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.

Monitoring wilderness stream ecosystems

Treesearch

Jeffrey C. Davis; G. Wayne Minshall; Christopher T. Robinson; Peter Landres

2001-01-01

A protocol and methods for monitoring the major physical, chemical, and biological components of stream ecosystems are presented. The monitoring protocol is organized into four stages. At stage 1 information is obtained on a basic set of parameters that describe stream ecosystems. Each following stage builds upon stage 1 by increasing the number of parameters and the...

Extended memory management under RTOS

NASA Technical Reports Server (NTRS)

Plummer, M.

1981-01-01

A technique for extended memory management in ROLM 1666 computers using FORTRAN is presented. A general software system is described for which the technique can be ideally applied. The memory manager interface with the system is described. The protocols by which the manager is invoked are presented, as well as the methods used by the manager.

A robust ECC based mutual authentication protocol with anonymity for session initiation protocol.

PubMed

Mehmood, Zahid; Chen, Gongliang; Li, Jianhua; Li, Linsen; Alzahrani, Bander

2017-01-01

Over the past few years, Session Initiation Protocol (SIP) is found as a substantial application-layer protocol for the multimedia services. It is extensively used for managing, altering, terminating and distributing the multimedia sessions. Authentication plays a pivotal role in SIP environment. Currently, Lu et al. presented an authentication protocol for SIP and profess that newly proposed protocol is protected against all the familiar attacks. However, the detailed analysis describes that the Lu et al.'s protocol is exposed against server masquerading attack and user's masquerading attack. Moreover, it also fails to protect the user's identity as well as it possesses incorrect login and authentication phase. In order to establish a suitable and efficient protocol, having ability to overcome all these discrepancies, a robust ECC-based novel mutual authentication mechanism with anonymity for SIP is presented in this manuscript. The improved protocol contains an explicit parameter for user to cope the issues of security and correctness and is found to be more secure and relatively effective to protect the user's privacy, user's masquerading and server masquerading as it is verified through the comprehensive formal and informal security analysis.

Zebrafish embryology and cartilage staining protocols for high school students.

PubMed

Emran, Farida; Brooks, Jacqueline M; Zimmerman, Steven R; Johnson, Susan L; Lue, Robert A

2009-06-01

The Life Sciences-Howard Hughes Medical Institute Outreach Program at Harvard University supports high school science education by offering an on-campus program for students and their teachers to participate in investigative, hands-on laboratory sessions. The outreach program has recently designed and launched a successful zebrafish embryology protocol that we present here. The main objectives of this protocol are to introduce students to zebrafish as a model research organism and to provide students with direct experience with current techniques used in embryological research. The content of the lab is designed to generate discussions on embryology, genetics, fertilization, natural selection, and animal adaptation. The protocol produces reliable results in a time-efficient manner using a minimum of reagents. The protocol presented here consists of three sections: observations of live zebrafish larvae at different developmental stages, cartilage staining of zebrafish larvae, and a mutant hunt involving identification of two zebrafish mutants (nacre and chokh). Here, we describe the protocol, show the results obtained for each section, and suggest possible alternatives for different lab settings.

OSI and TCP/IP

NASA Technical Reports Server (NTRS)

Randolph, Lynwood P.

1994-01-01

The Open Systems Interconnection Transmission Control Protocol/Internet Protocol (OSI TCP/IP) and the Government Open Systems Interconnection Profile (GOSIP) are compared and described in terms of Federal internetworking. The organization and functions of the Federal Internetworking Requirements Panel (FIRP) are discussed and the panel's conclusions and recommendations with respect to the standards and implementation of the National Information Infrastructure (NII) are presented.

A semi-nested real-time PCR method to detect low chimerism percentage in small quantity of hematopoietic stem cell transplant DNA samples.

PubMed

Aloisio, Michelangelo; Bortot, Barbara; Gandin, Ilaria; Severini, Giovanni Maria; Athanasakis, Emmanouil

2017-02-01

Chimerism status evaluation of post-allogeneic hematopoietic stem cell transplantation samples is essential to predict post-transplant relapse. The most commonly used technique capable of detecting small increments of chimerism is quantitative real-time PCR. Although this method is already used in several laboratories, previously described protocols often lack sensitivity and the amount of the DNA required for each chimerism analysis is too high. In the present study, we compared a novel semi-nested allele-specific real-time PCR (sNAS-qPCR) protocol with our in-house standard allele-specific real-time PCR (gAS-qPCR) protocol. We selected two genetic markers and analyzed technical parameters (slope, y-intercept, R2, and standard deviation) useful to determine the performances of the two protocols. The sNAS-qPCR protocol showed better sensitivity and precision. Moreover, the sNAS-qPCR protocol requires, as input, only 10 ng of DNA, which is at least 10-fold less than the gAS-qPCR protocols described in the literature. Finally, the proposed sNAS-qPCR protocol could prove very useful for performing chimerism analysis with a small amount of DNA, as in the case of blood cell subsets.

Preparation of BAC libraries from marine microbial populations.

PubMed

Sabehi, Gazalah; Béjà, Oded

2013-01-01

A protocol is presented here for the construction of BAC (bacterial artificial chromosome) libraries from planktonic microbial communities collected in marine environments. The protocol describes the collection and preparation of the planktonic microbial cells, high molecular weight DNA purification from those cells, the preparation of the BAC vector, and the special ligation and electrotransformation procedures required for successful library preparation. With small modifications, this protocol can be applied to microbes collected from other environments. © 2013 Elsevier Inc. All rights reserved.

Fiber optic control system integration

NASA Technical Reports Server (NTRS)

Poppel, G. L.; Glasheen, W. M.; Russell, J. C.

1987-01-01

A total fiber optic, integrated propulsion/flight control system concept for advanced fighter aircraft is presented. Fiber optic technology pertaining to this system is identified and evaluated for application readiness. A fiber optic sensor vendor survey was completed, and the results are reported. The advantages of centralized/direct architecture are reviewed, and the concept of the protocol branch is explained. Preliminary protocol branch selections are made based on the F-18/F404 application. Concepts for new optical tools are described. Development plans for the optical technology and the described system are included.

Quantum teleportation and entanglement swapping of electron spins in superconducting hybrid structures

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

Bubanja, Vladimir, E-mail: vladimir.bubanja@callaghaninnovation.govt.nz

2015-06-15

We present schemes for quantum teleportation and entanglement swapping of electronic spin states in hybrid superconductor–normal-metal systems. The proposed schemes employ subgap transport whereby the lowest order processes involve Cooper pair-electron and double Cooper-pair cotunneling in quantum teleportation and entanglement swapping protocols, respectively. The competition between elastic cotunneling and Cooper-pair splitting results in the success probability of 25% in both cases. Described implementations of these protocols are within reach of present-day experimental techniques.

Use of Flowchart for Automation of Clinical Protocols in mHealth.

PubMed

Dias, Karine Nóra; Welfer, Daniel; Cordeiro d'Ornellas, Marcos; Pereira Haygert, Carlos Jesus; Dotto, Gustavo Nogara

2017-01-01

For healthcare professionals to use mobile applications we need someone who knows software development, provide them. In healthcare institutions, health professionals use clinical protocols to govern care, and sometimes these documents are computerized through mobile applications to assist them. This work aims to present a proposal of an application of flow as a way of describing clinical protocols for automatic generation of mobile applications to assist health professionals. The purpose of this research is to enable health professionals to develop applications from the description of their own clinical protocols. As a result, we developed a web system that automates clinical protocols for an Android platform, and we validated with two clinical protocols used in a Brazilian hospital. Preliminary results of the developed architecture demonstrate the feasibility of this study.

Fast, efficient error reconciliation for quantum cryptography

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

Buttler, W.T.; Lamoreaux, S.K.; Torgerson, J.R.

2003-05-01

We describe an error-reconciliation protocol, which we call Winnow, based on the exchange of parity and Hamming's 'syndrome' for N-bit subunits of a large dataset. The Winnow protocol was developed in the context of quantum-key distribution and offers significant advantages and net higher efficiency compared to other widely used protocols within the quantum cryptography community. A detailed mathematical analysis of the Winnow protocol is presented in the context of practical implementations of quantum-key distribution; in particular, the information overhead required for secure implementation is one of the most important criteria in the evaluation of a particular error-reconciliation protocol. The increasemore » in efficiency for the Winnow protocol is largely due to the reduction in authenticated public communication required for its implementation.« less

Genome editing of bread wheat using biolistic delivery of CRISPR/Cas9 in vitro transcripts or ribonucleoproteins.

PubMed

Liang, Zhen; Chen, Kunling; Zhang, Yi; Liu, Jinxing; Yin, Kangquan; Qiu, Jin-Long; Gao, Caixia

2018-03-01

This protocol is an extension to: Nat. Protoc. 9, 2395-2410 (2014); doi:10.1038/nprot.2014.157; published online 18 September 2014In recent years, CRISPR/Cas9 has emerged as a powerful tool for improving crop traits. Conventional plant genome editing mainly relies on plasmid-carrying cassettes delivered by Agrobacterium or particle bombardment. Here, we describe DNA-free editing of bread wheat by delivering in vitro transcripts (IVTs) or ribonucleoprotein complexes (RNPs) of CRISPR/Cas9 by particle bombardment. This protocol serves as an extension of our previously published protocol on genome editing in bread wheat using CRISPR/Cas9 plasmids delivered by particle bombardment. The methods we describe not only eliminate random integration of CRISPR/Cas9 into genomic DNA, but also reduce off-target effects. In this protocol extension article, we present detailed protocols for preparation of IVTs and RNPs; validation by PCR/restriction enzyme (RE) and next-generation sequencing; delivery by biolistics; and recovery of mutants and identification of mutants by pooling methods and Sanger sequencing. To use these protocols, researchers should have basic skills and experience in molecular biology and biolistic transformation. By using these protocols, plants edited without the use of any foreign DNA can be generated and identified within 9-11 weeks.

Intelligent routing protocol for ad hoc wireless network

NASA Astrophysics Data System (ADS)

Peng, Chaorong; Chen, Chang Wen

2006-05-01

A novel routing scheme for mobile ad hoc networks (MANETs), which combines hybrid and multi-inter-routing path properties with a distributed topology discovery route mechanism using control agents is proposed in this paper. In recent years, a variety of hybrid routing protocols for Mobile Ad hoc wireless networks (MANETs) have been developed. Which is proactively maintains routing information for a local neighborhood, while reactively acquiring routes to destinations beyond the global. The hybrid protocol reduces routing discovery latency and the end-to-end delay by providing high connectivity without requiring much of the scarce network capacity. On the other side the hybrid routing protocols in MANETs likes Zone Routing Protocol still need route "re-discover" time when a route between zones link break. Sine the topology update information needs to be broadcast routing request on local zone. Due to this delay, the routing protocol may not be applicable for real-time data and multimedia communication. We utilize the advantages of a clustering organization and multi-routing path in routing protocol to achieve several goals at the same time. Firstly, IRP efficiently saves network bandwidth and reduces route reconstruction time when a routing path fails. The IRP protocol does not require global periodic routing advertisements, local control agents will automatically monitor and repair broke links. Secondly, it efficiently reduces congestion and traffic "bottlenecks" for ClusterHeads in clustering network. Thirdly, it reduces significant overheads associated with maintaining clusters. Fourthly, it improves clusters stability due to dynamic topology changing frequently. In this paper, we present the Intelligent Routing Protocol. First, we discuss the problem of routing in ad hoc networks and the motivation of IRP. We describe the hierarchical architecture of IRP. We describe the routing process and illustrate it with an example. Further, we describe the control manage mechanisms, which are used to control active route and reduce the traffic amount in the route discovery procedure. Finial, the numerical experiments are given to show the effectiveness of IRP routing protocol.

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.

Protocol for Short- and Longer-term Spatial Learning and Memory in Mice

PubMed Central

Willis, Emily F.; Bartlett, Perry F.; Vukovic, Jana

2017-01-01

Studies on the role of the hippocampus in higher cognitive functions such as spatial learning and memory in rodents are reliant upon robust and objective behavioral tests. This protocol describes one such test—the active place avoidance (APA) task. This behavioral task involves the mouse continuously integrating visual cues to orientate itself within a rotating arena in order to actively avoid a shock zone, the location of which remains constant relative to the room. This protocol details the step-by-step procedures for a novel paradigm of the hippocampal-dependent APA task, measuring acquisition of spatial learning during a single 20-min trial (i.e., short-term memory), with spatial memory encoding and retrieval (i.e., long-term memory) assessed by trials conducted over consecutive days. Using the APA task, cognitive flexibility can be assessed using the reversal learning paradigm, as this increases the cognitive load required for efficient performance in the task. In addition to a detailed experimental protocol, this paper also describes the range of its possible applications, the expected key results, as well as the analytical methods to assess the data, and the pitfalls/troubleshooting measures. The protocol described herein is highly robust and produces replicable results, thus presenting an important paradigm that enables the assessment of subtle short-term changes in spatial learning and memory, such as those observed for many experimental interventions. PMID:29089878

A universal TaqMan-based RT-PCR protocol for cost-efficient detection of small noncoding RNA.

PubMed

Jung, Ulrike; Jiang, Xiaoou; Kaufmann, Stefan H E; Patzel, Volker

2013-12-01

Several methods for the detection of RNA have been developed over time. For small RNA detection, a stem-loop reverse primer-based protocol relying on TaqMan RT-PCR has been described. This protocol requires an individual specific TaqMan probe for each target RNA and, hence, is highly cost-intensive for experiments with small sample sizes or large numbers of different samples. We describe a universal TaqMan-based probe protocol which can be used to detect any target sequence and demonstrate its applicability for the detection of endogenous as well as artificial eukaryotic and bacterial small RNAs. While the specific and the universal probe-based protocol showed the same sensitivity, the absolute sensitivity of detection was found to be more than 100-fold lower for both than previously reported. In subsequent experiments, we found previously unknown limitations intrinsic to the method affecting its feasibility in determination of mature template RISC incorporation as well as in multiplexing. Both protocols were equally specific in discriminating between correct and incorrect small RNA targets or between mature miRNA and its unprocessed RNA precursor, indicating the stem-loop RT-primer, but not the TaqMan probe, triggers target specificity. The presented universal TaqMan-based RT-PCR protocol represents a cost-efficient method for the detection of small RNAs.

Differences in handgrip strength protocols to identify sarcopenia and frailty - a systematic review.

PubMed

Sousa-Santos, A R; Amaral, T F

2017-10-16

Hand grip strength (HGS) is used for the diagnosis of sarcopenia and frailty. Several factors have been shown to influence HGS values during measurement. Therefore, variations in the protocols used to assess HGS, as part of the diagnosis of sarcopenia and frailty, may lead to the identification of different individuals with low HGS, introducing bias. The aim of this systematic review is to gather all the relevant studies that measured HGS to diagnose sarcopenia and frailty and to identify the differences between the protocols used. A systematic review was carried out following the recommendations of The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement. PubMed and Web of Science were systematically searched, until August 16, 2016. The evidence regarding HGS measurement protocols used to diagnose sarcopenia and frailty was summarised and the most recent protocols regarding the procedure were compared. From the described search 4393 articles were identified. Seventy-two studies were included in this systematic review, in which 37 referred to sarcopenia articles, 33 to frailty and two evaluated both conditions. Most studies presented limited information regarding the protocols used. The majority of the studies included did not describe a complete procedure of HGS measurement. The high heterogeneity between the protocols used, in sarcopenia and frailty studies, create an enormous difficulty in drawing comparative conclusions among them.

Protocol and standard operating procedures for common use in a worldwide multicenter study on reference values.

PubMed

Ozarda, Yesim; Ichihara, Kiyoshi; Barth, Julian H; Klee, George

2013-05-01

The reference intervals (RIs) given in laboratory reports have an important role in aiding clinicians in interpreting test results in reference to values of healthy populations. In this report, we present a proposed protocol and standard operating procedures (SOPs) for common use in conducting multicenter RI studies on a national or international scale. The protocols and consensus on their contents were refined through discussions in recent C-RIDL meetings. The protocol describes in detail (1) the scheme and organization of the study, (2) the target population, inclusion/exclusion criteria, ethnicity, and sample size, (3) health status questionnaire, (4) target analytes, (5) blood collection, (6) sample processing and storage, (7) assays, (8) cross-check testing, (9) ethics, (10) data analyses, and (11) reporting of results. In addition, the protocol proposes the common measurement of a panel of sera when no standard materials exist for harmonization of test results. It also describes the requirements of the central laboratory, including the method of cross-check testing between the central laboratory of each country and local laboratories. This protocol and the SOPs remain largely exploratory and may require a reevaluation from the practical point of view after their implementation in the ongoing worldwide study. The paper is mainly intended to be a basis for discussion in the scientific community.

Bilateral Ossified Chronic Subdural Hematoma Presenting as Diabetes Insipidus-Case Report and Literature Review.

PubMed

Siddiqui, Saquib A; Singh, Pankaj Kumar; Sawarkar, Dattaraj; Singh, Manmohanjit; Sharma, Bhawani S

2017-02-01

Calcified chronic subdural hematomas are an occurrence rarely seen in neurosurgical clinical practice. And when they occur bilaterally, the radiologic image they present is fascinating, as is the clinical presentation, but their management may be challenging. They have been reported to present with a multitude of neurologic deficits but never with diabetes insipidus, which is described here. Due to the rarity of this pathology, the management protocol is not well defined, though there have been quite a few papers on this condition. This review article gathers information published over the years on this rare entity to suggest a treatment protocol. Copyright © 2016 Elsevier Inc. All rights reserved.

A model protocol for a diabetes and other noncommunicable disease field survey.

PubMed

Dowse, G K; Zimmet, P

1992-01-01

Field surveys of diabetes and other noncommunicable diseases and their risk factors are increasingly being performed in both developed and developing countries. Although individual priorities and circumstances will influence survey design, a model survey manual and protocol is described which might assist investigators in formulating plans and preparing manuals for their own surveys. The model presented has been successfully used in developing countries, for both rural and urban communities, over more than a decade. It describes examples of survey objectives, and gives specific details of survey procedures and measurement techniques which may be utilized. It contains sufficient flexibility to allow its adaptation to local circumstances.

CT protocol management: simplifying the process by using a master protocol concept.

PubMed

Szczykutowicz, Timothy P; Bour, Robert K; Rubert, Nicholas; Wendt, Gary; Pozniak, Myron; Ranallo, Frank N

2015-07-08

This article explains a method for creating CT protocols for a wide range of patient body sizes and clinical indications, using detailed tube current information from a small set of commonly used protocols. Analytical expressions were created relating CT technical acquisition parameters which can be used to create new CT protocols on a given scanner or customize protocols from one scanner to another. Plots of mA as a function of patient size for specific anatomical regions were generated and used to identify the tube output needs for patients as a function of size for a single master protocol. Tube output data were obtained from the DICOM header of clinical images from our PACS and patient size was measured from CT localizer radiographs under IRB approval. This master protocol was then used to create 11 additional master protocols. The 12 master protocols were further combined to create 39 single and multiphase clinical protocols. Radiologist acceptance rate of exams scanned using the clinical protocols was monitored for 12,857 patients to analyze the effectiveness of the presented protocol management methods using a two-tailed Fisher's exact test. A single routine adult abdominal protocol was used as the master protocol to create 11 additional master abdominal protocols of varying dose and beam energy. Situations in which the maximum tube current would have been exceeded are presented, and the trade-offs between increasing the effective tube output via 1) decreasing pitch, 2) increasing the scan time, or 3) increasing the kV are discussed. Out of 12 master protocols customized across three different scanners, only one had a statistically significant acceptance rate that differed from the scanner it was customized from. The difference, however, was only 1% and was judged to be negligible. All other master protocols differed in acceptance rate insignificantly between scanners. The methodology described in this paper allows a small set of master protocols to be adapted among different clinical indications on a single scanner and among different CT scanners.

Arthroscopic management of the painful total elbow arthroplasty.

PubMed

Phadnis, Joideep; Bain, Gregory I

2016-01-01

Failure of total elbow arthroplasty is more common than after other major joint arthroplasties and is often a result of aseptic loosening, peri-prosthetic infection, fracture and instability. Infection can be a devastating complication, yet there are no established guidelines for the pre-operative diagnosis of total elbow peri-prosthetic infection. This is because pre-operative clinical, radiographic and biochemical tests are often unreliable. Using three case examples, a standardized protocol for the clinical and arthroscopic assessment of the painful total elbow arthroplasty is described. This is used to provide a mechanical and microbiological diagnosis of the patient's pain. There have been no complications resulting from the use of this technique in the three patients described, nor in any other patient to date. The staged protocol described in the present study, utilizing arthroscopic assessment, has refined the approach to the painful total elbow arthroplasty because it directly influences the definitive surgical management of the patient. It is recommended that other surgeons follow the principles outlined in the present study when faced with this challenging problem.

Conducting a successful residency research project.

PubMed

Barletta, Jeffrey F

2008-08-15

The residency research project can be a challenging endeavor for pharmacy residents since they typically have limited experience in this area. Furthermore, as the number of accredited residency programs has increased, so has the demand for preceptors with research experience. This review is intended to assist the resident and preceptor by providing steps and guidance with conducting a successful residency research project. Items such as idea generation, proposing the right type of project, departmental review, and project management skills are discussed and guidance with writing the research protocol is provided. Items that must be addressed in every research protocol are described and a generalized protocol template is presented. In addition, the institutional review board review process is described and tips and pointers for obtaining approval are included. Finally, useful tools and resources are provided that can be used up front or throughout each phase of the research project.

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).

Decoherence estimation in quantum theory and beyond

NASA Astrophysics Data System (ADS)

Pfister, Corsin

The quantum physics literature provides many different characterizations of decoherence. Most of them have in common that they describe decoherence as a kind of influence on a quantum system upon interacting with an another system. In the spirit of quantum information theory, we adapt a particular viewpoint on decoherence which describes it as the loss of information into a system that is possibly controlled by an adversary. We use a quantitative framework for decoherence that builds on operational characterizations of the min-entropy that have been developed in the quantum information literature. It characterizes decoherence as an influence on quantum channels that reduces their suitability for a variety of quantifiable tasks such as the distribution of secret cryptographic keys of a certain length or the distribution of a certain number of maximally entangled qubit pairs. This allows for a quantitative and operational characterization of decoherence via operational characterizations of the min-entropy. In this thesis, we present a series of results about the estimation of the minentropy, subdivided into three parts. The first part concerns the estimation of a quantum adversary's uncertainty about classical information--expressed by the smooth min-entropy--as it is done in protocols for quantum key distribution (QKD). We analyze this form of min-entropy estimation in detail and find that some of the more recently suggested QKD protocols have previously unnoticed security loopholes. We show that the specifics of the sifting subroutine of a QKD protocol are crucial for security by pointing out mistakes in the security analysis in the literature and by presenting eavesdropping attacks on those problematic protocols. We provide solutions to the identified problems and present a formalized analysis of the min-entropy estimate that incorporates the sifting stage of QKD protocols. In the second part, we extend ideas from QKD to a protocol that allows to estimate an adversary's uncertainty about quantum information, expressed by the fully quantum smooth min-entropy. Roughly speaking, we show that a protocol that resembles the parallel execution of two QKD protocols can be used to lower bound the min-entropy of some unmeasured qubits. We explain how this result may influence the ongoing search for protocols for entanglement distribution. The third part is dedicated to the development of a framework that allows the estimation of decoherence even in experiments that cannot be correctly described by quantum theory. Inspired by an equivalent formulation of the min-entropy that relates it to the fidelity with a maximally entangled state, we define a decoherence quantity for a very general class of probabilistic theories that reduces to the min-entropy in the special case of quantum theory. This entails a definition of maximal entanglement for generalized probabilistic theories. Using techniques from semidefinite and linear programming, we show how bounds on this quantity can be estimated through Bell-type experiments. This allows to test models for decoherence that cannot be described by quantum theory. As an example application, we devise an experimental test of a model for gravitational decoherence that has been suggested in the literature.

Measurement of Basal and Forskolin-stimulated Lipolysis in Inguinal Adipose Fat Pads.

PubMed

Baskaran, Padmamalini; Thyagarajan, Baskaran

2017-07-21

Lipolysis is a process by which the lipid stored as triglycerides in adipose tissues are hydrolyzed into glycerol and fatty acids. This article describes the method for the measurement of basal and forskolin (FSK)-stimulated lipolysis in the inguinal fat pads isolated from wild type mice fed either normal chow diet (NCD), high fat diet (HFD) or a high fat diet containing 0.01% of capsaicin (CAP; transient receptor potential vanilloid subfamily 1 (TRPV1) agonist) for 32 weeks. The method described here for performing ex vivo lipolysis is adopted from Schweiger et al. 1 We present a detailed protocol for measuring glycerol levels by UV-Visible (UV/VIS) spectrophotometry. The method described here can be used to successfully isolate inguinal fat pads for lipolysis measurements to obtain consistent results. The protocol described for inguinal fat pads can readily be extended to measure lipolysis in other tissues.

Referral Patterns for Chronic Groin Pain and Athletic Pubalgia/Sports Hernia: Magnetic Resonance Imaging Findings, Treatment, and Outcomes.

PubMed

Zoland, Mark P; Maeder, Matthew E; Iraci, Joseph C; Klein, Devon A

Chronic groin pain is a common problem and has been well-described in high-performance athletes. Its presentation in the recreational athlete has been less frequently described. We present the experience of a tertiary group of physicians specializing in groin pain and athletic pubalgia. Dynamic magnetic resonance imaging (MRI) protocol was employed. Surgery was performed in patients failing non-surgical management. A retrospective review was performed. Of 117 mostly non-professional athletes, there were 79 MRI-positive cases of athletic pubalgia (68%). Other common findings were acetabular labral tear (57%) and inguinal hernia (35%). Employment of a dynamic MRI protocol increased sensitivity for certain pathologies. Of positive athletic pubalgia cases, 49% went on to have surgical repair. The satisfaction rate in the surgical group was 90% at follow up. Advances in MRI have increased our ability to characterize and diagnose specific injuries causing groin pain. We present our diagnostic algorithm, including an MRI protocol that not only evaluates the groin, but has increased sensitivity for additional findings such as inguinal hernia and abdominal wall deficiencies. A targeted work-up and subsequent surgical treatment in the appropriate patient, even in the recreational athletic population, has yielded a 90% satisfaction rate.

[The intervention mapping protocol: A structured process to develop, implement and evaluate health promotion programs].

PubMed

Fassier, J-B; Lamort-Bouché, M; Sarnin, P; Durif-Bruckert, C; Péron, J; Letrilliart, L; Durand, M-J

2016-02-01

Health promotion programs are expected to improve population health and reduce social inequalities in health. However, their theoretical foundations are frequently ill-defined, and their implementation faces many obstacles. The aim of this article is to describe the intervention mapping protocol in health promotion programs planning, used recently in several countries. The challenges of planning health promotion programs are presented, and the six steps of the intervention mapping protocol are described with an example. Based on a literature review, the use of this protocol, its requirements and potential limitations are discussed. The intervention mapping protocol has four essential characteristics: an ecological perspective (person-environment), a participative approach, the use of theoretical models in human and social sciences and the use of scientific evidence. It comprises six steps: conduct a health needs assessment, define change objectives, select theory-based change techniques and practical applications, organize techniques and applications into an intervention program (logic model), plan for program adoption, implementation, and sustainability, and generate an evaluation plan. This protocol was used in different countries and domains such as obesity, tobacco, physical activity, cancer and occupational health. Although its utilization requires resources and a critical stance, this protocol was used to develop interventions which efficacy was demonstrated. The intervention mapping protocol is an integrated process that fits the scientific and practical challenges of health promotion. It could be tested in France as it was used in other countries, in particular to reduce social inequalities in health. Copyright © 2016. Published by Elsevier Masson SAS.

The Development of the Unified Protocol for the Transdiagnostic Treatment of Emotional Disorders: A Case Study

PubMed Central

Boisseau, Christina L.; Farchione, Todd J.; Fairholme, Christopher P.; Ellard, Kristen K.; Barlow, David H.

2013-01-01

A detailed description of treatment utilizing the Unified Protocol (UP), a transdiagnostic emotion-focused cognitive-behavioral treatment, is presented using a clinical case example treated during the most current phase of an ongoing randomized controlled trial of the UP. The implementation of the UP in its current, modular version is illustrated. A working case conceptualization is presented from the perspective of the UP drawing from theory and research that underlies current transdiagnostic approaches to treatment and consistent with recent dimensional classification proposals (Brown & Barlow, in press). Treatment is illustrated module-by-module describing how the principles of the UP were applied in the presented case. PMID:23997572

An architecture and protocol for communications satellite constellations regarded as multi-agent systems

NASA Technical Reports Server (NTRS)

Lindley, Craig A.

1995-01-01

This paper presents an architecture for satellites regarded as intercommunicating agents. The architecture is based upon a postmodern paradigm of artificial intelligence in which represented knowledge is regarded as text, inference procedures are regarded as social discourse and decision making conventions and the semantics of representations are grounded in the situated behaviour and activity of agents. A particular protocol is described for agent participation in distributed search and retrieval operations conducted as joint activities.

Local network assessment

NASA Astrophysics Data System (ADS)

Glen, D. V.

1985-04-01

Local networks, related standards activities of the Institute of Electrical and Electronics Engineers the American National Standards Institute and other elements are presented. These elements include: (1) technology choices such as topology, transmission media, and access protocols; (2) descriptions of standards for the 802 local area networks (LAN's); high speed local networks (HSLN's) and military specification local networks; and (3) intra- and internetworking using bridges and gateways with protocols Interconnection (OSI) reference model. The convergence of LAN/PBX technology is also described.

Internet Data Delivery for Future Space Missions

NASA Technical Reports Server (NTRS)

Rash, James; Hogie, Keith; Casasanta, Ralph; Hennessy, Joseph F. (Technical Monitor)

2002-01-01

This paper presents work being done at NASA/GSFC (Goddard Space Flight Center) on applying standard Internet applications and protocols to meet the technology challenge of future satellite missions. Internet protocols (IP) can provide seamless dynamic communication among heterogeneous instruments, spacecraft, ground stations, and constellations of spacecraft. A primary component of this work is to design and demonstrate automated end-to-end transport of files in a dynamic space environment using off-the-shelf, low-cost, commodity-level standard applications and protocols. These functions and capabilities will become increasingly significant in the years to come as both Earth and space science missions fly more sensors and the present labor-intensive, mission-specific techniques for processing and routing data become prohibitively expensive. This paper describes how an IP-based communication architecture can support existing operations concepts and how it will enable some new and complex communication and science concepts. The authors identify specific end-to-end file transfers all the way from instruments to control centers and scientists, and then describe how each data flow can be supported using standard Internet protocols and applications. The scenarios include normal data downlink and command uplink as well as recovery scenarios for both onboard and ground failures. The scenarios are based on an Earth orbiting spacecraft with data rates and downlink capabilities from 300 Kbps to 4 Mbps. Many examples are based on designs currently being investigated for the Global Precipitation Measurement (GPM) mission.

Protocols for the delivery of small molecules to the two-spotted spider mite, Tetranychus urticae

PubMed Central

Nunes, Maria Andreia; Zhurov, Vladimir; Dermauw, Wannes; Osakabe, Masahiro; Van Leeuwen, Thomas; Grbic, Miodrag

2017-01-01

The two-spotted spider mite, Tetranychus urticae, is a chelicerate herbivore with an extremely wide host range and an extraordinary ability to develop pesticide resistance. Due to its responsiveness to natural and synthetic xenobiotics, the spider mite is becoming a prime pest herbivore model for studies of the evolution of host range, plant-herbivore interactions and mechanisms of xenobiotic resistance. The spider mite genome has been sequenced and its transcriptional responses to developmental and various biotic and abiotic cues have been documented. However, to identify biological and evolutionary roles of T. urticae genes and proteins, it is necessary to develop methods for the efficient manipulation of mite gene function or protein activity. Here, we describe protocols developed for the delivery of small molecules into spider mites. Starting with mite maintenance and the preparation of the experimental mite populations of developmentally synchronized larvae and adults, we describe 3 methods for delivery of small molecules including artificial diet, leaf coating, and soaking. The presented results define critical steps in these methods and demonstrate that they can successfully deliver tracer dyes into mites. Described protocols provide guidelines for high-throughput setups for delivery of experimental compounds that could be used in reverse genetics platforms to modulate gene expression or protein activity, or for screens focused on discovery of new molecules for mite control. In addition, described protocols could be adapted for other Tetranychidae and related species of economic importance such as Varroa, dust and poultry mites. PMID:28686745

Modelling and regulating of cardio-respiratory response for the enhancement of interval training

PubMed Central

2014-01-01

Background The interval training method has been a well known exercise protocol which helps strengthen and improve one’s cardiovascular fitness. Purpose To develop an effective training protocol to improve cardiovascular fitness based on modelling and analysis of Heart Rate (HR) and Oxygen Uptake (VO2) dynamics. Methods In order to model the cardiorespiratory response to the onset and offset exercises, the (K4b2, Cosmed) gas analyzer was used to monitor and record the heart rate and oxygen uptake for ten healthy male subjects. An interval training protocol was developed for young health users and was simulated using a proposed RC switching model which was presented to accommodate the variations of the cardiorespiratory dynamics to running exercises. A hybrid system model was presented to describe the adaptation process and a multi-loop PI control scheme was designed for the tuning of interval training regime. Results By observing the original data for each subject, we can clearly identify that all subjects have similar HR and VO2 profiles. The proposed model is capable to simulate the exercise responses during onset and offset exercises; it ensures the continuity of the outputs within the interval training protocol. Under some mild assumptions, a hybrid system model can describe the adaption process and accordingly a multi-loop PI controller can be designed for the tuning of interval training protocol. The self-adaption feature of the proposed controller gives the exerciser the opportunity to reach his desired setpoints after a certain number of training sessions. Conclusions The established interval training protocol targets a range of 70-80% of HRmax which is mainly a training zone for the purpose of cardiovascular system development and improvement. Furthermore, the proposed multi-loop feedback controller has the potential to tune the interval training protocol according to the feedback from an individual exerciser. PMID:24499131

Understanding Skill in EVA Mass Handling. Volume 2; Empirical Investigation

NASA Technical Reports Server (NTRS)

Riccio, Gary; McDonald, Vernon; Peters, Brian; Layne, Charles; Bloomberg, Jacob

1997-01-01

In this report we describe the details of our empirical protocol effort investigating skill in extravehicular mass handling using NASA's principal mass handling simulator, the precision air bearing floor. Contents of this report include a description of the necessary modifications to the mass handling simulator; choice of task, and the description of an operationally relevant protocol. Our independent variables are presented in the context of the specific operational issues they were designed to simulate. The explanation of our dependent variables focuses on the specific data processing procedures used to transform data from common laboratory instruments into measures that are relevant to a special class of nested control systems (discussed in Volume 1): manual interactions between an individual and the substantial environment. The data reduction is explained in the context of the theoretical foundation described in Volume 1. Finally as a preface to the presentation of the empirical data in Volume 3 of this report series, a set of detailed hypotheses is presented.

How to write a surgical clinical research protocol: literature review and practical guide.

PubMed

Rosenthal, Rachel; Schäfer, Juliane; Briel, Matthias; Bucher, Heiner C; Oertli, Daniel; Dell-Kuster, Salome

2014-02-01

The study protocol is the core document of every clinical research project. Clinical research in studies involving surgical interventions presents some specific challenges, which need to be accounted for and described in the study protocol. The aim of this review is to provide a practical guide for developing a clinical study protocol for surgical interventions with a focus on methodologic issues. On the basis of an in-depth literature search of methodologic literature and on some cardinal published surgical trials and observational studies, the authors provides a 10-step guide for developing a clinical study protocol in surgery. This practical guide outlines key methodologic issues important when planning an ethically and scientifically sound research project involving surgical interventions, with the ultimate goal of providing high-level evidence relevant for health care decision making in surgery. Copyright © 2014 Elsevier Inc. All rights reserved.

Draft guidelines for measurement and assessment of low-level ambient noise

DOT National Transportation Integrated Search

1998-03-31

This document describes an ambient noise measurement protocol, a detailed methodology for characterizing ambient noise in low-level environments such as the National Parks. It presents definitions of terminology useful for understanding the mea...

The 10 Hottest Technologies in Telecom.

ERIC Educational Resources Information Center

Flanagan, Patrick

1997-01-01

Presents the fourth annual listing of the 10 "hottest" telecommunications technologies. Describes Web broadcasting, remote-access servers, extranets, Internet telephony, enterprise network directory services, Web site management tools, IP (Internet Protocols) switching, wavelength division multiplexing, digital subscriber lines, and…

Enhanced just-in-time plus protocol for optical burst switching networks

NASA Astrophysics Data System (ADS)

Rodrigues, Joel J. P. C.; Gregório, José M. B.; Vasilakos, Athanasios V.

2010-07-01

We propose a new one-way resource reservation protocol for optical burst switching (OBS) networks, called Enhanced Just-in-Time Plus (E-JIT+). The protocol is described in detail, and its formal specification is presented, following an extended finite state machine approach. The performance evaluation of E-JIT+ is analyzed in comparison with other proposed OBS protocols (JIT+ and E-JIT) for the following network topologies: rings; degree-two, degree-three, and degree-four chordal rings; mesh-torus; NSFNET; ARPANET; FCCN-NET; and the European Optical Network. We evaluate and compare the performance of the different protocols in terms of burst loss probability, taking into account the most important OBS network parameters. It was shown that E-JIT+ performs better than available one-way resource reservation protocols for all the evaluated network topologies. Moreover, the scalability of E-JIT+ was observed, and when the network traffic increases, the burst loss probability also increases, leading to a worse network performance.

Protein-Coated Microcrystals, Combi-Protein-Coated Microcrystals, and Cross-Linked Protein-Coated Microcrystals of Enzymes for Use in Low-Water Media.

PubMed

Mukherjee, Joyeeta; Gupta, Munishwar N

2017-01-01

Protein-coated microcrystals (PCMC) are a high-activity preparation of enzymes for use in low-water media. The protocols for the preparation of PCMCs of Subtilisin Carlsberg and Candida antarctica lipase B (CAL B) are described. The combi-PCMC concept is useful both for cascade and non-cascade reactions. It can also be beneficial to combine two different specificities of a lipase when the substrate requires it. Combi-PCMC of CALB and Palatase used for the conversion of coffee oil present in spent coffee grounds to biodiesel is described. Cross-linked protein-coated microcrystals (CL-PCMC) in some cases can give better results than PCMC. Protocols for the CLPCMC of Subtilisin Carlsberg and Candida antarctica lipase B (CAL B) are described. A discussion of their applications is also provided.

Replacement of missing teeth with fiber-reinforced composite FPDs: clinical protocol.

PubMed

Bouillaguet, Serge; Schütt, Andrea; Marin, Isabelle; Etechami, Leila; Di Salvo, Giancarlo; Krejci, Ivo

2003-04-01

The concept of minimally invasive preparation protocols has resulted in reduced loss of critical tooth structures and maintenance of optimal strength, form, and aesthetics. While various treatment options have been described for single-tooth replacement, fiber-reinforced composite (FRC) fixed partial dentures (FPDs) provide a viable treatment alternative with proven mechanical properties, aesthetics, and function. This article presents several clinical scenarios in which minimally invasive adhesive FRC FPDs are provided to deliver enhanced predictability, strength, and durability.

Diastereoselective chain-elongation reactions using microreactors for applications in complex molecule assembly.

PubMed

Carter, Catherine F; Lange, Heiko; Sakai, Daiki; Baxendale, Ian R; Ley, Steven V

2011-03-14

Diastereoselective chain-elongation reactions are important transformations for the assembly of complex molecular structures, such as those present in polyketide natural products. Here we report new methods for performing crotylation reactions and homopropargylation reactions by using newly developed low-temperature flow-chemistry technology. In-line purification protocols are described, as well as the application of the crotylation protocol in an automated multi-step sequence. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Anther Culture in Pepper (Capsicum annuum L.).

PubMed

Parra-Vega, Verónica; Seguí-Simarro, Jose M

2016-01-01

Anther culture is the most popular of the techniques used to induce microspore embryogenesis. This technique is well set up in a wide range of crops, including pepper. In this chapter, a protocol for anther culture in pepper is described. The protocol presented hereby includes the steps from the selection of buds from donor plants to the regeneration and acclimatization of doubled haploid plants derived from the embryos, as well as a description of how to analyze the ploidy level of the regenerated plants.

CT protocol management: simplifying the process by using a master protocol concept

PubMed Central

Bour, Robert K.; Rubert, Nicholas; Wendt, Gary; Pozniak, Myron; Ranallo, Frank N.

2015-01-01

This article explains a method for creating CT protocols for a wide range of patient body sizes and clinical indications, using detailed tube current information from a small set of commonly used protocols. Analytical expressions were created relating CT technical acquisition parameters which can be used to create new CT protocols on a given scanner or customize protocols from one scanner to another. Plots of mA as a function of patient size for specific anatomical regions were generated and used to identify the tube output needs for patients as a function of size for a single master protocol. Tube output data were obtained from the DICOM header of clinical images from our PACS and patient size was measured from CT localizer radiographs under IRB approval. This master protocol was then used to create 11 additional master protocols. The 12 master protocols were further combined to create 39 single and multiphase clinical protocols. Radiologist acceptance rate of exams scanned using the clinical protocols was monitored for 12,857 patients to analyze the effectiveness of the presented protocol management methods using a two‐tailed Fisher's exact test. A single routine adult abdominal protocol was used as the master protocol to create 11 additional master abdominal protocols of varying dose and beam energy. Situations in which the maximum tube current would have been exceeded are presented, and the trade‐offs between increasing the effective tube output via 1) decreasing pitch, 2) increasing the scan time, or 3) increasing the kV are discussed. Out of 12 master protocols customized across three different scanners, only one had a statistically significant acceptance rate that differed from the scanner it was customized from. The difference, however, was only 1% and was judged to be negligible. All other master protocols differed in acceptance rate insignificantly between scanners. The methodology described in this paper allows a small set of master protocols to be adapted among different clinical indications on a single scanner and among different CT scanners. PACS number: 87.57.Q PMID:26219005

Scoring System for the Management of Acute Gallstone Pancreatitis: Cost Analysis of a Prospective Study.

PubMed

Prigoff, Jake G; Swain, Gary W; Divino, Celia M

2016-05-01

Predicting the presence of a persistent common bile duct (CBD) stone is a difficult and expensive task. The aim of this study is to determine if a previously described protocol-based scoring system is a cost-effective strategy. The protocol includes all patients with gallstone pancreatitis and stratifies them based on laboratory values and imaging to high, medium, and low likelihood of persistent stones. The patient's stratification then dictates the next course of management. A decision analytic model was developed to compare the costs for patients who followed the protocol versus those that did not. Clinical data model inputs were obtained from a prospective study conducted at The Mount Sinai Medical Center to validate the protocol from Oct 2009 to May 2013. The study included all patients presenting with gallstone pancreatitis regardless of disease severity. Seventy-three patients followed the proposed protocol and 32 did not. The protocol group cost an average of $14,962/patient and the non-protocol group cost $17,138/patient for procedural costs. Mean length of stay for protocol and non-protocol patients was 5.6 and 7.7 days, respectively. The proposed protocol is a cost-effective way to determine the course for patients with gallstone pancreatitis, reducing total procedural costs over 12 %.

Arthroscopic management of the painful total elbow arthroplasty

PubMed Central

Bain, Gregory I

2015-01-01

Background Failure of total elbow arthroplasty is more common than after other major joint arthroplasties and is often a result of aseptic loosening, peri-prosthetic infection, fracture and instability. Infection can be a devastating complication, yet there are no established guidelines for the pre-operative diagnosis of total elbow peri-prosthetic infection. This is because pre-operative clinical, radiographic and biochemical tests are often unreliable. Methods Using three case examples, a standardized protocol for the clinical and arthroscopic assessment of the painful total elbow arthroplasty is described. This is used to provide a mechanical and microbiological diagnosis of the patient’s pain. Results There have been no complications resulting from the use of this technique in the three patients described, nor in any other patient to date. Conclusions The staged protocol described in the present study, utilizing arthroscopic assessment, has refined the approach to the painful total elbow arthroplasty because it directly influences the definitive surgical management of the patient. It is recommended that other surgeons follow the principles outlined in the present study when faced with this challenging problem. PMID:27583000

Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement.

PubMed

Moher, David; Shamseer, Larissa; Clarke, Mike; Ghersi, Davina; Liberati, Alessandro; Petticrew, Mark; Shekelle, Paul; Stewart, Lesley A

2015-01-01

Systematic reviews should build on a protocol that describes the rationale, hypothesis, and planned methods of the review; few reviews report whether a protocol exists. Detailed, well-described protocols can facilitate the understanding and appraisal of the review methods, as well as the detection of modifications to methods and selective reporting in completed reviews. We describe the development of a reporting guideline, the Preferred Reporting Items for Systematic reviews and Meta-Analyses for Protocols 2015 (PRISMA-P 2015). PRISMA-P consists of a 17-item checklist intended to facilitate the preparation and reporting of a robust protocol for the systematic review. Funders and those commissioning reviews might consider mandating the use of the checklist to facilitate the submission of relevant protocol information in funding applications. Similarly, peer reviewers and editors can use the guidance to gauge the completeness and transparency of a systematic review protocol submitted for publication in a journal or other medium.

A sessional blind signature based on quantum cryptography

NASA Astrophysics Data System (ADS)

Khodambashi, Siavash; Zakerolhosseini, Ali

2014-01-01

In this paper, we present a sessional blind signature protocol whose security is guaranteed by fundamental principles of quantum physics. It allows a message owner to get his message signed by an authorized signatory. However, the signatory is not capable of reading the message contents and everyone can verify authenticity of the message. For this purpose, we took advantage of a sessional signature as well as quantum entangled pairs which are generated with respect to it in our proposed protocol. We describe our proposed blind signature through an example and briefly discuss about its unconditional security. Due to the feasibility of the protocol, it can be widely employed for e-payment, e-government, e-business and etc.

Salvage immunotherapy of malignant glioma.

PubMed

Ingram, M; Jacques, S; Freshwater, D B; Techy, G B; Shelden, C H; Helsper, J T

1987-12-01

We present the preliminary results of a phase I trial of adoptive immunotherapy for recurrent or residual malignant glioma. The protocol is based on surgical debulking followed by implantation into the tumor bed of autologous lymphocytes that have been stimulated with phytohemagglutinin-P and then cultured in vitro in the presence of interleukin 2. Fifty-five patients with a mean Karnofsky rating of 64 were treated between February 1985 and March 1987. No significant toxicity was associated with the immunotherapy. Fifty patients had a positive initial response to therapy, nine patients had early recurrence (two to four months after treatment), and 22 patients died. We comment on major differences between the protocol described and other immunotherapy protocols.

An Instructional Consultation Service for Graduate Teaching Assistants.

ERIC Educational Resources Information Center

Habel, J. C.; Graveel, J. G.

1988-01-01

Described is a support program that guides prospective college teachers in teaching an introductory soil science laboratory course. Ideas are presented about the preparation for teaching and concerns of teaching assistants. A table citing classroom observation protocol is included. (RT)

A distributed computing model for telemetry data processing

NASA Astrophysics Data System (ADS)

Barry, Matthew R.; Scott, Kevin L.; Weismuller, Steven P.

1994-05-01

We present a new approach to distributing processed telemetry data among spacecraft flight controllers within the control centers at NASA's Johnson Space Center. This approach facilitates the development of application programs which integrate spacecraft-telemetered data and ground-based synthesized data, then distributes this information to flight controllers for analysis and decision-making. The new approach combines various distributed computing models into one hybrid distributed computing model. The model employs both client-server and peer-to-peer distributed computing models cooperating to provide users with information throughout a diverse operations environment. Specifically, it provides an attractive foundation upon which we are building critical real-time monitoring and control applications, while simultaneously lending itself to peripheral applications in playback operations, mission preparations, flight controller training, and program development and verification. We have realized the hybrid distributed computing model through an information sharing protocol. We shall describe the motivations that inspired us to create this protocol, along with a brief conceptual description of the distributed computing models it employs. We describe the protocol design in more detail, discussing many of the program design considerations and techniques we have adopted. Finally, we describe how this model is especially suitable for supporting the implementation of distributed expert system applications.

A distributed computing model for telemetry data processing

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Scott, Kevin L.; Weismuller, Steven P.

1994-01-01

We present a new approach to distributing processed telemetry data among spacecraft flight controllers within the control centers at NASA's Johnson Space Center. This approach facilitates the development of application programs which integrate spacecraft-telemetered data and ground-based synthesized data, then distributes this information to flight controllers for analysis and decision-making. The new approach combines various distributed computing models into one hybrid distributed computing model. The model employs both client-server and peer-to-peer distributed computing models cooperating to provide users with information throughout a diverse operations environment. Specifically, it provides an attractive foundation upon which we are building critical real-time monitoring and control applications, while simultaneously lending itself to peripheral applications in playback operations, mission preparations, flight controller training, and program development and verification. We have realized the hybrid distributed computing model through an information sharing protocol. We shall describe the motivations that inspired us to create this protocol, along with a brief conceptual description of the distributed computing models it employs. We describe the protocol design in more detail, discussing many of the program design considerations and techniques we have adopted. Finally, we describe how this model is especially suitable for supporting the implementation of distributed expert system applications.

A platform for population-based weight management: description of a health plan-based integrated systems approach.

PubMed

Pronk, Nicolaas P; Boucher, Jackie L; Gehling, Eve; Boyle, Raymond G; Jeffery, Robert W

2002-10-01

To describe an integrated, operational platform from which mail- and telephone-based health promotion programs are implemented and to specifically relate this approach to weight management programming in a managed care setting. In-depth description of essential systems structures, including people, computer technology, and decision-support protocols. The roles of support staff, counselors, a librarian, and a manager in delivering a weight management program are described. Information availability using computer technology is a critical component in making this system effective and is presented according to its architectural layout and design. Protocols support counselors and administrative support staff in decision making, and a detailed flowchart presents the layout of this part of the system. This platform is described in the context of a weight management program, and we present baseline characteristics of 1801 participants, their behaviors, self-reported medical conditions, and initial pattern of enrollment in the various treatment options. Considering the prevalence and upward trend of overweight and obesity in the United States, a need exists for robust intervention platforms that can systematically support multiple types of programs. Weight management interventions implemented using this platform are scalable to the population level and are sustainable over time despite the limits of defined resources and budgets. The present article describes an innovative approach to reaching a large population with effective programs in an integrated, coordinated, and systematic manner. This comprehensive, robust platform represents an example of how obesity prevention and treatment research may be translated into the applied setting.

Formative research in a school-based obesity prevention program for Native American school children (Pathways)

PubMed Central

Gittelsohn, Joel; Evans, Marguerite; Helitzer, Deborah; Anliker, Jean; Story, Mary; Metcalfe, Lauve; Davis, Sally; Cloud, Patty Iron

2016-01-01

This paper describes how formative research was developed and implemented to produce obesity prevention interventions among school children in six different Native American nations that are part of the Pathways study. The formative assessment work presented here was unique in several ways: (1) it represents the first time formative research methods have been applied across multiple Native American tribes; (2) it is holistic, including data collection from parents, children, teachers, administrators and community leaders; and (3) it was developed by a multi-disciplinary group, including substantial input from Native American collaborators. The paper describes the process of developing the different units of the protocol, how data collection was implemented and how analyses were structured around the identification of risk behaviors. An emphasis is placed on describing which units of the formative assessment protocol were most effective and which were less effective. PMID:10181023

Developments in fiber optics for distribution automation

NASA Technical Reports Server (NTRS)

Kirkham, H.; Friend, H.; Jackson, S.; Johnston, A.

1991-01-01

An optical fiber based communications system of unusual design is described. The system consists of a network of optical fibers overlaid on the distribution system. It is configured as a large number of interconnected rings, with some spurs. Protocols for access to and control of the network are described. Because of the way they function, the protocols are collectively called AbNET, in commemoration of the microbiologists' abbreviation Ab for antibody. Optical data links that could be optically powered are described. There are two versions, each of which has a good frequency response and minimal filtering requirements. In one, a conventional FM pulse train is used at the transmitter, and a novel form of phase-locked loop is used as demodulator. In the other, the FM transmitter is replaced with a pulse generator arranged so that the period between pulses represents the modulating signal. Transmitter and receiver designs, including temperature compensation methods, are presented. Experimental results are given.

Time-domain diffuse optics using bioresorbable fibers: a proof-of-principle study

NASA Astrophysics Data System (ADS)

Di Sieno, Laura; Boetti, Nadia G.; Dalla Mora, Alberto; Pugliese, Diego; Farina, Andrea; Konugolu Venkata Sekar, Sanathana; Ceci-Ginistrelli, Edoardo; Janner, Davide; Pifferi, Antonio; Milanese, Daniel

2017-07-01

We show for the first time the aptness of Calcium Phosphate Glass-based bioresorbable fibers for time-domain diffuse optics using tests described by a standardized protocol and we also present a spectroscopic measurement on a chicken breast.

Attacks on quantum key distribution protocols that employ non-ITS authentication

NASA Astrophysics Data System (ADS)

Pacher, C.; Abidin, A.; Lorünser, T.; Peev, M.; Ursin, R.; Zeilinger, A.; Larsson, J.-Å.

2016-01-01

We demonstrate how adversaries with large computing resources can break quantum key distribution (QKD) protocols which employ a particular message authentication code suggested previously. This authentication code, featuring low key consumption, is not information-theoretically secure (ITS) since for each message the eavesdropper has intercepted she is able to send a different message from a set of messages that she can calculate by finding collisions of a cryptographic hash function. However, when this authentication code was introduced, it was shown to prevent straightforward man-in-the-middle (MITM) attacks against QKD protocols. In this paper, we prove that the set of messages that collide with any given message under this authentication code contains with high probability a message that has small Hamming distance to any other given message. Based on this fact, we present extended MITM attacks against different versions of BB84 QKD protocols using the addressed authentication code; for three protocols, we describe every single action taken by the adversary. For all protocols, the adversary can obtain complete knowledge of the key, and for most protocols her success probability in doing so approaches unity. Since the attacks work against all authentication methods which allow to calculate colliding messages, the underlying building blocks of the presented attacks expose the potential pitfalls arising as a consequence of non-ITS authentication in QKD post-processing. We propose countermeasures, increasing the eavesdroppers demand for computational power, and also prove necessary and sufficient conditions for upgrading the discussed authentication code to the ITS level.

Nd:YAG photovaporization of residual equine guttural-pouch mycotic lesions after internal carotid occlusion

NASA Astrophysics Data System (ADS)

Tate, Lloyd P.; Tudor, R. A.; Little, Edwina D. E.

1998-07-01

Hospital records reviewed over a 12-year period determined that 6 horses had been presented for guttural pouch mycosis. All had a history of epistaxis and several had accompanying neurologic signs, including dysphagia. Initially, conformation of the disease was obtained by radiographic and endoscopic examinations. Surgical treatment was directed at controlling and preventing additional hemorrhage by occluding the arterial source of the hemorrhage. Direct treatment of the mycotic plaque present within the guttural pouch was conducted using transendoscopic technique to direct irradiation from the Nd:YAG laser. The protocol described for the laser application was successful in resolving the lesions and was less complicated and stressful than previously reported topically applied chemical protocols.

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.

The Simulation of Read-time Scalable Coherent Interface

NASA Technical Reports Server (NTRS)

Li, Qiang; Grant, Terry; Grover, Radhika S.

1997-01-01

Scalable Coherent Interface (SCI, IEEE/ANSI Std 1596-1992) (SCI1, SCI2) is a high performance interconnect for shared memory multiprocessor systems. In this project we investigate an SCI Real Time Protocols (RTSCI1) using Directed Flow Control Symbols. We studied the issues of efficient generation of control symbols, and created a simulation model of the protocol on a ring-based SCI system. This report presents the results of the study. The project has been implemented using SES/Workbench. The details that follow encompass aspects of both SCI and Flow Control Protocols, as well as the effect of realistic client/server processing delay. The report is organized as follows. Section 2 provides a description of the simulation model. Section 3 describes the protocol implementation details. The next three sections of the report elaborate on the workload, results and conclusions. Appended to the report is a description of the tool, SES/Workbench, used in our simulation, and internal details of our implementation of the protocol.

Analysis of Nuclear RNA Interference (RNAi) in Human Cells by Subcellular Fractionation and Argonaute Loading

PubMed Central

Gagnon, Keith T.; Li, Liande; Janowski, Bethany A.; Corey, David R.

2014-01-01

RNA interference (RNAi) is well known for its ability to regulate gene expression in the cytoplasm of mammalian cells. In mammalian cell nuclei, however, the impact of RNAi has remained more controversial. A key technical hurdle has been a lack of optimized protocols for the isolation and analysis of cell nuclei. Here we describe a simplified protocol for nuclei isolation from cultured cells that incorporates a method for obtaining nucleoplasmic and chromatin fractions and removing cytoplasmic contamination. Cell fractions can then be used to detect the presence and activity of RNAi factors in the nucleus. We present a protocol for investigating an early step in RNAi, Argonaute protein loading with small RNAs, which is enabled by our improved extract preparations. These protocols facilitate characterization of nuclear RNAi and can be applied to the analysis of other nuclear proteins and pathways. From cellular fractionation to analysis of Argonaute loading results, this protocol takes 4–6 d to complete. PMID:25079428

High-throughput microfluidics to control and measure signaling dynamics in single yeast cells

PubMed Central

Hansen, Anders S.; Hao, Nan; O'Shea, Erin K.

