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...

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.

A systematic review of postoperative hand therapy management of basal joint arthritis.

PubMed

Wolfe, Terri; Chu, Jennifer Y; Woods, Tammy; Lubahn, John D

2014-04-01

There are a variety of postoperative immobilization and therapy options for patients with basal joint arthritis. Although prior systematic reviews have compared surgical procedures used to treat basal joint arthritis, none to our knowledge compares therapy protocols for this condition, which are considered an important part of the treatment. (1) We sought to determine whether differences in the length and type of postoperative immobilization affect clinical results after basal joint arthritis surgery. (2) We also compared specific therapy protocols that were prescribed. (3) Finally, we evaluated published protocols to determine when patients were released to full activity to see whether these appeared to affect clinical results. A systematic review of English-language studies in the PubMed and Cochrane databases was performed. Studies were then reviewed to determine what postoperative immobilization and therapy protocols the authors used and when patients were released to full activities. A total of 19 studies were identified using the search criteria. All but one of the studies included a postoperative period of immobilization in either a cast or splint. Immobilization time varied depending on whether Kirschner wires were used for the surgery and whether an implant was placed. Postoperative therapy protocols also varied but followed three general patterns. Some therapy protocols involved teaching patients a home exercise program only, whereas some authors described routine referral to a therapist. The third group consisted of studies in which patients were only referred for therapy if the physicians determined it was necessary during followup. Many studies did not give a specific time for full return to activity and instead described a gradual transition to full activity after immobilization was discontinued. Because of the variability and small numbers, no conclusive recommendations could be made on any of the three study questions. Comparative, multicenter studies comparing different immobilization and therapy protocols after the surgical treatment of basal joint arthritis would be helpful for both surgeons and therapists looking to refine their treatment protocols.

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.

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.

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 %.

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.

Race to the Top--Early Learning Challenge (RTT-ELC): Descriptive Study of Tiered Quality Rating and Improvement Systems (TQRIS). Master Data Collection Protocol

ERIC Educational Resources Information Center

Mathematica Policy Research, Inc., 2015

2015-01-01

This master data collection protocol describes the data that Mathematica collected for the Race to the Top-Early Learning Challenge Study of Tiered Quality Rating and Improvement Systems. This study was conducted for the Department of Education's Institute of Education Sciences. The data were collected from reviews of applications, documents, and…

Where Words Fail, Music Speaks: A Mixed Method Study of an Evidence-Based Music Protocol.

PubMed

Daniels, Ruby A; Torres, David; Reeser, Cathy

2016-01-01

Despite numerous studies documenting the benefits of music, hospice social workers are often unfamiliar with evidence-based music practices that may improve end of life care. This mixed method study tested an intervention to teach hospice social workers and chaplains (N = 10) an evidence-based music protocol. Participants used the evidence-based practice (EBP) for 30 days, recording 226 journal entries that described observations of 84 patients and their families. There was a significant increase in EBP knowledge (35%). Prompting behavioral and emotional responses, music was described frequently as a catalyst that facilitated deeper dialogue between patients, families, social workers, and chaplains.

Connecting Levels of Representation: Emergent versus Submergent Perspective

ERIC Educational Resources Information Center

Rappoport, Lana T.; Ashkenazi, Guy

2008-01-01

Chemical phenomena can be described using three representation modes: macro, submicro, and symbolic. The way students use and connect these modes when solving conceptual problems was studied, using a think-aloud interview protocol. The protocol was validated through interviews with six faculty members, and then applied to four graduate and six…

Managerial Attention Patterns: A Micro-Behavioral Analysis.

ERIC Educational Resources Information Center

Sproull, Lee S.

This paper describes a study of managerial behavior in educational organizations that focused on managerial attention as an organizational coupling mechanism. Structured observation was used to collect minute-by-minute time allocation protocols for five first-line education program managers over 20 working days, and these protocols were analyzed…

Electroencephalography for children with autistic spectrum disorder: a sedation protocol.

PubMed

Keidan, Ilan; Ben-Menachem, Erez; Tzadok, Michal; Ben-Zeev, Bruria; Berkenstadt, Haim

2015-02-01

To report the effectiveness and efficiency of a predetermined sedation protocol for providing sedation for electroencephalograph (EEG) studies in children with autism. Sleep EEG has been advocated for the majority of children with autism spectrum disorder. In most cases, sedation is required to allow adequate studies. Most sedation drugs have negative effects on the EEG pattern. The sedation protocol we adopted included chloral hydrate, dexmedetomidine, and ketamine and was evaluated prospectively for 2 years. One hundred and eighty-three children with autistic spectrum disorder were sedated with the described drug protocol that was efficient, provided adequate EEG readings, and was not associated with serious adverse events. Our protocol kept costs to a minimum but provided appropriate escalation in care when required. © 2014 John Wiley & Sons Ltd.

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

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.

A standard protocol for describing individual-based and agent-based models

USGS Publications Warehouse

Grimm, Volker; Berger, Uta; Bastiansen, Finn; Eliassen, Sigrunn; Ginot, Vincent; Giske, Jarl; Goss-Custard, John; Grand, Tamara; Heinz, Simone K.; Huse, Geir; Huth, Andreas; Jepsen, Jane U.; Jorgensen, Christian; Mooij, Wolf M.; Muller, Birgit; Pe'er, Guy; Piou, Cyril; Railsback, Steven F.; Robbins, Andrew M.; Robbins, Martha M.; Rossmanith, Eva; Ruger, Nadja; Strand, Espen; Souissi, Sami; Stillman, Richard A.; Vabo, Rune; Visser, Ute; DeAngelis, Donald L.

2006-01-01

Simulation models that describe autonomous individual organisms (individual based models, IBM) or agents (agent-based models, ABM) have become a widely used tool, not only in ecology, but also in many other disciplines dealing with complex systems made up of autonomous entities. However, there is no standard protocol for describing such simulation models, which can make them difficult to understand and to duplicate. This paper presents a proposed standard protocol, ODD, for describing IBMs and ABMs, developed and tested by 28 modellers who cover a wide range of fields within ecology. This protocol consists of three blocks (Overview, Design concepts, and Details), which are subdivided into seven elements: Purpose, State variables and scales, Process overview and scheduling, Design concepts, Initialization, Input, and Submodels. We explain which aspects of a model should be described in each element, and we present an example to illustrate the protocol in use. In addition, 19 examples are available in an Online Appendix. We consider ODD as a first step for establishing a more detailed common format of the description of IBMs and ABMs. Once initiated, the protocol will hopefully evolve as it becomes used by a sufficiently large proportion of modellers.

A protocol for rheological characterization of hydrogels for tissue engineering strategies.

PubMed

Zuidema, Jonathan M; Rivet, Christopher J; Gilbert, Ryan J; Morrison, Faith A

2014-07-01

Hydrogels are studied extensively for many tissue engineering applications, and their mechanical properties influence both cellular and tissue compatibility. However, it is difficult to compare the mechanical properties of hydrogels between studies due to a lack of continuity between rheological protocols. This study outlines a straightforward protocol to accurately determine hydrogel equilibrium modulus and gelation time using a series of rheological tests. These protocols are applied to several hydrogel systems used within tissue engineering applications: agarose, collagen, fibrin, Matrigel™, and methylcellulose. The protocol is outlined in four steps: (1) Time sweep to determine the gelation time of the hydrogel. (2) Strain sweep to determine the linear-viscoelastic region of the hydrogel with respect to strain. (3) Frequency sweep to determine the linear equilibrium modulus plateau of the hydrogel. (4) Time sweep with values obtained from strain and frequency sweeps to accurately report the equilibrium moduli and gelation time. Finally, the rheological characterization protocol was evaluated using a composite Matrigel™-methylcellulose hydrogel blend whose mechanical properties were previously unknown. The protocol described herein provides a standardized approach for proper analysis of hydrogel rheological properties. © 2013 Wiley Periodicals, Inc.

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.

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.

Optimized protocols for Mycobacterium leprae strain management: frozen stock preservation and maintenance in athymic nude mice.

PubMed

Trombone, Ana Paula Fávaro; Pedrini, Sílvia Cristina Barbosa; Diório, Suzana Madeira; Belone, Andréa de Faria Fernandes; Fachin, Luciana Raquel Vicenzi; do Nascimento, Dejair Caitano; Rosa, Patricia Sammarco

2014-03-23

Leprosy, caused by Mycobacterium leprae, is an important infectious disease that is still endemic in many countries around the world, including Brazil. There are currently no known methods for growing M. leprae in vitro, presenting a major obstacle in the study of this pathogen in the laboratory. Therefore, the maintenance and growth of M. leprae strains are preferably performed in athymic nude mice (NU-Foxn1(nu)). The laboratory conditions for using mice are readily available, easy to perform, and allow standardization and development of protocols for achieving reproducible results. In the present report, we describe a simple protocol for purification of bacilli from nude mouse footpads using trypsin, which yields a suspension with minimum cell debris and with high bacterial viability index, as determined by fluorescent microscopy. A modification to the standard method for bacillary counting by Ziehl-Neelsen staining and light microscopy is also demonstrated. Additionally, we describe a protocol for freezing and thawing bacillary stocks as an alternative protocol for maintenance and storage of M. leprae strains.

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

Interventions developed with the Intervention Mapping protocol in the field of cancer: A systematic review.

PubMed

Lamort-Bouché, Marion; Sarnin, Philippe; Kok, Gerjo; Rouat, Sabrina; Péron, Julien; Letrilliart, Laurent; Fassier, Jean-Baptiste

2018-04-01

The Intervention Mapping (IM) protocol provides a structured framework to develop, implement, and evaluate complex interventions. The main objective of this review was to identify and describe the content of the interventions developed in the field of cancer with the IM protocol. Secondary objectives were to assess their fidelity to the IM protocol and to review their theoretical frameworks. Medline, Web of Science, PsycINFO, PASCAL, FRANCIS, and BDSP databases were searched. All titles and abstracts were reviewed. A standardized extraction form was developed. All included studies were reviewed by 2 reviewers blinded to each other. Sixteen studies were identified, and these reported 15 interventions. The objectives were to increase cancer screening participation (n = 7), early consultation (n = 1), and aftercare/quality of life among cancer survivors (n = 7). Six reported a complete participatory planning group, and 7 described a complete logic model of the problem. Ten studies described a complete logic model of change. The main theoretical frameworks used were the theory of planned behaviour (n = 8), the transtheoretical model (n = 6), the health belief model (n = 6), and the social cognitive theory (n = 6). The environment was rarely integrated in the interventions (n = 4). Five interventions were reported as effective. Culturally relevant interventions were developed with the IM protocol that were effective to increase cancer screening and reduce social disparities, particularly when they were developed through a participative approach and integrated the environment. Stakeholders' involvement and the role of the environment were heterogeneously integrated in the interventions. Copyright © 2017 John Wiley & Sons, Ltd.

Imaging Tumor Cell Movement In Vivo

PubMed Central

Entenberg, David; Kedrin, Dmitriy; Wyckoff, Jeffrey; Sahai, Erik; Condeelis, John; Segall, Jeffrey E.

2013-01-01

This unit describes the methods that we have been developing for analyzing tumor cell motility in mouse and rat models of breast cancer metastasis. Rodents are commonly used both to provide a mammalian system for studying human tumor cells (as xenografts in immunocompromised mice) as well as for following the development of tumors from a specific tissue type in transgenic lines. The Basic Protocol in this unit describes the standard methods used for generation of mammary tumors and imaging them. Additional protocols for labeling macrophages, blood vessel imaging, and image analysis are also included. PMID:23456602

Cardiac risk stratification in cardiac rehabilitation programs: a review of protocols

PubMed Central

da Silva, Anne Kastelianne França; Barbosa, Marianne Penachini da Costa de Rezende; Bernardo, Aline Fernanda Barbosa; Vanderlei, Franciele Marques; Pacagnelli, Francis Lopes; Vanderlei, Luiz Carlos Marques

2014-01-01

Objective Gather and describe general characteristics of different protocols of risk stratification for cardiac patients undergoing exercise. Methods We conducted searches in LILACS, IBECS, MEDLINE, Cochrane Library, and SciELO electronic databases, using the following descriptors: Cardiovascular Disease, Rehabilitation Centers, Practice Guideline, Exercise and Risk Stratification in the past 20 years. Results Were selected eight studies addressing methods of risk stratification in patients undergoing exercise. Conclusion None of the methods described could cover every situation the patient can be subjected to; however, they are essential to exercise prescription. PMID:25140477

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.

Development and Pilot-Testing of a Cognitive Behavioral Coping Skills Group Intervention for Patients with Chronic Hepatitis C.

PubMed

Evon, Donna M; Golin, Carol E; Ruffin, Rachel; Fried, Michael W

2017-06-01

Psychosocial interventions for patients with chronic hepatitis C viral (HCV) infection are needed to attenuate the impact of extrahepatic symptoms, comorbid conditions, and treatment side effects on HCV health outcomes. We adapted empirically-supported interventions for similar patient populations to develop a Cognitive Behavioral Coping Skills group intervention for HCV patients (CBCS-HCV) undergoing treatment. The objectives of this paper are to describe the research activities associated with CBCS-HCV development and pilot testing, including: (1) formative work leading to intervention development; (2) preliminary study protocol; and (3) pilot feasibility testing of the intervention and study design. Formative work included a literature review, qualitative interviews, and adaption, development, and review of study materials. A preliminary study protocol is described. We evaluate the feasibility of conducting a randomized controlled trial (RCT) of the CBCS-HCV with 12 study participants in Wave 1 testing to examine: (a) feasibility of intervention delivery; (b) patient acceptability; (c) recruitment, enrollment, retention; (d) feasibility of conducting a RCT; (d) therapist protocol fidelity; and (e) feasibility of data collection. Numerous lessons were learned. We found very high rates of data collection, participant attendance, engagement, retention and acceptability, and therapist protocol fidelity. We conclude that many aspects of the CBCS-HCV intervention and study protocol were highly feasible. The greatest challenge during this Wave 1 pilot study was efficiency of participant enrollment due to changes in standard of care treatment. These findings informed two additional waves of pilot testing to examine effect sizes and potential improvements in clinical outcomes, with results forthcoming.

Pharmaceutical care for patients with COPD in Belgium and views on protocol implementation.

PubMed

Tommelein, Eline; Tollenaere, Kathleen; Mehuys, Els; Boussery, Koen

2014-08-01

A protocol-based pharmaceutical care program (the PHARMACOP-protocol) focusing on patient counselling during prescription filling has shown to be effective in patients with chronic obstructive pulmonary disease (COPD). However, implementation of this protocol in daily practice has not yet been studied. To describe current implementation level of the items included in the PHARMACOP-protocol in Belgian community pharmacies and to evaluate pharmacists' perspectives on the implementation of this protocol in daily practice. A cross-sectional study was conducted from April to June 2012, in randomly selected community pharmacies in Flanders. Pharmacists were questionned using structured interviews. 125 pharmacies were contacted and 80 managing pharmacists (64 %) participated. In >70 % of pharmacies, 4/7 protocol items for first prescriptions and 3/5 protocol items for follow-up prescriptions were already routinely implemented. For first and follow-up prescriptions, respectively 39 (49 %) and 34 pharmacists (43 %) stated they would need to spend at least 5 min extra to offer optimal patient counselling. Most mentioned barriers preventing protocol implementation included lack of time (80 %), no integration in pharmacy software (61 %) and too much administrative burden (58 %). Approximately 50 % of the PHARMACOP-protocol items are currently routinely provided in Belgian community pharmacies. Nearly all interviewed pharmacists are willing to implement the protocol fully or partially in daily practice.

Protocol dependence of mechanical properties in granular systems.

PubMed

Inagaki, S; Otsuki, M; Sasa, S

2011-11-01

We study the protocol dependence of the mechanical properties of granular media by means of computer simulations. We control a protocol of realizing disk packings in a systematic manner. In 2D, by keeping material properties of the constituents identical, we carry out compaction with various strain rates. The disk packings exhibit the strain rate dependence of the critical packing fraction above which the pressure becomes non-zero. The observed behavior contrasts with the well-studied jamming transitions for frictionless disk packings. We also observe that the elastic moduli of the disk packings depend on the strain rate logarithmically. Our results suggest that there exists a time-dependent state variable to describe macroscopic material properties of disk packings, which depend on its protocol.

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.

Integrating landscape system and meta-ecosystem frameworks to advance the understanding of ecosystem function in heterogeneous landscapes: An analysis on the carbon fluxes in the Northern Highlands Lake District (NHLD) of Wisconsin and Michigan.

PubMed

Yang, Haile; Chen, Jiakuan

2018-01-01

The successful integration of ecosystem ecology with landscape ecology would be conducive to understanding how landscapes function. There have been several attempts at this, with two main approaches: (1) an ecosystem-based approach, such as the meta-ecosystem framework and (2) a landscape-based approach, such as the landscape system framework. These two frameworks are currently disconnected. To integrate these two frameworks, we introduce a protocol, and then demonstrate application of the protocol using a case study. The protocol includes four steps: 1) delineating landscape systems; 2) classifying landscape systems; 3) adjusting landscape systems to meta-ecosystems and 4) integrating landscape system and meta-ecosystem frameworks through meta-ecosystems. The case study is the analyzing of the carbon fluxes in the Northern Highlands Lake District (NHLD) of Wisconsin and Michigan using this protocol. The application of this protocol revealed that one could follow this protocol to construct a meta-ecosystem and analyze it using the integrative framework of landscape system and meta-ecosystem frameworks. That is, one could (1) appropriately describe and analyze the spatial heterogeneity of the meta-ecosystem; (2) understand the emergent properties arising from spatial coupling of local ecosystems in the meta-ecosystem. In conclusion, this protocol is a useful approach for integrating the meta-ecosystem framework and the landscape system framework, which advances the describing and analyzing of the spatial heterogeneity and ecosystem function of interconnected ecosystems.

Integrating landscape system and meta-ecosystem frameworks to advance the understanding of ecosystem function in heterogeneous landscapes: An analysis on the carbon fluxes in the Northern Highlands Lake District (NHLD) of Wisconsin and Michigan

PubMed Central

Chen, Jiakuan

2018-01-01

The successful integration of ecosystem ecology with landscape ecology would be conducive to understanding how landscapes function. There have been several attempts at this, with two main approaches: (1) an ecosystem-based approach, such as the meta-ecosystem framework and (2) a landscape-based approach, such as the landscape system framework. These two frameworks are currently disconnected. To integrate these two frameworks, we introduce a protocol, and then demonstrate application of the protocol using a case study. The protocol includes four steps: 1) delineating landscape systems; 2) classifying landscape systems; 3) adjusting landscape systems to meta-ecosystems and 4) integrating landscape system and meta-ecosystem frameworks through meta-ecosystems. The case study is the analyzing of the carbon fluxes in the Northern Highlands Lake District (NHLD) of Wisconsin and Michigan using this protocol. The application of this protocol revealed that one could follow this protocol to construct a meta-ecosystem and analyze it using the integrative framework of landscape system and meta-ecosystem frameworks. That is, one could (1) appropriately describe and analyze the spatial heterogeneity of the meta-ecosystem; (2) understand the emergent properties arising from spatial coupling of local ecosystems in the meta-ecosystem. In conclusion, this protocol is a useful approach for integrating the meta-ecosystem framework and the landscape system framework, which advances the describing and analyzing of the spatial heterogeneity and ecosystem function of interconnected ecosystems. PMID:29415066

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

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--STANDARD OPERATING PROCEDURE FOR LABORATORY ANALYSIS OF HAIR SAMPLES FOR MERCURY (RTI-L-1.0)

EPA Science Inventory

The purpose of this protocol is to provide guidelines for the analysis of hair samples for total mercury by cold vapor atomic fluorescence (CVAFS) spectrometry. This protocol describes the methodology and all other analytical aspects involved in the analysis. Keywords: hair; s...

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

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…

Instruments for Assessment of Instructional Practices in Standards-Based Teaching

NASA Astrophysics Data System (ADS)

Wainwright, Camille L.

2006-12-01

This paper describes the development of two forms of an instrument used as a classroom observation protocol, designed to document the impact of reform-based professional development with undergraduate mathematics and science faculty and its impact on the resultant preparation of teachers (PreK 12). A rationale for the development and utilization of this instrument (known as the OTOP, or the Oregon Teacher Observation Protocol) is provided. Constructed upon review of the research on teaching and standards documents in mathematics and science, the protocol formed the basis for data collection in a three-year longitudinal study of teaching practice among early career teachers as well as undergraduate college faculty. In addition, this paper suggests further applications of the observation protocol beyond the original research study purpose. One prominent use for the protocol is in supervisor observations of mathematics and science student teachers.

[Protocol of the animal assisted activity program at a university hospital].

PubMed

Silveira, Isa Rodrigues; Santos, Nanci Cristiano; Linhares, Daniela Ribeiro

2011-03-01

Animal-Assisted Activity (AAA) consists in visitation and recreation through contact with animals, aiming at entertainment and improving the interpersonal relationship between patients and staff. Permission for the animals to visit an Institution requires a protocol with rules and safety routines to avoid accidents and zoonoses. The objective of this study is to describe the important points of the protocol to implement the AAA program. The protocol includes: introduction, objectives, inclusion and exclusion criteria for animals, drivers and patients; recommendations to the handlers and the health team, responsibilities of the Nosocomial Infection Control Committee, zoonoses posters, vaccination schedule for dogs and cats, free-informed consent to take part in the program and records with behavioral analysis of the animals. We believe that disclosing the protocol, based on scientific studies, favors the implementation of new programs in institutions considering the lack of national publications.

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.

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...

Bioindicators in the MIDUS National Study: Protocol, Measures, Sample, and Comparative Context

PubMed Central

Love, Gayle Dienberg; Seeman, Teresa E.; Weinstein, Maxine; Ryff, Carol D.

2010-01-01

Objectives MIDUS is a national study of health and aging among individuals aged 25 to 74 at baseline(1995/96). Longitudinal survey assessments (2004/05), were followed by biological assessments on a subsample aged 35–85. To facilitate public use, we describe the protocol, measures, and sample. Methods Respondents traveled to clinics for a two-day data collection protocol that included fasting blood specimens, 12-hour urine specimen, medical history, physical exam, bone densitometry, a laboratory challenge (heart rate variability, blood pressure, respiration, salivary cortisol). Results Response rates for the biological protocol (N = 1,255) were 39.3%, or 43.1% (adjusting for those who could not be located or contacted). Reasons for non-participation were travel, family obligations, and being too busy. Respondents were comparable to the recruitment pool on most demographic characteristics and health assessments. Discussion Strengths of the protocol vis-à-vis other similar studies include opportunities to link biological factors with diverse content from other MIDUS projects. PMID:20876364

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

Using Zebrafish Models of Human Influenza A Virus Infections to Screen Antiviral Drugs and Characterize Host Immune Cell Responses.

PubMed

Sullivan, Con; Jurcyzszak, Denise; Goody, Michelle F; Gabor, Kristin A; Longfellow, Jacob R; Millard, Paul J; Kim, Carol H

2017-01-20

Each year, seasonal influenza outbreaks profoundly affect societies worldwide. In spite of global efforts, influenza remains an intractable healthcare burden. The principle strategy to curtail infections is yearly vaccination. In individuals who have contracted influenza, antiviral drugs can mitigate symptoms. There is a clear and unmet need to develop alternative strategies to combat influenza. Several animal models have been created to model host-influenza interactions. Here, protocols for generating zebrafish models for systemic and localized human influenza A virus (IAV) infection are described. Using a systemic IAV infection model, small molecules with potential antiviral activity can be screened. As a proof-of-principle, a protocol that demonstrates the efficacy of the antiviral drug Zanamivir in IAV-infected zebrafish is described. It shows how disease phenotypes can be quantified to score the relative efficacy of potential antivirals in IAV-infected zebrafish. In recent years, there has been increased appreciation for the critical role neutrophils play in the human host response to influenza infection. The zebrafish has proven to be an indispensable model for the study of neutrophil biology, with direct impacts on human medicine. A protocol to generate a localized IAV infection in the Tg(mpx:mCherry) zebrafish line to study neutrophil biology in the context of a localized viral infection is described. Neutrophil recruitment to localized infection sites provides an additional quantifiable phenotype for assessing experimental manipulations that may have therapeutic applications. Both zebrafish protocols described faithfully recapitulate aspects of human IAV infection. The zebrafish model possesses numerous inherent advantages, including high fecundity, optical clarity, amenability to drug screening, and availability of transgenic lines, including those in which immune cells such as neutrophils are labeled with fluorescent proteins. The protocols detailed here exploit these advantages and have the potential to reveal critical insights into host-IAV interactions that may ultimately translate into the clinic.

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

Mandible condylar hyperplasia: a review of diagnosis and treatment protocol

PubMed Central

Olate, Sergio; Netto, Henrique Duque; Rodriguez-Chessa, Jaime; Alister, Juan Pablo; de Albergaria-Barbosa, Jose; de Moraes, Márcio

2013-01-01

Condylar hyperplasia (CH) is a bone disease characterized by the increased development of one mandibular condyle. It regularly presents as an active growth with facial asymmetry generally without pain. Statistically it affects more women in adolescence, although it does not discriminate by age or gender. Its best-known consequence is asymmetric facial deformity (AFD), which combined with alteration of the dental occlusion with unilateral crossbite or open bite. It is not known when CH begins and how long it lasts; diagnostic examinations are described and are efficient in some research about diagnosis. Protocol treatment is not well studie and depends on the criteria described in this paper. The aim of this research is to provide up-to-date information about the diagnosis of this disease and to analyze the treatment protocol, visualizing the CH and AFD presented. PMID:24179565

Solid-State NMR Studies of Amyloid Materials: A Protocol to Define an Atomic Model of Aβ(1-42) in Amyloid Fibrils.

PubMed

Xiao, Yiling; McElheny, Dan; Hoshi, Minako; Ishii, Yoshitaka

2018-01-01

Intense efforts have been made to understand the molecular structures of misfolded amyloid β (Aβ) in order to gain insight into the pathological mechanism of Alzheimer's disease. Solid-state NMR spectroscopy (SSNMR) is considered a primary tool for elucidating the structures of insoluble and noncrystalline amyloid fibrils and other amyloid assemblies. In this chapter, we describe a detailed protocol to obtain the first atomic model of the 42-residue human Aβ peptide Aβ(1-42) in structurally homogeneous amyloid fibrils from our recent SSNMR study (Nat Struct Mol Biol 22:499-505, 2015). Despite great biological and clinical interest in Aβ(1-42) fibrils, their structural details have been long-elusive until this study. The protocol is divided into four sections. First, the solid-phase peptide synthesis (SPPS) and purification of monomeric Aβ(1-42) is described. We illustrate a controlled incubation method to prompt misfolding of Aβ(1-42) into homogeneous amyloid fibrils in an aqueous solution with fragmented Aβ(1-42) fibrils as seeds. Next, we detail analysis of Aβ(1-42) fibrils by SSNMR to obtain structural restraints. Finally, we describe methods to construct atomic models of Aβ(1-42) fibrils based on SSNMR results through two-stage molecular dynamics calculations.

Revised Methods for Characterizing Stream Habitat in the National Water-Quality Assessment Program

USGS Publications Warehouse

Fitzpatrick, Faith A.; Waite, Ian R.; D'Arconte, Patricia J.; Meador, Michael R.; Maupin, Molly A.; Gurtz, Martin E.

1998-01-01

Stream habitat is characterized in the U.S. Geological Survey's National Water-Quality Assessment (NAWQA) Program as part of an integrated physical, chemical, and biological assessment of the Nation's water quality. The goal of stream habitat characterization is to relate habitat to other physical, chemical, and biological factors that describe water-quality conditions. To accomplish this goal, environmental settings are described at sites selected for water-quality assessment. In addition, spatial and temporal patterns in habitat are examined at local, regional, and national scales. This habitat protocol contains updated methods for evaluating habitat in NAWQA Study Units. Revisions are based on lessons learned after 6 years of applying the original NAWQA habitat protocol to NAWQA Study Unit ecological surveys. Similar to the original protocol, these revised methods for evaluating stream habitat are based on a spatially hierarchical framework that incorporates habitat data at basin, segment, reach, and microhabitat scales. This framework provides a basis for national consistency in collection techniques while allowing flexibility in habitat assessment within individual Study Units. Procedures are described for collecting habitat data at basin and segment scales; these procedures include use of geographic information system data bases, topographic maps, and aerial photographs. Data collected at the reach scale include channel, bank, and riparian characteristics.

Quality assurance of data collection in the multi-site community randomized trial and prevalence survey of the children's healthy living program.

PubMed

Yamanaka, Ashley; Fialkowski, Marie Kainoa; Wilkens, Lynne; Li, Fenfang; Ettienne, Reynolette; Fleming, Travis; Power, Julianne; Deenik, Jonathan; Coleman, Patricia; Leon Guerrero, Rachael; Novotny, Rachel

2016-09-02

Quality assurance plays an important role in research by assuring data integrity, and thus, valid study results. We aim to describe and share the results of the quality assurance process used to guide the data collection process in a multi-site childhood obesity prevalence study and intervention trial across the US Affiliated Pacific Region. Quality assurance assessments following a standardized protocol were conducted by one assessor in every participating site. Results were summarized to examine and align the implementation of protocol procedures across diverse settings. Data collection protocols focused on food and physical activity were adhered to closely; however, protocols for handling completed forms and ensuring data security showed more variability. Quality assurance protocols are common in the clinical literature but are limited in multi-site community-based studies, especially in underserved populations. The reduction in the number of QA problems found in the second as compared to the first data collection periods for the intervention study attest to the value of this assessment. This paper can serve as a reference for similar studies wishing to implement quality assurance protocols of the data collection process to preserve data integrity and enhance the validity of study findings. NIH clinical trial #NCT01881373.

Systematic Review Protocol to Assess the Effectiveness of Usability Questionnaires in mHealth App Studies.

PubMed

Zhou, Leming; Bao, Jie; Parmanto, Bambang

2017-08-01

Usability questionnaires have a wide use in mobile health (mHealth) app usability studies. However, no systematic review has been conducted for assessing the effectiveness of these questionnaires. This paper describes a protocol for conducting a systematic review of published questionnaire-based mHealth app usability studies. In this systematic review, we will select recently published (2008-2017) articles from peer-reviewed journals and conferences that describe mHealth app usability studies and implement at least one usability questionnaire. The search strategy will include terms such as "mobile app" and "usability." Multiple databases such as PubMed, CINAHL, IEEE Xplore, ACM Digital Library, and INSPEC will be searched. There will be 2 independent reviewers in charge of screening titles and abstracts as well as determining those articles that should be included for a full-text review. The third reviewer will act as a mediator between the other 2 reviewers. Moreover, a data extraction form will be created and used during the full article data analysis. Notably, the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P) guidelines will be followed in reporting this protocol. A preliminary search produced 1271 articles, 40 of which are duplicate records. The inclusion-exclusion criteria are being strictly followed in performing the ongoing study selection. Usability questionnaires are an important tool in mHealth app usability studies. This review will summarize the usability questionnaires used in published research articles while assessing the efficacy of these questionnaires in determining the usability of mHealth apps. ©Leming Zhou, Jie Bao, Bambang Parmanto. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 01.08.2017.

Development of a manualized protocol of massage therapy for clinical trials in osteoarthritis.

PubMed

Ali, Ather; Kahn, Janet; Rosenberger, Lisa; Perlman, Adam I

2012-10-04

Clinical trial design of manual therapies may be especially challenging as techniques are often individualized and practitioner-dependent. This paper describes our methods in creating a standardized Swedish massage protocol tailored to subjects with osteoarthritis of the knee while respectful of the individualized nature of massage therapy, as well as implementation of this protocol in two randomized clinical trials. The manualization process involved a collaborative process between methodologic and clinical experts, with the explicit goals of creating a reproducible semi-structured protocol for massage therapy, while allowing some latitude for therapists' clinical judgment and maintaining consistency with a prior pilot study. The manualized protocol addressed identical specified body regions with distinct 30- and 60-min protocols, using standard Swedish strokes. Each protocol specifies the time allocated to each body region. The manualized 30- and 60-min protocols were implemented in a dual-site 24-week randomized dose-finding trial in patients with osteoarthritis of the knee, and is currently being implemented in a three-site 52-week efficacy trial of manualized Swedish massage therapy. In the dose-finding study, therapists adhered to the protocols and significant treatment effects were demonstrated. The massage protocol was manualized, using standard techniques, and made flexible for individual practitioner and subject needs. The protocol has been applied in two randomized clinical trials. This manualized Swedish massage protocol has real-world utility and can be readily utilized both in the research and clinical settings. Clinicaltrials.gov NCT00970008 (18 August 2009).

Regional gastrointestinal transit and pH studied in 215 healthy volunteers using the wireless motility capsule: influence of age, gender, study country and testing protocol.

PubMed

Wang, Y T; Mohammed, S D; Farmer, A D; Wang, D; Zarate, N; Hobson, A R; Hellström, P M; Semler, J R; Kuo, B; Rao, S S; Hasler, W L; Camilleri, M; Scott, S M

2015-09-01

The wireless motility capsule (WMC) offers the ability to investigate luminal gastrointestinal (GI) physiology in a minimally invasive manner. To investigate the effect of testing protocol, gender, age and study country on regional GI transit times and associated pH values using the WMC. Regional GI transit times and pH values were determined in 215 healthy volunteers from USA and Sweden studied using the WMC over a 6.5-year period. The effects of test protocol, gender, age and study country were examined. For GI transit times, testing protocol was associated with differences in gastric emptying time (GET; shorter with protocol 2 (motility capsule ingested immediately after meal) vs. protocol 1 (motility capsule immediately before): median difference: 52 min, P = 0.0063) and colonic transit time (CTT; longer with protocol 2: median 140 min, P = 0.0189), but had no overall effect on whole gut transit time. Females had longer GET (by median 17 min, P = 0.0307), and also longer CTT by (104 min, P = 0.0285) and whole gut transit time by (263 min, P = 0.0077). Increasing age was associated with shorter small bowel transit time (P = 0.002), and study country also influenced small bowel and CTTs. Whole gut and CTTs showed clustering of data at values separated by 24 h, suggesting that describing these measures as continuous variables is invalid. Testing protocol, gender and study country also significantly influenced pH values. Regional GI transit times and pH values, delineated using the wireless motility capsule (WMC), vary based on testing protocol, gender, age and country. Standardisation of testing is crucial for cross-referencing in clinical practice and future research. © 2015 John Wiley & Sons Ltd.

Empirical Examinations of Modifications and Adaptations to Evidence-Based Psychotherapies: Methodologies, Impact, and Future Directions.

PubMed

Stirman, Shannon Wiltsey; Gamarra, Jennifer; Bartlett, Brooke; Calloway, Amber; Gutner, Cassidy

2017-12-01

This review describes methods used to examine the modifications and adaptations to evidence-based psychological treatments (EBPTs), assesses what is known about the impact of modifications and adaptations to EBPTs, and makes recommendations for future research and clinical care. One hundred eight primary studies and three meta-analyses were identified. All studies examined planned adaptations, and many simultaneously investigated multiple types of adaptations. With the exception of studies on adding or removing specific EBPT elements, few studies compared adapted EBPTs to the original protocols. There was little evidence that adaptations in the studies were detrimental, but there was also limited consistent evidence that adapted protocols outperformed the original protocols, with the exception of adding components to EBPTs. Implications for EBPT delivery and future research are discussed.

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.

