A Lightweight Protocol for Secure Video Streaming.

PubMed

Venčkauskas, Algimantas; Morkevicius, Nerijus; Bagdonas, Kazimieras; Damaševičius, Robertas; Maskeliūnas, Rytis

2018-05-14

The Internet of Things (IoT) introduces many new challenges which cannot be solved using traditional cloud and host computing models. A new architecture known as fog computing is emerging to address these technological and security gaps. Traditional security paradigms focused on providing perimeter-based protections and client/server point to point protocols (e.g., Transport Layer Security (TLS)) are no longer the best choices for addressing new security challenges in fog computing end devices, where energy and computational resources are limited. In this paper, we present a lightweight secure streaming protocol for the fog computing "Fog Node-End Device" layer. This protocol is lightweight, connectionless, supports broadcast and multicast operations, and is able to provide data source authentication, data integrity, and confidentiality. The protocol is based on simple and energy efficient cryptographic methods, such as Hash Message Authentication Codes (HMAC) and symmetrical ciphers, and uses modified User Datagram Protocol (UDP) packets to embed authentication data into streaming data. Data redundancy could be added to improve reliability in lossy networks. The experimental results summarized in this paper confirm that the proposed method efficiently uses energy and computational resources and at the same time provides security properties on par with the Datagram TLS (DTLS) standard.

A self-paced motor imagery based brain-computer interface for robotic wheelchair control.

PubMed

Tsui, Chun Sing Louis; Gan, John Q; Hu, Huosheng

2011-10-01

This paper presents a simple self-paced motor imagery based brain-computer interface (BCI) to control a robotic wheelchair. An innovative control protocol is proposed to enable a 2-class self-paced BCI for wheelchair control, in which the user makes path planning and fully controls the wheelchair except for the automatic obstacle avoidance based on a laser range finder when necessary. In order for the users to train their motor imagery control online safely and easily, simulated robot navigation in a specially designed environment was developed. This allowed the users to practice motor imagery control with the core self-paced BCI system in a simulated scenario before controlling the wheelchair. The self-paced BCI can then be applied to control a real robotic wheelchair using a protocol similar to that controlling the simulated robot. Our emphasis is on allowing more potential users to use the BCI controlled wheelchair with minimal training; a simple 2-class self paced system is adequate with the novel control protocol, resulting in a better transition from offline training to online control. Experimental results have demonstrated the usefulness of the online practice under the simulated scenario, and the effectiveness of the proposed self-paced BCI for robotic wheelchair control.

Simple and Sensitive Paper-Based Device Coupling Electrochemical Sample Pretreatment and Colorimetric Detection.

PubMed

Silva, Thalita G; de Araujo, William R; Muñoz, Rodrigo A A; Richter, Eduardo M; Santana, Mário H P; Coltro, Wendell K T; Paixão, Thiago R L C

2016-05-17

We report the development of a simple, portable, low-cost, high-throughput visual colorimetric paper-based analytical device for the detection of procaine in seized cocaine samples. The interference of most common cutting agents found in cocaine samples was verified, and a novel electrochemical approach was used for sample pretreatment in order to increase the selectivity. Under the optimized experimental conditions, a linear analytical curve was obtained for procaine concentrations ranging from 5 to 60 μmol L(-1), with a detection limit of 0.9 μmol L(-1). The accuracy of the proposed method was evaluated using seized cocaine samples and an addition and recovery protocol.

Accuracy of binding mode prediction with a cascadic stochastic tunneling method.

PubMed

Fischer, Bernhard; Basili, Serena; Merlitz, Holger; Wenzel, Wolfgang

2007-07-01

We investigate the accuracy of the binding modes predicted for 83 complexes of the high-resolution subset of the ASTEX/CCDC receptor-ligand database using the atomistic FlexScreen approach with a simple forcefield-based scoring function. The median RMS deviation between experimental and predicted binding mode was just 0.83 A. Over 80% of the ligands dock within 2 A of the experimental binding mode, for 60 complexes the docking protocol locates the correct binding mode in all of ten independent simulations. Most docking failures arise because (a) the experimental structure clashed in our forcefield and is thus unattainable in the docking process or (b) because the ligand is stabilized by crystal water. 2007 Wiley-Liss, Inc.

Everything should be as simple as possible, but no simpler: towards a protocol for accumulating evidence regarding the active content of health behaviour change interventions.

PubMed

Peters, Gjalt-Jorn Ygram; de Bruin, Marijn; Crutzen, Rik

2015-01-01

There is a need to consolidate the evidence base underlying our toolbox of methods of behaviour change. Recent efforts to this effect have conducted meta-regressions on evaluations of behaviour change interventions, deriving each method's effectiveness from its association to intervention effect size. However, there are a range of issues that raise concern about whether this approach is actually furthering or instead obstructing the advancement of health psychology theories and the quality of health behaviour change interventions. Using examples from theory, the literature and data from previous meta-analyses, these concerns and their implications are explained and illustrated. An iterative protocol for evidence base accumulation is proposed that integrates evidence derived from both experimental and applied behaviour change research, and combines theory development in experimental settings with theory testing in applied real-life settings. As evidence gathered in this manner accumulates, a cumulative science of behaviour change can develop.

Everything should be as simple as possible, but no simpler: towards a protocol for accumulating evidence regarding the active content of health behaviour change interventions

PubMed Central

Peters, Gjalt-Jorn Ygram; de Bruin, Marijn; Crutzen, Rik

2015-01-01

There is a need to consolidate the evidence base underlying our toolbox of methods of behaviour change. Recent efforts to this effect have conducted meta-regressions on evaluations of behaviour change interventions, deriving each method's effectiveness from its association to intervention effect size. However, there are a range of issues that raise concern about whether this approach is actually furthering or instead obstructing the advancement of health psychology theories and the quality of health behaviour change interventions. Using examples from theory, the literature and data from previous meta-analyses, these concerns and their implications are explained and illustrated. An iterative protocol for evidence base accumulation is proposed that integrates evidence derived from both experimental and applied behaviour change research, and combines theory development in experimental settings with theory testing in applied real-life settings. As evidence gathered in this manner accumulates, a cumulative science of behaviour change can develop. PMID:25793484

PubSearch and PubFetch: a simple management system for semiautomated retrieval and annotation of biological information from the literature.

PubMed

Yoo, Danny; Xu, Iris; Berardini, Tanya Z; Rhee, Seung Yon; Narayanasamy, Vijay; Twigger, Simon

2006-03-01

For most systems in biology, a large body of literature exists that describes the complexity of the system based on experimental results. Manual review of this literature to extract targeted information into biological databases is difficult and time consuming. To address this problem, we developed PubSearch and PubFetch, which store literature, keyword, and gene information in a relational database, index the literature with keywords and gene names, and provide a Web user interface for annotating the genes from experimental data found in the associated literature. A set of protocols is provided in this unit for installing, populating, running, and using PubSearch and PubFetch. In addition, we provide support protocols for performing controlled vocabulary annotations. Intended users of PubSearch and PubFetch are database curators and biology researchers interested in tracking the literature and capturing information about genes of interest in a more effective way than with conventional spreadsheets and lab notebooks.

Using Simple Linear Regression to Assess the Success of the Montreal Protocol in Reducing Atmospheric Chlorofluorocarbons

ERIC Educational Resources Information Center

Nelson, Dean

2009-01-01

Following the Guidelines for Assessment and Instruction in Statistics Education (GAISE) recommendation to use real data, an example is presented in which simple linear regression is used to evaluate the effect of the Montreal Protocol on atmospheric concentration of chlorofluorocarbons. This simple set of data, obtained from a public archive, can…

Decarboxylative Fluorination of Aliphatic Carboxylic Acids via Photoredox Catalysis.

PubMed

Ventre, Sandrine; Petronijevic, Filip R; MacMillan, David W C

2015-05-06

The direct conversion of aliphatic carboxylic acids to the corresponding alkyl fluorides has been achieved via visible light-promoted photoredox catalysis. This operationally simple, redox-neutral fluorination method is amenable to a wide variety of carboxylic acids. Photon-induced oxidation of carboxylates leads to the formation of carboxyl radicals, which upon rapid CO2-extrusion and F(•) transfer from a fluorinating reagent yield the desired fluoroalkanes with high efficiency. Experimental evidence indicates that an oxidative quenching pathway is operable in this broadly applicable fluorination protocol.

Faster experimental validation of microRNA targets using cold fusion cloning and a dual firefly-Renilla luciferase reporter assay.

PubMed

Alvarez, M Lucrecia

2014-01-01

Different target prediction algorithms have been developed to provide a list of candidate target genes for a given animal microRNAs (miRNAs). However, these computational approaches provide both false-positive and false-negative predictions. Therefore, the target genes of a specific miRNA identified in silico should be experimentally validated. In this chapter, we describe a step-by-step protocol for the experimental validation of a direct miRNA target using a faster Dual Firefly-Renilla Luciferase Reporter Assay. We describe how to construct reporter plasmids using the simple, fast, and highly efficient cold fusion cloning technology, which does not require ligase, phosphatase, or restriction enzymes. In addition, we provide a protocol for co-transfection of reporter plasmids with either miRNA mimics or miRNA inhibitors in human embryonic kidney 293 (HEK293) cells, as well as a description on how to measure Firefly and Renilla luciferase activity using the Dual-Glo Luciferase Assay kit. As an example of the use of this technology, we will validate glucose-6-phosphate dehydrogenase (G6PD) as a direct target of miR-1207-5p.

A Simple XML Producer-Consumer Protocol

NASA Technical Reports Server (NTRS)

Smith, Warren; Gunter, Dan; Quesnel, Darcy

2000-01-01

This document describes a simple XML-based protocol that can be used for producers of events to communicate with consumers of events. The protocol described here is not meant to be the most efficient protocol, the most logical protocol, or the best protocol in any way. This protocol was defined quickly and it's intent is to give us a reasonable protocol that we can implement relatively easily and then use to gain experience in distributed event services. This experience will help us evaluate proposals for event representations, XML-based encoding of information, and communication protocols. The next section of this document describes how we represent events in this protocol and then defines the two events that we choose to use for our initial experiments. These definitions are made by example so that they are informal and easy to understand. The following section then proceeds to define the producer-consumer protocol we have agreed upon for our initial experiments.

Route to one-step microstructure mold fabrication for PDMS microfluidic chip

NASA Astrophysics Data System (ADS)

Lv, Xiaoqing; Geng, Zhaoxin; Fan, Zhiyuan; Wang, Shicai; Su, Yue; Fang, Weihao; Pei, Weihua; Chen, Hongda

2018-04-01

The microstructure mold fabrication for PDMS microfluidic chip remains complex and time-consuming process requiring special equipment and protocols: photolithography and etching. Thus, a rapid and cost-effective method is highly needed. Comparing with the traditional microfluidic chip fabricating process based on the micro-electromechanical system (MEMS), this method is simple and easy to implement, and the whole fabrication process only requires 1-2 h. Different size of microstructure from 100 to 1000 μm was fabricated, and used to culture four kinds of breast cancer cell lines. Cell viability and morphology was assessed when they were cultured in the micro straight channels, micro square holes and the bonding PDMS-glass microfluidic chip. The experimental results indicate that the microfluidic chip is good and meet the experimental requirements. This method can greatly reduce the process time and cost of the microfluidic chip, and provide a simple and effective way for the structure design and in the field of biological microfabrications and microfluidic chips.

Telemetry Standards, RCC Standard 106-17. Chapter 21. Telemetry Network Standard Introduction

DTIC Science & Technology

2017-07-01

Critical RF radio frequency RFC Request for Comment SNMP Simple Network Management Protocol TA test article TCP Transmission Control Protocol...chapters might be of most interest for a particular reader. In order to guide the reader toward the chapters of further interest , the applicable... Simple Network Management Protocol (SNMP) to pass management information through the system. The SNMP management information bases (MIBs) provide

A Simple and Reproducible Method to Prepare Membrane Samples from Freshly Isolated Rat Brain Microvessels.

PubMed

Brzica, Hrvoje; Abdullahi, Wazir; Reilly, Bianca G; Ronaldson, Patrick T

2018-05-07

The blood-brain barrier (BBB) is a dynamic barrier tissue that responds to various pathophysiological and pharmacological stimuli. Such changes resulting from these stimuli can greatly modulate drug delivery to the brain and, by extension, cause considerable challenges in the treatment of central nervous system (CNS) diseases. Many BBB changes that affect pharmacotherapy, involve proteins that are localized and expressed at the level of endothelial cells. Indeed, such knowledge on BBB physiology in health and disease has sparked considerable interest in the study of these membrane proteins. From a basic science research standpoint, this implies a requirement for a simple but robust and reproducible method for isolation of microvessels from brain tissue harvested from experimental animals. In order to prepare membrane samples from freshly isolated microvessels, it is essential that sample preparations be enriched in endothelial cells but limited in the presence of other cell types of the neurovascular unit (i.e., astrocytes, microglia, neurons, pericytes). An added benefit is the ability to prepare samples from individual animals in order to capture the true variability of protein expression in an experimental population. In this manuscript, details regarding a method that is utilized for isolation of rat brain microvessels and preparation of membrane samples are provided. Microvessel enrichment, from samples derived, is achieved by using four centrifugation steps where dextran is included in the sample buffer. This protocol can easily be adapted by other laboratories for their own specific applications. Samples generated from this protocol have been shown to yield robust experimental data from protein analysis experiments that can greatly aid the understanding of BBB responses to physiological, pathophysiological, and pharmacological stimuli.

Using semantics for representing experimental protocols.

PubMed

Giraldo, Olga; García, Alexander; López, Federico; Corcho, Oscar

2017-11-13

An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protocols often include references to equipment, reagents, descriptions of critical steps, troubleshooting and tips, as well as any other information that researchers deem important for facilitating the reusability of the protocol. Although experimental protocols are central to reproducibility, the descriptions are often cursory. There is the need for a unified framework with respect to the syntactic structure and the semantics for representing experimental protocols. In this paper we present "SMART Protocols ontology", an ontology for representing experimental protocols. Our ontology represents the protocol as a workflow with domain specific knowledge embedded within a document. We also present the S ample I nstrument R eagent O bjective (SIRO) model, which represents the minimal common information shared across experimental protocols. SIRO was conceived in the same realm as the Patient Intervention Comparison Outcome (PICO) model that supports search, retrieval and classification purposes in evidence based medicine. We evaluate our approach against a set of competency questions modeled as SPARQL queries and processed against a set of published and unpublished protocols modeled with the SP Ontology and the SIRO model. Our approach makes it possible to answer queries such as Which protocols use tumor tissue as a sample. Improving reporting structures for experimental protocols requires collective efforts from authors, peer reviewers, editors and funding bodies. The SP Ontology is a contribution towards this goal. We build upon previous experiences and bringing together the view of researchers managing protocols in their laboratory work. Website: https://smartprotocols.github.io/ .

Virtual hybrid test control of sinuous crack

NASA Astrophysics Data System (ADS)

Jailin, Clément; Carpiuc, Andreea; Kazymyrenko, Kyrylo; Poncelet, Martin; Leclerc, Hugo; Hild, François; Roux, Stéphane

2017-05-01

The present study aims at proposing a new generation of experimental protocol for analysing crack propagation in quasi brittle materials. The boundary conditions are controlled in real-time to conform to a predefined crack path. Servo-control is achieved through a full-field measurement technique to determine the pre-set fracture path and a simple predictor model based on linear elastic fracture mechanics to prescribe the boundary conditions on the fly so that the actual crack path follows at best the predefined trajectory. The final goal is to identify, for instance, non-local damage models involving internal lengths. The validation of this novel procedure is performed via a virtual test-case based on an enriched damage model with an internal length scale, a prior chosen sinusoidal crack path and a concrete sample. Notwithstanding the fact that the predictor model selected for monitoring the test is a highly simplified picture of the targeted constitutive law, the proposed protocol exhibits a much improved sensitivity to the sought parameters such as internal lengths as assessed from the comparison with other available experimental tests.

Quantum internet: the certifiable road ahead

NASA Astrophysics Data System (ADS)

Elkouss, David; Lipinska, Victoria; Goodenough, Kenneth; Rozpedek, Filip; Kalb, Norbert; van Dam, Suzanne; Le Phuc, Thinh; Murta, Glaucia; Humphreys, Peter; Taminiau, Tim; Hanson, Ronald; Wehner, Stephanie

A future quantum internet enables quantum communication between any two points on earth in order to solve problems which are provably impossible using classical communication. The most well-known application of quantum communication is quantum key distribution, which allows two users to establish an encryption key. However, many other applications are known ranging from protocols for clock synchronization, extending the baselines of telescopes to exponential savings in communication. Due to recent technological progress, we are now on the verge of seeing the first small-scale quantum communication networks being realized. Here, we present a roadmap towards the ultimate form of a quantum internet. Specifically, we identify stages of development that are distinguished by an ever increasing amount of functionality. Each stage supports a certain class of quantum protocols and is interesting in its own right. What's more, we propose a series of simple tests to certify that an experimental implementation has achieved a certain stage. Jointly, the stages and the certification tests will allow us to track and benchmark experimental progress in the years to come. This work is supported by STW, NWO VIDI and ERC Starting Grant.

Simple protocols for oblivious transfer and secure identification in the noisy-quantum-storage model

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

Schaffner, Christian

2010-09-15

We present simple protocols for oblivious transfer and password-based identification which are secure against general attacks in the noisy-quantum-storage model as defined in R. Koenig, S. Wehner, and J. Wullschleger [e-print arXiv:0906.1030]. We argue that a technical tool from Koenig et al. suffices to prove security of the known protocols. Whereas the more involved protocol for oblivious transfer from Koenig et al. requires less noise in storage to achieve security, our ''canonical'' protocols have the advantage of being simpler to implement and the security error is easier control. Therefore, our protocols yield higher OT rates for many realistic noise parameters.more » Furthermore, a proof of security of a direct protocol for password-based identification against general noisy-quantum-storage attacks is given.« less

A note on quantum teleportation without the Bell-state measurement in superconducting qubits

NASA Astrophysics Data System (ADS)

Gomes, R. M.; Cardoso, W. B.; Avelar, A. T.; Baseia, B.

2014-02-01

In this paper, we offer a simple scheme to teleport a quantum state from a superconducting qubit to another spatially separated qubit, both coupled to coplanar waveguide microwave resonator. In this scheme the Bell-state measurement is not necessary, which simplifies the experimental observation. We revisit the effective model that describes such a coupled system and present the teleportation scheme with 98.7% of fidelity and 25% of success probability. We also verify the feasibility of this protocol for the transmon qubit parameters.

Decarboxylative Fluorination of Aliphatic Carboxylic Acids via Photoredox Catalysis

PubMed Central

Ventre, Sandrine; Petronijevic, Filip R.; MacMillan, David W. C.

2016-01-01

The direct conversion of aliphatic carboxylic acids to the corresponding alkyl fluorides has been achieved via visible light-promoted photoredox catalysis. This operationally simple, redox-neutral fluorination method is amenable to a wide variety of carboxylic acids. Photon-induced oxidation of carboxylates leads to the formation of carboxyl radicals, which upon rapid CO2-extrusion and F• transfer from a fluorinating reagent yield the desired fluoroalkanes with high efficiency. Experimental evidence indicates that an oxidative quenching pathway is operable in this broadly applicable fluorination protocol. PMID:25881929

High-fidelity readout in circuit quantum electrodynamics using the Jaynes-Cummings nonlinearity.

PubMed

Reed, M D; DiCarlo, L; Johnson, B R; Sun, L; Schuster, D I; Frunzio, L; Schoelkopf, R J

2010-10-22

We demonstrate a qubit readout scheme that exploits the Jaynes-Cummings nonlinearity of a superconducting cavity coupled to transmon qubits. We find that, in the strongly driven dispersive regime of this system, there is the unexpected onset of a high-transmission "bright" state at a critical power which depends sensitively on the initial qubit state. A simple and robust measurement protocol exploiting this effect achieves a single-shot fidelity of 87% using a conventional sample design and experimental setup, and at least 61% fidelity to joint correlations of three qubits.

Statistical models for causation: what inferential leverage do they provide?

PubMed

Freedman, David A

2006-12-01

Experiments offer more reliable evidence on causation than observational studies, which is not to gainsay the contribution to knowledge from observation. Experiments should be analyzed as experiments, not as observational studies. A simple comparison of rates might be just the right tool, with little value added by "sophisticated" models. This article discusses current models for causation, as applied to experimental and observational data. The intention-to-treat principle and the effect of treatment on the treated will also be discussed. Flaws in per-protocol and treatment-received estimates will be demonstrated.

Experimentally feasible security check for n-qubit quantum secret sharing

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

Schauer, Stefan; Huber, Marcus; Hiesmayr, Beatrix C.

In this article we present a general security strategy for quantum secret sharing (QSS) protocols based on the scheme presented by Hillery, Buzek, and Berthiaume (HBB) [Phys. Rev. A 59, 1829 (1999)]. We focus on a generalization of the HBB protocol to n communication parties thus including n-partite Greenberger-Horne-Zeilinger states. We show that the multipartite version of the HBB scheme is insecure in certain settings and impractical when going to large n. To provide security for such QSS schemes in general we use the framework presented by some of the authors [M. Huber, F. Mintert, A. Gabriel, B. C. Hiesmayr,more » Phys. Rev. Lett. 104, 210501 (2010)] to detect certain genuine n-partite entanglement between the communication parties. In particular, we present a simple inequality which tests the security.« less

Spin glass model for cell reprogramming

NASA Astrophysics Data System (ADS)

Pusuluri, Sai Teja; Castillo, Horacio E.

2014-03-01

Recent experiments show that differentiated cells can be reprogrammed to become pluripotent stem cells. The possible cell fates can be modeled as attractors in a dynamical system, the ``epigenetic landscape.'' Both cellular differentiation and reprogramming can be described in the landscape picture as motion from one attractor state to another attractor state. We use a simple model based on spin glass theory that can construct a simulated epigenetic landscape starting from the experimental genomic data. We modify the model to incorporate experimental reprogramming protocols. Our simulations successfully reproduce several reprogramming experiments. We probe the robustness of the results against random changes in the model, explore the importance of asymmetric interactions between transcription factors and study the importance of histone modification errors in reprogramming.

Lasting improvements in left spatial neglect following a protocol combining neck-muscle vibration and voluntary arm movements: a case-study.

PubMed

Ceyte, Hadrien; Beis, Jean-Marie; Simon, Mathilde; Rémy, Ariane; Anxionnat, René; Paysant, Jean; Caudron, Sébastien

2018-01-22

Beyond promising experimental results of sensory passive stimulations in spatial cognition disorders, some questions still remain regarding interests of these stimulations during the daily activities in neglect. The aim of this case-study was to evaluate the effects of a protocol combining left neck-muscle vibration with daily simple movements, like arm pointing movements, on perceptivo-locomotor deficits in a left spatial neglect patient. Two neuropsychological tests, one subjective straight-ahead pointing (SSA) test and one wheelchair navigation test were carried out before the combination protocol, immediately after, 1 h later, and 24 h later. The results showed a reduction of neglect spatial bias following the protocol lasted at least 24 h in all the tests (except for the SSA test due to the unavailability of the pointing device). The range of improvements in the symptoms of spatial neglect suggests that this therapeutic intervention based on the combining neck-muscle vibration to voluntary arm movements could be a useful treatment for this condition. One of future investigation axes should be the development of a vibratory tool in order to facilitate the combining this proprioceptive stimulation to daily activities. Implications for rehabilitation Spatial neglect is a perplexing neuropsychological syndrome, affecting different domains of spatial cognition and impacting also the functional domain. The treatments based on neck-muscle vibration are simple to use, non-invasive and requires none active participation of patient. A therapeutic intervention based on the combining left neck-muscle vibration and voluntary arm movements in a left-spatial-neglect show a lasting reduction of symptoms especially in daily activities. The combination of treatments based on the Bottom-Up approach opens innovative perspectives in rehabilitation.

Determination of hydrazine in drinking water: Development and multivariate optimization of a rapid and simple solid phase microextraction-gas chromatography-triple quadrupole mass spectrometry protocol.

PubMed

Gionfriddo, Emanuela; Naccarato, Attilio; Sindona, Giovanni; Tagarelli, Antonio

2014-07-04

In this work, the capabilities of solid phase microextraction were exploited in a fully optimized SPME-GC-QqQ-MS analytical approach for hydrazine assay. A rapid and easy method was obtained by a simple derivatization reaction with propyl chloroformate and pyridine carried out directly in water samples, followed by automated SPME analysis in the same vial without further sample handling. The affinity of the different derivatized compounds obtained towards five commercially available SPME coatings was evaluated, in order to achieve the best extraction efficiency. GC analyses were carried out using a GC-QqQ-MS instrument in selected reaction monitoring (SRM) acquisition mode which has allowed the achievement of high specificity by selecting appropriate precursor-product ion couples improving the capability in analyte identification. The multivariate approach of experimental design was crucial in order to optimize derivatization reaction, SPME process and tandem mass spectrometry parameters. Accuracy of the proposed protocol, tested at 60, 200 and 800 ng L(-1), provided satisfactory values (114.2%, 83.6% and 98.6%, respectively), whereas precision (RSD%) at the same concentration levels were of 10.9%, 7.9% and 7.7% respectively. Limit of detection and quantification of 4.4 and 8.3 ng L(-1) were obtained. The reliable application of the proposed protocol to real drinking water samples confirmed its capability to be used as analytical tool for routine analyses. Copyright © 2014 Elsevier B.V. All rights reserved.

cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches.

PubMed

Martin-Herranz, Daniel E; Ribeiro, António J M; Krueger, Felix; Thornton, Janet M; Reik, Wolf; Stubbs, Thomas M

2017-11-16

DNA methylation is an important epigenetic modification in many species that is critical for development, and implicated in ageing and many complex diseases, such as cancer. Many cost-effective genome-wide analyses of DNA modifications rely on restriction enzymes capable of digesting genomic DNA at defined sequence motifs. There are hundreds of restriction enzyme families but few are used to date, because no tool is available for the systematic evaluation of restriction enzyme combinations that can enrich for certain sites of interest in a genome. Herein, we present customised Reduced Representation Bisulfite Sequencing (cuRRBS), a novel and easy-to-use computational method that solves this problem. By computing the optimal enzymatic digestions and size selection steps required, cuRRBS generalises the traditional MspI-based Reduced Representation Bisulfite Sequencing (RRBS) protocol to all restriction enzyme combinations. In addition, cuRRBS estimates the fold-reduction in sequencing costs and provides a robustness value for the personalised RRBS protocol, allowing users to tailor the protocol to their experimental needs. Moreover, we show in silico that cuRRBS-defined restriction enzymes consistently out-perform MspI digestion in many biological systems, considering both CpG and CHG contexts. Finally, we have validated the accuracy of cuRRBS predictions for single and double enzyme digestions using two independent experimental datasets. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Protocols Utilizing Constant pH Molecular Dynamics to Compute pH-Dependent Binding Free Energies

PubMed Central

2015-01-01

In protein–ligand binding, the electrostatic environments of the two binding partners may vary significantly in bound and unbound states, which may lead to protonation changes upon binding. In cases where ligand binding results in a net uptake or release of protons, the free energy of binding is pH-dependent. Nevertheless, conventional free energy calculations and molecular docking protocols typically do not rigorously account for changes in protonation that may occur upon ligand binding. To address these shortcomings, we present a simple methodology based on Wyman’s binding polynomial formalism to account for the pH dependence of binding free energies and demonstrate its use on cucurbit[7]uril (CB[7]) host–guest systems. Using constant pH molecular dynamics and a reference binding free energy that is taken either from experiment or from thermodynamic integration computations, the pH-dependent binding free energy is determined. This computational protocol accurately captures the large pKa shifts observed experimentally upon CB[7]:guest association and reproduces experimental binding free energies at different levels of pH. We show that incorrect assignment of fixed protonation states in free energy computations can give errors of >2 kcal/mol in these host–guest systems. Use of the methods presented here avoids such errors, thus suggesting their utility in computing proton-linked binding free energies for protein–ligand complexes. PMID:25134690

Open source software to control Bioflo bioreactors.

PubMed

Burdge, David A; Libourel, Igor G L

2014-01-01

Bioreactors are designed to support highly controlled environments for growth of tissues, cell cultures or microbial cultures. A variety of bioreactors are commercially available, often including sophisticated software to enhance the functionality of the bioreactor. However, experiments that the bioreactor hardware can support, but that were not envisioned during the software design cannot be performed without developing custom software. In addition, support for third party or custom designed auxiliary hardware is often sparse or absent. This work presents flexible open source freeware for the control of bioreactors of the Bioflo product family. The functionality of the software includes setpoint control, data logging, and protocol execution. Auxiliary hardware can be easily integrated and controlled through an integrated plugin interface without altering existing software. Simple experimental protocols can be entered as a CSV scripting file, and a Python-based protocol execution model is included for more demanding conditional experimental control. The software was designed to be a more flexible and free open source alternative to the commercially available solution. The source code and various auxiliary hardware plugins are publicly available for download from https://github.com/LibourelLab/BiofloSoftware. In addition to the source code, the software was compiled and packaged as a self-installing file for 32 and 64 bit windows operating systems. The compiled software will be able to control a Bioflo system, and will not require the installation of LabVIEW.

Open Source Software to Control Bioflo Bioreactors

PubMed Central

Burdge, David A.; Libourel, Igor G. L.

2014-01-01

Bioreactors are designed to support highly controlled environments for growth of tissues, cell cultures or microbial cultures. A variety of bioreactors are commercially available, often including sophisticated software to enhance the functionality of the bioreactor. However, experiments that the bioreactor hardware can support, but that were not envisioned during the software design cannot be performed without developing custom software. In addition, support for third party or custom designed auxiliary hardware is often sparse or absent. This work presents flexible open source freeware for the control of bioreactors of the Bioflo product family. The functionality of the software includes setpoint control, data logging, and protocol execution. Auxiliary hardware can be easily integrated and controlled through an integrated plugin interface without altering existing software. Simple experimental protocols can be entered as a CSV scripting file, and a Python-based protocol execution model is included for more demanding conditional experimental control. The software was designed to be a more flexible and free open source alternative to the commercially available solution. The source code and various auxiliary hardware plugins are publicly available for download from https://github.com/LibourelLab/BiofloSoftware. In addition to the source code, the software was compiled and packaged as a self-installing file for 32 and 64 bit windows operating systems. The compiled software will be able to control a Bioflo system, and will not require the installation of LabVIEW. PMID:24667828

Cell-based quantification of biomarkers from an ultra-fast microfluidic immunofluorescent staining: application to human breast cancer cell lines

NASA Astrophysics Data System (ADS)

Migliozzi, D.; Nguyen, H. T.; Gijs, M. A. M.

2018-02-01

Immunohistochemistry (IHC) is one of the main techniques currently used in the clinics for biomarker characterization. It consists in colorimetric labeling with specific antibodies followed by microscopy analysis. The results are then used for diagnosis and therapeutic targeting. Well-known drawbacks of such protocols are their limited accuracy and precision, which prevent the clinicians from having quantitative and robust IHC results. With our work, we combined rapid microfluidic immunofluorescent staining with efficient image-based cell segmentation and signal quantification to increase the robustness of both experimental and analytical protocols. The experimental protocol is very simple and based on fast-fluidic-exchange in a microfluidic chamber created on top of the formalin-fixed-paraffin-embedded (FFPE) slide by clamping it a silicon chip with a polydimethyl siloxane (PDMS) sealing ring. The image-processing protocol is based on enhancement and subsequent thresholding of the local contrast of the obtained fluorescence image. As a case study, given that the human epidermal growth factor receptor 2 (HER2) protein is often used as a biomarker for breast cancer, we applied our method to HER2+ and HER2- cell lines. We report very fast (5 minutes) immunofluorescence staining of both HER2 and cytokeratin (a marker used to define the tumor region) on FFPE slides. The image-processing program can segment cells correctly and give a cell-based quantitative immunofluorescent signal. With this method, we found a reproducible well-defined separation for the HER2-to-cytokeratin ratio for positive and negative control samples.

J-Plus Web Portal

NASA Astrophysics Data System (ADS)

Civera Lorenzo, Tamara

2017-10-01

Brief presentation about the J-PLUS EDR data access web portal (http://archive.cefca.es/catalogues/jplus-edr) where the different services available to retrieve images and catalogues data have been presented.J-PLUS Early Data Release (EDR) archive includes two types of data: images and dual and single catalogue data which include parameters measured from images. J-PLUS web portal offers catalogue data and images through several different online data access tools or services each suited to a particular need. The different services offered are: Coverage map Sky navigator Object visualization Image search Cone search Object list search Virtual observatory services: Simple Cone Search Simple Image Access Protocol Simple Spectral Access Protocol Table Access Protocol

Ca2+ current vs. Ca2+ channel cooperativity of exocytosis

PubMed Central

Matveev, Victor; Bertram, Richard; Sherman, Arthur

2009-01-01

Recently there has been significant interest and progress in the study of spatio-temporal dynamics of Ca2+ that triggers exocytosis at a fast chemical synapse, which requires understanding the contribution of individual calcium channels to the release of a single vesicle. Experimental protocols provide insight into this question by probing the sensitivity of exocytosis to Ca2+ influx. While varying extracellular or intracellular Ca2+ concentration assesses the intrinsic biochemical Ca2+ cooperativity of neurotransmitter release, varying the number of open Ca2+ channels using pharmacological channel block or the tail current titration probes the cooperativity between individual Ca2+ channels in triggering exocytosis. Despite the wide use of these Ca2+ sensitivity measurements, their interpretation often relies on heuristic arguments. Here we provide a detailed analysis of the Ca2+ sensitivity measures probed by these experimental protocols, present simple expressions for special cases, and demonstrate the distinction between the Ca2+ current cooperativity, defined by the relationship between exocytosis rate and the whole-terminal Ca2+ current magnitude, and the underlying Ca2+ channel cooperativity, defined as the average number of channels involved in the release of a single vesicle. We find simple algebraic expressions that show that the two are different but linearly related. Further, we use 3D computational modeling of buffered Ca2+ diffusion to analyze these distinct Ca2+ cooperativity measures, and demonstrate the role of endogenous Ca2+ buffers on such measures. We show that buffers can either increase or decrease the Ca2+ current cooperativity of exocytosis, depending on their concentration and the single-channel Ca2+ current. PMID:19793978

Cortical Plasticity Induced by Spike-Triggered Microstimulation in Primate Somatosensory Cortex

PubMed Central

Song, Weiguo; Kerr, Cliff C.; Lytton, William W.; Francis, Joseph T.

2013-01-01

Electrical stimulation of the nervous system for therapeutic purposes, such as deep brain stimulation in the treatment of Parkinson’s disease, has been used for decades. Recently, increased attention has focused on using microstimulation to restore functions as diverse as somatosensation and memory. However, how microstimulation changes the neural substrate is still not fully understood. Microstimulation may cause cortical changes that could either compete with or complement natural neural processes, and could result in neuroplastic changes rendering the region dysfunctional or even epileptic. As part of our efforts to produce neuroprosthetic devices and to further study the effects of microstimulation on the cortex, we stimulated and recorded from microelectrode arrays in the hand area of the primary somatosensory cortex (area 1) in two awake macaque monkeys. We applied a simple neuroprosthetic microstimulation protocol to a pair of electrodes in the area 1 array, using either random pulses or pulses time-locked to the recorded spiking activity of a reference neuron. This setup was replicated using a computer model of the thalamocortical system, which consisted of 1980 spiking neurons distributed among six cortical layers and two thalamic nuclei. Experimentally, we found that spike-triggered microstimulation induced cortical plasticity, as shown by increased unit-pair mutual information, while random microstimulation did not. In addition, there was an increased response to touch following spike-triggered microstimulation, along with decreased neural variability. The computer model successfully reproduced both qualitative and quantitative aspects of the experimental findings. The physiological findings of this study suggest that even simple microstimulation protocols can be used to increase somatosensory information flow. PMID:23472086

Simple Spectral Lines Data Model Version 1.0

NASA Astrophysics Data System (ADS)

Osuna, Pedro; Salgado, Jesus; Guainazzi, Matteo; Dubernet, Marie-Lise; Roueff, Evelyne; Osuna, Pedro; Salgado, Jesus

2010-12-01

This document presents a Data Model to describe Spectral Line Transitions in the context of the Simple Line Access Protocol defined by the IVOA (c.f. Ref[13] IVOA Simple Line Access protocol) The main objective of the model is to integrate with and support the Simple Line Access Protocol, with which it forms a compact unit. This integration allows seamless access to Spectral Line Transitions available worldwide in the VO context. This model does not provide a complete description of Atomic and Molecular Physics, which scope is outside of this document. In the astrophysical sense, a line is considered as the result of a transition between two energy levels. Under the basis of this assumption, a whole set of objects and attributes have been derived to define properly the necessary information to describe lines appearing in astrophysical contexts. The document has been written taking into account available information from many different Line data providers (see acknowledgments section).

Teaching Beer's Law and Absorption Spectrophotometry with a Smart Phone: A Substantially Simplified Protocol

ERIC Educational Resources Information Center

Kuntzleman, Thomas S.; Jacobson, Erik C.

2016-01-01

A very simple protocol for teaching Beer's Law and absorption spectrophotometry using a smart phone is described. Materials commonly found in high school chemistry laboratories or even around the house may be used. Data collection and analysis is quick and easy. Despite the simple nature of the experiment, excellent results can be achieved.

Simple Protocol for Secondary School Hands-On Activity: Electrophoresis of Pre-Stained Nucleic Acids on Agar-Agar Borate Gels

ERIC Educational Resources Information Center

Britos, Leticia; Goyenola, Guillermo; Orono, Silvia Umpierrez

2004-01-01

An extremely simple, inexpensive, and safe method is presented, which emulates nucleic acids isolation and electrophoretic analysis as performed in a research environment, in the context of a secondary school hands-on activity. The protocol is amenable to an interdisciplinary approach, taking into consideration the electrical and chemical…

Virioplankton 'pegylation': use of PEG (polyethylene glycol) to concentrate and purify viruses in pelagic ecosystems.

PubMed

Colombet, J; Robin, A; Lavie, L; Bettarel, Y; Cauchie, H M; Sime-Ngando, T

2007-12-01

We have described the use of Polyethylene glycol (PEG) for the precipitation of natural communities of aquatic viruses, and its comparison with the usual concentration method based on ultracentrifugation. Experimental samples were obtained from different freshwater ecosystems whose trophic status varied. Based on transmission electron microscope observations and counting of phage-shaped particles, our results showed that the greatest recovery efficiency for all ecosystems was obtained when we used the PEG protocol. On average, this protocol allowed the recovery of >2-fold more viruses, compared to ultracentrifugation. In addition, the diversity of virioplankton, based on genomic size profiling using pulsed field gel electrophoresis, was higher and better discriminated when we used the PEG method. We conclude that pegylation offers a valid, simple and cheaper alternative method to ultracentrifugation, for the concentration and the purification of pelagic viruses.

Refined Dummy Atom Model of Mg(2+) by Simple Parameter Screening Strategy with Revised Experimental Solvation Free Energy.

PubMed

Jiang, Yang; Zhang, Haiyang; Feng, Wei; Tan, Tianwei

2015-12-28

Metal ions play an important role in the catalysis of metalloenzymes. To investigate metalloenzymes via molecular modeling, a set of accurate force field parameters for metal ions is highly imperative. To extend its application range and improve the performance, the dummy atom model of metal ions was refined through a simple parameter screening strategy using the Mg(2+) ion as an example. Using the AMBER ff03 force field with the TIP3P model, the refined model accurately reproduced the experimental geometric and thermodynamic properties of Mg(2+). Compared with point charge models and previous dummy atom models, the refined dummy atom model yields an enhanced performance for producing reliable ATP/GTP-Mg(2+)-protein conformations in three metalloenzyme systems with single or double metal centers. Similar to other unbounded models, the refined model failed to reproduce the Mg-Mg distance and favored a monodentate binding of carboxylate groups, and these drawbacks needed to be considered with care. The outperformance of the refined model is mainly attributed to the use of a revised (more accurate) experimental solvation free energy and a suitable free energy correction protocol. This work provides a parameter screening strategy that can be readily applied to refine the dummy atom models for metal ions.

Fiber fault location utilizing traffic signal in optical network.

PubMed

Zhao, Tong; Wang, Anbang; Wang, Yuncai; Zhang, Mingjiang; Chang, Xiaoming; Xiong, Lijuan; Hao, Yi

2013-10-07

We propose and experimentally demonstrate a method for fault location in optical communication network. This method utilizes the traffic signal transmitted across the network as probe signal, and then locates the fault by correlation technique. Compared with conventional techniques, our method has a simple structure and low operation expenditure, because no additional device is used, such as light source, modulator and signal generator. The correlation detection in this method overcomes the tradeoff between spatial resolution and measurement range in pulse ranging technique. Moreover, signal extraction process can improve the location result considerably. Experimental results show that we achieve a spatial resolution of 8 cm and detection range of over 23 km with -8-dBm mean launched power in optical network based on synchronous digital hierarchy protocols.

Practical purification scheme for decohered coherent-state superpositions via partial homodyne detection

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

Suzuki, Shigenari; Department of Electronics and Electrical Engineering, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama, 223-8522; Takeoka, Masahiro

2006-04-15

We present a simple protocol to purify a coherent-state superposition that has undergone a linear lossy channel. The scheme constitutes only a single beam splitter and a homodyne detector, and thus is experimentally feasible. In practice, a superposition of coherent states is transformed into a classical mixture of coherent states by linear loss, which is usually the dominant decoherence mechanism in optical systems. We also address the possibility of producing a larger amplitude superposition state from decohered states, and show that in most cases the decoherence of the states are amplified along with the amplitude.

Generalized energy measurements and modified transient quantum fluctuation theorems

NASA Astrophysics Data System (ADS)

Watanabe, Gentaro; Venkatesh, B. Prasanna; Talkner, Peter

2014-05-01

Determining the work which is supplied to a system by an external agent provides a crucial step in any experimental realization of transient fluctuation relations. This, however, poses a problem for quantum systems, where the standard procedure requires the projective measurement of energy at the beginning and the end of the protocol. Unfortunately, projective measurements, which are preferable from the point of view of theory, seem to be difficult to implement experimentally. We demonstrate that, when using a particular type of generalized energy measurements, the resulting work statistics is simply related to that of projective measurements. This relation between the two work statistics entails the existence of modified transient fluctuation relations. The modifications are exclusively determined by the errors incurred in the generalized energy measurements. They are universal in the sense that they do not depend on the force protocol. Particularly simple expressions for the modified Crooks relation and Jarzynski equality are found for Gaussian energy measurements. These can be obtained by a sequence of sufficiently many generalized measurements which need not be Gaussian. In accordance with the central limit theorem, this leads to an effective error reduction in the individual measurements and even yields a projective measurement in the limit of infinite repetitions.

A simple protocol for NMR analysis of the enantiomeric purity of chiral hydroxylamines.

PubMed

Tickell, David A; Mahon, Mary F; Bull, Steven D; James, Tony D

2013-02-15

A practically simple three-component chiral derivatization protocol for determining the enantiopurity of chiral hydroxylamines by (1)H NMR spectroscopic analysis is described, involving their treatment with 2-formylphenylboronic acid and enantiopure BINOL to afford a mixture of diastereomeric nitrono-boronate esters whose ratio is an accurate reflection of the enantiopurity of the parent hydroxylamine.

If SWORD Is the Answer, What Is the Question?: Use of the Simple Web-Service Offering Repository Deposit Protocol

ERIC Educational Resources Information Center

Lewis, Stuart; Hayes, Leonie; Newton-Wade, Vanessa; Corfield, Antony; Davis, Richard; Donohue, Tim; Wilson, Scott

2009-01-01

Purpose: The purpose of this paper is to describe the repository deposit protocol, Simple Web-service Offering Repository Deposit (SWORD), its development iteration, and some of its potential use cases. In addition, seven case studies of institutional use of SWORD are provided. Design/methodology/approach: The paper describes the recent…

Exploitation of Existing Voice Over Internet Protocol Technology for Department of the Navy Application

DTIC Science & Technology

2002-09-01

Protocol LAN Local Area Network LDAP Lightweight Directory Access Protocol LLQ Low Latency Queuing MAC Media Access Control MarCorSysCom Marine...Description Protocol SIP Session Initiation Protocol SMTP Simple Mail Transfer Protocol SPAWAR Space and Naval Warfare Systems Center SS7 ...PSTN infrastructure previously required to carry the conversation. The cost of accessing the PSTN is thereby eliminated. In cases where Internet

Thermodynamic equilibrium solubility measurements in simulated fluids by 96-well plate method in early drug discovery.

PubMed

Bharate, Sonali S; Vishwakarma, Ram A

2015-04-01

An early prediction of solubility in physiological media (PBS, SGF and SIF) is useful to predict qualitatively bioavailability and absorption of lead candidates. Despite of the availability of multiple solubility estimation methods, none of the reported method involves simplified fixed protocol for diverse set of compounds. Therefore, a simple and medium-throughput solubility estimation protocol is highly desirable during lead optimization stage. The present work introduces a rapid method for assessment of thermodynamic equilibrium solubility of compounds in aqueous media using 96-well microplate. The developed protocol is straightforward to set up and takes advantage of the sensitivity of UV spectroscopy. The compound, in stock solution in methanol, is introduced in microgram quantities into microplate wells followed by drying at an ambient temperature. Microplates were shaken upon addition of test media and the supernatant was analyzed by UV method. A plot of absorbance versus concentration of a sample provides saturation point, which is thermodynamic equilibrium solubility of a sample. The established protocol was validated using a large panel of commercially available drugs and with conventional miniaturized shake flask method (r(2)>0.84). Additionally, the statistically significant QSPR models were established using experimental solubility values of 52 compounds. Copyright © 2015 Elsevier Ltd. All rights reserved.

Experimental considerations for fast kurtosis imaging.

PubMed

Hansen, Brian; Lund, Torben E; Sangill, Ryan; Stubbe, Ebbe; Finsterbusch, Jürgen; Jespersen, Sune Nørhøj

2016-11-01

The clinical use of kurtosis imaging is impeded by long acquisitions and postprocessing. Recently, estimation of mean kurtosis tensor W¯ and mean diffusivity ( D¯) was made possible from 13 distinct diffusion weighted MRI acquisitions (the 1-3-9 protocol) with simple postprocessing. Here, we analyze the effects of noise and nonideal diffusion encoding, and propose a new correction strategy. We also present a 1-9-9 protocol with increased robustness to experimental imperfections and minimal additional scan time. This refinement does not affect computation time and also provides a fast estimate of fractional anisotropy (FA). 1-3-9/1-9-9 data are acquired in rat and human brains, and estimates of D¯, FA, W¯ from human brains are compared with traditional estimates from an extensive diffusion kurtosis imaging data set. Simulations are used to evaluate the influence of noise and diffusion encodings deviating from the scheme, and the performance of the correction strategy. Optimal b-values are determined from simulations and data. Accuracy and precision in D¯ and W¯ are comparable to nonlinear least squares estimation, and is improved with the 1-9-9 protocol. The compensation strategy vastly improves parameter estimation in nonideal data. The framework offers a robust and compact method for estimating several diffusion metrics. The protocol is easily implemented. Magn Reson Med 76:1455-1468, 2016. © 2015 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2015 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies.

PubMed

DeMaere, Matthew Z; Darling, Aaron E

2018-02-01

Chromosome conformation capture (3C) and Hi-C DNA sequencing methods have rapidly advanced our understanding of the spatial organization of genomes and metagenomes. Many variants of these protocols have been developed, each with their own strengths. Currently there is no systematic means for simulating sequence data from this family of sequencing protocols, potentially hindering the advancement of algorithms to exploit this new datatype. We describe a computational simulator that, given simple parameters and reference genome sequences, will simulate Hi-C sequencing on those sequences. The simulator models the basic spatial structure in genomes that is commonly observed in Hi-C and 3C datasets, including the distance-decay relationship in proximity ligation, differences in the frequency of interaction within and across chromosomes, and the structure imposed by cells. A means to model the 3D structure of randomly generated topologically associating domains is provided. The simulator considers several sources of error common to 3C and Hi-C library preparation and sequencing methods, including spurious proximity ligation events and sequencing error. We have introduced the first comprehensive simulator for 3C and Hi-C sequencing protocols. We expect the simulator to have use in testing of Hi-C data analysis algorithms, as well as more general value for experimental design, where questions such as the required depth of sequencing, enzyme choice, and other decisions can be made in advance in order to ensure adequate statistical power with respect to experimental hypothesis testing.

Data transmission protocol for Pi-of-the-Sky cameras

NASA Astrophysics Data System (ADS)

Uzycki, J.; Kasprowicz, G.; Mankiewicz, M.; Nawrocki, K.; Sitek, P.; Sokolowski, M.; Sulej, R.; Tlaczala, W.

2006-10-01

The large amount of data collected by the automatic astronomical cameras has to be transferred to the fast computers in a reliable way. The method chosen should ensure data streaming in both directions but in nonsymmetrical way. The Ethernet interface is very good choice because of its popularity and proven performance. However it requires TCP/IP stack implementation in devices like cameras for full compliance with existing network and operating systems. This paper describes NUDP protocol, which was made as supplement to standard UDP protocol and can be used as a simple-network protocol. The NUDP does not need TCP protocol implementation and makes it possible to run the Ethernet network with simple devices based on microcontroller and/or FPGA chips. The data transmission idea was created especially for the "Pi of the Sky" project.

Strategies for Achieving High Sequencing Accuracy for Low Diversity Samples and Avoiding Sample Bleeding Using Illumina Platform

PubMed Central

Mitra, Abhishek; Skrzypczak, Magdalena; Ginalski, Krzysztof; Rowicka, Maga

2015-01-01

Sequencing microRNA, reduced representation sequencing, Hi-C technology and any method requiring the use of in-house barcodes result in sequencing libraries with low initial sequence diversity. Sequencing such data on the Illumina platform typically produces low quality data due to the limitations of the Illumina cluster calling algorithm. Moreover, even in the case of diverse samples, these limitations are causing substantial inaccuracies in multiplexed sample assignment (sample bleeding). Such inaccuracies are unacceptable in clinical applications, and in some other fields (e.g. detection of rare variants). Here, we discuss how both problems with quality of low-diversity samples and sample bleeding are caused by incorrect detection of clusters on the flowcell during initial sequencing cycles. We propose simple software modifications (Long Template Protocol) that overcome this problem. We present experimental results showing that our Long Template Protocol remarkably increases data quality for low diversity samples, as compared with the standard analysis protocol; it also substantially reduces sample bleeding for all samples. For comprehensiveness, we also discuss and compare experimental results from alternative approaches to sequencing low diversity samples. First, we discuss how the low diversity problem, if caused by barcodes, can be avoided altogether at the barcode design stage. Second and third, we present modified guidelines, which are more stringent than the manufacturer’s, for mixing low diversity samples with diverse samples and lowering cluster density, which in our experience consistently produces high quality data from low diversity samples. Fourth and fifth, we present rescue strategies that can be applied when sequencing results in low quality data and when there is no more biological material available. In such cases, we propose that the flowcell be re-hybridized and sequenced again using our Long Template Protocol. Alternatively, we discuss how analysis can be repeated from saved sequencing images using the Long Template Protocol to increase accuracy. PMID:25860802

Three Dimensional (3D) Printing: A Straightforward, User-Friendly Protocol to Convert Virtual Chemical Models to Real-Life Objects

ERIC Educational Resources Information Center

Rossi, Sergio; Benaglia, Maurizio; Brenna, Davide; Porta, Riccardo; Orlandi, Manuel

2015-01-01

A simple procedure to convert protein data bank files (.pdb) into a stereolithography file (.stl) using VMD software (Virtual Molecular Dynamic) is reported. This tutorial allows generating, with a very simple protocol, three-dimensional customized structures that can be printed by a low-cost 3D-printer, and used for teaching chemical education…

Using a Simple, Free Voice-over-Internet Protocol Service to Add Interest to Lectures and Enhance Student Engagement

ERIC Educational Resources Information Center

Beaton, Susan J.; Forster, Peter M.

2013-01-01

A large proportion of students in higher education report feeling bored during lectures, for example, Mann and Robinson (2009) put this figure at 60 per cent. This short article reviews our experiences of using a simple, free Voice-over-Internet Protocol (VoIP) service, Skype, to enhance the interest and engagement of students by holding a…

Linearization of the bradford protein assay.

PubMed

Ernst, Orna; Zor, Tsaffrir

2010-04-12

Determination of microgram quantities of protein in the Bradford Coomassie brilliant blue assay is accomplished by measurement of absorbance at 590 nm. This most common assay enables rapid and simple protein quantification in cell lysates, cellular fractions, or recombinant protein samples, for the purpose of normalization of biochemical measurements. However, an intrinsic nonlinearity compromises the sensitivity and accuracy of this method. It is shown that under standard assay conditions, the ratio of the absorbance measurements at 590 nm and 450 nm is strictly linear with protein concentration. This simple procedure increases the accuracy and improves the sensitivity of the assay about 10-fold, permitting quantification down to 50 ng of bovine serum albumin. Furthermore, the interference commonly introduced by detergents that are used to create the cell lysates is greatly reduced by the new protocol. A linear equation developed on the basis of mass action and Beer's law perfectly fits the experimental data.

Space Wire Upper Layer Protocols

NASA Technical Reports Server (NTRS)

Rakow, Glenn; Schnurr, Richard; Gilley, Daniel; Parkes, Steve

2004-01-01

This viewgraph presentation addresses efforts to provide a streamlined approach for developing SpaceWire Upper layer protocols which allows industry to drive standardized communication solutions for real projects. The presentation proposes a simple packet header that will allow flexibility in implementing a diverse range of protocols.

Optimisation of a Generic Ionic Model of Cardiac Myocyte Electrical Activity

PubMed Central

Guo, Tianruo; Al Abed, Amr; Lovell, Nigel H.; Dokos, Socrates

2013-01-01

A generic cardiomyocyte ionic model, whose complexity lies between a simple phenomenological formulation and a biophysically detailed ionic membrane current description, is presented. The model provides a user-defined number of ionic currents, employing two-gate Hodgkin-Huxley type kinetics. Its generic nature allows accurate reconstruction of action potential waveforms recorded experimentally from a range of cardiac myocytes. Using a multiobjective optimisation approach, the generic ionic model was optimised to accurately reproduce multiple action potential waveforms recorded from central and peripheral sinoatrial nodes and right atrial and left atrial myocytes from rabbit cardiac tissue preparations, under different electrical stimulus protocols and pharmacological conditions. When fitted simultaneously to multiple datasets, the time course of several physiologically realistic ionic currents could be reconstructed. Model behaviours tend to be well identified when extra experimental information is incorporated into the optimisation. PMID:23710254

Simple proof that Gaussian attacks are optimal among collective attacks against continuous-variable quantum key distribution with a Gaussian modulation

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

Leverrier, Anthony; Grangier, Philippe; Laboratoire Charles Fabry, Institut d'Optique, CNRS, University Paris-Sud, Campus Polytechnique, RD 128, F-91127 Palaiseau Cedex

2010-06-15

In this article, we give a simple proof of the fact that the optimal collective attacks against continuous-variable quantum key distribution with a Gaussian modulation are Gaussian attacks. Our proof, which makes use of symmetry properties of the protocol in phase space, is particularly relevant for the finite-key analysis of the protocol and therefore for practical applications.

Latency correction of event-related potentials between different experimental protocols

NASA Astrophysics Data System (ADS)

Iturrate, I.; Chavarriaga, R.; Montesano, L.; Minguez, J.; Millán, JdR

2014-06-01

Objective. A fundamental issue in EEG event-related potentials (ERPs) studies is the amount of data required to have an accurate ERP model. This also impacts the time required to train a classifier for a brain-computer interface (BCI). This issue is mainly due to the poor signal-to-noise ratio and the large fluctuations of the EEG caused by several sources of variability. One of these sources is directly related to the experimental protocol or application designed, and may affect the amplitude or latency of ERPs. This usually prevents BCI classifiers from generalizing among different experimental protocols. In this paper, we analyze the effect of the amplitude and the latency variations among different experimental protocols based on the same type of ERP. Approach. We present a method to analyze and compensate for the latency variations in BCI applications. The algorithm has been tested on two widely used ERPs (P300 and observation error potentials), in three experimental protocols in each case. We report the ERP analysis and single-trial classification. Main results. The results obtained show that the designed experimental protocols significantly affect the latency of the recorded potentials but not the amplitudes. Significance. These results show how the use of latency-corrected data can be used to generalize the BCIs, reducing the calibration time when facing a new experimental protocol.

Fourier-space TEM reconstructions with symmetry adapted functions for all rotational point groups.

PubMed

Trapani, Stefano; Navaza, Jorge

2013-05-01

A general-purpose and simple expression for the coefficients of symmetry adapted functions referred to conveniently oriented symmetry axes is given for all rotational point groups. The expression involves the computation of reduced Wigner-matrix elements corresponding to an angle specific to each group and has the computational advantage of leading to Fourier-space TEM (transmission electron microscopy) reconstruction procedures involving only real valued unknowns. Using this expression, a protocol for ab initio view and center assignment and reconstruction so far used for icosahedral particles has been tested with experimental data in other point groups. Copyright © 2013 Elsevier Inc. All rights reserved.

ShareSync: A Solution for Deterministic Data Sharing over Ethernet

NASA Technical Reports Server (NTRS)

Dunn, Daniel J., II; Koons, William A.; Kennedy, Richard D.; Davis, Philip A.

2007-01-01

As part of upgrading the Contact Dynamics Simulation Laboratory (CDSL) at the NASA Marshall Space Flight Center (MSFC), a simple, cost effective method was needed to communicate data among the networked simulation machines and I/O controllers used to run the facility. To fill this need and similar applicable situations, a generic protocol was developed, called ShareSync. ShareSync is a lightweight, real-time, publish-subscribe Ethernet protocol for simple and deterministic data sharing across diverse machines and operating systems. ShareSync provides a simple Application Programming Interface (API) for simulation programmers to incorporate into their code. The protocol is compatible with virtually all Ethernet-capable machines, is flexible enough to support a variety of applications, is fast enough to provide soft real-time determinism, and is a low-cost resource for distributed simulation development, deployment, and maintenance. The first design cycle iteration of ShareSync has been completed, and the protocol has undergone several testing procedures including endurance and benchmarking tests and approaches the 2001ts data synchronization design goal for the CDSL.

An air transfer experiment confirms the role of volatile cues in communication between plants.

PubMed

Karban, Richard; Shiojiri, Kaori; Ishizaki, Satomi

2010-09-01

Previous studies reported that sagebrush plants near experimentally clipped neighbors experienced less herbivory than did plants near unclipped neighbors. Blocking air flow with plastic bags made this effect undetectable. However, some scientists remained skeptical about the possibility of volatile communication between plants since the existence and identity of a cue that operates in nature have never been demonstrated. We conducted an air transfer experiment that collected air from the headspace of an experimentally clipped donor plant and delivered it to the headspace of an unclipped assay plant. We found that assay plants treated with air from clipped donors were less likely to be damaged by naturally occurring herbivores in a field experiment. This simple air transfer experiment fulfills the most critical of Koch's postulates and provides more definitive evidence for volatile communication between plants. It also provides an inexpensive experimental protocol that can be used to screen plants for interplant communication in the field.

EXACT2: the semantics of biomedical protocols

PubMed Central

2014-01-01

Background The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. Methods We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously 'unseen' (not used for the construction of EXACT2) protocols. Results The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. Conclusions The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format. PMID:25472549

Simple proof of security of the BB84 quantum key distribution protocol

PubMed

Shor; Preskill

2000-07-10

We prove that the 1984 protocol of Bennett and Brassard (BB84) for quantum key distribution is secure. We first give a key distribution protocol based on entanglement purification, which can be proven secure using methods from Lo and Chau's proof of security for a similar protocol. We then show that the security of this protocol implies the security of BB84. The entanglement purification based protocol uses Calderbank-Shor-Steane codes, and properties of these codes are used to remove the use of quantum computation from the Lo-Chau protocol.

A Family of Quantum Protocols

NASA Astrophysics Data System (ADS)

Devetak, Igor; Harrow, Aram W.; Winter, Andreas

2004-12-01

We introduce three new quantum protocols involving noisy quantum channels and entangled states, and relate them operationally and conceptually with four well-known old protocols. Two of the new protocols (the mother and father) can generate the other five “child” protocols by direct application of teleportation and superdense coding, and can be derived in turn by making the old protocols “coherent.” This gives very simple proofs for two famous old protocols (the hashing inequality and quantum channel capacity) and provides the basis for optimal trade-off curves in several quantum information processing tasks.

Experimental Determination of Demand Response Control Models and Cost of Control for Ensembles of Window-Mount Air Conditioners

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

Geller, Drew Adam; Backhaus, Scott N.

Control of consumer electrical devices for providing electrical grid services is expanding in both the scope and the diversity of loads that are engaged in control, but there are few experimentally-based models of these devices suitable for control designs and for assessing the cost of control. A laboratory-scale test system is developed to experimentally evaluate the use of a simple window-mount air conditioner for electrical grid regulation services. The experimental test bed is a single, isolated air conditioner embedded in a test system that both emulates the thermodynamics of an air conditioned room and also isolates the air conditioner frommore » the real-world external environmental and human variables that perturb the careful measurements required to capture a model that fully characterizes both the control response functions and the cost of control. The control response functions and cost of control are measured using harmonic perturbation of the temperature set point and a test protocol that further isolates the air conditioner from low frequency environmental variability.« less

Experimental QR code optical encryption: noise-free data recovering.

PubMed

Barrera, John Fredy; Mira-Agudelo, Alejandro; Torroba, Roberto

2014-05-15

We report, to our knowledge for the first time, the experimental implementation of a quick response (QR) code as a "container" in an optical encryption system. A joint transform correlator architecture in an interferometric configuration is chosen as the experimental scheme. As the implementation is not possible in a single step, a multiplexing procedure to encrypt the QR code of the original information is applied. Once the QR code is correctly decrypted, the speckle noise present in the recovered QR code is eliminated by a simple digital procedure. Finally, the original information is retrieved completely free of any kind of degradation after reading the QR code. Additionally, we propose and implement a new protocol in which the reception of the encrypted QR code and its decryption, the digital block processing, and the reading of the decrypted QR code are performed employing only one device (smartphone, tablet, or computer). The overall method probes to produce an outcome far more attractive to make the adoption of the technique a plausible option. Experimental results are presented to demonstrate the practicality of the proposed security system.

Accurate measurements of the true column efficiency and of the instrument band broadening contributions in the presence of a chromatographic column.

