in situ component of lesions with co-existing invasive ductal carcinoma as very similar to cells from invasive lesions. Additionally, we identified 147 genes that were differentially expressed between pure DCIS and in situ component of lesions with co-existing invasive ductal carcinoma, which can discriminate samples representative of in situ component of lesions with co-existing invasive ductal carcinoma from 60% of pure DCIS samples. A gene subset was evaluated using quantitative RT-PCR, which confirmed differential expression for 62.5% and 60.0% of them using initial and partial independent sample groups, respectively. Among these genes, LOX and SULF-1 exhibited features that identify them as potential participants in the malignant process of DCIS. Conclusions We identified new genes that are potentially involved in the malignant transformation of DCIS, and our findings strongly suggest that cells from the in situ component of lesions with co-existing invasive ductal carcinoma exhibit molecular alterations that enable them to invade the surrounding tissue before morphological changes in the lesion become apparent. PMID:18928525

Evidence that molecular changes in cells occur before morphological alterations during the progression of breast ductal carcinoma.

PubMed

Castro, Nadia P; Osório, Cynthia A B T; Torres, César; Bastos, Elen P; Mourão-Neto, Mário; Soares, Fernando A; Brentani, Helena P; Carraro, Dirce M

2008-01-01

Ductal carcinoma in situ (DCIS) of the breast includes a heterogeneous group of preinvasive tumors with uncertain evolution. Definition of the molecular factors necessary for progression to invasive disease is crucial to determining which lesions are likely to become invasive. To obtain insight into the molecular basis of DCIS, we compared the gene expression pattern of cells from the following samples: non-neoplastic, pure DCIS, in situ component of lesions with co-existing invasive ductal carcinoma, and invasive ductal carcinoma. Forty-one samples were evaluated: four non-neoplastic, five pure DCIS, 22 in situ component of lesions with co-existing invasive ductal carcinoma, and 10 invasive ductal carcinoma. Pure cell populations were isolated using laser microdissection. Total RNA was purified, DNase treated, and amplified using the T7-based method. Microarray analysis was conducted using a customized cDNA platform. The concept of molecular divergence was applied to classify the sample groups using analysis of variance followed by Tukey's test. Among the tumor sample groups, cells from pure DCIS exhibited the most divergent molecular profile, consequently identifying cells from in situ component of lesions with co-existing invasive ductal carcinoma as very similar to cells from invasive lesions. Additionally, we identified 147 genes that were differentially expressed between pure DCIS and in situ component of lesions with co-existing invasive ductal carcinoma, which can discriminate samples representative of in situ component of lesions with co-existing invasive ductal carcinoma from 60% of pure DCIS samples. A gene subset was evaluated using quantitative RT-PCR, which confirmed differential expression for 62.5% and 60.0% of them using initial and partial independent sample groups, respectively. Among these genes, LOX and SULF-1 exhibited features that identify them as potential participants in the malignant process of DCIS. We identified new genes that are potentially involved in the malignant transformation of DCIS, and our findings strongly suggest that cells from the in situ component of lesions with co-existing invasive ductal carcinoma exhibit molecular alterations that enable them to invade the surrounding tissue before morphological changes in the lesion become apparent.

A Microfluidic Platform for High-Throughput Multiplexed Protein Quantitation

PubMed Central

Volpetti, Francesca; Garcia-Cordero, Jose; Maerkl, Sebastian J.

2015-01-01

We present a high-throughput microfluidic platform capable of quantitating up to 384 biomarkers in 4 distinct samples by immunoassay. The microfluidic device contains 384 unit cells, which can be individually programmed with pairs of capture and detection antibody. Samples are quantitated in each unit cell by four independent MITOMI detection areas, allowing four samples to be analyzed in parallel for a total of 1,536 assays per device. We show that the device can be pre-assembled and stored for weeks at elevated temperature and we performed proof-of-concept experiments simultaneously quantitating IL-6, IL-1β, TNF-α, PSA, and GFP. Finally, we show that the platform can be used to identify functional antibody combinations by screening 64 antibody combinations requiring up to 384 unique assays per device. PMID:25680117

Rapid Development of Bespoke Unmanned Platforms for Atmospheric Science

NASA Astrophysics Data System (ADS)

Sobester, A.; Johnston, S. J.; Scanlan, J. P.; Hart, E. E.; O'Brien, N. S.

2012-04-01

The effective deployment of airborne atmospheric science instruments often hinges on the development cycle time of a suitable platform, one that is capable of delivering them to the desired altitude range for a specified amount of time, along a pre-determined trajectory. This could be driven by the need to respond rapidly to sudden, unexpected events (e.g., volcano eruptions, nuclear fallout, etc.) or simply to accommodate the iterative design and flight test cycle of the instrument developer. A shorter development cycle time would also afford us the ability to quickly adapt the hardware and control logic in response to unexpected results during an experimental campaign. We report on recent developments aimed at meeting this demand. As part of the Atmospheric Science Through Robotic Aircraft (ASTRA) initiative we have investigated the use of rapid prototyping technologies to this end, both on the 'airframe' of the platform itself and on the on-board systems. We show how fast multi-disciplinary design optimization techniques, coupled with computer-controlled additive manufacturing (3D printing) and laser cutting methods and electronic prototyping (using standard, modular, programmable building blocks) can lead to the delivery of a fully customized platform integrating a given instrument in a timescale of the order of ten days. Specific examples include the design and testing of a balloon-launched glider sensorcraft and a stratospheric balloon system. The 'vehicle' for the latter was built on a 3D printer using a copolymer thermoplastic material and fitted with a sacrificial protective 'cage' laser-cut from an open-cell foam. The data logging, tracking, sensor integration and communications services of the platform were constructed using the .net Gadgeteer open source hardware kit. The flight planning and eventual post-flight recovery of the system is enabled by a generic, stochastic trajectory simulation tool, also developed as part of the ASTRA initiative. This also demonstrated the feasibility of retrieving instrument platforms after the observations are complete, either through self-recovery (in the case of the glider) or accurate pre-flight prediction and real-time tracking, in the case of the balloon platform. We also review developments in progress, including a balloon-launched flock of sensorcraft designed for the effective mapping of aerosol concentrations or other atmospheric measurements across a target airspace block. At the heart of this effort lies the optimization of the (pre-programmed or dynamically re-designed) trajectories such that they combine to approximate space-filling curves that maximize sampling efficiency (a 3D 'travelling salesman'-type calculus of variations problem).

Micron-Scale Differential Scanning Calorimeter on a Chip

DOEpatents

Cavicchi, Richard E; Poirier, Gregory Ernest; Suehle, John S; Gaitan, Michael; Tea, Nim H

1998-06-30

A differential scanning microcalorimeter produced on a silicon chip enables microscopic scanning calorimetry measurements of small samples and thin films. The chip may be fabricated using standard CMOS processes. The microcalorimeter includes a reference zone and a sample zone. The reference and sample zones may be at opposite ends of a suspended platform or may reside on separate platforms. An integrated polysilicon heater provides heat to each zone. A thermopile consisting of a succession of thermocouple junctions generates a voltage representing the temperature difference between the reference and sample zones. Temperature differences between the zones provide information about the chemical reactions and phase transitions that occur in a sample placed in the sample zone.

A global reference database of crowdsourced cropland data collected using the Geo-Wiki platform.

PubMed

Laso Bayas, Juan Carlos; Lesiv, Myroslava; Waldner, François; Schucknecht, Anne; Duerauer, Martina; See, Linda; Fritz, Steffen; Fraisl, Dilek; Moorthy, Inian; McCallum, Ian; Perger, Christoph; Danylo, Olha; Defourny, Pierre; Gallego, Javier; Gilliams, Sven; Akhtar, Ibrar Ul Hassan; Baishya, Swarup Jyoti; Baruah, Mrinal; Bungnamei, Khangsembou; Campos, Alfredo; Changkakati, Trishna; Cipriani, Anna; Das, Krishna; Das, Keemee; Das, Inamani; Davis, Kyle Frankel; Hazarika, Purabi; Johnson, Brian Alan; Malek, Ziga; Molinari, Monia Elisa; Panging, Kripal; Pawe, Chandra Kant; Pérez-Hoyos, Ana; Sahariah, Parag Kumar; Sahariah, Dhrubajyoti; Saikia, Anup; Saikia, Meghna; Schlesinger, Peter; Seidacaru, Elena; Singha, Kuleswar; Wilson, John W

2017-09-26

A global reference data set on cropland was collected through a crowdsourcing campaign using the Geo-Wiki crowdsourcing tool. The campaign lasted three weeks, with over 80 participants from around the world reviewing almost 36,000 sample units, focussing on cropland identification. For quality assessment purposes, two additional data sets are provided. The first is a control set of 1,793 sample locations validated by students trained in satellite image interpretation. This data set was used to assess the quality of the crowd as the campaign progressed. The second data set contains 60 expert validations for additional evaluation of the quality of the contributions. All data sets are split into two parts: the first part shows all areas classified as cropland and the second part shows cropland average per location and user. After further processing, the data presented here might be suitable to validate and compare medium and high resolution cropland maps generated using remote sensing. These could also be used to train classification algorithms for developing new maps of land cover and cropland extent.

Hepatozoon canis and Leishmania spp. coinfection in dogs diagnosed with visceral leishmaniasis.

PubMed

Morgado, Fernanda Nazaré; Cavalcanti, Amanda Dos Santos; Miranda, Luisa Helena de; O'Dwyer, Lúcia Helena; Silva, Maria Regina Lucas da; Menezes, Rodrigo Caldas; Andrade da Silva, Aurea Virgínia; Boité, Mariana Côrtes; Cupolillo, Elisa; Porrozzi, Renato

2016-01-01

This study describes the occurrence of dogs naturally co-infected with Hepatozoon canis and two Leishmania species: L. infantum or L. braziliensis. Four dogs serologically diagnosed with Visceral Leishmaniasis were euthanized. Liver and spleen samples were collected for histopathological analysis and DNA isolation. H. canis meronts were observed in tissues from all four dogs. H. canis infection was confirmed by PCR followed by sequencing of a fragment of 18S rRNA gene. Leishmania detection and typing was confirmed by ITS1' PCR-RFLP and parasite burden was calculated using ssrRNA quantitative qPCR. A DPP - Dual Path platform test was performed. One out (Dog #2) of four animals was asymptomatic. Dogs #1 and #4 were infected by L. infantum and were DPP test positive. Dogs #2 and #3 were infected by L. braziliensis and were DPP test negative. Furthermore, visceral dissemination was observed in Dogs #2 and #3, since L. braziliensis was detected in liver and spleen samples. The visceral dissemination of L. braziliensis associated with systemic signs suggested that this co-infection could influence the parasite burden and disease progression.

A global reference database of crowdsourced cropland data collected using the Geo-Wiki platform

PubMed Central

Laso Bayas, Juan Carlos; Lesiv, Myroslava; Waldner, François; Schucknecht, Anne; Duerauer, Martina; See, Linda; Fritz, Steffen; Fraisl, Dilek; Moorthy, Inian; McCallum, Ian; Perger, Christoph; Danylo, Olha; Defourny, Pierre; Gallego, Javier; Gilliams, Sven; Akhtar, Ibrar ul Hassan; Baishya, Swarup Jyoti; Baruah, Mrinal; Bungnamei, Khangsembou; Campos, Alfredo; Changkakati, Trishna; Cipriani, Anna; Das, Krishna; Das, Keemee; Das, Inamani; Davis, Kyle Frankel; Hazarika, Purabi; Johnson, Brian Alan; Malek, Ziga; Molinari, Monia Elisa; Panging, Kripal; Pawe, Chandra Kant; Pérez-Hoyos, Ana; Sahariah, Parag Kumar; Sahariah, Dhrubajyoti; Saikia, Anup; Saikia, Meghna; Schlesinger, Peter; Seidacaru, Elena; Singha, Kuleswar; Wilson, John W

2017-01-01

A global reference data set on cropland was collected through a crowdsourcing campaign using the Geo-Wiki crowdsourcing tool. The campaign lasted three weeks, with over 80 participants from around the world reviewing almost 36,000 sample units, focussing on cropland identification. For quality assessment purposes, two additional data sets are provided. The first is a control set of 1,793 sample locations validated by students trained in satellite image interpretation. This data set was used to assess the quality of the crowd as the campaign progressed. The second data set contains 60 expert validations for additional evaluation of the quality of the contributions. All data sets are split into two parts: the first part shows all areas classified as cropland and the second part shows cropland average per location and user. After further processing, the data presented here might be suitable to validate and compare medium and high resolution cropland maps generated using remote sensing. These could also be used to train classification algorithms for developing new maps of land cover and cropland extent. PMID:28949323

A global reference database of crowdsourced cropland data collected using the Geo-Wiki platform

NASA Astrophysics Data System (ADS)

Laso Bayas, Juan Carlos; Lesiv, Myroslava; Waldner, François; Schucknecht, Anne; Duerauer, Martina; See, Linda; Fritz, Steffen; Fraisl, Dilek; Moorthy, Inian; McCallum, Ian; Perger, Christoph; Danylo, Olha; Defourny, Pierre; Gallego, Javier; Gilliams, Sven; Akhtar, Ibrar Ul Hassan; Baishya, Swarup Jyoti; Baruah, Mrinal; Bungnamei, Khangsembou; Campos, Alfredo; Changkakati, Trishna; Cipriani, Anna; Das, Krishna; Das, Keemee; Das, Inamani; Davis, Kyle Frankel; Hazarika, Purabi; Johnson, Brian Alan; Malek, Ziga; Molinari, Monia Elisa; Panging, Kripal; Pawe, Chandra Kant; Pérez-Hoyos, Ana; Sahariah, Parag Kumar; Sahariah, Dhrubajyoti; Saikia, Anup; Saikia, Meghna; Schlesinger, Peter; Seidacaru, Elena; Singha, Kuleswar; Wilson, John W.

2017-09-01

A global reference data set on cropland was collected through a crowdsourcing campaign using the Geo-Wiki crowdsourcing tool. The campaign lasted three weeks, with over 80 participants from around the world reviewing almost 36,000 sample units, focussing on cropland identification. For quality assessment purposes, two additional data sets are provided. The first is a control set of 1,793 sample locations validated by students trained in satellite image interpretation. This data set was used to assess the quality of the crowd as the campaign progressed. The second data set contains 60 expert validations for additional evaluation of the quality of the contributions. All data sets are split into two parts: the first part shows all areas classified as cropland and the second part shows cropland average per location and user. After further processing, the data presented here might be suitable to validate and compare medium and high resolution cropland maps generated using remote sensing. These could also be used to train classification algorithms for developing new maps of land cover and cropland extent.

Sample Handling and Instruments for the In-Situ Exploration of Ice-Rich Planets. Chapter 9

NASA Technical Reports Server (NTRS)

Castillo, Julie C.; Bar-Cohen, Yoseph; Vance, Steve; Choukroun, Mathieu; Lee, Hyeong Jae; Bao, Xiaoqi; Badescu, Mircea; Sherrit, Stewart; Trainer, Melissa G.; Getty, Stephanie A.

2016-01-01

NASA's key science goals for the exploration of the solar system seek a better understanding of the formation and evolutionary processes that have shaped planetary bodies and emphasize the search for habitable environments. Efforts are also made to detect and quantify resources that could be used for the support of human exploration. These themes call for chemistry and physical property observations that may be best approached by in situ measurements. NASA's planetary missions have progressively evolved from remote reconnaissance to in situ exploration with the ultimate goal to return samples. This chapter focuses on the techniques, available or in development, for advanced geophysical and chemical characterization of icy bodies, especially Mars polar areas, Enceladus, Titan, Europa, and Ceres. These astrobiological targets are the objects of recent or ongoing exploration whose findings are driving the formulation of new missions that involve in situ exploration. After reviewing the overall objectives of icy body exploration (Section 9.1) we describe key techniques used for addressing these objectives from surface platforms via geophysical observations (Section 9.2) and chemical measurements (Section 9.3).

On-Chip, Amplification-Free Quantification of Nucleic Acid for Point-of-Care Diagnosis

NASA Astrophysics Data System (ADS)

Yen, Tony Minghung

This dissertation demonstrates three physical device concepts to overcome limitations in point-of-care quantification of nucleic acids. Enabling sensitive, high throughput nucleic acid quantification on a chip, outside of hospital and centralized laboratory setting, is crucial for improving pathogen detection and cancer diagnosis and prognosis. Among existing platforms, microarray have the advantages of being amplification free, low instrument cost, and high throughput, but are generally less sensitive compared to sequencing and PCR assays. To bridge this performance gap, this dissertation presents theoretical and experimental progress to develop a platform nucleic acid quantification technology that is drastically more sensitive than current microarrays while compatible with microarray architecture. The first device concept explores on-chip nucleic acid enrichment by natural evaporation of nucleic acid solution droplet. Using a micro-patterned super-hydrophobic black silicon array device, evaporative enrichment is coupled with nano-liter droplet self-assembly workflow to produce a 50 aM concentration sensitivity, 6 orders of dynamic range, and rapid hybridization time at under 5 minutes. The second device concept focuses on improving target copy number sensitivity, instead of concentration sensitivity. A comprehensive microarray physical model taking into account of molecular transport, electrostatic intermolecular interactions, and reaction kinetics is considered to guide device optimization. Device pattern size and target copy number are optimized based on model prediction to achieve maximal hybridization efficiency. At a 100-mum pattern size, a quantum leap in detection limit of 570 copies is achieved using black silicon array device with self-assembled pico-liter droplet workflow. Despite its merits, evaporative enrichment on black silicon device suffers from coffee-ring effect at 100-mum pattern size, and thus not compatible with clinical patient samples. The third device concept utilizes an integrated optomechanical laser system and a Cytop microarray device to reverse coffee-ring effect during evaporative enrichment at 100-mum pattern size. This method, named "laser-induced differential evaporation" is expected to enable 570 copies detection limit for clinical samples in near future. While the work is ongoing as of the writing of this dissertation, a clear research plan is in place to implement this method on microarray platform toward clinical sample testing for disease applications and future commercialization.

Characterization of Hepatitis C Virus (HCV) Envelope Diversification from Acute to Chronic Infection within a Sexually Transmitted HCV Cluster by Using Single-Molecule, Real-Time Sequencing

PubMed Central

Ho, Cynthia K. Y.; Raghwani, Jayna; Koekkoek, Sylvie; Liang, Richard H.; Van der Meer, Jan T. M.; Van Der Valk, Marc; De Jong, Menno; Pybus, Oliver G.

2016-01-01

ABSTRACT In contrast to other available next-generation sequencing platforms, PacBio single-molecule, real-time (SMRT) sequencing has the advantage of generating long reads albeit with a relatively higher error rate in unprocessed data. Using this platform, we longitudinally sampled and sequenced the hepatitis C virus (HCV) envelope genome region (1,680 nucleotides [nt]) from individuals belonging to a cluster of sexually transmitted cases. All five subjects were coinfected with HIV-1 and a closely related strain of HCV genotype 4d. In total, 50 samples were analyzed by using SMRT sequencing. By using 7 passes of circular consensus sequencing, the error rate was reduced to 0.37%, and the median number of sequences was 612 per sample. A further reduction of insertions was achieved by alignment against a sample-specific reference sequence. However, in vitro recombination during PCR amplification could not be excluded. Phylogenetic analysis supported close relationships among HCV sequences from the four male subjects and subsequent transmission from one subject to his female partner. Transmission was characterized by a strong genetic bottleneck. Viral genetic diversity was low during acute infection and increased upon progression to chronicity but subsequently fluctuated during chronic infection, caused by the alternate detection of distinct coexisting lineages. SMRT sequencing combines long reads with sufficient depth for many phylogenetic analyses and can therefore provide insights into within-host HCV evolutionary dynamics without the need for haplotype reconstruction using statistical algorithms. IMPORTANCE Next-generation sequencing has revolutionized the study of genetically variable RNA virus populations, but for phylogenetic and evolutionary analyses, longer sequences than those generated by most available platforms, while minimizing the intrinsic error rate, are desired. Here, we demonstrate for the first time that PacBio SMRT sequencing technology can be used to generate full-length HCV envelope sequences at the single-molecule level, providing a data set with large sequencing depth for the characterization of intrahost viral dynamics. The selection of consensus reads derived from at least 7 full circular consensus sequencing rounds significantly reduced the intrinsic high error rate of this method. We used this method to genetically characterize a unique transmission cluster of sexually transmitted HCV infections, providing insight into the distinct evolutionary pathways in each patient over time and identifying the transmission-associated genetic bottleneck as well as fluctuations in viral genetic diversity over time, accompanied by dynamic shifts in viral subpopulations. PMID:28077634

A 3D-Printed, Portable, Optical-Sensing Platform for Smartphones Capable of Detecting the Herbicide 2,4-Dichlorophenoxyacetic Acid.

PubMed

Wang, Yijia; Zeinhom, Mohamed M A; Yang, Mingming; Sun, Rongrong; Wang, Shengfu; Smith, Jordan N; Timchalk, Charles; Li, Lei; Lin, Yuehe; Du, Dan

2017-09-05

Onsite rapid detection of herbicides and herbicide residuals in environmental and biological specimens are important for agriculture, environmental concerns, food safety, and health care. The traditional method for herbicide detection requires expensive laboratory equipment and a long turnaround time. In this work, we developed a single-stripe microliter plate smartphone-based colorimetric device for rapid and low-cost in-field tests. This portable smartphone platform is capable of screening eight samples in a single-stripe microplate. The device combined the advantages of small size (50 × 100 × 160 mm 3 ) and low cost ($10). The platform was calibrated by using two different dye solutions, i.e. methyl blue (MB) and rhodamine B, for the red and green channels. The results showed good correlation with results attained from a traditional laboratory reader. We demonstrated the application of this platform for detection of the herbicide 2,4-dichlorophenoxyacetic acid in the range of 1 to 80 ppb. Spiked samples of tap water, rat serum, plasma, and human serum were tested by our device. Recoveries obtained varied from 95.6% to 105.2% for all of the spiked samples using the microplate reader and from 93.7% to 106.9% for all of the samples using the smartphone device. This work validated that the smartphone optical-sensing platform is comparable to the commercial microplate reader; it is eligible for onsite, rapid, and low-cost detection of herbicides for environmental evaluation and biological monitoring.

Monitoring Progress and Adherence with Positive Airway Pressure Therapy for Obstructive Sleep Apnea: The Roles of Telemedicine and Mobile Health Applications.

PubMed

Hwang, Dennis

2016-06-01

Technology is changing the way health care is delivered and how patients are approaching their own health. Given the challenge within sleep medicine of optimizing adherence to continuous positive airway pressure (CPAP) therapy in patients with obstructive sleep apnea (OSA), implementation of telemedicine-based mechanisms is a critical component toward developing a comprehensive and cost-effective solution for OSA management. Key elements include the use of electronic messaging, remote monitoring, automated care mechanisms, and patient self-management platforms. Current practical sleep-related telemedicine platforms include Web-based educational programs, automated CPAP follow-up platforms that promote self-management, and peer-based patient-driven Internet support forums. Copyright © 2016 Elsevier Inc. All rights reserved.

Electronic Self-report Assessment--Cancer (ESRA-C): Working towards an integrated survey system.

PubMed

Karras, Bryant T; Wolpin, Seth; Lober, William B; Bush, Nigel; Fann, Jesse R; Berry, Donna L

2006-01-01

The Clinical Informatics Research Group and Biobehavioral Nursing and Health Systems at the University of Washington are working with interdisciplinary teams to improve patient care and tracking of patient-reported symptoms and outcomes by creating an extensible web-based survey and intervention platform. The findings and cumulative experience from these processes have led to incremental improvements and variations in each new implementation of the platform. This paper presents progress in the first year of a three-year NIH study entitled Electronic Self Report Assessment--Cancer (ESRA-C). The project's goals are to enhance and evaluate the web-based computerized patient self-reporting and assessment system at the Seattle Cancer Care Alliance. Preliminary work and lessons learned in the modification of the platform and enhancements to the system will be described.

On the way to commercializing plant cell culture platform for biopharmaceuticals: present status and prospect.

PubMed

Xu, Jianfeng; Zhang, Ningning

2014-12-01

Plant cell culture is emerging as an alternative bioproduction system for recombinant pharmaceuticals. Growing plant cells in vitro under controlled environmental conditions allows for precise control over cell growth and protein production, batch-to-batch product consistency and a production process aligned with current good manufacturing practices. With the recent US FDA approval and commercialization of the world's first plant cell-based recombinant pharmaceutical for human use, β-glucocerebrosidase for treatment of Gaucher's disease, a new era has come in which plant cell culture shows high potential to displace some established platform technologies in niche markets. This review updates the progress in plant cell culture processing technology, highlights recent commercial successes and discusses the challenges that must be overcome to make this platform commercially viable.

Bacterial diversity in water injection systems of Brazilian offshore oil platforms.

PubMed

Korenblum, Elisa; Valoni, Erika; Penna, Mônica; Seldin, Lucy

2010-01-01

Biogenic souring and microbial-influenced corrosion is a common scenario in water-flooded petroleum reservoirs. Water injection systems are continuously treated to control bacterial contamination, but some bacteria that cause souring and corrosion can persist even after different treatments have been applied. Our aim was to increase our knowledge of the bacterial communities that persist in the water injection systems of three offshore oil platforms in Brazil. To achieve this goal, we used a culture-independent molecular approach (16S ribosomal RNA gene clone libraries) to analyze seawater samples that had been subjected to different treatments. Phylogenetic analyses revealed that the bacterial communities from the different platforms were taxonomically different. A predominance of bacterial clones affiliated with Gammaproteobacteria, mostly belonging to the genus Marinobacter (60.7%), were observed in the platform A samples. Clones from platform B were mainly related to the genera Colwellia (37.9%) and Achromobacter (24.6%), whereas clones obtained from platform C were all related to unclassified bacteria. Canonical correspondence analyses showed that different treatments such as chlorination, deoxygenation, and biocide addition did not significantly influence the bacterial diversity in the platforms studied. Our results demonstrated that the injection water used in secondary oil recovery procedures contained potentially hazardous bacteria, which may ultimately cause souring and corrosion.

Computer Simulation of Developmental Processes and Toxicities (SOT)

EPA Science Inventory

Rationale: Recent progress in systems toxicology and synthetic biology have paved the way to new thinking about in vitro/in silico modeling of developmental processes and toxicities, both for embryological and reproductive impacts. Novel in vitro platforms such as 3D organotypic ...

Implementation of a protein profiling platform developed as an academic-pharmaceutical industry collaborative effort.

PubMed

Végvári, Akos; Magnusson, Mattias; Wallman, Lars; Ekström, Simon; Bolmsjö, Gunnar; Nilsson, Johan; Miliotis, Tasso; Ostling, Jörgen; Kjellström, Sven; Ottervald, Jan; Franzén, Bo; Hultberg, Hans; Marko-Varga, György; Laurell, Thomas

2008-06-01

As much attention has devoted to the proteome research during the last few years, biomarker discovery has become an increasingly hot area, potentially enabling the development of new assays for diagnosis and prognosis of severe diseases. This is the field of research interest where efforts originating from both academic and industrial groups should jointly work on solutions. In this paper, we would like to demonstrate the fruitful combination of both research domains where the scientific crossroads sprout fresh ideas from the basic research domain and how these are refined and tethered to industrial standards. We will present an approach that is based on novel microfluidic devices, utilizing their benefits in processing small-volume samples. Our biomarker discovery strategy, built around this platform, involves optimized samples processing (based on SPE and sample enrichment) and fast MALDI-MS readout. The identification of novel biomarkers at low-abundance level has been achieved by the utilization of a miniaturized sample handling platform, which offers clean-up and enrichment of proteins in one step. Complete automation has been realized in the form of a unique robotic instrumentation that is able to extract and transfer 96 samples onto standard MALDI target plates with high throughput. The developed platform was operated with a 60 sample turnaround per hour allowing sensitivities in femtomol regions of medium- and low-abundant target proteins from clinical studies on samples of multiple sclerosis and gastroesophageal reflux disease. Several proteins have been identified as new biomarkers from cerebrospinal fluid and esophagus epithelial cells.

Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.

PubMed

Luo, Chengwei; Tsementzi, Despina; Kyrpides, Nikos; Read, Timothy; Konstantinidis, Konstantinos T

2012-01-01

Next-generation sequencing (NGS) is commonly used in metagenomic studies of complex microbial communities but whether or not different NGS platforms recover the same diversity from a sample and their assembled sequences are of comparable quality remain unclear. We compared the two most frequently used platforms, the Roche 454 FLX Titanium and the Illumina Genome Analyzer (GA) II, on the same DNA sample obtained from a complex freshwater planktonic community. Despite the substantial differences in read length and sequencing protocols, the platforms provided a comparable view of the community sampled. For instance, derived assemblies overlapped in ~90% of their total sequences and in situ abundances of genes and genotypes (estimated based on sequence coverage) correlated highly between the two platforms (R(2)>0.9). Evaluation of base-call error, frameshift frequency, and contig length suggested that Illumina offered equivalent, if not better, assemblies than Roche 454. The results from metagenomic samples were further validated against DNA samples of eighteen isolate genomes, which showed a range of genome sizes and G+C% content. We also provide quantitative estimates of the errors in gene and contig sequences assembled from datasets characterized by different levels of complexity and G+C% content. For instance, we noted that homopolymer-associated, single-base errors affected ~1% of the protein sequences recovered in Illumina contigs of 10× coverage and 50% G+C; this frequency increased to ~3% when non-homopolymer errors were also considered. Collectively, our results should serve as a useful practical guide for choosing proper sampling strategies and data possessing protocols for future metagenomic studies.

Quantum dot enabled detection of Escherichia coli using a cell-phone†

PubMed Central

Zhu, Hongying; Sikora, Uzair; Ozcan, Aydogan

2013-01-01

We report a cell-phone based Escherichia coli (E. coli) detection platform for screening of liquid samples. In this compact and cost-effective design attached to a cell-phone, we utilize anti-E. coli O157:H7 antibody functionalized glass capillaries as solid substrates to perform a quantum dot based sandwich assay for specific detection of E. coli O157:H7 in liquid samples. Using battery-powered inexpensive light-emitting-diodes (LEDs) we excite/pump these labelled E. coli particles captured on the capillary surface, where the emission from the quantum dots is then imaged using the cell-phone camera unit through an additional lens that is inserted between the capillary and the cell-phone. By quantifying the fluorescent light emission from each capillary tube, the concentration of E. coli in the sample is determined. We experimentally confirmed the detection limit of this cell-phone based fluorescent imaging and sensing platform as ~5 to 10 cfu mL−1 in buffer solution. We also tested the specificity of this E. coli detection platform by spiking samples with different species (e.g., Salmonella) to confirm that non-specific binding/detection is negligible. We further demonstrated the proof-of-concept of our approach in a complex food matrix, e.g., fat-free milk, where a similar detection limit of ~5 to 10 cfu mL−1 was achieved despite challenges associated with the density of proteins that exist in milk. Our results reveal the promising potential of this cell-phone enabled field-portable and cost-effective E. coli detection platform for e.g., screening of water and food samples even in resource limited environments. The presented platform can also be applicable to other pathogens of interest through the use of different antibodies. PMID:22396952

Quantum dot enabled detection of Escherichia coli using a cell-phone.

PubMed

Zhu, Hongying; Sikora, Uzair; Ozcan, Aydogan

2012-06-07

We report a cell-phone based Escherichia coli (E. coli) detection platform for screening of liquid samples. In this compact and cost-effective design attached to a cell-phone, we utilize anti-E. coli O157:H7 antibody functionalized glass capillaries as solid substrates to perform a quantum dot based sandwich assay for specific detection of E. coli O157:H7 in liquid samples. Using battery-powered inexpensive light-emitting-diodes (LEDs) we excite/pump these labelled E. coli particles captured on the capillary surface, where the emission from the quantum dots is then imaged using the cell-phone camera unit through an additional lens that is inserted between the capillary and the cell-phone. By quantifying the fluorescent light emission from each capillary tube, the concentration of E. coli in the sample is determined. We experimentally confirmed the detection limit of this cell-phone based fluorescent imaging and sensing platform as ∼5 to 10 cfu mL(-1) in buffer solution. We also tested the specificity of this E. coli detection platform by spiking samples with different species (e.g., Salmonella) to confirm that non-specific binding/detection is negligible. We further demonstrated the proof-of-concept of our approach in a complex food matrix, e.g., fat-free milk, where a similar detection limit of ∼5 to 10 cfu mL(-1) was achieved despite challenges associated with the density of proteins that exist in milk. Our results reveal the promising potential of this cell-phone enabled field-portable and cost-effective E. coli detection platform for e.g., screening of water and food samples even in resource limited environments. The presented platform can also be applicable to other pathogens of interest through the use of different antibodies.

Creating A Nationwide Nonpartisan Initiative for Family Caregivers in Political Party Platforms.

PubMed

Scribner, Ben; Lynn, Joanne; Walker, Victoria; Morgan, Les; Montgomery, Anne; Blair, Elizabeth; Baird, Davis; Goldschmidt, Barbara; Kirschenbaum, Naomi

2017-06-01

Policymakers have been slow to support family caregivers, and political agendas mostly fail to address the cost burdens, impact on employment and productivity, and other challenges in taking on long-term care tasks. This project set out to raise policymakers' awareness of family caregivers through proposals to Republican and Democratic party platforms during the 2016 political season. The Family Caregiver Platform Project (FCPP) reviewed the state party platform submission process for Democratic and Republican parties in all 50 states and the District of Columbia. We built a website to make each process understandable by caregiver advocates. We designed model submissions to help volunteers tailor a proposal and recruited caregiver advocates participating in their state process. Finally, we mobilized a ground operation in many states and followed the progress of submissions in each state, as well as the formation of the national platforms. In 39 states, at least one party, Republican or Democrat, hosted a state party platform process. As of September 2016 FCPP volunteers submitted proposals to 29 state parties in 22 states. Family caregiver language was added to eight state party platforms, one state party resolution, two bipartisan legislative resolutions, and one national party platform. The FCPP generated a non-partisan grassroots effort to educate and motivate policymakers to address caregiving issues and solutions. Democratic party leaders provided more opportunities to connect with political leaders, with seven Democratic parties and one Republican party, addressing family caregiver issues in their party platforms. © 2017, Copyright the Authors Journal compilation © 2017, The American Geriatrics Society.

Towards Autonomous Inspection of Space Systems Using Mobile Robotic Sensor Platforms

NASA Technical Reports Server (NTRS)

Wong, Edmond; Saad, Ashraf; Litt, Jonathan S.

2007-01-01

The space transportation systems required to support NASA's Exploration Initiative will demand a high degree of reliability to ensure mission success. This reliability can be realized through autonomous fault/damage detection and repair capabilities. It is crucial that such capabilities are incorporated into these systems since it will be impractical to rely upon Extra-Vehicular Activity (EVA), visual inspection or tele-operation due to the costly, labor-intensive and time-consuming nature of these methods. One approach to achieving this capability is through the use of an autonomous inspection system comprised of miniature mobile sensor platforms that will cooperatively perform high confidence inspection of space vehicles and habitats. This paper will discuss the efforts to develop a small scale demonstration test-bed to investigate the feasibility of using autonomous mobile sensor platforms to perform inspection operations. Progress will be discussed in technology areas including: the hardware implementation and demonstration of robotic sensor platforms, the implementation of a hardware test-bed facility, and the investigation of collaborative control algorithms.

Progress on Platforms, Sensors and Applications with Unmanned Aerial Vehicles in soil science and geomorphology

NASA Astrophysics Data System (ADS)

Anders, Niels; Suomalainen, Juha; Seeger, Manuel; Keesstra, Saskia; Bartholomeus, Harm; Paron, Paolo

2014-05-01

The recent increase of performance and endurance of electronically controlled flying platforms, such as multi-copters and fixed-wing airplanes, and decreasing size and weight of different sensors and batteries leads to increasing popularity of Unmanned Aerial Systems (UAS) for scientific purposes. Modern workflows that implement UAS include guided flight plan generation, 3D GPS navigation for fully automated piloting, and automated processing with new techniques such as "Structure from Motion" photogrammetry. UAS are often equipped with normal RGB cameras, multi- and hyperspectral sensors, radar, or other sensors, and provide a cheap and flexible solution for creating multi-temporal data sets. UAS revolutionized multi-temporal research allowing new applications related to change analysis and process monitoring. The EGU General Assembly 2014 is hosting a session on platforms, sensors and applications with UAS in soil science and geomorphology. This presentation briefly summarizes the outcome of this session, addressing the current state and future challenges of small-platform data acquisition in soil science and geomorphology.

Paper-based electrochemical sensing platform with integral battery and electrochromic read-out.

PubMed

Liu, Hong; Crooks, Richard M

2012-03-06

We report a battery-powered, microelectrochemical sensing platform that reports its output using an electrochromic display. The platform is fabricated based on paper fluidics and uses a Prussian blue spot electrodeposited on an indium-doped tin oxide thin film as the electrochromic indicator. The integrated metal/air battery powers both the electrochemical sensor and the electrochromic read-out, which are in electrical contact via a paper reservoir. The sample activates the battery and the presence of analyte in the sample initiates the color change of the Prussian blue spot. The entire system is assembled on the lab bench, without the need for cleanroom facilities. The applicability of the device to point-of-care sensing is demonstrated by qualitative detection of 0.1 mM glucose and H(2)O(2) in artificial urine samples.

Microfluidic Lab-on-a-Chip Platforms: Requirements, Characteristics and Applications

NASA Astrophysics Data System (ADS)

Mark, D.; Haeberle, S.; Roth, G.; Von Stetten, F.; Zengerle, R.

This review summarizes recent developments in microfluidic platform approaches. In contrast to isolated application-specific solutions, a microfluidic platform provides a set of fluidic unit operations, which are designed for easy combination within a well-defined fabrication technology. This allows the implementation of different application-specific (bio-) chemical processes, automated by microfluidic process integration [1]. A brief introduction into technical advances, major market segments and promising applications is followed by a detailed characterization of different microfluidic platforms, comprising a short definition, the functional principle, microfluidic unit operations, application examples as well as strengths and limitations. The microfluidic platforms in focus are lateral flow tests, linear actuated devices, pressure driven laminar flow, microfluidic large scale integration, segmented flow microfluidics, centrifugal microfluidics, electro-kinetics, electrowetting, surface acoustic waves, and systems for massively parallel analysis. The review concludes with the attempt to provide a selection scheme for microfluidic platforms which is based on their characteristics according to key requirements of different applications and market segments. Applied selection criteria comprise portability, costs of instrument and disposable, sample throughput, number of parameters per sample, reagent consumption, precision, diversity of microfluidic unit operations and the flexibility in programming different liquid handling protocols.

Effects of different foot progression angles and platform settings on postural stability and fall risk in healthy and medial knee osteoarthritic adults.

PubMed

Khan, Saad Jawaid; Khan, Soobia Saad; Usman, Juliana; Mokhtar, Abdul Halim; Abu Osman, Noor Azuan

2018-02-01

This study aims to investigate the effects of varying toe angles at different platform settings on Overall Stability Index of postural stability and fall risk using Biodex Balance System in healthy participants and medial knee osteoarthritis patients. Biodex Balance System was employed to measure postural stability and fall risk at different foot progression angles (ranging from -20° to 40°, with 10° increments) on 20 healthy (control group) and 20 knee osteoarthritis patients (osteoarthritis group) randomly (age: 59.50 ± 7.33 years and 61.50 ± 8.63 years; body mass: 69.95 ± 9.86 kg and 70.45 ± 8.80 kg). Platform settings used were (1) static, (2) postural stability dynamic level 8 (PS8), (3) fall risk levels 12 to 8 (FR12) and (4) fall risk levels 8 to 2 (FR8). Data from the tests were analysed using three-way mixed repeated measures analysis of variance. The participant group, platform settings and toe angles all had a significant main effect on balance ( p ≤ 0.02). Platform settings had a significant interaction effect with participant group F(3, 144) = 6.97, p < 0.01 and toe angles F(21, 798) = 2.83, p < 0.01. Non-significant interactions were found for group × toe angles, F(7, 266) = 0.89, p = 0.50, and for group × toe angles × settings, F(21, 798) = 1.07, p = 0.36. The medial knee osteoarthritis group has a poorer postural stability and increased fall risk as compared to the healthy group. Changing platform settings has a more pronounced effect on balance in knee osteoarthritis group than in healthy participants. Changing toe angles produced similar effects in both the participant groups, with decreased stability and increased fall risk at extreme toe-in and toe-out angles.

Operation of Lanzhou all permanent electron cyclotron resonance ion source No. 2 on 320 kV platform with highly charged ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, W., E-mail: luwang@impcas.ac.cn; University of Chinese Academy of Sciences, Beijing 100049; Li, J. Y.

2014-02-15

The 320 kV platform for multi-discipline research with highly charged ions is a heavy ion beam acceleration instrument developed by Institute of Modern Physics, which is dedicated to basic scientific researches such as plasma, atom, material physics, and astrophysics, etc. The platform has delivered ion beams of 400 species for 36 000 h. The average operation time is around 5000 h/year. With the beams provided by the platform, lots of outstanding progresses were made in various research fields. The ion source of the platform is an all-permanent magnet electron cyclotron resonance ion source, LAPECR2 (Lanzhou All Permanent ECR ion source No.more » 2). The maximum axial magnetic fields are 1.28 T at injection and 1.07 T at extraction, and the radial magnetic field is up to 1.21 T at the inner wall of the plasma chamber. The ion source is capable to produce low, medium, and high charge state gaseous and metallic ion beams, such as H{sup +}, {sup 40}Ar{sup 8+}, {sup 129}Xe{sup 30+}, {sup 209}Bi{sup 33+}, etc. This paper will present the latest result of LAPECR2 and the routine operation status for the high voltage platform.« less

Metabolomics for laboratory diagnostics.

PubMed

Bujak, Renata; Struck-Lewicka, Wiktoria; Markuszewski, Michał J; Kaliszan, Roman

2015-09-10

Metabolomics is an emerging approach in a systems biology field. Due to continuous development in advanced analytical techniques and in bioinformatics, metabolomics has been extensively applied as a novel, holistic diagnostic tool in clinical and biomedical studies. Metabolome's measurement, as a chemical reflection of a current phenotype of a particular biological system, is nowadays frequently implemented to understand pathophysiological processes involved in disease progression as well as to search for new diagnostic or prognostic biomarkers of various organism's disorders. In this review, we discussed the research strategies and analytical platforms commonly applied in the metabolomics studies. The applications of the metabolomics in laboratory diagnostics in the last 5 years were also reviewed according to the type of biological sample used in the metabolome's analysis. We also discussed some limitations and further improvements which should be considered taking in mind potential applications of metabolomic research and practice. Copyright © 2014 Elsevier B.V. All rights reserved.

Efficient finite element simulation of slot spirals, slot radomes and microwave structures

NASA Technical Reports Server (NTRS)

Gong, J.; Volakis, J. L.

1995-01-01

This progress report contains the following two documents: (1) 'Efficient Finite Element Simulation of Slot Antennas using Prismatic Elements' - A hybrid finite element-boundary integral (FE-BI) simulation technique is discussed to treat narrow slot antennas etched on a planar platform. Specifically, the prismatic elements are used to reduce the redundant sampling rates and ease the mesh generation process. Numerical results for an antenna slot and frequency selective surfaces are presented to demonstrate the validity and capability of the technique; and (2) 'Application and Design Guidelines of the PML Absorber for Finite Element Simulations of Microwave Packages' - The recently introduced perfectly matched layer (PML) uniaxial absorber for frequency domain finite element simulations has several advantages. In this paper we present the application of PML for microwave circuit simulations along with design guidelines to obtain a desired level of absorption. Different feeding techniques are also investigated for improved accuracy.