2015-01-01

Microfluidics coupled to quantitative time-lapse fluorescence microscopy is transforming our ability to control, measure, and understand signaling dynamics in single living cells. Here we describe a pipeline that incorporates multiplexed microfluidic cell culture, automated programmable fluid handling for cell perturbation, quantitative time-lapse microscopy, and computational analysis of time-lapse movies. We illustrate how this setup can be used to control the nuclear localization of the budding yeast transcription factor Msn2. Using this protocol, we generate oscillations of Msn2 localization and measure the dynamic gene expression response of individual genes in single cells. The protocol allows a single researcher to perform up to 20 different experiments in a single day, whilst collecting data for thousands of single cells. Compared to other protocols, the present protocol is relatively easy to adopt and higher-throughput. The protocol can be widely used to control and monitor single-cell signaling dynamics in other signal transduction systems in microorganisms. PMID:26158443

Optimization of Native and Formaldehyde iPOND Techniques for Use in Suspension Cells.

PubMed

Wiest, Nathaniel E; Tomkinson, Alan E

2017-01-01

The isolation of proteins on nascent DNA (iPOND) technique developed by the Cortez laboratory allows a previously unparalleled ability to examine proteins associated with replicating and newly synthesized DNA in mammalian cells. Both the original, formaldehyde-based iPOND technique and a more recent derivative, accelerated native iPOND (aniPOND), have mostly been performed in adherent cell lines. Here, we describe modifications to both protocols for use with suspension cell lines. These include cell culture, pulse, and chase conditions that optimize sample recovery in both protocols using suspension cells and several key improvements to the published aniPOND technique that reduce sample loss, increase signal to noise, and maximize sample recovery. Additionally, we directly and quantitatively compare the iPOND and aniPOND protocols to test the strengths and limitations of both. Finally, we present a detailed protocol to perform the optimized aniPOND protocol in suspension cell lines. © 2017 Elsevier Inc. All rights reserved.

Realist theory construction for a mixed method multilevel study of neighbourhood context and postnatal depression.

PubMed

Eastwood, John G; Kemp, Lynn A; Jalaludin, Bin B

2016-01-01

We have recently described a protocol for a study that aims to build a theory of neighbourhood context and postnatal depression. That protocol proposed a critical realist Explanatory Theory Building Method comprising of an: (1) emergent phase, (2) construction phase, and (3) confirmatory phase. A concurrent triangulated mixed method multilevel cross-sectional study design was described. The protocol also described in detail the Theory Construction Phase which will be presented here. The Theory Construction Phase will include: (1) defining stratified levels; (2) analytic resolution; (3) abductive reasoning; (4) comparative analysis (triangulation); (5) retroduction; (6) postulate and proposition development; (7) comparison and assessment of theories; and (8) conceptual frameworks and model development. The stratified levels of analysis in this study were predominantly social and psychological. The abductive analysis used the theoretical frames of: Stress Process; Social Isolation; Social Exclusion; Social Services; Social Capital, Acculturation Theory and Global-economic level mechanisms. Realist propositions are presented for each analysis of triangulated data. Inference to best explanation is used to assess and compare theories. A conceptual framework of maternal depression, stress and context is presented that includes examples of mechanisms at psychological, social, cultural and global-economic levels. Stress was identified as a necessary mechanism that has the tendency to cause several outcomes including depression, anxiety, and health harming behaviours. The conceptual framework subsequently included conditional mechanisms identified through the retroduction including the stressors of isolation and expectations and buffers of social support and trust. The meta-theory of critical realism is used here to generate and construct social epidemiological theory using stratified ontology and both abductive and retroductive analysis. The findings will be applied to the development of a middle range theory and subsequent programme theory for local perinatal child and family interventions.

Optimal early active mobilisation protocol after extensor tendon repairs in zones V and VI: A systematic review of literature.

PubMed

Collocott, Shirley Jf; Kelly, Edel; Ellis, Richard F

2018-03-01

Early mobilisation protocols after repair of extensor tendons in zone V and VI provide better outcomes than immobilisation protocols. This systematic review investigated different early active mobilisation protocols used after extensor tendon repair in zone V and VI. The purpose was to determine whether any one early active mobilisation protocol provides superior results. An extensive literature search was conducted to identify articles investigating the outcomes of early active mobilisation protocols after extensor tendon repair in zone V and VI. Databases searched were AMED, Embase, Medline, Cochrane and CINAHL. Studies were included if they involved participants with extensor tendon repairs in zone V and VI in digits 2-5 and described a post-operative rehabilitation protocol which allowed early active metacarpophalangeal joint extension. Study designs included were randomised controlled trials, observational studies, cohort studies and case series. The Structured Effectiveness Quality Evaluation Scale was used to evaluate the methodological quality of the included studies. Twelve articles met the inclusion criteria. Two types of early active mobilisation protocols were identified: controlled active motion protocols and relative motion extension splinting protocols. Articles describing relative motion extension splinting protocols were more recent but of lower methodological quality than those describing controlled active motion protocols. Participants treated with controlled active motion and relative motion extension splinting protocols had similar range of motion outcomes, but those in relative motion extension splinting groups returned to work earlier. The evidence reviewed suggested that relative motion extension splinting protocols may allow an earlier return to function than controlled active motion protocols without a greater risk of complication.

Protocol: realist synthesis of the impact of unemployment insurance policies on poverty and health.

PubMed

Molnar, Agnes; O'Campo, Patricia; Ng, Edwin; Mitchell, Christiane; Muntaner, Carles; Renahy, Emilie; St John, Alexander; Shankardass, Ketan

2015-02-01

Unemployment insurance is an important social protection policy that buffers unemployed workers against poverty and poor health. Most unemployment insurance studies focus on whether increases in unemployment insurance generosity are predictive of poverty and health outcomes. Less work has used theory-driven approaches to understand and explain how and why unemployment insurance works, for whom, and under what circumstances. Given this, we present a realist synthesis protocol that seeks to unpack how contextual influences trigger relevant mechanisms to generate poverty and health outcomes. In this protocol, we conceptualize unemployment insurance as a key social protection policy; provide a supporting rationale on the need for a realist synthesis; and describe our process on identifying context-mechanism-outcome pattern configurations. Six methodological steps are described: initial theory development, search strategy; selection and appraisal of documents; data extraction; analysis and synthesis process; and presentation and dissemination of revised theory. Our forthcoming realist synthesis will be the first to build and test theory on the intended and unintended outcomes of unemployment insurance policies. Anticipated findings will allow policymakers to move beyond 'black box' approaches to consider 'mechanism-based' explanations that explicate the logic on how and why unemployment insurance matters. Copyright © 2014 Elsevier Ltd. All rights reserved.

A Protocol for Generation of a Corticosterone Model of Psychiatric Disorders.

PubMed

Guest, Paul C

2017-01-01

Some patients with psychiatric disorders show hyperactivity of the hypothalamic-pituitary-adrenal (HPA) axis. This may be due to an impaired feedback inhibition and can be seen through increased levels of circulating cortisol. Here a protocol is described to mimic this situation by subcutaneous implantation of corticosterone pellets in mice. We also present characterization of the model by looking at effects on neuronal proliferation in hippocampus, one of the main tissues known to be affected by HPA axis hyper-activation. Such tissues could be used in analyses by proteomic platforms.

A Protocol for Safe Lithiation Reactions Using Organolithium Reagents

PubMed Central

Gau, Michael R.; Zdilla, Michael J.

2016-01-01

Organolithium reagents are powerful tools in the synthetic chemist's toolbox. However, the extreme pyrophoric nature of the most reactive reagents warrants proper technique, thorough training, and proper personal protective equipment. To aid in the training of researchers using organolithium reagents, a thorough, step-by-step protocol for the safe and effective use of tert-butyllithium on an inert gas line or within a glovebox is described. As a model reaction, preparation of lithium tert-butyl amide by the reaction of tert-butyl amine with one equivalent of tert-butyl lithium is presented. PMID:27911386

School violence: effective response protocols for maximum safety and minimum liability.

PubMed

Miller, Laurence

2007-01-01

Despite the recent preoccupation with terrorism, most Americans are still killed by our own citizens, and school violence continues to be a significant source of mortality and trauma. This article describes the basic facts, features, and dynamics of school violence and presents a prevention, response, and recovery protocol adapted from the related field of workplace violence. This model may be used by educators, law enforcement professionals, and mental health clinicians in their collaborative efforts to make our academic institutions safer and healthier places to learn.

Patient perspectives: Kundalini yoga meditation techniques for psycho-oncology and as potential therapies for cancer.

PubMed

Shannahoff-Khalsa, David S

2005-03-01

The ancient system of Kundalini Yoga (KY) includes a vast array of meditation techniques. Some were discovered to be specific for treating psychiatric disorders and others are supposedly beneficial for treating cancers. To date, 2 clinical trials have been conducted for treating obsessive-compulsive disorder (OCD). The first was an open uncontrolled trial and the second a single-blinded randomized controlled trial (RCT) comparing a KY protocol against the Relaxation Response and Mindfulness Meditation (RRMM) techniques combined. Both trials showed efficacy on all psychological scales using the KY protocol; however, the RCT showed no efficacy on any scale with the RRMM control group. The KY protocol employed an OCD-specific meditation technique combined with other techniques that are individually specific for anxiety, low energy, fear, anger, meeting mental challenges, and turning negative thoughts into positive thoughts. In addition to OCD symptoms, other symptoms, including anxiety and depression, were also significantly reduced. Elements of the KY protocol other than the OCD-specific technique also may have applications for psycho-oncology patients and are described here. Two depression-specific KY techniques are described that also help combat mental fatigue and low energy. A 7-part protocol is described that would be used in KY practice to affect the full spectrum of emotions and distress that complicate a cancer diagnosis. In addition, there are KY techniques that practitioners have used in treating cancer. These techniques have not yet been subjected to formal clinical trials but are described here as potential adjunctive therapies. A case history demonstrating rapid onset of acute relief of intense fear in a terminal breast cancer patient using a KY technique specific for fear is presented. A second case history is reported for a surviving male diagnosed in 1988 with terminal prostate cancer who has used KY therapy long term as part of a self-directed integrative care approach.

High-throughput process development: II. Membrane chromatography.

PubMed

Rathore, Anurag S; Muthukumar, Sampath

2014-01-01

Membrane chromatography is gradually emerging as an alternative to conventional column chromatography. It alleviates some of the major disadvantages associated with the latter including high pressure drop across the column bed and dependence on intra-particle diffusion for the transport of solute molecules to their binding sites within the pores of separation media. In the last decade, it has emerged as a method of choice for final polishing of biopharmaceuticals, in particular monoclonal antibody products. The relevance of such a platform is high in view of the constraints with respect to time and resources that the biopharma industry faces today. This protocol describes the steps involved in performing HTPD of a membrane chromatography step. It describes operation of a commercially available device (AcroPrep™ Advance filter plate with Mustang S membrane from Pall Corporation). This device is available in 96-well format with 7 μL membrane in each well. We discuss the challenges that one faces when performing such experiments as well as possible solutions to alleviate them. Besides describing the operation of the device, the protocol also presents an approach for statistical analysis of the data that is gathered from such a platform. A case study involving use of the protocol for examining ion exchange chromatography of Granulocyte Colony Stimulating Factor (GCSF), a therapeutic product, is briefly discussed. This is intended to demonstrate the usefulness of this protocol in generating data that is representative of the data obtained at the traditional lab scale. The agreement in the data is indeed very significant (regression coefficient 0.99). We think that this protocol will be of significant value to those involved in performing high-throughput process development of membrane chromatography.

Cislan-2 extension final document by University of Twente (Netherlands)

NASA Astrophysics Data System (ADS)

Niemegeers, Ignas; Baumann, Frank; Beuwer, Wim; Jordense, Marcel; Pras, Aiko; Schutte, Leon; Tracey, Ian

1992-01-01

Results of worked performed under the so called Cislan extension contract are presented. The adaptation of the Cislan 2 prototype design to an environment of interconnected Local Area Networks (LAN's) instead of a single 802.5 token ring LAN is considered. In order to extend the network architecture, the Interconnection Function (IF) protocol layer was subdivided into two protocol layers: a new IF layer, and below the Medium Enhancement (ME) protocol layer. Some small enhancements to the distributed bandwidth allocation protocol were developed, which in fact are also applicable to the 'normal' Cislan 2 system. The new services and protocols are described together with some scenarios and requirements for the new internetting Cislan 2 system. How to overcome the degradation of the quality of speech due to packet loss on the LAN subsystem was studied. Experiments were planned in order to measure this speech quality degradation. Simulations were performed of two Cislan subsystems, the bandwidth allocation protocol and the clock synchronization mechanism. Results on both simulations, performed on SUN workstations using QNAP as a simulation tool, are given. Results of the simulations of the clock synchronization mechanism, and results of the simulation of the distributed bandwidth allocation protocol are given.

Multitask protocols to evaluate activities of daily living performance in people with COPD: a systematic review.

PubMed

Paes, Thaís; Machado, Felipe Vilaça Cavallari; Cavalheri, Vinícius; Pitta, Fabio; Hernandes, Nidia Aparecida

2017-07-01

People with chronic obstructive pulmonary disease (COPD) present symptoms such as dyspnea and fatigue, which hinder their performance in activities of daily living (ADL). A few multitask protocols have been developed to assess ADL performance in this population, although measurement properties of such protocols were not yet systematically reviewed. Areas covered: Studies were included if an assessment of the ability to perform ADL was conducted in people with COPD using a (objective) performance-based protocol. The search was conducted in the following databases: Pubmed, EMBASE, Cochrane Library, PEDro, CINAHL and LILACS. Furthermore, hand searches were conducted. Expert commentary: Up to this moment, only three protocols had measurement properties described: the Glittre ADL Test, the Monitored Functional Task Evaluation and the Londrina ADL Protocol were shown to be valid and reliable whereas only the Glittre ADL Test was shown to be responsive to change after pulmonary rehabilitation. These protocols can be used in laboratory settings and clinical practice to evaluate ADL performance in people with COPD, although there is need for more in-depth information on their validity, reliability and especially responsiveness due to the growing interest in the accurate assessment of ADL performance in this population.

The Virtual Insect Brain protocol: creating and comparing standardized neuroanatomy

PubMed Central

Jenett, Arnim; Schindelin, Johannes E; Heisenberg, Martin

2006-01-01

Background In the fly Drosophila melanogaster, new genetic, physiological, molecular and behavioral techniques for the functional analysis of the brain are rapidly accumulating. These diverse investigations on the function of the insect brain use gene expression patterns that can be visualized and provide the means for manipulating groups of neurons as a common ground. To take advantage of these patterns one needs to know their typical anatomy. Results This paper describes the Virtual Insect Brain (VIB) protocol, a script suite for the quantitative assessment, comparison, and presentation of neuroanatomical data. It is based on the 3D-reconstruction and visualization software Amira, version 3.x (Mercury Inc.) [1]. Besides its backbone, a standardization procedure which aligns individual 3D images (series of virtual sections obtained by confocal microscopy) to a common coordinate system and computes average intensities for each voxel (volume pixel) the VIB protocol provides an elaborate data management system for data administration. The VIB protocol facilitates direct comparison of gene expression patterns and describes their interindividual variability. It provides volumetry of brain regions and helps to characterize the phenotypes of brain structure mutants. Using the VIB protocol does not require any programming skills since all operations are carried out at an intuitively usable graphical user interface. Although the VIB protocol has been developed for the standardization of Drosophila neuroanatomy, the program structure can be used for the standardization of other 3D structures as well. Conclusion Standardizing brains and gene expression patterns is a new approach to biological shape and its variability. The VIB protocol provides a first set of tools supporting this endeavor in Drosophila. The script suite is freely available at [2] PMID:17196102

Elder Abuse Identification in the Prehospital Setting: An Examination of State Emergency Medical Services Protocols.

PubMed

Namboodri, Brooke L; Rosen, Tony; Dayaa, Joseph A; Bischof, Jason J; Ramadan, Nadeem; Patel, Mehul D; Grover, Joseph; Brice, Jane H; Platts-Mills, Timothy F

2018-03-22

To describe statewide emergency medical service (EMS) protocols relating to identification, management, and reporting of elder abuse in the prehospital setting. Cross-sectional analysis. Statewide EMS protocols in the United States. Publicly available statewide EMS protocols identified from published literature, http://EMSprotocols.org, and each state's public health website. Protocols were reviewed to determine whether elder abuse was mentioned, elder abuse was defined, potential indicators of elder abuse were listed, management of older adults experiencing abuse was described, and instructions regarding reporting were provided. EMS protocols for child abuse were reviewed in the same manner for the purpose of comparison. Of the 35 publicly available statewide EMS protocols, only 14 (40.0%) mention elder abuse. Of protocols that mention elder abuse, 6 (42.9%) define elder abuse, 10 (71.4%) describe indicators of elder abuse, 8 (57.1%) provide instruction regarding management, and 12 (85.7%) provide instruction regarding reporting. Almost twice as many states met each of these metrics for child abuse. Statewide EMS protocols for elder abuse vary in regard to identification, management, and reporting, with the majority of states having no content on this subject. Expansion and standardization of protocols may increase the identification of elder abuse. © 2018, Copyright the Authors Journal compilation © 2018, The American Geriatrics Society.

ASCOT: a text mining-based web-service for efficient search and assisted creation of clinical trials

PubMed Central

2012-01-01

Clinical trials are mandatory protocols describing medical research on humans and among the most valuable sources of medical practice evidence. Searching for trials relevant to some query is laborious due to the immense number of existing protocols. Apart from search, writing new trials includes composing detailed eligibility criteria, which might be time-consuming, especially for new researchers. In this paper we present ASCOT, an efficient search application customised for clinical trials. ASCOT uses text mining and data mining methods to enrich clinical trials with metadata, that in turn serve as effective tools to narrow down search. In addition, ASCOT integrates a component for recommending eligibility criteria based on a set of selected protocols. PMID:22595088

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.

ASCOT: a text mining-based web-service for efficient search and assisted creation of clinical trials.

PubMed

Korkontzelos, Ioannis; Mu, Tingting; Ananiadou, Sophia

2012-04-30

Clinical trials are mandatory protocols describing medical research on humans and among the most valuable sources of medical practice evidence. Searching for trials relevant to some query is laborious due to the immense number of existing protocols. Apart from search, writing new trials includes composing detailed eligibility criteria, which might be time-consuming, especially for new researchers. In this paper we present ASCOT, an efficient search application customised for clinical trials. ASCOT uses text mining and data mining methods to enrich clinical trials with metadata, that in turn serve as effective tools to narrow down search. In addition, ASCOT integrates a component for recommending eligibility criteria based on a set of selected protocols.

THE EFFECTS OF SCALE, DISTANCE AND TIME ON DRINKING WATER SYSTEMS RESEARCH

EPA Science Inventory

This presentation introduces and describes many components related to what generates and/or controls the concentrations of metals and other constituents in drinking water. Emphasis is placed on ways in which sampling protocol affects apparent levels of constituents, and the magn...

A Practicum for Oral Cancer Teaching.

ERIC Educational Resources Information Center

Barr, Charles E.; Goldberg, Marshal D.

1983-01-01

A hospital-based method for teaching general practice dental residents, involving patients for whom the residents are responsible, is described. Residents present prepared cases of dental patients according to a predetermined protocol: a talk, complete documentation of clinical history and laboratory findings, and discussion of therapy and…

ECOLOGICALLY-RELEVANT QUANTIFICATION OF STREAMFLOW REGIMES IN WESTERN STREAMS

EPA Science Inventory

This report describes the rationale for and application of a protocol for estimation of ecologically-relevant streamflow metrics that quantify streamflow regime for ungaged sites subject to a range of human impact. The analysis presented here is focused on sites sampled by the U....

A mechanized process algebra for verification of device synchronization protocols

NASA Technical Reports Server (NTRS)

Schubert, E. Thomas

1992-01-01

We describe the formalization of a process algebra based on CCS within the Higher Order Logic (HOL) theorem-proving system. The representation of four types of device interactions and a correctness proof of the communication between a microprocessor and MMU is presented.

Preliminary clinical trial of immunotherapy for malignant glioma.

PubMed

Ingram, M; Shelden, C H; Jacques, S; Skillen, R G; Bradley, W G; Techy, G B; Freshwater, D B; Abts, R M; Rand, R W

1987-10-01

An immunotherapy protocol based on intracranial implantation of stimulated, autologous lymphocytes into the tumor bed following surgical debulking of malignant glioma is described. Phase I clinical trials in human patients are now in progress. Preliminary data representing the first 39 patients treated are presented briefly.

Orchids (Cymbidium spp., Oncidium, and Phalaenopsis).

PubMed

Chan, Ming-Tsair; Chan, Yuan-Li; Sanjaya

2006-01-01

Recent advances in genetic engineering have made the transformation and regeneration of plants into a powerful tool for orchid improvement. This chapter presents a simple and reproducible Agrobacterium tumefaciens-mediated transformation protocol and molecular screening technique of transgenics for two orchid species, Oncidium and Phalaenopsis. The target tissues for gene transfer were protocorm-like bodies (PLBs) derived from protocorms, into which constructed foreign genes were successfully introduced. To establish stable transformants, two stages of selection were applied on the PLBs co-cultivated with A. tumefaciens. About 10% transformation efficiency was achieved in Oncidium orchid, as 108 antibiotic resistant independent PLBs were proliferated from 1000 infected PLBs. In Phalaenopsis orchid about 11 to 12% of transformation efficiency was achieved by using the present protocol. Different molecular methods and GUS-staining used to screen putative transgenic plants to confirm the integration of foreign DNA into the orchid genome were also described in detail. The methods described would also be useful for transformation of desired genes into other orchid species.

Vital pulp therapy with bipolar electrocoagulation after intentional pulp exposure of fixed prosthodontic abutments: a clinical report.

PubMed

Livaditis, G J

2001-10-01

A clinical protocol is described for the treatment of intentional and unavoidable exposed pulps during crown preparation. The protocol includes a definitive cavity preparation to create space in the exposed dentin for an adhesive pulp barrier; procedures to develop the highly desirable hybrid zone to prevent microleakage; the use of a specific resinous material that serves as a long-term pulp barrier with a relatively neutral and biocompatible impact on the pulp; and the use of precise bipolar electrocoagulation to provide durable hemostasis for restoration of the pulp wall and a relatively clot-free surgical wound to facilitate healing. The protocol involves the application of gentle surgical and restorative procedures to support the inherent healing process to restore the health of the pulp. The patient presented was part of a larger investigation and was selected in an attempt to identify a fixed prosthodontic application of the proposed pulp therapy protocol.

Use of Medaka in Toxicity Testing

PubMed Central

Cowden, John; Hinton, David E.; Johnson, Rodney; Flynn, Kevin; Hardman, Ronald C.; Yuen, Bonny; Law, Sheran; Kullman, Seth W.; Au, Doris W.T.

2015-01-01

Small aquarium fishes are increasingly used as animal models, and one of these, Japanese Medaka (Oryzias latipes), is frequently utilized for toxicity testing. While these vertebrates have many similarities with their terrestrial counterparts, there are differences that must be considered if these organisms are to be used to their highest potential. Testing commonly may employ either the developing embryo or adults; both are easy to use and to work with. We present here three main protocols to illustrate the utility and breadth of toxicity testing possible using medaka fish. The first protocol assesses neurotoxicity in developing embryos. The second protocol describes the sexual genotyping of medaka to evaluate toxicant effects on sexual phenotype after treatment with endocrine disrupting chemicals. The third protocol assesses hepatotoxicity in adult fish after treatment with a model hepatotoxicant. The methods run the gamut from immunohistology through PCR to basic histological techniques. PMID:20922755

Protocol for concomitant temporomandibular joint custom-fitted total joint reconstruction and orthognathic surgery utilizing computer-assisted surgical simulation.

PubMed

Movahed, Reza; Teschke, Marcus; Wolford, Larry M

2013-12-01

Clinicians who address temporomandibular joint (TMJ) pathology and dentofacial deformities surgically can perform the surgery in 1 stage or 2 separate stages. The 2-stage approach requires the patient to undergo 2 separate operations and anesthesia, significantly prolonging the overall treatment. However, performing concomitant TMJ and orthognathic surgery (CTOS) in these cases requires careful treatment planning and surgical proficiency in the 2 surgical areas. This article presents a new treatment protocol for the application of computer-assisted surgical simulation in CTOS cases requiring reconstruction with patient-fitted total joint prostheses. The traditional and new CTOS protocols are described and compared. The new CTOS protocol helps decrease the preoperative workup time and increase the accuracy of model surgery. Copyright © 2013 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

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.

Copper(I)/TEMPO Catalyzed Aerobic Oxidation of Primary Alcohols to Aldehydes with Ambient Air

PubMed Central

Hoover, Jessica M.; Steves, Janelle E.; Stahl, Shannon S.

2012-01-01

This protocol describes a practical laboratory-scale method for aerobic oxidation of primary alcohols to aldehydes, using a chemoselective CuI/TEMPO catalyst system. The catalyst is prepared in situ from commercially available reagents, and the reactions are performed in a common organic solvent (acetonitrile) with ambient air as the oxidant. Three different reaction conditions and three procedures for the isolation and purification of the aldehyde product are presented. The oxidations of eight different alcohols, described here, include representative examples of each reaction condition and purification method. Reaction times vary from 20 min to 24 h, depending on the alcohol, while the purification methods each take about 2 h. The total time necessary for the complete protocol ranges from 3 – 26 h. PMID:22635108

High speed bus technology development

NASA Astrophysics Data System (ADS)

Modrow, Marlan B.; Hatfield, Donald W.

1989-09-01

The development and demonstration of the High Speed Data Bus system, a 50 Million bits per second (Mbps) local data network intended for avionics applications in advanced military aircraft is described. The Advanced System Avionics (ASA)/PAVE PILLAR program provided the avionics architecture concept and basic requirements. Designs for wire and fiber optic media were produced and hardware demonstrations were performed. An efficient, robust token-passing protocol was developed and partially demonstrated. The requirements specifications, the trade-offs made, and the resulting designs for both a coaxial wire media system and a fiber optics design are examined. Also, the development of a message-oriented media access protocol is described, from requirements definition through analysis, simulation and experimentation. Finally, the testing and demonstrations conducted on the breadboard and brassboard hardware is presented.

Design of durability test protocol for vehicular fuel cell systems operated in power-follow mode based on statistical results of on-road data

NASA Astrophysics Data System (ADS)

Xu, Liangfei; Reimer, Uwe; Li, Jianqiu; Huang, Haiyan; Hu, Zunyan; Jiang, Hongliang; Janßen, Holger; Ouyang, Minggao; Lehnert, Werner

2018-02-01

City buses using polymer electrolyte membrane (PEM) fuel cells are considered to be the most likely fuel cell vehicles to be commercialized in China. The technical specifications of the fuel cell systems (FCSs) these buses are equipped with will differ based on the powertrain configurations and vehicle control strategies, but can generally be classified into the power-follow and soft-run modes. Each mode imposes different levels of electrochemical stress on the fuel cells. Evaluating the aging behavior of fuel cell stacks under the conditions encountered in fuel cell buses requires new durability test protocols based on statistical results obtained during actual driving tests. In this study, we propose a systematic design method for fuel cell durability test protocols that correspond to the power-follow mode based on three parameters for different fuel cell load ranges. The powertrain configurations and control strategy are described herein, followed by a presentation of the statistical data for the duty cycles of FCSs in one city bus in the demonstration project. Assessment protocols are presented based on the statistical results using mathematical optimization methods, and are compared to existing protocols with respect to common factors, such as time at open circuit voltage and root-mean-square power.

Protocols for Image Processing based Underwater Inspection of Infrastructure Elements

NASA Astrophysics Data System (ADS)

O'Byrne, Michael; Ghosh, Bidisha; Schoefs, Franck; Pakrashi, Vikram

2015-07-01

Image processing can be an important tool for inspecting underwater infrastructure elements like bridge piers and pile wharves. Underwater inspection often relies on visual descriptions of divers who are not necessarily trained in specifics of structural degradation and the information may often be vague, prone to error or open to significant variation of interpretation. Underwater vehicles, on the other hand can be quite expensive to deal with for such inspections. Additionally, there is now significant encouragement globally towards the deployment of more offshore renewable wind turbines and wave devices and the requirement for underwater inspection can be expected to increase significantly in the coming years. While the merit of image processing based assessment of the condition of underwater structures is understood to a certain degree, there is no existing protocol on such image based methods. This paper discusses and describes an image processing protocol for underwater inspection of structures. A stereo imaging image processing method is considered in this regard and protocols are suggested for image storage, imaging, diving, and inspection. A combined underwater imaging protocol is finally presented which can be used for a variety of situations within a range of image scenes and environmental conditions affecting the imaging conditions. An example of detecting marine growth is presented of a structure in Cork Harbour, Ireland.

Correlation Between Iron and alpha and pi Glutathione-S-Transferase Levels in Humans

DTIC Science & Technology

2012-09-01

assays were performed as described in the Biotrin High Sensitivity Alpha GST EIA kit protocol. First, serum samples were diluted 1:10 with wash solution...immunosorbent assays were performed as described in the Biotrin Pi GST EIA kit protocol. First, plasma samples were diluted 1:5 with sample diluent...immunosorbent assays were performed as described in the AssayMax Human Transferrin ELISA kit protocol. First, serum samples were diluted 1:2000 with MIX

Revisiting the ALA/N (alpha-lipoic acid/low-dose naltrexone) protocol for people with metastatic and nonmetastatic pancreatic cancer: a report of 3 new cases.

PubMed

Berkson, Burton M; Rubin, Daniel M; Berkson, Arthur J

2009-12-01

The authors, in a previous article, described the long-term survival of a man with pancreatic cancer and metastases to the liver, treated with intravenous alpha-lipoic acid and oral low-dose naltrexone (ALA/N) without any adverse effects. He is alive and well 78 months after initial presentation. Three additional pancreatic cancer case studies are presented in this article. At the time of this writing, the first patient, GB, is alive and well 39 months after presenting with adenocarcinoma of the pancreas with metastases to the liver. The second patient, JK, who presented to the clinic with the same diagnosis was treated with the ALA/N protocol and after 5 months of therapy, PET scan demonstrated no evidence of disease. The third patient, RC, in addition to his pancreatic cancer with liver and retroperitoneal metastases, has a history of B-cell lymphoma and prostate adenocarcinoma. After 4 months of the ALA/N protocol his PET scan demonstrated no signs of cancer. In this article, the authors discuss the poly activity of ALA: as an agent that reduces oxidative stress, its ability to stabilize NF(k)B, its ability to stimulate pro-oxidant apoptosic activity, and its discriminative ability to discourage the proliferation of malignant cells. In addition, the ability of lowdose naltrexone to modulate an endogenous immune response is discussed. This is the second article published on the ALA/N protocol and the authors believe the protocol warrants clinical trial.

Small-molecule ligand docking into comparative models with Rosetta

PubMed Central

Combs, Steven A; DeLuca, Samuel L; DeLuca, Stephanie H; Lemmon, Gordon H; Nannemann, David P; Nguyen, Elizabeth D; Willis, Jordan R; Sheehan, Jonathan H; Meiler, Jens

2017-01-01

Structure-based drug design is frequently used to accelerate the development of small-molecule therapeutics. Although substantial progress has been made in X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, the availability of high-resolution structures is limited owing to the frequent inability to crystallize or obtain sufficient NMR restraints for large or flexible proteins. Computational methods can be used to both predict unknown protein structures and model ligand interactions when experimental data are unavailable. This paper describes a comprehensive and detailed protocol using the Rosetta modeling suite to dock small-molecule ligands into comparative models. In the protocol presented here, we review the comparative modeling process, including sequence alignment, threading and loop building. Next, we cover docking a small-molecule ligand into the protein comparative model. In addition, we discuss criteria that can improve ligand docking into comparative models. Finally, and importantly, we present a strategy for assessing model quality. The entire protocol is presented on a single example selected solely for didactic purposes. The results are therefore not representative and do not replace benchmarks published elsewhere. We also provide an additional tutorial so that the user can gain hands-on experience in using Rosetta. The protocol should take 5–7 h, with additional time allocated for computer generation of models. PMID:23744289

Guidelines for randomized clinical trial protocol content: a systematic review

PubMed Central

2012-01-01

Background All randomized clinical trials (RCTs) require a protocol; however, numerous studies have highlighted protocol deficiencies. Reporting guidelines may improve the content of research reports and, if developed using robust methods, may increase the utility of reports to stakeholders. The objective of this study was to systematically identify and review RCT protocol guidelines, to assess their characteristics and methods of development, and to compare recommendations. Methods We conducted a systematic review of indexed literature (MEDLINE, EMBASE and the Cochrane Methodology Register from inception to September 2010; reference lists; related article features; forward citation searching) and a targeted search of supplementary sources, including a survey of major trial funding agencies in six countries. Records were eligible if they described a content guideline in English or French relevant to RCT protocols. Guidelines were excluded if they specified content for protocols for trials of specific procedures or conditions or were intended to assess trial quality. We extracted guideline characteristics and methods. Content was mapped for a subset of guidelines that described development methods or had institutional endorsement. Results Forty guidelines published in journals, books and institutional reports were included in the review; seven were specific to RCT protocols. Only eight (20%) described development methods which included informal consensus methods, pilot testing and formal validation; no guideline described all of these methods. No guideline described formal consensus methods or a systematic retrieval of empirical evidence to inform its development. The guidelines included a median of 23 concepts per guideline (interquartile range (IQR) = 14 to 34; range = 7 to 109). Among the subset of guidelines (n = 23) for which content was mapped, approximately 380 concepts were explicitly addressed (median concepts per guideline IQR = 31 (24,80); range = 16 to 150); most concepts were addressed in a minority of guidelines. Conclusions Existing guidelines for RCT protocol content varied substantially in their recommendations. Few reports described the methods of guideline development, limiting comparisons of guideline validity. Given the importance of protocols to diverse stakeholders, we believe a systematically developed, evidence-informed guideline for clinical trial protocols is needed. PMID:23006870

Guidelines for randomized clinical trial protocol content: a systematic review.

PubMed

Tetzlaff, Jennifer M; Chan, An-Wen; Kitchen, Jessica; Sampson, Margaret; Tricco, Andrea C; Moher, David

2012-09-24

All randomized clinical trials (RCTs) require a protocol; however, numerous studies have highlighted protocol deficiencies. Reporting guidelines may improve the content of research reports and, if developed using robust methods, may increase the utility of reports to stakeholders. The objective of this study was to systematically identify and review RCT protocol guidelines, to assess their characteristics and methods of development, and to compare recommendations. We conducted a systematic review of indexed literature (MEDLINE, EMBASE and the Cochrane Methodology Register from inception to September 2010; reference lists; related article features; forward citation searching) and a targeted search of supplementary sources, including a survey of major trial funding agencies in six countries. Records were eligible if they described a content guideline in English or French relevant to RCT protocols. Guidelines were excluded if they specified content for protocols for trials of specific procedures or conditions or were intended to assess trial quality. We extracted guideline characteristics and methods. Content was mapped for a subset of guidelines that described development methods or had institutional endorsement. Forty guidelines published in journals, books and institutional reports were included in the review; seven were specific to RCT protocols. Only eight (20%) described development methods which included informal consensus methods, pilot testing and formal validation; no guideline described all of these methods. No guideline described formal consensus methods or a systematic retrieval of empirical evidence to inform its development. The guidelines included a median of 23 concepts per guideline (interquartile range (IQR) = 14 to 34; range = 7 to 109). Among the subset of guidelines (n = 23) for which content was mapped, approximately 380 concepts were explicitly addressed (median concepts per guideline IQR = 31 (24,80); range = 16 to 150); most concepts were addressed in a minority of guidelines. Existing guidelines for RCT protocol content varied substantially in their recommendations. Few reports described the methods of guideline development, limiting comparisons of guideline validity. Given the importance of protocols to diverse stakeholders, we believe a systematically developed, evidence-informed guideline for clinical trial protocols is needed.

Telemetry in bundles: delay-tolerant networking for delay-challenged applications

NASA Technical Reports Server (NTRS)

Burleigh, S.

2003-01-01

This paper presents an overview of DTN concepts, including bundles and the Bundling overlay protocol. One possible scenario for the application of DTN to a telemetry return problem is described, and there is a brief discussion of the current state of DTN technology development.

Re-Framing the World Wide Web

ERIC Educational Resources Information Center

Black, August

2011-01-01

The research presented in this dissertation studies and describes how technical standards, protocols, and application programming interfaces (APIs) shape the aesthetic, functional, and affective nature of our most dominant mode of online communication, the World Wide Web (WWW). I examine the politically charged and contentious battle over browser…

Optimized imaging of the midface and orbits

PubMed Central

Langner, Sönke

2015-01-01

A variety of imaging techniques are available for imaging the midface and orbits. This review article describes the different imaging techniques based on the recent literature and discusses their impact on clinical routine imaging. Imaging protocols are presented for different diseases and the different imaging modalities. PMID:26770279

DoS detection in IEEE 802.11 with the presence of hidden nodes

PubMed Central

Soryal, Joseph; Liu, Xijie; Saadawi, Tarek

2013-01-01

The paper presents a novel technique to detect Denial of Service (DoS) attacks applied by misbehaving nodes in wireless networks with the presence of hidden nodes employing the widely used IEEE 802.11 Distributed Coordination Function (DCF) protocols described in the IEEE standard [1]. Attacker nodes alter the IEEE 802.11 DCF firmware to illicitly capture the channel via elevating the probability of the average number of packets transmitted successfully using up the bandwidth share of the innocent nodes that follow the protocol standards. We obtained the theoretical network throughput by solving two-dimensional Markov Chain model as described by Bianchi [2], and Liu and Saadawi [3] to determine the channel capacity. We validated the results obtained via the theoretical computations with the results obtained by OPNET simulator [4] to define the baseline for the average attainable throughput in the channel under standard conditions where all nodes follow the standards. The main goal of the DoS attacker is to prevent the innocent nodes from accessing the channel and by capturing the channel’s bandwidth. In addition, the attacker strives to appear as an innocent node that follows the standards. The protocol resides in every node to enable each node to police other nodes in its immediate wireless coverage area. All innocent nodes are able to detect and identify the DoS attacker in its wireless coverage area. We applied the protocol to two Physical Layer technologies: Direct Sequence Spread Spectrum (DSSS) and Frequency Hopping Spread Spectrum (FHSS) and the results are presented to validate the algorithm. PMID:25685510

DoS detection in IEEE 802.11 with the presence of hidden nodes.

PubMed

Soryal, Joseph; Liu, Xijie; Saadawi, Tarek

2014-07-01

The paper presents a novel technique to detect Denial of Service (DoS) attacks applied by misbehaving nodes in wireless networks with the presence of hidden nodes employing the widely used IEEE 802.11 Distributed Coordination Function (DCF) protocols described in the IEEE standard [1]. Attacker nodes alter the IEEE 802.11 DCF firmware to illicitly capture the channel via elevating the probability of the average number of packets transmitted successfully using up the bandwidth share of the innocent nodes that follow the protocol standards. We obtained the theoretical network throughput by solving two-dimensional Markov Chain model as described by Bianchi [2], and Liu and Saadawi [3] to determine the channel capacity. We validated the results obtained via the theoretical computations with the results obtained by OPNET simulator [4] to define the baseline for the average attainable throughput in the channel under standard conditions where all nodes follow the standards. The main goal of the DoS attacker is to prevent the innocent nodes from accessing the channel and by capturing the channel's bandwidth. In addition, the attacker strives to appear as an innocent node that follows the standards. The protocol resides in every node to enable each node to police other nodes in its immediate wireless coverage area. All innocent nodes are able to detect and identify the DoS attacker in its wireless coverage area. We applied the protocol to two Physical Layer technologies: Direct Sequence Spread Spectrum (DSSS) and Frequency Hopping Spread Spectrum (FHSS) and the results are presented to validate the algorithm.

Securing the AliEn File Catalogue - Enforcing authorization with accountable file operations

NASA Astrophysics Data System (ADS)

Schreiner, Steffen; Bagnasco, Stefano; Sankar Banerjee, Subho; Betev, Latchezar; Carminati, Federico; Vladimirovna Datskova, Olga; Furano, Fabrizio; Grigoras, Alina; Grigoras, Costin; Mendez Lorenzo, Patricia; Peters, Andreas Joachim; Saiz, Pablo; Zhu, Jianlin

2011-12-01

The AliEn Grid Services, as operated by the ALICE Collaboration in its global physics analysis grid framework, is based on a central File Catalogue together with a distributed set of storage systems and the possibility to register links to external data resources. This paper describes several identified vulnerabilities in the AliEn File Catalogue access protocol regarding fraud and unauthorized file alteration and presents a more secure and revised design: a new mechanism, called LFN Booking Table, is introduced in order to keep track of access authorization in the transient state of files entering or leaving the File Catalogue. Due to a simplification of the original Access Envelope mechanism for xrootd-protocol-based storage systems, fundamental computational improvements of the mechanism were achieved as well as an up to 50% reduction of the credential's size. By extending the access protocol with signed status messages from the underlying storage system, the File Catalogue receives trusted information about a file's size and checksum and the protocol is no longer dependent on client trust. Altogether, the revised design complies with atomic and consistent transactions and allows for accountable, authentic, and traceable file operations. This paper describes these changes as part and beyond the development of AliEn version 2.19.

From Expert Protocols to Standardized Management of Infectious Diseases.

PubMed

Lagier, Jean-Christophe; Aubry, Camille; Delord, Marion; Michelet, Pierre; Tissot-Dupont, Hervé; Million, Matthieu; Brouqui, Philippe; Raoult, Didier; Parola, Philippe

2017-08-15

We report here 4 examples of management of infectious diseases (IDs) at the University Hospital Institute Méditerranée Infection in Marseille, France, to illustrate the value of expert protocols feeding standardized management of IDs. First, we describe our experience on Q fever and Tropheryma whipplei infection management based on in vitro data and clinical outcome. Second, we describe our management-based approach for the treatment of infective endocarditis, leading to a strong reduction of mortality rate. Third, we report our use of fecal microbiota transplantation to face severe Clostridium difficile infections and to perform decolonization of patients colonized by emerging highly resistant bacteria. Finally, we present the standardized management of the main acute infections in patients admitted in the emergency department, promoting antibiotics by oral route, checking compliance with the protocol, and avoiding the unnecessary use of intravenous and urinary tract catheters. Overall, the standardization of the management is the keystone to reduce both mortality and morbidity related to IDs. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

Preparation of Low-Input and Ligation-Free ChIP-seq Libraries Using Template-Switching Technology.

PubMed

Bolduc, Nathalie; Lehman, Alisa P; Farmer, Andrew

2016-10-10

Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) has become the gold standard for mapping of transcription factors and histone modifications throughout the genome. However, for ChIP experiments involving few cells or targeting low-abundance transcription factors, the small amount of DNA recovered makes ligation of adapters very challenging. In this unit, we describe a ChIP-seq workflow that can be applied to small cell numbers, including a robust single-tube and ligation-free method for preparation of sequencing libraries from sub-nanogram amounts of ChIP DNA. An example ChIP protocol is first presented, resulting in selective enrichment of DNA-binding proteins and cross-linked DNA fragments immobilized on beads via an antibody bridge. This is followed by a protocol for fast and easy cross-linking reversal and DNA recovery. Finally, we describe a fast, ligation-free library preparation protocol, featuring DNA SMART technology, resulting in samples ready for Illumina sequencing. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

Hydroponics: A Versatile System to Study Nutrient Allocation and Plant Responses to Nutrient Availability and Exposure to Toxic Elements

PubMed Central

Nguyen, Nga T.; McInturf, Samuel A.; Mendoza-Cózatl, David G.

2016-01-01

Hydroponic systems have been utilized as one of the standard methods for plant biology research and are also used in commercial production for several crops, including lettuce and tomato. Within the plant research community, numerous hydroponic systems have been designed to study plant responses to biotic and abiotic stresses. Here we present a hydroponic protocol that can be easily implemented in laboratories interested in pursuing studies on plant mineral nutrition. This protocol describes the hydroponic system set up in detail and the preparation of plant material for successful experiments. Most of the materials described in this protocol can be found outside scientific supply companies, making the set up for hydroponic experiments less expensive and convenient. The use of a hydroponic growth system is most advantageous in situations where the nutrient media need to be well controlled and when intact roots need to be harvested for downstream applications. We also demonstrate how nutrient concentrations can be modified to induce plant responses to both essential nutrients and toxic non-essential elements. PMID:27500800

Hydroponics: A Versatile System to Study Nutrient Allocation and Plant Responses to Nutrient Availability and Exposure to Toxic Elements.

PubMed

Nguyen, Nga T; McInturf, Samuel A; Mendoza-Cózatl, David G

2016-07-13

Hydroponic systems have been utilized as one of the standard methods for plant biology research and are also used in commercial production for several crops, including lettuce and tomato. Within the plant research community, numerous hydroponic systems have been designed to study plant responses to biotic and abiotic stresses. Here we present a hydroponic protocol that can be easily implemented in laboratories interested in pursuing studies on plant mineral nutrition. This protocol describes the hydroponic system set up in detail and the preparation of plant material for successful experiments. Most of the materials described in this protocol can be found outside scientific supply companies, making the set up for hydroponic experiments less expensive and convenient. The use of a hydroponic growth system is most advantageous in situations where the nutrient media need to be well controlled and when intact roots need to be harvested for downstream applications. We also demonstrate how nutrient concentrations can be modified to induce plant responses to both essential nutrients and toxic non-essential elements.

Dissemination of compressed satellite imagery within the Navy SPAWAR Central Site Product Display environment

NASA Technical Reports Server (NTRS)

Kiselyov, Oleg; Fisher, Paul

1995-01-01

This paper presents a case study of integration of compression techniques within a satellite image communication component of an actual tactical weather information dissemination system. The paper describes history and requirements of the project, and discusses the information flow, request/reply protocols, error handling, and, especially, system integration issues: specification of compression parameters and the place and time for compressor/decompressor plug-ins. A case for a non-uniform compression of satellite imagery is presented, and its implementation in the current system id demonstrated. The paper gives special attention to challenges of moving the system towards the use of standard, non-proprietary protocols (smtp and http) and new technologies (OpenDoc), and reports the ongoing work in this direction.

The Deployment of IPv6 in an IPv4 World and Transition Strategies.

ERIC Educational Resources Information Center

Bouras, C.; Ganos, P.; Karaliotas, A.

2003-01-01

The current version of the IP protocol, IPv4, is the most widely used protocol in computer networks. This article describes mechanisms that can be used to facilitate the transition to the new version of the IP protocol, IPv6, and examines usability, usefulness and manageability. Describes how some of these mechanisms were applied to the Greek…

Informal trail monitoring protocols: Denali National Park and Preserve. Final Report, October 2011

USGS Publications Warehouse

Marion, Jeffrey L.; Wimpey, Jeremy F.

2011-01-01

Managers at Alaska?s Denali National Park and Preserve (DENA) sponsored this research to assess and monitor visitor-created informal trails (ITs). DENA is located in south-central Alaska and managed as a six million acre wilderness park. This program of research was guided by the following objectives: (1) Investigate alternative methods for monitoring the spatial distribution, aggregate lineal extent, and tread conditions of informal (visitor-created) trails within the park. (2) In consultation with park staff, develop, pilot test, and refine cost-effective and scientifically defensible trail monitoring procedures that are fully integrated with the park?s Geographic Information System. (3) Prepare a technical report that compiles and presents research results and their management implications. This report presents the protocol development and field testing process, illustrates the types of data produced by their application, and provides guidance for their application and use. The protocols described provide managers with an efficient means to document and monitor IT conditions in settings ranging from pristine to intensively visited.

Derivation of Thymic Lymphoma T-cell Lines from Atm-/- and p53-/- Mice

PubMed Central

Jinadasa, Rasika; Balmus, Gabriel; Gerwitz, Lee; Roden, Jamie; Weiss, Robert; Duhamel, Gerald

2011-01-01

Established cell lines are a critical research tool that can reduce the use of laboratory animals in research. Certain strains of genetically modified mice, such as Atm-/- and p53-/- consistently develop thymic lymphoma early in life 1,2, and thus, can serve as a reliable source for derivation of murine T-cell lines. Here we present a detailed protocol for the development of established murine thymic lymphoma T-cell lines without the need to add interleukins as described in previous protocols 1,3. Tumors were harvested from mice aged three to six months, at the earliest indication of visible tumors based on the observation of hunched posture, labored breathing, poor grooming and wasting in a susceptible strain 1,4. We have successfully established several T-cell lines using this protocol and inbred strains ofAtm-/- [FVB/N-Atmtm1Led/J] 2 and p53-/- [129/S6-Trp53tm1Tyj/J] 5 mice. We further demonstrate that more than 90% of the established T-cell population expresses CD3, CD4 and CD8. Consistent with stably established cell lines, the T-cells generated by using the present protocol have been passaged for over a year. PMID:21490582

Network Quality of Service Monitoring for IP Telephony.

ERIC Educational Resources Information Center

Ghita, B. V.; Furnell, S. M.; Lines, B. M.; Le-Foll, D.; Ifeachor, E. C.

2001-01-01

Discusses the development of real-time applications on the Internet for telecommunications and presents a non-intrusive way of determining network performance parameters for voice packet flows within a voice over IP (Internet Protocol), or Internet telephony call. Considers measurement of quality of service and describes results of a preliminary…

Measurement of cell viability in in vitro cultures.

PubMed

Castro-Concha, Lizbeth A; Escobedo, Rosa María; Miranda-Ham, María de Lourdes

2006-01-01

An overview of the methods for assessing cell viability in in vitro cultures is presented. The protocols of four of the most commonly used assays are described in detail, so the readers may be able to determine which assay is suitable for their own projects using plant cell cultures.

300 area TEDF NPDES Permit Compliance Monitoring Plan

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

Loll, C.M.

1995-09-05

This document presents the 300 Area Treated Effluent Disposal Facility (TEDF) National Pollutant Discharge Elimination System (NPDES) Permit Compliance Monitoring Plan (MP). The MP describes how ongoing monitoring of the TEDF effluent stream for compliance with the NPDES permit will occur. The MP also includes Quality Assurance protocols to be followed.

21 CFR 312.30 - Protocol amendments.

Code of Federal Regulations, 2011 CFR

2011-04-01

.... (b) Changes in a protocol. (1) A sponsor shall submit a protocol amendment describing any change in a Phase 1 protocol that significantly affects the safety of subjects or any change in a Phase 2 or 3... forth the provisions under which new protocols may be submitted and changes in previously submitted...

21 CFR 312.30 - Protocol amendments.

Code of Federal Regulations, 2010 CFR

2010-04-01

.... (b) Changes in a protocol. (1) A sponsor shall submit a protocol amendment describing any change in a Phase 1 protocol that significantly affects the safety of subjects or any change in a Phase 2 or 3... forth the provisions under which new protocols may be submitted and changes in previously submitted...

Administration of medicines by emergency nurse practitioners according to protocols in an accident and emergency department.

PubMed Central

Marshall, J; Edwards, C; Lambert, M

1997-01-01

OBJECTIVE: To present the legal and professional issues related to nurse administration of drugs according to protocols, and describe the implementation and initial audit findings of such a scheme. SETTING: Accident and emergency (A&E) department of a district general hospital. METHODS: Analysis of legal and professional opinion. Protocols acceptable to the medical, nursing, and pharmacy professions were developed across a wide range of drugs appropriate for administration by accident and emergency nurse practitioners (ENPs). The first six months of the scheme were audited. Audit initially addressed general compliance with protocols and later the specific areas of tetanus immunisation and emergency contraception. RESULTS: ENPs assessed 2925 patients in six months (10.9% of all new patients); 455 patients (15.5% of the ENP patients) were given drugs according to protocols. There were no breaches of the protocols. Subsequent audit of tetanus immunisation showed 94-100% compliance with protocol standards and 71-100% compliance for emergency contraception. CONCLUSIONS: There are no legal or professional obstacles to the development of protocols for the administration of drugs to patients by nurses without reference to a doctor, providing the protocols meet all the requirements of the UKCC and have the support of consultant medical staff. Such a system must be subject to regular audit to promote a dynamic approach to protocols and training. The system safely enhanced the quality of care of patients treated by ENPs in A&E. Images Figure 1 PMID:9248912

Multiphoton Intravital Calcium Imaging.

PubMed

Cheetham, Claire E J

2018-06-26

Multiphoton intravital calcium imaging is a powerful technique that enables high-resolution longitudinal monitoring of cellular and subcellular activity hundreds of microns deep in the living organism. This unit addresses the application of 2-photon microscopy to imaging of genetically encoded calcium indicators (GECIs) in the mouse brain. The protocols in this unit enable real-time intravital imaging of intracellular calcium concentration simultaneously in hundreds of neurons, or at the resolution of single synapses, as mice respond to sensory stimuli or perform behavioral tasks. Protocols are presented for implantation of a cranial imaging window to provide optical access to the brain and for 2-photon image acquisition. Protocols for implantation of both open skull and thinned skull windows for single or multi-session imaging are described. © 2018 by John Wiley & Sons, Inc. © 2018 John Wiley & Sons, Inc.

Gene Delivery to the Airway

PubMed Central

Keiser, Nicholas W.; Engelhardt, John F.

2013-01-01

This unit describes generation of and gene transfer to several commonly used airway models. Isolation and transduction of primary airway epithelial cells are first described. Next, the preparation of polarized airway epithelial monolayers is outlined. Transduction of these polarized cells is also described. Methods are presented for generation of tracheal xenografts as well as both ex vivo and in vivo gene transfer to these xenografts. Finally, a method for in vivo gene delivery to the lungs of rodents is included. Methods for evaluating transgene expression are given in the support protocols. PMID:23853081

Preclinical experimental stress studies: protocols, assessment and comparison.

PubMed

Bali, Anjana; Jaggi, Amteshwar Singh

2015-01-05

Stress is a state of threatened homeostasis during which a variety of adaptive processes are activated to produce physiological and behavioral changes. Preclinical models are pivotal for understanding these physiological or pathophysiological changes in the body in response to stress. Furthermore, these models are also important for the development of novel pharmacological agents for stress management. The well described preclinical stress models include immobilization, restraint, electric foot shock and social isolation stress. Stress assessment in animals is done at the behavioral level using open field, social interaction, hole board test; at the biochemical level by measuring plasma corticosterone and ACTH; at the physiological level by measuring food intake, body weight, adrenal gland weight and gastric ulceration. Furthermore the comparison between different stressors including electric foot shock, immobilization and cold stressor is described in terms of intensity, hormonal release, protein changes in brain, adaptation and sleep pattern. This present review describes these preclinical stress protocols, and stress assessment at different levels. Copyright © 2014 Elsevier B.V. All rights reserved.

Chapter 10: Peak Demand and Time-Differentiated Energy Savings Cross-Cutting Protocol. The Uniform Methods Project: Methods for Determining Energy Efficiency Savings for Specific Measures

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

Kurnik, Charles W; Stern, Frank; Spencer, Justin

Savings from electric energy efficiency measures and programs are often expressed in terms of annual energy and presented as kilowatt-hours per year (kWh/year). However, for a full assessment of the value of these savings, it is usually necessary to consider the measure or program's impact on peak demand as well as time-differentiated energy savings. This cross-cutting protocol describes methods for estimating the peak demand and time-differentiated energy impacts of measures implemented through energy efficiency programs.

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.

Advanced tools for the analysis of protein phosphorylation in yeast mitochondria.

PubMed

Walter, Corvin; Gonczarowska-Jorge, Humberto; Sickmann, Albert; Zahedi, René P; Meisinger, Chris; Schmidt, Oliver

2018-05-24

The biochemical analysis of protein phosphorylation in mitochondria lags behind that of cytosolic signaling events. One reason is the poor stability of many phosphorylation sites during common isolation procedures for mitochondria. We present here an optimized, fast protocol for the purification of yeast mitochondria that greatly increases recovery of phosphorylated mitochondrial proteins. Moreover, we describe improved protocols for the biochemical analysis of mitochondrial protein phosphorylation by Zn 2+ -Phos-tag electrophoresis under both denaturing and - for the first time - native conditions, and demonstrate that they outperform previously applied methods. Copyright © 2018. Published by Elsevier Inc.

Ethical dilemmas in genetic testing: examples from the Cuban program for predictive diagnosis of hereditary ataxias.

PubMed

Mariño, Tania Cruz; Armiñán, Rubén Reynaldo; Cedeño, Humberto Jorge; Mesa, José Miguel Laffita; Zaldivar, Yanetza González; Rodríguez, Raúl Aguilera; Santos, Miguel Velázquez; Mederos, Luis Enrique Almaguer; Herrera, Milena Paneque; Pérez, Luis Velázquez

2011-06-01

Predictive testing protocols are intended to help patients affected with hereditary conditions understand their condition and make informed reproductive choices. However, predictive protocols may expose clinicians and patients to ethical dilemmas that interfere with genetic counseling and the decision making process. This paper describes ethical dilemmas in a series of five cases involving predictive testing for hereditary ataxias in Cuba. The examples herein present evidence of the deeply controversial situations faced by both individuals at risk and professionals in charge of these predictive studies, suggesting a need for expanded guidelines to address such complexities.

Systems Imaging of the Immune Synapse.

PubMed

Ambler, Rachel; Ruan, Xiangtao; Murphy, Robert F; Wülfing, Christoph

2017-01-01

Three-dimensional live cell imaging of the interaction of T cells with antigen-presenting cells (APCs) visualizes the subcellular distributions of signaling intermediates during T cell activation at thousands of resolved positions within a cell. These information-rich maps of local protein concentrations are a valuable resource in understanding T cell signaling. Here, we describe a protocol for the efficient acquisition of such imaging data and their computational processing to create four-dimensional maps of local concentrations. This protocol allows quantitative analysis of T cell signaling as it occurs inside live cells with resolution in time and space across thousands of cells.