PubMed

Gritti, Fabrice; Guiochon, Georges

2014-01-31

A rapid and simple validated experimental protocol is proposed for the accurate determination of the true intrinsic column efficiency and for that of the variance of the extra-column volume of the instrument used, the latter being obtained without requiring the removal of the chromatographic column from the HPLC system. This protocol was applied to 2.1mm×100mm columns packed with sub-3 (2.7μm Halo Peptide ES-C18) and sub-2μm (1.6μm prototype) core-shell particles. It was validated by observing the linear behavior of the plot of the apparent column plate height versus the reciprocal of (1+k')(2) for at least three homologous compounds, with a linear regression coefficient R(2) larger than 0.999. Irrespective of the contribution of the several, different instruments used to the total band broadening, the same column HETP value was obtained within 5%. This new protocol outperform the classical one in which the chromatographic column is replaced with a zero dead volume (ZDV) union connector to measure the extra-column volume variance, which is subtracted from the variance measured with the column to measure the intrinsic HETP. This protocol fails because it significantly underestimates the system volume variance. Copyright © 2013 Elsevier B.V. All rights reserved.

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics.

PubMed

Tyanova, Stefka; Temu, Tikira; Cox, Juergen

2016-12-01

MaxQuant is one of the most frequently used platforms for mass-spectrometry (MS)-based proteomics data analysis. Since its first release in 2008, it has grown substantially in functionality and can be used in conjunction with more MS platforms. Here we present an updated protocol covering the most important basic computational workflows, including those designed for quantitative label-free proteomics, MS1-level labeling and isobaric labeling techniques. This protocol presents a complete description of the parameters used in MaxQuant, as well as of the configuration options of its integrated search engine, Andromeda. This protocol update describes an adaptation of an existing protocol that substantially modifies the technique. Important concepts of shotgun proteomics and their implementation in MaxQuant are briefly reviewed, including different quantification strategies and the control of false-discovery rates (FDRs), as well as the analysis of post-translational modifications (PTMs). The MaxQuant output tables, which contain information about quantification of proteins and PTMs, are explained in detail. Furthermore, we provide a short version of the workflow that is applicable to data sets with simple and standard experimental designs. The MaxQuant algorithms are efficiently parallelized on multiple processors and scale well from desktop computers to servers with many cores. The software is written in C# and is freely available at http://www.maxquant.org.

Harmonic force spectroscopy measures load-dependent kinetics of individual human β-cardiac myosin molecules.

PubMed

Sung, Jongmin; Nag, Suman; Mortensen, Kim I; Vestergaard, Christian L; Sutton, Shirley; Ruppel, Kathleen; Flyvbjerg, Henrik; Spudich, James A

2015-08-04

Molecular motors are responsible for numerous cellular processes from cargo transport to heart contraction. Their interactions with other cellular components are often transient and exhibit kinetics that depend on load. Here, we measure such interactions using 'harmonic force spectroscopy'. In this method, harmonic oscillation of the sample stage of a laser trap immediately, automatically and randomly applies sinusoidally varying loads to a single motor molecule interacting with a single track along which it moves. The experimental protocol and the data analysis are simple, fast and efficient. The protocol accumulates statistics fast enough to deliver single-molecule results from single-molecule experiments. We demonstrate the method's performance by measuring the force-dependent kinetics of individual human β-cardiac myosin molecules interacting with an actin filament at physiological ATP concentration. We show that a molecule's ADP release rate depends exponentially on the applied load, in qualitative agreement with cardiac muscle, which contracts with a velocity inversely proportional to external load.

Harmonic force spectroscopy measures load-dependent kinetics of individual human β-cardiac myosin molecules

PubMed Central

Sung, Jongmin; Nag, Suman; Mortensen, Kim I.; Vestergaard, Christian L.; Sutton, Shirley; Ruppel, Kathleen; Flyvbjerg, Henrik; Spudich, James A.

2015-01-01

Molecular motors are responsible for numerous cellular processes from cargo transport to heart contraction. Their interactions with other cellular components are often transient and exhibit kinetics that depend on load. Here, we measure such interactions using ‘harmonic force spectroscopy'. In this method, harmonic oscillation of the sample stage of a laser trap immediately, automatically and randomly applies sinusoidally varying loads to a single motor molecule interacting with a single track along which it moves. The experimental protocol and the data analysis are simple, fast and efficient. The protocol accumulates statistics fast enough to deliver single-molecule results from single-molecule experiments. We demonstrate the method's performance by measuring the force-dependent kinetics of individual human β-cardiac myosin molecules interacting with an actin filament at physiological ATP concentration. We show that a molecule's ADP release rate depends exponentially on the applied load, in qualitative agreement with cardiac muscle, which contracts with a velocity inversely proportional to external load. PMID:26239258

PaR-PaR Laboratory Automation Platform

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

Linshiz, G; Stawski, N; Poust, S

2013-05-01

Labor-intensive multistep biological tasks, such as the construction and cloning of DNA molecules, are prime candidates for laboratory automation. Flexible and biology-friendly operation of robotic equipment is key to its successful integration in biological laboratories, and the efforts required to operate a robot must be much smaller than the alternative manual lab work. To achieve these goals, a simple high-level biology-friendly robot programming language is needed. We have developed and experimentally validated such a language: Programming a Robot (PaR-PaR). The syntax and compiler for the language are based on computer science principles and a deep understanding of biological workflows. PaR-PaRmore » allows researchers to use liquid-handling robots effectively, enabling experiments that would not have been considered previously. After minimal training, a biologist can independently write complicated protocols for a robot within an hour. Adoption of PaR-PaR as a standard cross-platform language would enable hand-written or software-generated robotic protocols to be shared across laboratories.« less

Domain and nanoridge growth kinetics in stratifying foam films

NASA Astrophysics Data System (ADS)

Zhang, Yiran; Sharma, Vivek

Ultrathin films exhibit stratification due to confinement-induced structuring and layering of small molecules in simple fluids, and of supramolecular structures like micelles, lipid layers and nanoparticles in complex fluids. Stratification proceeds by the formation and growth of thinner domains at the expense of surrounding thicker film, and results in formation of nanoscopic terraces and mesas within a film. The detailed mechanisms underlying stratification are still under debate, and are resolved in this contribution by addressing long-standing experimental and theoretical challenges. Thickness variations in stratifying films are visualized and analyzed using interferometry, digital imaging and optical microscopy (IDIOM) protocols, with unprecedented high spatial (thickness <100 nm, lateral 500 nm) and temporal resolution (<1 ms). Using IDIOM protocols we developed recently, we characterize the shape and the growth dynamics of nanoridges that flank the expanding domains in micellar thin films. We show that topographical changes including nanoridge growth, and the overall stratification dynamics, can be described quantitatively by nonlinear thin film equation, amended with supramolecular oscillatory surface forces.

PaR-PaR laboratory automation platform.

PubMed

Linshiz, Gregory; Stawski, Nina; Poust, Sean; Bi, Changhao; Keasling, Jay D; Hillson, Nathan J

2013-05-17

Labor-intensive multistep biological tasks, such as the construction and cloning of DNA molecules, are prime candidates for laboratory automation. Flexible and biology-friendly operation of robotic equipment is key to its successful integration in biological laboratories, and the efforts required to operate a robot must be much smaller than the alternative manual lab work. To achieve these goals, a simple high-level biology-friendly robot programming language is needed. We have developed and experimentally validated such a language: Programming a Robot (PaR-PaR). The syntax and compiler for the language are based on computer science principles and a deep understanding of biological workflows. PaR-PaR allows researchers to use liquid-handling robots effectively, enabling experiments that would not have been considered previously. After minimal training, a biologist can independently write complicated protocols for a robot within an hour. Adoption of PaR-PaR as a standard cross-platform language would enable hand-written or software-generated robotic protocols to be shared across laboratories.

Command-line cellular electrophysiology for conventional and real-time closed-loop experiments.

PubMed

Linaro, Daniele; Couto, João; Giugliano, Michele

2014-06-15

Current software tools for electrophysiological experiments are limited in flexibility and rarely offer adequate support for advanced techniques such as dynamic clamp and hybrid experiments, which are therefore limited to laboratories with a significant expertise in neuroinformatics. We have developed lcg, a software suite based on a command-line interface (CLI) that allows performing both standard and advanced electrophysiological experiments. Stimulation protocols for classical voltage and current clamp experiments are defined by a concise and flexible meta description that allows representing complex waveforms as a piece-wise parametric decomposition of elementary sub-waveforms, abstracting the stimulation hardware. To perform complex experiments lcg provides a set of elementary building blocks that can be interconnected to yield a large variety of experimental paradigms. We present various cellular electrophysiological experiments in which lcg has been employed, ranging from the automated application of current clamp protocols for characterizing basic electrophysiological properties of neurons, to dynamic clamp, response clamp, and hybrid experiments. We finally show how the scripting capabilities behind a CLI are suited for integrating experimental trials into complex workflows, where actual experiment, online data analysis and computational modeling seamlessly integrate. We compare lcg with two open source toolboxes, RTXI and RELACS. We believe that lcg will greatly contribute to the standardization and reproducibility of both simple and complex experiments. Additionally, on the long run the increased efficiency due to a CLI will prove a great benefit for the experimental community. Copyright © 2014 Elsevier B.V. All rights reserved.

Efficient and simple approaches towards direct oxidative esterification of alcohols.

PubMed

Ray, Ritwika; Jana, Rahul Dev; Bhadra, Mayukh; Maiti, Debabrata; Lahiri, Goutam Kumar

2014-11-17

The present article describes novel oxidative protocols for direct esterification of alcohols. The protocols involve successful demonstrations of both "cross" and "self" esterification of a wide variety of alcohols. The cross-esterification proceeds under a simple transition-metal-free condition, containing catalytic amounts of TEMPO (2,2,6,6-tetramethyl-1-piperidinyloxy)/TBAB (tetra-n-butylammonium bromide) in combination with oxone (potassium peroxo monosulfate) as the oxidant, whereas the self-esterification is achieved through simple induction of Fe(OAc)2 /dipic (dipic=2,6-pyridinedicarboxylic acid) as the active catalyst under an identical oxidizing environment. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A simple protocol for attenuating the auto-fluorescence of cyanobacteria for optimized fluorescence in situ hybridization (FISH) imaging.

PubMed

Zeller, Perrine; Ploux, Olivier; Méjean, Annick

2016-03-01

Cyanobacteria contain pigments, which generate auto-fluorescence that interferes with fluorescence in situ hybridization (FISH) imaging of cyanobacteria. We describe simple chemical treatments using CuSO4 or H2O2 that significantly reduce the auto-fluorescence of Microcystis strains. These protocols were successfully applied in FISH experiments using 16S rRNA specific probes and filamentous cyanobacteria. Copyright © 2016 Elsevier B.V. All rights reserved.

How to Catch a Smurf? - Ageing and Beyond… In vivo Assessment of Intestinal Permeability in Multiple Model Organisms.

PubMed

Martins, Raquel R; McCracken, Andrew W; Simons, Mirre J P; Henriques, Catarina M; Rera, Michael

2018-02-05

The Smurf Assay (SA) was initially developed in the model organism Drosophila melanogaster where a dramatic increase of intestinal permeability has been shown to occur during aging (Rera et al. , 2011). We have since validated the protocol in multiple other model organisms (Dambroise et al. , 2016) and have utilized the assay to further our understanding of aging (Tricoire and Rera, 2015; Rera et al. , 2018). The SA has now also been used by other labs to assess intestinal barrier permeability (Clark et al. , 2015; Katzenberger et al. , 2015; Barekat et al. , 2016; Chakrabarti et al. , 2016; Gelino et al. , 2016). The SA in itself is simple; however, numerous small details can have a considerable impact on its experimental validity and subsequent interpretation. Here, we provide a detailed update on the SA technique and explain how to catch a Smurf while avoiding the most common experimental fallacies.

The chicken chorioallantoic membrane model in biology, medicine and bioengineering

PubMed Central

Nowak-Sliwinska, Patrycja; Segura, Tatiana; Iruela-Arispe, M. Luisa

2015-01-01

The chicken chorioallantoic membrane (CAM) is a simple, highly vascularized extraembryonic membrane, which performs multiple functions during embryonic development, including but not restricted to gas exchange. Over the last two decades, interest in the CAM as a robust experimental platform to study blood vessels has been shared by specialists working in bioengineering, development, morphology, biochemistry, transplant biology, cancer research and drug development. The tissue composition and accessibility of the CAM for experimental manipulation, makes it an attractive preclinical in vivo model for drug screening and / or for studies of vascular growth. In this article we provide a detailed review of the use of the CAM to study vascular biology and response of blood vessels to a variety of agonists. We also present distinct cultivation protocols discussing their advantages and limitations and provide a summarized update on the use of the CAM in vascular imaging, drug delivery, pharmacokinetics and toxicology. PMID:25138280

Nonblocking and orphan free message logging protocols

NASA Technical Reports Server (NTRS)

Alvisi, Lorenzo; Hoppe, Bruce; Marzullo, Keith

1992-01-01

Currently existing message logging protocols demonstrate a classic pessimistic vs. optimistic tradeoff. We show that the optimistic-pessimistic tradeoff is not inherent to the problem of message logging. We construct a message-logging protocol that has the positive features of both optimistic and pessimistic protocol: our protocol prevents orphans and allows simple failure recovery; however, it requires no blocking in failure-free runs. Furthermore, this protocol does not introduce any additional message overhead as compared to one implemented for a system in which messages may be lost but processes do not crash.

Nonblocking and orphan free message logging protocols

NASA Astrophysics Data System (ADS)

Alvisi, Lorenzo; Hoppe, Bruce; Marzullo, Keith

1992-12-01

Currently existing message logging protocols demonstrate a classic pessimistic vs. optimistic tradeoff. We show that the optimistic-pessimistic tradeoff is not inherent to the problem of message logging. We construct a message-logging protocol that has the positive features of both optimistic and pessimistic protocol: our protocol prevents orphans and allows simple failure recovery; however, it requires no blocking in failure-free runs. Furthermore, this protocol does not introduce any additional message overhead as compared to one implemented for a system in which messages may be lost but processes do not crash.

SAMP, the Simple Application Messaging Protocol: Letting applications talk to each other

NASA Astrophysics Data System (ADS)

Taylor, M. B.; Boch, T.; Taylor, J.

2015-06-01

SAMP, the Simple Application Messaging Protocol, is a hub-based communication standard for the exchange of data and control between participating client applications. It has been developed within the context of the Virtual Observatory with the aim of enabling specialised data analysis tools to cooperate as a loosely integrated suite, and is now in use by many and varied desktop and web-based applications dealing with astronomical data. This paper reviews the requirements and design principles that led to SAMP's specification, provides a high-level description of the protocol, and discusses some of its common and possible future usage patterns, with particular attention to those factors that have aided its success in practice.

An efficacious oral health care protocol for immunocompromised patients.

PubMed

Solomon, C S; Shaikh, A B; Arendorf, T M

1995-01-01

A twice-weekly oral and perioral examination was provided to 120 patients receiving antineoplastic therapy. Sixty patients were monitored while following the traditional hospital oral care protocol (chlorhexidine, hydrogen peroxide, sodium bicarbonate, thymol glycol, benzocaine mouthrinse, and nystatin). The mouth care protocol was then changed (experimental protocol = chlorhexidine, benzocaine lozenges, amphotericin B lozenges), and patients were monitored until the sample size matched that of the hospital mouth care regime. There was a statistically significant reduction in oral complications upon introduction and maintenance of the experimental protocol.

Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications

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

Zhou, Jianying; Dann, Geoffrey P.; Shi, Tujin

2012-03-10

Sodium dodecyl sulfate (SDS) is one of the most popular laboratory reagents used for highly efficient biological sample extraction; however, SDS presents a significant challenge to LC-MS-based proteomic analyses due to its severe interference with reversed-phase LC separations and electrospray ionization interfaces. This study reports a simple SDS-assisted proteomic sample preparation method facilitated by a novel peptide-level SDS removal protocol. After SDS-assisted protein extraction and digestion, SDS was effectively (>99.9%) removed from peptides through ion substitution-mediated DS- precipitation with potassium chloride (KCl) followed by {approx}10 min centrifugation. Excellent peptide recovery (>95%) was observed for less than 20 {mu}g of peptides.more » Further experiments demonstrated the compatibility of this protocol with LC-MS/MS analyses. The resulting proteome coverage from this SDS-assisted protocol was comparable to or better than those obtained from other standard proteomic preparation methods in both mammalian tissues and bacterial samples. These results suggest that this SDS-assisted protocol is a practical, simple, and broadly applicable proteomic sample processing method, which can be particularly useful when dealing with samples difficult to solubilize by other methods.« less

Simple and economic colloidal centrifugation protocols may be incorporated into the clinical equine sperm processing procedure.

PubMed

Gutiérrez-Cepeda, L; Fernández, A; Crespo, F; Gosálvez, J; Serres, C

2011-03-01

For many years in human assisted-reproduction procedures there have been special protocols to prepare and improve sperm quality. Colloidal centrifugation (CC) is a useful technique that has been proved to enhance semen quality by selection of the best spermatozoa for different species. Its use is recommended to improve fertility of subfertile stallions but current CC protocols are clinically complicated in the equine sperm processing technique due to economic and technical difficulties. The aim of this study was to determine the optimal processing procedures to adapt the use of a CC product (EquiPure™) in the equine reproduction industry. A total of nineteen ejaculates were collected from 10 Purebred Spanish Horses (P.R.E horses) using a Missouri artificial vagina. Gel-free semen aliquots were analyzed prior to treatment (control). Semen was subjected to one of six CC protocols with EquiPure™ and centrifuged samples were statistically evaluated by ANOVA and Duncan tests (p<0.05) for sperm quality and recovery rate. We obtained higher values by colloidal centrifugation in LIN, STR and BCF variables and DNA fragmentation index trended to be lower in most of the CC protocols. The studied protocols were shown to be as efficient in improving equine sperm quality as the current commercial EquiPure™, with the added advantage of being much more economical and simple to use. According to these results it seems to be possible to incorporate single layer and or high colloidal centrifugation volume protocols what would make them simple, economic and clinically viable for the equine sperm processing procedure. Copyright © 2011 Elsevier B.V. All rights reserved.

An adaptable chromosome preparation methodology for use in invertebrate research organisms.

PubMed

Guo, Longhua; Accorsi, Alice; He, Shuonan; Guerrero-Hernández, Carlos; Sivagnanam, Shamilene; McKinney, Sean; Gibson, Matthew; Sánchez Alvarado, Alejandro

2018-02-26

The ability to efficiently visualize and manipulate chromosomes is fundamental to understanding the genome architecture of organisms. Conventional chromosome preparation protocols developed for mammalian cells and those relying on species-specific conditions are not suitable for many invertebrates. Hence, a simple and inexpensive chromosome preparation protocol, adaptable to multiple invertebrate species, is needed. We optimized a chromosome preparation protocol and applied it to several planarian species (phylum Platyhelminthes), the freshwater apple snail Pomacea canaliculata (phylum Mollusca), and the starlet sea anemone Nematostella vectensis (phylum Cnidaria). We demonstrated that both mitotically active adult tissues and embryos can be used as sources of metaphase chromosomes, expanding the potential use of this technique to invertebrates lacking cell lines and/or with limited access to the complete life cycle. Simple hypotonic treatment with deionized water was sufficient for karyotyping; growing cells in culture was not necessary. The obtained karyotypes allowed the identification of differences in ploidy and chromosome architecture among otherwise morphologically indistinguishable organisms, as in the case of a mixed population of planarians collected in the wild. Furthermore, we showed that in all tested organisms representing three different phyla this protocol could be effectively coupled with downstream applications, such as chromosome fluorescent in situ hybridization. Our simple and inexpensive chromosome preparation protocol can be readily adapted to new invertebrate research organisms to accelerate the discovery of novel genomic patterns across the branches of the tree of life.

In vitro selection and amplification protocols for isolation of aptameric sensors for small molecules

PubMed Central

Yang, Kyung-Ae; Pei, Renjun; Stojanovic, Milan N.

2016-01-01

We recently optimized a procedure that directly yields aptameric sensors for small molecules in so-called structure-switching format. The protocol has a high success rate, short time, and is sufficiently simple to be readily implemented in a non-specialist laboratory. We provide a stepwise guide to this selection protocol. PMID:27155227

A simple protocol for protein extraction of recalcitrant fruit tissues suitable for 2-DE and MS analysis.

PubMed

Song, Jun; Braun, Gordon; Bevis, Eric; Doncaster, Kristen

2006-08-01

Fruit tissues are considered recalcitrant plant tissue for proteomic analysis. Three phenol-free protein extraction procedures for 2-DE were compared and evaluated on apple fruit proteins. Incorporation of hot SDS buffer, extraction with TCA/acetone precipitation was found to be the most effective protocol. The results from SDS-PAGE and 2-DE analysis showed high quality proteins. More than 500 apple polypeptides were separated on a small scale 2-DE gel. The successful protocol was further tested on banana fruit, in which 504 and 386 proteins were detected in peel and flesh tissues, respectively. To demonstrate the quality of the extracted proteins, several protein spots from apple and banana peels were cut from 2-DE gels, analyzed by MS and have been tentatively identified. The protocol described in this study is a simple procedure which could be routinely used in proteomic studies of many types of recalcitrant fruit tissues.

A Simple Method for High Throughput Chemical Screening in Caenorhabditis Elegans

PubMed Central

Lucanic, Mark; Garrett, Theo; Gill, Matthew S.; Lithgow, Gordon J.

2018-01-01

Caenorhabditis elegans is a useful organism for testing chemical effects on physiology. Whole organism small molecule screens offer significant advantages for identifying biologically active chemical structures that can modify complex phenotypes such as lifespan. Described here is a simple protocol for producing hundreds of 96-well culture plates with fairly consistent numbers of C. elegans in each well. Next, we specified how to use these cultures to screen thousands of chemicals for effects on the lifespan of the nematode C. elegans. This protocol makes use of temperature sensitive sterile strains, agar plate conditions, and simple animal handling to facilitate the rapid and high throughput production of synchronized animal cultures for screening. PMID:29630057

Periodic table-based descriptors to encode cytotoxicity profile of metal oxide nanoparticles: a mechanistic QSTR approach.

PubMed

Kar, Supratik; Gajewicz, Agnieszka; Puzyn, Tomasz; Roy, Kunal; Leszczynski, Jerzy

2014-09-01

Nanotechnology has evolved as a frontrunner in the development of modern science. Current studies have established toxicity of some nanoparticles to human and environment. Lack of sufficient data and low adequacy of experimental protocols hinder comprehensive risk assessment of nanoparticles (NPs). In the present work, metal electronegativity (χ), the charge of the metal cation corresponding to a given oxide (χox), atomic number and valence electron number of the metal have been used as simple molecular descriptors to build up quantitative structure-toxicity relationship (QSTR) models for prediction of cytotoxicity of metal oxide NPs to bacteria Escherichia coli. These descriptors can be easily obtained from molecular formula and information acquired from periodic table in no time. It has been shown that a simple molecular descriptor χox can efficiently encode cytotoxicity of metal oxides leading to models with high statistical quality as well as interpretability. Based on this model and previously published experimental results, we have hypothesized the most probable mechanism of the cytotoxicity of metal oxide nanoparticles to E. coli. Moreover, the required information for descriptor calculation is independent of size range of NPs, nullifying a significant problem that various physical properties of NPs change for different size ranges. Copyright © 2014 Elsevier Inc. All rights reserved.

Excimer-based peptide beacons: a convenient experimental approach for monitoring polypeptide-protein and polypeptide-oligonucleotide interactions.

PubMed

Oh, Kenneth J; Cash, Kevin J; Plaxco, Kevin W

2006-11-01

While protein-polypeptide and nucleic acid-polypeptide interactions are of significant experimental interest, quantitative methods for the characterization of such interactions are often cumbersome. Here we described a relatively simple means of optically monitoring such interactions using excimer-based peptide beacons (PBs). The design of PBs is based on the observation that, whereas short peptides are almost invariably unfolded and highly dynamic, they become rigid when complexed with macromolecular targets. Using this binding-induced folding to segregate two pyrene moieties and therefore inhibit excimer formation, we have produced PBs directed against both anti-HIV antibodies and the retroviral transactive response (TAR) RNA hairpin. For both polypeptides, target recognition is accompanied by a roughly 2-fold decrease in excimer emission, thus allowing the detection of their respective targets at concentrations of a few nanomolar. Because excimer emission requires the formation of a tight, precisely oriented pyrene dimer, even relatively trivial binding-induced segregation reduces fluorescence significantly. This suggests that the PB approach will be suitable for monitoring a wide range of peptide-macromolecule recognition events. Moreover, the synthesis of excimer-based PBs utilizes commercially available modified pyrenes in a simple and well-established protocol, making the approach well suited for routine laboratory applications.

Scope and mechanism in palladium-catalyzed isomerizations of highly substituted allylic, homoallylic, and alkenyl alcohols.

PubMed

Larionov, Evgeny; Lin, Luqing; Guénée, Laure; Mazet, Clément

2014-12-03

Herein we report the palladium-catalyzed isomerization of highly substituted allylic alcohols and alkenyl alcohols by means of a single catalytic system. The operationally simple reaction protocol is applicable to a broad range of substrates and displays a wide functional group tolerance, and the products are usually isolated in high chemical yield. Experimental and computational mechanistic investigations provide complementary and converging evidence for a chain-walking process consisting of repeated migratory insertion/β-H elimination sequences. Interestingly, the catalyst does not dissociate from the substrate in the isomerization of allylic alcohols, whereas it disengages during the isomerization of alkenyl alcohols when additional substituents are present on the alkyl chain.

Cellular reprogramming dynamics follow a simple 1D reaction coordinate

NASA Astrophysics Data System (ADS)

Teja Pusuluri, Sai; Lang, Alex H.; Mehta, Pankaj; Castillo, Horacio E.

2018-01-01

Cellular reprogramming, the conversion of one cell type to another, induces global changes in gene expression involving thousands of genes, and understanding how cells globally alter their gene expression profile during reprogramming is an ongoing problem. Here we reanalyze time-course data on cellular reprogramming from differentiated cell types to induced pluripotent stem cells (iPSCs) and show that gene expression dynamics during reprogramming follow a simple 1D reaction coordinate. This reaction coordinate is independent of both the time it takes to reach the iPSC state as well as the details of the experimental protocol used. Using Monte-Carlo simulations, we show that such a reaction coordinate emerges from epigenetic landscape models where cellular reprogramming is viewed as a ‘barrier-crossing’ process between cell fates. Overall, our analysis and model suggest that gene expression dynamics during reprogramming follow a canonical trajectory consistent with the idea of an ‘optimal path’ in gene expression space for reprogramming.

NADA Protocol for Behavioral Health. Putting Tools in the Hands of Behavioral Health Providers: The Case for Auricular Detoxification Specialists.

PubMed

Stuyt, Elizabeth B; Voyles, Claudia A; Bursac, Sara

2018-02-07

Background: The National Acupuncture Detoxification Association (NADA) protocol, a simple standardized auricular treatment has the potential to provide vast public health relief on issues currently challenging our world. This includes but is not limited to addiction, such as the opioid epidemic, but also encompasses mental health, trauma, PTSD, chronic stress, and the symptoms associated with these conditions. Simple accessible tools that improve outcomes can make profound differences. We assert that the NADA protocol can have greatest impact when broadly applied by behavioral health professionals, Auricular Detoxification Specialists (ADSes). Methods: The concept of ADS is described and how current laws vary from state to state. Using available national data, a survey of practitioners in three selected states with vastly different laws regarding ADSes, and interviews of publicly funded programs which are successfully incorporating the NADA protocol, we consider possible effects of ADS-friendly conditions. Results: Data presented supports the idea that conditions conducive to ADS practice lead to greater implementation. Program interviews reflect settings in which adding ADSes can in turn lead to improved outcomes. Discussion: The primary purpose of non-acupuncturist ADSes is to expand the access of this simple but effective treatment to all who are suffering from addictions, stress, or trauma and to allow programs to incorporate acupuncture in the form of the NADA protocol at minimal cost, when and where it is needed. States that have changed laws to allow ADS practice for this standardized ear acupuncture protocol have seen increased access to this treatment, benefiting both patients and the programs.

The Behavior of TCP and Its Extensions in Space

NASA Technical Reports Server (NTRS)

Wang, Ruhai; Horan, Stephen

2001-01-01

The performance of Transmission Control Protocol (TCP) in space has been examined from the observations of simulation and experimental tests for several years at National Aeronautics and Space Administration (NASA), Department of Defense (DoD) and universities. At New Mexico State University (NMSU), we have been concentrating on studying the performance of two protocol suites: the file transfer protocol (ftp) running over Transmission Control Protocol/Internet Protocol (TCP/IP) stack and the file protocol (fp) running over the Space Communications Protocol Standards (SCPS)-Transport Protocol (TP) developed under the Consultative Committee for Space Data Systems (CCSDS) standards process. SCPS-TP is considered to be TCP's extensions for space communications. This dissertation experimentally studies the behavior of TCP and SCPS-TP by running the protocol suites over both the Space-to-Ground Link Simulator (SGLS) test-bed and realistic satellite link. The study concentrates on comparing protocol behavior by plotting the averaged file transfer times for different experimental configurations and analyzing them using Statistical Analysis System (SAS) based procedures. The effects of different link delays and various Bit-Error-Rates (BERS) on each protocol performance are also studied and linear regression models are built for experiments over SGLS test-bed to reflect the relationships between the file transfer time and various transmission conditions.

Experimental purification of single qubits.

PubMed

Ricci, M; De Martini, F; Cerf, N J; Filip, R; Fiurásek, J; Macchiavello, C

2004-10-22

We report the experimental realization of the purification protocol for single qubits sent through a depolarizing channel. The qubits are associated with polarization states of single photons and the protocol is achieved by means of passive linear optical elements. The present approach may represent a convenient alternative to the distillation and error correction protocols of quantum information.

Isolation of exosomes by differential centrifugation: Theoretical analysis of a commonly used protocol

NASA Astrophysics Data System (ADS)

Livshts, Mikhail A.; Khomyakova, Elena; Evtushenko, Evgeniy G.; Lazarev, Vassili N.; Kulemin, Nikolay A.; Semina, Svetlana E.; Generozov, Edward V.; Govorun, Vadim M.

2015-11-01

Exosomes, small (40-100 nm) extracellular membranous vesicles, attract enormous research interest because they are carriers of disease markers and a prospective delivery system for therapeutic agents. Differential centrifugation, the prevalent method of exosome isolation, frequently produces dissimilar and improper results because of the faulty practice of using a common centrifugation protocol with different rotors. Moreover, as recommended by suppliers, adjusting the centrifugation duration according to rotor K-factors does not work for “fixed-angle” rotors. For both types of rotors - “swinging bucket” and “fixed-angle” - we express the theoretically expected proportion of pelleted vesicles of a given size and the “cut-off” size of completely sedimented vesicles as dependent on the centrifugation force and duration and the sedimentation path-lengths. The proper centrifugation conditions can be selected using relatively simple theoretical estimates of the “cut-off” sizes of vesicles. Experimental verification on exosomes isolated from HT29 cell culture supernatant confirmed the main theoretical statements. Measured by the nanoparticle tracking analysis (NTA) technique, the concentration and size distribution of the vesicles after centrifugation agree with those theoretically expected. To simplify this “cut-off”-size-based adjustment of centrifugation protocol for any rotor, we developed a web-calculator.

Dynamic Spectrum Management for Military Wireless Networks

DTIC Science & Technology

2010-09-01

auctions, and protocols and etiquettes . Command and control assignments are provided by the regulatory agency by reviewing specific licensing...devices and amateur licensees do not have specific frequency assignments. The Protocols and Etiquettes methods allow these devices to operate within a...with Collision Avoidance (CSMA/CA) a protocol . Etiquettes are rules that are followed without explicit interaction between devices. Simple etiquettes

Counterfactual Quantum Deterministic Key Distribution

NASA Astrophysics Data System (ADS)

Zhang, Sheng; Wang, Jian; Tang, Chao-Jing

2013-01-01

We propose a new counterfactual quantum cryptography protocol concerning about distributing a deterministic key. By adding a controlled blocking operation module to the original protocol [T.G. Noh, Phys. Rev. Lett. 103 (2009) 230501], the correlation between the polarizations of the two parties, Alice and Bob, is extended, therefore, one can distribute both deterministic keys and random ones using our protocol. We have also given a simple proof of the security of our protocol using the technique we ever applied to the original protocol. Most importantly, our analysis produces a bound tighter than the existing ones.

One Step Quantum Key Distribution Based on EPR Entanglement.

PubMed

Li, Jian; Li, Na; Li, Lei-Lei; Wang, Tao

2016-06-30

A novel quantum key distribution protocol is presented, based on entanglement and dense coding and allowing asymptotically secure key distribution. Considering the storage time limit of quantum bits, a grouping quantum key distribution protocol is proposed, which overcomes the vulnerability of first protocol and improves the maneuverability. Moreover, a security analysis is given and a simple type of eavesdropper's attack would introduce at least an error rate of 46.875%. Compared with the "Ping-pong" protocol involving two steps, the proposed protocol does not need to store the qubit and only involves one step.

Protocols for second-generation business satellites systems

NASA Astrophysics Data System (ADS)

Evans, B. G.; Coakley, F. P.; El Amin, M. H. M.

The paper discusses the nature and mix of traffic in business satellite systems and describes the limitations on the protocol imposed by the differing impairments of speech, video, and data. A simple TDMA system protocol is presented which meets the requirements of mixed-service operation. The efficiency of the protocol together with implications for allocation, scheduling and synchronisation are discussed. Future-generation satellites will probably use on-board processing. Some initial work on protocols that make use of on-board processing and the implications for satellite and earth-station equipment are presented.

A Matter of Timing: Identifying Significant Multi-Dose Radiotherapy Improvements by Numerical Simulation and Genetic Algorithm Search

PubMed Central

Angus, Simon D.; Piotrowska, Monika Joanna

2014-01-01

Multi-dose radiotherapy protocols (fraction dose and timing) currently used in the clinic are the product of human selection based on habit, received wisdom, physician experience and intra-day patient timetabling. However, due to combinatorial considerations, the potential treatment protocol space for a given total dose or treatment length is enormous, even for relatively coarse search; well beyond the capacity of traditional in-vitro methods. In constrast, high fidelity numerical simulation of tumor development is well suited to the challenge. Building on our previous single-dose numerical simulation model of EMT6/Ro spheroids, a multi-dose irradiation response module is added and calibrated to the effective dose arising from 18 independent multi-dose treatment programs available in the experimental literature. With the developed model a constrained, non-linear, search for better performing cadidate protocols is conducted within the vicinity of two benchmarks by genetic algorithm (GA) techniques. After evaluating less than 0.01% of the potential benchmark protocol space, candidate protocols were identified by the GA which conferred an average of 9.4% (max benefit 16.5%) and 7.1% (13.3%) improvement (reduction) on tumour cell count compared to the two benchmarks, respectively. Noticing that a convergent phenomenon of the top performing protocols was their temporal synchronicity, a further series of numerical experiments was conducted with periodic time-gap protocols (10 h to 23 h), leading to the discovery that the performance of the GA search candidates could be replicated by 17–18 h periodic candidates. Further dynamic irradiation-response cell-phase analysis revealed that such periodicity cohered with latent EMT6/Ro cell-phase temporal patterning. Taken together, this study provides powerful evidence towards the hypothesis that even simple inter-fraction timing variations for a given fractional dose program may present a facile, and highly cost-effecitive means of significantly improving clinical efficacy. PMID:25460164

A matter of timing: identifying significant multi-dose radiotherapy improvements by numerical simulation and genetic algorithm search.

PubMed

Angus, Simon D; Piotrowska, Monika Joanna

2014-01-01

Multi-dose radiotherapy protocols (fraction dose and timing) currently used in the clinic are the product of human selection based on habit, received wisdom, physician experience and intra-day patient timetabling. However, due to combinatorial considerations, the potential treatment protocol space for a given total dose or treatment length is enormous, even for relatively coarse search; well beyond the capacity of traditional in-vitro methods. In constrast, high fidelity numerical simulation of tumor development is well suited to the challenge. Building on our previous single-dose numerical simulation model of EMT6/Ro spheroids, a multi-dose irradiation response module is added and calibrated to the effective dose arising from 18 independent multi-dose treatment programs available in the experimental literature. With the developed model a constrained, non-linear, search for better performing cadidate protocols is conducted within the vicinity of two benchmarks by genetic algorithm (GA) techniques. After evaluating less than 0.01% of the potential benchmark protocol space, candidate protocols were identified by the GA which conferred an average of 9.4% (max benefit 16.5%) and 7.1% (13.3%) improvement (reduction) on tumour cell count compared to the two benchmarks, respectively. Noticing that a convergent phenomenon of the top performing protocols was their temporal synchronicity, a further series of numerical experiments was conducted with periodic time-gap protocols (10 h to 23 h), leading to the discovery that the performance of the GA search candidates could be replicated by 17-18 h periodic candidates. Further dynamic irradiation-response cell-phase analysis revealed that such periodicity cohered with latent EMT6/Ro cell-phase temporal patterning. Taken together, this study provides powerful evidence towards the hypothesis that even simple inter-fraction timing variations for a given fractional dose program may present a facile, and highly cost-effecitive means of significantly improving clinical efficacy.

Experimental eavesdropping attack against Ekert's protocol based on Wigner's inequality

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

Bovino, F. A.; Colla, A. M.; Castagnoli, G.

2003-09-01

We experimentally implemented an eavesdropping attack against the Ekert protocol for quantum key distribution based on the Wigner inequality. We demonstrate a serious lack of security of this protocol when the eavesdropper gains total control of the source. In addition we tested a modified Wigner inequality which should guarantee a secure quantum key distribution.

A Simple Method to Measure Renal Function in Swine by the Plasma Clearance of Iohexol

PubMed Central

Luis-Lima, Sergio; García-Contreras, Consolación; Carrara, Fabiola; Negrín-Mena, Natalia; Jiménez-Sosa, Alejandro; Jiménez-Hernández, Hugo; Porrini, Esteban

2018-01-01

There is no simple method to measure glomerular filtration rate (GFR) in swine, an established model for studying renal disease. We developed a protocol to measure GFR in conscious swine by using the plasma clearance of iohexol. We used two groups, test and validation, with eight animals each. Ten milliliters of iohexol (6.47 g) was injected into the marginal auricular vein and blood samples (3 mL) were collected from the orbital sinus at different points after injection. GFR was determined using two models: two-compartment (CL2: all samples) and one-compartment (CL1: the last six samples). In the test group, CL1 overestimated CL2 by ~30%: CL2 = 245 ± 93 and CL1 = 308 ± 123 mL/min. This error was corrected by a first-order polynomial quadratic equation to CL1, which was considered the simplified method: SM = −47.909 + (1.176xCL1) − (0.00063968xCL12). The SM showed narrow limits of agreement with CL2, a concordance correlation of 0.97, and a total deviation index of 14.73%. Similar results were obtained for the validation group. This protocol is reliable, reproducible, can be performed in conscious animals, uses a single dose of the marker, and requires a reduced number of samples, and avoids urine collection. Finally, it presents a significant improvement in animal welfare conditions and handling necessities in experimental trials. PMID:29329247

Multivariate Analysis of High Through-Put Adhesively Bonded Single Lap Joints: Experimental and Workflow Protocols

DTIC Science & Technology

2016-06-01

unlimited. v List of Tables Table 1 Single-lap-joint experimental parameters ..............................................7 Table 2 Survey ...Joints: Experimental and Workflow Protocols by Robert E Jensen, Daniel C DeSchepper, and David P Flanagan Approved for...TR-7696 ● JUNE 2016 US Army Research Laboratory Multivariate Analysis of High Through-Put Adhesively Bonded Single Lap Joints: Experimental

Apheresis product identification in the transplant center: development of point-of-care protocols for extended blood typing of stem cell apheresis products.

PubMed

Cummerow, C; Schwind, P; Spicher, M; Spohn, G; Geisen, C; Seifried, E; Bönig, H

2012-06-01

Transfusion of the 'wrong' stem cell product would almost inevitably be lethal, yet assays to confirm the contents of the product bag, except by checking labels and paperwork, are lacking. To increase the likelihood that a product mix-up would be detected in the transplant center, we developed a simple protocol for extended blood typing and hence, for confirmation of donor/product identity, on a tube segment. Apheresis samples were applied, directly or after erythrocyte enrichment, to commercially available blood typing assays, including lateral flow cards and gel agglutination cards. Without sample modification, low hematocrit and high leukocyte count obviated definitive blood typing. Using the most simple erythrocyte enrichment protocol, that is, centrifugation, reliable blood group analysis became possible with either assay. Other, more cumbersome pre-analytical protocols were also successful but provided no advantage. The preferred method was validated on 100 samples; ABD was correctly identified in 100% of cases. Of the other Rh Ags, all except two 'small e', in both cases in heterozygous individuals, were detected; there were no false positives. A simple, inexpensive point-of-care assay for extended blood typing of apheresis products is available, which can reduce the fatal risk of administering the wrong stem cell product.

A data driven method for estimation of B(avail) and appK(D) using a single injection protocol with [¹¹C]raclopride in the mouse.

PubMed

Wimberley, Catriona J; Fischer, Kristina; Reilhac, Anthonin; Pichler, Bernd J; Gregoire, Marie Claude

2014-10-01

The partial saturation approach (PSA) is a simple, single injection experimental protocol that will estimate both B(avail) and appK(D) without the use of blood sampling. This makes it ideal for use in longitudinal studies of neurodegenerative diseases in the rodent. The aim of this study was to increase the range and applicability of the PSA by developing a data driven strategy for determining reliable regional estimates of receptor density (B(avail)) and in vivo affinity (1/appK(D)), and validate the strategy using a simulation model. The data driven method uses a time window guided by the dynamic equilibrium state of the system as opposed to using a static time window. To test the method, simulations of partial saturation experiments were generated and validated against experimental data. The experimental conditions simulated included a range of receptor occupancy levels and three different B(avail) and appK(D) values to mimic diseases states. Also the effect of using a reference region and typical PET noise on the stability and accuracy of the estimates was investigated. The investigations showed that the parameter estimates in a simulated healthy mouse, using the data driven method were within 10±30% of the simulated input for the range of occupancy levels simulated. Throughout all experimental conditions simulated, the accuracy and robustness of the estimates using the data driven method were much improved upon the typical method of using a static time window, especially at low receptor occupancy levels. Introducing a reference region caused a bias of approximately 10% over the range of occupancy levels. Based on extensive simulated experimental conditions, it was shown the data driven method provides accurate and precise estimates of B(avail) and appK(D) for a broader range of conditions compared to the original method. Copyright © 2014 Elsevier Inc. All rights reserved.

Optimizing Libraries’ Content Findability Using Simple Object Access Protocol (SOAP) With Multi-Tier Architecture

NASA Astrophysics Data System (ADS)

Lahinta, A.; Haris, I.; Abdillah, T.

2017-03-01

The aim of this paper is to describe a developed application of Simple Object Access Protocol (SOAP) as a model for improving libraries’ digital content findability on the library web. The study applies XML text-based protocol tools in the collection of data about libraries’ visibility performance in the search results of the book. Model from the integrated Web Service Document Language (WSDL) and Universal Description, Discovery and Integration (UDDI) are applied to analyse SOAP as element within the system. The results showed that the developed application of SOAP with multi-tier architecture can help people simply access the website in the library server Gorontalo Province and support access to digital collections, subscription databases, and library catalogs in each library in Regency or City in Gorontalo Province.

Reference system for scanning probe tip fingerprinting

NASA Astrophysics Data System (ADS)

Turansky, Robert; Bamidele, Joseph; Sugawara, Yasuhiro; Kantorovitch, Lev; Stich, Ivan

2012-02-01

Knowledge of the chemical structure of the tip asperity in Non-Contact Atomic Force Microscopy (NC-AFM) is crucial as controlled manipulation of atoms and/or molecules on surfaces can only be performed if this information is available. However, a simple and robust protocol for ensuring a specific tip termination has not yet been developed. We propose a procedure for chemical tip finger printing and an example of a reference system, the oxygen-terminated Cu(110) surface, that enables one to ensure a specific tip termination with Si, Cu, or O atoms. To follow this up and unambiguously determine tip types, we performed a theoretical DFT study of the line scans with the tip models in question and found that the tip characterization made based on experimental results (Cu/O-terminated tip imaging Cu/O atoms) is in fact incorrect and the opposite is true (Cu/O-terminated tip imaging O/Cu atoms). This protocol allows the tip asperity's chemical structure to be verified and established both before as well as at any stage of the manipulation experiment when numerous tip changes may take place.

Practical quantum key distribution protocol without monitoring signal disturbance.

PubMed

Sasaki, Toshihiko; Yamamoto, Yoshihisa; Koashi, Masato

2014-05-22

Quantum cryptography exploits the fundamental laws of quantum mechanics to provide a secure way to exchange private information. Such an exchange requires a common random bit sequence, called a key, to be shared secretly between the sender and the receiver. The basic idea behind quantum key distribution (QKD) has widely been understood as the property that any attempt to distinguish encoded quantum states causes a disturbance in the signal. As a result, implementation of a QKD protocol involves an estimation of the experimental parameters influenced by the eavesdropper's intervention, which is achieved by randomly sampling the signal. If the estimation of many parameters with high precision is required, the portion of the signal that is sacrificed increases, thus decreasing the efficiency of the protocol. Here we propose a QKD protocol based on an entirely different principle. The sender encodes a bit sequence onto non-orthogonal quantum states and the receiver randomly dictates how a single bit should be calculated from the sequence. The eavesdropper, who is unable to learn the whole of the sequence, cannot guess the bit value correctly. An achievable rate of secure key distribution is calculated by considering complementary choices between quantum measurements of two conjugate observables. We found that a practical implementation using a laser pulse train achieves a key rate comparable to a decoy-state QKD protocol, an often-used technique for lasers. It also has a better tolerance of bit errors and of finite-sized-key effects. We anticipate that this finding will give new insight into how the probabilistic nature of quantum mechanics can be related to secure communication, and will facilitate the simple and efficient use of conventional lasers for QKD.

Immunosuppression for in vivo research: state-of-the-art protocols and experimental approaches

PubMed Central

Diehl, Rita; Ferrara, Fabienne; Müller, Claudia; Dreyer, Antje Y; McLeod, Damian D; Fricke, Stephan; Boltze, Johannes

2017-01-01

Almost every experimental treatment strategy using non-autologous cell, tissue or organ transplantation is tested in small and large animal models before clinical translation. Because these strategies require immunosuppression in most cases, immunosuppressive protocols are a key element in transplantation experiments. However, standard immunosuppressive protocols are often applied without detailed knowledge regarding their efficacy within the particular experimental setting and in the chosen model species. Optimization of such protocols is pertinent to the translation of experimental results to human patients and thus warrants further investigation. This review summarizes current knowledge regarding immunosuppressive drug classes as well as their dosages and application regimens with consideration of species-specific drug metabolization and side effects. It also summarizes contemporary knowledge of novel immunomodulatory strategies, such as the use of mesenchymal stem cells or antibodies. Thus, this review is intended to serve as a state-of-the-art compendium for researchers to refine applied experimental immunosuppression and immunomodulation strategies to enhance the predictive value of preclinical transplantation studies. PMID:27721455

Cryptanalysis and Improvements for the Quantum Private Comparison Protocol Using EPR Pairs

NASA Astrophysics Data System (ADS)

Wang, Cong; Xu, Gang; Yang, Yi-Xian

2013-07-01

In this paper, we carry out an in-depth analysis of the quantum private comparison (QPC) protocol with the semi-honest third party (TP). The security of QPC protocol using the EPR pairs is re-examined. Unfortunately, we find that TP can use the fake EPR pairs to steal all the secret information. Furthermore, we give two simple and feasible solutions to improve the original QPC protocol. It is shown that the improved protocol is secure, which can resist various kinds of attacks from both the outside eavesdroppers and the inside participants, even the semi-honest TP.

One Step Quantum Key Distribution Based on EPR Entanglement

PubMed Central

Li, Jian; Li, Na; Li, Lei-Lei; Wang, Tao

2016-01-01

A novel quantum key distribution protocol is presented, based on entanglement and dense coding and allowing asymptotically secure key distribution. Considering the storage time limit of quantum bits, a grouping quantum key distribution protocol is proposed, which overcomes the vulnerability of first protocol and improves the maneuverability. Moreover, a security analysis is given and a simple type of eavesdropper’s attack would introduce at least an error rate of 46.875%. Compared with the “Ping-pong” protocol involving two steps, the proposed protocol does not need to store the qubit and only involves one step. PMID:27357865

Simple and cost-effective fabrication of microvalve arrays in PDMS using laser cut molds with application to C. elegans manipulation in microfluidics

NASA Astrophysics Data System (ADS)

Samuel, R.; Thacker, C. M.; Maricq, A. V.; Gale, B. K.

2014-09-01

We present a new fabrication protocol for fabricating pneumatically controlled microvalve arrays (consisting of 100 s of microvalves) in PDMS substrates. The protocol utilizes rapid and cost-effective fabrication of molds using laser cutting of adhesive vinyl tapes and replica molding of PDMS. Hence the protocol is fast, simple and avoids cleanroom use. The results show that effective doormat-style microvalves can be easily fabricated in arrays by manipulating the stiffness of the actuating membrane through varying the valve-chamber area/shape. Three frequently used valve-chamber shapes (circle, square and capsule) were tested and all showed advantages in different situations. Circular valve chambers were best for small valves, square valves were best for medium-sized valves, and the capsule valves were best for larger valves. An application of this protocol has been demonstrated in the fabrication of a microfluidic 32-well plate for high-throughput manipulation of C. elegans for biomedical research.

Two-qubit correlations revisited: average mutual information, relevant (and useful) observables and an application to remote state preparation

NASA Astrophysics Data System (ADS)

Giorda, Paolo; Allegra, Michele

2017-07-01

Understanding how correlations can be used for quantum communication protocols is a central goal of quantum information science. While many authors have linked the global measures of correlations such as entanglement or discord to the performance of specific protocols, in general the latter may require only correlations between specific observables. In this work, we first introduce a general measure of correlations for two-qubit states, based on the classical mutual information between local observables. Our measure depends on the state’s purity and the symmetry in the correlation distribution, according to which we provide a classification of maximally mixed marginal states (MMMS). We discuss the complementarity relation between correlations and coherence. By focusing on a simple yet paradigmatic example, i.e. the remote state preparation protocol, we introduce a method to systematically define the proper protocol-tailored measures of the correlations. The method is based on the identification of those correlations that are relevant (useful) for the protocol. On the one hand, the approach allows the role of the symmetry of the correlation distribution to be discussed in determining the efficiency of the protocol, both for MMMS and general two-qubit quantum states, and on the other hand, it allows an optimized protocol for non-MMMS to be devised, which is more efficient with respect to the standard one. Overall, our findings clarify how the key resources in simple communication protocols are the purity of the state used and the symmetry of the correlation distribution.

Boolean Dynamic Modeling Approaches to Study Plant Gene Regulatory Networks: Integration, Validation, and Prediction.

PubMed

Velderraín, José Dávila; Martínez-García, Juan Carlos; Álvarez-Buylla, Elena R

2017-01-01

Mathematical models based on dynamical systems theory are well-suited tools for the integration of available molecular experimental data into coherent frameworks in order to propose hypotheses about the cooperative regulatory mechanisms driving developmental processes. Computational analysis of the proposed models using well-established methods enables testing the hypotheses by contrasting predictions with observations. Within such framework, Boolean gene regulatory network dynamical models have been extensively used in modeling plant development. Boolean models are simple and intuitively appealing, ideal tools for collaborative efforts between theorists and experimentalists. In this chapter we present protocols used in our group for the study of diverse plant developmental processes. We focus on conceptual clarity and practical implementation, providing directions to the corresponding technical literature.

Tube-Forming Assays.

PubMed

Brown, Ryan M; Meah, Christopher J; Heath, Victoria L; Styles, Iain B; Bicknell, Roy

2016-01-01

Angiogenesis involves the generation of new blood vessels from the existing vasculature and is dependent on many growth factors and signaling events. In vivo angiogenesis is dynamic and complex, meaning assays are commonly utilized to explore specific targets for research into this area. Tube-forming assays offer an excellent overview of the molecular processes in angiogenesis. The Matrigel tube forming assay is a simple-to-implement but powerful tool for identifying biomolecules involved in angiogenesis. A detailed experimental protocol on the implementation of the assay is described in conjunction with an in-depth review of methods that can be applied to the analysis of the tube formation. In addition, an ImageJ plug-in is presented which allows automatic quantification of tube images reducing analysis times while removing user bias and subjectivity.

Analysis of protein and lipid dynamics using confocal fluorescence recovery after photobleaching (FRAP)

PubMed Central

Day, Charles A.; Kraft, Lewis J.; Kang, Minchul; Kenworthy, Anne K.

2012-01-01

Fluorescence recovery after photobleaching (FRAP) is a powerful, versatile and widely accessible tool to monitor molecular dynamics in living cells that can be performed using modern confocal microscopes. Although the basic principles of FRAP are simple, quantitative FRAP analysis requires careful experimental design, data collection and analysis. In this review we discuss the theoretical basis for confocal FRAP, followed by step-by-step protocols for FRAP data acquisition using a laser scanning confocal microscope for (1) measuring the diffusion of a membrane protein, (2) measuring the diffusion of a soluble protein, and (3) analysis of intracellular trafficking. Finally, data analysis procedures are discussed and an equation for determining the diffusion coefficient of a molecular species undergoing pure diffusion is presented. PMID:23042527

Reprogramming of Somatic Cells Towards Pluripotency by Cell Fusion.

PubMed

Malinowski, Andrzej R; Fisher, Amanda G

2016-01-01

Pluripotent reprogramming can be dominantly induced in a somatic nucleus upon fusion with a pluripotent cell such as embryonic stem (ES) cell. Cell fusion between ES cells and somatic cells results in the formation of heterokaryons, in which the somatic nuclei begin to acquire features of the pluripotent partner. The generation of interspecies heterokaryons between mouse ES- and human somatic cells allows an experimenter to distinguish the nuclear events occurring specifically within the reprogrammed nucleus. Therefore, cell fusion provides a simple and rapid approach to look at the early nuclear events underlying pluripotent reprogramming. Here, we describe a polyethylene glycol (PEG)-mediated cell fusion protocol to generate interspecies heterokaryons and intraspecies hybrids between ES cells and B lymphocytes or fibroblasts.

Simple algorithm for improved security in the FDDI protocol

NASA Astrophysics Data System (ADS)

Lundy, G. M.; Jones, Benjamin

1993-02-01

We propose a modification to the Fiber Distributed Data Interface (FDDI) protocol based on a simple algorithm which will improve confidential communication capability. This proposed modification provides a simple and reliable system which exploits some of the inherent security properties in a fiber optic ring network. This method differs from conventional methods in that end to end encryption can be facilitated at the media access control sublayer of the data link layer in the OSI network model. Our method is based on a variation of the bit stream cipher method. The transmitting station takes the intended confidential message and uses a simple modulo two addition operation against an initialization vector. The encrypted message is virtually unbreakable without the initialization vector. None of the stations on the ring will have access to both the encrypted message and the initialization vector except the transmitting and receiving stations. The generation of the initialization vector is unique for each confidential transmission and thus provides a unique approach to the key distribution problem. The FDDI protocol is of particular interest to the military in terms of LAN/MAN implementations. Both the Army and the Navy are considering the standard as the basis for future network systems. A simple and reliable security mechanism with the potential to support realtime communications is a necessary consideration in the implementation of these systems. The proposed method offers several advantages over traditional methods in terms of speed, reliability, and standardization.

A protocol for the production of gliadin-cyanoacrylate nanoparticles for hydrophilic coating

USDA-ARS?s Scientific Manuscript database

This article presents a protocol for the production of protein-based nanoparticles that change the hydrophobic surface to hydrophilic by a simple spray coating. These nanoparticles are produced by the polymerization reaction of alkyl cyanoacrylate on the surface of cereal protein (gliadin) molecules...

Making Microbiology Even Smaller!

ERIC Educational Resources Information Center

Young, Linda Mull; Motz, Vicki Abrams

2013-01-01

We outline protocols for producing slant-minis (SLINIs) and mini-deeps (MEEPs) and examples of their use in simple microbiology experiments suitable for high school students. The principal benefits of these protocols are decreased cost associated with significantly reduced media use; easier, less expensive disposal of waste; and increased safety…

Link-state-estimation-based transmission power control in wireless body area networks.

PubMed

Kim, Seungku; Eom, Doo-Seop

2014-07-01

This paper presents a novel transmission power control protocol to extend the lifetime of sensor nodes and to increase the link reliability in wireless body area networks (WBANs). We first experimentally investigate the properties of the link states using the received signal strength indicator (RSSI). We then propose a practical transmission power control protocol based on both short- and long-term link-state estimations. Both the short- and long-term link-state estimations enable the transceiver to adapt the transmission power level and target the RSSI threshold range, respectively, to simultaneously satisfy the requirements of energy efficiency and link reliability. Finally, the performance of the proposed protocol is experimentally evaluated in two experimental scenarios-body posture change and dynamic body motion-and compared with the typical WBAN transmission power control protocols, a real-time reactive scheme, and a dynamic postural position inference mechanism. From the experimental results, it is found that the proposed protocol increases the lifetime of the sensor nodes by a maximum of 9.86% and enhances the link reliability by reducing the packet loss by a maximum of 3.02%.

Continuous-variable protocol for oblivious transfer in the noisy-storage model.

PubMed

Furrer, Fabian; Gehring, Tobias; Schaffner, Christian; Pacher, Christoph; Schnabel, Roman; Wehner, Stephanie

2018-04-13

Cryptographic protocols are the backbone of our information society. This includes two-party protocols which offer protection against distrustful players. Such protocols can be built from a basic primitive called oblivious transfer. We present and experimentally demonstrate here a quantum protocol for oblivious transfer for optical continuous-variable systems, and prove its security in the noisy-storage model. This model allows us to establish security by sending more quantum signals than an attacker can reliably store during the protocol. The security proof is based on uncertainty relations which we derive for continuous-variable systems, that differ from the ones used in quantum key distribution. We experimentally demonstrate in a proof-of-principle experiment the proposed oblivious transfer protocol for various channel losses by using entangled two-mode squeezed states measured with balanced homodyne detection. Our work enables the implementation of arbitrary two-party quantum cryptographic protocols with continuous-variable communication systems.

The theory of granular packings for coarse soils

NASA Astrophysics Data System (ADS)

Yanqui, Calixtro

2013-06-01

Coarse soils are substances made of grains of different shape, size and orientation. In this paper, new massive-measurable grain indexes are defined to develop a simple and systematic theory for the ideal packing of grains. First, a linear relationship between an assemblage of monodisperse spheres and an assemblage of polydisperse grains is deduced. Then, a general formula for the porosity of linearly ordered packings of spheres in contact is settled down by the appropriated choosing of eight neighboring spheres located at the vertices of the unit parallelepiped. The porosity of axisymmetric packings of grains, related to sand piles and axisymmetric compression tests, is proposed to be determined averaging the respective linear parameters. Since they can be tested experimentally, porosities of the densest state and the loosest state of a granular soil can be used to verify the accuracy of the present theory. Diagrams for these extreme quantities show a good agreement between the theoretical lines and the experimental data, no matter the dependency on the protocols and mineral composition.

Probing noncommutative theories with quantum optical experiments

NASA Astrophysics Data System (ADS)

Dey, Sanjib; Bhat, Anha; Momeni, Davood; Faizal, Mir; Ali, Ahmed Farag; Dey, Tarun Kumar; Rehman, Atikur

2017-11-01

One of the major difficulties of modern science underlies at the unification of general relativity and quantum mechanics. Different approaches towards such theory have been proposed. Noncommutative theories serve as the root of almost all such approaches. However, the identification of the appropriate passage to quantum gravity is suffering from the inadequacy of experimental techniques. It is beyond our ability to test the effects of quantum gravity thorough the available scattering experiments, as it is unattainable to probe such high energy scale at which the effects of quantum gravity appear. Here we propose an elegant alternative scheme to test such theories by detecting the deformations emerging from the noncommutative structures. Our protocol relies on the novelty of an opto-mechanical experimental setup where the information of the noncommutative oscillator is exchanged via the interaction with an optical pulse inside an optical cavity. We also demonstrate that our proposal is within the reach of current technology and, thus, it could uncover a feasible route towards the realization of quantum gravitational phenomena thorough a simple table-top experiment.

Sampling and measurement protocols for long-term silvicultural studies on the Penobscot Experimental Forest

Treesearch

Justin D. Waskiewicz; Laura S. Kenefic; Nicole S. Rogers; Joshua J. Puhlick; John C. Brissette; Richard J. Dionne

2015-01-01

The U.S. Forest Service, Northern Research Station has been conducting research on the silviculture of northern conifers on the Penobscot Experimental Forest (PEF) in Maine since 1950. Formal study plans provide guidance and specifications for the experimental treatments, but documentation is also needed to ensure consistency in data collection and sampling protocols....

Development of a fast and simple gas chromatographic protocol based on the combined use of alkyl chloroformate and solid phase microextraction for the assay of polyamines in human urine.

PubMed

Naccarato, Attilio; Elliani, Rosangela; Cavaliere, Brunella; Sindona, Giovanni; Tagarelli, Antonio

2018-05-11

Polyamines are aliphatic amines with low molecular weight that are widely recognized as one of the most important cancer biomarkers for early diagnosis and treatment. The goal of the work herein presented is the development of a rapid and simple method for the quantification of free polyamines (i.e., putrescine, cadaverine, spermidine, spermine) and N-monoacetylated polyamines (i.e., N 1 -Acetylspermidine, N 8 -Acetylspermidine, and N 1 -Acetylspermine) in human urine. A preliminary derivatization with propyl chloroformate combined with the use of solid phase microextraction (SPME) allowed for an easy and automatable protocol involving minimal sample handling and no consumption of organic solvents. The affinity of the analytes toward five commercial SPME coatings was evaluated in univariate mode, and the best result in terms of analyte extraction was achieved using the divinylbenzene/carboxen/polydimethylsiloxane fiber. The variables affecting the performance of SPME analysis were optimized by the multivariate approach of experimental design and, in particular, using a central composite design (CCD). The optimal working conditions in terms of response values are the following: extraction temperature 40 °C, extraction time of 15 min and no addition of NaCl. Analyses were carried out by gas chromatography-triple quadrupole mass spectrometry (GC-QqQ-MS) in selected reaction monitoring (SRM) acquisition mode. The developed method was validated according to the guidelines issued by the Food and Drug Administration (FDA). The satisfactory performances reached in terms of linearity, sensitivity (LOQs between 0.01 and 0.1 μg/mL), matrix effect (68-121%), accuracy, and precision (inter-day values between -24% and +16% and in the range 3.3-28.4%, respectively) make the proposed protocol suitable to be adopted for quantification of these important biomarkers in urine samples. Copyright © 2018 Elsevier B.V. All rights reserved.