Purification of complex samples: Implementation of a modular and reconfigurable droplet-based microfluidic platform with cascaded deterministic lateral displacement separation modules

PubMed Central

Pudda, Catherine; Boizot, François; Verplanck, Nicolas; Revol-Cavalier, Frédéric; Berthier, Jean; Thuaire, Aurélie

2018-01-01

Particle separation in microfluidic devices is a common problematic for sample preparation in biology. Deterministic lateral displacement (DLD) is efficiently implemented as a size-based fractionation technique to separate two populations of particles around a specific size. However, real biological samples contain components of many different sizes and a single DLD separation step is not sufficient to purify these complex samples. When connecting several DLD modules in series, pressure balancing at the DLD outlets of each step becomes critical to ensure an optimal separation efficiency. A generic microfluidic platform is presented in this paper to optimize pressure balancing, when DLD separation is connected either to another DLD module or to a different microfluidic function. This is made possible by generating droplets at T-junctions connected to the DLD outlets. Droplets act as pressure controllers, which perform at the same time the encapsulation of DLD sorted particles and the balance of output pressures. The optimized pressures to apply on DLD modules and on T-junctions are determined by a general model that ensures the equilibrium of the entire platform. The proposed separation platform is completely modular and reconfigurable since the same predictive model applies to any cascaded DLD modules of the droplet-based cartridge. PMID:29768490

Continuous pCO2 time series from Ocean Networks Canada cabled observatories at the northeast Pacific shelf edge and in the sub-tidal Arctic

NASA Astrophysics Data System (ADS)

Juniper, S. Kim; Sastri, Akash; Mihaly, Steven; Duke, Patrick; Else, Brent; Thomas, Helmuth; Miller, Lisa

2017-04-01

Marine pCO2 sensor technology has progressed to the point where months-long time series from remotely-deployed pCO2 sensors can be used to document seasonal and higher frequency variability in pCO2 and its relationship to oceanographic processes. Ocean Networks Canada recently deployed pCO2 sensors on two cabled platforms: a bottom-moored (400 m depth), vertical profiler at the edge of the northeast Pacific continental shelf off Vancouver Island, Canada, and a subtidal seafloor platform in the Canadian High Arctic (69˚ N) at Cambridge Bay, Nunavut. Both platforms streamed continuous data to a shore-based archive from Pro-Oceanus pCO2 sensors and other oceanographic instruments. The vertical profiler time series revealed substantial intrusions of corrosive (high CO2/low O2), saltier, colder water masses during the summertime upwelling season and during winter-time reversals of along-slope currents. Step-wise profiles during the downcast provided the most reliable pCO2 data, permitting the sensor to equilibrate to the broad range of pCO2 concentrations encountered over the 400 metre depth interval. The Arctic pCO2 sensor was deployed in August 2015. Reversing seasonal trends in pCO2 and dissolved oxygen values can be related to the changing balance of photosynthesis and respiration under sea ice, as influenced by irradiance. Correlation of pCO2 and dissolved oxygen sensor data and the collection of calibration samples have permitted evaluation of sensor performance in relation to operational conditions encountered in vertical profiling and lengthy exposure to subzero seawater.

Paleomagnetic Investigations on the Tectonic Evolution of the Southeastern Anatolian Ophiolites in Late Cretaceous

NASA Astrophysics Data System (ADS)

Cengiz Cinku, M.; Karabulut, S.; Parlak, O.; Cabuk, B. S.; Ustaömer, T.; Hisarli, M. Z.

2016-12-01

Two E-W trending ophiolite belts crop out in SE Turkey, The southerly located ophiolites (Hatay, Koçali) were emplaced onto the Arabian Platform in Late Cretaceous whereas the northerly located ophiolites (Göksun, İspendere, Kömürhan, Guleman) were underthrust the S Tauride margin (i.e. Malatya-Keban Platform) in Late Cretaceous. Here we report our first paleomagnetic results from 155 different sites which was was focused on to the sheeted dyke complex, cumulate gabbros and extrusive sequences of each ophiolite from the N and S belts, while the cover units where sampled to distinguish emplacement related tectonic rotations from post-emplacement tectonic rotations. Rock magnetic experiments showed evidence of magnetite/titanomagnetite as the main magnetic carriers at the majority of sites. Progressive thermal and alternating demagnetization revealed that the characteristic remanent component is removed between 500 and 580 °C or 30-100 mT, respectively. Our new paleomagnetic results from the ophiolitic rocks emplaced in Arabian platform and the SE Anatolia show important implications to the spreading centre of the former ocean (s). Large counterclockwise rotations up to 100° are obtained from the sheeded dykes of the Hatay ophiolite in the Arabian plate with a paleolatitude of 16°, in contrast to the sheeded dykes of the Göksun ophiolite emplaced in the SE Anatolian with clockwise rotation of 90° and a paleolatitude of 22°. The relative movement of the ophiolitic series show their emplacement in the different zones. This study was financially supported by the project of the Scientific and Technical Research Council of Turkey (TUBITAK) with Project number 114R024.

Evaluation of zirconium as a permanent chemical modifier using synchrotron radiation and imaging techniques for lithium determination in sediment slurry samples by ET AAS.

PubMed

Flores, Araceli V; Pérez, Carlos A; Arruda, Marco A Z

2004-02-27

In the present paper, lithium was determined in river sediment using slurry sampling and electrothermal atomic absorption spectrometry (ET AAS) after L'vov platform coating with zirconium (as a permanent chemical modifier). The performance of this modifier and its distribution on the L'vov platform after different heating cycles were evaluated using synchrotron radiation X-ray fluorescence (SRXRF) and imaging scanning electron microscopy (SEM) techniques. The analytical conditions for lithium determination in river sediment slurries were also investigated and the best conditions were obtained employing 1300 and 2300 degrees C for pyrolysis and atomization temperatures, respectively. In addition, 100mg of sediment samples were prepared using 4.0moll(-1) HNO(3). The Zr-coating permitted lithium determination with good precision and accuracy after 480 heating cycles using the same platform for slurry samples. The sediment samples were collected from five different points of the Cachoeira river, São Paulo, Brazil. The detection and quantification limits were, respectively, 0.07 and 0.23mugl(-1).

Cdk1 activity acts as a quantitative platform for coordinating cell cycle progression with periodic transcription

PubMed Central

Banyai, Gabor; Baïdi, Feriel; Coudreuse, Damien; Szilagyi, Zsolt

2016-01-01

Cell proliferation is regulated by cyclin-dependent kinases (Cdks) and requires the periodic expression of particular gene clusters in different cell cycle phases. However, the interplay between the networks that generate these transcriptional oscillations and the core cell cycle machinery remains largely unexplored. In this work, we use a synthetic regulable Cdk1 module to demonstrate that periodic expression is governed by quantitative changes in Cdk1 activity, with different clusters directly responding to specific activity levels. We further establish that cell cycle events neither participate in nor interfere with the Cdk1-driven transcriptional program, provided that cells are exposed to the appropriate Cdk1 activities. These findings contrast with current models that propose self-sustained and Cdk1-independent transcriptional oscillations. Our work therefore supports a model in which Cdk1 activity serves as a quantitative platform for coordinating cell cycle transitions with the expression of critical genes to bring about proper cell cycle progression. PMID:27045731

Progress in Development of the ITER Plasma Control System Simulation Platform

NASA Astrophysics Data System (ADS)

Walker, Michael; Humphreys, David; Sammuli, Brian; Ambrosino, Giuseppe; de Tommasi, Gianmaria; Mattei, Massimiliano; Raupp, Gerhard; Treutterer, Wolfgang; Winter, Axel

2017-10-01

We report on progress made and expected uses of the Plasma Control System Simulation Platform (PCSSP), the primary test environment for development of the ITER Plasma Control System (PCS). PCSSP will be used for verification and validation of the ITER PCS Final Design for First Plasma, to be completed in 2020. We discuss the objectives of PCSSP, its overall structure, selected features, application to existing devices, and expected evolution over the lifetime of the ITER PCS. We describe an archiving solution for simulation results, methods for incorporating physics models of the plasma and physical plant (tokamak, actuator, and diagnostic systems) into PCSSP, and defining characteristics of models suitable for a plasma control development environment such as PCSSP. Applications of PCSSP simulation models including resistive plasma equilibrium evolution are demonstrated. PCSSP development supported by ITER Organization under ITER/CTS/6000000037. Resistive evolution code developed under General Atomics' Internal funding. The views and opinions expressed herein do not necessarily reflect those of the ITER Organization.

Design of a portable electronic nose for real-fake detection of liquors

NASA Astrophysics Data System (ADS)

Qi, Pei-Feng; Zeng, Ming; Li, Zhi-Hua; Sun, Biao; Meng, Qing-Hao

2017-09-01

Portability is a major issue that influences the practical application of electronic noses (e-noses). For liquors detection, an e-nose must preprocess the liquid samples (e.g., using evaporation and thermal desorption), which makes the portable design even more difficult. To realize convenient and rapid detection of liquors, we designed a portable e-nose platform that consists of hardware and software systems. The hardware system contains an evaporation/sampling module, a reaction module, a control/data acquisition and analysis module, and a power module. The software system provides a user-friendly interface and can achieve automatic sampling and data processing. This e-nose platform has been applied to the real-fake recognition of Chinese liquors. Through parameter optimization of a one-class support vector machine classifier, the error rate of the negative samples is greatly reduced, and the overall recognition accuracy is improved. The results validated the feasibility of the designed portable e-nose platform.

Synthesis, characterization and nitrite ion sensing performance of reclaimable composite samples through a core-shell structure

NASA Astrophysics Data System (ADS)

Cui, Xiao; Yuqing, Zhao; Cui, Jiantao; Zheng, Qian; Bo, Wang

2018-02-01

The following paper reported and discussed a nitrite ion optical sensing platform based on a core-shell structure, using superamagnetic nanoparticles as the core, a silica molecular sieve MCM-41 as the shell and two rhodamine derivatives as probe, respectively. This superamagnetic core made this sensing platform reclaimable after finishing nitrite ion sensing procedure. This sensing platform was carefully characterized by means of electron microscopy images, porous structure analysis, magnetic response, IR spectra and thermal stability analysis. Detailed analysis suggested that the emission of these composite samples was quenchable by nitrite ion, showing emission turn off effect. A static sensing mechanism based on an additive reaction between chemosensors and nitrite ion was proposed. These composite samples followed Demas quenching equation against different nitrite ion concentrations. Limit of detection value was obtained as low as 0.4 μM. It was found that, after being quenched by nitrite ion, these composite samples could be reclaimed and recovered by sulphamic acid, confirming their recyclability.

Historical Population Estimates For Several Fish Species At Offshore Oil and Gas Structures in the US Gulf of Mexico

NASA Astrophysics Data System (ADS)

Gitschlag, G.

2016-02-01

Population estimates were calculated for four fish species occurring at offshore oil and gas structures in water depths of 14-32 m off the Louisiana and upper Texas coasts in the US Gulf of Mexico. From 1993-1999 sampling was conducted at eight offshore platforms in conjunction with explosive salvage of the structures. To estimate fish population size prior to detonation of explosives, a fish mark-recapture study was conducted. Fish were captured on rod and reel using assorted hook sizes. Traps were occasionally used to supplement catches. Fish were tagged below the dorsal fin with plastic t-bar tags using tagging guns. Only fish that were alive and in good condition were released. Recapture sampling was conducted after explosives were detonated during salvage operations. Personnel operating from inflatable boats used dip nets to collect all dead fish that floated to the surface. Divers collected representative samples of dead fish that sank to the sea floor. Data provided estimates for red snapper (Lutjanus campechanus), Atlantic spadefish (Chaetodipterus faber), gray triggerfish (Balistes capriscus), and blue runner (Caranx crysos) at one or more of the eight platforms studied. At seven platforms, population size for red snapper was calculated at 503-1,943 with a 95% CI of 478. Abundance estimates for Atlantic spadefish at three platforms ranged from 1,432-1,782 with a 95% CI of 473. At three platforms, population size of gray triggerfish was 63-129 with a 95% CI of 82. Blue runner abundance at one platform was 558. Unlike the other three species which occur close to the platforms, blue runner range widely and recapture of this species was dependent on fish schools being in close proximity to the platform at the time explosives were detonated. Tag recapture was as high as 73% for red snapper at one structure studied.

Hybrid Integrated Platforms for Silicon Photonics

PubMed Central

Liang, Di; Roelkens, Gunther; Baets, Roel; Bowers, John E.

2010-01-01

A review of recent progress in hybrid integrated platforms for silicon photonics is presented. Integration of III-V semiconductors onto silicon-on-insulator substrates based on two different bonding techniques is compared, one comprising only inorganic materials, the other technique using an organic bonding agent. Issues such as bonding process and mechanism, bonding strength, uniformity, wafer surface requirement, and stress distribution are studied in detail. The application in silicon photonics to realize high-performance active and passive photonic devices on low-cost silicon wafers is discussed. Hybrid integration is believed to be a promising technology in a variety of applications of silicon photonics.

Establishment and Comparison of Two Different Diagnostic Platforms for Detection of DENV1 NS1 Protein

PubMed Central

Tang, Yin-Liang; Chiu, Chien-Yu; Lin, Chun-Yu; Huang, Chung-Hao; Chen, Yen-Hsu; Destura, Raul V.; Chao, Day-Yu; Wu, Han-Chung

2015-01-01

Dengue virus (DENV) infection is currently at pandemic levels, with populations in tropical and subtropical regions at greatest risk of infection. Early diagnosis and management remain the cornerstone for good clinical outcomes, thus efficient and accurate diagnostic technology in the early stage of the disease is urgently needed. Serotype-specific monoclonal antibodies (mAbs) against the DENV1 nonstructural protein 1 (NS1), DA12-4, DA13-2, and DA15-3, which were recently generated using the hybridoma technique, are suitable for use in diagnostic platforms. Immunofluorescence assay (IFA), enzyme-linked immunosorbent assay (ELISA) and Western blot analysis further confirmed the serotype specificity of these three monoclonal antibodies. The ELISA-based diagnostic platform was established using the combination of two highly sensitive mAbs (DA15-3 and DB20-6). The same combination was also used for the flow cytometry-based diagnostic platform. We report here the detection limits of flow cytometry-based and ELISA-based diagnostic platforms using these mAbs to be 0.1 and 1 ng/mL, respectively. The collected clinical patient serum samples were also assayed by these two serotyping diagnostic platforms. The sensitivity and specificity for detecting NS1 protein of DENV1 are 90% and 96%, respectively. The accuracy of our platform for testing clinical samples is more advanced than that of the two commercial NS1 diagnostic platforms. In conclusion, our platforms are suitable for the early detection of NS1 protein in DENV1 infected patients. PMID:26610481

A whole-process progressive training mode to foster optoelectronic students' innovative practical ability

NASA Astrophysics Data System (ADS)

Zhong, Hairong; Xu, Wei; Hu, Haojun; Duan, Chengfang

2017-08-01

This article analyzes the features of fostering optoelectronic students' innovative practical ability based on the knowledge structure of optoelectronic disciplines, which not only reveals the common law of cultivating students' innovative practical ability, but also considers the characteristics of the major: (1) The basic theory is difficult, and the close combination of science and technology is obvious; (2)With the integration of optics, mechanics, electronics and computer, the system technology is comprehensive; (3) It has both leading-edge theory and practical applications, so the benefit of cultivating optoelectronic students is high ; (4) The equipment is precise and the practice is costly. Considering the concept and structural characteristics of innovative and practical ability, and adhering to the idea of running practice through the whole process, we put forward the construction of three-dimensional innovation and practice platform which consists of "Synthetically Teaching Laboratory + Innovation Practice Base + Scientific Research Laboratory + Major Practice Base + Joint Teaching and Training Base", and meanwhile build a whole-process progressive training mode to foster optoelectronic students' innovative practical ability, following the process of "basic experimental skills training - professional experimental skills training - system design - innovative practice - scientific research project training - expanded training - graduation project": (1) To create an in - class practical ability cultivation environment that has distinctive characteristics of the major, with the teaching laboratory as the basic platform; (2) To create an extra-curricular innovation practice activities cultivation environment that is closely linked to the practical application, with the innovation practice base as a platform for improvement; (3) To create an innovation practice training cultivation environment that leads the development of cutting-edge, with the scientific research laboratory as a platform to explore; (4) To create an out-campus expanded training environment of optoelectronic major practice and optoelectronic system teaching and training, with the major practice base as an expansion of the platform; (5) To break students' "pre-job training barriers" between school and work, with graduation design as the comprehensive training and testing link.

Evaluation of red blood cell and platelet antigen genotyping platforms (ID CORE XT/ID HPA XT) in routine clinical practice.

PubMed

Finning, Kirstin; Bhandari, Radhika; Sellers, Fiona; Revelli, Nicoletta; Villa, Maria Antonietta; Muñiz-Díaz, Eduardo; Nogués, Núria

2016-03-01

High-throughput genotyping platforms enable simultaneous analysis of multiple polymorphisms for blood group typing. BLOODchip® ID is a genotyping platform based on Luminex® xMAP technology for simultaneous determination of 37 red blood cell (RBC) antigens (ID CORE XT) and 18 human platelet antigens (HPA) (ID HPA XT) using the BIDS XT software. In this international multicentre study, the performance of ID CORE XT and ID HPA XT, using the centres' current genotyping methods as the reference for comparison, and the usability and practicality of these systems, were evaluated under working laboratory conditions. DNA was extracted from whole blood in EDTA with Qiagen methodologies. Ninety-six previously phenotyped/genotyped samples were processed per assay: 87 testing samples plus five positive controls and four negative controls. Results were available for 519 samples: 258 with ID CORE XT and 261 with ID HPA XT. There were three "no calls" that were either caused by human error or resolved after repeating the test. Agreement between the tests and reference methods was 99.94% for ID CORE XT (9,540/9,546 antigens determined) and 100% for ID HPA XT (all 4,698 alleles determined). There were six discrepancies in antigen results in five RBC samples, four of which (in VS, N, S and Do(a)) could not be investigated due to lack of sufficient sample to perform additional tests and two of which (in S and C) were resolved in favour of ID CORE XT (100% accuracy). The total hands-on time was 28-41 minutes for a batch of 16 samples. Compared with the reference platforms, ID CORE XT and ID HPA XT were considered simpler to use and had shorter processing times. ID CORE XT and ID HPA XT genotyping platforms for RBC and platelet systems were accurate and user-friendly in working laboratory settings.

Radionuclides, Metals, and Hydrocarbons in Oil and Gas Operational Discharges and Environmental Samples Associated with Offshore Production Facilities on the Texas/Louisiana Continental Shelf with an Environmental Assessment of Metals and Hydrocarbons.

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1997-06-01

This report presents concentrations of radionuclides, metals, and hydrocarbons in samples of produced water and produced sand from oil and gas production platforms located offshore Texas and Louisiana. concentrations in produced water discharge plume / receiving water, ambient seawater, sediment, interstitial water, and marine animal tissue samples collected in the vicinity of discharging platforms and reference sites distant from discharges are also reported and discussed. An environmental risk assessment is made on the basis of the concentration of metals and hydrocarbons determined in the samples.

Radionuclides, Metals, and Hydrocarbons in Oil and Gas Operational Discharges and Environmental Samples Associated with Offshore Production Facilities on the Texas/Louisiana Continental Shelf with an Environmental Assessment of Metals and Hydrocarbons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Continental Shelf Associates, Inc.

1999-08-16

This report presents concentrations of radionuclides, metals, and hydrocarbons in samples of produced water and produced sand from oil and gas production platforms located offshore Texas and Louisiana. Concentrations in produced water discharge plume/receiving water, ambient seawater, sediment, interstitial water, and marine animal tissue samples collected in the vicinity of discharging platforms and reference sites distant from discharges are also reported and discussed. An environmental risk assessment is made on the basis of the concentrations of metals and hydrocarbons determined in the samples.

The BioFIND study: Characteristics of a clinically typical Parkinson's disease biomarker cohort

PubMed Central

Goldman, Jennifer G.; Alcalay, Roy N.; Xie, Tao; Tuite, Paul; Henchcliffe, Claire; Hogarth, Penelope; Amara, Amy W.; Frank, Samuel; Rudolph, Alice; Casaceli, Cynthia; Andrews, Howard; Gwinn, Katrina; Sutherland, Margaret; Kopil, Catherine; Vincent, Lona; Frasier, Mark

2016-01-01

ABSTRACT Background Identifying PD‐specific biomarkers in biofluids will greatly aid in diagnosis, monitoring progression, and therapeutic interventions. PD biomarkers have been limited by poor discriminatory power, partly driven by heterogeneity of the disease, variability of collection protocols, and focus on de novo, unmedicated patients. Thus, a platform for biomarker discovery and validation in well‐characterized, clinically typical, moderate to advanced PD cohorts is critically needed. Methods BioFIND (Fox Investigation for New Discovery of Biomarkers in Parkinson's Disease) is a cross‐sectional, multicenter biomarker study that established a repository of clinical data, blood, DNA, RNA, CSF, saliva, and urine samples from 118 moderate to advanced PD and 88 healthy control subjects. Inclusion criteria were designed to maximize diagnostic specificity by selecting participants with clinically typical PD symptoms, and clinical data and biospecimen collection utilized standardized procedures to minimize variability across sites. Results We present the study methodology and data on the cohort's clinical characteristics. Motor scores and biospecimen samples including plasma are available for practically defined off and on states and thus enable testing the effects of PD medications on biomarkers. Other biospecimens are available from off state PD assessments and from controls. Conclusion Our cohort provides a valuable resource for biomarker discovery and validation in PD. Clinical data and biospecimens, available through The Michael J. Fox Foundation for Parkinson's Research and the National Institute of Neurological Disorders and Stroke, can serve as a platform for discovering biomarkers in clinically typical PD and comparisons across PD's broad and heterogeneous spectrum. © 2016 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society PMID:27113479

Patient-Customized Drug Combination Prediction and Testing for T-cell Prolymphocytic Leukemia Patients.

PubMed

He, Liye; Tang, Jing; Andersson, Emma I; Timonen, Sanna; Koschmieder, Steffen; Wennerberg, Krister; Mustjoki, Satu; Aittokallio, Tero

2018-05-01

The molecular pathways that drive cancer progression and treatment resistance are highly redundant and variable between individual patients with the same cancer type. To tackle this complex rewiring of pathway cross-talk, personalized combination treatments targeting multiple cancer growth and survival pathways are required. Here we implemented a computational-experimental drug combination prediction and testing (DCPT) platform for efficient in silico prioritization and ex vivo testing in patient-derived samples to identify customized synergistic combinations for individual cancer patients. DCPT used drug-target interaction networks to traverse the massive combinatorial search spaces among 218 compounds (a total of 23,653 pairwise combinations) and identified cancer-selective synergies by using differential single-compound sensitivity profiles between patient cells and healthy controls, hence reducing the likelihood of toxic combination effects. A polypharmacology-based machine learning modeling and network visualization made use of baseline genomic and molecular profiles to guide patient-specific combination testing and clinical translation phases. Using T-cell prolymphocytic leukemia (T-PLL) as a first case study, we show how the DCPT platform successfully predicted distinct synergistic combinations for each of the three T-PLL patients, each presenting with different resistance patterns and synergy mechanisms. In total, 10 of 24 (42%) of selective combination predictions were experimentally confirmed to show synergy in patient-derived samples ex vivo The identified selective synergies among approved drugs, including tacrolimus and temsirolimus combined with BCL-2 inhibitor venetoclax, may offer novel drug repurposing opportunities for treating T-PLL. Significance: An integrated use of functional drug screening combined with genomic and molecular profiling enables patient-customized prediction and testing of drug combination synergies for T-PLL patients. Cancer Res; 78(9); 2407-18. ©2018 AACR . ©2018 American Association for Cancer Research.

Topography-Assisted Electromagnetic Platform for Blood-to-PCR in a Droplet

PubMed Central

Chiou, Chi-Han; Shin, Dong Jin; Zhang, Yi; Wang, Tza-Huei

2013-01-01

This paper presents an electromagnetically actuated platform for automated sample preparation and detection of nucleic acids. The proposed platform integrates nucleic acid extraction using silica-coated magnetic particles with real-time polymerase chain reaction (PCR) on a single cartridge. Extraction of genomic material was automated by manipulating magnetic particles in droplets using a series of planar coil electromagnets assisted by topographical features, enabling efficient fluidic processing over a variety of buffers and reagents. The functionality of the platform was demonstrated by performing nucleic acid extraction from whole blood, followed by real-time PCR detection of KRAS oncogene. Automated sample processing from whole blood to PCR-ready droplet was performed in 15 minutes. We took a modular approach of decoupling the modules of magnetic manipulation and optical detection from the device itself, enabling a low-complexity cartridge that operates in tandem with simple external instruments. PMID:23835223

Iron Opacity Platform Performance Characterization at the National Ignition Facility

NASA Astrophysics Data System (ADS)

Opachich, Y. P.; Ross, P. W.; Heeter, R. F.; Barrios, M. A.; Liedahl, D. A.; May, M. J.; Schneider, M. B.; Craxton, R. S.; Garcia, E. M.; McKenty, P. W.; Zhang, R.; Weaver, J. L.; Flippo, K. A.; Kline, J. L.; Perry, T. S.; Los Alamos National Laboratory Collaboration; Naval Research Laboratory Collaboration; University of Rochester LaboratoryLaser Energetics Collaboration; Lawrence Livermore National Lab Collaboration; National Security Technologies, LLC Collaboration

2016-10-01

A high temperature opacity platform has been fielded at the National Ignition Facility (NIF). The platform will be used to study opacity in iron at a temperature of 160 eV. The platform uses a 6 mm diameter hohlraum driven by 128 laser beams with 530 kJ of energy in a 3 ns pulse to heat an iron sample. Absorption spectra of the heated sample are generated with a broadband pulsed X-ray backlighter produced by imploding a vacuum-filled CH shell. The shell is 2 mm in diameter and 20 microns thick, driven by 64 beams with 250 kJ in a 2.5 ns pulse. The hohlraum and backlighter performance have both been investigated recently and will be discussed in this presentation. This work was performed by National Security Technologies, LLC, under Contract No. DE-AC52-06NA25946 with the U.S. Department of Energy. DOE/NV/25946-2892.

The pitfalls of platform comparison: DNA copy number array technologies assessed

PubMed Central

2009-01-01

Background The accurate and high resolution mapping of DNA copy number aberrations has become an important tool by which to gain insight into the mechanisms of tumourigenesis. There are various commercially available platforms for such studies, but there remains no general consensus as to the optimal platform. There have been several previous platform comparison studies, but they have either described older technologies, used less-complex samples, or have not addressed the issue of the inherent biases in such comparisons. Here we describe a systematic comparison of data from four leading microarray technologies (the Affymetrix Genome-wide SNP 5.0 array, Agilent High-Density CGH Human 244A array, Illumina HumanCNV370-Duo DNA Analysis BeadChip, and the Nimblegen 385 K oligonucleotide array). We compare samples derived from primary breast tumours and their corresponding matched normals, well-established cancer cell lines, and HapMap individuals. By careful consideration and avoidance of potential sources of bias, we aim to provide a fair assessment of platform performance. Results By performing a theoretical assessment of the reproducibility, noise, and sensitivity of each platform, notable differences were revealed. Nimblegen exhibited between-replicate array variances an order of magnitude greater than the other three platforms, with Agilent slightly outperforming the others, and a comparison of self-self hybridizations revealed similar patterns. An assessment of the single probe power revealed that Agilent exhibits the highest sensitivity. Additionally, we performed an in-depth visual assessment of the ability of each platform to detect aberrations of varying sizes. As expected, all platforms were able to identify large aberrations in a robust manner. However, some focal amplifications and deletions were only detected in a subset of the platforms. Conclusion Although there are substantial differences in the design, density, and number of replicate probes, the comparison indicates a generally high level of concordance between platforms, despite differences in the reproducibility, noise, and sensitivity. In general, Agilent tended to be the best aCGH platform and Affymetrix, the superior SNP-CGH platform, but for specific decisions the results described herein provide a guide for platform selection and study design, and the dataset a resource for more tailored comparisons. PMID:19995423

Automation of Silica Bead-based Nucleic Acid Extraction on a Centrifugal Lab-on-a-Disc Platform

NASA Astrophysics Data System (ADS)

Kinahan, David J.; Mangwanya, Faith; Garvey, Robert; Chung, Danielle WY; Lipinski, Artur; Julius, Lourdes AN; King, Damien; Mohammadi, Mehdi; Mishra, Rohit; Al-Ofi, May; Miyazaki, Celina; Ducrée, Jens

2016-10-01

We describe a centrifugal microfluidic ‘Lab-on-a-Disc’ (LoaD) technology for DNA purification towards eventual integration into a Sample-to-Answer platform for detection of the pathogen Escherichia coli O157:H7 from food samples. For this application, we use a novel microfluidic architecture which combines ‘event-triggered’ dissolvable film (DF) valves with a reaction chamber gated by a centrifugo-pneumatic siphon valve (CPSV). This architecture permits comprehensive flow control by simple changes in the speed of the platform innate spindle motor. Even before method optimisation, characterisation by DNA fluorescence reveals an extraction efficiency of 58%, which is close to commercial spin columns.

Robotic platform for traveling on vertical piping network

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nance, Thomas A; Vrettos, Nick J; Krementz, Daniel

This invention relates generally to robotic systems and is specifically designed for a robotic system that can navigate vertical pipes within a waste tank or similar environment. The robotic system allows a process for sampling, cleaning, inspecting and removing waste around vertical pipes by supplying a robotic platform that uses the vertical pipes to support and navigate the platform above waste material contained in the tank.

Chemical Conversions of Biomass-Derived Platform Chemicals over Copper-Silica Nanocomposite Catalysts.

PubMed

Upare, Pravin P; Hwang, Young Kyu; Lee, Jong-Min; Hwang, Dong Won; Chang, Jong-San

2015-07-20

Biomass and biomass-derived carbohydrates have a high extent of functionality, unlike petroleum, which has limited functionality. In biorefinery applications, the development of methods to control the extent of functionality in final products intended for use as fuels and chemicals is a challenge. In the chemical industry, heterogeneous catalysis is an important tool for the defunctionalization of functionalized feedstocks and biomass-derived platform chemicals to produce value-added chemicals. Herein, we review the recent progress in this field, mainly of vapor phase chemical conversion of biomass-derived C4 -C6 carboxylic acids and esters using copper-silica nanocomposite catalysts. We also demonstrate that these nanocomposite catalysts very efficiently convert biomass-derived platform chemicals into cyclic compounds, such as lactones and hydrofurans, with high selectivities and yields. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

On the way to commercializing plant cell culture platform for biopharmaceuticals: present status and prospect

PubMed Central

Xu, Jianfeng; Zhang, Ningning

2014-01-01

Plant cell culture is emerging as an alternative bioproduction system for recombinant pharmaceuticals. Growing plant cells in vitro under controlled environmental conditions allows for precise control over cell growth and protein production, batch-to-batch product consistency and a production process aligned with current good manufacturing practices. With the recent US FDA approval and commercialization of the world’s first plant cell-based recombinant pharmaceutical for human use, β-glucocerebrosidase for treatment of Gaucher’s disease, a new era has come in which plant cell culture shows high potential to displace some established platform technologies in niche markets. This review updates the progress in plant cell culture processing technology, highlights recent commercial successes and discusses the challenges that must be overcome to make this platform commercially viable. PMID:25621170

Metagenomic analysis of medicinal Cannabis samples; pathogenic bacteria, toxigenic fungi, and beneficial microbes grow in culture-based yeast and mold tests.

PubMed

McKernan, Kevin; Spangler, Jessica; Helbert, Yvonne; Lynch, Ryan C; Devitt-Lee, Adrian; Zhang, Lei; Orphe, Wendell; Warner, Jason; Foss, Theodore; Hudalla, Christopher J; Silva, Matthew; Smith, Douglas R

2016-01-01

Background : The presence of bacteria and fungi in medicinal or recreational Cannabis poses a potential threat to consumers if those microbes include pathogenic or toxigenic species. This study evaluated two widely used culture-based platforms for total yeast and mold (TYM) testing marketed by 3M Corporation and Biomérieux, in comparison with a quantitative PCR (qPCR) approach marketed by Medicinal Genomics Corporation. Methods : A set of 15 medicinal Cannabis samples were analyzed using 3M and Biomérieux culture-based platforms and by qPCR to quantify microbial DNA. All samples were then subjected to next-generation sequencing and metagenomics analysis to enumerate the bacteria and fungi present before and after growth on culture-based media. Results : Several pathogenic or toxigenic bacterial and fungal species were identified in proportions of >5% of classified reads on the samples, including Acinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa, Ralstonia pickettii, Salmonella enterica, Stenotrophomonas maltophilia, Aspergillus ostianus, Aspergillus sydowii, Penicillium citrinum and Penicillium steckii. Samples subjected to culture showed substantial shifts in the number and diversity of species present, including the failure of Aspergillus species to grow well on either platform. Substantial growth of Clostridium botulinum and other bacteria were frequently observed on one or both of the culture-based TYM platforms. The presence of plant growth promoting (beneficial) fungal species further influenced the differential growth of species in the microbiome of each sample. Conclusions : These findings have important implications for the Cannabis and food safety testing industries.

Integrated sample-to-detection chip for nucleic acid test assays.

PubMed

Prakash, R; Pabbaraju, K; Wong, S; Tellier, R; Kaler, K V I S

2016-06-01

Nucleic acid based diagnostic techniques are routinely used for the detection of infectious agents. Most of these assays rely on nucleic acid extraction platforms for the extraction and purification of nucleic acids and a separate real-time PCR platform for quantitative nucleic acid amplification tests (NATs). Several microfluidic lab on chip (LOC) technologies have been developed, where mechanical and chemical methods are used for the extraction and purification of nucleic acids. Microfluidic technologies have also been effectively utilized for chip based real-time PCR assays. However, there are few examples of microfluidic systems which have successfully integrated these two key processes. In this study, we have implemented an electro-actuation based LOC micro-device that leverages multi-frequency actuation of samples and reagents droplets for chip based nucleic acid extraction and real-time, reverse transcription (RT) PCR (qRT-PCR) amplification from clinical samples. Our prototype micro-device combines chemical lysis with electric field assisted isolation of nucleic acid in a four channel parallel processing scheme. Furthermore, a four channel parallel qRT-PCR amplification and detection assay is integrated to deliver the sample-to-detection NAT chip. The NAT chip combines dielectrophoresis and electrostatic/electrowetting actuation methods with resistive micro-heaters and temperature sensors to perform chip based integrated NATs. The two chip modules have been validated using different panels of clinical samples and their performance compared with standard platforms. This study has established that our integrated NAT chip system has a sensitivity and specificity comparable to that of the standard platforms while providing up to 10 fold reduction in sample/reagent volumes.

Metagenomic analysis of medicinal Cannabis samples; pathogenic bacteria, toxigenic fungi, and beneficial microbes grow in culture-based yeast and mold tests

PubMed Central

McKernan, Kevin; Spangler, Jessica; Helbert, Yvonne; Lynch, Ryan C.; Devitt-Lee, Adrian; Zhang, Lei; Orphe, Wendell; Warner, Jason; Foss, Theodore; Hudalla, Christopher J.; Silva, Matthew; Smith, Douglas R.

2016-01-01

Background: The presence of bacteria and fungi in medicinal or recreational Cannabis poses a potential threat to consumers if those microbes include pathogenic or toxigenic species. This study evaluated two widely used culture-based platforms for total yeast and mold (TYM) testing marketed by 3M Corporation and Biomérieux, in comparison with a quantitative PCR (qPCR) approach marketed by Medicinal Genomics Corporation. Methods: A set of 15 medicinal Cannabis samples were analyzed using 3M and Biomérieux culture-based platforms and by qPCR to quantify microbial DNA. All samples were then subjected to next-generation sequencing and metagenomics analysis to enumerate the bacteria and fungi present before and after growth on culture-based media. Results: Several pathogenic or toxigenic bacterial and fungal species were identified in proportions of >5% of classified reads on the samples, including Acinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa, Ralstonia pickettii, Salmonella enterica, Stenotrophomonas maltophilia, Aspergillus ostianus, Aspergillus sydowii, Penicillium citrinum and Penicillium steckii. Samples subjected to culture showed substantial shifts in the number and diversity of species present, including the failure of Aspergillus species to grow well on either platform. Substantial growth of Clostridium botulinum and other bacteria were frequently observed on one or both of the culture-based TYM platforms. The presence of plant growth promoting (beneficial) fungal species further influenced the differential growth of species in the microbiome of each sample. Conclusions: These findings have important implications for the Cannabis and food safety testing industries. PMID:27853518

FLIPPED: A Case Study in Fundamental of Accounting in Malaysian Polytechnic

ERIC Educational Resources Information Center

Jamaludin, Rozinah; Osman, Siti Zuraidah Md; Yusof, Wan Mustaffa Wan; Jasni, Nur Farrah Azwa

2016-01-01

The new pedagogical flipped classroom was designed, developed and implemented using Flexible environments, Learning culture, Intentional content, Professional educators, Progressive activities, Engaging experiences, and Diversified platforms, also known as the FLIPPED model. The objective of this study is to investigate the effect of student…

Designing Asynchronous Online Discussion Environments: Recent Progress and Possible Future Directions

ERIC Educational Resources Information Center

Gao, Fei; Zhang, Tianyi; Franklin, Teresa

2013-01-01

Asynchronous online discussion environments are important platforms to support learning. Research suggests, however, threaded forums, one of the most popular asynchronous discussion environments, do not often foster productive online discussions naturally. This paper explores how certain properties of threaded forums have affected or constrained…

Wearable Platform for Real-time Monitoring of Sodium in Sweat.

PubMed

McCaul, Margaret; Porter, Adam; Barrett, Ruairi; White, Paddy; Stroiescu, Florien; Wallace, Gordon; Diamond, Dermot

2018-06-19

A fully integrated and wearable platform for harvesting and analysing sweat sodium concentration in real time during exercise has been developed and tested. The platform was largely produced using 3D printing, which greatly simplifies fabrication and operation compared to previous versions generated with traditional production techniques. The 3D printed platform doubles the capacity of the sample storage reservoir to about 1.3 ml, reduces the assembly time and provides simple and precise component alignment and contact of the integrated solid-state ion-selective and reference electrodes with the sorbent material. The sampling flowrate in the device can be controlled by introducing threads to enhance wicking of sweat from the skin, across the electrodes to the storage area. The platform was characterised in the lab and in exercise trials over a period of about 60 minutes continuous monitoring. Sweat sodium concentration was found to rise initially to approximately 17 mM and decline gradually over the period of the trial to about 11-12 mM. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gold Nanostructures as a Platform for Combinational Therapy in Future Cancer Therapeutics

PubMed Central

Jelveh, Salomeh; Chithrani, Devika B.

2011-01-01

The field of nanotechnology is currently undergoing explosive development on many fronts. The technology is expected to generate innovations and play a critical role in cancer therapeutics. Among other nanoparticle (NP) systems, there has been tremendous progress made in the use of spherical gold NPs (GNPs), gold nanorods (GNRs), gold nanoshells (GNSs) and gold nanocages (GNCs) in cancer therapeutics. In treating cancer, radiation therapy and chemotherapy remain the most widely used treatment options and recent developments in cancer research show that the incorporation of gold nanostructures into these protocols has enhanced tumor cell killing. These nanostructures further provide strategies for better loading, targeting, and controlling the release of drugs to minimize the side effects of highly toxic anticancer drugs used in chemotherapy and photodynamic therapy. In addition, the heat generation capability of gold nanostructures upon exposure to UV or near infrared light is being used to damage tumor cells locally in photothermal therapy. Hence, gold nanostructures provide a versatile platform to integrate many therapeutic options leading to effective combinational therapy in the fight against cancer. In this review article, the recent progress in the development of gold-based NPs towards improved therapeutics will be discussed. A multifunctional platform based on gold nanostructures with targeting ligands, therapeutic molecules, and imaging contrast agents, holds an array of promising directions for cancer research. PMID:24212654

Pneumatic Microvalve-Based Hydrodynamic Sample Injection for High-Throughput, Quantitative Zone Electrophoresis in Capillaries

PubMed Central

2015-01-01

A hybrid microchip/capillary electrophoresis (CE) system was developed to allow unbiased and lossless sample loading and high-throughput repeated injections. This new hybrid CE system consists of a poly(dimethylsiloxane) (PDMS) microchip sample injector featuring a pneumatic microvalve that separates a sample introduction channel from a short sample loading channel, and a fused-silica capillary separation column that connects seamlessly to the sample loading channel. The sample introduction channel is pressurized such that when the pneumatic microvalve opens briefly, a variable-volume sample plug is introduced into the loading channel. A high voltage for CE separation is continuously applied across the loading channel and the fused-silica capillary separation column. Analytes are rapidly separated in the fused-silica capillary, and following separation, high-sensitivity MS detection is accomplished via a sheathless CE/ESI-MS interface. The performance evaluation of the complete CE/ESI-MS platform demonstrated that reproducible sample injection with well controlled sample plug volumes could be achieved by using the PDMS microchip injector. The absence of band broadening from microchip to capillary indicated a minimum dead volume at the junction. The capabilities of the new CE/ESI-MS platform in performing high-throughput and quantitative sample analyses were demonstrated by the repeated sample injection without interrupting an ongoing separation and a linear dependence of the total analyte ion abundance on the sample plug volume using a mixture of peptide standards. The separation efficiency of the new platform was also evaluated systematically at different sample injection times, flow rates, and CE separation voltages. PMID:24865952

Pneumatic Microvalve-Based Hydrodynamic Sample Injection for High-Throughput, Quantitative Zone Electrophoresis in Capillaries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kelly, Ryan T.; Wang, Chenchen; Rausch, Sarah J.

2014-07-01

A hybrid microchip/capillary CE system was developed to allow unbiased and lossless sample loading and high throughput repeated injections. This new hybrid CE system consists of a polydimethylsiloxane (PDMS) microchip sample injector featuring a pneumatic microvalve that separates a sample introduction channel from a short sample loading channel and a fused silica capillary separation column that connects seamlessly to the sample loading channel. The sample introduction channel is pressurized such that when the pneumatic microvalve opens briefly, a variable-volume sample plug is introduced into the loading channel. A high voltage for CE separation is continuously applied across the loading channelmore » and the fused silica capillary separation column. Analytes are rapidly separated in the fused silica capillary with high resolution. High sensitivity MS detection after CE separation is accomplished via a sheathless CE/ESI-MS interface. The performance evaluation of the complete CE/ESI-MS platform demonstrated that reproducible sample injection with well controlled sample plug volumes could be achieved by using the PDMS microchip injector. The absence of band broadening from microchip to capillary indicated a minimum dead volume at the junction. The capabilities of the new CE/ESI-MS platform in performing high throughput and quantitative sample analyses were demonstrated by the repeated sample injection without interrupting an ongoing separation and a good linear dependence of the total analyte ion abundance on the sample plug volume using a mixture of peptide standards. The separation efficiency of the new platform was also evaluated systematically at different sample injection times, flow rates and CE separation voltages.« less

Capillary nano-immunoassays: advancing quantitative proteomics analysis, biomarker assessment, and molecular diagnostics.

PubMed

Chen, Jin-Qiu; Wakefield, Lalage M; Goldstein, David J

2015-06-06

There is an emerging demand for the use of molecular profiling to facilitate biomarker identification and development, and to stratify patients for more efficient treatment decisions with reduced adverse effects. In the past decade, great strides have been made to advance genomic, transcriptomic and proteomic approaches to address these demands. While there has been much progress with these large scale approaches, profiling at the protein level still faces challenges due to limitations in clinical sample size, poor reproducibility, unreliable quantitation, and lack of assay robustness. A novel automated capillary nano-immunoassay (CNIA) technology has been developed. This technology offers precise and accurate measurement of proteins and their post-translational modifications using either charge-based or size-based separation formats. The system not only uses ultralow nanogram levels of protein but also allows multi-analyte analysis using a parallel single-analyte format for increased sensitivity and specificity. The high sensitivity and excellent reproducibility of this technology make it particularly powerful for analysis of clinical samples. Furthermore, the system can distinguish and detect specific protein post-translational modifications that conventional Western blot and other immunoassays cannot easily capture. This review will summarize and evaluate the latest progress to optimize the CNIA system for comprehensive, quantitative protein and signaling event characterization. It will also discuss how the technology has been successfully applied in both discovery research and clinical studies, for signaling pathway dissection, proteomic biomarker assessment, targeted treatment evaluation and quantitative proteomic analysis. Lastly, a comparison of this novel system with other conventional immuno-assay platforms is performed.