Government Open Systems Interconnection Profile (GOSIP) Transition Strategy

DTIC Science & Technology

1993-09-01

it explores some of the GOSIP protocol details and discusses the process by which standards organizations have developed their...version 1 and 2. Additionally, it explores some of the GOSIP protocol details and discusses the process by which standards organizations have developed ...ORGANIZATION OF STUDY 1. The Standards Process Chapter II describes the process whereby standards are developed and adopted by the ISO and how the

A Think-Aloud Protocols Investigation of Dictionary Processing Strategies among Saudi EFL Students

ERIC Educational Resources Information Center

Alhaysony, Maha

2012-01-01

This paper aims to examine qualitatively how Saudi EFL female students look-up word meanings in their dictionaries while reading. We aimed to identify and describe the look-up strategies used by these students. The subjects of the study were ten third-year English major students. A think-aloud protocol was used in order to gain insights into the…

Effectiveness of muscle strengthening and description of protocols for preventing falls in the elderly: a systematic review

PubMed Central

Ishigaki, Erika Y.; Ramos, Lidiane G.; Carvalho, Elisa S.; Lunardi, Adriana C.

2014-01-01

Background Falls are a geriatric syndrome that is considered a significant public health problem in terms of morbidity and mortality because they lead to a decline in functional capacity and an impaired quality of life in the elderly. Lower limb muscle strengthening seems to be an effective intervention for preventing falls; however, there is no consensus regarding the best method for increasing lower limb muscle strength. Objectives To analyze the effectiveness of lower limb muscle strengthening and to investigate and describe the protocols used for preventing falls in elderly subjects. Method We performed a systematic review of randomized and controlled clinical trials published between 2002 and 2012 in the databases PubMed, EMBASE, Scopus, Web of Science, and PEDro that cited some type of lower limb muscle strengthening protocol and that evaluated the incidence of falls as the primary outcome exclusively in elderly subjects. Twelve studies met the inclusion criteria. Qualitative analysis was performed by independent reviewers applying the PEDro scale. Results The data obtained from the selected studies showed lower fall rates in the intervention groups compared to controls. Six studies described the lower limb muscle strengthening protocol in detail. High methodological quality was found in 6 studies (PEDro score ≥7/10 points). Conclusions The methodological quality of the studies in this area appears to leave little doubt regarding the effectiveness of lower limb strengthening exercises for preventing falls in elderly subjects, however the interventions in these studies were poorly reported. PMID:24760166

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

Place and Response Learning in the Open-field Tower Maze.

PubMed

Lipatova, Olga; Campolattaro, Matthew M; Toufexis, Donna J; Mabry, Erin A

2015-10-28

This protocol describes how the Open-field Tower Maze (OFTM) paradigm is used to study spatial learning in rodents. This maze is especially useful for examining how rats learn to use a place- or response-learning to successfully navigate in an open-field arena. Additionally, this protocol describes how the OFTM differs from other behavioral maze paradigms that are commonly used to study spatial learning in rodents. The OFTM described in this article was adapted from the one previously described by Cole, Clipperton, and Walt (2007). Specifically, the OFTM was created to test spatial learning in rodents without the experimenter having to consider how "stress" might play a role as a confounding variable. Experiments have shown that stress-alone can significantly affect cognitive function(1). The representative results section contains data from an experiment that used the OFTM to examine the effects of estradiol treatment on place- and response-learning in adult female Sprague Dawley rats(2). Future studies will be designed to examine the role of the hippocampus and striatum in place- and response-learning in the OFTM.

Level of adherence to an extravasation protocol over 10 years in a tertiary care hospital.

PubMed

Molas-Ferrer, Gloria; Farré-Ayuso, Elisabet; doPazo-Oubiña, Fernando; deAndrés-Lázaro, Ana; Guell-Picazo, Jaume; Borrás-Maixenchs, Núria; Corominas-Bosch, Lourdes; Valverde-Bosch, Montserrat; Creus-Baró, Natalia

2015-04-01

Extravasation of chemotherapy is an undesirable complication related to the administration of antineoplastic therapy. Establishing the real incidence is difficult. Because of the importance of a quick intervention after an extravasation, every hospital should have an extravasation protocol. The purpose of this study was to determine the degree of observance of an extravasation protocol by nursing staff and to determine extravasation incidence. This descriptive, longitudinal, retrospective study was set in a tertiary-level hospital. The researchers reviewed 117 extravasation notification forms received by the pharmacy department during a 10-year period. Nursing actuation, particularly observance of the extravasation protocol, was analyzed. Protocol adherence was 89%. Twelve deviations from the protocol in the application of recommended measures were detected. An antidote was used in 41 patients, and temperature measures were applied in 14 cases. Ninety-nine patients had at least one episode of reported follow-up. No cases of necrosis or skin ulcers were described, except by one patient, who developed a delayed skin ulcer to vinorelbine. Drugs most frequently reported were etoposide, carboplatin, and paclitaxel. Nursing staff should be continuously trained in extravasation protocol because a rapid actuation can prevent skin lesions.

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.

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.

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.

Atlas-based analysis of cardiac shape and function: correction of regional shape bias due to imaging protocol for population studies.

PubMed

Medrano-Gracia, Pau; Cowan, Brett R; Bluemke, David A; Finn, J Paul; Kadish, Alan H; Lee, Daniel C; Lima, Joao A C; Suinesiaputra, Avan; Young, Alistair A

2013-09-13

Cardiovascular imaging studies generate a wealth of data which is typically used only for individual study endpoints. By pooling data from multiple sources, quantitative comparisons can be made of regional wall motion abnormalities between different cohorts, enabling reuse of valuable data. Atlas-based analysis provides precise quantification of shape and motion differences between disease groups and normal subjects. However, subtle shape differences may arise due to differences in imaging protocol between studies. A mathematical model describing regional wall motion and shape was used to establish a coordinate system registered to the cardiac anatomy. The atlas was applied to data contributed to the Cardiac Atlas Project from two independent studies which used different imaging protocols: steady state free precession (SSFP) and gradient recalled echo (GRE) cardiovascular magnetic resonance (CMR). Shape bias due to imaging protocol was corrected using an atlas-based transformation which was generated from a set of 46 volunteers who were imaged with both protocols. Shape bias between GRE and SSFP was regionally variable, and was effectively removed using the atlas-based transformation. Global mass and volume bias was also corrected by this method. Regional shape differences between cohorts were more statistically significant after removing regional artifacts due to imaging protocol bias. Bias arising from imaging protocol can be both global and regional in nature, and is effectively corrected using an atlas-based transformation, enabling direct comparison of regional wall motion abnormalities between cohorts acquired in separate studies.

Proteomic Analysis of Cytoskeleton Proteins in Fish.

PubMed

Gotesman, Michael; Menanteau-Ledouble, Simon; El-Matbouli, Mansour

2016-01-01

In this chapter, we describe laboratory protocols for rearing fish and a simple and efficient method of extracting and identifying pathogen and host proteins that may be involved in entry and replication of commercially important fish viruses. We have used the common carp (Cyprinus carpio L.) and goldfish (Cyprinus auratus) as a model system for studies of proteins involved in viral entry and replication. The chapter describes detailed protocols for maintenance of carp, cell culture, antibody purification of proteins, and use of electrospray-ionization mass spectrometry analysis to screen and identify cytoskeleton and other proteins that may be involved in viral infection and propagation in fish.

Current fluctuations in periodically driven systems

NASA Astrophysics Data System (ADS)

Barato, Andre C.; Chetrite, Raphael

2018-05-01

Small nonequelibrium systems driven by an external periodic protocol can be described by Markov processes with time-periodic transition rates. In general, current fluctuations in such small systems are large and may play a crucial role. We develop a theoretical formalism to evaluate the rate of such large deviations in periodically driven systems. We show that the scaled cumulant generating function that characterizes current fluctuations is given by a maximal Floquet exponent. Comparing deterministic protocols with stochastic protocols, we show that, with respect to large deviations, systems driven by a stochastic protocol with an infinitely large number of jumps are equivalent to systems driven by deterministic protocols. Our results are illustrated with three case studies: a two-state model for a heat engine, a three-state model for a molecular pump, and a biased random walk with a time-periodic affinity.

An Efficient and Reproducible Protocol for Distraction Osteogenesis in a Rat Model Leading to a Functional Regenerated Femur.

PubMed

Pithioux, Martine; Roseren, Flavy; Jalain, Christian; Launay, Franck; Charpiot, Philippe; Chabrand, Patrick; Roffino, Sandrine; Lamy, Edouard

2017-10-23

This protocol describes the use of a newly developed external fixator for distraction osteogenesis in a rat femoral model. Distraction osteogenesis (DO) is a surgical technique leading to bone regeneration after an osteotomy. The osteotomized extremities are moved away from each other by gradual distraction to reach the desired elongation. This procedure is widely used in humans for lower and upper limb lengthening, treatment after a bone nonunion, or the regeneration of a bone defect following surgery for bone tumor excision, as well as in maxillofacial reconstruction. Only a few studies clearly demonstrate the efficiency of their protocol in obtaining a functional regenerated bone, i.e., bone that will support physiological weight-bearing without fracture after removal of the external fixator. Moreover, protocols for DO vary and reproducibility is limited by lack of information, making comparison between studies difficult. The aim of this study was to develop a reproducible protocol comprising an appropriate external fixator design for rat limb lengthening, with a detailed surgical technique that permits physiological weight-bearing by the animal after removal of the external fixator.

Aspirin Allergy Desensitization in Cerebrovascular Disease

PubMed Central

Zuckerman, Scott L; Seder, David B; Tsujiura, Crystiana; Cushing, Deborah; Gallup, Holly; Mocco, J; Hanel, Richard A; Ecker, Robert D

2014-01-01

Summary Aspirin (ASA) is the mainstay of treatment in cerebrovascular and systemic vascular disease. ASA hypersensitivity can pose a challenge to achieving optimum medical management prior to and after neurointerventional treatment. Desensitization to ASA is well described in the allergy and cardiovascular literature, but there are no similar discussions specific to neurointervention. The purpose of our study was to describe our experience with ASA hypersensitivity management and review the relevant literature. Two cases of patients with symptomatic cerebrovascular disease requiring neurointervention who were successfully desensitized to their ASA hypersensitivity prior to treatment are described. The subsequent literature is reviewed. Several ASA desensitization protocols exist and have been proven to successfully treat ASA hypersensitivity and allow for ASA therapy to be safely initiated. We describe several previously published protocols. ASA desensitization is a safe and simple way to manage ASA hypersensitivity. We provide comprehensive management guidelines for the neurointerventionalist engaging in ASA desensitization. PMID:24556294

21 CFR 50.3 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-04-01

... section 515. (19) A product development protocol for a medical device, described in section 515. (20) Data...) Data and information about a clinical study of an infant formula when submitted as part of an infant... investigations involving children submitted in a new dietary ingredient notification, described in § 190.6 of...

21 CFR 50.3 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-04-01

... section 515. (19) A product development protocol for a medical device, described in section 515. (20) Data...) Data and information about a clinical study of an infant formula when submitted as part of an infant... investigations involving children submitted in a new dietary ingredient notification, described in § 190.6 of...

21 CFR 50.3 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-04-01

... section 515. (19) A product development protocol for a medical device, described in section 515. (20) Data...) Data and information about a clinical study of an infant formula when submitted as part of an infant... investigations involving children submitted in a new dietary ingredient notification, described in § 190.6 of...

21 CFR 50.3 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... section 515. (19) A product development protocol for a medical device, described in section 515. (20) Data...) Data and information about a clinical study of an infant formula when submitted as part of an infant... investigations involving children submitted in a new dietary ingredient notification, described in § 190.6 of...

21 CFR 50.3 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-04-01

... section 515. (19) A product development protocol for a medical device, described in section 515. (20) Data...) Data and information about a clinical study of an infant formula when submitted as part of an infant... investigations involving children submitted in a new dietary ingredient notification, described in § 190.6 of...

Quarantine and protocol

NASA Technical Reports Server (NTRS)

1981-01-01

The purpose of the Orbiting Quarantine Facility is to provide maximum protection of the terrestrial biosphere by ensuring that the returned Martian samples are safe to bring to Earth. The protocol designed to detect the presence of biologically active agents in the Martian soil is described. The protocol determines one of two things about the sample: (1) that it is free from nonterrestrial life forms and can be sent to a terrestrial containment facility where extensive chemical, biochemical, geological, and physical investigations can be conducted; or (2) that it exhibits "biological effects" of the type that dictate second order testing. The quarantine protocol is designed to be conducted on a small portion of the returned sample, leaving the bulk of the sample undisturbed for study on Earth.

Systematic Evaluation of the Patient-Reported Outcome (PRO) Content of Clinical Trial Protocols

PubMed Central

Kyte, Derek; Duffy, Helen; Fletcher, Benjamin; Gheorghe, Adrian; Mercieca-Bebber, Rebecca; King, Madeleine; Draper, Heather; Ives, Jonathan; Brundage, Michael; Blazeby, Jane; Calvert, Melanie

2014-01-01

Background Qualitative evidence suggests patient-reported outcome (PRO) information is frequently absent from clinical trial protocols, potentially leading to inconsistent PRO data collection and risking bias. Direct evidence regarding PRO trial protocol content is lacking. The aim of this study was to systematically evaluate the PRO-specific content of UK National Institute for Health Research (NIHR) Health Technology Assessment (HTA) programme trial protocols. Methods and Findings We conducted an electronic search of the NIHR HTA programme database (inception to August 2013) for protocols describing a randomised controlled trial including a primary/secondary PRO. Two investigators independently reviewed the content of each protocol, using a specially constructed PRO-specific protocol checklist, alongside the ‘Standard Protocol Items: Recommendations for Interventional Trials’ (SPIRIT) checklist. Disagreements were resolved through discussion with a third investigator. 75 trial protocols were included in the analysis. Protocols included a mean of 32/51 (63%) SPIRIT recommendations (range 16–41, SD 5.62) and 11/33 (33%) PRO-specific items (range 4–18, SD 3.56). Over half (61%) of the PRO items were incomplete. Protocols containing a primary PRO included slightly more PRO checklist items (mean 14/33 (43%)). PRO protocol content was not associated with general protocol completeness; thus, protocols judged as relatively ‘complete’ using SPIRIT were still likely to have omitted a large proportion of PRO checklist items. Conclusions The PRO components of HTA clinical trial protocols require improvement. Information on the PRO rationale/hypothesis, data collection methods, training and management was often absent. This low compliance is unsurprising; evidence shows existing PRO guidance for protocol developers remains difficult to access and lacks consistency. Study findings suggest there are a number of PRO protocol checklist items that are not fully addressed by the current SPIRIT statement. We therefore advocate the development of consensus-based supplementary guidelines, aimed at improving the completeness and quality of PRO content in clinical trial protocols. PMID:25333349

Factors affecting adoption, implementation fidelity, and sustainability of the Redesigned Community Health Fund in Tanzania: a mixed methods protocol for process evaluation in the Dodoma region

PubMed Central

Kalolo, Albino; Radermacher, Ralf; Stoermer, Manfred; Meshack, Menoris; De Allegri, Manuela

2015-01-01

Background Despite the implementation of various initiatives to address low enrollment in voluntary micro health insurance (MHI) schemes in sub-Saharan Africa, the problem of low enrollment remains unresolved. The lack of process evaluations of such interventions makes it difficult to ascertain whether their poor results are because of design failures or implementation weaknesses. Objective In this paper, we describe a process evaluation protocol aimed at opening the ‘black box’ to evaluate the implementation processes of the Redesigned Community Health Fund (CHF) program in the Dodoma region of Tanzania. Design The study employs a cross-sectional mixed methods design and is being carried out 3 years after the launch of the Redesigned CHF program. The study is grounded in a conceptual framework which rests on the Diffusion of Innovation Theory and the Implementation Fidelity Framework. The study utilizes a mixture of quantitative and qualitative data collection tools (questionnaires, focus group discussions, in-depth interviews, and document review), and aligns the evaluation to the Theory of Intervention developed by our team. Quantitative data will be used to measure program adoption, implementation fidelity, and their moderating factors. Qualitative data will be used to explore the responses of stakeholders to the intervention, contextual factors, and moderators of adoption, implementation fidelity, and sustainability. Discussion This protocol describes a systematic process evaluation in relation to the implementation of a reformed MHI. We trust that the theoretical approaches and methodologies described in our protocol may be useful to inform the design of future process evaluations focused on the assessment of complex interventions, such as MHI schemes. PMID:26679408

Automated monitoring of medical protocols: a secure and distributed architecture.

PubMed

Alsinet, T; Ansótegui, C; Béjar, R; Fernández, C; Manyà, F

2003-03-01

The control of the right application of medical protocols is a key issue in hospital environments. For the automated monitoring of medical protocols, we need a domain-independent language for their representation and a fully, or semi, autonomous system that understands the protocols and supervises their application. In this paper we describe a specification language and a multi-agent system architecture for monitoring medical protocols. We model medical services in hospital environments as specialized domain agents and interpret a medical protocol as a negotiation process between agents. A medical service can be involved in multiple medical protocols, and so specialized domain agents are independent of negotiation processes and autonomous system agents perform monitoring tasks. We present the detailed architecture of the system agents and of an important domain agent, the database broker agent, that is responsible of obtaining relevant information about the clinical history of patients. We also describe how we tackle the problems of privacy, integrity and authentication during the process of exchanging information between agents.

Reporting on blinding in trial protocols and corresponding publications was often inadequate but rarely contradictory.

PubMed

Hróbjartsson, Asbjørn; Pildal, Julie; Chan, An-Wen; Haahr, Mette T; Altman, Douglas G; Gøtzsche, Peter C

2009-09-01

To compare the reporting on blinding in protocols and articles describing randomized controlled trials. We studied 73 protocols of trials approved by the scientific/ethical committees for Copenhagen and Frederiksberg, 1994 and 1995, and their corresponding publications. Three out of 73 trials (4%) reported blinding in the protocol that contradicted that in the publication (e.g., "open" vs. "double blind"). The proportion of "double-blind" trials with a clear description of the blinding of participants increased from 11 out of 58 (19%) when based on publications alone to 39 (67%) when adding the information in the protocol. The similar proportions for the blinding of health care providers were 2 (3%) and 22 (38%); and for the blinding of data collectors, they were 8 (14%) and 14 (24%). In 52 of 58 publications (90%), it was unclear whether all patients, health care providers, and data collectors had been blinded. In 4 of the 52 trials (7%), the protocols clarified that all three key trial persons had been blinded. The reporting on blinding in both trial protocols and publications is often inadequate. We suggest developing international guidelines for the reporting of trial protocols and public access to protocols.

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…

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

PubMed

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

2006-08-01

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

A protocol for isolating insect mitochondrial genomes: a case study of NUMT in Melipona flavolineata (Hymenoptera: Apidae).

PubMed

Françoso, Elaine; Gomes, Fernando; Arias, Maria Cristina

2016-07-01

Nuclear mitochondrial DNA insertions (NUMTs) are mitochondrial DNA sequences that have been transferred into the nucleus and are recognized by the presence of indels and stop codons. Although NUMTs have been identified in a diverse range of species, their discovery was frequently accidental. Here, our initial goal was to develop and standardize a simple method for isolating NUMTs from the nuclear genome of a single bee. Subsequently, we tested our new protocol by determining whether the indels and stop codons of the cytochrome c oxidase subunit I (COI) sequence of Melipona flavolineata are of nuclear origin. The new protocol successfully demonstrated the presence of a COI NUMT. In addition to NUMT investigations, the protocol described here will also be very useful for studying mitochondrial mutations related to diseases and for sequencing complete mitochondrial genomes with high read coverage by Next-Generation technology.

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)

Redactions in protocols for drug trials: what industry sponsors concealed.

PubMed

Marquardsen, Mikkel; Ogden, Michelle; Gøtzsche, Peter C

2018-04-01

Objective To describe the redactions in contemporary protocols for industry-sponsored randomised drug trials with patient relevant outcomes and to evaluate whether there was a legitimate rationale for the redactions. Design Cohort study. Under the Freedom of Information Act, we requested access to trial protocols approved by a research ethics committee in Denmark from October 2012 to March 2013. We received 17 consecutive protocols, which had been redacted before we got them, and nine protocols without redactions. In five additional cases, the companies refused to let the committees give us access, and in three other cases, documents were missing. Participants Not applicable. Setting Not applicable. Main outcome measure Amount and nature of redactions in 22 predefined key protocol variables. Results The redactions were most widespread in those sections of the protocol where there is empirical evidence of substantial problems with the trustworthiness of published drug trials: data analysis, handling of missing data, detection and analysis of adverse events, definition of the outcomes, interim analyses and premature termination of the study, sponsor's access to incoming data while the study is running, ownership to the data and investigators' publication rights. The parts of the text that were redacted differed widely, both between companies and within the same company. Conclusions We could not identify any legitimate rationale for the redactions. The current mistrust in industry-sponsored drug trials can only change if the industry offers unconditional access to its trial protocols and other relevant documents and data.

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.

Systematic Review Protocol to Assess the Effectiveness of Usability Questionnaires in mHealth App Studies

PubMed Central

Bao, Jie; Parmanto, Bambang

2017-01-01

Background Usability questionnaires have a wide use in mobile health (mHealth) app usability studies. However, no systematic review has been conducted for assessing the effectiveness of these questionnaires. Objective This paper describes a protocol for conducting a systematic review of published questionnaire-based mHealth app usability studies. Methods In this systematic review, we will select recently published (2008-2017) articles from peer-reviewed journals and conferences that describe mHealth app usability studies and implement at least one usability questionnaire. The search strategy will include terms such as “mobile app” and “usability.” Multiple databases such as PubMed, CINAHL, IEEE Xplore, ACM Digital Library, and INSPEC will be searched. There will be 2 independent reviewers in charge of screening titles and abstracts as well as determining those articles that should be included for a full-text review. The third reviewer will act as a mediator between the other 2 reviewers. Moreover, a data extraction form will be created and used during the full article data analysis. Notably, the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P) guidelines will be followed in reporting this protocol. Results A preliminary search produced 1271 articles, 40 of which are duplicate records. The inclusion-exclusion criteria are being strictly followed in performing the ongoing study selection. Conclusions Usability questionnaires are an important tool in mHealth app usability studies. This review will summarize the usability questionnaires used in published research articles while assessing the efficacy of these questionnaires in determining the usability of mHealth apps. PMID:28765101

A review of protocols for 308 nm excimer laser phototherapy in psoriasis.

PubMed

Mudigonda, Tejaswi; Dabade, Tushar S; Feldman, Steven R

2012-01-01

308 nm excimer laser phototherapy is efficacious in the treatment of localized psoriasis. Different approaches regarding dose fluency, number of treatments, and maintenance have been utilized, and there is yet to be a consensus on standard protocol. To characterize treatment parameters for 308 nm excimer laser phototherapy. We performed a PubMed search for studies describing excimer laser treatment protocol with particular attention to dosage determination, dose adjustment, dose fluency, number of treatments, and maintenance. Seven prospective studies were found describing the excimer efficacy for psoriasis. All studies determined the initial treatment dose using either the minimal erythema dose (MED) or induration. Fluency ranged from 0.5 MED (low) to 16 MED (high); one study demonstrated that medium to high fluencies yielded better improvement in fewer number of treatments. Fluency adjustments during the course of treatment were important to minimize phototherapy-associated side effects. The use of higher fluencies was reported to result in higher occurrences of blistering. One study implemented a maintenance tapering of dose-frequency phase to better manage psoriasis flare-ups. The 308 nm excimer laser is an effective therapy for psoriasis regardless of the method used to determine initial dosage, dose fluency, or number of treatments. As its usage as a targeted monotherapy increases, future trials should consider evaluating and modifying these parameters to determine the most optimal management of localized psoriasis. Based on our reviewed studies, there is no consensus for a single excimer laser therapy protocol and as a result, patient preferences should continue to be an important consideration for phototherapy regimen planning.

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…

Dual sensory loss: development of a dual sensory loss protocol and design of a randomized controlled trial

PubMed Central

2013-01-01

Background Dual sensory loss (DSL) has a negative impact on health and wellbeing and its prevalence is expected to increase due to demographic aging. However, specialized care or rehabilitation programs for DSL are scarce. Until now, low vision rehabilitation does not sufficiently target concurrent impairments in vision and hearing. This study aims to 1) develop a DSL protocol (for occupational therapists working in low vision rehabilitation) which focuses on optimal use of the senses and teaches DSL patients and their communication partners to use effective communication strategies, and 2) describe the multicenter parallel randomized controlled trial (RCT) designed to test the effectiveness and cost-effectiveness of the DSL protocol. Methods/design To develop a DSL protocol, literature was reviewed and content was discussed with professionals in eye/ear care (interviews/focus groups) and DSL patients (interviews). A pilot study was conducted to test and confirm the DSL protocol. In addition, a two-armed international multi-center RCT will evaluate the effectiveness and cost-effectiveness of the DSL protocol compared to waiting list controls, in 124 patients in low vision rehabilitation centers in the Netherlands and Belgium. Discussion This study provides a treatment protocol for rehabilitation of DSL within low vision rehabilitation, which aims to be a valuable addition to the general low vision rehabilitation care. Trial registration Netherlands Trial Register (NTR) identifier: NTR2843 PMID:23941667

Returning Individual Research Results: Development of a Cancer Genetics Education and Risk Communication Protocol

PubMed Central

Roberts, J. Scott; Shalowitz, David I.; Christensen, Kurt D.; Everett, Jessica N.; Kim, Scott Y. H.; Raskin, Leon; Gruber, Stephen B.

2011-01-01

The obligations of researchers to disclose clinically and/or personally significant individual research results are highly debated, but few empirical studies have addressed this topic. We describe the development of a protocol for returning research results to participants at one site of a multicenter study of the genetic epidemiology of melanoma. Protocol development involved numerous challenges: (1) deciding whether genotype results merited disclosure; (2) achieving an appropriate format for communicating results; (3) developing education materials; (4) deciding whether to retest samples for additional laboratory validation; (5) identifying and notifying selected participants; and (6) assessing the impact of disclosure. Our experience suggests potential obstacles depending on researcher resources and the design of the parent study, but offers a process by which researchers can responsibly return individual study results and evaluate the impact of disclosure. PMID:20831418

Validation of a new radiographic protocol for Asian elephant feet and description of their radiographic anatomy.

PubMed

Mumby, C; Bouts, T; Sambrook, L; Danika, S; Rees, E; Parry, A; Rendle, M; Masters, N; Weller, R

2013-10-05

Foot problems are extremely common in elephants and radiography is the only imaging method available but the radiographic anatomy has not been described in detail. The aims of this study were to develop a radiographic protocol for elephant feet using digital radiography, and to describe the normal radiographic anatomy of the Asian elephant front and hind foot. A total of fifteen cadaver foot specimens from captive Asian elephants were radiographed using a range of projections and exposures to determine the best radiographic technique. This was subsequently tested in live elephants in a free-contact setting. The normal radiographic anatomy of the Asian elephant front and hind foot was described with the use of three-dimensional models based on CT reconstructions. The projection angles that were found to be most useful were 65-70° for the front limb and 55-60° in the hind limb. The beam was centred 10-15 cm proximal to the cuticle in the front and 10-15 cm dorsal to the plantar edge of the sole in the hind foot depending on the size of the foot. The protocol developed can be used for larger-scale diagnostic investigations of captive elephant foot disorders, while the normal radiographic anatomy described can improve the diagnostic reliability of elephant feet radiography.

High-efficiency transformation by biolistics of soybean, common bean and cotton transgenic plants.

PubMed

Rech, Elibio L; Vianna, Giovanni R; Aragão, Francisco J L

2008-01-01

This protocol describes a method for high-frequency recovery of transgenic soybean, bean and cotton plants, by combining resistance to the herbicide imazapyr as a selectable marker, multiple shoot induction from embryonic axes of mature seeds and biolistics techniques. This protocol involves the following stages: plasmid design, preparation of soybean, common bean and cotton apical meristems for bombardment, microparticle-coated DNA bombardment of apical meristems and in vitro culture and selection of transgenic plants. The average frequencies (the total number of fertile transgenic plants divided by the total number of bombarded embryonic axes) of producing germline transgenic soybean and bean and cotton plants using this protocol are 9, 2.7 and 0.55%, respectively. This protocol is suitable for studies of gene function as well as the production of transgenic cultivars carrying different traits for breeding programs. This protocol can be completed in 7-10 months.

A New Cellular Architecture for Information Retrieval from Sensor Networks through Embedded Service and Security Protocols

PubMed Central

Shahzad, Aamir; Landry, René; Lee, Malrey; Xiong, Naixue; Lee, Jongho; Lee, Changhoon

2016-01-01

Substantial changes have occurred in the Information Technology (IT) sectors and with these changes, the demand for remote access to field sensor information has increased. This allows visualization, monitoring, and control through various electronic devices, such as laptops, tablets, i-Pads, PCs, and cellular phones. The smart phone is considered as a more reliable, faster and efficient device to access and monitor industrial systems and their corresponding information interfaces anywhere and anytime. This study describes the deployment of a protocol whereby industrial system information can be securely accessed by cellular phones via a Supervisory Control And Data Acquisition (SCADA) server. To achieve the study goals, proprietary protocol interconnectivity with non-proprietary protocols and the usage of interconnectivity services are considered in detail. They support the visualization of the SCADA system information, and the related operations through smart phones. The intelligent sensors are configured and designated to process real information via cellular phones by employing information exchange services between the proprietary protocol and non-proprietary protocols. SCADA cellular access raises the issue of security flaws. For these challenges, a cryptography-based security method is considered and deployed, and it could be considered as a part of a proprietary protocol. Subsequently, transmission flows from the smart phones through a cellular network. PMID:27314351

A New Cellular Architecture for Information Retrieval from Sensor Networks through Embedded Service and Security Protocols.

PubMed

Shahzad, Aamir; Landry, René; Lee, Malrey; Xiong, Naixue; Lee, Jongho; Lee, Changhoon

2016-06-14

Substantial changes have occurred in the Information Technology (IT) sectors and with these changes, the demand for remote access to field sensor information has increased. This allows visualization, monitoring, and control through various electronic devices, such as laptops, tablets, i-Pads, PCs, and cellular phones. The smart phone is considered as a more reliable, faster and efficient device to access and monitor industrial systems and their corresponding information interfaces anywhere and anytime. This study describes the deployment of a protocol whereby industrial system information can be securely accessed by cellular phones via a Supervisory Control And Data Acquisition (SCADA) server. To achieve the study goals, proprietary protocol interconnectivity with non-proprietary protocols and the usage of interconnectivity services are considered in detail. They support the visualization of the SCADA system information, and the related operations through smart phones. The intelligent sensors are configured and designated to process real information via cellular phones by employing information exchange services between the proprietary protocol and non-proprietary protocols. SCADA cellular access raises the issue of security flaws. For these challenges, a cryptography-based security method is considered and deployed, and it could be considered as a part of a proprietary protocol. Subsequently, transmission flows from the smart phones through a cellular network.

Lessons learned on the design and the conduct of Post-Authorization Safety Studies: review of 3 years of PRAC oversight.

PubMed

Engel, Pierre; Almas, Mariana Ferreira; De Bruin, Marieke Louise; Starzyk, Kathryn; Blackburn, Stella; Dreyer, Nancy Ann

2017-04-01

To describe and characterize the first cohort of Post-Authorization Safety Study (PASS) protocols reviewed under the recent European pharmacovigilance legislation. A systematic approach was used to compile all publicly available information on PASS protocols and assessments submitted from July 2012 to July 2015 from Pharmacovigilance Risk Assessment Committee (PRAC) minutes, European Medicines Agency (EMA) and European Network of Pharmacovigilance and Pharmacoepidemiology (ENCePP) webpages. During the study period, 189 different PASS protocols were submitted to the PRAC, half of which were entered in the ENCePP electronic register of post-authorization studies (EU-PAS) by July 2015. Those protocols were assessed during 353 PRAC reviews. The EMA published only 31% of the PRAC feedback, of which the main concerns were study design (37%) and feasibility (30%). Among the 189 PASS, slightly more involved primary data capture (58%). PASS assessing drug utilization mainly leveraged secondary data sources (58%). The majority of the PASS did not include a comparator (65%) and 35% of PASS also evaluated clinical effectiveness endpoints. To the best of our knowledge this is the first comprehensive review of three years of PASS protocols submitted under the new pharmacovigilance legislation. Our results show that both EMA and PASS sponsors could respectively increase the availability of protocol assessments and documents in the EU-PAS. Protocol content review and the high number of PRAC comments related to methodological issues and feasibility concerns should raise awareness among PASS stakeholders to design more thoughtful studies according to pharmacoepidemiological principles and existing guidelines. © 2016 The British Pharmacological Society.

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

PubMed

Cheikh Ismail, L; Knight, H E; Ohuma, E O; Hoch, L; 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 anthropometric training, standardisation and quality control procedures used to collect data for these new standards. The initial standardisation session was in Nairobi, Kenya, using newborns, which was followed by similar sessions in the eight participating study sites in Brazil, China, India, Italy, Kenya, Oman, UK and USA. The intraobserver and inter-observer technical error of measurement values for head circumference range from 0.3 to 0.4 cm, and for recumbent length from 0.3 to 0.5 cm. These standardisation protocols implemented at each study site worldwide ensure that the anthropometric data collected are of the highest quality to construct international growth standards. © 2013 Royal College of Obstetricians and Gynaecologists.

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.

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.

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.

Crystallization of Macromolecules

PubMed Central

Friedmann, David; Messick, Troy; Marmorstein, Ronen

2014-01-01

X-ray crystallography has evolved into a very powerful tool to determine the three-dimensional structure of macromolecules and macromolecular complexes. The major bottleneck in structure determination by X-ray crystallography is the preparation of suitable crystalline samples. This unit outlines steps for the crystallization of a macromolecule, starting with a purified, homogeneous sample. The first protocols describe preparation of the macromolecular sample (i.e., proteins, nucleic acids, and macromolecular complexes). The preparation and assessment of crystallization trials is then described, along with a protocol for confirming whether the crystals obtained are composed of macromolecule as opposed to a crystallization reagent . Next, the optimization of crystallization conditions is presented. Finally, protocols that facilitate the growth of larger crystals through seeding are described. PMID:22045560

Solution Strategies, Modes of Representation and Justifications of Primary Five Pupils in Solving Pre Algebra Problems: An Experience of Using Task-Based Interview and Verbal Protocol Analysis

ERIC Educational Resources Information Center

Ling, Gan We; Ghazali, Munirah

2007-01-01

This descriptive study was aimed at looking into how Primary 5 pupils solve pre-algebra problems concerning patterns and unknown quantities. Specifically, objectives of this study were to describe Primary 5 pupils' solution strategies, modes of representations and justifications in: (a) discovering, describing and using numerical and geometrical…

Expression, Biochemistry, and Stabilization with Camel Antibodies of Membrane Proteins: Case Study of the Mouse 5-HT3 Receptor.

PubMed

Hassaïne, Ghérici; Deluz, Cédric; Grasso, Luigino; Wyss, Romain; Hovius, Ruud; Stahlberg, Henning; Tomizaki, Takashi; Desmyter, Aline; Moreau, Christophe; Peclinovska, Lucie; Minniberger, Sonja; Mebarki, Lamia; Li, Xiao-Dan; Vogel, Horst; Nury, Hugues

2017-01-01

There is growing interest in the use of mammalian protein expression systems, and in the use of antibody-derived chaperones, for structural studies. Here, we describe protocols ranging from the production of recombinant membrane proteins in stable inducible cell lines to biophysical characterization of purified membrane proteins in complex with llama antibody domains. These protocols were used to solve the structure of the mouse 5-HT3 serotonin receptor but are of broad applicability for crystallization or cryo-electron microscopy projects.