A Proactive Approach to High Risk Delirium Patients Undergoing Total Joint Arthroplasty.

PubMed

Duque, Andres F; Post, Zachary D; Orozco, Fabio R; Lutz, Rex W; Ong, Alvin C

2018-04-01

Delirium is a common complication among elderly patients undergoing total joint arthroplasty (TJA). Its incidence has been reported from 4% to 53%. The Centers for Medicare and Medicaid Services consider delirium following TJA a "never-event." The purpose of this study is to evaluate a simple perioperative protocol used to identify delirium risk patients and prevent its incidence following TJA. Our group developed a protocol to identify and prevent delirium in patients undergoing TJA. All patients were screened and scored in the preoperative assessment, on criteria such as age, history of forgetfulness, history of agitation or visual hallucinations, history of falls, history of postoperative confusion, and inability to perform higher brain functions. Patients were scored on performance in a simple mental examination. The patients were classified as low, medium, or high risk. Patients who were identified as high risk were enrolled in a delirium avoidance protocol that minimized narcotics and emphasized nursing involvement and fluids administration. Five of 7659 (0.065%) consecutive TJA patients from 2010 to 2015 developed delirium. A total of 422 patients were identified as high risk. All 5 patients who suffered delirium were within the high risk group. No low or medium risk patients suffered a delirium complication. Three (0.039%) patients suffered drug-induced delirium, 1 (0.013%) had delirium related to alcohol withdrawal, and 1 (0.013%) had delirium after a systemic infection. This protocol is effective in identifying patients at high delirium risk and diminishing the incidence of this complication by utilizing a simple screening tool and perioperative protocol. Copyright © 2017 Elsevier Inc. All rights reserved.

Simple Perfusion Apparatus (SPA) for Manipulation, Tracking and Study of Oocytes and Embryos

PubMed Central

Angione, Stephanie L.; Oulhen, Nathalie; Brayboy, Lynae M.; Tripathi, Anubhav; Wessel, Gary M.

2016-01-01

Objective To develop and implement a device and protocol for oocyte analysis at a single cell level. The device must be capable of high resolution imaging, temperature control, perfusion of media, drugs, sperm, and immunolabeling reagents all at defined flow-rates. Each oocyte and resultant embryo must remain spatially separated and defined. Design Experimental laboratory study Setting University and Academic Center for reproductive medicine. Patients/Animals Women with eggs retrieved for ICSI cycles, adult female FVBN and B6C3F1 mouse strains, sea stars. Intervention Real-time, longitudinal imaging of oocytes following fluorescent labeling, insemination, and viability tests. Main outcome measure(s) Cell and embryo viability, immunolabeling efficiency, live cell endocytosis quantitation, precise metrics of fertilization and embryonic development. Results Single oocytes were longitudinally imaged following significant changes in media, markers, endocytosis quantitation, and development, all with supreme control by microfluidics. Cells remained viable, enclosed, and separate for precision measurements, repeatability, and imaging. Conclusions We engineered a simple device to load, visualize, experiment, and effectively record individual oocytes and embryos, without loss of cells. Prolonged incubation capabilities provide longitudinal studies without need for transfer and potential loss of cells. This simple perfusion apparatus (SPA) provides for careful, precise, and flexible handling of precious samples facilitating clinical in vitro fertilization approaches. PMID:25450296

Why standard brain-computer interface (BCI) training protocols should be changed: an experimental study.

PubMed

Jeunet, Camille; Jahanpour, Emilie; Lotte, Fabien

2016-06-01

While promising, electroencephaloraphy based brain-computer interfaces (BCIs) are barely used due to their lack of reliability: 15% to 30% of users are unable to control a BCI. Standard training protocols may be partly responsible as they do not satisfy recommendations from psychology. Our main objective was to determine in practice to what extent standard training protocols impact users' motor imagery based BCI (MI-BCI) control performance. We performed two experiments. The first consisted in evaluating the efficiency of a standard BCI training protocol for the acquisition of non-BCI related skills in a BCI-free context, which enabled us to rule out the possible impact of BCIs on the training outcome. Thus, participants (N = 54) were asked to perform simple motor tasks. The second experiment was aimed at measuring the correlations between motor tasks and MI-BCI performance. The ten best and ten worst performers of the first study were recruited for an MI-BCI experiment during which they had to learn to perform two MI tasks. We also assessed users' spatial ability and pre-training μ rhythm amplitude, as both have been related to MI-BCI performance in the literature. Around 17% of the participants were unable to learn to perform the motor tasks, which is close to the BCI illiteracy rate. This suggests that standard training protocols are suboptimal for skill teaching. No correlation was found between motor tasks and MI-BCI performance. However, spatial ability played an important role in MI-BCI performance. In addition, once the spatial ability covariable had been controlled for, using an ANCOVA, it appeared that participants who faced difficulty during the first experiment improved during the second while the others did not. These studies suggest that (1) standard MI-BCI training protocols are suboptimal for skill teaching, (2) spatial ability is confirmed as impacting on MI-BCI performance, and (3) when faced with difficult pre-training, subjects seemed to explore more strategies and therefore learn better.

EXPERIMENTAL PROTOCOL FOR DETERMINING PROTOLYSIS REACTION RATE CONSTANTS

EPA Science Inventory

An experimental protocol to determine photolysis rates of chemicals which photolyze relatively rapidly in the gas phase has been developed. This procedure provides a basis for evaluating the relative importance of one atmospheric reaction pathway (i.e., photolysis) for organic su...

Indoor radon regulation using tabulated values of temporal radon variation.

PubMed

Tsapalov, Andrey; Kovler, Konstantin

2018-03-01

Mass measurements of indoor radon concentrations have been conducted for about 30 years. In most of the countries, a national reference/action/limit level is adopted, limiting the annual average indoor radon (AAIR) concentration. However, until now, there is no single and generally accepted international protocol for determining the AAIR with a known confidence interval, based on measurements of different durations. Obviously, as the duration of measurements increases, the uncertainty of the AAIR estimation decreases. The lack of the information about the confidence interval of the determined AAIR level does not allow correct comparison with the radon reference level. This greatly complicates development of an effective indoor radon measurement protocol and strategy. The paper proposes a general principle of indoor radon regulation, based on the simple criteria widely used in metrology, and introduces a new parameter - coefficient of temporal radon variation K V (t) that depends on the measurement duration and determines the uncertainty of the AAIR. An algorithm for determining K V (t) based on the results of annual continuous radon monitoring in experimental rooms is proposed. Included are indoor radon activity concentrations and equilibrium equivalent concentration (EEC) of radon progeny. The monitoring was conducted in 10 selected experimental rooms located in 7 buildings, mainly in the Moscow region (Russia), from 2006 to 2013. The experimental and tabulated values of K V (t) and also the values of the coefficient of temporal EEC variation depending on the mode and duration of the measurements were obtained. The recommendations to improve the efficiency and reliability of indoor radon regulation are given. The importance of taking into account the geological factors is discussed. The representativity of the results of the study is estimated and the approach for their verification is proposed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Hard real-time closed-loop electrophysiology with the Real-Time eXperiment Interface (RTXI)

PubMed Central

George, Ansel; Dorval, Alan D.; Christini, David J.

2017-01-01

The ability to experimentally perturb biological systems has traditionally been limited to static pre-programmed or operator-controlled protocols. In contrast, real-time control allows dynamic probing of biological systems with perturbations that are computed on-the-fly during experimentation. Real-time control applications for biological research are available; however, these systems are costly and often restrict the flexibility and customization of experimental protocols. The Real-Time eXperiment Interface (RTXI) is an open source software platform for achieving hard real-time data acquisition and closed-loop control in biological experiments while retaining the flexibility needed for experimental settings. RTXI has enabled users to implement complex custom closed-loop protocols in single cell, cell network, animal, and human electrophysiology studies. RTXI is also used as a free and open source, customizable electrophysiology platform in open-loop studies requiring online data acquisition, processing, and visualization. RTXI is easy to install, can be used with an extensive range of external experimentation and data acquisition hardware, and includes standard modules for implementing common electrophysiology protocols. PMID:28557998

Entanglement-Assisted Weak Value Amplification

NASA Astrophysics Data System (ADS)

Pang, Shengshi; Dressel, Justin; Brun, Todd A.

2014-07-01

Large weak values have been used to amplify the sensitivity of a linear response signal for detecting changes in a small parameter, which has also enabled a simple method for precise parameter estimation. However, producing a large weak value requires a low postselection probability for an ancilla degree of freedom, which limits the utility of the technique. We propose an improvement to this method that uses entanglement to increase the efficiency. We show that by entangling and postselecting n ancillas, the postselection probability can be increased by a factor of n while keeping the weak value fixed (compared to n uncorrelated attempts with one ancilla), which is the optimal scaling with n that is expected from quantum metrology. Furthermore, we show the surprising result that the quantum Fisher information about the detected parameter can be almost entirely preserved in the postselected state, which allows the sensitive estimation to approximately saturate the relevant quantum Cramér-Rao bound. To illustrate this protocol we provide simple quantum circuits that can be implemented using current experimental realizations of three entangled qubits.

On the security of a simple three-party key exchange protocol without server's public keys.

PubMed

Nam, Junghyun; Choo, Kim-Kwang Raymond; Park, Minkyu; Paik, Juryon; Won, Dongho

2014-01-01

Authenticated key exchange protocols are of fundamental importance in securing communications and are now extensively deployed for use in various real-world network applications. In this work, we reveal major previously unpublished security vulnerabilities in the password-based authenticated three-party key exchange protocol according to Lee and Hwang (2010): (1) the Lee-Hwang protocol is susceptible to a man-in-the-middle attack and thus fails to achieve implicit key authentication; (2) the protocol cannot protect clients' passwords against an offline dictionary attack; and (3) the indistinguishability-based security of the protocol can be easily broken even in the presence of a passive adversary. We also propose an improved password-based authenticated three-party key exchange protocol that addresses the security vulnerabilities identified in the Lee-Hwang protocol.

On the Security of a Simple Three-Party Key Exchange Protocol without Server's Public Keys

PubMed Central

Nam, Junghyun; Choo, Kim-Kwang Raymond; Park, Minkyu; Paik, Juryon; Won, Dongho

2014-01-01

Authenticated key exchange protocols are of fundamental importance in securing communications and are now extensively deployed for use in various real-world network applications. In this work, we reveal major previously unpublished security vulnerabilities in the password-based authenticated three-party key exchange protocol according to Lee and Hwang (2010): (1) the Lee-Hwang protocol is susceptible to a man-in-the-middle attack and thus fails to achieve implicit key authentication; (2) the protocol cannot protect clients' passwords against an offline dictionary attack; and (3) the indistinguishability-based security of the protocol can be easily broken even in the presence of a passive adversary. We also propose an improved password-based authenticated three-party key exchange protocol that addresses the security vulnerabilities identified in the Lee-Hwang protocol. PMID:25258723

Improving cerebellar segmentation with statistical fusion

NASA Astrophysics Data System (ADS)

Plassard, Andrew J.; Yang, Zhen; Prince, Jerry L.; Claassen, Daniel O.; Landman, Bennett A.

2016-03-01

The cerebellum is a somatotopically organized central component of the central nervous system well known to be involved with motor coordination and increasingly recognized roles in cognition and planning. Recent work in multiatlas labeling has created methods that offer the potential for fully automated 3-D parcellation of the cerebellar lobules and vermis (which are organizationally equivalent to cortical gray matter areas). This work explores the trade offs of using different statistical fusion techniques and post hoc optimizations in two datasets with distinct imaging protocols. We offer a novel fusion technique by extending the ideas of the Selective and Iterative Method for Performance Level Estimation (SIMPLE) to a patch-based performance model. We demonstrate the effectiveness of our algorithm, Non- Local SIMPLE, for segmentation of a mixed population of healthy subjects and patients with severe cerebellar anatomy. Under the first imaging protocol, we show that Non-Local SIMPLE outperforms previous gold-standard segmentation techniques. In the second imaging protocol, we show that Non-Local SIMPLE outperforms previous gold standard techniques but is outperformed by a non-locally weighted vote with the deeper population of atlases available. This work advances the state of the art in open source cerebellar segmentation algorithms and offers the opportunity for routinely including cerebellar segmentation in magnetic resonance imaging studies that acquire whole brain T1-weighted volumes with approximately 1 mm isotropic resolution.

Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1

PubMed Central

Vangone, A.; Rodrigues, J. P. G. L. M.; Xue, L. C.; van Zundert, G. C. P.; Geng, C.; Kurkcuoglu, Z.; Nellen, M.; Narasimhan, S.; Karaca, E.; van Dijk, M.; Melquiond, A. S. J.; Visscher, K. M.; Trellet, M.; Kastritis, P. L.

2016-01-01

ABSTRACT Our information‐driven docking approach HADDOCK is a consistent top predictor and scorer since the start of its participation in the CAPRI community‐wide experiment. This sustained performance is due, in part, to its ability to integrate experimental data and/or bioinformatics information into the modelling process, and also to the overall robustness of the scoring function used to assess and rank the predictions. In the CASP‐CAPRI Round 1 scoring experiment we successfully selected acceptable/medium quality models for 18/14 of the 25 targets – a top‐ranking performance among all scorers. Considering that for only 20 targets acceptable models were generated by the community, our effective success rate reaches as high as 90% (18/20). This was achieved using the standard HADDOCK scoring function, which, thirteen years after its original publication, still consists of a simple linear combination of intermolecular van der Waals and Coulomb electrostatics energies and an empirically derived desolvation energy term. Despite its simplicity, this scoring function makes sense from a physico‐chemical perspective, encoding key aspects of biomolecular recognition. In addition to its success in the scoring experiment, the HADDOCK server takes the first place in the server prediction category, with 16 successful predictions. Much like our scoring protocol, because of the limited time per target, the predictions relied mainly on either an ab initio center‐of‐mass and symmetry restrained protocol, or on a template‐based approach whenever applicable. These results underline the success of our simple but sensible prediction and scoring scheme. Proteins 2017; 85:417–423. © 2016 Wiley Periodicals, Inc. PMID:27802573

Comment on 'Quantum direct communication with authentication'

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

Zhang, Zhan-jun; Key Laboratory of Optoelectronic Information Acquisition and Manipulation of Ministry of Education of China, School of Physics and Material Science, Anhui University, Hefei 230039; Liu, Jun

2007-02-15

Two protocols of quantum direct communication with authentication [Phys. Rev. A 73, 042305 (2006)] were recently proposed by Lee, Lim, and Yang. In this paper we will show that in the two protocols the authenticator Trent should be prevented from knowing the secret message. The first protocol can be eavesdropped on by Trent using the intercept-measure-resend attack, while the second protocol can be eavesdropped on by Trent using a simple single-qubit measurement. To fix these leaks, we revise the original versions of the protocols by using the Pauli Z operation {sigma}{sub z} instead of the original bit-flip operation X. Asmore » a consequence, the attacks we present can be prevented and accordingly the protocol securities are improved.« less

A Simple Approach To Assessing Copper Pitting Corrosion Tendenices and Developing Control Strategies

EPA Science Inventory

The objective of this research was to assess the effectiveness of a simple pipe loop system and protocol to predict localized corrosion, and to assess treatment alternatives for a drinking water that has been associated with customer complaints of pinhole leaks.

Shortcuts to Adiabaticity in Transport of a Single Trapped Ion

NASA Astrophysics Data System (ADS)

An, Shuoming; Lv, Dingshun; Campo, Adolfo Del; Kim, Kihwan

2015-05-01

We report an experimental study on shortcuts to adiabaticity in the transport of a single 171Yb+ ion trapped in a harmonic potential. In these driving schemes, the application of a force induces a nonadiabatic dynamics in which excitations are tailored so as to preserve the ion motional state in the ground state upon completion of the process. We experimentally apply the laser induced force and realize three different protocols: (1) a transitionless driving with a counterdiabatic term out of phase with the displacement force, (2) a classical protocol assisted by counterdiabatic fields in phase with the main force, (3) and an engineered transport protocol based on the Fourier transform of the trap acceleration. We experimentally compare and discuss the robustness of these protocols under given experimental limitations such as trap frequency drifts. This work was supported by the National Basic Research Program of China under Grants No. 2011CBA00300 (No. 2011CBA00301), the National Natural Science Foundation of China 11374178, and the University of Massachusetts Boston (No. P20150000029279).

Experimentally superposing two pure states with partial prior knowledge

NASA Astrophysics Data System (ADS)

Li, Keren; Long, Guofei; Katiyar, Hemant; Xin, Tao; Feng, Guanru; Lu, Dawei; Laflamme, Raymond

2017-02-01

Superposition, arguably the most fundamental property of quantum mechanics, lies at the heart of quantum information science. However, how to create the superposition of any two unknown pure states remains as a daunting challenge. Recently, it was proved that such a quantum protocol does not exist if the two input states are completely unknown, whereas a probabilistic protocol is still available with some prior knowledge about the input states [M. Oszmaniec et al., Phys. Rev. Lett. 116, 110403 (2016), 10.1103/PhysRevLett.116.110403]. The knowledge is that both of the two input states have nonzero overlaps with some given referential state. In this work, we experimentally realize the probabilistic protocol of superposing two pure states in a three-qubit nuclear magnetic resonance system. We demonstrate the feasibility of the protocol by preparing a families of input states, and the average fidelity between the prepared state and expected superposition state is over 99%. Moreover, we experimentally illustrate the limitation of the protocol that it is likely to fail or yields very low fidelity, if the nonzero overlaps are approaching zero. Our experimental implementation can be extended to more complex situations and other quantum systems.

Iterative tailoring of optical quantum states with homodyne measurements.

PubMed

Etesse, Jean; Kanseri, Bhaskar; Tualle-Brouri, Rosa

2014-12-01

As they can travel long distances, free space optical quantum states are good candidates for carrying information in quantum information technology protocols. These states, however, are often complex to produce and require protocols whose success probability drops quickly with an increase of the mean photon number. Here we propose a new protocol for the generation and growth of arbitrary states, based on one by one coherent adjunctions of the simple state superposition α|0〉 + β|1〉. Due to the nature of the protocol, which allows for the use of quantum memories, it can lead to high performances.

A double candidate survivable routing protocol for HAP network

NASA Astrophysics Data System (ADS)

He, Panfeng; Li, Chunyue; Ni, Shuyan

2016-11-01

To improve HAP network invulnerability, and at the same time considering the quasi-dynamic topology in HAP network, a simple and reliable routing protocol is proposed in the paper. The protocol firstly uses a double-candidate strategy for the next-node select to provide better robustness. Then during the maintenance stage, short hello packets instead of long routing packets are used only to check link connectivity in the quasi-dynamic HAP network. The route maintenance scheme based on short hello packets can greatly reduce link spending. Simulation results based on OPNET demonstrate the effectiveness of the proposed routing protocol.

40 CFR 792.120 - Protocol.

Code of Federal Regulations, 2010 CFR

2010-07-01

... the test system. (8) A description of the experimental design, including methods for the control of... 40 Protection of Environment 31 2010-07-01 2010-07-01 true Protocol. 792.120 Section 792.120... at which the study is being conducted. (4) The proposed experimental start and termination dates. (5...

Effectiveness of the implementation of a simple radiation reduction protocol in the catheterization laboratory.

PubMed

Jurado-Román, Alfonso; Sánchez-Pérez, Ignacio; Lozano Ruíz-Poveda, Fernando; López-Lluva, María T; Pinilla-Echeverri, Natalia; Moreno Arciniegas, Andrea; Agudo-Quilez, Pilar; Gil Agudo, Antonio

2016-01-01

A reduction in radiation doses at the catheterization laboratory, maintaining the quality of procedures is essential. Our objective was to analyze the results of a simple radiation reduction protocol at a high-volume interventional cardiology unit. We analyzed 1160 consecutive procedures: 580 performed before the implementation of the protocol and 580 after it. The protocol consisted in: the reduction of the number of ventriculographies and aortographies, the optimization of the collimation and the geometry of the X ray tube-patient-receptor, the use of low dose-rate fluoroscopy and the reduction of the number of cine sequences using the software "last fluoroscopy hold". There were no significant differences in clinical baseline features or in the procedural characteristics with the exception of a higher percentage of radial approach (30.7% vs 69.6%; p<0.001) and of percutaneous coronary interventions of chronic total occlusions after the implementation of the protocol (2.1% vs 6.7%; p=0,001). Angiographic success was similar during both periods (98.3% vs 99.2%; p=0.2). There were no significant differences between both periods regarding the overall duration of the procedures (26.9 vs 29.6min; p=0.14), or the fluoroscopy time (13.3 vs 13.2min; p=0.8). We observed a reduction in the percentage of procedures with ventriculography (80.9% vs 7.1%; p<0.0001) or aortography (15.4% vs 4.4%; p<0.0001), the cine runs (21.8 vs 6.9; p<0.0001) and the dose-area product (165 vs 71 Gyxcm(2); p<0.0001). With the implementation of a simple radiation reduction protocol, a 57% reduction of dose-area product was observed without a reduction in the quality or the complexity of procedures. Copyright © 2016 Elsevier Inc. All rights reserved.

Multiple functionalities of Ni nanoparticles embedded in carboxymethyl guar gum polymer: catalytic activity and superparamagnetism

NASA Astrophysics Data System (ADS)

Sardar, Debasmita; Sengupta, Manideepa; Bordoloi, Ankur; Ahmed, Md. A.; Neogi, S. K.; Bandyopadhyay, Sudipta; Jain, Ruchi; Gopinath, Chinnakonda S.; Bala, Tanushree

2017-05-01

Composites comprising of metallic nanoparticles in polymer matrices have allured significant importance due to multifunctionalities. Here a simple protocol has been described to embed Ni nanoparticles in carboxymethyl guar gum (CMGG) polymer. The composite formation helps in the stabilization of Ni nanoparticles which are otherwise prone towards aerial oxidation. Further the nanoparticles retain their superparamagnetic nature and catalytic capacity. Ni-Polymer composite catalyses the reduction of 4-Nitrophenol to 4-Aminophenol very efficiently in presence of NaBH4, attaining a complete conversion under some experimental conditions. Ni-Polymer composite is well characterized using UV-vis spectroscopy, FTIR, XPS, powder XRD, TGA, SEM and TEM. A detailed magnetic measurement using superconducting quantum interference device-vibrating sample magnetometer (SQUID-VSM) reveals superparamagnetic behaviour of the composite.

A practical approach for linearity assessment of calibration curves under the International Union of Pure and Applied Chemistry (IUPAC) guidelines for an in-house validation of method of analysis.

PubMed

Sanagi, M Marsin; Nasir, Zalilah; Ling, Susie Lu; Hermawan, Dadan; Ibrahim, Wan Aini Wan; Naim, Ahmedy Abu

2010-01-01

Linearity assessment as required in method validation has always been subject to different interpretations and definitions by various guidelines and protocols. However, there are very limited applicable implementation procedures that can be followed by a laboratory chemist in assessing linearity. Thus, this work proposes a simple method for linearity assessment in method validation by a regression analysis that covers experimental design, estimation of the parameters, outlier treatment, and evaluation of the assumptions according to the International Union of Pure and Applied Chemistry guidelines. The suitability of this procedure was demonstrated by its application to an in-house validation for the determination of plasticizers in plastic food packaging by GC.

Developing science gateways for drug discovery in a grid environment.

PubMed

Pérez-Sánchez, Horacio; Rezaei, Vahid; Mezhuyev, Vitaliy; Man, Duhu; Peña-García, Jorge; den-Haan, Helena; Gesing, Sandra

2016-01-01

Methods for in silico screening of large databases of molecules increasingly complement and replace experimental techniques to discover novel compounds to combat diseases. As these techniques become more complex and computationally costly we are faced with an increasing problem to provide the research community of life sciences with a convenient tool for high-throughput virtual screening on distributed computing resources. To this end, we recently integrated the biophysics-based drug-screening program FlexScreen into a service, applicable for large-scale parallel screening and reusable in the context of scientific workflows. Our implementation is based on Pipeline Pilot and Simple Object Access Protocol and provides an easy-to-use graphical user interface to construct complex workflows, which can be executed on distributed computing resources, thus accelerating the throughput by several orders of magnitude.

Lipid Extraction and Cholesterol Quantification: A Simple Protocol

ERIC Educational Resources Information Center

Barreto, M. Carmo

2005-01-01

Enzymatic methods are used to measure cholesterol levels but a simple and inexpensive method is described, which is particularly important when one has repeated lab sessions during the week. It can be carried out on the organic phase containing the lipids, without evaporating the solvent, yielding quick results.

A Practical Workshop for Generating Simple DNA Fingerprints of Plants

ERIC Educational Resources Information Center

Rouziere, A.-S.; Redman, J. E.

2011-01-01

Gel electrophoresis DNA fingerprints offer a graphical and visually appealing illumination of the similarities and differences between DNA sequences of different species and individuals. A polymerase chain reaction (PCR) and restriction digest protocol was designed to give high-school students the opportunity to generate simple fingerprints of…

Practical State Machine Replication with Confidentiality

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

Duan, Sisi; Zhang, Haibin

2016-01-01

We study how to enable arbitrary randomized algorithms in Byzantine fault-tolerant (BFT) settings. We formalize a randomized BFT protocol and provide a simple and efficient construction that can be built on any existing BFT protocols while adding practically no overhead. We go one step further to revisit a confidential BFT protocol (Yin et al., SOSP '03). We show that their scheme is potentially susceptible to safety and confidentiality attacks. We then present a new protocol that is secure in the stronger model we formalize, by extending the idea of a randomized BFT protocol. Our protocol uses only efficient symmetric cryptography,more » while Yin et al.'s uses costly threshold signatures. We implemented and evaluated our protocols on microbenchmarks and real-world use cases. We show that our randomized BFT protocol is as efficient as conventional BFT protocols, and our confidential BFT protocol is two to three orders of magnitude faster than Yin et al.'s, which is less secure than ours.« less

In silico simulations of experimental protocols for cardiac modeling.

PubMed

Carro, Jesus; Rodriguez, Jose Felix; Pueyo, Esther

2014-01-01

A mathematical model of the AP involves the sum of different transmembrane ionic currents and the balance of intracellular ionic concentrations. To each ionic current corresponds an equation involving several effects. There are a number of model parameters that must be identified using specific experimental protocols in which the effects are considered as independent. However, when the model complexity grows, the interaction between effects becomes increasingly important. Therefore, model parameters identified considering the different effects as independent might be misleading. In this work, a novel methodology consisting in performing in silico simulations of the experimental protocol and then comparing experimental and simulated outcomes is proposed for parameter model identification and validation. The potential of the methodology is demonstrated by validating voltage-dependent L-type calcium current (ICaL) inactivation in recently proposed human ventricular AP models with different formulations. Our results show large differences between ICaL inactivation as calculated from the model equation and ICaL inactivation from the in silico simulations due to the interaction between effects and/or to the experimental protocol. Our results suggest that, when proposing any new model formulation, consistency between such formulation and the corresponding experimental data that is aimed at being reproduced needs to be first verified considering all involved factors.

Experimental Quantum Coin Tossing

NASA Astrophysics Data System (ADS)

Molina-Terriza, G.; Vaziri, A.; Ursin, R.; Zeilinger, A.

2005-01-01

In this Letter we present the first implementation of a quantum coin-tossing protocol. This protocol belongs to a class of “two-party” cryptographic problems, where the communication partners distrust each other. As with a number of such two-party protocols, the best implementation of the quantum coin tossing requires qutrits, resulting in a higher security than using qubits. In this way, we have also performed the first complete quantum communication protocol with qutrits. In our experiment the two partners succeeded to remotely toss a row of coins using photons entangled in the orbital angular momentum. We also show the experimental bounds of a possible cheater and the ways of detecting him.

Quantum fingerprinting with coherent states and a constant mean number of photons

NASA Astrophysics Data System (ADS)

Arrazola, Juan Miguel; Lütkenhaus, Norbert

2014-06-01

We present a protocol for quantum fingerprinting that is ready to be implemented with current technology and is robust to experimental errors. The basis of our scheme is an implementation of the signal states in terms of a coherent state in a superposition of time-bin modes. Experimentally, this requires only the ability to prepare coherent states of low amplitude and to interfere them in a balanced beam splitter. The states used in the protocol are arbitrarily close in trace distance to states of O (log2n) qubits, thus exhibiting an exponential separation in abstract communication complexity compared to the classical case. The protocol uses a number of optical modes that is proportional to the size n of the input bit strings but a total mean photon number that is constant and independent of n. Given the expended resources, our protocol achieves a task that is provably impossible using classical communication only. In fact, even in the presence of realistic experimental errors and loss, we show that there exist a large range of input sizes for which our quantum protocol transmits an amount of information that can be more than two orders of magnitude smaller than a classical fingerprinting protocol.

Tribology of flexible and sliding spinal implants: Development of experimental and numerical models.

PubMed

Le Cann, Sophie; Chaves-Jacob, Julien; Rossi, Jean-Marie; Linares, Jean-Marc; Chabrand, Patrick

2018-01-01

New fusionless devices are being developed to get over the limits of actual spinal surgical treatment, based on arthrodesis. However, due to their recentness, no standards exist to test and validate those devices, especially concerning the wear. A new tribological first approach to the definition of an in vitro wear protocol to study wear of flexible and sliding spinal devices is presented in this article, and was applied to a new concept. A simplified synthetic spine portion (polyethylene) was developed to reproduce a simple supra-physiological spinal flexion (10° between two vertebrae). The device studied with this protocol was tested in wet environment until 1 million cycles (Mc). We obtained an encouraging estimated wear volume of same order of magnitude compared to similar devices. An associated finite element (FE) numerical model has permitted to access contact information and study the effect of misalignment of one screw. First results could point out how to improve the design and suggest that a vertical misalignment of a screw (under or over-screwing) has more impact than a horizontal one. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 104-111, 2018. © 2016 Wiley Periodicals, Inc.

Integrative Bioengineering Institute

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

Eddington, David; Magin,L,Richard; Hetling, John

2009-01-09

Microfabrication enables many exciting experimental possibilities for medicine and biology that are not attainable through traditional methods. However, in order for microfabricated devices to have an impact they must not only provide a robust solution to a current unmet need, but also be simple enough to seamlessly integrate into standard protocols. Broad dissemination of bioMEMS has been stymied by the common aim of replacing established and well accepted protocols with equally or more complex devices, methods, or materials. The marriage of a complex, difficult to fabricate bioMEMS device with a highly variable biological system is rarely successful. Instead, the designmore » philosophy of my lab aims to leverage a beneficial microscale phenomena (e.g. fast diffusion at the microscale) within a bioMEMS device and adapt to established methods (e.g. multiwell plate cell culture) and demonstrate a new paradigm for the field (adapt instead of replace). In order for the field of bioMEMS to mature beyond novel proof-of-concept demonstrations, researchers must focus on developing systems leveraging these phenomena and integrating into standard labs, which have largely been ignored. Towards this aim, the Integrative Bioengineering Institute has been established.« less

Measurement profiles of nano-scale ion beam for optimized radiation energy losses

NASA Astrophysics Data System (ADS)

Woo, T. H.; Cho, H. S.

2011-10-01

The behavior of charged particles is investigated for nano-scale ion beam therapy using a medical accelerator. Computational work is performed for the Bragg-peak simulation, which is focused on human organ material of pancreas and thyroid. The Results show that the trends of the dose have several different kinds of distributions. Before constructing a heavy ion collider, this study can give us the reliability of the therapeutic effect. Realistic treatment using human organs is calculated in a simple and cost effective manner using the computational code, the Stopping and Range of Ions in Matter 2008 (SRIM 2008). Considering the safety of the therapy, it is suggested to give a patient orient planning of the cancer therapy. The energy losses in ionization and phonon are analyzed, which are the behaviors in the molecular level nano-scopic investigation. The different fluctuations are shown at 150 MeV, where the lowest temperature is found in proton and pancreas case. Finally, the protocol for the radiation therapy is constructed by the simulation in which the procedure for a better therapy is selected. An experimental measurement incorporated with the simulations could be programmed by this protocol.

Predicting the behavior of microfluidic circuits made from discrete elements

PubMed Central

Bhargava, Krisna C.; Thompson, Bryant; Iqbal, Danish; Malmstadt, Noah

2015-01-01

Microfluidic devices can be used to execute a variety of continuous flow analytical and synthetic chemistry protocols with a great degree of precision. The growing availability of additive manufacturing has enabled the design of microfluidic devices with new functionality and complexity. However, these devices are prone to larger manufacturing variation than is typical of those made with micromachining or soft lithography. In this report, we demonstrate a design-for-manufacturing workflow that addresses performance variation at the microfluidic element and circuit level, in context of mass-manufacturing and additive manufacturing. Our approach relies on discrete microfluidic elements that are characterized by their terminal hydraulic resistance and associated tolerance. Network analysis is employed to construct simple analytical design rules for model microfluidic circuits. Monte Carlo analysis is employed at both the individual element and circuit level to establish expected performance metrics for several specific circuit configurations. A protocol based on osmometry is used to experimentally probe mixing behavior in circuits in order to validate these approaches. The overall workflow is applied to two application circuits with immediate use at on the bench-top: series and parallel mixing circuits that are modularly programmable, virtually predictable, highly precise, and operable by hand. PMID:26516059

Spectrophotometric calibration procedures to enable calibration-free measurements of seawater calcium carbonate saturation states.

PubMed

Cuyler, Erin E; Byrne, Robert H

2018-08-22

A simple protocol was developed to measure seawater calcium carbonate saturation states (Ω spec ) spectrophotometrically. Saturation states are typically derived from the separate measurement of two other carbon system parameters, with each requiring unique instrumentation and often complex measurement protocols. Using the new protocol, the only required equipment is a thermostatted laboratory spectrophotometer. For each seawater sample, spectrophotometric measurements of pH (visible absorbance) are made in paired optical cells, one with and one without added nitric acid. Ultraviolet absorbance is measured to determine the amount of added acid based on the direct proportionality between nitrate concentration and UV absorbance. Coupled measurements of pH and the alkalinity change that accompanies the nitric acid addition allow calculation of a seawater sample's original carbonate ion concentration and saturation state. These paired absorbance measurements yield Ω spec (and other carbonate system parameters), with each sample requiring about 12 min processing time. Initially, an instrument-specific nitrate molar absorptivity coefficient must be determined (due to small but significant discrepancies in instrumental wavelength calibrations), but thereafter no further calibration is needed. In this work, the 1σ precision of replicate measurements of aragonite saturation state was found to be 0.020, and the average difference between Ω spec and Ω calculated conventionally from measured total alkalinity and pH (Ω calc ) was -0.11% ± 0.96% (a level of accuracy comparable to that obtained from spectrophotometric measurements of carbonate ion concentration). Over the entire range of experimental conditions, 0.97 < Ω < 3.17 (n = 125), all measurements attained the Global Ocean Acidification Observing Network's "weather level" goal for accuracy and 90% attained the more stringent "climate level" goal. When Ω spec was calculated from averages of duplicate samples (n = 56), the precision improved to 0.014 and the average difference between Ω spec and Ω calc improved to -0.11% ± 0.73%. Additionally, 97% of the duplicate-based Ω spec measurements attained the "climate level" accuracy goal. These results indicate that the simple measurement protocol developed in this work should be widely applicable for monitoring fundamental seawater changes associated with ocean acidification. Copyright © 2018 Elsevier B.V. All rights reserved.

Design and Evaluation of Complex Moving HIFU Treatment Protocols

NASA Astrophysics Data System (ADS)

Kargl, Steven G.; Andrew, Marilee A.; Kaczkowski, Peter J.; Brayman, Andrew A.; Crum, Lawrence A.

2005-03-01

The use of moving high-intensity focused ultrasound (HIFU) treatment protocols is of interest in achieving efficient formation of large-volume thermal lesions in tissue. Judicious protocol design is critical in order to avoid collateral damage to healthy tissues outside the treatment zone. A KZK-BHTE model, extended to simulate multiple, moving scans in tissue, is used to investigate protocol design considerations. Prediction and experimental observations are presented which 1) validate the model, 2) illustrate how to assess the effects of acoustic nonlinearity, and 3) demonstrate how to assess and control collateral damage such as prefocal lesion formation and lesion formation resulting from thermal conduction without direct HIFU exposure. Experimental data consist of linear and circular scan protocols delivered over a range of exposure regimes in ex vivo bovine liver.

Crowd Sourcing Data Collection through Amazon Mechanical Turk

DTIC Science & Technology

2013-09-01

The first recognition study consisted of a Panel Study using a simple detection protocol, in which participants were presented with vignettes and, for...variability than the crowdsourcing data set, hewing more closely to the year 1 verbs of interest and simple description grammar . The DT:PS data were...Study RT: PS Recognition Task: Panel Study RT: RT Recognition Task: Round Table S3 Amazon Simple Storage Service SVPA Single Verb Present /Absent

Using Mouse Mammary Tumor Cells to Teach Core Biology Concepts: A Simple Lab Module.

PubMed

McIlrath, Victoria; Trye, Alice; Aguanno, Ann

2015-06-18

Undergraduate biology students are required to learn, understand and apply a variety of cellular and molecular biology concepts and techniques in preparation for biomedical, graduate and professional programs or careers in science. To address this, a simple laboratory module was devised to teach the concepts of cell division, cellular communication and cancer through the application of animal cell culture techniques. Here the mouse mammary tumor (MMT) cell line is used to model for breast cancer. Students learn to grow and characterize these animal cells in culture and test the effects of traditional and non-traditional chemotherapy agents on cell proliferation. Specifically, students determine the optimal cell concentration for plating and growing cells, learn how to prepare and dilute drug solutions, identify the best dosage and treatment time course of the antiproliferative agents, and ascertain the rate of cell death in response to various treatments. The module employs both a standard cell counting technique using a hemocytometer and a novel cell counting method using microscopy software. The experimental procedure lends to open-ended inquiry as students can modify critical steps of the protocol, including testing homeopathic agents and over-the-counter drugs. In short, this lab module requires students to use the scientific process to apply their knowledge of the cell cycle, cellular signaling pathways, cancer and modes of treatment, all while developing an array of laboratory skills including cell culture and analysis of experimental data not routinely taught in the undergraduate classroom.

Establishing the first institutional animal care and use committee in Egypt.

PubMed

Fahmy, Sohair R; Gaafar, Khadiga

2016-04-09

Although animal research ethics committees (AREC) are well established in Western countries, this field is weakly developed and its concept is poorly understood in the Middle East and North Africa region. Our main objective was to introduce the concept and requirements of ethical approaches in dealing with experimental animal in research and teaching in Egypt. Due to its very recent inception, Cairo University, Faculty of Science IACUC decided to operate in accordance with Guide for the Care and Use of Laboratory Animals 8th Edition 2011 (the Guide) since Egypt has not yet compiled its own guide. Fifty protocols were reviewed in 2013-2014. Only ten protocols were reviewed in 2013, but in 2014, forty protocols were reviewed. In 2013 all protocols were approved and in 2014, number of approvals were 35, the number of deferrals were 4, and one refused protocol. Master's theses (MSc) research protocols constituted the majority of the total reviewed protocols. This is attributed to the decision of the Board of the Faculty of Science, Cairo University in September, 2013 that the approval of the IACUC is mandatory before conducting any research involving animals or theses registration. The first IACUC was established in the Cairo University, Faculty of Science, since 2012. The challenges encountered by the committee were diverse, such as the absence of laws that control the use of animal models in scientific research, lack of guidelines (protocols for experimental animals in research) and, mandatory ethical approval for any experimental animal research.

Real-time Electrophysiology: Using Closed-loop Protocols to Probe Neuronal Dynamics and Beyond

PubMed Central

Linaro, Daniele; Couto, João; Giugliano, Michele

2015-01-01

Experimental neuroscience is witnessing an increased interest in the development and application of novel and often complex, closed-loop protocols, where the stimulus applied depends in real-time on the response of the system. Recent applications range from the implementation of virtual reality systems for studying motor responses both in mice1 and in zebrafish2, to control of seizures following cortical stroke using optogenetics3. A key advantage of closed-loop techniques resides in the capability of probing higher dimensional properties that are not directly accessible or that depend on multiple variables, such as neuronal excitability4 and reliability, while at the same time maximizing the experimental throughput. In this contribution and in the context of cellular electrophysiology, we describe how to apply a variety of closed-loop protocols to the study of the response properties of pyramidal cortical neurons, recorded intracellularly with the patch clamp technique in acute brain slices from the somatosensory cortex of juvenile rats. As no commercially available or open source software provides all the features required for efficiently performing the experiments described here, a new software toolbox called LCG5 was developed, whose modular structure maximizes reuse of computer code and facilitates the implementation of novel experimental paradigms. Stimulation waveforms are specified using a compact meta-description and full experimental protocols are described in text-based configuration files. Additionally, LCG has a command-line interface that is suited for repetition of trials and automation of experimental protocols. PMID:26132434

Design of freeze-drying processes for pharmaceuticals: practical advice.

PubMed

Tang, Xiaolin; Pikal, Michael J

2004-02-01

Design of freeze-drying processes is often approached with a "trial and error" experimental plan or, worse yet, the protocol used in the first laboratory run is adopted without further attempts at optimization. Consequently, commercial freeze-drying processes are often neither robust nor efficient. It is our thesis that design of an "optimized" freeze-drying process is not particularly difficult for most products, as long as some simple rules based on well-accepted scientific principles are followed. It is the purpose of this review to discuss the scientific foundations of the freeze-drying process design and then to consolidate these principles into a set of guidelines for rational process design and optimization. General advice is given concerning common stability issues with proteins, but unusual and difficult stability issues are beyond the scope of this review. Control of ice nucleation and crystallization during the freezing step is discussed, and the impact of freezing on the rest of the process and final product quality is reviewed. Representative freezing protocols are presented. The significance of the collapse temperature and the thermal transition, denoted Tg', are discussed, and procedures for the selection of the "target product temperature" for primary drying are presented. Furthermore, guidelines are given for selection of the optimal shelf temperature and chamber pressure settings required to achieve the target product temperature without thermal and/or mass transfer overload of the freeze dryer. Finally, guidelines and "rules" for optimization of secondary drying and representative secondary drying protocols are presented.

Deterministic generation of remote entanglement with active quantum feedback

DOE PAGES

Martin, Leigh; Motzoi, Felix; Li, Hanhan; ...

2015-12-10

We develop and study protocols for deterministic remote entanglement generation using quantum feedback, without relying on an entangling Hamiltonian. In order to formulate the most effective experimentally feasible protocol, we introduce the notion of average-sense locally optimal feedback protocols, which do not require real-time quantum state estimation, a difficult component of real-time quantum feedback control. We use this notion of optimality to construct two protocols that can deterministically create maximal entanglement: a semiclassical feedback protocol for low-efficiency measurements and a quantum feedback protocol for high-efficiency measurements. The latter reduces to direct feedback in the continuous-time limit, whose dynamics can bemore » modeled by a Wiseman-Milburn feedback master equation, which yields an analytic solution in the limit of unit measurement efficiency. Our formalism can smoothly interpolate between continuous-time and discrete-time descriptions of feedback dynamics and we exploit this feature to derive a superior hybrid protocol for arbitrary nonunit measurement efficiency that switches between quantum and semiclassical protocols. Lastly, we show using simulations incorporating experimental imperfections that deterministic entanglement of remote superconducting qubits may be achieved with current technology using the continuous-time feedback protocol alone.« less

106-17 Telemetry Management Resources Chapter 25

DTIC Science & Technology

2017-07-01

aspects of the TmNS system . There are two primary protocols for accessing the management resources: Simple Network Management Protocol (SNMP) and... management resources as well as a basic HTTP clients and servers for a more RESTful approach to system management . Both tools are available from the...Telemetry Standards, RCC Standard 106-17 Chapter 25, July 2017 i CHAPTER 25 Management Resources Acronyms

A Laboratory Exercise to Illustrate Protein-Membrane Interactions

ERIC Educational Resources Information Center

Weers, Paul M. M.; Prenner, Elmar J.; Curic, Spomenka; Lohmeier-Vogel, Elke M.

2016-01-01

The laboratory protocol presented here takes about 3 hours to perform and investigates protein and lipid interactions. Students first purify His6-tagged human apolipoprotein A-I (apoA-I) with Ni-NTA affinity resin in a simple batch protocol and prepare multilamellar vesicles (MLV) from pre-dried phospholipid films. When apoA-I is added to the MLV,…

A Protocol for NMR Analysis of the Enantiomeric Excess of Chiral Diols Using an Achiral Diboronic Acid Template.

PubMed

Tickell, David A; Lampard, Emma V; Lowe, John P; James, Tony D; Bull, Steven D

2016-08-05

A practically simple derivatization protocol for determining the enantiopurity of chiral diols by (1)H NMR spectroscopic analysis is described. Diols were treated with 0.5 equiv of 1,3-phenyldiboronic acid to afford mixtures of diastereomeric boronate esters whose homochiral/heterochiral ratios are an accurate reflection of the diol's enantiopurity.

High-resolution Episcopic Microscopy (HREM) - Simple and Robust Protocols for Processing and Visualizing Organic Materials

PubMed Central

Geyer, Stefan H.; Maurer-Gesek, Barbara; Reissig, Lukas F.; Weninger, Wolfgang J.

2017-01-01

We provide simple protocols for generating digital volume data with the high-resolution episcopic microscopy (HREM) method. HREM is capable of imaging organic materials with volumes up to 5 x 5 x 7 mm3 in typical numeric resolutions between 1 x 1 x 1 and 5 x 5 x 5 µm3. Specimens are embedded in methacrylate resin and sectioned on a microtome. After each section an image of the block surface is captured with a digital video camera that sits on the phototube connected to the compound microscope head. The optical axis passes through a green fluorescent protein (GFP) filter cube and is aligned with a position, at which the bock holder arm comes to rest after each section. In this way, a series of inherently aligned digital images, displaying subsequent block surfaces are produced. Loading such an image series in three-dimensional (3D) visualization software facilitates the immediate conversion to digital volume data, which permit virtual sectioning in various orthogonal and oblique planes and the creation of volume and surface rendered computer models. We present three simple, tissue specific protocols for processing various groups of organic specimens, including mouse, chick, quail, frog and zebra fish embryos, human biopsy material, uncoated paper and skin replacement material. PMID:28715372

High-resolution Episcopic Microscopy (HREM) - Simple and Robust Protocols for Processing and Visualizing Organic Materials.

PubMed

Geyer, Stefan H; Maurer-Gesek, Barbara; Reissig, Lukas F; Weninger, Wolfgang J

2017-07-07

We provide simple protocols for generating digital volume data with the high-resolution episcopic microscopy (HREM) method. HREM is capable of imaging organic materials with volumes up to 5 x 5 x 7 mm 3 in typical numeric resolutions between 1 x 1 x 1 and 5 x 5 x 5 µm 3 . Specimens are embedded in methacrylate resin and sectioned on a microtome. After each section an image of the block surface is captured with a digital video camera that sits on the phototube connected to the compound microscope head. The optical axis passes through a green fluorescent protein (GFP) filter cube and is aligned with a position, at which the bock holder arm comes to rest after each section. In this way, a series of inherently aligned digital images, displaying subsequent block surfaces are produced. Loading such an image series in three-dimensional (3D) visualization software facilitates the immediate conversion to digital volume data, which permit virtual sectioning in various orthogonal and oblique planes and the creation of volume and surface rendered computer models. We present three simple, tissue specific protocols for processing various groups of organic specimens, including mouse, chick, quail, frog and zebra fish embryos, human biopsy material, uncoated paper and skin replacement material.

A randomized controlled clinical trial evaluating quality of life when using a simple acupressure protocol in women with primary dysmenorrhea.

PubMed

Bazarganipour, Fatemeh; Taghavi, Seyed-Abdolvahab; Allan, Helen; Hosseini, Nazafarin; Khosravi, Ahmad; Asadi, Rahimeh; Salari, Shohreh; Dehghani, Raziyeh; Jamshidi, Zahra; Rezaei, Marziyeh; Saberian, Mansoreh; Javedan, Fatemeh; Salari, Zahra; Miri, Fahimeh

2017-10-01

To evaluate a simple acupressure protocol in LIV3 and LI4 acupoints in women with primary dysmenorrhea. This paper reports a randomized, single blinded clinical trial. 90 young women with dysmenorrhea were recruited to three groups to receive 20min acupressure every day in either LIV3 or LI4, or placebo points. Acupressure was timed five days before menstruation for three successive menstrual cycles. On menstruation, each participant completed the Wong Baker faces pain scale, and the quality of life short form -12 (QOL SF-12). Intensity and duration of pain between the three groups in the second and third cycles during the intervention (p<0.05) differed significantly. Significant differences were seen in all domains of QOL except for mental health (p=0.4), general health (p=0.7) and mental subscale component (p=0.12) in the second cycle, and mental health (p=0.9), and mental subscale component (p=0.14) in the third cycle. Performing the simple acupressure protocol is an effective method to decrease the intensity and duration of dysmenorrhea, and improve the QOL. Registration ID in IRCT: IRCT2016052428038N1. Copyright © 2017. Published by Elsevier Ltd.

A simple protocol for Matrix Assisted Laser Desorption Ionization- time of flight-mass spectrometry (MALDI-TOF-MS) analysis of lipids and proteins in single microsamples of paintings.

PubMed

van der Werf, Inez D; Calvano, Cosima D; Palmisano, Francesco; Sabbatini, Luigia

2012-03-09

A simple protocol, based on Bligh-Dyer (BD) extraction followed by MALDI-TOF-MS analysis, for fast identification of paint binders in single microsamples is proposed. For the first time it is demonstrated that the BD method is effective for the simultaneous extraction of lipids and proteins from complex, and atypical matrices, such as pigmented paint layers. The protocol makes use of an alternative denaturing anionic detergent (RapiGest™) in order to improve efficiency of protein digestion and purification step. Detection of various lipid classes, such as triacylglycerols (TAGs) and phospholipids (PLs), and their oxidation by-products was accomplished, whereas proteins could be identified by peptide mass fingerprinting. The effect of pigments on ageing of lipids and proteins was also investigated. Finally, the proposed protocol was successfully applied to the study of a late-15th century Italian panel painting allowing the identification of various proteinaceous and lipid sections in organic binders, such as egg yolk, egg white, animal glue, casein, and drying oil. Copyright © 2011 Elsevier B.V. All rights reserved.

A Mismatch-Based Model for Memory Reconsolidation and Extinction in Attractor Networks

PubMed Central

Amaral, Olavo B.

2011-01-01

The processes of memory reconsolidation and extinction have received increasing attention in recent experimental research, as their potential clinical applications begin to be uncovered. A number of studies suggest that amnestic drugs injected after reexposure to a learning context can disrupt either of the two processes, depending on the behavioral protocol employed. Hypothesizing that reconsolidation represents updating of a memory trace in the hippocampus, while extinction represents formation of a new trace, we have built a neural network model in which either simple retrieval, reconsolidation or extinction of a stored attractor can occur upon contextual reexposure, depending on the similarity between the representations of the original learning and reexposure sessions. This is achieved by assuming that independent mechanisms mediate Hebbian-like synaptic strengthening and mismatch-driven labilization of synaptic changes, with protein synthesis inhibition preferentially affecting the former. Our framework provides a unified mechanistic explanation for experimental data showing (a) the effect of reexposure duration on the occurrence of reconsolidation or extinction and (b) the requirement of memory updating during reexposure to drive reconsolidation. PMID:21826231

Fusion of footsteps and face biometrics on an unsupervised and uncontrolled environment

NASA Astrophysics Data System (ADS)

Vera-Rodriguez, Ruben; Tome, Pedro; Fierrez, Julian; Ortega-Garcia, Javier

2012-06-01

This paper reports for the first time experiments on the fusion of footsteps and face on an unsupervised and not controlled environment for person authentication. Footstep recognition is a relatively new biometric based on signals extracted from people walking over floor sensors. The idea of the fusion between footsteps and face starts from the premise that in an area where footstep sensors are installed it is very simple to place a camera to capture also the face of the person that walks over the sensors. This setup may find application in scenarios like ambient assisted living, smart homes, eldercare, or security access. The paper reports a comparative assessment of both biometrics using the same database and experimental protocols. In the experimental work we consider two different applications: smart homes (small group of users with a large set of training data) and security access (larger group of users with a small set of training data) obtaining results of 0.9% and 5.8% EER respectively for the fusion of both modalities. This is a significant performance improvement compared with the results obtained by the individual systems.

Compensatory Limb Use and Behavioral Assessment of Motor Skill Learning Following Sensorimotor Cortex Injury in a Mouse Model of Ischemic Stroke

PubMed Central

Kerr, Abigail L.; Tennant, Kelly A.

2014-01-01

Mouse models have become increasingly popular in the field of behavioral neuroscience, and specifically in studies of experimental stroke. As models advance, it is important to develop sensitive behavioral measures specific to the mouse. The present protocol describes a skilled motor task for use in mouse models of stroke. The Pasta Matrix Reaching Task functions as a versatile and sensitive behavioral assay that permits experimenters to collect accurate outcome data and manipulate limb use to mimic human clinical phenomena including compensatory strategies (i.e., learned non-use) and focused rehabilitative training. When combined with neuroanatomical tools, this task also permits researchers to explore the mechanisms that support behavioral recovery of function (or lack thereof) following stroke. The task is both simple and affordable to set up and conduct, offering a variety of training and testing options for numerous research questions concerning functional outcome following injury. Though the task has been applied to mouse models of stroke, it may also be beneficial in studies of functional outcome in other upper extremity injury models. PMID:25045916

Toward the design of alkynylimidazole fluorophores: computational and experimental characterization of spectroscopic features in solution and in poly(methyl methacrylate).

PubMed

Barone, Vincenzo; Bellina, Fabio; Biczysko, Malgorzata; Bloino, Julien; Fornaro, Teresa; Latouche, Camille; Lessi, Marco; Marianetti, Giulia; Minei, Pierpaolo; Panattoni, Alessandro; Pucci, Andrea

2015-10-28

The possibilities offered by organic fluorophores in the preparation of advanced plastic materials have been increased by designing novel alkynylimidazole dyes, featuring different push and pull groups. This new family of fluorescent dyes was synthesized by means of a one-pot sequential bromination-alkynylation of the heteroaromatic core, and their optical properties were investigated in tetrahydrofuran and in poly(methyl methacrylate). An efficient in silico pre-screening scheme was devised as consisting of a step-by-step procedure employing computational methodologies by simulation of electronic spectra within simple vertical energy and more sophisticated vibronic approaches. Such an approach was also extended to efficiently simulate one-photon absorption and emission spectra of the dyes in the polymer environment for their potential application in luminescent solar concentrators. Besides the specific applications of this novel material, the integration of computational and experimental techniques reported here provides an efficient protocol that can be applied to make a selection among similar dye candidates, which constitute the essential responsive part of those fluorescent plastic materials.

The Design of Finite State Machine for Asynchronous Replication Protocol

NASA Astrophysics Data System (ADS)

Wang, Yanlong; Li, Zhanhuai; Lin, Wei; Hei, Minglei; Hao, Jianhua

Data replication is a key way to design a disaster tolerance system and to achieve reliability and availability. It is difficult for a replication protocol to deal with the diverse and complex environment. This means that data is less well replicated than it ought to be. To reduce data loss and to optimize replication protocols, we (1) present a finite state machine, (2) run it to manage an asynchronous replication protocol and (3) report a simple evaluation of the asynchronous replication protocol based on our state machine. It's proved that our state machine is applicable to guarantee the asynchronous replication protocol running in the proper state to the largest extent in the event of various possible events. It also can helpful to build up replication-based disaster tolerance systems to ensure the business continuity.

Cryptography in the Bounded-Quantum-Storage Model

NASA Astrophysics Data System (ADS)

Schaffner, Christian

2007-09-01

This thesis initiates the study of cryptographic protocols in the bounded-quantum-storage model. On the practical side, simple protocols for Rabin Oblivious Transfer, 1-2 Oblivious Transfer and Bit Commitment are presented. No quantum memory is required for honest players, whereas the protocols can only be broken by an adversary controlling a large amount of quantum memory. The protocols are efficient, non-interactive and can be implemented with today's technology. On the theoretical side, new entropic uncertainty relations involving min-entropy are established and used to prove the security of protocols according to new strong security definitions. For instance, in the realistic setting of Quantum Key Distribution (QKD) against quantum-memory-bounded eavesdroppers, the uncertainty relation allows to prove the security of QKD protocols while tolerating considerably higher error rates compared to the standard model with unbounded adversaries.

Multi-stimuli responsive Cu2S nanocrystals as trimodal imaging and synergistic chemo-photothermal therapy agents

NASA Astrophysics Data System (ADS)

Poulose, Aby Cheruvathoor; Veeranarayanan, Srivani; Mohamed, M. Sheikh; Nagaoka, Yutaka; Romero Aburto, Rebeca; Mitcham, Trevor; Ajayan, Pulickel M.; Bouchard, Richard R.; Sakamoto, Yasushi; Yoshida, Yasuhiko; Maekawa, Toru; Sakthi Kumar, D.

2015-04-01

A size and shape tuned, multifunctional metal chalcogenide, Cu2S-based nanotheranostic agent is developed for trimodal imaging and multimodal therapeutics against brain cancer cells. This theranostic agent was highly efficient in optical, photoacoustic and X-ray contrast imaging systems. The folate targeted NIR-responsive photothermal ablation in synergism with the chemotherapeutic action of doxorubicin proved to be a rapid precision guided cancer-killing module. The multi-stimuli, i.e., pH-, thermo- and photo-responsive drug release behavior of the nanoconjugates opens up a wider corridor for on-demand triggered drug administration. The simple synthesis protocol, combined with the multitudes of interesting features packed into a single nanoformulation, clearly demonstrates the competing role of this Cu2S nanosystem in future cancer treatment strategies.A size and shape tuned, multifunctional metal chalcogenide, Cu2S-based nanotheranostic agent is developed for trimodal imaging and multimodal therapeutics against brain cancer cells. This theranostic agent was highly efficient in optical, photoacoustic and X-ray contrast imaging systems. The folate targeted NIR-responsive photothermal ablation in synergism with the chemotherapeutic action of doxorubicin proved to be a rapid precision guided cancer-killing module. The multi-stimuli, i.e., pH-, thermo- and photo-responsive drug release behavior of the nanoconjugates opens up a wider corridor for on-demand triggered drug administration. The simple synthesis protocol, combined with the multitudes of interesting features packed into a single nanoformulation, clearly demonstrates the competing role of this Cu2S nanosystem in future cancer treatment strategies. Electronic supplementary information (ESI) available: Methodology and additional experimental results. See DOI: 10.1039/c4nr07139e

Rehabilitation Approaches in Macular Degeneration Patients

PubMed Central

Maniglia, Marcello; Cottereau, Benoit R.; Soler, Vincent; Trotter, Yves

2016-01-01

Age related macular degeneration (AMD) is a visual disease that affects elderly population. It entails a progressive loss of central vision whose consequences are dramatic for the patient’s quality of life. Current rehabilitation programs are restricted to technical aids based on visual devices. They only temporarily improve specific visual functions such as reading skills. Considering the rapid increase of the aging population worldwide, it is crucial to intensify clinical research on AMD in order to develop simple and efficient methods that improve the patient’s visual performances in many different contexts. One very promising approach to face this challenge is based on perceptual learning (PL). Through intensive practice, PL can induce neural plasticity in sensory cortices and result in long-lasting enhancements for various perceptual tasks in both normal and visually impaired populations. A growing number of studies showed how appropriate PL protocols improve visual functions in visual disorders, namely amblyopia, presbyopia or myopia. In order to successfully apply these approaches to more severe conditions such as AMD, numerous challenges have to be overcome. Indeed, the overall elderly age of patients and the reduced cortical surface that is devoted to peripheral vision potentially limit neural plasticity in this population. In addition, ocular fixation becomes much less stable because patients have to rely on peripheral fixation spots outside the scotoma whose size keeps on evolving. The aim of this review article is to discuss the recent literature on this topic and to offer a unified approach for developing new rehabilitation programs of AMD using PL. We argue that with an appropriate experimental and training protocol that is adapted to each patient needs, PL can offer fascinating opportunities for the development of simple, non-expensive rehabilitation approaches a large spectrum of visual functions in AMD patients. PMID:28082876

High-Throughput Cryopreservation of Plant Cell Cultures for Functional Genomics

PubMed Central

Ogawa, Yoichi; Sakurai, Nozomu; Oikawa, Akira; Kai, Kosuke; Morishita, Yoshihiko; Mori, Kumiko; Moriya, Kanami; Fujii, Fumiko; Aoki, Koh; Suzuki, Hideyuki; Ohta, Daisaku; Saito, Kazuki; Shibata, Daisuke

2012-01-01

Suspension-cultured cell lines from plant species are useful for genetic engineering. However, maintenance of these lines is laborious, involves routine subculturing and hampers wider use of transgenic lines, especially when many lines are required for a high-throughput functional genomics application. Cryopreservation of these lines may reduce the need for subculturing. Here, we established a simple protocol for cryopreservation of cell lines from five commonly used plant species, Arabidopsis thaliana, Daucus carota, Lotus japonicus, Nicotiana tabacum and Oryza sativa. The LSP solution (2 M glycerol, 0.4 M sucrose and 86.9 mM proline) protected cells from damage during freezing and was only mildly toxic to cells kept at room temperature for at least 2 h. More than 100 samples were processed for freezing simultaneously. Initially, we determined the conditions for cryopreservation using a programmable freezer; we then developed a modified simple protocol that did not require a programmable freezer. In the simple protocol, a thick expanded polystyrene (EPS) container containing the vials with the cell–LSP solution mixtures was kept at −30°C for 6 h to cool the cells slowly (pre-freezing); samples from the EPS containers were then plunged into liquid nitrogen before long-term storage. Transgenic Arabidopsis cells were subjected to cryopreservation, thawed and then re-grown in culture; transcriptome and metabolome analyses indicated that there was no significant difference in gene expression or metabolism between cryopreserved cells and control cells. The simplicity of the protocol will accelerate the pace of research in functional plant genomics. PMID:22437846

Micropropagation of African violet (Saintpaulia ionantha Wendl.).