Electricity-Free, Sequential Nucleic Acid and Protein Isolation

PubMed Central

Pawlowski, David R.; Karalus, Richard J.

2012-01-01

Traditional and emerging pathogens such as Enterohemorrhagic Escherichia coli (EHEC), Yersinia pestis, or prion-based diseases are of significant concern for governments, industries and medical professionals worldwide. For example, EHECs, combined with Shigella, are responsible for the deaths of approximately 325,000 children each year and are particularly prevalent in the developing world where laboratory-based identification, common in the United States, is unavailable 1. The development and distribution of low cost, field-based, point-of-care tools to aid in the rapid identification and/or diagnosis of pathogens or disease markers could dramatically alter disease progression and patient prognosis. We have developed a tool to isolate nucleic acids and proteins from a sample by solid-phase extraction (SPE) without electricity or associated laboratory equipment 2. The isolated macromolecules can be used for diagnosis either in a forward lab or using field-based point-of-care platforms. Importantly, this method provides for the direct comparison of nucleic acid and protein data from an un-split sample, offering a confidence through corroboration of genomic and proteomic analysis. Our isolation tool utilizes the industry standard for solid-phase nucleic acid isolation, the BOOM technology, which isolates nucleic acids from a chaotropic salt solution, usually guanidine isothiocyanate, through binding to silica-based particles or filters 3. CUBRC's proprietary solid-phase extraction chemistry is used to purify protein from chaotropic salt solutions, in this case, from the waste or flow-thru following nucleic acid isolation4. By packaging well-characterized chemistries into a small, inexpensive and simple platform, we have generated a portable system for nucleic acid and protein extraction that can be performed under a variety of conditions. The isolated nucleic acids are stable and can be transported to a position where power is available for PCR amplification while the protein content can immediately be analyzed by hand held or other immunological-based assays. The rapid identification of disease markers in the field could significantly alter the patient's outcome by directing the proper course of treatment at an earlier stage of disease progression. The tool and method described are suitable for use with virtually any infectious agent and offer the user the redundancy of multi-macromolecule type analyses while simultaneously reducing their logistical burden. PMID:22635135

Electricity-free, sequential nucleic acid and protein isolation.

PubMed

Pawlowski, David R; Karalus, Richard J

2012-05-15

Traditional and emerging pathogens such as Enterohemorrhagic Escherichia coli (EHEC), Yersinia pestis, or prion-based diseases are of significant concern for governments, industries and medical professionals worldwide. For example, EHECs, combined with Shigella, are responsible for the deaths of approximately 325,000 children each year and are particularly prevalent in the developing world where laboratory-based identification, common in the United States, is unavailable (1). The development and distribution of low cost, field-based, point-of-care tools to aid in the rapid identification and/or diagnosis of pathogens or disease markers could dramatically alter disease progression and patient prognosis. We have developed a tool to isolate nucleic acids and proteins from a sample by solid-phase extraction (SPE) without electricity or associated laboratory equipment (2). The isolated macromolecules can be used for diagnosis either in a forward lab or using field-based point-of-care platforms. Importantly, this method provides for the direct comparison of nucleic acid and protein data from an un-split sample, offering a confidence through corroboration of genomic and proteomic analysis. Our isolation tool utilizes the industry standard for solid-phase nucleic acid isolation, the BOOM technology, which isolates nucleic acids from a chaotropic salt solution, usually guanidine isothiocyanate, through binding to silica-based particles or filters (3). CUBRC's proprietary solid-phase extraction chemistry is used to purify protein from chaotropic salt solutions, in this case, from the waste or flow-thru following nucleic acid isolation(4). By packaging well-characterized chemistries into a small, inexpensive and simple platform, we have generated a portable system for nucleic acid and protein extraction that can be performed under a variety of conditions. The isolated nucleic acids are stable and can be transported to a position where power is available for PCR amplification while the protein content can immediately be analyzed by hand held or other immunological-based assays. The rapid identification of disease markers in the field could significantly alter the patient's outcome by directing the proper course of treatment at an earlier stage of disease progression. The tool and method described are suitable for use with virtually any infectious agent and offer the user the redundancy of multi-macromolecule type analyses while simultaneously reducing their logistical burden.

A mixed signal ECG processing platform with an adaptive sampling ADC for portable monitoring applications.

PubMed

Kim, Hyejung; Van Hoof, Chris; Yazicioglu, Refet Firat

2011-01-01

This paper describes a mixed-signal ECG processing platform with an 12-bit ADC architecture that can adapt its sampling rate according to the input signals rate of change. This enables the sampling of ECG signals with significantly reduced data rate without loss of information. The presented adaptive sampling scheme reduces the ADC power consumption, enables the processing of ECG signals with lower power consumption, and reduces the power consumption of the radio while streaming the ECG signals. The test results show that running a CWT-based R peak detection algorithm using the adaptively sampled ECG signals consumes only 45.6 μW and it leads to 36% less overall system power consumption.

Computational On-Chip Imaging of Nanoparticles and Biomolecules using Ultraviolet Light.

PubMed

Daloglu, Mustafa Ugur; Ray, Aniruddha; Gorocs, Zoltan; Xiong, Matthew; Malik, Ravinder; Bitan, Gal; McLeod, Euan; Ozcan, Aydogan

2017-03-09

Significant progress in characterization of nanoparticles and biomolecules was enabled by the development of advanced imaging equipment with extreme spatial-resolution and sensitivity. To perform some of these analyses outside of well-resourced laboratories, it is necessary to create robust and cost-effective alternatives to existing high-end laboratory-bound imaging and sensing equipment. Towards this aim, we have designed a holographic on-chip microscope operating at an ultraviolet illumination wavelength (UV) of 266 nm. The increased forward scattering from nanoscale objects at this short wavelength has enabled us to detect individual sub-30 nm nanoparticles over a large field-of-view of >16 mm 2 using an on-chip imaging platform, where the sample is placed at ≤0.5 mm away from the active area of an opto-electronic sensor-array, without any lenses in between. The strong absorption of this UV wavelength by biomolecules including nucleic acids and proteins has further enabled high-contrast imaging of nanoscopic aggregates of biomolecules, e.g., of enzyme Cu/Zn-superoxide dismutase, abnormal aggregation of which is linked to amyotrophic lateral sclerosis (ALS) - a fatal neurodegenerative disease. This UV-based wide-field computational imaging platform could be valuable for numerous applications in biomedical sciences and environmental monitoring, including disease diagnostics, viral load measurements as well as air- and water-quality assessment.

Development and validation of a comprehensive genomic diagnostic tool for myeloid malignancies

PubMed Central

McKerrell, Thomas; Moreno, Thaidy; Ponstingl, Hannes; Bolli, Niccolo; Dias, João M. L.; Tischler, German; Colonna, Vincenza; Manasse, Bridget; Bench, Anthony; Bloxham, David; Herman, Bram; Fletcher, Danielle; Park, Naomi; Quail, Michael A.; Manes, Nicla; Hodkinson, Clare; Baxter, Joanna; Sierra, Jorge; Foukaneli, Theodora; Warren, Alan J.; Chi, Jianxiang; Costeas, Paul; Rad, Roland; Huntly, Brian; Grove, Carolyn; Ning, Zemin; Tyler-Smith, Chris; Varela, Ignacio; Scott, Mike; Nomdedeu, Josep; Mustonen, Ville

2016-01-01

The diagnosis of hematologic malignancies relies on multidisciplinary workflows involving morphology, flow cytometry, cytogenetic, and molecular genetic analyses. Advances in cancer genomics have identified numerous recurrent mutations with clear prognostic and/or therapeutic significance to different cancers. In myeloid malignancies, there is a clinical imperative to test for such mutations in mainstream diagnosis; however, progress toward this has been slow and piecemeal. Here we describe Karyogene, an integrated targeted resequencing/analytical platform that detects nucleotide substitutions, insertions/deletions, chromosomal translocations, copy number abnormalities, and zygosity changes in a single assay. We validate the approach against 62 acute myeloid leukemia, 50 myelodysplastic syndrome, and 40 blood DNA samples from individuals without evidence of clonal blood disorders. We demonstrate robust detection of sequence changes in 49 genes, including difficult-to-detect mutations such as FLT3 internal-tandem and mixed-lineage leukemia (MLL) partial-tandem duplications, and clinically significant chromosomal rearrangements including MLL translocations to known and unknown partners, identifying the novel fusion gene MLL-DIAPH2 in the process. Additionally, we identify most significant chromosomal gains and losses, and several copy neutral loss-of-heterozygosity mutations at a genome-wide level, including previously unreported changes such as homozygosity for DNMT3A R882 mutations. Karyogene represents a dependable genomic diagnosis platform for translational research and for the clinical management of myeloid malignancies, which can be readily adapted for use in other cancers. PMID:27121471

Computational On-Chip Imaging of Nanoparticles and Biomolecules using Ultraviolet Light

NASA Astrophysics Data System (ADS)

Daloglu, Mustafa Ugur; Ray, Aniruddha; Gorocs, Zoltan; Xiong, Matthew; Malik, Ravinder; Bitan, Gal; McLeod, Euan; Ozcan, Aydogan

2017-03-01

Significant progress in characterization of nanoparticles and biomolecules was enabled by the development of advanced imaging equipment with extreme spatial-resolution and sensitivity. To perform some of these analyses outside of well-resourced laboratories, it is necessary to create robust and cost-effective alternatives to existing high-end laboratory-bound imaging and sensing equipment. Towards this aim, we have designed a holographic on-chip microscope operating at an ultraviolet illumination wavelength (UV) of 266 nm. The increased forward scattering from nanoscale objects at this short wavelength has enabled us to detect individual sub-30 nm nanoparticles over a large field-of-view of >16 mm2 using an on-chip imaging platform, where the sample is placed at ≤0.5 mm away from the active area of an opto-electronic sensor-array, without any lenses in between. The strong absorption of this UV wavelength by biomolecules including nucleic acids and proteins has further enabled high-contrast imaging of nanoscopic aggregates of biomolecules, e.g., of enzyme Cu/Zn-superoxide dismutase, abnormal aggregation of which is linked to amyotrophic lateral sclerosis (ALS) - a fatal neurodegenerative disease. This UV-based wide-field computational imaging platform could be valuable for numerous applications in biomedical sciences and environmental monitoring, including disease diagnostics, viral load measurements as well as air- and water-quality assessment.

Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers

PubMed Central

Pabinger, Stephan; Ernst, Karina; Pulverer, Walter; Kallmeyer, Rainer; Valdes, Ana M.; Metrustry, Sarah; Katic, Denis; Nuzzo, Angelo; Kriegner, Albert; Vierlinger, Klemens; Weinhaeusel, Andreas

2016-01-01

Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM). Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage. TABSAT is freely available under a GNU General Public License version 3.0 (GPLv3) at https://github.com/tadkeys/tabsat/ and http://demo.platomics.com/. PMID:27467908

Integrated chemical/biochemical sample collection, pre-concentration, and analysis on a digital microfluidic lab-on-a-chip platform

NASA Astrophysics Data System (ADS)

Fair, Richard B.; Khlystov, A.; Srinivasan, Vijay; Pamula, Vamsee K.; Weaver, Kathryn N.

2004-12-01

An ideal on-site chemical/biochemical analysis system must be inexpensive, sensitive, fully automated and integrated, reliable, and compatible with a broad range of samples. The advent of digital microfluidic lab-on-a-chip (LoC) technology offers such a detection system due to the advantages in portability, reduction of the volumes of the sample and reagents, faster analysis times, increased automation, low power consumption, compatibility with mass manufacturing, and high throughput. We describe progress towards integrating sample collection onto a digital microfluidic LoC that is a component of a cascade impactor device. The sample collection is performed by impacting airborne particles directly onto the surface of the chip. After the collection phase, the surface of the chip is washed with a micro-droplet of solvent. The droplet will be digitally directed across the impaction surface, dissolving sample constituents. Because of the very small droplet volume used for extraction of the sample from a wide colection area, the resulting solution is realatively concentrated and the analytes can be detected after a very short sampling time (1 min) due to such pre-concentration. After the washing phase, the droplet is mixed with specific reagents that produce colored reaction products. The concentration of the analyte is quantitatively determined by measuring absorption at target wavelengths using a simple light emitting diode and photodiode setup. Specific applications include automatic measurements of major inorganic ions in aerosols, such as sulfate, nitrate and ammonium, with a time resolution of 1 min and a detection limit of 30 nm/m3. We have already demonstrated the detection and quantification of nitroaromatic explosives without integrating the sample collection. Other applications being developed include airborne bioagent detection.

Sediment porewater toxicity assessment studies in the vicinity of offshore oil and gas production platforms in the Gulf of Mexico

USGS Publications Warehouse

Carr, R.S.; Chapman, D.C.; Presley, B.J.; Biedenbach, J.M.; Robertson, L.; Boothe, P.; Kilada, R.; Wade, T.; Montagna, P.

1996-01-01

As part of a multidisciplinary program to assess the potential long-term impacts of offshore oil and gas exploration and production activities in the Gulf of Mexico, sediment chemical analyses and porewater toxicity tests were conducted in the vicinity of five offshore platforms. Based on data from sea urchin fertilization and embryological development assays, toxicity was observed near four of the five platforms sampled; the majority of the toxic samples were collected within 150 m of a platform. There was excellent agreement among the results of porewater tests with three different species (sea urchin embryological development, polychaete reproduction, and copepod nauplii survival). The sediment concentrations of several metals were well in excess of sediment quality assessment guidelines at a number of stations, and good agreement was observed between predicted and observed toxicity. Porewater metal concentrations compared with EC50, LOEC, and NOEC values generated for water-only exposures indicated that the porewater concentrations for several metals were high enough to account for the observed toxicity. Results of these studies utilizing highly sensitive toxicity tests suggest that the contaminant-induced impacts from offshore platforms are limited to a localized area in the immediate vicinity of the platforms. 

Comprehensive Study of the Flow Control Strategy in a Wirelessly Charged Centrifugal Microfluidic Platform with Two Rotation Axes.

PubMed

Zhu, Yunzeng; Chen, Yiqi; Meng, Xiangrui; Wang, Jing; Lu, Ying; Xu, Youchun; Cheng, Jing

2017-09-05

Centrifugal microfluidics has been widely applied in the sample-in-answer-out systems for the analyses of nucleic acids, proteins, and small molecules. However, the inherent characteristic of unidirectional fluid propulsion limits the flexibility of these fluidic chips. Providing an extra degree of freedom to allow the unconstrained and reversible pumping of liquid is an effective strategy to address this limitation. In this study, a wirelessly charged centrifugal microfluidic platform with two rotation axes has been constructed and the flow control strategy in such platform with two degrees of freedom was comprehensively studied for the first time. Inductively coupled coils are installed on the platform to achieve wireless power transfer to the spinning stage. A micro servo motor is mounted on both sides of the stage to alter the orientation of the device around a secondary rotation axis on demand during stage rotation. The basic liquid operations on this platform, including directional transport of liquid, valving, metering, and mixing, are comprehensively studied and realized. Finally, a chip for the simultaneous determination of hexavalent chromium [Cr(VI)] and methanal in water samples is designed and tested based on the strategy presented in this paper, demonstrating the potential use of this platform for on-site environmental monitoring, food safety testing, and other life science applications.

SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids

DOE PAGES

Zhang, Xing; Romm, Michelle; Zheng, Xueyun; ...

2016-12-29

Characterization of endogenous metabolites and xenobiotics is essential to deconvoluting the genetic and environmental causes of disease. However, surveillance of chemical exposure and disease-related changes in large cohorts requires an analytical platform that offers rapid measurement, high sensitivity, efficient separation, broad dynamic range, and application to an expansive chemical space. Here in this article, we present a novel platform for small molecule analyses that addresses these requirements by combining solid-phase extraction with ion mobility spectrometry and mass spectrometry (SPE-IMS-MS). This platform is capable of performing both targeted and global measurements of endogenous metabolites and xenobiotics in human biofluids with highmore » reproducibility (CV ≤ 3%), sensitivity (LODs in the pM range in biofluids) and throughput (10-s sample-to-sample duty cycle). We report application of this platform to the analysis of human urine from patients with and without type 1 diabetes, where we observed statistically significant variations in the concentration of disaccharides and previously unreported chemical isomers. Lastly, this SPE-IMS-MS platform overcomes many of the current challenges of large-scale metabolomic and exposomic analyses and offers a viable option for population and patient cohort screening in an effort to gain insights into disease processes and human environmental chemical exposure.« less

SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids.

PubMed

Zhang, Xing; Romm, Michelle; Zheng, Xueyun; Zink, Erika M; Kim, Young-Mo; Burnum-Johnson, Kristin E; Orton, Daniel J; Apffel, Alex; Ibrahim, Yehia M; Monroe, Matthew E; Moore, Ronald J; Smith, Jordan N; Ma, Jian; Renslow, Ryan S; Thomas, Dennis G; Blackwell, Anne E; Swinford, Glenn; Sausen, John; Kurulugama, Ruwan T; Eno, Nathan; Darland, Ed; Stafford, George; Fjeldsted, John; Metz, Thomas O; Teeguarden, Justin G; Smith, Richard D; Baker, Erin S

2016-12-01

Characterization of endogenous metabolites and xenobiotics is essential to deconvoluting the genetic and environmental causes of disease. However, surveillance of chemical exposure and disease-related changes in large cohorts requires an analytical platform that offers rapid measurement, high sensitivity, efficient separation, broad dynamic range, and application to an expansive chemical space. Here, we present a novel platform for small molecule analyses that addresses these requirements by combining solid-phase extraction with ion mobility spectrometry and mass spectrometry (SPE-IMS-MS). This platform is capable of performing both targeted and global measurements of endogenous metabolites and xenobiotics in human biofluids with high reproducibility (CV 6 3%), sensitivity (LODs in the pM range in biofluids) and throughput (10-s sample-to-sample duty cycle). We report application of this platform to the analysis of human urine from patients with and without type 1 diabetes, where we observed statistically significant variations in the concentration of disaccharides and previously unreported chemical isomers. This SPE-IMS-MS platform overcomes many of the current challenges of large-scale metabolomic and exposomic analyses and offers a viable option for population and patient cohort screening in an effort to gain insights into disease processes and human environmental chemical exposure.

SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids

PubMed Central

Zhang, Xing; Romm, Michelle; Zheng, Xueyun; Zink, Erika M.; Kim, Young-Mo; Burnum-Johnson, Kristin E.; Orton, Daniel J.; Apffel, Alex; Ibrahim, Yehia M.; Monroe, Matthew E.; Moore, Ronald J.; Smith, Jordan N.; Ma, Jian; Renslow, Ryan S.; Thomas, Dennis G.; Blackwell, Anne E.; Swinford, Glenn; Sausen, John; Kurulugama, Ruwan T.; Eno, Nathan; Darland, Ed; Stafford, George; Fjeldsted, John; Metz, Thomas O.; Teeguarden, Justin G.; Smith, Richard D.; Baker, Erin S.

2017-01-01

Characterization of endogenous metabolites and xenobiotics is essential to deconvoluting the genetic and environmental causes of disease. However, surveillance of chemical exposure and disease-related changes in large cohorts requires an analytical platform that offers rapid measurement, high sensitivity, efficient separation, broad dynamic range, and application to an expansive chemical space. Here, we present a novel platform for small molecule analyses that addresses these requirements by combining solid-phase extraction with ion mobility spectrometry and mass spectrometry (SPE-IMS-MS). This platform is capable of performing both targeted and global measurements of endogenous metabolites and xenobiotics in human biofluids with high reproducibility (CV 6 3%), sensitivity (LODs in the pM range in biofluids) and throughput (10-s sample-to-sample duty cycle). We report application of this platform to the analysis of human urine from patients with and without type 1 diabetes, where we observed statistically significant variations in the concentration of disaccharides and previously unreported chemical isomers. This SPE-IMS-MS platform overcomes many of the current challenges of large-scale metabolomic and exposomic analyses and offers a viable option for population and patient cohort screening in an effort to gain insights into disease processes and human environmental chemical exposure. PMID:29276770

Earth Orbital Science, Space in the Seventies.

ERIC Educational Resources Information Center

Corliss, William R.

This publication is part of the "Space in the Seventies" series and reviews the National Aeronautics and Space Administration's (NASA) earth orbital scientific research programs in progress and those to be pursued in the coming decade. Research in space physics is described in Part One in these areas: interplanetary monitoring platforms, small…

DISTINGUISHING CONTAMINANT FROM REEF EFFECTS ON MEIOFAUNA NEAR OFFSHORE HYDROCARBON PLATFORMS IN THE GULF OF MEXICO. (R825355)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Genome editing: progress and challenges for medical applications.

PubMed

Carroll, Dana

2016-11-15

The development of the CRISPR-Cas platform for genome editing has greatly simplified the process of making targeted genetic modifications. Applications of genome editing are expected to have a substantial impact on human therapies through the development of better animal models, new target discovery, and direct therapeutic intervention.

Comparison of plasma ammonia results from seven different automated platforms in use throughout Central Australia.

PubMed

Markus, Corey; Metz, Michael

2017-04-01

The clinical catchment area for the Metabolic service at the Women's and Children's Hospital in Adelaide, South Australia, covers nearly 2.5millionkm 2 . Care of children with metabolic disorders in these remote areas is assisted from Adelaide, and at times, using plasma ammonia results from laboratories up to 3000km away. There are seven different platforms measuring plasma ammonia within this vast clinical catchment area. Hence, a correlation study was conducted to examine the relationship between plasma ammonia results from the seven different platforms in use throughout central Australia. Multiple aliquots of plasma from remainder EDTA samples for haematological investigations were frozen. Samples were then dispatched on dry ice to the laboratories being correlated. At an agreed date and time correlation samples were thawed and plasma ammonia measured. Passing-Bablok regression analysis showed slopes ranging from 1.00 to 1.10 and y-intercepts ranging from -10μmol/L to 1μmol/L. Despite the absence of a reference method or reference material and troublesome pre-analytical effects in ammonia measurement, plasma ammonia results from the different platforms in general compare well. The study also demonstrates that samples for ammonia measurement can be transported over great distances and still correlate well. Furthermore, a common reference interval for plasma ammonia may be a possibility. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

Integration of reconfigurable potentiometric electrochemical sensors into a digital microfluidic platform.

PubMed

Farzbod, Ali; Moon, Hyejin

2018-05-30

This paper presents the demonstration of on-chip fabrication of a potassium-selective sensor array enabled by electrowetting on dielectric digital microfluidics for the first time. This demonstration proves the concept that electrochemical sensors can be seamlessly integrated with sample preparation units in a digital microfluidic platform. More significantly, the successful on-chip fabrication of a sensor array indicates that sensors become reconfigurable and have longer lifetime in a digital microfluidic platform. The on-chip fabrication of ion-selective electrodes includes electroplating Ag followed by forming AgCl layer by chemical oxidation and depositing a thin layer of desired polymer-based ion selective membrane on one of the sensor electrodes. In this study, potassium ionophores work as potassium ion channels and make the membrane selective to potassium ions. This selectiveness results in the voltage difference across the membrane layer, which is correlated with potassium ion concentration. The calibration curve of the fabricated potassium-selective electrode demonstrates the slope of 58 mV/dec for potassium concentration in KCl sample solutions and shows good agreement with the ideal Nernstian response. The proposed sensor platform is an outstanding candidate for a portable home-use for continuous monitoring of ions thanks to its advantages such as easy automation of sample preparation and detection processes, elongated sensor lifetime, minimal membrane and sample consumption, and user-definable/reconfigurable sensor array. Copyright © 2018 Elsevier B.V. All rights reserved.

Design and Performance of a Spectrometer for Deployment on MISSE 7

NASA Technical Reports Server (NTRS)

Pippin, Gary; Beymer, Jim; Robb, Andrew; Longino, James; Perry, George; Stewart, Alan; Finkenor, Miria

2009-01-01

A spectrometer for reflectance and transmission measurements of samples exposed to the space environment has been developed for deployment on the Materials on the International Space Station Experiment (MISSE) 7. The instrument incorporates a miniature commercial fiber optic coupled spectrometer with a computer control system for detector operation, sample motion and illumination. A set of three spectrometers were recently integrated on the MISSE7 platform with launch and deployment on the International Space Station scheduled for summer of this year. The instrument is one of many active experiments on the platform. The performance of the instrument prior to launch will be discussed. Data from samples measured in the laboratory will be compared to those from the instrument prior to launch. These comparisons will illustrate the capabilities of the current design. The space environment challenges many materials. When in operation on the MISSE 7 platform, the new spectrometer will provide real time data on the how the space environment affects the optical properties of thermal control paints and optical coatings. Data obtained from comparison of pre and post flight measurements on hundreds of samples exposed on previous MISSE platforms have been reported at these meetings. With the new spectrometer and the ability to correlate measured changes with time on orbit and the occurrence of both natural events and human activities, a better understanding of the processes responsible for degradation of materials in space will be possible.

Genetic connectivity in scleractinian corals across the Northern Gulf of Mexico: oil/gas platforms, and relationship to the Flower Garden Banks.

PubMed

Sammarco, Paul W; Brazeau, Daniel A; Sinclair, James

2012-01-01

The 3,000 oil/gas structures currently deployed in the northern Gulf of Mexico (GOM) provide hard substratum for marine organisms in a region where such has been rare since the Holocene. The major exception to this are the Flower Garden Banks (FGB). Corals are known to have colonized oil/gas platforms around the FGB, facilitating biogeographic expansion. We ask the question, what are the patterns of genetic affinity in these coral populations. We sampled coral tissue from populations of two species occurring on oil and gas platforms: Madracis decactis (hermatype) and Tubastraea coccinea (invasive ahermatype). We sampled 28 platforms along four transects from 20 km offshore to the continental shelf edge off 1) Matagorda Island, TX; 2) Lake Sabine, TX; 3) Terrebonne Bay, LA; and 4) Mobile, AL. The entire population of M. decactis was sampled between depths of 5 m and 37 m. T. coccinea populations were sub-sampled. Genetic variation was assessed using the PCR-based Amplified Fragment Length Polymorphisms (AFLPs). Data were analyzed via AFLPOP and STRUCTURE. Genetic connectivity among M. decactis platform populations was highest near the FGB and decreased to the east. Connectivity increased again in the eastern sector, indicating isolation between the populations from different sides of the Mississippi River (Transects 3 and 4). A point-drop in genetic affinity (relatedness) at the shelf edge south of Terrebonne Bay, LA indicated a population differing from all others in the northern GOM. Genetic affinities among T. coccinea were highest in the west and decreased to the east. Very low genetic affinities off Mobile, AL indicated a dramatic difference between those populations and those west of the Mississippi River, apparently a formidable barrier to larval dispersal.

Dissolution Rates of Biogenic Carbonate Sediments from the Bermuda Platform

NASA Astrophysics Data System (ADS)

Finlay, A. J.; Andersson, A. J.

2016-02-01

The contribution of biogenic carbonate sediment dissolution rates to overall net reef accretion/erosion (under both present and future oceanic pCO2 levels) has been strikingly neglected, despite experimental results indicating that sediment dissolution might be more sensitive to ocean acidification (OA) than calcification. Dissolution of carbonate sediments could impact net reef accretion rates as well as the formation and preservation of valuable marine and terrestrial ecosystems. Bulk sediment dissolution rates of samples from the Bermuda carbonate platform were measured in natural seawater at pCO2 values ranging from approximately 3500 μatm to 9000 μatm. This range of pCO2 levels incorporates values currently observed in porewaters on the Bermuda carbonate platform as well as a potential future increase in porewater pCO2 levels due to OA. Sediment samples from two different stations on the reef platform were analyzed for grain size and mineralogy. Dissolution rates of sediments in the dominant grain size fraction of the platform (500-1000 μm) from both stations ranged between 16.25 and 47.19 (± 0.27 to 0.79) μmoles g-1 hr-1 and are comparable to rates previously obtained from laboratory experiments on other natural carbonate sediments. At a pCO2 of 3500 μatm, rates from both samples were similar, despite their differing mineralogy. However, at pCO2 levels above 3500 μatm, the sediment sample with a greater weight percent of Mg-calcite had slightly higher dissolution rates. Despite many laboratory studies on biogenic carbonate dissolution, a significant disparity still exists between laboratory measurements and field observations. Performing additional controlled, laboratory experiments on natural sediment may help to elucidate the reasons for this disparity.

Genetic Connectivity in Scleractinian Corals across the Northern Gulf of Mexico: Oil/Gas Platforms, and Relationship to the Flower Garden Banks

PubMed Central

Sammarco, Paul W.; Brazeau, Daniel A.; Sinclair, James

2012-01-01

The 3,000 oil/gas structures currently deployed in the northern Gulf of Mexico (GOM) provide hard substratum for marine organisms in a region where such has been rare since the Holocene. The major exception to this are the Flower Garden Banks (FGB). Corals are known to have colonized oil/gas platforms around the FGB, facilitating biogeographic expansion. We ask the question, what are the patterns of genetic affinity in these coral populations. We sampled coral tissue from populations of two species occurring on oil and gas platforms: Madracis decactis (hermatype) and Tubastraea coccinea (invasive ahermatype). We sampled 28 platforms along four transects from 20 km offshore to the continental shelf edge off 1) Matagorda Island, TX; 2) Lake Sabine, TX; 3) Terrebonne Bay, LA; and 4) Mobile, AL. The entire population of M. decactis was sampled between depths of 5 m and 37 m. T. coccinea populations were sub-sampled. Genetic variation was assessed using the PCR-based Amplified Fragment Length Polymorphisms (AFLPs). Data were analyzed via AFLPOP and STRUCTURE. Genetic connectivity among M. decactis platform populations was highest near the FGB and decreased to the east. Connectivity increased again in the eastern sector, indicating isolation between the populations from different sides of the Mississippi River (Transects 3 and 4). A point-drop in genetic affinity (relatedness) at the shelf edge south of Terrebonne Bay, LA indicated a population differing from all others in the northern GOM. Genetic affinities among T. coccinea were highest in the west and decreased to the east. Very low genetic affinities off Mobile, AL indicated a dramatic difference between those populations and those west of the Mississippi River, apparently a formidable barrier to larval dispersal. PMID:22558066

The High-Throughput Protein Sample Production Platform of the Northeast Structural Genomics Consortium

PubMed Central

Xiao, Rong; Anderson, Stephen; Aramini, James; Belote, Rachel; Buchwald, William A.; Ciccosanti, Colleen; Conover, Ken; Everett, John K.; Hamilton, Keith; Huang, Yuanpeng Janet; Janjua, Haleema; Jiang, Mei; Kornhaber, Gregory J.; Lee, Dong Yup; Locke, Jessica Y.; Ma, Li-Chung; Maglaqui, Melissa; Mao, Lei; Mitra, Saheli; Patel, Dayaban; Rossi, Paolo; Sahdev, Seema; Sharma, Seema; Shastry, Ritu; Swapna, G.V.T.; Tong, Saichu N.; Wang, Dongyan; Wang, Huang; Zhao, Li; Montelione, Gaetano T.; Acton, Thomas B.

2014-01-01

We describe the core Protein Production Platform of the Northeast Structural Genomics Consortium (NESG) and outline the strategies used for producing high-quality protein samples. The platform is centered on the cloning, expression and purification of 6X-His-tagged proteins using T7-based Escherichia coli systems. The 6X-His tag allows for similar purification procedures for most targets and implementation of high-throughput (HTP) parallel methods. In most cases, the 6X-His-tagged proteins are sufficiently purified (> 97% homogeneity) using a HTP two-step purification protocol for most structural studies. Using this platform, the open reading frames of over 16,000 different targeted proteins (or domains) have been cloned as > 26,000 constructs. Over the past nine years, more than 16,000 of these expressed protein, and more than 4,400 proteins (or domains) have been purified to homogeneity in tens of milligram quantities (see Summary Statistics, http://nesg.org/statistics.html). Using these samples, the NESG has deposited more than 900 new protein structures to the Protein Data Bank (PDB). The methods described here are effective in producing eukaryotic and prokaryotic protein samples in E. coli. This paper summarizes some of the updates made to the protein production pipeline in the last five years, corresponding to phase 2 of the NIGMS Protein Structure Initiative (PSI-2) project. The NESG Protein Production Platform is suitable for implementation in a large individual laboratory or by a small group of collaborating investigators. These advanced automated and/or parallel cloning, expression, purification, and biophysical screening technologies are of broad value to the structural biology, functional proteomics, and structural genomics communities. PMID:20688167

Microfluidic-Based Platform for Universal Sample Preparation and Biological Assays Automation for Life-Sciences Research and Remote Medical Applications

NASA Astrophysics Data System (ADS)

Brassard, D.; Clime, L.; Daoud, J.; Geissler, M.; Malic, L.; Charlebois, D.; Buckley, N.; Veres, T.

2018-02-01

An innovative centrifugal microfluidic universal platform for remote bio-analytical assays automation required in life-sciences research and medical applications, including purification and analysis from body fluids of cellular and circulating markers.

Implementation of Arithmetic and Nonarithmetic Functions on a Label-free and DNA-based Platform

NASA Astrophysics Data System (ADS)

Wang, Kun; He, Mengqi; Wang, Jin; He, Ronghuan; Wang, Jianhua

2016-10-01

A series of complex logic gates were constructed based on graphene oxide and DNA-templated silver nanoclusters to perform both arithmetic and nonarithmetic functions. For the purpose of satisfying the requirements of progressive computational complexity and cost-effectiveness, a label-free and universal platform was developed by integration of various functions, including half adder, half subtractor, multiplexer and demultiplexer. The label-free system avoided laborious modification of biomolecules. The designed DNA-based logic gates can be implemented with readout of near-infrared fluorescence, and exhibit great potential applications in the field of bioimaging as well as disease diagnosis.

Space-based sensor management and geostationary satellites tracking

NASA Astrophysics Data System (ADS)

El-Fallah, A.; Zatezalo, A.; Mahler, R.; Mehra, R. K.; Donatelli, D.

2007-04-01

Sensor management for space situational awareness presents a daunting theoretical and practical challenge as it requires the use of multiple types of sensors on a variety of platforms to ensure that the space environment is continuously monitored. We demonstrate a new approach utilizing the Posterior Expected Number of Targets (PENT) as the sensor management objective function, an observation model for a space-based EO/IR sensor platform, and a Probability Hypothesis Density Particle Filter (PHD-PF) tracker. Simulation and results using actual Geostationary Satellites are presented. We also demonstrate enhanced performance by applying the ProgressiveWeighting Correction (PWC) method for regularization in the implementation of the PHD-PF tracker.

The Ree and ɛNd of 40-70 Ma old fish debris from the west-African platform

NASA Astrophysics Data System (ADS)

Grandjean, Patricia; Cappetta, Henri; Albarède, Francis

1988-04-01

REE concentrations and Nd isotopic compositions have been determined in Late Cretaceous-Early Cenozoic fish debris from West African and Israeli platform sediments and show a strong regional control independent of time, except for those from the Northern Morocco. It is suggested that, although diagenetic fluids do not contribute REE's directly to the phosphatic debris, they may significantly change the Ce anomaly and the ɛNd(T) value of the epicontinental seas, which, in turn, control the REE in marine phosphates. It is shown that, over the investigated period, the North Moroccan shelf seawater was progressively flushed by deep North-Atlantic water.

Nanoparticle Approaches against Bacterial Infections

PubMed Central

Gao, Weiwei; Thamphiwatana, Soracha; Angsantikul, Pavimol; Zhang, Liangfang

2014-01-01

Despite the wide success of antibiotics, the treatment of bacterial infection still faces significant challenges, particularly the emergence of antibiotic resistance. As a result, nanoparticle drug delivery platforms including liposomes, polymeric nanoparticles, dendrimers, and various inorganic nanoparticles have been increasingly exploited to enhance the therapeutic effectiveness of existing antibiotics. This review focuses on areas where nanoparticle approaches hold significant potential to advance the treatment of bacterial infection. These areas include targeted antibiotic delivery, environmentally responsive antibiotic delivery, combinatorial antibiotic delivery, nanoparticle-enabled antibacterial vaccination, and nanoparticle-based bacterial detection. In each area we highlight the innovative antimicrobial nanoparticle platforms and review their progress made against bacterial infections. PMID:25044325

Scheduling whole-air samples above the Trade Wind Inversion from SUAS using real-time sensors

NASA Astrophysics Data System (ADS)

Freer, J. E.; Greatwood, C.; Thomas, R.; Richardson, T.; Brownlow, R.; Lowry, D.; MacKenzie, A. R.; Nisbet, E. G.

2015-12-01

Small Unmanned Air Systems (SUAS) are increasingly being used in science applications for a range of applications. Here we explore their use to schedule the sampling of air masses up to 2.5km above ground using computer controlled bespoked Octocopter platforms. Whole-air sampling is targeted above, within and below the Trade Wind Inversion (TWI). On-board sensors profiled the TWI characteristics in real time on ascent and, hence, guided the altitudes at which samples were taken on descent. The science driver for this research is investigation of the Southern Methane Anomaly and, more broadly, the hemispheric-scale transport of long-lived atmospheric tracers in the remote troposphere. Here we focus on the practical application of SUAS for this purpose. Highlighting the need for mission planning, computer control, onboard sensors and logistics in deploying such technologies for out of line-of-sight applications. We show how such a platform can be deployed successfully, resulting in some 60 sampling flights within a 10 day period. Challenges remain regarding the deployment of such platforms routinely and cost-effectively, particularly regarding training and support. We present some initial results from the methane sampling and its implication for exploring and understanding the Southern Methane Anomaly.

Impact E-Learning Platform Moodle on the Physic's Learning Process in the High School's Students

NASA Astrophysics Data System (ADS)

Torres-Montealban, Jonas; Ruiz-Chavarria, Gregorio; Gomez-Lozoya, Enrique Armando

2011-03-01

As a didactic proposal, moodle e-learning platform was implemented in one of two Physics High School's group at UACH, in order to show how the use of new technologies can improve the learning progress linked to physics concepts. As a result, the first group worked at the same time with inside class activities as well as outside resources from the moodle e-platform. The second group only worked with inside class activities. This teaching application was developed in six sections. Section I defines the educational framework. Section II identifies the key physic's concepts to be studied in each proposed activity. Section III describes the didactic model. Section IV displays the compared results between similarities and differences in both groups. Section VI shows the gathered information in order to be discussed as a topic related on how new technologies improve the Physic's learning process in the high school' students.

Opportunity and Challenges for Migrating Big Data Analytics in Cloud

NASA Astrophysics Data System (ADS)

Amitkumar Manekar, S.; Pradeepini, G., Dr.

2017-08-01

Big Data Analytics is a big word now days. As per demanding and more scalable process data generation capabilities, data acquisition and storage become a crucial issue. Cloud storage is a majorly usable platform; the technology will become crucial to executives handling data powered by analytics. Now a day’s trend towards “big data-as-a-service” is talked everywhere. On one hand, cloud-based big data analytics exactly tackle in progress issues of scale, speed, and cost. But researchers working to solve security and other real-time problem of big data migration on cloud based platform. This article specially focused on finding possible ways to migrate big data to cloud. Technology which support coherent data migration and possibility of doing big data analytics on cloud platform is demanding in natute for new era of growth. This article also gives information about available technology and techniques for migration of big data in cloud.

Strategies to Maximize the Potential of Marine Biomaterials as a Platform for Cell Therapy

PubMed Central

Kim, Hyeongmin; Lee, Jaehwi

2016-01-01

Marine biopolymers have been explored as a promising cell therapy system for efficient cell delivery and tissue engineering. However, the marine biomaterial-based systems themselves have exhibited limited performance in terms of maintenance of cell viability and functions, promotion of cell proliferation and differentiation as well as cell delivery efficiency. Thus, numerous novel strategies have been devised to improve cell therapy outcomes. The strategies include optimization of physical and biochemical properties, provision of stimuli-responsive functions, and design of platforms for efficient cell delivery and tissue engineering. These approaches have demonstrated substantial improvement of therapeutic outcomes in a variety of research settings. In this review, therefore, research progress made with marine biomaterials as a platform for cell therapy is reported along with current research directions to further advance cell therapies as a tool to cure incurable diseases. PMID:26821034

Space platform expendables resupply concept definition study. Volume 3: Work breakdown structure and work breakdown structure dictionary

NASA Technical Reports Server (NTRS)

1984-01-01

The work breakdown structure (WBS) for the Space Platform Expendables Resupply Concept Definition Study is described. The WBS consists of a list of WBS elements, a dictionary of element definitions, and an element logic diagram. The list and logic diagram identify the interrelationships of the elements. The dictionary defines the types of work that may be represented by or be classified under each specific element. The Space Platform Expendable Resupply WBS was selected mainly to support the program planning, scheduling, and costing performed in the programmatics task (task 3). The WBS is neither a statement-of-work nor a work authorization document. Rather, it is a framework around which to define requirements, plan effort, assign responsibilities, allocate and control resources, and report progress, expenditures, technical performance, and schedule performance. The WBS element definitions are independent of make-or-buy decisions, organizational structure, and activity locations unless exceptions are specifically stated.

Near-Infrared Ag2S Quantum Dots-Based DNA Logic Gate Platform for miRNA Diagnostics.

PubMed

Miao, Peng; Tang, Yuguo; Wang, Bidou; Meng, Fanyu

2016-08-02

Dysregulation of miRNA expression is correlated with the development and progression of many diseases. These miRNAs are regarded as promising biomarkers. However, it is challenging to measure these low abundant molecules without employing time-consuming radioactive labeling or complex amplification strategies. Here, we present a DNA logic gate platform for miRNA diagnostics with fluorescence outputs from near-infrared (NIR) Ag2S quantum dots (QDs). Carefully designed toehold exchange-mediated strand displacements with different miRNA inputs occur on a solid-state interface, which control QDs release from solid-state interface to solution, responding to multiplex information on initial miRNAs. Excellent fluorescence emission properties of NIR Ag2S QDs certify the great prospect for amplification-free and sensitive miRNA assay. We demonstrate the potential of this platform by achieving femtomolar level miRNA analysis and the versatility of a series of logic circuits computation.

EdREC: Design and Development of Adaptive Platform for Scaling-up Flipped Mastery Learning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gautam, Thakur

EdREC is an adaptive learning and management platform designed to enhance the adoption of differential classroom and mastery flipped learning in K-12 school system. The platform is an innovative approach to teaching and learning that addresses education needs of each student separately by providing customized education plans and adaptive learning methodologies that tunes to the students abilities as well as giving students freedom to learn in their own way. On one side, EdREC provides innovative ways to help students learn; on the other side, it reduces educators' workload and empowers them to understand their students better. EdREC comes with amore » state-of-the-art computer algorithm package that enables educators to store and retrieve their students' information and augment their abilities to individualize student attention, get real-time feedback about student education progress, and provide corrective actions. The platform provides approaches to design and develop a differential classroom concept that frees much needed time by the teachers to focus more on the students at the individual level and to increase communication and collaboration opportunities among them.« less

Microcarrier-based platforms for in vitro expansion and differentiation of human pluripotent stem cells in bioreactor culture systems.

PubMed

Badenes, Sara M; Fernandes, Tiago G; Rodrigues, Carlos A V; Diogo, Maria Margarida; Cabral, Joaquim M S

2016-09-20

Human pluripotent stem cells (hPSC) have attracted a great attention as an unlimited source of cells for cell therapies and other in vitro biomedical applications such as drug screening, toxicology assays and disease modeling. The implementation of scalable culture platforms for the large-scale production of hPSC and their derivatives is mandatory to fulfill the requirement of obtaining large numbers of cells for these applications. Microcarrier technology has been emerging as an effective approach for the large scale ex vivo hPSC expansion and differentiation. This review presents recent achievements in hPSC microcarrier-based culture systems and discusses the crucial aspects that influence the performance of these culture platforms. Recent progress includes addressing chemically-defined culture conditions for manufacturing of hPSC and their derivatives, with the development of xeno-free media and microcarrier coatings to meet good manufacturing practice (GMP) quality requirements. Finally, examples of integrated platforms including hPSC expansion and directed differentiation to specific lineages are also presented in this review. Copyright © 2016 Elsevier B.V. All rights reserved.