A Modified Protocol for High-Quality RNA Extraction from Oleoresin-Producing Adult Pines.

PubMed

de Lima, Júlio César; Füller, Thanise Nogueira; de Costa, Fernanda; Rodrigues-Corrêa, Kelly C S; Fett-Neto, Arthur G

2016-01-01

RNA extraction resulting in good yields and quality is a fundamental step for the analyses of transcriptomes through high-throughput sequencing technologies, microarray, and also northern blots, RT-PCR, and RTqPCR. Even though many specific protocols designed for plants with high content of secondary metabolites have been developed, these are often expensive, time consuming, and not suitable for a wide range of tissues. Here we present a modification of the method previously described using the commercially available Concert™ Plant RNA Reagent (Invitrogen) buffer for field-grown adult pine trees with high oleoresin content.

An evaluation plan of bus architectures and protocols using the NASA Ames intelligent redundant actuation system

NASA Technical Reports Server (NTRS)

Defeo, P.; Chen, M.

1987-01-01

Means for evaluating data bus architectures and protocols for highly integrated flight control system applications are needed. Described are the criteria and plans to do this by using the NASA/Ames Intelligent Redundant Actuation System (IRAS) experimental set-up. Candidate bus architectures differ from one another in terms of: topology, access control, message transfer schemes, message characteristics, initialization. data flow control, transmission rates, fault tolerance, and time synchronization. The evaluation criteria are developed relative to these features. A preliminary, analytical evaluation of four candidate busses (MIL-STD-1553B, DATAC, Ethernet, and HSIS) is described. A bus must be exercised in a real-time environment to evaluate its dynamic characteristics. A plan for real-time evaluation of these four busses using a combination of hardware and simulation techniques is presented.

A Protocol for Collecting Human Cardiac Tissue for Research.

PubMed

Blair, Cheavar A; Haynes, Premi; Campbell, Stuart G; Chung, Charles; Mitov, Mihail I; Dennis, Donna; Bonnell, Mark R; Hoopes, Charles W; Guglin, Maya; Campbell, Kenneth S

2016-01-01

This manuscript describes a protocol at the University of Kentucky that allows a translational research team to collect human myocardium that can be used for biological research. We have gained a great deal of practical experience since we started this protocol in 2008, and we hope that other groups might be able to learn from our endeavors. To date, we have procured ~4000 samples from ~230 patients. The tissue that we collect comes from organ donors and from patients who are receiving a heart transplant or a ventricular assist device because they have heart failure. We begin our manuscript by describing the importance of human samples in cardiac research. Subsequently, we describe the process for obtaining consent from patients, the cost of running the protocol, and some of the issues and practical difficulties that we have encountered. We conclude with some suggestions for other researchers who may be considering starting a similar protocol.

A Protocol for Collecting Human Cardiac Tissue for Research

PubMed Central

Blair, Cheavar A.; Haynes, Premi; Campbell, Stuart G.; Chung, Charles; Mitov, Mihail I.; Dennis, Donna; Bonnell, Mark R.; Hoopes, Charles W.; Guglin, Maya; Campbell, Kenneth S.

2016-01-01

This manuscript describes a protocol at the University of Kentucky that allows a translational research team to collect human myocardium that can be used for biological research. We have gained a great deal of practical experience since we started this protocol in 2008, and we hope that other groups might be able to learn from our endeavors. To date, we have procured ~4000 samples from ~230 patients. The tissue that we collect comes from organ donors and from patients who are receiving a heart transplant or a ventricular assist device because they have heart failure. We begin our manuscript by describing the importance of human samples in cardiac research. Subsequently, we describe the process for obtaining consent from patients, the cost of running the protocol, and some of the issues and practical difficulties that we have encountered. We conclude with some suggestions for other researchers who may be considering starting a similar protocol. PMID:28042604

Emulation Platform for Cyber Analysis of Wireless Communication Network Protocols

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

Van Leeuwen, Brian P.; Eldridge, John M.

Wireless networking and mobile communications is increasing around the world and in all sectors of our lives. With increasing use, the density and complexity of the systems increase with more base stations and advanced protocols to enable higher data throughputs. The security of data transported over wireless networks must also evolve with the advances in technologies enabling more capable wireless networks. However, means for analysis of the effectiveness of security approaches and implementations used on wireless networks are lacking. More specifically a capability to analyze the lower-layer protocols (i.e., Link and Physical layers) is a major challenge. An analysis approachmore » that incorporates protocol implementations without the need for RF emissions is necessary. In this research paper several emulation tools and custom extensions that enable an analysis platform to perform cyber security analysis of lower layer wireless networks is presented. A use case of a published exploit in the 802.11 (i.e., WiFi) protocol family is provided to demonstrate the effectiveness of the described emulation platform.« less

THE MASTER PROTOCOL CONCEPT

PubMed Central

Allegra, Carmen J.

2015-01-01

During the past decade, biomedical technologies have undergone an explosive evolution---from the publication of the first complete human genome in 2003, after more than a decade of effort and at a cost of hundreds of millions of dollars---to the present time, where a complete genomic sequence can be available in less than a day and at a small fraction of the cost of the original sequence. The widespread availability of next generation genomic sequencing has opened the door to the development of precision oncology. The need to test multiple new targeted agents both alone and in combination with other targeted therapies, as well as classic cytotoxic agents, demand the development of novel therapeutic platforms (particularly Master Protocols) capable of efficiently and effectively testing multiple targeted agents or targeted therapeutic strategies in relatively small patient subpopulations. Here, we describe the Master Protocol concept, with a focus on the expected gains and complexities of the use of this design. An overview of Master Protocols currently active or in development is provided along with a more extensive discussion of the Lung Master Protocol (Lung-MAP study). PMID:26433553

Examining a New Method to Studying Velopharyngeal Structures in a Child With 22q11.2 Deletion Syndrome.

PubMed

Kollara, Lakshmi; Schenck, Graham; Jaskolka, Michael; Perry, Jamie L

2017-04-14

To date, no studies have imaged the velopharynx in children with 22q11.2 deletion syndrome (22q11.2 DS) without the use of sedation. Dysmorphology in velopharyngeal structures has been shown to have significant negative implications on speech among these individuals. This single case study was designed to assess the feasibility of a child-friendly magnetic resonance imaging (MRI) scanning protocol in this clinically challenging population and to determine the utility of this MRI protocol for future work in this area. One 6-year-old White girl diagnosed with 22q11.2 DS was imaged using a child-friendly, nonsedated MRI protocol. Quantitative and qualitative measures of the velopharyngeal area and associated structures were evaluated, and comparisons were made to age-matched control subjects with normal velopharyngeal anatomy. MRI data were successfully obtained using the child-friendly scanning protocol in the subject in the present study. Quantitative and qualitative differences of the levator muscle and associated velopharyngeal structures were noted. Using these MRI and structural analyses methods, insights related to muscle morphology can be obtained and considered as part of the research and clinical examination of children with 22q11.2 DS. The imaging protocol described in this study presents an effective means to counteract difficulties in imaging young children.

Majority of systematic reviews published in high-impact journals neglected to register the protocols: a meta-epidemiological study.

PubMed

Tsujimoto, Yasushi; Tsujimoto, Hiraku; Kataoka, Yuki; Kimachi, Miho; Shimizu, Sayaka; Ikenoue, Tatsuyoshi; Fukuma, Shingo; Yamamoto, Yosuke; Fukuhara, Shunichi

2017-04-01

To describe the registration of systematic review (SR) protocols and examine whether or not registration reduced the outcome reporting bias in high-impact journals. We searched MEDLINE via PubMed to identify SRs of randomized controlled trials of interventions. We included SRs published between August 2009 and June 2015 in the 10 general and internal medicinal journals with the highest impact factors in 2013. We examined the proportion of SR protocol registration and investigated the relationship between registration and outcome reporting bias using multivariable logistic regression. Among the 284 included reviews, 60 (21%) protocols were registered. The proportion of registration increased from 5.6% in 2009 to 27% in 2015 (P for trend <0.001). Protocol registration was not associated with outcome reporting bias (adjusted odds ratio [OR] 0.85, 95% confidence interval [CI] 0.39-1.86). The association between Preferred Reporting Items for Systematic review and Meta-Analysis (PRISMA) adherence and protocol registration was not statistically significant (OR 1.09, 95% CI 0.59-2.01). Six years after the launch of the PRISMA statement, the proportion of protocol registration in high-impact journals has increased some but remains low. The present study found no evidence suggesting that protocol registration reduced outcome reporting bias. Copyright © 2017 Elsevier Inc. All rights reserved.

Three-particle hyper-entanglement: teleportation and quantum key distribution

NASA Astrophysics Data System (ADS)

Perumangatt, Chithrabhanu; Abdul Rahim, Aadhi; Salla, Gangi Reddy; Prabhakar, Shashi; Samanta, Goutam Kumar; Paul, Goutam; Singh, Ravindra Pratap

2015-10-01

We present a scheme to generate three-particle hyper-entanglement utilizing polarization and orbital angular momentum (OAM) of photons. We show that the generated state can be used to teleport a two-qubit state described by the polarization and the OAM. The proposed quantum system has also been used to describe a new efficient quantum key distribution (QKD) protocol. We give a sketch of the experimental arrangement to realize the proposed teleportation and the QKD.

Quantum Communication with a High-Rate Entangled Photon Source

NASA Technical Reports Server (NTRS)

Wilson, Nathaniel C.; Chaffee, Dalton W.; Lekki, John D.; Wilson, Jeffrey D.

2016-01-01

A high generation rate photon-pair source using a dual element periodically-poled potassium titanyl phosphate (PP KTP) waveguide is described. The photon-pair source features a high pair generation rate, a compact power-efficient package, and continuous wave (CW) or pulsed operation. Characterization and test results are presented. Details and preliminary results of a laboratory free-space QKD experiment with the B92 protocol are also presented.

Efficient Isolation Protocol for B and T Lymphocytes from Human Palatine Tonsils

PubMed Central

Assadian, Farzaneh; Sandström, Karl; Laurell, Göran; Svensson, Catharina; Akusjärvi, Göran; Punga, Tanel

2015-01-01

Tonsils form a part of the immune system providing the first line of defense against inhaled pathogens. Usually the term “tonsils” refers to the palatine tonsils situated at the lateral walls of the oral part of the pharynx. Surgically removed palatine tonsils provide a convenient accessible source of B and T lymphocytes to study the interplay between foreign pathogens and the host immune system. This video protocol describes the dissection and processing of surgically removed human palatine tonsils, followed by the isolation of the individual B and T cell populations from the same tissue sample. We present a method, which efficiently separates tonsillar B and T lymphocytes using an antibody-dependent affinity protocol. Further, we use the method to demonstrate that human adenovirus infects specifically the tonsillar T cell fraction. The established protocol is generally applicable to efficiently and rapidly isolate tonsillar B and T cell populations to study the role of different types of pathogens in tonsillar immune responses. PMID:26650582

Quantification of protein carbonylation.

PubMed

Wehr, Nancy B; Levine, Rodney L

2013-01-01

Protein carbonylation is the most commonly used measure of oxidative modification of proteins. It is most often measured spectrophotometrically or immunochemically by derivatizing proteins with the classical carbonyl reagent 2,4 dinitrophenylhydrazine (DNPH). We present protocols for the derivatization and quantification of protein carbonylation with these two methods, including a newly described dot blot with greatly increased sensitivity.

RORSCHACH'S TEST. VOLUME II, A VARIETY OF PERSONALITY PICTURES.

ERIC Educational Resources Information Center

BECK, SAMUEL J.; MOLISH, HERMAN B.

REVISED AND REWRITTEN FROM THE 1945 EDITION, THE TEXT DESCRIBES AND ANALYZES THE RORSCHACH TEST. PART 1 OF THE VOLUME WAS WRITTEN BY SAMUEL J. BECK AND PRESENTS A VARIETY OF PERSONALITY PICTURES DRAWN FROM RORSCHACH PROTOCOLS AND THEIR INTERPRETATION. EXCERPTS FROM 29 CASE STUDIES ARE INCLUDED ON FIVE DIMENSIONS--THE INTELLIGENCE CURVE, YOUNG…

Constructing the Components of a Lab Report Using Peer Review

ERIC Educational Resources Information Center

Berry, David E.; Fawkes, Kelli L.

2010-01-01

A protocol that emphasizes lab report writing using a piecemeal approach coupled with peer review is described. As the lab course progresses, the focus of the report writing changes sequentially through the abstract and introduction, the discussion, and the procedure. Two styles of lab programs are presented. One style rotates the students through…

Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes

PubMed Central

Robert, Catherine; Pascalis, Hervé; Michelle, Caroline; Jardot, Priscilla; Charrel, Rémi; Raoult, Didier; Desnues, Christelle

2015-01-01

Background Metagenomic analyses have been widely used in the last decade to describe viral communities in various environments or to identify the etiology of human, animal, and plant pathologies. Here, we present a simple and standardized protocol that allows for the purification and sequencing of RNA viromes from complex biological samples with an important reduction of host DNA and RNA contaminants, while preserving the infectivity of viral particles. Principal Findings We evaluated different viral purification steps, random reverse transcriptions and sequence-independent amplifications of a pool of representative RNA viruses. Viruses remained infectious after the purification process. We then validated the protocol by sequencing the RNA virome of human body lice engorged in vitro with artificially contaminated human blood. The full genomes of the most abundant viruses absorbed by the lice during the blood meal were successfully sequenced. Interestingly, random amplifications differed in the genome coverage of segmented RNA viruses. Moreover, the majority of reads were taxonomically identified, and only 7–15% of all reads were classified as “unknown”, depending on the random amplification method. Conclusion The protocol reported here could easily be applied to generate RNA viral metagenomes from complex biological samples of different origins. Our protocol allows further virological characterizations of the described viral communities because it preserves the infectivity of viral particles and allows for the isolation of viruses. PMID:26431175

Radiation safety protocol using real-time dose reporting reduces patient exposure in pediatric electrophysiology procedures.

PubMed

Patel, Akash R; Ganley, Jamie; Zhu, Xiaowei; Rome, Jonathan J; Shah, Maully; Glatz, Andrew C

2014-10-01

Radiation exposure during pediatric catheterization is significant. We sought to describe radiation exposure and the effectiveness of radiation safety protocols in reducing exposure during catheter ablations with electrophysiology studies in children and patients with congenital heart disease. We additionally sought to identify at-risk patients. We retrospectively reviewed all interventional electrophysiology procedures performed from April 2009 to September 2011 (6 months preceding intervention, 12 months following implementation of initial radiation safety protocol, and 8 months following implementation of modified protocol). The protocols consisted of low pulse rate fluoroscopy settings, operator notification of skin entrance dose every 1,000 mGy, adjusting cameras by >5 at every 1,000 mGy, and appropriate collimation. The cohort consisted of 291 patients (70 pre-intervention, 137 after initial protocol implementation, 84 after modified protocol implementation) at a median age of 14.9 years with congenital heart disease present in 11 %. Diagnoses included atrioventricular nodal reentrant tachycardia (25 %), atrioventricular reentrant tachycardia (61 %), atrial tachycardias (12 %), and ventricular tachycardia (2 %). There were no differences between groups based on patient, arrhythmia, and procedural characteristics. Following implementation of the protocols, there were significant reductions in all measures of radiation exposure: fluoroscopy time (17.8 %), dose area product (80.2 %), skin entry dose (81.0 %), and effective dose (76.9 %), p = 0.0001. Independent predictors of increased radiation exposure included larger patient weight, longer fluoroscopy time, and lack of radiation safety protocol. Implementation of a radiation safety protocol for pediatric and congenital catheter ablations can drastically reduce radiation exposure to patients without affecting procedural success.

WE-G-19A-01: Radiologists and Medical Physicists: Working Together to Achieve Common Goals

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

Jones, A; Ma, J; Steele, J

It is vitally important that medical physicists understand the clinical questions that radiologists are trying to answer with patient images. Knowledge of the types of information the radiologist needs helps medical physicists configure imaging protocols that appropriately balance radiation dose, time, and image quality. The ability to communicate with radiologists and understand medical terminology, anatomy, and physiology is key to creating such imaging protocols. In this session, radiologists will present clinical cases and describe the information they are seeking in the clinical images. Medical physicists will then discuss how imaging protocols are configured. Learning Objectives: Understand the types of informationmore » that radiologists seek in medical images. Apply this understanding in configuring the imaging equipment to deliver this information. Develop strategies for working with physician colleagues.« less

Electrical stimulation systems for cardiac tissue engineering

PubMed Central

Tandon, Nina; Cannizzaro, Christopher; Chao, Pen-Hsiu Grace; Maidhof, Robert; Marsano, Anna; Au, Hoi Ting Heidi; Radisic, Milica; Vunjak-Novakovic, Gordana

2009-01-01

We describe a protocol for tissue engineering of synchronously contractile cardiac constructs by culturing cardiac cells with the application of pulsatile electrical fields designed to mimic those present in the native heart. Tissue culture is conducted in a customized chamber built to allow for cultivation of (i) engineered three-dimensional (3D) cardiac tissue constructs, (ii) cell monolayers on flat substrates or (iii) cells on patterned substrates. This also allows for analysis of the individual and interactive effects of pulsatile electrical field stimulation and substrate topography on cell differentiation and assembly. The protocol is designed to allow for delivery of predictable electrical field stimuli to cells, monitoring environmental parameters, and assessment of cell and tissue responses. The duration of the protocol is 5 d for two-dimensional cultures and 10 d for 3D cultures. PMID:19180087

Quantum State Transfer via Noisy Photonic and Phononic Waveguides

NASA Astrophysics Data System (ADS)

Vermersch, B.; Guimond, P.-O.; Pichler, H.; Zoller, P.

2017-03-01

We describe a quantum state transfer protocol, where a quantum state of photons stored in a first cavity can be faithfully transferred to a second distant cavity via an infinite 1D waveguide, while being immune to arbitrary noise (e.g., thermal noise) injected into the waveguide. We extend the model and protocol to a cavity QED setup, where atomic ensembles, or single atoms representing quantum memory, are coupled to a cavity mode. We present a detailed study of sensitivity to imperfections, and apply a quantum error correction protocol to account for random losses (or additions) of photons in the waveguide. Our numerical analysis is enabled by matrix product state techniques to simulate the complete quantum circuit, which we generalize to include thermal input fields. Our discussion applies both to photonic and phononic quantum networks.

Network acceleration techniques

NASA Technical Reports Server (NTRS)

Crowley, Patricia (Inventor); Maccabe, Arthur Barney (Inventor); Awrach, James Michael (Inventor)

2012-01-01

Splintered offloading techniques with receive batch processing are described for network acceleration. Such techniques offload specific functionality to a NIC while maintaining the bulk of the protocol processing in the host operating system ("OS"). The resulting protocol implementation allows the application to bypass the protocol processing of the received data. Such can be accomplished this by moving data from the NIC directly to the application through direct memory access ("DMA") and batch processing the receive headers in the host OS when the host OS is interrupted to perform other work. Batch processing receive headers allows the data path to be separated from the control path. Unlike operating system bypass, however, the operating system still fully manages the network resource and has relevant feedback about traffic and flows. Embodiments of the present disclosure can therefore address the challenges of networks with extreme bandwidth delay products (BWDP).

Analysis of In Vivo Chromatin and Protein Interactions of Arabidopsis Transcript Elongation Factors.

PubMed

Pfab, Alexander; Antosz, Wojciech; Holzinger, Philipp; Bruckmann, Astrid; Griesenbeck, Joachim; Grasser, Klaus D

2017-01-01

A central step to elucidate the function of proteins commonly comprises the analysis of their molecular interactions in vivo. For nuclear regulatory proteins this involves determining protein-protein interactions as well as mapping of chromatin binding sites. Here, we present two protocols to identify protein-protein and chromatin interactions of transcript elongation factors (TEFs) in Arabidopsis. The first protocol (Subheading 3.1) describes protein affinity-purification coupled to mass spectrometry (AP-MS) that utilizes suspension cultured cells as experimental system. This approach provides an unbiased view of proteins interacting with epitope-tagged TEFs. The second protocol (Subheading 3.2) depicts details about a chromatin immunoprecipitation (ChIP) procedure to characterize genomic binding sites of TEFs. These methods should be valuable tools for the analysis of a broad variety of nuclear proteins.

Simultaneous brightness contrast of foraging Papilio butterflies

PubMed Central

Kinoshita, Michiyo; Takahashi, Yuki; Arikawa, Kentaro

2012-01-01

This study focuses on the sense of brightness in the foraging Japanese yellow swallowtail butterfly, Papilio xuthus. We presented two red discs of different intensity on a grey background to butterflies, and trained them to select one of the discs. They were successfully trained to select either a high intensity or a low intensity disc. The trained butterflies were tested on their ability to perceive brightness in two different protocols: (i) two orange discs of different intensity presented on the same intensity grey background and (ii) two orange discs of the same intensity separately presented on a grey background that was either higher or lower in intensity than the training background. The butterflies trained to high intensity red selected the orange disc of high intensity in protocol 1, and the disc on the background of low intensity grey in protocol 2. We obtained similar results in another set of experiments with purple discs instead of orange discs. The choices of the butterflies trained to low intensity red were opposite to those just described. Taken together, we conclude that Papilio has the ability to learn brightness and darkness of targets independent of colour, and that they have the so-called simultaneous brightness contrast. PMID:22179808

High-throughput process development: I. Process chromatography.

PubMed

Rathore, Anurag S; Bhambure, Rahul

2014-01-01

Chromatographic separation serves as "a workhorse" for downstream process development and plays a key role in removal of product-related, host cell-related, and process-related impurities. Complex and poorly characterized raw materials and feed material, low feed concentration, product instability, and poor mechanistic understanding of the processes are some of the critical challenges that are faced during development of a chromatographic step. Traditional process development is performed as trial-and-error-based evaluation and often leads to a suboptimal process. High-throughput process development (HTPD) platform involves an integration of miniaturization, automation, and parallelization and provides a systematic approach for time- and resource-efficient chromatography process development. Creation of such platforms requires integration of mechanistic knowledge of the process with various statistical tools for data analysis. The relevance of such a platform is high in view of the constraints with respect to time and resources that the biopharma industry faces today. This protocol describes the steps involved in performing HTPD of process chromatography step. It described operation of a commercially available device (PreDictor™ plates from GE Healthcare). This device is available in 96-well format with 2 or 6 μL well size. We also discuss the challenges that one faces when performing such experiments as well as possible solutions to alleviate them. Besides describing the operation of the device, the protocol also presents an approach for statistical analysis of the data that is gathered from such a platform. A case study involving use of the protocol for examining ion-exchange chromatography of granulocyte colony-stimulating factor (GCSF), a therapeutic product, is briefly discussed. This is intended to demonstrate the usefulness of this protocol in generating data that is representative of the data obtained at the traditional lab scale. The agreement in the data is indeed very significant (regression coefficient 0.93). We think that this protocol will be of significant value to those involved in performing high-throughput process development of process chromatography.

An Action-Based Fine-Grained Access Control Mechanism for Structured Documents and Its Application

PubMed Central

Su, Mang; Li, Fenghua; Tang, Zhi; Yu, Yinyan; Zhou, Bo

2014-01-01

This paper presents an action-based fine-grained access control mechanism for structured documents. Firstly, we define a describing model for structured documents and analyze the application scenarios. The describing model could support the permission management on chapters, pages, sections, words, and pictures of structured documents. Secondly, based on the action-based access control (ABAC) model, we propose a fine-grained control protocol for structured documents by introducing temporal state and environmental state. The protocol covering different stages from document creation, to permission specification and usage control are given by using the Z-notation. Finally, we give the implementation of our mechanism and make the comparisons between the existing methods and our mechanism. The result shows that our mechanism could provide the better solution of fine-grained access control for structured documents in complicated networks. Moreover, it is more flexible and practical. PMID:25136651

An action-based fine-grained access control mechanism for structured documents and its application.

PubMed

Su, Mang; Li, Fenghua; Tang, Zhi; Yu, Yinyan; Zhou, Bo

2014-01-01

This paper presents an action-based fine-grained access control mechanism for structured documents. Firstly, we define a describing model for structured documents and analyze the application scenarios. The describing model could support the permission management on chapters, pages, sections, words, and pictures of structured documents. Secondly, based on the action-based access control (ABAC) model, we propose a fine-grained control protocol for structured documents by introducing temporal state and environmental state. The protocol covering different stages from document creation, to permission specification and usage control are given by using the Z-notation. Finally, we give the implementation of our mechanism and make the comparisons between the existing methods and our mechanism. The result shows that our mechanism could provide the better solution of fine-grained access control for structured documents in complicated networks. Moreover, it is more flexible and practical.

Creating fractional quantum Hall states with atomic clusters using light-assisted insertion of angular momentum

NASA Astrophysics Data System (ADS)

Zhang, Junyi; Beugnon, Jerome; Nascimbene, Sylvain

We describe a protocol to prepare clusters of ultracold bosonic atoms in strongly interacting states reminiscent of fractional quantum Hall states. Our scheme consists in injecting a controlled amount of angular momentum to an atomic gas using Raman transitions carrying orbital angular momentum. By injecting one unit of angular momentum per atom, one realizes a single-vortex state, which is well described by mean-field theory for large enough particle numbers. We also present schemes to realize fractional quantum Hall states, namely, the bosonic Laughlin and Moore-Read states. We investigate the requirements for adiabatic nucleation of such topological states, in particular comparing linear Landau-Zener ramps and arbitrary ramps obtained from optimized control methods. We also show that this protocol requires excellent control over the isotropic character of the trapping potential. ERC-Synergy Grant UQUAM, ANR-10-IDEX-0001-02, DIM NanoK Atocirc project.

The reliable multicast protocol application programming interface

NASA Technical Reports Server (NTRS)

Montgomery , Todd; Whetten, Brian

1995-01-01

The Application Programming Interface for the Berkeley/WVU implementation of the Reliable Multicast Protocol is described. This transport layer protocol is implemented as a user library that applications and software buses link against.

In vivo imaging and analysis of cerebrovascular hemodynamic responses and tissue oxygenation in the mouse brain.

PubMed

Kisler, Kassandra; Lazic, Divna; Sweeney, Melanie D; Plunkett, Shane; El Khatib, Mirna; Vinogradov, Sergei A; Boas, David A; Sakadži, Sava; Zlokovic, Berislav V

2018-06-01

Cerebrovascular dysfunction has an important role in the pathogenesis of multiple brain disorders. Measurement of hemodynamic responses in vivo can be challenging, particularly as techniques are often not described in sufficient detail and vary between laboratories. We present a set of standardized in vivo protocols that describe high-resolution two-photon microscopy and intrinsic optical signal (IOS) imaging to evaluate capillary and arteriolar responses to a stimulus, regional hemodynamic responses, and oxygen delivery to the brain. The protocol also describes how to measure intrinsic NADH fluorescence to understand how blood O 2 supply meets the metabolic demands of activated brain tissue, and to perform resting-state absolute oxygen partial pressure (pO 2 ) measurements of brain tissue. These methods can detect cerebrovascular changes at far higher resolution than MRI techniques, although the optical nature of these techniques limits their achievable imaging depths. Each individual procedure requires 1-2 h to complete, with two to three procedures typically performed per animal at a time. These protocols are broadly applicable in studies of cerebrovascular function in healthy and diseased brain in any of the existing mouse models of neurological and vascular disorders. All these procedures can be accomplished by a competent graduate student or experienced technician, except the two-photon measurement of absolute pO 2 level, which is better suited to a more experienced, postdoctoral-level researcher.

A Simple XML Producer-Consumer Protocol

NASA Technical Reports Server (NTRS)

Smith, Warren; Gunter, Dan; Quesnel, Darcy; Biegel, Bryan (Technical Monitor)

2001-01-01

There are many different projects from government, academia, and industry that provide services for delivering events in distributed environments. The problem with these event services is that they are not general enough to support all uses and they speak different protocols so that they cannot interoperate. We require such interoperability when we, for example, wish to analyze the performance of an application in a distributed environment. Such an analysis might require performance information from the application, computer systems, networks, and scientific instruments. In this work we propose and evaluate a standard XML-based protocol for the transmission of events in distributed systems. One recent trend in government and academic research is the development and deployment of computational grids. Computational grids are large-scale distributed systems that typically consist of high-performance compute, storage, and networking resources. Examples of such computational grids are the DOE Science Grid, the NASA Information Power Grid (IPG), and the NSF Partnerships for Advanced Computing Infrastructure (PACIs). The major effort to deploy these grids is in the area of developing the software services to allow users to execute applications on these large and diverse sets of resources. These services include security, execution of remote applications, managing remote data, access to information about resources and services, and so on. There are several toolkits for providing these services such as Globus, Legion, and Condor. As part of these efforts to develop computational grids, the Global Grid Forum is working to standardize the protocols and APIs used by various grid services. This standardization will allow interoperability between the client and server software of the toolkits that are providing the grid services. The goal of the Performance Working Group of the Grid Forum is to standardize protocols and representations related to the storage and distribution of performance data. These standard protocols and representations must support tasks such as profiling parallel applications, monitoring the status of computers and networks, and monitoring the performance of services provided by a computational grid. This paper describes a proposed protocol and data representation for the exchange of events in a distributed system. The protocol exchanges messages formatted in XML and it can be layered atop any low-level communication protocol such as TCP or UDP Further, we describe Java and C++ implementations of this protocol and discuss their performance. The next section will provide some further background information. Section 3 describes the main communication patterns of our protocol. Section 4 describes how we represent events and related information using XML. Section 5 describes our protocol and Section 6 discusses the performance of two implementations of the protocol. Finally, an appendix provides the XML Schema definition of our protocol and event information.

Use of luciferase probes to measure ATP in living cells and animals.

PubMed

Morciano, Giampaolo; Sarti, Alba Clara; Marchi, Saverio; Missiroli, Sonia; Falzoni, Simonetta; Raffaghello, Lizzia; Pistoia, Vito; Giorgi, Carlotta; Di Virgilio, Francesco; Pinton, Paolo

2017-08-01

ATP, the energy exchange factor that connects anabolism and catabolism, is required for major reactions and processes that occur in living cells, such as muscle contraction, phosphorylation and active transport. ATP is also the key molecule in extracellular purinergic signaling mechanisms, with an established crucial role in inflammation and several additional disease conditions. Here, we describe detailed protocols to measure the ATP concentration in isolated living cells and animals using luminescence techniques based on targeted luciferase probes. In the presence of magnesium, oxygen and ATP, the protein luciferase catalyzes oxidation of the substrate luciferin, which is associated with light emission. Recombinantly expressed wild-type luciferase is exclusively cytosolic; however, adding specific targeting sequences can modify its cellular localization. Using this strategy, we have constructed luciferase chimeras targeted to the mitochondrial matrix and the outer surface of the plasma membrane. Here, we describe optimized protocols for monitoring ATP concentrations in the cytosol, mitochondrial matrix and pericellular space in living cells via an overall procedure that requires an average of 3 d. In addition, we present a detailed protocol for the in vivo detection of extracellular ATP in mice using luciferase-transfected reporter cells. This latter procedure may require up to 25 d to complete.

Micropatterning hydroxy-PAAm hydrogels and Sylgard 184 silicone elastomers with tunable elastic moduli.

PubMed

Versaevel, Marie; Grevesse, Thomas; Riaz, Maryam; Lantoine, Joséphine; Gabriele, Sylvain

2014-01-01

This protocol describes a simple method to deposit protein micropatterns over a wide range of culture substrate stiffness (three orders of magnitude) by using two complementary polymeric substrates. In the first part, we introduce a novel polyacrylamide hydrogel, called hydroxy-polyacrylamide (PAAm), that permits to surmount the intrinsically nonadhesive properties of polyacrylamide with minimal requirements in cost or expertize. We present a protocol for tuning easily the rigidity of "soft" hydroxy-PAAm hydrogels between ~0.5 and 50 kPa and a micropatterning method to locally deposit protein micropatterns on these hydrogels. In a second part, we describe a protocol for tuning the rigidity of "stiff" silicone elastomers between ~100 and 1000 kPa and printing efficiently proteins from the extracellular matrix. Finally, we investigate the effect of the matrix rigidity on the nucleus of primary endothelial cells by tuning the rigidity of both polymeric substrates. We envision that the complementarity of these two polymeric substrates, combined with an efficient microprinting technique, can be further developed in the future as a powerful mechanobiology platform to investigate in vitro the effect of mechanotransduction cues on cellular functions, gene expression, and stem cell differentiation. Copyright © 2014 Elsevier Inc. All rights reserved.

An Identity Based Key Exchange Protocol in Cloud Computing

NASA Astrophysics Data System (ADS)

Molli, Venkateswara Rao; Tiwary, Omkar Nath

2012-10-01

Workflow systems often use delegation to enhance the flexibility of authorization; delegation transfers privileges among users across different administrative domains and facilitates information sharing. We present an independently verifiable delegation mechanism, where a delegation credential can be verified without the participation of domain administrators. This protocol, called role-based cascaded delegation (RBCD), supports simple and efficient cross-domain delegation of authority. RBCD enables a role member to create delegations based on the dynamic needs of collaboration; in the meantime, a delegation chain canbe verified by anyone without the participation of role administrators. We also propose the Measurable Risk Adaptive decentralized Role-based Delegation framework to address this problem. Describe an efficient realization of RBCD by using aggregate signatures, where the authentication information for an arbitrarily long role-based delegation chain is captured by one short signature of constant size. RBCD enables a role member to create delegations based on the need of collaboration; in the meantime anyone can verify a delegation chain without the participation of role administrators. The protocol is general and can be realized by any signature scheme. We have described a specific realization with a hierarchical certificate-based encryption scheme that gives delegation compact credentials.

PEP: patient-supported esthetic protocol.

PubMed

Gebhard-Achilles, Walter

2013-01-01

Nowadays, materials and process engineering, especially digital-based techniques, are becoming more and more important for esthetic dentistry. Digital communication is also increasing, which is accompanied by a change from a personal contact to a more technocratic and less emotional and empathic communication. Sometimes our personal experiences and perceptions, based on dental, empirical knowledge, collide with this development. It also happens very often, that the patients - with their perceptions, concerns and not least their esthetic preferences - feel neglected by the treatment team. Patient's wishes often cannot be described adequately. The patient-supported esthetic protocol (PEP) described in this article is a simple tool with which the patients are involved in the esthetic concerns of their treatment. The patient feels to be more perceived, respected, and their wishes implemented, without affecting the medical therapy. At the same time, PEP is used for communication within the health care team, such as the dentist and the dental technician. Because of the clear record it is easy to recognize the changes the patient desires, and the suggestions a teammate developed with the patient, without having been present at the session. Furthermore, the protocol can be attached to the patient's medical history and, therefore, could be a tool for quality management.

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

Aurich, Maike K.; Fleming, Ronan M. T.; Thiele, Ines

Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Previous work, by us and others, revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. With the MetaboTools, we make our methods available to the broader scientific community. The MetaboTools consist of a protocol, a toolbox, and tutorials of two use cases. The protocol describes, in a step-wise manner, the workflow of data integration, and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorialsmore » explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, the MetaboTools constitute a comprehensive guide to the intra-model analysis of extracellular metabolomic data from microbial, plant, or human cells. In conclusion, this computational modeling resource offers a broad set of computational analysis tools for a wide biomedical and non-biomedical research community.« less

Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols.

PubMed

Li, Minghui; Goncearenco, Alexander; Panchenko, Anna R

2017-01-01

In this review we describe a protocol to annotate the effects of missense mutations on proteins, their functions, stability, and binding. For this purpose we present a collection of the most comprehensive databases which store different types of sequencing data on missense mutations, we discuss their relationships, possible intersections, and unique features. Next, we suggest an annotation workflow using the state-of-the art methods and highlight their usability, advantages, and limitations for different cases. Finally, we address a particularly difficult problem of deciphering the molecular mechanisms of mutations on proteins and protein complexes to understand the origins and mechanisms of diseases.

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

Lima Bernardo, Bertúlio de, E-mail: bertulio.fisica@gmail.com

We describe a novel quantum information protocol, which probabilistically entangles two distant photons that have never interacted. Different from the entanglement swapping protocol, which requires two pairs of maximally entangled photons as the input states, as well as a Bell-state measurement (BSM), the present scheme only requires three photons: two to be entangled and another to mediate the correlation, and no BSM, in a process that we call “entanglement mediation”. Furthermore, in analyzing the paths of the photons in our arrangement, we conclude that one of them, the mediator, exchanges information with the two others simultaneously, which seems to bemore » a new quantum-mechanical feature.« less

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 computer-aided movement analysis system.

PubMed

Fioretti, S; Leo, T; Pisani, E; Corradini, M L

1990-08-01

Interaction with biomechanical data concerning human movement analysis implies the adoption of various experimental equipments and the choice of suitable models, data processing, and graphical data restitution techniques. The integration of measurement setups with the associated experimental protocols and the relative software procedures constitutes a computer-aided movement analysis (CAMA) system. In the present paper such integration is mapped onto the causes that limit the clinical acceptance of movement analysis methods. The structure of the system is presented. A specific CAMA system devoted to posture analysis is described in order to show the attainable features. Scientific results obtained with the support of the described system are also reported.

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.

Preparation of Hydrophobic Metal-Organic Frameworks via Plasma Enhanced Chemical Vapor Deposition of Perfluoroalkanes for the Removal of Ammonia

PubMed Central

DeCoste, Jared B.; Peterson, Gregory W.

2013-01-01

Plasma enhanced chemical vapor deposition (PECVD) of perfluoroalkanes has long been studied for tuning the wetting properties of surfaces. For high surface area microporous materials, such as metal-organic frameworks (MOFs), unique challenges present themselves for PECVD treatments. Herein the protocol for development of a MOF that was previously unstable to humid conditions is presented. The protocol describes the synthesis of Cu-BTC (also known as HKUST-1), the treatment of Cu-BTC with PECVD of perfluoroalkanes, the aging of materials under humid conditions, and the subsequent ammonia microbreakthrough experiments on milligram quantities of microporous materials. Cu-BTC has an extremely high surface area (~1,800 m2/g) when compared to most materials or surfaces that have been previously treated by PECVD methods. Parameters such as chamber pressure and treatment time are extremely important to ensure the perfluoroalkane plasma penetrates to and reacts with the inner MOF surfaces. Furthermore, the protocol for ammonia microbreakthrough experiments set forth here can be utilized for a variety of test gases and microporous materials. PMID:24145623

Control of size and aspect ratio in hydroquinone-based synthesis of gold nanorods

NASA Astrophysics Data System (ADS)

Morasso, Carlo; Picciolini, Silvia; Schiumarini, Domitilla; Mehn, Dora; Ojea-Jiménez, Isaac; Zanchetta, Giuliano; Vanna, Renzo; Bedoni, Marzia; Prosperi, Davide; Gramatica, Furio

2015-08-01

In this article, we describe how it is possible to tune the size and the aspect ratio of gold nanorods obtained using a highly efficient protocol based on the use of hydroquinone as a reducing agent by varying the amounts of CTAB and silver ions present in the "seed-growth" solution. Our approach not only allows us to prepare nanorods with a four times increased Au3+ reduction yield, when compared with the commonly used protocol based on ascorbic acid, but also allows a remarkable reduction of 50-60 % of the amount of CTAB needed. In fact, according to our findings, the concentration of CTAB present in the seed-growth solution do not linearly influence the final aspect ratio of the obtained nanorods, and an optimal concentration range between 30 and 50 mM has been identified as the one that is able to generate particles with more elongated shapes. On the optimized protocol, the effect of the concentration of Ag+ ions in the seed-growth solution and the stability of the obtained particles has also been investigated.

Intravenous Ketamine Infusions for Neuropathic Pain Management: A Promising Therapy in Need of Optimization.

PubMed

Maher, Dermot P; Chen, Lucy; Mao, Jianren

2017-02-01

Intravenous ketamine infusions have been used extensively to treat often-intractable neuropathic pain conditions. Because there are many widely divergent ketamine infusion protocols described in the literature, the variation in these protocols presents a challenge for direct comparison of one protocol with another and in discerning an optimal protocol. Careful examination of the published literature suggests that ketamine infusions can be useful to treat neuropathic pain and that certain characteristics of ketamine infusions may be associated with better clinical outcomes. Increased duration of relief from neuropathic pain is associated with (1) higher total infused doses of ketamine; (2) prolonged infusion durations, although the rate of infusion does not appear to be a factor; and (3) coadministration of adjunct medications such as midazolam and/or clonidine that mitigate some of the unpleasant psychomimetic side effects. However, there are few studies designed to optimize ketamine infusion protocols by defining what an effective infusion protocol entails with regard to a respective neuropathic pain condition. Therefore, despite common clinical practice, the current state of the literature leaves the use of ketamine infusions without meaningful guidance from high-quality comparative evidence. The objectives of this topical review are to (1) analyze the available clinical evidence related to ketamine infusion protocols and (2) call for clinical studies to identify optimal ketamine infusion protocols tailored for individual neuropathic pain conditions. The Oxford Center for Evidence-Based Medicine classification for levels of evidence was used to stratify the grades of clinical recommendation for each infusion variable studied.

Diagnosing a Failed Proof in Fault-Tolerance: A Disproving Challenge Problem

NASA Technical Reports Server (NTRS)

Pike, Lee; Miner, Paul; Torres-Pomales, Wilfredo

2006-01-01

This paper proposes a challenge problem in disproving. We describe a fault-tolerant distributed protocol designed at NASA for use in a fly-by-wire system for next-generation commercial aircraft. An early design of the protocol contains a subtle bug that is highly unlikely to be caught in fault injection testing. We describe a failed proof of the protocol's correctness in a mechanical theorem prover (PVS) with a complex unfinished proof conjecture. We use a model checking suite (SAL) to generate a concrete counterexample to the unproven conjecture to demonstrate the existence of a bug. However, we argue that the effort required in our approach is too high and propose what conditions a better solution would satisfy. We carefully describe the protocol and bug to provide a challenging but feasible case study for disproving research.

Caesarean of Lion (Panthera leo) at Dulahajra Safari Park, Bangladesh

PubMed Central

Khan, S.A.; Hassan, M.M.; Uddin, M.B.; Rahman, Z.M.M.; Yasin, G.; Epstein, J.H.

2011-01-01

A six years eight months pregnant lioness at the Dulahajara Safari Park, Chakoria, Cox’s Bazar, Bangladesh, was presented with dystocia. This paper described the pre-, intra- and postoperative procedures including anesthetic protocol carried out and performing a caesarean section to remove dead fetuses and the successful recovery of the lioness without complications. PMID:26623273

Iridium-catalysed ortho-H/D and -H/T exchange under basic conditions: C-H activation of unprotected tetrazoles.

PubMed

Kerr, William J; Lindsay, David M; Reid, Marc; Atzrodt, Jens; Derdau, Volker; Rojahn, Patrick; Weck, Remo

2016-05-10

The first examples of selective ortho-directed C-H activation with unprotected 2-aryltetrazoles are described. A new base-assisted protocol for iridium(i) hydrogen isotope exchange catalysis allows access to ortho-deuterated and tritiated tetrazoles, including the tetrazole-containing pharmaceutical, Valsartan. Preliminary mechanistic studies are also presented.

Virtual Reality Exposure in the Treatment of Panic Disorder with Agoraphobia: A Case Study

ERIC Educational Resources Information Center

Martin, Helena Villa; Botella, Cristina; Garcia-Palacios, Azucena; Osma, Jorge

2007-01-01

In this work we present a case example of the use of virtual reality exposure for the treatment of panic disorder with agoraphobia. The assessment protocol and procedure (including a baseline period) and the cognitive-behavioral treatment program are described. The clinical measures were categorized into target behaviors, panic and agoraphobia…

The Interlibrary Loan Protocol: An OSI Solution to ILL Messaging.

ERIC Educational Resources Information Center

Turner, Fay

1990-01-01

Discusses the interlibrary loan (ILL) protocol, a standard based on the principles of the Open Systems Interconnection (OSI) Reference Model. Benefits derived from protocol use are described, the status of the protocol as an international standard is reviewed, and steps taken by the National Library of Canada to facilitate migration to an ILL…

Point-to-Point Multicast Communications Protocol

NASA Technical Reports Server (NTRS)

Byrd, Gregory T.; Nakano, Russell; Delagi, Bruce A.

1987-01-01

This paper describes a protocol to support point-to-point interprocessor communications with multicast. Dynamic, cut-through routing with local flow control is used to provide a high-throughput, low-latency communications path between processors. In addition multicast transmissions are available, in which copies of a packet are sent to multiple destinations using common resources as much as possible. Special packet terminators and selective buffering are introduced to avoid a deadlock during multicasts. A simulated implementation of the protocol is also described.

A Deconstructive Pedagogy

ERIC Educational Resources Information Center

Uba, Laura

2008-01-01

This article describes a four-pronged pedagogical protocol for teaching undergraduates how to deconstruct statements, including a list of deconstructive considerations students learn to apply. The protocol also encourages oral participation in class discussions. Three assessment measures demonstrate the protocol's effectiveness: (1) a qualitative…

Gigabit Ethernet: A Technical Assessment.

ERIC Educational Resources Information Center

Axner, David

1997-01-01

Describes gigabit ethernet for LAN (local area network) technology that will expand ethernet bandwidth. Technical details are discussed, including protocol stacks, optical fiber, deployment strategy for performance improvement, ATM (Asynchronous Transfer Mode), real-time protocol, reserve reservation protocol, and standards. (LRW)

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

Bauer, Gerry; et al.

The DAQ system of the CMS experiment at CERN collects data from more than 600 custom detector Front-End Drivers (FEDs). During 2013 and 2014 the CMS DAQ system will undergo a major upgrade to address the obsolescence of current hardware and the requirements posed by the upgrade of the LHC accelerator and various detector components. For a loss-less data collection from the FEDs a new FPGA based card implementing the TCP/IP protocol suite over 10Gbps Ethernet has been developed. To limit the TCP hardware implementation complexity the DAQ group developed a simplified and unidirectional but RFC 793 compliant version ofmore » the TCP protocol. This allows to use a PC with the standard Linux TCP/IP stack as a receiver. We present the challenges and protocol modifications made to TCP in order to simplify its FPGA implementation. We also describe the interaction between the simplified TCP and Linux TCP/IP stack including the performance measurements.« less

Instituting a music listening intervention for critically ill patients receiving mechanical ventilation: Exemplars from two patient cases

PubMed Central

Heiderscheit, Annie; Chlan, Linda; Donley, Kim

2011-01-01

Music is an ideal intervention to reduce anxiety and promote relaxation in critically ill patients receiving mechanical ventilatory support. This article reviews the basis for a music listening intervention and describes two case examples with patients utilizing a music listening intervention to illustrate the implementation and use of the music listening protocol in this dynamic environment. The case examples illustrate the importance and necessity of engaging a music therapist in not only assessing the music preferences of patients, but also for implementing a music listening protocol to manage the varied and challenging needs of patients in the critical care setting. Additionally, the case examples presented in this paper demonstrate the wide array of music patients prefer and how the ease of a music listening protocol allows mechanically ventilated patients to engage in managing their own anxiety during this distressful experience. PMID:22081788

Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services: an example with ChIP-chip data.

PubMed

Sand, Olivier; Thomas-Chollier, Morgane; Vervisch, Eric; van Helden, Jacques

2008-01-01

This protocol shows how to access the Regulatory Sequence Analysis Tools (RSAT) via a programmatic interface in order to automate the analysis of multiple data sets. We describe the steps for writing a Perl client that connects to the RSAT Web services and implements a workflow to discover putative cis-acting elements in promoters of gene clusters. In the presented example, we apply this workflow to lists of transcription factor target genes resulting from ChIP-chip experiments. For each factor, the protocol predicts the binding motifs by detecting significantly overrepresented hexanucleotides in the target promoters and generates a feature map that displays the positions of putative binding sites along the promoter sequences. This protocol is addressed to bioinformaticians and biologists with programming skills (notions of Perl). Running time is approximately 6 min on the example data set.

A protocol for generating a high-quality genome-scale metabolic reconstruction.

PubMed

Thiele, Ines; Palsson, Bernhard Ø

2010-01-01

Network reconstructions are a common denominator in systems biology. Bottom-up metabolic network reconstructions have been developed over the last 10 years. These reconstructions represent structured knowledge bases that abstract pertinent information on the biochemical transformations taking place within specific target organisms. The conversion of a reconstruction into a mathematical format facilitates a myriad of computational biological studies, including evaluation of network content, hypothesis testing and generation, analysis of phenotypic characteristics and metabolic engineering. To date, genome-scale metabolic reconstructions for more than 30 organisms have been published and this number is expected to increase rapidly. However, these reconstructions differ in quality and coverage that may minimize their predictive potential and use as knowledge bases. Here we present a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction, as well as the common trials and tribulations. Therefore, this protocol provides a helpful manual for all stages of the reconstruction process.

A protocol for generating a high-quality genome-scale metabolic reconstruction

PubMed Central

Thiele, Ines; Palsson, Bernhard Ø.

2011-01-01

Network reconstructions are a common denominator in systems biology. Bottom-up metabolic network reconstructions have developed over the past 10 years. These reconstructions represent structured knowledge-bases that abstract pertinent information on the biochemical transformations taking place within specific target organisms. The conversion of a reconstruction into a mathematical format facilitates myriad computational biological studies including evaluation of network content, hypothesis testing and generation, analysis of phenotypic characteristics, and metabolic engineering. To date, genome-scale metabolic reconstructions for more than 30 organisms have been published and this number is expected to increase rapidly. However, these reconstructions differ in quality and coverage that may minimize their predictive potential and use as knowledge-bases. Here, we present a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction as well as common trials and tribulations. Therefore, this protocol provides a helpful manual for all stages of the reconstruction process. PMID:20057383

A protocol for the creation of useful geometric shape metrics illustrated with a newly derived geometric measure of leaf circularity.

PubMed

Krieger, Jonathan D

2014-08-01

I present a protocol for creating geometric leaf shape metrics to facilitate widespread application of geometric morphometric methods to leaf shape measurement. • To quantify circularity, I created a novel shape metric in the form of the vector between a circle and a line, termed geometric circularity. Using leaves from 17 fern taxa, I performed a coordinate-point eigenshape analysis to empirically identify patterns of shape covariation. I then compared the geometric circularity metric to the empirically derived shape space and the standard metric, circularity shape factor. • The geometric circularity metric was consistent with empirical patterns of shape covariation and appeared more biologically meaningful than the standard approach, the circularity shape factor. The protocol described here has the potential to make geometric morphometrics more accessible to plant biologists by generalizing the approach to developing synthetic shape metrics based on classic, qualitative shape descriptors.

Reliable multicast protocol specifications flow control and NACK policy

NASA Technical Reports Server (NTRS)

Callahan, John R.; Montgomery, Todd L.; Whetten, Brian

1995-01-01

This appendix presents the flow and congestion control schemes recommended for RMP and a NACK policy based on the whiteboard tool. Because RMP uses a primarily NACK based error detection scheme, there is no direct feedback path through which receivers can signal losses through low buffer space or congestion. Reliable multicast protocols also suffer from the fact that throughput for a multicast group must be divided among the members of the group. This division is usually very dynamic in nature and therefore does not lend itself well to a priori determination. These facts have led the flow and congestion control schemes of RMP to be made completely orthogonal to the protocol specification. This allows several differing schemes to be used in different environments to produce the best results. As a default, a modified sliding window scheme based on previous algorithms are suggested and described below.

Secure Publish-Subscribe Protocols for Heterogeneous Medical Wireless Body Area Networks

PubMed Central

Picazo-Sanchez, Pablo; Tapiador, Juan E.; Peris-Lopez, Pedro; Suarez-Tangil, Guillermo

2014-01-01

Security and privacy issues in medical wireless body area networks (WBANs) constitute a major unsolved concern because of the challenges posed by the scarcity of resources in WBAN devices and the usability restrictions imposed by the healthcare domain. In this paper, we describe a WBAN architecture based on the well-known publish-subscribe paradigm. We present two protocols for publishing data and sending commands to a sensor that guarantee confidentiality and fine-grained access control. Both protocols are based on a recently proposed ciphertext policy attribute-based encryption (CP-ABE) scheme that is lightweight enough to be embedded into wearable sensors. We show how sensors can implement lattice-based access control (LBAC) policies using this scheme, which are highly appropriate for the eHealth domain. We report experimental results with a prototype implementation demonstrating the suitability of our proposed solution. PMID:25460814

A RESTful image gateway for multiple medical image repositories.

PubMed

Valente, Frederico; Viana-Ferreira, Carlos; Costa, Carlos; Oliveira, José Luis

2012-05-01

Mobile technologies are increasingly important components in telemedicine systems and are becoming powerful decision support tools. Universal access to data may already be achieved by resorting to the latest generation of tablet devices and smartphones. However, the protocols employed for communicating with image repositories are not suited to exchange data with mobile devices. In this paper, we present an extensible approach to solving the problem of querying and delivering data in a format that is suitable for the bandwidth and graphic capacities of mobile devices. We describe a three-tiered component-based gateway that acts as an intermediary between medical applications and a number of Picture Archiving and Communication Systems (PACS). The interface with the gateway is accomplished using Hypertext Transfer Protocol (HTTP) requests following a Representational State Transfer (REST) methodology, which relieves developers from dealing with complex medical imaging protocols and allows the processing of data on the server side.

A reference protocol for comparing the biocidal properties of gas plasma generating devices

NASA Astrophysics Data System (ADS)

Shaw, A.; Seri, P.; Borghi, C. A.; Shama, G.; Iza, F.

2015-12-01

Growing interest in the use of non-thermal, atmospheric pressure gas plasmas for decontamination purposes has resulted in a multiplicity of plasma-generating devices. There is currently no universally approved method of comparing the biocidal performance of such devices and in the work described here spores of the Gram positive bacterium Bacillus subtilis (ATCC 6633) are proposed as a suitable reference biological agent. In order to achieve consistency in the form in which the biological agent in question is presented to the plasma, a polycarbonate membrane loaded with a monolayer of spores is proposed. The advantages of the proposed protocol are evaluated by comparing inactivation tests in which an alternative microorganism (methicillin resistant Staphylococcus aureus—MRSA) and the widely-used sample preparation technique of directly pipetting cell suspensions onto membranes are employed. In all cases, inactivation tests with either UV irradiation or plasma exposure were more reproducible when the proposed protocol was followed.

In vitro skin models and tissue engineering protocols for skin graft applications.

PubMed

Naves, Lucas B; Dhand, Chetna; Almeida, Luis; Rajamani, Lakshminarayanan; Ramakrishna, Seeram

2016-11-30

In this review, we present a brief introduction of the skin structure, a concise compilation of skin-related disorders, and a thorough discussion of different in vitro skin models, artificial skin substitutes, skin grafts, and dermal tissue engineering protocols. The advantages of the development of in vitro skin disorder models, such as UV radiation and the prototype model, melanoma model, wound healing model, psoriasis model, and full-thickness model are also discussed. Different types of skin grafts including allografts, autografts, allogeneic, and xenogeneic are described in detail with their associated applications. We also discuss different tissue engineering protocols for the design of various types of skin substitutes and their commercial outcomes. Brief highlights are given of the new generation three-dimensional printed scaffolds for tissue regeneration applications. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

Laboratory procedures to generate viral metagenomes.

PubMed

Thurber, Rebecca V; Haynes, Matthew; Breitbart, Mya; Wegley, Linda; Rohwer, Forest

2009-01-01

This collection of laboratory protocols describes the steps to collect viruses from various samples with the specific aim of generating viral metagenome sequence libraries (viromes). Viral metagenomics, the study of uncultured viral nucleic acid sequences from different biomes, relies on several concentration, purification, extraction, sequencing and heuristic bioinformatic methods. No single technique can provide an all-inclusive approach, and therefore the protocols presented here will be discussed in terms of hypothetical projects. However, care must be taken to individualize each step depending on the source and type of viral-particles. This protocol is a description of the processes we have successfully used to: (i) concentrate viral particles from various types of samples, (ii) eliminate contaminating cells and free nucleic acids and (iii) extract, amplify and purify viral nucleic acids. Overall, a sample can be processed to isolate viral nucleic acids suitable for high-throughput sequencing in approximately 1 week.

Task based rehabilitation protocol for elite athletes following Anterior Cruciate ligament reconstruction: a clinical commentary.

PubMed

Herrington, Lee; Myer, Gregory; Horsley, Ian

2013-11-01

Anterior Cruciate ligament (ACL) injuries are one of the most common and devastating knee injuries sustained whilst participating in sport. ACL reconstruction (ACLR) remains the standard approach for athletes who aim to return to high level sporting activities but the outcome from surgery is not assured. Secondary morbidities and an inability to return to the same competitive level are common following ACLR. One factor which might be linked to these sub-optimal outcomes may be a failure to have clearly defined performance criteria for return to activity and sport. This paper presents a commentary describing a structured return to sport rehabilitation protocol for athletes following ACLR. The protocol was developed from synthesis of the available literature and consensus of physiotherapists and strength and conditioning coaches based in the home country Institute of Sports within the United Kingdom. Copyright © 2013 Elsevier Ltd. All rights reserved.