PubMed

Shukla, Mukund; Sullivan, J Alan; Jain, Shri Mohan; Murch, Susan J; Saxena, Praveen K

2013-01-01

Micropropagation is an important tool for rapid multiplication and the creation of genetic variability in African violets (Saintpaulia ionantha Wendl.). Successful in vitro propagation depends on the specific requirements and precise manipulation of various factors such as the type of explants used, physiological state of the mother plant, plant growth regulators in the culture medium, and growth conditions. Development of cost-effective protocols with a high rate of multiplication is a crucial requirement for commercial application of micropropagation. The current chapter describes an optimized protocol for micropropagation of African violets using leaf explants obtained from in vitro grown plants. In this process, plant regeneration occurs via both somatic embryogenesis and shoot organogenesis simultaneously in the explants induced with the growth regulator thidiazuron (TDZ; N-phenyl-N'-1,2,3-thidiazol-5-ylurea). The protocol is simple, rapid, and efficient for large-scale propagation of African violet and the dual routes of regeneration allow for multiple applications of the technology from simple clonal propagation to induction or selection of variants to the production of synthetic seeds.

The Power of Proofs-of-Possession: Securing Multiparty Signatures against Rogue-Key Attacks

NASA Astrophysics Data System (ADS)

Ristenpart, Thomas; Yilek, Scott

Multiparty signature protocols need protection against rogue-key attacks, made possible whenever an adversary can choose its public key(s) arbitrarily. For many schemes, provable security has only been established under the knowledge of secret key (KOSK) assumption where the adversary is required to reveal the secret keys it utilizes. In practice, certifying authorities rarely require the strong proofs of knowledge of secret keys required to substantiate the KOSK assumption. Instead, proofs of possession (POPs) are required and can be as simple as just a signature over the certificate request message. We propose a general registered key model, within which we can model both the KOSK assumption and in-use POP protocols. We show that simple POP protocols yield provable security of Boldyreva's multisignature scheme [11], the LOSSW multisignature scheme [28], and a 2-user ring signature scheme due to Bender, Katz, and Morselli [10]. Our results are the first to provide formal evidence that POPs can stop rogue-key attacks.

Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review.

PubMed

Emwas, Abdul-Hamid; Luchinat, Claudio; Turano, Paola; Tenori, Leonardo; Roy, Raja; Salek, Reza M; Ryan, Danielle; Merzaban, Jasmeen S; Kaddurah-Daouk, Rima; Zeri, Ana Carolina; Nagana Gowda, G A; Raftery, Daniel; Wang, Yulan; Brennan, Lorraine; Wishart, David S

The metabolic composition of human biofluids can provide important diagnostic and prognostic information. Among the biofluids most commonly analyzed in metabolomic studies, urine appears to be particularly useful. It is abundant, readily available, easily stored and can be collected by simple, noninvasive techniques. Moreover, given its chemical complexity, urine is particularly rich in potential disease biomarkers. This makes it an ideal biofluid for detecting or monitoring disease processes. Among the metabolomic tools available for urine analysis, NMR spectroscopy has proven to be particularly well-suited, because the technique is highly reproducible and requires minimal sample handling. As it permits the identification and quantification of a wide range of compounds, independent of their chemical properties, NMR spectroscopy has been frequently used to detect or discover disease fingerprints and biomarkers in urine. Although protocols for NMR data acquisition and processing have been standardized, no consensus on protocols for urine sample selection, collection, storage and preparation in NMR-based metabolomic studies have been developed. This lack of consensus may be leading to spurious biomarkers being reported and may account for a general lack of reproducibility between laboratories. Here, we review a large number of published studies on NMR-based urine metabolic profiling with the aim of identifying key variables that may affect the results of metabolomics studies. From this survey, we identify a number of issues that require either standardization or careful accounting in experimental design and provide some recommendations for urine collection, sample preparation and data acquisition.

Experimental aspect of solid-state nuclear magnetic resonance studies of biomaterials such as bones.

PubMed

Singh, Chandan; Rai, Ratan Kumar; Sinha, Neeraj

2013-01-01

Solid-state nuclear magnetic resonance (SSNMR) spectroscopy is increasingly becoming a popular technique to probe micro-structural details of biomaterial such as bone with pico-meter resolution. Due to high-resolution structural details probed by SSNMR methods, handling of bone samples and experimental protocol are very crucial aspects of study. We present here first report of the effect of various experimental protocols and handling methods of bone samples on measured SSNMR parameters. Various popular SSNMR experiments were performed on intact cortical bone sample collected from fresh animal, immediately after removal from animal systems, and results were compared with bone samples preserved in different conditions. We find that the best experimental conditions for SSNMR parameters of bones correspond to preservation at -20 °C and in 70% ethanol solution. Various other SSNMR parameters were compared corresponding to different experimental conditions. Our study has helped in finding best experimental protocol for SSNMR studies of bone. This study will be of further help in the application of SSNMR studies on large bone disease related animal model systems for statistically significant results. © 2013 Elsevier Inc. All rights reserved.

Effect of the material properties on the crumpling of a thin sheet.

PubMed

Habibi, Mehdi; Adda-Bedia, Mokhtar; Bonn, Daniel

2017-06-07

While simple at first glance, the dense packing of sheets is a complex phenomenon that depends on material parameters and the packing protocol. We study the effect of plasticity on the crumpling of sheets of different materials by performing isotropic compaction experiments on sheets of different sizes and elasto-plastic properties. First, we quantify the material properties using a dimensionless foldability index. Then, the compaction force required to crumple a sheet into a ball as well as the average number of layers inside the ball are measured. For each material, both quantities exhibit a power-law dependence on the diameter of the crumpled ball. We experimentally establish the power-law exponents and find that both depend nonlinearly on the foldability index. However the exponents that characterize the mechanical response and morphology of the crumpled materials are related linearly. A simple scaling argument explains this in terms of the buckling of the sheets, and recovers the relation between the crumpling force and the morphology of the crumpled structure. Our results suggest a new approach to tailor the mechanical response of the crumpled objects by carefully selecting their material properties.

Why standard brain-computer interface (BCI) training protocols should be changed: an experimental study

NASA Astrophysics Data System (ADS)

Jeunet, Camille; Jahanpour, Emilie; Lotte, Fabien

2016-06-01

Objective. While promising, electroencephaloraphy based brain-computer interfaces (BCIs) are barely used due to their lack of reliability: 15% to 30% of users are unable to control a BCI. Standard training protocols may be partly responsible as they do not satisfy recommendations from psychology. Our main objective was to determine in practice to what extent standard training protocols impact users’ motor imagery based BCI (MI-BCI) control performance. Approach. We performed two experiments. The first consisted in evaluating the efficiency of a standard BCI training protocol for the acquisition of non-BCI related skills in a BCI-free context, which enabled us to rule out the possible impact of BCIs on the training outcome. Thus, participants (N = 54) were asked to perform simple motor tasks. The second experiment was aimed at measuring the correlations between motor tasks and MI-BCI performance. The ten best and ten worst performers of the first study were recruited for an MI-BCI experiment during which they had to learn to perform two MI tasks. We also assessed users’ spatial ability and pre-training μ rhythm amplitude, as both have been related to MI-BCI performance in the literature. Main results. Around 17% of the participants were unable to learn to perform the motor tasks, which is close to the BCI illiteracy rate. This suggests that standard training protocols are suboptimal for skill teaching. No correlation was found between motor tasks and MI-BCI performance. However, spatial ability played an important role in MI-BCI performance. In addition, once the spatial ability covariable had been controlled for, using an ANCOVA, it appeared that participants who faced difficulty during the first experiment improved during the second while the others did not. Significance. These studies suggest that (1) standard MI-BCI training protocols are suboptimal for skill teaching, (2) spatial ability is confirmed as impacting on MI-BCI performance, and (3) when faced with difficult pre-training, subjects seemed to explore more strategies and therefore learn better.

No significant effect of transcranial direct current stimulation (tDCS) found on simple motor reaction time comparing 15 different simulation protocols.

PubMed

Horvath, Jared Cooney; Carter, Olivia; Forte, Jason D

2016-10-01

Research exploring the behavioral impact of transcranial direct current stimulation (tDCS) over M1 has produced homogenous results. The most common explanations to address this homogeneity concerns the differential impact of varied tDCS parameters (such as stimulation intensity or electrode montage). To explore this, we systematically examined the effects of 15 different tDCS protocols on a well-elucidated neurobehavioral system: simple visual motor reaction time (smRT). For the initial phase of this study, 150 healthy participants were randomly assigned to one of 5 experimental groups (2mA anodal, 2mA cathodal, 1mA anodal, 1mA cathodal, or sham) across 3 different conditions (orbitofrontal, bilateral, or extracephalic reference electrode location). The active electrode was always placed over M1 and tDCS lasted for 20min. Starting ~5min prior to stimulation and running continuously for ~30min, participants were repeatedly presented with a visual cue centered on a computer monitor and asked to press a response button as quickly as possible at stimulus onset (stimuli number: 100 pre-, 400 during-, and 100-post stimulation - interstimulus interval: 1-3s). Ex-gaussian distribution curves, miss, and error rates were determined for each normalized batch of 100 RTs and compared using a two-way ANOVA. As the largest group differences were seen with 2mA anodal (compared to sham) stimulation using an orbitofrontal montage, an additional 60 healthy participants were recruited to further test for significance in this condition. No significant impact of tDCS was seen on any parameter of smRT distribution, error rate, or miss rate, regardless of polarity, stimulation intensity, electrode montage, or stimulation-to-task relationship. Our results suggest that tDCS over M1 might not have a predictable or reliable effect on short duration smRT. Our results raise interesting questions regarding the mechanisms by which tDCS might modulate more complex motor behaviors. Additional research utilizing multiple tDCS protocols as undertaken here will help address and clarify these concerns. Copyright © 2016 Elsevier Ltd. All rights reserved.

A protocol for rat in vitro fertilization during conventional laboratory working hours.

PubMed

Aoto, Toshihiro; Takahashi, Ri-ichi; Ueda, Masatsugu

2011-12-01

In vitro fertilization (IVF) is a valuable technique for the propagation of experimental animals. IVF has typically been used in mice to rapidly expand breeding colonies and create large numbers of embryos. However, applications of IVF in rat breeding experiments have stalled due to the inconvenient laboratory work schedules imposed by current IVF protocols for this species. Here, we developed a new rat IVF protocol that consists of experimental steps performed during common laboratory working hours. Our protocol can be completed within 12 h by shortening the period of sperm capacitation from 5 to 1 h and the fertilization time from 10 to 8 h in human tubal fluid (HTF) medium. This new protocol generated an excellent birth rate and was applicable not only to closed colony rat strains, such as Wistar, Long-Evans, and Sprague-Dawley (SD), but also to the inbred Lewis strain. Moreover, Wistar and Long-Evans embryos prepared by this protocol were successfully frozen by vitrification and later successfully thawed and resuscitated. This protocol is practical and can be easily adopted by laboratory workers.

Theoretical and Experimental Investigation of Random Gust Loads Part I : Aerodynamic Transfer Function of a Simple Wing Configuration in Incompressible Flow

NASA Technical Reports Server (NTRS)

Hakkinen, Raimo J; Richardson, A S , Jr

1957-01-01

Sinusoidally oscillating downwash and lift produced on a simple rigid airfoil were measured and compared with calculated values. Statistically stationary random downwash and the corresponding lift on a simple rigid airfoil were also measured and the transfer functions between their power spectra determined. The random experimental values are compared with theoretically approximated values. Limitations of the experimental technique and the need for more extensive experimental data are discussed.

Experimental Optimal Single Qubit Purification in an NMR Quantum Information Processor

PubMed Central

Hou, Shi-Yao; Sheng, Yu-Bo; Feng, Guan-Ru; Long, Gui-Lu

2014-01-01

High quality single qubits are the building blocks in quantum information processing. But they are vulnerable to environmental noise. To overcome noise, purification techniques, which generate qubits with higher purities from qubits with lower purities, have been proposed. Purifications have attracted much interest and been widely studied. However, the full experimental demonstration of an optimal single qubit purification protocol proposed by Cirac, Ekert and Macchiavello [Phys. Rev. Lett. 82, 4344 (1999), the CEM protocol] more than one and half decades ago, still remains an experimental challenge, as it requires more complicated networks and a higher level of precision controls. In this work, we design an experiment scheme that realizes the CEM protocol with explicit symmetrization of the wave functions. The purification scheme was successfully implemented in a nuclear magnetic resonance quantum information processor. The experiment fully demonstrated the purification protocol, and showed that it is an effective way of protecting qubits against errors and decoherence. PMID:25358758

Permutation parity machines for neural cryptography.

PubMed

Reyes, Oscar Mauricio; Zimmermann, Karl-Heinz

2010-06-01

Recently, synchronization was proved for permutation parity machines, multilayer feed-forward neural networks proposed as a binary variant of the tree parity machines. This ability was already used in the case of tree parity machines to introduce a key-exchange protocol. In this paper, a protocol based on permutation parity machines is proposed and its performance against common attacks (simple, geometric, majority and genetic) is studied.

Permutation parity machines for neural cryptography

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

Reyes, Oscar Mauricio; Escuela de Ingenieria Electrica, Electronica y Telecomunicaciones, Universidad Industrial de Santander, Bucaramanga; Zimmermann, Karl-Heinz

2010-06-15

Recently, synchronization was proved for permutation parity machines, multilayer feed-forward neural networks proposed as a binary variant of the tree parity machines. This ability was already used in the case of tree parity machines to introduce a key-exchange protocol. In this paper, a protocol based on permutation parity machines is proposed and its performance against common attacks (simple, geometric, majority and genetic) is studied.

Evaluating the Process of Generating a Clinical Trial Protocol

PubMed Central

Franciosi, Lui G.; Butterfield, Noam N.; MacLeod, Bernard A.

2002-01-01

The research protocol is the principal document in the conduct of a clinical trial. Its generation requires knowledge about the research problem, the potential experimental confounders, and the relevant Good Clinical Practices for conducting the trial. However, such information is not always available to authors during the writing process. A checklist of over 80 items has been developed to better understand the considerations made by authors in generating a protocol. It is based on the most cited requirements for designing and implementing the randomised controlled trial. Items are categorised according to the trial's research question, experimental design, statistics, ethics, and standard operating procedures. This quality assessment tool evaluates the extent that a generated protocol deviates from the best-planned clinical trial.

Data aggregation in wireless sensor networks using the SOAP protocol

NASA Astrophysics Data System (ADS)

Al-Yasiri, A.; Sunley, A.

2007-07-01

Wireless sensor networks (WSN) offer an increasingly attractive method of data gathering in distributed system architectures and dynamic access via wireless connectivity. Wireless sensor networks have physical and resource limitations, this leads to increased complexity for application developers and often results in applications that are closely coupled with network protocols. In this paper, a data aggregation framework using SOAP (Simple Object Access Protocol) on wireless sensor networks is presented. The framework works as a middleware for aggregating data measured by a number of nodes within a network. The aim of the study is to assess the suitability of the protocol in such environments where resources are limited compared to traditional networks.

Reliable transfer of data from ground to space

NASA Technical Reports Server (NTRS)

Brosi, Fred

1993-01-01

This paper describes the problems involved in uplink of data from control centers on the ground to spacecraft, and explores the solutions to those problems, past. present. and future. The evolution of this process, from simple commanding to transfer of large volumes of data and commands is traced. The need for reliable end-to-end protocols for commanding and file transfer is demonstrated, and the shortcomings of both existing telecommand protocols and commercial products to meet this need are discussed. Recent developments in commercial protocols that may be adaptable to the mentioned operations environment are surveyed, and current efforts to develop a suite of protocols for reliable transfer in this environment are presented.

Status and trends monitoring of riparian and aquatic habitat in the Olympic Experimental State Forest: Monitoring protocols

Treesearch

Teodora Minkova; Alex D. Foster

2017-01-01

Presented here are the monitoring protocols for the Status and Trends Monitoring of Riparian and Aquatic Habitats project in the Olympic Experimental State Forest (OESF). The procedures yield the empirical data needed to address key uncertainties regarding the integration of timber production and habitat conservation across landscapes and assess progress toward...

Weight training in youth-growth, maturation, and safety: an evidence-based review.

PubMed

Malina, Robert M

2006-11-01

To review the effects of resistance training programs on pre- and early-pubertal youth in the context of response, potential influence on growth and maturation, and occurrence of injury. Evidence-based review. Twenty-two reports dealing with experimental resistance training protocols, excluding isometric programs, in pre- and early-pubertal youth, were reviewed in the context of subject characteristics, training protocol, responses, and occurrence of injury. Experimental programs most often used isotonic machines and free weights, 2- and 3-day protocols, and 8- and 12-week durations, with significant improvements in muscular strength during childhood and early adolescence. Strength gains were lost during detraining. Experimental resistance training programs did not influence growth in height and weight of pre- and early-adolescent youth, and changes in estimates of body composition were variable and quite small. Only 10 studies systematically monitored injuries, and only three injuries were reported. Estimated injury rates were 0.176, 0.053, and 0.055 per 100 participant-hours in the respective programs. Experimental training protocols with weights and resistance machines and with supervision and low instructor/participant ratios are relatively safe and do not negatively impact growth and maturation of pre- and early-pubertal youth.

Level Alignment as Descriptor for Semiconductor/Catalyst Systems in Water Splitting: The Case of Hematite/Cobalt Hexacyanoferrate Photoanodes.

PubMed

Hegner, Franziska Simone; Cardenas-Morcoso, Drialys; Giménez, Sixto; López, Núria; Galan-Mascaros, Jose Ramon

2017-11-23

The realization of artificial photosynthesis may depend on the efficient integration of photoactive semiconductors and catalysts to promote photoelectrochemical water splitting. Many efforts are currently devoted to the processing of multicomponent anodes and cathodes in the search for appropriate synergy between light absorbers and active catalysts. No single material appears to combine both features. Many experimental parameters are key to achieve the needed synergy between both systems, without clear protocols for success. Herein, we show how computational chemistry can shed some light on this cumbersome problem. DFT calculations are useful to predict adequate energy-level alignment for thermodynamically favored hole transfer. As proof of concept, we experimentally confirmed the limited performance enhancement in hematite photoanodes decorated with cobalt hexacyanoferrate as a competent water-oxidation catalyst. Computational methods describe the misalignment of their energy levels, which is the origin of this mismatch. Photoelectrochemical studies indicate that the catalyst exclusively shifts the hematite surface state to lower potentials, which therefore reduces the onset for water oxidation. Although kinetics will still depend on interface architecture, our simple theoretical approach may identify and predict plausible semiconductor/catalyst combinations, which will speed up experimental work towards promising photoelectrocatalytic systems. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Health surveillance under adverse ergonomics conditions--validity of a screening method adapted for the occupational health service.

PubMed

Jonker, Dirk; Gustafsson, Ewa; Rolander, Bo; Arvidsson, Inger; Nordander, Catarina

2015-01-01

A new health surveillance protocol for work-related upper-extremity musculoskeletal disorders has been validated by comparing the results with a reference protocol. The studied protocol, Health Surveillance in Adverse Ergonomics Conditions (HECO), is a new version of the reference protocol modified for application in the Occupational Health Service (OHS). The HECO protocol contains both a screening part and a diagnosing part. Sixty-three employees were examined. The screening in HECO did not miss any diagnosis found when using the reference protocol, but in comparison to the reference protocol considerable time savings could be achieved. Fair to good agreement between the protocols was obtained for one or more diagnoses in neck/shoulders (86%, k = 0.62) and elbow/hands (84%, k = 0.49). Therefore, the results obtained using the HECO protocol can be compared with a reference material collected with the reference protocol, and thus provide information of the magnitude of disorders in an examined work group. Practitioner Summary: The HECO protocol is a relatively simple physical examination protocol for identification of musculoskeletal disorders in the neck and upper extremities. The protocol is a reliable and cost-effective tool for the OHS to use for occupational health surveillance in order to detect workplaces at high risk for developing musculoskeletal disorders.

A simple protocol using underwater epoxy to install annual temperature monitoring sites in rivers and streams

Treesearch

Daniel J. Isaak; Dona L. Horan; Sherry P. Wollrab

2013-01-01

Thermal regimes in rivers and streams are fundamental determinants of biological processes and are often monitored for regulatory compliance. Here, we describe a simple technique for establishing annual monitoring sites that uses underwater epoxy to attach miniature sensors to large rocks and cement bridge supports, which then serve as protective anchors. More than 500...

A simple, effective media access protocol system for integrated, high data rate networks

NASA Technical Reports Server (NTRS)

Foudriat, E. C.; Maly, K.; Overstreet, C. M.; Khanna, S.; Zhang, L.

1992-01-01

The operation and performance of a dual media access protocol for integrated, gigabit networks are described. Unlike other dual protocols, each protocol supports a different class of traffic. The Carrier Sensed Multiple Access-Ring Network (CSMA/RN) protocol and the Circulating Reservation Packet (CRP) protocol support asynchronous and synchronous traffic, respectively. The two protocols operate with minimal impact upon each other. Performance information demonstrates that they support a complete range of integrated traffic loads, do not require call setup/termination or a special node for synchronous traffic control, and provide effective pre-use and recovery. The CRP also provides guaranteed access and fairness control for the asynchronous system. The paper demonstrates that the CSMA-CRP system fulfills many of the requirements for gigabit LAN-MAN networks most effectively and simply. To accomplish this, CSMA-CRP features are compared against similar ring and bus systems, such as Cambridge Fast Ring, Metaring, Cyclic Reservation Multiple Access, and Distributed Dual Queue Data Bus (DQDB).

Performance in complex motor tasks deteriorates in hyperthermic humans.

PubMed

Piil, Jacob F; Lundbye-Jensen, Jesper; Trangmar, Steven J; Nybo, Lars

2017-01-01

Heat stress, leading to elevations in whole-body temperature, has a marked impact on both physical performance and cognition in ecological settings. Lab experiments confirm this for physically demanding activities, whereas observations are inconsistent for tasks involving cognitive processing of information or decision-making prior to responding. We hypothesized that divergences could relate to task complexity and developed a protocol consisting of 1) simple motor task [TARGET_pinch], 2) complex motor task [Visuo-motor tracking], 3) simple math task [MATH_type], 4) combined motor-math task [MATH_pinch]. Furthermore, visuo-motor tracking performance was assessed both in a separate- and a multipart protocol (complex motor tasks alternating with the three other tasks). Following familiarization, each of the 10 male subjects completed separate and multipart protocols in randomized order in the heat (40°C) or control condition (20°C) with testing at baseline (seated rest) and similar seated position, following exercise-induced hyperthermia (core temperature ∼ 39.5°C in the heat and 38.2°C in control condition). All task scores were unaffected by control exercise or passive heat exposure, but visuo-motor tracking performance was reduced by 10.7 ± 6.5% following exercise-induced hyperthermia when integrated in the multipart protocol and 4.4 ± 5.7% when tested separately (both P < 0.05 ). TARGET_pinch precision declined by 2.6 ± 1.3% ( P < 0.05 ), while no significant changes were observed for the math tasks. These results indicate that heat per se has little impact on simple motor or cognitive test performance, but complex motor performance is impaired by hyperthermia and especially so when multiple tasks are combined.

Backup key generation model for one-time password security protocol

NASA Astrophysics Data System (ADS)

Jeyanthi, N.; Kundu, Sourav

2017-11-01

The use of one-time password (OTP) has ushered new life into the existing authentication protocols used by the software industry. It introduced a second layer of security to the traditional username-password authentication, thus coining the term, two-factor authentication. One of the drawbacks of this protocol is the unreliability of the hardware token at the time of authentication. This paper proposes a simple backup key model that can be associated with the real world applications’user database, which would allow a user to circumvent the second authentication stage, in the event of unavailability of the hardware token.

Using a CLIPS expert system to automatically manage TCP/IP networks and their components

NASA Technical Reports Server (NTRS)

Faul, Ben M.

1991-01-01

A expert system that can directly manage networks components on a Transmission Control Protocol/Internet Protocol (TCP/IP) network is described. Previous expert systems for managing networks have focused on managing network faults after they occur. However, this proactive expert system can monitor and control network components in near real time. The ability to directly manage network elements from the C Language Integrated Production System (CLIPS) is accomplished by the integration of the Simple Network Management Protocol (SNMP) and a Abstract Syntax Notation (ASN) parser into the CLIPS artificial intelligence language.

A new rapid kindling variant for induction of cortical epileptogenesis in freely moving rats

PubMed Central

Morales, Juan Carlos; Álvarez-Ferradas, Carla; Roncagliolo, Manuel; Fuenzalida, Marco; Wellmann, Mario; Nualart, Francisco Javier; Bonansco, Christian

2014-01-01

Kindling, one of the most used models of experimental epilepsy is based on daily electrical stimulation in several brain structures. Unlike the classic or slow kindling protocols (SK), the rapid kindling types (RK) described until now require continuous stimulation at suprathreshold intensities applied directly to the same brain structure used for subsequent electrophysiological and immunohistochemical studies, usually the hippocampus. However, the cellular changes observed in these rapid protocols, such as astrogliosis and neuronal loss, could be due to experimental manipulation more than to epileptogenesis-related alterations. Here, we developed a new RK protocol in order to generate an improved model of temporal lobe epilepsy (TLE) which allows gradual progression of the epilepsy as well as obtaining an epileptic hippocampus, thus avoiding direct surgical manipulation and electric stimulation over this structure. This new protocol consists of basolateral amygdala (BLA) stimulation with 10 trains of biphasic pulses (10 s; 50 Hz) per day with 20 min-intervals, during 3 consecutive days, using a subconvulsive and subthreshold intensity, which guarantees tissue integrity. The progression of epileptic activity was evaluated in freely moving rats through electroencephalographic (EEG) recordings from cortex and amygdala, accompanied with synchronized video recordings. Moreover, we assessed the effectiveness of RK protocol and the establishment of epilepsy by evaluating cellular alterations of hippocampal slices from kindled rats. RK protocol induced convulsive states similar to SK protocols but in 3 days, with persistently lowered threshold to seizure induction and epileptogenic-dependent cellular changes in amygdala projection areas. We concluded that this novel RK protocol introduces a new variant of the chronic epileptogenesis models in freely moving rats, which is faster, highly reproducible and causes minimum cell damage with respect to that observed in other experimental models of epilepsy. PMID:25100948

A new rapid kindling variant for induction of cortical epileptogenesis in freely moving rats.

PubMed

Morales, Juan Carlos; Alvarez-Ferradas, Carla; Roncagliolo, Manuel; Fuenzalida, Marco; Wellmann, Mario; Nualart, Francisco Javier; Bonansco, Christian

2014-01-01

Kindling, one of the most used models of experimental epilepsy is based on daily electrical stimulation in several brain structures. Unlike the classic or slow kindling protocols (SK), the rapid kindling types (RK) described until now require continuous stimulation at suprathreshold intensities applied directly to the same brain structure used for subsequent electrophysiological and immunohistochemical studies, usually the hippocampus. However, the cellular changes observed in these rapid protocols, such as astrogliosis and neuronal loss, could be due to experimental manipulation more than to epileptogenesis-related alterations. Here, we developed a new RK protocol in order to generate an improved model of temporal lobe epilepsy (TLE) which allows gradual progression of the epilepsy as well as obtaining an epileptic hippocampus, thus avoiding direct surgical manipulation and electric stimulation over this structure. This new protocol consists of basolateral amygdala (BLA) stimulation with 10 trains of biphasic pulses (10 s; 50 Hz) per day with 20 min-intervals, during 3 consecutive days, using a subconvulsive and subthreshold intensity, which guarantees tissue integrity. The progression of epileptic activity was evaluated in freely moving rats through electroencephalographic (EEG) recordings from cortex and amygdala, accompanied with synchronized video recordings. Moreover, we assessed the effectiveness of RK protocol and the establishment of epilepsy by evaluating cellular alterations of hippocampal slices from kindled rats. RK protocol induced convulsive states similar to SK protocols but in 3 days, with persistently lowered threshold to seizure induction and epileptogenic-dependent cellular changes in amygdala projection areas. We concluded that this novel RK protocol introduces a new variant of the chronic epileptogenesis models in freely moving rats, which is faster, highly reproducible and causes minimum cell damage with respect to that observed in other experimental models of epilepsy.

Systematic Assessment of the Impact of User Roles on Network Flow Patterns

DTIC Science & Technology

2017-09-01

Protocol SNMP Simple Network Management Protocol SQL Structured Query Language SSH Secure Shell SYN TCP Sync Flag SVDD Support Vector Data Description SVM...and evaluating users based on roles provide the best approach for defining normal digital behaviors? People are individuals, with different interests...activities on the network. We evaluate the assumption that users sharing similar roles exhibit similar network behaviors, and contrast the level of similarity

Can SNMP be Used to Create a Silent SS in an 802.16 Implementation

DTIC Science & Technology

2008-09-01

wireless transmissions by using the Simple Network Management Protocol (SNMP). SNMP is a networking protocol that can be used by network ...802.16 as a unique networking technology. In a more familiar wireless networking environment like Wi-Fi, there is no central scheduler for access to...much a concern due to the scheduling algorithm , this power saving method provides good transmission security as a

Finite-key analysis for quantum key distribution with weak coherent pulses based on Bernoulli sampling

NASA Astrophysics Data System (ADS)

Kawakami, Shun; Sasaki, Toshihiko; Koashi, Masato

2017-07-01

An essential step in quantum key distribution is the estimation of parameters related to the leaked amount of information, which is usually done by sampling of the communication data. When the data size is finite, the final key rate depends on how the estimation process handles statistical fluctuations. Many of the present security analyses are based on the method with simple random sampling, where hypergeometric distribution or its known bounds are used for the estimation. Here we propose a concise method based on Bernoulli sampling, which is related to binomial distribution. Our method is suitable for the Bennett-Brassard 1984 (BB84) protocol with weak coherent pulses [C. H. Bennett and G. Brassard, Proceedings of the IEEE Conference on Computers, Systems and Signal Processing (IEEE, New York, 1984), Vol. 175], reducing the number of estimated parameters to achieve a higher key generation rate compared to the method with simple random sampling. We also apply the method to prove the security of the differential-quadrature-phase-shift (DQPS) protocol in the finite-key regime. The result indicates that the advantage of the DQPS protocol over the phase-encoding BB84 protocol in terms of the key rate, which was previously confirmed in the asymptotic regime, persists in the finite-key regime.

Efficient Regular Perovskite Solar Cells Based on Pristine [70]Fullerene as Electron-Selective Contact.

PubMed

Collavini, Silvia; Kosta, Ivet; Völker, Sebastian F; Cabanero, German; Grande, Hans J; Tena-Zaera, Ramón; Delgado, Juan Luis

2016-06-08

[70]Fullerene is presented as an efficient alternative electron-selective contact (ESC) for regular-architecture perovskite solar cells (PSCs). A smart and simple, well-described solution processing protocol for the preparation of [70]- and [60]fullerene-based solar cells, namely the fullerene saturation approach (FSA), allowed us to obtain similar power conversion efficiencies for both fullerene materials (i.e., 10.4 and 11.4 % for [70]- and [60]fullerene-based devices, respectively). Importantly, despite the low electron mobility and significant visible-light absorption of [70]fullerene, the presented protocol allows the employment of [70]fullerene as an efficient ESC. The [70]fullerene film thickness and its solubility in the perovskite processing solutions are crucial parameters, which can be controlled by the use of this simple solution processing protocol. The damage to the [70]fullerene film through dissolution during the perovskite deposition is avoided through the saturation of the perovskite processing solution with [70]fullerene. Additionally, this fullerene-saturation strategy improves the performance of the perovskite film significantly and enhances the power conversion efficiency of solar cells based on different ESCs (i.e., [60]fullerene, [70]fullerene, and TiO2 ). Therefore, this universal solution processing protocol widens the opportunities for the further development of PSCs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Protocols for efficient simulations of long-time protein dynamics using coarse-grained CABS model.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2014-01-01

Coarse-grained (CG) modeling is a well-acknowledged simulation approach for getting insight into long-time scale protein folding events at reasonable computational cost. Depending on the design of a CG model, the simulation protocols vary from highly case-specific-requiring user-defined assumptions about the folding scenario-to more sophisticated blind prediction methods for which only a protein sequence is required. Here we describe the framework protocol for the simulations of long-term dynamics of globular proteins, with the use of the CABS CG protein model and sequence data. The simulations can start from a random or a selected (e.g., native) structure. The described protocol has been validated using experimental data for protein folding model systems-the prediction results agreed well with the experimental results.

The Role of Additional Pulses in Electropermeabilization Protocols

PubMed Central

Suárez, Cecilia; Soba, Alejandro; Maglietti, Felipe; Olaiz, Nahuel; Marshall, Guillermo

2014-01-01

Electropermeabilization (EP) based protocols such as those applied in medicine, food processing or environmental management, are well established and widely used. The applied voltage, as well as tissue electric conductivity, are of utmost importance for assessing final electropermeabilized area and thus EP effectiveness. Experimental results from literature report that, under certain EP protocols, consecutive pulses increase tissue electric conductivity and even the permeabilization amount. Here we introduce a theoretical model that takes into account this effect in the application of an EP-based protocol, and its validation with experimental measurements. The theoretical model describes the electric field distribution by a nonlinear Laplace equation with a variable conductivity coefficient depending on the electric field, the temperature and the quantity of pulses, and the Penne's Bioheat equation for temperature variations. In the experiments, a vegetable tissue model (potato slice) is used for measuring electric currents and tissue electropermeabilized area in different EP protocols. Experimental measurements show that, during sequential pulses and keeping constant the applied voltage, the electric current density and the blackened (electropermeabilized) area increase. This behavior can only be attributed to a rise in the electric conductivity due to a higher number of pulses. Accordingly, we present a theoretical modeling of an EP protocol that predicts correctly the increment in the electric current density observed experimentally during the addition of pulses. The model also demonstrates that the electric current increase is due to a rise in the electric conductivity, in turn induced by temperature and pulse number, with no significant changes in the electric field distribution. The EP model introduced, based on a novel formulation of the electric conductivity, leads to a more realistic description of the EP phenomenon, hopefully providing more accurate predictions of treatment outcomes. PMID:25437512

Experimental Demonstration of a Cheap and Accurate Phase Estimation

DOE PAGES

Rudinger, Kenneth; Kimmel, Shelby; Lobser, Daniel; ...

2017-05-11

We demonstrate an experimental implementation of robust phase estimation (RPE) to learn the phase of a single-qubit rotation on a trapped Yb + ion qubit. Here, we show this phase can be estimated with an uncertainty below 4 × 10 -4 rad using as few as 176 total experimental samples, and our estimates exhibit Heisenberg scaling. Unlike standard phase estimation protocols, RPE neither assumes perfect state preparation and measurement, nor requires access to ancillae. We crossvalidate the results of RPE with the more resource-intensive protocol of gate set tomography.

Feasibility and Emotional Impact of Experimentally Extending Sleep in Short-Sleeping Adolescents.

PubMed

Van Dyk, Tori R; Zhang, Nanhua; Catlin, Perry A; Cornist, Kaylin; McAlister, Shealan; Whitacre, Catharine; Beebe, Dean W

2017-09-01

Published experimental sleep manipulation protocols for adolescents have been limited to the summer, limiting causal conclusions about how short sleep affects them on school nights, when they are most likely to restrict their sleep. This study assesses the feasibility and emotional impact of a school-night sleep manipulation protocol to test the effects of lengthening sleep in habitually short-sleeping adolescents. High school students aged 14-18 years who habitually slept 5-7 hours on school nights participated in a 5-week experimental sleep manipulation protocol. Participants completed a baseline week followed in randomized counterbalanced order by two experimental conditions lasting 2 weeks each: prescribed habitual sleep (HAB; sleep time set to match baseline) and sleep extension (EXT; 1.5-hour increase in time in bed from HAB). All sleep was obtained at home, monitored with actigraphy. Data on adherence, protocol acceptability, mood and behavior were collected at the end of each condition. Seventy-six adolescents enrolled in the study, with 54 retained through all 5 weeks. Compared to HAB, during EXT, participants averaged an additional 72.6 minutes/night of sleep (p < .001) and had reduced symptoms of sleepiness, anger, vigor, fatigue, and confusion (p < .05). The large majority of parents (98%) and adolescents (100%) said they would "maybe" or "definitely" recommend the study to another family. An experimental, school-night sleep manipulation protocol can be feasibly implemented which directly tests the potential protective effects of lengthening sleep. Many short-sleeping adolescents would benefit emotionally from sleeping longer, supporting public health efforts to promote adolescent sleep on school nights. © Sleep Research Society 2017. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.

Analysis of the contribution of experimental bias, experimental noise, and inter-subject biological variability on the assessment of developmental trajectories in diffusion MRI studies of the brain.

PubMed

Sadeghi, Neda; Nayak, Amritha; Walker, Lindsay; Okan Irfanoglu, M; Albert, Paul S; Pierpaoli, Carlo

2015-04-01

Metrics derived from the diffusion tensor, such as fractional anisotropy (FA) and mean diffusivity (MD) have been used in many studies of postnatal brain development. A common finding of previous studies is that these tensor-derived measures vary widely even in healthy populations. This variability can be due to inherent inter-individual biological differences as well as experimental noise. Moreover, when comparing different studies, additional variability can be introduced by different acquisition protocols. In this study we examined scans of 61 individuals (aged 4-22 years) from the NIH MRI study of normal brain development. Two scans were collected with different protocols (low and high resolution). Our goal was to separate the contributions of biological variability and experimental noise to the overall measured variance, as well as to assess potential systematic effects related to the use of different protocols. We analyzed FA and MD in seventeen regions of interest. We found that biological variability for both FA and MD varies widely across brain regions; biological variability is highest for FA in the lateral part of the splenium and body of the corpus callosum along with the cingulum and the superior longitudinal fasciculus, and for MD in the optic radiations and the lateral part of the splenium. These regions with high inter-individual biological variability are the most likely candidates for assessing genetic and environmental effects in the developing brain. With respect to protocol-related effects, the lower resolution acquisition resulted in higher MD and lower FA values for the majority of regions compared with the higher resolution protocol. However, the majority of the regions did not show any age-protocol interaction, indicating similar trajectories were obtained irrespective of the protocol used. Published by Elsevier Inc.

Spectral reconstruction of dental X-ray tubes using laplace inverse transform of the attenuation curve

NASA Astrophysics Data System (ADS)

Malezan, A.; Tomal, A.; Antoniassi, M.; Watanabe, P. C. A.; Albino, L. D.; Poletti, M. E.

2015-11-01

In this work, a spectral reconstruction methodology for diagnostic X-ray, using Laplace inverse transform of the attenuation, was successfully applied to dental X-ray equipments. The attenuation curves of 8 commercially available dental X-ray equipment, from 3 different manufactures (Siemens, Gnatus and Dabi Atlante), were obtained by using an ionization chamber and high purity aluminium filters, while the kVp was obtained with a specific meter. A computational routine was implemented in order to adjust a model function, whose inverse Laplace transform is analytically known, to the attenuation curve. This methodology was validated by comparing the reconstructed and the measured (using semiconductor detector of cadmium telluride) spectra of a given dental X-ray unit. The spectral reconstruction showed the Dabi Atlante equipments generating similar shape spectra. This is a desirable feature from clinic standpoint because it produces similar levels of image quality and dose. We observed that equipments from Siemens and Gnatus generate significantly different spectra, suggesting that, for a given operating protocol, these units will present different levels of image quality and dose. This fact claims for the necessity of individualized operating protocols that maximize image quality and dose. The proposed methodology is suitable to perform a spectral reconstruction of dental X-ray equipments from the simple measurements of attenuation curve and kVp. The simplified experimental apparatus and the low level of technical difficulty make this methodology accessible to a broad range of users. The knowledge of the spectral distribution can help in the development of operating protocols that maximize image quality and dose.

Infection control in healthcare settings: perspectives for mfDNA analysis in monitoring sanitation procedures.

PubMed

Valeriani, Federica; Protano, Carmela; Gianfranceschi, Gianluca; Cozza, Paola; Campanella, Vincenzo; Liguori, Giorgio; Vitali, Matteo; Divizia, Maurizio; Romano Spica, Vincenzo

2016-08-09

Appropriate sanitation procedures and monitoring of their actual efficacy represent critical points for improving hygiene and reducing the risk of healthcare-associated infections. Presently, surveillance is based on traditional protocols and classical microbiology. Innovation in monitoring is required not only to enhance safety or speed up controls but also to prevent cross infections due to novel or uncultivable pathogens. In order to improve surveillance monitoring, we propose that biological fluid microflora (mf) on reprocessed devices is a potential indicator of sanitation failure, when tested by an mfDNA-based approach. The survey focused on oral microflora traces in dental care settings. Experimental tests (n = 48) and an "in field" trial (n = 83) were performed on dental instruments. Conventional microbiology and amplification of bacterial genes by multiple real-time PCR were applied to detect traces of salivary microflora. Six different sanitation protocols were considered. A monitoring protocol was developed and performance of the mfDNA assay was evaluated by sensitivity and specificity. Contaminated samples resulted positive for saliva traces by the proposed approach (CT < 35). In accordance with guidelines, only fully sanitized samples were considered negative (100 %). Culture-based tests confirmed disinfectant efficacy, but failed in detecting incomplete sanitation. The method provided sensitivity and specificity over 95 %. The principle of detecting biological fluids by mfDNA analysis seems promising for monitoring the effectiveness of instrument reprocessing. The molecular approach is simple, fast and can provide a valid support for surveillance in dental care or other hospital settings.

[Enhanced Recovery after Surgery from Theory to Practice
What do We Need to Do?

PubMed

Che, Guowei; Liu, Lunxu; Zhou, Qinghua

2017-04-20

Enhanced recovery after surgery (ERAS) is a paradigm shift in perioperative care, resulting in substantial improvements in clinical outcomes, shorter length of hospital stay and cost savings. But the current ERAS either by application of breadth or depth is not enough, why? The main reason is the lack of "operability, evaluation, repetition" ERAS protocol and suitable for clinical extensive application protocol. How to form the clinical available protocol? Operational mainly refers to the clinical scheme is simple and feasible, and protocol compliance is good; Evaluate refers to the methods used before, during and after are the objective evaluation criteria and plan; Repeatable is clinical scheme repeatability in the process of single or multiple center.

Electro-Optic Quantum Memory for Light Using Two-Level Atoms

NASA Astrophysics Data System (ADS)

Hétet, G.; Longdell, J. J.; Alexander, A. L.; Lam, P. K.; Sellars, M. J.

2008-01-01

We present a simple quantum memory scheme that allows for the storage of a light field in an ensemble of two-level atoms. The technique is analogous to the NMR gradient echo for which the imprinting and recalling of the input field are performed by controlling a linearly varying broadening. Our protocol is perfectly efficient in the limit of high optical depths and the output pulse is emitted in the forward direction. We provide a numerical analysis of the protocol together with an experiment performed in a solid state system. In close agreement with our model, the experiment shows a total efficiency of up to 15%, and a recall efficiency of 26%. We suggest simple realizable improvements for the experiment to surpass the no-cloning limit.

Electro-optic quantum memory for light using two-level atoms.

PubMed

Hétet, G; Longdell, J J; Alexander, A L; Lam, P K; Sellars, M J

2008-01-18

We present a simple quantum memory scheme that allows for the storage of a light field in an ensemble of two-level atoms. The technique is analogous to the NMR gradient echo for which the imprinting and recalling of the input field are performed by controlling a linearly varying broadening. Our protocol is perfectly efficient in the limit of high optical depths and the output pulse is emitted in the forward direction. We provide a numerical analysis of the protocol together with an experiment performed in a solid state system. In close agreement with our model, the experiment shows a total efficiency of up to 15%, and a recall efficiency of 26%. We suggest simple realizable improvements for the experiment to surpass the no-cloning limit.

Conducting Miller-Urey Experiments

NASA Technical Reports Server (NTRS)

Parker, Eric Thomas; Cleaves, Henderson James; Burton, Aaron S.; Glavin, Daniel P.; Dworkin, Jason; Zhou, Manshui; Bada, Jeffrey L.; Fernandez, Facundo M.

2014-01-01

In 1953, Stanley Miller reported the production of biomolecules from simple gaseous starting materials, using apparatus constructed to simulate the primordial Earth's atmosphere-ocean system. Miller introduced 200 ml of water, 100 mmHg of H2, 200mmHg of CH4, and 200mmHg of NH3 into the apparatus, then subjected this mixture, under reflux, to an electric discharge for a week, while the water was simultaneously heated. The purpose of this manuscript is to provide the reader with a general experimental protocol that can be used to conduct a Miller-Urey type spark discharge experiment, using a simplified 3 L reaction flask. Since the experiment involves exposing inflammable gases to a high voltage discharge, it is worth highlighting important steps that reduce the risk of explosion. The general procedures described in this work can be extrapolated to design and conduct a wide variety of electric discharge experiments simulating primitive planetary environments.

Magnetic domain wall creep and depinning: A scalar field model approach

NASA Astrophysics Data System (ADS)

Caballero, Nirvana B.; Ferrero, Ezequiel E.; Kolton, Alejandro B.; Curiale, Javier; Jeudy, Vincent; Bustingorry, Sebastian

2018-06-01

Magnetic domain wall motion is at the heart of new magnetoelectronic technologies and hence the need for a deeper understanding of domain wall dynamics in magnetic systems. In this context, numerical simulations using simple models can capture the main ingredients responsible for the complex observed domain wall behavior. We present a scalar field model for the magnetization dynamics of quasi-two-dimensional systems with a perpendicular easy axis of magnetization which allows a direct comparison with typical experimental protocols, used in polar magneto-optical Kerr effect microscopy experiments. We show that the thermally activated creep and depinning regimes of domain wall motion can be reached and the effect of different quenched disorder implementations can be assessed with the model. In particular, we show that the depinning field increases with the mean grain size of a Voronoi tessellation model for the disorder.

A multiparallel bioreactor for the cultivation of mammalian cells in a 3D-ceramic matrix.

PubMed

Goralczyk, Vicky; Driemel, Gregor; Bischof, Andreas; Peter, Andrea; Berthold, Almuth; Kroh, Lothar; Blessing, Lucienne; Schubert, Helmut; King, Rudibert

2010-01-01

For adherently growing cells, cultivation is limited by the provided growth surface. Excellent surface-to-volume ratios are found in highly porous matrices, which have to face the challenge of nutrient supply inside the matrices' caverns. Therefore, perfusion strategies are recommended which often have to deal with the need of developing an encompassing bioreactor periphery. We present a modular bioreactor system based on a porous ceramic matrix that enables the supply of cells with oxygen and nutrients by perfusion. The present version of the reactor system focuses on simple testing of various inoculation and operation modes. Moreover, it can be used to efficiently test different foam structures. Protocols are given to set-up the system together with handling procedures for long-time cultivation of a CHO cell line. Experimental results confirm vital growth of cells inside the matrices' caverns.

[Learning to solve a spatial task in a water maze in aggressive and submissive mice].

PubMed

Dubrovina, N I; Tomilenko, R A

2007-01-01

Learning and retention of the spatial memory were studied in mice with alternative under conditions of various experimental protocols. Visible and hidden platform acquisition in a simple model of the water maze was similarly fast both in aggressive and submissive mice, but extinction differed. Retention of the platform location preference persisted in aggressive mice in four testing trials. In submissive mice, extiction of the spatial memory was accompanied with a prolongation of search with parallel production of episodes of "passive drift". Differences in spatial learning between aggressive and submissive mice were revealed in a water maze complicated with partitions. In this case, aggressors were able to learn the position of a hidden platform (in contrast to submissive mice with the dominant response of "passive drift"). During testing the response, aggressive mice longer retained the spatial preference without extinction.

A Reusable, Compliant, Small Volume Blood Reservoir for In Vitro Hemolysis Testing.

PubMed

Olia, Salim E; Herbertson, Luke H; Malinauskas, Richard A; Kameneva, Marina V

2017-02-01

Bench-top in vitro hemolysis testing is a fundamental tool during the design and regulatory safety evaluation of blood-contacting medical devices. While multiple published experimental protocols exist, descriptions of the test loop reservoir remain ambiguous. A critical fixture within the circuit, there is no readily available blood reservoir that ensures thorough mixing and complete air evacuation: two major factors which can affect results. As part of the Food and Drug Administration (FDA) Critical Path Initiative, we developed a three-piece reservoir consisting of a 3D-printed base, a plastic clamp set, and a medical-grade blood bag. This simple, reusable, and cost-effective design was used successfully in the hemolysis assessment of FDA benchmark nozzles and prototype rotary blood pumps, and may be useful as an integral component to any in vitro blood circulation loop. © 2016 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Relativistic quantum cryptography

NASA Astrophysics Data System (ADS)

Molotkov, S. N.; Nazin, S. S.

2003-07-01

The problem of unconditional security of quantum cryptography (i.e. the security which is guaranteed by the fundamental laws of nature rather than by technical limitations) is one of the central points in quantum information theory. We propose a relativistic quantum cryptosystem and prove its unconditional security against any eavesdropping attempts. Relativistitic causality arguments allow to demonstrate the security of the system in a simple way. Since the proposed protocol does not empoly collective measurements and quantum codes, the cryptosystem can be experimentally realized with the present state-of-art in fiber optics technologies. The proposed cryptosystem employs only the individual measurements and classical codes and, in addition, the key distribution problem allows to postpone the choice of the state encoding scheme until after the states are already received instead of choosing it before sending the states into the communication channel (i.e. to employ a sort of "antedate" coding).

Core structure and dynamics of non-Abelian vortices in a biaxial nematic spinor Bose-Einstein condensate

NASA Astrophysics Data System (ADS)

Borgh, Magnus O.; Ruostekoski, Janne

2016-05-01

We demonstrate that multiple interaction-dependent defect core structures as well as dynamics of non-Abelian vortices can be realized in the biaxial nematic (BN) phase of a spin-2 atomic Bose-Einstein condensate (BEC). An experimentally simple protocol may be used to break degeneracy with the uniaxial nematic phase. We show that a discrete spin-space symmetry in the core may be reflected in a breaking of its spatial symmetry. The discrete symmetry of the BN order parameter leads to non-commuting vortex charges. We numerically simulate reconnection of non-Abelian vortices, demonstrating formation of the obligatory rung vortex. In addition to atomic BECs, non-Abelian vortices are theorized in, e.g., liquid crystals and cosmic strings. Our results suggest the BN spin-2 BEC as a prime candidate for their realization. We acknowledge financial support from the EPSRC.

Anharmonic Vibrational Spectroscopy on Metal Transition Complexes

NASA Astrophysics Data System (ADS)

Latouche, Camille; Bloino, Julien; Barone, Vincenzo

2014-06-01

Advances in hardware performance and the availability of efficient and reliable computational models have made possible the application of computational spectroscopy to ever larger molecular systems. The systematic interpretation of experimental data and the full characterization of complex molecules can then be facilitated. Focusing on vibrational spectroscopy, several approaches have been proposed to simulate spectra beyond the double harmonic approximation, so that more details become available. However, a routine use of such tools requires the preliminary definition of a valid protocol with the most appropriate combination of electronic structure and nuclear calculation models. Several benchmark of anharmonic calculations frequency have been realized on organic molecules. Nevertheless, benchmarks of organometallics or inorganic metal complexes at this level are strongly lacking despite the interest of these systems due to their strong emission and vibrational properties. Herein we report the benchmark study realized with anharmonic calculations on simple metal complexes, along with some pilot applications on systems of direct technological or biological interest.

Atomic scale simulations of vapor cooled carbon clusters

NASA Astrophysics Data System (ADS)

Bogana, M. P.; Colombo, L.

2007-03-01

By means of atomistic simulations we observed the formation of many topologically non-equivalent carbon clusters formed by the condensation of liquid droplets, including: (i) standard fullerenes and onion-like structures, (ii) clusters showing extremely complex surfaces with both positive and negative curvatures and (iii) complex endohedral structures. In this work we offer a thorough structural characterization of the above systems, as well as an attempt to correlate the resulting structure to the actual protocol of growth. The IR and Raman responses of some exotic linear carbon structures have been further investigated, finding good agreement with experimental evidence of carbinoid structures in cluster-assembled films. Towards the aim of fully understanding the process of cluster-to-cluster coalescence dynamics, we further simulated an aerosol of amorphous carbon clusters at controlled temperatures. Various annealing temperatures and times have been observed, identifying different pathways for cluster ripening, ranging from simple coalescence to extensive reconstruction.

Histomorphometric assessment of bone necrosis produced by two cryosurgery protocols using liquid nitrogen: an experimental study on rat femurs.

PubMed

Costa, Fábio Wildson Gurgel; Brito, Gerly Anne de Castro; Pessoa, Rosana Maria Andrade; Studart-Soares, Eduardo Costa

2011-01-01

The aim of this study was to evaluate the effects of liquid nitrogen cryosurgery on the femoral diaphysis of rats. The femoral diaphyses of 42 Wistar rats were exposed to three local and sequential applications of liquid nitrogen for 1 or 2 min, intercalated with periods of 5 min of passive thawing. The animals were sacrificed after 1, 2, 4 and 12 weeks and the specimens obtained were processed and analyzed histomorphometrically. The depth and extent of peak bone necrosis were 124.509 µm and 2087.094 µm for the 1-min protocol, respectively, and 436.424 µm and 12046.426 µm for the 2-min protocol. Peak necrosis was observed in the second experimental week with both cryotherapy protocols. The present results indicate that the 2-min protocol produced more marked bone necrosis than the 1-min protocol. Although our results cannot be entirely extrapolated to clinical practice, they contribute to the understanding of the behavior of bone tissue submitted to different cycles of liquid nitrogen freezing and may serve as a basis for new studies.

Simulation-based Randomized Comparative Assessment of Out-of-Hospital Cardiac Arrest Resuscitation Bundle Completion by Emergency Medical Service Teams Using Standard Life Support or an Experimental Automation-assisted Approach.

PubMed

Choi, Bryan; Asselin, Nicholas; Pettit, Catherine C; Dannecker, Max; Machan, Jason T; Merck, Derek L; Merck, Lisa H; Suner, Selim; Williams, Kenneth A; Jay, Gregory D; Kobayashi, Leo

2016-12-01

Effective resuscitation of out-of-hospital cardiac arrest (OHCA) patients is challenging. Alternative resuscitative approaches using electromechanical adjuncts may improve provider performance. Investigators applied simulation to study the effect of an experimental automation-assisted, goal-directed OHCA management protocol on EMS providers' resuscitation performance relative to standard protocols and equipment. Two-provider (emergency medical technicians (EMT)-B and EMT-I/C/P) teams were randomized to control or experimental group. Each team engaged in 3 simulations: baseline simulation (standard roles); repeat simulation (standard roles); and abbreviated repeat simulation (reversed roles, i.e., basic life support provider performing ALS tasks). Control teams used standard OHCA protocols and equipment (with high-performance cardiopulmonary resuscitation training intervention); for second and third simulations, experimental teams performed chest compression, defibrillation, airway, pulmonary ventilation, vascular access, medication, and transport tasks with goal-directed protocol and resuscitation-automating devices. Videorecorders and simulator logs collected resuscitation data. Ten control and 10 experimental teams comprised 20 EMT-B's; 1 EMT-I, 8 EMT-C's, and 11 EMT-P's; study groups were not fully matched. Both groups suboptimally performed chest compressions and ventilations at baseline. For their second simulations, control teams performed similarly except for reduced on-scene time, and experimental teams improved their chest compressions (P=0.03), pulmonary ventilations (P<0.01), and medication administration (P=0.02); changes in their performance of chest compression, defibrillation, airway, and transport tasks did not attain significance against control teams' changes. Experimental teams maintained performance improvements during reversed-role simulations. Simulation-based investigation into OHCA resuscitation revealed considerable variability and improvable deficiencies in small EMS teams. Goal-directed, automation-assisted OHCA management augmented select resuscitation bundle element performance without comprehensive improvement.

Biodistribution of the boron carriers boronophenylalanine (BPA) and/or decahydrodecaborate (GB-10) for Boron Neutron Capture Therapy (BNCT) in an experimental model of lung metastases.

PubMed

Trivillin, V A; Garabalino, M A; Colombo, L L; González, S J; Farías, R O; Monti Hughes, A; Pozzi, E C C; Bortolussi, S; Altieri, S; Itoiz, M E; Aromando, R F; Nigg, D W; Schwint, A E

2014-06-01

BNCT was proposed for the treatment of diffuse, non-resectable tumors in the lung. We performed boron biodistribution studies with 5 administration protocols employing the boron carriers BPA and/or GB-10 in an experimental model of disseminated lung metastases in rats. All 5 protocols were non-toxic and showed preferential tumor boron uptake versus lung. Absolute tumor boron concentration values were therapeutically useful (25-76ppm) for 3 protocols. Dosimetric calculations indicate that BNCT at RA-3 would be potentially therapeutic without exceeding radiotolerance in the lung. © 2013 Published by Elsevier Ltd.

Biodistribution of the boron carriers boronophenylalanine (BPA) and/or decahydrodecaborate (GB-10) for Boron Neutron Capture Therapy (BNCT) in an experimental model of lung metastases

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

D.W. Nigg; Various Others

BNCT was proposed for the treatment of diffuse, non-resectable tumors in the lung. We performed boron biodistribution studies with 5 administration protocols employing the boron carriers BPA and/or GB-10 in an experimental model of disseminated lung metastases in rats. All 5 protocols were non-toxic and showed preferential tumor boron uptake versus lung. Absolute tumor boron concentration values were therapeutically useful (25–76 ppm) for 3 protocols. Dosimetric calculations indicate that BNCT at RA-3 would be potentially therapeutic without exceeding radiotolerance in the lung.

One for all: A standardized protocol for ex vivo culture of limbal, conjunctival and oral mucosal epithelial cells into corneal lineage.

PubMed

Dhamodaran, Kamesh; Subramani, Murali; Matalia, Himanshu; Jayadev, Chaitra; Shetty, Rohit; Das, Debashish

2016-04-01

Autologous transplantation of ex vivo cultured cells the treatment of choice for patients with limbal stem cell deficiency. The most commonly used cell sources for transplantation limbal, conjunctival or oral mucosal tissue. Protocols vary for culturing each tissue type, and there are no comparative studies on transplantation outcomes using these different culture techniques. To overcome this limitation, we devised a simple protocol that can uniformly promote growth and differentiation of cells from a limbal, conjunctival or oral mucosal biopsy into the corneal lineage. Biopsies were cultured as explants on de-epithelialized human amniotic membrane in the presence of recombinant epidermal growth factor and insulin. Cultured cells were characterized using immunohistochemistry and quantitative reverse transcriptase polymerase chain reaction for stem/progenitor markers (ABCG2 and P63α) and differentiation markers (CK3, CK12, CK4, CK13, CK15 and CONNEXIN 43). Fluorescence-activated cell sorter analysis was performed for ABCG2. The results revealed that cells of all three biopsies differentiated into the corneal lineage. Positivity of CK3/12, CK4, CK12 and CONNEXIN 43 immunostaining and the relative mRNA expression of CK3, CK4, CK12, CK13, CK15 and CONNEXIN 43 could be detected in the cultured biopsies. Unlike tissue-specific protocols, our protocol can unequivocally promote differentiation of cells from a limbal, conjunctival or oral mucosal biopsy into the corneal lineage. This simple standardized protocol can be adapted for ocular surface reconstruction using stem cell transplantation. Copyright © 2016 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

Password-only authenticated three-party key exchange proven secure against insider dictionary attacks.

PubMed

Nam, Junghyun; Choo, Kim-Kwang Raymond; Paik, Juryon; Won, Dongho

2014-01-01

While a number of protocols for password-only authenticated key exchange (PAKE) in the 3-party setting have been proposed, it still remains a challenging task to prove the security of a 3-party PAKE protocol against insider dictionary attacks. To the best of our knowledge, there is no 3-party PAKE protocol that carries a formal proof, or even definition, of security against insider dictionary attacks. In this paper, we present the first 3-party PAKE protocol proven secure against both online and offline dictionary attacks as well as insider and outsider dictionary attacks. Our construct can be viewed as a protocol compiler that transforms any 2-party PAKE protocol into a 3-party PAKE protocol with 2 additional rounds of communication. We also present a simple and intuitive approach of formally modelling dictionary attacks in the password-only 3-party setting, which significantly reduces the complexity of proving the security of 3-party PAKE protocols against dictionary attacks. In addition, we investigate the security of the well-known 3-party PAKE protocol, called GPAKE, due to Abdalla et al. (2005, 2006), and demonstrate that the security of GPAKE against online dictionary attacks depends heavily on the composition of its two building blocks, namely a 2-party PAKE protocol and a 3-party key distribution protocol.

M13-Tailed Simple Sequence Repeat (SSR) Markers in Studies of Genetic Diversity and Population Structure of Common Oat Germplasm.

PubMed

Onyśk, Agnieszka; Boczkowska, Maja

2017-01-01

Simple Sequence Repeat (SSR) markers are one of the most frequently used molecular markers in studies of crop diversity and population structure. This is due to their uniform distribution in the genome, the high polymorphism, reproducibility, and codominant character. Additional advantages are the possibility of automatic analysis and simple interpretation of the results. The M13 tagged PCR reaction significantly reduces the costs of analysis by the automatic genetic analyzers. Here, we also disclose a short protocol of SSR data analysis.

Modeling Collective Animal Behavior with a Cognitive Perspective: A Methodological Framework

PubMed Central

Weitz, Sebastian; Blanco, Stéphane; Fournier, Richard; Gautrais, Jacques; Jost, Christian; Theraulaz, Guy

2012-01-01

The last decades have seen an increasing interest in modeling collective animal behavior. Some studies try to reproduce as accurately as possible the collective dynamics and patterns observed in several animal groups with biologically plausible, individual behavioral rules. The objective is then essentially to demonstrate that the observed collective features may be the result of self-organizing processes involving quite simple individual behaviors. Other studies concentrate on the objective of establishing or enriching links between collective behavior researches and cognitive or physiological ones, which then requires that each individual rule be carefully validated. Here we discuss the methodological consequences of this additional requirement. Using the example of corpse clustering in ants, we first illustrate that it may be impossible to discriminate among alternative individual rules by considering only observational data collected at the group level. Six individual behavioral models are described: They are clearly distinct in terms of individual behaviors, they all reproduce satisfactorily the collective dynamics and distribution patterns observed in experiments, and we show theoretically that it is strictly impossible to discriminate two of these models even in the limit of an infinite amount of data whatever the accuracy level. A set of methodological steps are then listed and discussed as practical ways to partially overcome this problem. They involve complementary experimental protocols specifically designed to address the behavioral rules successively, conserving group-level data for the overall model validation. In this context, we highlight the importance of maintaining a sharp distinction between model enunciation, with explicit references to validated biological concepts, and formal translation of these concepts in terms of quantitative state variables and fittable functional dependences. Illustrative examples are provided of the benefits expected during the often long and difficult process of refining a behavioral model, designing adapted experimental protocols and inversing model parameters. PMID:22761685

Modeling collective animal behavior with a cognitive perspective: a methodological framework.