Near real time water resources data for river basin management

NASA Technical Reports Server (NTRS)

Paulson, R. W. (Principal Investigator)

1973-01-01

The author has identified the following significant results. Twenty Data Collection Platforms (DCP) are being field installed on USGS water resources stations in the Delaware River Basin. DCP's have been successfully installed and are operating well on five stream gaging stations, three observation wells, and one water quality monitor in the basin. DCP's have been installed at nine additional water quality monitors, and work is progressing on interfacing the platforms to the monitors. ERTS-related water resources data from the platforms are being provided in near real time, by the Goddard Space Flight Center to the Pennsylvania district, Water Resources Division, U.S. Geological Survey. On a daily basis, the data are computer processed by the Survey and provided to the Delaware River Basin Commission. Each daily summary contains data that were relayed during 4 or 5 of the 15 orbits made by ERTS-1 during the previous day. Water resources parameters relays by the platforms include dissolved oxygen concentrations, temperature, pH, specific conductance, well level, and stream gage height, which is used to compute stream flow for the daily summary.

Detection and characterization of invasive circulating tumor cells derived from men with metastatic castration-resistant prostate cancer.

PubMed

Friedlander, Terence W; Ngo, Vy T; Dong, Huan; Premasekharan, Gayatri; Weinberg, Vivian; Doty, Shaun; Zhao, Qiang; Gilbert, Elizabeth G; Ryan, Charles J; Chen, Wen-Tien; Paris, Pamela L

2014-05-15

The Vitatex cell-adhesion matrix (CAM) platform allows for isolation of invasive circulating tumor cells (iCTCs). Here we sought to determine the utility of prostate-specific membrane antigen (PSMA) as a metastatic castration-resistant prostate cancer (mCRPC) iCTC biomarker, to identify solitary cells and clusters of iCTCs expressing either epithelial, mesenchymal, or stem cell markers, and to explore the feasibility of iCTC epigenomic analysis. CTCs were isolated and enumerated simultaneously using the Vitatex and CellSearch platforms in 23 men with mCRPC. CAM-avid iCTCs were identified as nucleated cells capable of CAM uptake, but without detectable expression of hematopoietic lineage (HL) markers including CD45. iCTCs were enumerated immunocytochemically (ICC) and by flow cytometry. Whole-genome methylation status was determined for iCTCs using the Illumina HumanMethylation27 BeadChip. Thirty-four samples were collected for iCTC analysis. A median of 27 (range 0-800) and 23 (range 2-390) iCTCs/mL were detected by ICC and flow, respectively. In a subset of 20 samples, a median of seven CTCs/mL (range 0-85) were detected by the CellSearch platform compared to 26 by the CAM platform. iCTC clusters were observed in 17% of samples. iCTCs expressing PSMA as well as markers of EMT and stemness were detectable. The iCTC methylation profile highly resembled mCRPC. More CTCs were recovered using the CAM platform than the CellSearch platform, and the CAM platform allowed for the detection of iCTC clusters, iCTCs expressing EMT and stem-cell markers, and characterization of the iCTC methylome. Correlation with clinical data in future studies may yield further insight into the functional significance of these findings. © 2013 UICC.

Trace gas measurements from tethered balloon platforms

NASA Technical Reports Server (NTRS)

Bandy, Alan R.; Bandy, Terese L.; Youngbluth, Otto; Owens, Thomas L.

1987-01-01

Instrumentation and chemical sampling and analysis procedures are described for making measurements of atmospheric carbon disulfide in the concentration range 1-1000 pptv from tethered balloon platforms. Results of a study on the CS2 composition of air downward of a saltwater marsh are reported. A method for obtaining the necessary data for solving the budget equations for surface fluxes, chemical formation rates and chemical destruction rates using data acquired from tethered balloon platforms is presented.

Mass spectrometry-based monitoring of millisecond protein–ligand binding dynamics using an automated microfluidic platform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cong, Yongzheng; Katipamula, Shanta; Trader, Cameron D.

2016-01-01

Characterizing protein-ligand binding dynamics is crucial for understanding protein function and developing new therapeutic agents. We have developed a novel microfluidic platform that features rapid mixing of protein and ligand solutions, variable incubation times, and on-chip electrospray ionization to perform label-free, solution-based monitoring of protein-ligand binding dynamics. This platform offers many advantages including automated processing, rapid mixing, and low sample consumption.

Next generation platforms for high-throughput biodosimetry

PubMed Central

Repin, Mikhail; Turner, Helen C.; Garty, Guy; Brenner, David J.

2014-01-01

Here the general concept of the combined use of plates and tubes in racks compatible with the American National Standards Institute/the Society for Laboratory Automation and Screening microplate formats as the next generation platforms for increasing the throughput of biodosimetry assays was described. These platforms can be used at different stages of biodosimetry assays starting from blood collection into microtubes organised in standardised racks and ending with the cytogenetic analysis of samples in standardised multiwell and multichannel plates. Robotically friendly platforms can be used for different biodosimetry assays in minimally equipped laboratories and on cost-effective automated universal biotech systems. PMID:24837249

A 3D-Printed, Portable, Optical-Sensing Platform for Smartphones Capable of Detecting the Herbicide 2,4-Dichlorophenoxyacetic Acid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yijia; Zeinhom, Mohamed M. A.; Yang, Mingming

Onsite rapid detection of herbicide and herbicide residuals in environmental and biological specimens is important for agriculture, environment, food safety, and health care. Traditional method for herbicide detection requires expensive laboratory equipment and a long turn-round time. In this work, we developed a single-stripe microliter plate smartphone colorimetric device for rapid and low-cost in-field test. This portable smartphone platform is capable of screening 8 samples in a microplate single-stripe. The device combined the advantages of small size (50×100×160 mm3) and low cost ($10). The platform was calibrated by using two different dye solutions, i.e. methyl blue (MB) and Rhodamine B,more » for green and red channels. The results showed good correlation with results attained from a traditional laboratory reader. We demonstrated the application of this platform for an herbicide, 2,4-Dichlorophenoxyacetic acid detection in the range of 1 ppb to 80 ppb. Spiked samples of tap water, rat serum, plasma and human serum were tested by our device. Recoveries obtained varied from 95.6% to 105.2% for all spiked samples using the microplate reader and from 93.7% to 106.9% using the smartphone device. This work validated that the smartphone optical sensing platform is comparable to the commercial microplate reader, it is eligible for onsite rapid and low-cost detection of herbicide for environmental evaluation and biological monitoring.« less

Genetic mutations in human rectal cancers detected by targeted sequencing.

PubMed

Bai, Jun; Gao, Jinglong; Mao, Zhijun; Wang, Jianhua; Li, Jianhui; Li, Wensheng; Lei, Yu; Li, Shuaishuai; Wu, Zhuo; Tang, Chuanning; Jones, Lindsey; Ye, Hua; Lou, Feng; Liu, Zhiyuan; Dong, Zhishou; Guo, Baishuai; Huang, Xue F; Chen, Si-Yi; Zhang, Enke

2015-10-01

Colorectal cancer (CRC) is widespread with significant mortality. Both inherited and sporadic mutations in various signaling pathways influence the development and progression of the cancer. Identifying genetic mutations in CRC is important for optimal patient treatment and many approaches currently exist to uncover these mutations, including next-generation sequencing (NGS) and commercially available kits. In the present study, we used a semiconductor-based targeted DNA-sequencing approach to sequence and identify genetic mutations in 91 human rectal cancer samples. Analysis revealed frequent mutations in KRAS (58.2%), TP53 (28.6%), APC (16.5%), FBXW7 (9.9%) and PIK3CA (9.9%), and additional mutations in BRAF, CTNNB1, ERBB2 and SMAD4 were also detected at lesser frequencies. Thirty-eight samples (41.8%) also contained two or more mutations, with common combination mutations occurring between KRAS and TP53 (42.1%), and KRAS and APC (31.6%). DNA sequencing for individual cancers is of clinical importance for targeted drug therapy and the advantages of such targeted gene sequencing over other NGS platforms or commercially available kits in sensitivity, cost and time effectiveness may aid clinicians in treating CRC patients in the near future.

Study of cellular oncometabolism via multidimensional protein identification technology.

PubMed

Aukim-Hastie, Claire; Garbis, Spiros D

2014-01-01

Cellular proteomics is becoming a widespread clinical application, matching the definition of bench-to-bedside translation. Among various fields of investigation, this approach can be applied to the study of the metabolic alterations that accompany oncogenesis and tumor progression, which are globally referred to as oncometabolism. Here, we describe a multidimensional protein identification technology (MuDPIT)-based strategy that can be employed to study the cellular proteome of malignant cells and tissues. This method has previously been shown to be compatible with the reproducible, in-depth analysis of up to a thousand proteins in clinical samples. The possibility to employ this technique to study clinical specimens demonstrates its robustness. MuDPIT is advantageous as compared to other approaches because it is direct, highly sensitive, and reproducible, it provides high resolution with ultra-high mass accuracy, it allows for relative quantifications, and it is compatible with multiplexing (thus limiting costs).This method enables the direct assessment of the proteomic profile of neoplastic cells and tissues and could be employed in the near future as a high-throughput, rapid, quantitative, and cost-effective screening platform for clinical samples. © 2014 Elsevier Inc. All rights reserved.

Comparison of standard- and nano-flow liquid chromatography platforms for MRM-based quantitation of putative plasma biomarker proteins.

PubMed

Percy, Andrew J; Chambers, Andrew G; Yang, Juncong; Domanski, Dominik; Borchers, Christoph H

2012-09-01

The analytical performance of a standard-flow ultra-high-performance liquid chromatography (UHPLC) and a nano-flow high-performance liquid chromatography (HPLC) system, interfaced to the same state-of-the-art triple-quadrupole mass spectrometer, were compared for the multiple reaction monitoring (MRM)-mass spectrometry (MS)-based quantitation of a panel of 48 high-to-moderate-abundance cardiovascular disease-related plasma proteins. After optimization of the MRM transitions for sensitivity and testing for chemical interference, the optimum sensitivity, loading capacity, gradient, and retention-time reproducibilities were determined. We previously demonstrated the increased robustness of the standard-flow platform, but we expected that the standard-flow platform would have an overall lower sensitivity. This study was designed to determine if this decreased sensitivity could be compensated for by increased sample loading. Significantly fewer interferences with the MRM transitions were found for the standard-flow platform than for the nano-flow platform (2 out of 103 transitions compared with 42 out of 103 transitions, respectively), which demonstrates the importance of interference-testing when nano-flow systems are used. Using only interference-free transitions, 36 replicate LC/MRM-MS analyses resulted in equal signal reproducibilities between the two platforms (9.3 % coefficient of variation (CV) for 88 peptide targets), with superior retention-time precision for the standard-flow platform (0.13 vs. 6.1 % CV). Surprisingly, for 41 of the 81 proteotypic peptides in the final assay, the standard-flow platform was more sensitive while for 9 of 81 the nano-flow platform was more sensitive. For these 81 peptides, there was a good correlation between the two sets of results (R(2) = 0.98, slope = 0.97). Overall, the standard-flow platform had superior performance metrics for most peptides, and is a good choice if sufficient sample is available.

A differential mobility spectrometry/mass spectrometry platform for the rapid detection and quantitation of DNA adduct dG-ABP.

PubMed

Kafle, Amol; Klaene, Joshua; Hall, Adam B; Glick, James; Coy, Stephen L; Vouros, Paul

2013-07-15

There is continued interest in exploring new analytical technologies for the detection and quantitation of DNA adducts, biomarkers which provide direct evidence of exposure and genetic damage in cells. With the goal of reducing clean-up steps and improving sample throughput, a Differential Mobility Spectrometry/Mass Spectrometry (DMS/MS) platform has been introduced for adduct analysis. A DMS/MS platform has been utilized for the analysis of dG-ABP, the deoxyguanosine adduct of the bladder carcinogen 4-aminobiphenyl (4-ABP). After optimization of the DMS parameters, each sample was analyzed in just 30 s following a simple protein precipitation step of the digested DNA. A detection limit of one modification in 10^6 nucleosides has been achieved using only 2 µg of DNA. A brief comparison (quantitative and qualitative) with liquid chromatography/mass spectrometry is also presented highlighting the advantages of using the DMS/MS method as a high-throughput platform. The data presented demonstrate the successful application of a DMS/MS/MS platform for the rapid quantitation of DNA adducts using, as a model analyte, the deoxyguanosine adduct of the bladder carcinogen 4-aminobiphenyl. Copyright © 2013 John Wiley & Sons, Ltd.

Micro-UAV tracking framework for EO exploitation

NASA Astrophysics Data System (ADS)

Browning, David; Wilhelm, Joe; Van Hook, Richard; Gallagher, John

2012-06-01

Historically, the Air Force's research into aerial platforms for sensing systems has focused on low-, mid-, and highaltitude platforms. Though these systems are likely to comprise the majority of the Air Force's assets for the foreseeable future, they have limitations. Specifically, these platforms, their sensor packages, and their data exploitation software are unsuited for close-quarter surveillance, such as in alleys and inside of buildings. Micro-UAVs have been gaining in popularity, especially non-fixed-wing platforms such as quad-rotors. These platforms are much more appropriate for confined spaces. However, the types of video exploitation techniques that can effectively be used are different from the typical nadir-looking aerial platform. This paper discusses the creation of a framework for testing existing and new video exploitation algorithms, as well as describes a sample micro-UAV-based tracker.

3-2-1 Ignition*: Making Science Creative, Accessible and Fun

ERIC Educational Resources Information Center

Reichardt, Oliver

2013-01-01

For over 250 years, the RSA (Royal Society for the Encouragement of Arts, Manufactures and Commerce) has been committed to finding practical solutions to today's social challenges. The Society's way of working consists of providing a platform for critical debate and new ideas; working with partners to translate knowledge and progressive thinking…

Creating a Collaborative Culture.

ERIC Educational Resources Information Center

Edmonson, Stacey; Fisher, Alice; Brown, Genevieve; Irby, Beverly; Lunenburg, Fred; Creighton, Ted; Czaja, Marion; Merchant, Jimmy; Christianson, Judy

More and more research is focusing on the importance of a healthy work environment and its impact on workers' well-being and productivity. A culture of collaboration has been shown to have an important impact on school-reform efforts and is recognized by several authors as an effective platform for progress within an organization. A collaborative…

The Relationship between Research Method and Visual Display: A Study of Conference Proceedings in the Field of Knowledge Organization

ERIC Educational Resources Information Center

Friedman, Alon

2014-01-01

Introduction: "Research method" refers to how to conduct research, how to measure progress, and what constitutes success. Visualisation has become the platform for communicating research findings according to Friedman and Smiraglia. Knowledge organization aims to organize knowledge and many researchers employ visualisation in their…

The role of academia and industry in nurturing women in physics in Kenya

NASA Astrophysics Data System (ADS)

Nyamwandha, Cecilia A.; Kasina, Angeline; Muthui, Zipporah W.; Awuor, Emily; Baki, Paul

2015-12-01

The authors look at some of the primary initiatives taken by the government, academia, and industry to nurture the goals and dreams of Kenyan women physicists. They discuss key transformative lines of progress as evidenced by statistics, and the enabling environments and platforms upon which these were made possible.

Study on an Interactive Truck Crane Simulation Platform Based on Virtual Reality Technology

ERIC Educational Resources Information Center

Sang, Yong; Zhu, Yu; Zhao, Honghua; Tang, Mingyan

2016-01-01

The modern web-based distance education overcomes space-time restriction of the traditional teaching forms. However, being short of specifically observable and operable experimental equipment makes the web-based education lack advantages in the knowledge learning progress, which needs strong stereoscopic effect and operability. Truck crane is the…

Health Advocacy: A Vital Step in Attaining Human Rights for Adults with Intellectual Disability

ERIC Educational Resources Information Center

Brolan, C. E.; Boyle, F. M.; Dean, J. H.; Gomez, M. Taylor; Ware, R. S.; Lennox, N. G.

2012-01-01

Background: People with intellectual disability (ID) experience health inequity compared with the general population, a key contributing factor being disparities in social determinants of health. The enactment of the United Nations Convention on the Rights of Persons with Disabilities (CRPD) provides a platform for the progression and promotion of…

30 years of progress toward increased biomass yield of switchgrass and big bluestem

USDA-ARS?s Scientific Manuscript database

Breeding to improved biomass production of switchgrass and big bluestem for conversion to bioenergy began in 1992. The purpose of this study was (1) to develop a platform for uniform regional testing of cultivars and experimental populations for these species and (2) to estimate the gains made by br...

Blended Learning Environments: Using Social Networking Sites to Enhance the First Year Experience

ERIC Educational Resources Information Center

McCarthy, Joshua

2010-01-01

This study explores blending virtual and physical learning environments to enhance the experience of first year by immersing students into university culture through social and academic interaction between peers. It reports on the progress made from 2008 to 2009 using an existing academic platform, the first year design elective course…

Design and Evaluation of a Pervasive Coaching and Gamification Platform for Young Diabetes Patients.

PubMed

Klaassen, Randy; Bul, Kim C M; Op den Akker, Rieks; van der Burg, Gert Jan; Kato, Pamela M; Di Bitonto, Pierpaolo

2018-01-30

Self monitoring, personal goal-setting and coaching, education and social support are strategies to help patients with chronic conditions in their daily care. Various tools have been developed, e.g., mobile digital coaching systems connected with wearable sensors, serious games and patient web portals to personal health records, that aim to support patients with chronic conditions and their caregivers in realizing the ideal of self-management. We describe a platform that integrates these tools to support young patients in diabetes self-management through educational game playing, monitoring and motivational feedback. We describe the design of the platform referring to principles from healthcare, persuasive system design and serious game design. The virtual coach is a game guide that can also provide personalized feedback about the user's daily care related activities which have value for making progress in the game world. User evaluations with patients under pediatric supervision revealed that the use of mobile technology in combination with web-based elements is feasible but some assumptions made about how users would connect to the platform were not satisfied in reality, resulting in less than optimal user experiences. We discuss challenges with suggestions for further development of integrated pervasive coaching and gamification platforms in medical practice.

Design and Evaluation of a Pervasive Coaching and Gamification Platform for Young Diabetes Patients †

PubMed Central

Klaassen, Randy; Bul, Kim C. M.; op den Akker, Rieks; van der Burg, Gert Jan; Di Bitonto, Pierpaolo

2018-01-01

Self monitoring, personal goal-setting and coaching, education and social support are strategies to help patients with chronic conditions in their daily care. Various tools have been developed, e.g., mobile digital coaching systems connected with wearable sensors, serious games and patient web portals to personal health records, that aim to support patients with chronic conditions and their caregivers in realizing the ideal of self-management. We describe a platform that integrates these tools to support young patients in diabetes self-management through educational game playing, monitoring and motivational feedback. We describe the design of the platform referring to principles from healthcare, persuasive system design and serious game design. The virtual coach is a game guide that can also provide personalized feedback about the user’s daily care related activities which have value for making progress in the game world. User evaluations with patients under pediatric supervision revealed that the use of mobile technology in combination with web-based elements is feasible but some assumptions made about how users would connect to the platform were not satisfied in reality, resulting in less than optimal user experiences. We discuss challenges with suggestions for further development of integrated pervasive coaching and gamification platforms in medical practice. PMID:29385750

Recent progress in design and hybridization of planar grating-based transceivers

NASA Astrophysics Data System (ADS)

Bidnyk, S.; Pearson, M.; Balakrishnan, A.; Gao, M.

2007-06-01

We report on recent progress in simulations, physical layout, fabrication and hybridization of planar grating-based transceivers for passive optical networks (PONs). Until recently, PON transceivers have been manufactured using bulk micro-optical components. Today, advancements in modeling and simulation techniques has made it possible to design complex elements in the same silica-on silicon PLC platform and create an alternative platform for manufacturing of bi-directional transceivers. In our chips we simulated an integrated chip that monolithically combined planar reflective gratings and cascaded Mach-Zehnder interferometers. We used a combination of the finite element method and beam propagation method to model cascaded interferometers with enhanced coupling coefficients. Our simulations show that low-diffraction order planar reflective gratings, designed for small incidence and reflection angles, possess the required dispersion strength to meet the PON specifications. Subsequently, we created structures for passive alignment and hybridized photodetectors and lasers. We believe that advancements in simulation of planar lightwave circuits with embedded planar reflective gratings will result in displacement of the thin-film filters (TFFs) technology in many applications that require a high degree of monolithic and hybrid integration.

Recent advances in nanoplasmonic biosensors: applications and lab-on-a-chip integration

NASA Astrophysics Data System (ADS)

Lopez, Gerardo A.; Estevez, M.-Carmen; Soler, Maria; Lechuga, Laura M.

2017-01-01

Motivated by the recent progress in the nanofabrication field and the increasing demand for cost-effective, portable, and easy-to-use point-of-care platforms, localized surface plasmon resonance (LSPR) biosensors have been subjected to a great scientific interest in the last few years. The progress observed in the research of this nanoplasmonic technology is remarkable not only from a nanostructure fabrication point of view but also in the complete development and integration of operative devices and their application. The potential benefits that LSPR biosensors can offer, such as sensor miniaturization, multiplexing opportunities, and enhanced performances, have quickly positioned them as an interesting candidate in the design of lab-on-a-chip (LOC) optical biosensor platforms. This review covers specifically the most significant achievements that occurred in recent years towards the integration of this technology in compact devices, with views of obtaining LOC devices. We also discuss the most relevant examples of the use of the nanoplasmonic biosensors for real bioanalytical and clinical applications from assay development and validation to the identification of the implications, requirements, and challenges to be surpassed to achieve fully operative devices.

Research on propane leak detection system and device based on mid infrared laser

NASA Astrophysics Data System (ADS)

Jiang, Meng; Wang, Xuefeng; Wang, Junlong; Wang, Yizhao; Li, Pan; Feng, Qiaoling

2017-10-01

Propane is a key component of liquefied petroleum gas (LPG) and crude oil volatile. This issue summarizes the recent progress of propane detection technology. Meanwhile, base on the development trend, our latest progress is also provided. We demonstrated a mid infrared propane sensor system, which is based on wavelength modulation spectroscopy (WMS) technique with a CW interband cascade laser (ICL) emitting at 3370.4nm. The ICL laser scanned over a sharp feature in the broader spectrum of propane, and harmonic signals are obtained by lock-in amplifier for gas concentration deduction. The surrounding gas is extracted into the fine optical absorption cell through the pump to realize online detection. The absorption cell is designed in mid infrared windows range. An example experimental setup is shown. The second harmonic signals 2f and first harmonic signals1f are obtained. We present the sensor performance test data including dynamic precision and temperature stability. The propane detection sensor system and device is portable can carried on the mobile inspection vehicle platforms or intelligent robot inspection platform to realize the leakage monitoring of whole oil gas tank area.

Undergraduate Laboratory Module for Implementing ELISA on the High Performance Microfluidic Platform

ERIC Educational Resources Information Center

Giri, Basant; Peesara, Ravichander R.; Yanagisawa, Naoki; Dutta, Debashis

2015-01-01

Implementing enzyme-linked immunosorbent assays (ELISA) in microchannels offers several advantages over its traditional microtiter plate-based format, including a reduced sample volume requirement, shorter incubation period, and greater sensitivity. Moreover, microfluidic ELISA platforms are inexpensive to fabricate and allow integration of…

The LabTube - a novel microfluidic platform for assay automation in laboratory centrifuges.

PubMed

Kloke, A; Fiebach, A R; Zhang, S; Drechsel, L; Niekrawietz, S; Hoehl, M M; Kneusel, R; Panthel, K; Steigert, J; von Stetten, F; Zengerle, R; Paust, N

2014-05-07

Assay automation is the key for successful transformation of modern biotechnology into routine workflows. Yet, it requires considerable investment in processing devices and auxiliary infrastructure, which is not cost-efficient for laboratories with low or medium sample throughput or point-of-care testing. To close this gap, we present the LabTube platform, which is based on assay specific disposable cartridges for processing in laboratory centrifuges. LabTube cartridges comprise interfaces for sample loading and downstream applications and fluidic unit operations for release of prestored reagents, mixing, and solid phase extraction. Process control is achieved by a centrifugally-actuated ballpen mechanism. To demonstrate the workflow and functionality of the LabTube platform, we show two LabTube automated sample preparation assays from laboratory routines: DNA extractions from whole blood and purification of His-tagged proteins. Equal DNA and protein yields were observed compared to manual reference runs, while LabTube automation could significantly reduce the hands-on-time to one minute per extraction.

jsc2018m000314_Spinning_Science_Multi-use_Variable-g_Platform_Arrives_at_the_Space_Station-MP4

NASA Image and Video Library

2018-05-09

Spinning Science: Multi-use Variable-g Platform Arrives at the Space Station --- The Multi-use Variable-gravity Platform (MVP) Validation mission will install and test the MVP, a new hardware platform developed and owned by Techshot Inc., on the International Space Station (ISS). Though the MVP is designed for research with many different kinds of organisms and cell types, this validation mission will focus on Drosophila melanogaster, more commonly known as the fruit fly. This platform will be especially important for fruit fly research, as it will allow researchers to study larger sample sizes of Drosophila melanogaster than in other previous hardware utilizing centrifuges and it will be able to support fly colonies for multiple generations.

High resolution computational on-chip imaging of biological samples using sparsity constraint (Conference Presentation)

NASA Astrophysics Data System (ADS)

Rivenson, Yair; Wu, Chris; Wang, Hongda; Zhang, Yibo; Ozcan, Aydogan

2017-03-01

Microscopic imaging of biological samples such as pathology slides is one of the standard diagnostic methods for screening various diseases, including cancer. These biological samples are usually imaged using traditional optical microscopy tools; however, the high cost, bulkiness and limited imaging throughput of traditional microscopes partially restrict their deployment in resource-limited settings. In order to mitigate this, we previously demonstrated a cost-effective and compact lens-less on-chip microscopy platform with a wide field-of-view of >20-30 mm^2. The lens-less microscopy platform has shown its effectiveness for imaging of highly connected biological samples, such as pathology slides of various tissue samples and smears, among others. This computational holographic microscope requires a set of super-resolved holograms acquired at multiple sample-to-sensor distances, which are used as input to an iterative phase recovery algorithm and holographic reconstruction process, yielding high-resolution images of the samples in phase and amplitude channels. Here we demonstrate that in order to reconstruct clinically relevant images with high resolution and image contrast, we require less than 50% of the previously reported nominal number of holograms acquired at different sample-to-sensor distances. This is achieved by incorporating a loose sparsity constraint as part of the iterative holographic object reconstruction. We demonstrate the success of this sparsity-based computational lens-less microscopy platform by imaging pathology slides of breast cancer tissue and Papanicolaou (Pap) smears.

Progressive simplification and transmission of building polygons based on triangle meshes

NASA Astrophysics Data System (ADS)

Li, Hongsheng; Wang, Yingjie; Guo, Qingsheng; Han, Jiafu

2010-11-01

Digital earth is a virtual representation of our planet and a data integration platform which aims at harnessing multisource, multi-resolution, multi-format spatial data. This paper introduces a research framework integrating progressive cartographic generalization and transmission of vector data. The progressive cartographic generalization provides multiple resolution data from coarse to fine as key scales and increments between them which is not available in traditional generalization framework. Based on the progressive simplification algorithm, the building polygons are triangulated into meshes and encoded according to the simplification sequence of two basic operations, edge collapse and vertex split. The map data at key scales and encoded increments between them are stored in a multi-resolution file. As the client submits requests to the server, the coarsest map is transmitted first and then the increments. After data decoding and mesh refinement the building polygons with more details will be visualized. Progressive generalization and transmission of building polygons is demonstrated in the paper.

Quality control of next-generation sequencing library through an integrative digital microfluidic platform.

PubMed

Thaitrong, Numrin; Kim, Hanyoup; Renzi, Ronald F; Bartsch, Michael S; Meagher, Robert J; Patel, Kamlesh D

2012-12-01

We have developed an automated quality control (QC) platform for next-generation sequencing (NGS) library characterization by integrating a droplet-based digital microfluidic (DMF) system with a capillary-based reagent delivery unit and a quantitative CE module. Using an in-plane capillary-DMF interface, a prepared sample droplet was actuated into position between the ground electrode and the inlet of the separation capillary to complete the circuit for an electrokinetic injection. Using a DNA ladder as an internal standard, the CE module with a compact LIF detector was capable of detecting dsDNA in the range of 5-100 pg/μL, suitable for the amount of DNA required by the Illumina Genome Analyzer sequencing platform. This DMF-CE platform consumes tenfold less sample volume than the current Agilent BioAnalyzer QC technique, preserving precious sample while providing necessary sensitivity and accuracy for optimal sequencing performance. The ability of this microfluidic system to validate NGS library preparation was demonstrated by examining the effects of limited-cycle PCR amplification on the size distribution and the yield of Illumina-compatible libraries, demonstrating that as few as ten cycles of PCR bias the size distribution of the library toward undesirable larger fragments. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

eSensor: an electrochemical detection-based DNA microarray technology enabling sample-to-answer molecular diagnostics

NASA Astrophysics Data System (ADS)

Liu, Robin H.; Longiaru, Mathew

2009-05-01

DNA microarrays are becoming a widespread tool used in life science and drug screening due to its many benefits of miniaturization and integration. Microarrays permit a highly multiplexed DNA analysis. Recently, the development of new detection methods and simplified methodologies has rapidly expanded the use of microarray technologies from predominantly gene expression analysis into the arena of diagnostics. Osmetech's eSensor® is an electrochemical detection platform based on a low-to- medium density DNA hybridization array on a cost-effective printed circuit board substrate. eSensor® has been cleared by FDA for Warfarin sensitivity test and Cystic Fibrosis Carrier Detection. Other genetic-based diagnostic and infectious disease detection tests are under development. The eSensor® platform eliminates the need for an expensive laser-based optical system and fluorescent reagents. It allows one to perform hybridization and detection in a single and small instrument without any fluidic processing and handling. Furthermore, the eSensor® platform is readily adaptable to on-chip sample-to-answer genetic analyses using microfluidics technology. The eSensor® platform provides a cost-effective solution to direct sample-to-answer genetic analysis, and thus have a potential impact in the fields of point-of-care genetic analysis, environmental testing, and biological warfare agent detection.

Species classifier choice is a key consideration when analysing low-complexity food microbiome data.

PubMed

Walsh, Aaron M; Crispie, Fiona; O'Sullivan, Orla; Finnegan, Laura; Claesson, Marcus J; Cotter, Paul D

2018-03-20

The use of shotgun metagenomics to analyse low-complexity microbial communities in foods has the potential to be of considerable fundamental and applied value. However, there is currently no consensus with respect to choice of species classification tool, platform, or sequencing depth. Here, we benchmarked the performances of three high-throughput short-read sequencing platforms, the Illumina MiSeq, NextSeq 500, and Ion Proton, for shotgun metagenomics of food microbiota. Briefly, we sequenced six kefir DNA samples and a mock community DNA sample, the latter constructed by evenly mixing genomic DNA from 13 food-related bacterial species. A variety of bioinformatic tools were used to analyse the data generated, and the effects of sequencing depth on these analyses were tested by randomly subsampling reads. Compositional analysis results were consistent between the platforms at divergent sequencing depths. However, we observed pronounced differences in the predictions from species classification tools. Indeed, PERMANOVA indicated that there was no significant differences between the compositional results generated by the different sequencers (p = 0.693, R 2  = 0.011), but there was a significant difference between the results predicted by the species classifiers (p = 0.01, R 2  = 0.127). The relative abundances predicted by the classifiers, apart from MetaPhlAn2, were apparently biased by reference genome sizes. Additionally, we observed varying false-positive rates among the classifiers. MetaPhlAn2 had the lowest false-positive rate, whereas SLIMM had the greatest false-positive rate. Strain-level analysis results were also similar across platforms. Each platform correctly identified the strains present in the mock community, but accuracy was improved slightly with greater sequencing depth. Notably, PanPhlAn detected the dominant strains in each kefir sample above 500,000 reads per sample. Again, the outputs from functional profiling analysis using SUPER-FOCUS were generally accordant between the platforms at different sequencing depths. Finally, and expectedly, metagenome assembly completeness was significantly lower on the MiSeq than either on the NextSeq (p = 0.03) or the Proton (p = 0.011), and it improved with increased sequencing depth. Our results demonstrate a remarkable similarity in the results generated by the three sequencing platforms at different sequencing depths, and, in fact, the choice of bioinformatics methodology had a more evident impact on results than the choice of sequencer did.

Predicting Droplet Formation on Centrifugal Microfluidic Platforms

NASA Astrophysics Data System (ADS)

Moebius, Jacob Alfred

Centrifugal microfluidics is a widely known research tool for biological sample and water quality analysis. Currently, the standard equipment used for such diagnostic applications include slow, bulky machines controlled by multiple operators. These machines can be condensed into a smaller, faster benchtop sample-to-answer system. Sample processing is an important step taken to extract, isolate, and convert biological factors, such as nucleic acids or proteins, from a raw sample to an analyzable solution. Volume definition is one such step. The focus of this thesis is the development of a model predicting monodispersed droplet formation and the application of droplets as a technique for volume definition. First, a background of droplet microfluidic platforms is presented, along with current biological analysis technologies and the advantages of integrating such technologies onto microfluidic platforms. Second, background and theories of centrifugal microfluidics is given, followed by theories relevant to droplet emulsions. Third, fabrication techniques for centrifugal microfluidic designs are discussed. Finally, the development of a model for predicting droplet formation on the centrifugal microfluidic platform are presented for the rest of the thesis. Predicting droplet formation analytically based on the volumetric flow rates of the continuous and dispersed phases, the ratios of these two flow rates, and the interfacial tension between the continuous and dispersed phases presented many challenges, which will be discussed in this work. Experimental validation was completed using continuous phase solutions of different interfacial tensions. To conclude, prospective applications are discussed with expected challenges.

The Organization of European Cancer Institute Pathobiology Working Group and its support of European biobanking infrastructures for translational cancer research.

PubMed

Riegman, Peter H J; de Jong, Bas W D; Llombart-Bosch, Antonio

2010-04-01

Today's translational cancer research increasingly depends on international multi-center studies. Biobanking infrastructure or comprehensive sample exchange platforms to enable networking of clinical cancer biobanks are instrumental to facilitate communication, uniform sample quality, and rules for exchange. The Organization of European Cancer Institutes (OECI) Pathobiology Working Group supports European biobanking infrastructure by maintaining the OECI-TuBaFrost exchange platform and organizing regular meetings. This platform originated from a European Commission project and is updated with knowledge from ongoing and new biobanking projects. This overview describes how European biobanking projects that have a large impact on clinical biobanking, including EuroBoNeT, SPIDIA, and BBMRI, contribute to the update of the OECI-TuBaFrost exchange platform. Combining the results of these European projects enabled the creation of an open (upon valid registration only) catalogue view of cancer biobanks and their available samples to initiate research projects. In addition, closed environments supporting active projects could be developed together with the latest views on quality, access rules, ethics, and law. With these contributions, the OECI Pathobiology Working Group contributes to and stimulates a professional attitude within biobanks at the European comprehensive cancer centers. Improving the fundamentals of cancer sample exchange in Europe stimulates the performance of large multi-center studies, resulting in experiments with the desired statistical significance outcome. With this approach, future innovation in cancer patient care can be realized faster and more reliably.

ART-ML: a new markup language for modelling and representation of biological processes in cardiovascular diseases.

PubMed

Karvounis, E C; Exarchos, T P; Fotiou, E; Sakellarios, A I; Iliopoulou, D; Koutsouris, D; Fotiadis, D I

2013-01-01

With an ever increasing number of biological models available on the internet, a standardized modelling framework is required to allow information to be accessed and visualized. In this paper we propose a novel Extensible Markup Language (XML) based format called ART-ML that aims at supporting the interoperability and the reuse of models of geometry, blood flow, plaque progression and stent modelling, exported by any cardiovascular disease modelling software. ART-ML has been developed and tested using ARTool. ARTool is a platform for the automatic processing of various image modalities of coronary and carotid arteries. The images and their content are fused to develop morphological models of the arteries in 3D representations. All the above described procedures integrate disparate data formats, protocols and tools. ART-ML proposes a representation way, expanding ARTool, for interpretability of the individual resources, creating a standard unified model for the description of data and, consequently, a format for their exchange and representation that is machine independent. More specifically, ARTool platform incorporates efficient algorithms which are able to perform blood flow simulations and atherosclerotic plaque evolution modelling. Integration of data layers between different modules within ARTool are based upon the interchange of information included in the ART-ML model repository. ART-ML provides a markup representation that enables the representation and management of embedded models within the cardiovascular disease modelling platform, the storage and interchange of well-defined information. The corresponding ART-ML model incorporates all relevant information regarding geometry, blood flow, plaque progression and stent modelling procedures. All created models are stored in a model repository database which is accessible to the research community using efficient web interfaces, enabling the interoperability of any cardiovascular disease modelling software models. ART-ML can be used as a reference ML model in multiscale simulations of plaque formation and progression, incorporating all scales of the biological processes.

Astrophysical Computation in Research, the Classroom and Beyond

NASA Astrophysics Data System (ADS)

Frank, Adam

2009-03-01

In this talk I review progress in the use of simulations as a tool for astronomical research, for education and public outreach. The talk will include the basic elements of numerical simulations as well as advances in algorithms which have led to recent dramatic progress such as the use of Adaptive Mesh Refinement methods. The scientific focus of the talk will be star formation jets and outflows while the educational emphasis will be on the use of advanced platforms for simulation based learning in lecture and integrated homework. Learning modules for science outreach websites such as DISCOVER magazine will also be highlighted.

Highly sensitive and multiplexed platforms for allergy diagnostics

NASA Astrophysics Data System (ADS)

Monroe, Margo R.

Allergy is a disorder of the immune system caused by an immune response to otherwise harmless environmental allergens. Currently 20% of the US population is allergic and 90% of pediatric patients and 60% of adult patients with asthma have allergies. These percentages have increased by 18.5% in the past decade, with predicted similar trends for the future. Here we design sensitive, multiplexed platforms to detect allergen-specific IgE using the Interferometric Reflectance Imaging Sensor (IRIS) for various clinical settings. A microarray platform for allergy diagnosis allows for testing of specific IgE sensitivity to a multitude of allergens, while requiring only small volumes of patient blood sample. However, conventional fluorescent microarray technology is limited by i) the variation of probe immobilization, which hinders the ability to make quantitative, assertive, and statistically relevant conclusions necessary in immunodiagnostics and ii) the use of fluorophore labels, which is not suitable for some clinical applications due to the tendency of fluorophores to stick to blood particulates and require daily calibration methods. This calibrated fluorescence enhancement (CaFE) method integrates the low magnification modality of IRIS with enhanced fluorescence sensing in order to directly correlate immobilized probe (major allergens) density to allergen-specific IgE in patient serum. However, this platform only operates in processed serum samples, which is not ideal for point of care testing. Thus, a high magnification modality of IRIS was adapted as an alternative allergy diagnostic platform to automatically discriminate and size single nanoparticles bound to specific IgE in unprocessed, characterized human blood and serum samples. These features make IRIS an ideal candidate for clinical and diagnostic applications, such a POC testing. The high magnification (nanoparticle counting) modality in conjunction with low magnification of IRIS in a combined instrument offers four significant advantages compared to existing sensing technologies: IRIS i) corrects for any variation in probe immobilization, ii) detects proteins from attomolar to nanomolar concentrations in unprocessed biological samples, iii) unambiguously discriminates nanoparticles tags on a robust and physically large sensor area, iv) detects protein targets with conjugated nanoparticle tags (~40nm diameter), which minimally affect assay kinetics compared to conventional microparticle tagging methods, and v) utilizes components that make the instrument inexpensive, robust, and portable. This platform was successfully validated on patient serum and whole blood samples with documented allergy profiles (ImmunoCAPRTM, ThermoFisher Scientific).

Portable life support for instrumentation of an offshore platform

NASA Technical Reports Server (NTRS)

Mull, M. M.; Coffin, C. L.

1972-01-01

A compressor was used to supply air through a nylon hose to the offshore platform field engineer working at the bottom of the piling. Air quality in the pile was sampled periodically for carbon dioxide, carbon monoxide, hydrogen sulfide, and combustible gases by an universal tester and an explosion meter.

Fluorescent microarray for multiplexed quantification of environmental contaminants in seawater samples

USDA-ARS?s Scientific Manuscript database

The development of a fluorescent multiplexed microarray platform able to detect and quantify a wide variety of pollutants in seawater is reported. The microarray platform has been manufactured by spotting 6 different bioconjugate competitors and it uses a cocktail of 6 monoclonal and polyclonal anti...

MICROARRAY QUALITY CONTROL PROJECT: A COMPREHENSIVE GENE EXPRESSION TECHNOLOGY SURVEY DEMONSTRATES MEASURABLE CONSISTENCY AND CONCORDANT RESULTS BETWEEN PLATFORMS

EPA Science Inventory

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, h...

Centrifugal microfluidic platform for ultrasensitive detection of botulinum toxin

DOE PAGES

Koh, Chung -Yan; Schaff, Ulrich Y.; Sandstone Diagnostics, Livermore, CA; ...

2014-12-18

In this study, we present an innovative centrifugal microfluidic immunoassay platform (SpinDx) to address the urgent biodefense and public health need for ultrasensitive point-of-care/incident detection of botulinum toxin. The simple, sample-to-answer centrifugal microfluidic immunoassay approach is based on binding of toxins to antibody-laden capture particles followed by sedimentation of the particles through a density-media in a microfluidic disk and quantification by laser-induced fluorescence. A blind, head-to-head comparison study of SpinDx versus the gold-standard mouse bioassay demonstrates 100-fold improvement in sensitivity (limit of detection = 0.09 pg/mL), while achieving total sample-to-answer time of <30 min with 2-μL required volume of themore » unprocessed sample. We further demonstrate quantification of botulinum toxin in both exogeneous (human blood and serum spiked with toxins) and endogeneous (serum from mice intoxicated via oral, intranasal, and intravenous routes) samples. SpinDx can analyze, without any sample preparation, multiple sample types including whole blood, serum, and food. It is readily expandable to additional analytes as the assay reagents (i.e., the capture beads and detection antibodies) are disconnected from the disk architecture and the reader, facilitating rapid development of new assays. SpinDx can also serve as a general-purpose immunoassay platform applicable to diagnosis of other conditions and diseases.« less

Integrated Spintronic Platforms for Biomolecular Recognition Detection

NASA Astrophysics Data System (ADS)

Martins, V. C.; Cardoso, F. A.; Loureiro, J.; Mercier, M.; Germano, J.; Cardoso, S.; Ferreira, R.; Fonseca, L. P.; Sousa, L.; Piedade, M. S.; Freitas, P. P.

2008-06-01

This paper covers recent developments in magnetoresistive based biochip platforms fabricated at INESC-MN, and their application to the detection and quantification of pathogenic waterborn microorganisms in water samples for human consumption. Such platforms are intended to give response to the increasing concern related to microbial contaminated water sources. The presented results concern the development of biological active DNA chips and protein chips and the demonstration of the detection capability of the present platforms. Two platforms are described, one including spintronic sensors only (spin-valve based or magnetic tunnel junction based), and the other, a fully scalable platform where each probe site consists of a MTJ in series with a thin film diode (TFD). Two microfluidic systems are described, for cell separation and concentration, and finally, the read out and control integrated electronics are described, allowing the realization of bioassays with a portable point of care unit. The present platforms already allow the detection of complementary biomolecular target recognition with 1 pM concentration.

Point-of-Care Quantitative Measure of Glucose-6-Phosphate Dehydrogenase Enzyme Deficiency.