Developing a guideline for clinical trial protocol content: Delphi consensus survey

PubMed Central

2012-01-01

Background Recent evidence has highlighted deficiencies in clinical trial protocols, having implications for many groups. Existing guidelines for randomized clinical trial (RCT) protocol content vary substantially and most do not describe systematic methodology for their development. As one of three prespecified steps for the systematic development of a guideline for trial protocol content, the objective of this study was to conduct a three-round Delphi consensus survey to develop and refine minimum content for RCT protocols. Methods Panellists were identified using a multistep iterative approach, met prespecified minimum criteria and represented key stakeholders who develop or use clinical trial protocols. They were asked to rate concepts for importance in a minimum set of items for RCT protocols. The main outcome measures were degree of importance (scale of 1 to 10; higher scores indicating higher importance) and level of consensus for items. Results were presented as medians, interquartile ranges, counts and percentages. Results Ninety-six expert panellists participated in the Delphi consensus survey including trial investigators, methodologists, research ethics board members, funders, industry, regulators and journal editors. Response rates were between 88 and 93% per round. Overall, panellists rated 63 of 88 concepts of high importance (of which 50 had a 25th percentile rating of 8 or greater), 13 of moderate importance (median 6 or 7) and 12 of low importance (median less than or equal to 5) for minimum trial protocol content. General and item-specific comments and subgroup results provided valuable insight for further discussions. Conclusions This Delphi process achieved consensus from a large panel of experts from diverse stakeholder groups on essential content for RCT protocols. It also highlights areas of divergence. These results, complemented by other empirical research and consensus meetings, are helping guide the development of a guideline for protocol content. PMID:23006145

Description of bipolar charge transport in polyethylene using a fluid model with a constant mobility: model prediction

NASA Astrophysics Data System (ADS)

LeRoy, S.; Segur, P.; Teyssedre, G.; Laurent, C.

2004-01-01

We present a conduction model aimed at describing bipolar transport and space charge phenomena in low density polyethylene under dc stress. In the first part we recall the basic requirements for the description of charge transport and charge storage in disordered media with emphasis on the case of polyethylene. A quick review of available conduction models is presented and our approach is compared with these models. Then, the bases of the model are described and related assumptions are discussed. Finally, results on external current, trapped and free space charge distributions, field distribution and recombination rate are presented and discussed, considering a constant dc voltage, a step-increase of the voltage, and a polarization-depolarization protocol for the applied voltage. It is shown that the model is able to describe the general features reported for external current, electroluminescence and charge distribution in polyethylene.

Supported Lipid Bilayer Technology for the Study of Cellular Interfaces

PubMed Central

Crites, Travis J.; Maddox, Michael; Padhan, Kartika; Muller, James; Eigsti, Calvin; Varma, Rajat

2015-01-01

Glass-supported lipid bilayers presenting freely diffusing proteins have served as a powerful tool for studying cell-cell interfaces, in particular, T cell–antigen presenting cell (APC) interactions, using optical microscopy. Here we expand upon existing protocols and describe the preparation of liposomes by an extrusion method, and describe how this system can be used to study immune synapse formation by Jurkat cells. We also present a method for forming such lipid bilayers on silica beads for the study of signaling responses by population methods, such as western blotting, flow cytometry, and gene-expression analysis. Finally, we describe how to design and prepare transmembrane-anchored protein-laden liposomes, following expression in suspension CHO (CHOs) cells, a mammalian expression system alternative to insect and bacterial cell lines, which do not produce mammalian glycosylation patterns. Such transmembrane-anchored proteins may have many novel applications in cell biology and immunology. PMID:26331983

Forest Soil Disturbance Monitoring Protocol: Volume I: Rapid assessment

Treesearch

Deborah S. Page-Dumroese; Ann M. Abbott; Thomas M. Rice

2009-01-01

This volume of the Forest Soil Disturbance Monitoring Protocol (FSDMP) describes how to monitor forest sites before and after ground disturbing management activities for physical attributes that could influence site resilience and long-term sustainability. The attributes describe surface conditions that affect site sustainability and hydrologic function. Monitoring the...

Nonbibliographic Applications of Z39.50.

ERIC Educational Resources Information Center

Kunze, John A.

1992-01-01

Describes the use of the Z39.50 information retrieval protocol as the basis for Infocal, a read-only, client/server-based campus information system. Technical considerations in adapting the protocol to nonbibliographic data, including semantic modules, dynamic attribute sets, and dynamic record syntax, are described in detail. (Contains 11…

Subclassification and Clinical Management of Extraction Sockets with Labial Dentoalveolar Dehiscence Defects.

PubMed

Chu, Stephen J; Sarnachiaro, Guido O; Hochman, Mark N; Tarnow, Dennis P

2015-01-01

Immediate implant therapy involving implants placed into intact Type 1 extraction sockets has become a consistent clinical technique. The classification of Type 2 extraction sockets, where the mucosal tissues are present but there is a midfacial osseous dehiscence defect, has been described according to the extent of the buccal bone plate absence. The literature has offered different techniques in the treatment of Type 2 sockets; however, the extent of the defect has never been defined or delineated. In this article, the authors describe a subclassification of Type 2 sockets: Type 2A presents with a dehiscence defect roughly 5 mm to 6 mm from the free gingival margin (FGM) involving the coronal one-third of the labial bone plate; Type 2B presents with a dehiscence defect involving the middle one-third of the labial plate, approximately 7 mm to 9 mm from the FGM; and in Type 2C the dehiscence defect involves the apical one-third of the labial osseous plate roughly 10 mm or greater from the FGM. The authors also offer a protocol and technique employing immediate implant placement, guided bone regeneration, and bone graft containment with a custom two-piece healing abutment that can lead to consistent and satisfactory clinical outcomes in low-smile-line patients. The treatment protocol and sequence is outlined in a clinical case presentation involving a Type 2B socket.

Contemporary management and surveillance strategy after shunt or endoscopic third ventriculostomy procedures for hydrocephalus.

PubMed

Janjua, M Burhan; Hoffman, Caitlin E; Souweidane, Mark M

2017-11-01

The management of hydrocephalus can be challenging even in expert hands. Due to acute presentation, recurrence, accompanying complications, the need for urgent diagnosis; a robust management plan is an absolute necessity. We devised a novel time efficient surveillance strategy during emergency, and clinic follow up settings which has never been described in the literature. We searched all articles embracing management/surveillance protocol on pediatric hydrocephalus utilizing the terms "hydrocephalus follow up" or "surveillance protocol after hydrocephalus treatment". The authors present their own strategy based on vast experience in the hydrocephalus management at a single institution. The need for the diagnostic laboratory testing, age and presentation based radiological imaging, significance of neuro-opthalmological exam, and when to consider the emergent exploration have been discussed in detail. Moreover, a definitive triaging strategy has been described with the help of flow chart diagrams for clinicians, and the neurosurgeons in practice. The triage starts from detail history, physical exam, necessary labs, radiological imaging depending on the presentation, and the age of the child. A quick head CT scan helps after shunt surgery while, a FAST sequence MRI scan (fsMRI) is important in post ETV patients. The need for neuro-opthalmological exam, and the shunt series stays vital in asymptomatic patients during regular follow up. Copyright © 2017 Elsevier Ltd. All rights reserved.

Internet Technology for Future Space Missions

NASA Technical Reports Server (NTRS)

Hennessy, Joseph F. (Technical Monitor); Rash, James; Casasanta, Ralph; Hogie, Keith

2002-01-01

Ongoing work at National Aeronautics and Space Administration Goddard Space Flight Center (NASA/GSFC), seeks to apply standard Internet applications and protocols to meet the technology challenge of future satellite missions. Internet protocols and technologies are under study as a future means to provide seamless dynamic communication among heterogeneous instruments, spacecraft, ground stations, constellations of spacecraft, and science investigators. The primary objective is to design and demonstrate in the laboratory the automated end-to-end transport of files in a simulated dynamic space environment using off-the-shelf, low-cost, commodity-level standard applications and protocols. The demonstrated functions and capabilities will become increasingly significant in the years to come as both earth and space science missions fly more sensors and the present labor-intensive, mission-specific techniques for processing and routing data become prohibitively. This paper describes how an IP-based communication architecture can support all existing operations concepts and how it will enable some new and complex communication and science concepts. The authors identify specific end-to-end data flows from the instruments to the control centers and scientists, and then describe how each data flow can be supported using standard Internet protocols and applications. The scenarios include normal data downlink and command uplink as well as recovery scenarios for both onboard and ground failures. The scenarios are based on an Earth orbiting spacecraft with downlink data rates from 300 Kbps to 4 Mbps. Included examples are based on designs currently being investigated for potential use by the Global Precipitation Measurement (GPM) mission.

Protocol for the management of psychiatric patients with psychomotor agitation.

PubMed

Vieta, Eduard; Garriga, Marina; Cardete, Laura; Bernardo, Miquel; Lombraña, María; Blanch, Jordi; Catalán, Rosa; Vázquez, Mireia; Soler, Victòria; Ortuño, Noélia; Martínez-Arán, Anabel

2017-09-08

Psychomotor agitation (PMA) is a state of motor restlessness and mental tension that requires prompt recognition, appropriate assessment and management to minimize anxiety for the patient and reduce the risk for escalation to aggression and violence. Standardized and applicable protocols and algorithms can assist healthcare providers to identify patients at risk of PMA, achieve timely diagnosis and implement minimally invasive management strategies to ensure patient and staff safety and resolution of the episode. Spanish experts in PMA from different disciplines (psychiatrists, psychologists and nurses) convened in Barcelona for a meeting in April 2016. Based on recently issued international consensus guidelines on the standard of care for psychiatric patients with PMA, the meeting provided the opportunity to address the complexities in the assessment and management of PMA from different perspectives. The attendees worked towards producing a consensus for a unified approach to PMA according to the local standards of care and current local legislations. The draft protocol developed was reviewed and ratified by all members of the panel prior to its presentation to the Catalan Society of Psychiatry and Mental Health, the Spanish Society of Biological Psychiatry (SEPB) and the Spanish Network Centre for Research in Mental Health (CIBERSAM) for input. The final protocol and algorithms were then submitted to these organizations for endorsement. The protocol presented here provides guidance on the appropriate selection and use of pharmacological agents (inhaled/oral/IM), seclusion, and physical restraint for psychiatric patients suspected of or presenting with PMA. The protocol is applicable within the Spanish healthcare system. Implementation of the protocol and the constituent algorithms described here should ensure the best standard of care of patients at risk of PMA. Episodes of PMA could be identified earlier in their clinical course and patients could be managed in the least invasive and coercive manner, ensuring their own safety and that of others around them. Establishing specialized teams in agitation and providing them with continued training on the identification of agitation, patient management and therapeutic alternatives might reduce the burden of PMA for both the patient and the healthcare system.

Pyrrole-Imidazole Polyamides: Manual Solid-Phase Synthesis.

PubMed

Pauff, Steven M; Fallows, Andrew J; Mackay, Simon P; Su, Wu; Cullis, Paul M; Burley, Glenn A

2015-12-01

Pyrrole-imidazole polyamides (PAs) are a family of DNA-binding peptides that bind in the minor groove of double-stranded DNA (dsDNA) in a sequence-selective, programmable fashion. This protocol describes a detailed manual procedure for the solid-phase synthesis of this family of compounds. The protocol entails solution-phase synthesis of the Boc-protected pyrrole (Py) and imidazole (Im) carboxylic acid building blocks. This unit also describes the importance of choosing the appropriate condensing agent to form the amide linkages between each building block. Finally, a monomeric coupling protocol and a fragment-based approach are described that delivers PAs in 13% to 30% yield in 8 days. Copyright © 2015 John Wiley & Sons, Inc.

An optimised procedure for prenatal ethanol exposure with determination of its effects on central nervous system connections.

PubMed

Sbriccoli, A; Carretta, D; Santarelli, M; Granato, A; Minciacchi, D

1999-01-01

We describe the protocol set-up to investigate an experimental model of foetal alcohol syndrome in the rat. The protocol has been devised to expose specific cell populations of the central nervous system to ethanol during their neurogenesis and has been applied to the study of diencephalo-telencephalic connections. We were able to demonstrate specific permanent changes of the adult thalamo-cortical circuitry. Our protocol can be applied to study other aspects of central nervous system-ethanol interactions, such as neurotransmitter and receptor patterns. It can also represent a useful tool to test the effects of different diets to prevent nutritional deficiencies and the efficacy of drug treatments to prevent foetal alcohol syndrome. We have shown in fact that ethanol-induced thalamo-cortical alterations are partially prevented by concurrent administration of acetyl-L-carnitine. Finally, the present protocol can be used to investigate the effects of ethanol exposure on the development of different brain structures. To this purpose, the gestational period for ethanol exposure must be chosen according to the peak of neurogenesis for the investigated structure.

Multiplex Droplet Digital PCR Protocols for Quantification of GM Maize Events.

PubMed

Dobnik, David; Spilsberg, Bjørn; Bogožalec Košir, Alexandra; Štebih, Dejan; Morisset, Dany; Holst-Jensen, Arne; Žel, Jana

2018-01-01

The standard-curve based simplex quantitative polymerase chain reaction (qPCR) has been the gold standard for DNA target quantification for more than a decade. The large and growing number of individual analyses needed to test for genetically modified organisms (GMOs) is reducing the cost-effectiveness of qPCR. Droplet digital PCR (ddPCR) enables absolute quantification without standard curves, avoids the amplification efficiency bias observed with qPCR, allows more accurate estimations at low target copy numbers and, in combination with multiplexing, significantly improves cost efficiency. Here we describe two protocols for multiplex quantification of GM maize events: (1) nondiscriminating, with multiplex quantification of targets as a group (12 GM maize lines) and (2) discriminating, with multiplex quantification of individual targets (events). The first enables the quantification of twelve European Union authorized GM maize events as a group with only two assays, but does not permit determination of the individual events present. The second protocol enables the quantification of four individual targets (three GM events and one endogene) in a single reaction. Both protocols can be modified for quantification of any other DNA target.

Electroencephalographic reactivity testing in unconscious patients: a systematic review of methods and definitions.

PubMed

Admiraal, M M; van Rootselaar, A-F; Horn, J

2017-02-01

Electroencephalographic (EEG) reactivity testing is often presented as a clear-cut element of electrophysiological testing. Absence of EEG reactivity is generally considered an indicator of poor outcome, especially in patients after cardiac arrest. However, guidelines do not clearly describe how to test for reactivity and how to evaluate the results. In a quest for clear guidelines, we performed a systematic review aimed at identifying testing methods and definitions of EEG reactivity. We systematically searched the literature between 1970 and May 2016. Methodological quality of the studies was assessed using the QUality In Prognostic Studies tool. Quality of the descriptions of stimulus protocol and reactivity definition was rated on a four-category grading scale based on reproducibility. We found that protocols for EEG reactivity testing vary greatly and descriptions of protocols are almost never replicable. Furthermore, replicable definitions of presence or absence of EEG reactivity are never provided. In order to draw firm conclusions on EEG reactivity as a prognostic factor, future studies should include a precise stimulation protocol and reactivity definition to facilitate guideline formation. © 2016 EAN.

Criteria for the Collection of Useful Respirator Performance Data in the Workplace

PubMed Central

Janssen, Larry; Zhuang, Ziqing; Shaffer, Ronald

2016-01-01

Workplace protection factors (WPFs) are intended to measure the ability of a respiratory protective device (RPD) to reduce contaminant exposure when used in the context of an effective respiratory protection program. In 1992, members of the American Industrial Hygiene Association Respiratory Protection Committee (RPC) published a review of important issues and considerations for measuring respirator performance in the workplace. The RPC recognized that respirator testing in workplaces can have a variety of objectives and endpoints, and that not all workplace measurements are WPFs. That paper addressed concerns in the general categories of 1) study objectives; 2) site selection; 3) subject selection and preparation; 4) sampling and analytical methods; and 5) data analysis. No specific protocol for measuring WPFs was recommended by the RPC, and attempts to reach a U.S. consensus on a WPF protocol since 1992 have not succeeded. Numerous studies have implemented the principles for WPF measurement described in the RPC paper. Modifications to the original recommendations have been made to reflect the current state of the art. This article describes what has been learned in recent years in each of the five categories identified in the 1992 discussion. Because of the wide variety of workplaces and work activities, contaminants and respiratory protective devices, a strict protocol is not appropriate for collecting WPF data. Rather, the minimum requirements for the collection and presentation of meaningful respirator performance data in the workplace are described. Understanding of these principles will permit useful RPD performance data to be generated. PMID:24579751

3D printing of versatile reactionware for chemical synthesis.

PubMed

Kitson, Philip J; Glatzel, Stefan; Chen, Wei; Lin, Chang-Gen; Song, Yu-Fei; Cronin, Leroy

2016-05-01

In recent decades, 3D printing (also known as additive manufacturing) techniques have moved beyond their traditional applications in the fields of industrial manufacturing and prototyping to increasingly find roles in scientific research contexts, such as synthetic chemistry. We present a general approach for the production of bespoke chemical reactors, termed reactionware, using two different approaches to extrusion-based 3D printing. This protocol describes the printing of an inert polypropylene (PP) architecture with the concurrent printing of soft material catalyst composites, using two different 3D printer setups. The steps of the PROCEDURE describe the design and preparation of a 3D digital model of the desired reactionware device and the preparation of this model for use with fused deposition modeling (FDM) type 3D printers. The protocol then further describes the preparation of composite catalyst-silicone materials for incorporation into the 3D-printed device and the steps required to fabricate a reactionware device. This combined approach allows versatility in the design and use of reactionware based on the specific needs of the experimental user. To illustrate this, we present a detailed procedure for the production of one such reactionware device that will result in the production of a sealed reactor capable of effecting a multistep organic synthesis. Depending on the design time of the 3D model, and including time for curing and drying of materials, this procedure can be completed in ∼3 d.

Optical protocols for advanced spacecraft networks

NASA Technical Reports Server (NTRS)

Bergman, Larry A.

1991-01-01

Most present day fiber optic networks are in fact extensions of copper wire networks. As a result, their speed is still limited by electronics even though optics is capable of running three orders of magnitude faster. Also, the fact that photons do not interact with one another (as electrons do) provides optical communication systems with some unique properties or new functionality that is not readily taken advantage of with conventional approaches. Some of the motivation for implementing network protocols in the optical domain, a few possible approaches including optical code-division multiple-access (CDMA), and how this class of networks can extend the technology life cycle of the Space Station Freedom (SSF) with increased performance and functionality are described.

Esthetic Rehabilitation of Anterior Teeth with Laminates Composite Veneers

PubMed Central

Riva, Giancarlo

2014-01-01

No- or minimal-preparation veneers associated with enamel preservation offer predictable results in esthetic dentistry; indirect additive anterior composite restorations represent a quick, minimally invasive, inexpensive, and repairable option for a smile enhancement treatment plan. Current laboratory techniques associated with a strict clinical protocol satisfy patients' restorative and esthetic needs. The case report presented describes minimal invasive treatment of four upper incisors with laminate nanohybrid resin composite veneers. A step-by-step protocol is proposed for diagnostic evaluation, mock-up fabrication and trial, teeth preparation and impression, and adhesive cementation. The resolution of initial esthetic issues, patient satisfaction, and nice integration of indirect restorations confirmed the success of this anterior dentition rehabilitation. PMID:25013730

ChIP-seq and RNA-seq methods to study circadian control of transcription in mammals

PubMed Central

Takahashi, Joseph S.; Kumar, Vivek; Nakashe, Prachi; Koike, Nobuya; Huang, Hung-Chung; Green, Carla B.; Kim, Tae-Kyung

2015-01-01

Genome-wide analyses have revolutionized our ability to study the transcriptional regulation of circadian rhythms. The advent of next-generation sequencing methods has facilitated the use of two such technologies, ChIP-seq and RNA-seq. In this chapter, we describe detailed methods and protocols for these two techniques, with emphasis on their usage in circadian rhythm experiments in the mouse liver, a major target organ of the circadian clock system. Critical factors for these methods are highlighted and issues arising with time series samples for ChIP-seq and RNA-seq are discussed. Finally detailed protocols for library preparation suitable for Illumina sequencing platforms are presented. PMID:25662462

Local network interconnection through a satellite point-to-multipoint link. Ph.D. Thesis - Ecole Nationale Superieure des Telecommunications, 6 Jul. 1985

NASA Technical Reports Server (NTRS)

Duarte, O. Muniz Bandeira

1986-01-01

Four architectures to implement a point to multipoint satellite link protocol for communication services offered by the Telecom 1 satellite network are presented. A safe communication service with error correction and flow control facilities is described. It is shown that a time transparent communication system combines simplicity and cost advantages.

Flexible Strategy Use by Students Who Learn Much versus Little from Text: Transitions within Think-Aloud Protocols

ERIC Educational Resources Information Center

Cromley, Jennifer G.; Wills, Theodore W.

2016-01-01

Van den Broek's landscape model explicitly posits sequences of moves during reading in real time. Two other models that implicitly describe sequences of processes during reading are tested in the present research. Coded think-aloud data from 24 undergraduate students reading scientific text were analysed with lag-sequential techniques to compare…

ALT-114 and ALT-118 Alternative Approaches to NIST ...

EPA Pesticide Factsheets

In 2016, US EPA approved two separate alternatives (ALT 114 and ALT 118) for the preparation and certification of Hydrogen Chloride (HCl) and Mercury (Hg) cylinder reference gas standards that can serve as EPA Protocol gases where EPA Protocol are required, but unavailable. The alternatives were necessary due to the unavailability of NIST reference materials (SRM, NTRM, CRM or RGM) or VSL reference materials (VSL PRM or VSL CRM), reference materials identified in EPA’s Green Book as necessary to establish the traceability of EPA protocol gases. ALT 114 and ALT 118 provides a pathway for gas vendors to prepare and certify traceable gas cylinder standards for use in certifying Hg and HCl CEMS. In this presentation, EPA will describe the mechanics and requirements of the performance-based approach, provide an update on the availability of these gas standards and also discuss the potential for producing and certifying gas standards for other compounds using this approach. This presentation discusses the importance of NIST-traceable reference gases relative to regulatory source compliance emissions monitoring. Specifically this presentation discusses 2 new approaches for making necessary reference gases available in the absence of NIST reference materials. Moreover, these approaches provide an alternative approach to rapidly make available new reference gases for additional HAPS regulatory compliance emissions measurement and monitoring.

SUBSTANCE-ABUSING PREGNANT WOMEN: PRENATAL INTERVENTION USING ULTRASOUND CONSULTATION AND MENTALIZATION TO ENHANCE THE MOTHER-CHILD RELATIONSHIP AND REDUCE SUBSTANCE USE.

PubMed

Pajulo, Helena; Pajulo, Marjukka; Jussila, Heidi; Ekholm, Eeva

2016-07-01

Substance-abusing pregnant and parenting women are considered one of the most challenging, but important, target groups for developing early parenting interventions. Some valuable efforts to develop such interventions have been made in the organizational sector in Finland. However, there is a great need for new ways of work that would simultaneously concentrate in substance-abuse treatment and enhance parenting in public healthcare settings. The present article describes the background, content, and protocol of a new prenatal intervention developed for substance-abusing pregnant women in a hospital setting in public healthcare. The intervention includes two new elements and pathways aimed to enhance the mothers' curiosity toward her developing child and provide motivation to stay abstinent from substance use. The pathways are interactive ultrasound consultation and a new pregnancy diary, both using a parental mentalization focus. The intervention elements, experiences from running the intervention, evaluation protocol, and general characteristics of the study sample gained (n = 90) are described and discussed. Two case vignettes from the study sample are presented, and the applicability of this prenatal work with other groups and settings is considered. © 2016 Michigan Association for Infant Mental Health.

Aptamers and methods for their in vitro selection and uses thereof

DOEpatents

Doyle, Sharon A [Walnut Creek, CA; Murphy, Michael B [Severna Park, MD

2008-02-12

The present method is an improved in vitro selection protocol that relies on magnetic separations for DNA aptamer production that is relatively easy and scalable without the need for expensive robotics. The ability of aptamers selected by this method to recognize and bind their target protein with high affinity and specificity, and detail their uses in a number of assays is also described. Specific TTF1 and His6 aptamers were selected using the method described, and shown to be useful for enzyme-linked assays, Western blots, and affinity purification.

Aptamers and methods for their in vitro selection and uses thereof

DOEpatents

Doyle, Sharon A [Walnut Creek, CA; Murphy, Michael B [Severna Park, MD

2012-01-31

The present method is an improved in vitro selection protocol that relies on magnetic separations for DNA aptamer production that is relatively easy and scalable without the need for expensive robotics. The ability of aptamers selected by this method to recognize and bind their target protein with high affinity and specificity, and detail their uses in a number of assays is also described. Specific TTF1 and His6 aptamers were selected using the method described, and shown to be useful for enzyme-linked assays, Western blots, and affinity purification.

Drug delivery optimization through Bayesian networks.

PubMed Central

Bellazzi, R.

1992-01-01

This paper describes how Bayesian Networks can be used in combination with compartmental models to plan Recombinant Human Erythropoietin (r-HuEPO) delivery in the treatment of anemia of chronic uremic patients. Past measurements of hematocrit or hemoglobin concentration in a patient during the therapy can be exploited to adjust the parameters of a compartmental model of the erythropoiesis. This adaptive process allows more accurate patient-specific predictions, and hence a more rational dosage planning. We describe a drug delivery optimization protocol, based on our approach. Some results obtained on real data are presented. PMID:1482938

A Public-Use, Full-Screen Interface for SPIRES Databases.

ERIC Educational Resources Information Center

Kriz, Harry M.

This paper describes the techniques for implementing a full-screen, custom SPIRES interface for a public-use library database. The database-independent protocol that controls the system is described in detail. Source code for an entire working application using this interface is included. The protocol, with less than 170 lines of procedural code,…

Design exploration and verification platform, based on high-level modeling and FPGA prototyping, for fast and flexible digital communication in physics experiments

NASA Astrophysics Data System (ADS)

Magazzù, G.; Borgese, G.; Costantino, N.; Fanucci, L.; Incandela, J.; Saponara, S.

2013-02-01

In many research fields as high energy physics (HEP), astrophysics, nuclear medicine or space engineering with harsh operating conditions, the use of fast and flexible digital communication protocols is becoming more and more important. The possibility to have a smart and tested top-down design flow for the design of a new protocol for control/readout of front-end electronics is very useful. To this aim, and to reduce development time, costs and risks, this paper describes an innovative design/verification flow applied as example case study to a new communication protocol called FF-LYNX. After the description of the main FF-LYNX features, the paper presents: the definition of a parametric SystemC-based Integrated Simulation Environment (ISE) for high-level protocol definition and validation; the set up of figure of merits to drive the design space exploration; the use of ISE for early analysis of the achievable performances when adopting the new communication protocol and its interfaces for a new (or upgraded) physics experiment; the design of VHDL IP cores for the TX and RX protocol interfaces; their implementation on a FPGA-based emulator for functional verification and finally the modification of the FPGA-based emulator for testing the ASIC chipset which implements the rad-tolerant protocol interfaces. For every step, significant results will be shown to underline the usefulness of this design and verification approach that can be applied to any new digital protocol development for smart detectors in physics experiments.

Biolistic Transformation of Wheat.

PubMed

Tassy, Caroline; Barret, Pierre

2017-01-01

The wheat genome encodes some 100,000 genes. To understand how the expression of these genes is regulated it will be necessary to carry out many genetic transformation experiments. Robust protocols that allow scientists to transform a wide range of wheat genotypes are therefore required. In this chapter, we describe a protocol for biolistic transformation of wheat that uses immature embryos and small quantities of DNA cassettes. An original method for DNA cassette purification is also described. This protocol can be used to transform a wide range of wheat genotypes and other related species.

Network Upgrade for the SLC: Control System Modifications

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

Crane, M.; Mackenzie, R.; Sass, R.

2011-09-09

Current communications between the SLAC Linear Collider control system central host and the SLCmicros is built upon the SLAC developed SLCNET communication hardware and protocols. We will describe how the Internet Suite of protocols (TCP/IP) are used to replace the SLCNET protocol interface. The major communication pathways and their individual requirements are described. A proxy server is used to reduce the number of total system TCP/IP connections. The SLCmicros were upgraded to use Ethernet and TCP/IP as well as SLCNET. Design choices and implementation experiences are addressed.

Enhancing creative cognition with a rapid right-parietal neurofeedback procedure.

PubMed

Agnoli, Sergio; Zanon, Marco; Mastria, Serena; Avenanti, Alessio; Corazza, Giovanni Emanuele

2018-02-14

The present article describes an innovative neurofeedback training (NFT) procedure aimed at increasing creative cognition through the enhancement of specific brain activities previously associated with divergent thinking. We designed and tested two NFT protocols based on training alpha and beta EEG oscillations selectively measured over the right parietal region. A total of 80 participants were involved, 40 in the alpha NFT protocol and 40 in the beta NFT protocol. The NFT loop was closed on a video stream that would advance only when oscillation power exceeded a normalized threshold. The total duration of the protocol was two hours in a single day, hence its classification as rapid. Changes in ideational fluency and originality, measured with a divergent thinking task, were compared between participants receiving real video feedback and participants receiving sham feedback. We controlled for individual differences in creative achievement level. Results showed that the protocols were effective at enhancing alpha and beta activities in the targeted area. Differences between the two protocols emerged in their effectiveness at promoting divergent thinking. While no significant changes in originality resulted from the rapid alpha NFT, increases in both originality and fluency emerged as a consequence of the rapid beta NFT. These results were particularly evident in participants starting with a low creative achievement level. Possible interpretations and future directions are proposed and discussed. Copyright © 2018 Elsevier Ltd. All rights reserved.

SITE-SPECIFIC PROTOCOL FOR MEASURING SOIL RADON POTENTIALS FOR FLORIDA HOUSES

EPA Science Inventory

The report describes a protocol for site-specific measurement of radon potentials for Florida houses that is consistent with existing residential radon protection maps. The protocol gives further guidance on the possible need for radon-protective house construction features. In a...

Post-trial period surveillance for randomised controlled cardiovascular studies: submitted protocols, consent forms and the role of the ethics board.

PubMed

Zia, Mohammad I; Heslegrave, Ronald; Newton, Gary E

2011-12-01

The post-trial period is the time period after the end of study drug administration. It is unclear whether post-trial arrangements for patient surveillance are routinely included in study protocols and consents, and whether research ethics boards (REB) consider the post-trial period. The objective was to determine whether trial protocols and consent forms reviewed by the REB describe procedures for post-trial period surveillance. An observational study of protocols of randomised trials of chronic therapies for cardiac conditions, approved by the REB of two academic institutions affiliated with the University of Toronto in Canada (University Health Network and Mount Sinai Hospital) from 1995 to 2007. Plans for patient surveillance in the post-trial period described in the protocol or in the consent form before and after REB approval were recorded. 42 studies were identified including 18 heart failure and 15 coronary artery disease trials. Only four studies planned a clinical visit after trial termination, and an additional three planned a telephone contact after trial completion. Five trials submitted consent forms to the REB with a discussion of the post-trial period. The majority of protocols and consent forms did not discuss plans for post-trial period surveillance. The post-trial period and the REB approval process could be improved by systematic follow-up being described in the protocol and consent form. The small number of trial protocols evaluated in the study may impair the degree to which the results can be generalised.

Polyethylene glycol 3350 based colon cleaning protocol: 2 d vs 4 d head to head comparison.

PubMed

Elitsur, Rotem; Butcher, Lisa; Vicki, Lund; Elitsur, Yoram

2013-04-16

To compare between 2 and 4 d colon cleansing protocols. Children who were scheduled for colonoscopy procedure (2010-2012) for various medical reasons, were recruited from the pediatric gastroenterology clinic at Marshall University School of Medicine, Huntington, WV. Exclusion criteria were patients who were allergic to the medication used in the protocols [polyethylene glycol (PEG) 3350, Bisacodyl], or children with metabolic or renal diseases. Two PEG 3350 protocols for 4 d (A) and 2 d (B) were prescribed as previously described. A questionnaire describing the volume of PEG consumed, clinical data, and side effects were recorded. Colon preparation was graded by two observers according to previously described method. Rate of adequate colon preparation. A total of 78 patients were considered for final calculation (group A: 40, group B: 38). Age and stool consistency at the last day was comparable in both groups, but the number of stools/day was significantly higher in group B (P = 0.001). Adequate colon preparation was reached in 57.5% (A) and 73.6% (B), respectively (P = 0.206). Side effects were minimal and comparable in both groups. There was no difference in children's age, stool characteristics, or side effects between the children with adequate or inadequate colon preparation. Correlation and agreement between observers was excellent (Pearson correlation = 0.972, kappa = 1.0). No difference between protocols was observed, but the 2 d protocol was superior for its shorter time. Direct comparison between different colon cleansing protocols is crucial in order to establish the "gold standard" protocol for children.

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.

FISH-Flow, a protocol for the concurrent detection of mRNA and protein in single cells using fluorescence in situ hybridization and flow cytometry

PubMed Central

Arrigucci, Riccardo; Bushkin, Yuri; Radford, Felix; Lakehal, Karim; Vir, Pooja; Pine, Richard; Martin, December; Sugarman, Jeffrey; Zhao, Yanlin; Yap, George S; Lardizabal, Alfred A; Tyagi, Sanjay; Gennaro, Maria Laura

2017-01-01

We describe a flow-cytometry-based protocol for intracellular mRNA measurements in nonadherent mammalian cells using fluorescence in situ hybridization (FISH) probes. The method, which we call FISH-Flow, allows for high-throughput multiparametric measurements of gene expression, a task that was not feasible with earlier, microscopy-based approaches. The FISH-Flow protocol involves cell fixation, permeabilization and hybridization with a set of fluorescently labeled oligonucleotide probes. In this protocol, surface and intracellular protein markers can also be stained with fluorescently labeled antibodies for simultaneous protein and mRNA measurement. Moreover, a semiautomated, single-tube version of the protocol can be performed with a commercially available cell-wash device that reduces cell loss, operator time and interoperator variability. It takes ~30 h to perform this protocol. An example of FISH-Flow measurements of cytokine mRNA induction by ex vivo stimulation of primed T cells with specific antigens is described. PMID:28518171

Southern blotting.

PubMed

Brown, T

2001-05-01

Southern blotting is the transfer of DNA fragments from an electrophoresis gel to a membrane support (the properties and advantages of the different types of membrane, transfer buffer, and transfer method are discussed in detail), resulting in immobilization of the DNA fragments, so the membrane carries a semipermanent reproduction of the banding pattern of the gel. After immobilization, the DNA can be subjected to hybridization analysis, enabling bands with sequence similarity to a labeled probe to be identified. This appendix describes Southern blotting via upward capillary transfer of DNA from an agarose gel onto a nylon or nitrocellulose membrane, using a high-salt transfer buffer to promote binding of DNA to the membrane. With the high-salt buffer, the DNA becomes bound to the membrane during transfer but not permanently immobilized. Immobilization is achieved by UV irradiation (for nylon) or baking (for nitrocellulose). A Support Protocol describes how to calibrate a UV transilluminator for optimal UV irradiation of a nylon membrane. An alternate protocol details transfer using nylon membranes and an alkaline buffer, and is primarily used with positively charged nylon membranes. The advantage of this combination is that no post-transfer immobilization step is required, as the positively charged membrane binds DNA irreversibly under alkaline transfer conditions. The method can also be used with neutral nylon membranes but less DNA will be retained. A second alternate protocol describes a transfer method based on a different transfer-stack setup. The traditional method of upward capillary transfer of DNA from gel to membrane described in the first basic and alternate protocols has certain disadvantages, notably the fact that the gel can become crushed by the weighted filter papers and paper towels that are laid on top of it. This slows down the blotting process and may reduce the amount of DNA that can be transferred. The downward capillary method described in the second alternate protocol is therefore more rapid than the basic protocol and can result in more complete transfer. Although the ease and reliability of capillary transfer methods makes this far and away the most popular system for Southern blotting with agarose gels, it unfortunately does not work with polyacrylamide gels, whose smaller pore size impedes the transverse movement of the DNA molecules. The third alternate protocol describes an electroblotting procedure that is currently the most reliable method for transfer of DNA from a polyacrylamide gel. Dot and slot blotting are also described.

The role of hypnosis in the detection of psychogenic seizures.

PubMed

Martínez-Taboas, Alfonso

2002-07-01

In this preliminary clinical investigation, hypnosis was used in the differential diagnosis of epileptic versus psychogenic seizures (PS). Eight patients with a clinical profile suggesting the presence of PS were given a hypnotic suggestion in which they had to go back in time to the exact moment of their last seizure. They were then asked to concentrate their attention on any unusual feeling or bodily sensation. All 8 patients presented a PS during the age regression protocol. In 6 cases, independent testimony from family members corroborated the morphological similarity of the induced attack and the ones presented in their natural environment. Also, the seizures ended abruptly after a command was given to stop them. A control group of 5 epileptic subjects did not present any signs of discomfort or seizure behavior during the hypnotic protocol. It is argued that a simple procedure as the one described in this investigation can be useful as a diagnostic tool in the differentiation of epileptic from PS attacks.

MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models

DOE PAGES

Aurich, Maike K.; Fleming, Ronan M. T.; Thiele, Ines

2016-08-03

Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Previous work, by us and others, revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. With the MetaboTools, we make our methods available to the broader scientific community. The MetaboTools consist of a protocol, a toolbox, and tutorials of two use cases. The protocol describes, in a step-wise manner, the workflow of data integration, and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorialsmore » explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, the MetaboTools constitute a comprehensive guide to the intra-model analysis of extracellular metabolomic data from microbial, plant, or human cells. In conclusion, this computational modeling resource offers a broad set of computational analysis tools for a wide biomedical and non-biomedical research community.« less

Derivation and Implementation of a Protocol in Israel for Organ Donation after Cardio-Circulatory Death.

PubMed

Cohen, Jonathan; Rahamimov, Ruth; Hoffman, Aaron; Katvan, Eyal; Grozovski, Kyril; Ashkenazi, Tamar

2017-09-01

Strategies aimed at expanding the organ donor pool have been sought, which has resulted in renewed interest in donation after cardio-circulatory death (DCCD), also known as non-heart beating donors (NHBDs). To describe the derivation and implementation of a protocol for DCCD in Israel and report on the results with the first six cases. After receiving approval from an extraordinary ethics committee, Ministry of Health, the steering committee of the National Transplant Center defined and reached consensus on the unique challenges presented by a DCCD program. These protocol included medical aspects (construction of a clinical pathway), social and ethical aspects (presentation of the protocol at a public gathering(, legal/ethical aspects (consent for organ preservation procedures being either implied if the donor had signed an organ donor card or received directly from a surrogate decision maker), and logistical aspects (pilot study confined to kidney retrieval and to four medical centers). Data regarding organ donors and recipients were recorded. The protocol was implemented at four medical centers. Consent for organ donation was received from four of the six potential donors meeting criteria for inclusion, in all cases, from a surrogate decision maker. Of the eight kidneys retrieved, only four were suitable for transplantation, which was carried out successfully for four recipients. Graft function remained normal in all cases in 6-12 months follow-up. The DCCD program was successfully implemented and initial results are encouraging, suggesting that expansion of the program might further aid in decreasing the gap between needs and availability of organs.

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.

Anti-Hu paraneoplastic brainstem encephalitis caused by a pancreatic neuroendocrine tumor presenting with central hypoventilation.

PubMed

Najjar, Marc; Taylor, Andrew; Agrawal, Surbhi; Fojo, Tito; Merkler, Alexander E; Rosenblum, Marc K; Lennihan, Laura; Kluger, Michael D

2017-06-01

Paraneoplastic neurological syndromes are rare autoimmune manifestations of malignancies associated with specific antibodies. Anti-Hu associated brainstem encephalitis, a well-described syndrome, usually presents subacutely with preferential involvement of the medulla. Anti-Hu antibodies target intraneuronal antigens and are therefore highly correlated with neurological syndromes when present concomitantly with a neoplasm. Reported is a case of anti-Hu brainstem encephalitis associated with a pancreatic neuroendocrine tumor (PNET) presenting with central hypoventilation. This is the first described case of brainstem encephalitis associated with a well-differentiated PNET as well as the first case of Anti-Hu antibodies associated with a PNET. There are no standardized protocols for the treatment of paraneoplastic brainstem encephalitis however, as in the present case, surgical resection and oncological treatment of the tumor is the first line treatment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Automated generation of patient-tailored electronic care pathways by translating computer-interpretable guidelines into hierarchical task networks.

PubMed

González-Ferrer, Arturo; ten Teije, Annette; Fdez-Olivares, Juan; Milian, Krystyna

2013-02-01

This paper describes a methodology which enables computer-aided support for the planning, visualization and execution of personalized patient treatments in a specific healthcare process, taking into account complex temporal constraints and the allocation of institutional resources. To this end, a translation from a time-annotated computer-interpretable guideline (CIG) model of a clinical protocol into a temporal hierarchical task network (HTN) planning domain is presented. The proposed method uses a knowledge-driven reasoning process to translate knowledge previously described in a CIG into a corresponding HTN Planning and Scheduling domain, taking advantage of HTNs known ability to (i) dynamically cope with temporal and resource constraints, and (ii) automatically generate customized plans. The proposed method, focusing on the representation of temporal knowledge and based on the identification of workflow and temporal patterns in a CIG, makes it possible to automatically generate time-annotated and resource-based care pathways tailored to the needs of any possible patient profile. The proposed translation is illustrated through a case study based on a 70 pages long clinical protocol to manage Hodgkin's disease, developed by the Spanish Society of Pediatric Oncology. We show that an HTN planning domain can be generated from the corresponding specification of the protocol in the Asbru language, providing a running example of this translation. Furthermore, the correctness of the translation is checked and also the management of ten different types of temporal patterns represented in the protocol. By interpreting the automatically generated domain with a state-of-art HTN planner, a time-annotated care pathway is automatically obtained, customized for the patient's and institutional needs. The generated care pathway can then be used by clinicians to plan and manage the patients long-term care. The described methodology makes it possible to automatically generate patient-tailored care pathways, leveraging an incremental knowledge-driven engineering process that starts from the expert knowledge of medical professionals. The presented approach makes the most of the strengths inherent in both CIG languages and HTN planning and scheduling techniques: for the former, knowledge acquisition and representation of the original clinical protocol, and for the latter, knowledge reasoning capabilities and an ability to deal with complex temporal and resource constraints. Moreover, the proposed approach provides immediate access to technologies such as business process management (BPM) tools, which are increasingly being used to support healthcare processes. Copyright © 2012 Elsevier B.V. All rights reserved.

Preparation and Fluorescent Analysis of Plant Metaphase Chromosomes.

PubMed

Schwarzacher, Trude

2016-01-01

Good preparations are essential for informative analysis of both somatic and meiotic chromosomes, cytogenetics, and cell divisions. Fluorescent chromosome staining allows even small chromosomes to be visualized and counted, showing their morphology. Aneuploidies and polyploidies can be established for species, populations, or individuals while changes occurring in breeding lines during hybridization or tissue culture and transformation protocols can be assessed. The process of division can be followed during mitosis and meiosis including pairing and chiasma distribution, as well as DNA organization and structure during the evolution of chromosomes can be studied. This chapter presents protocols for pretreatment and fixation of material, including tips of how to grow plants to get good and healthy meristem with many divisions. The chromosome preparation technique is described using proteolytic enzymes, but acids can be used instead. Chromosome slide preparations are suitable for fluorochrome staining for fast screening (described in the chapter) or fluorescent in situ hybridization (see Schwarzacher and Heslop-Harrison, In situ hybridization. BIOS Scientific Publishers, Oxford, 2000).

A Quantitative Microscopy Technique for Determining the Number of Specific Proteins in Cellular Compartments

PubMed Central

Mutch, Sarah A.; Gadd, Jennifer C.; Fujimoto, Bryant S.; Kensel-Hammes, Patricia; Schiro, Perry G.; Bajjalieh, Sandra M.; Chiu, Daniel T.

2013-01-01

This protocol describes a method to determine both the average number and variance of proteins in the few to tens of copies in isolated cellular compartments, such as organelles and protein complexes. Other currently available protein quantification techniques either provide an average number but lack information on the variance or are not suitable for reliably counting proteins present in the few to tens of copies. This protocol entails labeling the cellular compartment with fluorescent primary-secondary antibody complexes, TIRF (total internal reflection fluorescence) microscopy imaging of the cellular compartment, digital image analysis, and deconvolution of the fluorescence intensity data. A minimum of 2.5 days is required to complete the labeling, imaging, and analysis of a set of samples. As an illustrative example, we describe in detail the procedure used to determine the copy number of proteins in synaptic vesicles. The same procedure can be applied to other organelles or signaling complexes. PMID:22094731

Cyclotide isolation and characterization.

PubMed

Craik, David J; Henriques, Sonia Troeira; Mylne, Joshua S; Wang, Conan K

2012-01-01

Cyclotides are disulfide-rich cyclic peptides produced by plants with the presumed natural function of defense agents against insect pests. They are present in a wide range of plant tissues, being ribosomally synthesized via precursor proteins that are posttranslationally processed to produce mature peptides with a characteristic cyclic backbone and cystine knot motif associated with their six conserved cysteine residues. Their processing is not fully understood but involves asparaginyl endoproteinase activity. In addition to interest in their defense roles and their unique topologies, cyclotides have attracted attention as potential templates in peptide-based drug design applications. This chapter provides protocols for the isolation of cyclotides from plants, their detection and sequencing by mass spectrometry, and their structural analysis by NMR, as well as describing methods for the isolation of nucleic acid sequences that encode their precursor proteins. Assays to assess their membrane-binding interactions are also described. These protocols provide a "starter kit" for researchers entering the cyclotide field. Copyright © 2012 Elsevier Inc. All rights reserved.

NHEXAS PHASE I REGION 5 STUDY--STANDARD OPERATING PROCEDURE--HANDLING QUALITY CONTROL SAMPLES IN THE FIELD (RTI/ACS-AP-209-090)

EPA Science Inventory

This protocol describes how quality control samples should be handled in the field, and was designed as a quick reference source for the field staff. The protocol describes quality control samples for air-VOCs, air-particles, water samples, house dust, soil, urine, blood, hair, a...

Assessing the detection, reporting and investigation of adverse events in clinical trial protocols implemented in Cameroon: a documentary review of clinical trial protocols.

PubMed

Ebile, Akoh Walter; Ateudjieu, Jerome; Yakum, Martin Ndinakie; Djuidje, Marceline Ngounoue; Watcho, Pierre

2015-09-29

International guidelines recommend ethical and scientific quality standards for managing and reporting adverse events occurring during clinical trials to competent research ethics committees and regulatory authorities. The purpose of this study was to determine whether clinical trial protocols in Cameroon are developed in line with national requirements and international guidelines as far as detecting, reporting and investigating of adverse events is concerned. It was a documentary review of all approved clinical trial protocols that were submitted at the Cameroon National Ethics Committee for evaluation from 1997 through 2012. Data were extracted using a preconceived and validated grid. Protocol review process targeted the title, abstract, objectives, methodology, resources, and the chapter on safety. In total, 106 (4.9 %) clinical trial protocols were identified from 2173 protocols seen in the archive and 104 (4.8 %) included for review. Seventy six (73.1 %) trials did not include the surveillance of adverse events as part of their objective. A total of 91 (87.5 %) protocols did not budget for adverse event surveillance, 76 (73.1 %) did not have a data safety management board (DSMB), 11(10.6 %) included insurance for participants, 47 (45.2 %) did not include a case definition for serious adverse events, 33 (31.7 %) described procedures to detect adverse events, 33 (31.7 %) described procedure for reporting and 22 (21.2 %) described procedure for investigating adverse events. Most clinical trial protocols in Cameroon are developed to focus on benefits and pay little attention to harms. The development of national guidelines can improve the surveillance of adverse events in clinical trial research conducted in Cameroon. Adverse events surveillance tools and a budget are critical for an adequate planning for adverse event surveillance when developing trial protocols. Clinical trial protocols submitted in the Cameroon National Ethics Committee do not adequately plan to assess adverse events in clinical trial protocols. In order to improve on the safety of participants and marketed drug, there is a need to develop national guidelines for clinical trials by the government, and to improve evaluation procedures and monitoring of ongoing trials by the ethics committee.

Introduction to multiprotocol over ATM (MPOA)

NASA Astrophysics Data System (ADS)

Fredette, Andre N.

1997-10-01

Multiprotocol over ATM (MPOA) is a new protocol specified by the ATM Forum. MPOA provides a framework for effectively synthesizing bridging and routing with ATM in an environment of diverse protocols and network technologies. The primary goal of MPOA is the efficient transfer of inter-subnet unicast data in a LAN Emulation (LANE) environment. MPOA integrates LANE and the next hop resolution protocol (NHRP) to preserve the benefits of LAN Emulation, while allowing inter-subnet, internetwork layer protocol communication over ATM VCCs without requiring routers in the data path. It reduces latency and the internetwork layer forwarding load on backbone routers by enabling direct connectivity between ATM-attached edge devices (i.e., shortcuts). To establish these shortcuts, MPOA uses both routing and bridging information to locate the edge device closest to the addressed end station. By integrating LANE and NHRP, MPOA allows the physical separation of internetwork layer route calculation and forwarding, a technique known as virtual routing. This separation provides a number of key benefits including enhanced manageability and reduced complexity of internetwork layer capable edge devices. This paper provides an overview of MPOA that summarizes the goals, architecture, and key attributes of the protocol. In presenting this overview, the salient attributes of LANE and NHRP are described as well.

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.

Implementation and Evaluation of Four Interoperable Open Standards for the Internet of Things.

PubMed

Jazayeri, Mohammad Ali; Liang, Steve H L; Huang, Chih-Yuan

2015-09-22

Recently, researchers are focusing on a new use of the Internet called the Internet of Things (IoT), in which enabled electronic devices can be remotely accessed over the Internet. As the realization of IoT concept is still in its early stages, manufacturers of Internet-connected devices and IoT web service providers are defining their proprietary protocols based on their targeted applications. Consequently, IoT becomes heterogeneous in terms of hardware capabilities and communication protocols. Addressing these heterogeneities by following open standards is a necessary step to communicate with various IoT devices. In this research, we assess the feasibility of applying existing open standards on resource-constrained IoT devices. The standard protocols developed in this research are OGC PUCK over Bluetooth, TinySOS, SOS over CoAP, and OGC SensorThings API. We believe that by hosting open standard protocols on IoT devices, not only do the devices become self-describable, self-contained, and interoperable, but innovative applications can also be easily developed with standardized interfaces. In addition, we use memory consumption, request message size, response message size, and response latency to benchmark the efficiency of the implemented protocols. In all, this research presents and evaluates standard-based solutions to better understand the feasibility of applying existing standards to the IoT vision.

Pelvic Muscle Rehabilitation: A Standardized Protocol for Pelvic Floor Dysfunction

PubMed Central

Pedraza, Rodrigo; Nieto, Javier; Ibarra, Sergio; Haas, Eric M.

2014-01-01

Introduction. Pelvic floor dysfunction syndromes present with voiding, sexual, and anorectal disturbances, which may be associated with one another, resulting in complex presentation. Thus, an integrated diagnosis and management approach may be required. Pelvic muscle rehabilitation (PMR) is a noninvasive modality involving cognitive reeducation, modification, and retraining of the pelvic floor and associated musculature. We describe our standardized PMR protocol for the management of pelvic floor dysfunction syndromes. Pelvic Muscle Rehabilitation Program. The diagnostic assessment includes electromyography and manometry analyzed in 4 phases: (1) initial baseline phase; (2) rapid contraction phase; (3) tonic contraction and endurance phase; and (4) late baseline phase. This evaluation is performed at the onset of every session. PMR management consists of 6 possible therapeutic modalities, employed depending on the diagnostic evaluation: (1) down-training; (2) accessory muscle isolation; (3) discrimination training; (4) muscle strengthening; (5) endurance training; and (6) electrical stimulation. Eight to ten sessions are performed at one-week intervals with integration of home exercises and lifestyle modifications. Conclusions. The PMR protocol offers a standardized approach to diagnose and manage pelvic floor dysfunction syndromes with potential advantages over traditional biofeedback, involving additional interventions and a continuous pelvic floor assessment with management modifications over the clinical course. PMID:25006337

MTP: An atomic multicast transport protocol

NASA Technical Reports Server (NTRS)

Freier, Alan O.; Marzullo, Keith

1990-01-01

Multicast transport protocol (MTP); a reliable transport protocol that utilizes the multicast strategy of applicable lower layer network architectures is described. In addition to transporting data reliably and efficiently, MTP provides the client synchronization necessary for agreement on the receipt of data and the joining of the group of communicants.

A Model Based Security Testing Method for Protocol Implementation

PubMed Central

Fu, Yu Long; Xin, Xiao Long

2014-01-01

The security of protocol implementation is important and hard to be verified. Since the penetration testing is usually based on the experience of the security tester and the specific protocol specifications, a formal and automatic verification method is always required. In this paper, we propose an extended model of IOLTS to describe the legal roles and intruders of security protocol implementations, and then combine them together to generate the suitable test cases to verify the security of protocol implementation. PMID:25105163

Refinement for fault-tolerance: An aircraft hand-off protocol

NASA Technical Reports Server (NTRS)

Marzullo, Keith; Schneider, Fred B.; Dehn, Jon

1994-01-01

Part of the Advanced Automation System (AAS) for air-traffic control is a protocol to permit flight hand-off from one air-traffic controller to another. The protocol must be fault-tolerant and, therefore, is subtle -- an ideal candidate for the application of formal methods. This paper describes a formal method for deriving fault-tolerant protocols that is based on refinement and proof outlines. The AAS hand-off protocol was actually derived using this method; that derivation is given.

A model based security testing method for protocol implementation.

PubMed

Fu, Yu Long; Xin, Xiao Long

2014-01-01

The security of protocol implementation is important and hard to be verified. Since the penetration testing is usually based on the experience of the security tester and the specific protocol specifications, a formal and automatic verification method is always required. In this paper, we propose an extended model of IOLTS to describe the legal roles and intruders of security protocol implementations, and then combine them together to generate the suitable test cases to verify the security of protocol implementation.

Polyethylene glycol 3350 based colon cleaning protocol: 2 d vs 4 d head to head comparison

PubMed Central

Elitsur, Rotem; Butcher, Lisa; Vicki, Lund; Elitsur, Yoram

2013-01-01

AIM: To compare between 2 and 4 d colon cleansing protocols. METHODS: Children who were scheduled for colonoscopy procedure (2010-2012) for various medical reasons, were recruited from the pediatric gastroenterology clinic at Marshall University School of Medicine, Huntington, WV. Exclusion criteria were patients who were allergic to the medication used in the protocols [polyethylene glycol (PEG) 3350, Bisacodyl], or children with metabolic or renal diseases. Two PEG 3350 protocols for 4 d (A) and 2 d (B) were prescribed as previously described. A questionnaire describing the volume of PEG consumed, clinical data, and side effects were recorded. Colon preparation was graded by two observers according to previously described method. Main outcome measurements: Rate of adequate colon preparation. RESULTS: A total of 78 patients were considered for final calculation (group A: 40, group B: 38). Age and stool consistency at the last day was comparable in both groups, but the number of stools/day was significantly higher in group B (P = 0.001). Adequate colon preparation was reached in 57.5% (A) and 73.6% (B), respectively (P = 0.206). Side effects were minimal and comparable in both groups. There was no difference in children’s age, stool characteristics, or side effects between the children with adequate or inadequate colon preparation. Correlation and agreement between observers was excellent (Pearson correlation = 0.972, kappa = 1.0). CONCLUSION: No difference between protocols was observed, but the 2 d protocol was superior for its shorter time. Direct comparison between different colon cleansing protocols is crucial in order to establish the “gold standard” protocol for children. PMID:23596539

Reconstitution of mouse oogenesis in a dish from pluripotent stem cells.

PubMed

Hayashi, Katsuhiko; Hikabe, Orie; Obata, Yayoi; Hirao, Yuji

2017-09-01

This protocol is an extension to: Nat. Protoc. 8, 1513-1524 (2013); doi: 10.1038/nprot.2013.090; published online 11 July 2013Generation of functional oocytes in culture from pluripotent stem cells should provide a useful model system for improving our understanding of the basic mechanisms underlying oogenesis. In addition, it has potential applications as an alternative source of oocytes for reproduction. Using the most advanced mouse model in regard to reproductive engineering and stem cell biology, we previously developed a culture method that produces functional primorial germ cells starting from pluripotent cells in culture and described it in a previous protocol. This Protocol Extension describes an adaptation of this existing Protocol in which oogenesis also occurs in vitro, thus substantially modifying the technique. Oocytes generated from embryonic stem cells (ESCs) or induced pluripotent stem cells give rise to healthy pups. Here, we describe the protocol for oocyte generation in culture. The protocol is mainly composed of three different culture stages: in vitro differentiation (IVDi), in vitro growth (IVG), and in vitro maturation (IVM), which in total take ∼5 weeks. In each culture period, there are several checkpoints that enable the number of oocytes being produced in the culture to be monitored. The basic structure of the culture system should provide a useful tool for clarifying the complicated sequence of oogenesis in mammals.

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…

Chemokine receptor binding and signal transduction in native cells of the central nervous system.

PubMed

Davis, Christopher N; Chen, Shuzhen; Boehme, Stefen A; Bacon, Kevin B; Harrison, Jeffrey K

2003-04-01

Chemokine receptors belong to the superfamily of seven-transmembrane-spanning, G-protein-coupled receptors, and their expression by central nervous system cells is clearly documented. As this gene family has become the target of novel therapeutic development, the analysis of these receptors requires radioligand binding techniques as well as methods that entail assessing receptor stimulation of signal transduction pathways. Herein, we describe specific protocols for measuring radiolabeled chemokine binding to their cognate receptors on cultured glial cells as well as to receptors expressed in heterologous cell systems. Multiple downstream signaling pathways, including intracellular calcium influx and receptor-dependent kinase activation, are associated with chemokine receptor stimulation. Protocols for measuring these signaling events in chemokine-receptor-expressing cells are also presented.