PubMed

Weitz, Sebastian; Blanco, Stéphane; Fournier, Richard; Gautrais, Jacques; Jost, Christian; Theraulaz, Guy

2012-01-01

The last decades have seen an increasing interest in modeling collective animal behavior. Some studies try to reproduce as accurately as possible the collective dynamics and patterns observed in several animal groups with biologically plausible, individual behavioral rules. The objective is then essentially to demonstrate that the observed collective features may be the result of self-organizing processes involving quite simple individual behaviors. Other studies concentrate on the objective of establishing or enriching links between collective behavior researches and cognitive or physiological ones, which then requires that each individual rule be carefully validated. Here we discuss the methodological consequences of this additional requirement. Using the example of corpse clustering in ants, we first illustrate that it may be impossible to discriminate among alternative individual rules by considering only observational data collected at the group level. Six individual behavioral models are described: They are clearly distinct in terms of individual behaviors, they all reproduce satisfactorily the collective dynamics and distribution patterns observed in experiments, and we show theoretically that it is strictly impossible to discriminate two of these models even in the limit of an infinite amount of data whatever the accuracy level. A set of methodological steps are then listed and discussed as practical ways to partially overcome this problem. They involve complementary experimental protocols specifically designed to address the behavioral rules successively, conserving group-level data for the overall model validation. In this context, we highlight the importance of maintaining a sharp distinction between model enunciation, with explicit references to validated biological concepts, and formal translation of these concepts in terms of quantitative state variables and fittable functional dependences. Illustrative examples are provided of the benefits expected during the often long and difficult process of refining a behavioral model, designing adapted experimental protocols and inversing model parameters.

Exploiting the acylating nature of the imide-Ugi intermediate: a straightforward synthesis of tetrahydro-1,4-benzodiazepin-2-ones.

PubMed

Mossetti, Riccardo; Saggiorato, Dèsirèe; Tron, Gian Cesare

2011-12-16

We describe a simple and novel protocol for the synthesis of tetrahydro-1,4-benzodiazepin-2-ones with three points of diversity, exploiting the acylating properties of the recently rediscovered Ugi-imide. The final compounds can be easily prepared in three synthetic steps using a multicomponent reaction, a Staudinger reduction, and an acylative protocol, with good to excellent yields for each synthetic step.

A Framework for Building and Reasoning with Adaptive and Interoperable PMESII Models

DTIC Science & Technology

2007-11-01

Description Logic SOA Service Oriented Architecture SPARQL Simple Protocol And RDF Query Language SQL Standard Query Language SROM Stability and...another by providing a more expressive ontological structure for one of the models, e.g., semantic networks can be mapped to first- order logical...Pellet is an open-source reasoner that works with OWL-DL. It accepts the SPARQL protocol and RDF query language ( SPARQL ) and provides a Java API to

Health surveillance under adverse ergonomics conditions – validity of a screening method adapted for the occupational health service

PubMed Central

Jonker, Dirk; Gustafsson, Ewa; Rolander, Bo; Arvidsson, Inger; Nordander, Catarina

2015-01-01

A new health surveillance protocol for work-related upper-extremity musculoskeletal disorders has been validated by comparing the results with a reference protocol. The studied protocol, Health Surveillance in Adverse Ergonomics Conditions (HECO), is a new version of the reference protocol modified for application in the Occupational Health Service (OHS). The HECO protocol contains both a screening part and a diagnosing part. Sixty-three employees were examined. The screening in HECO did not miss any diagnosis found when using the reference protocol, but in comparison to the reference protocol considerable time savings could be achieved. Fair to good agreement between the protocols was obtained for one or more diagnoses in neck/shoulders (86%, k = 0.62) and elbow/hands (84%, k = 0.49). Therefore, the results obtained using the HECO protocol can be compared with a reference material collected with the reference protocol, and thus provide information of the magnitude of disorders in an examined work group. Practitioner Summary: The HECO protocol is a relatively simple physical examination protocol for identification of musculoskeletal disorders in the neck and upper extremities. The protocol is a reliable and cost-effective tool for the OHS to use for occupational health surveillance in order to detect workplaces at high risk for developing musculoskeletal disorders. PMID:25761380

Guidelines for experimental design protocol and validation procedure for the measurement of heat resistance of microorganisms in milk.

PubMed

Condron, Robin; Farrokh, Choreh; Jordan, Kieran; McClure, Peter; Ross, Tom; Cerf, Olivier

2015-01-02

Studies on the heat resistance of dairy pathogens are a vital part of assessing the safety of dairy products. However, harmonized methodology for the study of heat resistance of food pathogens is lacking, even though there is a need for such harmonized experimental design protocols and for harmonized validation procedures for heat treatment studies. Such an approach is of particular importance to allow international agreement on appropriate risk management of emerging potential hazards for human and animal health. This paper is working toward establishment of a harmonized protocol for the study of the heat resistance of pathogens, identifying critical issues for establishment of internationally agreed protocols, including a harmonized framework for reporting and interpretation of heat inactivation studies of potentially pathogenic microorganisms. Copyright © 2014 Elsevier B.V. All rights reserved.

Defining standardized protocols for determining the efficacy of a postmilking teat disinfectant following experimental exposure of teats to mastitis pathogens.

PubMed

Schukken, Y H; Rauch, B J; Morelli, J

2013-04-01

The objective of this paper was to define standardized protocols for determining the efficacy of a postmilking teat disinfectant following experimental exposure of teats to both Staphylococcus aureus and Streptococcus agalactiae. The standardized protocols describe the selection of cows and herds and define the critical points in performing experimental exposure, performing bacterial culture, evaluating the culture results, and finally performing statistical analyses and reporting of the results. The protocols define both negative control and positive control trials. For negative control trials, the protocol states that an efficacy of reducing new intramammary infections (IMI) of at least 40% is required for a teat disinfectant to be considered effective. For positive control trials, noninferiority to a control disinfectant with a published efficacy of reducing new IMI of at least 70% is required. Sample sizes for both negative and positive control trials are calculated. Positive control trials are expected to require a large trial size. Statistical analysis methods are defined and, in the proposed methods, the rate of IMI may be analyzed using generalized linear mixed models. The efficacy of the test product can be evaluated while controlling for important covariates and confounders in the trial. Finally, standards for reporting are defined and reporting considerations are discussed. The use of the defined protocol is shown through presentation of the results of a recent trial of a test product against a negative control. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

An operational open-end file transfer protocol for mobile satellite communications

NASA Technical Reports Server (NTRS)

Wang, Charles; Cheng, Unjeng; Yan, Tsun-Yee

1988-01-01

This paper describes an operational open-end file transfer protocol which includes the connecting procedure, data transfer, and relinquishment procedure for mobile satellite communications. The protocol makes use of the frame level and packet level formats of the X.25 standard for the data link layer and network layer, respectively. The structure of a testbed for experimental simulation of this protocol over a mobile fading channel is also introduced.

Reliability of Vibrating Mesh Technology.

PubMed

Gowda, Ashwin A; Cuccia, Ann D; Smaldone, Gerald C

2017-01-01

For delivery of inhaled aerosols, vibrating mesh systems are more efficient than jet nebulizers are and do not require added gas flow. We assessed the reliability of a vibrating mesh nebulizer (Aerogen Solo, Aerogen Ltd, Galway Ireland) suitable for use in mechanical ventilation. An initial observational study was performed with 6 nebulizers to determine run time and efficiency using normal saline and distilled water. Nebulizers were run until cessation of aerosol production was noted, with residual volume and run time recorded. Three controllers were used to assess the impact of the controller on nebulizer function. Following the observational study, a more detailed experimental protocol was performed using 20 nebulizers. For this analysis, 2 controllers were used, and time to cessation of aerosol production was noted. Gravimetric techniques were used to measure residual volume. Total nebulization time and residual volume were recorded. Failure was defined as premature cessation of aerosol production represented by residual volume of > 10% of the nebulizer charge. In the initial observational protocol, an unexpected sporadic failure rate was noted of 25% in 55 experimental runs. In the experimental protocol, a failure rate was noted of 30% in 40 experimental runs. Failed runs in the experimental protocol exhibited a wide range of retained volume averaging ± SD 36 ± 21.3% compared with 3.2 ± 1.5% (P = .001) in successful runs. Small but significant differences existed in nebulization time between controllers. Aerogen Solo nebulization was often randomly interrupted with a wide range of retained volumes. Copyright © 2017 by Daedalus Enterprises.

Direction based Hazard Routing Protocol (DHRP) for disseminating road hazard information using road side infrastructures in VANETs.

PubMed

Berlin, M A; Anand, Sheila

2014-01-01

This paper presents Direction based Hazard Routing Protocol (DHRP) for disseminating information about fixed road hazards such as road blocks, tree fall, boulders on road, snow pile up, landslide, road maintenance work and other obstacles to the vehicles approaching the hazardous location. The proposed work focuses on dissemination of hazard messages on highways with sparse traffic. The vehicle coming across the hazard would report the presence of the hazard. It is proposed to use Road Side fixed infrastructure Units for reliable and timely delivery of hazard messages to vehicles. The vehicles can then take appropriate safety action to avoid the hazardous location. The proposed protocol has been implemented and tested using SUMO simulator to generate road traffic and NS 2.33 network simulator to analyze the performance of DHRP. The performance of the proposed protocol was also compared with simple flooding protocol and the results are presented.

Study on Cloud Security Based on Trust Spanning Tree Protocol

NASA Astrophysics Data System (ADS)

Lai, Yingxu; Liu, Zenghui; Pan, Qiuyue; Liu, Jing

2015-09-01

Attacks executed on Spanning Tree Protocol (STP) expose the weakness of link layer protocols and put the higher layers in jeopardy. Although the problems have been studied for many years and various solutions have been proposed, many security issues remain. To enhance the security and credibility of layer-2 network, we propose a trust-based spanning tree protocol aiming at achieving a higher credibility of LAN switch with a simple and lightweight authentication mechanism. If correctly implemented in each trusted switch, the authentication of trust-based STP can guarantee the credibility of topology information that is announced to other switch in the LAN. To verify the enforcement of the trusted protocol, we present a new trust evaluation method of the STP using a specification-based state model. We implement a prototype of trust-based STP to investigate its practicality. Experiment shows that the trusted protocol can achieve security goals and effectively avoid STP attacks with a lower computation overhead and good convergence performance.

Practical quantum appointment scheduling

NASA Astrophysics Data System (ADS)

Touchette, Dave; Lovitz, Benjamin; Lütkenhaus, Norbert

2018-04-01

We propose a protocol based on coherent states and linear optics operations for solving the appointment-scheduling problem. Our main protocol leaks strictly less information about each party's input than the optimal classical protocol, even when considering experimental errors. Along with the ability to generate constant-amplitude coherent states over two modes, this protocol requires the ability to transfer these modes back-and-forth between the two parties multiple times with very low losses. The implementation requirements are thus still challenging. Along the way, we develop tools to study quantum information cost of interactive protocols in the finite regime.

Virtual Reality for Research in Social Neuroscience

PubMed Central

Parsons, Thomas D.; Gaggioli, Andrea; Riva, Giuseppe

2017-01-01

The emergence of social neuroscience has significantly advanced our understanding of the relationship that exists between social processes and their neurobiological underpinnings. Social neuroscience research often involves the use of simple and static stimuli lacking many of the potentially important aspects of real world activities and social interactions. Whilst this research has merit, there is a growing interest in the presentation of dynamic stimuli in a manner that allows researchers to assess the integrative processes carried out by perceivers over time. Herein, we discuss the potential of virtual reality for enhancing ecological validity while maintaining experimental control in social neuroscience research. Virtual reality is a technology that allows for the creation of fully interactive, three-dimensional computerized models of social situations that can be fully controlled by the experimenter. Furthermore, the introduction of interactive virtual characters—either driven by a human or by a computer—allows the researcher to test, in a systematic and independent manner, the effects of various social cues. We first introduce key technical features and concepts related to virtual reality. Next, we discuss the potential of this technology for enhancing social neuroscience protocols, drawing on illustrative experiments from the literature. PMID:28420150

NLSdb-major update for database of nuclear localization signals and nuclear export signals.

PubMed

Bernhofer, Michael; Goldberg, Tatyana; Wolf, Silvana; Ahmed, Mohamed; Zaugg, Julian; Boden, Mikael; Rost, Burkhard

2018-01-04

NLSdb is a database collecting nuclear export signals (NES) and nuclear localization signals (NLS) along with experimentally annotated nuclear and non-nuclear proteins. NES and NLS are short sequence motifs related to protein transport out of and into the nucleus. The updated NLSdb now contains 2253 NLS and introduces 398 NES. The potential sets of novel NES and NLS have been generated by a simple 'in silico mutagenesis' protocol. We started with motifs annotated by experiments. In step 1, we increased specificity such that no known non-nuclear protein matched the refined motif. In step 2, we increased the sensitivity trying to match several different families with a motif. We then iterated over steps 1 and 2. The final set of 2253 NLS motifs matched 35% of 8421 experimentally verified nuclear proteins (up from 21% for the previous version) and none of 18 278 non-nuclear proteins. We updated the web interface providing multiple options to search protein sequences for NES and NLS motifs, and to evaluate your own signal sequences. NLSdb can be accessed via Rostlab services at: https://rostlab.org/services/nlsdb/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Fragmentation modeling of a resin bonded sand

NASA Astrophysics Data System (ADS)

Hilth, William; Ryckelynck, David

2017-06-01

Cemented sands exhibit a complex mechanical behavior that can lead to sophisticated models, with numerous parameters without real physical meaning. However, using a rather simple generalized critical state bonded soil model has proven to be a relevant compromise between an easy calibration and good results. The constitutive model formulation considers a non-associated elasto-plastic formulation within the critical state framework. The calibration procedure, using standard laboratory tests, is complemented by the study of an uniaxial compression test observed by tomography. Using finite elements simulations, this test is simulated considering a non-homogeneous 3D media. The tomography of compression sample gives access to 3D displacement fields by using image correlation techniques. Unfortunately these fields have missing experimental data because of the low resolution of correlations for low displacement magnitudes. We propose a recovery method that reconstructs 3D full displacement fields and 2D boundary displacement fields. These fields are mandatory for the calibration of the constitutive parameters by using 3D finite element simulations. The proposed recovery technique is based on a singular value decomposition of available experimental data. This calibration protocol enables an accurate prediction of the fragmentation of the specimen.

Virtual Reality for Research in Social Neuroscience.

PubMed

Parsons, Thomas D; Gaggioli, Andrea; Riva, Giuseppe

2017-04-16

The emergence of social neuroscience has significantly advanced our understanding of the relationship that exists between social processes and their neurobiological underpinnings. Social neuroscience research often involves the use of simple and static stimuli lacking many of the potentially important aspects of real world activities and social interactions. Whilst this research has merit, there is a growing interest in the presentation of dynamic stimuli in a manner that allows researchers to assess the integrative processes carried out by perceivers over time. Herein, we discuss the potential of virtual reality for enhancing ecological validity while maintaining experimental control in social neuroscience research. Virtual reality is a technology that allows for the creation of fully interactive, three-dimensional computerized models of social situations that can be fully controlled by the experimenter. Furthermore, the introduction of interactive virtual characters-either driven by a human or by a computer-allows the researcher to test, in a systematic and independent manner, the effects of various social cues. We first introduce key technical features and concepts related to virtual reality. Next, we discuss the potential of this technology for enhancing social neuroscience protocols, drawing on illustrative experiments from the literature.

Design optimization of a brush turbine with a cleaner/water based solution

NASA Technical Reports Server (NTRS)

Kim, Rhyn H.

1994-01-01

Recently, a fluid turbine which has a brush attached to it has been designed and tested with water as fluid. The purpose of the turbine-brush is to clean up fouling in a tube. The Montreal Protocol prohibits the use of CFC products from refrigeration industry or from industry in general as a cleanser in 1996. Alternatives for the cleansers, devices or a combination of alternative devices with a cleanser should be found. One of the methods is to develop a device which cleans fouling with a cleaning medium. In this paper, we describe a turbine connected with a brush. However, the turbine with the brush should be simple and easy to install. This device is a combined small liquid turbine with a brush. The turbine is activated by the liquid flowing through the tube. Then the turbine turns the brush cleaning fouling along the tube. Based on the energy conservation and the Bernoulli equation along with an empirical relationship of drag force obtained from an experimental apparatus, a relationship of the rotational speed, the number of blades, and geometric variables of the turbine-brush was obtained. The predicted rotational speeds were compared with the experimental observations. Further work was recommended for improvements.

Optimal protocols for slowly driven quantum systems.

PubMed

Zulkowski, Patrick R; DeWeese, Michael R

2015-09-01

The design of efficient quantum information processing will rely on optimal nonequilibrium transitions of driven quantum systems. Building on a recently developed geometric framework for computing optimal protocols for classical systems driven in finite time, we construct a general framework for optimizing the average information entropy for driven quantum systems. Geodesics on the parameter manifold endowed with a positive semidefinite metric correspond to protocols that minimize the average information entropy production in finite time. We use this framework to explicitly compute the optimal entropy production for a simple two-state quantum system coupled to a heat bath of bosonic oscillators, which has applications to quantum annealing.

Noisy processing and distillation of private quantum States.

PubMed

Renes, Joseph M; Smith, Graeme

2007-01-12

We provide a simple security proof for prepare and measure quantum key distribution protocols employing noisy processing and one-way postprocessing of the key. This is achieved by showing that the security of such a protocol is equivalent to that of an associated key distribution protocol in which, instead of the usual maximally entangled states, a more general private state is distilled. In addition to a more general target state, the usual entanglement distillation tools are employed (in particular, Calderbank-Shor-Steane-like codes), with the crucial difference that noisy processing allows some phase errors to be left uncorrected without compromising the privacy of the key.

Simple and effective exercise design for assessing in vivo mitochondrial function in clinical applications using (31)P magnetic resonance spectroscopy.

PubMed

Sleigh, Alison; Lupson, Victoria; Thankamony, Ajay; Dunger, David B; Savage, David B; Carpenter, T Adrian; Kemp, Graham J

2016-01-11

The growing recognition of diseases associated with dysfunction of mitochondria poses an urgent need for simple measures of mitochondrial function. Assessment of the kinetics of replenishment of the phosphocreatine pool after exercise using (31)P magnetic resonance spectroscopy can provide an in vivo measure of mitochondrial function; however, the wider application of this technique appears limited by complex or expensive MR-compatible exercise equipment and protocols not easily tolerated by frail participants or those with reduced mental capacity. Here we describe a novel in-scanner exercise method which is patient-focused, inexpensive, remarkably simple and highly portable. The device exploits an MR-compatible high-density material (BaSO4) to form a weight which is attached directly to the ankle, and a one-minute dynamic knee extension protocol produced highly reproducible measurements of post-exercise PCr recovery kinetics in both healthy subjects and patients. As sophisticated exercise equipment is unnecessary for this measurement, our extremely simple design provides an effective and easy-to-implement apparatus that is readily translatable across sites. Its design, being tailored to the needs of the patient, makes it particularly well suited to clinical applications, and we argue the potential of this method for investigating in vivo mitochondrial function in new cohorts of growing clinical interest.

Analysis of pre-service physics teacher skills designing simple physics experiments based technology

NASA Astrophysics Data System (ADS)

Susilawati; Huda, C.; Kurniawan, W.; Masturi; Khoiri, N.

2018-03-01

Pre-service physics teacher skill in designing simple experiment set is very important in adding understanding of student concept and practicing scientific skill in laboratory. This study describes the skills of physics students in designing simple experiments based technologicall. The experimental design stages include simple tool design and sensor modification. The research method used is descriptive method with the number of research samples 25 students and 5 variations of simple physics experimental design. Based on the results of interviews and observations obtained the results of pre-service physics teacher skill analysis in designing simple experimental physics charged technology is good. Based on observation result, pre-service physics teacher skill in designing simple experiment is good while modification and sensor application are still not good. This suggests that pre-service physics teacher still need a lot of practice and do experiments in designing physics experiments using sensor modifications. Based on the interview result, it is found that students have high enough motivation to perform laboratory activities actively and students have high curiosity to be skilled at making simple practicum tool for physics experiment.

Firewall Traversal for CORBA Applications Using an Implementation of Bidirectional IIOP in MICO

NASA Technical Reports Server (NTRS)

Griffin, Robert I.; Lopez, Isaac (Technical Monitor)

2002-01-01

The Object Management Group (OMG) has added specifications to the General Inter-ORB Protocol (GIOP 1.2), specifically the Internet Inter-ORB Protocol (IIOP 1.2), that allow servers and clients on opposing sides of a firewall to reverse roles and still communicate freely. This addition to the GIOP specifications is referred to as Bidirectional GIOP. The implementation of these specifications as applied to communication over TCP/IP connections is referred to as 'Bidirectional Internet Inter-ORB Protocol' or BiDirIIOP. This paper details the implementation and testing of the BiDirIIOP Specification in an open source ORB, MICO, that did not previously support Bidirectional GIOP. It also provides simple contextual information and a description of the OMG GIOP/IIOP messaging protocols.

Two-dimensional distributed-phase-reference protocol for quantum key distribution

NASA Astrophysics Data System (ADS)

Bacco, Davide; Christensen, Jesper Bjerge; Castaneda, Mario A. Usuga; Ding, Yunhong; Forchhammer, Søren; Rottwitt, Karsten; Oxenløwe, Leif Katsuo

2016-12-01

Quantum key distribution (QKD) and quantum communication enable the secure exchange of information between remote parties. Currently, the distributed-phase-reference (DPR) protocols, which are based on weak coherent pulses, are among the most practical solutions for long-range QKD. During the last 10 years, long-distance fiber-based DPR systems have been successfully demonstrated, although fundamental obstacles such as intrinsic channel losses limit their performance. Here, we introduce the first two-dimensional DPR-QKD protocol in which information is encoded in the time and phase of weak coherent pulses. The ability of extracting two bits of information per detection event, enables a higher secret key rate in specific realistic network scenarios. Moreover, despite the use of more dimensions, the proposed protocol remains simple, practical, and fully integrable.

Two-dimensional distributed-phase-reference protocol for quantum key distribution.

PubMed

Bacco, Davide; Christensen, Jesper Bjerge; Castaneda, Mario A Usuga; Ding, Yunhong; Forchhammer, Søren; Rottwitt, Karsten; Oxenløwe, Leif Katsuo

2016-12-22

Quantum key distribution (QKD) and quantum communication enable the secure exchange of information between remote parties. Currently, the distributed-phase-reference (DPR) protocols, which are based on weak coherent pulses, are among the most practical solutions for long-range QKD. During the last 10 years, long-distance fiber-based DPR systems have been successfully demonstrated, although fundamental obstacles such as intrinsic channel losses limit their performance. Here, we introduce the first two-dimensional DPR-QKD protocol in which information is encoded in the time and phase of weak coherent pulses. The ability of extracting two bits of information per detection event, enables a higher secret key rate in specific realistic network scenarios. Moreover, despite the use of more dimensions, the proposed protocol remains simple, practical, and fully integrable.

Two-dimensional distributed-phase-reference protocol for quantum key distribution

PubMed Central

Bacco, Davide; Christensen, Jesper Bjerge; Castaneda, Mario A. Usuga; Ding, Yunhong; Forchhammer, Søren; Rottwitt, Karsten; Oxenløwe, Leif Katsuo

2016-01-01

Quantum key distribution (QKD) and quantum communication enable the secure exchange of information between remote parties. Currently, the distributed-phase-reference (DPR) protocols, which are based on weak coherent pulses, are among the most practical solutions for long-range QKD. During the last 10 years, long-distance fiber-based DPR systems have been successfully demonstrated, although fundamental obstacles such as intrinsic channel losses limit their performance. Here, we introduce the first two-dimensional DPR-QKD protocol in which information is encoded in the time and phase of weak coherent pulses. The ability of extracting two bits of information per detection event, enables a higher secret key rate in specific realistic network scenarios. Moreover, despite the use of more dimensions, the proposed protocol remains simple, practical, and fully integrable. PMID:28004821

SIMPL Systems, or: Can We Design Cryptographic Hardware without Secret Key Information?

NASA Astrophysics Data System (ADS)

Rührmair, Ulrich

This paper discusses a new cryptographic primitive termed SIMPL system. Roughly speaking, a SIMPL system is a special type of Physical Unclonable Function (PUF) which possesses a binary description that allows its (slow) public simulation and prediction. Besides this public key like functionality, SIMPL systems have another advantage: No secret information is, or needs to be, contained in SIMPL systems in order to enable cryptographic protocols - neither in the form of a standard binary key, nor as secret information hidden in random, analog features, as it is the case for PUFs. The cryptographic security of SIMPLs instead rests on (i) a physical assumption on their unclonability, and (ii) a computational assumption regarding the complexity of simulating their output. This novel property makes SIMPL systems potentially immune against many known hardware and software attacks, including malware, side channel, invasive, or modeling attacks.

Development, implementation, and experimentation of parametric routing protocol for sensor networks

NASA Astrophysics Data System (ADS)

Nassr, Matthew S.; Jun, Jangeun; Eidenbenz, Stephan J.; Frigo, Janette R.; Hansson, Anders A.; Mielke, Angela M.; Smith, Mark C.

2006-09-01

The development of a scalable and reliable routing protocol for sensor networks is traced from a theoretical beginning to positive simulation results to the end of verification experiments in large and heavily loaded networks. Design decisions and explanations as well as implementation hurdles are presented to give a complete picture of protocol development. Additional software and hardware is required to accurately test the performance of our protocol in field experiments. In addition, the developed protocol is tested in TinyOS on Mica2 motes against well-established routing protocols frequently used in sensor networks. Our protocol proves to outperform the standard (MINTRoute) and the trivial (Gossip) in a variety of different scenarios.

Analysis of OPACITY and PLAID Protocols for Contactless Smart Cards

DTIC Science & Technology

2012-09-01

9 3. Access Control ........................................................................ 9 E . THREATS AND...Synchronization .............................. 23 c. Simple Integration and Interoperability ..................... 24 E . MODES OF OPERATION...Interoperability ..................... 47 E . MODES OF OPERATIONS ................................................................ 47 F. SUGGESTED KEY

The impact of posture and prolonged cyclic compressive loading on vertebral joint mechanics.

PubMed

Gooyers, Chad E; McMillan, Robert D; Howarth, Samuel J; Callaghan, Jack P

2012-08-01

An in vitro biomechanics investigation exposing porcine functional spinal units (FSUs) to submaximal cyclic or static compressive forces while in a flexed, neutral, or extended posture. To investigate the combined effect of cyclically applied compressive force (e.g., vibration) and postural deviation on intervertebral joint mechanics. Independently, prolonged vibration exposure and non-neutral postures are known risk factors for development of low back pain and injury. However, there is limited basic scientific evidence to explain how the risk of low back injury from vibration exposure is modified by other mechanical factors. This work examined the influence of static postural deviation on vertebral joint height loss and compressive stiffness under cyclically applied compressive force. Forty-eight FSUs, consisting of 2 adjacent vertebrae, ligaments, and the intervening intervertebral disc were included in the study. Each specimen was randomized to 1 of 3 experimental posture conditions (neutral, flexed, or extended) and assigned to 1 of 2 loading protocols, consisting of (1) cyclic (1500 ± 1200 N applied at 5 Hz using a sinusoidal waveform, resulting in 0.2 g rms acceleration) or (2) 1500 N of static compressive force. RESULTS.: As expected, FSU height loss followed a typical first-order response in both the static and cyclic loading protocols, with the majority (~50%) of the loss occurring in the first 20 minutes of testing. A significant interaction between posture and loading protocol (P < 0.001) was noted in the magnitude of FSU height loss. Subsequent analysis of simple effects revealed significant differences between cyclic and static loading protocols in both a neutral (P = 0.016) and a flexed posture (P < 0.0001). No significant differences (P = 0.320) were noted between pre/postmeasurements of FSU compressive stiffness. Posture is an important mechanical factor to consider when assessing the risk of injury from cyclic loading to the lumbar spine.

Usefulness of a simple sleep-deprived EEG protocol for epilepsy diagnosis in de novo subjects.

PubMed

Giorgi, Filippo S; Perini, Daria; Maestri, Michelangelo; Guida, Melania; Pizzanelli, Chiara; Caserta, Anna; Iudice, Alfonso; Bonanni, Enrica

2013-11-01

In case series concerning the role of EEG after sleep deprivation (SD-EEG) in epilepsy, patients' features and protocols vary dramatically from one report to another. In this study, we assessed the usefulness of a simple SD-EEG method in well characterized patients. Among the 963 adult subjects submitted to SD-EEG at our Center, in the period 2003-2010, we retrospectively selected for analysis only those: (1) evaluated for suspected epileptic seizures; (2) with a normal/non-specific baseline EEG; (3) still drug-free at the time of SD-EEG; (4) with an MRI analysis; (5) with at least 1 year follow-up. SD-EEG consisted in SD from 2:00 AM and laboratory EEG from 8:00 AM to 10:30 AM. We analyzed epileptic interictal abnormalities (IIAs) and their correlations with patients' features. Epilepsy was confirmed in 131 patients. SD-EEG showed IIAs in 41.2% of all patients with epilepsy, and a 91.1% specificity for epilepsy diagnosis; IIAs types observed during SD-EEG are different in generalized versus focal epilepsies; for focal epilepsies, the IIAs yield in SD-EEG is higher than in second routine EEG. This simple SD-EEG protocol is very useful in de novo patients with suspected seizures. This study sheds new light on the role of SD-EEG in specific epilepsy populations. Copyright © 2013 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Effects of Guided Written Disclosure Protocol on mood states and psychological symptoms among parents of off-therapy acute lymphoblastic leukemia children.

PubMed

Martino, Maria Luisa; Freda, Maria Francesca; Camera, Flavia

2013-06-01

This study assesses the effects of Guided Written Disclosure Protocol on psychological distress in mothers and fathers of off-therapy acute lymphoblastic leukemia children. An experimental group participated in the writing intervention with a control group subject only to test-taking standards. The Symptom Questionnaire and Profile of Mood States were administered at baseline, post-intervention, and follow-up. Guided Written Disclosure Protocol had significant effects on the progressive reduction of anxiety, depression, somatic symptoms, hostility, tension-anxiety, and fatigue-inertia within the experimental group. However, the control group distress levels tended to worsen over time. The mediating role of emotional processing was highlighted.

An Eco-Friendly Improved Protocol for the Synthesis of Bis(3-indolyl)methanes Using Poly(4-vinylpyridinium)hydrogen Sulfate as Efficient, Heterogeneous, and Recyclable Solid Acid Catalyst

PubMed Central

Banothu, Janardhan; Gali, Rajitha; Velpula, Ravibabu; Bavantula, Rajitha; Crooks, Peter A.

2013-01-01

Highly efficient and eco-friendly protocol for the synthesis of bis(3-indolyl)methanes by the electrophilic substitution reaction of indole with aldehydes catalyzed by poly(4-vinylpyridinium)hydrogen sulfate was described. Excellent yields, shorter reaction times, simple work-up procedure, avoiding hazardous organic solvents, and reusability of the catalyst are the most obvious advantages of this method. PMID:24052864

Nonpainful wide-area compression inhibits experimental pain.

PubMed

Honigman, Liat; Bar-Bachar, Ofrit; Yarnitsky, David; Sprecher, Elliot; Granovsky, Yelena

2016-09-01

Compression therapy, a well-recognized treatment for lymphoedema and venous disorders, pressurizes limbs and generates massive non-noxious afferent sensory barrages. The aim of this study was to study whether such afferent activity has an analgesic effect when applied on the lower limbs, hypothesizing that larger compression areas will induce stronger analgesic effects, and whether this effect correlates with conditioned pain modulation (CPM). Thirty young healthy subjects received painful heat and pressure stimuli (47°C for 30 seconds, forearm; 300 kPa for 15 seconds, wrist) before and during 3 compression protocols of either SMALL (up to ankles), MEDIUM (up to knees), or LARGE (up to hips) compression areas. Conditioned pain modulation (heat pain conditioned by noxious cold water) was tested before and after each compression protocol. The LARGE protocol induced more analgesia for heat than the SMALL protocol (P < 0.001). The analgesic effect interacted with gender (P = 0.015). The LARGE protocol was more efficient for females, whereas the MEDIUM protocol was more efficient for males. Pressure pain was reduced by all protocols (P < 0.001) with no differences between protocols and no gender effect. Conditioned pain modulation was more efficient than the compression-induced analgesia. For the LARGE protocol, precompression CPM efficiency positively correlated with compression-induced analgesia. Large body area compression exerts an area-dependent analgesic effect on experimental pain stimuli. The observed correlation with pain inhibition in response to robust non-noxious sensory stimulation may suggest that compression therapy shares similar mechanisms with inhibitory pain modulation assessed through CPM.

Assessment of three AC electroosmotic flow protocols for mixing in microfluidic channel.

PubMed

Chen, Jia-Kun; Weng, Chi-Neng; Yang, Ruey-Jen

2009-05-07

This study performs an experimental investigation into the micromixer capabilities of three different protocols of AC electroosmotic flow (AC EOF), namely capacitive charging (CC), Faradaic charging (FC) and asymmetric polarization (AP). The results reveal that the vortices generated by the FC protocol (the frequency is around 50-350 Hz) are stronger than those induced by the CC protocol (the frequency is higher than 350 Hz), and therefore provide an improved mixing effect. However, in the FC protocol, the frequency of the external AC voltage must be carefully controlled to avoid damaging electrodes as a result of Faradaic reactions. The experimental results indicate that the AP polarization effect (the applied voltage and frequency are V(1) = 1 V(pp) and V(2) = 20 V(pp)/5 kHz) induces more powerful vortices than either the CC protocol or the FC protocol, and therefore yields a better mixing performance. Two AP-based micromixers are fabricated with symmetric and asymmetric electrode configurations, respectively. The mixing indices achieved by the two devices after an elapsed time of 60 seconds are found to be 56.49 % and 71.77 %, respectively. This result shows that of the two devices, an asymmetric electrode configuration represents a more suitable choice for micromixer in microfluidic devices.

Lifespan development of the bilateral deficit in a simple reaction time task.

PubMed

Vieluf, Solveig; Aschersleben, Gisa; Panzer, Stefan

2017-04-01

Performing an action at a maximum speed or with a maximum strength simultaneously with two limbs leads to a lower performance than the sum of unimanual performances. This phenomenon is known as bilateral deficit. There is some evidence that the bilateral deficit changes over the lifespan, in a way that children and older adults show lower deficits than young adults. Inverse developmental changes of childrens' and older adults' brain structures connecting both hemispheres, i.e., the corpus callosum, might importantly contribute to this phenomenon. The seemingly similar developments have been observed with different experimental protocols in the different age groups, respectively. To test for similarities and differences in changes of the bilateral deficit at critical periods of the lifespan development of bimanual actions, children, young adults, and older adults performed a simple reaction time task uni- and bimanually. Reaction times and the resulting bilateral deficit, as well as reaction time variability were analyzed. As expected, reaction times were different for the young adults between the uni- and the bimanual task. Children and older adults performed both conditions with similar reaction times. However, a difference in the direction of the %bilateral deficit occurred between the two age groups. The findings demonstrated an absence of the bilateral deficit for children, but not for younger and older adults.

OpenKnowledge for peer-to-peer experimentation in protein identification by MS/MS

PubMed Central

2011-01-01

Background Traditional scientific workflow platforms usually run individual experiments with little evaluation and analysis of performance as required by automated experimentation in which scientists are being allowed to access numerous applicable workflows rather than being committed to a single one. Experimental protocols and data under a peer-to-peer environment could potentially be shared freely without any single point of authority to dictate how experiments should be run. In such environment it is necessary to have mechanisms by which each individual scientist (peer) can assess, locally, how he or she wants to be involved with others in experiments. This study aims to implement and demonstrate simple peer ranking under the OpenKnowledge peer-to-peer infrastructure by both simulated and real-world bioinformatics experiments involving multi-agent interactions. Methods A simulated experiment environment with a peer ranking capability was specified by the Lightweight Coordination Calculus (LCC) and automatically executed under the OpenKnowledge infrastructure. The peers such as MS/MS protein identification services (including web-enabled and independent programs) were made accessible as OpenKnowledge Components (OKCs) for automated execution as peers in the experiments. The performance of the peers in these automated experiments was monitored and evaluated by simple peer ranking algorithms. Results Peer ranking experiments with simulated peers exhibited characteristic behaviours, e.g., power law effect (a few dominant peers dominate), similar to that observed in the traditional Web. Real-world experiments were run using an interaction model in LCC involving two different types of MS/MS protein identification peers, viz., peptide fragment fingerprinting (PFF) and de novo sequencing with another peer ranking algorithm simply based on counting the successful and failed runs. This study demonstrated a novel integration and useful evaluation of specific proteomic peers and found MASCOT to be a dominant peer as judged by peer ranking. Conclusion The simulated and real-world experiments in the present study demonstrated that the OpenKnowledge infrastructure with peer ranking capability can serve as an evaluative environment for automated experimentation. PMID:22192521

Technical Note: Procedure for the calibration and validation of kilo-voltage cone-beam CT models

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

Vilches-Freixas, Gloria; Létang, Jean Michel; Rit,

2016-09-15

Purpose: The aim of this work is to propose a general and simple procedure for the calibration and validation of kilo-voltage cone-beam CT (kV CBCT) models against experimental data. Methods: The calibration and validation of the CT model is a two-step procedure: the source model then the detector model. The source is described by the direction dependent photon energy spectrum at each voltage while the detector is described by the pixel intensity value as a function of the direction and the energy of incident photons. The measurements for the source consist of a series of dose measurements in air performedmore » at each voltage with varying filter thicknesses and materials in front of the x-ray tube. The measurements for the detector are acquisitions of projection images using the same filters and several tube voltages. The proposed procedure has been applied to calibrate and assess the accuracy of simple models of the source and the detector of three commercial kV CBCT units. If the CBCT system models had been calibrated differently, the current procedure would have been exclusively used to validate the models. Several high-purity attenuation filters of aluminum, copper, and silver combined with a dosimeter which is sensitive to the range of voltages of interest were used. A sensitivity analysis of the model has also been conducted for each parameter of the source and the detector models. Results: Average deviations between experimental and theoretical dose values are below 1.5% after calibration for the three x-ray sources. The predicted energy deposited in the detector agrees with experimental data within 4% for all imaging systems. Conclusions: The authors developed and applied an experimental procedure to calibrate and validate any model of the source and the detector of a CBCT unit. The present protocol has been successfully applied to three x-ray imaging systems. The minimum requirements in terms of material and equipment would make its implementation suitable in most clinical environments.« less

Extended charge banking model of dual path shocks for implantable cardioverter defibrillators

PubMed Central

Dosdall, Derek J; Sweeney, James D

2008-01-01

Background Single path defibrillation shock methods have been improved through the use of the Charge Banking Model of defibrillation, which predicts the response of the heart to shocks as a simple resistor-capacitor (RC) circuit. While dual path defibrillation configurations have significantly reduced defibrillation thresholds, improvements to dual path defibrillation techniques have been limited to experimental observations without a practical model to aid in improving dual path defibrillation techniques. Methods The Charge Banking Model has been extended into a new Extended Charge Banking Model of defibrillation that represents small sections of the heart as separate RC circuits, uses a weighting factor based on published defibrillation shock field gradient measures, and implements a critical mass criteria to predict the relative efficacy of single and dual path defibrillation shocks. Results The new model reproduced the results from several published experimental protocols that demonstrated the relative efficacy of dual path defibrillation shocks. The model predicts that time between phases or pulses of dual path defibrillation shock configurations should be minimized to maximize shock efficacy. Discussion Through this approach the Extended Charge Banking Model predictions may be used to improve dual path and multi-pulse defibrillation techniques, which have been shown experimentally to lower defibrillation thresholds substantially. The new model may be a useful tool to help in further improving dual path and multiple pulse defibrillation techniques by predicting optimal pulse durations and shock timing parameters. PMID:18673561

The effect of repeated laser stimuli to ink-marked skin on skin temperature-recommendations for a safe experimental protocol in humans.

PubMed

Madden, Victoria J; Catley, Mark J; Grabherr, Luzia; Mazzola, Francesca; Shohag, Mohammad; Moseley, G Lorimer

2016-01-01

Background. Nd:YAP laser is widely used to investigate the nociceptive and pain systems, generating perpetual and laser-evoked neurophysiological responses. A major procedural concern for the use of Nd:YAP laser stimuli in experimental research is the risk of skin damage. The absorption of Nd:YAP laser stimuli is greater in darker skin, or in pale skin that has been darkened with ink, prompting some ethics boards to refuse approval to experimenters wishing to track stimulus location by marking the skin with ink. Some research questions, however, require laser stimuli to be delivered at particular locations or within particular zones, a requirement that is very difficult to achieve if marking the skin is not possible. We thoroughly searched the literature for experimental evidence and protocol recommendations for safe delivery of Nd:YAP laser stimuli over marked skin, but found nothing. Methods. We designed an experimental protocol to define safe parameters for the use of Nd:YAP laser stimuli over skin that has been marked with black dots, and used thermal imaging to assess the safety of the procedure at the forearm and the back. Results. Using thermal imaging and repeated laser stimulation to ink-marked skin, we demonstrated that skin temperature did not increase progressively across the course of the experiment, and that the small change in temperature seen at the forearm was reversed during the rest periods between blocks. Furthermore, no participant experienced skin damage due to the procedure. Conclusion. This protocol offers parameters for safe, confident and effective experimentation using repeated Nd:YAP laser on skin marked with ink, thus paving the way for investigations that depend on it.

BioBlocks: Programming Protocols in Biology Made Easier.

PubMed

Gupta, Vishal; Irimia, Jesús; Pau, Iván; Rodríguez-Patón, Alfonso

2017-07-21

The methods to execute biological experiments are evolving. Affordable fluid handling robots and on-demand biology enterprises are making automating entire experiments a reality. Automation offers the benefit of high-throughput experimentation, rapid prototyping, and improved reproducibility of results. However, learning to automate and codify experiments is a difficult task as it requires programming expertise. Here, we present a web-based visual development environment called BioBlocks for describing experimental protocols in biology. It is based on Google's Blockly and Scratch, and requires little or no experience in computer programming to automate the execution of experiments. The experiments can be specified, saved, modified, and shared between multiple users in an easy manner. BioBlocks is open-source and can be customized to execute protocols on local robotic platforms or remotely, that is, in the cloud. It aims to serve as a de facto open standard for programming protocols in Biology.

DTN routing in body sensor networks with dynamic postural partitioning.

PubMed

Quwaider, Muhannad; Biswas, Subir

2010-11-01

This paper presents novel store-and-forward packet routing algorithms for Wireless Body Area Networks ( WBAN ) with frequent postural partitioning. A prototype WBAN has been constructed for experimentally characterizing on-body topology disconnections in the presence of ultra short range radio links, unpredictable RF attenuation, and human postural mobility. On-body DTN routing protocols are then developed using a stochastic link cost formulation, capturing multi-scale topological localities in human postural movements. Performance of the proposed protocols are evaluated experimentally and via simulation, and are compared with a number of existing single-copy DTN routing protocols and an on-body packet flooding mechanism that serves as a performance benchmark with delay lower-bound. It is shown that via multi-scale modeling of the spatio-temporal locality of on-body link disconnection patterns, the proposed algorithms can provide better routing performance compared to a number of existing probabilistic, opportunistic, and utility-based DTN routing protocols in the literature.

Selection for production-related traits in Pelargonium zonale: improved design and analysis make all the difference

PubMed Central

Molenaar, Heike; Glawe, Martin; Boehm, Robert; Piepho, Hans-Peter

2017-01-01

Ornamental plant variety improvement is limited by current phenotyping approaches and neglected use of experimental designs. The present study was conducted to show the benefits of using an experimental design and corresponding analysis in ornamental breeding regarding simulated response to selection in Pelargonium zonale for production-related traits. This required establishment of phenotyping protocols for root formation and stem cutting counts, with which 974 genotypes were assessed in a two-phase experimental design. The present paper evaluates this protocol. The possibility of varietal improvement through indirect selection on secondary traits such as branch count and flower count was assessed by genetic correlations. Simulated response to selection varied greatly, depending on the genotypic variances of the breeding population and traits. A varietal improvement of over 20% is possible for stem cutting count, root formation, branch count and flower count. In contrast, indirect selection of stem cutting count by branch count or flower count was found to be ineffective. The established phenotypic protocols and two-phase experimental designs are valuable tools for breeding of P. zonale. PMID:28243453

Selection for production-related traits in Pelargonium zonale: improved design and analysis make all the difference.

PubMed

Molenaar, Heike; Glawe, Martin; Boehm, Robert; Piepho, Hans-Peter

2017-01-01

Ornamental plant variety improvement is limited by current phenotyping approaches and neglected use of experimental designs. The present study was conducted to show the benefits of using an experimental design and corresponding analysis in ornamental breeding regarding simulated response to selection in Pelargonium zonale for production-related traits. This required establishment of phenotyping protocols for root formation and stem cutting counts, with which 974 genotypes were assessed in a two-phase experimental design. The present paper evaluates this protocol. The possibility of varietal improvement through indirect selection on secondary traits such as branch count and flower count was assessed by genetic correlations. Simulated response to selection varied greatly, depending on the genotypic variances of the breeding population and traits. A varietal improvement of over 20% is possible for stem cutting count, root formation, branch count and flower count. In contrast, indirect selection of stem cutting count by branch count or flower count was found to be ineffective. The established phenotypic protocols and two-phase experimental designs are valuable tools for breeding of P. zonale .

Quantum dense key distribution

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

Degiovanni, I.P.; Ruo Berchera, I.; Castelletto, S.

2004-03-01

This paper proposes a protocol for quantum dense key distribution. This protocol embeds the benefits of a quantum dense coding and a quantum key distribution and is able to generate shared secret keys four times more efficiently than the Bennet-Brassard 1984 protocol. We hereinafter prove the security of this scheme against individual eavesdropping attacks, and we present preliminary experimental results, showing its feasibility.

Proof-of-principle experimental realization of a qubit-like qudit-based quantum key distribution scheme

NASA Astrophysics Data System (ADS)

Wang, Shuang; Yin, Zhen-Qiang; Chau, H. F.; Chen, Wei; Wang, Chao; Guo, Guang-Can; Han, Zheng-Fu

2018-04-01

In comparison to qubit-based protocols, qudit-based quantum key distribution ones generally allow two cooperative parties to share unconditionally secure keys under a higher channel noise. However, it is very hard to prepare and measure the required quantum states in qudit-based protocols in general. One exception is the recently proposed highly error tolerant qudit-based protocol known as the Chau15 (Chau 2015 Phys. Rev. A 92 062324). Remarkably, the state preparation and measurement in this protocol can be done relatively easily since the required states are phase encoded almost like the diagonal basis states of a qubit. Here we report the first proof-of-principle demonstration of the Chau15 protocol. One highlight of our experiment is that its post-processing is based on practical one-way manner, while the original proposal in Chau (2015 Phys. Rev. A 92 062324) relies on complicated two-way post-processing, which is a great challenge in experiment. In addition, by manipulating time-bin qudit and measurement with a variable delay interferometer, our realization is extensible to qudit with high-dimensionality and confirms the experimental feasibility of the Chau15 protocol.

EASE (Experimental Assembly of Structures in EVA) overview of selected results

NASA Technical Reports Server (NTRS)

Akin, David L.

1987-01-01

Experimental Assembly of Structures in EVA (EASE) objectives, experimental protocol, neutral buoyancy simulation, task time distribution, assembly task performance, metabolic rate/biomedical readouts are summarized. This presentation is shown in charts, figures, and graphs.

iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis

PubMed Central

2009-01-01

Background In recent years, the genome biology community has expended considerable effort to confront the challenges of managing heterogeneous data in a structured and organized way and developed laboratory information management systems (LIMS) for both raw and processed data. On the other hand, electronic notebooks were developed to record and manage scientific data, and facilitate data-sharing. Software which enables both, management of large datasets and digital recording of laboratory procedures would serve a real need in laboratories using medium and high-throughput techniques. Results We have developed iLAP (Laboratory data management, Analysis, and Protocol development), a workflow-driven information management system specifically designed to create and manage experimental protocols, and to analyze and share laboratory data. The system combines experimental protocol development, wizard-based data acquisition, and high-throughput data analysis into a single, integrated system. We demonstrate the power and the flexibility of the platform using a microscopy case study based on a combinatorial multiple fluorescence in situ hybridization (m-FISH) protocol and 3D-image reconstruction. iLAP is freely available under the open source license AGPL from http://genome.tugraz.at/iLAP/. Conclusion iLAP is a flexible and versatile information management system, which has the potential to close the gap between electronic notebooks and LIMS and can therefore be of great value for a broad scientific community. PMID:19941647

Unification of quantum information theory

NASA Astrophysics Data System (ADS)

Abeyesinghe, Anura

We present the unification of many previously disparate results in noisy quantum Shannon theory and the unification of all of noiseless quantum Shannon theory. More specifically we deal here with bipartite, unidirectional, and memoryless quantum Shannon theory. We find all the optimal protocols and quantify the relationship between the resources used, both for the one-shot and for the ensemble case, for what is arguably the most fundamental task in quantum information theory: sharing entangled states between a sender and a receiver. We find that all of these protocols are derived from our one-shot superdense coding protocol and relate nicely to each other. We then move on to noisy quantum information theory and give a simple, direct proof of the "mother" protocol, or rather her generalization to the Fully Quantum Slepian-Wolf protocol (FQSW). FQSW simultaneously accomplishes two goals: quantum communication-assisted entanglement distillation, and state transfer from the sender to the receiver. As a result, in addition to her other "children," the mother protocol generates the state merging primitive of Horodecki, Oppenheim, and Winter as well as a new class of distributed compression protocols for correlated quantum sources, which are optimal for sources described by separable density operators. Moreover, the mother protocol described here is easily transformed into the so-called "father" protocol, demonstrating that the division of single-sender/single-receiver protocols into two families was unnecessary: all protocols in the family are children of the mother.

Password-Only Authenticated Three-Party Key Exchange Proven Secure against Insider Dictionary Attacks

PubMed Central

Nam, Junghyun; Choo, Kim-Kwang Raymond

2014-01-01

While a number of protocols for password-only authenticated key exchange (PAKE) in the 3-party setting have been proposed, it still remains a challenging task to prove the security of a 3-party PAKE protocol against insider dictionary attacks. To the best of our knowledge, there is no 3-party PAKE protocol that carries a formal proof, or even definition, of security against insider dictionary attacks. In this paper, we present the first 3-party PAKE protocol proven secure against both online and offline dictionary attacks as well as insider and outsider dictionary attacks. Our construct can be viewed as a protocol compiler that transforms any 2-party PAKE protocol into a 3-party PAKE protocol with 2 additional rounds of communication. We also present a simple and intuitive approach of formally modelling dictionary attacks in the password-only 3-party setting, which significantly reduces the complexity of proving the security of 3-party PAKE protocols against dictionary attacks. In addition, we investigate the security of the well-known 3-party PAKE protocol, called GPAKE, due to Abdalla et al. (2005, 2006), and demonstrate that the security of GPAKE against online dictionary attacks depends heavily on the composition of its two building blocks, namely a 2-party PAKE protocol and a 3-party key distribution protocol. PMID:25309956

Effects of a peer support programme for youth social services employees experiencing potentially traumatic events: a protocol for a prospective cohort study

PubMed Central

Guay, Stephane; Tremblay, Nicole; Goncalves, Jane; Bilodeau, Henriette; Geoffrion, Steve

2017-01-01

Introduction The use of peer support programmes to help workers experiencing potentially traumatic events (PTE) has increased in high-risk organisations in the last decades. However, the scientific evidence of its effectiveness is still very limited. This paper aims to describe the protocol of a prospective cohort study that assesses the efficacy of a peer support programme among youth social services employees exposed to a PTE at work on psychological well-being, work functioning and needs of support. Methods and analysis This is a mixed-methods prospective study that will examine workers' evolution four times over a 12-month period in Canada. This study involves: (1) quantitative data obtained through self-administrated questionnaires among 222 workers, and (2) qualitative in-depth interviews with a subsample of 45 workers. This study will compare findings from a cohort who received the support of a peer following a PTE (peer support–experimental protocol) as part of the experimental protocol of the Montreal Youth Social Services-University Institute (MYSS-UI), the second group of workers did not ask for the peer support (no peer support-experimental protocol) but was part of MYSS-UI, and the third group received standard organisational support from the Monteregie Youth Social Services (MYSS) (standard organisational protocol). Ethics and dissemination The protocol and informed consent form complied with the ethics guidelines of the MYSS-UI. The Research Ethics Board of MYSS-UI and MYSS reviewed and accepted the protocol as required. The results of the study will be published in peer-reviewed journals, presented at research and general public conferences, disseminated via a public report for the institute that funded the project and for all workers. Results of this study will influence decision making regarding intervention policies following PTE and peer support interventions may be expanded throughout the youth social services in Canada and worldwide. PMID:28647721

Note: a simple experimental arrangement to generate optical vortex beams.

PubMed

Kumar, Dhirendra; Das, Abhijit; Boruah, Bosanta R

2013-02-01

In this Note, we present a simple experimental arrangement to generate optical vortex beams. We have demonstrated how by taking print of an interferogram on a transparent sheet, vortex beams with various topological charges can be generated. Experimental results show that the vortex beam indeed carries the topological charge that is used to compute the interferograms. In addition to being simple and inexpensive, one major advantage of the arrangement is that it makes it possible to generate different vortex beams quickly, unlike using the photographic process to create the holograms.

Quantum Computer Science

NASA Astrophysics Data System (ADS)

Mermin, N. David

2007-08-01

Preface; 1. Cbits and Qbits; 2. General features and some simple examples; 3. Breaking RSA encryption with a quantum computer; 4. Searching with a quantum computer; 5. Quantum error correction; 6. Protocols that use just a few Qbits; Appendices; Index.

Virtual laboratories: new opportunities for collaborative water science

NASA Astrophysics Data System (ADS)

Ceola, Serena; Arheimer, Berit; Bloeschl, Guenter; Baratti, Emanuele; Capell, Rene; Castellarin, Attilio; Freer, Jim; Han, Dawei; Hrachowitz, Markus; Hundecha, Yeshewatesfa; Hutton, Christopher; Lindström, Goran; Montanari, Alberto; Nijzink, Remko; Parajka, Juraj; Toth, Elena; Viglione, Alberto; Wagener, Thorsten

2015-04-01

Reproducibility and repeatability of experiments are the fundamental prerequisites that allow researchers to validate results and share hydrological knowledge, experience and expertise in the light of global water management problems. Virtual laboratories offer new opportunities to enable these prerequisites since they allow experimenters to share data, tools and pre-defined experimental procedures (i.e. protocols). Here we present the outcomes of a first collaborative numerical experiment undertaken by five different international research groups in a virtual laboratory to address the key issues of reproducibility and repeatability. Moving from the definition of accurate and detailed experimental protocols, a rainfall-runoff model was independently applied to 15 European catchments by the research groups and model results were collectively examined through a web-based discussion. We found that a detailed modelling protocol was crucial to ensure the comparability and reproducibility of the proposed experiment across groups. Our results suggest that sharing comprehensive and precise protocols and running the experiments within a controlled environment (e.g. virtual laboratory) is as fundamental as sharing data and tools for ensuring experiment repeatability and reproducibility across the broad scientific community and thus advancing hydrology in a more coherent way.

Of taps and toilets: quasi-experimental protocol for evaluating community-demand-driven projects.

PubMed

Pattanayak, Subhrendu K; Poulos, Christine; Yang, Jui-Chen; Patil, Sumeet R; Wendland, Kelly J

2009-09-01

Sustainable and equitable access to safe water and adequate sanitation are widely acknowledged as vital, yet neglected, development goals. Water supply and sanitation (WSS) policies are justified because of the usual efficiency criteria, but also major equity concerns. Yet, to date there are few scientific impact evaluations showing that WSS policies are effective in delivering social welfare outcomes. This lack of an evaluation culture is partly because WSS policies are characterized by diverse mechanisms, broad goals and the increasing importance of decentralized delivery, and partly because programme administrators are unaware of appropriate methods. We describe a protocol for a quasi-experimental evaluation of a community-demand-driven programme for water and sanitation in rural India, which addresses several evaluation challenges. After briefly reviewing policy and implementation issues in the sector, we describe key features of our protocol, including control group identification, pre-post measurement, programme theory, sample sufficiency and robust indicators. At its core, our protocol proposes to combine propensity score matching and difference-in-difference estimation. We conclude by briefly summarizing how quasi-experimental impact evaluations can address key issues in WSS policy design and when such evaluations are needed.

Generation of concatenated Greenberger-Horne-Zeilinger-type entangled coherent state based on linear optics

NASA Astrophysics Data System (ADS)

Guo, Rui; Zhou, Lan; Gu, Shi-Pu; Wang, Xing-Fu; Sheng, Yu-Bo

2017-03-01

The concatenated Greenberger-Horne-Zeilinger (C-GHZ) state is a new type of multipartite entangled state, which has potential application in future quantum information. In this paper, we propose a protocol of constructing arbitrary C-GHZ entangled state approximatively. Different from previous protocols, each logic qubit is encoded in the coherent state. This protocol is based on the linear optics, which is feasible in experimental technology. This protocol may be useful in quantum information based on the C-GHZ state.

A model-guided symbolic execution approach for network protocol implementations and vulnerability detection.

PubMed

Wen, Shameng; Meng, Qingkun; Feng, Chao; Tang, Chaojing

2017-01-01

Formal techniques have been devoted to analyzing whether network protocol specifications violate security policies; however, these methods cannot detect vulnerabilities in the implementations of the network protocols themselves. Symbolic execution can be used to analyze the paths of the network protocol implementations, but for stateful network protocols, it is difficult to reach the deep states of the protocol. This paper proposes a novel model-guided approach to detect vulnerabilities in network protocol implementations. Our method first abstracts a finite state machine (FSM) model, then utilizes the model to guide the symbolic execution. This approach achieves high coverage of both the code and the protocol states. The proposed method is implemented and applied to test numerous real-world network protocol implementations. The experimental results indicate that the proposed method is more effective than traditional fuzzing methods such as SPIKE at detecting vulnerabilities in the deep states of network protocol implementations.

Finite-key analysis for the 1-decoy state QKD protocol

NASA Astrophysics Data System (ADS)

Rusca, Davide; Boaron, Alberto; Grünenfelder, Fadri; Martin, Anthony; Zbinden, Hugo

2018-04-01

It has been shown that in the asymptotic case of infinite-key length, the 2-decoy state Quantum Key Distribution (QKD) protocol outperforms the 1-decoy state protocol. Here, we present a finite-key analysis of the 1-decoy method. Interestingly, we find that for practical block sizes of up to 108 bits, the 1-decoy protocol achieves for almost all experimental settings higher secret key rates than the 2-decoy protocol. Since using only one decoy is also easier to implement, we conclude that it is the best choice for QKD, in most common practical scenarios.

Detecting gait abnormalities after concussion or mild traumatic brain injury: A systematic review of single-task, dual-task, and complex gait.

PubMed

Fino, Peter C; Parrington, Lucy; Pitt, Will; Martini, Douglas N; Chesnutt, James C; Chou, Li-Shan; King, Laurie A

2018-05-01

While a growing number of studies have investigated the effects of concussion or mild traumatic brain injury (mTBI) on gait, many studies use different experimental paradigms and outcome measures. The path for translating experimental studies for objective clinical assessments of gait is unclear. This review asked 2 questions: 1) is gait abnormal after concussion/mTBI, and 2) what gait paradigms (single-task, dual-task, complex gait) detect abnormalities after concussion. Data sources included MEDLINE/PubMed, Scopus, Web of Science, and Cumulative Index to Nursing and Allied Health Literature (CINAHL) accessed on March 14, 2017. Original research articles reporting gait outcomes in people with concussion or mTBI were included. Studies of moderate, severe, or unspecified TBI, and studies without a comparator were excluded. After screening 233 articles, 38 studies were included and assigned to one or more sections based on the protocol and reported outcomes. Twenty-six articles reported single-task simple gait outcomes, 24 reported dual-task simple gait outcomes, 21 reported single-task complex gait outcomes, and 10 reported dual-task complex gait outcomes. Overall, this review provides evidence for two conclusions: 1) gait is abnormal acutely after concussion/mTBI but generally resolves over time; and 2) the inconsistency of findings, small sample sizes, and small number of studies examining homogenous measures at the same time-period post-concussion highlight the need for replication across independent populations and investigators. Future research should concentrate on dual-task and complex gait tasks, as they showed promise for detecting abnormal locomotor function outside of the acute timeframe. Additionally, studies should provide detailed demographic and clinical characteristics to enable more refined comparisons across studies. Copyright © 2018 Elsevier B.V. All rights reserved.

Decoding DNA labels by melting curve analysis using real-time PCR.

PubMed

Balog, József A; Fehér, Liliána Z; Puskás, László G

2017-12-01

Synthetic DNA has been used as an authentication code for a diverse number of applications. However, existing decoding approaches are based on either DNA sequencing or the determination of DNA length variations. Here, we present a simple alternative protocol for labeling different objects using a small number of short DNA sequences that differ in their melting points. Code amplification and decoding can be done in two steps using quantitative PCR (qPCR). To obtain a DNA barcode with high complexity, we defined 8 template groups, each having 4 different DNA templates, yielding 158 (>2.5 billion) combinations of different individual melting temperature (Tm) values and corresponding ID codes. The reproducibility and specificity of the decoding was confirmed by using the most complex template mixture, which had 32 different products in 8 groups with different Tm values. The industrial applicability of our protocol was also demonstrated by labeling a drone with an oil-based paint containing a predefined DNA code, which was then successfully decoded. The method presented here consists of a simple code system based on a small number of synthetic DNA sequences and a cost-effective, rapid decoding protocol using a few qPCR reactions, enabling a wide range of authentication applications.

Relative Motion of the WDS 05110+3203 STF 648 System, With a Protocol for Calculating Relative Motion

NASA Astrophysics Data System (ADS)

Wiley, E. O.

2010-07-01

Relative motion studies of visual double stars can be investigated using least squares regression techniques and readily accessible programs such as Microsoft Excel and a calculator. Optical pairs differ from physical pairs under most geometries in both their simple scatter plots and their regression models. A step-by-step protocol for estimating the rectilinear elements of an optical pair is presented. The characteristics of physical pairs using these techniques are discussed.