PubMed

Bhutani, Vinod K; Kaplan, Michael; Glader, Bertil; Cotten, Michael; Kleinert, Jairus; Pamula, Vamsee

2015-11-01

Widespread newborn screening on a point-of-care basis could prevent bilirubin neurotoxicity in newborns with glucose-6-phosphate dehydrogenase (G6PD) deficiency. We evaluated a quantitative G6PD assay on a digital microfluidic platform by comparing its performance with standard clinical methods. G6PD activity was measured quantitatively by using digital microfluidic fluorescence and the gold standard fluorescence biochemical test on a convenience sample of 98 discarded blood samples. Twenty-four samples were designated as G6PD deficient. Mean ± SD G6PD activity for normal samples using the digital microfluidic method and the standard method, respectively, was 9.7 ± 2.8 and 11.1 ± 3.0 U/g hemoglobin (Hb), respectively; for G6PD-deficient samples, it was 0.8 ± 0.7 and 1.4 ± 0.9 U/g Hb. Bland-Altman analysis determined a mean difference of -0.96 ± 1.8 U/g Hb between the digital microfluidic fluorescence results and the standard biochemical test results. The lower and upper limits for the digital microfluidic platform were 4.5 to 19.5 U/g Hb for normal samples and 0.2 to 3.7 U/g Hb for G6PD-deficient samples. The lower and upper limits for the Stanford method were 5.5 to 20.7 U/g Hb for normal samples and 0.1 to 2.8 U/g Hb for G6PD-deficient samples. The measured activity discriminated between G6PD-deficient samples and normal samples with no overlap. Pending further validation, a digital microfluidics platform could be an accurate point-of-care screening tool for rapid newborn G6PD screening. Copyright © 2015 by the American Academy of Pediatrics.

Real-time label-free quantitative fluorescence microscopy-based detection of ATP using a tunable fluorescent nano-aptasensor platform

NASA Astrophysics Data System (ADS)

Shrivastava, Sajal; Sohn, Il-Yung; Son, Young-Min; Lee, Won-Il; Lee, Nae-Eung

2015-11-01

Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules.Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr05839b

ProteoCloud: a full-featured open source proteomics cloud computing pipeline.

PubMed

Muth, Thilo; Peters, Julian; Blackburn, Jonathan; Rapp, Erdmann; Martens, Lennart

2013-08-02

We here present the ProteoCloud pipeline, a freely available, full-featured cloud-based platform to perform computationally intensive, exhaustive searches in a cloud environment using five different peptide identification algorithms. ProteoCloud is entirely open source, and is built around an easy to use and cross-platform software client with a rich graphical user interface. This client allows full control of the number of cloud instances to initiate and of the spectra to assign for identification. It also enables the user to track progress, and to visualize and interpret the results in detail. Source code, binaries and documentation are all available at http://proteocloud.googlecode.com. Copyright © 2012 Elsevier B.V. All rights reserved.

Analysis and design of energy monitoring platform for smart city

NASA Astrophysics Data System (ADS)

Wang, Hong-xia

2016-09-01

The development and utilization of energy has greatly promoted the development and progress of human society. It is the basic material foundation for human survival. City running is bound to consume energy inevitably, but it also brings a lot of waste discharge. In order to speed up the process of smart city, improve the efficiency of energy saving and emission reduction work, maintain the green and livable environment, a comprehensive management platform of energy monitoring for government departments is constructed based on cloud computing technology and 3-tier architecture in this paper. It is assumed that the system will provide scientific guidance for the environment management and decision making in smart city.

Microcantilever-based platforms as biosensing tools.

PubMed

Alvarez, Mar; Lechuga, Laura M

2010-05-01

The fast and progressive growth of the biotechnology and pharmaceutical fields forces the development of new and powerful sensing techniques for process optimization and detection of biomolecules at very low concentrations. During the last years, the simplest MEMS structures, i.e. microcantilevers, have become an emerging and promising technology for biosensing applications, due to their small size, fast response, high sensitivity and their compatible integration into "lab-on-a-chip" devices. This article provides an overview of some of the most interesting bio-detections carried out during the last 2-3 years with the microcantilever-based platforms, which highlight the continuous expansion of this kind of sensor in the medical diagnosis field, reaching limits of detection at the single molecule level.

The current status of alternatives to animal testing and predictive toxicology methods using liver microfluidic biochips.

PubMed

Prot, Jean Matthieu; Leclerc, Eric

2012-06-01

In this paper, we will consider new in vitro cell culture platforms and the progress made, based on the microfluidic liver biochips dedicated to pharmacological and toxicological studies. Particular emphasis will be given to recent developments in the microfluidic tools dedicated to cell culture (more particularly liver cell culture), in silico opportunities for Physiologically Based PharmacoKinetic (PBPK) modelling, the challenge of the mechanistic interpretations offered by the approaches resulting from "multi-omics" data (transcriptomics, proteomics, metabolomics, cytomics) and imaging microfluidic platforms. Finally, we will discuss the critical features regarding microfabrication, design and materials, and cell functionality as the key points for the future development of new microfluidic liver biochips.

[Current situation and prospect of breast cancer liquid biopsy].

PubMed

Zhou, B; Xin, L; Xu, L; Ye, J M; Liu, Y H

2018-02-01

Liquid biopsy is a diagnostic approach by analyzing body fluid samples. Peripheral blood is the most common sample. Urine, saliva, pleural effusion and ascites are also used. Now liquid biopsy is mainly used in the area of neoplasm diagnosis and treatment. Compared with traditional tissue biopsy, liquid biopsy is minimally invasive, convenient to sample and easy to repeat. Liquid biopsy mainly includes circulating tumor cells and circulating tumor DNA (ctDNA) detection. Detection of ctDNA requires sensitive and accurate methods. The progression of next-generation sequencing (NGS) and digital PCR promote the process of studies in ctDNA. In 2016, Nature published the result of whole-genome sequencing study of breast cancer. The study found 1 628 mutations of 93 protein-coding genes which may be driver mutations of breast cancer. The result of this study provided a new platform for breast cancer ctDNA studies. In recent years, there were many studies using ctDNA detection to monitor therapeutic effect and guide treatment. NGS is a promising technique in accessing genetic information and guiding targeted therapy. It must be emphasized that ctDNA detection using NGS is still at research stage. It is important to standardize ctDNA detection technique and perform prospective clinical researches. The time is not ripe for using ctDNA detection to guide large-scale breast cancer clinical practice at present.

Mechanistic and Technical Challenges in Studying the Human Microbiome and Cancer Epidemiology.

PubMed

Verma, Mukesh

2017-04-01

This article reviews the significance of the microbiome in cancer epidemiology, mechanistic and technical challenges in the field, and characterization of the microbiome in different tumor types to identify biomarkers of risk, progression, and prognosis. Publications on the microbiome and cancer epidemiology were reviewed to analyze sample collection and processing, microbiome taxa characterization by 16S ribosomal RNA sequencing, and microbiome metabolite characterization (metabotyping) by nuclear magnetic resonance and mass spectrometry. The analysis identified methodology types, research design, sample types, and issues in integrating data from different platforms. Aerodigestive cancer epidemiology studies conducted by different groups demonstrated the significance of microbiome information in developing approaches to improve health. Challenges exist in sample preparation and processing (eg, standardization of methods for collection and analysis). These challenges relate to technology, data integration from "omics" studies, inherent bias in primer selection during 16S ribosomal RNA sequencing, the need for large consortia with well-characterized biospecimens, cause and effect issues, resilience of microbiota to exposure events (requires longitudinal studies), and expanding studies for fungal and viral diversity (most studies used bacterial 16S ribosomal RNA sequencing for microbiota characterization). Despite these challenges, microbiome and cancer epidemiology studies are significant and may facilitate cancer risk assessment, diagnosis, and prognosis. In the future, clinical trials likely will use microbiota modifications to improve the efficacy of existing treatments.

Mechanistic and Technical Challenges in Studying the Human Microbiome and Cancer Epidemiology

PubMed Central

2016-01-01

This article reviews the significance of the microbiome in cancer epidemiology, mechanistic and technical challenges in the field, and characterization of the microbiome in different tumor types to identify biomarkers of risk, progression, and prognosis. Publications on the microbiome and cancer epidemiology were reviewed to analyze sample collection and processing, microbiome taxa characterization by 16S ribosomal RNA sequencing, and microbiome metabolite characterization (metabotyping) by nuclear magnetic resonance and mass spectrometry. The analysis identified methodology types, research design, sample types, and issues in integrating data from different platforms. Aerodigestive cancer epidemiology studies conducted by different groups demonstrated the significance of microbiome information in developing approaches to improve health. Challenges exist in sample preparation and processing (eg, standardization of methods for collection and analysis). These challenges relate to technology, data integration from “omics” studies, inherent bias in primer selection during 16S ribosomal RNA sequencing, the need for large consortia with well-characterized biospecimens, cause and effect issues, resilience of microbiota to exposure events (requires longitudinal studies), and expanding studies for fungal and viral diversity (most studies used bacterial 16S ribosomal RNA sequencing for microbiota characterization). Despite these challenges, microbiome and cancer epidemiology studies are significant and may facilitate cancer risk assessment, diagnosis, and prognosis. In the future, clinical trials likely will use microbiota modifications to improve the efficacy of existing treatments. PMID:27121074

Self-digitization microfluidic chip for absolute quantification of mRNA in single cells.

PubMed

Thompson, Alison M; Gansen, Alexander; Paguirigan, Amy L; Kreutz, Jason E; Radich, Jerald P; Chiu, Daniel T

2014-12-16

Quantification of mRNA in single cells provides direct insight into how intercellular heterogeneity plays a role in disease progression and outcomes. Quantitative polymerase chain reaction (qPCR), the current gold standard for evaluating gene expression, is insufficient for providing absolute measurement of single-cell mRNA transcript abundance. Challenges include difficulties in handling small sample volumes and the high variability in measurements. Microfluidic digital PCR provides far better sensitivity for minute quantities of genetic material, but the typical format of this assay does not allow for counting of the absolute number of mRNA transcripts samples taken from single cells. Furthermore, a large fraction of the sample is often lost during sample handling in microfluidic digital PCR. Here, we report the absolute quantification of single-cell mRNA transcripts by digital, one-step reverse transcription PCR in a simple microfluidic array device called the self-digitization (SD) chip. By performing the reverse transcription step in digitized volumes, we find that the assay exhibits a linear signal across a wide range of total RNA concentrations and agrees well with standard curve qPCR. The SD chip is found to digitize a high percentage (86.7%) of the sample for single-cell experiments. Moreover, quantification of transferrin receptor mRNA in single cells agrees well with single-molecule fluorescence in situ hybridization experiments. The SD platform for absolute quantification of single-cell mRNA can be optimized for other genes and may be useful as an independent control method for the validation of mRNA quantification techniques.

Lensfree fluorescent on-chip imaging of transgenic Caenorhabditis elegans over an ultra-wide field-of-view.

PubMed

Coskun, Ahmet F; Sencan, Ikbal; Su, Ting-Wei; Ozcan, Aydogan

2011-01-06

We demonstrate lensfree on-chip fluorescent imaging of transgenic Caenorhabditis elegans (C. elegans) over an ultra-wide field-of-view (FOV) of e.g., >2-8 cm(2) with a spatial resolution of ∼10 µm. This is the first time that a lensfree on-chip platform has successfully imaged fluorescent C. elegans samples. In our wide-field lensfree imaging platform, the transgenic samples are excited using a prism interface from the side, where the pump light is rejected through total internal reflection occurring at the bottom facet of the substrate. The emitted fluorescent signal from C. elegans samples is then recorded on a large area opto-electronic sensor-array over an FOV of e.g., >2-8 cm(2), without the use of any lenses, thin-film interference filters or mechanical scanners. Because fluorescent emission rapidly diverges, such lensfree fluorescent images recorded on a chip look blurred due to broad point-spread-function of our platform. To combat this resolution challenge, we use a compressive sampling algorithm to uniquely decode the recorded lensfree fluorescent patterns into higher resolution images, demonstrating ∼10 µm resolution. We tested the efficacy of this compressive decoding approach with different types of opto-electronic sensors to achieve a similar resolution level, independent of the imaging chip. We further demonstrate that this wide FOV lensfree fluorescent imaging platform can also perform sequential bright-field imaging of the same samples using partially-coherent lensfree digital in-line holography that is coupled from the top facet of the same prism used in fluorescent excitation. This unique combination permits ultra-wide field dual-mode imaging of C. elegans on a chip which could especially provide a useful tool for high-throughput screening applications in biomedical research.

Lensfree Fluorescent On-Chip Imaging of Transgenic Caenorhabditis elegans Over an Ultra-Wide Field-of-View

PubMed Central

Ozcan, Aydogan

2011-01-01

We demonstrate lensfree on-chip fluorescent imaging of transgenic Caenorhabditis elegans (C. elegans) over an ultra-wide field-of-view (FOV) of e.g., >2–8 cm2 with a spatial resolution of ∼10µm. This is the first time that a lensfree on-chip platform has successfully imaged fluorescent C. elegans samples. In our wide-field lensfree imaging platform, the transgenic samples are excited using a prism interface from the side, where the pump light is rejected through total internal reflection occurring at the bottom facet of the substrate. The emitted fluorescent signal from C. elegans samples is then recorded on a large area opto-electronic sensor-array over an FOV of e.g., >2–8 cm2, without the use of any lenses, thin-film interference filters or mechanical scanners. Because fluorescent emission rapidly diverges, such lensfree fluorescent images recorded on a chip look blurred due to broad point-spread-function of our platform. To combat this resolution challenge, we use a compressive sampling algorithm to uniquely decode the recorded lensfree fluorescent patterns into higher resolution images, demonstrating ∼10 µm resolution. We tested the efficacy of this compressive decoding approach with different types of opto-electronic sensors to achieve a similar resolution level, independent of the imaging chip. We further demonstrate that this wide FOV lensfree fluorescent imaging platform can also perform sequential bright-field imaging of the same samples using partially-coherent lensfree digital in-line holography that is coupled from the top facet of the same prism used in fluorescent excitation. This unique combination permits ultra-wide field dual-mode imaging of C. elegans on a chip which could especially provide a useful tool for high-throughput screening applications in biomedical research. PMID:21253611

A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments.

PubMed

Robinson, Mark D; De Souza, David P; Keen, Woon Wai; Saunders, Eleanor C; McConville, Malcolm J; Speed, Terence P; Likić, Vladimir A

2007-10-29

Gas chromatography-mass spectrometry (GC-MS) is a robust platform for the profiling of certain classes of small molecules in biological samples. When multiple samples are profiled, including replicates of the same sample and/or different sample states, one needs to account for retention time drifts between experiments. This can be achieved either by the alignment of chromatographic profiles prior to peak detection, or by matching signal peaks after they have been extracted from chromatogram data matrices. Automated retention time correction is particularly important in non-targeted profiling studies. A new approach for matching signal peaks based on dynamic programming is presented. The proposed approach relies on both peak retention times and mass spectra. The alignment of more than two peak lists involves three steps: (1) all possible pairs of peak lists are aligned, and similarity of each pair of peak lists is estimated; (2) the guide tree is built based on the similarity between the peak lists; (3) peak lists are progressively aligned starting with the two most similar peak lists, following the guide tree until all peak lists are exhausted. When two or more experiments are performed on different sample states and each consisting of multiple replicates, peak lists within each set of replicate experiments are aligned first (within-state alignment), and subsequently the resulting alignments are aligned themselves (between-state alignment). When more than two sets of replicate experiments are present, the between-state alignment also employs the guide tree. We demonstrate the usefulness of this approach on GC-MS metabolic profiling experiments acquired on wild-type and mutant Leishmania mexicana parasites. We propose a progressive method to match signal peaks across multiple GC-MS experiments based on dynamic programming. A sensitive peak similarity function is proposed to balance peak retention time and peak mass spectra similarities. This approach can produce the optimal alignment between an arbitrary number of peak lists, and models explicitly within-state and between-state peak alignment. The accuracy of the proposed method was close to the accuracy of manually-curated peak matching, which required tens of man-hours for the analyzed data sets. The proposed approach may offer significant advantages for processing of high-throughput metabolomics data, especially when large numbers of experimental replicates and multiple sample states are analyzed.

Semiautomated confocal imaging of fungal pathogenesis on plants: Microscopic analysis of macroscopic specimens.

PubMed

Minker, Katharine R; Biedrzycki, Meredith L; Kolagunda, Abhishek; Rhein, Stephen; Perina, Fabiano J; Jacobs, Samuel S; Moore, Michael; Jamann, Tiffany M; Yang, Qin; Nelson, Rebecca; Balint-Kurti, Peter; Kambhamettu, Chandra; Wisser, Randall J; Caplan, Jeffrey L

2018-02-01

The study of phenotypic variation in plant pathogenesis provides fundamental information about the nature of disease resistance. Cellular mechanisms that alter pathogenesis can be elucidated with confocal microscopy; however, systematic phenotyping platforms-from sample processing to image analysis-to investigate this do not exist. We have developed a platform for 3D phenotyping of cellular features underlying variation in disease development by fluorescence-specific resolution of host and pathogen interactions across time (4D). A confocal microscopy phenotyping platform compatible with different maize-fungal pathosystems (fungi: Setosphaeria turcica, Cochliobolus heterostrophus, and Cercospora zeae-maydis) was developed. Protocols and techniques were standardized for sample fixation, optical clearing, species-specific combinatorial fluorescence staining, multisample imaging, and image processing for investigation at the macroscale. The sample preparation methods presented here overcome challenges to fluorescence imaging such as specimen thickness and topography as well as physiological characteristics of the samples such as tissue autofluorescence and presence of cuticle. The resulting imaging techniques provide interesting qualitative and quantitative information not possible with conventional light or electron 2D imaging. Microsc. Res. Tech., 81:141-152, 2018. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Handbook of Research on Emerging Priorities and Trends in Distance Education: Communication, Pedagogy, and Technology

ERIC Educational Resources Information Center

Yuzer, T. Volkan, Ed.; Eby, Gulsun, Ed.

2014-01-01

With the rise of distance education in the post-modern world, progressive research on the best methods, tools, and technologies in the field is necessary to continue to take advantage of the pedagogical opportunities and improvements offered through remote learning platforms. The "Handbook of Research on Emerging Priorities and Trends in…

A Framework for the Design of Computer-Assisted Simulation Training for Complex Police Situations

ERIC Educational Resources Information Center

Söderström, Tor; Åström, Jan; Anderson, Greg; Bowles, Ron

2014-01-01

Purpose: The purpose of this paper is to report progress concerning the design of a computer-assisted simulation training (CAST) platform for developing decision-making skills in police students. The overarching aim is to outline a theoretical framework for the design of CAST to facilitate police students' development of search techniques in…

Gaming as a Platform for the Development of Innovative Problem-Based Learning Opportunities

ERIC Educational Resources Information Center

Echeverri, J. Felipe; Sadler, Troy D.

2011-01-01

The state of education in the United States, particularly in the areas of science, mathematics and technology, has been a consistent source of concern since at least the early 1980s when student performance on the 1986 National Assessment of Educational Progress (NAEP) revealed that science proficiency was lower than comparable measures from the…

Rapid, portable, multiplexed detection of bacterial pathogens directly from clinical sample matrices

DOE PAGES

Phaneuf, Christopher R.; Mangadu, Betty Lou Bosano; Piccini, Matthew E.; ...

2016-09-23

Enteric and diarrheal diseases are a major cause of childhood illness and death in countries with developing economies. Each year, more than half of a million children under the age of five die from these diseases. We have developed a portable, microfluidic platform capable of simultaneous, multiplexed detection of several of the bacterial pathogens that cause these diseases. Furthermore, this platform can perform fast, sensitive immunoassays directly from relevant, complex clinical matrices such as stool without extensive sample cleanup or preparation. Using only 1 µL of sample per assay, we demonstrate simultaneous multiplexed detection of four bacterial pathogens implicated inmore » diarrheal and enteric diseases in less than 20 min.« less

Rapid, portable, multiplexed detection of bacterial pathogens directly from clinical sample matrices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Phaneuf, Christopher R.; Mangadu, Betty Lou Bosano; Piccini, Matthew E.

Enteric and diarrheal diseases are a major cause of childhood illness and death in countries with developing economies. Each year, more than half of a million children under the age of five die from these diseases. We have developed a portable, microfluidic platform capable of simultaneous, multiplexed detection of several of the bacterial pathogens that cause these diseases. Furthermore, this platform can perform fast, sensitive immunoassays directly from relevant, complex clinical matrices such as stool without extensive sample cleanup or preparation. Using only 1 µL of sample per assay, we demonstrate simultaneous multiplexed detection of four bacterial pathogens implicated inmore » diarrheal and enteric diseases in less than 20 min.« less

Micro-RNAs as diagnostic or prognostic markers in human epithelial malignancies

PubMed Central

2011-01-01

Micro-RNAs (miRs) are important regulators of mRNA and protein expression; the ability of miR expression profilings to distinguish different cancer types and classify their sub-types has been well-described. They also represent a novel biological entity with potential value as tumour biomarkers, which can improve diagnosis, prognosis, and monitoring of treatment response for human cancers. This endeavour has been greatly facilitated by the stability of miRs in formalin-fixed paraffin-embedded (FFPE) tissues, and their detection in circulation. This review will summarize some of the key dysregulated miRs described to date in human epithelial malignancies, and their potential value as molecular bio-markers in FFPE tissues and blood samples. There remain many challenges in this domain, however, with the evolution of different platforms, the complexities of normalizing miR profiling data, and the importance of evaluating sufficiently-powered training and validation cohorts. Nonetheless, well-conducted miR profiling studies should contribute important insights into the molecular aberrations driving human cancer development and progression. PMID:22128797

Exploring the Kibble-Zurek mechanism with homogeneous Bose gases

NASA Astrophysics Data System (ADS)

Beugnon, Jérôme; Navon, Nir

2017-01-01

Out-of-equilibrium phenomena are a subject of considerable interest in many fields of physics. Ultracold quantum gases, which are extremely clean, well-isolated and highly controllable systems, offer ideal platforms to investigate this topic. The recent progress in tailoring trapping potentials now allows the experimental production of homogeneous samples in custom geometries, which is a key advance for studies of the emergence of coherence in interacting quantum systems. Here we review recent experiments in which temperature quenches have been performed across the Bose-Einstein condensation phase transition in an annular geometry and in homogeneous 3D and quasi-2D gases. Combined, these experiments comprehensively explore and validate the Kibble-Zurek (KZ) scenario through complementary measurements of correlation functions and density of topological defects. They allow the measurement of KZ scaling laws, the direct confirmation of the ‘freeze-out’ hypothesis that underlies the KZ theory, and the extraction of critical exponents of the Bose-Einstein condensation transition.

Amyloid Beta and Tau as Alzheimer's Disease Blood Biomarkers: Promise From New Technologies.

PubMed

Lue, Lih-Fen; Guerra, Andre; Walker, Douglas G

2017-07-01

The utility of the levels of amyloid beta (Aβ) peptide and tau in blood for diagnosis, drug development, and assessment of clinical trials for Alzheimer's disease (AD) has not been established. The lack of availability of ultra-sensitive assays is one critical issue that has impeded progress. The levels of Aβ species and tau in plasma and serum are much lower than levels in cerebrospinal fluid. Furthermore, plasma or serum contain high levels of assay-interfering factors, resulting in difficulties in the commonly used singulex or multiplex ELISA platforms. In this review, we focus on two modern immune-complex-based technologies that show promise to advance this field. These innovative technologies are immunomagnetic reduction technology and single molecule array technology. We describe the technologies and discuss the published studies using these technologies. Currently, the potential of utilizing these technologies to advance Aβ and tau as blood-based biomarkers for AD requires further validation using already collected large sets of samples, as well as new cohorts and population-based longitudinal studies.

Consistency of biological networks inferred from microarray and sequencing data.

PubMed

Vinciotti, Veronica; Wit, Ernst C; Jansen, Rick; de Geus, Eco J C N; Penninx, Brenda W J H; Boomsma, Dorret I; 't Hoen, Peter A C

2016-06-24

Sparse Gaussian graphical models are popular for inferring biological networks, such as gene regulatory networks. In this paper, we investigate the consistency of these models across different data platforms, such as microarray and next generation sequencing, on the basis of a rich dataset containing samples that are profiled under both techniques as well as a large set of independent samples. Our analysis shows that individual node variances can have a remarkable effect on the connectivity of the resulting network. Their inconsistency across platforms and the fact that the variability level of a node may not be linked to its regulatory role mean that, failing to scale the data prior to the network analysis, leads to networks that are not reproducible across different platforms and that may be misleading. Moreover, we show how the reproducibility of networks across different platforms is significantly higher if networks are summarised in terms of enrichment amongst functional groups of interest, such as pathways, rather than at the level of individual edges. Careful pre-processing of transcriptional data and summaries of networks beyond individual edges can improve the consistency of network inference across platforms. However, caution is needed at this stage in the (over)interpretation of gene regulatory networks inferred from biological data.

A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry.

PubMed

Li, Xiao-jun; Yi, Eugene C; Kemp, Christopher J; Zhang, Hui; Aebersold, Ruedi

2005-09-01

There is an increasing interest in the quantitative proteomic measurement of the protein contents of substantially similar biological samples, e.g. for the analysis of cellular response to perturbations over time or for the discovery of protein biomarkers from clinical samples. Technical limitations of current proteomic platforms such as limited reproducibility and low throughput make this a challenging task. A new LC-MS-based platform is able to generate complex peptide patterns from the analysis of proteolyzed protein samples at high throughput and represents a promising approach for quantitative proteomics. A crucial component of the LC-MS approach is the accurate evaluation of the abundance of detected peptides over many samples and the identification of peptide features that can stratify samples with respect to their genetic, physiological, or environmental origins. We present here a new software suite, SpecArray, that generates a peptide versus sample array from a set of LC-MS data. A peptide array stores the relative abundance of thousands of peptide features in many samples and is in a format identical to that of a gene expression microarray. A peptide array can be subjected to an unsupervised clustering analysis to stratify samples or to a discriminant analysis to identify discriminatory peptide features. We applied the SpecArray to analyze two sets of LC-MS data: one was from four repeat LC-MS analyses of the same glycopeptide sample, and another was from LC-MS analysis of serum samples of five male and five female mice. We demonstrate through these two study cases that the SpecArray software suite can serve as an effective software platform in the LC-MS approach for quantitative proteomics.

Satellite Image Classification of Building Damages Using Airborne and Satellite Image Samples in a Deep Learning Approach

NASA Astrophysics Data System (ADS)

Duarte, D.; Nex, F.; Kerle, N.; Vosselman, G.

2018-05-01

The localization and detailed assessment of damaged buildings after a disastrous event is of utmost importance to guide response operations, recovery tasks or for insurance purposes. Several remote sensing platforms and sensors are currently used for the manual detection of building damages. However, there is an overall interest in the use of automated methods to perform this task, regardless of the used platform. Owing to its synoptic coverage and predictable availability, satellite imagery is currently used as input for the identification of building damages by the International Charter, as well as the Copernicus Emergency Management Service for the production of damage grading and reference maps. Recently proposed methods to perform image classification of building damages rely on convolutional neural networks (CNN). These are usually trained with only satellite image samples in a binary classification problem, however the number of samples derived from these images is often limited, affecting the quality of the classification results. The use of up/down-sampling image samples during the training of a CNN, has demonstrated to improve several image recognition tasks in remote sensing. However, it is currently unclear if this multi resolution information can also be captured from images with different spatial resolutions like satellite and airborne imagery (from both manned and unmanned platforms). In this paper, a CNN framework using residual connections and dilated convolutions is used considering both manned and unmanned aerial image samples to perform the satellite image classification of building damages. Three network configurations, trained with multi-resolution image samples are compared against two benchmark networks where only satellite image samples are used. Combining feature maps generated from airborne and satellite image samples, and refining these using only the satellite image samples, improved nearly 4 % the overall satellite image classification of building damages.

Sample positioning apparatus

DOEpatents

Bell, Thomas H.; Johnson, Jr., Charles H.; Lane, Robert L.; Martin, Bradley E.; Tyree, William H.

1976-01-06

Apparatus for use in alpha particle counting with such as photomultiplier tubes, comprising a platform and linkage mechanism whereby samples are moved in linear manner toward and away from ends of the photomultiplier tubes.

Line-scan Raman imaging and spectroscopy platform for surface and subsurface evaluation of food safety and quality

USDA-ARS?s Scientific Manuscript database

Both surface and subsurface food inspection is important since interesting safety and quality attributes can be at different sample locations. This paper presents a multipurpose line-scan Raman platform for food safety and quality research, which can be configured for Raman chemical imaging (RCI) mo...

Topographical and Chemical Imaging of a Phase Separated Polymer Using a Combined Atomic Force Microscopy/Infrared Spectroscopy/Mass Spectrometry Platform

DOE PAGES

Tai, Tamin; Karácsony, Orsolya; Bocharova, Vera; ...

2016-02-18

This article describes how the use of a hybrid atomic force microscopy/infrared spectroscopy/mass spectrometry imaging platform was demonstrated for the acquisition and correlation of nanoscale sample surface topography and chemical images based on infrared spectroscopy and mass spectrometry.

ICECAP: an integrated, general-purpose, automation-assisted IC50/EC50 assay platform.

PubMed

Li, Ming; Chou, Judy; King, Kristopher W; Jing, Jing; Wei, Dong; Yang, Liyu

2015-02-01

IC50 and EC50 values are commonly used to evaluate drug potency. Mass spectrometry (MS)-centric bioanalytical and biomarker labs are now conducting IC50/EC50 assays, which, if done manually, are tedious and error-prone. Existing bioanalytical sample preparation automation systems cannot meet IC50/EC50 assay throughput demand. A general-purpose, automation-assisted IC50/EC50 assay platform was developed to automate the calculations of spiking solutions and the matrix solutions preparation scheme, the actual spiking and matrix solutions preparations, as well as the flexible sample extraction procedures after incubation. In addition, the platform also automates the data extraction, nonlinear regression curve fitting, computation of IC50/EC50 values, graphing, and reporting. The automation-assisted IC50/EC50 assay platform can process the whole class of assays of varying assay conditions. In each run, the system can handle up to 32 compounds and up to 10 concentration levels per compound, and it greatly improves IC50/EC50 assay experimental productivity and data processing efficiency. © 2014 Society for Laboratory Automation and Screening.

Performance Evaluation of Block Acquisition and Tracking Algorithms Using an Open Source GPS Receiver Platform

NASA Technical Reports Server (NTRS)

Ramachandran, Ganesh K.; Akopian, David; Heckler, Gregory W.; Winternitz, Luke B.

2011-01-01

Location technologies have many applications in wireless communications, military and space missions, etc. US Global Positioning System (GPS) and other existing and emerging Global Navigation Satellite Systems (GNSS) are expected to provide accurate location information to enable such applications. While GNSS systems perform very well in strong signal conditions, their operation in many urban, indoor, and space applications is not robust or even impossible due to weak signals and strong distortions. The search for less costly, faster and more sensitive receivers is still in progress. As the research community addresses more and more complicated phenomena there exists a demand on flexible multimode reference receivers, associated SDKs, and development platforms which may accelerate and facilitate the research. One of such concepts is the software GPS/GNSS receiver (GPS SDR) which permits a facilitated access to algorithmic libraries and a possibility to integrate more advanced algorithms without hardware and essential software updates. The GNU-SDR and GPS-SDR open source receiver platforms are such popular examples. This paper evaluates the performance of recently proposed block-corelator techniques for acquisition and tracking of GPS signals using open source GPS-SDR platform.

20170312 - Computer Simulation of Developmental ...

EPA Pesticide Factsheets

Rationale: Recent progress in systems toxicology and synthetic biology have paved the way to new thinking about in vitro/in silico modeling of developmental processes and toxicities, both for embryological and reproductive impacts. Novel in vitro platforms such as 3D organotypic culture models, engineered microscale tissues and complex microphysiological systems (MPS), together with computational models and computer simulation of tissue dynamics, lend themselves to a integrated testing strategies for predictive toxicology. As these emergent methodologies continue to evolve, they must be integrally tied to maternal/fetal physiology and toxicity of the developing individual across early lifestage transitions, from fertilization to birth, through puberty and beyond. Scope: This symposium will focus on how the novel technology platforms can help now and in the future, with in vitro/in silico modeling of complex biological systems for developmental and reproductive toxicity issues, and translating systems models into integrative testing strategies. The symposium is based on three main organizing principles: (1) that novel in vitro platforms with human cells configured in nascent tissue architectures with a native microphysiological environments yield mechanistic understanding of developmental and reproductive impacts of drug/chemical exposures; (2) that novel in silico platforms with high-throughput screening (HTS) data, biologically-inspired computational models of

Computer Simulation of Developmental Processes and ...

EPA Pesticide Factsheets

Rationale: Recent progress in systems toxicology and synthetic biology have paved the way to new thinking about in vitro/in silico modeling of developmental processes and toxicities, both for embryological and reproductive impacts. Novel in vitro platforms such as 3D organotypic culture models, engineered microscale tissues and complex microphysiological systems (MPS), together with computational models and computer simulation of tissue dynamics, lend themselves to a integrated testing strategies for predictive toxicology. As these emergent methodologies continue to evolve, they must be integrally tied to maternal/fetal physiology and toxicity of the developing individual across early lifestage transitions, from fertilization to birth, through puberty and beyond. Scope: This symposium will focus on how the novel technology platforms can help now and in the future, with in vitro/in silico modeling of complex biological systems for developmental and reproductive toxicity issues, and translating systems models into integrative testing strategies. The symposium is based on three main organizing principles: (1) that novel in vitro platforms with human cells configured in nascent tissue architectures with a native microphysiological environments yield mechanistic understanding of developmental and reproductive impacts of drug/chemical exposures; (2) that novel in silico platforms with high-throughput screening (HTS) data, biologically-inspired computational models of

An economic analysis of the processing technologies in CDW recycling platforms.

PubMed

Oliveira Neto, Raul; Gastineau, Pascal; Cazacliu, Bogdan Grigore; Le Guen, Lauredan; Paranhos, Régis Sebben; Petter, Carlos Otávio

2017-02-01

This paper proposes an economic analysis of three different types of processing in CDW (construction and demolition waste) recycling platforms, according to the sophistication of the processing technologies (current advanced, advanced and advanced sorting). The methodology that is adopted is in the economic evaluation concept of projects and is classified with a scoping study phase. In these contexts, three levels of CDW processing capabilities for recycling platforms are analyzed (100, 300 and 600 thousand tons per year). This article considers databases obtained from similar projects that have been published in the specialized literature; the data sources are primarily from the European continent. The paper shows that current advanced process has better economic performance, in terms of IRR, related to the other two processes. The IRR associated with advanced and advanced sorting processes could be raised by, (i) higher price of secondary primary material, and/or (ii) higher capacity of platforms, and/or (iii) higher sharing of secondary primary material in the total production. The first two points depend on the market conditions (prices and total quantity of CDW available) and (potential) fiscal or incentive policies. The last one depends on technological progress. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

PubMed Central

Mak, Sarah Siu Tze; Gopalakrishnan, Shyam; Carøe, Christian; Geng, Chunyu; Liu, Shanlin; Sinding, Mikkel-Holger S; Kuderna, Lukas F K; Zhang, Wenwei; Fu, Shujin; Vieira, Filipe G; Germonpré, Mietje; Bocherens, Hervé; Fedorov, Sergey; Petersen, Bent; Sicheritz-Pontén, Thomas; Marques-Bonet, Tomas; Zhang, Guojie; Jiang, Hui; Gilbert, M Thomas P

2017-01-01

Abstract Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform on DNA extracted from 8 historic and ancient dog and wolf samples. The data generated were largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (P = 0.371) and average sequence length (P = 0718) of endogenous nuclear DNA, sequence GC content (P = 0.311), double-stranded DNA damage rate (v. 0.309), and sequence clonality (P = 0.093). Small significant differences were found in single-strand DNA damage rate (δS; slightly lower for the BGISEQ-500, P = 0.011) and the background rate of difference from the reference genome (θ; slightly higher for BGISEQ-500, P = 0.012). This may result from the differences in amplification cycles used to polymerase chain reaction–amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (P = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from 3 of the samples with overall very low levels of endogenous DNA. Although we acknowledge that our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent a valid and potentially valuable alternative platform for palaeogenomic data generation that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA. PMID:28854615

Progress Towards a Global Understanding of Plankton Dynamics: The Global Alliance of CPR Surveys (GACS)

NASA Astrophysics Data System (ADS)

Batten, S.; Richardson, A.; Melrose, C.; Muxagata, E.; Hosie, G.; Verheye, H.; Hall, J.; Edwards, M.; Koubbi, P.; Abu-Alhaija, R.; Chiba, S.; Wilson, W.; Nagappa, R.; Takahashi, K.

2016-02-01

The Continuous Plankton Recorder (CPR) was first used in 1931 to routinely sample plankton and its continued deployment now sustains the longest-running, and spatially most extensive marine biological sampling programme in the world. Towed behind, for the most part commercial, ships it collects plankton samples from the surface waters that are subsequently analysed to provide taxonomically-resolved abundance data on a broad range of planktonic organisms from the size of coccolithophores to euphausiids. Plankton appear to integrate changes in the physical environment and by underpinning most marine food-webs, pass on this variability to higher trophic levels which have societal value. CPRs are deployed increasingly around the globe in discrete regional surveys that until recently interacted in an informal way. In 2011 the Global Alliance of CPR Surveys (GACS) was launched to bring these surveys together to collaborate more productively and address issues such as: methodological standardization, data integration, capacity building, and data analysis. Early products include a combined global database and regularly-released global marine ecological status reports. There are, of course, limitations to the exploitation of CPR data as well as the current geographic coverage. A current focus of GACS is integration of the data with models to meaningfully extrapolate across time and space. In this way the output could be used to provide more robust synoptic representations of key plankton variables. Recent years have also seen the CPR used as a platform in itself with the inclusion of additional sensors and water samplers that can sample the microplankton. The archive of samples has already been used for some molecular investigations and curation of samples is maintained for future studies. Thus the CPR is a key element of any regional to global ocean observing system of biodiversity.

Real-Time Cellular Exometabolome Analysis with a Microfluidic-Mass Spectrometry Platform

PubMed Central

Marasco, Christina C.; Enders, Jeffrey R.; Seale, Kevin T.; McLean, John A.; Wikswo, John P.

2015-01-01

To address the challenges of tracking the multitude of signaling molecules and metabolites that is the basis of biological complexity, we describe a strategy to expand the analytical techniques for dynamic systems biology. Using microfluidics, online desalting, and mass spectrometry technologies, we constructed and validated a platform well suited for sampling the cellular microenvironment with high temporal resolution. Our platform achieves success in: automated cellular stimulation and microenvironment control; reduced non-specific adsorption to polydimethylsiloxane due to surface passivation; real-time online sample collection; near real-time sample preparation for salt removal; and real-time online mass spectrometry. When compared against the benchmark of “in-culture” experiments combined with ultraperformance liquid chromatography-electrospray ionization-ion mobility-mass spectrometry (UPLC-ESI-IM-MS), our platform alleviates the volume challenge issues caused by dilution of autocrine and paracrine signaling and dramatically reduces sample preparation and data collection time, while reducing undesirable external influence from various manual methods of manipulating cells and media (e.g., cell centrifugation). To validate this system biologically, we focused on cellular responses of Jurkat T cells to microenvironmental stimuli. Application of these stimuli, in conjunction with the cell’s metabolic processes, results in changes in consumption of nutrients and secretion of biomolecules (collectively, the exometabolome), which enable communication with other cells or tissues and elimination of waste. Naïve and experienced T-cell metabolism of cocaine is used as an exemplary system to confirm the platform’s capability, highlight its potential for metabolite discovery applications, and explore immunological memory of T-cell drug exposure. Our platform proved capable of detecting metabolomic variations between naïve and experienced Jurkat T cells and highlights the dynamics of the exometabolome over time. Upregulation of the cocaine metabolite, benzoylecgonine, was noted in experienced T cells, indicating potential cellular memory of cocaine exposure. These metabolomics distinctions were absent from the analogous, traditional “in-culture” UPLC-ESI-IM-MS experiment, further demonstrating this platform’s capabilities. PMID:25723555

Opportunities and Challenges for Pancreatic Circulating Tumor Cells.

PubMed

Nagrath, Sunitha; Jack, Rhonda M; Sahai, Vaibhav; Simeone, Diane M

2016-09-01

Sensitive and reproducible platforms have been developed for detection, isolation, and enrichment of circulating tumor cells (CTCs)-rare cells that enter the blood from solid tumors, including those of the breast, prostate gland, lung, pancreas, and colon. These might be used as biomarkers in diagnosis or determination of prognosis. CTCs are no longer simply detected and quantified; they are now used in ex vivo studies of anticancer agents and early detection. We review what we have recently learned about CTCs from pancreatic tumors, describing advances in their isolation and analysis and challenges to their clinical utility. We summarize technologies used to isolate CTCs from blood samples of patients with pancreatic cancer, including immunoaffinity and label-free physical attribute-based capture. We explain methods of CTC analysis and how findings from these studies might be used to detect cancer at earlier stages, monitor disease progression, and determine prognosis. We review studies that have expanded CTCs for testing of anticancer agents and how these approaches might be used to personalize treatment. Advances in the detection, isolation, and analysis of CTCs have increased our understanding of the dissemination and progression of pancreatic cancer. However, standardization of methodologies and prospective studies are needed for this emerging technology to have a significant effect on clinical care. Copyright © 2016 AGA Institute. Published by Elsevier Inc. All rights reserved.

Natural Hazards characterisation in industrial practice

NASA Astrophysics Data System (ADS)

Bernardara, Pietro

2017-04-01

The definition of rare hydroclimatic extremes (up to 10-4 annual probability of occurrence) is of the utmost importance for the design of high value industrial infrastructures, such as grids, power plants, offshore platforms. The underestimation as well as the overestimation of the risk may lead to huge costs (ex. mid-life expensive works or overdesign) which may even prevent the project to happen. Nevertheless, the uncertainty associated to the extrapolation towards the rare frequencies are huge and manifold. They are mainly due to the scarcity of observations, the lack of quality on the extreme value records and on the arbitrary choice of the models used for extrapolations. This often put the design engineers in uncomfortable situations when they must choose the design values to use. Providentially, the recent progresses in the earth observation techniques, information technology, historical data collection and weather and ocean modelling are making huge datasets available. A careful use of big datasets of observations and modelled data are leading towards a better understanding of the physics of the underlying phenomena, the complex interactions between them and thus of the extreme events frequency extrapolations. This will move the engineering practice from the single site, small sample, application of statistical analysis to a more spatially coherent, physically driven extrapolation of extreme values. Few examples, from the EDF industrial practice are given to illustrate these progresses and their potential impact on the design approaches.

Principle considerations for the use of transcriptomics in doping research.

PubMed

Neuberger, Elmo W I; Moser, Dirk A; Simon, Perikles

2011-10-01

Over the course of the past decade, technical progress has enabled scientists to investigate genome-wide RNA expression using microarray platforms. This transcriptomic approach represents a promising tool for the discovery of basic gene expression patterns and for identification of cellular signalling pathways under various conditions. Since doping substances have been shown to influence mRNA expression, it has been suggested that these changes can be detected by screening the blood transcriptome. In this review, we critically discuss the potential but also the pitfalls of this application as a tool in doping research. Transcriptomic approaches were considered to potentially provide researchers with a unique gene expression signature or with a specific biomarker for various physiological and pathophysiological conditions. Since transcriptomic approaches are considerably prone to biological and technical confounding factors that act on study subjects or samples, very strict guidelines for the use of transcriptomics in human study subjects have been developed. Typical field conditions associated with doping controls limit the feasibility of following these strict guidelines as there are too many variables counteracting a standardized procedure. After almost a decade of research using transcriptomic tools, it still remains a matter of future technological progress to identify the ultimate biomarker using technologies and/or methodologies that are sufficiently robust against typical biological and technical bias and that are valid in a court of law. Copyright © 2011 John Wiley & Sons, Ltd.

The progress in the cholinesterase quantification methods.

PubMed

Holas, Ondrej; Musilek, Kamil; Pohanka, Miroslav; Kuca, Kamil

2012-12-01

Determination of acetylcholinesterase and butyrylcholinesterase activity has become an important tool in drug design and discovery as well as in medicine and toxicology. There are a large number of compounds that are able to modulate cholinesterase activity. These compounds can be used for pharmacological management of various disorders (e.g., Alzheimer's disease, myasthenia Gravis). Moreover, organophosphate poisoning is frequently diagnosed via a cholinesterase activity assay. This broad variety of methods has been developed over the past decades for cholinesterase activity quantification. This review provides a summary of the methods that are based on specific properties of cholinesterases and their interactions with native or artificial substrates. The authors also aim to provide an overview of different techniques used for the determination of quantitative cholinesterase activity. Specifically, the authors describe and discuss the manometric, potentiometric, titrimetric, photometric, fluorometric, and radioisotopic methods. Existing methods are able to cover most of the problems that arise during cholinesterase activity determination. Colorimetry according to Ellman has proved to be the most useful and versatile approach. It may be used in various protocols for the determination of pesticide or nerve agent exposure or for the development of new drugs. Its possible improvement lies in optimization of hemoglobin-rich samples. The progress of the most common methods (including Ellman) depends on miniaturization and modern physical platforms (e.g., optical fibers, chip methods, or nanotechnologies).