Conceptual framework for drought phenotyping during molecular breeding.

PubMed

Salekdeh, Ghasem Hosseini; Reynolds, Matthew; Bennett, John; Boyer, John

2009-09-01

Drought is a major threat to agricultural production and drought tolerance is a prime target for molecular approaches to crop improvement. To achieve meaningful results, these approaches must be linked with suitable phenotyping protocols at all stages, such as the screening of germplasm collections, mutant libraries, mapping populations, transgenic lines and breeding materials and the design of OMICS and quantitative trait loci (QTLs) experiments. Here we present a conceptual framework for molecular breeding for drought tolerance based on the Passioura equation of expressing yield as the product of water use (WU), water use efficiency (WUE) and harvest index (HI). We identify phenotyping protocols that address each of these factors, describe their key features and illustrate their integration with different molecular approaches.

A novel protocol for generating intact, whole-head spider cephalothorax tissue sections.

PubMed

Long, Skye M

2018-04-01

The diversity of spider behavior and sensory systems provides an excellent opportunity for comparative studies of the relationship between the brain and behavior. However, the morphology of spiders poses a challenge for histologists since the spider cephalothorax contains heterogeneous tissues and has both tough external and internal sclerotized regions. Unlike the heads of insects, the cephalothorax is highly pressurized, which can cause tissues to shift during processing and can reduce tissue cohesion in thick sections. This work describes a novel protocol for producing thick whole-head sections for morphological study by softening the exoskeleton and stabilizing friable tissue, without freezing or dehydration. It also presents an effective whole-head DiI staining method that uses minimal dehydration and highlights neural structures.

Comprehensive protocols for CRISPR/Cas9-based gene editing in human pluripotent stem cells

PubMed Central

Santos, David P.; Kiskinis, Evangelos; Eggan, Kevin; Merkle, Florian T.

2016-01-01

Application of the CRISPR/Cas9 system to edit the genomes of human pluripotent stem cells (hPSCs) has the potential to revolutionize hPSC-based disease modeling, drug screening, and transplantation therapy. Here, we aim to provide a single resource to enable groups, even those with limited experience with hPSC culture or the CRISPR/Cas9 system, to successfully perform genome editing. The methods are presented in detail and are supported by a theoretical framework to allow for the incorporation of inevitable improvements in the rapidly evolving gene-editing field. We describe protocols to generate hPSC lines with gene-specific knock-outs, small targeted mutations, or knock-in reporters. PMID:27532820

Timing module for MTCA MCH

NASA Astrophysics Data System (ADS)

Gumiński, M.; Kasprowicz, G.

2016-09-01

White Rabbit is an extension of Precise Time Protocol for synchronous Ethernet networks. Network created with dedicated WR switches enable synchronisation of WR capable devices with 1 ns precision. MicroTCA on the other hand is open standard defining cost efficient shelves capable of housing AMC modules used for data processing. Presented article give further introduction to WR and MTCA standard. The most important aspects of MTCA system are described, with focus on shelf controller and its functionality. Following part describes timing difficulties in MTCA systems and possible solutions. Main section describes extension module for MCH, capable of implementing White Rabbit node and distributing acquired timing to all modules connected to MTCA. Conclusions are given at the end of the article.

INEL BNCT Research Program, March/April 1992

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

Venhuizen, J.R.

1992-09-01

This report presents summaries for two months of current research for the Idaho National Engineering Laboratory (INEL) Boron Neutron Capture Therapy (BNCT) Program. Information is presented on development and murino screening experiments of low-density lipoprotein, carboranyl alanine, and liposome boron containing compounds. Pituitary tumor call culture studies are described. Drug stability, pharmacology and toxicity evaluation of borocaptate sodium (BSH) and boronopheoylalanine (BPA) are described. Treatment protocol development via the large animal (canine) model studies and physiological response evaluation in rats are discussed. Supporting technology development and technical support activities for boron drug biochemistry and purity, analytical and measurement dosimetry, andmore » noninvasive boron quantification activities are included for the current time period. Current publications for the two months are listed.« less

Anthropometric protocols for the construction of new international fetal and newborn growth standards: the INTERGROWTH-21st Project.

PubMed

Cheikh Ismail, L; Knight, H E; Bhutta, Z; Chumlea, W C

2013-09-01

The primary aim of the INTERGROWTH-21(st) Project is to construct new, prescriptive standards describing optimal fetal and preterm postnatal growth. The anthropometric measurements include the head circumference, recumbent length and weight of the infants, and the stature and weight of the parents. In such a large, international, multicentre project, it is critical that all study sites follow standardised protocols to ensure maximal validity of the growth and nutrition indicators used. This paper describes, in detail, the selection of anthropometric personnel, equipment, and measurement and calibration protocols used to construct the new standards. Implementing these protocols at each study site ensures that the anthropometric data are of the highest quality to construct the international standards. © 2013 Royal College of Obstetricians and Gynaecologists.

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.

Reproducible model development in the cardiac electrophysiology Web Lab.

PubMed

Daly, Aidan C; Clerx, Michael; Beattie, Kylie A; Cooper, Jonathan; Gavaghan, David J; Mirams, Gary R

2018-05-26

The modelling of the electrophysiology of cardiac cells is one of the most mature areas of systems biology. This extended concentration of research effort brings with it new challenges, foremost among which is that of choosing which of these models is most suitable for addressing a particular scientific question. In a previous paper, we presented our initial work in developing an online resource for the characterisation and comparison of electrophysiological cell models in a wide range of experimental scenarios. In that work, we described how we had developed a novel protocol language that allowed us to separate the details of the mathematical model (the majority of cardiac cell models take the form of ordinary differential equations) from the experimental protocol being simulated. We developed a fully-open online repository (which we termed the Cardiac Electrophysiology Web Lab) which allows users to store and compare the results of applying the same experimental protocol to competing models. In the current paper we describe the most recent and planned extensions of this work, focused on supporting the process of model building from experimental data. We outline the necessary work to develop a machine-readable language to describe the process of inferring parameters from wet lab datasets, and illustrate our approach through a detailed example of fitting a model of the hERG channel using experimental data. We conclude by discussing the future challenges in making further progress in this domain towards our goal of facilitating a fully reproducible approach to the development of cardiac cell models. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Measuring Reform Practices in Science and Mathematics Classrooms: The Reformed Teaching Observation Protocol.

ERIC Educational Resources Information Center

Sawada, Daiyo; Piburn, Michael D.; Judson, Eugene; Turley, Jeff; Falconer, Kathleen; Benford, Russell; Bloom, Irene

2002-01-01

Describes the Reformed Teaching Observation Protocol (RTOP), a 25-item classroom observation protocol that is standards-based, inquiry-oriented, and student-centered. Provides the definition for reform and the basis for evaluation of the Arizona Collaborative for Excellence in the Preparation of Teachers (ACEPT). Concludes that reform, as defined…

Teaching Integrity in Empirical Research: A Protocol for Documenting Data Management and Analysis

ERIC Educational Resources Information Center

Ball, Richard; Medeiros, Norm

2012-01-01

This article describes a protocol the authors developed for teaching undergraduates to document their statistical analyses for empirical research projects so that their results are completely reproducible and verifiable. The protocol is guided by the principle that the documentation prepared to accompany an empirical research project should be…

Quantum error correction of continuous-variable states against Gaussian noise

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

Ralph, T. C.

2011-08-15

We describe a continuous-variable error correction protocol that can correct the Gaussian noise induced by linear loss on Gaussian states. The protocol can be implemented using linear optics and photon counting. We explore the theoretical bounds of the protocol as well as the expected performance given current knowledge and technology.

Space-Based Telemetry and Range Safety (STARS) Study

NASA Technical Reports Server (NTRS)

Hogie, Keith; Crisuolo, Ed; Parise, Ron

2004-01-01

This presentation will describe the design, development, and testing of a system to collect telemetry, format it into UDP/IP packets, and deliver it to a ground test range using standard IP technologies over a TDRSS link. This presentation will discuss the goal of the STARS IP Formatter along with the overall design. It will also present performance results of the current version of the IP formatter. Finally, it will discuss key issues for supporting constant rate telemetry data delivery when using standard components such as PCI/104 processors, the Linux operating system, Internet Protocols, and synchronous serial interfaces.

Extraction of High Quality DNA from Seized Moroccan Cannabis Resin (Hashish)

PubMed Central

El Alaoui, Moulay Abdelaziz; Melloul, Marouane; Alaoui Amine, Sanaâ; Stambouli, Hamid; El Bouri, Aziz; Soulaymani, Abdelmajid; El Fahime, Elmostafa

2013-01-01

The extraction and purification of nucleic acids is the first step in most molecular biology analysis techniques. The objective of this work is to obtain highly purified nucleic acids derived from Cannabis sativa resin seizure in order to conduct a DNA typing method for the individualization of cannabis resin samples. To obtain highly purified nucleic acids from cannabis resin (Hashish) free from contaminants that cause inhibition of PCR reaction, we have tested two protocols: the CTAB protocol of Wagner and a CTAB protocol described by Somma (2004) adapted for difficult matrix. We obtained high quality genomic DNA from 8 cannabis resin seizures using the adapted protocol. DNA extracted by the Wagner CTAB protocol failed to give polymerase chain reaction (PCR) amplification of tetrahydrocannabinolic acid (THCA) synthase coding gene. However, the extracted DNA by the second protocol permits amplification of THCA synthase coding gene using different sets of primers as assessed by PCR. We describe here for the first time the possibility of DNA extraction from (Hashish) resin derived from Cannabis sativa. This allows the use of DNA molecular tests under special forensic circumstances. PMID:24124454

[3.0 T MRI with a high resolution protocol for the study of benign disease of the anus and rectum. Part one: High resolution protocol for 3.0 T MRI, anatomic review, benign tumors, and congenital or acquired alterations of the sphincter complex].

PubMed

Herráiz Hidalgo, L; Cano Alonso, R; Carrascoso Arranz, J; Álvarez Moreno, E; Martínez de Vega Fernández, V

2014-01-01

Benign anorectal disease comprises a broad group of processes with very diverse origins; these processes may be congenital or acquired as well as inflammatory or tumor related. However, benign anorectal disease has received less attention in the scientific literature than malignant disease. We present an image-based review of the most common benign diseases of the anus and rectum. In this first part, we review the anatomy of the region and provide a brief description of the peculiarities of the high resolution protocol that we use with 3.0 T MRI. We go on to describe the most common benign anorectal tumors and developmental cystic lesions, together with their differential diagnoses, as well as congenital and acquired anomalies of the anorectal sphincter complex. Copyright © 2011 SERAM. Published by Elsevier Espana. All rights reserved.

Neonatal euthanasia.

PubMed

Kon, Alexander A

2009-12-01

Despite advances in the care of infants, there remain many newborns whose medical conditions are incompatible with sustained life. At times, healthcare providers and parents may agree that prolonging life is not an appropriate goal of care, and they may redirect treatment to alleviate suffering. While pediatric palliative treatment protocols are gaining greater acceptance, there remain some children whose suffering is unrelenting despite maximal efforts. Due to the realization that some infants suffer unbearably (ie, the burdens of suffering outweigh the benefits of life), the Dutch have developed a protocol for euthanizing these newborns. In this review, I examine the ethical aspects of 6 forms of end of life care, explain the ethical arguments in support of euthanasia, review the history and verbiage of the United States regulations governing limiting and withdrawing life-prolonging interventions in infants, describe the 3 categories of neonates for whom the Dutch provide euthanasia, review the published analyses of the Dutch protocol, and finally present some practical considerations should some form of euthanasia ever be deemed appropriate.

Is the Prosthetic Homologue Necessary for Embodiment?

PubMed Central

Dornfeld, Chelsea; Swanston, Michelle; Cassella, Joseph; Beasley, Casey; Green, Jacob; Moshayev, Yonatan; Wininger, Michael

2016-01-01

Embodiment is the process by which patients with limb loss come to accept their peripheral device as a natural extension of self. However, there is little guidance as to how exacting the prosthesis must be in order for embodiment to take place: is it necessary for the prosthetic hand to look just like the absent hand? Here, we describe a protocol for testing whether an individual would select a hand that looks like their own from among a selection of five hands, and whether the hand selection (regardless of homology) is consistent across multiple exposures to the same (but reordered) set of candidate hands. Pilot results using healthy volunteers reveals that hand selection is only modestly consistent, and that selection of the prosthetic homologue is atypical (61 of 192 total exposures). Our protocol can be executed in minutes, and makes use of readily available equipment and softwares. We present both a face-to-face and a virtual protocol, for maximum flexibility of implementation. PMID:28066228

Protocol for monitoring metals in Ozark National Scenic Riverways, Missouri: Version 1.0

USGS Publications Warehouse

Schmitt, Christopher J.; Brumbaugh, William G.; Besser, John M.; Hinck, Jo Ellen; Bowles, David E.; Morrison, Lloyd W.; Williams, Michael H.

2008-01-01

The National Park Service is developing a monitoring plan for the Ozark National Scenic Riverways in southeastern Missouri. Because of concerns about the release of lead, zinc, and other metals from lead-zinc mining to streams, the monitoring plan will include mining-related metals. After considering a variety of alternatives, the plan will consist of measuring the concentrations of cadmium, cobalt, lead, nickel, and zinc in composite samples of crayfish (Orconectes luteus or alternate species) and Asian clam (Corbicula fluminea) collected periodically from selected sites. This document, which comprises a protocol narrative and supporting standard operating procedures, describes the methods to be employed prior to, during, and after collection of the organisms, along with procedures for their chemical analysis and quality assurance; statistical analysis, interpretation, and reporting of the data; and for modifying the protocol narrative and supporting standard operating procedures. A list of supplies and equipment, data forms, and sample labels are also included. An example based on data from a pilot study is presented.

Sequential ChIP Protocol for Profiling Bivalent Epigenetic Modifications (ReChIP).

PubMed

Desvoyes, Bénédicte; Sequeira-Mendes, Joana; Vergara, Zaida; Madeira, Sofia; Gutierrez, Crisanto

2018-01-01

Identification of chromatin modifications, e.g., histone acetylation and methylation, among others, is widely carried out by using a chromatin immunoprecipitation (ChIP) strategy. The information obtained with these procedures is useful to gain an overall picture of modifications present in all cells of the population under study. It also serves as a basis to figure out the mechanisms of chromatin organization and gene regulation at the population level. However, the ultimate goal is to understand gene regulation at the level of single chromatin fibers. This requires the identification of chromatin modifications that occur at a given genomic location and within the same chromatin fiber. This is achieved by following a sequential ChIP strategy using two antibodies to distinguish different chromatin modifications. Here, we describe a sequential ChIP protocol (Re-ChIP), paying special attention to the controls needed and the required steps to obtain meaningful and reproducible results. The protocol is developed for young Arabidopsis seedlings but could be adapted to other plant materials.

Synthesis of immunotargeted magneto-plasmonic nanoclusters.

PubMed

Wu, Chun-Hsien; Sokolov, Konstantin

2014-08-22

Magnetic and plasmonic properties combined in a single nanoparticle provide a synergy that is advantageous in a number of biomedical applications including contrast enhancement in novel magnetomotive imaging modalities, simultaneous capture and detection of circulating tumor cells (CTCs), and multimodal molecular imaging combined with photothermal therapy of cancer cells. These applications have stimulated significant interest in development of protocols for synthesis of magneto-plasmonic nanoparticles with optical absorbance in the near-infrared (NIR) region and a strong magnetic moment. Here, we present a novel protocol for synthesis of such hybrid nanoparticles that is based on an oil-in-water microemulsion method. The unique feature of the protocol described herein is synthesis of magneto-plasmonic nanoparticles of various sizes from primary blocks which also have magneto-plasmonic characteristics. This approach yields nanoparticles with a high density of magnetic and plasmonic functionalities which are uniformly distributed throughout the nanoparticle volume. The hybrid nanoparticles can be easily functionalized by attaching antibodies through the Fc moiety leaving the Fab portion that is responsible for antigen binding available for targeting.

Effect of test exercises and mask donning on measured respirator fit.

PubMed

Crutchfield, C D; Fairbank, E O; Greenstein, S L

1999-12-01

Quantitative respirator fit test protocols are typically defined by a series of fit test exercises. A rationale for the protocols that have been developed is generally not available. There also is little information available that describes the effect or effectiveness of the fit test exercises currently specified in respiratory protection standards. This study was designed to assess the relative impact of fit test exercises and mask donning on respirator fit as measured by a controlled negative pressure and an ambient aerosol fit test system. Multiple donnings of two different sizes of identical respirator models by each of 14 test subjects showed that donning affects respirator fit to a greater degree than fit test exercises. Currently specified fit test protocols emphasize test exercises, and the determination of fit is based on a single mask donning. A rationale for a modified fit test protocol based on fewer, more targeted test exercises and multiple mask donnings is presented. The modified protocol identified inadequately fitting respirators as effectively as the currently specified Occupational Safety and Health Administration (OSHA) quantitative fit test protocol. The controlled negative pressure system measured significantly (p < 0.0001) more respirator leakage than the ambient aerosol fit test system. The bend over fit test exercise was found to be predictive of poor respirator fit by both fit test systems. For the better fitting respirators, only the talking exercise generated aerosol fit factors that were significantly lower (p < 0.0001) than corresponding donning fit factors.

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.

Interdisciplinary development and implementation of communication checklist for postoperative management of pediatric airway patients.

PubMed

Kim, Sang W; Maturo, Stephen; Dwyer, Danielle; Monash, Bradley; Yager, Phoebe H; Zanger, Kerstin; Hartnick, Christopher J

2012-01-01

The authors describe their multidisciplinary experience in applying the Institute of Health Improvement methodology to develop a protocol and checklist to reduce communication error during transfer of care for postoperative pediatric surgical airway patients. Preliminary outcome data following implementation of the protocol and checklist are also presented. Prospective study from July 1, 2009, to February 1, 2011. Tertiary care center. Subjects. One hundred twenty-six pediatric airway patients who required coordinated care between Massachusetts Eye and Ear Infirmary and Massachusetts General Hospital. Two sentinel events involving airway emergencies demonstrated a critical need for a standardized, comprehensive instrument that would ensure safe transfer of care. After development and implementation of the protocol and checklist, an initial pilot period on the first set of 9 pediatric airway patients was reassessed. Subsequent prospective 11-month follow-up data of 93 pediatric airway patients were collected and analyzed. A multidisciplinary pediatric team developed and implemented a formalized, postoperative checklist and transfer protocol. After implementation of the checklist and transfer protocol, prospective analysis showed no adverse events from miscommunication during transfer of care over the subsequent 11-month period involving 93 pediatric airway patients. There has been very little written in the quality and safety patient literature about coordinating effective transfer of care between the pediatric surgical and medical subspecialty realms. After design and implementation of a simple, electronically based transfer-of-care checklist and protocol, the number of postsurgical pediatric airway information transfer and communication errors decreased significantly.

Human MAIT-cell responses to Escherichia coli: activation, cytokine production, proliferation, and cytotoxicity.

PubMed

Dias, Joana; Sobkowiak, Michał J; Sandberg, Johan K; Leeansyah, Edwin

2016-07-01

Mucosa-associated invariant T cells are a large and relatively recently described innate-like antimicrobial T-cell subset in humans. These cells recognize riboflavin metabolites from a range of microbes presented by evolutionarily conserved major histocompatibility complex, class I-related molecules. Given the innate-like characteristics of mucosa-associated invariant T cells and the novel type of antigens they recognize, new methodology must be developed and existing methods refined to allow comprehensive studies of their role in human immune defense against microbial infection. In this study, we established protocols to examine a range of mucosa-associated invariant T-cell functions as they respond to antigen produced by Escherichia coli These improved and dose- and time-optimized experimental protocols allow detailed studies of MR1-dependent mucosa-associated invariant T-cell responses to Escherichia coli pulsed antigen-presenting cells, as assessed by expression of activation markers and cytokines, by proliferation, and by induction of apoptosis and death in major histocompatibility complex, class I-related-expressing target cells. The novel and optimized protocols establish a framework of methods and open new possibilities to study mucosa-associated invariant T-cell immunobiology, using Escherichia coli as a model antigen. Furthermore, we propose that these robust experimental systems can also be adapted to study mucosa-associated invariant T-cell responses to other microbes and types of antigen-presenting cells. © The Author(s).

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.

Telerobotic system performance measurement - Motivation and methods

NASA Technical Reports Server (NTRS)

Kondraske, George V.; Khoury, George J.

1992-01-01

A systems performance-based strategy for modeling and conducting experiments relevant to the design and performance characterization of telerobotic systems is described. A developmental testbed consisting of a distributed telerobotics network and initial efforts to implement the strategy described is presented. Consideration is given to the general systems performance theory (GSPT) to tackle human performance problems as a basis for: measurement of overall telerobotic system (TRS) performance; task decomposition; development of a generic TRS model; and the characterization of performance of subsystems comprising the generic model. GSPT employs a resource construct to model performance and resource economic principles to govern the interface of systems to tasks. It provides a comprehensive modeling/measurement strategy applicable to complex systems including both human and artificial components. Application is presented within the framework of a distributed telerobotics network as a testbed. Insight into the design of test protocols which elicit application-independent data is described.

Implementation of AICAR analysis by GC-C-IRMS for anti-doping purposes.

PubMed

Buisson, C; Frelat, C; Mongongu, C; Martinat, N; Audran, M

2017-11-01

AICAR (5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside), is a naturally occurring substance which is part to the World Anti-Doping Agency (WADA) Prohibited List. It is claimed to improve physical performance when administered as a supplement. As for other endogenous compounds such as steroids, the gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) analysis remains an efficient tool to differentiate endogenous substances from exogenous ones. A protocol was described in the literature for the analysis of AICAR by GC-C-IRMS. The aim of the present study was to implement this protocol in our laboratory and to propose solutions to avoid the difficulties encountered. The first point discussed in this study is the derivatization step. Due to the structure of the AICAR molecule, conventional derivatization for GC-C-IRMS such as acetylation could not be applied and silylation was preferred. The improvement of the derivatives stability was achieved thanks to several derivatization conditions tested. This adjustment led to a reproducible derivatization pattern with the 3-TMS form as major derivative product. The second point discussed in this study is the diminution of extracts' background noise. Indeed, the implementation of the published protocol was not easy due to high performance liquid chromatography (HPLC) problems encountered when concentrated urine was injected into our system. Also, too many interferences in the endogenous reference compound fractions were observed. The addition of both a wash step before the HPLC purification and a HPLC purification step for the endogenous reference compound (ERC) fraction allowed us to increase the robustness of the method. This study presents the modified protocol compared to the original protocol as well as the evaluation of the whole method performances. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Novel quantitative real-time LCR for the sensitive detection of SNP frequencies in pooled DNA: method development, evaluation and application.

PubMed

Psifidi, Androniki; Dovas, Chrysostomos; Banos, Georgios

2011-01-19

Single nucleotide polymorphisms (SNP) have proven to be powerful genetic markers for genetic applications in medicine, life science and agriculture. A variety of methods exist for SNP detection but few can quantify SNP frequencies when the mutated DNA molecules correspond to a small fraction of the wild-type DNA. Furthermore, there is no generally accepted gold standard for SNP quantification, and, in general, currently applied methods give inconsistent results in selected cohorts. In the present study we sought to develop a novel method for accurate detection and quantification of SNP in DNA pooled samples. The development and evaluation of a novel Ligase Chain Reaction (LCR) protocol that uses a DNA-specific fluorescent dye to allow quantitative real-time analysis is described. Different reaction components and thermocycling parameters affecting the efficiency and specificity of LCR were examined. Several protocols, including gap-LCR modifications, were evaluated using plasmid standard and genomic DNA pools. A protocol of choice was identified and applied for the quantification of a polymorphism at codon 136 of the ovine PRNP gene that is associated with susceptibility to a transmissible spongiform encephalopathy in sheep. The real-time LCR protocol developed in the present study showed high sensitivity, accuracy, reproducibility and a wide dynamic range of SNP quantification in different DNA pools. The limits of detection and quantification of SNP frequencies were 0.085% and 0.35%, respectively. The proposed real-time LCR protocol is applicable when sensitive detection and accurate quantification of low copy number mutations in DNA pools is needed. Examples include oncogenes and tumour suppressor genes, infectious diseases, pathogenic bacteria, fungal species, viral mutants, drug resistance resulting from point mutations, and genetically modified organisms in food.

Novel Quantitative Real-Time LCR for the Sensitive Detection of SNP Frequencies in Pooled DNA: Method Development, Evaluation and Application

PubMed Central

Psifidi, Androniki; Dovas, Chrysostomos; Banos, Georgios

2011-01-01

Background Single nucleotide polymorphisms (SNP) have proven to be powerful genetic markers for genetic applications in medicine, life science and agriculture. A variety of methods exist for SNP detection but few can quantify SNP frequencies when the mutated DNA molecules correspond to a small fraction of the wild-type DNA. Furthermore, there is no generally accepted gold standard for SNP quantification, and, in general, currently applied methods give inconsistent results in selected cohorts. In the present study we sought to develop a novel method for accurate detection and quantification of SNP in DNA pooled samples. Methods The development and evaluation of a novel Ligase Chain Reaction (LCR) protocol that uses a DNA-specific fluorescent dye to allow quantitative real-time analysis is described. Different reaction components and thermocycling parameters affecting the efficiency and specificity of LCR were examined. Several protocols, including gap-LCR modifications, were evaluated using plasmid standard and genomic DNA pools. A protocol of choice was identified and applied for the quantification of a polymorphism at codon 136 of the ovine PRNP gene that is associated with susceptibility to a transmissible spongiform encephalopathy in sheep. Conclusions The real-time LCR protocol developed in the present study showed high sensitivity, accuracy, reproducibility and a wide dynamic range of SNP quantification in different DNA pools. The limits of detection and quantification of SNP frequencies were 0.085% and 0.35%, respectively. Significance The proposed real-time LCR protocol is applicable when sensitive detection and accurate quantification of low copy number mutations in DNA pools is needed. Examples include oncogenes and tumour suppressor genes, infectious diseases, pathogenic bacteria, fungal species, viral mutants, drug resistance resulting from point mutations, and genetically modified organisms in food. PMID:21283808

Radiographic protocol and normal anatomy of the hind feet in the white rhinoceros (Ceratotherium simum).

PubMed

Dudley, Robert J; Wood, Simon P; Hutchinson, John R; Weller, Renate

2015-01-01

Foot pathology is a common and important health concern in captive rhinoceroses worldwide, but osteopathologies are rarely diagnosed, partly because of a lack of radiographic protocols. Here, we aimed to develop the first radiographic protocol for rhinoceros feet and describe the radiographic anatomy of the white rhinoceros (Ceratotherium simum) hind foot (pes). Computed tomographic images were obtained of nine cadaver pedes from seven different white rhinoceroses and assessed for pathology. A single foot deemed free of pathology was radiographed using a range of different projections and exposures to determine the best protocol. 3D models were produced from the CT images and were displayed with the real radiographs to describe the normal radiographic anatomy of the white rhinoceros pes. An optimal radiographic projection was determined for each bone in the rhinoceros pes focusing on highlighting areas where pathology has been previously described. The projections deemed to be most useful were D60Pr-PlDiO (digit III), D45Pr45M-PlDiLO (digit II), and D40Pr35L-PlDiLO (digit IV). The primary beam was centered 5-7 cm proximal to the cuticle on the digit of interest. Articular surfaces, ridges, grooves, tubercles, processes and fossae were identified. The radiographic protocol we have developed along with the normal radiographic anatomy we have described will allow for more accessible and effective diagnosis of white rhinoceros foot osteopathologies. © 2014 American College of Veterinary Radiology.

Error characterization and quantum control benchmarking in liquid state NMR using quantum information processing techniques

NASA Astrophysics Data System (ADS)

Laforest, Martin

Quantum information processing has been the subject of countless discoveries since the early 1990's. It is believed to be the way of the future for computation: using quantum systems permits one to perform computation exponentially faster than on a regular classical computer. Unfortunately, quantum systems that not isolated do not behave well. They tend to lose their quantum nature due to the presence of the environment. If key information is known about the noise present in the system, methods such as quantum error correction have been developed in order to reduce the errors introduced by the environment during a given quantum computation. In order to harness the quantum world and implement the theoretical ideas of quantum information processing and quantum error correction, it is imperative to understand and quantify the noise present in the quantum processor and benchmark the quality of the control over the qubits. Usual techniques to estimate the noise or the control are based on quantum process tomography (QPT), which, unfortunately, demands an exponential amount of resources. This thesis presents work towards the characterization of noisy processes in an efficient manner. The protocols are developed from a purely abstract setting with no system-dependent variables. To circumvent the exponential nature of quantum process tomography, three different efficient protocols are proposed and experimentally verified. The first protocol uses the idea of quantum error correction to extract relevant parameters about a given noise model, namely the correlation between the dephasing of two qubits. Following that is a protocol using randomization and symmetrization to extract the probability that a given number of qubits are simultaneously corrupted in a quantum memory, regardless of the specifics of the error and which qubits are affected. Finally, a last protocol, still using randomization ideas, is developed to estimate the average fidelity per computational gates for single and multi qubit systems. Even though liquid state NMR is argued to be unsuitable for scalable quantum information processing, it remains the best test-bed system to experimentally implement, verify and develop protocols aimed at increasing the control over general quantum information processors. For this reason, all the protocols described in this thesis have been implemented in liquid state NMR, which then led to further development of control and analysis techniques.

CNES-NASA Disruption-Tolerant Networking (DTN) Interoperability

NASA Technical Reports Server (NTRS)

Mortensen, Dale; Eddy, Wesley M.; Reinhart, Richard C.; Lassere, Francois

2014-01-01

Future missions requiring robust internetworking services may use Delay-Disruption-Tolerant Networking (DTN) technology. CNES, NASA, and other international space agencies are committed to using CCSDS standards in their space and ground mission communications systems. The experiment described in this presentation will evaluate operations concepts, system performance, and advance technology readiness for the use of DTN protocols in conjunction with CCSDS ground systems, CCSDS data links, and CCSDS file transfer applications

CD-ROM-aided Databases

NASA Astrophysics Data System (ADS)

Sano, Tomoyuki; Suzuki, Masataka; Nishida, Hideo

The Development of CAI system using CD-ROM and NAPLPS (North American Presentation Level Protocol Syntax) was taken place by Himeji Dokkyo University. The characteristics of CAI using CD-ROM as information processing series for the department of liberal arts student are described. The system is that the computer program, vast amount of voice data and graphics data are stored in a CD-ROM. It is very effective to improve learning ability of student.

Detection of EEG electrodes in brain volumes.

PubMed

Graffigna, Juan P; Gómez, M Eugenia; Bustos, José J

2010-01-01

This paper presents a method to detect 128 EEG electrodes in image study and to merge with the Nuclear Magnetic Resonance volume for better diagnosis. First we propose three hypotheses to define a specific acquisition protocol in order to recognize the electrodes and to avoid distortions in the image. In the second instance we describe a method for segmenting the electrodes. Finally, registration is performed between volume of the electrodes and NMR.

Model-Driven Test Generation of Distributed Systems

NASA Technical Reports Server (NTRS)

Easwaran, Arvind; Hall, Brendan; Schweiker, Kevin

2012-01-01

This report describes a novel test generation technique for distributed systems. Utilizing formal models and formal verification tools, spe cifically the Symbolic Analysis Laboratory (SAL) tool-suite from SRI, we present techniques to generate concurrent test vectors for distrib uted systems. These are initially explored within an informal test validation context and later extended to achieve full MC/DC coverage of the TTEthernet protocol operating within a system-centric context.

An Extensible NetLogo Model for Visualizing Message Routing Protocols

DTIC Science & Technology

2017-08-01

the hard sciences to the social sciences to computer-generated art. NetLogo represents the world as a set of...describe the model is shown here; for the supporting methods , refer to the source code. Approved for public release; distribution is unlimited. 4 iv...if ticks - last-inject > time-to-inject [inject] if run# > #runs [stop] end Next, we present some basic statistics collected for the

PrOtocols for WatERmarking (POWER)

DTIC Science & Technology

2011-03-01

22. Page 57 of 94 Figure 22: Exemplary watermark structure incl. the structure of the embedded ToC The segmented watermarking approach for...somewhere within the cover. The addresses addressSLji belonging to the different access levels Li are stored in a table of contents ( ToC ) entry, along...then embedded into the ToC -segment Stoc. Several assumptions have to be made before describing the actual functions of the presented system

[Hemiparesis and facial palsy caused by methotrexate].

PubMed

Rueda Arenas, E; García Corzo, J; Franco Ospina, L

2013-12-01

Methotrexate used in the treatment of acute lymphocytic leukemia, can cause neurotoxicity, including a rare presentation with hemiparesis. We describe two teenagers, who during the implementation of the M phase of the protocol, suffered hemiparesis, facial paresis and dysarthria which quickly reversed. Leukemia involvement of the central nervous system and stroke, were ruled out. We briefly review the pathophysiology of methotrexate neurotoxicity, the characteristics of the focal paresis presentation and magnetic resonance image findings. Copyright © 2013 Asociación Española de Pediatría. Published by Elsevier Espana. All rights reserved.

Protocol for Detection of Bacillus anthracis in Environmental Samples

EPA Pesticide Factsheets

This pProtocol Method describes proceduresintended for the analyses of swabs, wipes, Sponge-Sticks, vacuum socks and filters, air filters, drinking water, and decontamination waste water for Bacillus anthracis spores.

Chapter 2: Commercial and Industrial Lighting Evaluation Protocol. The Uniform Methods Project: Methods for Determining Energy Efficiency Savings for Specific Measures

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

Kurnik, Charles W; Gowans, Dakers; Telarico, Chad

The Commercial and Industrial Lighting Evaluation Protocol (the protocol) describes methods to account for gross energy savings resulting from the programmatic installation of efficient lighting equipment in large populations of commercial, industrial, and other nonresidential facilities. This protocol does not address savings resulting from changes in codes and standards, or from education and training activities. A separate Uniform Methods Project (UMP) protocol, Chapter 3: Commercial and Industrial Lighting Controls Evaluation Protocol, addresses methods for evaluating savings resulting from lighting control measures such as adding time clocks, tuning energy management system commands, and adding occupancy sensors.

Outpatient desensitization in selected patients with platinum hypersensitivity reactions.

PubMed

O'Malley, David M; Vetter, Monica Hagan; Cohn, David E; Khan, Ambar; Hays, John L

2017-06-01

Platinum-based chemotherapies are a standard treatment for both initial and recurrent gynecologic cancers. Given this widespread use, it is important to be aware of the features of platinum hypersensitivity reactions and the subsequent treatment of these reactions. There is also increasing interest in the development of desensitization protocols to allow patients with a history of platinum hypersensitivity to receive further platinum based therapy. In this review, we describe the management of platinum hypersensitivity reactions and the desensitization protocols utilized at our institution. We also describe the clinical categorizations utilized to triage patients to appropriate desensitization protocols. Copyright © 2017 Elsevier Inc. All rights reserved.

A Method to Identify Nucleolus-Associated Chromatin Domains (NADs).

PubMed

Carpentier, Marie-Christine; Picart-Picolo, Ariadna; Pontvianne, Frédéric

2018-01-01

The nuclear context needs to be taken into consideration to better understand the mechanisms shaping the epigenome and its organization, and therefore its impact on gene expression. For example, in Arabidopsis, heterochromatin is preferentially localized at the nuclear and the nucleolar periphery. Although chromatin domains associating with the nuclear periphery remain to be identified in plant cells, Nucleolus Associated chromatin Domains (NADs) can be identified thanks to a protocol allowing the isolation of pure nucleoli. We describe here the protocol enabling the identification of NADs in Arabidopsis. Providing the transfer of a nucleolus marker as described here in other crop species, this protocol is broadly applicable.

MRML: an extensible communication protocol for interoperability and benchmarking of multimedia information retrieval systems

NASA Astrophysics Data System (ADS)

Mueller, Wolfgang; Mueller, Henning; Marchand-Maillet, Stephane; Pun, Thierry; Squire, David M.; Pecenovic, Zoran; Giess, Christoph; de Vries, Arjen P.

2000-10-01

While in the area of relational databases interoperability is ensured by common communication protocols (e.g. ODBC/JDBC using SQL), Content Based Image Retrieval Systems (CBIRS) and other multimedia retrieval systems are lacking both a common query language and a common communication protocol. Besides its obvious short term convenience, interoperability of systems is crucial for the exchange and analysis of user data. In this paper, we present and describe an extensible XML-based query markup language, called MRML (Multimedia Retrieval markup Language). MRML is primarily designed so as to ensure interoperability between different content-based multimedia retrieval systems. Further, MRML allows researchers to preserve their freedom in extending their system as needed. MRML encapsulates multimedia queries in a way that enable multimedia (MM) query languages, MM content descriptions, MM query engines, and MM user interfaces to grow independently from each other, reaching a maximum of interoperability while ensuring a maximum of freedom for the developer. For benefitting from this, only a few simple design principles have to be respected when extending MRML for one's fprivate needs. The design of extensions withing the MRML framework will be described in detail in the paper. MRML has been implemented and tested for the CBIRS Viper, using the user interface Snake Charmer. Both are part of the GNU project and can be downloaded at our site.

Simulation of axonal excitability using a Spreadsheet template created in Microsoft Excel.

PubMed

Brown, A M

2000-08-01

The objective of this present study was to implement an established simulation protocol (A.M. Brown, A methodology for simulating biological systems using Microsoft Excel, Comp. Methods Prog. Biomed. 58 (1999) 181-90) to model axonal excitability. The simulation protocol involves the use of in-cell formulas directly typed into a spreadsheet and does not require any programming skills or use of the macro language. Once the initial spreadsheet template has been set up the simulations described in this paper can be executed with a few simple keystrokes. The model axon contained voltage-gated ion channels that were modeled using Hodgkin Huxley style kinetics. The basic properties of axonal excitability modeled were: (1) threshold of action potential firing, demonstrating that not only are the stimulus amplitude and duration critical in the generation of an action potential, but also the resting membrane potential; (2) refractoriness, the phenomenon of reduced excitability immediately following an action potential. The difference between the absolute refractory period, when no amount of stimulus will elicit an action potential, and relative refractory period, when an action potential may be generated by applying increased stimulus, was demonstrated with regard to the underlying state of the Na(+) and K(+) channels; (3) temporal summation, a process by which two sub-threshold stimuli can unite to elicit an action potential was shown to be due to conductance changes outlasting the first stimulus and summing with the second stimulus-induced conductance changes to drive the membrane potential past threshold; (4) anode break excitation, where membrane hyperpolarization was shown to produce an action potential by removing Na(+) channel inactivation that is present at resting membrane potential. The simulations described in this paper provide insights into mechanisms of axonal excitation that can be carried out by following an easily understood protocol.

Successful implementation of a perioperative glycemic control protocol in cardiac surgery: barrier analysis and intervention using lean six sigma.

PubMed

Martinez, Elizabeth A; Chavez-Valdez, Raul; Holt, Natalie F; Grogan, Kelly L; Khalifeh, Katherine W; Slater, Tammy; Winner, Laura E; Moyer, Jennifer; Lehmann, Christoph U

2011-01-01

Although the evidence strongly supports perioperative glycemic control among cardiac surgical patients, there is scant literature to describe the practical application of such a protocol in the complex ICU environment. This paper describes the use of the Lean Six Sigma methodology to implement a perioperative insulin protocol in a cardiac surgical intensive care unit (CSICU) in a large academic hospital. A preintervention chart audit revealed that fewer than 10% of patients were admitted to the CSICU with glucose <200 mg/dL, prompting the initiation of the quality improvement project. Following protocol implementation, more than 90% of patients were admitted with a glucose <200 mg/dL. Key elements to success include barrier analysis and intervention, provider education, and broadening the project scope to address the intraoperative period.

Successful Implementation of a Perioperative Glycemic Control Protocol in Cardiac Surgery: Barrier Analysis and Intervention Using Lean Six Sigma

PubMed Central

Martinez, Elizabeth A.; Chavez-Valdez, Raul; Holt, Natalie F.; Grogan, Kelly L.; Khalifeh, Katherine W.; Slater, Tammy; Winner, Laura E.; Moyer, Jennifer; Lehmann, Christoph U.

2011-01-01

Although the evidence strongly supports perioperative glycemic control among cardiac surgical patients, there is scant literature to describe the practical application of such a protocol in the complex ICU environment. This paper describes the use of the Lean Six Sigma methodology to implement a perioperative insulin protocol in a cardiac surgical intensive care unit (CSICU) in a large academic hospital. A preintervention chart audit revealed that fewer than 10% of patients were admitted to the CSICU with glucose <200 mg/dL, prompting the initiation of the quality improvement project. Following protocol implementation, more than 90% of patients were admitted with a glucose <200 mg/dL. Key elements to success include barrier analysis and intervention, provider education, and broadening the project scope to address the intraoperative period. PMID:22091218

Chapter 15: Commercial New Construction Evaluation Protocol. The Uniform Methods Project: Methods for Determining Energy Efficiency Savings for Specific Measures

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

Kurnik, Charles W.; Keates, Steven

This protocol is intended to describe the recommended method when evaluating the whole-building performance of new construction projects in the commercial sector. The protocol focuses on energy conservation measures (ECMs) or packages of measures where evaluators can analyze impacts using building simulation. These ECMs typically require the use of calibrated building simulations under Option D of the International Performance Measurement and Verification Protocol (IPMVP).

Research protocol for the Picture Talk Project: a qualitative study on research and consent with remote Australian Aboriginal communities

PubMed Central

Fitzpatrick, Emily F M; Carter, Maureen; Oscar, June; Lawford, Tom; Martiniuk, Alexandra L C; D’Antoine, Heather A; Elliott, Elizabeth J

2017-01-01

Introduction Research with Indigenous populations is not always designed with cultural sensitivity. Few publications evaluate or describe in detail seeking consent for research with Indigenous participants. When potential participants are not engaged in a culturally respectful manner, participation rates and research quality can be adversely affected. It is unethical to proceed with research without truly informed consent. Methods and analysis We describe a culturally appropriate research protocol that is invited by Aboriginal communities of the Fitzroy Valley in Western Australia. The Picture Talk Project is a research partnership with local Aboriginal leaders who are also chief investigators. We will interview Aboriginal leaders about research, community engagement and the consent process and hold focus groups with Aboriginal community members about individual consent. Cultural protocols will be applied to recruit and conduct research with participants. Transcripts will be analysed using NVivo10 qualitative software and themes synthesised to highlight the key issues raised by the community about the research process. This protocol will guide future research with the Aboriginal communities of the Fitzroy Valley and may inform the approach to research with other Indigenous communities of Australia or the world. It must be noted that no community is the same and all research requires local consultation and input. To conduct culturally sensitive research, respected local people from the community who have knowledge of cultural protocol and language are engaged to guide each step of the research process from the project design to the delivery of results. Ethics and dissemination Ethics approval was granted by the University of Sydney Human Research Ethics Committee (No. 2012/348, reference:14760), the Western Australia Country Health Service Ethics Committee (No. 2012:15), the Western Australian Aboriginal Health Ethics Committee and reviewed by the Kimberley Aboriginal Health Planning Forum Research Sub-Committee (No. 2012–008). Results will be disseminated through peer review articles, a local Fitzroy Valley report and conference presentations. PMID:29288181

Implementation and Evaluation of Four Interoperable Open Standards for the Internet of Things

PubMed Central

Jazayeri, Mohammad Ali; Liang, Steve H. L.; Huang, Chih-Yuan

2015-01-01

Recently, researchers are focusing on a new use of the Internet called the Internet of Things (IoT), in which enabled electronic devices can be remotely accessed over the Internet. As the realization of IoT concept is still in its early stages, manufacturers of Internet-connected devices and IoT web service providers are defining their proprietary protocols based on their targeted applications. Consequently, IoT becomes heterogeneous in terms of hardware capabilities and communication protocols. Addressing these heterogeneities by following open standards is a necessary step to communicate with various IoT devices. In this research, we assess the feasibility of applying existing open standards on resource-constrained IoT devices. The standard protocols developed in this research are OGC PUCK over Bluetooth, TinySOS, SOS over CoAP, and OGC SensorThings API. We believe that by hosting open standard protocols on IoT devices, not only do the devices become self-describable, self-contained, and interoperable, but innovative applications can also be easily developed with standardized interfaces. In addition, we use memory consumption, request message size, response message size, and response latency to benchmark the efficiency of the implemented protocols. In all, this research presents and evaluates standard-based solutions to better understand the feasibility of applying existing standards to the IoT vision. PMID:26402683

The Best of Both Worlds: Building on the COPUS and RTOP Observation Protocols to Easily and Reliably Measure Various Levels of Reformed Instructional Practice

PubMed Central

Lund, Travis J.; Pilarz, Matthew; Velasco, Jonathan B.; Chakraverty, Devasmita; Rosploch, Kaitlyn; Undersander, Molly; Stains, Marilyne

2015-01-01

Researchers, university administrators, and faculty members are increasingly interested in measuring and describing instructional practices provided in science, technology, engineering, and mathematics (STEM) courses at the college level. Specifically, there is keen interest in comparing instructional practices between courses, monitoring changes over time, and mapping observed practices to research-based teaching. While increasingly common observation protocols (Reformed Teaching Observation Protocol [RTOP] and Classroom Observation Protocol in Undergraduate STEM [COPUS]) at the postsecondary level help achieve some of these goals, they also suffer from weaknesses that limit their applicability. In this study, we leverage the strengths of these protocols to provide an easy method that enables the reliable and valid characterization of instructional practices. This method was developed empirically via a cluster analysis using observations of 269 individual class periods, corresponding to 73 different faculty members, 28 different research-intensive institutions, and various STEM disciplines. Ten clusters, called COPUS profiles, emerged from this analysis; they represent the most common types of instructional practices enacted in the classrooms observed for this study. RTOP scores were used to validate the alignment of the 10 COPUS profiles with reformed teaching. Herein, we present a detailed description of the cluster analysis method, the COPUS profiles, and the distribution of the COPUS profiles across various STEM courses at research-intensive universities. PMID:25976654

The Roadmap to Climate Stability Based on IPCC Fifth Assessment Climate Accounting Protocols

NASA Astrophysics Data System (ADS)

Schultz, T.

2016-12-01

The Climate Stabilization Council recognizes the severe impact consequences of a rapidly warming climate and the challenging mitigation requirements of reaching the COP21 aspirational goal of +1.5°C. To address this challenge, we have used the IPCC Fifth Assessment Report which presents new methods for projecting increases in average global temperature and new metrics to update global climate accounting protocols. The updated protocols allow us to assess the full spectrum of climate mitigation projects available and identify the ability of specific projects to achieve various climate warming targets at different points in time. This assessment demonstrates the need to continue focusing on reducing and removing the major sources of overall excess heat linked to CO2, methane, black carbon, and tropospheric ozone. These findings also highlight the importance of solar radiation management (SRM) and earth radiation management (ERM) to achieve climate stabilization in the near-term. By integrating advanced life-cycle assessment (LCA) into the protocols, unintended environmental or human health impact trade-offs that may be associated with deployment of specific mitigation options can be identified. These protocols have also been introduced for standardization to the international ISO 14000 process. We conclude by describing the Climate Stabilization Council's role in establishing a platform for the scientific research, evaluation, and implementation of the identified climate mitigation projects.

ACIX: Atmospheric Correction Inter-comparison Exercise

NASA Astrophysics Data System (ADS)

Doxani, Georgia; Gascon, Ferran; Vermote, Éric; Roger, Jean-Claude

2017-04-01

The free and open data access policy to Sentinel-2 (S-2) and Landsat-8 (L-8) satellite imagery has stimulated the development of atmospheric correction (AC) processors for generating Bottom-of-Atmosphere (BOA) products. Several entities have started to generate (or plan to generate in the short term) BOA reflectance products at global scale for S-2 and L-8 missions. To this end, the European Space Agency (ESA) and NASA are organizing an exercise on AC processors inter-comparison. The results of the exercise are expected to point out the strengths and weaknesses, as well as communalities and discrepancies of various AC processors, in order to suggest and define ways for their further improvement. In particular, 13 atmospheric processors from five different countries participate in ACIX with the aim to inter-compare their performance when applied to L-8 and S-2 data. A protocol describing the inter-comparison process and the test dataset, which is based on the AERONET sites, will be presented. The protocol has been defined according to what was agreed among the participants during the 1st ACIX workshop held in June 2016. It includes the comparison of aerosol optical thickness and water vapour products of the processors with the AERONET measurements. Moreover, concerning the surface reflectances, the protocol describes the inter-comparison among the processors, as well as the comparison with the MODIS surface reflectance and with a reference surface reflectance product. Such a reference product will be obtained using the AERONET characterization of the aerosol (size distribution and refractive indices) and an accurate radiative transfer code. The inter-comparison outcomes will be presented and discussed among the participants in the 2nd ACIX workshop, which will be held on 11-12 April 2017 (ESRIN/ESA). The proposed presentation is an opportunity for the user community to be informed for the first time about the ACIX results and conclusions.

Accuracy of prehospital triage protocols in selecting severely injured patients: A systematic review.

PubMed

van Rein, Eveline A J; Houwert, R Marijn; Gunning, Amy C; Lichtveld, Rob A; Leenen, Luke P H; van Heijl, Mark

2017-08-01

Prehospital trauma triage ensures proper transport of patients at risk of severe injury to hospitals with an appropriate corresponding level of trauma care. Incorrect triage results in undertriage and overtriage. The American College of Surgeons Committee on Trauma recommends an undertriage rate below 5% and an overtriage rate below 50% for prehospital trauma triage protocols. To find the most accurate prehospital trauma triage protocol, a clear overview of all currently available protocols and corresponding outcomes is necessary. The aim of this systematic review was to evaluate the current literature on all available prehospital trauma triage protocols and determine accuracy of protocol-based triage quality in terms of sensitivity and specificity. A search of Pubmed, Embase, and Cochrane Library databases was performed to identify all studies describing prehospital trauma triage protocols before November 2016. The search terms included "trauma," "trauma center," or "trauma system" combined with "triage," "undertriage," or "overtriage." All studies describing protocol-based triage quality were reviewed. To assess the quality of these type of studies, a new critical appraisal tool was developed. In this review, 21 articles were included with numbers of patients ranging from 130 to over 1 million. Significant predictors for severe injury were: vital signs, suspicion of certain anatomic injuries, mechanism of injury, and age. Sensitivity ranged from 10% to 100%; specificity from 9% to 100%. Nearly all protocols had a low sensitivity, thereby failing to identify severely injured patients. Additionally, the critical appraisal showed poor quality of the majority of included studies. This systematic review shows that nearly all protocols are incapable of identifying severely injured patients. Future studies of high methodological quality should be performed to improve prehospital trauma triage protocols. Systematic review, level III.

The Virtual Cosmos Project: Astronomical Data access for General Public via the National Virtual Observatory

NASA Astrophysics Data System (ADS)

Craig, N.; Mendez, B. J.; Hanisch, R. J.; Christian, C. A.; Summers, F.; Haisch, B.; Lindblom, J.

2005-05-01

We will describe the development of protocols to make Astronomy press-release quality images from HST and other sources publicly available through compatibility with the National Virtual Observatory (NVO). We will present the designs for a public portal to these resources, based on a robust evaluation of our intended audience. The availability of press-release quality materials via the NVO through a simplified interface will greatly enhance the utility of these materials for the public. Behind any portal to NVO data there is a standard registry and data structures that allow collections of data (such as the press release images) to be located and acquired. We will describe our design of the necessary protocols and metadata being used within the NVO framework for this project. We base our meta-tags on the considerable existing work done in the science community as well as the NASA education community. These refined metadata are applied to new HST press-release images as they are produced and registered with the NVO. We will describe methods for retrofitting pre-existing imagery with the metadata standards. The rich media, 3D navigation and visualization capabilities of the browser created by ManyOne Network Inc. are particularly well suited to the presentation of astronomical information and ever more detailed models of the local neighborhood, the Milky Way, etc. We will discuss the 3D navigation and visualization capabilities of the browser with particular focus on the Milky Way Galaxy. Development of an online encyclopedia to accompany the ManyOne portals as part of the Virtual Cosmos will also be described. Support from NASA's AISR Program is gratefully acknowledged.

Southern blotting.

PubMed

Brown, T

2001-05-01

Southern blotting is the transfer of DNA fragments from an electrophoresis gel to a membrane support, resulting in immobilization of the DNA fragments, so the membrane carries a semipermanent reproduction of the banding pattern of the gel. After immobilization, the DNA can be subjected to hybridization analysis, enabling bands with sequence similarity to a labeled probe to be identified. This unit describes Southern blotting via upward capillary transfer of DNA from an agarose gel onto a nylon or nitrocellulose membrane, and subsequent immobilization by UV irradiation (for nylon) or baking (for nitrocellulose). A Support Protocol describes how to calibrate a UV transilluminator for optimal UV irradiation of a nylon membrane. An alternate protocol details transfer using nylon membranes and an alkaline buffer, and is primarily used with positively charged nylon membranes. A second alternate protocol describes a transfer method based on a different transfer-stack setup. The traditional method of upward capillary transfer of DNA from gel to membrane has certain disadvantages, notably the fact that the gel can become crushed by the weighted filter papers and paper towels that are laid on top of it. This slows down the blotting process and may reduce the amount of DNA that can be transferred. The downward capillary method described in the second alternate protocol is therefore more rapid and can result in more complete transfer.

Maternal-Fetal Monitoring of Opioid-Exposed Pregnancies: Analysis of a Pilot Community-Based Protocol and Review of the Literature.

PubMed

Ryan, Gareth; Dooley, Joe; Windrim, Rory; Bollinger, Megan; Gerber Finn, Lianne; Kelly, Len

2017-06-01

To describe/analyse a novel, community-based prenatal monitoring protocol for opioid-exposed pregnancies developed by our centre in 2014 to optimize prenatal care for this population. A literature review of published monitoring protocols for this population is also presented. Retrospective comparison of pre-protocol (n = 215) and post-protocol (n = 251) cohorts. Medline and Embase were searched between 2000-2016 using MeSH terms: [fetal monitoring OR prenatal care] AND [opioid-related disorders OR substance-related disorders] in Medline and [fetal monitoring OR prenatal care] AND [opiate addiction OR substance abuse] in Embase, producing 518 results. Thirteen studies included protocols for monitoring opioid-exposed pregnancies. No comprehensive monitoring protocols with high-quality supporting evidence were found. We evaluated 466 opioid-exposed pregnancies, 215 before and 251 after introduction of the protocol. Since implementation, there was a significant increase in the number of opioid-exposed patients who have underwent urine drug screening (72.6% to 89.2%, P < 0.0001); a significant reduction in the number of urine drug screenings positive for illicit opioids (50.2% to 29.1%, P < 0.0001); and a significant increase in the number of patients who discontinued illicit opioid use by the time of delivery (24.7% to 39.4%, P < 0.01). There was no difference in the CS rate (27.4% vs. 26.3%, P > 0.05). There were no observed differences in the rate of preterm birth, birth weight <2500 g, or Apgar score <7 (P > 0.05). Care of women with increased opioid use during pregnancy is an important but under-studied health issue. A novel protocol for focused antenatal care provision for women with opioid-exposed pregnancies improves standard of care and maternal/fetal outcomes. Copyright © 2017. Published by Elsevier Inc.

Fuzzy adaptive iterative learning coordination control of second-order multi-agent systems with imprecise communication topology structure

NASA Astrophysics Data System (ADS)

Chen, Jiaxi; Li, Junmin

2018-02-01

In this paper, we investigate the perfect consensus problem for second-order linearly parameterised multi-agent systems (MAS) with imprecise communication topology structure. Takagi-Sugeno (T-S) fuzzy models are presented to describe the imprecise communication topology structure of leader-following MAS, and a distributed adaptive iterative learning control protocol is proposed with the dynamic of leader unknown to any of the agent. The proposed protocol guarantees that the follower agents can track the leader perfectly on [0,T] for the consensus problem. Under alignment condition, a sufficient condition of the consensus for closed-loop MAS is given based on Lyapunov stability theory. Finally, a numerical example and a multiple pendulum system are given to illustrate the effectiveness of the proposed algorithm.

Comprehensive Protocols for CRISPR/Cas9-based Gene Editing in Human Pluripotent Stem Cells.

PubMed

Santos, David P; Kiskinis, Evangelos; Eggan, Kevin; Merkle, Florian T

2016-08-17

Genome editing of human pluripotent stem cells (hPSCs) with the CRISPR/Cas9 system has the potential to revolutionize hPSC-based disease modeling, drug screening, and transplantation therapy. Here, we aim to provide a single resource to enable groups, even those with limited experience with hPSC culture or the CRISPR/Cas9 system, to successfully perform genome editing. The methods are presented in detail and are supported by a theoretical framework to allow for the incorporation of inevitable improvements in the rapidly evolving gene-editing field. We describe protocols to generate hPSC lines with gene-specific knock-outs, small targeted mutations, or knock-in reporters. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

Library preparation and data analysis packages for rapid genome sequencing.