Tandem Aldol-Michael Reactions in Aqueous Diethylamine Medium: A Greener and Efficient Approach to Bis-Pyrimidine Derivatives

PubMed Central

Al-Majid, Abdullah M.; Barakat, Assem; AL-Najjar, Hany J.; Mabkhot, Yahia N.; Ghabbour, Hazem A.; Fun, Hoong-Kun

2013-01-01

A simple protocol, involving the green synthesis for the construction of novel bis-pyrimidine derivatives, 3a–i and 4a–e are accomplished by the aqueous diethylamine media promoted tandem Aldol-Michael reaction between two molecules of barbituric acid derivatives 1a,b with various aldehydes. This efficient synthetic protocol using an economic and environmentally friendly reaction media with versatility and shorter reaction time provides bis-pyrimidine derivatives with high yields (88%–99%). PMID:24317435

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

Sivak, David; Crooks, Gavin

A fundamental problem in modern thermodynamics is how a molecular-scale machine performs useful work, while operating away from thermal equilibrium without excessive dissipation. To this end, we derive a friction tensor that induces a Riemannian manifold on the space of thermodynamic states. Within the linear-response regime, this metric structure controls the dissipation of finite-time transformations, and bestows optimal protocols with many useful properties. We discuss the connection to the existing thermodynamic length formalism, and demonstrate the utility of this metric by solving for optimal control parameter protocols in a simple nonequilibrium model.

An improved silver staining procedure for schizodeme analysis in polyacrylamide gradient gels.

PubMed

Gonçalves, A M; Nehme, N S; Morel, C M

1990-01-01

A simple protocol is described for the silver staining of polyacrylamide gradient gels used for the separation of restriction fragments of kinetoplast DNA [schizodeme analysis of trypanosomatids (Morel et al., 1980)]. The method overcomes the problems of non-uniform staining and strong background color which are frequently encountered when conventional protocols for silver staining of linear gels are applied to gradient gels. The method described has proven to be of general applicability for DNA, RNA and protein separations in gradient gels.

The Surviving Sepsis Campaign: Where have we been and where are we going?

PubMed

Dellinger, R Phillip

2015-04-01

The Surviving Sepsis Campaign develops and promotes evidence-based guidelines and performance-improvement practices aimed at reducing deaths from sepsis worldwide. The most recent guidelines, published in 2013, provide detailed management strategies for acute care, fluid resuscitation, and vasopressor use. In addition, the campaign has developed simple, short protocols for what to do within 3 and 6 hours of recognition of sepsis. These protocols are associated with reduced mortality rates. Copyright © 2015 Cleveland Clinic.

Achieving High Throughput for Data Transfer over ATM Networks

NASA Technical Reports Server (NTRS)

Johnson, Marjory J.; Townsend, Jeffrey N.

1996-01-01

File-transfer rates for ftp are often reported to be relatively slow, compared to the raw bandwidth available in emerging gigabit networks. While a major bottleneck is disk I/O, protocol issues impact performance as well. Ftp was developed and optimized for use over the TCP/IP protocol stack of the Internet. However, TCP has been shown to run inefficiently over ATM. In an effort to maximize network throughput, data-transfer protocols can be developed to run over UDP or directly over IP, rather than over TCP. If error-free transmission is required, techniques for achieving reliable transmission can be included as part of the transfer protocol. However, selected image-processing applications can tolerate a low level of errors in images that are transmitted over a network. In this paper we report on experimental work to develop a high-throughput protocol for unreliable data transfer over ATM networks. We attempt to maximize throughput by keeping the communications pipe full, but still keep packet loss under five percent. We use the Bay Area Gigabit Network Testbed as our experimental platform.

40 CFR 160.120 - Protocol.

Code of Federal Regulations, 2010 CFR

2010-07-01

... system. (8) A description of the experimental design, including methods for the control of bias. (9... being conducted. (4) The proposed experimental start and termination dates. (5) Justification for...

40 CFR 160.120 - Protocol.

Code of Federal Regulations, 2013 CFR

2013-07-01

... system. (8) A description of the experimental design, including methods for the control of bias. (9... being conducted. (4) The proposed experimental start and termination dates. (5) Justification for...

40 CFR 160.120 - Protocol.

Code of Federal Regulations, 2012 CFR

2012-07-01

... system. (8) A description of the experimental design, including methods for the control of bias. (9... being conducted. (4) The proposed experimental start and termination dates. (5) Justification for...

40 CFR 160.120 - Protocol.

Code of Federal Regulations, 2011 CFR

2011-07-01

... system. (8) A description of the experimental design, including methods for the control of bias. (9... being conducted. (4) The proposed experimental start and termination dates. (5) Justification for...

40 CFR 160.120 - Protocol.

Code of Federal Regulations, 2014 CFR

2014-07-01

... system. (8) A description of the experimental design, including methods for the control of bias. (9... being conducted. (4) The proposed experimental start and termination dates. (5) Justification for...

Two Quantum Protocols for Oblivious Set-member Decision Problem

NASA Astrophysics Data System (ADS)

Shi, Run-Hua; Mu, Yi; Zhong, Hong; Cui, Jie; Zhang, Shun

2015-10-01

In this paper, we defined a new secure multi-party computation problem, called Oblivious Set-member Decision problem, which allows one party to decide whether a secret of another party belongs to his private set in an oblivious manner. There are lots of important applications of Oblivious Set-member Decision problem in fields of the multi-party collaborative computation of protecting the privacy of the users, such as private set intersection and union, anonymous authentication, electronic voting and electronic auction. Furthermore, we presented two quantum protocols to solve the Oblivious Set-member Decision problem. Protocol I takes advantage of powerful quantum oracle operations so that it needs lower costs in both communication and computation complexity; while Protocol II takes photons as quantum resources and only performs simple single-particle projective measurements, thus it is more feasible with the present technology.

A flexible acquisition cycle for incompletely defined fieldbus protocols.

PubMed

Gaitan, Vasile-Gheorghita; Gaitan, Nicoleta-Cristina; Ungurean, Ioan

2014-05-01

Real time data-acquisition from fieldbuses strongly depends on the network type and protocol used. Currently, there is an impressive number of fieldbuses, some of them are completely defined and others are incompletely defined. In those from the second category, the time variable, the main element in real-time data acquisition, does not appear explicitly. Examples include protocols such as Modbus ASCII/RTU, M-bus, ASCII character-based, and so on. This paper defines a flexible acquisition cycle based on the Master-Slave architecture that can be implemented on a Master station, called a Base Station Gateway (BSG). The BSG can add a timestamp for temporal location of data. It also presents a possible extension for the Modbus protocol, developed as simple and low cost solution based on existing hardware. Copyright © 2014 ISA. Published by Elsevier Ltd. All rights reserved.

FISH-in-CHIPS: A Microfluidic Platform for Molecular Typing of Cancer Cells.

PubMed

Perez-Toralla, Karla; Mottet, Guillaume; Tulukcuoglu-Guneri, Ezgi; Champ, Jérôme; Bidard, François-Clément; Pierga, Jean-Yves; Klijanienko, Jerzy; Draskovic, Irena; Malaquin, Laurent; Viovy, Jean-Louis; Descroix, Stéphanie

2017-01-01

Microfluidics offer powerful tools for the control, manipulation, and analysis of cells, in particular for the assessment of cell malignancy or the study of cell subpopulations. However, implementing complex biological protocols on chip remains a challenge. Sample preparation is often performed off chip using multiple manually performed steps, and protocols usually include different dehydration and drying steps that are not always compatible with a microfluidic format.Here, we report the implementation of a Fluorescence in situ Hybridization (FISH) protocol for the molecular typing of cancer cells in a simple and low-cost device. The geometry of the chip allows integrating the sample preparation steps to efficiently assess the genomic content of individual cells using a minute amount of sample. The FISH protocol can be fully automated, thus enabling its use in routine clinical practice.

Two Quantum Protocols for Oblivious Set-member Decision Problem

PubMed Central

Shi, Run-hua; Mu, Yi; Zhong, Hong; Cui, Jie; Zhang, Shun

2015-01-01

In this paper, we defined a new secure multi-party computation problem, called Oblivious Set-member Decision problem, which allows one party to decide whether a secret of another party belongs to his private set in an oblivious manner. There are lots of important applications of Oblivious Set-member Decision problem in fields of the multi-party collaborative computation of protecting the privacy of the users, such as private set intersection and union, anonymous authentication, electronic voting and electronic auction. Furthermore, we presented two quantum protocols to solve the Oblivious Set-member Decision problem. Protocol I takes advantage of powerful quantum oracle operations so that it needs lower costs in both communication and computation complexity; while Protocol II takes photons as quantum resources and only performs simple single-particle projective measurements, thus it is more feasible with the present technology. PMID:26514668

Two Quantum Protocols for Oblivious Set-member Decision Problem.

PubMed

Shi, Run-Hua; Mu, Yi; Zhong, Hong; Cui, Jie; Zhang, Shun

2015-10-30

In this paper, we defined a new secure multi-party computation problem, called Oblivious Set-member Decision problem, which allows one party to decide whether a secret of another party belongs to his private set in an oblivious manner. There are lots of important applications of Oblivious Set-member Decision problem in fields of the multi-party collaborative computation of protecting the privacy of the users, such as private set intersection and union, anonymous authentication, electronic voting and electronic auction. Furthermore, we presented two quantum protocols to solve the Oblivious Set-member Decision problem. Protocol I takes advantage of powerful quantum oracle operations so that it needs lower costs in both communication and computation complexity; while Protocol II takes photons as quantum resources and only performs simple single-particle projective measurements, thus it is more feasible with the present technology.

Equipment and Protocols for Quasi-Static and Dynamic Tests of Very-High-Strength Concrete (VHSC) and High-Strength High-Ductility Concrete (HSHDC)

DTIC Science & Technology

2016-08-01

quasi -static mechanical properties, deformation behavior, and damage mechanisms in HSHDC and compare the behavior with VHSC. 2. Develop experimental ...using the experimental setup described in Chapter 6. The quasi -static strain rate was approximately 10-4/s. All panels tested have nominal dimensions...ER D C TR -1 6- 13 Force Protection Basing; TeCD 1a Equipment and Protocols for Quasi -Static and Dynamic Tests of Very-High-Strength

Extended Theories of Gravitation. Observation Protocols and Experimental Tests

NASA Astrophysics Data System (ADS)

Fatibene, Lorenzo; Ferraris, Marco; Francaviglia, Mauro; Magnano, Guido

2013-09-01

Within the framework of extended theories of gravitation we shall discuss physical equivalences among different formalisms and classical tests. As suggested by the Ehlers-Pirani-Schild framework, the conformal invariance will be preserved and its effect on observational protocols discussed. Accordingly, we shall review standard tests showing how Palatini f(R)-theories naturally passes solar system tests. Observation protocols will be discussed in this wider framework.

Location-oblivious data transfer with flying entangled qudits

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

Kent, Adrian

2011-07-15

We present a simple and practical quantum protocol involving two mistrustful agencies in Minkowski space, which allows Alice to transfer data to Bob at a space-time location that neither can predict in advance. The location depends on both Alice's and Bob's actions. The protocol guarantees unconditionally to Alice that Bob learns the data at a randomly determined location; it guarantees to Bob that Alice will not learn the transfer location even after the protocol is complete. The task implemented, transferring data at a space-time location that remains hidden from the transferrer, has no precise analog in nonrelativistic quantum cryptography. Itmore » illustrates further the scope for novel cryptographic applications of relativistic quantum theory.« less

EEG-based workload estimation across affective contexts

PubMed Central

Mühl, Christian; Jeunet, Camille; Lotte, Fabien

2014-01-01

Workload estimation from electroencephalographic signals (EEG) offers a highly sensitive tool to adapt the human–computer interaction to the user state. To create systems that reliably work in the complexity of the real world, a robustness against contextual changes (e.g., mood), has to be achieved. To study the resilience of state-of-the-art EEG-based workload classification against stress we devise a novel experimental protocol, in which we manipulated the affective context (stressful/non-stressful) while the participant solved a task with two workload levels. We recorded self-ratings, behavior, and physiology from 24 participants to validate the protocol. We test the capability of different, subject-specific workload classifiers using either frequency-domain, time-domain, or both feature varieties to generalize across contexts. We show that the classifiers are able to transfer between affective contexts, though performance suffers independent of the used feature domain. However, cross-context training is a simple and powerful remedy allowing the extraction of features in all studied feature varieties that are more resilient to task-unrelated variations in signal characteristics. Especially for frequency-domain features, across-context training is leading to a performance comparable to within-context training and testing. We discuss the significance of the result for neurophysiology-based workload detection in particular and for the construction of reliable passive brain–computer interfaces in general. PMID:24971046

Controlling for confounding variables in MS-omics protocol: why modularity matters.

PubMed

Smith, Rob; Ventura, Dan; Prince, John T

2014-09-01

As the field of bioinformatics research continues to grow, more and more novel techniques are proposed to meet new challenges and improvements upon solutions to long-standing problems. These include data processing techniques and wet lab protocol techniques. Although the literature is consistently thorough in experimental detail and variable-controlling rigor for wet lab protocol techniques, bioinformatics techniques tend to be less described and less controlled. As the validation or rejection of hypotheses rests on the experiment's ability to isolate and measure a variable of interest, we urge the importance of reducing confounding variables in bioinformatics techniques during mass spectrometry experimentation. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Free-space quantum key distribution at night

NASA Astrophysics Data System (ADS)

Buttler, William T.; Hughes, Richard J.; Kwiat, Paul G.; Lamoreaux, Steve K.; Luther, Gabriel G.; Morgan, George L.; Nordholt, Jane E.; Peterson, C. Glen; Simmons, Charles M.

1998-07-01

An experimental free-space quantum key distribution (QKD) system has been tested over an outdoor optical path of approximately 1 km under nighttime conditions at Los Alamos National Laboratory. This system employs the Bennett 92 protocol; here we give a brief overview of this protocol, and describe our experimental implementation of it. An analysis of the system efficiency is presented as well as a description of our error detection protocol, which employs a 2D parity check scheme. Finally, the susceptibility of this system to eavesdropping by various techniques is determined, and the effectiveness of privacy amplification procedures is discussed. Our conclusions are that free-space QKD is both effective and secure; possible applications include the rekeying of satellites in low earth orbit.

Separation of Chloroplast Pigments Using Reverse Phase Chromatography.

ERIC Educational Resources Information Center

Reese, R. Neil

1997-01-01

Presents a protocol that uses reverse phase chromatography for the separation of chloroplast pigments. Provides a simple and relatively safe procedure for use in teaching laboratories. Discusses pigment extraction, chromatography, results, and advantages of the process. (JRH)

Internal Corrosion Detection in Liquids Pipelines

DOT National Transportation Integrated Search

2012-01-01

PHMSA project DTRS56-05-T-0005 "Development of ICDA for Liquid Petroleum Pipelines" led to the development of a Direct Assessment (DA) protocol to prioritize locations of possible internal corrosion. The underlying basis LP-ICDA is simple; corrosion ...

Molecular Identification of Date Palm Cultivars Using Random Amplified Polymorphic DNA (RAPD) Markers.

PubMed

Al-Khalifah, Nasser S; Shanavaskhan, A E

2017-01-01

Ambiguity in the total number of date palm cultivars across the world is pointing toward the necessity for an enumerative study using standard morphological and molecular markers. Among molecular markers, DNA markers are more suitable and ubiquitous to most applications. They are highly polymorphic in nature, frequently occurring in genomes, easy to access, and highly reproducible. Various molecular markers such as restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), simple sequence repeats (SSR), inter-simple sequence repeats (ISSR), and random amplified polymorphic DNA (RAPD) markers have been successfully used as efficient tools for analysis of genetic variation in date palm. This chapter explains a stepwise protocol for extracting total genomic DNA from date palm leaves. A user-friendly protocol for RAPD analysis and a table showing the primers used in different molecular techniques that produce polymorphisms in date palm are also provided.

Modeling helical proteins using residual dipolar couplings, sparse long-range distance constraints and a simple residue-based force field

PubMed Central

Eggimann, Becky L.; Vostrikov, Vitaly V.; Veglia, Gianluigi; Siepmann, J. Ilja

2013-01-01

We present a fast and simple protocol to obtain moderate-resolution backbone structures of helical proteins. This approach utilizes a combination of sparse backbone NMR data (residual dipolar couplings and paramagnetic relaxation enhancements) or EPR data with a residue-based force field and Monte Carlo/simulated annealing protocol to explore the folding energy landscape of helical proteins. By using only backbone NMR data, which are relatively easy to collect and analyze, and strategically placed spin relaxation probes, we show that it is possible to obtain protein structures with correct helical topology and backbone RMS deviations well below 4 Å. This approach offers promising alternatives for the structural determination of proteins in which nuclear Overha-user effect data are difficult or impossible to assign and produces initial models that will speed up the high-resolution structure determination by NMR spectroscopy. PMID:24639619

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

Fox, Kevin

The software provides a simple web api to allow users to request a time window where a file will not be removed from cache. HPSS provides the concept of a "purge lock". When a purge lock is set on a file, the file will not be removed from disk, entering tape only state. A lot of network file protocols assume a file is on disk so it is good to purge lock a file before transferring using one of those protocols. HPSS's purge lock system is very coarse grained though. A file is either purge locked or not. Nothing enforcesmore » quotas, timely unlocking of purge locks, or managing the races inherent with multiple users wanting to lock/unlock the same file. The Purge Lock Server lets you, through a simple REST API, specify a list of files to purge lock and an expire time, and the system will ensure things happen properly.« less

Nonpainful wide-area compression inhibits experimental pain

PubMed Central

Honigman, Liat; Bar-Bachar, Ofrit; Yarnitsky, David; Sprecher, Elliot; Granovsky, Yelena

2016-01-01

Abstract Compression therapy, a well-recognized treatment for lymphoedema and venous disorders, pressurizes limbs and generates massive non-noxious afferent sensory barrages. The aim of this study was to study whether such afferent activity has an analgesic effect when applied on the lower limbs, hypothesizing that larger compression areas will induce stronger analgesic effects, and whether this effect correlates with conditioned pain modulation (CPM). Thirty young healthy subjects received painful heat and pressure stimuli (47°C for 30 seconds, forearm; 300 kPa for 15 seconds, wrist) before and during 3 compression protocols of either SMALL (up to ankles), MEDIUM (up to knees), or LARGE (up to hips) compression areas. Conditioned pain modulation (heat pain conditioned by noxious cold water) was tested before and after each compression protocol. The LARGE protocol induced more analgesia for heat than the SMALL protocol (P < 0.001). The analgesic effect interacted with gender (P = 0.015). The LARGE protocol was more efficient for females, whereas the MEDIUM protocol was more efficient for males. Pressure pain was reduced by all protocols (P < 0.001) with no differences between protocols and no gender effect. Conditioned pain modulation was more efficient than the compression-induced analgesia. For the LARGE protocol, precompression CPM efficiency positively correlated with compression-induced analgesia. Large body area compression exerts an area-dependent analgesic effect on experimental pain stimuli. The observed correlation with pain inhibition in response to robust non-noxious sensory stimulation may suggest that compression therapy shares similar mechanisms with inhibitory pain modulation assessed through CPM. PMID:27152691

FDA approved drugs complexed to their targets: evaluating pose prediction accuracy of docking protocols.

PubMed

Bohari, Mohammed H; Sastry, G Narahari

2012-09-01

Efficient drug discovery programs can be designed by utilizing existing pools of knowledge from the already approved drugs. This can be achieved in one way by repositioning of drugs approved for some indications to newer indications. Complex of drug to its target gives fundamental insight into molecular recognition and a clear understanding of putative binding site. Five popular docking protocols, Glide, Gold, FlexX, Cdocker and LigandFit have been evaluated on a dataset of 199 FDA approved drug-target complexes for their accuracy in predicting the experimental pose. Performance for all the protocols is assessed at default settings, with root mean square deviation (RMSD) between the experimental ligand pose and the docked pose of less than 2.0 Å as the success criteria in predicting the pose. Glide (38.7 %) is found to be the most accurate in top ranked pose and Cdocker (58.8 %) in top RMSD pose. Ligand flexibility is a major bottleneck in failure of docking protocols to correctly predict the pose. Resolution of the crystal structure shows an inverse relationship with the performance of docking protocol. All the protocols perform optimally when a balanced type of hydrophilic and hydrophobic interaction or dominant hydrophilic interaction exists. Overall in 16 different target classes, hydrophobic interactions dominate in the binding site and maximum success is achieved for all the docking protocols in nuclear hormone receptor class while performance for the rest of the classes varied based on individual protocol.

Evaluation of two clinical protocols for the management of women with vaginal discharge in southern Thailand.

PubMed

Chandeying, V; Skov, S; Kemapunmanus, M; Law, M; Geater, A; Rowe, P

1998-06-01

(1) To compare the effectiveness of two clinical protocols for the management of vaginal discharge in the situations where no laboratory facilities are available but speculum examination is possible and where basic laboratory facilities are available. (2) To determine clinical and simple laboratory indicators for diagnosis of patients with vaginal discharge in the local setting. Alternate allocation of subjects to one of two management protocols. Women presenting to university gynaecology outpatients department with a complaint of vaginal discharge. Subjects were alternately allocated management according to one of two protocols: one without (group A) and one with (group B) immediate access to results of basic laboratory tests. Full clinical assessment including speculum examination and microbiological assessment for infection with gonorrhoea, chlamydia, candida, trichomonas, and bacterial vaginosis was performed on all women. Follow up assessment of clinical and microbiological response was performed 1-2 weeks later. At initial assessment, both groups were similar in all respects except that more group B women had inflammation of the vulva. The prevalences of various conditions were: candidiasis 22%, bacterial vaginosis 38%, trichomoniasis 4%, chlamydia 4%, gonorrhoea 0.4%. There was no association between any demographic characteristic and diagnosis of cause of the discharge. Both protocols resulted in clinically and statistically significant improvements for women with candidiasis, bacterial vaginosis, and trichomoniasis. There were no clinically important differences in outcomes between the two protocols. The sensitivities and specificities of various indicators were: curd-like vaginal discharge for candidiasis, 72% and 100%; homogeneous vaginal discharge for bacterial vaginosis or trichomoniasis, 94% and 88%; absent or scanty lactobacilli for bacterial vaginosis, 99% and 68%; > 20% clue cells for bacterial vaginosis, 81% and 99%; visible endocervical mucopus for chlamydia or gonorrhoea, 36% and 86%; microscopic endocervical mucopus for chlamydia or gonorrhoea, 64% and 69%. Both protocols were equally effective in managing women with abnormal vaginal discharge. Simple clinical indicators for candidiasis, bacterial vaginosis, or trichomonas as in protocol A are sufficiently sensitive and specific for use in situations with no laboratory support. A modification to protocol A could increase detection of bacterial vaginosis at basic health service level. Further work is needed to identify appropriate indicators for infection with chlamydia or gonorrhoea.

Evaluation of two clinical protocols for the management of women with vaginal discharge in southern Thailand

PubMed Central

Chandeying, V.; Skov, S.; Kemapunmanus, M.; Law, M.; Geater, A.; Rowe, P.

1998-01-01

OBJECTIVES: (1) To compare the effectiveness of two clinical protocols for the management of vaginal discharge in the situations where no laboratory facilities are available but speculum examination is possible and where basic laboratory facilities are available. (2) To determine clinical and simple laboratory indicators for diagnosis of patients with vaginal discharge in the local setting. DESIGN: Alternate allocation of subjects to one of two management protocols. SUBJECTS: Women presenting to university gynaecology outpatients department with a complaint of vaginal discharge. METHODS: Subjects were alternately allocated management according to one of two protocols: one without (group A) and one with (group B) immediate access to results of basic laboratory tests. Full clinical assessment including speculum examination and microbiological assessment for infection with gonorrhoea, chlamydia, candida, trichomonas, and bacterial vaginosis was performed on all women. Follow up assessment of clinical and microbiological response was performed 1-2 weeks later. RESULTS: At initial assessment, both groups were similar in all respects except that more group B women had inflammation of the vulva. The prevalences of various conditions were: candidiasis 22%, bacterial vaginosis 38%, trichomoniasis 4%, chlamydia 4%, gonorrhoea 0.4%. There was no association between any demographic characteristic and diagnosis of cause of the discharge. Both protocols resulted in clinically and statistically significant improvements for women with candidiasis, bacterial vaginosis, and trichomoniasis. There were no clinically important differences in outcomes between the two protocols. The sensitivities and specificities of various indicators were: curd-like vaginal discharge for candidiasis, 72% and 100%; homogeneous vaginal discharge for bacterial vaginosis or trichomoniasis, 94% and 88%; absent or scanty lactobacilli for bacterial vaginosis, 99% and 68%; > 20% clue cells for bacterial vaginosis, 81% and 99%; visible endocervical mucopus for chlamydia or gonorrhoea, 36% and 86%; microscopic endocervical mucopus for chlamydia or gonorrhoea, 64% and 69%. CONCLUSIONS: Both protocols were equally effective in managing women with abnormal vaginal discharge. Simple clinical indicators for candidiasis, bacterial vaginosis, or trichomonas as in protocol A are sufficiently sensitive and specific for use in situations with no laboratory support. A modification to protocol A could increase detection of bacterial vaginosis at basic health service level. Further work is needed to identify appropriate indicators for infection with chlamydia or gonorrhoea. 


 PMID:9849555

Continuous-variable quantum key distribution based on a plug-and-play dual-phase-modulated coherent-states protocol

NASA Astrophysics Data System (ADS)

Huang, Duan; Huang, Peng; Wang, Tao; Li, Huasheng; Zhou, Yingming; Zeng, Guihua

2016-09-01

We propose and experimentally demonstrate a continuous-variable quantum key distribution (CV-QKD) protocol using dual-phase-modulated coherent states. We show that the modulation scheme of our protocol works equivalently to that of the Gaussian-modulated coherent-states (GMCS) protocol, but shows better experimental feasibility in the plug-and-play configuration. Besides, it waives the necessity of propagation of a local oscillator (LO) between legitimate users and generates a real local LO for quantum measurement. Our protocol is proposed independent of the one-way GMCS QKD without sending a LO [Opt. Lett. 40, 3695 (2015), 10.1364/OL.40.003695; Phys. Rev. X 5, 041009 (2015), 10.1103/PhysRevX.5.041009; Phys. Rev. X 5, 041010 (2015), 10.1103/PhysRevX.5.041010]. In those recent works, the system stability will suffer the impact of polarization drifts induced by environmental perturbations, and two independent frequency-locked laser sources are necessary to achieve reliable coherent detection. In the proposed protocol, these previous problems can be resolved. We derive the security bounds for our protocol against collective attacks, and we also perform a proof-of-principle experiment to confirm the utility of our proposal in real-life applications. Such an efficient scheme provides a way of removing the security loopholes associated with the transmitting LO, which have been a notoriously hard problem in continuous-variable quantum communication.

Efficient model checking of network authentication protocol based on SPIN

NASA Astrophysics Data System (ADS)

Tan, Zhi-hua; Zhang, Da-fang; Miao, Li; Zhao, Dan

2013-03-01

Model checking is a very useful technique for verifying the network authentication protocols. In order to improve the efficiency of modeling and verification on the protocols with the model checking technology, this paper first proposes a universal formalization description method of the protocol. Combined with the model checker SPIN, the method can expediently verify the properties of the protocol. By some modeling simplified strategies, this paper can model several protocols efficiently, and reduce the states space of the model. Compared with the previous literature, this paper achieves higher degree of automation, and better efficiency of verification. Finally based on the method described in the paper, we model and verify the Privacy and Key Management (PKM) authentication protocol. The experimental results show that the method of model checking is effective, which is useful for the other authentication protocols.

ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments.

PubMed

Khan, Imtiaz A; Fraser, Adam; Bray, Mark-Anthony; Smith, Paul J; White, Nick S; Carpenter, Anne E; Errington, Rachel J

2014-12-01

Experimental reproducibility is fundamental to the progress of science. Irreproducible research decreases the efficiency of basic biological research and drug discovery and impedes experimental data reuse. A major contributing factor to irreproducibility is difficulty in interpreting complex experimental methodologies and designs from written text and in assessing variations among different experiments. Current bioinformatics initiatives either are focused on computational research reproducibility (i.e. data analysis) or laboratory information management systems. Here, we present a software tool, ProtocolNavigator, which addresses the largely overlooked challenges of interpretation and assessment. It provides a biologist-friendly open-source emulation-based tool for designing, documenting and reproducing biological experiments. ProtocolNavigator was implemented in Python 2.7, using the wx module to build the graphical user interface. It is a platform-independent software and freely available from http://protocolnavigator.org/index.html under the GPL v2 license. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A reconfigurable visual-programming library for real-time closed-loop cellular electrophysiology

PubMed Central

Biró, István; Giugliano, Michele

2015-01-01

Most of the software platforms for cellular electrophysiology are limited in terms of flexibility, hardware support, ease of use, or re-configuration and adaptation for non-expert users. Moreover, advanced experimental protocols requiring real-time closed-loop operation to investigate excitability, plasticity, dynamics, are largely inaccessible to users without moderate to substantial computer proficiency. Here we present an approach based on MATLAB/Simulink, exploiting the benefits of LEGO-like visual programming and configuration, combined to a small, but easily extendible library of functional software components. We provide and validate several examples, implementing conventional and more sophisticated experimental protocols such as dynamic-clamp or the combined use of intracellular and extracellular methods, involving closed-loop real-time control. The functionality of each of these examples is demonstrated with relevant experiments. These can be used as a starting point to create and support a larger variety of electrophysiological tools and methods, hopefully extending the range of default techniques and protocols currently employed in experimental labs across the world. PMID:26157385

Spina Bifida

MedlinePlus

... of myelomeningocele through a National Institutes of Health experimental protocol (Management of Myelomeningocele Study, or MOMS). Fetal ... additional loss from occurring. The surgery is considered experimental and there are risks to the fetus as ...

Comparison of Gluten Extraction Protocols Assessed by LC-MS/MS Analysis.

PubMed

Fallahbaghery, Azadeh; Zou, Wei; Byrne, Keren; Howitt, Crispin A; Colgrave, Michelle L

2017-04-05

The efficiency of gluten extraction is of critical importance to the results derived from any analytical method for gluten detection and quantitation, whether it employs reagent-based technology (antibodies) or analytical instrumentation (mass spectrometry). If the target proteins are not efficiently extracted, the end result will be an under-estimation in the gluten content posing a health risk to people affected by conditions such as celiac disease (CD) and nonceliac gluten sensitivity (NCGS). Five different extraction protocols were investigated using LC-MRM-MS for their ability to efficiently and reproducibly extract gluten. The rapid and simple "IPA/DTT" protocol and related "two-step" protocol were enriched for gluten proteins, 55/86% (trypsin/chymotrypsin) and 41/68% of all protein identifications, respectively, with both methods showing high reproducibility (CV < 15%). When using multistep protocols, it was critical to examine all fractions, as coextraction of proteins occurred across fractions, with significant levels of proteins existing in unexpected fractions and not all proteins within a particular gluten class behaving the same.

Lightweight UDP Pervasive Protocol in Smart Home Environment Based on Labview

NASA Astrophysics Data System (ADS)

Kurniawan, Wijaya; Hannats Hanafi Ichsan, Mochammad; Rizqika Akbar, Sabriansyah; Arwani, Issa

2017-04-01

TCP (Transmission Control Protocol) technology in a reliable environment was not a problem, but not in an environment where the entire Smart Home network connected locally. Currently employing pervasive protocols using TCP technology, when data transmission is sent, it would be slower because they have to perform handshaking process in advance and could not broadcast the data. On smart home environment, it does not need large size and complex data transmission between monitoring site and monitoring center required in Smart home strain monitoring system. UDP (User Datagram Protocol) technology is quick and simple on data transmission process. UDP can broadcast messages because the UDP did not require handshaking and with more efficient memory usage. LabVIEW is a programming language software for processing and visualization of data in the field of data acquisition. This paper proposes to examine Pervasive UDP protocol implementations in smart home environment based on LabVIEW. UDP coded in LabVIEW and experiments were performed on a PC and can work properly.

A data transmission method for particle physics experiments based on Ethernet physical layer

NASA Astrophysics Data System (ADS)

Huang, Xi-Ru; Cao, Ping; Zheng, Jia-Jun

2015-11-01

Due to its advantages of universality, flexibility and high performance, fast Ethernet is widely used in readout system design for modern particle physics experiments. However, Ethernet is usually used together with the TCP/IP protocol stack, which makes it difficult to implement readout systems because designers have to use the operating system to process this protocol. Furthermore, TCP/IP degrades the transmission efficiency and real-time performance. To maximize the performance of Ethernet in physics experiment applications, a data readout method based on the physical layer (PHY) is proposed. In this method, TCP/IP is replaced with a customized and simple protocol, which makes it easier to implement. On each readout module, data from the front-end electronics is first fed into an FPGA for protocol processing and then sent out to a PHY chip controlled by this FPGA for transmission. This kind of data path is fully implemented by hardware. From the side of the data acquisition system (DAQ), however, the absence of a standard protocol causes problems for the network related applications. To solve this problem, in the operating system kernel space, data received by the network interface card is redirected from the traditional flow to a specified memory space by a customized program. This memory space can easily be accessed by applications in user space. For the purpose of verification, a prototype system has been designed and implemented. Preliminary test results show that this method can meet the requirements of data transmission from the readout module to the DAQ with an efficient and simple manner. Supported by National Natural Science Foundation of China (11005107) and Independent Projects of State Key Laboratory of Particle Detection and Electronics (201301)

Protocol: a rapid and economical procedure for purification of plasmid or plant DNA with diverse applications in plant biology

PubMed Central

2010-01-01

Research in plant molecular biology involves DNA purification on a daily basis. Although different commercial kits enable convenient extraction of high-quality DNA from E. coli cells, PCR and agarose gel samples as well as plant tissues, each kit is designed for a particular type of DNA extraction work, and the cost of purchasing these kits over a long run can be considerable. Furthermore, a simple method for the isolation of binary plasmid from Agrobacterium tumefaciens cells with satisfactory yield is lacking. Here we describe an easy protocol using homemade silicon dioxide matrix and seven simple solutions for DNA extraction from E. coli and A. tumefaciens cells, PCR and restriction digests, agarose gel slices, and plant tissues. Compared with the commercial kits, this protocol allows rapid DNA purification from diverse sources with comparable yield and purity at negligible cost. Following this protocol, we have demonstrated: (1) DNA fragments as small as a MYC-epitope tag coding sequence can be successfully recovered from an agarose gel slice; (2) Miniprep DNA from E. coli can be eluted with as little as 5 μl water, leading to high DNA concentrations (>1 μg/μl) for efficient biolistic bombardment of Arabidopsis seedlings, polyethylene glycol (PEG)-mediated Arabidopsis protoplast transfection and maize protoplast electroporation; (3) Binary plasmid DNA prepared from A. tumefaciens is suitable for verification by restriction analysis without the need for large scale propagation; (4) High-quality genomic DNA is readily isolated from several plant species including Arabidopsis, tobacco and maize. Thus, the silicon dioxide matrix-based DNA purification protocol offers an easy, efficient and economical way to extract DNA for various purposes in plant research. PMID:20180960

CT and MR Protocol Standardization Across a Large Health System: Providing a Consistent Radiologist, Patient, and Referring Provider Experience.

PubMed

Sachs, Peter B; Hunt, Kelly; Mansoubi, Fabien; Borgstede, James

2017-02-01

Building and maintaining a comprehensive yet simple set of standardized protocols for a cross-sectional image can be a daunting task. A single department may have difficulty preventing "protocol creep," which almost inevitably occurs when an organized "playbook" of protocols does not exist and individual radiologists and technologists alter protocols at will and on a case-by-case basis. When multiple departments or groups function in a large health system, the lack of uniformity of protocols can increase exponentially. In 2012, the University of Colorado Hospital formed a large health system (UCHealth) and became a 5-hospital provider network. CT and MR imaging studies are conducted at multiple locations by different radiology groups. To facilitate consistency in ordering, acquisition, and appearance of a given study, regardless of location, we minimized the number of protocols across all scanners and sites of practice with a clinical indication-driven protocol selection and standardization process. Here we review the steps utilized to perform this process improvement task and insure its stability over time. Actions included creation of a standardized protocol template, which allowed for changes in electronic storage and management of protocols, designing a change request form, and formation of a governance structure. We utilized rapid improvement events (1 day for CT, 2 days for MR) and reduced 248 CT protocols into 97 standardized protocols and 168 MR protocols to 66. Additional steps are underway to further standardize output and reporting of imaging interpretation. This will result in an improved, consistent radiologist, patient, and provider experience across the system.

Modeling of Receptor Tyrosine Kinase Signaling: Computational and Experimental Protocols.

PubMed

Fey, Dirk; Aksamitiene, Edita; Kiyatkin, Anatoly; Kholodenko, Boris N

2017-01-01

The advent of systems biology has convincingly demonstrated that the integration of experiments and dynamic modelling is a powerful approach to understand the cellular network biology. Here we present experimental and computational protocols that are necessary for applying this integrative approach to the quantitative studies of receptor tyrosine kinase (RTK) signaling networks. Signaling by RTKs controls multiple cellular processes, including the regulation of cell survival, motility, proliferation, differentiation, glucose metabolism, and apoptosis. We describe methods of model building and training on experimentally obtained quantitative datasets, as well as experimental methods of obtaining quantitative dose-response and temporal dependencies of protein phosphorylation and activities. The presented methods make possible (1) both the fine-grained modeling of complex signaling dynamics and identification of salient, course-grained network structures (such as feedback loops) that bring about intricate dynamics, and (2) experimental validation of dynamic models.

Patient and professional user experiences of simple telehealth for hypertension, medication reminders and smoking cessation: a service evaluation

PubMed Central

Cottrell, Elizabeth; Cox, Tracey; O'Connell, Phil; Chambers, Ruth

2015-01-01

Objectives To establish patient and professional user satisfaction with the Advice & Interactive Messaging (AIM) for Health programme delivered using a mobile phone-based, simple telehealth intervention, ‘Florence’. Design A service evaluation using data extracted from Florence and from a professional user electronic survey. Setting 425 primary care practices across 31 Clinical Commissioning Groups in England. Participants 3381 patients registered on 1 of 10 AIM protocols between March 2013 and January 2014 and 77 professional users. Intervention The AIM programme offered 10 clinical protocols, in three broad groups: (1) hypertension diagnosis/monitoring, (2) medication reminders and (3) smoking cessation. Florence sent patients prompts to submit clinical information, educational messages and user satisfaction questions. Patient responses were reviewed by their primary healthcare providers. Primary outcome measures Patients and professional user experiences of using AIM, and within this, Florence. Results Patient activity using Florence was generally good at month 1 for the hypertension protocols (71–80%), but reduced over 2–3 months (31–60%). For the other protocols, patient activity was 0–39% at 3 months. Minimum target days of texting were met for half the hypertension protocols. 1707/2304 (74%) patients sent evaluative texts responded at least once. Among responders, agreement with the adapted friends and family statement generally exceeded preproject aspirations. Professional responders were generally positive or equivocal about the programme. Conclusions Satisfaction with AIM appeared optimal when patients were carefully selected for the protocol; professional users were familiar with the system, the programme addressed a problem with the previous service delivery that was identified by users and users took an active approach to achieve clinical goals. However, there was a significant decrease in patients’ use of Florence over time. Future applications may be optimised by identifying and addressing reasons for the waning use of the service and enhancing support during implementation of the service. PMID:25795698

Engineering platform and experimental protocol for design and evaluation of a neurally-controlled powered transfemoral prosthesis.

PubMed

Zhang, Fan; Liu, Ming; Harper, Stephen; Lee, Michael; Huang, He

2014-07-22

To enable intuitive operation of powered artificial legs, an interface between user and prosthesis that can recognize the user's movement intent is desired. A novel neural-machine interface (NMI) based on neuromuscular-mechanical fusion developed in our previous study has demonstrated a great potential to accurately identify the intended movement of transfemoral amputees. However, this interface has not yet been integrated with a powered prosthetic leg for true neural control. This study aimed to report (1) a flexible platform to implement and optimize neural control of powered lower limb prosthesis and (2) an experimental setup and protocol to evaluate neural prosthesis control on patients with lower limb amputations. First a platform based on a PC and a visual programming environment were developed to implement the prosthesis control algorithms, including NMI training algorithm, NMI online testing algorithm, and intrinsic control algorithm. To demonstrate the function of this platform, in this study the NMI based on neuromuscular-mechanical fusion was hierarchically integrated with intrinsic control of a prototypical transfemoral prosthesis. One patient with a unilateral transfemoral amputation was recruited to evaluate our implemented neural controller when performing activities, such as standing, level-ground walking, ramp ascent, and ramp descent continuously in the laboratory. A novel experimental setup and protocol were developed in order to test the new prosthesis control safely and efficiently. The presented proof-of-concept platform and experimental setup and protocol could aid the future development and application of neurally-controlled powered artificial legs.

What if Finding Data was as Easy as Subscribing to the News?

NASA Astrophysics Data System (ADS)

Duerr, R. E.

2011-12-01

Data are the "common wealth of humanity," the fuel that drives the sciences; but much of the data that exist are inaccessible, buried in one of numerous stove-piped data systems, or entirely hidden unless you have direct knowledge of and contact with the investigator that acquired them. Much of the "wealth" is squandered and overall scientific progress inhibited, a situation that is becoming increasingly untenable with the openness required by data-driven science. What are needed are simple interoperability protocols and advertising mechanisms that allow data from disparate data systems to be easily discovered, explored, and accessed. The tools must be simple enough that individual investigators can use them without IT support. The tools cannot rely on centralized repositories or registries but must enable the development of ad-hoc or special purpose aggregations of data and services tailored to individual community needs. In addition, the protocols must scale to support the discovery of and access to the holdings of the global, interdisciplinary community, be they individual investigators or major data centers. NSIDC, in conjunction with other members of the Federation of Earth Science Information Partners and the Polar Information Commons, are working on just such a suite of tools and protocols. In this talk, I discuss data and service casting, aggregation, data badging, and OpenSearch - a suite of tools and protocols which, when used in conjunction with each other, have the potential of completely changing the way that data and services worldwide are discovered and used.

Self-referenced continuous-variable quantum key distribution protocol

DOE PAGES

Soh, Daniel Beom Soo; Sarovar, Mohan; Brif, Constantin; ...

2015-10-21

We introduce a new continuous-variable quantum key distribution (CV-QKD) protocol, self-referenced CV-QKD, that eliminates the need for transmission of a high-power local oscillator between the communicating parties. In this protocol, each signal pulse is accompanied by a reference pulse (or a pair of twin reference pulses), used to align Alice’s and Bob’s measurement bases. The method of phase estimation and compensation based on the reference pulse measurement can be viewed as a quantum analog of intradyne detection used in classical coherent communication, which extracts the phase information from the modulated signal. We present a proof-of-principle, fiber-based experimental demonstration of themore » protocol and quantify the expected secret key rates by expressing them in terms of experimental parameters. Our analysis of the secret key rate fully takes into account the inherent uncertainty associated with the quantum nature of the reference pulse(s) and quantifies the limit at which the theoretical key rate approaches that of the respective conventional protocol that requires local oscillator transmission. The self-referenced protocol greatly simplifies the hardware required for CV-QKD, especially for potential integrated photonics implementations of transmitters and receivers, with minimum sacrifice of performance. Furthermore, it provides a pathway towards scalable integrated CV-QKD transceivers, a vital step towards large-scale QKD networks.« less

Self-referenced continuous-variable quantum key distribution protocol

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

Soh, Daniel Beom Soo; Sarovar, Mohan; Brif, Constantin

We introduce a new continuous-variable quantum key distribution (CV-QKD) protocol, self-referenced CV-QKD, that eliminates the need for transmission of a high-power local oscillator between the communicating parties. In this protocol, each signal pulse is accompanied by a reference pulse (or a pair of twin reference pulses), used to align Alice’s and Bob’s measurement bases. The method of phase estimation and compensation based on the reference pulse measurement can be viewed as a quantum analog of intradyne detection used in classical coherent communication, which extracts the phase information from the modulated signal. We present a proof-of-principle, fiber-based experimental demonstration of themore » protocol and quantify the expected secret key rates by expressing them in terms of experimental parameters. Our analysis of the secret key rate fully takes into account the inherent uncertainty associated with the quantum nature of the reference pulse(s) and quantifies the limit at which the theoretical key rate approaches that of the respective conventional protocol that requires local oscillator transmission. The self-referenced protocol greatly simplifies the hardware required for CV-QKD, especially for potential integrated photonics implementations of transmitters and receivers, with minimum sacrifice of performance. Furthermore, it provides a pathway towards scalable integrated CV-QKD transceivers, a vital step towards large-scale QKD networks.« less

Self-Referenced Continuous-Variable Quantum Key Distribution Protocol

NASA Astrophysics Data System (ADS)

Soh, Daniel B. S.; Brif, Constantin; Coles, Patrick J.; Lütkenhaus, Norbert; Camacho, Ryan M.; Urayama, Junji; Sarovar, Mohan

2015-10-01

We introduce a new continuous-variable quantum key distribution (CV-QKD) protocol, self-referenced CV-QKD, that eliminates the need for transmission of a high-power local oscillator between the communicating parties. In this protocol, each signal pulse is accompanied by a reference pulse (or a pair of twin reference pulses), used to align Alice's and Bob's measurement bases. The method of phase estimation and compensation based on the reference pulse measurement can be viewed as a quantum analog of intradyne detection used in classical coherent communication, which extracts the phase information from the modulated signal. We present a proof-of-principle, fiber-based experimental demonstration of the protocol and quantify the expected secret key rates by expressing them in terms of experimental parameters. Our analysis of the secret key rate fully takes into account the inherent uncertainty associated with the quantum nature of the reference pulse(s) and quantifies the limit at which the theoretical key rate approaches that of the respective conventional protocol that requires local oscillator transmission. The self-referenced protocol greatly simplifies the hardware required for CV-QKD, especially for potential integrated photonics implementations of transmitters and receivers, with minimum sacrifice of performance. As such, it provides a pathway towards scalable integrated CV-QKD transceivers, a vital step towards large-scale QKD networks.

A neural networks-based hybrid routing protocol for wireless mesh networks.

PubMed

Kojić, Nenad; Reljin, Irini; Reljin, Branimir

2012-01-01

The networking infrastructure of wireless mesh networks (WMNs) is decentralized and relatively simple, but they can display reliable functioning performance while having good redundancy. WMNs provide Internet access for fixed and mobile wireless devices. Both in urban and rural areas they provide users with high-bandwidth networks over a specific coverage area. The main problems affecting these networks are changes in network topology and link quality. In order to provide regular functioning, the routing protocol has the main influence in WMN implementations. In this paper we suggest a new routing protocol for WMN, based on good results of a proactive and reactive routing protocol, and for that reason it can be classified as a hybrid routing protocol. The proposed solution should avoid flooding and creating the new routing metric. We suggest the use of artificial logic-i.e., neural networks (NNs). This protocol is based on mobile agent technologies controlled by a Hopfield neural network. In addition to this, our new routing metric is based on multicriteria optimization in order to minimize delay and blocking probability (rejected packets or their retransmission). The routing protocol observes real network parameters and real network environments. As a result of artificial logic intelligence, the proposed routing protocol should maximize usage of network resources and optimize network performance.

A Neural Networks-Based Hybrid Routing Protocol for Wireless Mesh Networks

PubMed Central

Kojić, Nenad; Reljin, Irini; Reljin, Branimir

2012-01-01

The networking infrastructure of wireless mesh networks (WMNs) is decentralized and relatively simple, but they can display reliable functioning performance while having good redundancy. WMNs provide Internet access for fixed and mobile wireless devices. Both in urban and rural areas they provide users with high-bandwidth networks over a specific coverage area. The main problems affecting these networks are changes in network topology and link quality. In order to provide regular functioning, the routing protocol has the main influence in WMN implementations. In this paper we suggest a new routing protocol for WMN, based on good results of a proactive and reactive routing protocol, and for that reason it can be classified as a hybrid routing protocol. The proposed solution should avoid flooding and creating the new routing metric. We suggest the use of artificial logic—i.e., neural networks (NNs). This protocol is based on mobile agent technologies controlled by a Hopfield neural network. In addition to this, our new routing metric is based on multicriteria optimization in order to minimize delay and blocking probability (rejected packets or their retransmission). The routing protocol observes real network parameters and real network environments. As a result of artificial logic intelligence, the proposed routing protocol should maximize usage of network resources and optimize network performance. PMID:22969360

40 CFR 792.120 - Protocol.

Code of Federal Regulations, 2014 CFR

2014-07-01

... the test system. (8) A description of the experimental design, including methods for the control of... at which the study is being conducted. (4) The proposed experimental start and termination dates. (5...

40 CFR 792.120 - Protocol.

Code of Federal Regulations, 2012 CFR

2012-07-01

... the test system. (8) A description of the experimental design, including methods for the control of... at which the study is being conducted. (4) The proposed experimental start and termination dates. (5...

40 CFR 792.120 - Protocol.

Code of Federal Regulations, 2013 CFR

2013-07-01

... the test system. (8) A description of the experimental design, including methods for the control of... at which the study is being conducted. (4) The proposed experimental start and termination dates. (5...

40 CFR 792.120 - Protocol.

Code of Federal Regulations, 2011 CFR

2011-07-01

... the test system. (8) A description of the experimental design, including methods for the control of... at which the study is being conducted. (4) The proposed experimental start and termination dates. (5...

Optimizing Standard Sequential Extraction Protocol With Lake And Ocean Sediments

EPA Science Inventory

The environmental mobility/availability behavior of radionuclides in soils and sediments depends on their speciation. Experiments have been carried out to develop a simple but robust radionuclide sequential extraction method for identification of radionuclide partitioning in sed...

A facile and eco-friendly synthesis of diarylthiazoles and diarylimidazoles in water

EPA Science Inventory

A simple, efficient and high yielding greener protocol for the synthesis of substituted thiazoles and imidazoles is described that utilizes the reaction of readily available α-tosyloxy ketones with variety of thioamides/amidines in water

A shorter and more specific oral sensitization-based experimental model of food allergy in mice.

PubMed

Bailón, Elvira; Cueto-Sola, Margarita; Utrilla, Pilar; Rodríguez-Ruiz, Judith; Garrido-Mesa, Natividad; Zarzuelo, Antonio; Xaus, Jordi; Gálvez, Julio; Comalada, Mònica

2012-07-31

Cow's milk protein allergy (CMPA) is one of the most prevalent human food-borne allergies, particularly in children. Experimental animal models have become critical tools with which to perform research on new therapeutic approaches and on the molecular mechanisms involved. However, oral food allergen sensitization in mice requires several weeks and is usually associated with unspecific immune responses. To overcome these inconveniences, we have developed a new food allergy model that takes only two weeks while retaining the main characters of allergic response to food antigens. The new model is characterized by oral sensitization of weaned Balb/c mice with 5 doses of purified cow's milk protein (CMP) plus cholera toxin (CT) for only two weeks and posterior challenge with an intraperitoneal administration of the allergen at the end of the sensitization period. In parallel, we studied a conventional protocol that lasts for seven weeks, and also the non-specific effects exerted by CT in both protocols. The shorter protocol achieves a similar clinical score as the original food allergy model without macroscopically affecting gut morphology or physiology. Moreover, the shorter protocol caused an increased IL-4 production and a more selective antigen-specific IgG1 response. Finally, the extended CT administration during the sensitization period of the conventional protocol is responsible for the exacerbated immune response observed in that model. Therefore, the new model presented here allows a reduction not only in experimental time but also in the number of animals required per experiment while maintaining the features of conventional allergy models. We propose that the new protocol reported will contribute to advancing allergy research. Copyright © 2012 Elsevier B.V. All rights reserved.

Design and Implementation of a Secure Modbus Protocol

NASA Astrophysics Data System (ADS)

Fovino, Igor Nai; Carcano, Andrea; Masera, Marcelo; Trombetta, Alberto

The interconnectivity of modern and legacy supervisory control and data acquisition (SCADA) systems with corporate networks and the Internet has significantly increased the threats to critical infrastructure assets. Meanwhile, traditional IT security solutions such as firewalls, intrusion detection systems and antivirus software are relatively ineffective against attacks that specifically target vulnerabilities in SCADA protocols. This paper describes a secure version of the Modbus SCADA protocol that incorporates integrity, authentication, non-repudiation and anti-replay mechanisms. Experimental results using a power plant testbed indicate that the augmented protocol provides good security functionality without significant overhead.

Mutation-based learning to improve student autonomy and scientific inquiry skills in a large genetics laboratory course.

PubMed

Wu, Jinlu

2013-01-01

Laboratory education can play a vital role in developing a learner's autonomy and scientific inquiry skills. In an innovative, mutation-based learning (MBL) approach, students were instructed to redesign a teacher-designed standard experimental protocol by a "mutation" method in a molecular genetics laboratory course. Students could choose to delete, add, reverse, or replace certain steps of the standard protocol to explore questions of interest to them in a given experimental scenario. They wrote experimental proposals to address their rationales and hypotheses for the "mutations"; conducted experiments in parallel, according to both standard and mutated protocols; and then compared and analyzed results to write individual lab reports. Various autonomy-supportive measures were provided in the entire experimental process. Analyses of student work and feedback suggest that students using the MBL approach 1) spend more time discussing experiments, 2) use more scientific inquiry skills, and 3) find the increased autonomy afforded by MBL more enjoyable than do students following regimented instructions in a conventional "cookbook"-style laboratory. Furthermore, the MBL approach does not incur an obvious increase in labor and financial costs, which makes it feasible for easy adaptation and implementation in a large class.

Design of efficient and simple interface testing equipment for opto-electric tracking system

NASA Astrophysics Data System (ADS)

Liu, Qiong; Deng, Chao; Tian, Jing; Mao, Yao

2016-10-01

Interface testing for opto-electric tracking system is one important work to assure system running performance, aiming to verify the design result of every electronic interface matching the communication protocols or not, by different levels. Opto-electric tracking system nowadays is more complicated, composed of many functional units. Usually, interface testing is executed between units manufactured completely, highly depending on unit design and manufacture progress as well as relative people. As a result, it always takes days or weeks, inefficiently. To solve the problem, this paper promotes an efficient and simple interface testing equipment for opto-electric tracking system, consisting of optional interface circuit card, processor and test program. The hardware cards provide matched hardware interface(s), easily offered from hardware engineer. Automatic code generation technique is imported, providing adaption to new communication protocols. Automatic acquiring items, automatic constructing code architecture and automatic encoding are used to form a new program quickly with adaption. After simple steps, a standard customized new interface testing equipment with matching test program and interface(s) is ready for a waiting-test system in minutes. The efficient and simple interface testing equipment for opto-electric tracking system has worked for many opto-electric tracking system to test entire or part interfaces, reducing test time from days to hours, greatly improving test efficiency, with high software quality and stability, without manual coding. Used as a common tool, the efficient and simple interface testing equipment for opto-electric tracking system promoted by this paper has changed traditional interface testing method and created much higher efficiency.

(abstract) Experimental Results From Internetworking Data Applications Over Various Wireless Networks Using a Single Flexible Error Control Protocol

NASA Technical Reports Server (NTRS)

Kanai, T.; Kramer, M.; McAuley, A. J.; Nowack, S.; Pinck, D. S.; Ramirez, G.; Stewart, I.; Tohme, H.; Tong, L.

1995-01-01

This paper describes results from several wireless field trials in New Jersey, California, and Colorado, conducted jointly by researchers at Bellcore, JPL, and US West over the course of 1993 and 1994. During these trials, applications communicated over multiple wireless networks including satellite, low power PCS, high power cellular, packet data, and the wireline Public Switched Telecommunications Network (PSTN). Key goals included 1) designing data applications and an API suited to mobile users, 2) investigating internetworking issues, 3) characterizing wireless networks under various field conditions, and 4) comparing the performance of different protocol mechanisms over the diverse networks and applications. We describe experimental results for different protocol mechanisms and parameters, such as acknowledgment schemes and packet sizes. We show the need for powerful error control mechanisms such as selective acknowledgements and combining data from multiple transmissions. We highlight the possibility of a common protocol for all wireless networks, from micro-cellular PCS to satellite networks.

Changes in morphology of long bone marrow tissue of rats submitted to cryotherapy with liquid nitrogen.

PubMed

Costa, Fábio Wildson Gurgel; Pessoa, Rosana Maria Andrade; Nogueira, Carlos Bruno Pinheiro; Pereira, Karuza Maria Alves; Brito, Gerly Anne de Castro; Soares, Eduardo Costa Studart

2012-02-01

To study the main effects of local use of liquid nitrogen on bone marrow tissue in rats. The femoral diaphyses of 42 Wistar rats were exposed to three local and sequential applications of liquid nitrogen for one or two minutes, intercalated with periods of five minutes of passive thawing. The animals were sacrificed after one, two, four and 12 weeks and the specimens obtained were analyzed histomorphologically. In the second experimental week of one-minute protocol, histological degree of inflammation obtained a mean score of one (mild), ranging from 0 (absent or scarce) and two (moderate) (Kruskal-Wallis test p=0.01). In the second experimental week of two-minute protocol, degree of inflammation to the medullar tissue obtained an average score of two (Kruskal-Wallis test p=0.01). The degree of inflammation of the bone marrow tissue was higher in protocol of three applications of two minutes compared to protocol of three applications of one minute.

Comparison of protocols for measuring and calculating postmortem submersion intervals for human analogs in fresh water.

PubMed

Humphreys, Michael K; Panacek, Edward; Green, William; Albers, Elizabeth

2013-03-01

Protocols for determining postmortem submersion interval (PMSI) have long been problematic for forensic investigators due to the wide variety of factors affecting the rate of decomposition of submerged carrion. Likewise, it has been equally problematic for researchers to develop standardized experimental protocols to monitor underwater decomposition without artificially affecting the decomposition rate. This study compares two experimental protocols: (i) underwater in situ evaluation with photographic documentation utilizing the Heaton et al. total aquatic decomposition (TAD) score and (ii) weighing the carrion before and after submersion. Complete forensic necropsies were performed as a control. Perinatal piglets were used as human analogs. The results of this study indicate that in order to objectively measure decomposition over time, the human analog should be examined at depth using the TAD scoring system rather than utilizing a carrion weight evaluation. The acquired TAD score can be used to calculate an approximate PMSI. © 2012 American Academy of Forensic Sciences.

Translational microsurgery. A new platform for transplantation research.

PubMed

Kobayashi, Eiji; Haga, Junko

2016-03-01

Clinical microsurgery has been introduced in many fields, while experimental microsurgery has the cross-disciplinary features of the sciences and techniques for growth of medicine, pharmacology, veterinary, engineering etc. Training protocol, proposing a new name as Translational Microsurgery, was introduced. Reconstructive skills of hepatic artery in pediatric living donor liver transplantation were summarized. Ex vivo training protocol using artificial blood vessel for surgeons was proposed. Clinical microsurgery requires anastomosis with delicate arteries and limited field of view. Our training protocol revealed that the relation between the score and speed was seen, while not all the surgeons with enough experience got high score. This training led to muster clinical skills and to apply excellent experimental works. Our microsurgical training protocol has been planned from the points of clinical setting. Training for vascular anastomosis led to rodent transplantation models. These models were used for immunology and immunosuppressant research. Microsurgical techniques led to master catheter technique and to inject various drugs or gene vectors.

Evaluating optimal therapy robustness by virtual expansion of a sample population, with a case study in cancer immunotherapy

PubMed Central

Barish, Syndi; Ochs, Michael F.; Sontag, Eduardo D.; Gevertz, Jana L.

2017-01-01

Cancer is a highly heterogeneous disease, exhibiting spatial and temporal variations that pose challenges for designing robust therapies. Here, we propose the VEPART (Virtual Expansion of Populations for Analyzing Robustness of Therapies) technique as a platform that integrates experimental data, mathematical modeling, and statistical analyses for identifying robust optimal treatment protocols. VEPART begins with time course experimental data for a sample population, and a mathematical model fit to aggregate data from that sample population. Using nonparametric statistics, the sample population is amplified and used to create a large number of virtual populations. At the final step of VEPART, robustness is assessed by identifying and analyzing the optimal therapy (perhaps restricted to a set of clinically realizable protocols) across each virtual population. As proof of concept, we have applied the VEPART method to study the robustness of treatment response in a mouse model of melanoma subject to treatment with immunostimulatory oncolytic viruses and dendritic cell vaccines. Our analysis (i) showed that every scheduling variant of the experimentally used treatment protocol is fragile (nonrobust) and (ii) discovered an alternative region of dosing space (lower oncolytic virus dose, higher dendritic cell dose) for which a robust optimal protocol exists. PMID:28716945

Automatized set-up procedure for transcranial magnetic stimulation protocols.

PubMed

Harquel, S; Diard, J; Raffin, E; Passera, B; Dall'Igna, G; Marendaz, C; David, O; Chauvin, A

2017-06-01

Transcranial Magnetic Stimulation (TMS) established itself as a powerful technique for probing and treating the human brain. Major technological evolutions, such as neuronavigation and robotized systems, have continuously increased the spatial reliability and reproducibility of TMS, by minimizing the influence of human and experimental factors. However, there is still a lack of efficient set-up procedure, which prevents the automation of TMS protocols. For example, the set-up procedure for defining the stimulation intensity specific to each subject is classically done manually by experienced practitioners, by assessing the motor cortical excitability level over the motor hotspot (HS) of a targeted muscle. This is time-consuming and introduces experimental variability. Therefore, we developed a probabilistic Bayesian model (AutoHS) that automatically identifies the HS position. Using virtual and real experiments, we compared the efficacy of the manual and automated procedures. AutoHS appeared to be more reproducible, faster, and at least as reliable as classical manual procedures. By combining AutoHS with robotized TMS and automated motor threshold estimation methods, our approach constitutes the first fully automated set-up procedure for TMS protocols. The use of this procedure decreases inter-experimenter variability while facilitating the handling of TMS protocols used for research and clinical routine. Copyright © 2017 Elsevier Inc. All rights reserved.

Numerical simulation of a relaxation test designed to fit a quasi-linear viscoelastic model for temporomandibular joint discs.