New Tools for New Research in Psychiatry: A Scalable and Customizable Platform to Empower Data Driven Smartphone Research.

PubMed

Torous, John; Kiang, Mathew V; Lorme, Jeanette; Onnela, Jukka-Pekka

2016-05-05

A longstanding barrier to progress in psychiatry, both in clinical settings and research trials, has been the persistent difficulty of accurately and reliably quantifying disease phenotypes. Mobile phone technology combined with data science has the potential to offer medicine a wealth of additional information on disease phenotypes, but the large majority of existing smartphone apps are not intended for use as biomedical research platforms and, as such, do not generate research-quality data. Our aim is not the creation of yet another app per se but rather the establishment of a platform to collect research-quality smartphone raw sensor and usage pattern data. Our ultimate goal is to develop statistical, mathematical, and computational methodology to enable us and others to extract biomedical and clinical insights from smartphone data. We report on the development and early testing of Beiwe, a research platform featuring a study portal, smartphone app, database, and data modeling and analysis tools designed and developed specifically for transparent, customizable, and reproducible biomedical research use, in particular for the study of psychiatric and neurological disorders. We also outline a proposed study using the platform for patients with schizophrenia. We demonstrate the passive data capabilities of the Beiwe platform and early results of its analytical capabilities. Smartphone sensors and phone usage patterns, when coupled with appropriate statistical learning tools, are able to capture various social and behavioral manifestations of illnesses, in naturalistic settings, as lived and experienced by patients. The ubiquity of smartphones makes this type of moment-by-moment quantification of disease phenotypes highly scalable and, when integrated within a transparent research platform, presents tremendous opportunities for research, discovery, and patient health.

New Tools for New Research in Psychiatry: A Scalable and Customizable Platform to Empower Data Driven Smartphone Research

PubMed Central

Torous, John; Kiang, Mathew V; Lorme, Jeanette

2016-01-01

Background A longstanding barrier to progress in psychiatry, both in clinical settings and research trials, has been the persistent difficulty of accurately and reliably quantifying disease phenotypes. Mobile phone technology combined with data science has the potential to offer medicine a wealth of additional information on disease phenotypes, but the large majority of existing smartphone apps are not intended for use as biomedical research platforms and, as such, do not generate research-quality data. Objective Our aim is not the creation of yet another app per se but rather the establishment of a platform to collect research-quality smartphone raw sensor and usage pattern data. Our ultimate goal is to develop statistical, mathematical, and computational methodology to enable us and others to extract biomedical and clinical insights from smartphone data. Methods We report on the development and early testing of Beiwe, a research platform featuring a study portal, smartphone app, database, and data modeling and analysis tools designed and developed specifically for transparent, customizable, and reproducible biomedical research use, in particular for the study of psychiatric and neurological disorders. We also outline a proposed study using the platform for patients with schizophrenia. Results We demonstrate the passive data capabilities of the Beiwe platform and early results of its analytical capabilities. Conclusions Smartphone sensors and phone usage patterns, when coupled with appropriate statistical learning tools, are able to capture various social and behavioral manifestations of illnesses, in naturalistic settings, as lived and experienced by patients. The ubiquity of smartphones makes this type of moment-by-moment quantification of disease phenotypes highly scalable and, when integrated within a transparent research platform, presents tremendous opportunities for research, discovery, and patient health. PMID:27150677

Next generation sensing platforms for extended deployments in large-scale, multidisciplinary, adaptive sampling and observational networks

NASA Astrophysics Data System (ADS)

Cross, J. N.; Meinig, C.; Mordy, C. W.; Lawrence-Slavas, N.; Cokelet, E. D.; Jenkins, R.; Tabisola, H. M.; Stabeno, P. J.

2016-12-01

New autonomous sensors have dramatically increased the resolution and accuracy of oceanographic data collection, enabling rapid sampling over extremely fine scales. Innovative new autonomous platofrms like floats, gliders, drones, and crawling moorings leverage the full potential of these new sensors by extending spatiotemporal reach across varied environments. During 2015 and 2016, The Innovative Technology for Arctic Exploration Program at the Pacific Marine Environmental Laboratory tested several new types of fully autonomous platforms with increased speed, durability, and power and payload capacity designed to deliver cutting-edge ecosystem assessment sensors to remote or inaccessible environments. The Expendable Ice-Tracking (EXIT) gloat developed by the NOAA Pacific Marine Environmental Laboratory (PMEL) is moored near bottom during the ice-free season and released on an autonomous timer beneath the ice during the following winter. The float collects a rapid profile during ascent, and continues to collect critical, poorly-accessible under-ice data until melt, when data is transmitted via satellite. The autonomous Oculus sub-surface glider developed by the University of Washington and PMEL has a large power and payload capacity and an enhanced buoyancy engine. This 'coastal truck' is designed for the rapid water column ascent required by optical imaging systems. The Saildrone is a solar and wind powered ocean unmanned surface vessel (USV) developed by Saildrone, Inc. in partnership with PMEL. This large-payload (200 lbs), fast (1-7 kts), durable (46 kts winds) platform was equipped with 15 sensors designed for ecosystem assessment during 2016, including passive and active acoustic systems specially redesigned for autonomous vehicle deployments. The senors deployed on these platforms achieved rigorous accuracy and precision standards. These innovative platforms provide new sampling capabilities and cost efficiencies in high-resolution sensor deployment, including reconnaissance for annual fisheries and marine mammal surveys; better linkages between sustained observing platforms; and adaptive deployments that can easily target anomalies as they arise.

Application of targeted quantitative proteomics analysis in human cerebrospinal fluid using a liquid chromatography matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometer (LC MALDI TOF/TOF) platform.

PubMed

Pan, Sheng; Rush, John; Peskind, Elaine R; Galasko, Douglas; Chung, Kathryn; Quinn, Joseph; Jankovic, Joseph; Leverenz, James B; Zabetian, Cyrus; Pan, Catherine; Wang, Yan; Oh, Jung Hun; Gao, Jean; Zhang, Jianpeng; Montine, Thomas; Zhang, Jing

2008-02-01

Targeted quantitative proteomics by mass spectrometry aims to selectively detect one or a panel of peptides/proteins in a complex sample and is particularly appealing for novel biomarker verification/validation because it does not require specific antibodies. Here, we demonstrated the application of targeted quantitative proteomics in searching, identifying, and quantifying selected peptides in human cerebrospinal spinal fluid (CSF) using a matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometer (MALDI TOF/TOF)-based platform. The approach involved two major components: the use of isotopic-labeled synthetic peptides as references for targeted identification and quantification and a highly selective mass spectrometric analysis based on the unique characteristics of the MALDI instrument. The platform provides high confidence for targeted peptide detection in a complex system and can potentially be developed into a high-throughput system. Using the liquid chromatography (LC) MALDI TOF/TOF platform and the complementary identification strategy, we were able to selectively identify and quantify a panel of targeted peptides in the whole proteome of CSF without prior depletion of abundant proteins. The effectiveness and robustness of the approach associated with different sample complexity, sample preparation strategies, as well as mass spectrometric quantification were evaluated. Other issues related to chromatography separation and the feasibility for high-throughput analysis were also discussed. Finally, we applied targeted quantitative proteomics to analyze a subset of previously identified candidate markers in CSF samples of patients with Parkinson's disease (PD) at different stages and Alzheimer's disease (AD) along with normal controls.

Multitarget, quantitative nanoplasmonic electrical field-enhanced resonating device (NE2RD) for diagnostics.

PubMed

Inci, Fatih; Filippini, Chiara; Baday, Murat; Ozen, Mehmet Ozgun; Calamak, Semih; Durmus, Naside Gozde; Wang, ShuQi; Hanhauser, Emily; Hobbs, Kristen S; Juillard, Franceline; Kuang, Ping Ping; Vetter, Michael L; Carocci, Margot; Yamamoto, Hidemi S; Takagi, Yuko; Yildiz, Umit Hakan; Akin, Demir; Wesemann, Duane R; Singhal, Amit; Yang, Priscilla L; Nibert, Max L; Fichorova, Raina N; Lau, Daryl T-Y; Henrich, Timothy J; Kaye, Kenneth M; Schachter, Steven C; Kuritzkes, Daniel R; Steinmetz, Lars M; Gambhir, Sanjiv S; Davis, Ronald W; Demirci, Utkan

2015-08-11

Recent advances in biosensing technologies present great potential for medical diagnostics, thus improving clinical decisions. However, creating a label-free general sensing platform capable of detecting multiple biotargets in various clinical specimens over a wide dynamic range, without lengthy sample-processing steps, remains a considerable challenge. In practice, these barriers prevent broad applications in clinics and at patients' homes. Here, we demonstrate the nanoplasmonic electrical field-enhanced resonating device (NE(2)RD), which addresses all these impediments on a single platform. The NE(2)RD employs an immunodetection assay to capture biotargets, and precisely measures spectral color changes by their wavelength and extinction intensity shifts in nanoparticles without prior sample labeling or preprocessing. We present through multiple examples, a label-free, quantitative, portable, multitarget platform by rapidly detecting various protein biomarkers, drugs, protein allergens, bacteria, eukaryotic cells, and distinct viruses. The linear dynamic range of NE(2)RD is five orders of magnitude broader than ELISA, with a sensitivity down to 400 fg/mL This range and sensitivity are achieved by self-assembling gold nanoparticles to generate hot spots on a 3D-oriented substrate for ultrasensitive measurements. We demonstrate that this precise platform handles multiple clinical samples such as whole blood, serum, and saliva without sample preprocessing under diverse conditions of temperature, pH, and ionic strength. The NE(2)RD's broad dynamic range, detection limit, and portability integrated with a disposable fluidic chip have broad applications, potentially enabling the transition toward precision medicine at the point-of-care or primary care settings and at patients' homes.

Multitarget, quantitative nanoplasmonic electrical field-enhanced resonating device (NE2RD) for diagnostics

PubMed Central

Inci, Fatih; Filippini, Chiara; Ozen, Mehmet Ozgun; Calamak, Semih; Durmus, Naside Gozde; Wang, ShuQi; Hanhauser, Emily; Hobbs, Kristen S.; Juillard, Franceline; Kuang, Ping Ping; Vetter, Michael L.; Carocci, Margot; Yamamoto, Hidemi S.; Takagi, Yuko; Yildiz, Umit Hakan; Akin, Demir; Wesemann, Duane R.; Singhal, Amit; Yang, Priscilla L.; Nibert, Max L.; Fichorova, Raina N.; Lau, Daryl T.-Y.; Henrich, Timothy J.; Kaye, Kenneth M.; Schachter, Steven C.; Kuritzkes, Daniel R.; Steinmetz, Lars M.; Gambhir, Sanjiv S.; Davis, Ronald W.; Demirci, Utkan

2015-01-01

Recent advances in biosensing technologies present great potential for medical diagnostics, thus improving clinical decisions. However, creating a label-free general sensing platform capable of detecting multiple biotargets in various clinical specimens over a wide dynamic range, without lengthy sample-processing steps, remains a considerable challenge. In practice, these barriers prevent broad applications in clinics and at patients’ homes. Here, we demonstrate the nanoplasmonic electrical field-enhanced resonating device (NE2RD), which addresses all these impediments on a single platform. The NE2RD employs an immunodetection assay to capture biotargets, and precisely measures spectral color changes by their wavelength and extinction intensity shifts in nanoparticles without prior sample labeling or preprocessing. We present through multiple examples, a label-free, quantitative, portable, multitarget platform by rapidly detecting various protein biomarkers, drugs, protein allergens, bacteria, eukaryotic cells, and distinct viruses. The linear dynamic range of NE2RD is five orders of magnitude broader than ELISA, with a sensitivity down to 400 fg/mL This range and sensitivity are achieved by self-assembling gold nanoparticles to generate hot spots on a 3D-oriented substrate for ultrasensitive measurements. We demonstrate that this precise platform handles multiple clinical samples such as whole blood, serum, and saliva without sample preprocessing under diverse conditions of temperature, pH, and ionic strength. The NE2RD’s broad dynamic range, detection limit, and portability integrated with a disposable fluidic chip have broad applications, potentially enabling the transition toward precision medicine at the point-of-care or primary care settings and at patients’ homes. PMID:26195743

Concentration and characterization of airborne particles in Tehran's subway system.

PubMed

Kamani, Hosein; Hoseini, Mohammad; Seyedsalehi, Mahdi; Mahdavi, Yousef; Jaafari, Jalil; Safari, Gholam Hosein

2014-06-01

Particulate matter is an important air pollutant, especially in closed environments like underground subway stations. In this study, a total of 13 elements were determined from PM10 and PM2.5 samples collected at two subway stations (Imam Khomeini and Sadeghiye) in Tehran's subway system. Sampling was conducted in April to August 2011 to measure PM concentrations in platform and adjacent outdoor air of the stations. In the Imam Khomeini station, the average concentrations of PM10 and PM2.5 were 94.4 ± 26.3 and 52.3 ± 16.5 μg m(-3) in the platform and 81.8 ± 22.2 and 35 ± 17.6 μg m(-3) in the outdoor air, respectively. In the Sadeghiye station, mean concentrations of PM10 and PM2.5 were 87.6 ± 23 and 41.3 ± 20.4 μg m(-3) in the platform and 73.9 ± 17.3 and 30 ± 15 μg m(-3), in the outdoor air, respectively. The relative contribution of elemental components in each particle fraction were accounted for 43% (PM10) and 47.7% (PM2.5) in platform of Imam Khomeini station and 15.9% (PM10) and 18.5% (PM2.5) in the outdoor air of this station. Also, at the Sadeghiye station, each fraction accounted for 31.6% (PM10) and 39.8% (PM2.5) in platform and was 11.7% (PM10) and 14.3% (PM2.5) in the outdoor. At the Imam Khomeini station, Fe was the predominant element to represent 32.4 and 36 % of the total mass of PM10 and PM2.5 in the platform and 11.5 and 13.3% in the outdoor, respectively. At the Sadeghiye station, this element represented 22.7 and 29.8% of total mass of PM10 and PM2.5 in the platform and 8.7 and 10.5% in the outdoor air, respectively. Other major crustal elements were 5.8% (PM10) and 5.3% (PM2.5) in the Imam Khomeini station platform and 2.3 and 2.4% in the outdoor air, respectively. The proportion of other minor elements was significantly lower, actually less than 7% in total samples, and V was the minor concentration in total mass of PM10 and PM2.5 in both platform stations.

Determination of lead in flour samples directly by solid sampling high resolution continuum source graphite furnace atomic absorption spectrometry

NASA Astrophysics Data System (ADS)

Tinas, Hande; Ozbek, Nil; Akman, Suleyman

2018-02-01

In this study, lead concentrations in various flour samples were determined by high-resolution continuum source graphite furnace atomic absorption spectrometry with solid sampling. Since samples were analyzed directly, the risks and disadvantages of sample digestion were eliminated. Solid flour samples were dried, weighed on the platforms, Pd was added as a modifier and introduced directly into a graphite tube using a manual solid sampler. Platforms and tubes were coated with Zr. The optimized pyrolysis and atomization temperatures were 800 °C and 2200 °C, respectively. The sensitivities of lead in various flour certified reference materials (CRMs) and aqueous standards were not significantly different. Therefore, aqueous standards were safely used for calibration. The absolute limit of detection and characteristic mass were 7.2 pg and 9.0 pg of lead, respectively. The lead concentrations in different types of flour samples were found in the range of 25-52 μg kg- 1. Finally, homogeneity factors representing the heterogeneity of analyte distribution for lead in flour samples were determined.

Data visualisation in surveillance for injury prevention and control: conceptual bases and case studies

PubMed Central

Martinez, Ramon; Ordunez, Pedro; Soliz, Patricia N; Ballesteros, Michael F

2016-01-01

Background The complexity of current injury-related health issues demands the usage of diverse and massive data sets for comprehensive analyses, and application of novel methods to communicate data effectively to the public health community, decision-makers and the public. Recent advances in information visualisation, availability of new visual analytic methods and tools, and progress on information technology provide an opportunity for shaping the next generation of injury surveillance. Objective To introduce data visualisation conceptual bases, and propose a visual analytic and visualisation platform in public health surveillance for injury prevention and control. Methods The paper introduces data visualisation conceptual bases, describes a visual analytic and visualisation platform, and presents two real-world case studies illustrating their application in public health surveillance for injury prevention and control. Results Application of visual analytic and visualisation platform is presented as solution for improved access to heterogeneous data sources, enhance data exploration and analysis, communicate data effectively, and support decision-making. Conclusions Applications of data visualisation concepts and visual analytic platform could play a key role to shape the next generation of injury surveillance. Visual analytic and visualisation platform could improve data use, the analytic capacity, and ability to effectively communicate findings and key messages. The public health surveillance community is encouraged to identify opportunities to develop and expand its use in injury prevention and control. PMID:26728006

A modular platform for targeted RNAi therapeutics.

PubMed

Kedmi, Ranit; Veiga, Nuphar; Ramishetti, Srinivas; Goldsmith, Meir; Rosenblum, Daniel; Dammes, Niels; Hazan-Halevy, Inbal; Nahary, Limor; Leviatan-Ben-Arye, Shani; Harlev, Michael; Behlke, Mark; Benhar, Itai; Lieberman, Judy; Peer, Dan

2018-03-01

Previous studies have identified relevant genes and signalling pathways that are hampered in human disorders as potential candidates for therapeutics. Developing nucleic acid-based tools to manipulate gene expression, such as short interfering RNAs 1-3 (siRNAs), opens up opportunities for personalized medicine. Yet, although major progress has been made in developing siRNA targeted delivery carriers, mainly by utilizing monoclonal antibodies (mAbs) for targeting 4-8 , their clinical translation has not occurred. This is in part because of the massive development and production requirements and the high batch-to-batch variability of current technologies, which rely on chemical conjugation. Here we present a self-assembled modular platform that enables the construction of a theoretically unlimited repertoire of siRNA targeted carriers. The self-assembly of the platform is based on a membrane-anchored lipoprotein that is incorporated into siRNA-loaded lipid nanoparticles that interact with the antibody crystallizable fragment (Fc) domain. We show that a simple switch of eight different mAbs redirects the specific uptake of siRNAs by diverse leukocyte subsets in vivo. The therapeutic potential of the platform is demonstrated in an inflammatory bowel disease model by targeting colon macrophages to reduce inflammatory symptoms, and in a Mantle Cell Lymphoma xenograft model by targeting cancer cells to induce cell death and improve survival. This modular delivery platform represents a milestone in the development of precision medicine.

A modular platform for targeted RNAi therapeutics

NASA Astrophysics Data System (ADS)

Kedmi, Ranit; Veiga, Nuphar; Ramishetti, Srinivas; Goldsmith, Meir; Rosenblum, Daniel; Dammes, Niels; Hazan-Halevy, Inbal; Nahary, Limor; Leviatan-Ben-Arye, Shani; Harlev, Michael; Behlke, Mark; Benhar, Itai; Lieberman, Judy; Peer, Dan

2018-01-01

Previous studies have identified relevant genes and signalling pathways that are hampered in human disorders as potential candidates for therapeutics. Developing nucleic acid-based tools to manipulate gene expression, such as short interfering RNAs1-3 (siRNAs), opens up opportunities for personalized medicine. Yet, although major progress has been made in developing siRNA targeted delivery carriers, mainly by utilizing monoclonal antibodies (mAbs) for targeting4-8, their clinical translation has not occurred. This is in part because of the massive development and production requirements and the high batch-to-batch variability of current technologies, which rely on chemical conjugation. Here we present a self-assembled modular platform that enables the construction of a theoretically unlimited repertoire of siRNA targeted carriers. The self-assembly of the platform is based on a membrane-anchored lipoprotein that is incorporated into siRNA-loaded lipid nanoparticles that interact with the antibody crystallizable fragment (Fc) domain. We show that a simple switch of eight different mAbs redirects the specific uptake of siRNAs by diverse leukocyte subsets in vivo. The therapeutic potential of the platform is demonstrated in an inflammatory bowel disease model by targeting colon macrophages to reduce inflammatory symptoms, and in a Mantle Cell Lymphoma xenograft model by targeting cancer cells to induce cell death and improve survival. This modular delivery platform represents a milestone in the development of precision medicine.

Modular development of a prototype point of care molecular diagnostic platform for sexually transmitted infections.

PubMed

Branavan, Manoharanehru; Mackay, Ruth E; Craw, Pascal; Naveenathayalan, Angel; Ahern, Jeremy C; Sivanesan, Tulasi; Hudson, Chris; Stead, Thomas; Kremer, Jessica; Garg, Neha; Baker, Mark; Sadiq, Syed T; Balachandran, Wamadeva

2016-08-01

This paper presents the design of a modular point of care test platform that integrates a proprietary sample collection device directly with a microfluidic cartridge. Cell lysis, within the cartridge, is conducted using a chemical method and nucleic acid purification is done on an activated cellulose membrane. The microfluidic device incorporates passive mixing of the lysis-binding buffers and sample using a serpentine channel. Results have shown extraction efficiencies for this new membrane of 69% and 57% compared to the commercial Qiagen extraction method of 85% and 59.4% for 0.1ng/µL and 100ng/µL salmon sperm DNA respectively spiked in phosphate buffered solution. Extraction experiments using the serpentine passive mixer cartridges incorporating lysis and nucleic acid purification showed extraction efficiency around 80% of the commercial Qiagen kit. Isothermal amplification was conducted using thermophillic helicase dependant amplification and recombinase polymerase amplification. A low cost benchtop real-time isothermal amplification platform has been developed capable of running six amplifications simultaneously. Results show that the platform is capable of detecting 1.32×10(6) of sample DNA through thermophillic helicase dependant amplification and 1×10(5) copy numbers Chlamydia trachomatis genomic DNA within 10min through recombinase polymerase nucleic acid amplification tests. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

C-SPECT - a Clinical Cardiac SPECT/Tct Platform: Design Concepts and Performance Potential

PubMed Central

Chang, Wei; Ordonez, Caesar E.; Liang, Haoning; Li, Yusheng; Liu, Jingai

2013-01-01

Because of scarcity of photons emitted from the heart, clinical cardiac SPECT imaging is mainly limited by photon statistics. The sub-optimal detection efficiency of current SPECT systems not only limits the quality of clinical cardiac SPECT imaging but also makes more advanced potential applications difficult to be realized. We propose a high-performance system platform - C-SPECT, which has its sampling geometry optimized for detection of emitted photons in quality and quantity. The C-SPECT has a stationary C-shaped gantry that surrounds the left-front side of a patient’s thorax. The stationary C-shaped collimator and detector systems in the gantry provide effective and efficient detection and sampling of photon emission. For cardiac imaging, the C-SPECT platform could achieve 2 to 4 times the system geometric efficiency of conventional SPECT systems at the same sampling resolution. This platform also includes an integrated transmission CT for attenuation correction. The ability of C-SPECT systems to perform sequential high-quality emission and transmission imaging could bring cost-effective high-performance to clinical imaging. In addition, a C-SPECT system could provide high detection efficiency to accommodate fast acquisition rate for gated and dynamic cardiac imaging. This paper describes the design concepts and performance potential of C-SPECT, and illustrates how these concepts can be implemented in a basic system. PMID:23885129

Development of Prototype Filovirus Recombinant Antigen Immunoassays

PubMed Central

Boisen, Matt L.; Oottamasathien, Darin; Jones, Abigail B.; Millett, Molly M.; Nelson, Diana S.; Bornholdt, Zachary A.; Fusco, Marnie L.; Abelson, Dafna M.; Oda, Shun-ichiro; Hartnett, Jessica N.; Rowland, Megan M.; Heinrich, Megan L.; Akdag, Marjan; Goba, Augustine; Momoh, Mambu; Fullah, Mohammed; Baimba, Francis; Gbakie, Michael; Safa, Sadiki; Fonnie, Richard; Kanneh, Lansana; Cross, Robert W.; Geisbert, Joan B.; Geisbert, Thomas W.; Kulakosky, Peter C.; Grant, Donald S.; Shaffer, Jeffery G.; Schieffelin, John S.; Wilson, Russell B.; Saphire, Erica Ollmann; Branco, Luis M.; Garry, Robert F.; Khan, S. Humarr; Pitts, Kelly R.

2015-01-01

Background. Throughout the 2014–2015 Ebola outbreak in West Africa, major gaps were exposed in the availability of validated rapid diagnostic platforms, protective vaccines, and effective therapeutic agents. These gaps potentiated the development of prototype rapid lateral flow immunodiagnostic (LFI) assays that are true point-of-contact platforms, for the detection of active Ebola infections in small blood samples. Methods. Recombinant Ebola and Marburg virus matrix VP40 and glycoprotein (GP) antigens were used to derive a panel of monoclonal and polyclonal antibodies. Antibodies were tested using a multivariate approach to identify antibody-antigen combinations suitable for enzyme-linked immunosorbent assay (ELISA) and LFI assay development. Results. Polyclonal antibodies generated in goats were superior reagents for capture and detection of recombinant VP40 in test sample matrices. These antibodies were optimized for use in antigen-capture ELISA and LFI assay platforms. Prototype immunoglobulin M (IgM)/immunoglobulin G (IgG) ELISAs were similarly developed that specifically detect Ebola virus–specific antibodies in the serum of experimentally infected nonhuman primates and in blood samples obtained from patients with Ebola from Sierra Leone. Conclusions. The prototype recombinant Ebola LFI assays developed in these studies have sensitivities that are useful for clinical diagnosis of acute ebolavirus infections. The antigen-capture and IgM/IgG ELISAs provide additional confirmatory assay platforms for detecting VP40 and other ebolavirus-specific immunoglobulins. PMID:26232440

Cross-platform validation and analysis environment for particle physics

NASA Astrophysics Data System (ADS)

Chekanov, S. V.; Pogrebnyak, I.; Wilbern, D.

2017-11-01

A multi-platform validation and analysis framework for public Monte Carlo simulation for high-energy particle collisions is discussed. The front-end of this framework uses the Python programming language, while the back-end is written in Java, which provides a multi-platform environment that can be run from a web browser and can easily be deployed at the grid sites. The analysis package includes all major software tools used in high-energy physics, such as Lorentz vectors, jet algorithms, histogram packages, graphic canvases, and tools for providing data access. This multi-platform software suite, designed to minimize OS-specific maintenance and deployment time, is used for online validation of Monte Carlo event samples through a web interface.

Waveguide infrared spectrometer platform for point and standoff chemical sensing

NASA Astrophysics Data System (ADS)

Chadha, Suneet; Henning, Pat; Landers, Frank; Weling, Ani

2004-03-01

Advanced autonomous detection of chemical warfare agents and toxic industrial chemicals has long been a major military concern. At present, our capability to rapidly assess the immediate environment is severely limited and our domestic infrastructure is burdened by the meticulous procedures required to rule out false threats. While significant advances have recently been accomplished in remote spectral sensing using rugged FTIRs and point detectors, efforts towards low cost chemical discrimination have been lacking. Foster-Miller has developed a unique waveguide spectrometer which is a paradigm shift from the conventional FTIR approach. The spectrometer provides spectral discrimination over the 3-14 μm range and will be the spectrometer platform for both active and passive detection. Foster-Miller has leveraged its innovations in infrared fiber-optic probes and the recent development of a waveguide spectrometer to build a novel infrared sensor platform for both point and stand-off chemical sensing. A monolithic wedge-grating optic provides the spectral dispersion with low cost thermopile point or array detectors picking off the diffracted wavelengths from the optic. The integrated optic provides spectral discrimination between 3-12 μm with resolution at 16 cm-1 or better and overall optical throughput approaching 35%. The device has a fixed cylindrical grating bonded to the edge of a ZnSe conditioning "wedge". The conditioning optic overcomes limitations of concave gratings as it accepts high angle (large FOV) light at the narrow end of the wedge and progressively conditions it to be near normal to the grating. On return, the diffracted wavelengths are concentrated on the discrete or array detector (pixel) elements by the wedge, providing throughput comparable to that of an FTIR. The waveguide spectrometer coupled to ATR probes, flow through liquid cells or multipass gas cells provides significant cost advantage over conventional sampling methodologies. We will present the enabling innovations along with present performance, sensitivity expectations and discrimination algorithm strategy.

DISCO-SCA and Properly Applied GSVD as Swinging Methods to Find Common and Distinctive Processes

PubMed Central

Van Deun, Katrijn; Van Mechelen, Iven; Thorrez, Lieven; Schouteden, Martijn; De Moor, Bart; van der Werf, Mariët J.; De Lathauwer, Lieven; Smilde, Age K.; Kiers, Henk A. L.

2012-01-01

Background In systems biology it is common to obtain for the same set of biological entities information from multiple sources. Examples include expression data for the same set of orthologous genes screened in different organisms and data on the same set of culture samples obtained with different high-throughput techniques. A major challenge is to find the important biological processes underlying the data and to disentangle therein processes common to all data sources and processes distinctive for a specific source. Recently, two promising simultaneous data integration methods have been proposed to attain this goal, namely generalized singular value decomposition (GSVD) and simultaneous component analysis with rotation to common and distinctive components (DISCO-SCA). Results Both theoretical analyses and applications to biologically relevant data show that: (1) straightforward applications of GSVD yield unsatisfactory results, (2) DISCO-SCA performs well, (3) provided proper pre-processing and algorithmic adaptations, GSVD reaches a performance level similar to that of DISCO-SCA, and (4) DISCO-SCA is directly generalizable to more than two data sources. The biological relevance of DISCO-SCA is illustrated with two applications. First, in a setting of comparative genomics, it is shown that DISCO-SCA recovers a common theme of cell cycle progression and a yeast-specific response to pheromones. The biological annotation was obtained by applying Gene Set Enrichment Analysis in an appropriate way. Second, in an application of DISCO-SCA to metabolomics data for Escherichia coli obtained with two different chemical analysis platforms, it is illustrated that the metabolites involved in some of the biological processes underlying the data are detected by one of the two platforms only; therefore, platforms for microbial metabolomics should be tailored to the biological question. Conclusions Both DISCO-SCA and properly applied GSVD are promising integrative methods for finding common and distinctive processes in multisource data. Open source code for both methods is provided. PMID:22693578

Low Cost High Value Mars Sample to Orbit

NASA Astrophysics Data System (ADS)

Adler, M.; Guernsey, C.; Sell, S.; Sengupta, A.; Shiraishi, L.

2012-06-01

A mid-size lander, rover, and MAV using the MSL CEDL architecture and a 3-stage Falcon 9 can collect scientifically high-quality Mars surface samples consisting of rock cores collected by a roving platform, and deliver those samples to Mars orbit.

Ebola Virus Vaccines – reality or fiction?

PubMed Central

Mire, Chad E.; Geisbert, Thomas W.; Feldmann, Heinz

2016-01-01

For 40 years ebolaviruses have been responsible for sporadic outbreaks of severe and often fatal hemorrhagic fever in humans and nonhuman primates. In December 2013 an unprecedented Zaire ebolavirus epidemic began in West Africa. Although “patient zero” has finally been reached after 2 years, the virus is again causing disease in the region. Currently there are no licensed vaccines or therapeutic countermeasures against ebolaviruses; however, the epidemic in West Africa has focused attention on the potential vaccine platforms developed over the past 15 years. There has been remarkable progress using a variety of platforms including DNA, subunit, and several viral vector approaches, replicating and non-replicating, which have shown varying degrees of protective efficacy in the “gold-standard” nonhuman primate models for Ebolavirus infections. A number of these vaccine platforms have moved into clinical trials over the past year with the hope of finding an efficacious vaccine to prevent future outbreaks/epidemics of Ebola hemorrhagic fever on the scale of the West African epidemic. PMID:27078187

Cardiovascular Organ-on-a-Chip Platforms for Drug Discovery and Development

PubMed Central

Ribas, João; Sadeghi, Hossein; Manbachi, Amir; Leijten, Jeroen; Brinegar, Katelyn; Zhang, Yu Shrike; Ferreira, Lino

2016-01-01

Abstract Cardiovascular diseases are prevalent worldwide and are the most frequent causes of death in the United States. Although spending in drug discovery/development has increased, the amount of drug approvals has seen a progressive decline. Particularly, adverse side effects to the heart and general vasculature have become common causes for preclinical project closures, and preclinical models do not fully recapitulate human in vivo dynamics. Recently, organs-on-a-chip technologies have been proposed to mimic the dynamic conditions of the cardiovascular system—in particular, heart and general vasculature. These systems pay particular attention to mimicking structural organization, shear stress, transmural pressure, mechanical stretching, and electrical stimulation. Heart- and vasculature-on-a-chip platforms have been successfully generated to study a variety of physiological phenomena, model diseases, and probe the effects of drugs. Here, we review and discuss recent breakthroughs in the development of cardiovascular organs-on-a-chip platforms, and their current and future applications in the area of drug discovery and development. PMID:28971113

Wafer-scale integrated micro-supercapacitors on an ultrathin and highly flexible biomedical platform.

PubMed

Maeng, Jimin; Meng, Chuizhou; Irazoqui, Pedro P

2015-02-01

We present wafer-scale integrated micro-supercapacitors on an ultrathin and highly flexible parylene platform, as progress toward sustainably powering biomedical microsystems suitable for implantable and wearable applications. All-solid-state, low-profile (<30 μm), and high-density (up to ~500 μF/mm(2)) micro-supercapacitors are formed on an ultrathin (~20 μm) freestanding parylene film by a wafer-scale parylene packaging process in combination with a polyaniline (PANI) nanowire growth technique assisted by surface plasma treatment. These micro-supercapacitors are highly flexible and shown to be resilient toward flexural stress. Further, direct integration of micro-supercapacitors into a radio frequency (RF) rectifying circuit is achieved on a single parylene platform, yielding a complete RF energy harvesting microsystem. The system discharging rate is shown to improve by ~17 times in the presence of the integrated micro-supercapacitors. This result suggests that the integrated micro-supercapacitor technology described herein is a promising strategy for sustainably powering biomedical microsystems dedicated to implantable and wearable applications.

MathWorks Simulink and C++ integration with the new VLT PLC-based standard development platform for instrument control systems

NASA Astrophysics Data System (ADS)

Kiekebusch, Mario J.; Di Lieto, Nicola; Sandrock, Stefan; Popovic, Dan; Chiozzi, Gianluca

2014-07-01

ESO is in the process of implementing a new development platform, based on PLCs, for upcoming VLT control systems (new instruments and refurbishing of existing systems to manage obsolescence issues). In this context, we have evaluated the integration and reuse of existing C++ libraries and Simulink models into the real-time environment of BECKHOFF Embedded PCs using the capabilities of the latest version of TwinCAT software and MathWorks Embedded Coder. While doing so the aim was to minimize the impact of the new platform by adopting fully tested solutions implemented in C++. This allows us to reuse the in house expertise, as well as extending the normal capabilities of the traditional PLC programming environments. We present the progress of this work and its application in two concrete cases: 1) field rotation compensation for instrument tracking devices like derotators, 2) the ESO standard axis controller (ESTAC), a generic model-based controller implemented in Simulink and used for the control of telescope main axes.

Integrated liquid-core optical fibers for ultra-efficient nonlinear liquid photonics.

PubMed

Kieu, K; Schneebeli, L; Norwood, R A; Peyghambarian, N

2012-03-26

We have developed a novel integrated platform for liquid photonics based on liquid core optical fiber (LCOF). The platform is created by fusion splicing liquid core optical fiber to standard single-mode optical fiber making it fully integrated and practical - a major challenge that has greatly hindered progress in liquid-photonic applications. As an example, we report here the realization of ultralow threshold Raman generation using an integrated CS₂ filled LCOF pumped with sub-nanosecond pulses at 532 nm and 1064 nm. The measured energy threshold for the Stokes generation is 1nJ, about three orders of magnitude lower than previously reported values in the literature for hydrogen gas, a popular Raman medium. The integrated LCOF platform opens up new possibilities for ultralow power nonlinear optics such as efficient white light generation for displays, mid-IR generation, slow light generation, parametric amplification, all-optical switching and wavelength conversion using liquids that have orders of magnitude larger optical nonlinearities compared with silica glass.

A Survey of Geosensor Networks: Advances in Dynamic Environmental Monitoring

PubMed Central

Nittel, Silvia

2009-01-01

In the recent decade, several technology trends have influenced the field of geosciences in significant ways. The first trend is the more readily available technology of ubiquitous wireless communication networks and progress in the development of low-power, short-range radio-based communication networks, the miniaturization of computing and storage platforms as well as the development of novel microsensors and sensor materials. All three trends have changed the type of dynamic environmental phenomena that can be detected, monitored and reacted to. Another important aspect is the real-time data delivery of novel platforms today. In this paper, I will survey the field of geosensor networks, and mainly focus on the technology of small-scale geosensor networks, example applications and their feasibility and lessons learnt as well as the current research questions posed by using this technology today. Furthermore, my objective is to investigate how this technology can be embedded in the current landscape of intelligent sensor platforms in the geosciences and identify its place and purpose. PMID:22346721

Late dislocation of rotating platform in New Jersey Low-Contact Stress knee prosthesis.

PubMed

Huang, Chun-Hsiung; Ma, Hon-Ming; Liau, Jiann-Jong; Ho, Fang-Yuan; Cheng, Cheng-Kung

2002-12-01

Five patients with late rotational dislocation of the rotating platform bearing in the New Jersey Low-Contact Stress total knee arthroplasty are reported. The prostheses had functioned well for 8 to 12 years before failure. Preoperative radiographs showed asymmetric femorotibial joint spaces. Entrapment of the dislocated bearing in three patients and spontaneous reduction of the dislocated bearing in another two patients were seen at revision. Femorotibial ligamentous instability was found after reduction. The retrieved polyethylene bearings showed advanced wear and cold flow deformities and the thickness was reduced. The revision arthroplasty was accomplished by replacement with a thicker bearing element. Progressive femorotibial ligament laxity and reduction of the thickness of polyethylene with wearing break down the originally well-balanced soft tissue tension of the knee. The rotational degree of the rotating platform bearing is unrestricted, which may result in late dislocation. Polyethylene wear is unavoidable in knee prostheses using metal contact with polyethylene even with a mobile-bearing design. Efforts to reduce polyethylene wear are mandatory.

The Mars Hopper: a radioisotope powered, impulse driven, long-range, long-lived mobile platform for exploration of Mars

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steven D. Howe; Robert C. O'Brien; William Taitano

Planetary exploration mission requirements are becoming more demanding. Due to the increasing cost, the missions that provide mobile platforms that can acquire data at multiple locations are becoming more attractive. Wheeled vehicles such as the MER rovers have proven extremely capable but have very limited range and cannot traverse rugged terrain. Flying vehicles such as balloons and airplanes have been proposed but are problematic due to the very thin atmospheric pressure and the strong, dusty winds present on Mars. The Center for Space Nuclear Research has designed an instrumented platform that can acquire detailed data at hundreds of locations duringmore » its lifetime - a Mars Hopper. The Mars Hopper concept utilizes energy from radioisotopic decay in a manner different from any existing radioisotopic power sources—as a thermal capacitor. By accumulating the heat from radioisotopic decay for long periods, the power of the source can be dramatically increased for short periods. The platform will be able to "hop" from one location to the next every 5-7 days with a separation of 5-10 km per hop. Preliminary designs show a platform that weighs around 52 kgs unfueled which is the condition at deployment. Consequently, several platforms may be deployed on a single launch from Earth. With sufficient lifetime, the entire surface of Mars can be mapped in detail by a couple dozen platforms. In addition, Hoppers can collect samples from all over the planet, including gorges, mountains and crevasses, and deliver them to a central location for eventual pick-up by a Mars Sample Return mission. The status of the Mars Hopper development project at the CSNR is discussed.« less

Integrated experimental platforms to study blast injuries: a bottom-up approach

NASA Astrophysics Data System (ADS)

Bo, C.; Williams, A.; Rankin, S.; Proud, W. G.; Brown, K. A.

2014-05-01

We are developing experimental models of blast injury using data from live biological samples. An integrated research strategy is followed to study material and biological properties of cells, tissues and organs, that are subjected to dynamic and static pressures, relevant to those of battlefield blast. We have developed a confined Split Hopkinson Pressure Bar (SHPB) system, which allows cells, either in suspension or as a monolayer, to be subjected to compression waves with pressures on the order of a few MPa and durations of hundreds of microseconds. The chamber design enables recovery of biological samples for cellular and molecular analysis. The SHPB platform, coupled with Quasi-Static experiments, is used to determine stress-strain curves of soft biological tissues under compression at low, medium and high strain rates. Tissue samples are examined, using histological techniques, to study macro- and microscopic changes induced by compression waves. In addition, a shock tube enables application of single or multiple air blasts with pressures on the order of kPa and a few milliseconds duration; this platform was used for initial studies on mesenchymal stem cells responses to blast pressures.

Surface engineering on mesoporous silica chips for enriching low molecular weight phosphorylated proteins

NASA Astrophysics Data System (ADS)

Hu, Ye; Peng, Yang; Lin, Kevin; Shen, Haifa; Brousseau, Louis C., III; Sakamoto, Jason; Sun, Tong; Ferrari, Mauro

2011-02-01

Phosphorylated peptides and proteins play an important role in normal cellular activities, e.g., gene expression, mitosis, differentiation, proliferation, and apoptosis, as well as tumor initiation, progression and metastasis. However, technical hurdles hinder the use of common fractionation methods to capture phosphopeptides from complex biological fluids such as human sera. Herein, we present the development of a dual strategy material that offers enhanced capture of low molecular weight phosphoproteins: mesoporous silica thin films with precisely engineered pore sizes that sterically select for molecular size combined with chemically selective surface modifications (i.e. Ga3+, Ti4+ and Zr4+) that target phosphoroproteins. These materials provide high reproducibility (CV = 18%) and increase the stability of the captured proteins by excluding degrading enzymes, such as trypsin. The chemical and physical properties of the composite mesoporous thin films were characterized by X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectroscopy, energy dispersive X-ray spectroscopy and ellipsometry. Using mass spectroscopy and biostatistics analysis, the enrichment efficiency of different metal ions immobilized on mesoporous silica chips was investigated. The novel technology reported provides a platform capable of efficiently profiling the serum proteome for biomarker discovery, forensic sampling, and routine diagnostic applications.Phosphorylated peptides and proteins play an important role in normal cellular activities, e.g., gene expression, mitosis, differentiation, proliferation, and apoptosis, as well as tumor initiation, progression and metastasis. However, technical hurdles hinder the use of common fractionation methods to capture phosphopeptides from complex biological fluids such as human sera. Herein, we present the development of a dual strategy material that offers enhanced capture of low molecular weight phosphoproteins: mesoporous silica thin films with precisely engineered pore sizes that sterically select for molecular size combined with chemically selective surface modifications (i.e. Ga3+, Ti4+ and Zr4+) that target phosphoroproteins. These materials provide high reproducibility (CV = 18%) and increase the stability of the captured proteins by excluding degrading enzymes, such as trypsin. The chemical and physical properties of the composite mesoporous thin films were characterized by X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectroscopy, energy dispersive X-ray spectroscopy and ellipsometry. Using mass spectroscopy and biostatistics analysis, the enrichment efficiency of different metal ions immobilized on mesoporous silica chips was investigated. The novel technology reported provides a platform capable of efficiently profiling the serum proteome for biomarker discovery, forensic sampling, and routine diagnostic applications. Electronic supplementary information (ESI) available. See DOI: 10.1039/c0nr00720j

Cancer cachexia: mediators, signaling, and metabolic pathways.