Health care access for rural youth on equal terms? A mixed methods study protocol in northern Sweden.

PubMed

Goicolea, Isabel; Carson, Dean; San Sebastian, Miguel; Christianson, Monica; Wiklund, Maria; Hurtig, Anna-Karin

2018-01-11

The purpose of this paper is to propose a protocol for researching the impact of rural youth health service strategies on health care access. There has been no published comprehensive assessment of the effectiveness of youth health strategies in rural areas, and there is no clearly articulated model of how such assessments might be conducted. The protocol described here aims to gather information to; i) Assess rural youth access to health care according to their needs, ii) Identify and understand the strategies developed in rural areas to promote youth access to health care, and iii) Propose actions for further improvement. The protocol is described with particular reference to research being undertaken in the four northernmost counties of Sweden, which contain a widely dispersed and diverse youth population. The protocol proposes qualitative and quantitative methodologies sequentially in four phases. First, to map youth access to health care according to their health care needs, including assessing horizontal equity (equal use of health care for equivalent health needs,) and vertical equity (people with greater health needs should receive more health care than those with lesser needs). Second, a multiple case study design investigates strategies developed across the region (youth clinics, internet applications, public health programs) to improve youth access to health care. Third, qualitative comparative analysis of the 24 rural municipalities in the region identifies the best combination of conditions leading to high youth access to health care. Fourth, a concept mapping study involving rural stakeholders, care providers and youth provides recommended actions to improve rural youth access to health care. The implementation of this research protocol will contribute to 1) generating knowledge that could contribute to strengthening rural youth access to health care, as well as to 2) advancing the application of mixed methods to explore access to health care.

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,…

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.

Simple Tools to Facilitate Project Management of a Nursing Research Project.

PubMed

Aycock, Dawn M; Clark, Patricia C; Thomas-Seaton, LaTeshia; Lee, Shih-Yu; Moloney, Margaret

2016-07-01

Highly organized project management facilitates rigorous study implementation. Research involves gathering large amounts of information that can be overwhelming when organizational strategies are not used. We describe a variety of project management and organizational tools used in different studies that may be particularly useful for novice researchers. The studies were a multisite study of caregivers of stroke survivors, an Internet-based diary study of women with migraines, and a pilot study testing a sleep intervention in mothers of low-birth-weight infants. Project management tools were used to facilitate enrollment, data collection, and access to results. The tools included protocol and eligibility checklists, event calendars, screening and enrollment logs, instrument scoring tables, and data summary sheets. These tools created efficiency, promoted a positive image, minimized errors, and provided researchers with a sense of control. For the studies described, there were no protocol violations, there were minimal missing data, and the integrity of data collection was maintained. © The Author(s) 2016.

A genotyping protocol for multiple tissue types from the polyploid tree species Sequoia sempervirens (Cupressaceae)1

PubMed Central

Narayan, Lakshmi; Dodd, Richard S.; O’Hara, Kevin L.

2015-01-01

Premise of the study: Identifying clonal lineages in asexually reproducing plants using microsatellite markers is complicated by the possibility of nonidentical genotypes from the same clonal lineage due to somatic mutations, null alleles, and scoring errors. We developed and tested a clonal identification protocol that is robust to these issues for the asexually reproducing hexaploid tree species coast redwood (Sequoia sempervirens). Methods: Microsatellite data from four previously published and two newly developed primers were scored using a modified protocol, and clones were identified using Bruvo genetic distances. The effectiveness of this clonal identification protocol was assessed using simulations and by genotyping a test set of paired samples of different tissue types from the same trees. Results: Data from simulations showed that our protocol allowed us to accurately identify clonal lineages. Multiple test samples from the same trees were identified correctly, although certain tissue type pairs had larger genetic distances on average. Discussion: The methods described in this paper will allow for the accurate identification of coast redwood clones, facilitating future studies of the reproductive ecology of this species. The techniques used in this paper can be applied to studies of other clonal organisms as well. PMID:25798341

Nurses' perceptions of involvement in Thunder Project. American Association of Critical-Care Nurses Thunder Project task force.

PubMed

1995-03-01

The American Association of Critical-Care Nurse's (AACN) Thunder Project was conceptualized and developed to provide critical-care nurses with a research protocol ready for institutional review and implementation. Project goals included providing a research package (protocol, educational, and data collection materials) and a topic of clinical significance to critical-care nurses. Site coordinators and research associates were identified at participating institutions to coordinate and implement all study activities. In this article, an evaluation study undertaken to recount perceptions of site coordinators and research associates in relation to project goals and research experience is described. Data demonstrated that study goals were achieved, and research experience was considered professionally enhancing. Written comments described barriers to project implementation at participating sites. Obtaining informed consent and physician approval and/or cooperation were identified as significant barriers to implementation at some sites.

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.

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.

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...

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.

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.

Protocols for the Initial Treatment of Moderately Severe Juvenile Dermatomyositis: Results of a Children's Arthritis and Rheumatology Research Alliance Consensus Conference

PubMed Central

Huber, Adam M.; Giannini, Edward H.; Bowyer, Suzanne L.; Kim, Susan; Lang, Bianca; Lindsley, Carol B.; Pachman, Lauren M.; Pilkington, Clarissa; Reed, Ann M.; Rennebohm, Robert M.; Rider, Lisa G.; Wallace, Carol A.; Feldman, Brian M.

2010-01-01

Objective To use juvenile dermatomyositis (JDM) survey data and expert opinion to develop a small number of consensus treatment protocols which reflect current initial treatment of moderately severe JDM. Methods A consensus meeting was held in Toronto, Ontario, Canada on December 1-2, 2007. Nominal group technique was used to achieve consensus on treatment protocols which represented typical management of moderately severe JDM. Consensus was also reached on which patients these protocols would be applicable to (inclusion and exclusion criteria), initial investigations which should be done prior to initiating one of these protocols, data which should be collected to evaluate these protocols, concomitant interventions that would be required or recommended. Results Three protocols were developed which described the first 2 months of treatment. All protocols included corticosteroids and methotrexate. One protocol also included intravenous gammaglobulin. Consensus was achieved for all issues that were addressed by conference participants, although there were some areas of controversy Conclusions This study shows that it is possible to achieve consensus on the initial treatment of JDM, despite considerable variation in clinical practice. Once these protocols are extended beyond 2 months, these protocols will be available for clinical use. By using methods which account for differences between patients (confounding by indication), the comparative effectiveness of the protocols will be evaluated. In the future, the goal will be to identify the optimal treatment of moderately severe JDM. PMID:20191521

Isolation of Primary Human Skeletal Muscle Cells

PubMed Central

Spinazzola, Janelle M.; Gussoni, Emanuela

2017-01-01

Primary myoblast culture is a valuable tool in research of muscle disease, pathophysiology, and pharmacology. This protocol describes techniques for dissociation of cells from human skeletal muscle biopsies and enrichment for a highly myogenic population by fluorescence-activated cell sorting (FACS). We also describe methods for assessing myogenicity and population expansion for subsequent in vitro study. PMID:29152538

Aspirin allergy desensitization in cerebrovascular disease. A report of two cases, literature review and management guide for the neurointerventionalist.

PubMed

Zuckerman, Scott L; Seder, David B; Tsujiura, Crystiana; Cushing, Deborah; Gallup, Holly; Mocco, J; Hanel, Richard A; Ecker, Robert D

2014-01-01

Aspirin (ASA) is the mainstay of treatment in cerebrovascular and systemic vascular disease. ASA hypersensitivity can pose a challenge to achieving optimum medical management prior to and after neurointerventional treatment. Desensitization to ASA is well described in the allergy and cardiovascular literature, but there are no similar discussions specific to neurointervention. The purpose of our study was to describe our experience with ASA hypersensitivity management and review the relevant literature. Two cases of patients with symptomatic cerebrovascular disease requiring neurointervention who were successfully desensitized to their ASA hypersensitivity prior to treatment are described. The subsequent literature is reviewed. Several ASA desensitization protocols exist and have been proven to successfully treat ASA hypersensitivity and allow for ASA therapy to be safely initiated. We describe several previously published protocols. ASA desensitization is a safe and simple way to manage ASA hypersensitivity. We provide comprehensive management guidelines for the neurointerventionalist engaging in ASA desensitization.

Peer Review and Publication of Research Protocols and Proposals: A Role for Open Access Journals

PubMed Central

2004-01-01

Peer-review and publication of research protocols offer several advantages to all parties involved. Among these are the following opportunities for authors: external expert opinion on the methods, demonstration to funding agencies of prior expert review of the protocol, proof of priority of ideas and methods, and solicitation of potential collaborators. We think that review and publication of protocols is an important role for Open Access journals. Because of their electronic form, openness for readers, and author-pays business model, they are better suited than traditional journals to ensure the sustainability and quality of protocol reviews and publications. In this editorial, we describe the workflow for investigators in eHealth research, from protocol submission to a funding agency, to protocol review and (optionally) publication at JMIR, to registration of trials at the International eHealth Study Registry (IESR), and to publication of the report. One innovation at JMIR is that protocol peer reviewers will be paid a honorarium, which will be drawn partly from a new submission fee for protocol reviews. Separating the article processing fee into a submission and a publishing fee will allow authors to opt for “peer-review only” (without subsequent publication) at reduced costs, if they wish to await a funding decision or for other reasons decide not to make the protocol public. PMID:15471763

Peer-review and publication of research protocols and proposals: a role for open access journals.

PubMed

Eysenbach, Gunther

2004-09-30

Peer-review and publication of research protocols offer several advantages to all parties involved. Among these are the following opportunities for authors: external expert opinion on the methods, demonstration to funding agencies of prior expert review of the protocol, proof of priority of ideas and methods, and solicitation of potential collaborators. We think that review and publication of protocols is an important role for Open Access journals. Because of their electronic form, openness for readers, and author-pays business model, they are better suited than traditional journals to ensure the sustainability and quality of protocol reviews and publications. In this editorial, we describe the workflow for investigators in eHealth research, from protocol submission to a funding agency, to protocol review and (optionally) publication at JMIR, to registration of trials at the International eHealth Study Registry (IESR), and to publication of the report. One innovation at JMIR is that protocol peer reviewers will be paid a honorarium, which will be drawn partly from a new submission fee for protocol reviews. Separating the article processing fee into a submission and a publishing fee will allow authors to opt for "peer-review only" (without subsequent publication) at reduced costs, if they wish to await a funding decision or for other reasons decide not to make the protocol public.

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.

Applying Adult Ventilator-associated Pneumonia Bundle Evidence to the Ventilated Neonate.

PubMed

Weber, Carla D

2016-06-01

Ventilator-associated pneumonia (VAP) in neonates can be reduced by implementing preventive care practices. Implementation of a group, or bundle, of evidence-based practices that improve processes of care has been shown to be cost-effective and to have better outcomes than implementation of individual single practices. The purpose of this article is to describe a safe, effective, and efficient neonatal VAP prevention protocol developed for caregivers in the neonatal intensive care unit (NICU). Improved understanding of VAP causes, effects of care practices, and rationale for interventions can help reduce VAP risk to neonatal patients. In order to improve care practices to affect VAP rates, initial and annual education occurred on improved protocol components after surveying staff practices and auditing documentation compliance. In 2009, a tertiary care level III NICU in the Midwestern United States had 14 VAP cases. Lacking evidence-based VAP prevention practices for neonates, effective adult strategies were modified to meet the complex needs of the ventilated neonate. A protocol was developed over time and resulted in an annual decrease in VAP until rates were zero for 20 consecutive months from October 2012 to May 2014. This article describes a VAP prevention protocol developed to address care practices surrounding hand hygiene, intubation, feeding, suctioning, positioning, oral care, and respiratory equipment in the NICU. Implementation of this VAP prevention protocol in other facilities with appropriate monitoring and tracking would provide broader support for standardization of care. Individual components of this VAP protocol could be studied to strengthen the inclusion of each; however, bundled interventions are often considered stronger when implemented as a whole.

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

Analysis of NASA communications (Nascom) II network protocols and performance

NASA Technical Reports Server (NTRS)

Omidyar, Guy C.; Butler, Thomas E.

1991-01-01

The NASA Communications (Nascom) Division of the Mission Operations and Data Systems Directorate is to undertake a major initiative to develop the Nascom II (NII) network to achieve its long-range service objectives for operational data transport to support the Space Station Freedom Program, the Earth Observing System, and other projects. NII is the Nascom ground communications network being developed to accommodate the operational traffic of the mid-1990s and beyond. The authors describe various baseline protocol architectures based on current and evolving technologies. They address the internetworking issues suggested for reliable transfer of data over heterogeneous segments. They also describe the NII architecture, topology, system components, and services. A comparative evaluation of the current and evolving technologies was made, and suggestions for further study are described. It is shown that the direction of the NII configuration and the subsystem component design will clearly depend on the advances made in the area of broadband integrated services.

Building Assessment Survey and Evaluation Study: Quality Assurance Project Plan

EPA Pesticide Factsheets

This supplement describes QA/QC aspects of the implementation of the Office of Radiation and Indoor Air's BASE protocol including: recruitment of study buildings, execution of field studies in each building, and the processing and coordination of each building's ata for final submittal to EPA.

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.

Evaluating the performance of vehicular platoon control under different network topologies of initial states

NASA Astrophysics Data System (ADS)

Li, Yongfu; Li, Kezhi; Zheng, Taixiong; Hu, Xiangdong; Feng, Huizong; Li, Yinguo

2016-05-01

This study proposes a feedback-based platoon control protocol for connected autonomous vehicles (CAVs) under different network topologies of initial states. In particularly, algebraic graph theory is used to describe the network topology. Then, the leader-follower approach is used to model the interactions between CAVs. In addition, feedback-based protocol is designed to control the platoon considering the longitudinal and lateral gaps simultaneously as well as different network topologies. The stability and consensus of the vehicular platoon is analyzed using the Lyapunov technique. Effects of different network topologies of initial states on convergence time and robustness of platoon control are investigated. Results from numerical experiments demonstrate the effectiveness of the proposed protocol with respect to the position and velocity consensus in terms of the convergence time and robustness. Also, the findings of this study illustrate the convergence time of the control protocol is associated with the initial states, while the robustness is not affected by the initial states significantly.

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

Methods to Assess Mitochondrial Morphology in Mammalian Cells Mounting Autophagic or Mitophagic Responses.

PubMed

Marchi, S; Bonora, M; Patergnani, S; Giorgi, C; Pinton, P

2017-01-01

It is widely acknowledged that mitochondria are highly active structures that rapidly respond to cellular and environmental perturbations by changing their shape, number, and distribution. Mitochondrial remodeling is a key component of diverse biological processes, ranging from cell cycle progression to autophagy. In this chapter, we describe different methodologies for the morphological study of the mitochondrial network. Instructions are given for the preparation of samples for fluorescent microscopy, based on genetically encoded strategies or the employment of synthetic fluorescent dyes. We also propose detailed protocols to analyze mitochondrial morphometric parameters from both three-dimensional and bidimensional datasets. Finally, we describe a protocol for the visualization and quantification of mitochondrial structures through electron microscopy. © 2017 Elsevier Inc. All rights reserved.

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

PubMed 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

Treatment of feline intermediate- to high-grade lymphoma with a modified university of Wisconsin-Madison protocol: 119 cases (2004-2012).

PubMed

Collette, S A; Allstadt, S D; Chon, E M; Vernau, W; Smith, A N; Garrett, L D; Choy, K; Rebhun, R B; Rodriguez, C O; Skorupski, K A

2016-08-01

CHOP-based (cyclophosphamide, doxorubicin, vinca alkaloid, prednisolone) chemotherapy protocols are often recommended for treatment of feline lymphoma. While maintenance-free CHOP-based protocols have been published and readily used in dogs, there is limited literature regarding similar maintenance-free protocols in cats. The purpose of this study was to describe the outcome of cats with intermediate- to high-grade lymphoma that were prescribed a modified 25-week University of Wisconsin-Madison (UW-25) chemotherapy protocol. A secondary objective was examination of potential prognostic factors. One hundred and nineteen cats from five institutions treated with a UW-25-based protocol were included. The Kaplan-Meier median progression-free interval (PFI) and survival time (MST) were 56 and 97 (range 2-2019) days, respectively. Cats assessed as having a complete response (CR) to therapy had significantly longer PFI and MST than those with partial or no response (PFI 205 versus 54 versus 21 days, respectively, P < 0.0001 and MST 318 versus 85 versus 27 days, respectively, P < 0.0001). © 2015 John Wiley & Sons Ltd.

Bacterial molecular networks: bridging the gap between functional genomics and dynamical modelling.

PubMed

van Helden, Jacques; Toussaint, Ariane; Thieffry, Denis

2012-01-01

This introductory review synthesizes the contents of the volume Bacterial Molecular Networks of the series Methods in Molecular Biology. This volume gathers 9 reviews and 16 method chapters describing computational protocols for the analysis of metabolic pathways, protein interaction networks, and regulatory networks. Each protocol is documented by concrete case studies dedicated to model bacteria or interacting populations. Altogether, the chapters provide a representative overview of state-of-the-art methods for data integration and retrieval, network visualization, graph analysis, and dynamical modelling.

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.

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

Subgroup analyses in randomised controlled trials: cohort study on trial protocols and journal publications.

PubMed

Kasenda, Benjamin; Schandelmaier, Stefan; Sun, Xin; von Elm, Erik; You, John; Blümle, Anette; Tomonaga, Yuki; Saccilotto, Ramon; Amstutz, Alain; Bengough, Theresa; Meerpohl, Joerg J; Stegert, Mihaela; Olu, Kelechi K; Tikkinen, Kari A O; Neumann, Ignacio; Carrasco-Labra, Alonso; Faulhaber, Markus; Mulla, Sohail M; Mertz, Dominik; Akl, Elie A; Bassler, Dirk; Busse, Jason W; Ferreira-González, Ignacio; Lamontagne, Francois; Nordmann, Alain; Gloy, Viktoria; Raatz, Heike; Moja, Lorenzo; Rosenthal, Rachel; Ebrahim, Shanil; Vandvik, Per O; Johnston, Bradley C; Walter, Martin A; Burnand, Bernard; Schwenkglenks, Matthias; Hemkens, Lars G; Bucher, Heiner C; Guyatt, Gordon H; Briel, Matthias

2014-07-16

To investigate the planning of subgroup analyses in protocols of randomised controlled trials and the agreement with corresponding full journal publications. Cohort of protocols of randomised controlled trial and subsequent full journal publications. Six research ethics committees in Switzerland, Germany, and Canada. 894 protocols of randomised controlled trial involving patients approved by participating research ethics committees between 2000 and 2003 and 515 subsequent full journal publications. Of 894 protocols of randomised controlled trials, 252 (28.2%) included one or more planned subgroup analyses. Of those, 17 (6.7%) provided a clear hypothesis for at least one subgroup analysis, 10 (4.0%) anticipated the direction of a subgroup effect, and 87 (34.5%) planned a statistical test for interaction. Industry sponsored trials more often planned subgroup analyses compared with investigator sponsored trials (195/551 (35.4%) v 57/343 (16.6%), P<0.001). Of 515 identified journal publications, 246 (47.8%) reported at least one subgroup analysis. In 81 (32.9%) of the 246 publications reporting subgroup analyses, authors stated that subgroup analyses were prespecified, but this was not supported by 28 (34.6%) corresponding protocols. In 86 publications, authors claimed a subgroup effect, but only 36 (41.9%) corresponding protocols reported a planned subgroup analysis. Subgroup analyses are insufficiently described in the protocols of randomised controlled trials submitted to research ethics committees, and investigators rarely specify the anticipated direction of subgroup effects. More than one third of statements in publications of randomised controlled trials about subgroup prespecification had no documentation in the corresponding protocols. Definitive judgments regarding credibility of claimed subgroup effects are not possible without access to protocols and analysis plans of randomised controlled trials. © The DISCO study group 2014.

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.

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.

Application of SEM and EDX in studying biomineralization in plant tissues.

PubMed

He, Honghua; Kirilak, Yaowanuj

2014-01-01

This chapter describes protocols using formalin-acetic acid-alcohol (FAA) to fix plant tissues for studying biomineralization by means of scanning electron microscopy (SEM) and qualitative energy-dispersive X-ray microanalysis (EDX). Specimen preparation protocols for SEM and EDX mainly include fixation, dehydration, critical point drying (CPD), mounting, and coating. Gold-coated specimens are used for SEM imaging, while gold- and carbon-coated specimens are prepared for qualitative X-ray microanalyses separately to obtain complementary information on the elemental compositions of biominerals. During the specimen preparation procedure for SEM, some biominerals may be dislodged or scattered, making it difficult to determine their accurate locations, and light microscopy is used to complement SEM studies. Specimen preparation protocols for light microscopy generally include fixation, dehydration, infiltration and embedding with resin, microtome sectioning, and staining. In addition, microwave processing methods are adopted here to speed up the specimen preparation process for both SEM and light microscopy.

A novel method of genomic DNA extraction for Cactaceae1

PubMed Central

Fehlberg, Shannon D.; Allen, Jessica M.; Church, Kathleen

2013-01-01

• Premise of the study: Genetic studies of Cactaceae can at times be impeded by difficult sampling logistics and/or high mucilage content in tissues. Simplifying sampling and DNA isolation through the use of cactus spines has not previously been investigated. • Methods and Results: Several protocols for extracting DNA from spines were tested and modified to maximize yield, amplification, and sequencing. Sampling of and extraction from spines resulted in a simplified protocol overall and complete avoidance of mucilage as compared to typical tissue extractions. Sequences from one nuclear and three plastid regions were obtained across eight genera and 20 species of cacti using DNA extracted from spines. • Conclusions: Genomic DNA useful for amplification and sequencing can be obtained from cactus spines. The protocols described here are valuable for any cactus species, but are particularly useful for investigators interested in sampling living collections, extensive field sampling, and/or conservation genetic studies. PMID:25202521

A habitat-based point-count protocol for terrestrial birds, emphasizing Washington and Oregon.

Treesearch

Mark H. Huff; Kelly A. Bettinger; Howard L. Ferguson; Martin J. Brown; Bob. Altman

2000-01-01

We describe a protocol and provide a summary for point-count monitoring of landbirds that is designed for habitat-based objectives. Presentation is in four steps: preparation and planning, selecting monitoring sites, establishing monitoring stations, and conducting point counts. We describe the basis for doing habitat-based point counts, how they are organized, and how...

Using NMR-based metabolomics to monitor the biochemical composition of agricultural soils: a pilot study

USDA-ARS?s Scientific Manuscript database

NMR-based metabolomics plays a major role studying complex living systems. However, very few studies describe the application of this technique to the evaluation of soil metabolome. Here, we introduce a protocol for analyzing the biochemical compounds from agricultural soils where the microbial comm...

In vitro microfluidic circulatory system for circulating cancer cells

PubMed Central

wan, jiandi; Fan, Rong; Emery, Travis; Zhang, Yongguo; Xia, Yuxuan; Sun, Jun; Wan, Jiandi

2016-01-01

Circulating tumor cells (CTCs) experience hemodynamic shear stress in circulation and play critical roles in cancer metastasis. The effect of shear on CTCs, however, remains less studied. Here, we described a protocol to circulate HCT116 human colon cancer cells in a microfluidic circulatory system mimicking physiologically relevant circulating conditions. This protocol represents a useful scaffold to mimic the transportation of CTCs in circulation and thus provides an effective means to study the effect of shear on CTCs. We anticipate that future studies using the developed system will help us to further investigate the regulatory roles of shear in molecular responses of CTCs. PMID:28690779

Animal Models of Mycobacteria Infection

PubMed Central

Ordway, Diane J.; Orme, Ian M.

2011-01-01

This unit describes the infection of mice and guinea pigs with mycobacteria via various routes, as well as necropsy methods for the determination of mycobacterial loads within target organs. Additionally, methods for cultivating mycobacteria and preparing stocks are described. The protocols outlined are primarily used for M. tuberculosis, but can also be used for the study of other non-tuberculosis mycobacterial species. PMID:18432756

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.

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.

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…

Using Green Star Metrics to Optimize the Greenness of Literature Protocols for Syntheses

ERIC Educational Resources Information Center

Duarte, Rita C. C.; Ribeiro, M. Gabriela T. C.; Machado, Adélio A. S. C.

2015-01-01

A procedure to improve the greenness of a synthesis, without performing laboratory work, using alternative protocols available in the literature is presented. The greenness evaluation involves the separate assessment of the different steps described in the available protocols--reaction, isolation, and purification--as well as the global process,…

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.

In-Space Networking on NASA's SCAN Testbed

NASA Technical Reports Server (NTRS)

Brooks, David E.; Eddy, Wesley M.; Clark, Gilbert J.; Johnson, Sandra K.

2016-01-01

The NASA Space Communications and Navigation (SCaN) Testbed, an external payload onboard the International Space Station, is equipped with three software defined radios and a flight computer for supporting in-space communication research. New technologies being studied using the SCaN Testbed include advanced networking, coding, and modulation protocols designed to support the transition of NASAs mission systems from primarily point to point data links and preplanned routes towards adaptive, autonomous internetworked operations needed to meet future mission objectives. Networking protocols implemented on the SCaN Testbed include the Advanced Orbiting Systems (AOS) link-layer protocol, Consultative Committee for Space Data Systems (CCSDS) Encapsulation Packets, Internet Protocol (IP), Space Link Extension (SLE), CCSDS File Delivery Protocol (CFDP), and Delay-Tolerant Networking (DTN) protocols including the Bundle Protocol (BP) and Licklider Transmission Protocol (LTP). The SCaN Testbed end-to-end system provides three S-band data links and one Ka-band data link to exchange space and ground data through NASAs Tracking Data Relay Satellite System or a direct-to-ground link to ground stations. The multiple data links and nodes provide several upgradable elements on both the space and ground systems. This paper will provide a general description of the testbeds system design and capabilities, discuss in detail the design and lessons learned in the implementation of the network protocols, and describe future plans for continuing research to meet the communication needs for evolving global space systems.

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

Lower limb muscle impairment in myotonic dystrophy type 1: the need for better guidelines.

PubMed

Petitclerc, Émilie; Hébert, Luc J; Desrosiers, Johanne; Gagnon, Cynthia

2015-04-01

In myotonic dystrophy type 1 (DM1), leg muscle weakness is a major impairment. There are challenges to obtaining a clear portrait of muscle strength impairment. A systematic literature review was conducted on lower limb strength impairment in late-onset and adult phenotypes to document variables which affect strength measurement. Thirty-two articles were reviewed using the COSMIN guidelines. Only a third of the studies described a reproducible protocol. Only 2 muscle groups have documented reliability for quantitative muscle testing and only 1 total score for manual muscle testing. Variables affecting muscle strength impairment are not described in most studies. This review illustrates the variability in muscle strength assessment in relation to DM1 characteristics and the questionable validity of the results with regard to undocumented methodological properties. There is therefore a clear need to adopt a consensus on the use of a standardized muscle strength assessment protocol. © 2015 Wiley Periodicals, Inc.

Novel methodology to isolate microplastics from vegetal-rich samples.

PubMed

Herrera, Alicia; Garrido-Amador, Paloma; Martínez, Ico; Samper, María Dolores; López-Martínez, Juan; Gómez, May; Packard, Theodore T

2018-04-01

Microplastics are small plastic particles, globally distributed throughout the oceans. To properly study them, all the methodologies for their sampling, extraction, and measurement should be standardized. For heterogeneous samples containing sediments, animal tissues and zooplankton, several procedures have been described. However, definitive methodologies for samples, rich in algae and plant material, have not yet been developed. The aim of this study was to find the best extraction protocol for vegetal-rich samples by comparing the efficacies of five previously described digestion methods, and a novel density separation method. A protocol using 96% ethanol for density separation was better than the five digestion methods tested, even better than using H 2 O 2 digestion. As it was the most efficient, simple, safe and inexpensive method for isolating microplastics from vegetal rich samples, we recommend it as a standard separation method. Copyright © 2018 Elsevier Ltd. All rights reserved.

Survival times for canine intranasal sarcomas treated with radiation therapy: 86 cases (1996-2011).

PubMed

Sones, Evan; Smith, Annette; Schleis, Stephanie; Brawner, William; Almond, Gregory; Taylor, Kathryn; Haney, Siobhan; Wypij, Jackie; Keyerleber, Michele; Arthur, Jennifer; Hamilton, Terrance; Lawrence, Jessica; Gieger, Tracy; Sellon, Rance; Wright, Zack

2013-01-01

Sarcomas comprise approximately one-third of canine intranasal tumors, however few veterinary studies have described survival times of dogs with histologic subtypes of sarcomas separately from other intranasal tumors. One objective of this study was to describe median survival times for dogs treated with radiation therapy for intranasal sarcomas. A second objective was to compare survival times for dogs treated with three radiation therapy protocols: daily-fractionated radiation therapy; Monday, Wednesday, and Friday fractionated radiation therapy; and palliative radiation therapy. Medical records were retrospectively reviewed for dogs that had been treated with radiation therapy for confirmed intranasal sarcoma. A total of 86 dogs met inclusion criteria. Overall median survival time for included dogs was 444 days. Median survival time for dogs with chondrosarcoma (n = 42) was 463 days, fibrosarcoma (n = 12) 379 days, osteosarcoma (n = 6) 624 days, and undifferentiated sarcoma (n = 22) 344 days. Dogs treated with daily-fractionated radiation therapy protocols; Monday, Wednesday and Friday fractionated radiation therapy protocols; and palliative radiation therapy protocols had median survival times of 641, 347, and 305 days, respectively. A significant difference in survival time was found for dogs receiving curative intent radiation therapy vs. palliative radiation therapy (P = 0.032). A significant difference in survival time was also found for dogs receiving daily-fractionated radiation therapy vs. Monday, Wednesday and Friday fractionated radiation therapy (P = 0.0134). Findings from this study support the use of curative intent radiation therapy for dogs with intranasal sarcoma. Future prospective, randomized trials are needed for confirmation of treatment benefits. © 2012 Veterinary Radiology & Ultrasound.

Self-organization of human embryonic stem cells on micropatterns

PubMed Central

Deglincerti, Alessia; Etoc, Fred; Guerra, M. Cecilia; Martyn, Iain; Metzger, Jakob; Ruzo, Albert; Simunovic, Mijo; Yoney, Anna; Brivanlou, Ali H.; Siggia, Eric; Warmflash, Aryeh

2018-01-01

Fate allocation in the gastrulating embryo is spatially organized as cells differentiate to specialized cell types depending on their positions with respect to the body axes. There is a need for in vitro protocols that allow the study of spatial organization associated with this developmental transition. While embryoid bodies and organoids can exhibit some spatial organization of differentiated cells, these methods do not yield consistent and fully reproducible results. Here, we describe a micropatterning approach where human embryonic stem cells are confined to disk-shaped, sub-millimeter colonies. After 42 hours of BMP4 stimulation, cells form self-organized differentiation patterns in concentric radial domains, which express specific markers associated with the embryonic germ layers, reminiscent of gastrulating embryos. Our protocol takes 3 days; it uses commercial microfabricated slides (CYTOO), human laminin-521 (LN-521) as extra-cellular matrix coating, and either conditioned or chemically-defined medium (mTeSR). Differentiation patterns within individual colonies can be determined by immunofluorescence and analyzed with cellular resolution. Both the size of the micropattern and the type of medium affect the patterning outcome. The protocol is appropriate for personnel with basic stem cell culture training. This protocol describes a robust platform for quantitative analysis of the mechanisms associated with pattern formation at the onset of gastrulation. PMID:27735934

Mandibular molar uprighting using mini-implants: different approaches for different clinical cases--two case reports.

PubMed

Derton, Nicola; Perini, Alessandro; Mutinelli, Sabrina; Gracco, Antonio

2012-01-01

To detail two different clinical protocols and case studies using mini-implant anchorage developed to respond to certain clinical conditions. Two clinical protocols are described to upright mesially tilted mandibular molars. In the first protocol, a single mini-implant is inserted distally to the molar to be uprighted, and an elastic traction chain is applied to the tooth. In the second clinical approach, two mini-implants are inserted mesially. A screw-suspended TMA sectional archwire is applied (Derton-Perini technique). Two cases, descriptive of the two different treatment protocols, are described. In the first case, the mandibular right second premolar was missing and the adjacent first molar needed to be uprighted. A single screw was inserted distally to the first molar, and an elastic chain was applied. In the second case, the mandibular left second molar was missing and the third molar needed to be uprighted. Two mini-implants were inserted mesially and a fully screw-supported sectional archwire was used to upright and bodily mesialize the third molar. Both uprighting approaches uprighted the molar axis without loss of anchorage. The two approaches to mandibular molar uprighting, developed as rational responses to different clinical cases, were both found to be effective.

A genotyping protocol for multiple tissue types from the polyploid tree species Sequoia sempervirens (Cupressaceae).

PubMed

Narayan, Lakshmi; Dodd, Richard S; O'Hara, Kevin L

2015-03-01

Identifying clonal lineages in asexually reproducing plants using microsatellite markers is complicated by the possibility of nonidentical genotypes from the same clonal lineage due to somatic mutations, null alleles, and scoring errors. We developed and tested a clonal identification protocol that is robust to these issues for the asexually reproducing hexaploid tree species coast redwood (Sequoia sempervirens). Microsatellite data from four previously published and two newly developed primers were scored using a modified protocol, and clones were identified using Bruvo genetic distances. The effectiveness of this clonal identification protocol was assessed using simulations and by genotyping a test set of paired samples of different tissue types from the same trees. Data from simulations showed that our protocol allowed us to accurately identify clonal lineages. Multiple test samples from the same trees were identified correctly, although certain tissue type pairs had larger genetic distances on average. The methods described in this paper will allow for the accurate identification of coast redwood clones, facilitating future studies of the reproductive ecology of this species. The techniques used in this paper can be applied to studies of other clonal organisms as well.

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.

Application of the Putting Women First protocol in a study on violence against immigrant women in Spain.

PubMed

Torrubiano-Domínguez, Jordi; Vives-Cases, Carmen

2013-01-01

In this paper, we describe our experience of using the Putting Women First protocol in the design and implementation of a cross-sectional study on violence against women (VAW) among 1607 immigrant women from Morocco, Ecuador and Romania living in Spain in 2011. The Putting Women First protocol is an ethical guideline for VAW research, which includes recommendations to ensure the safety of the women involved in studies on this subject. The response rate in this study was 59.3%. The prevalence of VAW cases last year was 11.7%, of which 15.6% corresponded to Ecuadorian women, 10.9% to Moroccan women and 8.6% to Romanian women. We consider that the most important goal for future research is the use of VAW scales validated in different languages, which would help to overcome the language barriers encountered in this study. Copyright © 2012 SESPAS. Published by Elsevier Espana. All rights reserved.

Worldwide trends in volume and quality of published protocols of randomized controlled trials

PubMed Central

Alldinger, Ingo; Cieslak, Kasia P.; Wennink, Roos; Clarke, Mike; Ali, Usama Ahmed; Besselink, Marc G. H.