PubMed

Commisso, Maria S; Martínez-Reina, Javier; Mayo, Juana; Domínguez, Jaime

2013-02-01

The main objectives of this work are: (a) to introduce an algorithm for adjusting the quasi-linear viscoelastic model to fit a material using a stress relaxation test and (b) to validate a protocol for performing such tests in temporomandibular joint discs. This algorithm is intended for fitting the Prony series coefficients and the hyperelastic constants of the quasi-linear viscoelastic model by considering that the relaxation test is performed with an initial ramp loading at a certain rate. This algorithm was validated before being applied to achieve the second objective. Generally, the complete three-dimensional formulation of the quasi-linear viscoelastic model is very complex. Therefore, it is necessary to design an experimental test to ensure a simple stress state, such as uniaxial compression to facilitate obtaining the viscoelastic properties. This work provides some recommendations about the experimental setup, which are important to follow, as an inadequate setup could produce a stress state far from uniaxial, thus, distorting the material constants determined from the experiment. The test considered is a stress relaxation test using unconfined compression performed in cylindrical specimens extracted from temporomandibular joint discs. To validate the experimental protocol, the test was numerically simulated using finite-element modelling. The disc was arbitrarily assigned a set of quasi-linear viscoelastic constants (c1) in the finite-element model. Another set of constants (c2) was obtained by fitting the results of the simulated test with the proposed algorithm. The deviation of constants c2 from constants c1 measures how far the stresses are from the uniaxial state. The effects of the following features of the experimental setup on this deviation have been analysed: (a) the friction coefficient between the compression plates and the specimen (which should be as low as possible); (b) the portion of the specimen glued to the compression plates (smaller areas glued are better); and (c) the variation in the thickness of the specimen. The specimen's faces should be parallel to ensure a uniaxial stress state. However, this is not possible in real specimens, and a criterion must be defined to accept the specimen in terms of the specimen's thickness variation and the deviation of the fitted constants arising from such a variation.

A protocol for isolating insect mitochondrial genomes: a case study of NUMT in Melipona flavolineata (Hymenoptera: Apidae).

PubMed

Françoso, Elaine; Gomes, Fernando; Arias, Maria Cristina

2016-07-01

Nuclear mitochondrial DNA insertions (NUMTs) are mitochondrial DNA sequences that have been transferred into the nucleus and are recognized by the presence of indels and stop codons. Although NUMTs have been identified in a diverse range of species, their discovery was frequently accidental. Here, our initial goal was to develop and standardize a simple method for isolating NUMTs from the nuclear genome of a single bee. Subsequently, we tested our new protocol by determining whether the indels and stop codons of the cytochrome c oxidase subunit I (COI) sequence of Melipona flavolineata are of nuclear origin. The new protocol successfully demonstrated the presence of a COI NUMT. In addition to NUMT investigations, the protocol described here will also be very useful for studying mitochondrial mutations related to diseases and for sequencing complete mitochondrial genomes with high read coverage by Next-Generation technology.

Network Configuration Analysis for Formation Flying Satellites

NASA Technical Reports Server (NTRS)

Knoblock, Eric J.; Wallett, Thomas M.; Konangi, Vijay K.; Bhasin, Kul B.

2001-01-01

The performance of two networks to support autonomous multi-spacecraft formation flying systems is presented. Both systems are comprised of a ten-satellite formation, with one of the satellites designated as the central or 'mother ship.' All data is routed through the mother ship to the terrestrial network. The first system uses a TCP/EP over ATM protocol architecture within the formation, and the second system uses the IEEE 802.11 protocol architecture within the formation. The simulations consist of file transfers using either the File Transfer Protocol (FTP) or the Simple Automatic File Exchange (SAFE) Protocol. The results compare the IP queuing delay, IP queue size and IP processing delay at the mother ship as well as end-to-end delay for both systems. In all cases, using IEEE 802.11 within the formation yields less delay. Also, the throughput exhibited by SAFE is better than FTP.

Protocol for fermionic positive-operator-valued measures

NASA Astrophysics Data System (ADS)

Arvidsson-Shukur, D. R. M.; Lepage, H. V.; Owen, E. T.; Ferrus, T.; Barnes, C. H. W.

2017-11-01

In this paper we present a protocol for the implementation of a positive-operator-valued measure (POVM) on massive fermionic qubits. We present methods for implementing nondispersive qubit transport, spin rotations, and spin polarizing beam-splitter operations. Our scheme attains linear opticslike control of the spatial extent of the qubits by considering ground-state electrons trapped in the minima of surface acoustic waves in semiconductor heterostructures. Furthermore, we numerically simulate a high-fidelity POVM that carries out Procrustean entanglement distillation in the framework of our scheme, using experimentally realistic potentials. Our protocol can be applied not only to pure ensembles with particle pairs of known identical entanglement, but also to realistic ensembles of particle pairs with a distribution of entanglement entropies. This paper provides an experimentally realizable design for future quantum technologies.

Experimental verification of multipartite entanglement in quantum networks

PubMed Central

McCutcheon, W.; Pappa, A.; Bell, B. A.; McMillan, A.; Chailloux, A.; Lawson, T.; Mafu, M.; Markham, D.; Diamanti, E.; Kerenidis, I.; Rarity, J. G.; Tame, M. S.

2016-01-01

Multipartite entangled states are a fundamental resource for a wide range of quantum information processing tasks. In particular, in quantum networks, it is essential for the parties involved to be able to verify if entanglement is present before they carry out a given distributed task. Here we design and experimentally demonstrate a protocol that allows any party in a network to check if a source is distributing a genuinely multipartite entangled state, even in the presence of untrusted parties. The protocol remains secure against dishonest behaviour of the source and other parties, including the use of system imperfections to their advantage. We demonstrate the verification protocol in a three- and four-party setting using polarization-entangled photons, highlighting its potential for realistic photonic quantum communication and networking applications. PMID:27827361

Compositional Verification of a Communication Protocol for a Remotely Operated Vehicle

NASA Technical Reports Server (NTRS)

Goodloe, Alwyn E.; Munoz, Cesar A.

2009-01-01

This paper presents the specification and verification in the Prototype Verification System (PVS) of a protocol intended to facilitate communication in an experimental remotely operated vehicle used by NASA researchers. The protocol is defined as a stack-layered com- position of simpler protocols. It can be seen as the vertical composition of protocol layers, where each layer performs input and output message processing, and the horizontal composition of different processes concurrently inhabiting the same layer, where each process satisfies a distinct requirement. It is formally proven that the protocol components satisfy certain delivery guarantees. Compositional techniques are used to prove these guarantees also hold in the composed system. Although the protocol itself is not novel, the methodology employed in its verification extends existing techniques by automating the tedious and usually cumbersome part of the proof, thereby making the iterative design process of protocols feasible.

A clinical pathway for the postoperative management of hypocalcemia after pediatric thyroidectomy reduces blood draws.

PubMed

Patel, Neha A; Bly, Randall A; Adams, Seth; Carlin, Kristen; Parikh, Sanjay R; Dahl, John P; Manning, Scott

2018-02-01

Postoperative calcium management is challenging following pediatric thyroidectomy given potential limitations in self-reporting symptoms and compliance with phlebotomy. A protocol was created at our tertiary children's institution utilizing intraoperative parathyroid hormone (PTH) levels to guide electrolyte management during hospitalization. The objective of this study was to determine the effect of a new thyroidectomy postoperative management protocol on two primary outcomes: (1) the number of postoperative calcium blood draws and (2) the length of hospital stay. Institutional review board approved retrospective study (2010-2016). Consecutive pediatric total thyroidectomy and completion thyroidectomy ± neck dissection cases from 1/1/2010 through 8/5/2016 at a single tertiary children's institution were retrospectively reviewed before and after initiation of a new management protocol. All cases after 2/1/2014 comprised the experimental group (post-protocol implementation). The pre-protocol control group consisted of cases prior to 2/1/2014. Multivariable linear and Poisson regression models were used to compare the control and experimental groups for outcome measure of number of calcium lab draws and hospital length of stay. 53 patients were included (n = 23, control group; n = 30 experimental group). The median age was 15 years. 41 patients (77.4%) were female. Postoperative calcium draws decreased from a mean of 5.2 to 3.6 per day post-protocol implementation (Rate Ratio = 0.70, p < .001), adjusting for covariates. The mean number of total inpatient calcium draws before protocol initiation was 13.3 (±13.20) compared to 7.2 (±4.25) in the post-protocol implementation group. Length of stay was 2.1 days in the control group and 1.8 days post-protocol implementation (p = .29). Patients who underwent concurrent neck dissection had a longer mean length of stay of 2.32 days compared to 1.66 days in those patients who did not undergo a neck dissection (p = .02). Hypocalcemia was also associated with a longer mean length of stay of 2.41 days compared to 1.60 days in patients who did not develop hypocalcemia (p < .01). The number of calcium blood draws was significantly reduced after introduction of a standardized protocol based on intraoperative PTH levels. The hospital length of stay did not change. Adoption of a standardized postoperative protocol based on intraoperative PTH levels may reduce the number of blood draws in children undergoing thyroidectomy. Copyright © 2017 Elsevier B.V. All rights reserved.

Compression-based aggregation model for medical web services.

PubMed

Al-Shammary, Dhiah; Khalil, Ibrahim

2010-01-01

Many organizations such as hospitals have adopted Cloud Web services in applying their network services to avoid investing heavily computing infrastructure. SOAP (Simple Object Access Protocol) is the basic communication protocol of Cloud Web services that is XML based protocol. Generally,Web services often suffer congestions and bottlenecks as a result of the high network traffic that is caused by the large XML overhead size. At the same time, the massive load on Cloud Web services in terms of the large demand of client requests has resulted in the same problem. In this paper, two XML-aware aggregation techniques that are based on exploiting the compression concepts are proposed in order to aggregate the medical Web messages and achieve higher message size reduction.

Understanding the antiangiogenic effect of metronomic chemotherapy through a simple mathematical model

NASA Astrophysics Data System (ADS)

Rodrigues, Diego S.; Mancera, Paulo F. A.; Pinho, Suani T. R.

2016-12-01

Despite the current and increasingly successful fight against cancer, there are some important questions concerning the efficiency of its treatment - in particular, the design of oncology chemotherapy protocols. Seeking efficiency, schedules based on more frequent, low-doses of drugs, known as metronomic chemotherapy, have been proposed as an alternative to the classical standard protocol of chemotherapy administration. The in silico approach may be very useful for providing a comparative analysis of these two kinds of protocols. In so doing, we found that metronomic schedules are more effective in eliminating tumour cells mainly due to their chemotherapeutic action on endothelial cells and that more frequent, low drug doses also entail outcomes in which the survival time of patient is increased.

Integrated protocol for reliable and fast quantification and documentation of electrophoresis gels.

PubMed

Rehbein, Peter; Schwalbe, Harald

2015-06-01

Quantitative analysis of electrophoresis gels is an important part in molecular cloning, as well as in protein expression and purification. Parallel quantifications in yield and purity can be most conveniently obtained from densitometric analysis. This communication reports a comprehensive, reliable and simple protocol for gel quantification and documentation, applicable for single samples and with special features for protein expression screens. As major component of the protocol, the fully annotated code of a proprietary open source computer program for semi-automatic densitometric quantification of digitized electrophoresis gels is disclosed. The program ("GelQuant") is implemented for the C-based macro-language of the widespread integrated development environment of IGOR Pro. Copyright © 2014 Elsevier Inc. All rights reserved.

Effects of a peer support programme for youth social services employees experiencing potentially traumatic events: a protocol for a prospective cohort study.

PubMed

Guay, Stephane; Tremblay, Nicole; Goncalves, Jane; Bilodeau, Henriette; Geoffrion, Steve

2017-06-24

The use of peer support programmes to help workers experiencing potentially traumatic events (PTE) has increased in high-risk organisations in the last decades. However, the scientific evidence of its effectiveness is still very limited. This paper aims to describe the protocol of a prospective cohort study that assesses the efficacy of a peer support programme among youth social services employees exposed to a PTE at work on psychological well-being, work functioning and needs of support. This is a mixed-methods prospective study that will examine workers' evolution four times over a 12-month period in Canada. This study involves: (1) quantitative data obtained through self-administrated questionnaires among 222 workers, and (2) qualitative in-depth interviews with a subsample of 45 workers. This study will compare findings from a cohort who received the support of a peer following a PTE (peer support-experimental protocol) as part of the experimental protocol of the Montreal Youth Social Services-University Institute (MYSS-UI), the second group of workers did not ask for the peer support (no peer support-experimental protocol) but was part of MYSS-UI, and the third group received standard organisational support from the Monteregie Youth Social Services (MYSS) (standard organisational protocol). The protocol and informed consent form complied with the ethics guidelines of the MYSS-UI. The Research Ethics Board of MYSS-UI and MYSS reviewed and accepted the protocol as required. The results of the study will be published in peer-reviewed journals, presented at research and general public conferences, disseminated via a public report for the institute that funded the project and for all workers. Results of this study will influence decision making regarding intervention policies following PTE and peer support interventions may be expanded throughout the youth social services in Canada and worldwide. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Coherent one-way quantum key distribution

NASA Astrophysics Data System (ADS)

Stucki, Damien; Fasel, Sylvain; Gisin, Nicolas; Thoma, Yann; Zbinden, Hugo

2007-05-01

Quantum Key Distribution (QKD) consists in the exchange of a secrete key between two distant points [1]. Even if quantum key distribution systems exist and commercial systems are reaching the market [2], there are still improvements to be made: simplify the construction of the system; increase the secret key rate. To this end, we present a new protocol for QKD tailored to work with weak coherent pulses and at high bit rates [3]. The advantages of this system are that the setup is experimentally simple and it is tolerant to reduced interference visibility and to photon number splitting attacks, thus resulting in a high efficiency in terms of distilled secret bits per qubit. After having successfully tested the feasibility of the system [3], we are currently developing a fully integrated and automated prototype within the SECOQC project [4]. We present the latest results using the prototype. We also discuss the issue of the photon detection, which still remains the bottleneck for QKD.

A Low-Cost and Energy-Efficient Multiprocessor System-on-Chip for UWB MAC Layer

NASA Astrophysics Data System (ADS)

Xiao, Hao; Isshiki, Tsuyoshi; Khan, Arif Ullah; Li, Dongju; Kunieda, Hiroaki; Nakase, Yuko; Kimura, Sadahiro

Ultra-wideband (UWB) technology has attracted much attention recently due to its high data rate and low emission power. Its media access control (MAC) protocol, WiMedia MAC, promises a lot of facilities for high-speed and high-quality wireless communication. However, these benefits in turn involve a large amount of computational load, which challenges the traditional uniprocessor architecture based implementation method to provide the required performance. However, the constrained cost and power budget, on the other hand, makes using commercial multiprocessor solutions unrealistic. In this paper, a low-cost and energy-efficient multiprocessor system-on-chip (MPSoC), which tackles at once the aspects of system design, software migration and hardware architecture, is presented for the implementation of UWB MAC layer. Experimental results show that the proposed MPSoC, based on four simple RISC processors and shared-memory infrastructure, achieves up to 45% performance improvement and 65% power saving, but takes 15% less area than the uniprocessor implementation.

Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling

NASA Astrophysics Data System (ADS)

Bhakat, Soumendranath; Åberg, Emil; Söderhjelm, Pär

2018-01-01

Advanced molecular docking methods often aim at capturing the flexibility of the protein upon binding to the ligand. In this study, we investigate whether instead a simple rigid docking method can be applied, if combined with multiple target structures to model the backbone flexibility and molecular dynamics simulations to model the sidechain and ligand flexibility. The methods are tested for the binding of 35 ligands to FXR as part of the first stage of the Drug Design Data Resource (D3R) Grand Challenge 2 blind challenge. The results show that the multiple-target docking protocol performs surprisingly well, with correct poses found for 21 of the ligands. MD simulations started on the docked structures are remarkably stable, but show almost no tendency of refining the structure closer to the experimentally found binding pose. Reconnaissance metadynamics enhances the exploration of new binding poses, but additional collective variables involving the protein are needed to exploit the full potential of the method.

Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling.

PubMed

Bhakat, Soumendranath; Åberg, Emil; Söderhjelm, Pär

2018-01-01

Advanced molecular docking methods often aim at capturing the flexibility of the protein upon binding to the ligand. In this study, we investigate whether instead a simple rigid docking method can be applied, if combined with multiple target structures to model the backbone flexibility and molecular dynamics simulations to model the sidechain and ligand flexibility. The methods are tested for the binding of 35 ligands to FXR as part of the first stage of the Drug Design Data Resource (D3R) Grand Challenge 2 blind challenge. The results show that the multiple-target docking protocol performs surprisingly well, with correct poses found for 21 of the ligands. MD simulations started on the docked structures are remarkably stable, but show almost no tendency of refining the structure closer to the experimentally found binding pose. Reconnaissance metadynamics enhances the exploration of new binding poses, but additional collective variables involving the protein are needed to exploit the full potential of the method.

ZyFISH: A Simple, Rapid and Reliable Zygosity Assay for Transgenic Mice

PubMed Central

McHugh, Donal; O’Connor, Tracy; Bremer, Juliane; Aguzzi, Adriano

2012-01-01

Microinjection of DNA constructs into fertilized mouse oocytes typically results in random transgene integration at a single genomic locus. The resulting transgenic founders can be used to establish hemizygous transgenic mouse lines. However, practical and experimental reasons often require that such lines be bred to homozygosity. Transgene zygosity can be determined by progeny testing assays which are expensive and time-consuming, by quantitative Southern blotting which is labor-intensive, or by quantitative PCR (qPCR) which requires transgene-specific design. Here, we describe a zygosity assessment procedure based on fluorescent in situ hybridization (zyFISH). The zyFISH protocol entails the detection of transgenic loci by FISH and the concomitant assignment of homozygosity using a concise and unbiased scoring system. The method requires small volumes of blood, is scalable to at least 40 determinations per assay, and produces results entirely consistent with the progeny testing assay. This combination of reliability, simplicity and cost-effectiveness makes zyFISH a method of choice for transgenic mouse zygosity determinations. PMID:22666404

Phase transitions and adiabatic preparation of a fractional Chern insulator in a boson cold-atom model

NASA Astrophysics Data System (ADS)

Motruk, Johannes; Pollmann, Frank

2017-10-01

We investigate the fate of hardcore bosons in a Harper-Hofstadter model which was experimentally realized by Aidelsburger et al. [Nat. Phys. 11, 162 (2015), 10.1038/nphys3171] at half-filling of the lowest band. We discuss the stability of an emergent fractional Chern insulator (FCI) state in a finite region of the phase diagram that is separated from a superfluid state by a first-order transition when tuning the band topology following the protocol used in the experiment. Since crossing a first-order transition is unfavorable for adiabatically preparing the FCI state, we extend the model to stabilize a featureless insulating state. The transition between this phase and the topological state proves to be continuous, providing a path in parameter space along which an FCI state could be adiabatically prepared. To further corroborate this statement, we perform time-dependent DMRG calculations which demonstrate that the FCI state may indeed be reached by adiabatically tuning a simple product state.

Quantum Optical Realization of Arbitrary Linear Transformations Allowing for Loss and Gain

NASA Astrophysics Data System (ADS)

Tischler, N.; Rockstuhl, C.; Słowik, K.

2018-04-01

Unitary transformations are routinely modeled and implemented in the field of quantum optics. In contrast, nonunitary transformations, which can involve loss and gain, require a different approach. In this work, we present a universal method to deal with nonunitary networks. An input to the method is an arbitrary linear transformation matrix of optical modes that does not need to adhere to bosonic commutation relations. The method constructs a transformation that includes the network of interest and accounts for full quantum optical effects related to loss and gain. Furthermore, through a decomposition in terms of simple building blocks, it provides a step-by-step implementation recipe, in a manner similar to the decomposition by Reck et al. [Experimental Realization of Any Discrete Unitary Operator, Phys. Rev. Lett. 73, 58 (1994), 10.1103/PhysRevLett.73.58] but applicable to nonunitary transformations. Applications of the method include the implementation of positive-operator-valued measures and the design of probabilistic optical quantum information protocols.

An efficient management system for wireless sensor networks.

PubMed

Ma, Yi-Wei; Chen, Jiann-Liang; Huang, Yueh-Min; Lee, Mei-Yu

2010-01-01

Wireless sensor networks have garnered considerable attention recently. Networks typically have many sensor nodes, and are used in commercial, medical, scientific, and military applications for sensing and monitoring the physical world. Many researchers have attempted to improve wireless sensor network management efficiency. A Simple Network Management Protocol (SNMP)-based sensor network management system was developed that is a convenient and effective way for managers to monitor and control sensor network operations. This paper proposes a novel WSNManagement system that can show the connections stated of relationships among sensor nodes and can be used for monitoring, collecting, and analyzing information obtained by wireless sensor networks. The proposed network management system uses collected information for system configuration. The function of performance analysis facilitates convenient management of sensors. Experimental results show that the proposed method enhances the alive rate of an overall sensor node system, reduces the packet lost rate by roughly 5%, and reduces delay time by roughly 0.2 seconds. Performance analysis demonstrates that the proposed system is effective for wireless sensor network management.

Buprenorphine During Pregnancy Reduces Neonate Distress

MedlinePlus

... supported clinical trial, the Maternal Opioid Treatment: Human Experimental Research (MOTHER) study, has found buprenorphine to be ... to the two medications. They surmise that the experimental treatment protocols may have moved patients from morphine ...

Experimental quantum fingerprinting with weak coherent pulses

PubMed Central

Xu, Feihu; Arrazola, Juan Miguel; Wei, Kejin; Wang, Wenyuan; Palacios-Avila, Pablo; Feng, Chen; Sajeed, Shihan; Lütkenhaus, Norbert; Lo, Hoi-Kwong

2015-01-01

Quantum communication holds the promise of creating disruptive technologies that will play an essential role in future communication networks. For example, the study of quantum communication complexity has shown that quantum communication allows exponential reductions in the information that must be transmitted to solve distributed computational tasks. Recently, protocols that realize this advantage using optical implementations have been proposed. Here we report a proof-of-concept experimental demonstration of a quantum fingerprinting system that is capable of transmitting less information than the best-known classical protocol. Our implementation is based on a modified version of a commercial quantum key distribution system using off-the-shelf optical components over telecom wavelengths, and is practical for messages as large as 100 Mbits, even in the presence of experimental imperfections. Our results provide a first step in the development of experimental quantum communication complexity. PMID:26515586

Experimental quantum fingerprinting with weak coherent pulses.

PubMed

Xu, Feihu; Arrazola, Juan Miguel; Wei, Kejin; Wang, Wenyuan; Palacios-Avila, Pablo; Feng, Chen; Sajeed, Shihan; Lütkenhaus, Norbert; Lo, Hoi-Kwong

2015-10-30

Quantum communication holds the promise of creating disruptive technologies that will play an essential role in future communication networks. For example, the study of quantum communication complexity has shown that quantum communication allows exponential reductions in the information that must be transmitted to solve distributed computational tasks. Recently, protocols that realize this advantage using optical implementations have been proposed. Here we report a proof-of-concept experimental demonstration of a quantum fingerprinting system that is capable of transmitting less information than the best-known classical protocol. Our implementation is based on a modified version of a commercial quantum key distribution system using off-the-shelf optical components over telecom wavelengths, and is practical for messages as large as 100 Mbits, even in the presence of experimental imperfections. Our results provide a first step in the development of experimental quantum communication complexity.

Experimental quantum fingerprinting with weak coherent pulses

NASA Astrophysics Data System (ADS)

Xu, Feihu; Arrazola, Juan Miguel; Wei, Kejin; Wang, Wenyuan; Palacios-Avila, Pablo; Feng, Chen; Sajeed, Shihan; Lütkenhaus, Norbert; Lo, Hoi-Kwong

2015-10-01

Quantum communication holds the promise of creating disruptive technologies that will play an essential role in future communication networks. For example, the study of quantum communication complexity has shown that quantum communication allows exponential reductions in the information that must be transmitted to solve distributed computational tasks. Recently, protocols that realize this advantage using optical implementations have been proposed. Here we report a proof-of-concept experimental demonstration of a quantum fingerprinting system that is capable of transmitting less information than the best-known classical protocol. Our implementation is based on a modified version of a commercial quantum key distribution system using off-the-shelf optical components over telecom wavelengths, and is practical for messages as large as 100 Mbits, even in the presence of experimental imperfections. Our results provide a first step in the development of experimental quantum communication complexity.

Protocol vulnerability detection based on network traffic analysis and binary reverse engineering.

PubMed

Wen, Shameng; Meng, Qingkun; Feng, Chao; Tang, Chaojing

2017-01-01

Network protocol vulnerability detection plays an important role in many domains, including protocol security analysis, application security, and network intrusion detection. In this study, by analyzing the general fuzzing method of network protocols, we propose a novel approach that combines network traffic analysis with the binary reverse engineering method. For network traffic analysis, the block-based protocol description language is introduced to construct test scripts, while the binary reverse engineering method employs the genetic algorithm with a fitness function designed to focus on code coverage. This combination leads to a substantial improvement in fuzz testing for network protocols. We build a prototype system and use it to test several real-world network protocol implementations. The experimental results show that the proposed approach detects vulnerabilities more efficiently and effectively than general fuzzing methods such as SPIKE.

A simple but powerful test of perseverative search in dogs and toddlers.

PubMed

Péter, András; Gergely, Anna; Topál, József; Miklósi, Ádám; Pongrácz, Péter

2015-01-01

Perseverative (A-not-B) errors during the search of a hidden object were recently described in both dogs and 10-month-old infants. It was found that ostensive cues indicating a communicative intent of the person who hides the object played a major role in eliciting perseverative errors in both species. However, the employed experimental set-up gave rise to several alternative explanations regarding the source of these errors. Here we present a simplified protocol that eliminates the ambiguities present in the original design. Using five consecutive object hiding events to one of two locations in a fixed order ("AABBA"), we tested adult companion dogs and human children (24 months old). The experimenter performed the hiding actions while giving ostensive cues in each trial and moved the target object to the given location in a straight line. Our results show that in the B trials, both 24-month-old children and dogs could not reliably find the hidden object, and their performance in the first B trials was significantly below that of any of the A trials. These results are the first to show that the tendency for perseverative errors in an ostensive-communicative context is a robust phenomenon among 2-year-old children and dogs, and not the by-product of a topographically elaborate hiding event.

Experimental vitrification of human compacted morulae and early blastocysts using fine diameter plastic micropipettes.

PubMed

Cremades, N; Sousa, M; Silva, J; Viana, P; Sousa, S; Oliveira, C; Teixeira da Silva, J; Barros, A

2004-02-01

Vitrification of human blastocysts has been successfully applied using grids, straws and cryoloops. We assessed the survival rate of human compacted morulae and early blastocysts vitrified in pipette tips with a smaller inner diameter and solution volume than the previously described open pulled straw (OPS) method. Excess day 5 human embryos (n = 63) were experimentally vitrified in vessels. Embryos were incubated at 37 degrees C with sperm preparation medium (SPM) for 1 min, SPM + 7.5% ethylene glycol (EG)/dimethylsulphoxide (DMSO) for 3 min, and SPM + 16.5% EG + 16.5% DMSO + 0.67 mol/l sucrose for 25 s. They were then aspirated (0.5 microl) into a plastic micropipette tip (0.36 mm inner diameter), exposed to liquid nitrogen (LN(2)) vapour for 2 min before being placed into a pre-cooled cryotube, which was then closed and plunged into LN(2). Embryos were warmed and diluted using 0.33 mol/l and 0.2 mol/l sucrose. The survival rate for compacted morulae was 73% (22/30) and 82% (27/33) for early blastocysts. The survival rates of human compacted morulae and early blastocysts after vitrification with this simple technique are similar to those reported in the literature achieved by slow cooling and other vitrification protocols.

Ultrasound assisted enzyme catalyzed hydrolysis of waste cooking oil under solvent free condition.

PubMed

Waghmare, Govind V; Rathod, Virendra K

2016-09-01

The present work demonstrates the hydrolysis of waste cooking oil (WCO) under solvent free condition using commercial available immobilized lipase (Novozyme 435) under the influence of ultrasound irradiation. The process parameters were optimized using a sequence of experimental protocol to evaluate the effects of temperature, molar ratios of substrates, enzyme loading, duty cycle and ultrasound intensity. It has been observed that ultrasound-assisted lipase-catalyzed hydrolysis of WCO would be a promising alternative for conventional methods. A maximum conversion of 75.19% was obtained at mild operating parameters: molar ratio of oil to water (buffer pH 7) 3:1, catalyst loading of 1.25% (w/w), lower ultrasound power 100W (ultrasound intensity - 7356.68Wm(-2)), duty cycle 50% and temperature (50°C) in a relatively short reaction time (2h). The activation energy and thermodynamic study shows that the hydrolysis reaction is more feasible when ultrasound is combined with mechanical agitation as compared with the ultrasound alone and simple conventional stirring technique. Application of ultrasound considerably reduced the reaction time as compared to conventional reaction. The successive use of the catalyst for repetitive cycles under the optimum experimental conditions resulted in a loss of enzymatic activity and also minimized the product conversion. Copyright © 2016. Published by Elsevier B.V.

Synthesis of Pyrrolo[1,2-a]pyrimidine Enantiomers via Domino Ring-Closure followed by Retro Diels-Alder Protocol.

PubMed

Fekete, Beáta; Palkó, Márta; Haukka, Matti; Fülöp, Ferenc

2017-04-13

From 2-aminonorbornene hydroxamic acids, a simple and efficient method for the preparation of pyrrolo[1,2- a ]pyrimidine enantiomers is reported. The synthesis is based on domino ring-closure followed by microwave-induced retro Diels-Alder (RDA) protocols, where the chirality of the desired products is transferred from norbornene derivatives. The stereochemistry of the synthesized compounds was proven by X-ray crystallography. The absolute configuration of the product is determined by the configuration of the starting amino hydroxamic acid.

Thermodynamic metrics and optimal paths.

PubMed

Sivak, David A; Crooks, Gavin E

2012-05-11

A fundamental problem in modern thermodynamics is how a molecular-scale machine performs useful work, while operating away from thermal equilibrium without excessive dissipation. To this end, we derive a friction tensor that induces a Riemannian manifold on the space of thermodynamic states. Within the linear-response regime, this metric structure controls the dissipation of finite-time transformations, and bestows optimal protocols with many useful properties. We discuss the connection to the existing thermodynamic length formalism, and demonstrate the utility of this metric by solving for optimal control parameter protocols in a simple nonequilibrium model.

The Instrumental Model

ERIC Educational Resources Information Center

Yeates, Devin Rodney

2011-01-01

The goal of this dissertation is to enable better predictive models by engaging raw experimental data through the Instrumental Model. The Instrumental Model captures the protocols and procedures of experimental data analysis. The approach is formalized by encoding the Instrumental Model in an XML record. Decoupling the raw experimental data from…

Rendering the "Not-So-Simple" Pendulum Experimentally Accessible.

ERIC Educational Resources Information Center

Jackson, David P.

1996-01-01

Presents three methods for obtaining experimental data related to acceleration of a simple pendulum. Two of the methods involve angular position measurements and the subsequent calculation of the acceleration while the third method involves a direct measurement of the acceleration. Compares these results with theoretical calculations and…

Effective Swimmer’s Action during the Grab Start Technique

PubMed Central

Mourão, Luis; de Jesus, Karla; Roesler, Hélio; Machado, Leandro J.; Fernandes, Ricardo J.; Vilas-Boas, João Paulo; Vaz, Mário A. P.

2015-01-01

The external forces applied in swimming starts have been often studied, but using direct analysis and simple interpretation data processes. This study aimed to develop a tool for vertical and horizontal force assessment based on the swimmers’ propulsive and structural forces (passive forces due to dead weight) applied during the block phase. Four methodological pathways were followed: the experimented fall of a rigid body, the swimmers’ inertia effect, the development of a mathematical model to describe the outcome of the rigid body fall and its generalization to include the effects of the inertia, and the experimental swimmers’ starting protocol analysed with the inclusion of the developed mathematical tool. The first three methodological steps resulted in the description and computation of the passive force components. At the fourth step, six well-trained swimmers performed three 15 m maximal grab start trials and three-dimensional (3D) kinetic data were obtained using a six degrees of freedom force plate. The passive force contribution to the start performance obtained from the model was subtracted from the experimental force due to the swimmers resulting in the swimmers’ active forces. As expected, the swimmers’ vertical and horizontal active forces accounted for the maximum variability contribution of the experimental forces. It was found that the active force profile for the vertical and horizontal components resembled one another. These findings should be considered in clarifying the active swimmers’ force variability and the respective geometrical profile as indicators to redefine steering strategies. PMID:25978370

A Range Finding Protocol to Support Design for Transcriptomics Experimentation: Examples of In-Vitro and In-Vivo Murine UV Exposure

PubMed Central

van Oostrom, Conny T.; Jonker, Martijs J.; de Jong, Mark; Dekker, Rob J.; Rauwerda, Han; Ensink, Wim A.; de Vries, Annemieke; Breit, Timo M.

2014-01-01

In transcriptomics research, design for experimentation by carefully considering biological, technological, practical and statistical aspects is very important, because the experimental design space is essentially limitless. Usually, the ranges of variable biological parameters of the design space are based on common practices and in turn on phenotypic endpoints. However, specific sub-cellular processes might only be partially reflected by phenotypic endpoints or outside the associated parameter range. Here, we provide a generic protocol for range finding in design for transcriptomics experimentation based on small-scale gene-expression experiments to help in the search for the right location in the design space by analyzing the activity of already known genes of relevant molecular mechanisms. Two examples illustrate the applicability: in-vitro UV-C exposure of mouse embryonic fibroblasts and in-vivo UV-B exposure of mouse skin. Our pragmatic approach is based on: framing a specific biological question and associated gene-set, performing a wide-ranged experiment without replication, eliminating potentially non-relevant genes, and determining the experimental ‘sweet spot’ by gene-set enrichment plus dose-response correlation analysis. Examination of many cellular processes that are related to UV response, such as DNA repair and cell-cycle arrest, revealed that basically each cellular (sub-) process is active at its own specific spot(s) in the experimental design space. Hence, the use of range finding, based on an affordable protocol like this, enables researchers to conveniently identify the ‘sweet spot’ for their cellular process of interest in an experimental design space and might have far-reaching implications for experimental standardization. PMID:24823911

[Surgery of lower third molars and lesions of the lingual nerve].

PubMed

Chiapasco, M; Pedrinazzi, M; Motta, J; Crescentini, M; Ramundo, G

1996-11-01

The authors describe a technical expedient applied during the removal of totally or partially impacted lower third molars, in order to prevent lingual nerve damage. EXPERIMENTAL ASSAY: Retrospective study. The sample includes 1835 extractions of totally or partially impacted lower third molars, performed on 1030 patients, 493 males and 537 females, aging between 12 and 72 years. All the operations were carried out under local anaesthesia with standardization of the surgical protocol. A mucoperiosteal paramarginal flap was used in case of germectomy, whereas a mucoperiosteal marginal flap with mesial releasing incision was used in case of fully mature teeth. Ostectomy and tooth sectioning were performed using a round and fissure bur respectively, assembled on a straight low-speed handpiece and under irrigation with sterile saline. The authors reported only one case of transient lingual nerve paresthesia (0.05%) which occurred in a 19-years old female presenting a totally impacted third molar mesial-lingual inclination. Symptoms disappeared spontaneously one week postoperatively. Therefore the overall incidence of permanent nerve damage was equal to 0%. The data reported in literature show a lingual nerve lesion incidence ranging between 0% and 22%. With this simple surgical expedient the incidence of permanent lingual damage was 0%. Thus, it is the authors' opinion that this simple expedient should be applied in all cases of impacted third molar removal.

A Simple Method To Demonstrate the Enzymatic Production of Hydrogen from Sugar

NASA Astrophysics Data System (ADS)

Hershlag, Natalie; Hurley, Ian; Woodward, Jonathan

1998-10-01

There is current interest in and concern for the development of environmentally friendly bioprocesses whereby biomass and the biodegradable content of municipal wastes can be converted to useful forms of energy. For example, cellulose, a glucose polymer that is the principal component of biomass and paper waste, can be enzymatically degraded to glucose, which can subsequently be converted by fermentation or further enzymatic reaction to fuels such as ethanol or hydrogen. These products represent alternative energy sources to fossil fuels such as oil. Demonstration of the relevant reactions in high-school and undergraduate college laboratories would have value not only in illustrating environmentally friendly biotechnology for the utilization of renewable energy sources, such as cellulosic wastes, but could also be used to teach the principles of enzyme-catalyzed reactions. In the experimental protocol described here, it has been demonstrated that the common sugar glucose can be used to produce hydrogen using two enzymes, glucose dehydrogenase and hydrogenase. No sophisticated or expensive hydrogen detection equipment is required-only a redox dye, benzyl viologen, which turns purple when it is reduced. The color can be detected by a simple colorimeter. Furthermore, it is shown that the renewable resource cellulose, in its soluble derivative from carboxymethylcellulose, as well as aspen-wood waste, is also a source of hydrogen if the enzyme cellulase is included in the reaction mixture.

A practical workshop for generating simple DNA fingerprints of plants.

PubMed

Rouzière, A-S; Redman, J E

2011-01-01

Gel electrophoresis DNA fingerprints offer a graphical and visually appealing illumination of the similarities and differences between DNA sequences of different species and individuals. A polymerase chain reaction (PCR) and restriction digest protocol was designed to give high-school students the opportunity to generate simple fingerprints of plants thereby illustrating concepts and techniques in genetics and molecular biology. Three combinations of primers/restriction enzyme targeting chloroplast DNA were sufficient to generate patterns that enabled visual discrimination of plant species. The protocol was tested with a range of common fruit, vegetable, and herb plants that could be easily cultivated and handled in the laboratory. Toxic or hazardous materials such as ethidium bromide and liquid nitrogen were avoided. The protocol was validated as a university outreach workshop targeted at a group of up to 10 high-school students. In a teaching laboratory, students sampled plants, setup the PCR reaction and restriction digest using microliter pipettes, and loaded the digested samples on an agarose gel. The workshop was structured as 2 × 2.5-hour sessions on separate days. The main challenges stemmed from the speed and accuracy of pipetting, especially at the gel loading stage. Feedback from students was largely positive, with the majority reporting that they had both enjoyed and learnt from the experience. Copyright © 2010 Wiley Periodicals, Inc.

The Phyre2 web portal for protein modelling, prediction and analysis

PubMed Central

Kelley, Lawrence A; Mezulis, Stefans; Yates, Christopher M; Wass, Mark N; Sternberg, Michael JE

2017-01-01

Summary Phyre2 is a suite of tools available on the web to predict and analyse protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a protocol. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites, and analyse the effect of amino-acid variants (e.g. nsSNPs) for a user’s protein sequence. Users are guided through results by a simple interface at a level of detail determined by them. This protocol will guide a user from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30mins and 2 hours after submission. PMID:25950237

Taking the Politics Out of Satellite and Space-Based Communications Protocols

NASA Technical Reports Server (NTRS)

Ivancic, William D.

2006-01-01

After many years of studies, experimentation, and deployment, large amounts of misinformation and misconceptions remain regarding applicability of various communications protocols for use in satellite and space-based networks. This paper attempts to remove much of the politics, misconceptions, and misinformation that have plagued spacebased communications protocol development and deployment. This paper provides a common vocabulary for communications; a general discussion of the requirements for various communication environments; an evaluation of tradeoffs between circuit and packet-switching technologies, and the pros and cons of various link, network, transport, application, and security protocols. Included is the applicability of protocol enhancing proxies to NASA, Department of Defense (DOD), and commercial space communication systems.

Performance Analysis of the HTTP Protocol on Geostationary Satellite Links

NASA Technical Reports Server (NTRS)

Krus, Hans; Allman, Mark; Griner, Jim; Tran, Diepchi

1998-01-01

Various issues associated with HTTP protocol on geostationary satellite links are presented in viewgraph form. Specific topics include: 1) Network reference points; 2) The HTTP 1.0 and 1.1 mechanisms; 3) Experimental setup; 4) TCP and HTTP configuration; 5) Modelling slow start and 6) Results and future work.

Toward a single nursery protocol for oak seedlings

Treesearch

Paul P. Kormanik; Shi-Jean S. Sung; T.L. Kormanik

1994-01-01

After a soil fertility baseline had been determined for the Georgia Forestry Commission's (GFC) Morgan Nursery, and single nursery protocol consistently produced high quality oak seedlings. The fertility baseline developed at the Institute of Tree Root Biology's Whitehall Experimental Nursery and adjusted for three GFC nurseries has a background target level...

Situated Naive Physics: Task Constraints Decide What Children Know about Density

ERIC Educational Resources Information Center

Kloos, Heidi; Fisher, Anna; Van Orden, Guy C.

2010-01-01

Children's understanding of density is riddled with misconceptions--or so it seems. Yet even preschoolers at times appear to understand density. This article seeks to reconcile these conflicting outcomes by investigating the nature of constraints available in different experimental protocols. Protocols that report misconceptions about density used…

A Simple Experimental Setup to Clearly Show that Light Does Not Recombine After Passing Through Two Prisms

NASA Astrophysics Data System (ADS)

Garcia-Molina, Rafael; del Mazo, Alejandro; Velasco, Santiago

2018-01-01

We present a simple and cheap experimental setup that clearly shows how the colors of the white light spectrum after passing a prism do not recombine when emerging from an identical second prism, as it is still found in many references.

A Simple Experimental Setup to Clearly Show That Light Does Not Recombine after Passing through Two Prisms

ERIC Educational Resources Information Center

Garcia-Molina, Rafael; del Mazo, Alejandro; Velasco, Santiago

2018-01-01

We present a simple and cheap experimental setup that clearly shows how the colors of the white light spectrum after passing a prism do not recombine when emerging from an identical second prism, as it is still found in many references.

A SIMPLE MULTIPLEX POLYMERASE CHAIN REACTION ASSAY FOR THE IDENTIFICATION OF FOUR ENVIRONMENTALLY RELEVANT FUNGAL CONTAMINANTS

EPA Science Inventory

Historically, identification of filamentous fungal (mold) species has been based on morphological characteristics, both macroscopic and microscopic. These methods have proven to be time consuming and inaccurate, necessitating the development of identification protocols that are ...

Synthesis of disulfides and diselenides by copper-catalyzed coupling reactions in water.

PubMed

Li, Zhengkai; Ke, Fang; Deng, Hang; Xu, Hualong; Xiang, Haifeng; Zhou, Xiangge

2013-05-14

A simple and efficient protocol for copper-catalyzed coupling reactions between aryl halides and elemental sulfur or selenium has been developed. A variety of disulfides and diselenides can be obtained in moderate to excellent yields up to 96%.

Experimental demonstration of the anti-maser

NASA Astrophysics Data System (ADS)

Mazzocco, Anthony; Aviles, Michael; Andrews, Jim; Dawson, Nathan; Crescimanno, Michael

2012-10-01

We denote by ``anti-maser'' a coherent perfect absorption (CPA) process in the radio frequency domain. We demonstrate several experimental realizations of the anti-maser suitable for an advanced undergraduate laboratory. Students designed, assembled and tested these devices, as well as the inexpensive laboratory setup and experimental protocol for displaying various CPA phenomenon.

75 FR 23775 - Agency Information Collection Activities; Proposed Collection; Comment Request; Experimental...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-04

... for research entitled ``Experimental Study of Patient Information Prototypes.'' This study is designed..., the working group refined several prototypes and designed a study to investigate the usefulness of... Design and Protocol The study is experimental and will have two independent variables in a 3 x 2 design...

SpaceWire Protocol ID: What Does It Mean To You?

NASA Technical Reports Server (NTRS)

Rakow, Glenn; Schnurr, Richard; Gilley, Daniel; Parks, Steve

2006-01-01

Spacewire is becoming a popular solution for satellite high-speed data buses because it is a simple standard that provides great flexibility for a wide range of system requirements. It is simple in packet format and protocol, allowing users to easily tailor their implementation for their specific application. Some of the attractive aspects of Spacewire that make it easy to implement also make it hard for future reuse. Protocol reuse is difficult because Spacewire does not have a defined mechanism to communicate with the higher layers of the protocol stack. This has forced users of Spacewire to define unique packet formats and define how these packets are to be processed. Each mission writes their own Interface Control Document (ICD) and tailors Spacewire for their specific requirements making reuse difficult. Part of the reason for this habit may be because engineers typically optimize designs for their own requirements in the absence of a standard. This is an inefficient use of project resources and costs more to develop missions. A new packet format for Spacewire has been defined as a solution for this problem. This new packet format is a compliment to the Spacewire standard that will support protocol development upon Spacewire. The new packet definition does not replace the current packet structure, i.e., does not make the standard obsolete, but merely extends the standard for those who want to develop protocols over Spacewire. The Spacewire packet is defined with the first part being the Destination Address, which may be one or more bytes. This is followed by the packet cargo, which is user defined. The cargo is truncated with an End-Of-Packet (EOP) marker. This packet structure offers low packet overhead and allows the user to define how the contents are to be formatted. It also provides for many different addressing schemes, which provide flexibility in the system. This packet flexibility is typically an attractive part of the Spacewire. The new extended packet format adds one new field to the packet that greatly enhances the capability of Spacewire. This new field called the Protocol Identifier (ID) is used to identify the packet contents and the associated processing for the packet. This feature along with the restriction in the packet format that uses the Protocol ID, allows a deterministic method of decoding packets that was not before possible. The first part of the packet is still the Destination Address, which still conforms to the original standard but with one restriction. The restriction is that the first byte seen at the destination by the user needs to be a logical address, independent of the addressing scheme used. The second field is defined as the Protocol ID, which is usually one byte in length. The packet cargo (user defined) follows the Protocol ID. After the packet cargo is the EOP, which defines the end of packet. The value of the Protocol ID is assigned by the Spacewire working group and the protocol description published for others to use. The development of Protocols for Spacewire is currently the area of greatest activity by the Spacewire working group. The first protocol definition by the working group has been completed and is now in the process of formal standardization. There are many other protocols in development for missions that have not yet received formal Protocol ID assignment, but even if the protocols are not formally assigned a value, this effort will provide synergism for future developments.

REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding.

PubMed

Mizutani, Hisashi; Sugawara, Hideaki; Buckle, Ashley M; Sangawa, Takeshi; Miyazono, Ken-Ichi; Ohtsuka, Jun; Nagata, Koji; Shojima, Tomoki; Nosaki, Shohei; Xu, Yuqun; Wang, Delong; Hu, Xiao; Tanokura, Masaru; Yura, Kei

2017-04-24

More than 7000 papers related to "protein refolding" have been published to date, with approximately 300 reports each year during the last decade. Whilst some of these papers provide experimental protocols for protein refolding, a survey in the structural life science communities showed a necessity for a comprehensive database for refolding techniques. We therefore have developed a new resource - "REFOLDdb" that collects refolding techniques into a single, searchable repository to help researchers develop refolding protocols for proteins of interest. We based our resource on the existing REFOLD database, which has not been updated since 2009. We redesigned the data format to be more concise, allowing consistent representations among data entries compared with the original REFOLD database. The remodeled data architecture enhances the search efficiency and improves the sustainability of the database. After an exhaustive literature search we added experimental refolding protocols from reports published 2009 to early 2017. In addition to this new data, we fully converted and integrated existing REFOLD data into our new resource. REFOLDdb contains 1877 entries as of March 17 th , 2017, and is freely available at http://p4d-info.nig.ac.jp/refolddb/ . REFOLDdb is a unique database for the life sciences research community, providing annotated information for designing new refolding protocols and customizing existing methodologies. We envisage that this resource will find wide utility across broad disciplines that rely on the production of pure, active, recombinant proteins. Furthermore, the database also provides a useful overview of the recent trends and statistics in refolding technology development.

Secure quantum private information retrieval using phase-encoded queries

NASA Astrophysics Data System (ADS)

Olejnik, Lukasz

2011-08-01

We propose a quantum solution to the classical private information retrieval (PIR) problem, which allows one to query a database in a private manner. The protocol offers privacy thresholds and allows the user to obtain information from a database in a way that offers the potential adversary, in this model the database owner, no possibility of deterministically establishing the query contents. This protocol may also be viewed as a solution to the symmetrically private information retrieval problem in that it can offer database security (inability for a querying user to steal its contents). Compared to classical solutions, the protocol offers substantial improvement in terms of communication complexity. In comparison with the recent quantum private queries [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.100.230502 100, 230502 (2008)] protocol, it is more efficient in terms of communication complexity and the number of rounds, while offering a clear privacy parameter. We discuss the security of the protocol and analyze its strengths and conclude that using this technique makes it challenging to obtain the unconditional (in the information-theoretic sense) privacy degree; nevertheless, in addition to being simple, the protocol still offers a privacy level. The oracle used in the protocol is inspired both by the classical computational PIR solutions as well as the Deutsch-Jozsa oracle.

Secure quantum private information retrieval using phase-encoded queries

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

Olejnik, Lukasz

We propose a quantum solution to the classical private information retrieval (PIR) problem, which allows one to query a database in a private manner. The protocol offers privacy thresholds and allows the user to obtain information from a database in a way that offers the potential adversary, in this model the database owner, no possibility of deterministically establishing the query contents. This protocol may also be viewed as a solution to the symmetrically private information retrieval problem in that it can offer database security (inability for a querying user to steal its contents). Compared to classical solutions, the protocol offersmore » substantial improvement in terms of communication complexity. In comparison with the recent quantum private queries [Phys. Rev. Lett. 100, 230502 (2008)] protocol, it is more efficient in terms of communication complexity and the number of rounds, while offering a clear privacy parameter. We discuss the security of the protocol and analyze its strengths and conclude that using this technique makes it challenging to obtain the unconditional (in the information-theoretic sense) privacy degree; nevertheless, in addition to being simple, the protocol still offers a privacy level. The oracle used in the protocol is inspired both by the classical computational PIR solutions as well as the Deutsch-Jozsa oracle.« less

Brazilian Samba Protocol for Individuals With Parkinson's Disease: A Clinical Non-Randomized Study.

PubMed

Tillmann, Ana Cristina; Andrade, Alexandro; Swarowsky, Alessandra; Guimarães, Adriana Coutinho De Azevedo

2017-07-04

In the 10 most populated countries in the world, Parkinson's disease (PD) affects more than 5 million individuals. Despite optimal treatment options already developed for the disease, concomitant involvement of other areas of health care plays an important role in complementing the treatment. From this perspective, dancing can be viewed as a non-drug alternative that can reduce falls by improving some motor skills, such as mobility, balance, gait, and posture, and can also improve the overall quality of life. Brazilian samba promotes improvement in motor and non-motor symptoms in individuals with PD, providing a new treatment option for this population. The main objective of this quasi-experimental study is to provide a 12-week samba protocol (2x/week) for individuals with PD and to compare its effects with the group without intervention. The hypothesis is that the Brazilian samba protocol will promote improvement in primary (motor) and secondary (non-motor) outcomes in individuals with PD. The sample will be selected at random from individuals diagnosed with PD in the city of Florianopolis (SC, Brazil). Sample size calculation was performed with the G*Power 3.1.9.2 software, with 0.447 effect size, at 5% significance level, power of 0.9, and test and sample loss of 20%. This yielded 60 individuals divided between the intervention and control groups. The questionnaires will be filled out before and after the dance intervention. The data collection for the control group will be held simultaneously to the intervention group. The classes will last for 1 hour, twice a week in the evening for 12 weeks, and all classes will be divided into warm-up, main part, and relaxation. Two-way analysis of variance with repeated measures and Sidak post-hoc comparison test will be used for a comparative analysis of the final results of the control group with the experimental group and of the within-group changes between pre- and postintervention period. We expect to complete follow-up in September 2017. The major inspiration for this study was to encourage the creation of new rehabilitation programs that do not emphasize doctor involvement. This is a unique protocol for PD and we believe it can be an important tool to alleviate the motor and non-motor symptoms of individuals with PD. Dance is a simple activity depending on little equipment and few financial resources, facilitating its implementation and improving the cost-benefit relationship. In addition, activities that have a cultural aspect for the population in question, and which are pleasant, enable the participants to commit long term. This can enhance patient's compliance with the therapy, which is often a problem for many rehabilitation programs. ©Ana Cristina Tillmann, Alexandro Andrade, Alessandra Swarowsky, Adriana Coutinho De Azevedo Guimarães. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 04.07.2017.

Security of Y-00 and Similar Quantum Cryptographic Protocols

DTIC Science & Technology

2004-11-16

security of Y-00 type protocols is clarified. Key words: Quantum cryptography PACS: 03.67.Dd Anew approach to quantum cryptog- raphy called KCQ, ( keyed ...classical- noise key generation [2] or the well known BB84 quantum protocol [3]. A special case called αη (or Y-00 in Japan) has been experimentally in... quantum noise for typical op- erating parameters. It weakens both the data and key security , possibly information-theoretically and cer- tainly

In silico toxicology protocols.

PubMed

Myatt, Glenn J; Ahlberg, Ernst; Akahori, Yumi; Allen, David; Amberg, Alexander; Anger, Lennart T; Aptula, Aynur; Auerbach, Scott; Beilke, Lisa; Bellion, Phillip; Benigni, Romualdo; Bercu, Joel; Booth, Ewan D; Bower, Dave; Brigo, Alessandro; Burden, Natalie; Cammerer, Zoryana; Cronin, Mark T D; Cross, Kevin P; Custer, Laura; Dettwiler, Magdalena; Dobo, Krista; Ford, Kevin A; Fortin, Marie C; Gad-McDonald, Samantha E; Gellatly, Nichola; Gervais, Véronique; Glover, Kyle P; Glowienke, Susanne; Van Gompel, Jacky; Gutsell, Steve; Hardy, Barry; Harvey, James S; Hillegass, Jedd; Honma, Masamitsu; Hsieh, Jui-Hua; Hsu, Chia-Wen; Hughes, Kathy; Johnson, Candice; Jolly, Robert; Jones, David; Kemper, Ray; Kenyon, Michelle O; Kim, Marlene T; Kruhlak, Naomi L; Kulkarni, Sunil A; Kümmerer, Klaus; Leavitt, Penny; Majer, Bernhard; Masten, Scott; Miller, Scott; Moser, Janet; Mumtaz, Moiz; Muster, Wolfgang; Neilson, Louise; Oprea, Tudor I; Patlewicz, Grace; Paulino, Alexandre; Lo Piparo, Elena; Powley, Mark; Quigley, Donald P; Reddy, M Vijayaraj; Richarz, Andrea-Nicole; Ruiz, Patricia; Schilter, Benoit; Serafimova, Rositsa; Simpson, Wendy; Stavitskaya, Lidiya; Stidl, Reinhard; Suarez-Rodriguez, Diana; Szabo, David T; Teasdale, Andrew; Trejo-Martin, Alejandra; Valentin, Jean-Pierre; Vuorinen, Anna; Wall, Brian A; Watts, Pete; White, Angela T; Wichard, Joerg; Witt, Kristine L; Woolley, Adam; Woolley, David; Zwickl, Craig; Hasselgren, Catrin

2018-07-01

The present publication surveys several applications of in silico (i.e., computational) toxicology approaches across different industries and institutions. It highlights the need to develop standardized protocols when conducting toxicity-related predictions. This contribution articulates the information needed for protocols to support in silico predictions for major toxicological endpoints of concern (e.g., genetic toxicity, carcinogenicity, acute toxicity, reproductive toxicity, developmental toxicity) across several industries and regulatory bodies. Such novel in silico toxicology (IST) protocols, when fully developed and implemented, will ensure in silico toxicological assessments are performed and evaluated in a consistent, reproducible, and well-documented manner across industries and regulatory bodies to support wider uptake and acceptance of the approaches. The development of IST protocols is an initiative developed through a collaboration among an international consortium to reflect the state-of-the-art in in silico toxicology for hazard identification and characterization. A general outline for describing the development of such protocols is included and it is based on in silico predictions and/or available experimental data for a defined series of relevant toxicological effects or mechanisms. The publication presents a novel approach for determining the reliability of in silico predictions alongside experimental data. In addition, we discuss how to determine the level of confidence in the assessment based on the relevance and reliability of the information. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2

NASA Astrophysics Data System (ADS)

Kurkcuoglu, Zeynep; Koukos, Panagiotis I.; Citro, Nevia; Trellet, Mikael E.; Rodrigues, J. P. G. L. M.; Moreira, Irina S.; Roel-Touris, Jorge; Melquiond, Adrien S. J.; Geng, Cunliang; Schaarschmidt, Jörg; Xue, Li C.; Vangone, Anna; Bonvin, A. M. J. J.

2018-01-01

We present the performance of HADDOCK, our information-driven docking software, in the second edition of the D3R Grand Challenge. In this blind experiment, participants were requested to predict the structures and binding affinities of complexes between the Farnesoid X nuclear receptor and 102 different ligands. The models obtained in Stage1 with HADDOCK and ligand-specific protocol show an average ligand RMSD of 5.1 Å from the crystal structure. Only 6/35 targets were within 2.5 Å RMSD from the reference, which prompted us to investigate the limiting factors and revise our protocol for Stage2. The choice of the receptor conformation appeared to have the strongest influence on the results. Our Stage2 models were of higher quality (13 out of 35 were within 2.5 Å), with an average RMSD of 4.1 Å. The docking protocol was applied to all 102 ligands to generate poses for binding affinity prediction. We developed a modified version of our contact-based binding affinity predictor PRODIGY, using the number of interatomic contacts classified by their type and the intermolecular electrostatic energy. This simple structure-based binding affinity predictor shows a Kendall's Tau correlation of 0.37 in ranking the ligands (7th best out of 77 methods, 5th/25 groups). Those results were obtained from the average prediction over the top10 poses, irrespective of their similarity/correctness, underscoring the robustness of our simple predictor. This results in an enrichment factor of 2.5 compared to a random predictor for ranking ligands within the top 25%, making it a promising approach to identify lead compounds in virtual screening.

Interplanetary Overlay Network Bundle Protocol Implementation

NASA Technical Reports Server (NTRS)

Burleigh, Scott C.

2011-01-01

The Interplanetary Overlay Network (ION) system's BP package, an implementation of the Delay-Tolerant Networking (DTN) Bundle Protocol (BP) and supporting services, has been specifically designed to be suitable for use on deep-space robotic vehicles. Although the ION BP implementation is unique in its use of zero-copy objects for high performance, and in its use of resource-sensitive rate control, it is fully interoperable with other implementations of the BP specification (Internet RFC 5050). The ION BP implementation is built using the same software infrastructure that underlies the implementation of the CCSDS (Consultative Committee for Space Data Systems) File Delivery Protocol (CFDP) built into the flight software of Deep Impact. It is designed to minimize resource consumption, while maximizing operational robustness. For example, no dynamic allocation of system memory is required. Like all the other ION packages, ION's BP implementation is designed to port readily between Linux and Solaris (for easy development and for ground system operations) and VxWorks (for flight systems operations). The exact same source code is exercised in both environments. Initially included in the ION BP implementations are the following: libraries of functions used in constructing bundle forwarders and convergence-layer (CL) input and output adapters; a simple prototype bundle forwarder and associated CL adapters designed to run over an IPbased local area network; administrative tools for managing a simple DTN infrastructure built from these components; a background daemon process that silently destroys bundles whose time-to-live intervals have expired; a library of functions exposed to applications, enabling them to issue and receive data encapsulated in DTN bundles; and some simple applications that can be used for system checkout and benchmarking.

Rehabilitation for the management of knee osteoarthritis using comprehensive traditional Chinese medicine in community health centers: study protocol for a randomized controlled trial

PubMed Central

2013-01-01

Background It is becoming increasingly necessary for community health centers to make rehabilitation services available to patients with osteoarthritis of the knee. However, for a number of reasons, including a lack of expertise, the small size of community health centers and the availability of only simple medical equipment, conventional rehabilitation therapy has not been widely used in China. Consequently, most patients with knee osteoarthritis seek treatment in high-grade hospitals. However, many patients cannot manage the techniques that they were taught in the hospital. Methods such as acupuncture, tuina, Chinese medical herb fumigation-washing and t’ai chi are easy to do and have been reported to have curative effects in those with knee osteoarthritis. To date, there have been no randomized controlled trials validating comprehensive traditional Chinese medicine for the rehabilitation of knee osteoarthritis in a community health center. Furthermore, there is no standard rehabilitation protocol using traditional Chinese medicine for knee osteoarthritis. The aim of the current study is to develop a comprehensive rehabilitation protocol using traditional Chinese medicine for the management of knee osteoarthritis in a community health center. Method/design This will be a randomized controlled clinical trial with blinded assessment. There will be a 4-week intervention utilizing rehabilitation protocols from traditional Chinese medicine and conventional therapy. Follow-up will be conducted for a period of 12 weeks. A total of 722 participants with knee osteoarthritis will be recruited. Participants will be randomly divided into two groups: experimental and control. Primary outcomes will include range of motion, girth measurement, the visual analogue scale, and results from the manual muscle, six-minute walking and stair-climbing tests. Secondary outcomes will include average daily consumption of pain medication, ability to perform daily tasks and health-related quality-of-life assessments. Other outcomes will include rate of adverse events and economic effects. Relative cost-effectiveness will be determined from health service usage and outcome data. Discussion The primary aim of this trial is to develop a standard protocol for traditional Chinese medicine, which can be adopted by community health centers in China and worldwide, for the rehabilitation of patients with knee osteoarthritis. Trial registration Clinical Trials Registration: ChiCTR-TRC-12002538 PMID:24188276

Rehabilitation for the management of knee osteoarthritis using comprehensive traditional Chinese medicine in community health centers: study protocol for a randomized controlled trial.

PubMed

Yan, Hu; Su, Youxin; Chen, Lidian; Zheng, Guohua; Lin, Xueyi; Chen, Baojun; Zhou, Bihong; Zhang, Qing

2013-11-04

It is becoming increasingly necessary for community health centers to make rehabilitation services available to patients with osteoarthritis of the knee. However, for a number of reasons, including a lack of expertise, the small size of community health centers and the availability of only simple medical equipment, conventional rehabilitation therapy has not been widely used in China. Consequently, most patients with knee osteoarthritis seek treatment in high-grade hospitals. However, many patients cannot manage the techniques that they were taught in the hospital. Methods such as acupuncture, tuina, Chinese medical herb fumigation-washing and t'ai chi are easy to do and have been reported to have curative effects in those with knee osteoarthritis. To date, there have been no randomized controlled trials validating comprehensive traditional Chinese medicine for the rehabilitation of knee osteoarthritis in a community health center. Furthermore, there is no standard rehabilitation protocol using traditional Chinese medicine for knee osteoarthritis. The aim of the current study is to develop a comprehensive rehabilitation protocol using traditional Chinese medicine for the management of knee osteoarthritis in a community health center. This will be a randomized controlled clinical trial with blinded assessment. There will be a 4-week intervention utilizing rehabilitation protocols from traditional Chinese medicine and conventional therapy. Follow-up will be conducted for a period of 12 weeks. A total of 722 participants with knee osteoarthritis will be recruited. Participants will be randomly divided into two groups: experimental and control. Primary outcomes will include range of motion, girth measurement, the visual analogue scale, and results from the manual muscle, six-minute walking and stair-climbing tests. Secondary outcomes will include average daily consumption of pain medication, ability to perform daily tasks and health-related quality-of-life assessments. Other outcomes will include rate of adverse events and economic effects. Relative cost-effectiveness will be determined from health service usage and outcome data. The primary aim of this trial is to develop a standard protocol for traditional Chinese medicine, which can be adopted by community health centers in China and worldwide, for the rehabilitation of patients with knee osteoarthritis. ChiCTR-TRC-12002538.