PubMed

Fearon, Kenneth C H; Glass, David J; Guttridge, Denis C

2012-08-08

Cancer cachexia is characterized by a significant reduction in body weight resulting predominantly from loss of adipose tissue and skeletal muscle. Cachexia causes reduced cancer treatment tolerance and reduced quality and length of life, and remains an unmet medical need. Therapeutic progress has been impeded, in part, by the marked heterogeneity of mediators, signaling, and metabolic pathways both within and between model systems and the clinical syndrome. Recent progress in understanding conserved, molecular mechanisms of skeletal muscle atrophy/hypertrophy has provided a downstream platform for circumventing the variations and redundancy in upstream mediators and may ultimately translate into new targeted therapies. Copyright © 2012 Elsevier Inc. All rights reserved.

Molecular and chemical engineering of bacteriophages for potential medical applications.

PubMed

Hodyra, Katarzyna; Dąbrowska, Krystyna

2015-04-01

Recent progress in molecular engineering has contributed to the great progress of medicine. However, there are still difficult problems constituting a challenge for molecular biology and biotechnology, e.g. new generation of anticancer agents, alternative biosensors or vaccines. As a biotechnological tool, bacteriophages (phages) offer a promising alternative to traditional approaches. They can be applied as anticancer agents, novel platforms in vaccine design, or as target carriers in drug discovery. Phages also offer solutions for modern cell imaging, biosensor construction or food pathogen detection. Here we present a review of bacteriophage research as a dynamically developing field with promising prospects for further development of medicine and biotechnology.

KSC-2012-1346

NASA Image and Video Library

2012-02-15

CAPE CANAVERAL, Fla. –– Inside the Vehicle Assembly Building at NASA’s Kennedy Space Center in Florida, technicians monitor the progress as a crane begins to lift an Apollo era diesel engine from crawler-transporter 2 CT-2). New engines will be installed later this month. Work is in progress in high bay 2 to upgrade CT-2 so that it can carry NASA’s Space Launch System heavy-lift rocket, which is under design, and new Orion spacecraft to the launch pad. The crawler-transporters were used to carry the mobile launcher platform and space shuttle to Launch Complex 39 for space shuttle launches for 30 years. Photo credit: NASA/Kim Shiflett

KSC-2012-1344

NASA Image and Video Library

2012-02-15

CAPE CANAVERAL, Fla. ––Inside the Vehicle Assembly Building at NASA’s Kennedy Space Center in Florida, a technician monitors the progress as a crane begins to lift an Apollo era diesel engine from crawler-transporter 2 CT-2). New engines will be installed later this month. Work is in progress in high bay 2 to upgrade CT-2 so that it can carry NASA’s Space Launch System heavy-lift rocket, which is under design, and new Orion spacecraft to the launch pad. The crawler-transporters were used to carry the mobile launcher platform and space shuttle to Launch Complex 39 for space shuttle launches for 30 years. Photo credit: NASA/Kim Shiflett

KSC-2012-1348

NASA Image and Video Library

2012-02-15

CAPE CANAVERAL, Fla. –– Inside the Vehicle Assembly Building at NASA’s Kennedy Space Center in Florida, a technician monitors the progress as a crane lifts an Apollo era diesel engine from crawler-transporter 2 CT-2). New engines will be installed later this month. Work is in progress in high bay 2 to upgrade CT-2 so that it can carry NASA’s Space Launch System heavy-lift rocket, which is under design, and new Orion spacecraft to the launch pad. The crawler-transporters were used to carry the mobile launcher platform and space shuttle to Launch Complex 39 for space shuttle launches for 30 years. Photo credit: NASA/Kim Shiflett

KSC-2012-1347

NASA Image and Video Library

2012-02-15

CAPE CANAVERAL, Fla. –– Inside the Vehicle Assembly Building at NASA’s Kennedy Space Center in Florida, technicians monitor the progress as a crane lifts an Apollo era diesel engine from crawler-transporter 2 CT-2). New engines will be installed later this month. Work is in progress in high bay 2 to upgrade CT-2 so that it can carry NASA’s Space Launch System heavy-lift rocket, which is under design, and new Orion spacecraft to the launch pad. The crawler-transporters were used to carry the mobile launcher platform and space shuttle to Launch Complex 39 for space shuttle launches for 30 years. Photo credit: NASA/Kim Shiflett

Analytical aspects of plant metabolite profiling platforms: current standings and future aims.

PubMed

Seger, Christoph; Sturm, Sonja

2007-02-01

Over the past years, metabolic profiling has been established as a comprehensive systems biology tool. Mass spectrometry or NMR spectroscopy-based technology platforms combined with unsupervised or supervised multivariate statistical methodologies allow a deep insight into the complex metabolite patterns of plant-derived samples. Within this review, we provide a thorough introduction to the analytical hard- and software requirements of metabolic profiling platforms. Methodological limitations are addressed, and the metabolic profiling workflow is exemplified by summarizing recent applications ranging from model systems to more applied topics.

Efficiency of Airborne Sample Analysis Platform (ASAP) bioaerosol sampler for pathogen detection

PubMed Central

Sharma, Anurag; Clark, Elizabeth; McGlothlin, James D.; Mittal, Suresh K.

2015-01-01

The threat of bioterrorism and pandemics has highlighted the urgency for rapid and reliable bioaerosol detection in different environments. Safeguarding against such threats requires continuous sampling of the ambient air for pathogen detection. In this study we investigated the efficacy of the Airborne Sample Analysis Platform (ASAP) 2800 bioaerosol sampler to collect representative samples of air and identify specific viruses suspended as bioaerosols. To test this concept, we aerosolized an innocuous replication-defective bovine adenovirus serotype 3 (BAdV3) in a controlled laboratory environment. The ASAP efficiently trapped the surrogate virus at 5 × 103 plaque-forming units (p.f.u.) [2 × 105 genome copy equivalent] concentrations or more resulting in the successful detection of the virus using quantitative PCR. These results support the further development of ASAP for bioaerosol pathogen detection. PMID:26074900

Robotics-assisted mass spectrometry assay platform enabled by open-source electronics.

PubMed

Chiu, Shih-Hao; Urban, Pawel L

2015-02-15

Mass spectrometry (MS) is an important analytical technique with numerous applications in clinical analysis, biochemistry, environmental analysis, geology and physics. Its success builds on the ability of MS to determine molecular weights of analytes, and elucidate their structures. However, sample handling prior to MS requires a lot of attention and labor. In this work we were aiming to automate processing samples for MS so that analyses could be conducted without much supervision of experienced analysts. The goal of this study was to develop a robotics and information technology-oriented platform that could control the whole analysis process including sample delivery, reaction-based assay, data acquisition, and interaction with the analyst. The proposed platform incorporates a robotic arm for handling sample vials delivered to the laboratory, and several auxiliary devices which facilitate and secure the analysis process. They include: multi-relay board, infrared sensors, photo-interrupters, gyroscopes, force sensors, fingerprint scanner, barcode scanner, touch screen panel, and internet interface. The control of all the building blocks is achieved through implementation of open-source electronics (Arduino), and enabled by custom-written programs in C language. The advantages of the proposed system include: low cost, simplicity, small size, as well as facile automation of sample delivery and processing without the intervention of the analyst. It is envisaged that this simple robotic system may be the forerunner of automated laboratories dedicated to mass spectrometric analysis of biological samples. Copyright © 2014 Elsevier B.V. All rights reserved.

Open tubular lab-on-column/mass spectrometry for targeted proteomics of nanogram sample amounts.

PubMed

Hustoft, Hanne Kolsrud; Vehus, Tore; Brandtzaeg, Ole Kristian; Krauss, Stefan; Greibrokk, Tyge; Wilson, Steven Ray; Lundanes, Elsa

2014-01-01

A novel open tubular nanoproteomic platform featuring accelerated on-line protein digestion and high-resolution nano liquid chromatography mass spectrometry (LC-MS) has been developed. The platform features very narrow open tubular columns, and is hence particularly suited for limited sample amounts. For enzymatic digestion of proteins, samples are passed through a 20 µm inner diameter (ID) trypsin + endoproteinase Lys-C immobilized open tubular enzyme reactor (OTER). Resulting peptides are subsequently trapped on a monolithic pre-column and transferred on-line to a 10 µm ID porous layer open tubular (PLOT) liquid chromatography LC separation column. Wnt/ß-catenein signaling pathway (Wnt-pathway) proteins of potentially diagnostic value were digested+detected in targeted-MS/MS mode in small cell samples and tumor tissues within 120 minutes. For example, a potential biomarker Axin1 was identifiable in just 10 ng of sample (protein extract of ∼1,000 HCT15 colon cancer cells). In comprehensive mode, the current OTER-PLOT set-up could be used to identify approximately 1500 proteins in HCT15 cells using a relatively short digestion+detection cycle (240 minutes), outperforming previously reported on-line digestion/separation systems. The platform is fully automated utilizing common commercial instrumentation and parts, while the reactor and columns are simple to produce and have low carry-over. These initial results point to automated solutions for fast and very sensitive MS based proteomics, especially for samples of limited size.

Towards a systems approach for chronic diseases, based on health state modeling

PubMed Central

Rebhan, Michael

2017-01-01

Rising pressure from chronic diseases means that we need to learn how to deal with challenges at a different level, including the use of systems approaches that better connect across fragments, such as disciplines, stakeholders, institutions, and technologies. By learning from progress in leading areas of health innovation (including oncology and AIDS), as well as complementary indications (Alzheimer’s disease), I try to extract the most enabling innovation paradigms, and discuss their extension to additional areas of application within a systems approach. To facilitate such work, a Precision, P4 or Systems Medicine platform is proposed, which is centered on the representation of health states that enable the definition of time in the vision to provide the right intervention for the right patient at the right time and dose. Modeling of such health states should allow iterative optimization, as longitudinal human data accumulate. This platform is designed to facilitate the discovery of links between opportunities related to a) the modernization of diagnosis, including the increased use of omics profiling, b) patient-centric approaches enabled by technology convergence, including digital health and connected devices, c) increasing understanding of the pathobiological, clinical and health economic aspects of disease progression stages, d) design of new interventions, including therapies as well as preventive measures, including sequential intervention approaches. Probabilistic Markov models of health states, e.g. those used for health economic analysis, are discussed as a simple starting point for the platform. A path towards extension into other indications, data types and uses is discussed, with a focus on regenerative medicine and relevant pathobiology. PMID:28529704

A Computational Systems Biology Software Platform for Multiscale Modeling and Simulation: Integrating Whole-Body Physiology, Disease Biology, and Molecular Reaction Networks

PubMed Central

Eissing, Thomas; Kuepfer, Lars; Becker, Corina; Block, Michael; Coboeken, Katrin; Gaub, Thomas; Goerlitz, Linus; Jaeger, Juergen; Loosen, Roland; Ludewig, Bernd; Meyer, Michaela; Niederalt, Christoph; Sevestre, Michael; Siegmund, Hans-Ulrich; Solodenko, Juri; Thelen, Kirstin; Telle, Ulrich; Weiss, Wolfgang; Wendl, Thomas; Willmann, Stefan; Lippert, Joerg

2011-01-01

Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multiscale by nature, project work, and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform consisting of PK-Sim® and MoBi® capable of building and simulating models that integrate across biological scales. A prototypical multiscale model for the progression of a pancreatic tumor and its response to pharmacotherapy is constructed and virtual patients are treated with a prodrug activated by hepatic metabolization. Tumor growth is driven by signal transduction leading to cell cycle transition and proliferation. Free tumor concentrations of the active metabolite inhibit Raf kinase in the signaling cascade and thereby cell cycle progression. In a virtual clinical study, the individual therapeutic outcome of the chemotherapeutic intervention is simulated for a large population with heterogeneous genomic background. Thereby, the platform allows efficient model building and integration of biological knowledge and prior data from all biological scales. Experimental in vitro model systems can be linked with observations in animal experiments and clinical trials. The interplay between patients, diseases, and drugs and topics with high clinical relevance such as the role of pharmacogenomics, drug–drug, or drug–metabolite interactions can be addressed using this mechanistic, insight driven multiscale modeling approach. PMID:21483730

Nanocalorimeter platform for in situ specific heat measurements and x-ray diffraction at low temperature

NASA Astrophysics Data System (ADS)

Willa, K.; Diao, Z.; Campanini, D.; Welp, U.; Divan, R.; Hudl, M.; Islam, Z.; Kwok, W.-K.; Rydh, A.

2017-12-01

Recent advances in electronics and nanofabrication have enabled membrane-based nanocalorimetry for measurements of the specific heat of microgram-sized samples. We have integrated a nanocalorimeter platform into a 4.5 T split-pair vertical-field magnet to allow for the simultaneous measurement of the specific heat and x-ray scattering in magnetic fields and at temperatures as low as 4 K. This multi-modal approach empowers researchers to directly correlate scattering experiments with insights from thermodynamic properties including structural, electronic, orbital, and magnetic phase transitions. The use of a nanocalorimeter sample platform enables numerous technical advantages: precise measurement and control of the sample temperature, quantification of beam heating effects, fast and precise positioning of the sample in the x-ray beam, and fast acquisition of x-ray scans over a wide temperature range without the need for time-consuming re-centering and re-alignment. Furthermore, on an YBa2Cu3O7-δ crystal and a copper foil, we demonstrate a novel approach to x-ray absorption spectroscopy by monitoring the change in sample temperature as a function of incident photon energy. Finally, we illustrate the new insights that can be gained from in situ structural and thermodynamic measurements by investigating the superheated state occurring at the first-order magneto-elastic phase transition of Fe2P, a material that is of interest for magnetocaloric applications.

Evaluating the Quality and Usability of Open Data for Public Health Research: A Systematic Review of Data Offerings on 3 Open Data Platforms.

PubMed

Martin, Erika G; Law, Jennie; Ran, Weijia; Helbig, Natalie; Birkhead, Guthrie S

Government datasets are newly available on open data platforms that are publicly accessible, available in nonproprietary formats, free of charge, and with unlimited use and distribution rights. They provide opportunities for health research, but their quality and usability are unknown. To describe available open health data, identify whether data are presented in a way that is aligned with best practices and usable for researchers, and examine differences across platforms. Two reviewers systematically reviewed a random sample of data offerings on NYC OpenData (New York City, all offerings, n = 37), Health Data NY (New York State, 25% sample, n = 71), and HealthData.gov (US Department of Health and Human Services, 5% sample, n = 75), using a standard coding guide. Three open health data platforms at the federal, New York State, and New York City levels. Data characteristics from the coding guide were aggregated into summary indices for intrinsic data quality, contextual data quality, adherence to the Dublin Core metadata standards, and the 5-star open data deployment scheme. One quarter of the offerings were structured datasets; other presentation styles included charts (14.7%), documents describing data (12.0%), maps (10.9%), and query tools (7.7%). Health Data NY had higher intrinsic data quality (P < .001), contextual data quality (P < .001), and Dublin Core metadata standards adherence (P < .001). All met basic "web availability" open data standards; fewer met higher standards of "hyperlinked to other data." Although all platforms need improvement, they already provide readily available data for health research. Sustained effort on improving open data websites and metadata is necessary for ensuring researchers use these data, thereby increasing their research value.

Authenticity screening of seized whiskey samples using electrophoresis microchips coupled with contactless conductivity detection.

PubMed

Rezende, Kariolanda C A; Moreira, Roger Cardoso; Logrado, Lucio Paulo Lima; Talhavini, Márcio; Coltro, Wendell K T

2016-10-01

This report describes for the first time the use of microchip electrophoresis (ME) devices integrated with capacitively coupled contactless conductivity detection (C 4 D) to investigate the authenticity of seized whiskey samples, which were probably adulterated by simple dilution with tap water. The proposed microfluidic platform was explored for the monitoring of anionic species (Cl - and F - ) in both original and tampered samples. The best separations were achieved within 70 s using a running buffer composed of lactic acid and histidine (pH = 5.9). ME-C 4 D devices were used to analyze samples from three different brands (five samples each). Based on the presence of inorganic anions like Cl - , F - , SO 4 2- and NO 2 - in different amounts, the authenticity of seized whiskeys was compared to original samples. According to the reported data, the proposed microfluidic platform can be useful to help regulatory authorities in the investigation and monitoring of authenticity of commercialized whiskey beverages. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

ACS sampling system: design, implementation, and performance evaluation

NASA Astrophysics Data System (ADS)

Di Marcantonio, Paolo; Cirami, Roberto; Chiozzi, Gianluca

2004-09-01

By means of ACS (ALMA Common Software) framework we designed and implemented a sampling system which allows sampling of every Characteristic Component Property with a specific, user-defined, sustained frequency limited only by the hardware. Collected data are sent to various clients (one or more Java plotting widgets, a dedicated GUI or a COTS application) using the ACS/CORBA Notification Channel. The data transport is optimized: samples are cached locally and sent in packets with a lower and user-defined frequency to keep network load under control. Simultaneous sampling of the Properties of different Components is also possible. Together with the design and implementation issues we present the performance of the sampling system evaluated on two different platforms: on a VME based system using VxWorks RTOS (currently adopted by ALMA) and on a PC/104+ embedded platform using Red Hat 9 Linux operating system. The PC/104+ solution offers, as an alternative, a low cost PC compatible hardware environment with free and open operating system.

Electrokinetic Sample Preconcentration and Hydrodynamic Sample Injection for Microchip Electrophoresis Using a Pneumatic Microvalve

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cong, Yongzheng; Katipamula, Shanta; Geng, Tao

2016-02-01

A microfluidic platform was developed to perform online electrokinetic sample preconcentration and rapid hydrodynamic sample injection for electrophoresis using a single microvalve. The PDMS microchip consists of a separation channel, a side channel for sample introduction, and a control channel which is used as a pneumatic microvalve aligned at the intersection of the two flow channels. The closed microvalve, created by multilayer soft lithography, can serve as a preconcentrator under an applied electric potential, enabling current to pass through while blocking bulk flow. Once analytes are concentrated, the valve is briefly opened and the stacked sample is pressure injected intomore » the separation channel for electrophoretic separation. Fluorescently labeled peptides were enriched by a factor of ~450 in 230 s. The performance of the platform was validated by the online preconcentration, injection and electrophoretic separation of fluorescently labeled peptides. This method enables both rapid analyte concentration and controlled injection volume for high sensitivity, high resolution capillary electrophoresis.« less

Automated centrifugal-microfluidic platform for DNA purification using laser burst valve and coriolis effect.

PubMed

Choi, Min-Seong; Yoo, Jae-Chern

2015-04-01

We report a fully automated DNA purification platform with a micropored membrane in the channel utilizing centrifugal microfluidics on a lab-on-a-disc (LOD). The microfluidic flow in the LOD, into which the reagents are injected for DNA purification, is controlled by a single motor and laser burst valve. The sample and reagents pass successively through the micropored membrane in the channel when each laser burst valve is opened. The Coriolis effect is used by rotating the LOD bi-directionally to increase the purity of the DNA, thereby preventing the mixing of the waste and elution solutions. The total process from the lysed sample injection into the LOD to obtaining the purified DNA was finished within 7 min with only one manual step. The experimental result for Salmonella shows that the proposed microfluidic platform is comparable to the existing devices in terms of the purity and yield of DNA.

Multiplexed analysis of protein-ligand interactions by fluorescence anisotropy in a microfluidic platform.

PubMed

Cheow, Lih Feng; Viswanathan, Ramya; Chin, Chee-Sing; Jennifer, Nancy; Jones, Robert C; Guccione, Ernesto; Quake, Stephen R; Burkholder, William F

2014-10-07

Homogeneous assay platforms for measuring protein-ligand interactions are highly valued due to their potential for high-throughput screening. However, the implementation of these multiplexed assays in conventional microplate formats is considerably expensive due to the large amounts of reagents required and the need for automation. We implemented a homogeneous fluorescence anisotropy-based binding assay in an automated microfluidic chip to simultaneously interrogate >2300 pairwise interactions. We demonstrated the utility of this platform in determining the binding affinities between chromatin-regulatory proteins and different post-translationally modified histone peptides. The microfluidic chip assay produces comparable results to conventional microtiter plate assays, yet requires 2 orders of magnitude less sample and an order of magnitude fewer pipetting steps. This approach enables one to use small samples for medium-scale screening and could ease the bottleneck of large-scale protein purification.

The Short Wave Aerostat-Mounted Imager (SWAMI): A novel platform for acquiring remotely sensed data from a tethered balloon

USGS Publications Warehouse

Vierling, L.A.; Fersdahl, M.; Chen, X.; Li, Z.; Zimmerman, P.

2006-01-01

We describe a new remote sensing system called the Short Wave Aerostat-Mounted Imager (SWAMI). The SWAMI is designed to acquire co-located video imagery and hyperspectral data to study basic remote sensing questions and to link landscape level trace gas fluxes with spatially and temporally appropriate spectral observations. The SWAMI can fly at altitudes up to 2 km above ground level to bridge the spatial gap between radiometric measurements collected near the surface and those acquired by other aircraft or satellites. The SWAMI platform consists of a dual channel hyperspectral spectroradiometer, video camera, GPS, thermal infrared sensor, and several meteorological and control sensors. All SWAMI functions (e.g. data acquisition and sensor pointing) can be controlled from the ground via wireless transmission. Sample data from the sampling platform are presented, along with several potential scientific applications of SWAMI data.

Centrifugal sedimentation immunoassays for multiplexed detection of enteric bacteria in ground water

PubMed Central

Litvinov, Julia; Moen, Scott T.; Koh, Chung-Yan; Singh, Anup K.

2016-01-01

Waterborne pathogens pose significant threat to the global population and early detection plays an important role both in making drinking water safe, as well as in diagnostics and treatment of water-borne diseases. We present an innovative centrifugal sedimentation immunoassay platform for detection of bacterial pathogens in water. Our approach is based on binding of pathogens to antibody-functionalized capture particles followed by sedimentation of the particles through a density-media in a microfluidic disk. Beads at the distal end of the disk are imaged to quantify the fluorescence and determine the bacterial concentration. Our platform is fast (20 min), can detect as few as ∼10 bacteria with minimal sample preparation, and can detect multiple pathogens simultaneously. The platform was used to detect a panel of enteric bacteria (Escherichia coli, Salmonella typhimurium, Shigella, Listeria, and Campylobacter) spiked in tap and ground water samples. PMID:26858815

Nanoparticle functionalised small-core suspended-core fibre - a novel platform for efficient sensing.

PubMed

Doherty, Brenda; Csáki, Andrea; Thiele, Matthias; Zeisberger, Matthias; Schwuchow, Anka; Kobelke, Jens; Fritzsche, Wolfgang; Schmidt, Markus A

2017-02-01

Detecting small quantities of specific target molecules is of major importance within bioanalytics for efficient disease diagnostics. One promising sensing approach relies on combining plasmonically-active waveguides with microfluidics yielding an easy-to-use sensing platform. Here we introduce suspended-core fibres containing immobilised plasmonic nanoparticles surrounding the guiding core as a concept for an entirely integrated optofluidic platform for efficient refractive index sensing. Due to the extremely small optical core and the large adjacent microfluidic channels, over two orders of magnitude of nanoparticle coverage densities have been accessed with millimetre-long sample lengths showing refractive index sensitivities of 170 nm/RIU for aqueous analytes where the fibre interior is functionalised by gold nanospheres. Our concept represents a fully integrated optofluidic sensing system demanding small sample volumes and allowing for real-time analyte monitoring, both of which are highly relevant within invasive bioanalytics, particularly within molecular disease diagnostics and environmental science.

Polymer platforms for selective detection of cocaine in street samples adulterated with levamisole.

PubMed

Florea, Anca; Cowen, Todd; Piletsky, Sergey; De Wael, Karolien

2018-08-15

Accurate drug detection is of utmost importance for fighting against drug abuse. With a high number of cutting agents and adulterants being added to cut or mask drugs in street powders the number of false results is increasing. We demonstrate for the first time the usefulness of employing polymers readily synthesized by electrodeposition to selectively detect cocaine in the presence of the commonly used adulterant levamisole. The polymers were selected by computational modelling to exhibit high binding affinity towards cocaine and deposited directly on the surface of graphene-modified electrodes via electropolymerization. The resulting platforms allowed a distinct electrochemical signal for cocaine, which is otherwise suppressed by levamisole. Square wave voltammetry was used to quantify cocaine alone and in the presence of levamisole. The usefulness of the platforms was demonstrated in the screening of real street samples. Copyright © 2018 Elsevier B.V. All rights reserved.

The Arctic Observing Viewer (AOV): Visualization, Data Discovery, Strategic Assessment, and Decision Support for Arctic Observing

NASA Astrophysics Data System (ADS)

Cody, R. P.; Manley, W. F.; Gaylord, A. G.; Kassin, A.; Villarreal, S.; Barba, M.; Dover, M.; Escarzaga, S. M.; Habermann, T.; Kozimor, J.; Score, R.; Tweedie, C. E.

2016-12-01

To better assess progress in Arctic Observing made by U.S. SEARCH, NSF AON, SAON, and related initiatives, an updated version of the Arctic Observing Viewer (AOV; http://ArcticObservingViewer.org) has been released. This web mapping application and information system conveys the who, what, where, and when of "data collection sites" - the precise locations of monitoring assets, observing platforms, and wherever repeat marine or terrestrial measurements have been taken. Over 8000 sites across the circum-arctic are documented including a range of boreholes, ship tracks, buoys, towers, sampling stations, sensor networks, vegetation plots, stream gauges, ice cores, observatories, and more. Contributing partners are the U.S. NSF, ACADIS, ADIwg, AOOS, a2dc, AON, CAFF, GINA, IASOA, INTERACT, NASA ABoVE, and USGS, among others. Users can visualize, navigate, select, search, draw, print, view details, and follow links to obtain a comprehensive perspective of environmental monitoring efforts. We continue to develop, populate, and enhance AOV. Recent improvements include: a more intuitive and functional search tool, a modern cross-platform interface using javascript and HTML5, and hierarchical ISO metadata coupled with RESTful web services & metadata XLinks to span the data life cycle (from project planning to establishment of data collection sites to release of scientific datasets). Additionally, through collaborations with the Barrow Area Information Database (BAID, www.barrowmapped.org) we are exploring linkages with datacenters and have developed a prototype dashboard application that allows users to explore data services in the AOV application. AOV is founded on principles of interoperability, such that agencies and organizations can use the AOV Viewer and web services for their own purposes. In this way, AOV complements other distributed yet interoperable cyber resources and helps science planners, funding agencies, investigators, data specialists, and others to: assess status, identify overlap, fill gaps, optimize sampling design, refine network performance, clarify directions, access data, coordinate logistics, and collaborate to meet Arctic Observing goals.

Utilization of Cloud Computing in Education and Research to the Attainment of Millennium Development Goals and Vision 2030 in Kenya

ERIC Educational Resources Information Center

Waga, Duncan; Makori, Esther; Rabah, Kefa

2014-01-01

Kenya Educational and Research fraternity has highly qualified human resource capacity with globally gained experiences. However each research entity works in disparity due to the absence of a common digital platform while educational units don't even have the basic infrastructure. For sustainability of Education and research progression,…

Development and Evaluation of a Web 2.0-Based Ubiquitous Learning Platform for Schoolyard Plant Identification

ERIC Educational Resources Information Center

Hwang, Gwo-Haur; Chu, Hui-Chun; Chen, Beyin; Cheng, Zheng Shan

2014-01-01

The rapid progress of wireless communication, sensing, and mobile technologies has enabled students to learn in an environment that combines learning resources from both the real world and the digital world. It can be viewed as a new learning style which has been called context-aware ubiquitous learning. Most context-aware ubiquitous learning…

Reconfigurable, Intelligently-Adaptive, Communication System, an SDR Platform

NASA Technical Reports Server (NTRS)

Roche, Rigoberto

2016-01-01

The Space Telecommunications Radio System (STRS) provides a common, consistent framework to abstract the application software from the radio platform hardware. STRS aims to reduce the cost and risk of using complex, configurable and reprogrammable radio systems across NASA missions. The Glenn Research Center (GRC) team made a software-defined radio (SDR) platform STRS compliant by adding an STRS operating environment and a field programmable gate array (FPGA) wrapper, capable of implementing each of the platforms interfaces, as well as a test waveform to exercise those interfaces. This effort serves to provide a framework toward waveform development on an STRS compliant platform to support future space communication systems for advanced exploration missions. Validated STRS compliant applications provided tested code with extensive documentation to potentially reduce risk, cost and efforts in development of space-deployable SDRs. This paper discusses the advantages of STRS, the integration of STRS onto a Reconfigurable, Intelligently-Adaptive, Communication System (RIACS) SDR platform, the sample waveform, and wrapper development efforts. The paper emphasizes the infusion of the STRS Architecture onto the RIACS platform for potential use in next generation SDRs for advance exploration missions.

Single Domain Antibodies as New Biomarker Detectors

PubMed Central

Fischer, Katja; Leow, Chiuan Yee; Chuah, Candy; McCarthy, James

2017-01-01

Biomarkers are defined as indicators of biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention. Biomarkers have been widely used for early detection, prediction of response after treatment, and for monitoring the progression of diseases. Antibodies represent promising tools for recognition of biomarkers, and are widely deployed as analytical tools in clinical settings. For immunodiagnostics, antibodies are now exploited as binders for antigens of interest across a range of platforms. More recently, the discovery of antibody surface display and combinatorial chemistry techniques has allowed the exploration of new binders from a range of animals, for instance variable domains of new antigen receptors (VNAR) from shark and variable heavy chain domains (VHH) or nanobodies from camelids. These single domain antibodies (sdAbs) have some advantages over conventional murine immunoglobulin owing to the lack of a light chain, making them the smallest natural biomarker binders thus far identified. In this review, we will discuss several biomarkers used as a means to validate diseases progress. The potential functionality of modern singe domain antigen binders derived from phylogenetically early animals as new biomarker detectors for current diagnostic and research platforms development will be described. PMID:29039819

Natural orifice translumenal endoscopic surgery: Progress in humans since white paper

PubMed Central

Santos, Byron F; Hungness, Eric S

2011-01-01

Since the first description of the concept of natural orifice translumenal endoscopic surgery (NOTES), a substantial number of clinical NOTES reports have appeared in the literature. This editorial reviews the available human data addressing research questions originally proposed by the white paper, including determining the optimal method of access for NOTES, developing safe methods of lumenal closure, suturing and anastomotic devices, advanced multitasking platforms, addressing the risk of infection, managing complications, addressing challenges with visualization, and training for NOTES procedures. An analysis of the literature reveals that so far transvaginal access and closure appear to be the most feasible techniques for NOTES, with a limited, but growing transgastric, transrectal, and transesophageal NOTES experience in humans. The theoretically increased risk of infection as a result of NOTES procedures has not been substantiated in transvaginal and transgastric procedures so far. Development of suturing and anastomotic devices and advanced platforms for NOTES has progressed slowly, with limited clinical data on their use so far. Data on the optimal management and incidence of intraoperative complications remain sparse, although possible factors contributing to complications are discussed. Finally, this editorial discusses the likely direction of future NOTES development and its possible role in clinical practice. PMID:21483624

WINCS Harmoni: Closed-loop dynamic neurochemical control of therapeutic interventions

NASA Astrophysics Data System (ADS)

Lee, Kendall H.; Lujan, J. Luis; Trevathan, James K.; Ross, Erika K.; Bartoletta, John J.; Park, Hyung Ook; Paek, Seungleal Brian; Nicolai, Evan N.; Lee, Jannifer H.; Min, Hoon-Ki; Kimble, Christopher J.; Blaha, Charles D.; Bennet, Kevin E.

2017-04-01

There has been significant progress in understanding the role of neurotransmitters in normal and pathologic brain function. However, preclinical trials aimed at improving therapeutic interventions do not take advantage of real-time in vivo neurochemical changes in dynamic brain processes such as disease progression and response to pharmacologic, cognitive, behavioral, and neuromodulation therapies. This is due in part to a lack of flexible research tools that allow in vivo measurement of the dynamic changes in brain chemistry. Here, we present a research platform, WINCS Harmoni, which can measure in vivo neurochemical activity simultaneously across multiple anatomical targets to study normal and pathologic brain function. In addition, WINCS Harmoni can provide real-time neurochemical feedback for closed-loop control of neurochemical levels via its synchronized stimulation and neurochemical sensing capabilities. We demonstrate these and other key features of this platform in non-human primate, swine, and rodent models of deep brain stimulation (DBS). Ultimately, systems like the one described here will improve our understanding of the dynamics of brain physiology in the context of neurologic disease and therapeutic interventions, which may lead to the development of precision medicine and personalized therapies for optimal therapeutic efficacy.

Progress toward development of a platform for studying burn in the presence of mix on the National Ignition Facility

NASA Astrophysics Data System (ADS)

Murphy, T. J.; Kyrala, G. A.; Bradley, P. A.; Krasheninnikova, N. S.; Cobble, J. A.; Tregillis, I. L.; Obrey, K. A. D.; Hsu, S. C.; Shah, R. C.; Hakel, P.; Kline, J. L.; Grim, G. P.; Baumgaertel, J. A.; Schmitt, M. J.; Kanzleiter, R. J.; Batha, S. H.

2013-10-01

Mix of shell material into ICF capsule fuel can degrade implosion performance through a number of mechanisms. One way is by dilution of the fusion fuel, which affects performance by an amount that is dependent on the degree of mix at the atomic level. Experiments are underway to quantify the mix of shell material into fuel using directly driven capsules on the National Ignition Facility. Deuterated plastic shells will be utilized with tritium fill so that the production of DT neutrons is indicative of mix at the atomic level. Neutron imaging will locate the burn region and spectroscopic imaging of the doped layers will reveal the location, temperature, and density of the shell material. Correlation of the two will be used to determine the degree of atomic mixing of the shell into the fuel and will be compared to models. This talk will review progress toward the development of an experimental platform to measure burn in the presence of measured mix. This work is supported by US DOE/NNSA, performed at LANL, operated by LANS LLC under contract DE-AC52-06NA25396.

Epigenetics of prostate cancer.

PubMed

McKee, Tawnya C; Tricoli, James V

2015-01-01

The introduction of novel technologies that can be applied to the investigation of the molecular underpinnings of human cancer has allowed for new insights into the mechanisms associated with tumor development and progression. They have also advanced the diagnosis, prognosis and treatment of cancer. These technologies include microarray and other analysis methods for the generation of large-scale gene expression data on both mRNA and miRNA, next-generation DNA sequencing technologies utilizing a number of platforms to perform whole genome, whole exome, or targeted DNA sequencing to determine somatic mutational differences and gene rearrangements, and a variety of proteomic analysis platforms including liquid chromatography/mass spectrometry (LC/MS) analysis to survey alterations in protein profiles in tumors. One other important advancement has been our current ability to survey the methylome of human tumors in a comprehensive fashion through the use of sequence-based and array-based methylation analysis (Bock et al., Nat Biotechnol 28:1106-1114, 2010; Harris et al., Nat Biotechnol 28:1097-1105, 2010). The focus of this chapter is to present and discuss the evidence for key genes involved in prostate tumor development, progression, or resistance to therapy that are regulated by methylation-induced silencing.

Novel drug discovery approaches for treating arenavirus infections.

PubMed

Pasquato, Antonella; Kunz, Stefan

2016-01-01

Arenaviruses are enveloped negative stranded viruses endemic in Africa, Europe and the Americas. Several arenaviruses cause severe viral hemorrhagic fever with high mortality in humans and pose serious public health threats. So far, there are no FDA-approved vaccines and therapeutic options are restricted to the off-label use of ribavirin. The major human pathogenic arenaviruses are classified as Category A agents and require biosafety level (BSL)-4 containment. Herein, the authors cover the recent progress in the development of BSL2 surrogate systems that recapitulate the entire or specific steps of the arenavirus life cycle and are serving as powerful platforms for drug discovery. Furthermore, they highlight the identification of selected novel drugs that target individual steps of arenavirus multiplication describing their discovery, their targets, and mode of action. The lack of effective drugs against arenaviruses is an unmatched challenge in current medical virology. Novel technologies have provided important insights into the basic biology of arenaviruses and the mechanisms underlying virus-host cell interaction. Significant progress of our understanding of how the virus invades the host cell paved the way to develop powerful novel screening platforms. Recent efforts have provided a range of promising drug candidates currently under evaluation for therapeutic intervention in vivo.

Direct assembling methodologies for high-throughput bioscreening

PubMed Central

Rodríguez-Dévora, Jorge I.; Shi, Zhi-dong; Xu, Tao

2012-01-01

Over the last few decades, high-throughput (HT) bioscreening, a technique that allows rapid screening of biochemical compound libraries against biological targets, has been widely used in drug discovery, stem cell research, development of new biomaterials, and genomics research. To achieve these ambitions, scaffold-free (or direct) assembly of biological entities of interest has become critical. Appropriate assembling methodologies are required to build an efficient HT bioscreening platform. The development of contact and non-contact assembling systems as a practical solution has been driven by a variety of essential attributes of the bioscreening system, such as miniaturization, high throughput, and high precision. The present article reviews recent progress on these assembling technologies utilized for the construction of HT bioscreening platforms. PMID:22021162

Design process of a photonics network for military platforms

NASA Astrophysics Data System (ADS)

Nelson, George F.; Rao, Nagarajan M.; Krawczak, John A.; Stevens, Rick C.

1999-02-01

Technology development in photonics is rapidly progressing. The concept of a Unified Network will provide re- configurable network access to platform sensors, Vehicle Management Systems, Stores and avionics. The re-configurable taps into the network will accommodate present interface standards and provide scaleability for the insertion of future interfaces. Significant to this development is the design and test of the Optical Backplane Interconnect System funded by Naval Air Systems Command and developed by Lockheed Martin Tactical Defense Systems - Eagan. OBIS results in the merging of the electrical backplane and the optical backplane, with interconnect fabric and card edge connectors finally providing adequate electrical and optical card access. Presently OBIS will support 1.2 Gb/s per fiber over multiples of 12 fibers per ribbon cable.

Automated distribution system management for multichannel space power systems

NASA Technical Reports Server (NTRS)

Fleck, G. W.; Decker, D. K.; Graves, J.

1983-01-01

A NASA sponsored study of space power distribution system technology is in progress to develop an autonomously managed power system (AMPS) for large space power platforms. The multichannel, multikilowatt, utility-type power subsystem proposed presents new survivability requirements and increased subsystem complexity. The computer controls under development for the power management system must optimize the power subsystem performance and minimize the life cycle cost of the platform. A distribution system management philosophy has been formulated which incorporates these constraints. Its implementation using a TI9900 microprocessor and FORTH as the programming language is presented. The approach offers a novel solution to the perplexing problem of determining the optimal combination of loads which should be connected to each power channel for a versatile electrical distribution concept.

Multifunctional Gold Nanostars for Molecular Imaging and Cancer Therapy

NASA Astrophysics Data System (ADS)

Liu, Yang; Yuan, Hsiangkuo; Fales, Andrew; Register, Janna; Vo-Dinh, Tuan

2015-08-01

Plasmonics-active gold nanoparticles offer excellent potential in molecular imaging and cancer therapy. Among them, gold nanostars (AuNS) exhibit cross-platform flexibility as multimodal contrast agents for macroscopic X-ray computer tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), as well as nanoprobes for photoacoustic tomography (PAT), two-photon photoluminescence (TPL) and surface-enhanced Raman spectroscopy (SERS). Their surfactant-free surface enables versatile functionalization to enhance cancer targeting, and allow triggered drug release. AuNS can also be used as an efficient platform for drug carrying, photothermal therapy, and photodynamic therapy. This review paper presents the latest progress regarding AuNS as a promising nanoplatform for cancer nanotheranostics. Future research directions with AuNS for biomedical applications will also be discussed.

Comparison of serum, EDTA plasma and P100 plasma for luminex-based biomarker multiplex assays in patients with chronic obstructive pulmonary disease in the SPIROMICS study.

PubMed

O'Neal, Wanda K; Anderson, Wayne; Basta, Patricia V; Carretta, Elizabeth E; Doerschuk, Claire M; Barr, R Graham; Bleecker, Eugene R; Christenson, Stephanie A; Curtis, Jeffrey L; Han, Meilan K; Hansel, Nadia N; Kanner, Richard E; Kleerup, Eric C; Martinez, Fernando J; Miller, Bruce E; Peters, Stephen P; Rennard, Stephen I; Scholand, Mary Beth; Tal-Singer, Ruth; Woodruff, Prescott G; Couper, David J; Davis, Sonia M

2014-01-08

As a part of the longitudinal Chronic Obstructive Pulmonary Disease (COPD) study, Subpopulations and Intermediate Outcome Measures in COPD study (SPIROMICS), blood samples are being collected from 3200 subjects with the goal of identifying blood biomarkers for sub-phenotyping patients and predicting disease progression. To determine the most reliable sample type for measuring specific blood analytes in the cohort, a pilot study was performed from a subset of 24 subjects comparing serum, Ethylenediaminetetraacetic acid (EDTA) plasma, and EDTA plasma with proteinase inhibitors (P100). 105 analytes, chosen for potential relevance to COPD, arranged in 12 multiplex and one simplex platform (Myriad-RBM) were evaluated in duplicate from the three sample types from 24 subjects. The reliability coefficient and the coefficient of variation (CV) were calculated. The performance of each analyte and mean analyte levels were evaluated across sample types. 20% of analytes were not consistently detectable in any sample type. Higher reliability and/or smaller CV were determined for 12 analytes in EDTA plasma compared to serum, and for 11 analytes in serum compared to EDTA plasma. While reliability measures were similar for EDTA plasma and P100 plasma for a majority of analytes, CV was modestly increased in P100 plasma for eight analytes. Each analyte within a multiplex produced independent measurement characteristics, complicating selection of sample type for individual multiplexes. There were notable detectability and measurability differences between serum and plasma. Multiplexing may not be ideal if large reliability differences exist across analytes measured within the multiplex, especially if values differ based on sample type. For some analytes, the large CV should be considered during experimental design, and the use of duplicate and/or triplicate samples may be necessary. These results should prove useful for studies evaluating selection of samples for evaluation of potential blood biomarkers.

Comparison of serum, EDTA plasma and P100 plasma for luminex-based biomarker multiplex assays in patients with chronic obstructive pulmonary disease in the SPIROMICS study

PubMed Central

2014-01-01

Background As a part of the longitudinal Chronic Obstructive Pulmonary Disease (COPD) study, Subpopulations and Intermediate Outcome Measures in COPD study (SPIROMICS), blood samples are being collected from 3200 subjects with the goal of identifying blood biomarkers for sub-phenotyping patients and predicting disease progression. To determine the most reliable sample type for measuring specific blood analytes in the cohort, a pilot study was performed from a subset of 24 subjects comparing serum, Ethylenediaminetetraacetic acid (EDTA) plasma, and EDTA plasma with proteinase inhibitors (P100™). Methods 105 analytes, chosen for potential relevance to COPD, arranged in 12 multiplex and one simplex platform (Myriad-RBM) were evaluated in duplicate from the three sample types from 24 subjects. The reliability coefficient and the coefficient of variation (CV) were calculated. The performance of each analyte and mean analyte levels were evaluated across sample types. Results 20% of analytes were not consistently detectable in any sample type. Higher reliability and/or smaller CV were determined for 12 analytes in EDTA plasma compared to serum, and for 11 analytes in serum compared to EDTA plasma. While reliability measures were similar for EDTA plasma and P100 plasma for a majority of analytes, CV was modestly increased in P100 plasma for eight analytes. Each analyte within a multiplex produced independent measurement characteristics, complicating selection of sample type for individual multiplexes. Conclusions There were notable detectability and measurability differences between serum and plasma. Multiplexing may not be ideal if large reliability differences exist across analytes measured within the multiplex, especially if values differ based on sample type. For some analytes, the large CV should be considered during experimental design, and the use of duplicate and/or triplicate samples may be necessary. These results should prove useful for studies evaluating selection of samples for evaluation of potential blood biomarkers. PMID:24397870

Centrifugal Microfluidic Platform for Rapid, Multiplexed Detection of TB and HIV Biomarkers in Whole Blood Samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Litvinov, Julia; Moen, Scott T.; Berry, Gregory J.