2017-01-01

Introduction Publishing protocols of randomized controlled trials (RCT) facilitates a more detailed description of study rational, design, and related ethical and safety issues, which should promote transparency. Little is known about how the practice of publishing protocols developed over time. Therefore, this study describes the worldwide trends in volume and methodological quality of published RCT protocols. Methods A systematic search was performed in PubMed and EMBASE, identifying RCT protocols published over a decade from 1 September 2001. Data were extracted on quality characteristics of RCT protocols. The primary outcome, methodological quality, was assessed by individual methodological characteristics (adequate generation of allocation, concealment of allocation and intention-to-treat analysis). A comparison was made by publication period (First, September 2001- December 2004; Second, January 2005-May 2008; Third, June 2008-September 2011), geographical region and medical specialty. Results The number of published RCT protocols increased from 69 in the first, to 390 in the third period (p<0.0001). Internal medicine and paediatrics were the most common specialty topics. Whereas most published RCT protocols in the first period originated from North America (n = 30, 44%), in the second and third period this was Europe (respectively, n = 65, 47% and n = 190, 48%, p = 0.02). Quality of RCT protocols was higher in Europe and Australasia, compared to North America (OR = 0.63, CI = 0.40–0.99, p = 0.04). Adequate generation of allocation improved with time (44%, 58%, 67%, p = 0.001), as did concealment of allocation (38%, 53%, 55%, p = 0.03). Surgical protocols had the highest quality among the three specialty topics used in this study (OR = 1.94, CI = 1.09–3.45, p = 0.02). Conclusion Publishing RCT protocols has become popular, with a five-fold increase in the past decade. The quality of published RCT protocols also improved, although variation between geographical regions and across medical specialties was seen. This emphasizes the importance of international standards of comprehensive training in RCT methodology. PMID:28296925

Adaptive tracking of a time-varying field with a quantum sensor

NASA Astrophysics Data System (ADS)

Bonato, Cristian; Berry, Dominic W.

2017-05-01

Sensors based on single spins can enable magnetic-field detection with very high sensitivity and spatial resolution. Previous work has concentrated on sensing of a constant magnetic field or a periodic signal. Here, we instead investigate the problem of estimating a field with nonperiodic variation described by a Wiener process. We propose and study, by numerical simulations, an adaptive tracking protocol based on Bayesian estimation. The tracking protocol updates the probability distribution for the magnetic field based on measurement outcomes and adapts the choice of sensing time and phase in real time. By taking the statistical properties of the signal into account, our protocol strongly reduces the required measurement time. This leads to a reduction of the error in the estimation of a time-varying signal by up to a factor of four compare with protocols that do not take this information into account.

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation.

PubMed

Belaghzal, Houda; Dekker, Job; Gibcus, Johan H

2017-07-01

Chromosome conformation capture-based methods such as Hi-C have become mainstream techniques for the study of the 3D organization of genomes. These methods convert chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions). Here, we describe an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (kb) resolution. It also includes steps to reduce random ligation and the generation of uninformative molecules, such as unligated ends, to improve the amount of valid intra-chromosomal read pairs. This protocol allows for obtaining information on conformational structures such as compartment and topologically associating domains, as well as high-resolution conformational features such as DNA loops. Copyright © 2017 Elsevier Inc. All rights reserved.

Protocols for second-generation business satellites systems

NASA Astrophysics Data System (ADS)

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

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

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.

A systematic review of risk factors associated with accidental falls, outcome measures and interventions to manage fall risk in non-ambulatory adults.

PubMed

Rice, Laura A; Ousley, Cherita; Sosnoff, Jacob J

2015-01-01

To systematically review peer-reviewed literature pertaining to risk factors, outcome measures and interventions managing fall risk in non-ambulatory adults. Twenty-one papers were selected for inclusion from databases including PubMed/Medline, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Cochrane Library, Scopus, Consumer Health Complete and Web of Science. Selected studies involved a description of fall related risk factors, outcomes to assess fall risk and intervention studies describing protocols to manage fall risk in non-ambulatory adults. Studies were selected by two reviewers and consultation provided by a third reviewer. The most frequently cited risk factors/characteristics associated with falls included: wheelchair related characteristics, transfer activities, impaired seated balance and environmental factors. The majority of the outcomes were found to evaluate seated postural control. One intervention study was identified describing a protocol targeting specific problems of individual participants. A global fall prevention program was not identified. Several risk factors associated with falls were identified and must be understood by clinicians to better serve their clients. To improve objective assessment, a comprehensive outcome assessment specific to non-ambulatory adults is needed. Finally, additional research is needed to examine the impact of structured protocols to manage fall risk in non-ambulatory adults. Falls are a common health concern for non-ambulatory adults. Risk factors commonly associated with falls include wheelchair related characteristics, transfer activities, impaired seated balance and environmental factors. Limited outcome measures are available to assess fall risk in non-ambulatory adults. Clinicians must be aware of the known risk factors and provide comprehensive education to their clients on the potential for falls. Additional research is needed to develop and evaluate protocols to clinically manage fall risk.

Lipids and Fatty Acids in Algae: Extraction, Fractionation into Lipid Classes, and Analysis by Gas Chromatography Coupled with Flame Ionization Detector (GC-FID).

PubMed

Guihéneuf, Freddy; Schmid, Matthias; Stengel, Dagmar B

2015-01-01

Despite the number of biochemical studies exploring algal lipids and fatty acid biosynthesis pathways and profiles, analytical methods used by phycologists for this purpose are often diverse and incompletely described. Potential confusion and potential variability of the results between studies can therefore occur due to change of protocols for lipid extraction and fractionation, as well as fatty acid methyl esters (FAME) preparation before gas chromatography (GC) analyses. Here, we describe a step-by-step procedure for the profiling of neutral and polar lipids using techniques such as solid-liquid extraction (SLE), thin-layer chromatography (TLC), and gas chromatography coupled with flame ionization detector (GC-FID). As an example, in this protocol chapter, analyses of neutral and polar lipids from the marine microalga Pavlova lutheri (an EPA/DHA-rich haptophyte) will be outlined to describe the distribution of fatty acid residues within its major lipid classes. This method has been proven to be a reliable technique to assess changes in lipid and fatty acid profiles in several other microalgal species and seaweeds.

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

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.

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

Might digital drains speed up the time to thoracic drain removal?

PubMed

Afoke, Jonathan; Tan, Carol; Hunt, Ian; Zakkar, Mustafa

2014-07-01

A best evidence topic in thoracic surgery was written according to a structured protocol. The question addressed was: might digital drains speed up the time to thoracic drain removal in terms of time till chest drain removal, hospital stay and overall cost? A total of 296 papers were identified as a result of the search as described below. Of these, five papers provided the best evidence to answer the clinical question. The author, date and country of publication, patient group studied, study type, relevant outcomes, results and study weaknesses of the papers are tabulated. A literature search revealed that several single-centre prospective randomized studies have shown significantly earlier removal of chest drains with digital drains ranging between 0.8 and 2.1 days sooner. However, there was heterogeneity in studies in the management protocol of chest drains in terms of the use of suction, number of drains and assessment for drain removal. Some protocols such as routinely keeping drains irrespective of the presence of air leak or drain output may have skewed results. Differences in exclusion criteria and protocols for discharging home with portable devices may have biased results. Due to heterogeneity in the management protocol of chest drains, there is conflicting evidence regarding hospital stay. The limited data on cost suggest that there may be significantly lower postoperative costs in the digital drain group. All the studies were single-centre series generally including patients with good preoperative lung function tests. Further larger studies with more robust chest drain management protocols are required especially to assess length of hospital stay, cost and whether the results are applicable to a larger patient population. © The Author 2014. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Investigation of the Study Characteristics Affecting Clinical Trial Quality Using the Protocol Deviations Leading to Exclusion of Subjects From the Per Protocol Set Data in Studies for New Drug Application: A Retrospective Analysis.

PubMed

Kohara, Norihito; Kaneko, Masayuki; Narukawa, Mamoru

2018-01-01

The concept of the risk-based approach has been introduced as an effort to secure the quality of clinical trials. In the risk-based approach, identification and evaluation of risk in advance are considered important. For recently completed clinical trials, we investigated the relationship between study characteristics and protocol deviations leading to the exclusion of subjects from Per Protocol Set (PPS) efficacy analysis. New drugs approved in Japan in the fiscal year 2014-2015 were targeted in the research. The reasons for excluding subjects from the PPS efficacy analysis were described in 102 trials out of 492 in the summary of new drug application documents, which was publicly disclosed after the drug's regulatory approval. The author extracted these reasons along with the numbers of the cases and the study characteristics of each clinical trial. Then, the direct comparison, univariate regression analysis, and multivariate regression analysis was carried out based on the exclusion rate. The study characteristics for which exclusion of subjects from the PPS efficacy analysis were frequently observed was multiregional clinical trials in study region; inhalant and external use in administration route; Anti-infective for systemic use; Respiratory system, Dermatologicals, and Nervous system in therapeutic drug under the Anatomical Therapeutic Chemical Classification. In the multivariate regression analysis, the clinical trial variables of inhalant, Respiratory system, or Dermatologicals were selected as study characteristics leading to a higher exclusion rate. The characteristics of the clinical trial that is likely to cause protocol deviations that will affect efficacy analysis were suggested. These studies should be considered for specific attention and priority observation in the trial protocol or its monitoring plan and execution, such as a clear description of inclusion/exclusion criteria in the protocol, development of training materials to site staff, and/or trial subjects as specific risk-alleviating measures.

Use of a Brine Shrimp Assay to Study Herbal Teas in the Classroom.

ERIC Educational Resources Information Center

Opler, Annette; Mizell, Rebecca; Robert, Alexander; Cervantes-Cervantes, Miguel; Kincaid, Dwight; Kennelly, Edward J.

2002-01-01

Introduces a brine shrimp assay to demonstrate the effects of the biological activity of herbal remedies. Describes two protocols, one using aqueous extracts and the other using methanol extracts. (Contains 21 references.) (YDS)

Development and validation of a remote home safety protocol.

PubMed

Romero, Sergio; Lee, Mi Jung; Simic, Ivana; Levy, Charles; Sanford, Jon

2018-02-01

Environmental assessments and subsequent modifications conducted by healthcare professionals can enhance home safety and promote independent living. However, travel time, expense and the availability of qualified professionals can limit the broad application of this intervention. Remote technology has the potential to increase access to home safety evaluations. This study describes the development and validation of a remote home safety protocol that can be used by a caregiver of an elderly person to video-record their home environment for later viewing and evaluation by a trained professional. The protocol was developed based on literature reviews and evaluations from clinical and content experts. Cognitive interviews were conducted with a group of six caregivers to validate the protocol. The final protocol included step-by-step directions to record indoor and outdoor areas of the home. The validation process resulted in modifications related to safety, clarity of the protocol, readability, visual appearance, technical descriptions and usability. Our final protocol includes detailed instructions that a caregiver should be able to follow to record a home environment for subsequent evaluation by a home safety professional. Implications for Rehabilitation The results of this study have several implications for rehabilitation practice The remote home safety evaluation protocol can potentially improve access to rehabilitation services for clients in remote areas and prevent unnecessary delays for needed care. Using our protocol, a patient's caregiver can partner with therapists to quickly and efficiently evaluate a patient's home before they are released from the hospital. Caregiver narration, which reflects a caregiver's own perspective, is critical to evaluating home safety. In-home safety evaluations, currently not available to all who need them due to access barriers, can enhance a patient's independence and provide a safer home environment.

Simplified follow-up after medical abortion using a low-sensitivity urinary pregnancy test and a pictorial instruction sheet in Rajasthan, India--study protocol and intervention adaptation of a randomised control trial.

PubMed

Paul, Mandira; Iyengar, Kirti; Iyengar, Sharad; Gemzell-Danielsson, Kristina; Essén, Birgitta; Klingberg-Allvin, Marie

2014-08-15

The World Health Organisation suggests that simplification of the medical abortion regime will contribute to an increased acceptability of medical abortion, among women as well as providers. It is expected that a home-based follow-up after a medical abortion will increase the willingness to opt for medical abortion as well as decrease the workload and service costs in the clinic. This study protocol describes a study that is a randomised, controlled, non-superiority trial. Women screened to participate in the study are those with unwanted pregnancies and gestational ages equal to or less than nine weeks. The randomisation list will be generated using a computerized random number generator and opaque sealed envelopes with group allocation will be prepared. Randomization of the study participants will occur after the first clinical encounter with the doctor. Eligible women randomised to the home-based assessment group will use a low-sensitivity pregnancy test and a pictorial instruction sheet at home, while the women in the clinic follow-up group will return to the clinic for routine follow-up carried out by a doctor. The primary objective of the study this study protocol describes is to evaluate the efficacy of home-based assessment using a low-sensitivity pregnancy test and a pictorial instruction sheet 10-14 days after an early medical abortion. Providers or research assistants will not be blinded during outcome assessment. To ensure feasibility of the self-assessment intervention an adaption phase took place at the selected study sites before study initiation. This resulted in an optimized, tailor-made intervention and in the development of the pictorial instruction sheet with a guide on how to use the low-sensitivity pregnancy test and the danger signs after a medical abortion. In this paper, we will describe the study protocol for a randomised control trial investigating the efficacy of simplified follow-up in terms of home-based assessment, 10-14 days after a medical abortion. Moreover, a description of the adaptation phase is included for a better understanding of the implementation of the intervention in a setting where literacy is low and the road-connections are poor. Clinicaltrials.gov NCT01827995. Registered 04 May 2013.

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.

Exercise for methamphetamine dependence: rationale, design, and methodology.

PubMed

Mooney, Larissa J; Cooper, Christopher; London, Edythe D; Chudzynski, Joy; Dolezal, Brett; Dickerson, Daniel; Brecht, Mary-Lynn; Peñate, Jose; Rawson, Richard A

2014-01-01

Effective pharmacotherapies to treat methamphetamine (MA) dependence have not been identified, and behavioral therapies are marginally effective. Based on behavioral studies demonstrating the potential efficacy of aerobic exercise for improving depressive symptoms, anxiety, cognitive deficits, and substance use outcomes, the study described here is examining exercise as a potential treatment for MA-dependent individuals. This study is randomizing 150 participants with MA dependence at a residential treatment facility for addictive disorders to receive either a thrice-weekly structured aerobic and resistance exercise intervention or a health education condition. Recruitment commenced in March, 2010. Enrollment and follow-up phases are ongoing, and recruitment is exceeding targeted enrollment rates. Seeking evidence for a possibly effective adjunct to traditional behavioral approaches for treatment of MA dependence, this study is assessing the ability of an 8-week aerobic and resistance exercise protocol to reduce relapse to MA use during a 12-week follow-up period after discharge from residential-based treatment. The study also is evaluating improvements in health and functional outcomes during and after the protocol. This paper describes the design and methods of the study. Copyright © 2013 Elsevier Inc. All rights reserved.

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).

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.

Communication and protocol compliance and their relation to the quality of cardiopulmonary resuscitation (CPR): A mixed-methods study of simulated telephone-assisted CPR.

PubMed

Nord-Ljungquist, Helena; Brännström, Margareta; Bohm, Katarina

2015-07-01

In the event of a cardiac arrest, emergency medical dispatchers (EMDs) play a critical role by providing telephone-assisted cardiopulmonary resuscitation (T-CPR) to laypersons. The aim of our investigation was to describe compliance with the T-CPR protocol, the performance of the laypersons in a simulated T-CPR situation, and the communication between laypersons and EMDs during these actions. We conducted a retrospective observational study by analysing 20 recorded video and audio files. In a simulation, EMDs provided laypersons with instructions following T-CPR protocols. These were then analysed using a mixed method with convergent parallel design. If the EMDs complied with the T-CPR protocol, the laypersons performed the correct procedures in 71% of the actions. The single most challenging instruction of the T-CPR protocol, for both EMDs and laypersons, was airway control. Mean values for compression depth and frequency did not reach established guideline goals for CPR. Proper application of T-CPR protocols by EMDs resulted in better performance by laypersons in CPR. The most problematic task for EMDs as well for laypersons was airway management. The study results did not establish that the quality of communication between EMDs and laypersons performing CPR in a cardiac arrest situation led to statistically different outcomes, as measured by the quality and effectiveness of the CPR delivered. Copyright © 2014 Elsevier Ltd. All rights reserved.

The View from Here: Emergence of Graphical Literacy

ERIC Educational Resources Information Center

Roberts, Kathryn L.; Brugar, Kristy A.

2017-01-01

The purpose of this study is to describe upper elementary students' understandings of four graphical devices that frequently occur in social studies texts: captioned images, maps, tables, and timelines. Using verbal protocol data collection procedures, we collected information on students' metacognitive processes when they were explicitly asked to…

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.

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.

Phonological outcome of laryngeal framework surgery by different anesthesia protocols: a single-surgeon experience.

PubMed

Kanazawa, Takeharu; Watanabe, Yusuke; Komazawa, Daigo; Indo, Kanako; Misawa, Kiyoshi; Nagatomo, Takafumi; Shimada, Mari; Iino, Yukiko; Ichimura, Keiichi

2014-02-01

Similar to combined arytenoid adduction and medialization laryngoplasty (i.e. combined surgery) under local anesthesia, general anesthesia by intubation or by the laryngeal mask airway (LMA) method significantly improves phonological outcome. Thus, laryngeal framework surgery under general anesthesia is a promising surgical approach for selected patients with unilateral vocal cord paralysis (UVCP). The advantages of laryngeal framework surgery under local anesthesia have been described, but no studies exist concerning the difference in phonological outcome of laryngeal framework surgery performed under general anesthesia. To add new information, we retrospectively investigated the phonological outcome of the combined surgery performed under three different anesthesia protocols. Thirty-nine consecutive patients with severe UVCP underwent the combined surgery under three anesthesia protocols performed by a single surgeon: (1) under general anesthesia by intubation, (2) under general anesthesia using LMA, and (3) under local anesthesia. Under all anesthesia protocols, the vocal cords of most patients could be positioned such that the best vocal outcome could be expected. Statistical analyses demonstrated improved maximum phonation time and mean airflow rate, and grade, roughness, breathiness, asthenia, and strain (GRBAS) scale in all patients, regardless of their anesthesia protocol. Furthermore, of the three protocols, local anesthesia had the shortest operation time.

Comparison between publicly accessible publications, registries, and protocols of phase III trials indicated persistence of selective outcome reporting.

PubMed

Zhang, Sheng; Liang, Fei; Li, Wenfeng

2017-11-01

The decision to make protocols of phase III randomized controlled trials (RCTs) publicly accessible by leading journals was a landmark event in clinical trial reporting. Here, we compared primary outcomes defined in protocols with those in publications describing the trials and in trial registration. We identified phase III RCTs published between January 1, 2012, and June 30, 2015, in The New England Journal of Medicine, The Lancet, The Journal of the American Medical Association, and The BMJ with available protocols. Consistency in primary outcomes between protocols and registries (articles) was evaluated. We identified 299 phase III RCTs with available protocols in this analysis. Out of them, 25 trials (8.4%) had some discrepancy for primary outcomes between publications and protocols. Types of discrepancies included protocol-defined primary outcome reported as nonprimary outcome in publication (11 trials, 3.7%), protocol-defined primary outcome omitted in publication (10 trials, 3.3%), new primary outcome introduced in publication (8 trials, 2.7%), protocol-defined nonprimary outcome reported as primary outcome in publication (4 trials, 1.3%), and different timing of assessment of primary outcome (4 trials, 1.3%). Out of trials with discrepancies in primary outcome, 15 trials (60.0%) had discrepancies that favored statistically significant results. Registration could be seen as a valid surrogate of protocol in 237 of 299 trials (79.3%) with regard to primary outcome. Despite unrestricted public access to protocols, selective outcome reporting persists in a small fraction of phase III RCTs. Only studies from four leading journals were included, which may cause selection bias and limit the generalizability of this finding. Copyright © 2017 Elsevier Inc. All rights reserved.

Lessons Learned from Decontamination Experiences

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

Sorensen, JH

2000-11-16

This interim report describes a DOE project currently underway to establish what is known about decontamination of buildings and people and the procedures and protocols used to determine when and how people or buildings are considered ''clean'' following decontamination. To fulfill this objective, the study systematically examined reported decontamination experiences to determine what procedures and protocols are currently employed for decontamination, the timeframe involved to initiate and complete the decontamination process, how the contaminants were identified, the problems encountered during the decontamination process, how response efforts of agencies were coordinated, and the perceived social psychological effects on people who weremore » decontaminated or who participated in the decontamination process. Findings and recommendations from the study are intended to aid decision-making and to improve the basis for determining appropriate decontamination protocols for recovery planners and policy makers for responding to chemical and biological events.« less

Establishing a novel single-copy primer-internal intron-spanning PCR (spiPCR) procedure for the direct detection of gene doping.

PubMed

Beiter, Thomas; Zimmermann, Martina; Fragasso, Annunziata; Armeanu, Sorin; Lauer, Ulrich M; Bitzer, Michael; Su, Hua; Young, William L; Niess, Andreas M; Simon, Perikles

2008-01-01

So far, the abuse of gene transfer technology in sport, so-called gene doping, is undetectable. However, recent studies in somatic gene therapy indicate that long-term presence of transgenic DNA (tDNA) following various gene transfer protocols can be found in DNA isolated from whole blood using conventional PCR protocols. Application of these protocols for the direct detection of gene doping would require almost complete knowledge about the sequence of the genetic information that has been transferred. Here, we develop and describe the novel single-copy primer-internal intron-spanning PCR (spiPCR) procedure that overcomes this difficulty. Apart from the interesting perspectives that this spiPCR procedure offers in the fight against gene doping, this technology could also be of interest in biodistribution and biosafety studies for gene therapeutic applications.

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 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.

Did low tube voltage CT combined with low contrast media burden protocols accomplish the goal of "double low" for patients? An overview of applications in vessels and abdominal parenchymal organs over the past 5 years.

PubMed

Shen, Yaqi; Hu, Xuemei; Zou, Xianlun; Zhu, Di; Li, Zhen; Hu, Daoyu

2016-09-01

Imaging communities have already reached a consensus that the radiation dose of computed tomography (CT) should be reduced as much as reasonably achievable to lower population risks. Increasing attention is being paid to iodinated contrast media (CM) induced nephrotoxicity (CIN); a decrease in the intake of iodinated CM is required by increasingly more radiologists. Theoretically, the radiation dose varies with the tube current time and square of the tube voltage, with higher iodine contrast at low photon energies (Huda et al. [2000] Radiology, 21 7, 430-435).The use of low tube voltage is a promising strategy to reduce both the radiation dose and CM burden. The term 'double low' has been coined to describe scanning protocols that reduce radiation dose and iodine intake synchronously. These protocols are becoming increasingly popular in the clinical setting. The aim of this review was to describe all original studies using the 'double low' strategy in the last 5 years. We searched an online electronic database (PubMed) from January 2011 to December 2015 for original studies published on the relationship of low tube voltage with low radiation dose and low iodine contrast media burden in patients undergoing CT scans. Studies that failed to reduce radiation dose or iodine CM burden were excluded in this study. Thirty-seven studies aimed at reducing radiation dose using low tube voltage combined with iodine CM reduced protocols were included in this study. Most studies evaluated conditions associated with arteries. Four were cerebral and neck computed tomography angiography (CTA) studies, 15 were pulmonary CTA (pCTA) and coronary CTA (cCTA) studies, one concerned myocardial perfusion, five studies focused on the thoracic and abdominal aorta, and one investigated renal arteries. Three studies consisted of CT venography (CTV) of the pelvis and lower extremities. Six publications examined the liver, and two focused on the kidney. Overall, this review demonstrates that the low tube voltage CT protocol is a powerful tool to reduce the radiation dose in CTA, especially with pCTA and cCTA. © 2016 John Wiley & Sons Ltd.

Routing Protocols for Underwater Wireless Sensor Networks: Taxonomy, Research Challenges, Routing Strategies and Future Directions.

PubMed

Khan, Anwar; Ali, Ihsan; Ghani, Abdullah; Khan, Nawsher; Alsaqer, Mohammed; Rahman, Atiq Ur; Mahmood, Hasan

2018-05-18

Recent research in underwater wireless sensor networks (UWSNs) has gained the attention of researchers in academia and industry for a number of applications. They include disaster and earthquake prediction, water quality and environment monitoring, leakage and mine detection, military surveillance and underwater navigation. However, the aquatic medium is associated with a number of limitations and challenges: long multipath delay, high interference and noise, harsh environment, low bandwidth and limited battery life of the sensor nodes. These challenges demand research techniques and strategies to be overcome in an efficient and effective fashion. The design of routing protocols for UWSNs is one of the promising solutions to cope with these challenges. This paper presents a survey of the routing protocols for UWSNs. For the ease of description, the addressed routing protocols are classified into two groups: localization-based and localization-free protocols. These groups are further subdivided according to the problems they address or the major parameters they consider during routing. Unlike the existing surveys, this survey considers only the latest and state-of-the-art routing protocols. In addition, every protocol is described in terms of its routing strategy and the problem it addresses and solves. The merit(s) of each protocol is (are) highlighted along with the cost. A description of the protocols in this fashion has a number of advantages for researchers, as compared to the existing surveys. Firstly, the description of the routing strategy of each protocol makes its routing operation easily understandable. Secondly, the demerit(s) of a protocol provides (provide) insight into overcoming its flaw(s) in future investigation. This, in turn, leads to the foundation of new protocols that are more intelligent, robust and efficient with respect to the desired parameters. Thirdly, a protocol can be selected for the appropriate application based on its described merit(s). Finally, open challenges and research directions are presented for future investigation.

Routing Protocols for Underwater Wireless Sensor Networks: Taxonomy, Research Challenges, Routing Strategies and Future Directions

PubMed Central

Ghani, Abdullah; Alsaqer, Mohammed; Rahman, Atiq Ur; Mahmood, Hasan

2018-01-01

Recent research in underwater wireless sensor networks (UWSNs) has gained the attention of researchers in academia and industry for a number of applications. They include disaster and earthquake prediction, water quality and environment monitoring, leakage and mine detection, military surveillance and underwater navigation. However, the aquatic medium is associated with a number of limitations and challenges: long multipath delay, high interference and noise, harsh environment, low bandwidth and limited battery life of the sensor nodes. These challenges demand research techniques and strategies to be overcome in an efficient and effective fashion. The design of routing protocols for UWSNs is one of the promising solutions to cope with these challenges. This paper presents a survey of the routing protocols for UWSNs. For the ease of description, the addressed routing protocols are classified into two groups: localization-based and localization-free protocols. These groups are further subdivided according to the problems they address or the major parameters they consider during routing. Unlike the existing surveys, this survey considers only the latest and state-of-the-art routing protocols. In addition, every protocol is described in terms of its routing strategy and the problem it addresses and solves. The merit(s) of each protocol is (are) highlighted along with the cost. A description of the protocols in this fashion has a number of advantages for researchers, as compared to the existing surveys. Firstly, the description of the routing strategy of each protocol makes its routing operation easily understandable. Secondly, the demerit(s) of a protocol provides (provide) insight into overcoming its flaw(s) in future investigation. This, in turn, leads to the foundation of new protocols that are more intelligent, robust and efficient with respect to the desired parameters. Thirdly, a protocol can be selected for the appropriate application based on its described merit(s). Finally, open challenges and research directions are presented for future investigation. PMID:29783686

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…

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.

On Robust Key Agreement Based on Public Key Authentication

NASA Astrophysics Data System (ADS)

Hao, Feng

We describe two new attacks on the HMQV protocol. The first attack raises a serious question on the basic definition of "authentication" in HMQV, while the second attack is generally applicable to many other protocols. In addition, we present a new authenticated key agreement protocol called YAK. Our approach is to depend on well-established techniques such as Schnorr's signature. Among all the related protocols, YAK appears to be the simplest so far. We believe simplicity is an important engineering principle.

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.

The characteristics of national health initiatives promoting earlier cancer diagnosis among adult populations: a systematic review protocol

PubMed Central

Calanzani, Natalia; Weller, David; Campbell, Christine

2017-01-01

Introduction The increasing burden of cancer morbidity and mortality has led to the development of national health initiatives to promote earlier cancer diagnosis and improve cancer survival. This protocol describes a systematic review aiming to identify the evidence about such initiatives among the adult population. We will describe their components, stakeholders and target populations, and summarise their outcomes. Methods and analysis We will search databases and websites for peer-reviewed publications and grey literature on national health initiatives in high-income countries as defined by the World Bank. Quantitative, qualitative and mixed-methods studies will be included and assessed for their methodological quality. Study selection, quality assessment and data extraction will be carried out independently by two reviewers. Narrative synthesis will be used to analyse the findings. Ethics and dissemination This systematic review analyses secondary data and ethical approval is not required. Review findings will be helpful to researchers, policy makers, governments and other key stakeholders developing similar initiatives and assessing cancer outcomes. The results will be submitted to a peer-reviewed journal in order to reach a diverse group of healthcare professionals, researchers and policy makers. This systematic review protocol is registered at PROSPERO (CRD42016047233). PMID:28698336

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.

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

PubMed

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

2017-06-24

The use of peer support programmes to help workers experiencing potentially traumatic events (PTE) has increased in high-risk organisations in the last decades. However, the scientific evidence of its effectiveness is still very limited. This paper aims to describe the protocol of a prospective cohort study that assesses the efficacy of a peer support programme among youth social services employees exposed to a PTE at work on psychological well-being, work functioning and needs of support. This is a mixed-methods prospective study that will examine workers' evolution four times over a 12-month period in Canada. This study involves: (1) quantitative data obtained through self-administrated questionnaires among 222 workers, and (2) qualitative in-depth interviews with a subsample of 45 workers. This study will compare findings from a cohort who received the support of a peer following a PTE (peer support-experimental protocol) as part of the experimental protocol of the Montreal Youth Social Services-University Institute (MYSS-UI), the second group of workers did not ask for the peer support (no peer support-experimental protocol) but was part of MYSS-UI, and the third group received standard organisational support from the Monteregie Youth Social Services (MYSS) (standard organisational protocol). The protocol and informed consent form complied with the ethics guidelines of the MYSS-UI. The Research Ethics Board of MYSS-UI and MYSS reviewed and accepted the protocol as required. The results of the study will be published in peer-reviewed journals, presented at research and general public conferences, disseminated via a public report for the institute that funded the project and for all workers. Results of this study will influence decision making regarding intervention policies following PTE and peer support interventions may be expanded throughout the youth social services in Canada and worldwide. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Description of the Protocols for Randomized Controlled Trials on Cancer Drugs Conducted in Spain (1999–2003)

PubMed Central

Bonfill, Xavier; Ballesteros, Mónica; Gich, Ignasi; Serrano, María Antonia; García López, Fernando; Urrútia, Gerard

2013-01-01

Objective To describe the characteristics of randomized controlled clinical trials (RCT) on cancer drugs conducted in Spain between 1999 and 2003 based on their protocols. Methods We conducted an observational retrospective cohort study to identify the protocols of RCTs on cancer drugs authorized by the Agencia Española del Medicamento y Productos Sanitarios (AEMPS) (Spanish Agency for Medicines and Medical Devices) during 1999-2003. A descriptive analysis was completed and the association between variables based on the study setting and sponsorship were assessed. Results We identified a total of 303 protocols, which included 176,835 potentially eligible patients. Three-quarter of the studies were internationally-based, 61.7% were phase III, and 76.2% were sponsored by pharmaceutical companies. The most frequently assessed outcomes were response rate (24.7%), overall survival (20.7%), and progression-free survival (14.5%). Of all protocols, 10.6% intended to include more than 1000 patients (mean: 2442, SD: 2724). Compared with their national counterparts, internationally-based studies were significantly larger (p<0.001) and were more likely to implement centralized randomization (p<0.001), blinding of the intervention (p<0.001), and survival as primary outcome (p<0.001). Additionally, most internationally-based studies were sponsored by pharmaceutical companies (p<0.01). In a high percentage of protocols, the available information was not explicit enough to assess the validity of each trial. Compared to other European countries, the proportion of Spanish cancer drugs protocols registered at www.clinicaltrials.gov (7%) was lower. Conclusion RCTs on cancer drugs conducted in Spain between 1999 and 2003 were more likely to be promoted by pharmaceutical companies rather than by non-profit national groups. The former were more often part of international studies, which generally had better methodological quality than national ones. There are some worldwide on-going initiatives that aim to increase the transparency and quality of future research. PMID:24236154

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

Improving the quality of perinatal mental health: a health visitor-led protocol.

PubMed

Lewis, Anne; Ilot, Irene; Lekka, Chrysanthi; Oluboyede, Yemi

2011-02-01

The mental health of mothers is of significant concern to community practitioners. This paper reports on a case study exploring the success factors of a well established, health visitor-led protocol to identify and treat women with mild to moderate depression. Data were collected through interviews with a purposive sample of 12 community practitioners, a focus group of four health visitors and observation of a multidisciplinary steering group meeting. The protocol was described as an evidence-based tool and safety net that could be used flexibly to support clinical judgments and tailored to individual needs. Success factors included frontline clinician engagement and ownership, continuity of leadership to drive development and maintain momentum, comprehensive and on-going staff training, and strategic support for the protocol as a quality indicator at a time of organisational change. Quality and clinical leadership are continuing policy priorities. The protocol enabled frontline staff to lead a service innovation, providing a standardised multiprofessional approach to women's mental health needs through effective support, advice and treatment that can be measured and quality assured.

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.

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.

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'.

Agreement protocol between the CNES (National French Space Study Center) and the Swedish Space Commission

NASA Technical Reports Server (NTRS)

1979-01-01

The detailed arrangements made between France and Sweden to develop a satellite (and the associated receiving stations) which will perform systematic, repetitive observations of land masses, with the purpose of terrestrial resource exploration are described.

21 CFR 58.35 - Quality assurance unit.

Code of Federal Regulations, 2013 CFR

2013-04-01

... the corrective actions taken. (5) Determine that no deviations from approved protocols or standard operating procedures were made without proper authorization and documentation. (6) Review the final study report to assure that such report accurately describes the methods and standard operating procedures, and...

21 CFR 58.35 - Quality assurance unit.

Code of Federal Regulations, 2010 CFR

2010-04-01

... the corrective actions taken. (5) Determine that no deviations from approved protocols or standard operating procedures were made without proper authorization and documentation. (6) Review the final study report to assure that such report accurately describes the methods and standard operating procedures, and...

21 CFR 58.35 - Quality assurance unit.

Code of Federal Regulations, 2012 CFR

2012-04-01

... the corrective actions taken. (5) Determine that no deviations from approved protocols or standard operating procedures were made without proper authorization and documentation. (6) Review the final study report to assure that such report accurately describes the methods and standard operating procedures, and...

21 CFR 58.35 - Quality assurance unit.

Code of Federal Regulations, 2011 CFR

2011-04-01

... the corrective actions taken. (5) Determine that no deviations from approved protocols or standard operating procedures were made without proper authorization and documentation. (6) Review the final study report to assure that such report accurately describes the methods and standard operating procedures, and...

21 CFR 58.35 - Quality assurance unit.

Code of Federal Regulations, 2014 CFR

2014-04-01

... the corrective actions taken. (5) Determine that no deviations from approved protocols or standard operating procedures were made without proper authorization and documentation. (6) Review the final study report to assure that such report accurately describes the methods and standard operating procedures, and...

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.

78 FR 12764 - Draft Office of Health Assessment and Translation Approach for Systematic Review and Evidence...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-25

... Approach--February 2013 might be needed, OHAT plans to apply it to two case-study evaluations. One case... Availability: Draft OHAT Approach--February 2013 will be available by February 26, 2013, and case-study... framework, describe the contents in the case-study protocols, and respond to questions from the public on...

Echocardiographic evaluation after pediatric heart transplant in Chile: initial application of a functional protocol with global longitudinal strain.