[Benefits of Decumanum Phlebodium intake on the muscle damage in the response to intense physical exercise in sedentary subjects].

PubMed

Vargas Corzo, M C; Aguilar Cordero, M J; de Teresa Galván, C; Segura Millán, D; Miranda Leon, M T; Castillo Rueda, G; Guisado Barrilao, R

2014-06-01

Intense physical exercise provoke muscle damage, that in sedentary people can increase cardiovascular risk. Phlebodium decumanum (PD) has shown to have immunomodulator effects in models of moderate intense physical activities in well conditioned groups. To evaluate the PD effects during eccentric exercise, as a model of muscle inflammation protocol, on a sedentary population with cardiovascular risk. This is an experimental, double-blind, multigroup randomized study. Experimental Group 1 (n = 17)received PD, 9 doses of 400 mg (total amount 3.6 g) every 8 hours during 3 days, and Control Group 2 (n = 16)received a placebo. All the subjects performed two treadmill ergoespirometry tests: first, a modified Bruce protocol to discard ischemic responses during exercise and to evaluate VO2max before the experimental phase;and second, with an eccentric protocol (14% descending ramp test) during 10 minutes in stable state at 70-80%VO2max, as experimental inflammatory protocol.We compared intra and inter groups to evaluate differences in the pre and post-test differences results on blood muscle damage variables. The study shown statistically significant differences in all pre-post intra-groups results in muscle damage variables (CK, LDH and Myoglobin, but not in Cardiac Troponin), and in functional lower-limb test (SJand CMJ). The comparison of inter-group results shown less muscle damage and less functional lower-limb deterioration in Group 1 compared with Control group, with statistical significance in both cases. Differences in handgrip dynamometry were no statistically significant. The eccentric exercise protocol in that study has proven to be a good model to induce muscle and functional damage in sedentary people. Short PD treatment has shown to reduce muscle and functional acute damages compared with placebo control group in this specific population. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Experimental investigation of factors affecting the absolute recovery coefficients in iodine-124 PET lesion imaging

NASA Astrophysics Data System (ADS)

Jentzen, Walter

2010-04-01

The use of recovery coefficients (RCs) in 124I PET lesion imaging is a simple method to correct the imaged activity concentration (AC) primarily for the partial-volume effect and, to a minor extent, for the prompt gamma coincidence effect. The aim of this phantom study was to experimentally investigate a number of various factors affecting the 124I RCs. Three RC-based correction approaches were considered. These approaches differ with respect to the volume of interest (VOI) drawn, which determines the imaged AC and the RCs: a single voxel VOI containing the maximum value (maximum RC), a spherical VOI with a diameter of the scanner resolution (resolution RC) and a VOI equaling the physical object volume (isovolume RC). Measurements were performed using mainly a stand-alone PET scanner (EXACT HR+) and a latest-generation PET/CT scanner (BIOGRAPH mCT). The RCs were determined using a cylindrical phantom containing spheres or rotational ellipsoids and were derived from images acquired with a reference acquisition protocol. For each type of RC, the influence of the following factors on the RC was assessed: object shape, background activity spill in and iterative image reconstruction parameters. To evaluate the robustness of the RC-based correction approaches, the percentage deviation between RC-corrected and true ACs was determined from images acquired with a clinical acquisition protocol of different AC regimes. The observed results of the shape and spill-in effects were compared with simulation data derived from a convolution-based model. The study demonstrated that the shape effect was negligible and, therefore, was in agreement with theoretical expectations. In contradiction to the simulation results, the observed spill-in effect was unexpectedly small. To avoid variations in the determination of RCs due to reconstruction parameter changes, image reconstruction with a pixel length of about one-third or less of the scanner resolution and an OSEM 1 × 32 algorithm or one with somewhat higher number of effective iterations are recommended. Using the clinical acquisition protocol, the phantom study indicated that the resolution- or isovolume-based recovery-correction approaches appeared to be more appropriate to recover the ACs from patient data; however, the application of the three RC-based correction approaches to small lesions containing low ACs was, in particular, associated with large underestimations. The phantom study had several limitations, which were discussed in detail.

Determining contrast medium dose and rate on basis of lean body weight: does this strategy improve patient-to-patient uniformity of hepatic enhancement during multi-detector row CT?

PubMed

Ho, Lisa M; Nelson, Rendon C; Delong, David M

2007-05-01

To prospectively evaluate the use of lean body weight (LBW) as the main determinant of the volume and rate of contrast material administration during multi-detector row computed tomography of the liver. This HIPAA-compliant study had institutional review board approval. All patients gave written informed consent. Four protocols were compared. Standard protocol involved 125 mL of iopamidol injected at 4 mL/sec. Total body weight (TBW) protocol involved 0.7 g iodine per kilogram of TBW. Calculated LBW and measured LBW protocols involved 0.86 g of iodine per kilogram and 0.92 g of iodine per kilogram calculated or measured LBW for men and women, respectively. Injection rate used for the three experimental protocols was determined proportionally on the basis of the calculated volume of contrast material. Postcontrast attenuation measurements during portal venous phase were obtained in liver, portal vein, and aorta for each group and were summed for each patient. Patient-to-patient enhancement variability in same group was measured with Levene test. Two-tailed t test was used to compare the three experimental protocols with the standard protocol. Data analysis was performed in 101 patients (25 or 26 patients per group), including 56 men and 45 women (mean age, 53 years). Average summed attenuation values for standard, TBW, calculated LBW, and measured LBW protocols were 419 HU +/- 50 (standard deviation), 443 HU +/- 51, 433 HU +/- 50, and 426 HU +/- 33, respectively (P = not significant for all). Levene test results for summed attenuation data for standard, TBW, calculated LBW, and measured LBW protocols were 40 +/- 29, 38 +/- 33 (P = .83), 35 +/- 35 (P = .56), and 26 +/- 19 (P = .05), respectively. By excluding highly variable but poorly perfused adipose tissue from calculation of contrast medium dose, the measured LBW protocol may lessen patient-to-patient enhancement variability while maintaining satisfactory hepatic and vascular enhancement.

MANEMO Routing in Practice: Protocol Selection, Expected Performance, and Experimental Evaluation

NASA Astrophysics Data System (ADS)

Tazaki, Hajime; van Meter, Rodney; Wakikawa, Ryuji; Wongsaardsakul, Thirapon; Kanchanasut, Kanchana; Dias de Amorim, Marcelo; Murai, Jun

Motivated by the deployment of post-disaster MANEMO (MANET for NEMO) composed of mobile routers and stations, we evaluate two candidate routing protocols through network simulation, theoretical performance analysis, and field experiments. The first protocol is the widely adopted Optimized Link State Routing protocol (OLSR) and the second is the combination of the Tree Discovery Protocol (TDP) with Network In Node Advertisement (NINA). To the best of our knowledge, this is the first time that these two protocols are compared in both theoretical and practical terms. We focus on the control overhead generated when mobile routers perform a handover. Our results confirm the correctness and operational robustness of both protocols. More interestingly, although in the general case OLSR leads to better results, TDP/NINA outperforms OLSR both in the case of sparse networks and in highly mobile networks, which correspond to the operation point of a large set of post-disaster scenarios.

Effect of different analyte diffusion/adsorption protocols on SERS signals

NASA Astrophysics Data System (ADS)

Li, Ruoping; Petschek, Rolfe G.; Han, Junhe; Huang, Mingju

2018-07-01

The effect of different analyte diffusion/adsorption protocols was studied which is often overlooked in surface-enhanced Raman scattering (SERS) technique. Three protocols: highly concentrated dilution (HCD) protocol, half-half dilution (HHD) protocol and layered adsorption (LA) protocol were studied and the SERS substrates were monolayer films of 80 nm Ag nanoparticles (NPs) which were modified by polyvinylpyrrolidone. The diffusion/adsorption mechanisms were modelled using the diffusion equation and the electromagnetic field distribution of two adjacent Ag NPs was simulated by the finite-different time-domain method. All experimental data and theoretical analysis suggest that different diffusion/adsorption behaviour of analytes will cause different SERS signal enhancements. HHD protocol could produce the most uniform and reproducible samples, and the corresponding signal intensity of the analyte is the strongest. This study will help to understand and promote the use of SERS technique in quantitative analysis.

The diagnosis of sepsis revisited - a challenge for young medical scientists in the 21st century

PubMed Central

2014-01-01

In 1991, a well-meaning consensus group of thought leaders derived a simple definition for sepsis which required the breach of only a few static thresholds. More than 20 years later, this simple definition has calcified to become the gold standard for sepsis protocols and research. Yet sepsis clearly comprises a complex, dynamic, and relational distortion of human life. Given the profound scope of the loss of life worldwide, there is a need to disengage from the simple concepts of the past. There is an acute need to develop 21st century approaches which engage sepsis in its true form, as a complex, dynamic, and relational pattern of death. PMID:24383420

Optimized protocols for Mycobacterium leprae strain management: frozen stock preservation and maintenance in athymic nude mice.

PubMed

Trombone, Ana Paula Fávaro; Pedrini, Sílvia Cristina Barbosa; Diório, Suzana Madeira; Belone, Andréa de Faria Fernandes; Fachin, Luciana Raquel Vicenzi; do Nascimento, Dejair Caitano; Rosa, Patricia Sammarco

2014-03-23

Leprosy, caused by Mycobacterium leprae, is an important infectious disease that is still endemic in many countries around the world, including Brazil. There are currently no known methods for growing M. leprae in vitro, presenting a major obstacle in the study of this pathogen in the laboratory. Therefore, the maintenance and growth of M. leprae strains are preferably performed in athymic nude mice (NU-Foxn1(nu)). The laboratory conditions for using mice are readily available, easy to perform, and allow standardization and development of protocols for achieving reproducible results. In the present report, we describe a simple protocol for purification of bacilli from nude mouse footpads using trypsin, which yields a suspension with minimum cell debris and with high bacterial viability index, as determined by fluorescent microscopy. A modification to the standard method for bacillary counting by Ziehl-Neelsen staining and light microscopy is also demonstrated. Additionally, we describe a protocol for freezing and thawing bacillary stocks as an alternative protocol for maintenance and storage of M. leprae strains.

Experiences with http/WebDAV protocols for data access in high throughput computing

NASA Astrophysics Data System (ADS)

Bernabeu, Gerard; Martinez, Francisco; Acción, Esther; Bria, Arnau; Caubet, Marc; Delfino, Manuel; Espinal, Xavier

2011-12-01

In the past, access to remote storage was considered to be at least one order of magnitude slower than local disk access. Improvement on network technologies provide the alternative of using remote disk. For those accesses one can today reach levels of throughput similar or exceeding those of local disks. Common choices as access protocols in the WLCG collaboration are RFIO, [GSI]DCAP, GRIDFTP, XROOTD and NFS. HTTP protocol shows a promising alternative as it is a simple, lightweight protocol. It also enables the use of standard technologies such as http caching or load balancing which can be used to improve service resilience and scalability or to boost performance for some use cases seen in HEP such as the "hot files". WebDAV extensions allow writing data, giving it enough functionality to work as a remote access protocol. This paper will show our experiences with the WebDAV door for dCache, in terms of functionality and performance, applied to some of the HEP work flows in the LHC Tier1 at PIC.

Mutation-Based Learning to Improve Student Autonomy and Scientific Inquiry Skills in a Large Genetics Laboratory Course

PubMed Central

Wu, Jinlu

2013-01-01

Laboratory education can play a vital role in developing a learner's autonomy and scientific inquiry skills. In an innovative, mutation-based learning (MBL) approach, students were instructed to redesign a teacher-designed standard experimental protocol by a “mutation” method in a molecular genetics laboratory course. Students could choose to delete, add, reverse, or replace certain steps of the standard protocol to explore questions of interest to them in a given experimental scenario. They wrote experimental proposals to address their rationales and hypotheses for the “mutations”; conducted experiments in parallel, according to both standard and mutated protocols; and then compared and analyzed results to write individual lab reports. Various autonomy-supportive measures were provided in the entire experimental process. Analyses of student work and feedback suggest that students using the MBL approach 1) spend more time discussing experiments, 2) use more scientific inquiry skills, and 3) find the increased autonomy afforded by MBL more enjoyable than do students following regimented instructions in a conventional “cookbook”-style laboratory. Furthermore, the MBL approach does not incur an obvious increase in labor and financial costs, which makes it feasible for easy adaptation and implementation in a large class. PMID:24006394

Attraction of Rotors to the Pulmonary Veins in Paroxysmal Atrial Fibrillation: A Modeling Study

PubMed Central

Calvo, Conrado J.; Deo, Makarand; Zlochiver, Sharon; Millet, José; Berenfeld, Omer

2014-01-01

Maintenance of paroxysmal atrial fibrillation (AF) by fast rotors in the left atrium (LA) or at the pulmonary veins (PVs) is not fully understood. To gain insight into this dynamic and complex process, we studied the role of the heterogeneous distribution of transmembrane currents in the PVs and LA junction (PV-LAJ) in the localization of rotors in the PVs. We also investigated whether simple pacing protocols could be used to predict rotor drift in the PV-LAJ. Experimentally observed heterogeneities in IK1, IKs, IKr, Ito, and ICaL in the PV-LAJ were incorporated into two- and pseudo three-dimensional models of Courtemanche-Ramirez-Nattel-Kneller human atrial kinetics to simulate various conditions and investigate rotor drifting mechanisms. Spatial gradients in the currents resulted in shorter action potential duration, minimum diastolic potential that was less negative, and slower upstroke and conduction velocity for rotors in the PV region than in the LA. Rotors under such conditions drifted toward the PV and stabilized at the shortest action potential duration and less-excitable region, consistent with drift direction under intercellular coupling heterogeneities and regardless of the geometrical constraint in the PVs. Simulations with various IK1 gradient conditions and current-voltage relationships substantiated its major role in the rotor drift. In our 1:1 pacing protocol, we found that among various action potential properties, only the minimum diastolic potential gradient was a rate-independent predictor of rotor drift direction. Consistent with experimental and clinical AF studies, simulations in an electrophysiologically heterogeneous model of the PV-LAJ showed rotor attraction toward the PV. Our simulations suggest that IK1 heterogeneity is dominant compared to other currents in determining the drift direction through its impact on the excitability gradient. These results provide a believed novel framework for understanding the complex dynamics of rotors in AF. PMID:24739180

Monitoring and Research of the Colorado River Ecosystem: When Is Enough Enough?

NASA Astrophysics Data System (ADS)

Schmidt, J. C.

2014-12-01

The Glen Canyon Dam Adaptive Management Program (GCDAMP) is a well-funded ( $10 million/yr.) river rehabilitation program with long-term monitoring and research focused on 400 km of the Colorado River in Glen, Marble, and Grand Canyons downstream from Lake Powell. More than 15 years of substantive science concerning hydrology, hydraulics, sediment transport, geomorphology, aquatic and fish ecology, riparian ecology, and socio-economics has yielded significant insights that guide experimental river management initiatives, such as a new protocol to annually release sediment-triggered controlled floods; administratively called the High Flow Experimental Protocol (HFEP). Implementation of the HFEP requires nearly real-time monitoring of sediment delivery from key sand producing tributaries, transport in and calculation of sand mass balance in segments of the Colorado River, and defined uncertainty of those processes and conditions (see: http://www.gcmrc.gov/). The HFEP aims to rebuild sandbars within the active channel, but many stakeholders remain focused on other aquatic ecosystem, riparian ecosystem, archaeological resources, or cultural values that are linked in complex ways to active channel conditions. Tension exists within the GCDAMP about how funding is allocated for innovative data collection, analysis, and publication strategies that allow implementation of the HFEP, and to also measure derivative resource conditions about which some stakeholders have concern. Monitoring and research initiatives that attempt to incorporate traditional cultural values also have high uncertainty when resource condition is linked with the simple implementation paradigm of the HFEP. Thus, the GCDAMP is faced with the complex challenge of allocating sufficient resources to monitor active channel processes and characteristics, resolve remaining scientific uncertainties, and develop new strategies for incorporating science insights into engineering and policy decisions, while also monitoring terrestrial resources supported by stakeholders but only indirectly linked with dam operations. The challenge of balancing these scientific and adaptive management objectives is substantial.

Attraction of rotors to the pulmonary veins in paroxysmal atrial fibrillation: a modeling study.

PubMed

Calvo, Conrado J; Deo, Makarand; Zlochiver, Sharon; Millet, José; Berenfeld, Omer

2014-04-15

Maintenance of paroxysmal atrial fibrillation (AF) by fast rotors in the left atrium (LA) or at the pulmonary veins (PVs) is not fully understood. To gain insight into this dynamic and complex process, we studied the role of the heterogeneous distribution of transmembrane currents in the PVs and LA junction (PV-LAJ) in the localization of rotors in the PVs. We also investigated whether simple pacing protocols could be used to predict rotor drift in the PV-LAJ. Experimentally observed heterogeneities in IK1, IKs, IKr, Ito, and ICaL in the PV-LAJ were incorporated into two- and pseudo three-dimensional models of Courtemanche-Ramirez-Nattel-Kneller human atrial kinetics to simulate various conditions and investigate rotor drifting mechanisms. Spatial gradients in the currents resulted in shorter action potential duration, minimum diastolic potential that was less negative, and slower upstroke and conduction velocity for rotors in the PV region than in the LA. Rotors under such conditions drifted toward the PV and stabilized at the shortest action potential duration and less-excitable region, consistent with drift direction under intercellular coupling heterogeneities and regardless of the geometrical constraint in the PVs. Simulations with various IK1 gradient conditions and current-voltage relationships substantiated its major role in the rotor drift. In our 1:1 pacing protocol, we found that among various action potential properties, only the minimum diastolic potential gradient was a rate-independent predictor of rotor drift direction. Consistent with experimental and clinical AF studies, simulations in an electrophysiologically heterogeneous model of the PV-LAJ showed rotor attraction toward the PV. Our simulations suggest that IK1 heterogeneity is dominant compared to other currents in determining the drift direction through its impact on the excitability gradient. These results provide a believed novel framework for understanding the complex dynamics of rotors in AF. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Organic synthesis via magnetic attraction: benign and sustainable protocols using magnetic nanoferrites

EPA Science Inventory

Magnetic nano-catalysts have been prepared using simple modification of iron ferrites wherein their quasi-homogeneous state, because of nm size range, facilitates the catalysis process as increased surface is available for reaction; the easy separation of the catalysts by externa...

DEVELOPMENT OF A PROTOCOL FOR TESTING EFFECTS OF TOXIC SUBSTANCES ON PLANTS

EPA Science Inventory

This study was designed to devise a rapid, simple, reproducible bioassay procedure to determine effects of so-called 'toxic substances in the environment' on vegetation and provide a standardized procedure for evaluation and comparison of effects of diverse compounds. Eight diffe...

Plasmid fermentation process for DNA immunization applications.

PubMed

Carnes, Aaron E; Williams, James A

2014-01-01

Plasmid DNA for immunization applications must be of the highest purity and quality. The ability of downstream purification to efficiently produce a pure final product is directly influenced by the performance of the upstream fermentation process. While several clinical manufacturing facilities already have validated fermentation processes in place to manufacture plasmid DNA for use in humans, a simple and inexpensive laboratory-scale fermentation process can be valuable for in-house production of plasmid DNA for use in animal efficacy studies. This chapter describes a simple fed-batch fermentation process for producing bacterial cell paste enriched with high-quality plasmid DNA. A constant feeding strategy results in a medium cell density culture with continuously increasing plasmid amplification towards the end of the process. Cell banking and seed culture preparation protocols, which can dramatically influence final product yield and quality, are also described. These protocols are suitable for production of research-grade plasmid DNA at the 100 mg-to-1.5 g scale from a typical 10 L laboratory benchtop fermentor.

Simple and Efficient Generation of Aryl Radicals from Aryl Triflates: Synthesis of Aryl Boronates and Aryl Iodides at Room Temperature.

PubMed

Liu, Wenbo; Yang, Xiaobo; Gao, Yang; Li, Chao-Jun

2017-06-28

Despite the wide use of aryl radicals in organic synthesis, current methods to prepare them from aryl halides, carboxylic acids, boronic acids, and diazonium salts suffer from limitations. Aryl triflates, easily obtained from phenols, are promising aryl radical progenitors but remain elusive in this regard. Inspired by the single electron transfer process for aryl halides to access aryl radicals, we developed a simple and efficient protocol to convert aryl triflates to aryl radicals. Our success lies in exploiting sodium iodide as the soft electron donor assisted by light. This strategy enables the scalable synthesis of two types of important organic molecules, i.e., aryl boronates and aryl iodides, in good to high yields, with broad functional group compatibility in a transition-metal-free manner at room temperature. This protocol is anticipated to find potential applications in other aryl-radical-involved reactions by using aryl triflates as aryl radical precursors.

Human granulocyte colony stimulating factor (hG-CSF): cloning, overexpression, purification and characterization.

PubMed

Vanz, Ana Ls; Renard, Gaby; Palma, Mario S; Chies, Jocelei M; Dalmora, Sérgio L; Basso, Luiz A; Santos, Diógenes S

2008-04-04

Biopharmaceutical drugs are mainly recombinant proteins produced by biotechnological tools. The patents of many biopharmaceuticals have expired, and biosimilars are thus currently being developed. Human granulocyte colony stimulating factor (hG-CSF) is a hematopoietic cytokine that acts on cells of the neutrophil lineage causing proliferation and differentiation of committed precursor cells and activation of mature neutrophils. Recombinant hG-CSF has been produced in genetically engineered Escherichia coli (Filgrastim) and successfully used to treat cancer patients suffering from chemotherapy-induced neutropenia. Filgrastim is a 175 amino acid protein, containing an extra N-terminal methionine, which is needed for expression in E. coli. Here we describe a simple and low-cost process that is amenable to scaling-up for the production and purification of homogeneous and active recombinant hG-CSF expressed in E. coli cells. Here we describe cloning of the human granulocyte colony-stimulating factor coding DNA sequence, protein expression in E. coli BL21(DE3) host cells in the absence of isopropyl-beta-D-thiogalactopyranoside (IPTG) induction, efficient isolation and solubilization of inclusion bodies by a multi-step washing procedure, and a purification protocol using a single cationic exchange column. Characterization of homogeneous rhG-CSF by size exclusion and reverse phase chromatography showed similar yields to the standard. The immunoassay and N-terminal sequencing confirmed the identity of rhG-CSF. The biological activity assay, in vivo, showed an equivalent biological effect (109.4%) to the standard reference rhG-CSF. The homogeneous rhG-CSF protein yield was 3.2 mg of bioactive protein per liter of cell culture. The recombinant protein expression in the absence of IPTG induction is advantageous since cost is reduced, and the protein purification protocol using a single chromatographic step should reduce cost even further for large scale production. The physicochemical, immunological and biological analyses showed that this protocol can be useful to develop therapeutic bioproducts. In summary, the combination of different experimental strategies presented here allowed an efficient and cost-effective protocol for rhG-CSF production. These data may be of interest to biopharmaceutical companies interested in developing biosimilars and healthcare community.

Human granulocyte colony stimulating factor (hG-CSF): cloning, overexpression, purification and characterization

PubMed Central

Vanz, Ana LS; Renard, Gaby; Palma, Mario S; Chies, Jocelei M; Dalmora, Sérgio L; Basso, Luiz A; Santos, Diógenes S

2008-01-01

Background Biopharmaceutical drugs are mainly recombinant proteins produced by biotechnological tools. The patents of many biopharmaceuticals have expired, and biosimilars are thus currently being developed. Human granulocyte colony stimulating factor (hG-CSF) is a hematopoietic cytokine that acts on cells of the neutrophil lineage causing proliferation and differentiation of committed precursor cells and activation of mature neutrophils. Recombinant hG-CSF has been produced in genetically engineered Escherichia coli (Filgrastim) and successfully used to treat cancer patients suffering from chemotherapy-induced neutropenia. Filgrastim is a 175 amino acid protein, containing an extra N-terminal methionine, which is needed for expression in E. coli. Here we describe a simple and low-cost process that is amenable to scaling-up for the production and purification of homogeneous and active recombinant hG-CSF expressed in E. coli cells. Results Here we describe cloning of the human granulocyte colony-stimulating factor coding DNA sequence, protein expression in E. coli BL21(DE3) host cells in the absence of isopropyl-β-D-thiogalactopyranoside (IPTG) induction, efficient isolation and solubilization of inclusion bodies by a multi-step washing procedure, and a purification protocol using a single cationic exchange column. Characterization of homogeneous rhG-CSF by size exclusion and reverse phase chromatography showed similar yields to the standard. The immunoassay and N-terminal sequencing confirmed the identity of rhG-CSF. The biological activity assay, in vivo, showed an equivalent biological effect (109.4%) to the standard reference rhG-CSF. The homogeneous rhG-CSF protein yield was 3.2 mg of bioactive protein per liter of cell culture. Conclusion The recombinant protein expression in the absence of IPTG induction is advantageous since cost is reduced, and the protein purification protocol using a single chromatographic step should reduce cost even further for large scale production. The physicochemical, immunological and biological analyses showed that this protocol can be useful to develop therapeutic bioproducts. In summary, the combination of different experimental strategies presented here allowed an efficient and cost-effective protocol for rhG-CSF production. These data may be of interest to biopharmaceutical companies interested in developing biosimilars and healthcare community. PMID:18394164

Two Phase Admission Control for QoS Mobile Ad Hoc Networks

NASA Astrophysics Data System (ADS)

Chen, Chien-Sheng; Su, Yi-Wen; Liu, Wen-Hsiung; Chi, Ching-Lung

In this paper a novel and effective two phase admission control (TPAC) for QoS mobile ad hoc networks is proposed that satisfies the real-time traffic requirements in mobile ad hoc networks. With a limited amount of extra overhead, TPAC can avoid network congestions by a simple and precise admission control which blocks most of the overloading flow-requests in the route discovery process. When compared with previous QoS routing schemes such as QoS-aware routing protocol and CACP protocols, it is shown from system simulations that the proposed scheme can increase the system throughput and reduce both the dropping rate and the end-to-end delay. Therefore, TPAC is surely an effective QoS-guarantee protocol to provide for real-time traffic.

Experimental system for computer network via satellite /CS/. III - Network control processor

NASA Astrophysics Data System (ADS)

Kakinuma, Y.; Ito, A.; Takahashi, H.; Uchida, K.; Matsumoto, K.; Mitsudome, H.

1982-03-01

A network control processor (NCP) has the functions of generating traffics, the control of links and the control of transmitting bursts. The NCP executes protocols, monitors of experiments, gathering and compiling data of measurements, of which programs are loaded on a minicomputer (MELCOM 70/40) with 512KB of memories. The NCP acts as traffic generators, instead of a host computer, in the experiment. For this purpose, 15 fake stations are realized by the software in each user station. This paper describes the configuration of the NCP and the implementation of the protocols for the experimental system.

Casting Protocols for the Production of Open Cell Aluminum Foams by the Replication Technique and the Effect on Porosity

PubMed Central

Elizondo Luna, Erardo M.; Barari, Farzad; Woolley, Robert; Goodall, Russell

2014-01-01

Metal foams are interesting materials from both a fundamental understanding and practical applications point of view. Uses have been proposed, and in many cases validated experimentally, for light weight or impact energy absorbing structures, as high surface area heat exchangers or electrodes, as implants to the body, and many more. Although great progress has been made in understanding their structure-properties relationships, the large number of different processing techniques, each producing material with different characteristics and structure, means that understanding of the individual effects of all aspects of structure is not complete. The replication process, where molten metal is infiltrated between grains of a removable preform material, allows a markedly high degree of control and has been used to good effect to elucidate some of these relationships. Nevertheless, the process has many steps that are dependent on individual “know-how”, and this paper aims to provide a detailed description of all stages of one embodiment of this processing method, using materials and equipment that would be relatively easy to set up in a research environment. The goal of this protocol and its variants is to produce metal foams in an effective and simple way, giving the possibility to tailor the outcome of the samples by modifying certain steps within the process. By following this, open cell aluminum foams with pore sizes of 1–2.36 mm diameter and 61% to 77% porosity can be obtained. PMID:25548938

Attention to baseline: does orienting visuospatial attention really facilitate target detection?

PubMed

Albares, Marion; Criaud, Marion; Wardak, Claire; Nguyen, Song Chi Trung; Ben Hamed, Suliann; Boulinguez, Philippe

2011-08-01

Standard protocols testing the orientation of visuospatial attention usually present spatial cues before targets and compare valid-cue trials with invalid-cue trials. The valid/invalid contrast results in a relative behavioral or physiological difference that is generally interpreted as a benefit of attention orientation. However, growing evidence suggests that inhibitory control of response is closely involved in this kind of protocol that requires the subjects to withhold automatic responses to cues, probably biasing behavioral and physiological baselines. Here, we used two experiments to disentangle the inhibitory control of automatic responses from orienting of visuospatial attention in a saccadic reaction time task in humans, a variant of the classical cue-target detection task and a sustained visuospatial attentional task. Surprisingly, when referring to a simple target detection task in which there is no need to refrain from reacting to avoid inappropriate responses, we found no consistent evidence of facilitation of target detection at the attended location. Instead, we observed a cost at the unattended location. Departing from the classical view, our results suggest that reaction time measures of visuospatial attention probably relie on the attenuation of elementary processes involved in visual target detection and saccade initiation away from the attended location rather than on facilitation at the attended location. This highlights the need to use proper control conditions in experimental designs to disambiguate relative from absolute cueing benefits on target detection reaction times, both in psychophysical and neurophysiological studies.

Generalized estimators of avian abundance from count survey data

USGS Publications Warehouse

Royle, J. Andrew

2004-01-01

I consider modeling avian abundance from spatially referenced bird count data collected according to common protocols such as capture?recapture, multiple observer, removal sampling and simple point counts. Small sample sizes and large numbers of parameters have motivated many analyses that disregard the spatial indexing of the data, and thus do not provide an adequate treatment of spatial structure. I describe a general framework for modeling spatially replicated data that regards local abundance as a random process, motivated by the view that the set of spatially referenced local populations (at the sample locations) constitute a metapopulation. Under this view, attention can be focused on developing a model for the variation in local abundance independent of the sampling protocol being considered. The metapopulation model structure, when combined with the data generating model, define a simple hierarchical model that can be analyzed using conventional methods. The proposed modeling framework is completely general in the sense that broad classes of metapopulation models may be considered, site level covariates on detection and abundance may be considered, and estimates of abundance and related quantities may be obtained for sample locations, groups of locations, unsampled locations. Two brief examples are given, the first involving simple point counts, and the second based on temporary removal counts. Extension of these models to open systems is briefly discussed.

Moving the Learning of Teaching Closer to Practice: Teacher Education Implications of School-Based Inquiry Teams

ERIC Educational Resources Information Center

Gallimore, Ronald; Ermeling, Bradley A.; Saunders, William M.; Goldenberg, Claude

2009-01-01

A 5-year prospective, quasi-experimental investigation demonstrated that grade-level teams in 9 Title 1 schools using an inquiry-focused protocol to solve instructional problems significantly increased achievement. Teachers applying the inquiry protocol shifted attribution of improved student performance to their teaching rather than external…

GUIDANCE FOR RESEARCH HOUSE STUDIES OF THE FLORIDA RADON RESEARCH PROGRAM, VOLUME 2: MODEL-BACKED EXPERIMENTAL PROTOCOL FOR DETERMINING RADON

EPA Science Inventory

The report provides guidance and a readily available reference to groups involved with the Florida Radon Research Program's (FRRP's) research house studies. It includes: 1): Lists of Parameters for continuous and periodic high and low resolution measurements; (2) Protocols for c...

Experimental Evaluation of Unicast and Multicast CoAP Group Communication

PubMed Central

Ishaq, Isam; Hoebeke, Jeroen; Moerman, Ingrid; Demeester, Piet

2016-01-01

The Internet of Things (IoT) is expanding rapidly to new domains in which embedded devices play a key role and gradually outnumber traditionally-connected devices. These devices are often constrained in their resources and are thus unable to run standard Internet protocols. The Constrained Application Protocol (CoAP) is a new alternative standard protocol that implements the same principals as the Hypertext Transfer Protocol (HTTP), but is tailored towards constrained devices. In many IoT application domains, devices need to be addressed in groups in addition to being addressable individually. Two main approaches are currently being proposed in the IoT community for CoAP-based group communication. The main difference between the two approaches lies in the underlying communication type: multicast versus unicast. In this article, we experimentally evaluate those two approaches using two wireless sensor testbeds and under different test conditions. We highlight the pros and cons of each of them and propose combining these approaches in a hybrid solution to better suit certain use case requirements. Additionally, we provide a solution for multicast-based group membership management using CoAP. PMID:27455262

Screening for Learning and Memory Mutations: A New Approach.

PubMed

Gallistel, C R; King, A P; Daniel, A M; Freestone, D; Papachristos, E B; Balci, F; Kheifets, A; Zhang, J; Su, X; Schiff, G; Kourtev, H

2010-01-30

We describe a fully automated, live-in 24/7 test environment, with experimental protocols that measure the accuracy and precision with which mice match the ratio of their expected visit durations to the ratio of the incomes obtained from two hoppers, the progress of instrumental and classical conditioning (trials-to-acquisition), the accuracy and precision of interval timing, the effect of relative probability on the choice of a timed departure target, and the accuracy and precision of memory for the times of day at which food is available. The system is compact; it obviates the handling of the mice during testing; it requires negligible amounts of experimenter/technician time; and it delivers clear and extensive results from 3 protocols within a total of 7-9 days after the mice are placed in the test environment. Only a single 24-hour period is required for the completion of first protocol (the matching protocol), which is strong test of temporal and spatial estimation and memory mechanisms. Thus, the system permits the extensive screening of many mice in a short period of time and in limited space. The software is publicly available.

Mobile Virtual Private Networking

NASA Astrophysics Data System (ADS)

Pulkkis, Göran; Grahn, Kaj; Mårtens, Mathias; Mattsson, Jonny

Mobile Virtual Private Networking (VPN) solutions based on the Internet Security Protocol (IPSec), Transport Layer Security/Secure Socket Layer (SSL/TLS), Secure Shell (SSH), 3G/GPRS cellular networks, Mobile IP, and the presently experimental Host Identity Protocol (HIP) are described, compared and evaluated. Mobile VPN solutions based on HIP are recommended for future networking because of superior processing efficiency and network capacity demand features. Mobile VPN implementation issues associated with the IP protocol versions IPv4 and IPv6 are also evaluated. Mobile VPN implementation experiences are presented and discussed.

A Mobility-Aware QoS Signaling Protocol for Ambient Networks

NASA Astrophysics Data System (ADS)

Jeong, Seong-Ho; Lee, Sung-Hyuck; Bang, Jongho

Mobility-aware quality of service (QoS) signaling is crucial to provide seamless multimedia services in the ambient environment where mobile nodes may move frequently between different wireless access networks. The mobility of an IP-based node in ambient networks affects routing paths, and as a result, can have a significant impact on the operation and state management of QoS signaling protocols. In this paper, we first analyze the impact of mobility on QoS signaling protocols and how the protocols operate in mobility scenarios. We then propose an efficient mobility-aware QoS signaling protocol which can operate adaptively in ambient networks. The key features of the protocol include the fast discovery of a crossover node where the old and new paths converge or diverge due to handover and the localized state management for seamless services. Our analytical and simulation/experimental results show that the proposed/implemented protocol works better than existing protocols in the IP-based mobile environment.

Continuous-variable measurement-device-independent quantum key distribution with photon subtraction

NASA Astrophysics Data System (ADS)

Ma, Hong-Xin; Huang, Peng; Bai, Dong-Yun; Wang, Shi-Yu; Bao, Wan-Su; Zeng, Gui-Hua

2018-04-01

It has been found that non-Gaussian operations can be applied to increase and distill entanglement between Gaussian entangled states. We show the successful use of the non-Gaussian operation, in particular, photon subtraction operation, on the continuous-variable measurement-device-independent quantum key distribution (CV-MDI-QKD) protocol. The proposed method can be implemented based on existing technologies. Security analysis shows that the photon subtraction operation can remarkably increase the maximal transmission distance of the CV-MDI-QKD protocol, which precisely make up for the shortcoming of the original CV-MDI-QKD protocol, and one-photon subtraction operation has the best performance. Moreover, the proposed protocol provides a feasible method for the experimental implementation of the CV-MDI-QKD protocol.

Initial non-operative management of uncomplicated appendicitis in children: a protocol for a multicentre randomised controlled trial (APAC trial)

PubMed Central

Knaapen, Max; van der Lee, Johanna H; Bakx, Roel; The, Sarah-May L; van Heurn, Ernst W E; Heij, Hugo A; Gorter, Ramon R

2017-01-01

Introduction Based on epidemiological, immunological and pathology data, the idea that appendicitis is not necessarily a progressive disease is gaining ground. Two types are distinguished: simple and complicated appendicitis. Non-operative treatment (NOT) of children with simple appendicitis has been investigated in several small studies. So far, it is deemed safe. However, its effectiveness and effect on quality of life (QoL) have yet to be established in an adequately powered randomised trial. In this article, we provide the study protocol for the APAC (Antibiotics versus Primary Appendectomy in Children) trial. Methods and analysis This multicentre, non-inferiority, randomised controlled trial randomises children aged 7–17 years with imaging-confirmed simple appendicitis between appendectomy and NOT. Patients are recruited in 15 hospitals. The intended sample size, based on the primary outcome, rate of complications and a non-inferiority margin of 5%, is 334 patients. NOT consists of intravenous antibiotics for 48–72 hours, daily blood tests and ultrasound follow-up. If the patient meets the predefined discharge criteria, antibiotic treatment is continued orally at home. Primary outcome is the rate of complications at 1-year follow-up. An independent adjudication committee will assess all complications and their relation to the allocated treatment. Secondary outcomes include, but are not limited to, delayed appendectomies, QoL, pain and (in)direct costs. The primary outcome will be analysed both according to the intention-to-treat principle and the per-protocol principle, and is presented with a one-sided 97.5% CI. We will use multiple logistic and linear regression for binary and continuous outcomes, respectively, to adjust for stratification factors. Ethics and dissemination The protocol has been approved by the Medical Ethics Review Committee of the Academic Medical Center, Amsterdam. Data monitoring is performed by an independent institute and a Data Safety Monitoring Board has been assigned. Results will be presented in peer-reviewed academic journals and at (international) conferences. Trial registration number NCT02848820; NTR5977; Pre-results. PMID:29146647

Fasting: a major limitation for resistance exercise training effects in rodents

PubMed Central

das Neves, W.; de Oliveira, L.F.; da Silva, R.P.; Alves, C.R.R.; Lancha, A.H.

2017-01-01

Protocols that mimic resistance exercise training (RET) in rodents present several limitations, one of them being the electrical stimulus, which is beyond the physiological context observed in humans. Recently, our group developed a conditioning system device that does not use electric shock to stimulate rats, but includes fasting periods before each RET session. The current study was designed to test whether cumulative fasting periods have some influence on skeletal muscle mass and function. Three sets of male Wistar rats were used in the current study. The first set of rats was submitted to a RET protocol without food restriction. However, rats were not able to perform exercise properly. The second and third sets were then randomly assigned into three experimental groups: 1) untrained control rats, 2) untrained rats submitted to fasting periods, and 3) rats submitted to RET including fasting periods before each RET session. While the second set of rats performed a short RET protocol (i.e., an adaptation protocol for 3 weeks), the third set of rats performed a longer RET protocol including overload (i.e., 8 weeks). After the short-term protocol, cumulative fasting periods promoted loss of weight (P<0.001). After the longer RET protocol, no difference was observed for body mass, extensor digitorum longus (EDL) morphology or skeletal muscle function (P>0.05 for all). Despite no effects on EDL mass, soleus muscle displayed significant atrophy in the fasting experimental groups (P<0.01). Altogether, these data indicate that fasting is a major limitation for RET in rats. PMID:29185588

Fasting: a major limitation for resistance exercise training effects in rodents.

PubMed

das Neves, W; de Oliveira, L F; da Silva, R P; Alves, C R R; Lancha, A H

2017-11-17

Protocols that mimic resistance exercise training (RET) in rodents present several limitations, one of them being the electrical stimulus, which is beyond the physiological context observed in humans. Recently, our group developed a conditioning system device that does not use electric shock to stimulate rats, but includes fasting periods before each RET session. The current study was designed to test whether cumulative fasting periods have some influence on skeletal muscle mass and function. Three sets of male Wistar rats were used in the current study. The first set of rats was submitted to a RET protocol without food restriction. However, rats were not able to perform exercise properly. The second and third sets were then randomly assigned into three experimental groups: 1) untrained control rats, 2) untrained rats submitted to fasting periods, and 3) rats submitted to RET including fasting periods before each RET session. While the second set of rats performed a short RET protocol (i.e., an adaptation protocol for 3 weeks), the third set of rats performed a longer RET protocol including overload (i.e., 8 weeks). After the short-term protocol, cumulative fasting periods promoted loss of weight (P<0.001). After the longer RET protocol, no difference was observed for body mass, extensor digitorum longus (EDL) morphology or skeletal muscle function (P>0.05 for all). Despite no effects on EDL mass, soleus muscle displayed significant atrophy in the fasting experimental groups (P<0.01). Altogether, these data indicate that fasting is a major limitation for RET in rats.

Experimental high-speed network

NASA Astrophysics Data System (ADS)

McNeill, Kevin M.; Klein, William P.; Vercillo, Richard; Alsafadi, Yasser H.; Parra, Miguel V.; Dallas, William J.

1993-09-01

Many existing local area networking protocols currently applied in medical imaging were originally designed for relatively low-speed, low-volume networking. These protocols utilize small packet sizes appropriate for text based communication. Local area networks of this type typically provide raw bandwidth under 125 MHz. These older network technologies are not optimized for the low delay, high data traffic environment of a totally digital radiology department. Some current implementations use point-to-point links when greater bandwidth is required. However, the use of point-to-point communications for a total digital radiology department network presents many disadvantages. This paper describes work on an experimental multi-access local area network called XFT. The work includes the protocol specification, and the design and implementation of network interface hardware and software. The protocol specifies the Physical and Data Link layers (OSI layers 1 & 2) for a fiber-optic based token ring providing a raw bandwidth of 500 MHz. The protocol design and implementation of the XFT interface hardware includes many features to optimize image transfer and provide flexibility for additional future enhancements which include: a modular hardware design supporting easy portability to a variety of host system buses, a versatile message buffer design providing 16 MB of memory, and the capability to extend the raw bandwidth of the network to 3.0 GHz.

Measurement-device-independent quantum key distribution for Scarani-Acin-Ribordy-Gisin 04 protocol

PubMed Central

Mizutani, Akihiro; Tamaki, Kiyoshi; Ikuta, Rikizo; Yamamoto, Takashi; Imoto, Nobuyuki

2014-01-01

The measurement-device-independent quantum key distribution (MDI QKD) was proposed to make BB84 completely free from any side-channel in detectors. Like in prepare & measure QKD, the use of other protocols in MDI setting would be advantageous in some practical situations. In this paper, we consider SARG04 protocol in MDI setting. The prepare & measure SARG04 is proven to be able to generate a key up to two-photon emission events. In MDI setting we show that the key generation is possible from the event with single or two-photon emission by a party and single-photon emission by the other party, but the two-photon emission event by both parties cannot contribute to the key generation. On the contrary to prepare & measure SARG04 protocol where the experimental setup is exactly the same as BB84, the measurement setup for SARG04 in MDI setting cannot be the same as that for BB84 since the measurement setup for BB84 in MDI setting induces too many bit errors. To overcome this problem, we propose two alternative experimental setups, and we simulate the resulting key rate. Our study highlights the requirements that MDI QKD poses on us regarding with the implementation of a variety of QKD protocols. PMID:24913431

Merging domino and redox chemistry: stereoselective access to di- and trisubstituted β,γ-unsaturated acids and esters.

PubMed

Tejedor, David; Méndez-Abt, Gabriela; Cotos, Leandro; García-Tellado, Fernando

2012-03-19

Merging is the game! The coupling of a domino reaction and an internal neutral redox reaction constitutes an excellent manifold for the stereoselective synthesis of di- and trisubstituted olefins featuring a malonate unit, an ester, or a free carboxylic acid as substituents at the allylic position (see scheme; MW=microwave). The reaction utilizes simple starting materials (propargyl vinyl ethers), methanol or water as solvents, and a very simple and bench-friendly protocol. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simple Automatic File Exchange (SAFE) to Support Low-Cost Spacecraft Operation via the Internet

NASA Technical Reports Server (NTRS)

Baker, Paul; Repaci, Max; Sames, David

1998-01-01

Various issues associated with Simple Automatic File Exchange (SAFE) are presented in viewgraph form. Specific topics include: 1) Packet telemetry, Internet IP networks and cost reduction; 2) Basic functions and technical features of SAFE; 3) Project goals, including low-cost satellite transmission to data centers to be distributed via an Internet; 4) Operations with a replicated file protocol; 5) File exchange operation; 6) Ground stations as gateways; 7) Lessons learned from demonstrations and tests with SAFE; and 8) Feedback and future initiatives.

Quantum processing by remote quantum control

NASA Astrophysics Data System (ADS)

Qiang, Xiaogang; Zhou, Xiaoqi; Aungskunsiri, Kanin; Cable, Hugo; O'Brien, Jeremy L.

2017-12-01

Client-server models enable computations to be hosted remotely on quantum servers. We present a novel protocol for realizing this task, with practical advantages when using technology feasible in the near term. Client tasks are realized as linear combinations of operations implemented by the server, where the linear coefficients are hidden from the server. We report on an experimental demonstration of our protocol using linear optics, which realizes linear combination of two single-qubit operations by a remote single-qubit control. In addition, we explain when our protocol can remain efficient for larger computations, as well as some ways in which privacy can be maintained using our protocol.

Catalytic Routes for the Conversion of Biomass Derivatives to Hydrocarbons and/or Platform Chemicals

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

Silks, III, Louis A.

Unprotected carbohydrates were reacted in amine-catalyzed cascade reactions with various methyl ketones to give a direct access to C-glycosides by an operationally simple protocol. As the reaction mechanism,an aldol condensation followed by an intramolecular conjugate addition is assumed.

Simple X-ray diffraction algorithm for direct determination of cotton crystallinity

USDA-ARS?s Scientific Manuscript database

Traditionally, XRD had been used to study the crystalline structure of cotton celluloses. Despite considerable efforts in developing the curve-fitting protocol to evaluate the crystallinity index (CI), in its present state, XRD measurement can only provide a qualitative or semi-quantitative assessme...

Time- and cost-saving apparatus for analytical sample filtration

Treesearch

William R. Kenealy; Joseph C. Destree

2005-01-01

Simple and cost-effective protocols were developed for removing particulates from samples prior to analysis by high performance liquid chromatography and gas chromatography. A filter and vial holder were developed for use with a 96-well filtration plate. The device saves preparation time and costs.

AN EFFICIENT AQUEOUS N-HETEROCYCLIZATION OF ANILINE DERIVATIVES: MICROWAVE-ASSISTED SYNTHESIS OF N-ARYL AZACYCLOALKANES

EPA Science Inventory

N-aryl azacycloalkanes, an important class of building blocks in natural product and pharmaceuticals, are synthesized via an efficient and simple eco-friendly protocol that involves double N-alkylation of aniline derivatives. The reaction is accelerated by exposure to microwaves ...

EVALUATION OF MIXING ENERGY IN FLASKS USED FOR DISPERSANT EFFECTIVENESS TESTING

EPA Science Inventory

A U.S. Environmental Protection Agency (EPA) laboratory screening protocol for dispersant effectiveness consists of placing water, oil, and a dispersant in a flask and mixing the contents on an orbital shaker. Two flasks are being investigated, a simple Erlenmeyer (used in EPA's...

SOLVENT-FREE PREPARATION OF IONIC LIQUIDS USING A HOUSEHOLD MICROWAVE OVEN

EPA Science Inventory

An efficient solventless protocol for the preparation of a wide variety of ionic liquids is described which requires a simple exposure of admixed 1-methylimidazole and alkyl halides to microwave irradiation in open glass containers. The details of this clean process using a commo...

A virtual experimenter to increase standardization for the investigation of placebo effects.

PubMed

Horing, Bjoern; Newsome, Nathan D; Enck, Paul; Babu, Sabarish V; Muth, Eric R

2016-07-18

Placebo effects are mediated by expectancy, which is highly influenced by psychosocial factors of a treatment context. These factors are difficult to standardize. Furthermore, dedicated placebo research often necessitates single-blind deceptive designs where biases are easily introduced. We propose a study protocol employing a virtual experimenter - a computer program designed to deliver treatment and instructions - for the purpose of standardization and reduction of biases when investigating placebo effects. To evaluate the virtual experimenter's efficacy in inducing placebo effects via expectancy manipulation, we suggest a partially blinded, deceptive design with a baseline/retest pain protocol (hand immersions in hot water bath). Between immersions, participants will receive an (actually inert) medication. Instructions pertaining to the medication will be delivered by one of three metaphors: The virtual experimenter, a human experimenter, and an audio/text presentation (predictor "Metaphor"). The second predictor includes falsely informing participants that the medication is an effective pain killer, or correctly informing them that it is, in fact, inert (predictor "Instruction"). Analysis will be performed with hierarchical linear modelling, with a sample size of N = 50. Results from two pilot studies are presented that indicate the viability of the pain protocol (N = 33), and of the virtual experimenter software and placebo manipulation (N = 48). It will be challenging to establish full comparability between all metaphors used for instruction delivery, and to account for participant differences in acceptance of their virtual interaction partner. Once established, the presence of placebo effects would suggest that the virtual experimenter exhibits sufficient cues to be perceived as a social agent. He could consequently provide a convenient platform to investigate effects of experimenter behavior, or other experimenter characteristics, e.g., sex, age, race/ethnicity or professional status. More general applications are possible, for example in psychological research such as bias research, or virtual reality research. Potential applications also exist for standardizing clinical research by documenting and communicating instructions used in clinical trials.

Action Observation Plus Sonification. A Novel Therapeutic Protocol for Parkinson’s Patient with Freezing of Gait

PubMed Central

Mezzarobba, Susanna; Grassi, Michele; Pellegrini, Lorella; Catalan, Mauro; Kruger, Bjorn; Furlanis, Giovanni; Manganotti, Paolo; Bernardis, Paolo

2018-01-01

Freezing of gait (FoG) is a disabling symptom associated with falls, with little or no responsiveness to pharmacological treatment. Current protocols used for rehabilitation are based on the use of external sensory cues. However, cued strategies might generate an important dependence on the environment. Teaching motor strategies without cues [i.e., action observation (AO) plus Sonification] could represent an alternative/innovative approach to rehabilitation that matters most on appropriate allocation of attention and lightening cognitive load. We aimed to test the effects of a novel experimental protocol to treat patients with Parkinson’s disease (PD) and FoG, using functional, and clinical scales. The experimental protocol was based on AO plus Sonification. 12 patients were treated with 8 motor gestures. They watched eight videos showing an actor performing the same eight gestures, and then tried to repeat each gesture. Each video was composed by images and sounds of the gestures. By means of the Sonification technique, the sounds of gestures were obtained by transforming kinematic data (velocity) recorded during gesture execution, into pitch variations. The same 8 motor gestures were also used in a second group of 10 patients; which were treated with a standard protocol based on a common sensory stimulation method. All patients were tested with functional and clinical scales before, after, at 1 month, and 3 months after the treatment. Data showed that the experimental protocol have positive effects on functional and clinical tests. In comparison with the baseline evaluations, significant performance improvements were seen in the NFOG questionnaire, and the UPDRS (parts II and III). Importantly, all these improvements were consistently observed at the end, 1 month, and 3 months after treatment. No improvement effects were found in the group of patients treated with the standard protocol. These data suggest that a multisensory approach based on AO plus Sonification, with the two stimuli semantically related, could help PD patients with FoG to relearn gait movements, to reduce freezing episodes, and that these effects could be prolonged over time. PMID:29354092

Protocol for Removal of Third Molar Root Tips from the Inferior Alveolar Canal-Crossing the line.

PubMed

Punga, Rohit; Keswani, Kiran

2014-12-01

The safe removal of third molars involved with the inferior alveolar canal (IAC) has been an area of concern since long. Many times we hesitate for the removal of third molars, fearing injury to the inferior alveolar nerve. The authors here describe a simple technique which can be used to remove third molars showing evidence of proximity to IAC on presurgical radiographic evaluation, as well as those root tips which, during removal, accidentally enter the IAC space. A step-by-step protocol is presented along with necessary precautions during the operative procedure.

Reply to ``Comment II on `Quantum secret sharing based on reusable Greenberger-Horne-Zeilinger states as secure carriers' ''

NASA Astrophysics Data System (ADS)

Karimipour, V.

2006-07-01

In the preceding Comment [Jian-Zhong Du, Su-Juan Qin, Qiao-Yan Wen, and Fu-Chen Zhu, Phys. Rev. A 74, 016301 (2006)], it has been shown that in a quantum secret sharing protocol proposed in [S. Bagherinezhad and V. Karimipour, Phys. Rev. A 67, 044302 (2003)], one of the receivers can cheat by splitting the entanglement of the carrier and intercepting the secret, without being detected. In this reply we show that a simple modification of the protocol prevents the receivers from this kind of cheating.

Risks and benefits of citrate anticoagulation for continuous renal replacement therapy.

PubMed

Shum, H P; Yan, W W; Chan, T M

2015-04-01

Heparin, despite its significant side-effects, is the most commonly used anticoagulant for continuous renal replacement therapy in critical care setting. In recent years, citrate has gained much popularity by improving continuous renal replacement therapy circuit survival and decreasing blood transfusion requirements. However, its complex metabolic consequences warrant modification in the design of the citrate-based continuous renal replacement therapy protocol. With thorough understanding of the therapeutic mechanism of citrate, a simple and practicable protocol can be devised. Citrate-based continuous renal replacement therapy can be safely and widely used in the clinical setting with appropriate clinical staff training.

Single-Molecule Fluorescence In Situ Hybridization (FISH) of Circular RNA CDR1as.

PubMed

Kocks, Christine; Boltengagen, Anastasiya; Piwecka, Monika; Rybak-Wolf, Agnieszka; Rajewsky, Nikolaus

2018-01-01

Individual mRNA molecules can be imaged in fixed cells by hybridization with multiple, singly labeled oligonucleotide probes, followed by computational identification of fluorescent signals. This approach, called single-molecule RNA fluorescence in situ hybridization (smRNA FISH), allows subcellular localization and absolute quantification of RNA molecules in individual cells. Here, we describe a simple smRNA FISH protocol for two-color imaging of a circular RNA, CDR1as, simultaneously with an unrelated messenger RNA. The protocol can be adapted to circRNAs that coexist with overlapping, noncircular mRNA isoforms produced from the same genetic locus.

Immunocytochemical detection of astrocytes in brain slices in combination with Nissl staining.

PubMed

Korzhevskii, D E; Otellin, V A

2005-07-01

The present study was performed to develop a simple and reliable method for the combined staining of specimens to allow the advantages of immunocytochemical detection of astrocytes and assessment of the functional state of neurons by the Nissl method to be assessed simultaneously. The protocol suggested for processing paraffin sections allows preservation of tissue structure at high quality and allows the selective identification of astrocytes with counterstaining of neurons by the Nissl method. The protocol can be used without modification for processing brain specimens from humans and various mammals--except mice and rabbits.

Changes in co-contraction during stair descent after manual therapy protocol in knee osteoarthritis: A pilot, single-blind, randomized study.

PubMed

Cruz-Montecinos, Carlos; Flores-Cartes, Rodrigo; Montt-Rodriguez, Agustín; Pozo, Esteban; Besoaín-Saldaña, Alvaro; Horment-Lara, Giselle

2016-10-01

Manual therapy has shown clinical results in patients with knee osteoarthritis. However, the biomechanical aspects during functional tasks have not been explored in depth. Through surface electromyography, the medial and lateral co-contractions of the knee were measured while descending stairs, prior and posterior to applying a manual therapy protocol in the knee, with emphasis on techniques of joint mobilization and soft-tissue management. Sixteen females with slight or moderate knee osteoarthritis were recruited (eight experimental, eight control). It was observed that the lateral co-contraction index of the experimental group, posterior to intervention, increased by 11.7% (p = 0.014). The application of a manual therapy protocol with emphasis on techniques of joint mobilization and soft-tissue management modified lateral co-contraction, which would have a protective effect on the joint. Copyright © 2016 Elsevier Ltd. All rights reserved.

Experimental measurement-device-independent verification of quantum steering

NASA Astrophysics Data System (ADS)

Kocsis, Sacha; Hall, Michael J. W.; Bennet, Adam J.; Saunders, Dylan J.; Pryde, Geoff J.

2015-01-01

Bell non-locality between distant quantum systems—that is, joint correlations which violate a Bell inequality—can be verified without trusting the measurement devices used, nor those performing the measurements. This leads to unconditionally secure protocols for quantum information tasks such as cryptographic key distribution. However, complete verification of Bell non-locality requires high detection efficiencies, and is not robust to typical transmission losses over long distances. In contrast, quantum or Einstein-Podolsky-Rosen steering, a weaker form of quantum correlation, can be verified for arbitrarily low detection efficiencies and high losses. The cost is that current steering-verification protocols require complete trust in one of the measurement devices and its operator, allowing only one-sided secure key distribution. Here we present measurement-device-independent steering protocols that remove this need for trust, even when Bell non-locality is not present. We experimentally demonstrate this principle for singlet states and states that do not violate a Bell inequality.

Continuous variable quantum key distribution with modulated entangled states.

PubMed

Madsen, Lars S; Usenko, Vladyslav C; Lassen, Mikael; Filip, Radim; Andersen, Ulrik L

2012-01-01

Quantum key distribution enables two remote parties to grow a shared key, which they can use for unconditionally secure communication over a certain distance. The maximal distance depends on the loss and the excess noise of the connecting quantum channel. Several quantum key distribution schemes based on coherent states and continuous variable measurements are resilient to high loss in the channel, but are strongly affected by small amounts of channel excess noise. Here we propose and experimentally address a continuous variable quantum key distribution protocol that uses modulated fragile entangled states of light to greatly enhance the robustness to channel noise. We experimentally demonstrate that the resulting quantum key distribution protocol can tolerate more noise than the benchmark set by the ideal continuous variable coherent state protocol. Our scheme represents a very promising avenue for extending the distance for which secure communication is possible.

Experimental measurement-device-independent verification of quantum steering.

PubMed

Kocsis, Sacha; Hall, Michael J W; Bennet, Adam J; Saunders, Dylan J; Pryde, Geoff J

2015-01-07

Bell non-locality between distant quantum systems--that is, joint correlations which violate a Bell inequality--can be verified without trusting the measurement devices used, nor those performing the measurements. This leads to unconditionally secure protocols for quantum information tasks such as cryptographic key distribution. However, complete verification of Bell non-locality requires high detection efficiencies, and is not robust to typical transmission losses over long distances. In contrast, quantum or Einstein-Podolsky-Rosen steering, a weaker form of quantum correlation, can be verified for arbitrarily low detection efficiencies and high losses. The cost is that current steering-verification protocols require complete trust in one of the measurement devices and its operator, allowing only one-sided secure key distribution. Here we present measurement-device-independent steering protocols that remove this need for trust, even when Bell non-locality is not present. We experimentally demonstrate this principle for singlet states and states that do not violate a Bell inequality.

Experimental plug and play quantum coin flipping.

PubMed

Pappa, Anna; Jouguet, Paul; Lawson, Thomas; Chailloux, André; Legré, Matthieu; Trinkler, Patrick; Kerenidis, Iordanis; Diamanti, Eleni

2014-04-24

Performing complex cryptographic tasks will be an essential element in future quantum communication networks. These tasks are based on a handful of fundamental primitives, such as coin flipping, where two distrustful parties wish to agree on a randomly generated bit. Although it is known that quantum versions of these primitives can offer information-theoretic security advantages with respect to classical protocols, a demonstration of such an advantage in a practical communication scenario has remained elusive. Here we experimentally implement a quantum coin flipping protocol that performs strictly better than classically possible over a distance suitable for communication over metropolitan area optical networks. The implementation is based on a practical plug and play system, developed by significantly enhancing a commercial quantum key distribution device. Moreover, we provide combined quantum coin flipping protocols that are almost perfectly secure against bounded adversaries. Our results offer a useful toolbox for future secure quantum communications.

Experimental study on all-fiber-based unidimensional continuous-variable quantum key distribution

NASA Astrophysics Data System (ADS)

Wang, Xuyang; Liu, Wenyuan; Wang, Pu; Li, Yongmin

2017-06-01

We experimentally demonstrated an all-fiber-based unidimensional continuous-variable quantum key distribution (CV QKD) protocol and analyzed its security under collective attack in realistic conditions. A pulsed balanced homodyne detector, which could not be accessed by eavesdroppers, with phase-insensitive efficiency and electronic noise, was considered. Furthermore, a modulation method and an improved relative phase-locking technique with one amplitude modulator and one phase modulator were designed. The relative phase could be locked precisely with a standard deviation of 0.5° and a mean of almost zero. Secret key bit rates of 5.4 kbps and 700 bps were achieved for transmission fiber lengths of 30 and 50 km, respectively. The protocol, which simplified the CV QKD system and reduced the cost, displayed a performance comparable to that of a symmetrical counterpart under realistic conditions. It is expected that the developed protocol can facilitate the practical application of the CV QKD.

Modelling the complete operation of a free-piston shock tunnel for a low enthalpy condition

NASA Astrophysics Data System (ADS)

McGilvray, M.; Dann, A. G.; Jacobs, P. A.

2013-07-01

Only a limited number of free-stream flow properties can be measured in hypersonic impulse facilities at the nozzle exit. This poses challenges for experimenters when subsequently analysing experimental data obtained from these facilities. Typically in a reflected shock tunnel, a simple analysis that requires small amounts of computational resources is used to calculate quasi-steady gas properties. This simple analysis requires initial fill conditions and experimental measurements in analytical calculations of each major flow process, using forward coupling with minor corrections to include processes that are not directly modeled. However, this simplistic approach leads to an unknown level of discrepancy to the true flow properties. To explore the simple modelling techniques accuracy, this paper details the use of transient one and two-dimensional numerical simulations of a complete facility to obtain more refined free-stream flow properties from a free-piston reflected shock tunnel operating at low-enthalpy conditions. These calculations were verified by comparison to experimental data obtained from the facility. For the condition and facility investigated, the test conditions at nozzle exit produced with the simple modelling technique agree with the time and space averaged results from the complete facility calculations to within the accuracy of the experimental measurements.