Infection with Mycobacterium Tuberculosis represents a significant threat to people with immune disorders, such as HIV-positive individuals, and can result in significant health complications or death if not diagnosed and treated early. We present a centrifugal microfluidic platform for multiplexed detection of tuberculosis and HIV biomarkers in human whole blood with minimal sample preparation and a sample-to-answer time of 30 minutes. This multiplexed assay was developed for the detection of two M.tuberculosis secreted proteins, whose secretion represents an active and ongoing infection, as well as detection of HIV p24 protein and human anti-p24 antibodies. The limit of detection for thismore » multiplex assay is in the pg/mL range for both HIV and M.tuberculosis proteins, making this assay potentially useful in the clinical diagnosis of both HIV and Tuberculosis proteins indicative of active infection. Antigen detection for the HIV assay sensitivity was 89%, the specificity 85%. Serological detection had 100% sensitivity and specificity for the limited sample pool. The centrifugal microfluidic platform presented here offers the potential for a portable, fast and inexpensive multiplexed diagnostic device that can be used in resource-limited settings for diagnosis of TB and HIV.« less

Centrifugal Microfluidic Platform for Rapid, Multiplexed Detection of TB and HIV Biomarkers in Whole Blood Samples

DOE PAGES

Litvinov, Julia; Moen, Scott T.; Berry, Gregory J.; ...

2017-05-30

Infection with Mycobacterium Tuberculosis represents a significant threat to people with immune disorders, such as HIV-positive individuals, and can result in significant health complications or death if not diagnosed and treated early. We present a centrifugal microfluidic platform for multiplexed detection of tuberculosis and HIV biomarkers in human whole blood with minimal sample preparation and a sample-to-answer time of 30 minutes. This multiplexed assay was developed for the detection of two M.tuberculosis secreted proteins, whose secretion represents an active and ongoing infection, as well as detection of HIV p24 protein and human anti-p24 antibodies. The limit of detection for thismore » multiplex assay is in the pg/mL range for both HIV and M.tuberculosis proteins, making this assay potentially useful in the clinical diagnosis of both HIV and Tuberculosis proteins indicative of active infection. Antigen detection for the HIV assay sensitivity was 89%, the specificity 85%. Serological detection had 100% sensitivity and specificity for the limited sample pool. The centrifugal microfluidic platform presented here offers the potential for a portable, fast and inexpensive multiplexed diagnostic device that can be used in resource-limited settings for diagnosis of TB and HIV.« less

Increased Bisecting N-Acetylglucosamine and Decreased Branched Chain Glycans of N-linked Glycoproteins in Expressed Prostatic Secretions Associated with Prostate Cancer Progression

PubMed Central

Nyalwidhe, Julius O.; Betesh, Lucy R.; Powers, Thomas W.; Jones, E. Ellen; White, Krista Y.; Burch, Tanya C.; Brooks, Jasmin; Watson, Megan T.; Lance, Raymond S.; Troyer, Dean A.; Semmes, O. John; Mehta, Anand; Drake, Richard R.

2013-01-01

Purpose Using prostatic fluids rich in glycoproteins like prostate specific antigen (PSA) and prostatic acid phosphatase (PAP) , the goal of this study was to identify the structural types and relative abundance of glycans associated with prostate cancer status for subsequent use in emerging mass spectrometry-based glycopeptide analysis platforms. Experimental Design A series of pooled samples of expressed prostatic secretions (EPS) and exosomes reflecting different stages of prostate cancer disease were used for N-linked glycan profiling by three complementary methods, MALDI-TOF profiling, normal-phase HPLC separation, and triple quadropole MS analysis of PAP glycopeptides. Results Glycan profiling of N-linked glycans from different EPS fluids indicated a global decrease in larger branched tri- and tetra-antennary glycans. Differential exoglycosidase treatments indicated a substantial increase in bisecting N-acetylglucosamines correlated with disease severity. A triple quadrupole MS analysis of the N-linked glycopeptides sites from PAP in aggressive prostate cancer pools was done to cross-reference with the glycan profiling data. Conclusion and clinical relevance Changes in glycosylation as detected in EPS fluids reflect the clinical status of prostate cancer. Defining these molecular signatures at the glycopeptide level in individual samples could improve current approaches of diagnosis and prognosis. PMID:23775902

Optical Biomarkers of Serous and Mucinous Human Ovarian Tumor Assessed with Nonlinear Optics Microscopies

PubMed Central

Adur, Javier; Pelegati, Vitor B.; de Thomaz, Andre A.; Baratti, Mariana O.; Almeida, Diogo B.; Andrade, L. A. L. A.; Bottcher-Luiz, Fátima; Carvalho, Hernandes F.; Cesar, Carlos L.

2012-01-01

Background Nonlinear optical (NLO) microscopy techniques have potential to improve the early detection of epithelial ovarian cancer. In this study we showed that multimodal NLO microscopies, including two-photon excitation fluorescence (TPEF), second-harmonic generation (SHG), third-harmonic generation (THG) and fluorescence lifetime imaging microscopy (FLIM) can detect morphological and metabolic changes associated with ovarian cancer progression. Methodology/Principal Findings We obtained strong TPEF + SHG + THG signals from fixed samples stained with Hematoxylin & Eosin (H&E) and robust FLIM signal from fixed unstained samples. Particularly, we imaged 34 ovarian biopsies from different patients (median age, 49 years) including 5 normal ovarian tissue, 18 serous tumors and 11 mucinous tumors with the multimodal NLO platform developed in our laboratory. We have been able to distinguish adenomas, borderline, and adenocarcinomas specimens. Using a complete set of scoring methods we found significant differences in the content, distribution and organization of collagen fibrils in the stroma as well as in the morphology and fluorescence lifetime from epithelial ovarian cells. Conclusions/Significance NLO microscopes provide complementary information about tissue microstructure, showing distinctive patterns for serous and mucinous ovarian tumors. The results provide a basis to interpret future NLO images of ovarian tissue and lay the foundation for future in vivo optical evaluation of premature ovarian lesions. PMID:23056557

The application of proteomics in different aspects of hepatocellular carcinoma research.

PubMed

Xing, Xiaohua; Liang, Dong; Huang, Yao; Zeng, Yongyi; Han, Xiao; Liu, Xiaolong; Liu, Jingfeng

2016-08-11

Hepatocellular carcinoma (HCC) is one of the most common malignant tumors, which is causing the second leading cancer-related death worldwide. With the significant advances of high-throughput protein analysis techniques, the proteomics offered an extremely useful and versatile analytical platform for biomedical researches. In recent years, different proteomic strategies have been widely applied in the various aspects of HCC studies, ranging from screening the early diagnostic and prognostic biomarkers to in-depth investigating the underlying molecular mechanisms. In this review, we would like to systematically summarize the current applications of proteomics in hepatocellular carcinoma study, and discuss the challenges of applying proteomics in study clinical samples, as well as discuss the possible application of proteomics in precision medicine. In this review, we have systematically summarized the current applications of proteomics in hepatocellular carcinoma study, ranging from screening biomarkers to in-depth investigating the underlying molecular mechanisms. In addition, we have discussed the challenges of applying proteomics in study clinical samples, as well as the possible applications of proteomics in precision medicine. We believe that this review would help readers to be better familiar with the recent progresses of clinical proteomics, especially in the field of hepatocellular carcinoma research. Copyright © 2016 Elsevier B.V. All rights reserved.

Development of a Shared Decision Making coding system for analysis of patient-healthcare provider encounters

PubMed Central

Clayman, Marla L.; Makoul, Gregory; Harper, Maya M.; Koby, Danielle G.; Williams, Adam R.

2012-01-01

Objectives Describe the development and refinement of a scheme, Detail of Essential Elements and Participants in Shared Decision Making (DEEP-SDM), for coding Shared Decision Making (SDM) while reporting on the characteristics of decisions in a sample of patients with metastatic breast cancer. Methods The Evidence-Based Patient Choice instrument was modified to reflect Makoul and Clayman’s Integrative Model of SDM. Coding was conducted on video recordings of 20 women at the first visit with their medical oncologists after suspicion of disease progression. Noldus Observer XT v.8, a video coding software platform, was used for coding. Results The sample contained 80 decisions (range: 1-11), divided into 150 decision making segments. Most decisions were physician-led, although patients and physicians initiated similar numbers of decision-making conversations. Conclusion DEEP-SDM facilitates content analysis of encounters between women with metastatic breast cancer and their medical oncologists. Despite the fractured nature of decision making, it is possible to identify decision points and to code each of the Essential Elements of Shared Decision Making. Further work should include application of DEEP-SDM to non-cancer encounters. Practice Implications: A better understanding of how decisions unfold in the medical encounter can help inform the relationship of SDM to patient-reported outcomes. PMID:22784391

Reduction of matrix interferences in furnace atomic absorption with the L'vov Platform

USGS Publications Warehouse

Kaiser, M.L.; Koirtyohann, S.R.; Hinderberger, E.J.; Taylor, Howard E.

1981-01-01

Use of a modified L'vov Platform and ammonium phosphate as a matrix modifier greatly reduced matrix interferences in a commercial Massmann-type atomic absorption furnace. Platforms were readily fabricated from furnace tubes and, once positioned in the furnace, caused no inconvenience in operation. Two volatile elements (Pb, Cd), two of intermediate volatility (Co, Cr) and two which form stable oxides (Al, Sn) were tested in natural water and selected synthetic matrices. In every case for which there was a significant matrix effect during atomization from the tube wall, the platform and platform plus modifier gave improved performance. With lead, for example, an average ratio of 0.48 ?? 0.11 was found when the slope of the standard additions plot for six different natural water samples was compared to the slope of the standard working curve in dilute acid. The average slope ratio between the natural water matrices and the dilute acid matrix was 0.94 ?? 0.03 with the L'vov Platform and 0.96 ?? 0.03 with the platform and matrix modifier. In none of the cases studied did the use of the platform or platform plus modifier cause an interference problem where none existed while atomizing from the tube wall. An additional benefit of the platform was a factor of about two improvement in peak height precision. ?? 1981.

Aerostat-Lofted Instrument Platform and Sampling Method for Determination of Emissions from Open Area Sources

EPA Science Inventory

Sampling emissions from open area sources, particularly sources of open burning, is difficult due to fast dilution of emissions and safety concerns for personnel. Representative emission samples can be difficult to obtain with flaming and explosive sources since personnel safety ...

Novel peptide-based platform for the dual presentation of biologically active peptide motifs on biomaterials.

PubMed

Mas-Moruno, Carlos; Fraioli, Roberta; Albericio, Fernando; Manero, José María; Gil, F Javier

2014-05-14

Biofunctionalization of metallic materials with cell adhesive molecules derived from the extracellular matrix is a feasible approach to improve cell-material interactions and enhance the biointegration of implant materials (e.g., osseointegration of bone implants). However, classical biomimetic strategies may prove insufficient to elicit complex and multiple biological signals required in the processes of tissue regeneration. Thus, newer strategies are focusing on installing multifunctionality on biomaterials. In this work, we introduce a novel peptide-based divalent platform with the capacity to simultaneously present distinct bioactive peptide motifs in a chemically controlled fashion. As a proof of concept, the integrin-binding sequences RGD and PHSRN were selected and introduced in the platform. The biofunctionalization of titanium with this platform showed a positive trend towards increased numbers of cell attachment, and statistically higher values of spreading and proliferation of osteoblast-like cells compared to control noncoated samples. Moreover, it displayed statistically comparable or improved cell responses compared to samples coated with the single peptides or with an equimolar mixture of the two motifs. Osteoblast-like cells produced higher levels of alkaline phosphatase on surfaces functionalized with the platform than on control titanium; however, these values were not statistically significant. This study demonstrates that these peptidic structures are versatile tools to convey multiple biofunctionality to biomaterials in a chemically defined manner.

Advancing the global proteome survey platform by using an oriented single chain antibody fragment immobilization approach.

PubMed

Säll, Anna; Persson, Helena; Ohlin, Mats; Borrebaeck, Carl A K; Wingren, Christer

2016-09-25

Increasing the understanding of a proteome and how its protein composition is affected by for example different diseases, such as cancer, has the potential to improve strategies for early diagnosis and therapeutics. The Global Proteome Survey or GPS is a method that combines mass spectrometry and affinity enrichment with the use of antibodies. The technology enables profiling of complex proteomes in a species independent manner. The sensitivity of GPS, and other methods relying on affinity enrichment, is largely affected by the activity of the exploited affinity reagent. We here present an improvement of the GPS platform by utilizing an antibody immobilization approach which ensures a controlled immobilization process of the antibody to the magnetic bead support. More specifically, we make use of an antibody format that enables site-directed biotinylation and use this in combination with streptavidin coated magnetic beads. The performance of the expanded GPS platform was evaluated by profiling yeast proteome samples. We demonstrate that the oriented antibody immobilization strategy increases the ability of the GPS platform and results in larger fraction of functional antibodies. Additionally, we show that this new antibody format enabled in-solution capture, i.e. immobilization of the antibodies after sample incubation. A workflow has been established that permit the use of an oriented immobilization strategy for the GPS platform. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Automation of diagnostic genetic testing: mutation detection by cyclic minisequencing.

PubMed

Alagrund, Katariina; Orpana, Arto K

2014-01-01

The rising role of nucleic acid testing in clinical decision making is creating a need for efficient and automated diagnostic nucleic acid test platforms. Clinical use of nucleic acid testing sets demands for shorter turnaround times (TATs), lower production costs and robust, reliable methods that can easily adopt new test panels and is able to run rare tests in random access principle. Here we present a novel home-brew laboratory automation platform for diagnostic mutation testing. This platform is based on the cyclic minisequecing (cMS) and two color near-infrared (NIR) detection. Pipetting is automated using Tecan Freedom EVO pipetting robots and all assays are performed in 384-well micro plate format. The automation platform includes a data processing system, controlling all procedures, and automated patient result reporting to the hospital information system. We have found automated cMS a reliable, inexpensive and robust method for nucleic acid testing for a wide variety of diagnostic tests. The platform is currently in clinical use for over 80 mutations or polymorphisms. Additionally to tests performed from blood samples, the system performs also epigenetic test for the methylation of the MGMT gene promoter, and companion diagnostic tests for analysis of KRAS and BRAF gene mutations from formalin fixed and paraffin embedded tumor samples. Automation of genetic test reporting is found reliable and efficient decreasing the work load of academic personnel.

Portable, one-step, and rapid GMR biosensor platform with smartphone interface.

PubMed

Choi, Joohong; Gani, Adi Wijaya; Bechstein, Daniel J B; Lee, Jung-Rok; Utz, Paul J; Wang, Shan X

2016-11-15

Quantitative immunoassay tests in clinical laboratories require trained technicians, take hours to complete with multiple steps, and the instruments used are generally immobile-patient samples have to be sent in to the labs for analysis. This prevents quantitative immunoassay tests to be performed outside laboratory settings. A portable, quantitative immunoassay device will be valuable in rural and resource-limited areas, where access to healthcare is scarce or far away. We have invented Eigen Diagnosis Platform (EDP), a portable quantitative immunoassay platform based on Giant Magnetoresistance (GMR) biosensor technology. The platform does not require a trained technician to operate, and only requires one-step user involvement. It displays quantitative results in less than 15min after sample insertion, and each test costs less than US$4. The GMR biosensor employed in EDP is capable of detecting multiple biomarkers in one test, enabling a wide array of immune diagnostics to be performed simultaneously. In this paper, we describe the design of EDP, and demonstrate its capability. Multiplexed assay of human immunoglobulin G and M (IgG and IgM) antibodies with EDP achieves sensitivities down to 0.07 and 0.33 nanomolar, respectively. The platform will allow lab testing to be performed in remote areas, and open up applications of immunoassay testing in other non-clinical settings, such as home, school, and office. Copyright © 2016 Elsevier B.V. All rights reserved.

Anthropometry as a predictor of vertical jump heights derived from an instrumented platform.

PubMed

Caruso, John F; Daily, Jeremy S; Mason, Melissa L; Shepherd, Catherine M; McLagan, Jessica R; Marshall, Mallory R; Walker, Ron H; West, Jason O

2012-01-01

The current study purpose examined the vertical height-anthropometry relationship with jump data obtained from an instrumented platform. Our methods required college-aged (n = 177) subjects to make 3 visits to our laboratory to measure the following anthropometric variables: height, body mass, upper arm length (UAL), lower arm length, upper leg length, and lower leg length. Per jump, maximum height was measured in 3 ways: from the subjects' takeoff, hang times, and as they landed on the platform. Standard multivariate regression assessed how well anthropometry predicted the criterion variance per gender (men, women, pooled) and jump height method (takeoff, hang time, landing) combination. Z-scores indicated that small amounts of the total data were outliers. The results showed that the majority of outliers were from jump heights calculated as women landed on the platform. With the genders pooled, anthropometry predicted a significant (p < 0.05) amount of variance from jump heights calculated from both takeoff and hang time. The anthropometry-vertical jump relationship was not significant from heights calculated as subjects landed on the platform, likely due to the female outliers. Yet anthropometric data of men did predict a significant amount of variance from heights calculated when they landed on the platform; univariate correlations of men's data revealed that UAL was the best predictor. It was concluded that the large sample of men's data led to greater data heterogeneity and a higher univariate correlation. Because of our sample size and data heterogeneity, practical applications suggest that coaches may find our results best predict performance for a variety of college-aged athletes and vertical jump enthusiasts.

Summer and winter plankton fish assemblages around offshore oil and gas platforms in south-eastern Australia

NASA Astrophysics Data System (ADS)

Neira, Francisco J.

2005-06-01

Opportunistic plankton surveys were conducted within a 5-nmi radius of nine offshore oil and gas platforms in Bass Strait, south-eastern Australia, in February 1998 and 1999 (summer) and August 1998 (winter). The 108 day-night samples collected alongside (vertical tows) and nearby (surface and oblique tows) platforms yielded 1526 larval and early juvenile fishes representing 55 taxa from 45 families. Epipelagic/mesopelagic taxa dominated the catches, whereas hard/soft habitat-associated taxa were uncommon. Carangidae (36.2%) and Myctophidae (31.5%) dominated in summer and winter, respectively. The most abundant taxon was Trachurus declivis (Carangidae, 35.1%), followed by Bovichtus angustifrons (Bovichtidae, 8.7%), Scomberesox saurus (Scomberesocidae, 3.7%), Centroberyx affinis (Berycidae, 3.0%) and Arripis trutta (Arripidae, 1.7%). Fish concentrations (nos. per 100 m 3) alongside platforms did not differ significantly between day and night across all surveys. Likewise, concentrations nearby platforms in February 1999, including those of T. declivis, did not vary significantly by tow type (surface vs. oblique) or day vs. night. The far greater diversity and abundance recorded in February 1999 are likely the result of upwelling conditions over the eastern Bass Strait shelf during the sampling period, and which were not detected in February 1998. In the absence of data on adult fishes associated with the Bass Strait platforms, and given the limited availability of reefs directly around the area, it could be argued that some of the taxa caught may originate from spawning around neighboring natural reefs, particularly those off the Gippsland coastline and the south-east corner of mainland Australia. However, the prime position of the platforms almost right in the center of a productivity "hotspot" would have a confounding effect on the potential source(s) of larval fishes in that region of south-eastern Australia. The role of platforms as potential de-facto reefs for juvenile fishes in Bass Strait, as well as spawning areas, is discussed based on the findings of this study, the first on early stages of fishes around oil and gas platforms in Australia.

Cross-platform validation and analysis environment for particle physics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chekanov, S. V.; Pogrebnyak, I.; Wilbern, D.

A multi-platform validation and analysis framework for public Monte Carlo simulation for high-energy particle collisions is discussed. The front-end of this framework uses the Python programming language, while the back-end is written in Java, which provides a multi-platform environment that can be run from a web browser and can easily be deployed at the grid sites. The analysis package includes all major software tools used in high-energy physics, such as Lorentz vectors, jet algorithms, histogram packages, graphic canvases, and tools for providing data access. This multi-platform software suite, designed to minimize OS-specific maintenance and deployment time, is used for onlinemore » validation of Monte Carlo event samples through a web interface.« less

Next generation platforms for high-throughput biodosimetry.

PubMed

Repin, Mikhail; Turner, Helen C; Garty, Guy; Brenner, David J

2014-06-01

Here the general concept of the combined use of plates and tubes in racks compatible with the American National Standards Institute/the Society for Laboratory Automation and Screening microplate formats as the next generation platforms for increasing the throughput of biodosimetry assays was described. These platforms can be used at different stages of biodosimetry assays starting from blood collection into microtubes organised in standardised racks and ending with the cytogenetic analysis of samples in standardised multiwell and multichannel plates. Robotically friendly platforms can be used for different biodosimetry assays in minimally equipped laboratories and on cost-effective automated universal biotech systems. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Real-time label-free quantitative fluorescence microscopy-based detection of ATP using a tunable fluorescent nano-aptasensor platform.

PubMed

Shrivastava, Sajal; Sohn, Il-Yung; Son, Young-Min; Lee, Won-Il; Lee, Nae-Eung

2015-12-14

Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules.

Identification of susceptibility genes and genetic modifiers of human diseases

NASA Astrophysics Data System (ADS)

Abel, Kenneth; Kammerer, Stefan; Hoyal, Carolyn; Reneland, Rikard; Marnellos, George; Nelson, Matthew R.; Braun, Andreas

2005-03-01

The completion of the human genome sequence enables the discovery of genes involved in common human disorders. The successful identification of these genes is dependent on the availability of informative sample sets, validated marker panels, a high-throughput scoring technology, and a strategy for combining these resources. We have developed a universal platform technology based on mass spectrometry (MassARRAY) for analyzing nucleic acids with high precision and accuracy. To fuel this technology, we generated more than 100,000 validated assays for single nucleotide polymorphisms (SNPs) covering virtually all known and predicted human genes. We also established a large DNA sample bank comprised of more than 50,000 consented healthy and diseased individuals. This combination of reagents and technology allows the execution of large-scale genome-wide association studies. Taking advantage of MassARRAY"s capability for quantitative analysis of nucleic acids, allele frequencies are estimated in sample pools containing large numbers of individual DNAs. To compare pools as a first-pass "filtering" step is a tremendous advantage in throughput and cost over individual genotyping. We employed this approach in numerous genome-wide, hypothesis-free searches to identify genes associated with common complex diseases, such as breast cancer, osteoporosis, and osteoarthritis, and genes involved in quantitative traits like high density lipoproteins cholesterol (HDL-c) levels and central fat. Access to additional well-characterized patient samples through collaborations allows us to conduct replication studies that validate true disease genes. These discoveries will expand our understanding of genetic disease predisposition, and our ability for early diagnosis and determination of specific disease subtype or progression stage.

Implementation and Evaluation of a Fully Automated Multiplex Real-Time PCR Assay on the BD Max Platform to Detect and Differentiate Herpesviridae from Cerebrospinal Fluids

PubMed Central

Köller, Thomas; Kurze, Daniel; Lange, Mirjam; Scherdin, Martin; Podbielski, Andreas; Warnke, Philipp

2016-01-01

A fully automated multiplex real-time PCR assay—including a sample process control and a plasmid based positive control—for the detection and differentiation of herpes simplex virus 1 (HSV1), herpes simplex virus 2 (HSV2) and varicella-zoster virus (VZV) from cerebrospinal fluids (CSF) was developed on the BD Max platform. Performance was compared to an established accredited multiplex real time PCR protocol utilizing the easyMAG and the LightCycler 480/II, both very common devices in viral molecular diagnostics. For clinical validation, 123 CSF specimens and 40 reference samples from national interlaboratory comparisons were examined with both methods, resulting in 97.6% and 100% concordance for CSF and reference samples, respectively. Utilizing the BD Max platform revealed sensitivities of 173 (CI 95%, 88–258) copies/ml for HSV1, 171 (CI 95%, 148–194) copies/ml for HSV2 and 84 (CI 95%, 5–163) copies/ml for VZV. Cross reactivity could be excluded by checking 25 common viral, bacterial and fungal human pathogens. Workflow analyses displayed shorter test duration as well as remarkable fewer and easier preparation steps with the potential to reduce error rates occurring when manually assessing patient samples. This protocol allows for a fully automated PCR assay on the BD Max platform for the simultaneously detection of herpesviridae from CSF specimens. Singular or multiple infections due to HSV1, HSV2 and VZV can reliably be differentiated with good sensitivities. Control parameters are included within the assay, thereby rendering its suitability for current quality management requirements. PMID:27092772

Highly-sensitive electrochemical sensing platforms for food colourants based on the property-tuning of porous carbon.

PubMed

Cheng, Qin; Xia, Shanhong; Tong, Jianhua; Wu, Kangbing

2015-08-05

It is very challenging to develop highly-sensitive analytical platforms for toxic synthetic colourants that widely added in food samples. Herein, a series of porous carbon (PC) was prepared using CaCO3 nanoparticles (nano-CaCO3) as the hard template and starch as the carbon precursor. Characterizations of scanning electron microscopy and transmission electron microscopy indicated that the morphology and porous structure were controlled by the weight ratio of starch and nano-CaCO3. The electrochemical behaviours of four kinds of widely-used food colourants, Sunset yellow, Tartrazine, Ponceau 4R and Allura red, were studied. On the surface of PC samples, the oxidation signals of colourants enhanced obviously, and more importantly, the signal enhancement abilities of PC were also dependent on the starch/nano-CaCO3 weight ratio. The greatly-increased electron transfer ability and accumulation efficiency were the main reason for the enhanced signals of colourants, as confirmed by electrochemical impedance spectroscopy and chronocoulometry. The prepared PC-2 sample by 1:1 starch/nano-CaCO3 weight ratio was more active for the oxidation of food colourtants, and increased the signals by 89.4-fold, 79.3-fold, 47.3-fold and 50.7-fold for Sunset yellow, Tartrazine, Ponceau 4R and Allura red. As a result, a highly-sensitive electrochemical sensing platform was developed, and the detection limits were 1.4, 3.5, 2.1 and 1.7 μg L(-1) for Sunset yellow, Tartrazine, Ponceau 4R and Allura red. The practical application of this new sensing platform was demonstrated using drink samples, and the detected results consisted with the values that obtained by high-performance liquid chromatography. Copyright © 2015 Elsevier B.V. All rights reserved.

Accuracy of genomic prediction for BCWD resistance in rainbow trout using different genotyping platforms and genomic selection models

USDA-ARS?s Scientific Manuscript database

In this study, we aimed to (1) predict genomic estimated breeding value (GEBV) for bacterial cold water disease (BCWD) resistance by genotyping training (n=583) and validation samples (n=53) with two genotyping platforms (24K RAD-SNP and 49K SNP) and using different genomic selection (GS) models (Ba...

A Versatile Integrated Ambient Ionization Source Platform.

PubMed

Ai, Wanpeng; Nie, Honggang; Song, Shiyao; Liu, Xiaoyun; Bai, Yu; Liu, Huwei

2018-04-30

The pursuit of high-throughput sample analysis from complex matrix demands development of multiple ionization techniques with complementary specialties. A versatile integrated ambient ionization source (iAmIS) platform is proposed in this work, based on the idea of integrating multiple functions, enhancing the efficiency of current ionization techniques, extending the applications, and decreasing the cost of the instrument. The design of the iAmIS platform combines flowing atmospheric pressure afterglow (FAPA) source/direct analysis in real time (DART), dielectric barrier discharge ionization (DBDI)/low-temperature plasma (LTP), desorption electrospray ionization (DESI), and laser desorption (LD) technique. All individual and combined ionization modes can be easily attained by modulating parameters. In particular, the FAPA/DART&DESI mode can realize the detection of polar and nonpolar compounds at the same time with two different ionization mechanisms: proton transfer and charge transfer. The introduction of LD contributes to the mass spectrometry imaging and the surface-assisted laser desorption (SALDI) under ambient condition. Compared with other individual or multi-mode ion source, the iAmIS platform provides the flexibility of choosing different ionization modes, broadens the scope of the analyte detection, and facilitates the analysis of complex samples. Graphical abstract ᅟ.

Doped and undoped graphene platforms: the influence of structural properties on the detection of polyphenols

PubMed Central

Chng, Chu’Er; Sofer, Zdenek; Pumera, Martin; Bonanni, Alessandra

2016-01-01

There is a huge interest in doped graphene and how doping can tune the material properties for the specific application. It was recently demonstrated that the effect of doping can have different influence on the electrochemical detection of electroactive probes, depending on the analysed probe, on the structural characteristics of the graphene materials and on the type and amount of heteroatom used for the doping. In this work we wanted to investigate the effect of doping on graphene materials used as platform for the detection of catechin, a standard probe which is commonly used for the measurement of polyphenols in food and beverages. To this aim we compared undoped graphene with boron-doped graphene and nitrogen doped graphene platforms for the electrochemical detection of standard catechin oxidation. Finally, the material providing the best electrochemical performance was employed for the analysis of real samples. We found that the undoped graphene, possessing lower amount of oxygen functionalities, higher density of defects and larger electroactive surface area provided the best electroanalytical performance for the determination of catechin in commercial beer samples. Our findings are important for the development of novel graphene platforms for the electrochemical assessment of food quality. PMID:26861507

Doped and undoped graphene platforms: the influence of structural properties on the detection of polyphenols

NASA Astrophysics Data System (ADS)

Chng, Chu'Er; Sofer, Zdenek; Pumera, Martin; Bonanni, Alessandra

2016-02-01

There is a huge interest in doped graphene and how doping can tune the material properties for the specific application. It was recently demonstrated that the effect of doping can have different influence on the electrochemical detection of electroactive probes, depending on the analysed probe, on the structural characteristics of the graphene materials and on the type and amount of heteroatom used for the doping. In this work we wanted to investigate the effect of doping on graphene materials used as platform for the detection of catechin, a standard probe which is commonly used for the measurement of polyphenols in food and beverages. To this aim we compared undoped graphene with boron-doped graphene and nitrogen doped graphene platforms for the electrochemical detection of standard catechin oxidation. Finally, the material providing the best electrochemical performance was employed for the analysis of real samples. We found that the undoped graphene, possessing lower amount of oxygen functionalities, higher density of defects and larger electroactive surface area provided the best electroanalytical performance for the determination of catechin in commercial beer samples. Our findings are important for the development of novel graphene platforms for the electrochemical assessment of food quality.

A Versatile Integrated Ambient Ionization Source Platform

NASA Astrophysics Data System (ADS)

Ai, Wanpeng; Nie, Honggang; Song, Shiyao; Liu, Xiaoyun; Bai, Yu; Liu, Huwei

2018-04-01

The pursuit of high-throughput sample analysis from complex matrix demands development of multiple ionization techniques with complementary specialties. A versatile integrated ambient ionization source (iAmIS) platform is proposed in this work, based on the idea of integrating multiple functions, enhancing the efficiency of current ionization techniques, extending the applications, and decreasing the cost of the instrument. The design of the iAmIS platform combines flowing atmospheric pressure afterglow (FAPA) source/direct analysis in real time (DART), dielectric barrier discharge ionization (DBDI)/low-temperature plasma (LTP), desorption electrospray ionization (DESI), and laser desorption (LD) technique. All individual and combined ionization modes can be easily attained by modulating parameters. In particular, the FAPA/DART&DESI mode can realize the detection of polar and nonpolar compounds at the same time with two different ionization mechanisms: proton transfer and charge transfer. The introduction of LD contributes to the mass spectrometry imaging and the surface-assisted laser desorption (SALDI) under ambient condition. Compared with other individual or multi-mode ion source, the iAmIS platform provides the flexibility of choosing different ionization modes, broadens the scope of the analyte detection, and facilitates the analysis of complex samples. [Figure not available: see fulltext.

Mechanical Abrasion as a Low Cost Technique for Contamination-Free Sample Acquisition from a Category IVA Clean Platform

NASA Technical Reports Server (NTRS)

Dolgin, B.; Yarbrough, C.; Carson, J.; Troy, R.

2000-01-01

The proposed Mars Sample Transfer Chain Architecture provides Planetary Protection Officers with clean samples that are required for the eventual release from confinement of the returned Martian samples. At the same time, absolute cleanliness and sterility requirement is not placed of any part of the Lander (including the deep drill), Mars Assent Vehicle (MAV), any part of the Orbiting Sample container (OS), Rover mobility platform, any part of the Minicorer, Robotic arm (including instrument sensors), and most of the caching equipment on the Rover. The removal of the strict requirements in excess of the Category IVa cleanliness (Pathfinder clean) is expected to lead to significant cost savings. The proposed architecture assumes that crosscontamination renders all surfaces in the vicinity of the rover(s) and the lander(s) contaminated. Thus, no accessible surface of Martian rocks and soil is Earth contamination free. As a result of the latter, only subsurface samples (either rock or soil) can be and will be collected for eventual return to Earth. Uncontaminated samples can be collected from a Category IVa clean platform. Both subsurface soil and rock samples can be maintained clean if they are collected by devices that are self-contained and clean and sterile inside only. The top layer of the sample is removed in a manner that does not contaminate the collection tools. Biobarrier (e.g., aluminum foil) covering the moving parts of these devices may be used as the only self removing bio-blanket that is required. The samples never leave the collection tools. The lids are placed on these tools inside the collection device. These single use tools with the lid and the sample inside are brought to Earth in the OS. The lids have to be designed impenetrable to the Earth organisms. The latter is a well established art.

Simultaneous analysis of cerebrospinal fluid biomarkers using microsphere-based xMAP multiplex technology for early detection of Alzheimer's disease.

PubMed

Kang, Ju-Hee; Vanderstichele, Hugo; Trojanowski, John Q; Shaw, Leslie M

2012-04-01

The xMAP-Luminex multiplex platform for measurement of Alzheimer's disease (AD) cerebrospinal fluid (CSF) biomarkers using Innogenetics AlzBio3 immunoassay reagents that are for research use only has been shown to be an effective tool for early detection of an AD-like biomarker signature based on concentrations of CSF Aβ(1-42), t-tau and p-tau(181). Among the several advantages of the xMAP-Luminex platform for AD CSF biomarkers are: a wide dynamic range of ready-to-use calibrators, time savings for the simultaneous analyses of three biomarkers in one analytical run, reduction of human error, potential of reduced cost of reagents, and a modest reduction of sample volume as compared to conventional enzyme-linked immunosorbant assay (ELISA) methodology. Recent clinical studies support the use of CSF Aβ(1-42), t-tau and p-tau(181) measurement using the xMAP-Luminex platform for the early detection of AD pathology in cognitively normal individuals, and for prediction of progression to AD dementia in subjects with mild cognitive impairment (MCI). Studies that have shown the prediction of risk for progression to AD dementia by MCI patients provide the basis for the use of CSF Aβ(1-42), t-tau and p-tau(181) testing to assign risk for progression in patients enrolled in therapeutic trials. Furthermore emerging study data suggest that these pathologic changes occur in cognitively normal subjects 20 or more years before the onset of clinically detectable memory changes thus providing an objective measurement for use in the assessment of treatment effects in primary treatment trials. However, numerous previous ELISA and Luminex-based multiplex studies reported a wide range of absolute values of CSF Aβ(1-42), t-tau and p-tau(181) indicative of substantial inter-laboratory variability as well as varying degrees of intra-laboratory imprecision. In order to address these issues a recent inter-laboratory investigation that included a common set of CSF pool aliquots from controls as well as AD patients over a range of normal and pathological Aβ(1-42), t-tau and p-tau(181) values as well as agreed-on standard operating procedures (SOPs) assessed the reproducibility of the multiplex methodology and Innogenetics AlzBio3 immunoassay reagents. This study showed within-center precision values of 5% to a little more than 10% and good inter-laboratory %CV values (10-20%). There are several likely factors influencing the variability of CSF Aβ(1-42), t-tau and p-tau(181) measurements. In this review, we describe the pre-analytical, analytical and post-analytical sources of variability including sources inherent to kits, and describe procedures to decrease the variability. A CSF AD biomarker Quality Control program has been established and funded by the Alzheimer Association, and global efforts are underway to further define optimal pre-analytical SOPs and best practices for the methodologies available or in development including plans for production of a standard reference material that could provide for a common standard against which manufacturers of immunoassay kits would assign calibration standard values. Copyright © 2012 Elsevier Inc. All rights reserved.

Experimental platform utilising melting curve technology for detection of mutations in Mycobacterium tuberculosis isolates.

PubMed

Broda, Agnieszka; Nikolayevskyy, Vlad; Casali, Nicki; Khan, Huma; Bowker, Richard; Blackwell, Gemma; Patel, Bhakti; Hume, James; Hussain, Waqar; Drobniewski, Francis

2018-04-20

Tuberculosis (TB) remains one of the most deadly infections with approximately a quarter of cases not being identified and/or treated mainly due to a lack of resources. Rapid detection of TB or drug-resistant TB enables timely adequate treatment and is a cornerstone of effective TB management. We evaluated the analytical performance of a single-tube assay for multidrug-resistant TB (MDR-TB) on an experimental platform utilising RT-PCR and melting curve analysis that could potentially be operated as a point-of-care (PoC) test in resource-constrained settings with a high burden of TB. Firstly, we developed and evaluated the prototype MDR-TB assay using specimens extracted from well-characterised TB isolates with a variety of distinct rifampicin and isoniazid resistance conferring mutations and nontuberculous Mycobacteria (NTM) strains. Secondly, we validated the experimental platform using 98 clinical sputum samples from pulmonary TB patients collected in high MDR-TB settings. The sensitivity of the platform for TB detection in clinical specimens was 75% for smear-negative and 92.6% for smear-positive sputum samples. The sensitivity of detection for rifampicin and isoniazid resistance was 88.9 and 96.0% and specificity was 87.5 and 100%, respectively. Observed limitations in sensitivity and specificity could be resolved by adjusting the sample preparation methodology and melting curve recognition algorithm. Overall technology could be considered a promising PoC methodology especially in resource-constrained settings based on its combined accuracy, convenience, simplicity, speed, and cost characteristics.

Field Programmable Gate Array Based Parallel Strapdown Algorithm Design for Strapdown Inertial Navigation Systems

PubMed Central

Li, Zong-Tao; Wu, Tie-Jun; Lin, Can-Long; Ma, Long-Hua

2011-01-01

A new generalized optimum strapdown algorithm with coning and sculling compensation is presented, in which the position, velocity and attitude updating operations are carried out based on the single-speed structure in which all computations are executed at a single updating rate that is sufficiently high to accurately account for high frequency angular rate and acceleration rectification effects. Different from existing algorithms, the updating rates of the coning and sculling compensations are unrelated with the number of the gyro incremental angle samples and the number of the accelerometer incremental velocity samples. When the output sampling rate of inertial sensors remains constant, this algorithm allows increasing the updating rate of the coning and sculling compensation, yet with more numbers of gyro incremental angle and accelerometer incremental velocity in order to improve the accuracy of system. Then, in order to implement the new strapdown algorithm in a single FPGA chip, the parallelization of the algorithm is designed and its computational complexity is analyzed. The performance of the proposed parallel strapdown algorithm is tested on the Xilinx ISE 12.3 software platform and the FPGA device XC6VLX550T hardware platform on the basis of some fighter data. It is shown that this parallel strapdown algorithm on the FPGA platform can greatly decrease the execution time of algorithm to meet the real-time and high precision requirements of system on the high dynamic environment, relative to the existing implemented on the DSP platform. PMID:22164058

Examining the scope and patterns of deliberate self-injurious cutting content in popular social media.

PubMed

Miguel, Elizabeth M; Chou, Tommy; Golik, Alejandra; Cornacchio, Danielle; Sanchez, Amanda L; DeSerisy, Mariah; Comer, Jonathan S

2017-09-01

Social networking services (SNS) have rapidly become a central platform for adolescents' social interactions and media consumption patterns. The present study examined a representative sample of publicly accessible content related to deliberate self-injurious cutting across three SNS platforms: Twitter, Tumblr, and Instagram. Data collection simulated searches for publicly available deliberate self-injury content on Twitter, Tumblr, and Instagram. Over a six-month period at randomly generated time points, data were obtained by searching "#cutting" on each SNS platform and collecting the first 10 posts generated. Independent evaluators coded posts for presence of the following: (a) graphic content, (b) negative self-evaluations, (c) references to mental health terms, (d) discouragement of deliberate self-injury, and (e) recovery-oriented resources. Differences across platforms were examined. Data collection yielded a sample of 1,155 public posts (770 of which were related to mental health). Roughly 60% of sampled posts depicted graphic content, almost half included negative self-evaluations, only 9.5% discouraged self-injury, and <1% included formal recovery resources. Instagram posts displayed the greatest proportion of graphic content and negative self-evaluations, whereas Twitter exhibited the smallest proportion of each. Findings characterize the graphic nature of online SNS deliberate self-injury content and the relative absence of SNS-posted resources for populations seeking out deliberate self-injurious cutting content. Mental health professionals must recognize the rapidly changing landscape of adolescent media consumption, influences, and social interaction as they may pertain to self-harm patterns. © 2017 Wiley Periodicals, Inc.

Site-specific characterization of beetle horn shell with micromechanical bending test in focused ion beam system.

PubMed

Lee, Hyun-Taek; Kim, Ho-Jin; Kim, Chung-Soo; Gomi, Kenji; Taya, Minoru; Nomura, Shûhei; Ahn, Sung-Hoon

2017-07-15

Biological materials are the result of years of evolution and possess a number of efficient features and structures. Researchers have investigated the possibility of designing biomedical structures that take advantage of these structural features. Insect shells, such as beetle shells, are among the most promising types of biological material for biomimetic development. However, due to their intricate geometries and small sizes, it is challenging to measure the mechanical properties of these microscale structures. In this study, we developed an in-situ testing platform for site-specific experiments in a focused ion beam (FIB) system. Multi-axis nano-manipulators and a micro-force sensor were utilized in the testing platform to allow better results in the sample preparation and data acquisition. The entire test protocol, consisting of locating sample, ion beam milling and micro-mechanical bending tests, can be carried out without sample transfer or reattachment. We used our newly devised test platform to evaluate the micromechanical properties and structural features of each separated layer of the beetle horn shell. The Young's modulus of both the exocuticle and endocuticle layers was measured. We carried out a bending test to characterize the layers mechanically. The exocuticle layer bent in a brick-like manner, while the endocuticle layer exhibited a crack blunting effect. This paper proposed an in-situ manipulation/test method in focused ion beam for characterizing micromechanical properties of beetle horn shell. The challenge in precise and accurate fabrication for the samples with complex geometry was overcome by using nano-manipulators having multi-degree of freedom and a micro-gripper. With the aid of this specially designed test platform, bending tests were carried out on cantilever-shaped samples prepared by focused ion beam milling. Structural differences between exocuticle and endocuticle layers of beetle horn shell were explored and the results provided insight into the structural advantages of each biocomposite structure. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

FY2011 Annual Progress Report for Vehicle and Systems Simulation and Testing

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

2012-01-15

The VSST team's mission is to evaluate the technologies and performance characteristics of advanced automotive powertrain components and subsystems in an integrated vehicle systems context. These evaluations address light-, medium-, and heavy-duty vehicle platforms. This work is directed toward evaluating and verifying the targets of the VTP R&D teams and to providing guidance in establishing roadmaps for achievement of these goals.

Microfluidic platform for assessing pancreatic islet functionality through dielectric spectroscopy

PubMed Central

Heileman, K.; Daoud, J.; Hasilo, C.; Gasparrini, M.; Paraskevas, S.; Tabrizian, M.

2015-01-01

Human pancreatic islets are seldom assessed for dynamic responses to external stimuli. Thus, the elucidation of human islet functionality would provide insights into the progression of diabetes mellitus, evaluation of preparations for clinical transplantation, as well as for the development of novel therapeutics. The objective of this study was to develop a microfluidic platform for in vitro islet culture, allowing the multi-parametric investigation of islet response to chemical and biochemical stimuli. This was accomplished through the fabrication and implementation of a microfluidic platform that allowed the perifusion of islet culture while integrating real-time monitoring using impedance spectroscopy, through microfabricated, interdigitated electrodes located along the microchamber arrays. Real-time impedance measurements provide important dielectric parameters, such as cell membrane capacitance and cytoplasmic conductivity, representing proliferation, differentiation, viability, and functionality. The perifusion of varying glucose concentrations and monitoring of the resulting impedance of pancreatic islets were performed as proof-of-concept validation of the lab-on-chip platform. This novel technique to elucidate the underlying mechanisms that dictate islet functionality is presented, providing new information regarding islet function that could improve the evaluation of islet preparations for transplantation. In addition, it will lead to a better understanding of fundamental diabetes-related islet dysfunction and the development of therapeutics through evaluation of potential drug effects. PMID:26339324