PubMed

Pomraning, Kyle R; Smith, Kristina M; Bredeweg, Erin L; Connolly, Lanelle R; Phatale, Pallavi A; Freitag, Michael

2012-01-01

High-throughput sequencing (HTS) has quickly become a valuable tool for comparative genetics and genomics and is now regularly carried out in laboratories that are not connected to large sequencing centers. Here we describe an updated version of our protocol for constructing single- and paired-end Illumina sequencing libraries, beginning with purified genomic DNA. The present protocol can also be used for "multiplexing," i.e. the analysis of several samples in a single flowcell lane by generating "barcoded" or "indexed" Illumina sequencing libraries in a way that is independent from Illumina-supported methods. To analyze sequencing results, we suggest several independent approaches but end users should be aware that this is a quickly evolving field and that currently many alignment (or "mapping") and counting algorithms are being developed and tested.

Simplified production and concentration of HIV-1-based lentiviral vectors using HYPERFlask vessels and anion exchange membrane chromatography

PubMed Central

Kutner, Robert H; Puthli, Sharon; Marino, Michael P; Reiser, Jakob

2009-01-01

Background During the past twelve years, lentiviral (LV) vectors have emerged as valuable tools for transgene delivery because of their ability to transduce nondividing cells and their capacity to sustain long-term transgene expression in target cells in vitro and in vivo. However, despite significant progress, the production and concentration of high-titer, high-quality LV vector stocks is still cumbersome and costly. Methods Here we present a simplified protocol for LV vector production on a laboratory scale using HYPERFlask vessels. HYPERFlask vessels are high-yield, high-performance flasks that utilize a multilayered gas permeable growth surface for efficient gas exchange, allowing convenient production of high-titer LV vectors. For subsequent concentration of LV vector stocks produced in this way, we describe a facile protocol involving Mustang Q anion exchange membrane chromatography. Results Our results show that unconcentrated LV vector stocks with titers in excess of 108 transduction units (TU) per ml were obtained using HYPERFlasks and that these titers were higher than those produced in parallel using regular 150-cm2 tissue culture dishes. We also show that up to 500 ml of an unconcentrated LV vector stock prepared using a HYPERFlask vessel could be concentrated using a single Mustang Q Acrodisc with a membrane volume of 0.18 ml. Up to 5.3 × 1010 TU were recovered from a single HYPERFlask vessel. Conclusion The protocol described here is easy to implement and should facilitate high-titer LV vector production for preclinical studies in animal models without the need for multiple tissue culture dishes and ultracentrifugation-based concentration protocols. PMID:19220915

Global Land Product Validation Protocols: An Initiative of the CEOS Working Group on Calibration and Validation to Evaluate Satellite-derived Essential Climate Variables

NASA Astrophysics Data System (ADS)

Guillevic, P. C.; Nickeson, J. E.; Roman, M. O.; camacho De Coca, F.; Wang, Z.; Schaepman-Strub, G.

2016-12-01

The Global Climate Observing System (GCOS) has specified the need to systematically produce and validate Essential Climate Variables (ECVs). The Committee on Earth Observation Satellites (CEOS) Working Group on Calibration and Validation (WGCV) and in particular its subgroup on Land Product Validation (LPV) is playing a key coordination role leveraging the international expertise required to address actions related to the validation of global land ECVs. The primary objective of the LPV subgroup is to set standards for validation methods and reporting in order to provide traceable and reliable uncertainty estimates for scientists and stakeholders. The Subgroup is comprised of 9 focus areas that encompass 10 land surface variables. The activities of each focus area are coordinated by two international co-leads and currently include leaf area index (LAI) and fraction of absorbed photosynthetically active radiation (FAPAR), vegetation phenology, surface albedo, fire disturbance, snow cover, land cover and land use change, soil moisture, land surface temperature (LST) and emissivity. Recent additions to the focus areas include vegetation indices and biomass. The development of best practice validation protocols is a core activity of CEOS LPV with the objective to standardize the evaluation of land surface products. LPV has identified four validation levels corresponding to increasing spatial and temporal representativeness of reference samples used to perform validation. Best practice validation protocols (1) provide the definition of variables, ancillary information and uncertainty metrics, (2) describe available data sources and methods to establish reference validation datasets with SI traceability, and (3) describe evaluation methods and reporting. An overview on validation best practice components will be presented based on the LAI and LST protocol efforts to date.

Simple immunoassay for detection of PCBs in transformer oil.

PubMed

Glass, Thomas R; Ohmura, Naoya; Taemi, Yukihiro; Joh, Takashi

2005-07-01

A rapid and inexpensive procedure to detect polychlorinated biphenyls (PCBs) in transformer oil is needed to facilitate identification and removal of PCB contaminated transformers. Here we describe a simple two-step liquid-liquid extraction using acidic dimethyl sulfoxide in conjunction with an immunoassay for detecting PCBs in transformer oil. The process described is faster and simpler than any previous immunoassay while maintaining comparable detection limit and false negative rate. Cross reactivity data, characterizing the immunoassay response to the four Kanechlor technical mixtures of PCBs in oil, are presented. Forty-five used transformer oil samples were analyzed by gas chromatography-high-resolution mass spectrometry and were also evaluated using the immunoassay protocol developed. Results presented show zero false negatives at a 1.4 ppm nominal cutoff for the transformer oils analyzed.

A fast and mild decellularization protocol for obtaining extracellular matrix.

PubMed

Mirzarafie, Ariana; Grainger, Rhian K; Thomas, Ben; Bains, William; Ustok, Fatma I; Lowe, Chris R

2014-04-01

Degradation of extracellular matrix (ECM) function with age is a major cause of loss of tissue function with age that we would wish to reverse. Tissue engineering to provide replacement tissue requires an ECM-mimicking scaffold for cell organization. The standard protocols for achieving this take 10 days and include steps that may change the protein structure of the ECM. Here we describe a much shorter protocol for decellularizing chicken muscle, skin, and tendon samples that achieves the same efficiency as the original protocol without protein cross-link interference. Our protocol can be completed in 72 hr.

Cell synchrony and chromosomal protocols for somatic cells of cotton gossypium hirsutum

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

Van`t Hof, J.; Lamm, S.S.

1994-10-10

The intent of this pamphlet is to share information with others who are interested in useful protocols for cotton cytogenetics and cytology. The protocols described are a beginning effort and they are expected to be improved. All methods, results and data given pertain to cultivar MD 51ne. We are not satisfied with our results of in situ hybridization.

Amplification of Chloroplast DNA Using the Polymerase Chain Reaction (PCR): A Practical Activity for Secondary School Students

ERIC Educational Resources Information Center

Hamilton, Kenny; Barfoot, Jan; Crawford, Kathleen E.; Simpson, Craig G.; Beaumont, Paul C.; Bownes, Mary

2006-01-01

We describe a polymerase chain reaction (PCR) protocol suitable for use in secondary schools and colleges. This PCR protocol can be used to investigate genetic variation between plants. The protocol makes use of primers which are complementary to sequences of nucleotides that are highly conserved across different plant genera. The regions of…

Architectural Methodology Report

NASA Technical Reports Server (NTRS)

Dhas, Chris

2000-01-01

The establishment of conventions between two communicating entities in the end systems is essential for communications. Examples of the kind of decisions that need to be made in establishing a protocol convention include the nature of the data representation, the for-mat and the speed of the date representation over the communications path, and the sequence of control messages (if any) which are sent. One of the main functions of a protocol is to establish a standard path between the communicating entities. This is necessary to create a virtual communications medium with certain desirable characteristics. In essence, it is the function of the protocol to transform the characteristics of the physical communications environment into a more useful virtual communications model. The final function of a protocol is to establish standard data elements for communications over the path; that is, the protocol serves to create a virtual data element for exchange. Other systems may be constructed in which the transferred element is a program or a job. Finally, there are special purpose applications in which the element to be transferred may be a complex structure such as all or part of a graphic display. NASA's Glenn Research Center (GRC) defines and develops advanced technology for high priority national needs in communications technologies for application to aeronautics and space. GRC tasked Computer Networks and Software Inc. (CNS) to describe the methodologies used in developing a protocol architecture for an in-space Internet node. The node would support NASA:s four mission areas: Earth Science; Space Science; Human Exploration and Development of Space (HEDS); Aerospace Technology. This report presents the methodology for developing the protocol architecture. The methodology addresses the architecture for a computer communications environment. It does not address an analog voice architecture.

A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design.

PubMed

Ó Conchúir, Shane; Barlow, Kyle A; Pache, Roland A; Ollikainen, Noah; Kundert, Kale; O'Meara, Matthew J; Smith, Colin A; Kortemme, Tanja

2015-01-01

The development and validation of computational macromolecular modeling and design methods depend on suitable benchmark datasets and informative metrics for comparing protocols. In addition, if a method is intended to be adopted broadly in diverse biological applications, there needs to be information on appropriate parameters for each protocol, as well as metrics describing the expected accuracy compared to experimental data. In certain disciplines, there exist established benchmarks and public resources where experts in a particular methodology are encouraged to supply their most efficient implementation of each particular benchmark. We aim to provide such a resource for protocols in macromolecular modeling and design. We present a freely accessible web resource (https://kortemmelab.ucsf.edu/benchmarks) to guide the development of protocols for protein modeling and design. The site provides benchmark datasets and metrics to compare the performance of a variety of modeling protocols using different computational sampling methods and energy functions, providing a "best practice" set of parameters for each method. Each benchmark has an associated downloadable benchmark capture archive containing the input files, analysis scripts, and tutorials for running the benchmark. The captures may be run with any suitable modeling method; we supply command lines for running the benchmarks using the Rosetta software suite. We have compiled initial benchmarks for the resource spanning three key areas: prediction of energetic effects of mutations, protein design, and protein structure prediction, each with associated state-of-the-art modeling protocols. With the help of the wider macromolecular modeling community, we hope to expand the variety of benchmarks included on the website and continue to evaluate new iterations of current methods as they become available.

Verification and validation of a reliable multicast protocol

NASA Technical Reports Server (NTRS)

Callahan, John R.; Montgomery, Todd L.

1995-01-01

This paper describes the methods used to specify and implement a complex communications protocol that provides reliable delivery of data in multicast-capable, packet-switching telecommunication networks. The protocol, called the Reliable Multicasting Protocol (RMP), was developed incrementally by two complementary teams using a combination of formal and informal techniques in an attempt to ensure the correctness of the protocol implementation. The first team, called the Design team, initially specified protocol requirements using a variant of SCR requirements tables and implemented a prototype solution. The second team, called the V&V team, developed a state model based on the requirements tables and derived test cases from these tables to exercise the implementation. In a series of iterative steps, the Design team added new functionality to the implementation while the V&V team kept the state model in fidelity with the implementation through testing. Test cases derived from state transition paths in the formal model formed the dialogue between teams during development and served as the vehicles for keeping the model and implementation in fidelity with each other. This paper describes our experiences in developing our process model, details of our approach, and some example problems found during the development of RMP.

A communication protocol for mobile satellite systems affected by rain attenuation

NASA Technical Reports Server (NTRS)

Lay, Norman; Dessouky, Khaled

1992-01-01

A communication protocol is described that has been developed as part of a K/Ka-band mobile terminal breadboard system to be demonstrated through NASA's Advanced Communications Technology Satellite (ACTS) in 1993. The protocol is aimed at providing the means for enhancing link availability and continuity by supporting real-time data rate selection and changes during rain events. Particular attention is given to the system architecture; types of links, connections, and packets; the protocol procedures; and design rationales.

Abbreviated MRI Protocols: Wave of the Future for Breast Cancer Screening.

PubMed

Chhor, Chloe M; Mercado, Cecilia L

2017-02-01

The purpose of this article is to describe the use of abbreviated breast MRI protocols for improving access to screening for women at intermediate risk. Breast MRI is not a cost-effective modality for screening women at intermediate risk, including those with dense breast tissue as the only risk. Abbreviated breast MRI protocols have been proposed as a way of achieving efficiency and rapid throughput. Use of these abbreviated protocols may increase availability and provide women with greater access to breast MRI.

Using pancreas tissue slices for in situ studies of islet of Langerhans and acinar cell biology.

PubMed

Marciniak, Anja; Cohrs, Christian M; Tsata, Vasiliki; Chouinard, Julie A; Selck, Claudia; Stertmann, Julia; Reichelt, Saskia; Rose, Tobias; Ehehalt, Florian; Weitz, Jürgen; Solimena, Michele; Slak Rupnik, Marjan; Speier, Stephan

2014-12-01

Studies on the cellular function of the pancreas are typically performed in vitro on its isolated functional units, the endocrine islets of Langerhans and the exocrine acini. However, these approaches are hampered by preparation-induced changes of cell physiology and the lack of an intact surrounding. We present here a detailed protocol for the preparation of pancreas tissue slices. This procedure is less damaging to the tissue and faster than alternative approaches, and it enables the in situ study of pancreatic endocrine and exocrine cell physiology in a conserved environment. Pancreas tissue slices facilitate the investigation of cellular mechanisms underlying the function, pathology and interaction of the endocrine and exocrine components of the pancreas. We provide examples for several experimental applications of pancreas tissue slices to study various aspects of pancreas cell biology. Furthermore, we describe the preparation of human and porcine pancreas tissue slices for the validation and translation of research findings obtained in the mouse model. Preparation of pancreas tissue slices according to the protocol described here takes less than 45 min from tissue preparation to receipt of the first slices.

Validation of quantitative and qualitative methods for detecting allergenic ingredients in processed foods in Japan.

PubMed

Sakai, Shinobu; Adachi, Reiko; Akiyama, Hiroshi; Teshima, Reiko

2013-06-19

A labeling system for food allergenic ingredients was established in Japan in April 2002. To monitor the labeling, the Japanese government announced official methods for detecting allergens in processed foods in November 2002. The official methods consist of quantitative screening tests using enzyme-linked immunosorbent assays (ELISAs) and qualitative confirmation tests using Western blotting or polymerase chain reactions (PCR). In addition, the Japanese government designated 10 μg protein/g food (the corresponding allergenic ingredient soluble protein weight/food weight), determined by ELISA, as the labeling threshold. To standardize the official methods, the criteria for the validation protocol were described in the official guidelines. This paper, which was presented at the Advances in Food Allergen Detection Symposium, ACS National Meeting and Expo, San Diego, CA, Spring 2012, describes the validation protocol outlined in the official Japanese guidelines, the results of interlaboratory studies for the quantitative detection method (ELISA for crustacean proteins) and the qualitative detection method (PCR for shrimp and crab DNAs), and the reliability of the detection methods.

An objective protocol for comparing the noise performance of silver halide film and digital sensor

NASA Astrophysics Data System (ADS)

Cao, Frédéric; Guichard, Frédéric; Hornung, Hervé; Tessière, Régis

2012-01-01

Digital sensors have obviously invaded the photography mass market. However, some photographers with very high expectancy still use silver halide film. Are they only nostalgic reluctant to technology or is there more than meets the eye? The answer is not so easy if we remark that, at the end of the golden age, films were actually scanned before development. Nowadays film users have adopted digital technology and scan their film to take advantage from digital processing afterwards. Therefore, it is legitimate to evaluate silver halide film "with a digital eye", with the assumption that processing can be applied as for a digital camera. The article will describe in details the operations we need to consider the film as a RAW digital sensor. In particular, we have to account for the film characteristic curve, the autocorrelation of the noise (related to film grain) and the sampling of the digital sensor (related to Bayer filter array). We also describe the protocol that was set, from shooting to scanning. We then present and interpret the results of sensor response, signal to noise ratio and dynamic range.

A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis

PubMed Central

Lawless, Craig; Hubbard, Simon J.; Fan, Jun; Bessant, Conrad; Hermjakob, Henning; Jones, Andrew R.

2012-01-01

Abstract New methods for performing quantitative proteome analyses based on differential labeling protocols or label-free techniques are reported in the literature on an almost monthly basis. In parallel, a correspondingly vast number of software tools for the analysis of quantitative proteomics data has also been described in the literature and produced by private companies. In this article we focus on the review of some of the most popular techniques in the field and present a critical appraisal of several software packages available to process and analyze the data produced. We also describe the importance of community standards to support the wide range of software, which may assist researchers in the analysis of data using different platforms and protocols. It is intended that this review will serve bench scientists both as a useful reference and a guide to the selection and use of different pipelines to perform quantitative proteomics data analysis. We have produced a web-based tool (http://www.proteosuite.org/?q=other_resources) to help researchers find appropriate software for their local instrumentation, available file formats, and quantitative methodology. PMID:22804616

A Graphical User Interface for Software-assisted Tracking of Protein Concentration in Dynamic Cellular Protrusions.

PubMed

Saha, Tanumoy; Rathmann, Isabel; Galic, Milos

2017-07-11

Filopodia are dynamic, finger-like cellular protrusions associated with migration and cell-cell communication. In order to better understand the complex signaling mechanisms underlying filopodial initiation, elongation and subsequent stabilization or retraction, it is crucial to determine the spatio-temporal protein activity in these dynamic structures. To analyze protein function in filopodia, we recently developed a semi-automated tracking algorithm that adapts to filopodial shape-changes, thus allowing parallel analysis of protrusion dynamics and relative protein concentration along the whole filopodial length. Here, we present a detailed step-by-step protocol for optimized cell handling, image acquisition and software analysis. We further provide instructions for the use of optional features during image analysis and data representation, as well as troubleshooting guidelines for all critical steps along the way. Finally, we also include a comparison of the described image analysis software with other programs available for filopodia quantification. Together, the presented protocol provides a framework for accurate analysis of protein dynamics in filopodial protrusions using image analysis software.

Postsurgical Orthodontic Treatment Planning: a Case Report with 20 Years Follow-up.

PubMed

Farronato, Giampietro; Garagiola, Umberto; Carletti, Vera; Cressoni, Paolo; Mortellaro, Carmen

2011-01-01

Traditionally, maxillofacial deformities are corrected surgically after an initial orthodontic treatment phase. However in, this article, the authors emphasize the postsurgical therapeutic protocol which is extremely important for determining the final and permanent retention of the corrected occlusion. A 55 year old female with severe skeletal Class II malocclusion is presented. Combined surgical and orthodontic correction of the malocclusion was used. : The step-by-step procedure the authors followed for the postsurgical therapy is described. The goals of the postoperative therapy were to restore and rehabilitate neuromuscular function, obtain occlusal stabilization, grind teeth selectively, and final occlusion retention. The importance of a surgical occlusal splint for rehabilitating stomatognathic neuromuscular function postoperatively was demonstrated. Furthermore, the orthodontic-prosthodontic treatment ensured occlusion stability after the surgical correction. The long-term results confirmed the efficacy of the treatment protocol presented here from both functional and aesthetical perspectives. Postsurgical orthodontic treatment is an important step in the surgical and orthodontic therapy of maxillofacial deformities.

INTEGRATED CIRCUITS FROM MOBILE PHONES AS POSSIBLE EMERGENCY OSL/TL DOSIMETERS.

PubMed

Sholom, S; McKeever, S W S

2016-09-01

In this article, optically stimulated luminescence (OSL) data are presented from integrated circuits (ICs) extracted from mobile phones. The purpose is to evaluate the potential of using OSL from components in personal electronic devices such as smart phones as a means of emergency dosimetry in the event of a large-scale radiological incident. ICs were extracted from five different makes and models of mobile phone. Sample preparation procedures are described, and OSL from the IC samples following irradiation using a (90)Sr/(90)Y source is presented. Repeatability, sensitivity, dose responses, minimum measureable doses, stability and fading data were examined and are described. A protocol for measuring absorbed dose is presented, and it was concluded that OSL from these components is a viable method for assessing dose in the days following a radiological incident. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

«Surgery first» or two stage complex rehabilitation plan for patients with malocclusions.

PubMed

Andreishchev, A R; Kavrayskaya, A Yu; Nikolaev, A V

2016-01-01

The article considers stages of complex rehabilitation treatment plans of patients with bite anomalies. The study included 515 patients with various complex malocclusions. Two and conventional three stage treatment plans are described. The article suggests indications for the two stage treatment protocol. The evaluation of efficiency and stability of achieved treatment results obtained with a help of the system of quantitative analysis of dentooralfacial disorders is presented.

How to benchmark methods for structure-based virtual screening of large compound libraries.

PubMed

Christofferson, Andrew J; Huang, Niu

2012-01-01

Structure-based virtual screening is a useful computational technique for ligand discovery. To systematically evaluate different docking approaches, it is important to have a consistent benchmarking protocol that is both relevant and unbiased. Here, we describe the designing of a benchmarking data set for docking screen assessment, a standard docking screening process, and the analysis and presentation of the enrichment of annotated ligands among a background decoy database.

ECHO Services: Foundational Middleware for a Science Cyberinfrastructure

NASA Technical Reports Server (NTRS)

Burnett, Michael

2005-01-01

This viewgraph presentation describes ECHO, an interoperability middleware solution. It uses open, XML-based APIs, and supports net-centric architectures and solutions. ECHO has a set of interoperable registries for both data (metadata) and services, and provides user accounts and a common infrastructure for the registries. It is built upon a layered architecture with extensible infrastructure for supporting community unique protocols. It has been operational since November, 2002 and it available as open source.

Cochlear implantation in children with Jervell and Lange-Nielsen syndrome - a cautionary tale.

PubMed

Broomfield, Stephen J; Bruce, Iain A; Henderson, Lise; Ramsden, Richard T; Green, Kevin M J

2012-08-01

Jervell and Lange-Nielsen (JLN) syndrome is a rare cause of congenital profound hearing loss associated with a prolonged QT interval on the electrocardiogram. Children presenting for cochlear implantation with this condition may be asymptomatic but are at risk of sudden death. SCREENING AND SUBSEQUENT: careful management is therefore required to ensure a successful outcome. We present our experience of cochlear implantation in children with JLN syndrome, including two who died unexpectedly, and suggest a protocol for management of such cases. Clinical presentation Four cases of cochlear implantation in JLN syndrome are described. None had any previous cardiological family history. Two were diagnosed pre-operatively but, despite appropriate management under a cardiologist, died from cardiac arrest; the first in the perioperative period following reimplantation for infection, and the second unrelated to his cochlear implant surgery. The other two patients were diagnosed only subsequent to their implantation and continue to use their implants successfully. These cases highlight the variation in presentation of JLN syndrome, and the spectrum of disease severity that exists. Our protocol stresses the importance of careful assessment and counselling of parents by an experienced implant team.

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.

Generic Verification Protocol for Verification of Online Turbidimeters

EPA Science Inventory

This protocol provides generic procedures for implementing a verification test for the performance of online turbidimeters. The verification tests described in this document will be conducted under the Environmental Technology Verification (ETV) Program. Verification tests will...

Growth on solid media.

PubMed

Elbing, Karen; Brent, Roger

2002-08-01

Detailed protocols are provided for titering and isolating bacterial colonies by serial dilutions, or alternatively by streaking or spreading a plate. Support protocols describe replica plating as well as methods for storing strains as agar stabs or frozen glycerol stocks.

Detection of isotype switch rearrangement in bulk culture by PCR.

PubMed

Max, E E; Mills, F C; Chu, C

2001-05-01

When a B lymphocyte changes from synthesizing IgM to synthesizing IgG, IgA, or IgE, this isotype switch is generally accompanied by a unique DNA rearrangement. The protocols in this unit describe two polymerase chain reaction (PCR)-based strategies for detecting switch rearrangements in bulk culture. The first involves direct PCR across the switch junctions, providing the opportunity for characterizing the recombination products by nucleotide sequence analysis; however, because of characteristics inherent to the PCR methodology this strategy cannot easily be used as a quantitative assay for recombination. A support protocol details the preparation of the 5' Su PCR probe for this protocol. The second basic protocol describes a method known as digestion-circularization PCR (DCPCR) that is more amenable to quantitation but yields no information on structure of the recombination products. Both techniques should be capable of detecting reciprocal deletion circles as well as functional recombination products remaining on the expressed chromosome.

j5 DNA assembly design automation.

PubMed

Hillson, Nathan J

2014-01-01

Modern standardized methodologies, described in detail in the previous chapters of this book, have enabled the software-automated design of optimized DNA construction protocols. This chapter describes how to design (combinatorial) scar-less DNA assembly protocols using the web-based software j5. j5 assists biomedical and biotechnological researchers construct DNA by automating the design of optimized protocols for flanking homology sequence as well as type IIS endonuclease-mediated DNA assembly methodologies. Unlike any other software tool available today, j5 designs scar-less combinatorial DNA assembly protocols, performs a cost-benefit analysis to identify which portions of an assembly process would be less expensive to outsource to a DNA synthesis service provider, and designs hierarchical DNA assembly strategies to mitigate anticipated poor assembly junction sequence performance. Software integrated with j5 add significant value to the j5 design process through graphical user-interface enhancement and downstream liquid-handling robotic laboratory automation.

Pepper, sweet (Capsicum annuum).

PubMed

Heidmann, Iris; Boutilier, Kim

2015-01-01

Capsicum (pepper) species are economically important crops that are recalcitrant to genetic transformation by Agrobacterium (Agrobacterium tumefaciens). A number of protocols for pepper transformation have been described but are not routinely applicable. The main bottleneck in pepper transformation is the low frequency of cells that are both susceptible for Agrobacterium infection and have the ability to regenerate. Here, we describe a protocol for the efficient regeneration of transgenic sweet pepper (C. annuum) through inducible activation of the BABY BOOM (BBM) AP2/ERF transcription factor. Using this approach, we can routinely achieve a transformation efficiency of at least 0.6 %. The main improvements in this protocol are the reproducibility in transforming different genotypes and the ability to produce fertile shoots. An added advantage of this protocol is that BBM activity can be induced subsequently in stable transgenic lines, providing a novel regeneration system for clonal propagation through somatic embryogenesis.

Supervision of Facilitators in a Multisite Study: Goals, Process, and Outcomes

PubMed Central

2010-01-01

Objective To describe the aims, implementation, and desired outcomes of facilitator supervision for both interventions (treatment and control) in Project Eban and to present the Eban Theoretical Framework for Supervision that guided the facilitators’ supervision. The qualifications and training of supervisors and facilitators are also described. Design This article provides a detailed description of supervision in a multisite behavioral intervention trial. The Eban Theoretical Framework for Supervision is guided by 3 theories: cognitive behavior therapy, the Life-long Model of Supervision, and “Empowering supervisees to empower others: a culturally responsive supervision model.” Methods Supervision is based on the Eban Theoretical Framework for Supervision, which provides guidelines for implementing both interventions using goals, process, and outcomes. Results Because of effective supervision, the interventions were implemented with fidelity to the protocol and were standard across the multiple sites. Conclusions Supervision of facilitators is a crucial aspect of multisite intervention research quality assurance. It provides them with expert advice, optimizes the effectiveness of facilitators, and increases adherence to the protocol across multiple sites. Based on the experience in this trial, some of the challenges that arise when conducting a multisite randomized control trial and how they can be handled by implementing the Eban Theoretical Framework for Supervision are described. PMID:18724192

Functional Profiling Using the Saccharomyces Genome Deletion Project Collections.

PubMed

Nislow, Corey; Wong, Lai Hong; Lee, Amy Huei-Yi; Giaever, Guri

2016-09-01

The ability to measure and quantify the fitness of an entire organism requires considerably more complex approaches than simply using traditional "omic" methods that examine, for example, the abundance of RNA transcripts, proteins, or metabolites. The yeast deletion collections represent the only systematic, comprehensive set of null alleles for any organism in which such fitness measurements can be assayed. Generated by the Saccharomyces Genome Deletion Project, these collections allow the systematic and parallel analysis of gene functions using any measurable phenotype. The unique 20-bp molecular barcodes engineered into the genome of each deletion strain facilitate the massively parallel analysis of individual fitness. Here, we present functional genomic protocols for use with the yeast deletion collections. We describe how to maintain, propagate, and store the deletion collections and how to perform growth fitness assays on single and parallel screening platforms. Phenotypic fitness analyses of the yeast mutants, described in brief here, provide important insights into biological functions, mechanisms of drug action, and response to environmental stresses. It is important to bear in mind that the specific assays described in this protocol represent some of the many ways in which these collections can be assayed, and in this description particular attention is paid to maximizing throughput using growth as the phenotypic measure. © 2016 Cold Spring Harbor Laboratory Press.

Strategies for successful trauma registry implementation in low- and middle-income countries-protocol for a systematic review.

PubMed

Paradis, Tiffany; St-Louis, Etienne; Landry, Tara; Poenaru, Dan

2018-02-21

The benefits of trauma registries have been well described. The crucial data they provide may guide injury prevention strategies, inform resource allocation, and support advocacy and policy. This has been shown to reduce trauma-related mortality in various settings. Trauma remains a leading cause of mortality in low- and middle-income countries (LMICs). However, the implementation of trauma registries in LMICs can be challenging due to lack of funding, specialized personnel, and infrastructure. This study explores strategies for successful trauma registry implementation in LMICs. The protocol was registered a priori (CRD42017058586). A peer-reviewed search strategy of multiple databases will be developed with a senior librarian. As per PRISMA guidelines, first screen of references based on abstract and title and subsequent full-text review will be conducted by two independent reviewers. Disagreements that cannot be resolved by discussion between reviewers shall be arbitrated by the principal investigator. Data extraction will be performed using a pre-defined data extraction sheet. Finally, bibliographies of included articles will be hand-searched. Studies of any design will be included if they describe or review development and implementation of a trauma registry in LMICs. No language or period restrictions will be applied. Summary statistics and qualitative meta-narrative analyses will be performed. The significant burden of trauma in LMIC environments presents unique challenges and limitations. Adapted strategies for deployment and maintenance of sustainable trauma registries are needed. Our methodology will systematically identify recommendations and strategies for successful trauma registry implementation in LMICs and describe threats and barriers to this endeavor. The protocol was registered on the PROSPERO international prospective register of systematic reviews ( CRD42017058586 ).

[Management of bluespotted stingray injuries in Djibouti from July 2008 to July 2009].

PubMed

Aigle, L; Lions, C; Mottier, F; Ollivier, L

2010-06-01

Although stingray injuries have always been frequent in the Republic of Djibouti, it was not until July 2008 that the Bouffard Hospital developed a standardised management protocol. The purpose of this report is to describe that protocol and evaluate its impact on the outcome of stingray injuries based on a prospective study for the period between July 2008 and July 2009. During the study period, 12 stingray stings were treated. The treatment protocol that is based on a multidisciplinary approach involving the intensivist, anaesthesiologist, and surgeon achieved wound healing within one month. This outcome contrasts with previous publications that have generally described longer healing times with frequent infectious complications.

Reverse transcription polymerase chain reaction protocols for cloning small circular RNAs.

PubMed

Navarro, B; Daròs, J A; Flores, R

1998-07-01

A protocol is described for general application for cloning small circular RNAs which requires only minimal amounts of template (approximately 50 ng) of unknown sequence. Both cDNA strands are synthesized with a 26-mer primer whose six 3'-terminal positions are totally degenerate in two consecutive reactions catalyzed by reverse transcriptase and DNA polymerase, respectively. The cDNAs are then PCR-amplified, using a 20-mer primer with the non-degenerate sequence of the previous primer, cloned and sequenced. This information permits the synthesis of one or more pairs of specific and adjacent primers for obtaining full-length cDNA clones by a protocol which is also described.

Somatic Embryogenesis in Two Orchid Genera (Cymbidium, Dendrobium).

PubMed

da Silva, Jaime A Teixeira; Winarto, Budi

2016-01-01

The protocorm-like body (PLB) is the de facto somatic embryo in orchids. Here we describe detailed protocols for two orchid genera (hybrid Cymbidium Twilight Moon 'Day Light' and Dendrobium 'Jayakarta', D. 'Gradita 31', and D. 'Zahra FR 62') for generating PLBs. These protocols will most likely have to be tweaked for different cultivars as the response of orchids in vitro tends to be dependent on genotype. In addition to primary somatic embryogenesis, secondary (or repetitive) somatic embryogenesis is also described for both genera. The use of thin cell layers as a sensitive tissue assay is outlined for hybrid Cymbidium while the protocol outlined is suitable for bioreactor culture of D. 'Zahra FR 62'.

New Protocol Based on UHPLC-MS/MS for Quantitation of Metabolites in Xylose-Fermenting Yeasts

NASA Astrophysics Data System (ADS)

Campos, Christiane Gonçalves; Veras, Henrique César Teixeira; de Aquino Ribeiro, José Antônio; Costa, Patrícia Pinto Kalil Gonçalves; Araújo, Katiúscia Pereira; Rodrigues, Clenilson Martins; de Almeida, João Ricardo Moreira; Abdelnur, Patrícia Verardi

2017-12-01

Xylose fermentation is a bottleneck in second-generation ethanol production. As such, a comprehensive understanding of xylose metabolism in naturally xylose-fermenting yeasts is essential for prospection and construction of recombinant yeast strains. The objective of the current study was to establish a reliable metabolomics protocol for quantification of key metabolites of xylose catabolism pathways in yeast, and to apply this protocol to Spathaspora arborariae. Ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS) was used to quantify metabolites, and afterwards, sample preparation was optimized to examine yeast intracellular metabolites. S. arborariae was cultivated using xylose as a carbon source under aerobic and oxygen-limited conditions. Ion pair chromatography (IPC) and hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) were shown to efficiently quantify 14 and 5 metabolites, respectively, in a more rapid chromatographic protocol than previously described. Thirteen and eleven metabolites were quantified in S. arborariae under aerobic and oxygen-limited conditions, respectively. This targeted metabolomics protocol is shown here to quantify a total of 19 metabolites, including sugars, phosphates, coenzymes, monosaccharides, and alcohols, from xylose catabolism pathways (glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle) in yeast. Furthermore, to our knowledge, this is the first time that intracellular metabolites have been quantified in S. arborariae after xylose consumption. The results indicated that fine control of oxygen levels during fermentation is necessary to optimize ethanol production by S. arborariae. The protocol presented here may be applied to other yeast species and could support yeast genetic engineering to improve second generation ethanol production. [Figure not available: see fulltext.

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.

Milrinone and homeostasis to treat cerebral vasospasm associated with subarachnoid hemorrhage: the Montreal Neurological Hospital protocol.

PubMed

Lannes, Marcelo; Teitelbaum, Jeanne; del Pilar Cortés, Maria; Cardoso, Mauro; Angle, Mark

2012-06-01

For the treatment of cerebral vasospasm, current therapies have focused on increasing blood flow through blood pressure augmentation, hypervolemia, the use of intra-arterial vasodilators, and angioplasty of proximal cerebral vessels. Through a large case series, we present our experience of treating cerebral vasospasm with a protocol based on maintenance of homeostasis (correction of electrolyte and glucose disturbances, prevention and treatment of hyperthermia, replacement of fluid losses), and the use of intravenous milrinone to improve microcirculation (the Montreal Neurological Hospital protocol). Our objective is to describe the use milrinone in our practice and the neurological outcomes associated with this approach. Large case series based on the review of all patients diagnosed with delayed ischemic neurologic deficits after aneurysmal subarachnoid hemorrhage between April 1999 and April 2006. 88 patients were followed for a mean time of 44.6 months. An intravenous milrinone infusion was used for a mean of 9.8 days without any significant side effects. No medical complications associated with this protocol were observed. There were five deaths; of the surviving patients, 48.9 % were able to go back to their previous baseline and 75 % had a good functional outcome (modified Rankin scale ≤ 2). A protocol using intravenous milrinone, and the maintenance of homeostasis is simple to use and requires less intensive monitoring and resources than the standard triple H therapy. Despite the obvious limitations of this study's design, we believe that it would be now appropriate to proceed with formal prospective studies of this protocol.

The Interface of Clinical Decision-Making With Study Protocols for Knowledge Translation From a Walking Recovery Trial.

PubMed

Hershberg, Julie A; Rose, Dorian K; Tilson, Julie K; Brutsch, Bettina; Correa, Anita; Gallichio, Joann; McLeod, Molly; Moore, Craig; Wu, Sam; Duncan, Pamela W; Behrman, Andrea L

2017-01-01

Despite efforts to translate knowledge into clinical practice, barriers often arise in adapting the strict protocols of a randomized, controlled trial (RCT) to the individual patient. The Locomotor Experience Applied Post-Stroke (LEAPS) RCT demonstrated equal effectiveness of 2 intervention protocols for walking recovery poststroke; both protocols were more effective than usual care physical therapy. The purpose of this article was to provide knowledge-translation tools to facilitate implementation of the LEAPS RCT protocols into clinical practice. Participants from 2 of the trial's intervention arms: (1) early Locomotor Training Program (LTP) and (2) Home Exercise Program (HEP) were chosen for case presentation. The two cases illustrate how the protocols are used in synergy with individual patient presentations and clinical expertise. Decision algorithms and guidelines for progression represent the interface between implementation of an RCT standardized intervention protocol and clinical decision-making. In each case, the participant presents with a distinct clinical challenge that the therapist addresses by integrating the participant's unique presentation with the therapist's expertise while maintaining fidelity to the LEAPS protocol. Both participants progressed through an increasingly challenging intervention despite their own unique presentation. Decision algorithms and exercise progression for the LTP and HEP protocols facilitate translation of the RCT protocol to the real world of clinical practice. The two case examples to facilitate translation of the LEAPS RCT into clinical practice by enhancing understanding of the protocols, their progression, and their application to individual participants.Video Abstract available for more insights from the authors (see Supplemental Digital Content 1, available at: http://links.lww.com/JNPT/A147).

Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols.

PubMed

Campagne, Fabien

2008-02-29

The evaluation of information retrieval techniques has traditionally relied on human judges to determine which documents are relevant to a query and which are not. This protocol is used in the Text Retrieval Evaluation Conference (TREC), organized annually for the past 15 years, to support the unbiased evaluation of novel information retrieval approaches. The TREC Genomics Track has recently been introduced to measure the performance of information retrieval for biomedical applications. We describe two protocols for evaluating biomedical information retrieval techniques without human relevance judgments. We call these protocols No Title Evaluation (NT Evaluation). The first protocol measures performance for focused searches, where only one relevant document exists for each query. The second protocol measures performance for queries expected to have potentially many relevant documents per query (high-recall searches). Both protocols take advantage of the clear separation of titles and abstracts found in Medline. We compare the performance obtained with these evaluation protocols to results obtained by reusing the relevance judgments produced in the 2004 and 2005 TREC Genomics Track and observe significant correlations between performance rankings generated by our approach and TREC. Spearman's correlation coefficients in the range of 0.79-0.92 are observed comparing bpref measured with NT Evaluation or with TREC evaluations. For comparison, coefficients in the range 0.86-0.94 can be observed when evaluating the same set of methods with data from two independent TREC Genomics Track evaluations. We discuss the advantages of NT Evaluation over the TRels and the data fusion evaluation protocols introduced recently. Our results suggest that the NT Evaluation protocols described here could be used to optimize some search engine parameters before human evaluation. Further research is needed to determine if NT Evaluation or variants of these protocols can fully substitute for human evaluations.

Feasibility and effect of home-based therapy programmes for children with cerebral palsy: a protocol for a systematic review.

PubMed

Beckers, L W M E; Schnackers, M L A P; Janssen-Potten, Y J; Kleijnen, J; Steenbergen, B

2017-02-24

Given the promising advantages of upper extremity home-based programmes in children with cerebral palsy (CP), a systematic review of the available literature on this topic is warranted. The purpose of the systematic review described in this protocol is to investigate currently available home-based occupational therapy and physiotherapy programmes regarding both their feasibility and effect. This protocol describes a systematic review, developed in accordance with the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P) 2015. Studies will be included in which primary data are collected, participants are children aged <18 years with any type of CP and the intervention of interest is a home-based occupational therapy or physiotherapy intervention. Comparators of interest are: no therapy, care as usual, centre-based occupational therapy or physiotherapy, an alternative home-based programme and a medical intervention. Studies will be included that report either on feasibility (ie, acceptability, demand, implementation, practicality, adaptation, expansion or integration) or on efficacy/effectiveness (ie, child-related upper extremity outcomes within all International Classification of Functioning, Disability and Health levels or parent-related/caregiver-related outcomes on the psychological and social domain). Relevant studies will be identified by searching the databases MEDLINE, EMBASE, CINAHL, PsycINFO, PEDro, OTSeeker and CPCI-S as well as the trial registers ICTRP and CENTRAL, the reference lists of included records and by circulating a bibliography of the included records to authors of included studies. There will be no restrictions on language or year of publication. The search strategy consists of terms related to the population and intervention. Data will be extracted in duplicate using a digital data extraction form. The proposed study does not involve collection of primary data. Accordingly, no ethical approval is required. The authors will disseminate the findings of this systematic review through publication in a peer-reviewed journal and conference presentation(s). CRD42016043743; pre-results. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

A protocol using coho salmon to monitor Tongass National Forest Land and Resource Management Plan standards and guidelines for fish habitat.

Treesearch

M.D. Bryant; Trent McDonald; R. Aho; B.E. Wright; Michelle Bourassa Stahl

2008-01-01

We describe a protocol to monitor the effectiveness of the Tongass Land Management Plan (TLMP) management standards for maintaining fish habitat. The protocol uses juvenile coho salmon (Oncorhynchus kisutch) in small tributary streams in forested watersheds. We used a 3-year pilot study to develop detailed methods to estimate juvenile salmonid...

Repetitive Transcranial Magnetic Stimulation for the Treatment of Executive Function Deficits in Autism Spectrum Disorder: Clinical Trial Approach.

PubMed

Ameis, Stephanie H; Daskalakis, Zafiris J; Blumberger, Daniel M; Desarkar, Pushpal; Drmic, Irene; Mabbott, Donald J; Lai, Meng-Chuan; Croarkin, Paul E; Szatmari, Peter

2017-06-01

Executive function (EF) deficits in patients with autism spectrum disorder (ASD) are ubiquitous and understudied. Further, there are no effective, neuroscience-based treatments to address this impairing feature of ASD. Repetitive transcranial magnetic stimulation (rTMS) has demonstrated promise in addressing EF deficits in adult neuropsychiatric disorders. This article will outline the design of a novel randomized-controlled trial of bilateral, 20 Hz, rTMS applied to the dorsolateral prefrontal cortex (DLPFC) for treatment of EF deficits in ASD that is currently ongoing. We describe prior therapeutic rTMS research for ASD and prior rTMS trials targeting EFs in adult neuropsychiatric disorders. A neurophysiological rationale for rTMS treatment of EF deficits in ASD is presented. An ongoing protocol will enroll participants aged 16-35 with ASD and no intellectual disability. Psychotropic medications will be continued during the 4-week trial of active 20 Hz versus sham rTMS applied to the DLPFC. Twenty, active treatment sessions consisting of 25 stimulation trains at a 90% motor threshold will be administered. The primary outcome measure is the Cambridge Neuropsychological Test Automated Battery (CANTAB) spatial working memory task. At present, recruitment, enrollment, and treatment within the described clinical trial are ongoing. EF deficits are common and impairing symptoms of ASD. There are no evidence-based treatments for EF deficits in ASD. The protocol described here will provide important preliminary data on the feasibility and efficacy of 20 Hz rTMS to DLPFC for EF deficits in ASD.

GreenChill Store Certification Protocol for Sub-Cooling Contained on Racks Separate from Refrigeration Equipment

EPA Pesticide Factsheets

Document describes the protocol used to determine the total load and refrigerant charge of stores that have placed all sub-cooling on a rack separate from all other commercial refrigeration equipment.

Protocol for selecting ASR-affected structures for lithium treatment

DOT National Transportation Integrated Search

2006-02-01

This TechBrief describes a protocol for evaluating damaged concrete structures to determine whether they are suitable candidates for lithium treatment to address alkali-silica reactivity (ASR). A major part of the TechBrief's source document, Protoco...

Agents Based e-Commerce and Securing Exchanged Information

NASA Astrophysics Data System (ADS)

Al-Jaljouli, Raja; Abawajy, Jemal

Mobile agents have been implemented in e-Commerce to search and filter information of interest from electronic markets. When the information is very sensitive and critical, it is important to develop a novel security protocol that can efficiently protect the information from malicious tampering as well as unauthorized disclosure or at least detect any malicious act of intruders. In this chapter, we describe robust security techniques that ensure a sound security of information gathered throughout agent’s itinerary against various security attacks, as well as truncation attacks. A sound security protocol is described, which implements the various security techniques that would jointly prevent or at least detect any malicious act of intruders. We reason about the soundness of the protocol usingSymbolic Trace Analyzer (STA), a formal verification tool that is based on symbolic techniques. We analyze the protocol in key configurations and show that it is free of flaws. We also show that the protocol fulfils the various security requirements of exchanged information in MAS, including data-integrity, data-confidentiality, data-authenticity, origin confidentiality and data non-repudiability.

The Xpress Transfer Protocol (XTP): A tutorial (expanded version)

NASA Technical Reports Server (NTRS)

Sanders, Robert M.; Weaver, Alfred C.

1990-01-01

The Xpress Transfer Protocol (XTP) is a reliable, real-time, light weight transfer layer protocol. Current transport layer protocols such as DoD's Transmission Control Protocol (TCP) and ISO's Transport Protocol (TP) were not designed for the next generation of high speed, interconnected reliable networks such as fiber distributed data interface (FDDI) and the gigabit/second wide area networks. Unlike all previous transport layer protocols, XTP is being designed to be implemented in hardware as a VLSI chip set. By streamlining the protocol, combining the transport and network layers and utilizing the increased speed and parallelization possible with a VLSI implementation, XTP will be able to provide the end-to-end data transmission rates demanded in high speed networks without compromising reliability and functionality. This paper describes the operation of the XTP protocol and in particular, its error, flow and rate control; inter-networking addressing mechanisms; and multicast support features, as defined in the XTP Protocol Definition Revision 3.4.

A Novel Quantum Solution to Privacy-Preserving Nearest Neighbor Query in Location-Based Services

NASA Astrophysics Data System (ADS)

Luo, Zhen-yu; Shi, Run-hua; Xu, Min; Zhang, Shun

2018-04-01

We present a cheating-sensitive quantum protocol for Privacy-Preserving Nearest Neighbor Query based on Oblivious Quantum Key Distribution and Quantum Encryption. Compared with the classical related protocols, our proposed protocol has higher security, because the security of our protocol is based on basic physical principles of quantum mechanics, instead of difficulty assumptions. Especially, our protocol takes single photons as quantum resources and only needs to perform single-photon projective measurement. Therefore, it is feasible to implement this protocol with the present technologies.

Dynamics of Nafion membrane swelling in H2O/D2O mixtures as studied using FTIR technique

NASA Astrophysics Data System (ADS)

Bunkin, Nikolai F.; Kozlov, Valeriy A.; Shkirin, Alexey V.; Ninham, Barry W.; Balashov, Anatoliy A.; Gudkov, Sergey V.

2018-03-01

Experiments with Fourier transform spectrometry of Nafion, a water-swollen polymeric membrane, are described. The transmittance spectra of liquid samples and Nafion, soaked in these samples, were studied, depending on the deuterium content in water in the spectral range 1.8-2.15 μm. The experiments were carried out using two protocols: in the first protocol we studied the dynamics of Nafion swelling in H2O + D2O mixtures for the deuterium concentrations 3 < C < 104 ppm, and in the second protocol we studied the dynamics of swelling in pure heavy water (C = 106 ppm). For liquid mixtures in the concentration range 3 < C < 104 ppm, the transmittance spectra are the same, but for Nafion soaked in these fluids, the corresponding spectra are different. It is shown that, in the range of deuterium contents C = 90-500 ppm, the behavior of transmittance of the polymer membrane is non-monotonic. In experiments using the second protocol, the dynamics of diffusion replacement of residual water, which is always present in the bulk of the polymer membrane inside closed cavities (i.e., without access to atmospheric air), were studied. The experimentally estimated diffusion coefficient for this process is ≈6.10-11 cm2/s.

Sampling protocol for post-landfall Deepwater Horizon oil release, Gulf of Mexico, 2010

USGS Publications Warehouse

Wilde, F.D.; Skrobialowski, S.C.; Hart, J.S.

2010-01-01

The protocols and procedures described in this report are designed to be used by U.S. Geological Survey (USGS) field teams for the collection of environmental data and samples in coastal areas affected by the 2010 Deepwater Horizon oil spill in the Gulf of Mexico. This sampling protocol focuses specifically on sampling for water, sediments, benthic invertebrates, and microorganisms (ambient bacterial populations) after shoreline arrival of petroleum-associated product on beach, barrier island, and wetland environments of the Gulf of Mexico coastal states. Deployment to sampling sites, site setup, and sample collection in these environments necessitates modifications to standard USGS sampling procedures in order to address the regulatory, logistical, and legal requirements associated with samples collected in oil-impacted coastal areas. This document, therefore, has been written as an addendum to the USGS National Field Manual for the Collection of Water-Quality Data (NFM) (http://pubs.water.usgs.gov/twri9A/), which provides the basis for training personnel in the use of standard USGS sampling protocols. The topics covered in this Gulf of Mexico oil-spill sampling protocol augment NFM protocols for field-deployment preparations, health and safety precautions, sampling and quality-assurance procedures, and decontamination requirements under potentially hazardous environmental conditions. Documentation procedures and maintenance of sample integrity by use of chain-of-custody procedures also are described in this protocol.

A lightweight neighbor-info-based routing protocol for no-base-station taxi-call system.

PubMed

Zhu, Xudong; Wang, Jinhang; Chen, Yunchao

2014-01-01

Since the quick topology change and short connection duration, the VANET has had unstable routing and wireless signal quality. This paper proposes a kind of lightweight routing protocol-LNIB for call system without base station, which is applicable to the urban taxis. LNIB maintains and predicts neighbor information dynamically, thus finding the reliable path between the source and the target. This paper describes the protocol in detail and evaluates the performance of this protocol by simulating under different nodes density and speed. The result of evaluation shows that the performance of LNIB is better than AODV which is a classic protocol in taxi-call scene.

Compliance with AAPM Practice Guideline 1.a: CT Protocol Management and Review — from the perspective of a university hospital

PubMed Central

Bour, Robert K.; Pozniak, Myron; Ranallo, Frank N.

2015-01-01

The purpose of this paper is to describe our experience with the AAPM Medical Physics Practice Guideline 1.a: “CT Protocol Management and Review Practice Guideline”. Specifically, we will share how our institution's quality management system addresses the suggestions within the AAPM practice report. We feel this paper is needed as it was beyond the scope of the AAPM practice guideline to provide specific details on fulfilling individual guidelines. Our hope is that other institutions will be able to emulate some of our practices and that this article would encourage other types of centers (e.g., community hospitals) to share their methodology for approaching CT protocol optimization and quality control. Our institution had a functioning CT protocol optimization process, albeit informal, since we began using CT. Recently, we made our protocol development and validation process compliant with a number of the ISO 9001:2008 clauses and this required us to formalize the roles of the members of our CT protocol optimization team. We rely heavily on PACS‐based IT solutions for acquiring radiologist feedback on the performance of our CT protocols and the performance of our CT scanners in terms of dose (scanner output) and the function of the automatic tube current modulation. Specific details on our quality management system covering both quality control and ongoing optimization have been provided. The roles of each CT protocol team member have been defined, and the critical role that IT solutions provides for the management of files and the monitoring of CT protocols has been reviewed. In addition, the invaluable role management provides by being a champion for the project has been explained; lack of a project champion will mitigate the efforts of a CT protocol optimization team. Meeting the guidelines set forth in the AAPM practice guideline was not inherently difficult, but did, in our case, require the cooperation of radiologists, technologists, physicists, IT, administrative staff, and hospital management. Some of the IT solutions presented in this paper are novel and currently unique to our institution. PACS number: 87.57.Q PMID:26103176

Phytoplankton IF-FISH: Species-specific labeling of cellular proteins by immunofluorescence (IF) with simultaneous species identification by fluorescence immunohybridization (FISH).

PubMed

Meek, Megan E; Van Dolah, Frances M

2016-05-01

Phytoplankton rarely occur as unialgal populations. Therefore, to study species-specific protein expression, indicative of physiological status in natural populations, methods are needed that will both assay for a protein of interest and identify the species expressing it. Here we describe a protocol for IF-FISH, a dual labeling procedure using immunofluorescence (IF) labeling of a protein of interest followed by fluorescence in situ hybridization (FISH) to identify the species expressing that protein. The protocol was developed to monitor expression of the cell cycle marker proliferating cell nuclear antigen (PCNA) in the red tide dinoflagellate, Karenia brevis, using a large subunit (LSU) rRNA probe to identify K. brevis in a mixed population of morphologically similar Karenia species. We present this protocol as proof of concept that IF-FISH can be successfully applied to phytoplankton cells. This method is widely applicable for the analysis of single-cell protein expression of any protein of interest within phytoplankton communities. Copyright © 2016 Elsevier B.V. All rights reserved.

Protocols and characterization data for 2D, 3D, and slice-based tumor models from the PREDECT project.

PubMed

de Hoogt, Ronald; Estrada, Marta F; Vidic, Suzana; Davies, Emma J; Osswald, Annika; Barbier, Michael; Santo, Vítor E; Gjerde, Kjersti; van Zoggel, Hanneke J A A; Blom, Sami; Dong, Meng; Närhi, Katja; Boghaert, Erwin; Brito, Catarina; Chong, Yolanda; Sommergruber, Wolfgang; van der Kuip, Heiko; van Weerden, Wytske M; Verschuren, Emmy W; Hickman, John; Graeser, Ralph

2017-11-21

Two-dimensional (2D) culture of cancer cells in vitro does not recapitulate the three-dimensional (3D) architecture, heterogeneity and complexity of human tumors. More representative models are required that better reflect key aspects of tumor biology. These are essential studies of cancer biology and immunology as well as for target validation and drug discovery. The Innovative Medicines Initiative (IMI) consortium PREDECT (www.predect.eu) characterized in vitro models of three solid tumor types with the goal to capture elements of tumor complexity and heterogeneity. 2D culture and 3D mono- and stromal co-cultures of increasing complexity, and precision-cut tumor slice models were established. Robust protocols for the generation of these platforms are described. Tissue microarrays were prepared from all the models, permitting immunohistochemical analysis of individual cells, capturing heterogeneity. 3D cultures were also characterized using image analysis. Detailed step-by-step protocols, exemplary datasets from the 2D, 3D, and slice models, and refined analytical methods were established and are presented.

Protocols and characterization data for 2D, 3D, and slice-based tumor models from the PREDECT project

PubMed Central

de Hoogt, Ronald; Estrada, Marta F.; Vidic, Suzana; Davies, Emma J.; Osswald, Annika; Barbier, Michael; Santo, Vítor E.; Gjerde, Kjersti; van Zoggel, Hanneke J. A. A.; Blom, Sami; Dong, Meng; Närhi, Katja; Boghaert, Erwin; Brito, Catarina; Chong, Yolanda; Sommergruber, Wolfgang; van der Kuip, Heiko; van Weerden, Wytske M.; Verschuren, Emmy W.; Hickman, John; Graeser, Ralph

2017-01-01

Two-dimensional (2D) culture of cancer cells in vitro does not recapitulate the three-dimensional (3D) architecture, heterogeneity and complexity of human tumors. More representative models are required that better reflect key aspects of tumor biology. These are essential studies of cancer biology and immunology as well as for target validation and drug discovery. The Innovative Medicines Initiative (IMI) consortium PREDECT (www.predect.eu) characterized in vitro models of three solid tumor types with the goal to capture elements of tumor complexity and heterogeneity. 2D culture and 3D mono- and stromal co-cultures of increasing complexity, and precision-cut tumor slice models were established. Robust protocols for the generation of these platforms are described. Tissue microarrays were prepared from all the models, permitting immunohistochemical analysis of individual cells, capturing heterogeneity. 3D cultures were also characterized using image analysis. Detailed step-by-step protocols, exemplary datasets from the 2D, 3D, and slice models, and refined analytical methods were established and are presented. PMID:29160867

Visualization of cortical, subcortical, and deep brain neural circuit dynamics during naturalistic mammalian behavior with head-mounted microscopes and chronically implanted lenses

PubMed Central

Resendez, Shanna L.; Jennings, Josh H.; Ung, Randall L.; Namboodiri, Vijay Mohan K.; Zhou, Zhe Charles; Otis, James M.; Nomura, Hiroshi; McHenry, Jenna A.; Kosyk, Oksana; Stuber, Garret D.

2016-01-01

Genetically encoded calcium indicators for visualizing dynamic cellular activity have greatly expanded our understanding of the brain. However, due to light scattering properties of the brain as well as the size and rigidity of traditional imaging technology, in vivo calcium imaging has been limited to superficial brain structures during head fixed behavioral tasks. This limitation can now be circumvented by utilizing miniature, integrated microscopes in conjunction with an implantable microendoscopic lens to guide light into and out of the brain, thus permitting optical access to deep brain (or superficial) neural ensembles during naturalistic behaviors. Here, we describe procedural steps to conduct such imaging studies using mice. However, we anticipate the protocol can be easily adapted for use in other small vertebrates. Successful completion of this protocol will permit cellular imaging of neuronal activity and the generation of data sets with sufficient statistical power to correlate neural activity with stimulus presentation, physiological state, and other aspects of complex behavioral tasks. This protocol takes 6–11 weeks to complete. PMID:26914316

Effectiveness of Serious Games for Leap Motion on the Functionality of the Upper Limb in Parkinson's Disease: A Feasibility Study.

PubMed

Oña, Edwin Daniel; Balaguer, Carlos; Cano-de la Cuerda, Roberto; Collado-Vázquez, Susana; Jardón, Alberto

2018-01-01

The design and application of Serious Games (SG) based on the Leap Motion sensor are presented as a tool to support the rehabilitation therapies for upper limbs. Initially, the design principles and their implementation are described, focusing on improving both unilateral and bilateral manual dexterity and coordination. The design of the games has been supervised by specialized therapists. To assess the therapeutic effectiveness of the proposed system, a protocol of trials with Parkinson's patients has been defined. Evaluations of the physical condition of the participants in the study, at the beginning and at the end of the treatment, are carried out using standard tests. The specific measurements of each game give the therapist more detailed information about the patients' evolution after finishing the planned protocol. The obtained results support the fact that the set of developed video games can be combined to define different therapy protocols and that the information obtained is richer than the one obtained through current clinical metrics, serving as method of motor function assessment.