PubMed

Trincado, Claudia; Molina, Víctor; Urcelay, Gonzalo; Dellepiane, Paulina

2018-02-01

The echocardiographic evaluation of patients after heart transplantation is a useful tool. However, it is still necessary to define an optimal follow-up protocol. To describe the results of the application of a functional echocardiographic protocol in patients being followed after pediatric heart transplantation. Alls patients being followed at our institution after pediatric heart transplantation underwent an echocardiographic examination with a functional protocol that included global longitudinal strain. Contemporaneous endomyocardial biopsy results and hemodynamic data were recorded. 9 patients were evaluated with our echocardiographic functional protocol. Of these patients, only 1 showed systolic left ventricular dysfunction according to classic parameters. However, almost all patients had an abnormal global longitudinal strain. Right ventricular systolic dysfunction was observed in all patients. No epidodes of moderate to severe rejectiom were recorded. No correlation was observed between these parameters and pulmonary artery pressure. Subclinical biventricular systolic dysfunction was observed in the majority of the patients in this study. No association with rejection episodes or pulmonary hypertension was observed, which may be related to the absence of moderate or severe rejection episodes during the study period, and to the small sample size. Long term follow-up of these patients may better define the clinical relevance of our findings.

Tissue Sampling Guides for Porcine Biomedical Models.

PubMed

Albl, Barbara; Haesner, Serena; Braun-Reichhart, Christina; Streckel, Elisabeth; Renner, Simone; Seeliger, Frank; Wolf, Eckhard; Wanke, Rüdiger; Blutke, Andreas

2016-04-01

This article provides guidelines for organ and tissue sampling adapted to porcine animal models in translational medical research. Detailed protocols for the determination of sampling locations and numbers as well as recommendations on the orientation, size, and trimming direction of samples from ∼50 different porcine organs and tissues are provided in the Supplementary Material. The proposed sampling protocols include the generation of samples suitable for subsequent qualitative and quantitative analyses, including cryohistology, paraffin, and plastic histology; immunohistochemistry;in situhybridization; electron microscopy; and quantitative stereology as well as molecular analyses of DNA, RNA, proteins, metabolites, and electrolytes. With regard to the planned extent of sampling efforts, time, and personnel expenses, and dependent upon the scheduled analyses, different protocols are provided. These protocols are adjusted for (I) routine screenings, as used in general toxicity studies or in analyses of gene expression patterns or histopathological organ alterations, (II) advanced analyses of single organs/tissues, and (III) large-scale sampling procedures to be applied in biobank projects. Providing a robust reference for studies of porcine models, the described protocols will ensure the efficiency of sampling, the systematic recovery of high-quality samples representing the entire organ or tissue as well as the intra-/interstudy comparability and reproducibility of results. © The Author(s) 2016.

In situ hybridization for the detection of rust fungi in paraffin embedded plant tissue sections.

PubMed

Ellison, Mitchell A; McMahon, Michael B; Bonde, Morris R; Palmer, Cristi L; Luster, Douglas G

2016-01-01

Rust fungi are obligate pathogens with multiple life stages often including different spore types and multiple plant hosts. While individual rust pathogens are often associated with specific plants, a wide range of plant species are infected with rust fungi. To study the interactions between these important pathogenic fungi and their host plants, one must be able to differentiate fungal tissue from plant tissue. This can be accomplished using the In situ hybridization (ISH) protocol described here. To validate reproducibility using the ISH protocol, samples of Chrysanthemum × morifolium infected with Puccinia horiana, Gladiolus × hortulanus infected with Uromyces transversalis and Glycine max infected with Phakopsora pachyrhizi were tested alongside uninfected leaf tissue samples. The results of these tests show that this technique clearly distinguishes between rust pathogens and their respective host plant tissues. This ISH protocol is applicable to rust fungi and potentially other plant pathogenic fungi as well. It has been shown here that this protocol can be applied to pathogens from different genera of rust fungi with no background staining of plant tissue. We encourage the use of this protocol for the study of plant pathogenic fungi in paraffin embedded sections of host plant tissue.

Improvements in Clinical Trials Information Will Improve the Reproductive Health and Fertility of Cancer Patients.

PubMed

Dauti, Angela; Gerstl, Brigitte; Chong, Serena; Chisholm, Orin; Anazodo, Antoinette

2017-06-01

There are a number of barriers that result in cancer patients not being referred for oncofertility care, which include knowledge about reproductive risks of antineoplastic agents. Without this information, clinicians do not always make recommendations for oncofertility care. The objective of this study was to describe the level of reproductive information and recommendations that clinicians have available in clinical trial protocols regarding oncofertility management and follow-up, and the information that patients may receive in clinical trials patient information sheets or consent forms. A literature review of the 71 antineoplastic drugs included in the 68 clinical trial protocols showed that 68% of the antineoplastic drugs had gonadotoxic animal data, 32% had gonadotoxic human data, 83% had teratogenic animal data, and 32% had teratogenic human data. When the clinical trial protocols were reviewed, only 22% of the protocols reported the teratogenic risks and 32% of the protocols reported the gonadotoxic risk. Only 56% of phase 3 protocols had gonadotoxic information and 13% of phase 3 protocols had teratogenic information. Nine percent of the protocols provided fertility preservation recommendations and 4% provided reproductive information in the follow-up and survivorship period. Twenty-six percent had a section in the clinical trials protocol, which identified oncofertility information easily. When gonadotoxic and teratogenic effects of treatment were known, they were not consistently included in the clinical trial protocols and the lack of data for new drugs was not reported. Very few protocols gave recommendations for oncofertility management and follow-up following the completion of cancer treatment. The research team proposes a number of recommendations that should be required for clinicians and pharmaceutical companies developing new trials.

Embedding, serial sectioning and staining of zebrafish embryos using JB-4 resin.

PubMed

Sullivan-Brown, Jessica; Bisher, Margaret E; Burdine, Rebecca D

2011-01-01

Histological techniques are critical for observing tissue and cellular morphology. In this paper, we outline our protocol for embedding, serial sectioning, staining and visualizing zebrafish embryos embedded in JB-4 plastic resin-a glycol methacrylate-based medium that results in excellent preservation of tissue morphology. In addition, we describe our procedures for staining plastic sections with toluidine blue or hematoxylin and eosin, and show how to couple these stains with whole-mount RNA in situ hybridization. We also describe how to maintain and visualize immunofluorescence and EGFP signals in JB-4 resin. The protocol we outline-from embryo preparation, embedding, sectioning and staining to visualization-can be accomplished in 3 d. Overall, we reinforce that plastic embedding can provide higher resolution of cellular details and is a valuable tool for cellular and morphological studies in zebrafish.

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

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

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.

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.

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.

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.

Patient-Centred Innovations for Persons with Multimorbidity: funded evaluation protocol.

PubMed

Stewart, Moira; Fortin, Martin

2017-05-09

The high prevalence of multimorbidity necessitates rethinking of the health care system. The overarching goal of the Patient-Centred Innovations for Persons with Multimorbidity program is to build on existing structures and find and evaluate patient-centred innovations relevant to multimorbidity. We describe the protocol for a proposed multijurisdictional (Quebec and Ontario) concurrent triangulation mixed-methods study. In both provinces, a qualitative descriptive study will be used to explore innovations in patient-centred multimorbidity care. Two randomized controlled trials, 1 in either province, will evaluate the innovations in a wait-list-controlled design using patient-reported outcomes. An additional control group, matched on age, sex, enrolment/index date (± 3 mo) and propensity score, will be created with the use of health administrative data. Patients will be 18-80 years of age and will have 3 or more chronic conditions. The innovations will have elements of relevance to multimorbidity care, patient-centred partnerships and integration of care. The primary outcome measures will be 2 patient-reported outcomes: patient education and self-efficacy. Secondary outcomes will include patient-reported health status, quality of life, psychological distress and health behaviours, and costs of care. This protocol describes a mixed-method study in 2 jurisdictions. The studies will answer the questions of what innovations work and how they work for patients, health care professionals and policy-makers. Trial registration: ClinicalTrials.gov, no NCT02789800 (Quebec Trial), NCT02742597 (Ontario Trial). Copyright 2017, Joule Inc. or its licensors.

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 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.

Behavioral Interventions to Prevent or Delay Dementia: Protocol for a Randomized Comparative Effectiveness Study.

PubMed

Smith, Glenn; Chandler, Melanie; Locke, Dona Ec; Fields, Julie; Phatak, Vaishali; Crook, Julia; Hanna, Sherrie; Lunde, Angela; Morris, Miranda; Graff-Radford, Michelle; Hughes, Christine A; Lepore, Susan; Cuc, Andrea; Caselli, Maria; Hurst, Duane; Wethe, Jennifer; Francone, Andrea; Eilertsen, Jeanne; Lucas, Pauline; Hoffman Snyder, Charlene; Kuang, LeeAnn; Becker, Marigrace; Dean, Pamela; Diehl, Nancy; Lofquist, Marvin; Vanderhook, Shirley; Myles, Diana; Cochran, Denise

2017-11-27

Currently, people at risk for dementia and their caregivers are confronted with confusing choices about what behavioral interventions are most effective. The objective of this study is to determine which empirically supported behavioral interventions most impact the outcomes highly valued by patients with mild cognitive impairment and their partners. This protocol describes a comparative effectiveness trial targeting 300 participants with mild cognitive impairment and their study partners. The trial is being conducted at the Mayo Clinic campuses in Arizona, Florida, Minnesota, and the University of Washington in Seattle. The study examines the contribution of five behavioral interventions (yoga, memory compensation training, computerized cognitive training, support groups, and wellness education) on primary outcomes of participant and partner quality of life and self-efficacy. In this unique 10-day multicomponent intervention, groups of couples were randomized to have one of the five interventions withheld while receiving the other four. Although the longitudinal follow-up is still under way, enrollment results are available and reported. In total, 272 couples have been enrolled in the trial and follow-up visits continue. Outcomes will be assessed at the end-of-intervention and 6-, 12-, and 18-month follow-ups. We anticipate reporting on our primary and secondary outcomes across time points in the next 2 years. This paper describes the protocol for a randomized comparative effectiveness study of behavioral interventions to prevent or delay dementia. We describe of the rationale, design, power analysis, and analysis plan. Also because enrollment is complete and we are in follow-up phases of the study, we have included enrollment data from the trial.  ClinicalTrials.gov NCT02265757; http://clinicaltrials.gov/ctsshow/ NCT02265757 (Archived by WebCite at http://www.webcitation.org/6ueRfwSYv). ©Glenn Smith, Melanie Chandler, Dona EC Locke, Julie Fields, Vaishali Phatak, Julia Crook, Sherrie Hanna, Angela Lunde, Miranda Morris, Michelle Graff-Radford, Christine A Hughes, Susan Lepore, Andrea Cuc, Maria Caselli, Duane Hurst, Jennifer Wethe, Andrea Francone, Jeanne Eilertsen, Pauline Lucas, Charlene Hoffman Snyder, LeeAnn Kuang, Marigrace Becker, Pamela Dean, Nancy Diehl, Marvin Lofquist, Shirley Vanderhook, Diana Myles, Denise Cochran. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 27.11.2017.

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.

Behavioral Interventions to Prevent or Delay Dementia: Protocol for a Randomized Comparative Effectiveness Study

PubMed Central

Chandler, Melanie; Locke, Dona EC; Fields, Julie; Phatak, Vaishali; Crook, Julia; Hanna, Sherrie; Lunde, Angela; Morris, Miranda; Graff-Radford, Michelle; Hughes, Christine A; Lepore, Susan; Cuc, Andrea; Caselli, Maria; Hurst, Duane; Wethe, Jennifer; Francone, Andrea; Eilertsen, Jeanne; Lucas, Pauline; Hoffman Snyder, Charlene; Kuang, LeeAnn; Becker, Marigrace; Dean, Pamela; Diehl, Nancy; Lofquist, Marvin; Vanderhook, Shirley; Myles, Diana; Cochran, Denise

2017-01-01

Background Currently, people at risk for dementia and their caregivers are confronted with confusing choices about what behavioral interventions are most effective. Objective The objective of this study is to determine which empirically supported behavioral interventions most impact the outcomes highly valued by patients with mild cognitive impairment and their partners. Methods This protocol describes a comparative effectiveness trial targeting 300 participants with mild cognitive impairment and their study partners. The trial is being conducted at the Mayo Clinic campuses in Arizona, Florida, Minnesota, and the University of Washington in Seattle. The study examines the contribution of five behavioral interventions (yoga, memory compensation training, computerized cognitive training, support groups, and wellness education) on primary outcomes of participant and partner quality of life and self-efficacy. In this unique 10-day multicomponent intervention, groups of couples were randomized to have one of the five interventions withheld while receiving the other four. Although the longitudinal follow-up is still under way, enrollment results are available and reported. Results In total, 272 couples have been enrolled in the trial and follow-up visits continue. Outcomes will be assessed at the end-of-intervention and 6-, 12-, and 18-month follow-ups. We anticipate reporting on our primary and secondary outcomes across time points in the next 2 years. Conclusions This paper describes the protocol for a randomized comparative effectiveness study of behavioral interventions to prevent or delay dementia. We describe of the rationale, design, power analysis, and analysis plan. Also because enrollment is complete and we are in follow-up phases of the study, we have included enrollment data from the trial. Trial Registration  ClinicalTrials.gov NCT02265757; http://clinicaltrials.gov/ctsshow/ NCT02265757 (Archived by WebCite at http://www.webcitation.org/6ueRfwSYv) PMID:29180344

DATA QUALITY OBJECTIVES AND STATISTICAL DESIGN SUPPORT FOR DEVELOPMENT OF A MONITORING PROTOCOL FOR RECREATIONAL WATERS

EPA Science Inventory

The purpose of this report is to describe the outputs of the Data Quality Objectives (DQOs) Process and discussions about developing a statistical design that will be used to implement the research study of recreational beach waters.

Dientamoeba fragilis DNA detection in Enterobius vermicularis eggs

PubMed Central

Ögren, Jessica; Dienus, Olaf; Löfgren, Sture; Iveroth, Peter; Matussek, Andreas

2013-01-01

Dientamoeba fragilis is an intestinal protozoan suspected of causing gastrointestinal symptoms, and its mode of transmission is unknown, although first described almost a century ago. A hypothesis is that Enterobius vermicularis is a vector for D. fragilis, and recently, D. fragilis DNA was detected within surface-sterilized eggs of E. vermicularis. Using real-time PCR, we detected D. fragilis DNA in 18 (85%) of 21 samples of E. vermicularis eggs collected from patients harbouring D. fragilis in faeces. This finding supports the hypothesis that E. vermicularis may have an important role in the transmission of D. fragilis. This paper describes a protocol to wash and surface-sterilize E. vermicularis eggs, with the aim of showing presence of both E. vermicularis and D. fragilis specific DNA within, and the results from 20 co-infected patients. The study has merit as a confirmatory study of the trials by Röser et al. (2013), and includes improvements of the protocol. PMID:23893951

Nuclear transfer to study the nuclear reprogramming of human stem cells.

PubMed

Saito, Shigeo; Sawai, Ken; Murayama, Yoshinobu; Fukuda, Keiichi; Yokoyama, Kazunari

2008-01-01

Research of stem cells will enable us to understand the development and function of tissues and organs in mammals. The ability to induce regeneration of new tissues from embryonic stem (ES) cells derived from cloned blastocysts via nuclear transfer can be expected in the not-too-distant future. The fact that there is no way except nuclear cloning for the return of differentiated cells to undifferentiated cells remains an interesting problem to be solved. We describe protocols for the production of cloned calves from bovine ES cells to study nuclear reprogramming ability of stem cells. The frequency of term pregnancies for blastocysts from ES cells is higher than those of early pregnancies and maintained pregnancies after nuclear transfer with bovine somatic cells. We also describe protocols for gene introduction into bovine ES cells in vitro, particularly the human leukocyte antigens (HLA). Bovine ES cells provide a powerful tool for the generation of transgenic clonal offspring. This technique, when perfected for humans, may be critical for neural stem cell transplantation.

Perceptual attributes for the comparison of head-related transfer functions.

PubMed

Simon, Laurent S R; Zacharov, Nick; Katz, Brian F G

2016-11-01

The benefit of using individual head-related transfer functions (HRTFs) in binaural audio is well documented with regards to improving localization precision. However, with the increased use of binaural audio in more complex scene renderings, cognitive studies, and virtual and augmented reality simulations, the perceptual impact of HRTF selection may go beyond simple localization. In this study, the authors develop a list of attributes which qualify the perceived differences between HRTFs, providing a qualitative understanding of the perceptual variance of non-individual binaural renderings. The list of attributes was designed using a Consensus Vocabulary Protocol elicitation method. Participants followed an Individual Vocabulary Protocol elicitation procedure, describing the perceived differences between binaural stimuli based on binauralized extracts of multichannel productions. This was followed by an automated lexical reduction and a series of consensus group meetings during which participants agreed on a list of relevant attributes. Finally, the proposed list of attributes was then evaluated through a listening test, leading to eight valid perceptual attributes for describing the perceptual dimensions affected by HRTF set variations.

Outcome and toxicity associated with a dose-intensified, maintenance-free CHOP-based chemotherapy protocol in canine lymphoma: 130 cases.

PubMed

Sorenmo, Karin; Overley, B; Krick, E; Ferrara, T; LaBlanc, A; Shofer, F

2010-09-01

A dose-intensified/dose-dense chemotherapy protocol for canine lymphoma was designed and implemented at the Veterinary Hospital of the University of Pennsylvania. In this study, we describe the clinical characteristics, prognostic factors, efficacy and toxicity in 130 dogs treated with this protocol. The majority of the dogs had advanced stage disease (63.1% stage V) and sub-stage b (58.5%). The median time to progression (TTP) and lymphoma-specific survival were 219 and 323 days, respectively. These results are similar to previous less dose-intense protocols. Sub-stage was a significant negative prognostic factor for survival. The incidence of toxicity was high; 53.9 and 45% of the dogs needed dose reductions and treatment delays, respectively. Dogs that required dose reductions and treatment delays had significantly longer TTP and lymphoma-specific survival times. These results suggest that dose density is important, but likely relative, and needs to be adjusted according to the individual patient's toxicity for optimal outcome.

Using the emergency department as a screening site for high blood pressure. A method for improving hypertension detection and appropriate referral.

PubMed

Mamon, J; Green, L; Levine, D M; Gibson, G; Gurley, H T

1987-08-01

This study describes the development and testing of a high blood pressure protocol for use in emergency departments (ED) to enhance detection of those patients appropriate for subsequent referral. The protocol involves two serial blood pressure measurements and a patient interview to determine: 1) previous history of high blood pressure (HBP), 2) treatment in past year for HBP, and 3) usual source of medical care. The accuracy of patient reporting was validated by comparison with the patients' hospital record (reflecting outpatient and inpatient visits). Results indicate that these self-reports have high levels of sensitivity (range 90-100%) and specificity (range 79-96%). Use of the additional patient information increased the sensitivity of the screening protocol in identifying when and where a patient should be referred. Use of this methodology indicates that the protocol is a simple and effective method for HBP screening. The findings also suggest that the ED is an ideal site for screening the "hard-to-reach" hypertensive population.

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 ...

Cognitive-Behavioral Therapy for Depression in an Older Gay Man: A Clinical Case Study

PubMed Central

Satterfield, Jason M.; Crabb, Rebecca

2012-01-01

Although strong evidence supports cognitive-behavioral therapy for late-life depression and depression in racial and ethnic minorities, there are no empirical studies on the treatment of depression in older sexual minorities. Three distinct literatures were tapped to create a depression treatment protocol for an older gay male. Interventions were deduced from the late-life depression literature, culturally adapted CBT protocols for racial minorities, and the emerging social and developmental psychological theories for lesbian, gay, and bisexual populations. Specific treatment interventions, processes, and outcomes are described to illustrate how these literatures may be used to provide more culturally appropriate and effective health care for the growing, older sexual minority population. PMID:23144559

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

How to Prepare SMC and BMC-like Compounds to Perform Relevant Rheological Experiments?

NASA Astrophysics Data System (ADS)

Guiraud, Olivier; Dumont, Pierre J. J.; Orgéas, Laurent

2013-04-01

The study of the rheology of injected or compression moulded compounds like SMC or BMC is made particularly difficult by the high content and the intricate arrangement of their fibrous reinforcement. For these two types of compounds, inappropriate rheological testing protocols and rheometers are often used, which leads to a very large scatter of the experimental data. This study describes specific sampling and specimen's preparation methods, as well as dedicated rheometry devices to test their rheology. Following the proposed protocols, it is possible to obtain rheological measurements showing low scatter of the recorded stress values: about ±10% for SMC and about ±15% for BMC-like compounds.

A framework for the definition of standardized protocols for measuring upper-extremity kinematics.

PubMed

Kontaxis, A; Cutti, A G; Johnson, G R; Veeger, H E J

2009-03-01

Increasing interest in upper extremity biomechanics has led to closer investigations of both segment movements and detailed joint motion. Unfortunately, conceptual and practical differences in the motion analysis protocols used up to date reduce compatibility for post data and cross validation analysis and so weaken the body of knowledge. This difficulty highlights a need for standardised protocols, each addressing a set of questions of comparable content. The aim of this work is therefore to open a discussion and propose a flexible framework to support: (1) the definition of standardised protocols, (2) a standardised description of these protocols, and (3) the formulation of general recommendations. Proposal of a framework for the definition of standardized protocols. The framework is composed by two nested flowcharts. The first defines what a motion analysis protocol is by pointing out its role in a motion analysis study. The second flowchart describes the steps to build a protocol, which requires decisions on the joints or segments to be investigated and the description of their mechanical equivalent model, the definition of the anatomical or functional coordinate frames, the choice of marker or sensor configuration and the validity of their use, the definition of the activities to be measured and the refinements that can be applied to the final measurements. Finally, general recommendations are proposed for each of the steps based on the current literature, and open issues are highlighted for future investigation and standardisation. Standardisation of motion analysis protocols is urgent. The proposed framework can guide this process through the rationalisation of the approach.

Colon cleansing protocol in children: research conditions vs. clinical practice.

PubMed

Elitsur, Yoram; Balfaqih, Yaslam; Preston, Deborah

2018-04-01

 Colon preparation rates are the limiting factor for a successful diagnostic colonoscopy in children. Different colon cleansing protocols have been published for use in children. Unfortunately, the applicability of those published research protocols has not been formally evaluated in routine clinical practice. We investigated the success rate of our previously published colon cleansing protocol as utilized in our clinical practice.  This was a retrospective study. In the clinical practice, the colon cleansing protocol included PEG-3350 at a dose of 2 g/kg/day plus Dulcolax (Bisacodyl, Boehringer Ingelheim, TX USA) 5 mg/day for 2 days. Adequate colon preparation was graded between 1 - 5, as previously described, and grade ≥ 4.0 was considered an adequate preparation. Patients were instructed to complete a questionnaire that included PEG-3350 dose, number of stools per day, consistency of each stool, and side effects (vomiting, abdominal pain). Clinical and endoscopic results were compared between the protocol under research conditions and routine practice.  The success rate of the colon preparation in our clinical practice was similar to the results observed under our research protocol (75 % vs. 73.6 %). Moreover, the total number of stools, stool consistency, and the intubation rate of the terminal ileum were also similar. We concluded, that in our experience, the colon cleansing protocol used under research conditions was effective and appropriate for use in routine clinical practice.  We recommend testing each new protocol under the routine conditions of clinical practice to confirm its applicability for general practitioners.

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.

Primary Culture System for Germ Cells from Caenorhabditis elegans Tumorous Germline Mutants

PubMed Central

Vagasi, Alexandra S.; Rahman, Mohammad M.; Chaudhari, Snehal N.; Kipreos, Edward T.

2017-01-01

The Caenorhabditis elegans germ line is an important model system for the study of germ stem cells. Wild-type C. elegans germ cells are syncytial and therefore cannot be isolated in in vitro cultures. In contrast, the germ cells from tumorous mutants can be fully cellularized and isolated intact from the mutant animals. Here we describe a detailed protocol for the isolation of germ cells from tumorous mutants that allows the germ cells to be maintained for extended periods in an in vitro primary culture. This protocol has been adapted from Chaudhari et al., 2016. PMID:28868332

Development methodology of the novel Endoscopic stone treatment step 1 (EST s1) training/assessment curriculum.

PubMed

Veneziano, Domenico; Ahmed, Kamran; Van Cleynenbreugel, Ben S E P; Gözen, Ali Serdar; Palou, Joan; Sarica, Kemal; Liatsikos, Evangelos N; Sanguedolce, Francesco; Honeck, Patrick; Alvarez-Maestro, Mario; Papatsoris, Athanasios; Kallidonis, Panagiotis; Greco, Francesco; Breda, Alberto; Somani, Bhaskar

2017-07-10

Background Simulation based technical-skill assessment is a core topic of debate, especially in high-risk environments. After the introduction of the E-BLUS exam for basic laparoscopy, no more technical training/assessment urological protocols have been developed in Europe. Objective We describe the methodology used in the development of the novel Endoscopic Stone Treatment step 1 (EST s1) assessment curriculum. Materials and Methods The "full life cycle curriculum development" template was followed for curriculum development. A CTA was run to define the most important steps and details of RIRS, in accordance with EAU Urolithiasis guidelines. Training tasks were created between April 2015 and September 2015. Tasks and metrics were further analyzed by a consensus meeting with the EULIS board in February 2016. A review, aimed to study available simulators and their accordance with task requirements, was subsequently run in London on March 2016. After initial feedback and further tests, content validity of this protocol was achieved during EUREP 2016. Results The EST s1 curriculum development, took 23 months. 72 participants tested the 5 preliminary tasks during EUREP 2015, with sessions of 45 minutes each. Likert-scale questionnaires were filled-out to score the quality of training. The protocol was modified accordingly and 25 participants tested the 4 tasks during the hands-on training sessions of the ESUT 2016 congress. 134 participants finally participated in the validation study in EUREP 2016. During the same event 10 experts confirmed content validity by filling-out a Likert-scale questionnaire. Conclusion We described a reliable and replicable methodology that can be followed to develop training/assessment protocols for surgical procedures. The expert consensus meetings, strict adherence to guidelines and updated literature search towards an Endourology curriculum allowed correct training and assessment protocol development. It is the first step towards standardized simulation training in Endourology with a potential for worldwide adoption.

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

Treatment outcomes after implementation of an adapted WHO protocol for severe sepsis and septic shock in Haiti.

PubMed

Papali, Alfred; Eoin West, T; Verceles, Avelino C; Augustin, Marc E; Nathalie Colas, L; Jean-Francois, Carl H; Patel, Devang M; Todd, Nevins W; McCurdy, Michael T

2017-10-01

The World Health Organization (WHO) has developed a simplified algorithm specific to resource-limited settings for the treatment of severe sepsis emphasizing early fluids and antibiotics. However, this protocol's clinical effectiveness is unknown. We describe patient outcomes before and after implementation of an adapted WHO severe sepsis protocol at a community hospital in Haiti. Using a before-and-after study design, we retrospectively enrolled 99 adult Emergency Department patients with severe sepsis from January through March 2012. After protocol implementation in January 2014, we compared outcomes to 67 patients with severe sepsis retrospectively enrolled from February to April 2014. We defined sepsis according to the WHO's Integrated Management of Adult Illness guidelines and severe sepsis as sepsis plus organ dysfunction. After protocol implementation, quantity of fluid administered increased and the physician's differential diagnoses more often included sepsis. Patients were more likely to have follow-up vital signs taken sooner, a radiograph performed, and a lactic acid tested. There were no improvements in mortality, time to fluids or antimicrobials. Use of a simplified sepsis protocol based primarily on physiologic parameters allows for substantial improvements in process measures in the care of severely septic patients in a resource-constrained setting. Copyright © 2017 Elsevier Inc. All rights reserved.

Slow histidine H/D exchange protocol for thermodynamic analysis of protein folding and stability using mass spectrometry.

PubMed

Tran, Duc T; Banerjee, Sambuddha; Alayash, Abdu I; Crumbliss, Alvin L; Fitzgerald, Michael C

2012-02-07

Described here is a mass spectrometry-based protocol to study the thermodynamic stability of proteins and protein-ligand complexes using the chemical denaturant dependence of the slow H/D exchange reaction of the imidazole C(2) proton in histidine side chains. The protocol is developed using several model protein systems including: ribonuclease (Rnase) A, myoglobin, bovine carbonic anhydrase (BCA) II, hemoglobin (Hb), and the hemoglobin-haptoglobin (Hb-Hp) protein complex. Folding free energies consistent with those previously determined by other more conventional techniques were obtained for the two-state folding proteins, Rnase A and myoglobin. The protocol successfully detected a previously observed partially unfolded intermediate stabilized in the BCA II folding/unfolding reaction, and it could be used to generate a K(d) value of 0.24 nM for the Hb-Hp complex. The compatibility of the protocol with conventional mass spectrometry-based proteomic sample preparation and analysis methods was also demonstrated in an experiment in which the protocol was used to detect the binding of zinc to superoxide dismutase in the yeast cell lysate sample. The yeast cell sample analyses also helped define the scope of the technique, which requires the presence of globally protected histidine residues in a protein's three-dimensional structure for successful application. © 2011 American Chemical Society

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

Static balance and function in children with cerebral palsy submitted to neuromuscular block and neuromuscular electrical stimulation: Study protocol for prospective, randomized, controlled trial

PubMed Central

2012-01-01

Background The use of botulinum toxin A (BT-A) for the treatment of lower limb spasticity is common in children with cerebral palsy (CP). Following the administration of BT-A, physical therapy plays a fundamental role in potentiating the functionality of the child. The balance deficit found in children with CP is mainly caused by muscle imbalance (spastic agonist and weak antagonist). Neuromuscular electrical stimulation (NMES) is a promising therapeutic modality for muscle strengthening in this population. The aim of the present study is to describe a protocol for a study aimed at analyzing the effects of NMES on dorsiflexors combined with physical therapy on static and functional balance in children with CP submitted to BT- A. Methods/Design Protocol for a prospective, randomized, controlled trial with a blinded evaluator. Eligible participants will be children with cerebral palsy (Levels I, II and III of the Gross Motor Function Classification System) between five and 12 years of age, with independent gait with or without a gait-assistance device. All participants will receive BT-A in the lower limbs (triceps surae). The children will then be randomly allocated for either treatment with motor physical therapy combined with NMES on the tibialis anterior or motor physical therapy alone. The participants will be evaluated on three occasions: 1) one week prior to the administration of BT-A; 2) one week after the administration of BT-A; and 3) four months after the administration of BT-A (end of intervention). Spasticity will be assessed by the Modified Ashworth Scale and Modified Tardieu Scale. Static balance will be assessed using the Medicapteurs Fusyo pressure platform and functional balance will be assessed using the Berg Balance Scale. Discussion The aim of this protocol study is to describe the methodology of a randomized, controlled, clinical trial comparing the effect of motor physical therapy combined with NMES on the tibialis anterior muscle or motor physical therapy alone on static and functional balance in children with CP submitted to BT-A in the lower limbs. This study describes the background, hypotheses, methodology of the procedures and measurement of the results. Trial registration RBR5qzs8h PMID:22591446

Multiple Access Schemes for Lunar Missions

NASA Technical Reports Server (NTRS)

Deutsch, Leslie; Hamkins, Jon; Stocklin, Frank J.

2010-01-01

Two years ago, the NASA Coding, Modulation, and Link Protocol (CMLP) study was completed. The study, led by the authors of this paper, recommended codes, modulation schemes, and desired attributes of link protocols for all space communication links in NASA's future space architecture. Portions of the NASA CMLP team were reassembled to resolve one open issue: the use of multiple access (MA) communication from the lunar surface. The CMLP-MA team analyzed and simulated two candidate multiple access schemes that were identified in the original CMLP study: Code Division MA (CDMA) and Frequency Division MA (FDMA) based on a bandwidth-efficient Continuous Phase Modulation (CPM) with a superimposed Pseudo-Noise (PN) ranging signal (CPM/PN). This paper summarizes the results of the analysis and simulation of the CMLP-MA study and describes the final recommendations.

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…

Twelve Middle-School Teachers' Planning.

ERIC Educational Resources Information Center

Brown, Deborah Sardo

1988-01-01

Case studies described 12 middle-school teachers' instructional yearly, unit, weekly, and daily planning on the basis of a background questionnaire, interview protocols, an analysis of written plans, think-aloud typescripts, and a questionnaire. A process model best characterized teachers long-term planning, while an agenda-formulation model fit…

The Hands and Reading: What Deafblind Adult Readers Tell Us

ERIC Educational Resources Information Center

Ingraham, Cynthia L.; Andrews, Jean F.

2010-01-01

Deafblind readers are heterogeneous in reading skill acquisition. This qualitative study uses in-depth interviews and protocol analyses and queries the three deafblind adult participants in describing their metacomprehension, metacognitive and metalinguistic strategies used when reading different types of text. Using retrospective analysis, the…

Qualitative and quantitative assessment of Unresolved Complex Mixture in PM2.5 of Bakersfield, CA.

EPA Science Inventory

The 2010 CalNex (California Nexus) field experiment offered an opportunity for detailed characterization of atmospheric particulate carbon composition and sources in Bakersfield, CA. In the current study, the authors describe and employ a new protocol for reporting unresolved com...

Purpose and Professional Writers.

ERIC Educational Resources Information Center

Blyler, Nancy Roundy

1989-01-01

Describes a protocol study of 10 professional writers which examined the meaning and influence of purpose on writers in the workplace. Explores the interactions of various purpose considerations derived from situation, reader, and text. Suggests that professional writers have a range of meanings in mind when they think about purpose. (MM)

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.

Methods and Management of the Healthy Brain Study: A Large Multisite Qualitative Research Project

ERIC Educational Resources Information Center

Laditka, Sarah B.; Corwin, Sara J.; Laditka, James N.; Liu, Rui; Friedman, Daniela B.; Mathews, Anna E.; Wilcox, Sara

2009-01-01

Purpose of the study: To describe processes used in the Healthy Brain project to manage data collection, coding, and data distribution in a large qualitative project, conducted by researchers at 9 universities in 9 states. Design and Methods: Project management protocols included: (a) managing audiotapes and surveys to ensure data confidentiality,…

Decisions Made in the Practice Room: A Qualitative Study of Middle School Students' Thought Processes while Practicing

ERIC Educational Resources Information Center

Oare, Steve

2012-01-01

The purpose of this study is to describe the decision-making processes of novice band students while engaged in individual practice. Five seventh- through ninth-grade students were videotaped while practicing and subsequently interviewed using retrospective verbal protocol. Students were asked to discuss the goals they had while practicing, their…

NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR STANDARD PROTOCOL FOR CLEANING LABORATORY AND FIELD SAMPLING APPARATUS (UA-L-5.1)

EPA Science Inventory

The purpose of this SOP is to describe the standard approach used for cleaning glassware and plasticware during the Arizona NHEXAS project and the "Border" study. Keywords: lab; equipment; cleaning.

The National Human Exposure Assessment Survey (NHEXAS) is a federal interagency...

Micropropagation of Asparagus by in vitro shoot culture.

PubMed

Stajner, Nataša

2013-01-01

Asparagus officinalis is most extensively studied species within the genus Asparagus, which is well known as garden asparagus. This species is dioecious with unisexual flowers, which means that generative propagation gives roughly equal number of male and female plants. Male plants are high yielders and preferred commercially over female plants. Tissue culture techniques could efficiently promote vegetative propagation of male plants and pave the way for efficient plant breeding.This chapter describes an efficient micropropagation protocol for developing rapid growing in vitro Asparagus shoot cultures. The source of explants, inoculation, and shoot proliferation, followed by shoot propagation, rooting, and acclimatization is described. The optimal medium for Asparagus micropropagation described in this chapter is composed of MS macro- and microelements and a combination of auxins and cytokinins. Plant growth regulators NAA, kinetin, and BA were used in various concentrations. Three different media representing the whole micropropagation protocol of Asparagus are described; medium for shoot initiation, medium for shoot multiplication, and medium for root formation. By in vitro propagation of Asparagus, root initiation is difficult, but can be promoted by adding growth retardant ancymidol which also greatly promotes shoot development and suppresses callus formation.