Effectiveness of Serious Games for Leap Motion on the Functionality of the Upper Limb in Parkinson's Disease: A Feasibility Study

PubMed Central

Balaguer, Carlos; Collado-Vázquez, Susana; Jardón, Alberto

2018-01-01

The design and application of Serious Games (SG) based on the Leap Motion sensor are presented as a tool to support the rehabilitation therapies for upper limbs. Initially, the design principles and their implementation are described, focusing on improving both unilateral and bilateral manual dexterity and coordination. The design of the games has been supervised by specialized therapists. To assess the therapeutic effectiveness of the proposed system, a protocol of trials with Parkinson's patients has been defined. Evaluations of the physical condition of the participants in the study, at the beginning and at the end of the treatment, are carried out using standard tests. The specific measurements of each game give the therapist more detailed information about the patients' evolution after finishing the planned protocol. The obtained results support the fact that the set of developed video games can be combined to define different therapy protocols and that the information obtained is richer than the one obtained through current clinical metrics, serving as method of motor function assessment. PMID:29849550

Synthesis of Immunotargeted Magneto-plasmonic Nanoclusters

PubMed Central

Wu, Chun-Hsien; Sokolov, Konstantin

2014-01-01

Magnetic and plasmonic properties combined in a single nanoparticle provide a synergy that is advantageous in a number of biomedical applications including contrast enhancement in novel magnetomotive imaging modalities, simultaneous capture and detection of circulating tumor cells (CTCs), and multimodal molecular imaging combined with photothermal therapy of cancer cells. These applications have stimulated significant interest in development of protocols for synthesis of magneto-plasmonic nanoparticles with optical absorbance in the near-infrared (NIR) region and a strong magnetic moment. Here, we present a novel protocol for synthesis of such hybrid nanoparticles that is based on an oil-in-water microemulsion method. The unique feature of the protocol described herein is synthesis of magneto-plasmonic nanoparticles of various sizes from primary blocks which also have magneto-plasmonic characteristics. This approach yields nanoparticles with a high density of magnetic and plasmonic functionalities which are uniformly distributed throughout the nanoparticle volume. The hybrid nanoparticles can be easily functionalized by attaching antibodies through the Fc moiety leaving the Fab portion that is responsible for antigen binding available for targeting. PMID:25177973

Bowel preparation for pediatric colonoscopy: report of the NASPGHAN endoscopy and procedures committee.

PubMed

Pall, Harpreet; Zacur, George M; Kramer, Robert E; Lirio, Richard A; Manfredi, Michael; Shah, Manoj; Stephen, Thomas C; Tucker, Neil; Gibbons, Troy E; Sahn, Benjamin; McOmber, Mark; Friedlander, Joel; Quiros, J A; Fishman, Douglas S; Mamula, Petar

2014-09-01

Pediatric bowel preparation protocols used before colonoscopy vary greatly, with no identified standard practice. The present clinical report reviews the evidence for several bowel preparations in children and reports on their use among North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition members. Publications in the pediatric literature for bowel preparation regimens are described, including mechanisms of action, efficacy and ease of use, and pediatric studies. A survey distributed to pediatric gastroenterology programs across the country reviews present national practice, and cleanout recommendations are provided. Finally, further areas for research are identified.

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

High-Performance CCSDS AOS Protocol Implementation in FPGA

NASA Technical Reports Server (NTRS)

Clare, Loren P.; Torgerson, Jordan L.; Pang, Jackson

2010-01-01

The Consultative Committee for Space Data Systems (CCSDS) Advanced Orbiting Systems (AOS) space data link protocol provides a framing layer between channel coding such as LDPC (low-density parity-check) and higher-layer link multiplexing protocols such as CCSDS Encapsulation Service, which is described in the following article. Recent advancement in RF modem technology has allowed multi-megabit transmission over space links. With this increase in data rate, the CCSDS AOS protocol implementation needs to be optimized to both reduce energy consumption and operate at a high rate.

Hybrid protocols plus natural treatments for inflammatory conditions.

PubMed

1998-01-01

Hybrid protocols combine one, two, or three pharmaceutical drugs with several nutritional or immune-based therapies. These protocols are not limited solely to FDA-approved drugs or strictly to alternative therapies. The rationale for using a hybrid protocol is to find an effective antiviral regimen that also restores immune function. The goal is to obtain the benefits of protease inhibitors without viral resistance and side effects which include problems with fat metabolism and cholesterol levels. Natural treatments for inflammatory conditions are also described. Options include licorice root, ginger root, and slippery elm.

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.

Efficient Group Coordination in Multicast Trees

DTIC Science & Technology

2001-01-01

describe a novel protocol to coordinate multipoint groupwork within the IP-multicast framework. The protocol supports Internet-wide coordination for large...and highly-interactive groupwork , relying on the dissemination of coordination directives among group members across a shared end-to-end multicast

GENERIC VERIFICATION PROTOCOL FOR AQUEOUS CLEANER RECYCLING TECHNOLOGIES

EPA Science Inventory

This generic verification protocol has been structured based on a format developed for ETV-MF projects. This document describes the intended approach and explain plans for testing with respect to areas such as test methodology, procedures, parameters, and instrumentation. Also ...

Thermolysis of Geminal Diazides: Reagent-Free Synthesis of 3-Hydroxypyridines.

PubMed

Erhardt, Hellmuth; Kunz, Kevin A; Kirsch, Stefan F

2017-01-06

An operationally simple protocol for the rapid and efficient construction of highly substituted 3-hydroxypyridines is presented. The thermally induced cyclization of easily constructed geminal diazides derived from β-ketoesters having an additional olefin moiety affords the title compounds in yields up to 97% under reagent-free conditions. The new method allows for the synthesis of preparative quantities of material. Additionally, the synthetic utility of the pyridine products for the synthesis of valuable heterocycles is described.

USEPA/USGS Sample Collection Protocol for Bacterial ...

EPA Pesticide Factsheets

Report/SOP This Sample Collection Procedure (SCP) describes the activities and considerations for the collection of bacterial pathogens from representative surface soil samples (0-5 cm). This sampling depth can be reached without the use of a drill rig, direct-push technology, or other mechanized equipment. Analizing soil samples for biothreat agents may, for instance, define the extent of contamination or determine whether the concentrations of contaminants present a risk to public health, welfare, or the environment.

Administration of egg-derived vaccines in patients with history of egg sensitivity.

PubMed

Kletz, M R; Holland, C L; Mendelson, J S; Bielory, L

1990-06-01

A history of a prior hypersensitivity reaction to egg has precluded patients from receiving egg-derived vaccines. We present three cases of successful administration of egg-derived vaccines; specifically influenza and measles, mumps, and rubella (MMR) to patients with egg hypersensitivity. Two were given influenza vaccine without incident and one was successfully desensitized to MMR. Skin testing and desensitization protocols are described. Desensitization to all three components of MMR has not been reported previously.

Research on mobile electronic commerce security technology based on WPKI

NASA Astrophysics Data System (ADS)

Zhang, Bo

2013-07-01

Through the in-depth study on the existing mobile e-commerce and WAP protocols, this paper presents a security solution of e-commerce system based on WPKI, and describes its implementation process and specific implementation details. This solution uniformly distributes the key used by the various participating entities , to fully ensure the confidentiality, authentication, fairness and integrity of mobile e-commerce payments, therefore has some pract ical value for improving the security of e-commerce system.

Quantification of biofilm in microtiter plates: overview of testing conditions and practical recommendations for assessment of biofilm production by staphylococci.

PubMed

Stepanović, Srdjan; Vuković, Dragana; Hola, Veronika; Di Bonaventura, Giovanni; Djukić, Slobodanka; Cirković, Ivana; Ruzicka, Filip

2007-08-01

The details of all steps involved in the quantification of biofilm formation in microtiter plates are described. The presented protocol incorporates information on assessment of biofilm production by staphylococci, gained both by direct experience as well as by analysis of methods for assaying biofilm production. The obtained results should simplify quantification of biofilm formation in microtiter plates, and make it more reliable and comparable among different laboratories.

Development of mini VSAT system

NASA Astrophysics Data System (ADS)

Lu, Shyue-Ching; Chiu, Wu-Jhy; Lin, Hen-Dao; Shih, Mu-Piao

1992-03-01

This paper presents the mini VSAT (very small aperture terminal) system, which is a low cost networking system providing economical alternatives to the business world's datacom needs. The system is designed to achieve the highest possible performance/price ratio for private VSAT networks that range from a few tens of remote terminals to large networks of several thousands remote terminals. The paper describes the system architecture, major features, hardware and software structure, access protocol and performance of the developed system.

A randomized controlled trial of culturally adapted motivational interviewing for Hispanic heavy drinkers: Theory of Adaptation and Study Protocol

PubMed Central

Lee, Christina S.; Colby, Suzanne M.; Magill, Molly; Almeida, Joanna; Tavares, Tonya; Rohsenow, Damaris J.

2016-01-01

Background The NIH Strategic Plan prioritizes health disparities research for socially disadvantaged Hispanics, to reduce the disproportionate burden of alcohol-related negative consequences compared to other racial/ethnic groups. Cultural adaptation of evidence-based treatments, such as motivational interviewing (MI), can improve access and response to alcohol treatment. However, the lack of rigorous clinical trials designed to test the efficacy and theoretical underpinnings of cultural adaptation has made proof of concept difficult. Objective The CAMI2 (Culturally Adapted Motivational Interviewing) study design and its theoretical model, is described to illustrate how MI adapted to social and cultural factors (CAMI) can be discriminated against non-adapted MI. Methods and Design CAMI2, a large, 12 month randomized prospective trial, examines the efficacy of CAMI and MI among heavy drinking Hispanics recruited from the community (n=257). Outcomes are reductions in heavy drinking days (Time Line Follow-Back) and negative consequences of drinking among Hispanics (Drinkers Inventory of Consequences). A second aim examines perceived acculturation stress as a moderator of treatment outcomes in the CAMI condition. Summary The CAMI2 study design protocol is presented and the theory of adaptation is presented. Findings from the trial described may yield important recommendations on the science of cultural adaptation and improve MI dissemination to Hispanics with alcohol risk. PMID:27565832

Robust generation and expansion of skeletal muscle progenitors and myocytes from human pluripotent stem cells.

PubMed

Shelton, Michael; Kocharyan, Avetik; Liu, Jun; Skerjanc, Ilona S; Stanford, William L

2016-05-15

Human pluripotent stem cells provide a developmental model to study early embryonic and tissue development, tease apart human disease processes, perform drug screens to identify potential molecular effectors of in situ regeneration, and provide a source for cell and tissue based transplantation. Highly efficient differentiation protocols have been established for many cell types and tissues; however, until very recently robust differentiation into skeletal muscle cells had not been possible unless driven by transgenic expression of master regulators of myogenesis. Nevertheless, several breakthrough protocols have been published in the past two years that efficiently generate cells of the skeletal muscle lineage from pluripotent stem cells. Here, we present an updated version of our recently described 50-day protocol in detail, whereby chemically defined media are used to drive and support muscle lineage development from initial CHIR99021-induced mesoderm through to PAX7-expressing skeletal muscle progenitors and mature skeletal myocytes. Furthermore, we report an optional method to passage and expand differentiating skeletal muscle progenitors approximately 3-fold every 2weeks using Collagenase IV and continued FGF2 supplementation. Both protocols have been optimized using a variety of human pluripotent stem cell lines including patient-derived induced pluripotent stem cells. Taken together, our differentiation and expansion protocols provide sufficient quantities of skeletal muscle progenitors and myocytes that could be used for a variety of studies. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

An Upgrade on the Rabbit Model of Anthracycline-Induced Cardiomyopathy: Shorter Protocol, Reduced Mortality, and Higher Incidence of Overt Dilated Cardiomyopathy

PubMed Central

Talavera, Jesús; Fernández-Del-Palacio, María Josefa; García-Nicolás, Obdulio; Seva, Juan; Brooks, Gavin; Moraleda, Jose M.

2015-01-01

Current protocols of anthracycline-induced cardiomyopathy in rabbits present with high premature mortality and nephrotoxicity, thus rendering them unsuitable for studies requiring long-term functional evaluation of myocardial function (e.g., stem cell therapy). We compared two previously described protocols to an in-house developed protocol in three groups: Group DOX2 received doxorubicin 2 mg/kg/week (8 weeks); Group DAU3 received daunorubicin 3 mg/kg/week (10 weeks); and Group DAU4 received daunorubicin 4 mg/kg/week (6 weeks). A cohort of rabbits received saline (control). Results of blood tests, cardiac troponin I, echocardiography, and histopathology were analysed. Whilst DOX2 and DAU3 rabbits showed high premature mortality (50% and 33%, resp.), DAU4 rabbits showed 7.6% premature mortality. None of DOX2 rabbits developed overt dilated cardiomyopathy; 66% of DAU3 rabbits developed overt dilated cardiomyopathy and quickly progressed to severe congestive heart failure. Interestingly, 92% of DAU4 rabbits showed overt dilated cardiomyopathy and 67% developed congestive heart failure exhibiting stable disease. DOX2 and DAU3 rabbits showed alterations of renal function, with DAU3 also exhibiting hepatic function compromise. Thus, a shortened protocol of anthracycline-induced cardiomyopathy as in DAU4 group results in high incidence of overt dilated cardiomyopathy, which insidiously progressed to congestive heart failure, associated to reduced systemic compromise and very low premature mortality. PMID:26788502

Aerobic interval exercise improves parameters of nonalcoholic fatty liver disease (NAFLD) and other alterations of metabolic syndrome in obese Zucker rats.

PubMed

Kapravelou, Garyfallia; Martínez, Rosario; Andrade, Ana M; Nebot, Elena; Camiletti-Moirón, Daniel; Aparicio, Virginia A; Lopez-Jurado, Maria; Aranda, Pilar; Arrebola, Francisco; Fernandez-Segura, Eduardo; Bermano, Giovanna; Goua, Marie; Galisteo, Milagros; Porres, Jesus M

2015-12-01

Metabolic syndrome (MS) is a group of metabolic alterations that increase the susceptibility to cardiovascular disease and type 2 diabetes. Nonalcoholic fatty liver disease has been described as the liver manifestation of MS. We aimed to test the beneficial effects of an aerobic interval training (AIT) protocol on different biochemical, microscopic, and functional liver alterations related to the MS in the experimental model of obese Zucker rat. Two groups of lean and obese animals (6 weeks old) followed a protocol of AIT (4 min at 65%-80% of maximal oxygen uptake, followed by 3 min at 50%-65% of maximal oxygen uptake for 45-60 min, 5 days/week, 8 weeks of experimental period), whereas 2 control groups remained sedentary. Obese rats had higher food intake and body weight (P < 0.0001) and suffered significant alterations in plasma lipid profile, area under the curve after oral glucose overload (P < 0.0001), liver histology and functionality, and antioxidant status. The AIT protocol reduced the severity of alterations related to glucose and lipid metabolism and increased the liver protein expression of PPARγ, as well as the gene expression of glutathione peroxidase 4 (P < 0.001). The training protocol also showed significant effects on the activity of hepatic antioxidant enzymes, although this action was greatly influenced by rat phenotype. The present data suggest that AIT protocol is a feasible strategy to improve some of the plasma and liver alterations featured by the MS.

Network-wide BGP route prediction for traffic engineering

NASA Astrophysics Data System (ADS)

Feamster, Nick; Rexford, Jennifer

2002-07-01

The Internet consists of about 13,000 Autonomous Systems (AS's) that exchange routing information using the Border Gateway Protocol (BGP). The operators of each AS must have control over the flow of traffic through their network and between neighboring AS's. However, BGP is a complicated, policy-based protocol that does not include any direct support for traffic engineering. In previous work, we have demonstrated that network operators can adapt the flow of traffic in an efficient and predictable fashion through careful adjustments to the BGP policies running on their edge routers. Nevertheless, many details of the BGP protocol and decision process make predicting the effects of these policy changes difficult. In this paper, we describe a tool that predicts traffic flow at network exit points based on the network topology, the import policy associated with each BGP session, and the routing advertisements received from neighboring AS's. We present a linear-time algorithm that computes a network-wide view of the best BGP routes for each destination prefix given a static snapshot of the network state, without simulating the complex details of BGP message passing. We describe how to construct this snapshot using the BGP routing tables and router configuration files available from operational routers. We verify the accuracy of our algorithm by applying our tool to routing and configuration data from AT&T's commercial IP network. Our route prediction techniques help support the operation of large IP backbone networks, where interdomain routing is an important aspect of traffic engineering.

A reference model for scientific information interchange

NASA Technical Reports Server (NTRS)

Reich, Lou; Sawyer, Don; Davis, Randy

1993-01-01

This paper presents an overview of an Information Interchange Reference Model (IIRM) currently being developed by individuals participating in the Consultative Committee for Space Data Systems (CCSDS) Panel 2, the Planetary Data Systems (PDS), and the Committee on Earth Observing Satellites (CEOS). This is an ongoing research activity and is not an official position by these bodies. This reference model provides a framework for describing and assessing current and proposed methodologies for information interchange within and among the space agencies. It is hoped that this model will improve interoperability between the various methodologies. As such, this model attempts to address key information interchange issues as seen by the producers and users of space-related data and to put them into a coherent framework. Information is understood as the knowledge (e.g., the scientific content) represented by data. Therefore, concern is not primarily on mechanisms for transferring data from user to user (e.g., compact disk read-only memory (CD-ROM), wide-area networks, optical tape, and so forth) but on how information is encoded as data and how the information content is maintained with minimal loss or distortion during transmittal. The model assumes open systems, which means that the protocols or methods used should be fully described and the descriptions publicly available. Ideally these protocols are promoted by recognized standards organizations using processes that permit involvement by those most likely to be affected, thereby enhancing the protocol's stability and the likelihood of wide support.

Biomimetic, Mild Chemical Synthesis of CdTe-GSH Quantum Dots with Improved Biocompatibility

PubMed Central

Pérez-Donoso, José M.; Monrás, Juan P.; Bravo, Denisse; Aguirre, Adam; Quest, Andrew F.; Osorio-Román, Igor O.; Aroca, Ricardo F.; Chasteen, Thomas G.; Vásquez, Claudio C.

2012-01-01

Multiple applications of nanotechnology, especially those involving highly fluorescent nanoparticles (NPs) or quantum dots (QDs) have stimulated the research to develop simple, rapid and environmentally friendly protocols for synthesizing NPs exhibiting novel properties and increased biocompatibility. In this study, a simple protocol for the chemical synthesis of glutathione (GSH)-capped CdTe QDs (CdTe-GSH) resembling conditions found in biological systems is described. Using only CdCl2, K2TeO3 and GSH, highly fluorescent QDs were obtained under pH, temperature, buffer and oxygen conditions that allow microorganisms growth. These CdTe-GSH NPs displayed similar size, chemical composition, absorbance and fluorescence spectra and quantum yields as QDs synthesized using more complicated and expensive methods. CdTe QDs were not freely incorporated into eukaryotic cells thus favoring their biocompatibility and potential applications in biomedicine. In addition, NPs entry was facilitated by lipofectamine, resulting in intracellular fluorescence and a slight increase in cell death by necrosis. Toxicity of the as prepared CdTe QDs was lower than that observed with QDs produced by other chemical methods, probably as consequence of decreased levels of Cd+2 and higher amounts of GSH. We present here the simplest, fast and economical method for CdTe QDs synthesis described to date. Also, this biomimetic protocol favors NPs biocompatibility and helps to establish the basis for the development of new, “greener” methods to synthesize cadmium-containing QDs. PMID:22292028

Applications of a hologram watermarking protocol: aging-aware biometric signature verification and time validity check with personal documents

NASA Astrophysics Data System (ADS)

Vielhauer, Claus; Croce Ferri, Lucilla

2003-06-01

Our paper addresses two issues of a biometric authentication algorithm for ID cardholders previously presented namely the security of the embedded reference data and the aging process of the biometric data. We describe a protocol that allows two levels of verification, combining a biometric hash technique based on handwritten signature and hologram watermarks with cryptographic signatures in a verification infrastructure. This infrastructure consists of a Trusted Central Public Authority (TCPA), which serves numerous Enrollment Stations (ES) in a secure environment. Each individual performs an enrollment at an ES, which provides the TCPA with the full biometric reference data and a document hash. The TCPA then calculates the authentication record (AR) with the biometric hash, a validity timestamp, and a document hash provided by the ES. The AR is then signed with a cryptographic signature function, initialized with the TCPA's private key and embedded in the ID card as a watermark. Authentication is performed at Verification Stations (VS), where the ID card will be scanned and the signed AR is retrieved from the watermark. Due to the timestamp mechanism and a two level biometric verification technique based on offline and online features, the AR can deal with the aging process of the biometric feature by forcing a re-enrollment of the user after expiry, making use of the ES infrastructure. We describe some attack scenarios and we illustrate the watermarking embedding, retrieval and dispute protocols, analyzing their requisites, advantages and disadvantages in relation to security requirements.

The emotional counting Stroop: a task for assessing emotional interference during brain imaging.

PubMed

Whalen, Paul J; Bush, George; Shin, Lisa M; Rauch, Scott L

2006-01-01

The emotional counting Stroop (ecStroop) is an emotional variant of the counting Stroop. Both of these tasks require a motor response instead of a spoken response for the purpose of minimizing head movement during functional MRI (fMRI). During this task, subjects report, by button press, the number of words (1-4) that appear on a screen, regardless of word meaning. Neutral word-control trials contain common words (e.g., 'cabinet' written three times), while interference trials contain emotional words (e.g., 'murder' written three times). The degree to which this task represents a true 'Stroop' interference task, in the sense that emotional words will increase motor-response times compared with neutral words, depends upon the subjects of the study and the words that are presented. Much research on the emotional Stroop task demonstrates that interference effects are observed in psychopathological groups in response to words that are specific to their disorder, and in normal subjects when the words are related to current concerns endorsed by them. The ecStroop task described here will produce reaction time-interference effects that are comparable to the traditional color-naming emotional Stroop. This protocol can be completed in approximately 20 min per subject. The protocol described here employs neutral words and emotional words that include general-negative words, as well as words specific to combat-related trauma. However, this protocol is amenable to any emotional word lists.

Organizational principles of cloud storage to support collaborative biomedical research.

PubMed

Kanbar, Lara J; Shalish, Wissam; Robles-Rubio, Carlos A; Precup, Doina; Brown, Karen; Sant'Anna, Guilherme M; Kearney, Robert E

2015-08-01

This paper describes organizational guidelines and an anonymization protocol for the management of sensitive information in interdisciplinary, multi-institutional studies with multiple collaborators. This protocol is flexible, automated, and suitable for use in cloud-based projects as well as for publication of supplementary information in journal papers. A sample implementation of the anonymization protocol is illustrated for an ongoing study dealing with Automated Prediction of EXtubation readiness (APEX).

Quantum Sensors for the Generating Functional of Interacting Quantum Field Theories

NASA Astrophysics Data System (ADS)

Bermudez, A.; Aarts, G.; Müller, M.

2017-10-01

Difficult problems described in terms of interacting quantum fields evolving in real time or out of equilibrium abound in condensed-matter and high-energy physics. Addressing such problems via controlled experiments in atomic, molecular, and optical physics would be a breakthrough in the field of quantum simulations. In this work, we present a quantum-sensing protocol to measure the generating functional of an interacting quantum field theory and, with it, all the relevant information about its in- or out-of-equilibrium phenomena. Our protocol can be understood as a collective interferometric scheme based on a generalization of the notion of Schwinger sources in quantum field theories, which make it possible to probe the generating functional. We show that our scheme can be realized in crystals of trapped ions acting as analog quantum simulators of self-interacting scalar quantum field theories.

Primary Characterization of Small RNAs in Symbiotic Nitrogen-Fixing Bacteria.

PubMed

Robledo, Marta; García-Tomsig, Natalia I; Jiménez-Zurdo, José I

2018-01-01

High-throughput transcriptome profiling (RNAseq) has uncovered large and heterogeneous populations of small noncoding RNA species (sRNAs) with potential regulatory roles in bacteria. A large fraction of sRNAs are differentially regulated and rely on protein-assisted antisense interactions to trans-encoded target mRNAs to fine-tune posttranscriptional reprogramming of gene expression in response to external cues. However, annotation and function of sRNAs are still largely overlooked in nonmodel bacteria with complex lifestyles. Here, we describe experimental protocols successfully applied for the accurate annotation, expression profiling and target mRNA identification of trans-acting sRNAs in the nitrogen-fixing α-rhizobium Sinorhizobium meliloti. The protocols presented here can be similarly applied for the characterization of trans-sRNAs in genetically tractable α-proteobacteria of agronomical or clinical relevance interacting with eukaryotic hosts.

Chemical warfare agent detection: a review of current trends and future perspective.

PubMed

Pacsial-Ong, Eden Joy; Aguilar, Zoraida P

2013-01-01

The World Health Organization recommends countries to create a public health system that can respond to the deliberate release of chemical warfare agents (CWAs). Procedures for preparedness, response, decontamination protocols and medical countermeasures against CWA attacks are described. Known CWAs, including their properties and pharmacological consequences upon exposure, are tabulated and discussed. Requirements imposed on detection systems by various applications and environmental needs are presented in order to assess the devices for detection and identification of specific CWAs. The review surveys current and near-term detection technologies and equipments, as well as devices that are currently available to the military and civilian first responders. Brief technical discussions of several detection technologies are presented, with emphasis placed in the principles of detection. Finally, enabling technologies that form the basis for advanced sensing systems and devices are described.

Composite material impregnation unit

NASA Technical Reports Server (NTRS)

Wilkinson, S. P.; Marchello, J. M.; Johnston, N. J.

1993-01-01

This memorandum presents an introduction to the NASA multi-purpose prepregging unit which is now installed and fully operational at the Langley Research Center in the Polymeric Materials Branch. A description of the various impregnation methods that are available to the prepregger are presented. Machine operating details and protocol are provided for its various modes of operation. These include, where appropriate, the related equations for predicting the desired prepreg specifications. Also, as the prepregger is modular in its construction, each individual section is described and discussed. Safety concerns are an important factor and a chapter has been included that highlights the major safety features. Initial experiences and observations for fiber impregnation are described. These first observations have given great insight into the areas of future work that need to be addressed. Future memorandums will focus on these individual processes and their related problems.

Experimental Analysis of hFACT Action during Pol II Transcription in vitro

PubMed Central

Hsieh, Fu-Kai; Kulaeva, Olga I.; Studitsky, Vasily M.

2016-01-01

Summary FACT (facilitates chromatin transcription) is a histone chaperone that facilitates transcription through chromatin and promotes histone recovery during transcription. Here, we describe a highly purified experimental system that recapitulates many important properties of transcribed chromatin and the key aspects of hFACT action during this process in vitro. We present the protocols describing how to prepare different forms of nucleosomes, including intact nucleosome, covalently conjugated nucleosome, nucleosome missing one of the two H2A/2B dimers (hexasome) and tetrasome (a nucleosome missing both H2A/2B dimers). These complexes allow analysis of various aspects of FACT’s function. These approaches and other methods described below can also be applied to the study of other chromatin remodelers and chromatin-targeted factors. PMID:25665573

Characterization of an Electroanalytical Instrument Suite Searching for Water and Life on Mars

NASA Technical Reports Server (NTRS)

Bostic, Heidi E.

2005-01-01

Seeking the existence of life on other planets is an essential part of NASA's research. Our terrestrial experience suggests that water is a mandatory resource for life to exist and thrive. However, instruments capable of detecting water at the levels likely to be present on Mars are lacking. This project tests the possibility of using electrical measurements of soils, at variable frequencies, as a water detector. Generally, the electrical resistance of soils can be described as a combination of resistance and capacitance, which can be described by a vector including a magnitude and (phase) angle. By specifically studying the impedance measurements and phase angles of different types of soil, spiked with varying concentrations of dissolved ions, measurements can be taken to provide an idea of the behavior of dry Martian soils. The presentation will describe the experimental technique, apparatus and procedures, as well as results conducted to calibrate the instrument and to establish sample preparation protocols.

SPIRIT 2013 Statement: defining standard protocol items for clinical trials.

PubMed

Chan, An-Wen; Tetzlaff, Jennifer M; Altman, Douglas G; Laupacis, Andreas; Gøtzsche, Peter C; Krle A-Jerić, Karmela; Hrobjartsson, Asbjørn; Mann, Howard; Dickersin, Kay; Berlin, Jesse A; Dore, Caroline J; Parulekar, Wendy R; Summerskill, William S M; Groves, Trish; Schulz, Kenneth F; Sox, Harold C; Rockhold, Frank W; Rennie, Drummond; Moher, David

2015-12-01

The protocol of a clinical trial serves as the foundation for study planning, conduct, reporting, and appraisal. However, trial protocols and existing protocol guidelines vary greatly in content and quality. This article describes the systematic development and scope of SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) 2013, a guideline for the minimum content of a clinical trial protocol. The 33-item SPIRIT checklist applies to protocols for all clinical trials and focuses on content rather than format. The checklist recommends a full description of what is planned; it does not prescribe how to design or conduct a trial. By providing guidance for key content, the SPIRIT recommendations aim to facilitate the drafting of high-quality protocols. Adherence to SPIRIT would also enhance the transparency and completeness of trial protocols for the benefit of investigators, trial participants, patients, sponsors, funders, research ethics committees or institutional review boards, peer reviewers, journals, trial registries, policymakers, regulators, and other key stakeholders.

SPIRIT 2013 Statement: Defining Standard Protocol Items for Clinical Trials

PubMed Central

Chan, An-Wen; Tetzlaff, Jennifer M.; Altman, Douglas G.; Laupacis, Andreas; Gøtzsche, Peter C.; Krleža-Jerić, Karmela; Hróbjartsson, Asbjørn; Mann, Howard; Dickersin, Kay; Berlin, Jesse A.; Doré, Caroline J.; Parulekar, Wendy R.; Summerskill, William S.M.; Groves, Trish; Schulz, Kenneth F.; Sox, Harold C.; Rockhold, Frank W.; Rennie, Drummond; Moher, David

2016-01-01

The protocol of a clinical trial serves as the foundation for study planning, conduct, reporting, and appraisal. However, trial protocols and existing protocol guidelines vary greatly in content and quality. This article describes the systematic development and scope of SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) 2013, a guideline for the minimum content of a clinical trial protocol. The 33-item SPIRIT checklist applies to protocols for all clinical trials and focuses on content rather than format. The checklist recommends a full description of what is planned; it does not prescribe how to design or conduct a trial. By providing guidance for key content, the SPIRIT recommendations aim to facilitate the drafting of high-quality protocols. Adherence to SPIRIT would also enhance the transparency and completeness of trial protocols for the benefit of investigators, trial participants, patients, sponsors, funders, research ethics committees or institutional review boards, peer reviewers, journals, trial registries, policymakers, regulators, and other key stakeholders. PMID:23295957

SPIRIT 2013 statement: defining standard protocol items for clinical trials.

PubMed

Chan, An-Wen; Tetzlaff, Jennifer M; Altman, Douglas G; Laupacis, Andreas; Gøtzsche, Peter C; Krleža-Jerić, Karmela; Hróbjartsson, Asbjørn; Mann, Howard; Dickersin, Kay; Berlin, Jesse A; Doré, Caroline J; Parulekar, Wendy R; Summerskill, William S M; Groves, Trish; Schulz, Kenneth F; Sox, Harold C; Rockhold, Frank W; Rennie, Drummond; Moher, David

2013-02-05

The protocol of a clinical trial serves as the foundation for study planning, conduct, reporting, and appraisal. However, trial protocols and existing protocol guidelines vary greatly in content and quality. This article describes the systematic development and scope of SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) 2013, a guideline for the minimum content of a clinical trial protocol.The 33-item SPIRIT checklist applies to protocols for all clinical trials and focuses on content rather than format. The checklist recommends a full description of what is planned; it does not prescribe how to design or conduct a trial. By providing guidance for key content, the SPIRIT recommendations aim to facilitate the drafting of high-quality protocols. Adherence to SPIRIT would also enhance the transparency and completeness of trial protocols for the benefit of investigators, trial participants, patients, sponsors, funders, research ethics committees or institutional review boards, peer reviewers, journals, trial registries, policymakers, regulators, and other key stakeholders.

The activity of French research ethics committees and characteristics of biomedical research protocols involving humans: a retrospective cohort study.

PubMed

Decullier, Evelyne; Lhéritier, Véronique; Chapuis, François

2005-10-17

Clinical trials throughout the world must be evaluated by research ethics committees. No one has yet attempted to clearly quantify at the national level the activity of ethics committees and describe the characteristics of the protocols submitted. The objectives of this study were to describe 1) the workload and the activity of Research Ethics Committees in France, and 2) the characteristics of protocols approved on a nation-wide basis. Retrospective cohort of 976 protocols approved by a representative sample of 25/48 of French Research Ethics Committees in 1994. Protocols characteristics (design, study size, investigator), number of revisions requested by the ethics committee before approval, time to approval and number of amendments after approval were collected for each protocol by trained research assistant using the committee's files and archives. Thirty-one percent of protocols were approved with no modifications requested in 16 days (95% CI: 14-17). The number of revisions requested by the committee, and amendments submitted by the investigator was on average respectively 39 (95% CI: 25-53) and 37 (95% CI: 27-46), per committee and per year. When revisions were requested, the main reasons were related to information to the patient (28%) and consent modalities (18%). Drugs were the object of research in 68% of the protocols examined. The majority of the research was national (80%) with a predominance of single-centre studies. Workload per protocol has been estimated at twelve and half hours on average for administrative support and at eleven and half hours for expertise. The estimated workload justifies specific and independent administrative and financial support for Research Ethics Committees.

PROTOCOL FOR EXAMINATION OF THE INNER CAN CLOSURE WELD REGION FOR 3013 DE CONTAINERS

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

Mickalonis, J.

2014-09-16

The protocol for the examination of the inner can closure weld region (ICCWR) for 3013 DE containers is presented within this report. The protocol includes sectioning of the inner can lid section, documenting the surface condition, measuring corrosion parameters, and storing of samples. This protocol may change as the investigation develops since findings may necessitate additional steps be taken. Details of the previous analyses, which formed the basis for this protocol, are also presented.

TMS communications software. Volume 2: Bus interface unit

NASA Technical Reports Server (NTRS)

Gregor, P. J.

1979-01-01

A data bus communication system to support the space shuttle's Trend Monitoring System (TMS) and to provide a basis for evaluation of the bus concept is described. Installation of the system included developing both hardware and software interfaces between the bus and the specific TMS computers and terminals. The software written for the microprocessor-based bus interface units is described. The software implements both the general bus communications protocol and also the specific interface protocols for the TMS computers and terminals.

Measuring the Levels of Ribonucleotides Embedded in Genomic DNA.

PubMed

Meroni, Alice; Nava, Giulia M; Sertic, Sarah; Plevani, Paolo; Muzi-Falconi, Marco; Lazzaro, Federico

2018-01-01

Ribonucleotides (rNTPs) are incorporated into genomic DNA at a relatively high frequency during replication. They have beneficial effects but, if not removed from the chromosomes, increase genomic instability. Here, we describe a fast method to easily estimate the amounts of embedded ribonucleotides into the genome. The protocol described is performed in Saccharomyces cerevisiae and allows us to quantify altered levels of rNMPs due to different mutations in the replicative polymerase ε. However, this protocol can be easily applied to cells derived from any organism.

Measuring Feedforward Inhibition and Its Impact on Local Circuit Function.

PubMed

Hull, Court

2017-05-01

This protocol describes a series of approaches to measure feedforward inhibition in acute brain slices from the cerebellar cortex. Using whole-cell voltage and current clamp recordings from Purkinje cells in conjunction with electrical stimulation of the parallel fibers, these methods demonstrate how to measure the relationship between excitation and inhibition in a feedforward circuit. This protocol also describes how to measure the impact of feedforward inhibition on Purkinje cell excitability, with an emphasis on spike timing. © 2017 Cold Spring Harbor Laboratory Press.

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 Montreal Protocol treaty and its illuminating history of science-policy decision-making

NASA Astrophysics Data System (ADS)

Grady, C.

2017-12-01

The Montreal Protocol on Substances that Deplete the Ozone Layer, hailed as one of the most effective environmental treaties of all time, has a thirty year history of science-policy decision-making. The partnership between Parties to the Montreal Protocol and its technical assessment panels serve as a basis for understanding successes and evaluating stumbles of global environmental decision-making. Real-world environmental treaty negotiations can be highly time-sensitive, politically motivated, and resource constrained thus scientists and policymakers alike are often unable to confront the uncertainties associated with the multitude of choices. The science-policy relationship built within the framework of the Montreal Protocol has helped constrain uncertainty and inform policy decisions but has also highlighted the limitations of the use of scientific understanding in political decision-making. This talk will describe the evolution of the scientist-policymaker relationship over the history of the Montreal Protocol. Examples will illustrate how the Montreal Protocol's technical panels inform decisions of the country governments and will characterize different approaches pursued by different countries with a particular focus on the recently adopted Kigali Amendment. In addition, this talk will take a deeper dive with an analysis of the historic technical panel assessments on estimating financial resources necessary to enable compliance to the Montreal Protocol compared to the political financial decisions made through the Protocol's Multilateral Fund replenishment negotiation process. Finally, this talk will describe the useful lessons and challenges from these interactions and how they may be applicable in other environmental management frameworks across multiple scales under changing climatic conditions.

Evaluation of telomere length in human cardiac tissues using cardiac quantitative FISH.

PubMed

Sharifi-Sanjani, Maryam; Meeker, Alan K; Mourkioti, Foteini

2017-09-01

Telomere length has been correlated with various diseases, including cardiovascular disease and cancer. The use of currently available telomere-length measurement techniques is often restricted by the requirement of a large amount of cells (Southern-based techniques) or the lack of information on individual cells or telomeres (PCR-based methods). Although several methods have been used to measure telomere length in tissues as a whole, the assessment of cell-type-specific telomere length provides valuable information on individual cell types. The development of fluorescence in situ hybridization (FISH) technologies enables the quantification of telomeres in individual chromosomes, but the use of these methods is dependent on the availability of isolated cells, which prevents their use with fixed archival samples. Here we describe an optimized quantitative FISH (Q-FISH) protocol for measuring telomere length that bypasses the previous limitations by avoiding contributions from undesired cell types. We have used this protocol on small paraffin-embedded cardiac-tissue samples. This protocol describes step-by-step procedures for tissue preparation, permeabilization, cardiac-tissue pretreatment and hybridization with a Cy3-labeled telomeric repeat complementing (CCCTAA) 3 peptide nucleic acid (PNA) probe coupled with cardiac-specific antibody staining. We also describe how to quantify telomere length by means of the fluorescence intensity and area of each telomere within individual nuclei. This protocol provides comparative cell-type-specific telomere-length measurements in relatively small human cardiac samples and offers an attractive technique to test hypotheses implicating telomere length in various cardiac pathologies. The current protocol (from tissue collection to image procurement) takes ∼28 h along with three overnight incubations. We anticipate that the protocol could be easily adapted for use on different tissue types.

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

Representing the work of medical protocols for organizational simulation.

PubMed Central

Fridsma, D. B.

1998-01-01

Developing and implementing patient care protocols within a specific organizational setting requires knowledge of the protocol, the organization, and the way in which the organization does its work. Computer-based simulation tools have been used in many industries to provide managers with prospective insight into problems of work process and organization design mismatch. Many of these simulation tools are designed for well-understood routine work processes in which there are few contingent tasks. In this paper, we describe theoretic that make it possible to simulate medical protocols using an information-processing theory framework. These simulations will allow medical administrators to test different protocol and organizational designs before actually using them within a particular clinical setting. PMID:9929231

Erratum: Development, appraisal, validation and implementation of a consensus protocol for the assessment of cerebral amyloid angiopathy in post-mortem brain tissue.

PubMed

Love, Seth; Chalmers, Katy; Ince, Paul; Esiri, Margaret; Attems, Johannes; Kalaria, Raj; Jellinger, Kurt; Yamada, Masahito; McCarron, Mark; Minett, Thais; Matthews, Fiona; Greenberg, Steven; Mann, David; Kehoe, Patrick Gavin

2015-01-01

In a collaboration involving 11 groups with research interests in cerebral amyloid angiopathy (CAA), we used a two-stage process to develop and in turn validate a new consensus protocol and scoring scheme for the assessment of CAA and associated vasculopathic abnormalities in post-mortem brain tissue. Stage one used an iterative Delphi-style survey to develop the consensus protocol. The resultant scoring scheme was tested on a series of digital images and paraffin sections that were circulated blind to a number of scorers. The scoring scheme and choice of staining methods were refined by open-forum discussion. The agreed protocol scored parenchymal and meningeal CAA on a 0-3 scale, capillary CAA as present/absent and vasculopathy on 0-2 scale, in the 4 cortical lobes that were scored separately. A further assessment involving three centres was then undertaken. Neuropathologists in three centres (Bristol, Oxford and Sheffield) independently scored sections from 75 cases (25 from each centre) and high inter-rater reliability was demonstrated. Stage two used the results of the three-centre assessment to validate the protocol by investigating previously described associations between APOE genotype (previously determined), and both CAA and vasculopathy. Association of capillary CAA with or without arteriolar CAA with APOE ε4 was confirmed. However APOE ε2 was also found to be a strong risk factor for the development of CAA, not only in AD but also in elderly non-demented controls. Further validation of this protocol and scoring scheme is encouraged, to aid its wider adoption to facilitate collaborative and replication studies of CAA.[This corrects the article on p. 19 in vol. 3, PMID: 24754000.].

The AgMIP Coordinated Global and Regional Assessments (CGRA) of Climate Change Impacts on Agriculture and Food Security

NASA Technical Reports Server (NTRS)

Ruane, Alex; Rosenzweig, Cynthia; Elliott, Joshua; Antle, John

2015-01-01

The Agricultural Model Intercomparison and Improvement Project (AgMIP) has been working since 2010 to construct a protocol-based framework enabling regional assessments (led by regional experts and modelers) that can provide consistent inputs to global economic and integrated assessment models. These global models can then relay important global-level information that drive regional decision-making and outcomes throughout an interconnected agricultural system. AgMIPs community of nearly 800 climate, crop, livestock, economics, and IT experts has improved the state-of-the-art through model intercomparisons, validation exercises, regional integrated assessments, and the launch of AgMIP programs on all six arable continents. AgMIP is now launching Coordinated Global and Regional Assessments (CGRA) of climate change impacts on agriculture and food security to link global and regional crop and economic models using a protocol-based framework. The CGRA protocols are being developed to utilize historical observations, climate projections, and RCPsSSPs from CMIP5 (and potentially CMIP6), and will examine stakeholder-driven agricultural development and adaptation scenarios to provide cutting-edge assessments of climate changes impact on agriculture and food security. These protocols will build on the foundation of established protocols from AgMIPs 30+ activities, and will emphasize the use of multiple models, scenarios, and scales to enable an accurate assessment of related uncertainties. The CGRA is also designed to provide the outputs necessary to feed into integrated assessment models (IAMs), nutrition and food security assessments, nitrogen and carbon cycle models, and additional impact-sector assessments (e.g., water resources, land-use, biomes, urban areas). This presentation will describe the current status of CGRA planning and initial prototype experiments to demonstrate key aspects of the protocols before wider implementation ahead of the IPCC Sixth Assessment Report.

Comparison of Four Protocols to Generate Chondrocyte-Like Cells from Human Induced Pluripotent Stem Cells (hiPSCs).

PubMed

Suchorska, Wiktoria Maria; Augustyniak, Ewelina; Richter, Magdalena; Trzeciak, Tomasz

2017-04-01

Stem cells (SCs) are a promising approach to regenerative medicine, with the potential to treat numerous orthopedic disorders, including osteo-degenerative diseases. The development of human-induced pluripotent stem cells (hiPSCs) has increased the potential of SCs for new treatments. However, current methods of differentiating hiPSCs into chondrocyte-like cells are suboptimal and better methods are needed. The aim of the present study was to assess four different chondrogenic differentiation protocols to identify the most efficient method of generating hiPSC-derived chondrocytes. For this study, hiPSCs were obtained from primary human dermal fibroblasts (PHDFs) and differentiated into chondrocyte-like cells using four different protocols: 1) monolayer culture with defined growth factors (GF); 2) embryoid bodies (EBs) in a chondrogenic medium with TGF-β3 cells; 3) EBs in chondrogenic medium conditioned with human chondrocytes (HC-402-05a cell line) and 4) EBs in chondrogenic medium conditioned with human chondrocytes and supplemented with TGF-β3. The cells obtained through these four protocols were evaluated and compared at the mRNA and protein levels. Although chondrogenic differentiation of hiPSCs was successfully achieved with all of these protocols, the two fastest and most cost-effective methods were the monolayer culture with GFs and the medium conditioned with human chondrocytes. Both of these methods are superior to other available techniques. The main advantage of the conditioned medium is that the technique is relatively simple and inexpensive while the directed method (i.e., monolayer culture with GFs) is faster than any protocol described to date because it is does not require additional steps such as EB formation.

Development, appraisal, validation and implementation of a consensus protocol for the assessment of cerebral amyloid angiopathy in post-mortem brain tissue

PubMed Central

Love, Seth; Chalmers, Katy; Ince, Paul; Esiri, Margaret; Attems, Johannes; Kalaria, Raj; Jellinger, Kurt; Yamada, Masahito; McCarron, Mark; Minett, Thais; Matthews, Fiona; Greenberg, Steven; Mann, David; Kehoe, Patrick Gavin

2015-01-01

In a collaboration involving 11 groups with research interests in cerebral amyloid angiopathy (CAA), we used a two-stage process to develop and in turn validate a new consensus protocol and scoring scheme for the assessment of CAA and associated vasculopathic abnormalities in post-mortem brain tissue. Stage one used an iterative Delphi-style survey to develop the consensus protocol. The resultant scoring scheme was tested on a series of digital images and paraffin sections that were circulated blind to a number of scorers. The scoring scheme and choice of staining methods were refined by open-forum discussion. The agreed protocol scored parenchymal and meningeal CAA on a 0-3 scale, capillary CAA as present/absent and vasculopathy on 0-2 scale, in the 4 cortical lobes that were scored separately. A further assessment involving three centres was then undertaken. Neuropathologists in three centres (Bristol, Oxford and Sheffield) independently scored sections from 75 cases (25 from each centre) and high inter-rater reliability was demonstrated. Stage two used the results of the three-centre assessment to validate the protocol by investigating previously described associations between APOE genotype (previously determined), and both CAA and vasculopathy. Association of capillary CAA with or without arteriolar CAA with APOE ε4 was confirmed. However APOE ε2 was also found to be a strong risk factor for the development of CAA, not only in AD but also in elderly non-demented controls. Further validation of this protocol and scoring scheme is encouraged, to aid its wider adoption to facilitate collaborative and replication studies of CAA. PMID:26807344

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

Platinum desensitization in patients with carboplatin hypersensitivity: A single-institution retrospective study.

PubMed

Altwerger, Gary; Gressel, Gregory M; English, Diana P; Nelson, Wendelin K; Carusillo, Nina; Silasi, Dan-Arin; Azodi, Masoud; Santin, Alessandro; Schwartz, Peter E; Ratner, Elena S

2017-01-01

The carboplatin desensitization (CD) protocol presented here allows patients with either a positive skin test or a prior hypersensitivity reaction (HSR) to safely, rapidly and effectively continue with carboplatin infusions. Newly described factors can identify patients at risk for developing adverse events during CD. A retrospective review was performed on patients with gynecologic cancer who underwent CD between 2005 and 2014. The CD protocol uses a four-step dilution process over 3.5h. 129 patients underwent CD and completed a total of 788cycles. The desensitization protocol prevented HSRs in 96% (753 out of 788) of these cycles. Patients achieved an average of 6.1cycles (SD±4.55, range 0-23) with CD. The CD protocol allowed 73% (94 of 129) of the patients to undergo carboplatin infusion without reaction. Patients with moderate to life-threatening HSRs (grade 2 through 4) were 10.5years younger at initial CD than patients with grades 0 or 1 HSRs (52.3 vs. 63, P = 0.0307). One patient death occurred during her thirteenth desensitization cycle. The HSR in this case was complicated by pre-exisiting pulmonary hypertension. This is the largest study of its kind showing a safe, effective and rapid (3.5h) CD protocol. The majority of patients with a history of either carboplatin hypersensitivity reaction or a positive skin test completed the CD protocol without HSRs. Age was identified as a risk factor for HSR severity during CD. Age can be employed along with pre-load dependent cardiac conditions as a way to help risk stratify patients undergoing CD. Copyright © 2016 Elsevier Inc. All rights reserved.

The AgMIP Coordinated Global and Regional Assessments (CGRA) of Climate Change Impacts on Agriculture and Food Security

NASA Astrophysics Data System (ADS)

Ruane, A. C.; Rosenzweig, C.; Antle, J. M.; Elliott, J. W.

2015-12-01

The Agricultural Model Intercomparison and Improvement Project (AgMIP) has been working since 2010 to construct a protocol-based framework enabling regional assessments (led by regional experts and modelers) that can provide consistent inputs to global economic and integrated assessment models. These global models can then relay important global-level information that drive regional decision-making and outcomes throughout an interconnected agricultural system. AgMIP's community of nearly 800 climate, crop, livestock, economics, and IT experts has improved the state-of-the-art through model intercomparisons, validation exercises, regional integrated assessments, and the launch of AgMIP programs on all six arable continents. AgMIP is now launching Coordinated Global and Regional Assessments (CGRA) of climate change impacts on agriculture and food security to link global and regional crop and economic models using a protocol-based framework. The CGRA protocols are being developed to utilize historical observations, climate projections, and RCPs/SSPs from CMIP5 (and potentially CMIP6), and will examine stakeholder-driven agricultural development and adaptation scenarios to provide cutting-edge assessments of climate change's impact on agriculture and food security. These protocols will build on the foundation of established protocols from AgMIP's 30+ activities, and will emphasize the use of multiple models, scenarios, and scales to enable an accurate assessment of related uncertainties. The CGRA is also designed to provide the outputs necessary to feed into integrated assessment models (IAMs), nutrition and food security assessments, nitrogen and carbon cycle models, and additional impact-sector assessments (e.g., water resources, land-use, biomes, urban areas). This presentation will describe the current status of CGRA planning and initial prototype experiments to demonstrate key aspects of the protocols before wider implementation ahead of the IPCC Sixth Assessment Report.

Development, appraisal, validation and implementation of a consensus protocol for the assessment of cerebral amyloid angiopathy in post-mortem brain tissue

PubMed Central

Love, Seth; Chalmers, Katy; Ince, Paul; Esiri, Margaret; Attems, Johannes; Jellinger, Kurt; Yamada, Masahito; McCarron, Mark; Minett, Thais; Matthews, Fiona; Greenberg, Steven; Mann, David; Kehoe, Patrick Gavin

2014-01-01

In a collaboration involving 11 groups with research interests in cerebral amyloid angiopathy (CAA), we used a two-stage process to develop and in turn validate a new consensus protocol and scoring scheme for the assessment of CAA and associated vasculopathic abnormalities in post-mortem brain tissue. Stage one used an iterative Delphi-style survey to develop the consensus protocol. The resultant scoring scheme was tested on a series of digital images and paraffin sections that were circulated blind to a number of scorers. The scoring scheme and choice of staining methods were refined by open-forum discussion. The agreed protocol scored parenchymal and meningeal CAA on a 0-3 scale, capillary CAA as present/absent and vasculopathy on 0-2 scale, in the 4 cortical lobes that were scored separately. A further assessment involving three centres was then undertaken. Neuropathologists in three centres (Bristol, Oxford and Sheffield) independently scored sections from 75 cases (25 from each centre) and high inter-rater reliability was demonstrated. Stage two used the results of the three-centre assessment to validate the protocol by investigating previously described associations between APOE genotype (previously determined), and both CAA and vasculopathy. Association of capillary CAA with or without arteriolar CAA with APOE ε4 was confirmed. However APOE ε2 was also found to be a strong risk factor for the development of CAA, not only in AD but also in elderly non-demented controls. Further validation of this protocol and scoring scheme is encouraged, to aid its wider adoption to facilitate collaborative and replication studies of CAA. PMID:24754000

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.

Robust Routing Protocol For Digital Messages

NASA Technical Reports Server (NTRS)

Marvit, Maclen

1994-01-01

Refinement of ditigal-message-routing protocol increases fault tolerance of polled networks. AbNET-3 is latest of generic AbNET protocols for transmission of messages among computing nodes. AbNET concept described in "Multiple-Ring Digital Communication Network" (NPO-18133). Specifically aimed at increasing fault tolerance of network in broadcast mode, in which one node broadcasts message to and receives responses from all other nodes. Communication in network of computers maintained even when links fail.

Power Conservation through Energy Efficient Routing in Wireless Sensor Networks.

PubMed

Kandris, Dionisis; Tsioumas, Panagiotis; Tzes, Anthony; Nikolakopoulos, George; Vergados, Dimitrios D

2009-01-01

The power awareness issue is the primary concern within the domain of Wireless Sensor Networks (WSNs). Most power dissipation ocurrs during communication, thus routing protocols in WSNs mainly aim at power conservation. Moreover, a routing protocol should be scalable, so that its effectiveness does not degrade as the network size increases. In response to these issues, this work describes the development of an efficient routing protocol, named SHPER (Scaling Hierarchical Power Efficient Routing).

FD/DAMA Scheme For Mobile/Satellite Communications

NASA Technical Reports Server (NTRS)

Yan, Tsun-Yee; Wang, Charles C.; Cheng, Unjeng; Rafferty, William; Dessouky, Khaled I.

1992-01-01

Integrated-Adaptive Mobile Access Protocol (I-AMAP) proposed to allocate communication channels to subscribers in first-generation MSAT-X mobile/satellite communication network. Based on concept of frequency-division/demand-assigned multiple access (FD/DAMA) where partition of available spectrum adapted to subscribers' demands for service. Requests processed, and competing requests resolved according to channel-access protocol, or free-access tree algorithm described in "Connection Protocol for Mobile/Satellite Communications" (NPO-17735). Assigned spectrum utilized efficiently.

A network identity authentication protocol of bank account system based on fingerprint identification and mixed encryption

NASA Astrophysics Data System (ADS)

Zhu, Lijuan; Liu, Jingao

2013-07-01

This paper describes a network identity authentication protocol of bank account system based on fingerprint identification and mixed encryption. This protocol can provide every bank user a safe and effective way to manage his own bank account, and also can effectively prevent the hacker attacks and bank clerk crime, so that it is absolute to guarantee the legitimate rights and interests of bank users.

Improved Protocols for Illumina Sequencing

PubMed Central

Bronner, Iraad F.; Quail, Michael A.; Turner, Daniel J.; Swerdlow, Harold

2013-01-01

In this unit, we describe a set of improvements we have made to the standard Illumina protocols to make the sequencing process more reliable in a high-throughput environment, reduce amplification bias, narrow the distribution of insert sizes, and reliably obtain high yields of data. PMID:19582764

Internet Connections: Understanding Your Access Options.

ERIC Educational Resources Information Center

Notess, Greg R.

1994-01-01

Describes levels of Internet connectivity, physical connections, and connection speeds. Compares options for connecting to the Internet, including terminal accounts, dial-up terminal accounts, direct connections through a local area network, and direct connections using SLIP (Serial Line Internet Protocol) or PPP (Point-to-Point Protocol). (eight…

Protocol Analysis: A Methodology for Exploring the Information Processing of Gifted Students.

ERIC Educational Resources Information Center

Anderson, Margaret A.

1986-01-01

Protocol analysis techniques, in which subjects are taught to think aloud, can provide information on the mental operations used by gifted learners. Concerns over the use of such data are described and new directions for the technique are proposed. (CL)

A protocol for the health and fitness assessment of NBA players.

PubMed

Scheller, A; Rask, B

1993-04-01

The assessment of the health and fitness of elite basketball players should be a multidisciplinary process. We have described an organized, efficient, and comprehensive protocol for preseason physical evaluations that could be used at the university as well as professional level.

Generic Verification Protocol for Determination of Emissions from Cleaner Outdoor Wood-Fired Hydronic Heaters

EPA Science Inventory

This protocol describes the Environmental Technology Verification Program's considerations and requirements for verification of emissions reduction provided by cleaner outdoor wood-fired hydronic heaters. Outdoor wood-burning units provide heat and hot water for homes and other b...

Exacerbated in vivo metabolic changes suggestive of a spontaneous muscular vaso-occlusive crisis in exercising muscle of a sickle cell mouse.

PubMed

Chatel, Benjamin; Messonnier, Laurent A; Bendahan, David

2017-06-01

While sickle cell disease (SCD) is characterized by frequent vaso-occlusive crisis (VOC), no direct observation of such an event in skeletal muscle has been performed in vivo. The present study reported exacerbated in vivo metabolic changes suggestive of a spontaneous muscular VOC in exercising muscle of a sickle cell mouse. Using magnetic resonance spectroscopy of phosphorus 31, phosphocreatine and inorganic phosphate concentrations and intramuscular pH were measured throughout two standardized protocols of rest - exercise - recovery at two different intensities in ten SCD mice. Among these mice, one single mouse presented divergent responses. A statistical analysis (based on confidence intervals) revealed that this single mouse presented slower phosphocreatine resynthesis and inorganic phosphate disappearance during the post-stimulation recovery of one of the protocols, what could suggest an ischemia. This study described, for the first time in a sickle cell mouse in vivo, exacerbated metabolic changes triggered by an exercise session that would be suggestive of a live observation of a muscular VOC. However, no evidence of a direct cause-effect relationship between exercise and VOC has been put forth. Copyright © 2017 Elsevier Inc. All rights reserved.

Purification of the Membrane Compartment for Endoplasmic Reticulum-associated Degradation of Exogenous Antigens in Cross-presentation.

PubMed

Imai, Jun; Otani, Mayu; Sakai, Takahiro; Hatta, Shinichi

2017-08-21

Dendritic cells (DCs) are highly capable of processing and presenting internalized exogenous antigens upon major histocompatibility class (MHC) I molecules also known as cross-presentation (CP). CP plays an important role not only in the stimulation of naïve CD8 + T cells and memory CD8 + T cells for infectious and tumor immunity but also in the inactivation of self-acting naïve T cells by T cell anergy or T cell deletion. Although the critical molecular mechanism of CP remains to be elucidated, accumulating evidence indicates that exogenous antigens are processed through endoplasmic reticulum-associated degradation (ERAD) after export from non-classical endocytic compartments. Until recently, characterizations of these endocytic compartments were limited because there were no specific molecular markers other than exogenous antigens. The method described here is a new vesicle isolation protocol, which allows for the purification of these endocytic compartments. Using this purified microsome, we reconstituted the ERAD-like transport, ubiquitination, and processing of the exogenous antigen in vitro, suggesting that the ubiquitin-proteasome system processed the exogenous antigen after export from this cellular compartment. This protocol can be further applied to other cell types to clarify the molecular mechanism of CP.

(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.

Protocol for Microplastics Sampling on the Sea Surface and Sample Analysis

PubMed Central

Kovač Viršek, Manca; Palatinus, Andreja; Koren, Špela; Peterlin, Monika; Horvat, Petra; Kržan, Andrej

2016-01-01

Microplastic pollution in the marine environment is a scientific topic that has received increasing attention over the last decade. The majority of scientific publications address microplastic pollution of the sea surface. The protocol below describes the methodology for sampling, sample preparation, separation and chemical identification of microplastic particles. A manta net fixed on an »A frame« attached to the side of the vessel was used for sampling. Microplastic particles caught in the cod end of the net were separated from samples by visual identification and use of stereomicroscopes. Particles were analyzed for their size using an image analysis program and for their chemical structure using ATR-FTIR and micro FTIR spectroscopy. The described protocol is in line with recommendations for microplastics monitoring published by the Marine Strategy Framework Directive (MSFD) Technical Subgroup on Marine Litter. This written protocol with video guide will support the work of researchers that deal with microplastics monitoring all over the world. PMID:28060297

Protocol for Microplastics Sampling on the Sea Surface and Sample Analysis.

PubMed

Kovač Viršek, Manca; Palatinus, Andreja; Koren, Špela; Peterlin, Monika; Horvat, Petra; Kržan, Andrej

2016-12-16

Microplastic pollution in the marine environment is a scientific topic that has received increasing attention over the last decade. The majority of scientific publications address microplastic pollution of the sea surface. The protocol below describes the methodology for sampling, sample preparation, separation and chemical identification of microplastic particles. A manta net fixed on an »A frame« attached to the side of the vessel was used for sampling. Microplastic particles caught in the cod end of the net were separated from samples by visual identification and use of stereomicroscopes. Particles were analyzed for their size using an image analysis program and for their chemical structure using ATR-FTIR and micro FTIR spectroscopy. The described protocol is in line with recommendations for microplastics monitoring published by the Marine Strategy Framework Directive (MSFD) Technical Subgroup on Marine Litter. This written protocol with video guide will support the work of researchers that deal with microplastics monitoring all over the world.

Biosafety assessment protocols for new organisms in New Zealand: Can they apply internationally to emerging technologies?

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

Barratt, B.I.P.; Moeed, A.; Malone, L.A.

2006-05-15

An analysis of established biosafety protocols for release into the environment of exotic plants and biological control agents for weeds and arthropod pests has been carried out to determine whether such protocols can be applied to relatively new and emerging technologies intended for the primary production industries, such as transgenic plants. Example case studies are described to indicate the scope of issues considered by regulators who make decisions on new organism releases. No transgenic plants have been released to date in New Zealand, but two field test approvals are described as examples. An analysis of the biosafety protocols has shownmore » that, while many of the risk criteria considered for decision-making by regulators are similar for all new organisms, a case-by-case examination of risks and potential impacts is required in order to fully assess risk. The value of post-release monitoring and validation of decisions made by regulators is emphasised.« less

Medium Access Control Protocols for Cognitive Radio Ad Hoc Networks: A Survey

PubMed Central

Islam, A. K. M. Muzahidul; Baharun, Sabariah; Mansoor, Nafees

2017-01-01

New wireless network paradigms will demand higher spectrum use and availability to cope with emerging data-hungry devices. Traditional static spectrum allocation policies cause spectrum scarcity, and new paradigms such as Cognitive Radio (CR) and new protocols and techniques need to be developed in order to have efficient spectrum usage. Medium Access Control (MAC) protocols are accountable for recognizing free spectrum, scheduling available resources and coordinating the coexistence of heterogeneous systems and users. This paper provides an ample review of the state-of-the-art MAC protocols, which mainly focuses on Cognitive Radio Ad Hoc Networks (CRAHN). First, a description of the cognitive radio fundamental functions is presented. Next, MAC protocols are divided into three groups, which are based on their channel access mechanism, namely time-slotted protocol, random access protocol and hybrid protocol. In each group, a detailed and comprehensive explanation of the latest MAC protocols is presented, as well as the pros and cons of each protocol. A discussion on future challenges for CRAHN MAC protocols is included with a comparison of the protocols from a functional perspective. PMID:28926952

Large Volume, Behaviorally-relevant Illumination for Optogenetics in Non-human Primates.

PubMed

Acker, Leah C; Pino, Erica N; Boyden, Edward S; Desimone, Robert

2017-10-03

This protocol describes a large-volume illuminator, which was developed for optogenetic manipulations in the non-human primate brain. The illuminator is a modified plastic optical fiber with etched tip, such that the light emitting surface area is > 100x that of a conventional fiber. In addition to describing the construction of the large-volume illuminator, this protocol details the quality-control calibration used to ensure even light distribution. Further, this protocol describes techniques for inserting and removing the large volume illuminator. Both superficial and deep structures may be illuminated. This large volume illuminator does not need to be physically coupled to an electrode, and because the illuminator is made of plastic, not glass, it will simply bend in circumstances when traditional optical fibers would shatter. Because this illuminator delivers light over behaviorally-relevant tissue volumes (≈ 10 mm 3 ) with no greater penetration damage than a conventional optical fiber, it facilitates behavioral studies using optogenetics in non-human primates.

Detection of Food Allergens by Taqman Real-Time PCR Methodology.

PubMed

García, Aina; Madrid, Raquel; García, Teresa; Martín, Rosario; González, Isabel

2017-01-01

Real-time PCR (polymerase chain reaction) has shown to be a very effective technology for the detection of food allergens. The protocol described herein consists on a real-time PCR assay targeting the plant ITS (Internal Transcribed Spacer) region, using species-specific primers and hydrolysis probes (Taqman) dual labeled with a reporter fluorophore at the 5' end (6-carboxyfluorescein, FAM) and a quencher fluorophore at the 3' end (Blackberry, BBQ). The species-specific real-time PCR systems (primers/probe) described in this work allowed the detection of different nuts (peanut, hazelnut, pistachio, almond, cashew, macadamia, walnut and pecan), common allergens present in commercial food products, with a detection limit of 0.1 mg/kg.

Real-time imaging of specific genomic loci in eukaryotic cells using the ANCHOR DNA labelling system.

PubMed

Germier, Thomas; Sylvain, Audibert; Silvia, Kocanova; David, Lane; Kerstin, Bystricky

2018-06-01

Spatio-temporal organization of the cell nucleus adapts to and regulates genomic processes. Microscopy approaches that enable direct monitoring of specific chromatin sites in single cells and in real time are needed to better understand the dynamics involved. In this chapter, we describe the principle and development of ANCHOR, a novel tool for DNA labelling in eukaryotic cells. Protocols for use of ANCHOR to visualize a single genomic locus in eukaryotic cells are presented. We describe an approach for live cell imaging of a DNA locus during the entire cell cycle in human breast cancer cells. Copyright © 2018 Elsevier Inc. All rights reserved.

National protocol framework for the inventory and monitoring of bees

USGS Publications Warehouse

Droege, Sam; Engler, Joseph D.; Sellers, Elizabeth A.; Lee O'Brien,

2016-01-01

This national protocol framework is a standardized tool for the inventory and monitoring of the approximately 4,200 species of native and non-native bee species that may be found within the National Wildlife Refuge System (NWRS) administered by the U.S. Fish and Wildlife Service (USFWS). However, this protocol framework may also be used by other organizations and individuals to monitor bees in any given habitat or location. Our goal is to provide USFWS stations within the NWRS (NWRS stations are land units managed by the USFWS such as national wildlife refuges, national fish hatcheries, wetland management districts, conservation areas, leased lands, etc.) with techniques for developing an initial baseline inventory of what bee species are present on their lands and to provide an inexpensive, simple technique for monitoring bees continuously and for monitoring and evaluating long-term population trends and management impacts. The latter long-term monitoring technique requires a minimal time burden for the individual station, yet can provide a good statistical sample of changing populations that can be investigated at the station, regional, and national levels within the USFWS’ jurisdiction, and compared to other sites within the United States and Canada. This protocol framework was developed in cooperation with the United States Geological Survey (USGS), the USFWS, and a worldwide network of bee researchers who have investigated the techniques and methods for capturing bees and tracking population changes. The protocol framework evolved from field and lab-based investigations at the USGS Bee Inventory and Monitoring Laboratory at the Patuxent Wildlife Research Center in Beltsville, Maryland starting in 2002 and was refined by a large number of USFWS, academic, and state groups. It includes a Protocol Introduction and a set of 8 Standard Operating Procedures or SOPs and adheres to national standards of protocol content and organization. The Protocol Narrative describes the history and need for the protocol framework and summarizes the basic elements of objectives, sampling design, field methods, training, data management, analysis, and reporting. The SOPs provide more detail and specific instructions for implementing the protocol framework. A central database, for managing all the resulting data is under development. We welcome use of this protocol framework by our partners, as appropriate for their bee inventory and monitoring objectives.

Development of pig welfare assessment protocol integrating animal-, environment-, and management-based measures.

PubMed

Renggaman, Anriansyah; Choi, Hong L; Sudiarto, Sartika Ia; Alasaarela, Laura; Nam, Ok S

2015-01-01

Due to increased interest in animal welfare, there is now a need for a comprehensive assessment protocol to be used in intensive pig farming systems. There are two current welfare assessment protocols for pigs: Welfare Quality® Assessment Protocols (applicable in the Europe Union), that mostly focuses on animal-based measures, and the Swine Welfare Assurance Program (applicable in the United States), that mostly focuses on management- and environment-based measures. In certain cases, however, animal-based measures might not be adequate for properly assessing pig welfare status. Similarly, welfare assessment that relies only on environment- and management-based measures might not represent the actual welfare status of pigs. Therefore, the objective of this paper was to develop a new welfare protocol by integrating animal-, environment-, and management-based measures. The background for selection of certain welfare criteria and modification of the scoring systems from existing welfare assessment protocols are described. The developed pig welfare assessment protocol consists of 17 criteria that are related to four main principles of welfare (good feeding, good housing, good health, and appropriate behavior). Good feeding, good housing, and good health were assessed using a 3-point scale: 0 (good welfare), 1 (moderate welfare), and 2 (poor welfare). In certain cases, only a 2-point scale was used: 0 (certain condition is present) or 2 (certain condition is absent). Appropriate behavior was assessed by scan sampling of positive and negative social behaviors based on qualitative behavior assessment and human-animal relationship tests. Modification of the body condition score into a 3-point scale revealed pigs with a moderate body condition (score 1). Moreover, additional criteria such as feed quality confirmed that farms had moderate (score 1) or poor feed quality (score 2), especially those farms located in a high relative humidity region. The developed protocol can be utilized to assess welfare status in an intensive pig farming system. Although further improvements are still needed, this study is a first step in developing a pig welfare assessment protocol that combines animal-, environment-, and management-based measures.

Multi-party Quantum Key Agreement without Entanglement

NASA Astrophysics Data System (ADS)

Cai, Bin-Bin; Guo, Gong-De; Lin, Song

2017-04-01

A new efficient quantum key agreement protocol without entanglement is proposed. In this protocol, each user encodes his secret key into the traveling particles by performing one of four rotation operations that one cannot perfectly distinguish. In the end, all users can simultaneously obtain the final shared key. The security of the presented protocol against some common attacks is discussed. It is shown that this protocol can effectively protect the privacy of each user and satisfy the requirement of fairness in theory. Moreover, the quantum carriers and the encoding operations used in the protocol can be achieved in realistic physical devices. Therefore, the presented protocol is feasible with current technology.

Clinical protocol with digital cad/cam chairside workflow for the rehabilitation of severely worn dentition patients

PubMed Central

GERMANO, FED.; GERMANO, FRA.; PIRO, M.; ARCURI, C.; OTTRIA, L.

2017-01-01

SUMMARY Objectives The purpose of this paper is to investigate the effectiveness and to describe a clinical protocol with digital CAD CAM chairside workflow for the rehabilitation of severely compromised and worn dentitions. Methods This article reports 4 consecutive cases, where a clinical digital chairside workflow is used for the rehabilitation of severely compromised and worn dentitions. Advantages and limitations of this method compared with the traditional prosthetic protocol are also described and discussed. Results With all four patients treated with this protocol, we obtained a good aesthetic and functional result, improvement in chewing function, loss of cold sensitivity, better preservation of most of the left hard tissue and a good level of satisfaction. In a two-year follow-up, all patients also maintained the condition obtained with prosthetic chairside rehabilitation, resulting in almost 100% cumulative survival rate. Conclusion Within the limitations of this study, we can assert that the aforementioned restorative treatment with digital CAD/CAM chairside workflow represents a valid alternative to rehabilitate this kind of patients, because it is a safe, predictable and personalized procedure but also it seems easier, faster and cheaper than traditional protocols. PMID:29285327

Toward fidelity between specification and implementation

NASA Technical Reports Server (NTRS)

Callahan, John R.; Montgomery, Todd L.; Morrison, Jeff; Wu, Yunqing

1994-01-01

This paper describes the methods used to specify and implement a complex communications protocol that provides reliable delivery of data in multicast-capable, packet-switching telecommunication networks. The protocol, called the Reliable Multicasting Protocol (RMP), was developed incrementally by two complementary teams using a combination of formal and informal techniques in an attempt to ensure the correctness of the protocol implementation. The first team, called the Design team, initially specified protocol requirements using a variant of SCR requirements tables and implemented a prototype solution. The second team, called the V&V team, developed a state model based on the requirements tables and derived test cases from these tables to exercise the implementation. In a series of iterative steps, the Design team added new functionality to the implementation while the V&V team kept the state model in fidelity with the implementation through testing. Test cases derived from state transition paths in the formal model formed the dialogue between teams during development and served as the vehicles for keeping the model and implementation in fidelity with each other. This paper describes our experiences in developing our process model, details of our approach, and some example problems found during the development of RMP.

Chapter 3: Commercial and Industrial Lighting Controls Evaluation Protocol. The Uniform Methods Project: Methods for Determining Energy Efficiency Savings for Specific Measures

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

Kurnik, Charles W.; Carlson, Stephen

This Commercial and Industrial Lighting Controls Evaluation Protocol (the protocol) describes methods to account for energy savings resulting from programmatic installation of lighting control equipment in large populations of commercial, industrial, government, institutional, and other nonresidential facilities. This protocol does not address savings resulting from changes in codes and standards, or from education and training activities. When lighting controls are installed in conjunction with a lighting retrofit project, the lighting control savings must be calculated parametrically with the lighting retrofit project so savings are not double counted.

Extremely high data-rate, reliable network systems research

NASA Technical Reports Server (NTRS)

Foudriat, E. C.; Maly, Kurt J.; Mukkamala, R.; Murray, Nicholas D.; Overstreet, C. Michael

1990-01-01

Significant progress was made over the year in the four focus areas of this research group: gigabit protocols, extensions of metropolitan protocols, parallel protocols, and distributed simulations. Two activities, a network management tool and the Carrier Sensed Multiple Access Collision Detection (CSMA/CD) protocol, have developed to the point that a patent is being applied for in the next year; a tool set for distributed simulation using the language SIMSCRIPT also has commercial potential and is to be further refined. The year's results for each of these areas are summarized and next year's activities are described.

IVOA Credential Delegation Protocol Version 1.0

NASA Astrophysics Data System (ADS)

Plante, Raymond; Graham, Matthew; Rixon, Guy; Taffoni, Giuliano; Plante, Raymond; Graham, Matthew

2010-02-01

The credential delegation protocol allows a client program to delegate a user's credentials to a service such that that service may make requests of other services in the name of that user. The protocol defines a REST service that works alongside other IVO services to enable such a delegation in a secure manner. In addition to defining the specifics of the service protocol, this document describes how a delegation service is registered in an IVOA registry along with the services it supports. The specification also explains how one can determine from a service registration that it requires the use of a supporting delegation service.

The TurboLAN project. Phase 1: Protocol choices for high speed local area networks. Phase 2: TurboLAN Intelligent Network Adapter Card, (TINAC) architecture

NASA Technical Reports Server (NTRS)

Alkhatib, Hasan S.

1991-01-01

The hardware and the software architecture of the TurboLAN Intelligent Network Adapter Card (TINAC) are described. A high level as well as detailed treatment of the workings of various components of the TINAC are presented. The TINAC is divided into the following four major functional units: (1) the network access unit (NAU); (2) the buffer management unit; (3) the host interface unit; and (4) the node processor unit.

Technologies for unattended network operations

NASA Technical Reports Server (NTRS)

Jaworski, Allan; Odubiyi, Jide; Holdridge, Mark; Zuzek, John

1991-01-01

The necessary network management functions for a telecommunications, navigation and information management (TNIM) system in the framework of an extension of the ISO model for communications network management are described. Various technologies that could substantially reduce the need for TNIM network management, automate manpower intensive functions, and deal with synchronization and control at interplanetary distances are presented. Specific technologies addressed include the use of the ISO Common Management Interface Protocol, distributed artificial intelligence for network synchronization and fault management, and fault-tolerant systems engineering.

Thermal-vacuum response of polymer matrix composites in space

NASA Technical Reports Server (NTRS)

Tennyson, R. C.; Matthews, R.

1993-01-01

This report describes a thermal-vacuum outgassing model and test protocol for predicting outgassing times and dimensional changes for polymer matrix composites. Experimental results derived from 'control' samples are used to provide the basis for analytical predictions to compare with the outgassing response of Long Duration Exposure Facility (LDEF) flight samples. Coefficient of thermal expansion (CTE) data are also presented. In addition, an example is given illustrating the dimensional change of a 'zero' CTE laminate due to moisture outgassing.

Breast Abscess Mimicking Breast Carcinoma in Male.

PubMed

Gochhait, Debasis; Dehuri, Priyadarshini; Umamahesweran, Sandyya; Kamat, Rohan

2018-01-01

Male breast can show almost all pathological entities described in female breast. Inflammatory conditions of the breast in male are not common; however, occasionally, it can be encountered in the form of an abscess. Clinically, gynecomastia always presents as a symmetric unilateral or bilateral lump in the retroareolar region, and any irregular asymmetric lump raises a possibility of malignancy. Radiology should be used as a part of the triple assessment protocol for breast lump along with fine-needle aspiration cytology for definite diagnosis and proper management.

Micro-chromatin Immunoprecipation (μChIP) Protocol for Real-time PCR Analysis of a Limited Amount of Cells.

PubMed

Gillotin, Sébastien; Guillemot, François

2016-06-20

Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is an important strategy to study gene regulation. When availability of cells is limited, however, it can be useful to focus on specific genes to investigate in depth the role of transcription factors or histone marks. Unfortunately, performing ChIP experiments to study transcription factors' binding to DNA can be difficult when biological material is restricted. This protocol describes a robust method to perform μChIP for over-expressed or endogenous transcription factors using ~100,000 cells per ChIP experiment (Masserdotti et al ., 2015). We also describe optimization steps, which we think are critical for this protocol to work and which can be used to further reduce the number of cells.

Efficient protocols for Stirling heat engines at the micro-scale

NASA Astrophysics Data System (ADS)

Muratore-Ginanneschi, Paolo; Schwieger, Kay

2015-10-01

We investigate the thermodynamic efficiency of sub-micro-scale Stirling heat engines operating under the conditions described by overdamped stochastic thermodynamics. We show how to construct optimal protocols such that at maximum power the efficiency attains for constant isotropic mobility the universal law η=2 ηC/(4-ηC) , where ηC is the efficiency of an ideal Carnot cycle. We show that these protocols are specified by the solution of an optimal mass transport problem. Such solution can be determined explicitly using well-known Monge-Ampère-Kantorovich reconstruction algorithms. Furthermore, we show that the same law describes the efficiency of heat engines operating at maximum work over short time periods. Finally, we illustrate the straightforward extension of these results to cases when the mobility is anisotropic and temperature dependent.

Revitalization of open apex teeth with apical periodontitis using a collagen-hydroxyapatite scaffold.

PubMed

Nevins, Alan J; Cymerman, Jerome J

2015-06-01

An enhanced revision of the revitalization endodontic technique for immature teeth with apical periodontitis has been described. It includes the addition of collagen-hydroxyapatite scaffold to the currently practiced revascularization technique. Four cases treated in series are presented in this report, 1 case involving 2 teeth. Periapical diagnoses of immature teeth included "asymptomatic apical periodontitis," "symptomatic apical periodontitis," and "acute apical abscess." Additionally, 1 fully developed tooth that had undergone root canal treatment that failed had a periapical diagnosis of acute apical abscess. An established revascularization protocol was used for all teeth. In addition to stimulating blood clots, all teeth were filled with collagen-hydroxyapatite scaffolds. Periapical radiolucencies healed in all teeth, and diffuse radiopacity developed within the coronal portions of canal spaces. Root development with root lengthening occurred in the immature nonvital maxillary premolar that had not undergone prior treatment. The technique of adding a collagen-hydroxyapatite scaffold to the existing revitalization protocol has been described in which substantial hard tissue repair has occurred. This may leave teeth more fully developed and less likely to fracture. Copyright © 2015 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Image-based Lagrangian Particle Tracking in Bed-load Experiments.

PubMed

Radice, Alessio; Sarkar, Sankar; Ballio, Francesco

2017-07-20

Image analysis has been increasingly used for the measurement of river flows due to its capabilities to furnish detailed quantitative depictions at a relatively low cost. This manuscript describes an application of particle tracking velocimetry (PTV) to a bed-load experiment with lightweight sediment. The key characteristics of the investigated sediment transport conditions were the presence of a covered flow and of a fixed rough bed above which particles were released in limited number at the flume inlet. Under the applied flow conditions, the motion of the individual bed-load particles was intermittent, with alternating movement and stillness terms. The flow pattern was preliminarily characterized by acoustic measurements of vertical profiles of the stream-wise velocity. During process visualization, a large field of view was obtained using two action-cameras placed at different locations along the flume. The experimental protocol is described in terms of channel calibration, experiment realization, image pre-processing, automatic particle tracking, and post-processing of particle track data from the two cameras. The presented proof-of-concept results include probability distributions of the particle hop length and duration. The achievements of this work are compared to those of existing literature to demonstrate the validity of the protocol.

Highball: A high speed, reserved-access, wide area network

NASA Technical Reports Server (NTRS)

Mills, David L.; Boncelet, Charles G.; Elias, John G.; Schragger, Paul A.; Jackson, Alden W.

1990-01-01

A network architecture called Highball and a preliminary design for a prototype, wide-area data network designed to operate at speeds of 1 Gbps and beyond are described. It is intended for applications requiring high speed burst transmissions where some latency between requesting a transmission and granting the request can be anticipated and tolerated. Examples include real-time video and disk-disk transfers, national filestore access, remote sensing, and similar applications. The network nodes include an intelligent crossbar switch, but have no buffering capabilities; thus, data must be queued at the end nodes. There are no restrictions on the network topology, link speeds, or end-end protocols. The end system, nodes, and links can operate at any speed up to the limits imposed by the physical facilities. An overview of an initial design approach is presented and is intended as a benchmark upon which a detailed design can be developed. It describes the network architecture and proposed access protocols, as well as functional descriptions of the hardware and software components that could be used in a prototype implementation. It concludes with a discussion of additional issues to be resolved in continuing stages of this project.

Agrobacterium- and Biolistic-Mediated Transformation of Maize B104 Inbred.

PubMed

Raji, Jennifer A; Frame, Bronwyn; Little, Daniel; Santoso, Tri Joko; Wang, Kan

2018-01-01

Genetic transformation of maize inbred genotypes remains non-routine for many laboratories due to variations in cell competency to induce embryogenic callus, as well as the cell's ability to receive and incorporate transgenes into the genome. This chapter describes two transformation protocols using Agrobacterium- and biolistic-mediated methods for gene delivery. Immature zygotic embryos of maize inbred B104, excised from ears harvested 10-14 days post pollination, are used as starting explant material. Disarmed Agrobacterium strains harboring standard binary vectors and the biolistic gun system Bio-Rad PDS-1000/He are used as gene delivery systems. The herbicide resistant bar gene and selection agent bialaphos are used for identifying putative transgenic type I callus events. Using the step-by-step protocols described here, average transformation frequencies (number of bialaphos resistant T 0 callus events per 100 explants infected or bombarded) of 4% and 8% can be achieved using the Agrobacterium- and biolistic-mediated methods, respectively. An estimated duration of 16-21 weeks is needed using either protocol from the start of transformation experiments to obtaining putative transgenic plantlets with established roots. In addition to laboratory in vitro procedures, detailed greenhouse protocols for producing immature ears as transformation starting material and caring for transgenic plants for seed production are also described.

Running TCP/IP over ATM Networks.

ERIC Educational Resources Information Center

Witt, Michael

1995-01-01

Discusses Internet protocol (IP) and subnets and describes how IP may operate over asynchronous transfer mode (ATM). Topics include TCP (transmission control protocol), ATM cells and adaptation layers, a basic architectural model for IP over ATM, address resolution, mapping IP to a subnet technology, and connection management strategy. (LRW)

Single-step affinity purification for fungal proteomics.

PubMed

Liu, Hui-Lin; Osmani, Aysha H; Ukil, Leena; Son, Sunghun; Markossian, Sarine; Shen, Kuo-Fang; Govindaraghavan, Meera; Varadaraj, Archana; Hashmi, Shahr B; De Souza, Colin P; Osmani, Stephen A

2010-05-01

A single-step protein affinity purification protocol using Aspergillus nidulans is described. Detailed protocols for cell breakage, affinity purification, and depending on the application, methods for protein release from affinity beads are provided. Examples defining the utility of the approaches, which should be widely applicable, are included.

Serious gaming during multidisciplinary rehabilitation for patients with complex chronic pain or fatigue complaints: study protocol for a controlled trial and process evaluation

PubMed Central

Joosen, Margot C W; Mert, Agali; Zedlitz, Aglaia; Vrijhoef, Hubertus J M

2017-01-01

Introduction Many individuals suffer from chronic pain or functional somatic syndromes and face boundaries for diminishing functional limitations by means of biopsychosocial interventions. Serious gaming could complement multidisciplinary interventions through enjoyment and independent accessibility. A study protocol is presented for studying whether, how, for which patients and under what circumstances, serious gaming improves patient health outcomes during regular multidisciplinary rehabilitation. Methods and analysis A mixed-methods design is described that prioritises a two-armed naturalistic quasi-experiment. An experimental group is composed of patients who follow serious gaming during an outpatient multidisciplinary programme at two sites of a Dutch rehabilitation centre. Control group patients follow the same programme without serious gaming in two similar sites. Multivariate mixed-modelling analysis is planned for assessing how much variance in 250 patient records of routinely monitored pain intensity, pain coping and cognition, fatigue and psychopathology outcomes is attributable to serious gaming. Embedded qualitative methods include unobtrusive collection and analyses of stakeholder focus group interviews, participant feedback and semistructured patient interviews. Process analyses are carried out by a systematic approach of mixing qualitative and quantitative methods at various stages of the research. Ethics and dissemination The Ethics Committee of the Tilburg School of Social and Behavioural Sciences approved the research after reviewing the protocol for the protection of patients’ interests in conformity to the letter and rationale of the applicable laws and research practice (EC 2016.25t). Findings will be presented in research articles and international scientific conferences. Trial registration number A prospective research protocol for the naturalistic quasi-experimental outcome evaluation was entered in the Dutch trial register (registration number: NTR6020; Pre-results). PMID:28600377

Desensitization Protocol in Recipients of Deceased Kidney Donor With Donor-Specific Antibody-Low Titers.

PubMed

Kanter Berga, J; Sancho Calabuig, A; Gavela Martinez, E; Puig Alcaraz, N; Avila Bernabeu, A; Crespo Albiach, J; Molina Vila, P; Beltrán Catalan, S; Pallardó Mateu, L

2016-11-01

Kidney transplantation is the better option for end-stage renal disease (ESRD), but for patients with human leukocyte antigen (HLA) sensitization, the wait times are significantly longer than for patients without antibodies. Many desensitization protocols have been described involving strong immunosuppression, the use of apheresis, and B-cell-modulating therapies. We have designed a desensitization protocol from day 0 for deceased donor kidney transplantation. Our aim was to present our initial experience with five kidney transplant patients. All patients had a negative complement-dependent cytotoxicity cross-match. The desensitization protocol included five to seven doses of thymoglobulin (1.25 mg/kg) and three sessions of plasmapheresis (PP) within the first week after transplantation, with intravenous immunoglobulin (500 mg/kg) after each PP session and one dose of rituximab on day 8. The presence of donor-specific antibodies (DSA) was analyzed by use of Luminex technology; levels between 1000 and 3000 mean fluorescence intensity were considered for desensitization. The median age was 44 years and median renal replacement therapy time was 9 years. All recipients presented 1 to 3 DSA specificities. There were no severe side effects related to PP, infusion of intravenous immunoglobulin, or rituximab. The median follow-up period was 19.3 months. Median serum creatinine level at last follow-up was 1.7 mg/dL. A kidney biopsy was performed in all patients. Graft and patient survival was 100%. Until now, few data are available concerning whether HLA-incompatible kidney transplantation after desensitization would benefit patients with ERSD. The desensitization strategy using the combination of PP, low doses of intravenous immunoglobulin, and rituximab at our center resulted in a satisfactory clinical outcome. Copyright © 2016 Elsevier Inc. All rights reserved.

The Geneva Protocol of 1925: Past and Present.

ERIC Educational Resources Information Center

Harbison, John L.

1982-01-01

Presents a position paper for use in high school social studies class debates on the Geneva Protocol of 1925. The Protocol was an international agreement to restrict chemical and biological warfare (CBW). The author traces the history of U.S. policies dealing with CBW since 1925. (AM)

Protocol for communications in potentially noisy environments

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

Boyd, Gerlad M.; Farrow, Jeffrey

2016-02-09

A communications protocol that is designed for transmission of data in networks that are subjected to harsh conditions is described herein. A network includes a plurality of devices, where the devices comprise respective nodes. The nodes are in communication with one another by way of a central network hub. The protocol causes the nodes to transmit data over a network bus at different data rates depending upon whether the nodes are operating normally or an arbitration procedure has been invoked.

Generation and customization of biosynthetic excitable tissues for electrophysiological studies and cell-based therapies.

PubMed

Nguyen, Hung X; Kirkton, Robert D; Bursac, Nenad

2018-05-01

We describe a two-stage protocol to generate electrically excitable and actively conducting cell networks with stable and customizable electrophysiological phenotypes. Using this method, we have engineered monoclonally derived excitable tissues as a robust and reproducible platform to investigate how specific ion channels and mutations affect action potential (AP) shape and conduction. In the first stage of the protocol, we combine computational modeling, site-directed mutagenesis, and electrophysiological techniques to derive optimal sets of mammalian and/or prokaryotic ion channels that produce specific AP shape and conduction characteristics. In the second stage of the protocol, selected ion channels are stably expressed in unexcitable human cells by means of viral or nonviral delivery, followed by flow cytometry or antibiotic selection to purify the desired phenotype. This protocol can be used with traditional heterologous expression systems or primary excitable cells, and application of this method to primary fibroblasts may enable an alternative approach to cardiac cell therapy. Compared with existing methods, this protocol generates a well-defined, relatively homogeneous electrophysiological phenotype of excitable cells that facilitates experimental and computational studies of AP conduction and can decrease arrhythmogenic risk upon cell transplantation. Although basic cell culture and molecular biology techniques are sufficient to generate excitable tissues using the described protocol, experience with patch-clamp techniques is required to characterize and optimize derived cell populations.

Practical Quantum Private Database Queries Based on Passive Round-Robin Differential Phase-shift Quantum Key Distribution.

PubMed

Li, Jian; Yang, Yu-Guang; Chen, Xiu-Bo; Zhou, Yi-Hua; Shi, Wei-Min

2016-08-19

A novel quantum private database query protocol is proposed, based on passive round-robin differential phase-shift quantum key distribution. Compared with previous quantum private database query protocols, the present protocol has the following unique merits: (i) the user Alice can obtain one and only one key bit so that both the efficiency and security of the present protocol can be ensured, and (ii) it does not require to change the length difference of the two arms in a Mach-Zehnder interferometer and just chooses two pulses passively to interfere with so that it is much simpler and more practical. The present protocol is also proved to be secure in terms of the user security and database security.

Standardisation of neonatal clinical practice.

PubMed

Bhutta, Z A; Giuliani, F; Haroon, A; Knight, H E; Albernaz, E; Batra, M; Bhat, B; Bertino, E; McCormick, K; Ochieng, R; Rajan, V; Ruyan, P; Cheikh Ismail, L; Paul, V

2013-09-01

The International Fetal and Newborn Growth Consortium for the 21(st) Century (INTERGROWTH-21(st) ) is a large-scale, population-based, multicentre project involving health institutions from eight geographically diverse countries, which aims to assess fetal, newborn and preterm growth under optimal conditions. Given the multicentre nature of the project and the expected number of preterm births, it is vital that all centres follow the same standardised clinical care protocols to assess and manage preterm infants, so as to ensure maximum validity of the resulting standards as indicators of growth and nutrition with minimal confounding. Moreover, it is well known that evidence-based clinical practice guidelines can reduce the delivery of inappropriate care and support the introduction of new knowledge into clinical practice. The INTERGROWTH-21(st) Neonatal Group produced an operations manual, which reflects the consensus reached by members of the group regarding standardised definitions of neonatal morbidities and the minimum standards of care to be provided by all centres taking part in the project. The operational definitions and summary management protocols were developed by consensus through a Delphi process based on systematic reviews of relevant guidelines and management protocols by authoritative bodies. This paper describes the process of developing the Basic Neonatal Care Manual, as well as the morbidity definitions and standardised neonatal care protocols applied across all the INTERGROWTH-21(st) participating centres. Finally, thoughts about implementation strategies are presented. © 2013 Royal College of Obstetricians and Gynaecologists.

A real-time polymerase chain reaction-based protocol for low/medium-throughput Y-chromosome microdeletions analysis.

PubMed

Segat, Ludovica; Padovan, Lara; Doc, Darja; Petix, Vincenzo; Morgutti, Marcello; Crovella, Sergio; Ricci, Giuseppe

2012-12-01

We describe a real-time polymerase chain reaction (PCR) protocol based on the fluorescent molecule SYBR Green chemistry, for a low- to medium-throughput analysis of Y-chromosome microdeletions, optimized according to the European guidelines and aimed at making the protocol faster, avoiding post-PCR processing, and simplifying the results interpretation. We screened 156 men from the Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Institute for Maternal and Child Health IRCCS Burlo Garofolo (Trieste, Italy), 150 not presenting Y-chromosome microdeletion, and 6 with microdeletions in different azoospermic factor (AZF) regions. For each sample, the Zinc finger Y-chromosomal protein (ZFY), sex-determining region Y (SRY), sY84, sY86, sY127, sY134, sY254, and sY255 loci were analyzed by performing one reaction for each locus. AZF microdeletions were successfully detected in six individuals, confirming the results obtained with commercial kits. Our real-time PCR protocol proved to be a rapid, safe, and relatively cheap method that was suitable for a low- to medium-throughput diagnosis of Y-chromosome microdeletion, which allows an analysis of approximately 10 samples (with the addition of positive and negative controls) in a 96-well plate format, or approximately 46 samples in a 384-well plate for all markers simultaneously, in less than 2 h without the need of post-PCR manipulation.

Applying the Intervention Mapping protocol to develop a kindergarten-based, family-involved intervention to increase European preschool children's physical activity levels: the ToyBox-study.

PubMed

De Craemer, M; De Decker, E; De Bourdeaudhuij, I; Verloigne, M; Duvinage, K; Koletzko, B; Ibrügger, S; Kreichauf, S; Grammatikaki, E; Moreno, L; Iotova, V; Socha, P; Szott, K; Manios, Y; Cardon, G

2014-08-01

Although sufficient physical activity is beneficial for preschoolers' health, activity levels in most preschoolers are low. As preschoolers spend a considerable amount of time at home and at kindergarten, interventions should target both environments to increase their activity levels. The aim of the current paper was to describe the six different steps of the Intervention Mapping protocol towards the systematic development and implementation of the physical activity component of the ToyBox-intervention. This intervention is a kindergarten-based, family-involved intervention implemented across six European countries. Based on the results of literature reviews and focus groups with parents/caregivers and kindergarten teachers, matrices of change objectives were created. Then, theory-based methods and practical strategies were selected to develop intervention materials at three different levels: (i) individual level (preschoolers); (ii) interpersonal level (parents/caregivers) and (iii) organizational level (teachers). This resulted in a standardized intervention with room for local and cultural adaptations in each participating country. Although the Intervention Mapping protocol is a time-consuming process, using this systematic approach may lead to an increase in intervention effectiveness. The presented matrices of change objectives are useful for future programme planners to develop and implement an intervention based on the Intervention Mapping protocol to increase physical activity levels in preschoolers. © 2014 World Obesity.

Quality assurance in the EORTC 22033-26033/CE5 phase III randomized trial for low grade glioma: the digital individual case review.

PubMed

Fairchild, Alysa; Weber, Damien C; Bar-Deroma, Raquel; Gulyban, Akos; Fenton, Paul A; Stupp, Roger; Baumert, Brigitta G

2012-06-01

The phase III EORTC 22033-26033/NCIC CE5 intergroup trial compares 50.4 Gy radiotherapy with up-front temozolomide in previously untreated low-grade glioma. We describe the digital EORTC individual case review (ICR) performed to evaluate protocol radiotherapy (RT) compliance. Fifty-eight institutions were asked to submit 1-2 randomly selected cases. Digital ICR datasets were uploaded to the EORTC server and accessed by three central reviewers. Twenty-seven parameters were analysed including volume delineation, treatment planning, organ at risk (OAR) dosimetry and verification. Consensus reviews were collated and summary statistics calculated. Fifty-seven of seventy-two requested datasets from forty-eight institutions were technically usable. 31/57 received a major deviation for at least one section. Relocation accuracy was according to protocol in 45. Just over 30% had acceptable target volumes. OAR contours were missing in an average of 25% of cases. Up to one-third of those present were incorrectly drawn while dosimetry was largely protocol compliant. Beam energy was acceptable in 97% and 48 patients had per protocol beam arrangements. Digital RT plan submission and review within the EORTC 22033-26033 ICR provide a solid foundation for future quality assurance procedures. Strict evaluation resulted in overall grades of minor and major deviation for 37% and 32%, respectively. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Measurements of clothing evaporative resistance using a sweating thermal manikin: an overview

PubMed Central

WANG, Faming

2017-01-01

Evaporative resistance has been widely used to describe the evaporative heat transfer property of clothing. It is also a critical variable in heat stress models for predicting human physiological responses in various environmental conditions. At present, sweating thermal manikins provide a fast and cost-effective way to determine clothing evaporative resistance. Unfortunately, the measurement repeatability and reproducibility of evaporative resistance are rather low due to the complicated moisture transfer processes through clothing. This review article presents a systematical overview on major influential factors affecting the measurement precision of clothing evaporative resistance measurements. It also illustrates the state-of-the-art knowledge on the development of test protocol to measure clothing evaporative resistance by means of a sweating manikin. Some feasible and robust test procedures for measurement of clothing evaporative resistance using a sweating manikin are described. Recommendations on how to improve the measurement accuracy of clothing evaporative resistance are addressed and expected future trends on development of advanced sweating thermal manikins are finally presented. PMID:28566566

Transferable residues from dog fur and plasma cholinesterase inhibition in dogs treated with a flea control dip containing chlorpyrifos.

PubMed Central

Boone, J S; Tyler, J W; Chambers, J E

2001-01-01

We studied chlorpyrifos, an insecticide present in a commercial dip for treating ectoparasites in dogs, to estimate the amount of transferable residues that children could obtain from their treated pets. Although the chlorpyrifos dip is no longer supported by the manufacturer, the methodology described herein can help determine transferable residues from other flea control insecticide formulations. Twelve dogs of different breeds and weights were dipped using the recommended guidelines with a commercial, nonprescription chlorpyrifos flea dip for 4 consecutive treatments at 3-week intervals (nonshampoo protocol) and another 12 dogs were dipped with shampooing between dips (shampoo protocol). The samples collected at 4 hr and 7, 14, and 21 days after treatment in the nonshampoo protocol averaged 971, 157, 70, and 26 microg chlorpyrifos, respectively; in the shampoo protocol the samples averaged 459, 49, 15, and 10 microg, respectively. The highest single sample was about 7,000 microg collected at 4 hr. The pretreatment specific activities in the plasma of the dogs were about 75 nmol/min/mg protein for butyrylcholinesterase (BChE), and 9 nmol/min/mg protein for acetylcholinesterase (AChE). BChE was inhibited 50-75% throughout the study, and AChE was inhibited 11-18% in the nonshampoo protocol; inhibition was not as great in the shampoo protocol. There was no correlation (p

A single-arm clinical trial of a 48-hour intravenous N-acetylcysteine protocol for treatment of acetaminophen poisoning.

PubMed

Heard, K; Rumack, B H; Green, J L; Bucher-Bartelson, B; Heard, S; Bronstein, A C; Dart, R C

2014-06-01

Acetylcysteine prevents hepatic injury when administered soon after acetaminophen overdose. The most commonly used treatment protocols are a 72-hour oral and a 21-hour intravenous (IV) protocol. Between 1984 and 1994, 409 patients were enrolled in a study to describe the outcomes of patients who were treated using a 48-hour IV protocol. In 1991, an interim analysis reported the first 223 patients. The objective of this manuscript is to report the rates of hepatotoxicity and adverse events occurring during a 48-hour IV acetylcysteine protocol in the entire 409 patient cohort. This was a multicenter, single-arm, open-label clinical trial enrolling patients who presented with a toxic serum acetaminophen concentration within 24 h of acute acetaminophen ingestion. Patients were treated with 140 mg/kg loading dose followed by 70 mg/kg every 4 h for 12 doses. Serum aminotransferase activities were measured every 8 h during the protocol, and adverse events were recorded. The primary outcome was the percentage of subjects who developed hepatotoxicity defined as a peak serum aminotransferase greater than 1000 IU/L. Four hundred and nine patients were enrolled, and 309 met inclusion for the outcome analysis. The overall percentage of patients developing hepatotoxicity was 18.1%, and 3.4% of patients treated within 10 h developed hepatotoxicity. One acetaminophen-related death occurred in a patient treated at 22 h. Adverse events occurred in 28.9% of enrolled subjects; the most common adverse events were nausea, vomiting, and flushing, and no events were rated as serious by the investigator. Acetaminophen-overdosed patients treated with IV acetylcysteine administered as 140 mg/kg loading dose followed by 70 mg/kg every 4 h for 12 doses had a low rate of hepatotoxicity and few adverse events. This protocol delivers a higher dose of acetylcysteine which may be useful in selected cases involving very large overdoses.

An Evaluation of Protocol Enhancing Proxies and File Transport Protocols for Satellite Communication

NASA Technical Reports Server (NTRS)

Finch, Patrick Eugene; Sullivan, Donald; Ivancic, William D.

2012-01-01

NASA is utilizing Global Hawk aircraft in high-altitude, long-duration Earth science missions. Communications with the onboard research equipment and sensors (the science payload) is via Ku-Band radio utilizing satellites in geostationary orbits. All payload communications use standard Internet Protocols and routing, and much of the data to be transferred is comprised of very large files. The science community is interested in fully utilizing these communication links to retrieve data as quickly and reliably as possible. A test bed was developed at NASA Ames to evaluate modern transport protocols as well as Protocol Enhancing Proxies (PEPs) to determine what tools best fit the needs of the science community. This paper describes the test bed used, the protocols, the PEPs that were evaluated, the particular tests performed and the results and conclusions.

Comparison of two DNA extraction protocols from leave samples of Cotinus coggygria, Citrus sinensis and Genus juglans.

PubMed

Fallah, F; Minaei Chenar, H; Amiri, H; Omodipour, S; Shirbande Ghods, F; Kahrizi, D; Sohrabi, M; Ghorbani, T; Kazemi, E

2017-02-28

High quality DNA is essential for molecular research. Secondary metabolites can affect the quantity and quality DNA. In current research two DNA isolation methods including CTAB and Delaporta (protocols 1 & 2 respectively) were applied in three leave samples from Cotinus coggygria, Citrus sinensis and Genus juglans that their leaves are rich of secondary metabolites. We successfully isolated DNA from C. coggygria, C. sinensis and Genus Juglans using the two protocols described above. Good quality DNA was isolated from C. coggygria, C. sinensis and Genus Juglans using protocol 1, while protocol 2 failed to produce usable DNA from these sources. The highest amount of DNA (1.3-1.6) was obtained from them using protocol 1. As we discovered, procedure 1 may work better for plants with secondary metabolites.

Recent advances in magnetofection and its potential to deliver siRNAs in vitro.

PubMed

Mykhaylyk, Olga; Zelphati, Olivier; Hammerschmid, Edelburga; Anton, Martina; Rosenecker, Joseph; Plank, Christian

2009-01-01

This chapter describes how to design and conduct experiments to deliver siRNA to adherent mammalian cells in vitro by magnetic force-assisted transfection using self-assembled complexes of small interfering RNA (siRNA) and cationic lipids or polymers that are associated with magnetic nanoparticles. These magnetic complexes are targeted to the cell surface by the application of a magnetic gradient field. In this chapter, first we describe the synthesis of magnetic nanoparticles for magnetofection and the association of siRNA with the magnetic components of the transfection complex. Second, a simple protocol is described in order to evaluate magnetic responsiveness of the magnetic siRNA transfection complexes and estimate the complex loading with magnetic nanoparticles. Third, protocols are provided for the preparation of magnetic lipoplexes and polyplexes of siRNA, magnetofection, downregulation of gene expression, and the determination of cell viability. The addition of INF-7 peptide, a fusogenic peptide, to the magnetic transfection triplexes improved gene silencing in HeLa cells. The described protocols are also valuable for screening vector compositions and novel magnetic nanoparticle preparations to optimize siRNA transfection by magnetofection in every cell type.

Well installation and documentation, and ground-water sampling protocols for the pilot National Water-Quality Assessment Program

USGS Publications Warehouse

Hardy, M.A.; Leahy, P.P.; Alley, W.M.

1989-01-01

Several pilot projects are being conducted as part of the National Water Quality Assessment (NAWQA) Program. The purpose of the pilot program is to test and refine concepts for a proposed full-scale program. Three of the pilot projects are specifically designed to assess groundwater. The purpose of this report is to describe the criteria that are being used in the NAWQA pilot projects for selecting and documenting wells, installing new wells, and sampling wells for different water quality constituents. Guidelines are presented for the selection of wells for sampling. Information needed to accurately document each well includes site characteristics related to the location of the well, land use near the well, and important well construction features. These guidelines ensure the consistency of the information collected and will provide comparable data for interpretive purposes. Guidelines for the installation of wells are presented and include procedures that need to be followed for preparations prior to drilling, the selection of the drilling technique and casing type, the grouting procedure, and the well-development technique. A major component of the protocols is related to water quality sampling. Tasks are identified that need to be completed prior to visiting the site for sampling. Guidelines are presented for purging the well prior t sampling, both in terms of the volume of water pumped and the chemical stability of field parameters. Guidelines are presented concerning sampler selection as related to both inorganic and organic constituents. Documentation needed to describe the measurements and observations related to sampling each well and treating and preserving the samples are also presented. Procedures are presented for the storage and shipping of water samples, equipment cleaning, and quality assurance. Quality assurance guidelines include the description of the general distribution of the various quality assurance samples (blanks, spikes, duplicates, and reference samples) that will be used in the pilot program. (Lantz-PTT)

NASA SpaceWire Activities/Comments/Recommendations

NASA Technical Reports Server (NTRS)

Rakow, Glenn

2006-01-01

This viewgraph presentation reviews NASA's activities, and proposes recommendations for the further use of the SpaceWire (SpW). The areas covered in this presentation are: (1) Protocol ID assignment, (2) Protocol development, (3) Plug & Play (PnP), (4) Recommended additions t o SpW protocol and (5) SpaceFibre trade.

Respiratory analysis of coupled mitochondria in cryopreserved liver biopsies.

PubMed

García-Roche, Mercedes; Casal, Alberto; Carriquiry, Mariana; Radi, Rafael; Quijano, Celia; Cassina, Adriana

2018-07-01

The aim of this work was to develop a cryopreservation method of small liver biopsies for in situ mitochondrial function assessment. Herein we describe a detailed protocol for tissue collection, cryopreservation, high-resolution respirometry using complex I and II substrates, calculation and interpretation of respiratory parameters. Liver biopsies from cow and rat were sequentially frozen in a medium containing dimethylsulfoxide as cryoprotectant and stored for up to 3 months at -80 °C. Oxygen consumption rate studies of fresh and cryopreserved samples revealed that most respiratory parameters remained unchanged. Additionally, outer mitochondrial membrane integrity was assessed adding cytochrome c, proving that our cryopreservation method does not harm mitochondrial structure. In sum, we present a reliable way to cryopreserve small liver biopsies without affecting mitochondrial function. Our protocol will enable the transport and storage of samples, extending and facilitating mitochondrial function analysis of liver biopsies. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Protocol Based Real-Time Continuous Electroencephalography for Detecting Vasospasm in Subarachnoid Hemorrhage.

PubMed

Hong, Jeong-Ho; Bang, Jae Seung; Chung, Jin-Heon; Han, Moon-Ku

2016-03-01

A continuous electroencephalography (cEEG) can be helpful in detecting vasospasm and delayed cerebral ischemia in aneurysmal subarachnoid hemorrhage (SAH). We describe a patient with an aneurysmal SAH whose symptomatic vasospasm was detected promptly by using a real-time cEEG. Patient was immediately treated by intraarterial vasodilator therapy. A 50-year-old woman without any significant medical history presented with a severe bifrontal headache due to acute SAH with a ruptured aneurysm on the anterior communicating artery (Fisher grade 3). On bleed day 6, she developed a sudden onset of global aphasia and left hemiparesis preceded by cEEG changes consistent with vasospasm. A stat chemical dilator therapy was performed and she recovered without significant neurological deficits. A real-time and protocol-based cEEG can be utilized in order to avoid any delay in detection of vasospasm in aneurysmal SAH and thereby improve clinical outcomes.

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

PubMed Central

Moriya, Toshio; Saur, Michael; Stabrin, Markus; Merino, Felipe; Voicu, Horatiu; Huang, Zhong; Penczek, Pawel A.; Raunser, Stefan; Gatsogiannis, Christos

2017-01-01

SPHIRE (SPARX for High-Resolution Electron Microscopy) is a novel open-source, user-friendly software suite for the semi-automated processing of single particle electron cryo-microscopy (cryo-EM) data. The protocol presented here describes in detail how to obtain a near-atomic resolution structure starting from cryo-EM micrograph movies by guiding users through all steps of the single particle structure determination pipeline. These steps are controlled from the new SPHIRE graphical user interface and require minimum user intervention. Using this protocol, a 3.5 Å structure of TcdA1, a Tc toxin complex from Photorhabdus luminescens, was derived from only 9500 single particles. This streamlined approach will help novice users without extensive processing experience and a priori structural information, to obtain noise-free and unbiased atomic models of their purified macromolecular complexes in their native state. PMID:28570515

Pre-flight sensorimotor adaptation protocols for suborbital flight.

PubMed

Shelhamer, Mark; Beaton, Kara

2012-01-01

Commercial suborbital flights, which include 3-5 minutes of 0 g between hyper-g launch and landing phases, will present suborbital passengers with a challenging sensorimotor experience. Based on the results of neurovestibular research in parabolic and orbital flight, and the anticipated wide range of fitness and experience levels of suborbital passengers, neurovestibular disturbances are likely to be problematic in this environment. Pre-flight adaptation protocols might alleviate some of these issues. Therefore, we describe a set of sensorimotor tests to evaluate passengers before suborbital flight, including assessment of the angular vestibulo-ocular reflex (VOR), ocular skew and disconjugate torsion, subjective visual vertical, and roll vection. Performance on these tests can be examined for correlations with in-flight experience, such as motion sickness, disorientation, and visual disturbances, based on questionnaires and cabin video recordings. Through an understanding of sensorimotor adaptation to parabolic and orbital flight, obtained from many previous studies, we can then suggest appropriate pre-flight adaptation procedures.

Practical Computer Security through Cryptography

NASA Technical Reports Server (NTRS)

McNab, David; Twetev, David (Technical Monitor)

1998-01-01

The core protocols upon which the Internet was built are insecure. Weak authentication and the lack of low level encryption services introduce vulnerabilities that propagate upwards in the network stack. Using statistics based on CERT/CC Internet security incident reports, the relative likelihood of attacks via these vulnerabilities is analyzed. The primary conclusion is that the standard UNIX BSD-based authentication system is by far the most commonly exploited weakness. Encryption of Sensitive password data and the adoption of cryptographically-based authentication protocols can greatly reduce these vulnerabilities. Basic cryptographic terminology and techniques are presented, with attention focused on the ways in which technology such as encryption and digital signatures can be used to protect against the most commonly exploited vulnerabilities. A survey of contemporary security software demonstrates that tools based on cryptographic techniques, such as Kerberos, ssh, and PGP, are readily available and effectively close many of the most serious security holes. Nine practical recommendations for improving security are described.

Tracheostomy and mechanical ventilation weaning in children affected by respiratory virus according to a weaning protocol in a pediatric intensive care unit in Argentina: an observational restrospective trial

PubMed Central

2011-01-01

We describe difficult weaning after prolonged mechanical ventilation in three tracheostomized children affected by respiratory virus infection. Although the spontaneous breathing trials were successful, the patients failed all extubations. Therefore a tracheostomy was performed and the weaning plan was begun. The strategy for weaning was the decrease of ventilation support combining pressure control ventilation (PCV) with increasing periods of continuous positive airway pressure + pressure support ventilation (CPAP + PSV) and then CPAP + PSV with increasing intervals of T-piece. They presented acute respiratory distress syndrome on admission with high requirements of mechanical ventilation (MV). Intervening factors in the capabilities and loads of the respiratory system were considered and optimized. The average MV time was 69 days and weaning time 31 days. We report satisfactory results within the context of a directed weaning protocol. PMID:21244710

Mutagenic and antimutagenic effects of aqueous extract of rosemary (Rosmarinus officinalis L.) on meristematic cells of Allium cepa.

PubMed

Felicidade, I; Lima, J D; Pesarini, J R; Monreal, A C D; Mantovani, M S; Ribeiro, L R; Oliveira, R J

2014-11-28

Polyphenolic compounds present in rosemary were found to have antioxidant properties, anticarcinogenic activity, and to increase the detoxification of pro-carcinogens. The aim of the study was to determine the effect the aqueous extract of rosemary (AER) on mutagenicity induced by methylmethane sulfonate in meristematic cells of Allium cepa, as well as to describe its mode of action. Anti-mutagenicity experiments were carried out with 3 different concentrations of AER, which alone showed no mutagenic effects. In antimutagenicity experiments, AER showed chemopreventive activity in cultured meristematic cells of A. cepa against exposure to methylmethane sulfonate. Additionally, post-treatment and simultaneous treatment using pre-incubation protocols were the most effective. Evaluation of different protocols and the percent reduction in DNA indicated bioantimutagenic as well desmutagenic modes of action for AER. AER may be chemopreventive and antimutagenic.

Drug-induced conditioned place preference and aversion in mice.

PubMed

Cunningham, Christopher L; Gremel, Christina M; Groblewski, Peter A

2006-01-01

This protocol describes the equipment and methods used to establish conditioned place preference (CPP) or aversion (CPA). Place conditioning is a form of Pavlovian conditioning routinely used to measure the rewarding or aversive motivational effects of objects or experiences (e.g., abused drugs). Here, we present a place conditioning procedure that has been used extensively to study the motivational effects of ethanol and other abused drugs in mice. This protocol involves three phases: (i) habituation (or a pretest), (ii) conditioning of an association between the drug and a tactile or visual stimulus and (iii) a test that offers a choice between the drug-associated cue and a neutral cue. If the drug has motivational significance, mice will spend significantly more time (CPP) or less time (CPA) in proximity to the drug-associated cue. Potential problems in the design and interpretation of place conditioning studies are discussed. A typical experiment lasts 2 weeks.