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 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 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.

A protocol for lifetime energy and environmental impact assessment of building insulation materials

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

Shrestha, Som S., E-mail: shresthass@ornl.gov; Biswas, Kaushik; Desjarlais, Andre O.

This article describes a proposed protocol that is intended to provide a comprehensive list of factors to be considered in evaluating the direct and indirect environmental impacts of building insulation materials, as well as detailed descriptions of standardized calculation methodologies to determine those impacts. The energy and environmental impacts of insulation materials can generally be divided into two categories: (1) direct impact due to the embodied energy of the insulation materials and other factors and (2) indirect or environmental impacts avoided as a result of reduced building energy use due to addition of insulation. Standards and product category rules exist,more » which provide guidelines about the life cycle assessment (LCA) of materials, including building insulation products. However, critical reviews have suggested that these standards fail to provide complete guidance to LCA studies and suffer from ambiguities regarding the determination of the environmental impacts of building insulation and other products. The focus of the assessment protocol described here is to identify all factors that contribute to the total energy and environmental impacts of different building insulation products and, more importantly, provide standardized determination methods that will allow comparison of different insulation material types. Further, the intent is not to replace current LCA standards but to provide a well-defined, easy-to-use comparison method for insulation materials using existing LCA guidelines. - Highlights: • We proposed a protocol to evaluate the environmental impacts of insulation materials. • The protocol considers all life cycle stages of an insulation material. • Both the direct environmental impacts and the indirect impacts are defined. • Standardized calculation methods for the ‘avoided operational energy’ is defined. • Standardized calculation methods for the ‘avoided environmental impact’ is defined.« less

Internet Data Delivery for Future Space Missions

NASA Technical Reports Server (NTRS)

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

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 as the need increases for more network-oriented mission operations. Another element of increasing significance will be the increased cost effectiveness of designing, building, integrating, and operating instruments and spacecraft that will come to the fore as more missions take up the approach of using commodity-level standard communications technologies. This paper describes how an IP (Internet Protocol)-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.

VZV Replication Assays

PubMed Central

Griffiths, Samantha J.; Haas, Jürgen

2017-01-01

Varicella zoster virus (VZV) is a human herpesvirus which causes Varicella (chickenpox) upon primary infection and Zoster (shingles) following reactivation from latency (von Bokay, 1909). Whilst VZV is extensively studied, inherent features of VZV replication, such as cell-association of virus particles during in vitro culture and a restricted host range (limited to humans and some other primates) mean the cellular and viral mechanisms underlying VZV reactivation and pathogenesis remain largely uncharacterised. Much remains to be learnt about VZV, interactions with its host, and the development of disease. This protocol describes a basic VZV replication assay using a recombinant VZV-GFP reporter virus. As VZV is highly cell-associated in tissue culture, the reporter virus inoculum described here is a preparation of infected cells. This reporter virus-infected cell line can be used in combination with siRNA gene depletion or cDNA overexpression transfection protocols to determine the effect of individual cellular genes on virus replication. PMID:29085851

Detection of human Dicer and Argonaute 2 catalytic activity

PubMed Central

Perron, Marjorie P.; Landry, Patricia; Plante, Isabelle; Provost, Patrick

2013-01-01

The microRNA (miRNA)-guided RNA silencing pathway is a central and well-defined cellular process involved in messenger RNA (mRNA) translational control. This complex regulatory process is achieved by a well orchestrated machinery composed of a relatively few protein components, among which the ribonuclease III (RNase III) Dicer and Argonaute 2 (Ago2) play a central role. These two proteins are essential and it is of particular interest to measure and detect their catalytic activity under various situations and/or conditions. In this chapter, we describe different protocols that aim to study and determine the catalytic activity of Dicer and Ago2 in cell extracts, immune complexes and size-fractionated cell extracts. Another protocol aimed at assessing miRNA binding to Ago2 is also described. These experimental approaches are likely to be useful to researchers investigating the main steps of miRNA biogenesis and function in human health and diseases. PMID:21528451

Molecular Typing of Borrelia burgdorferi

PubMed Central

Wang, Guiqing; Liveris, Dionysios; Mukherjee, Priyanka; Jungnick, Sabrina; Margos, Gabriele; Schwartz, Ira

2015-01-01

Borrelia burgdorferi sensu lato is a group of spirochetes belonging to the genus Borrelia in the family of Spirochaetaceae. The spirochete is transmitted between reservoirs and hosts by ticks of the family Ixodidae. Infection with B. burgdorferi in humans causes Lyme disease or Lyme borreliosis. Currently, 20 Lyme disease-associated Borrelia species and more than 20 relapsing fever-associated Borrelia species have been described. Identification and differentiation of different Borrelia species and strains is largely dependent on analyses of their genetic characteristics. A variety of molecular techniques have been described for Borrelia isolate speciation, molecular epidemiology, and pathogenicity studies. In this unit, we focus on three basic protocols, PCR-RFLP-based typing of the rrs-rrlA and rrfA-rrlB ribosomal spacer, ospC typing, and MLST. These protocols can be employed alone or in combination for characterization of B. burgdorferi isolates or directly on uncultivated organisms in ticks, mammalian host reservoirs, and human clinical specimens. PMID:25082003

Handwriting assessment of Franco-Quebec primary school-age students

PubMed

Couture, Mélanie; Morin, Marie-France; Coallier, Mélissa; Lavigne, Audrey; Archambault, Patricia; Bolduc, Émilie; Chartier, Émilie; Liard, Karolane; Jasmin, Emmanuelle

2016-12-01

Reasons for referring school-age children to occupational therapy mainly relate to handwriting problems. However, there are no validated tools or reference values for assessing handwriting in francophone children in Canada. This study aimed to adapt and validate the writing tasks described in an English Canadian handwriting assessment protocol and to develop reference values for handwriting speed for francophone children. Three writing tasks from the Handwriting Assessment Protocol-2nd Edition (near-point and far-point copying and dictation) were adapted for Québec French children and administered to 141 Grade 1 ( n = 73) and Grade 2 ( n = 68) students. Reference values for handwriting speed were obtained for near point and far point copying tasks. This adapted protocol and these reference values for speed will improve occupational therapy handwriting assessments for the target population.

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.

A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research.

PubMed

Weidner, Christopher; Steinfath, Matthias; Wistorf, Elisa; Oelgeschläger, Michael; Schneider, Marlon R; Schönfelder, Gilbert

2017-08-16

Recent studies that compared transcriptomic datasets of human diseases with datasets from mouse models using traditional gene-to-gene comparison techniques resulted in contradictory conclusions regarding the relevance of animal models for translational research. A major reason for the discrepancies between different gene expression analyses is the arbitrary filtering of differentially expressed genes. Furthermore, the comparison of single genes between different species and platforms often is limited by technical variance, leading to misinterpretation of the con/discordance between data from human and animal models. Thus, standardized approaches for systematic data analysis are needed. To overcome subjective gene filtering and ineffective gene-to-gene comparisons, we recently demonstrated that gene set enrichment analysis (GSEA) has the potential to avoid these problems. Therefore, we developed a standardized protocol for the use of GSEA to distinguish between appropriate and inappropriate animal models for translational research. This protocol is not suitable to predict how to design new model systems a-priori, as it requires existing experimental omics data. However, the protocol describes how to interpret existing data in a standardized manner in order to select the most suitable animal model, thus avoiding unnecessary animal experiments and misleading translational studies.

Components of Effective Cognitive-Behavioral Therapy for Pediatric Headache: A Mixed Methods Approach

PubMed Central

Law, Emily F.; Beals-Erickson, Sarah E.; Fisher, Emma; Lang, Emily A.; Palermo, Tonya M.

2017-01-01

Internet-delivered treatment has the potential to expand access to evidence-based cognitive-behavioral therapy (CBT) for pediatric headache, and has demonstrated efficacy in small trials for some youth with headache. We used a mixed methods approach to identify effective components of CBT for this population. In Study 1, component profile analysis identified common interventions delivered in published RCTs of effective CBT protocols for pediatric headache delivered face-to-face or via the Internet. We identified a core set of three treatment components that were common across face-to-face and Internet protocols: 1) headache education, 2) relaxation training, and 3) cognitive interventions. Biofeedback was identified as an additional core treatment component delivered in face-to-face protocols only. In Study 2, we conducted qualitative interviews to describe the perspectives of youth with headache and their parents on successful components of an Internet CBT intervention. Eleven themes emerged from the qualitative data analysis, which broadly focused on patient experiences using the treatment components and suggestions for new treatment components. In the Discussion, these mixed methods findings are integrated to inform the adaptation of an Internet CBT protocol for youth with headache. PMID:29503787

Components of Effective Cognitive-Behavioral Therapy for Pediatric Headache: A Mixed Methods Approach.

PubMed

Law, Emily F; Beals-Erickson, Sarah E; Fisher, Emma; Lang, Emily A; Palermo, Tonya M

2017-01-01

Internet-delivered treatment has the potential to expand access to evidence-based cognitive-behavioral therapy (CBT) for pediatric headache, and has demonstrated efficacy in small trials for some youth with headache. We used a mixed methods approach to identify effective components of CBT for this population. In Study 1, component profile analysis identified common interventions delivered in published RCTs of effective CBT protocols for pediatric headache delivered face-to-face or via the Internet. We identified a core set of three treatment components that were common across face-to-face and Internet protocols: 1) headache education, 2) relaxation training, and 3) cognitive interventions. Biofeedback was identified as an additional core treatment component delivered in face-to-face protocols only. In Study 2, we conducted qualitative interviews to describe the perspectives of youth with headache and their parents on successful components of an Internet CBT intervention. Eleven themes emerged from the qualitative data analysis, which broadly focused on patient experiences using the treatment components and suggestions for new treatment components. In the Discussion, these mixed methods findings are integrated to inform the adaptation of an Internet CBT protocol for youth with headache.

Study protocol: a randomized controlled trial investigating the effects of a psychosexual training program for adolescents with autism spectrum disorder.

PubMed

Visser, Kirsten; Greaves-Lord, Kirstin; Tick, Nouchka T; Verhulst, Frank C; Maras, Athanasios; van der Vegt, Esther J M

2015-08-28

Previous research shows that adolescents with autism spectrum disorder (ASD) run several risks in their psychosexual development and that these adolescents can have limited access to reliable information on puberty and sexuality, emphasizing the need for specific guidance of adolescents with ASD in their psychosexual development. Few studies have investigated the effects of psychosexual training programs for adolescents with ASD and to date no randomized controlled trials are available to study the effects of psychosexual interventions for this target group. The randomized controlled trial (RCT) described in this study protocol aims to investigate the effects of the Tackling Teenage Training (TTT) program on the psychosexual development of adolescents with ASD. This parallel clinical trial, conducted in the South-West of the Netherlands, has a simple equal randomization design with an intervention and a waiting-list control condition. Two hundred adolescents and their parents participate in this study. We assess the participants in both conditions using self-report as well as parent-report questionnaires at three time points during 1 year: at baseline (T1), post-treatment (T2), and for follow-up (T3). To our knowledge, the current study is the first that uses a randomized controlled design to study the effects of a psychosexual training program for adolescents with ASD. It has a number of methodological strengths, namely a large sample size, a wide range of functionally relevant outcome measures, the use of multiple informants, and a standardized research and intervention protocol. Also some limitations of the described study are identified, for instance not making a comparison between two treatment conditions, and no use of blinded observational measures to investigate the ecological validity of the research results. Dutch Trial Register NTR2860. Registered on 20 April 2011.

Tackling reliability and construct validity: the systematic development of a qualitative protocol for skill and incident analysis.

PubMed

Savage, Trevor Nicholas; McIntosh, Andrew Stuart

2017-03-01

It is important to understand factors contributing to and directly causing sports injuries to improve the effectiveness and safety of sports skills. The characteristics of injury events must be evaluated and described meaningfully and reliably. However, many complex skills cannot be effectively investigated quantitatively because of ethical, technological and validity considerations. Increasingly, qualitative methods are being used to investigate human movement for research purposes, but there are concerns about reliability and measurement bias of such methods. Using the tackle in Rugby union as an example, we outline a systematic approach for developing a skill analysis protocol with a focus on improving objectivity, validity and reliability. Characteristics for analysis were selected using qualitative analysis and biomechanical theoretical models and epidemiological and coaching literature. An expert panel comprising subject matter experts provided feedback and the inter-rater reliability of the protocol was assessed using ten trained raters. The inter-rater reliability results were reviewed by the expert panel and the protocol was revised and assessed in a second inter-rater reliability study. Mean agreement in the second study improved and was comparable (52-90% agreement and ICC between 0.6 and 0.9) with other studies that have reported inter-rater reliability of qualitative analysis of human movement.

A neurocognitive approach for recovering upper extremity movement following subacute stroke: a randomized controlled pilot study.

PubMed

Sallés, Laia; Martín-Casas, Patricia; Gironès, Xavier; Durà, María José; Lafuente, José Vicente; Perfetti, Carlo

2017-04-01

[Purpose] This study aims to describe a protocol based on neurocognitive therapeutic exercises and determine its feasibility and usefulness for upper extremity functionality when compared with a conventional protocol. [Subjects and Methods] Eight subacute stroke patients were randomly assigned to a conventional (control group) or neurocognitive (experimental group) treatment protocol. Both lasted 30 minutes, 3 times a week for 10 weeks and assessments were blinded. Outcome measures included: Motor Evaluation Scale for Upper Extremity in Stroke Patients, Motricity Index, Revised Nottingham Sensory Assessment and Kinesthetic and Visual Imagery Questionnaire. Descriptive measures and nonparametric statistical tests were used for analysis. [Results] The results indicate a more favorable clinical progression in the neurocognitive group regarding upper extremity functional capacity with achievement of the minimal detectable change. The functionality results are related with improvements on muscle strength and sensory discrimination (tactile and kinesthetic). [Conclusion] Despite not showing significant group differences between pre and post-treatment, the neurocognitive approach could be a safe and useful strategy for recovering upper extremity movement following stroke, especially regarding affected hands, with better and longer lasting results. Although this work shows this protocol's feasibility with the panel of scales proposed, larger studies are required to demonstrate its effectiveness.

CSMA/RN: A universal protocol for gigabit networks

NASA Technical Reports Server (NTRS)

Foudriat, E. C.; Maly, Kurt J.; Overstreet, C. Michael; Khanna, S.; Paterra, Frank

1990-01-01

Networks must provide intelligent access for nodes to share the communications resources. In the range of 100 Mbps to 1 Gbps, the demand access class of protocols were studied extensively. Many use some form of slot or reservation system and many the concept of attempt and defer to determine the presence or absence of incoming information. The random access class of protocols like shared channel systems (Ethernet), also use the concept of attempt and defer in the form of carrier sensing to alleviate the damaging effects of collisions. In CSMA/CD, the sensing of interference is on a global basis. All systems discussed above have one aspect in common, they examine activity on the network either locally or globally and react in an attempt and whatever mechanism. Of the attempt + mechanisms discussed, one is obviously missing; that is attempt and truncate. Attempt and truncate was studied in a ring configuration called the Carrier Sensed Multiple Access Ring Network (CSMA/RN). The system features of CSMA/RN are described including a discussion of the node operations for inserting and removing messages and for handling integrated traffic. The performance and operational features based on analytical and simulation studies which indicate that CSMA/RN is a useful and adaptable protocol over a wide range of network conditions are discussed. Finally, the research and development activities necessary to demonstrate and realize the potential of CSMA/RN as a universal, gigabit network protocol is outlined.

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

Whole genome sequence analysis of the arctic-lineage strain responsible for distemper in Italian wolves and dogs through a fast and robust next generation sequencing protocol.

PubMed

Marcacci, Maurilia; Ancora, Massimo; Mangone, Iolanda; Teodori, Liana; Di Sabatino, Daria; De Massis, Fabrizio; Camma', Cesare; Savini, Giovanni; Lorusso, Alessio

2014-06-01

Dynamic surveillance and characterization of canine distemper virus (CDV) circulating strains are essential against possible vaccine breakthroughs events. This study describes the setup of a fast and robust next-generation sequencing (NGS) Ion PGM™ protocol that was used to obtain the complete genome sequence of a CDV isolate (CDV2784/2013). CDV2784/2013 is the prototype of CDV strains responsible for severe clinical distemper in dogs and wolves in Italy during 2013. CDV2784/2013 was isolated on cell culture and total RNA was used for NGS sample preparation. A total of 112.3 Mb of reads were assembled de novo using MIRA version 4.0rc4, which yielded a total number of 403 contigs with 12.1% coverage. The whole genome (15,690 bp) was recovered successfully and compared to those of existing CDV whole genomes. CDV2784/2013 was shown to have 92% nt identity with the Onderstepoort vaccine strain. This study describes for the first time a fast and robust Ion PGM™ platform-based whole genome amplification protocol for non-segmented negative stranded RNA viruses starting from total cell-purified RNA. Additionally, this is the first study reporting the whole genome analysis of an Arctic lineage strain that is known to circulate widely in Europe, Asia and USA. Copyright © 2014 Elsevier B.V. All rights reserved.

The Dutch 'Focus on Strength' intervention study protocol: programme design and production, implementation and evaluation plan.

PubMed

Ten Hoor, G A; Kok, G; Rutten, G M; Ruiter, R A C; Kremers, S P J; Schols, A M J W; Plasqui, G

2016-06-10

Overweight youngsters are better in absolute strength exercises than their normal-weight counterparts; a physiological phenomenon with promising psychological impact. In this paper we describe the study protocol of the Dutch, school-based program 'Focus on Strength' that aims to improve body composition of 11-13 year old students, and with that to ultimately improve their quality of life. The development of this intervention is based on the Intervention Mapping (IM) protocol, which starts from a needs assessment, uses theory and empirical research to develop a detailed intervention plan, and anticipates program implementation and evaluation. This novel intervention targets first year students in preparatory secondary vocational education (11-13 years of age). Teachers are the program implementers. One part of the intervention involves a 30 % increase of strength exercises in the physical education lessons. The other part is based on Motivational Interviewing, promoting autonomous motivation of students to become more physically active outside school. Performance and change objectives are described for both teachers and students. The effectiveness of the intervention will be tested in a Randomized Controlled Trial in 9 Dutch high schools. Intervention Mapping is a useful framework for program planning a school-based program to improve body composition and motivation to exercise in 11-13 year old adolescents by a "Focus on Strength". NTR5676 , registered 8 February 2016 (retrospectively registered).

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

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)

Preparing Protocols for Institutional Review Boards.

ERIC Educational Resources Information Center

Lyons, Charles M.

1983-01-01

Introduces the process by which Institutional Review Boards (IRBs) review proposals for research involving human subjects. Describes the composition of IRBs. Presents the Nuremberg code, the elements of informed consent, the judging criteria for proposals, and a sample protocol format. References newly published regulations governing research with…

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...

(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.

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.

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

Vogt

This report describes a U.S. Department of Energy, (DOE) Chemical and Biological National Security Program project that sought to establish what is known about decontamination of structures, objects, and people following an exposure to chemical or biological materials. Specifically we sought to identify the procedures and protocols used to determine when and how people or buildings are considered ''clean'' following decontamination. To fulfill this objective, the study systematically examined reported decontamination experiences to determine what procedures and protocols are currently employed for decontamination, the timeframe involved to initiate and complete the decontamination process, how the contaminants were identified, the factorsmore » determining when people were (or were not) decontaminated, the problems encountered during the decontamination process, how response efforts of agencies were coordinated, and the perceived social psychological effects on people who were decontaminated or who participated in the decontamination process. Findings and recommendations from the study are intended to aid decision-making and to improve the basis for determining appropriate decontamination protocols for recovery planners and policy makers for responding to chemical and biological events.« less

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

Teaching the Microbial Growth Curve Concept Using Microalgal Cultures and Flow Cytometry

ERIC Educational Resources Information Center

Forget, Nathalie; Belzile, Claude; Rioux, Pierre; Nozais, Christian

2010-01-01

The microbial growth curve is widely studied within microbiology classes and bacteria are usually the microbial model used. Here, we describe a novel laboratory protocol involving flow cytometry to assess the growth dynamics of the unicellular microalgae "Isochrysis galbana." The algal model represents an appropriate alternative to…

Developing Recruitment Methods for Vulnerable, Traumatized Adolescents: A Feminist Evaluation Approach

ERIC Educational Resources Information Center

Campbell, Rebecca; Greeson, Megan R.; Fehler-Cabral, Giannina

2014-01-01

This article describes the process by which we created a recruitment protocol for engaging adolescent sexual assault victims in a qualitative evaluation study. Working in collaboration with forensic nurses, rape victim advocates, adolescent rape survivors, and our institutional review board (IRB), we created a prospective recruitment method…

Potato transformation and potato cyst nematode infection on potato plantlets in tissue culture

USDA-ARS?s Scientific Manuscript database

These two protocols describe the methods for generating transgenic potato plants and for evaluating potato cyst nematode (Globodera rostochiensis and G. pallida) infection on potato plantlets in tissue culture. These methods are useful tools that can be used in the study of the interactions between ...

ORGAN CULTURE OF MID-FACIAL TISSUE AND SECONDARY PALATE

EPA Science Inventory

Abstract: Palatal organ culture provides an in vitro model for the study of the formation of the secondary palate, which forms the roof of the mouth in the developing fetus. The protocol describes the steps for culture of the mid-facial region of the fetal mouse or rat. In cult...

Locked down and out: Crisis at Central High

ERIC Educational Resources Information Center

Barron Ausbrooks, Carrie Y.

2010-01-01

This case study is designed for preservice school administrators enrolled in principalship and school law courses in educational administration. It describes an incident in which a school's crisis management and communication protocol were challenged. One day, through a series of unanticipated events, an assistant principal is engulfed in a test…

The Missing Link: Peer Conferencing in Civics Education

ERIC Educational Resources Information Center

Anderson, Derek L.; Lubig, Joe

2012-01-01

This article describes a method--Collaborative Civics Conference Protocol (3CP)--that teachers can use with any civics education program to engage students in meaningful collaborative assessment of each others' thinking and writing and to make connections between civics activities and essential social studies content. Borrowing from the Writer's…

Production, concentration and titration of pseudotyped HIV-1-based lentiviral vectors.

PubMed

Kutner, Robert H; Zhang, Xian-Yang; Reiser, Jakob

2009-01-01

Over the past decade, lentiviral vectors have emerged as powerful tools for transgene delivery. The use of lentiviral vectors has become commonplace and applications in the fields of neuroscience, hematology, developmental biology, stem cell biology and transgenesis are rapidly emerging. Also, lentiviral vectors are at present being explored in the context of human clinical trials. Here we describe improved protocols to generate highly concentrated lentiviral vector pseudotypes involving different envelope glycoproteins. In this protocol, vector stocks are prepared by transient transfection using standard cell culture media or serum-free media. Such stocks are then concentrated by ultracentrifugation and/or ion exchange chromatography, or by precipitation using polyethylene glycol 6000, resulting in vector titers of up to 10(10) transducing units per milliliter and above. We also provide reliable real-time PCR protocols to titrate lentiviral vectors based on proviral DNA copies present in genomic DNA extracted from transduced cells or on vector RNA. These production/concentration methods result in high-titer vector preparations that show reduced toxicity compared with lentiviral vectors produced using standard protocols involving ultracentrifugation-based methods. The vector production and titration protocol described here can be completed within 8 d.

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.

Investigating nurse practitioners in the private sector: a theoretically informed research protocol.

PubMed

Adams, Margaret; Gardner, Glenn; Yates, Patsy

2017-06-01

To report a study protocol and the theoretical framework normalisation process theory that informs this protocol for a case study investigation of private sector nurse practitioners. Most research evaluating nurse practitioner service is focused on public, mainly acute care environments where nurse practitioner service is well established with strong structures for governance and sustainability. Conversely, there is lack of clarity in governance for emerging models in the private sector. In a climate of healthcare reform, nurse practitioner service is extending beyond the familiar public health sector. Further research is required to inform knowledge of the practice, operational framework and governance of new nurse practitioner models. The proposed research will use a multiple exploratory case study design to examine private sector nurse practitioner service. Data collection includes interviews, surveys and audits. A sequential mixed method approach to analysis of each case will be conducted. Findings from within-case analysis will lead to a meta-synthesis across all four cases to gain a holistic understanding of the cases under study, private sector nurse practitioner service. Normalisation process theory will be used to guide the research process, specifically coding and analysis of data using theory constructs and the relevant components associated with those constructs. This article provides a blueprint for the research and describes a theoretical framework, normalisation process theory in terms of its flexibility as an analytical framework. Consistent with the goals of best research practice, this study protocol will inform the research community in the field of primary health care about emerging research in this field. Publishing a study protocol ensures researcher fidelity to the analysis plan and supports research collaboration across teams. © 2016 John Wiley & Sons Ltd.

Recruitment failure and futility were the most common reasons for discontinuation of clinical drug trials. Results of a nationwide inception cohort study in the Netherlands.

PubMed

van den Bogert, Cornelis A; Souverein, Patrick C; Brekelmans, Cecile T M; Janssen, Susan W J; Koëter, Gerard H; Leufkens, Hubert G M; Bouter, Lex M

2017-08-01

The objective of the study was to identify the reasons for discontinuation of clinical drug trials and to evaluate whether efficacy-related discontinuations were adequately planned in the trial protocol. All clinical drug trials in the Netherlands, reviewed by institutional review boards in 2007, were followed until December 2015. Data were obtained through the database of the Dutch competent authority (Central Committee on Research Involving Human Subjects [CCMO]) and a questionnaire to the principal investigators. Reasons for trial discontinuation were the primary outcome of the study. Three reasons for discontinuation were analyzed separately: all cause, recruitment failure, and efficacy related (when an interim analysis had demonstrated futility or superiority). Among the efficacy-related discontinuations, we examined whether the data monitoring committee, the stopping rule, and the moment of the interim analysis in the trial progress were specified in the trial protocol. Of the 574 trials, 102 (17.8%) were discontinued. The most common reasons were recruitment failure (33 of 574; 5.7%) and solely efficacy related (30 of 574; 5.2%). Of the efficacy-related discontinuations, 10 of 30 (33.3%) of the trial protocols reported all three aspects in the trial protocol, and 20 of 30 (66.7%) reported at least one aspect in the trial protocol. One out of five clinical drug trials is discontinued before the planned trial end, with recruitment failure and futility as the most common reasons. The target sample size of trials should be feasible, and interim analyses should be adequately described in trial protocols. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

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.

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 ).

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.

The preparation of Drosophila embryos for live-imaging using the hanging drop protocol.

PubMed

Reed, Bruce H; McMillan, Stephanie C; Chaudhary, Roopali

2009-03-13

Green fluorescent protein (GFP)-based timelapse live-imaging is a powerful technique for studying the genetic regulation of dynamic processes such as tissue morphogenesis, cell-cell adhesion, or cell death. Drosophila embryos expressing GFP are readily imaged using either stereoscopic or confocal microscopy. A goal of any live-imaging protocol is to minimize detrimental effects such as dehydration and hypoxia. Previous protocols for preparing Drosophila embryos for live-imaging analysis have involved placing dechorionated embryos in halocarbon oil and sandwiching them between a halocarbon gas-permeable membrane and a coverslip. The introduction of compression through mounting embryos in this manner represents an undesirable complication for any biomechanical-based analysis of morphogenesis. Our method, which we call the hanging drop protocol, results in excellent viability of embryos during live imaging and does not require that embryos be compressed. Briefly, the hanging drop protocol involves the placement of embryos in a drop of halocarbon oil that is suspended from a coverslip, which is, in turn, fixed in position over a humid chamber. In addition to providing gas exchange and preventing dehydration, this arrangement takes advantage of the buoyancy of embryos in halocarbon oil to prevent them from drifting out of position during timelapse acquisition. This video describes in detail how to collect and prepare Drosophila embryos for live imaging using the hanging drop protocol. This protocol is suitable for imaging dechorionated embryos using stereomicroscopy or any upright compound fluorescence microscope.

Efficacy and Safety of Available Protocols for Aspirin Hypersensitivity for Patients Undergoing Percutaneous Coronary Intervention: A Survey and Systematic Review.

PubMed

Bianco, Matteo; Bernardi, Alessandro; D'Ascenzo, Fabrizio; Cerrato, Enrico; Omedè, Pierluigi; Montefusco, Antonio; DiNicolantonio, James J; Zoccai, Giuseppe Biondi; Varbella, Ferdinando; Carini, Giovanni; Moretti, Claudio; Pozzi, Roberto; Gaita, Fiorenzo

2016-01-01

The most suitable approach for patients with aspirin hypersensitivity undergoing percutaneous coronary intervention remains to be assessed. Pubmed, Google Scholar, and Cochrane were systematically searched for papers describing protocols about aspirin hypersensitivity in the percutaneous coronary intervention setting. Discharge from hospital with aspirin was the primary end point, whereas rates of adverse reactions being a secondary outcome. An online international survey was performed to critically analyze rates of aspirin hypersensitivity and its medical and interventional management. Eleven studies with 283 patients were included. An endovenous desensitization protocol was performed on one of them, with high efficacy rate (98%) and a low adverse reaction rate when compared with oral administration. No significant differences were reported among the oral protocols in terms of efficacy (less versus more fractionated [95.8% {95.4%-96.2%} versus 95.9% {95.2-96.5%}]), whereas higher incidence of rash and angioedema were reported for protocols with <6 doses escalation (2.6% [1.1%-4.1%] versus 2.6% [1.9%-3.2%]). In the survey, we collected answer from 86 physician of the 100 interviewed. Fifty-six percent of them managed aspirin hypersensitivity changing the therapeutic regimen (eg, clopidogrel monotherapy and indobufen). Despite the previous safety data, desensitization protocols were adopted by only 42% of surveyed cardiologist. Available protocols for aspirin hypersensitivity are effective and safe, representing a feasible approach for patients needing dual antiplatelet therapy. © 2016 American Heart Association, Inc.

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.

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.

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--STANDARD OPERATING PROCEDURE FOR STANDARD PROTOCOL FOR CLEANING LABORATORY AND FIELD SAMPLING APPARATUS (UA-L-5.1)

EPA Science Inventory

The purpose of this SOP is to describe the standard approach used for cleaning glassware and plasticware during the Arizona NHEXAS project and the Border study. Keywords: lab; equipment; cleaning.

The U.S.-Mexico Border Program is sponsored by the Environmental Health Workgroup...

Cognitive Behavioral Therapy and Functional and Metacognitive Outcomes in Schizophrenia: A Single Case Study

ERIC Educational Resources Information Center

Davis, Louanne W.; Lysaker, Paul H.

2005-01-01

While much attention has been paid to how CBT can address symptoms in schizophrenia spectrum disorders, less is known about how it might be applied to target psychosocial dysfunction. This case study describes the treatment of a man with schizophrenia over a 6-month period using the Indianapolis Vocational Intervention Protocol (IVIP). The IVIP…

Riparian buffer design guidelines for water quality and wildlife habitat functions on agricultural landscapes in the Intermountain West: Case Study

Treesearch

Craig W. Johnson; Susan Buffler

2008-01-01

This hypothetical case study illustrates how the riparian buffer planning protocol described in the RB handbook is used to plan a buffer for both water quality and wildlife conservation on a specific project site. The case study site includes riparian buffer characteristics typical of the study area-variable topography and soils, flood plain wetlands, seeps, springs,...

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.

Has dementia research lost its sense of reality? A descriptive analysis of eligibility criteria of Dutch dementia research protocols.

PubMed

Jongsma, K R; van Bruchem-Visser, R L; van de Vathorst, S; Mattace Raso, F U S

2016-06-01

A substantial proportion of dementia patients are excluded from research participation, while for extrapolation of the study findings, it is important that the research population represents the patient population. The aim of this study is to provide an analysis of dementia research and its exclusion criteria in order to get a clearer picture whether the research participants represent the general dementia population. Dementia studies registered at ToetsingOnline.nl between 2006-2015 were analysed. Study characteristics, funding and eligibility criteria were described and analysed using a standardised score sheet. The search yielded 103 usable study protocols. The number of trials has increased over the years, and 35% of the studies were industry-financed. Alzheimer's disease was the most researched type of dementia (84%). In observational studies the most frequently observed exclusion criterion is a neurological condition, while in drug studies and other intervention studies this is a somatic condition. Of all protocols, 86% had at least one exclusion criterion concerning comorbidity. Most studies focused on mild or moderate dementia (78%). Our study has shown that the distribution of dementia research over the different subtypes of dementia does not correspond with the prevalence of these subtypes in clinical practice. The research population in the protocols is not representative of the larger patient population. A greater number of dementia patients could derive benefit from the conducted research if the research agenda were more closely aligned with disease prevalence. A better representation of all dementia patients in research will help to meet the needs of these patients.

Development of risk reduction behavioral counseling for Ebola virus disease survivors enrolled in the Sierra Leone Ebola Virus Persistence Study, 2015-2016.

PubMed

Abad, Neetu; Malik, Tasneem; Ariyarajah, Archchun; Ongpin, Patricia; Hogben, Matthew; McDonald, Suzanna L R; Marrinan, Jaclyn; Massaquoi, Thomas; Thorson, Anna; Ervin, Elizabeth; Bernstein, Kyle; Ross, Christine; Liu, William J; Kroeger, Karen; Durski, Kara N; Broutet, Nathalie; Knust, Barbara; Deen, Gibrilla F

2017-09-01

During the 2014-2016 West Africa Ebola Virus Disease (EVD) epidemic, the public health community had concerns that sexual transmission of the Ebola virus (EBOV) from EVD survivors was a risk, due to EBOV persistence in body fluids of EVD survivors, particularly semen. The Sierra Leone Ebola Virus Persistence Study was initiated to investigate this risk by assessing EBOV persistence in numerous body fluids of EVD survivors and providing risk reduction counseling based on test results for semen, vaginal fluid, menstrual blood, urine, rectal fluid, sweat, tears, saliva, and breast milk. This publication describes implementation of the counseling protocol and the key lessons learned. The Ebola Virus Persistence Risk Reduction Behavioral Counseling Protocol was developed from a framework used to prevent transmission of HIV and other sexually transmitted infections. The framework helped to identify barriers to risk reduction and facilitated the development of a personalized risk-reduction plan, particularly around condom use and abstinence. Pre-test and post-test counseling sessions included risk reduction guidance, and post-test counseling was based on the participants' individual test results. The behavioral counseling protocol enabled study staff to translate the study's body fluid test results into individualized information for study participants. The Ebola Virus Persistence Risk Reduction Behavioral Counseling Protocol provided guidance to mitigate the risk of EBOV transmission from EVD survivors. It has since been shared with and adapted by other EVD survivor body fluid testing programs and studies in Ebola-affected countries.

Construction and Operation of a High-Speed, High-Precision Eye Tracker for Tight Stimulus Synchronization and Real-Time Gaze Monitoring in Human and Animal Subjects.

PubMed

Farivar, Reza; Michaud-Landry, Danny

2016-01-01

Measurements of the fast and precise movements of the eye-critical to many vision, oculomotor, and animal behavior studies-can be made non-invasively by video oculography. The protocol here describes the construction and operation of a research-grade video oculography system with ~0.1° precision over the full typical viewing range at over 450 Hz with tight synchronization with stimulus onset. The protocol consists of three stages: (1) system assembly, (2) calibration for both cooperative, and for minimally cooperative subjects (e.g., animals or infants), and (3) gaze monitoring and recording.

Evaluation of pollutant source strengths and control strategies in an innovative residential high-rise building

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

NONE

1998-12-31

Describes a study undertaken to assess the indoor air quality in the Clos St-Andre, a 78-unit residential complex in downtown Montreal, through the implementation of a monitoring protocol in three of the building`s suites; and to examine the relationships between mechanical ventilation, material emissions, occupant lifestyle, and indoor air pollutant concentrations. The monitoring protocol consisted of tracer gas, air exchange testing, material emission testing, airtightness testing, and the monitoring of air temperature, relative humidity, carbon dioxide, carbon monoxide, formaldehyde, and total volatile organic carbon in the suites. Trends in pollutant concentrations over time in the post-construction period are noted.

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.

Securing TCP/IP and Dial-up Access to Administrative Data.

ERIC Educational Resources Information Center

Conrad, L. Dean

1992-01-01

This article describes Arizona State University's solution to security risk inherent in general access systems such as TCP/IP (Transmission Control Protocol/INTERNET Protocol). Advantages and disadvantages of various options are compared, and the process of selecting a log-on authentication approach involving generation of a different password at…

Updated Draft Protocol for the Evaluation of Bactericidal Activity of Hard, Non-porous Copper Containing Surface Products

EPA Pesticide Factsheets

This document describes the updated draft testing protocol recommended by the EPA to support the registration of copper-containing surface products (such as door knobs, or other items that are not intended for food contact) that bear sanitizer claims.

GENERIC VERIFICATION PROTOCOL FOR DETERMINATION OF EMISSIONS REDUCTIONS FROM SELECTIVE CATALYTIC REDUCTIONS CONTROL TECHNOLOGIES FOR HIGHWAY, NONROAD, AND STATIONARY USE DIESEL ENGINES

EPA Science Inventory

The protocol describes the Environmental Technology Verification (ETV) Program's considerations and requirements for verification of emissions reduction provided by selective catalytic reduction (SCR) technologies. The basis of the ETV will be comparison of the emissions and perf...

Assessment of metabolic stability using the rainbow trout (Oncorhynchus mykiss) liver S9 fraction

EPA Science Inventory

Standard protocols are given for assessing metabolic stability in rainbow trout using the liver S9 fraction. These protocols describe the isolation of S9 fractions from trout livers, evaluation of metabolic stability using a substrate depletion approach, and expression of the res...

Recombinant DNA for Teachers.

ERIC Educational Resources Information Center

Duvall, James G., III

1992-01-01

A science teacher describes his experience at a workshop to learn to teach the Cold Spring Harbor DNA Science Laboratory Protocols. These protocols lead students through processes for taking E. coli cells and transforming them into a new antibiotic resistant strain. The workshop featured discussions of the role of DNA recombinant technology in…

Validation of Microbial Source Tracking Markers and Detection Protocols: Considerations for Effective Interpretation

EPA Science Inventory

The goal of this chapter is to provide an overview of MST marker characteristics, to describe performance criteria of detection protocols used and to offer guidelines for the effective interpretation of the results. Since the trend in the research community has shifted towards (q...

The Historian and Electronic Research: File Transfer Protocol (FTP).

ERIC Educational Resources Information Center

McCarthy, Michael J.

1993-01-01

Asserts that the Internet will become the academic communication medium for historians in the 1990s. Describes the "file transfer protocol" (FTP) access approach to the Internet and discusses its significant for historical research. Includes instructions for using FTP and a list of history-related FTP sites. (CFR)

Technical Analysis of SSP-21 Protocol

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

Bromberger, S.

As part of the California Energy Systems for the Twenty-First Century (CES-21) program, in December 2016 San Diego Gas and Electric (SDG&E) contracted with Lawrence Livermore National Laboratory (LLNL) to perform an independent verification and validation (IV&V) of a white paper describing their Secure SCADA Protocol for the Twenty-First Century (SSP-21) in order to analyze the effectiveness and propriety of cryptographic protocol use within the SSP-21 specification. SSP-21 is designed to use cryptographic protocols to provide (optional) encryption, authentication, and nonrepudiation, among other capabilities. The cryptographic protocols to be used reflect current industry standards; future versions of SSP-21 will usemore » other advanced technologies to provide a subset of security services.« less

Biofeedback treatment of constipation: a critical review.

PubMed

Heymen, Steve; Jones, Kenneth R; Scarlett, Yolanda; Whitehead, William E

2003-09-01

This review was designed to 1) critically examine the research design used in investigations of biofeedback for pelvic floor dyssynergia, 2) compare the various biofeedback treatment protocols for pelvic floor dyssynergia-type constipation used in this research, 3) identify factors that influence treatment outcome, and 4) identify goals for future biofeedback research for pelvic floor dyssynergia. A comprehensive review of both the pediatric and adult research from 1970 to 2002 on "biofeedback for constipation" was conducted using a Medline search in all languages. Only prospective studies including five or more subjects that described the treatment protocol were included. In addition, a meta-analysis of these studies was performed to compare the outcome of different biofeedback protocols for treating constipation. Thirty-eight studies were reviewed, and sample size, treatment protocol, outcome rates, number of sessions, and etiology are shown in a table. Ten studies using a parallel treatment design were reviewed in detail, including seven that randomized subjects to treatment groups. A meta-analysis (weighted by subjects) was performed to compare the results of two treatment protocols prevalent in the literature. The mean success rate of studies using pressure biofeedback (78 percent) was superior (P = 0.018) to the mean success rate for studies using electromyography biofeedback (70 percent). However, the mean success rates comparing studies using intra-anal electromyography sensors to studies using perianal electromyography sensors were 69 and 72 percent, respectively, indicating no advantages for one type of electromyography protocol over the other (P = 0.428). In addition to the varied protocols and instrumentation used, there also are inconsistencies in the literature regarding the severity and etiology of symptoms, patient selection criteria, and the definition of a successful outcome. Finally, no anatomic, physiologic, or demographic variables were identified that would assist in predicting successful outcome. Having significant psychological symptoms was identified as a factor that may influence treatment outcome, but this requires further study. Although most studies report positive results using biofeedback to treat constipation, quality research is lacking. Specific recommendations are made for future investigations to 1) improve experimental design, 2) clearly define outcome measures, 3) identify the etiology and severity of symptoms, 4) determine which treatment protocol and which component of treatment is most effective for different types of subjects, 5) systematically explore the role of psychopathology in this population, 6) use an adequate sample size that allows for meaningful analysis, and 7) include long-term follow-up data.

Protocol-based care: the standardisation of decision-making?

PubMed

Rycroft-Malone, Jo; Fontenla, Marina; Seers, Kate; Bick, Debra

2009-05-01

To explore how protocol-based care affects clinical decision-making. In the context of evidence-based practice, protocol-based care is a mechanism for facilitating the standardisation of care and streamlining decision-making through rationalising the information with which to make judgements and ultimately decisions. However, whether protocol-based care does, in the reality of practice, standardise decision-making is unknown. This paper reports on a study that explored the impact of protocol-based care on nurses' decision-making. Theoretically informed by realistic evaluation and the promoting action on research implementation in health services framework, a case study design using ethnographic methods was used. Two sites were purposively sampled; a diabetic and endocrine unit and a cardiac medical unit. Within each site, data collection included observation, postobservation semi-structured interviews with staff and patients, field notes, feedback sessions and document review. Data were inductively and thematically analysed. Decisions made by nurses in both sites were varied according to many different and interacting factors. While several standardised care approaches were available for use, in reality, a variety of information sources informed decision-making. The primary approach to knowledge exchange and acquisition was person-to-person; decision-making was a social activity. Rarely were standardised care approaches obviously referred to; nurses described following a mental flowchart, not necessarily linked to a particular guideline or protocol. When standardised care approaches were used, it was reported that they were used flexibly and particularised. While the logic of protocol-based care is algorithmic, in the reality of clinical practice, other sources of information supported nurses' decision-making process. This has significant implications for the political goal of standardisation. The successful implementation and judicious use of tools such as protocols and guidelines will likely be dependant on approaches that facilitate the development of nurses' decision-making processes in parallel to paying attention to the influence of context.

Variability in usual care mechanical ventilation for pediatric acute lung injury: the potential benefit of a lung protective computer protocol.

PubMed

Khemani, Robinder G; Sward, Katherine; Morris, Alan; Dean, J Michael; Newth, Christopher J L

2011-11-01

Although pediatric intensivists claim to embrace lung protective ventilation for acute lung injury (ALI), ventilator management is variable. We describe ventilator changes clinicians made for children with hypoxemic respiratory failure, and evaluate the potential acceptability of a pediatric ventilation protocol. This was a retrospective cohort study performed in a tertiary care pediatric intensive care unit (PICU). The study period was from January 2000 to July 2007. We included mechanically ventilated children with PaO(2)/FiO(2) (P/F) ratio less than 300. We assessed variability in ventilator management by evaluating actual changes to ventilator settings after an arterial blood gas (ABG). We evaluated the potential acceptability of a pediatric mechanical ventilation protocol we adapted from National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) Acute Respiratory Distress Syndrome (ARDS) Network protocols by comparing actual practice changes in ventilator settings to changes that would have been recommended by the protocol. A total of 2,719 ABGs from 402 patients were associated with 6,017 ventilator settings. Clinicians infrequently decreased FiO(2), even when the PaO(2) was high (>68 mmHg). The protocol would have recommended more positive end expiratory pressure (PEEP) than was used in actual practice 42% of the time in the mid PaO(2) range (55-68 mmHg) and 67% of the time in the low PaO(2) range (<55 mmHg). Clinicians often made no change to either peak inspiratory pressure (PIP) or ventilator rate (VR) when the protocol would have recommended a change, even when the pH was greater than 7.45 with PIP at least 35 cmH(2)O. There may be lost opportunities to minimize potentially injurious ventilator settings for children with ALI. A reproducible pediatric mechanical ventilation protocol could prompt clinicians to make ventilator changes that are consistent with lung protective ventilation.

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.

Mobile Router Technology Development

NASA Technical Reports Server (NTRS)

Ivancic, William D.; Stewart, David H.; Bell, Terry L.; Kachmar, Brian A.; Shell, Dan; Leung, Kent

2002-01-01

Cisco Systems and NASA have been performing joint research on mobile routing technology under a NASA Space Act Agreement. Cisco developed mobile router technology and provided that technology to NASA for applications to aeronautic and space-based missions. NASA has performed stringent performance testing of the mobile router, including the interaction of routing and transport-level protocols. This paper describes mobile routing, the mobile router, and some key configuration parameters. In addition, the paper describes the mobile routing test network and test results documenting the performance of transport protocols in dynamic routing environments.

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

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.

SYTO probes: markers of apoptotic cell demise.

PubMed

Wlodkowic, Donald; Skommer, Joanna

2007-10-01

As mechanistic studies on tumor cell death advance towards their ultimate translational goal, there is a need for specific, rapid, and high-throughput analytical tools to detect diverse cell demise modes. Patented DNA-binding SYTO probes, for example, are gaining increasing interest as easy-to-use markers of caspase-dependent apoptotic cell death. They are proving convenient for tracking apoptosis in diverse hematopoietic cell lines and primary tumor samples, and, due to their spectral characteristics, appear to be useful for the development of multiparameter flow cytometry assays. Herein, several protocols for multiparametric assessment of apoptotic events using SYTO probes are provided. There are protocols describing the use of green fluorescent SYTO 16 and red fluorescent SYTO 17 dyes in combination with plasma membrane permeability markers. Another protocol highlights the multiparametric use of SYTO 16 dye in conjunction with the mitochondrial membrane potential sensitive probe, tetramethylrhodamine methyl ester (TMRM), and the plasma membrane permeability marker, 7-aminoactinomycin D (7-AAD).

The Ontology of Clinical Research (OCRe): An Informatics Foundation for the Science of Clinical Research

PubMed Central

Sim, Ida; Tu, Samson W.; Carini, Simona; Lehmann, Harold P.; Pollock, Brad H.; Peleg, Mor; Wittkowski, Knut M.

2013-01-01

To date, the scientific process for generating, interpreting, and applying knowledge has received less informatics attention than operational processes for conducting clinical studies. The activities of these scientific processes — the science of clinical research — are centered on the study protocol, which is the abstract representation of the scientific design of a clinical study. The Ontology of Clinical Research (OCRe) is an OWL 2 model of the entities and relationships of study design protocols for the purpose of computationally supporting the design and analysis of human studies. OCRe’s modeling is independent of any specific study design or clinical domain. It includes a study design typology and a specialized module called ERGO Annotation for capturing the meaning of eligibility criteria. In this paper, we describe the key informatics use cases of each phase of a study’s scientific lifecycle, present OCRe and the principles behind its modeling, and describe applications of OCRe and associated technologies to a range of clinical research use cases. OCRe captures the central semantics that underlies the scientific processes of clinical research and can serve as an informatics foundation for supporting the entire range of knowledge activities that constitute the science of clinical research. PMID:24239612

Evaluation of Cyanea capillata Sting Management Protocols Using Ex Vivo and In Vitro Envenomation Models

PubMed Central

Headlam, Jasmine L.; MacLoughlin, Eoin

2017-01-01

Lion’s mane jellyfish (Cyanea capillata) stings cause severe pain and can lead to dangerous systemic effects, including Irukandji-like syndrome. As is the case for most cnidarian stings, recommended medical protocols in response to such stings lack rigorous scientific support. In this study, we sought to evaluate potential first aid care protocols using previously described envenomation models that allow for direct measurements of venom activity. We found that seawater rinsing, the most commonly recommended method of tentacle removal for this species, induced significant increases in venom delivery, while rinsing with vinegar or Sting No More® Spray did not. Post-sting temperature treatments affected sting severity, with 40 min of hot-pack treatment reducing lysis of sheep’s blood (in agar plates), a direct representation of venom load, by over 90%. Ice pack treatment had no effect on sting severity. These results indicate that sting management protocols for Cyanea need to be revised immediately to discontinue rinsing with seawater and include the use of heat treatment. PMID:28686221

Novel methods to estimate antiretroviral adherence: protocol for a longitudinal study.

PubMed

Saberi, Parya; Ming, Kristin; Legnitto, Dominique; Neilands, Torsten B; Gandhi, Monica; Johnson, Mallory O

2018-01-01

There is currently no gold standard for assessing antiretroviral (ARV) adherence, so researchers often resort to the most feasible and cost-effective methods possible (eg, self-report), which may be biased or inaccurate. The goal of our study was to evaluate the feasibility and acceptability of innovative and remote methods to estimate ARV adherence, which can potentially be conducted with less time and financial resources in a wide range of clinic and research settings. Here, we describe the research protocol for studying these novel methods and some lessons learned. The 6-month pilot study aimed to examine the feasibility and acceptability of a remotely conducted study to evaluate the correlation between: 1) text-messaged photographs of pharmacy refill dates for refill-based adherence; 2) text-messaged photographs of pills for pill count-based adherence; and 3) home-collected hair sample measures of ARV concentration for pharmacologic-based adherence. Participants were sent monthly automated text messages to collect refill dates and pill counts that were taken and sent via mobile telephone photographs, and hair collection kits every 2 months by mail. At the study end, feasibility was calculated by specific metrics, such as the receipt of hair samples and responses to text messages. Participants completed a quantitative survey and qualitative exit interviews to examine the acceptability of these adherence evaluation methods. The relationship between the 3 novel metrics of adherence and self-reported adherence will be assessed. Investigators conducting adherence research are often limited to using either self-reported adherence, which is subjective, biased, and often overestimated, or other more complex methods. Here, we describe the protocol for evaluating the feasibility and acceptability of 3 novel and remote methods of estimating adherence, with the aim of evaluating the relationships between them. Additionally, we note the lessons learned from the protocol implementation to date. We expect that these novel measures will be feasible and acceptable. The implications of this research will be the identification and evaluation of innovative and accurate metrics of ARV adherence for future implementation.

Novel methods to estimate antiretroviral adherence: protocol for a longitudinal study

PubMed Central

Saberi, Parya; Ming, Kristin; Legnitto, Dominique; Neilands, Torsten B; Gandhi, Monica; Johnson, Mallory O

2018-01-01

Background There is currently no gold standard for assessing antiretroviral (ARV) adherence, so researchers often resort to the most feasible and cost-effective methods possible (eg, self-report), which may be biased or inaccurate. The goal of our study was to evaluate the feasibility and acceptability of innovative and remote methods to estimate ARV adherence, which can potentially be conducted with less time and financial resources in a wide range of clinic and research settings. Here, we describe the research protocol for studying these novel methods and some lessons learned. Methods The 6-month pilot study aimed to examine the feasibility and acceptability of a remotely conducted study to evaluate the correlation between: 1) text-messaged photographs of pharmacy refill dates for refill-based adherence; 2) text-messaged photographs of pills for pill count-based adherence; and 3) home-collected hair sample measures of ARV concentration for pharmacologic-based adherence. Participants were sent monthly automated text messages to collect refill dates and pill counts that were taken and sent via mobile telephone photographs, and hair collection kits every 2 months by mail. At the study end, feasibility was calculated by specific metrics, such as the receipt of hair samples and responses to text messages. Participants completed a quantitative survey and qualitative exit interviews to examine the acceptability of these adherence evaluation methods. The relationship between the 3 novel metrics of adherence and self-reported adherence will be assessed. Discussion Investigators conducting adherence research are often limited to using either self-reported adherence, which is subjective, biased, and often overestimated, or other more complex methods. Here, we describe the protocol for evaluating the feasibility and acceptability of 3 novel and remote methods of estimating adherence, with the aim of evaluating the relationships between them. Additionally, we note the lessons learned from the protocol implementation to date. We expect that these novel measures will be feasible and acceptable. The implications of this research will be the identification and evaluation of innovative and accurate metrics of ARV adherence for future implementation. PMID:29950816

Breadth in Design Problem Scoping: Using Insights from Experts to Investigate Student Processes. Research Brief

ERIC Educational Resources Information Center

Morozov, Andrew; Kilgore, Deborah; Atman, Cynthia

2007-01-01

In this study, the authors used two methods for analyzing expert data: verbal protocol analysis (VPA) and narrative analysis. VPA has been effectively used to describe the design processes employed by engineering students, expert designers, and expert-novice comparative research. VPA involves asking participants to "think aloud" while…

NHEXAS PHASE I REGION 5 STUDY--STANDARD OPERATING PROCEDURE--SAMPLE SHIPPING PROCEDURES (RTI/ACS-AP-209-083)

EPA Science Inventory

This procedure summarizes the sample shipping procedures that have been described in the individual NHEXAS sample collection protocols. This procedure serves as a quick reference tool for the field staff when samples are prepared for shipment at the field lab/staging area. For ea...

Multifunctional Interface Facility for Receiving and Processing Planetary Surface Materials for Science Investigation and Resource Evaluation at the Deep Space Gateway

NASA Astrophysics Data System (ADS)

Sibille, L.; Mantovani, J. G.; Townsend, I. I.; Mueller, R. P.

2018-02-01

The concepts describe hardware and instrumentation for the study of planetary surface materials at the Deep Space Gateway as a progressive evolution of capabilities for eliminating the need for special handling and Planetary Protection (PP) protocols inside the habitats.

The Use of Constructive Modeling and Virtual Simulation in Large-Scale Team Training: A Military Case Study.

ERIC Educational Resources Information Center

Andrews, Dee H.; Dineen, Toni; Bell, Herbert H.

1999-01-01

Discusses the use of constructive modeling and virtual simulation in team training; describes a military application of constructive modeling, including technology issues and communication protocols; considers possible improvements; and discusses applications in team-learning environments other than military, including industry and education. (LRW)

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…

From Reactionary to Responsive: Applying the Internal Environmental Scan Protocol to Lifelong Learning Strategic Planning and Operational Model Selection

ERIC Educational Resources Information Center

Downing, David L.

2009-01-01

This study describes and implements a necessary preliminary strategic planning procedure, the Internal Environmental Scanning (IES), and discusses its relevance to strategic planning and university-sponsored lifelong learning program model selection. Employing a qualitative research methodology, a proposed lifelong learning-centric IES process…

NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR PREPARATION OF STANDARD OPERATING PROCEDURES (SOPS) (UA-G-1.0)

EPA Science Inventory

The purpose of this SOP is to establish a uniform format for the preparation of SOPs. Use of these protocols ensures consistent implementation of project tasks, documents the preparation and implementation of the procedures used, describes quality control measures and the limits...

A Qualitative Analysis of an Advanced Practice Nurse-Directed Transitional Care Model Intervention

ERIC Educational Resources Information Center

Bradway, Christine; Trotta, Rebecca; Bixby, M. Brian; McPartland, Ellen; Wollman, M. Catherine; Kapustka, Heidi; McCauley, Kathleen; Naylor, Mary D.

2012-01-01

Purpose: The purpose of this study was to describe barriers and facilitators to implementing a transitional care intervention for cognitively impaired older adults and their caregivers lead by advanced practice nurses (APNs). Design and Methods: APNs implemented an evidence-based protocol to optimize transitions from hospital to home. An…

Investigating Reading Metacognitive Strategy Awareness of Elementary Children: A Developmental Continuum Emerges

ERIC Educational Resources Information Center

Cobb, Jeanne B.

2017-01-01

This article describes a descriptive study utilizing a picture protocol technique that integrated the use of photographs of good readers and children's representational drawings with informal conversations about their habits and behaviors before, during, and after reading. The research participants included 228 children in kindergarten through 5th…

Constraint-Induced Movement Therapy (CIMT): Pediatric Applications

ERIC Educational Resources Information Center

Brady, Kathleen; Garcia, Teressa

2009-01-01

The purpose of this article is to describe theoretical and research bases for constraint-induced movement therapy (CIMT), to discuss key features and variations in protocols currently in use with children, and to review the results of studies of efficacy. CIMT has been found to be an effective intervention for increasing functional use of the…

Aerobic Capacity in Children and Adolescents with Cerebral Palsy

ERIC Educational Resources Information Center

Verschuren, Olaf; Takken, Tim

2010-01-01

This study described the aerobic capacity [VO[subscript 2peak] (ml/kg/min)] in contemporary children and adolescents with cerebral palsy (CP) using a maximal exercise test protocol. Twenty-four children and adolescents with CP classified at Gross Motor Functional Classification Scale (GMFCS) level I or level II and 336 typically developing…

Avian Semen Collection by Cloacal Massage and Isolation of DNA from Sperm.

PubMed

Kucera, Aurelia C; Heidinger, Britt J

2018-02-05

Collection of semen may be useful for a wide range of applications including studies involving sperm quality, sperm telomere dynamics, and epigenetics. Birds are widely used subjects in biological research and are ideal for studies involving repeated sperm samples. However, few resources are currently available for those wishing to learn how to collect and extract DNA from avian sperm. Here we describe cloacal massage, a gentle, non-invasive manual technique for collecting avian sperm. Although this technique is established in the literature, it can be difficult to learn from the available descriptions. We also provide information for extracting DNA from avian semen using a commercial extraction kit with modifications. Cloacal massage can be easily used on any small- to medium-sized male bird in reproductive condition. Following collection, the semen can be used immediately for motility assays, or frozen for DNA extraction following the protocol described herein. This extraction protocol was refined for avian sperm and has been successfully used on samples collected from several passerine species (Passer domesticus, Spizella passerina, Haemorhous mexicanus, and Turdus migratorius) and one columbid (Columba livia).

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.

Mobile Virtual Private Networking

NASA Astrophysics Data System (ADS)

Pulkkis, Göran; Grahn, Kaj; Mårtens, Mathias; Mattsson, Jonny

Mobile Virtual Private Networking (VPN) solutions based on the Internet Security Protocol (IPSec), Transport Layer Security/Secure Socket Layer (SSL/TLS), Secure Shell (SSH), 3G/GPRS cellular networks, Mobile IP, and the presently experimental Host Identity Protocol (HIP) are described, compared and evaluated. Mobile VPN solutions based on HIP are recommended for future networking because of superior processing efficiency and network capacity demand features. Mobile VPN implementation issues associated with the IP protocol versions IPv4 and IPv6 are also evaluated. Mobile VPN implementation experiences are presented and discussed.

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.

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

Effects of a Delphi consensus acupuncture treatment protocol on the levels of stress and vascular tone in women undergoing in-vitro fertilization: a randomized clinical trial protocol.

PubMed

Zhang, Yan; Phy, Jennifer; Scott-Johnson, Chris; Garos, Sheila; Orlando, Jennie; Prien, Samuel; Huang, Jaou-Chen

2017-04-04

The variability of published acupuncture protocols for patients undergoing In-Vitro Fertilization (IVF) complicates the interpretation of data and hinders our understanding of acupuncture's impact. In 2012, an acupuncture treatment protocol developed by a Delphi consensus process was published to describe the parameters of best practice acupuncture for Assisted Reproductive Technology and future research. However, there has been no clinical trial utilizing this protocol to assess the effects of acupuncture. This study aims to assess the implementation of Dephi consensus acupuncture protocol and to examine the impact of acupuncture on stress and uterine and ovarian blood flow among women between ages 21-42 years seeking IVF. This study is a one site prospective, two-arm randomized controlled non-blind clinical trial conducted in a medical school-affiliated fertility center . Participants will be randomized 1:1 into either the acupuncture group or the standard of care (no acupuncture) group using computer generated tables. Both groups will have 3 regular clinical visits as their standard IVF care during an approximately 2 to 3 weeks window. Women who are randomized into the acupuncture group would receive three sessions based on the Delphi consensus acupuncture protocol in addition to the standard care. The first treatment will be administered between days 6 to 8 of the stimulated IVF cycle. The second session will be performed on the day of embryo transfer at least 1 h prior to the transfer. The third session will be performed within 48 h post-embryo transfer. Participants will be followed for their pregnancy test and pregnancy outcome when applicable. The outcomes stress and blood flow will be measured by a validated perceived stress scale and vasoactive molecules, respectively. Although recruitment and scheduling could be challenging at times, the Delphi consensus acupuncture protocol was implemented as planned and well-accepted by the patients. Because of the time-specified sessions around patients' IVF cycle, it is highly recommended to have on-site study acupuncturist(s) to accommodate the schedule. ClinicalTrials NCT02591186 registered on October 7, 2015.

Engineering designer transcription activator-like effector nucleases (TALENs) by REAL or REAL-Fast assembly.

PubMed

Reyon, Deepak; Khayter, Cyd; Regan, Maureen R; Joung, J Keith; Sander, Jeffry D

2012-10-01

Engineered transcription activator-like effector nucleases (TALENs) are broadly useful tools for performing targeted genome editing in a wide variety of organisms and cell types including plants, zebrafish, C. elegans, rat, human somatic cells, and human pluripotent stem cells. Here we describe detailed protocols for the serial, hierarchical assembly of TALENs that require neither PCR nor specialized multi-fragment ligations and that can be implemented by any laboratory. These restriction enzyme and ligation (REAL)-based protocols can be practiced using plasmid libraries and user-friendly, Web-based software that both identifies target sites in sequences of interest and generates printable graphical guides that facilitate assembly of TALENs. With the described platform of reagents, protocols, and software, researchers can easily engineer multiple TALENs within 2 weeks using standard cloning techniques. 2012 by John Wiley & Sons, Inc.

Parental intimate partner homicide and its consequences for children: protocol for a population-based study.

PubMed

Alisic, Eva; Groot, Arend; Snetselaar, Hanneke; Stroeken, Tielke; van de Putte, Elise

2015-07-29

The loss of a parent due to intimate partner homicide has a major impact on children. Professionals involved have to make far-reaching decisions regarding placement, guardianship, mental health care and contact with the perpetrating parent, without an evidence base to guide these decisions. We introduce a study protocol to a) systematically describe the demographics, circumstances, mental health and wellbeing of children bereaved by intimate partner homicide and b) build a predictive model of factors associated with children's mental health and wellbeing after intimate partner homicide. This study focuses on children bereaved by parental intimate partner homicide in the Netherlands over a period of 20 years (1993 - 2012). It involves an incidence study to identify all Dutch intimate partner homicide cases between 1993 and 2012 by which children have been bereaved; systematic case reviews to describe the demographics, circumstances and care trajectories of these children; and a mixed-methods study to assess mental health, wellbeing, and experiences regarding decisions made and care provided. Clinical experience and initial research suggest that the children involved often need long-term intensive mental health and case management. The costs of these services are extensive and the stakes are high. This study lays the foundation for an international dataset and evidence-informed decision making.

A centric/non-centric impact protocol and finite element model methodology for the evaluation of American football helmets to evaluate risk of concussion.

PubMed

Post, Andrew; Oeur, Anna; Walsh, Evan; Hoshizaki, Blaine; Gilchrist, Michael D

2014-01-01

American football reports high incidences of head injuries, in particular, concussion. Research has described concussion as primarily a rotation dominant injury affecting the diffuse areas of brain tissue. Current standards do not measure how helmets manage rotational acceleration or how acceleration loading curves influence brain deformation from an impact and thus are missing important information in terms of how concussions occur. The purpose of this study was to investigate a proposed three-dimensional impact protocol for use in evaluating football helmets. The dynamic responses resulting from centric and non-centric impact conditions were examined to ascertain the influence they have on brain deformations in different functional regions of the brain that are linked to concussive symptoms. A centric and non-centric protocol was used to impact an American football helmet; the resulting dynamic response data was used in conjunction with a three-dimensional finite element analysis of the human brain to calculate brain tissue deformation. The direction of impact created unique loading conditions, resulting in peaks in different regions of the brain associated with concussive symptoms. The linear and rotational accelerations were not predictive of the brain deformation metrics used in this study. In conclusion, the test protocol used in this study revealed that impact conditions influences the region of loading in functional regions of brain tissue that are associated with the symptoms of concussion. The protocol also demonstrated that using brain deformation metrics may be more appropriate when evaluating risk of concussion than using dynamic response data alone.

Development of the Diabetes Technology Society Blood Glucose Monitor System Surveillance Protocol

PubMed Central

Klonoff, David C.; Lias, Courtney; Beck, Stayce; Parkes, Joan Lee; Kovatchev, Boris; Vigersky, Robert A.; Arreaza-Rubin, Guillermo; Burk, Robert D.; Kowalski, Aaron; Little, Randie; Nichols, James; Petersen, Matt; Rawlings, Kelly; Sacks, David B.; Sampson, Eric; Scott, Steve; Seley, Jane Jeffrie; Slingerland, Robbert; Vesper, Hubert W.

2015-01-01

Background: Inaccurate blood glucsoe monitoring systems (BGMSs) can lead to adverse health effects. The Diabetes Technology Society (DTS) Surveillance Program for cleared BGMSs is intended to protect people with diabetes from inaccurate, unreliable BGMS products that are currently on the market in the United States. The Surveillance Program will provide an independent assessment of the analytical performance of cleared BGMSs. Methods: The DTS BGMS Surveillance Program Steering Committee included experts in glucose monitoring, surveillance testing, and regulatory science. Over one year, the committee engaged in meetings and teleconferences aiming to describe how to conduct BGMS surveillance studies in a scientifically sound manner that is in compliance with good clinical practice and all relevant regulations. Results: A clinical surveillance protocol was created that contains performance targets and analytical accuracy-testing studies with marketed BGMS products conducted by qualified clinical and laboratory sites. This protocol entitled “Protocol for the Diabetes Technology Society Blood Glucose Monitor System Surveillance Program” is attached as supplementary material. Conclusion: This program is needed because currently once a BGMS product has been cleared for use by the FDA, no systematic postmarket Surveillance Program exists that can monitor analytical performance and detect potential problems. This protocol will allow identification of inaccurate and unreliable BGMSs currently available on the US market. The DTS Surveillance Program will provide BGMS manufacturers a benchmark to understand the postmarket analytical performance of their products. Furthermore, patients, health care professionals, payers, and regulatory agencies will be able to use the results of the study to make informed decisions to, respectively, select, prescribe, finance, and regulate BGMSs on the market. PMID:26481642

Development of the Diabetes Technology Society Blood Glucose Monitor System Surveillance Protocol.

PubMed

Klonoff, David C; Lias, Courtney; Beck, Stayce; Parkes, Joan Lee; Kovatchev, Boris; Vigersky, Robert A; Arreaza-Rubin, Guillermo; Burk, Robert D; Kowalski, Aaron; Little, Randie; Nichols, James; Petersen, Matt; Rawlings, Kelly; Sacks, David B; Sampson, Eric; Scott, Steve; Seley, Jane Jeffrie; Slingerland, Robbert; Vesper, Hubert W

2016-05-01

Inaccurate blood glucsoe monitoring systems (BGMSs) can lead to adverse health effects. The Diabetes Technology Society (DTS) Surveillance Program for cleared BGMSs is intended to protect people with diabetes from inaccurate, unreliable BGMS products that are currently on the market in the United States. The Surveillance Program will provide an independent assessment of the analytical performance of cleared BGMSs. The DTS BGMS Surveillance Program Steering Committee included experts in glucose monitoring, surveillance testing, and regulatory science. Over one year, the committee engaged in meetings and teleconferences aiming to describe how to conduct BGMS surveillance studies in a scientifically sound manner that is in compliance with good clinical practice and all relevant regulations. A clinical surveillance protocol was created that contains performance targets and analytical accuracy-testing studies with marketed BGMS products conducted by qualified clinical and laboratory sites. This protocol entitled "Protocol for the Diabetes Technology Society Blood Glucose Monitor System Surveillance Program" is attached as supplementary material. This program is needed because currently once a BGMS product has been cleared for use by the FDA, no systematic postmarket Surveillance Program exists that can monitor analytical performance and detect potential problems. This protocol will allow identification of inaccurate and unreliable BGMSs currently available on the US market. The DTS Surveillance Program will provide BGMS manufacturers a benchmark to understand the postmarket analytical performance of their products. Furthermore, patients, health care professionals, payers, and regulatory agencies will be able to use the results of the study to make informed decisions to, respectively, select, prescribe, finance, and regulate BGMSs on the market. © 2015 Diabetes Technology Society.

A question of authority

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

Morgan, Earl W.

A Question of Authority. This article deals with a certain scenario and several reviewers are to give their opinion. This one is in regards to - Suspending an IACUC approved animal use activity is about the last thing a research institution wants to do. Consider the predicament that the Great Eastern University IACUC faced when Dr. Janet Jenkins, the Attending Veterinarian, suspended all animal use activity on an approved protocol of Dr. Roy Maslo. Jenkins had the IACUCs authority to temporarily suspend a protocol, subject to review by a quorum of the full committee. She alleged that Maslo used micemore » from his breeding colony, not purchased rats, to begin a new study. Jenkins saw Maslos technicians bringing mouse cages to a procedure room and setting up for a minor survival surgery. She asked them to wait until she clarified things as she felt confident that the protocol called for rats. She called Maslo and asked him if the study had been approved for mice, to which he responded affirmatively. Still not feeling quite assured, she went to her office, reviewed the protocol, and found only rat studies described. She also called the IACUC office to see if there were any approved amendments which she may not have received, and was told that there were none. By the time she returned, one procedure was completed. Understandably upset, she informed the technicians and Maslo that any further activity on the protocol was suspended until the issue was resolved. Jenkins informed the IACUC chairman who in turned called an emergency meeting of the committee.« less

Assessment of Adverse Events in Protocols, Clinical Study Reports, and Published Papers of Trials of Orlistat: A Document Analysis.

PubMed

Schroll, Jeppe Bennekou; Penninga, Elisabeth I; Gøtzsche, Peter C

2016-08-01

Little is known about how adverse events are summarised and reported in trials, as detailed information is usually considered confidential. We have acquired clinical study reports (CSRs) from the European Medicines Agency through the Freedom of Information Act. The CSRs describe the results of studies conducted as part of the application for marketing authorisation for the slimming pill orlistat. The purpose of this study was to study how adverse events were summarised and reported in study protocols, CSRs, and published papers of orlistat trials. We received the CSRs from seven randomised placebo controlled orlistat trials (4,225 participants) submitted by Roche. The CSRs consisted of 8,716 pages and included protocols. Two researchers independently extracted data on adverse events from protocols and CSRs. Corresponding published papers were identified on PubMed and adverse event data were extracted from this source as well. All three sources were compared. Individual adverse events from one trial were summed and compared to the totals in the summary report. None of the protocols or CSRs contained instructions for investigators on how to question participants about adverse events. In CSRs, gastrointestinal adverse events were only coded if the participant reported that they were "bothersome," a condition that was not specified in the protocol for two of the trials. Serious adverse events were assessed for relationship to the drug by the sponsor, and all adverse events were coded by the sponsor using a glossary that could be updated by the sponsor. The criteria for withdrawal due to adverse events were in one case related to efficacy (high fasting glucose led to withdrawal), which meant that one trial had more withdrawals due to adverse events in the placebo group. Finally, only between 3% and 33% of the total number of investigator-reported adverse events from the trials were reported in the publications because of post hoc filters, though six of seven papers stated that "all adverse events were recorded." For one trial, we identified an additional 1,318 adverse events that were not listed or mentioned in the CSR itself but could be identified through manually counting individual adverse events reported in an appendix. We discovered that the majority of patients had multiple episodes of the same adverse event that were only counted once, though this was not described in the CSRs. We also discovered that participants treated with orlistat experienced twice as many days with adverse events as participants treated with placebo (22.7 d versus 14.9 d, p-value < 0.0001, Student's t test). Furthermore, compared with the placebo group, adverse events in the orlistat group were more severe. None of this was stated in the CSR or in the published paper. Our analysis was restricted to one drug tested in the mid-1990s; our results might therefore not be applicable for newer drugs. In the orlistat trials, we identified important disparities in the reporting of adverse events between protocols, clinical study reports, and published papers. Reports of these trials seemed to have systematically understated adverse events. Based on these findings, systematic reviews of drugs might be improved by including protocols and CSRs in addition to published articles.

Dog EEG for wake-promotion studies.

PubMed

Parmentier, Régis; Bricout, Denis; Brousseau, Emmanuel; Giboulot, Thierry

2006-10-01

Described in this unit is a protocol for investigating the wake-promoting activity of new chemical entities (NCEs) in dog. The experimental approach is based on scoring of sleep/wake stages in animals implanted with a telemetry device for recording EMG and cortical EEG signals. A major advantage of this procedure is that it is conducted in nontethered animals, limiting possible bias and complications encountered with conventional recording systems. In this procedure, polygraphic recording is conducted using four implanted beagles. Results of studies with modafinil, a wake-promoting agent, are described to demonstrate the utility of this test procedure.

Single-cell transcriptome conservation in cryopreserved cells and tissues.

PubMed

Guillaumet-Adkins, Amy; Rodríguez-Esteban, Gustavo; Mereu, Elisabetta; Mendez-Lago, Maria; Jaitin, Diego A; Villanueva, Alberto; Vidal, August; Martinez-Marti, Alex; Felip, Enriqueta; Vivancos, Ana; Keren-Shaul, Hadas; Heath, Simon; Gut, Marta; Amit, Ido; Gut, Ivo; Heyn, Holger

2017-03-01

A variety of single-cell RNA preparation procedures have been described. So far, protocols require fresh material, which hinders complex study designs. We describe a sample preservation method that maintains transcripts in viable single cells, allowing one to disconnect time and place of sampling from subsequent processing steps. We sequence single-cell transcriptomes from >1000 fresh and cryopreserved cells using 3'-end and full-length RNA preparation methods. Our results confirm that the conservation process did not alter transcriptional profiles. This substantially broadens the scope of applications in single-cell transcriptomics and could lead to a paradigm shift in future study designs.

Fall risk screening protocol for older hearing clinic patients.

PubMed

Criter, Robin E; Honaker, Julie A

2017-10-01

The primary purposes of this study were (1) to describe measures that may contrast audiology patients who fall from those who do not fall and (2) to evaluate the clinical performance of measures that could be easily used for fall risk screening in a mainstream audiology hearing clinic. Cross-sectional study Study sample: Thirty-six community-dwelling audiology patient participants and 27 community-dwelling non-audiology patients over 60 years of age. The Hearing Handicap Inventory for the Elderly (HHIE) most accurately identified patients with a recent fall (sensitivity: 76.0%), while the Dizziness Handicap Inventory (DHI) most accurately identified patients without a recent fall (specificity: 90.9%). A combination of measures used in a protocol-including HHIE, DHI, number of medications, and the Timed Up and Go test-resulted in good, accurate identification of patients with or without a recent history of falls (92.0% sensitivity, 100% specificity). This study reports good sensitivity and excellent specificity for identifying patients with and without a recent history of falls when measures were combined into a screening protocol. Despite previously reported barriers, effective fall risk screenings may be performed in hearing clinic settings with measures often readily accessible to audiologists.

The "Healthy Habits, Healthy Girls" randomized controlled trial for girls: study design, protocol, and baseline results.

PubMed

Leme, Ana Carolina Barco; Philippi, Sonia Tucunduva

2015-07-01

The purpose of this article is to describe the study design, protocol, and baseline results of the "Healthy Habits, Healthy Girls" program. The intervention is being evaluated through a randomized controlled trial in 10 public schools in the city of São Paulo, Brazil. Data on the following variables were collected and assessed at baseline and will be reevaluated at 7 and 12 months: body mass index, waist circumference, dietary intake, nutrition, physical activity, social cognitive mediators, physical activity level, sedentary behaviors, self-rated physical status, and overall self-esteem. According to the baseline results, 32.4% and 23.4% of girls were overweight in the intervention and control groups, respectively, and in both groups a higher percentage failed to meet daily recommendations for moderate and vigorous physical activity and maximum screen time (TV, computer, mobile devices). There were no significant differences between the groups for most of the variables, except age (p = 0.000) and waist circumference (p = 0.014). The study showed a gap in the Brazilian literature on protocols for randomized controlled trials to prevent obesity among youth. The current study may thus be an important initial contribution to the field.

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.

Near-optimal protocols in complex nonequilibrium transformations

DOE PAGES

Gingrich, Todd R.; Rotskoff, Grant M.; Crooks, Gavin E.; ...

2016-08-29

The development of sophisticated experimental means to control nanoscale systems has motivated efforts to design driving protocols that minimize the energy dissipated to the environment. Computational models are a crucial tool in this practical challenge. In this paper, we describe a general method for sampling an ensemble of finite-time, nonequilibrium protocols biased toward a low average dissipation. In addition, we show that this scheme can be carried out very efficiently in several limiting cases. As an application, we sample the ensemble of low-dissipation protocols that invert the magnetization of a 2D Ising model and explore how the diversity of themore » protocols varies in response to constraints on the average dissipation. In this example, we find that there is a large set of protocols with average dissipation close to the optimal value, which we argue is a general phenomenon.« less

The Classroom Observation Protocol for Undergraduate STEM (COPUS): a new instrument to characterize university STEM classroom practices.

PubMed

Smith, Michelle K; Jones, Francis H M; Gilbert, Sarah L; Wieman, Carl E

2013-01-01

Instructors and the teaching practices they employ play a critical role in improving student learning in college science, technology, engineering, and mathematics (STEM) courses. Consequently, there is increasing interest in collecting information on the range and frequency of teaching practices at department-wide and institution-wide scales. To help facilitate this process, we present a new classroom observation protocol known as the Classroom Observation Protocol for Undergraduate STEM or COPUS. This protocol allows STEM faculty, after a short 1.5-hour training period, to reliably characterize how faculty and students are spending their time in the classroom. We present the protocol, discuss how it differs from existing classroom observation protocols, and describe the process by which it was developed and validated. We also discuss how the observation data can be used to guide individual and institutional change.

A Push-pull Protocol to Reduce Colonization of Bird Nest Boxes by Honey Bees.

PubMed

Efstathion, Caroline A; Kern, William H

2016-09-04

Introduction of the invasive Africanized honey bee (AHB) into the Neotropics is a serious problem for many cavity nesting birds, specifically parrots. These bees select cavities that are suitable nest sites for birds, resulting in competition. The difficulty of removing bees and their defensive behavior makes a prevention protocol necessary. Here, we describe a push-pull integrated pest management protocol to deter bees from inhabiting bird boxes by applying a bird safe insecticide, permethrin, to repel bees from nest boxes, while simultaneously attracting them to pheromone-baited swarm traps. Shown here is an example experiment using Barn Owl nest boxes. This protocol successfully reduced colonization of Barn Owl nest boxes by Africanized honey bees. This protocol is flexible, allowing adjustments to accommodate a wide range of bird species and habitats. This protocol could benefit conservation efforts where AHB are located.

Proposal for founding mistrustful quantum cryptography on coin tossing

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

Kent, Adrian; Hewlett-Packard Laboratories, Filton Road, Stoke Gifford, Bristol BS34 8QZ,

2003-07-01

A significant branch of classical cryptography deals with the problems which arise when mistrustful parties need to generate, process, or exchange information. As Kilian showed a while ago, mistrustful classical cryptography can be founded on a single protocol, oblivious transfer, from which general secure multiparty computations can be built. The scope of mistrustful quantum cryptography is limited by no-go theorems, which rule out, inter alia, unconditionally secure quantum protocols for oblivious transfer or general secure two-party computations. These theorems apply even to protocols which take relativistic signaling constraints into account. The best that can be hoped for, in general, aremore » quantum protocols which are computationally secure against quantum attack. Here a method is described for building a classically certified bit commitment, and hence every other mistrustful cryptographic task, from a secure coin-tossing protocol. No security proof is attempted, but reasons are sketched why these protocols might resist quantum computational attack.« less

A Novel Re-keying Function Protocol (NRFP) For Wireless Sensor Network Security

PubMed Central

Abdullah, Maan Younis; Hua, Gui Wei; Alsharabi, Naif

2008-01-01

This paper describes a novel re-keying function protocol (NRFP) for wireless sensor network security. A re-keying process management system for sensor networks is designed to support in-network processing. The design of the protocol is motivated by decentralization key management for wireless sensor networks (WSNs), covering key deployment, key refreshment, and key establishment. NRFP supports the establishment of novel administrative functions for sensor nodes that derive/re-derive a session key for each communication session. The protocol proposes direct connection, in-direct connection and hybrid connection. NRFP also includes an efficient protocol for local broadcast authentication based on the use of one-way key chains. A salient feature of the authentication protocol is that it supports source authentication without precluding innetwork processing. Security and performance analysis shows that it is very efficient in computation, communication and storage and, that NRFP is also effective in defending against many sophisticated attacks. PMID:27873963

The Classroom Observation Protocol for Undergraduate STEM (COPUS): A New Instrument to Characterize University STEM Classroom Practices

PubMed Central

Smith, Michelle K.; Jones, Francis H. M.; Gilbert, Sarah L.; Wieman, Carl E.

2013-01-01

Instructors and the teaching practices they employ play a critical role in improving student learning in college science, technology, engineering, and mathematics (STEM) courses. Consequently, there is increasing interest in collecting information on the range and frequency of teaching practices at department-wide and institution-wide scales. To help facilitate this process, we present a new classroom observation protocol known as the Classroom Observation Protocol for Undergraduate STEM or COPUS. This protocol allows STEM faculty, after a short 1.5-hour training period, to reliably characterize how faculty and students are spending their time in the classroom. We present the protocol, discuss how it differs from existing classroom observation protocols, and describe the process by which it was developed and validated. We also discuss how the observation data can be used to guide individual and institutional change. PMID:24297289

A Novel Re-keying Function Protocol (NRFP) For Wireless Sensor Network Security.

PubMed

Abdullah, Maan Younis; Hua, Gui Wei; Alsharabi, Naif

2008-12-04

This paper describes a novel re-keying function protocol (NRFP) for wireless sensor network security. A re-keying process management system for sensor networks is designed to support in-network processing. The design of the protocol is motivated by decentralization key management for wireless sensor networks (WSNs), covering key deployment, key refreshment, and key establishment. NRFP supports the establishment of novel administrative functions for sensor nodes that derive/re-derive a session key for each communication session. The protocol proposes direct connection, in-direct connection and hybrid connection. NRFP also includes an efficient protocol for local broadcast authentication based on the use of one-way key chains. A salient feature of the authentication protocol is that it supports source authentication without precluding in-network processing. Security and performance analysis shows that it is very efficient in computation, communication and storage and, that NRFP is also effective in defending against many sophisticated attacks.

Secular trends and smoke-free policy development in rural Kentucky

PubMed Central

Fallin, Amanda; Parker, Lindsay; Lindgreen, Janine; Riker, Carol; Kercsmar, Sarah; Hahn, Ellen J.

2011-01-01

Secondhand smoke (SHS) exposure causes cardiovascular disease, lung cancer and pulmonary disorders. Smoke-free policies are the most effective way to prevent exposure to SHS. A 5-year community-based randomized control trial (RCT) is in progress to assess factors associated with smoke-free policy development in rural communities. Considering secular trends is critical when conducting community-based RCTs as they may threaten the internal validity of the study. For the purposes of this paper, secular trends are defined as patterns or recurring events that are not directly related to smoke-free policy but have the potential to influence policy development. There are no established protocols to monitor secular trends in the study of smoke-free policy in rural communities. The purpose of this paper is to (i) describe the development of a protocol to identify and monitor secular trends that may threaten the internal validity of a community-based RCT to promote smoke-free policy development and (ii) describe secular trends identified in the first 2 years of the RCT. The sample includes 854 secular events captured from media outlets covering the 40 study counties over the first 2 years of the RCT. Of these 854 events, there were 281 secular events in Year 1 and 573 in Year 2. This paper focuses on five specific categories: ‘tobacco use and cessation activities’, ‘farming’, ‘economics’, ‘city/county infrastructure’ and ‘wellness’. This protocol is a feasible yet time-intensive method of identifying events that may threaten the internal validity of a community-based RCT. PMID:21558440

Clinical protocol levels are required in laboratory animal surgery when using medical devices: experiences with ureteral replacement surgery in goats.

PubMed

de Jonge, Paul K J D; Sloff, Marije; Janke, Heinz P; Kortmann, Barbara B M; de Gier, Robert P E; Geutjes, Paul J; Oosterwijk, Egbert; Feitz, Wout F J

2017-10-01

It is common to test medical devices in large animal studies that are or could also be used in humans. In this short report we describe the use of a ureteral J-stent for the evaluation of biodegradable tubular constructs for tissue reconstruction, and the regeneration of ureters in Saanen goats. Similarly to a previous study in pigs, the ureteral J-stent was blindly inserted until some resistance was met. During evaluation of the goats after three months, perforation of the renal cortex by the stent was observed in four out of seven animals. These results indicated that blind stent placement was not possible in goats. In four new goats, clinical protocols were followed using X-ray and iodinated contrast fluids to visualize the kidney and stent during stent placement. With this adaptation the stents were successfully placed in the kidneys of these four new goats with minimal additional effort. It is likely that other groups in other fields ran into similar problems that could have been avoided by following clinical protocols. Therefore, we would like to stress the importance of following clinical protocols when using medical devices in animals to prevent unnecessary suffering and to reduce the number of animals needed.

Metal- and additive-free photoinduced borylation of haloarenes.

PubMed

Mfuh, Adelphe M; Schneider, Brett D; Cruces, Westley; Larionov, Oleg V

2017-03-01

Boronic acids and esters have critical roles in the areas of synthetic organic chemistry, molecular sensors, materials science, drug discovery, and catalysis. Many of the current applications of boronic acids and esters require materials with very low levels of transition metal contamination. Most of the current methods for the synthesis of boronic acids, however, require transition metal catalysts and ligands that must be removed via additional purification procedures. This protocol describes a simple, metal- and additive-free method of conversion of haloarenes directly to boronic acids and esters. This photoinduced borylation protocol does not require expensive and toxic metal catalysts or ligands, and it produces innocuous and easy-to-remove by-products. Furthermore, the reaction can be carried out on multigram scales in common-grade solvents without the need for reaction mixtures to be deoxygenated. The setup and purification steps are typically accomplished within 1-3 h. The reactions can be run overnight, and the protocol can be completed within 13-16 h. Two representative procedures that are described in this protocol provide details for preparation of a boronic acid (3-cyanopheylboronic acid) and a boronic ester (1,4-benzenediboronic acid bis(pinacol)ester). We also discuss additional details of the method that will be helpful in the application of the protocol to other haloarene substrates.

A field protocol to monitor cavity-nesting birds

Treesearch

J. Dudley; V. Saab

2003-01-01

We developed a field protocol to monitor populations of cavity-nesting birds in burned and unburned coniferous forests of western North America. Standardized field methods are described for implementing long-term monitoring strategies and for conducting field research to evaluate the effects of habitat change on cavity-nesting birds. Key references (but not...

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...

Deployment of the Space Internet on a Spacecraft: Hosting CFDP and/or DTN Protocol Engines and the Resulting Resource Utilization

NASA Astrophysics Data System (ADS)

Foswell, Stuart D.; McLaren, David; Paramanatham, Daran; Taylor, Chris; Stanton, Dai; Farrell, Stephen

2012-08-01

This paper describes the outcome of analysis and simulation of how to deploy CFDP and DTN protocol engines onboard a spacecraft, so as to support the Space Internet, and the resulting spacecraft resource utilisation, under an ESA TRP contract [1].

Interlibrary Loan, the Key to Resource Sharing: A Manual of Procedures and Protocols.

ERIC Educational Resources Information Center

Alaska State Dept. of Education, Juneau. Div. of State Libraries.

Intended for use by librarians in Alaska, this manual provides general guidelines for the maximum utilization of library resources through interlibrary loan service. The first of four major sections describes the Alaska Library Network (ALN), which provides protocols and procedures to libraries for resource sharing; points out that new protocols…

The Power of Protocols: An Educator's Guide to Better Practice. The Series on School Reform.

ERIC Educational Resources Information Center

McDonald, Joseph P.; Mohr, Nancy; Dichter, Alan; McDonald, Elizabeth C.

This book describes nearly 30 protocols or "scripts" for conducting meetings, conversations, and other learning experiences among educators. Chapter 1, "The Basic Ideas," explains the basic ideas underlying the rest of the book, discussing why educators should educate themselves and making the case for exploring student work as…

Analysis of the Impacts of an Early Start for Compliance with the Kyoto Protocol

EIA Publications

1999-01-01

This report describes the Energy Information Administration's analysis of the impacts of an early start, using the same methodology as in Impacts of the Kyoto Protocol on U.S. Energy Markets and Economic Activity, with only those changes in assumptions caused by the early start date.

Development of bull trout sampling protocols

Treesearch

R. F. Thurow; J. T. Peterson; J. W. Guzevich

2001-01-01

This report describes results of research conducted in Washington in 2000 through Interagency Agreement #134100H002 between the U.S. Fish and Wildlife Service (USFWS) and the U.S. Forest Service Rocky Mountain Research Station (RMRS). The purpose of this agreement is to develop a bull trout (Salvelinus confluentus) sampling protocol by integrating...

Adding Dimension to Evaluative Research Through the Use of Protocol Material.

ERIC Educational Resources Information Center

Tittle, Carol Kehr

A rationale and illustration of the use of original records or protocol materials in an evaluation research report are described. Records of school observations and audiotape transcripts were selected to represent the concepts or categories which were developed in the process of evaluation. These qualitative data were collected in a project which…

Demography of Honors: The Census of U.S. Honors Programs and Colleges

ERIC Educational Resources Information Center

Scott, Richard I.; Smith, Patricia J.; Cognard-Black, Andrew J.

2017-01-01

Beginning in 2013 and spanning four research articles, we have implemented an empirical analysis protocol for honors education that is rooted in demography (Scott; Scott and Smith; Smith and Scott "Growth"; Smith and Scott, "Demography"). The goal of this protocol is to describe the structure and distribution of the honors…

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

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles

PubMed Central

Schneidman-Duhovny, Dina; Hammel, Michal

2018-01-01

Small-angle X-ray scattering (SAXS) is an increasingly common and useful technique for structural characterization of molecules in solution. A SAXS experiment determines the scattering intensity of a molecule as a function of spatial frequency, termed SAXS profile. SAXS profiles can be utilized in a variety of molecular modeling applications, such as comparing solution and crystal structures, structural characterization of flexible proteins, assembly of multi-protein complexes, and modeling of missing regions in the high-resolution structure. Here, we describe protocols for modeling atomic structures based on SAXS profiles. The first protocol is for comparing solution and crystal structures including modeling of missing regions and determination of the oligomeric state. The second protocol performs multi-state modeling by finding a set of conformations and their weights that fit the SAXS profile starting from a single-input structure. The third protocol is for protein-protein docking based on the SAXS profile of the complex. We describe the underlying software, followed by demonstrating their application on interleukin 33 (IL33) with its primary receptor ST2 and DNA ligase IV-XRCC4 complex. PMID:29605933

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.

Miniaturization of the Clonogenic Assay Using Confluence Measurement

PubMed Central

Mayr, Christian; Beyreis, Marlena; Dobias, Heidemarie; Gaisberger, Martin; Pichler, Martin; Ritter, Markus; Jakab, Martin; Neureiter, Daniel; Kiesslich, Tobias

2018-01-01

The clonogenic assay is a widely used method to study the ability of cells to ‘infinitely’ produce progeny and is, therefore, used as a tool in tumor biology to measure tumor-initiating capacity and stem cell status. However, the standard protocol of using 6-well plates has several disadvantages. By miniaturizing the assay to a 96-well microplate format, as well as by utilizing the confluence detection function of a multimode reader, we here describe a new and modified protocol that allows comprehensive experimental setups and a non-endpoint, label-free semi-automatic analysis. Comparison of bright field images with confluence images demonstrated robust and reproducible detection of clones by the confluence detection function. Moreover, time-resolved non-endpoint confluence measurement of the same well showed that semi-automatic analysis was suitable for determining the mean size and colony number. By treating cells with an inhibitor of clonogenic growth (PTC-209), we show that our modified protocol is suitable for comprehensive (broad concentration range, addition of technical replicates) concentration- and time-resolved analysis of the effect of substances or treatments on clonogenic growth. In summary, this protocol represents a time- and cost-effective alternative to the commonly used 6-well protocol (with endpoint staining) and also provides additional information about the kinetics of clonogenic growth. PMID:29510509

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.

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.

Health-care management of an unexpected case of Ebola virus disease at the Alcorcón Foundation University Teaching Hospital.

PubMed

Rodríguez-Caravaca, Gil; Timermans, Rafael; Parra-Ramírez, Juan Manuel; Domínguez-Hernández, Francisco Javier; Algora-Weber, Alejandro; Delgado-Iribarren, Alberto; Hermida-Gutiérrez, Guillermo

2015-04-01

The first Ebola virus infected patient outside Africa was diagnosed and treated at Alcorcón Foundation University Teaching Hospital (AFUTH). We describe the integrated management strategy (medical, occupational health, preventive and public health) applied to the case. Descriptive study of health-care management of an unexpected case of Ebola virus disease (EVD) at AFUTH treated on 6 October 2014. We describe the clinical evolution of the patient while he was attended at the Emergency Department, the drawing-up process of the action protocol, the process of training of hospital staff, the administrative management for transferring the patient to the referral centre, and the measures implemented for cleaning, disinfection and management of waste. Qualitative variables are expressed as percentages. Our centre designed and updated, from May to October, five versions of the acting and care protocol for patients with EVD. The protocol was in force at the AFUTH when a nursing assistant was attended on 6 October 2014. All preventive, diagnostic and therapeutic measures outlined in the protocol were applied and 206 professionals had received training and information about care procedures with a suspect case. Health-care management of an unexpected case of EVD was adequate and there was no secondary cases in our staff as a result. All resources available should be used to fight EVD. Copyright © 2015 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Rationale, timeline, study design, and protocol overview of the therapeutic hypothermia after pediatric cardiac arrest trials.

PubMed

Moler, Frank W; Silverstein, Faye S; Meert, Kathleen L; Clark, Amy E; Holubkov, Richard; Browning, Brittan; Slomine, Beth S; Christensen, James R; Dean, J Michael

2013-09-01

To describe the rationale, timeline, study design, and protocol overview of the Therapeutic Hypothermia after Pediatric Cardiac Arrest trials. Multicenter randomized controlled trials. Pediatric intensive care and cardiac ICUs in the United States and Canada. Children from 48 hours to 18 years old, who have return of circulation after cardiac arrest, who meet trial eligibility criteria, and whose guardians provide written consent. Therapeutic hypothermia or therapeutic normothermia. From concept inception in 2002 until trial initiation in 2009, 7 years were required to plan and operationalize the Therapeutic Hypothermia after Pediatric Cardiac Arrest trials. Two National Institute of Child Health and Human Development clinical trial planning grants (R21 and R34) supported feasibility assessment and protocol development. Two clinical research networks, Pediatric Emergency Care Applied Research Network and Collaborative Pediatric Critical Care Research Network, provided infrastructure resources. Two National Heart Lung Blood Institute U01 awards provided funding to conduct separate trials of in-hospital and out-of-hospital cardiac arrest. A pilot vanguard phase that included half the clinical sites began on March 9, 2009, and this was followed by full trial funding through 2015. Over a decade will have been required to plan, design, operationalize, and conduct the Therapeutic Hypothermia after Pediatric Cardiac Arrest trials. Details described in this report, such as participation of clinical research networks and clinical trial planning grants utilization, may be of utility for individuals who are planning investigator-initiated, federally supported clinical trials.

Optimization of methods for the genetic modification of human T cells.

PubMed

Bilal, Mahmood Y; Vacaflores, Aldo; Houtman, Jon Cd

2015-11-01

CD4(+) T cells are not only critical in the fight against parasitic, bacterial and viral infections, but are also involved in many autoimmune and pathological disorders. Studies of protein function in human T cells are confined to techniques such as RNA interference (RNAi) owing to ethical reasons and relative simplicity of these methods. However, introduction of RNAi or genes into primary human T cells is often hampered by toxic effects from transfection or transduction methods that yield cell numbers inadequate for downstream assays. Additionally, the efficiency of recombinant DNA expression is frequently low because of multiple factors including efficacy of the method and strength of the targeting RNAs. Here, we describe detailed protocols that will aid in the study of primary human CD4(+) T cells. First, we describe a method for development of effective microRNA/shRNAs using available online algorithms. Second, we illustrate an optimized protocol for high efficacy retroviral or lentiviral transduction of human T-cell lines. Importantly, we demonstrate that activated primary human CD4(+) T cells can be transduced efficiently with lentiviruses, with a highly activated population of T cells receiving the largest number of copies of integrated DNA. We also illustrate a method for efficient lentiviral transduction of hard-to-transduce un-activated primary human CD4(+) T cells. These protocols will significantly assist in understanding the activation and function of human T cells and will ultimately aid in the development or improvement of current drugs that target human CD4(+) T cells.

Definition and evaluation of the data-link layer of PACnet

NASA Astrophysics Data System (ADS)

Alsafadi, Yasser H.; Martinez, Ralph; Sanders, William H.

1991-07-01

PACnet is a 200-500 Mbps dual-ring fiber optic network designed to implement a picture archiving and communication system (PACS) in a hospital environment. The network consists of three channels: an image transfer channel, a command and control channel, and a real-time data channel. An initial network interface unit (NIU) design for PACnet consisted of a functional description of the protocols and NIU major components. In order to develop a demonstration prototype, additional definition of protocol algorithms of each channel is necessary. Using the International Standards Organization/Open Systems Interconnection (ISO/OSI) reference model as a guide, the definition of the data link layer is extended. This definition covers interface service specifications for the two constituent sublayers: logical link control (LLC) and medium access control (MAC). Furthermore, it describes procedures for data transfer, mechanisms of error detection and fault recovery. A performance evaluation study was then made to determine how the network performs under various application scenarios. The performance evaluation study was performed using stochastic activity networks, which can formally describe the network behavior. The results of the study demonstrate the feasibility of PACnet as an integrated image, data, and voice network for PACS.

Fast protocol for radiochromic film dosimetry using a cloud computing web application.

PubMed

Calvo-Ortega, Juan-Francisco; Pozo, Miquel; Moragues, Sandra; Casals, Joan

2017-07-01

To investigate the feasibility of a fast protocol for radiochromic film dosimetry to verify intensity-modulated radiotherapy (IMRT) plans. EBT3 film dosimetry was conducted in this study using the triple-channel method implemented in the cloud computing application (Radiochromic.com). We described a fast protocol for radiochromic film dosimetry to obtain measurement results within 1h. Ten IMRT plans were delivered to evaluate the feasibility of the fast protocol. The dose distribution of the verification film was derived at 15, 30, 45min using the fast protocol and also at 24h after completing the irradiation. The four dose maps obtained per plan were compared using global and local gamma index (5%/3mm) with the calculated one by the treatment planning system. Gamma passing rates obtained for 15, 30 and 45min post-exposure were compared with those obtained after 24h. Small differences respect to the 24h protocol were found in the gamma passing rates obtained for films digitized at 15min (global: 99.6%±0.9% vs. 99.7%±0.5%; local: 96.3%±3.4% vs. 96.3%±3.8%), at 30min (global: 99.5%±0.9% vs. 99.7%±0.5%; local: 96.5%±3.2% vs. 96.3±3.8%) and at 45min (global: 99.2%±1.5% vs. 99.7%±0.5%; local: 96.1%±3.8% vs. 96.3±3.8%). The fast protocol permits dosimetric results within 1h when IMRT plans are verified, with similar results as those reported by the standard 24h protocol. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-01-01

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

Indication-Based Ordering: A New Paradigm for Glycemic Control in Hospitalized Inpatients

PubMed Central

Lee, Joshua; Clay, Brian; Zelazny, Ziband; Maynard, Gregory

2008-01-01

Background Inpatient glycemic control is a constant challenge. Institutional insulin management protocols and structured order sets are commonly advocated but poorly studied. Effective and validated methods to integrate algorithmic protocol guidance into the insulin ordering process are needed. Methods We introduced a basic structured set of computerized insulin orders (Version 1), and later introduced a paper insulin management protocol, to assist users with the order set. Metrics were devised to assess the impact of the protocol on insulin use, glycemic control, and hypoglycemia using pharmacy data and point of care glucose tests. When incremental improvement was seen (as described in the results), Version 2 of the insulin orders was created to further streamline the process. Results The percentage of regimens containing basal insulin improved with Version 1. The percentage of patient days with hypoglycemia improved from 3.68% at baseline to 2.59% with Version 1 plus the paper insulin management protocol, representing a relative risk for hypoglycemic day of 0.70 [confidence interval (CI) 0.62, 0.80]. The relative risk of an uncontrolled (mean glucose over 180 mg/dl) patient stay was reduced to 0.84 (CI 0.77, 0.91) with Version 1 and was reduced further to 0.73 (CI 0.66, 0.81) with the paper protocol. Version 2 used clinician-entered patient parameters to guide protocol-based insulin ordering and simultaneously improved the flexibility and ease of ordering over Version 1. Conclusion Patient parameter and protocol-based clinical decision support, added to computerized provider order entry, has a track record of improving glycemic control indices. This justifies the incorporation of these algorithms into online order management. PMID:19885198

Automation of metabolic stability studies in microsomes, cytosol and plasma using a 215 Gilson liquid handler.

PubMed

Linget, J M; du Vignaud, P

1999-05-01

A 215 Gilson liquid handler was used to automate enzymatic incubations using microsomes, cytosol and plasma. The design of automated protocols are described. They were based on the use of 96 deep well plates and on HPLC-based methods for assaying the substrate. The assessment of those protocols was made with comparison between manual and automated incubations, reliability and reproducibility of automated incubations in microsomes and cytosol. Examples of the use of those programs in metabolic studies in drug research, i.e. metabolic screening in microsomes and plasma were shown. Even rapid processes (with disappearance half lives as low as 1 min) can be analysed. This work demonstrates how stability studies can be automated to save time, render experiments involving human biological media less hazardous and may be improve inter-laboratory reproducibility.

Methods to study the biogenesis of membrane proteins in yeast mitochondria.

PubMed

Weckbecker, Daniel; Herrmann, Johannes M

2013-01-01

The biogenesis of mitochondrial membrane proteins is an intricate process that relies on the import and submitochondrial sorting of nuclear-encoded preproteins and on the synthesis of mitochondrial translation products in the matrix. Subsequently, these polypeptides need to be inserted into the outer and the inner membranes of the organelle where many of them assemble into multisubunit complexes. In this chapter we provide established protocols to study these different processes experimentally using mitochondria of budding yeast. In particular, methods are described in detail to purify mitochondria, to study mitochondrial protein synthesis, to follow the import of radiolabeled preproteins into isolated mitochondria, and to assess membrane association and the aggregation of mitochondrial proteins by fractionation. These protocols and a list of dos and don'ts shall enable beginners and experienced scientists to address the targeting and assembly of mitochondrial membrane proteins.

Electronic Entanglement Concentration for the Concatenated Greenberger-Horne-Zeilinger State

NASA Astrophysics Data System (ADS)

Ding, Shang-Ping; Zhou, Lan; Gu, Shi-Pu; Wang, Xing-Fu; Sheng, Yu-Bo

2017-06-01

Concatenated Greenberger-Horne-Zeilinger (C-GHZ) state, which encodes many physical qubits in a logic qubit will have important applications in both quantum communication and computation. In this paper, we will describe an entanglement concentration protocol (ECP) for electronic C-GHZ state, by exploiting the electronic polarization beam splitters (PBSs) and charge detection. This protocol has several advantages. First, the parties do not need to know the exact coefficients of the initial less-entangled C-GHZ state, which makes this protocol feasible. Second, with the help of charge detection, the distilled maximally entangled C-GHZ state can be remained for future application. Third, this protocol can be repeated to obtain a higher success probability. We hope that this protocol can be useful in future quantum computation based on electrons.

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/.

Detection of Drug-Resistant Mycobacterium tuberculosis.

PubMed

Engström, Anna; Juréen, Pontus

2015-01-01

Tuberculosis (TB) remains a global health problem. The increasing prevalence of drug-resistant Mycobacterium tuberculosis, the causative agent of TB, demands new measures to combat the situation. Rapid and accurate diagnosis of the pathogen and its drug susceptibility pattern is essential for timely initiation of optimal treatment, and, ultimately, control of the disease. We have developed a molecular method for detection of first- and second-line drug resistance in M. tuberculosis by Pyrosequencing(®). The method consists of seven Pyrosequencing assays for the detection of mutations in the genes or promoter regions, which are most commonly responsible for resistance to the drugs rifampicin, isoniazid, ethambutol, amikacin, kanamycin, capreomycin, and fluoroquinolones. The method was validated on clinical isolates and it was shown that the sensitivity and specificity of the method were comparable to those of Sanger sequencing. In the protocol in this chapter we describe the steps necessary for setting up and performing Pyrosequencing for M. tuberculosis. The first part of the protocol describes the assay development and the second part of the protocol describes utilization of the method.

Cryptographic Protocol for Comparing Sets without Leaking Them: Applications in Astronomy

NASA Astrophysics Data System (ADS)

McCullough, Peter R.

2011-09-01

We describe a cryptographic protocol for two or more persons to compare individual lists of astronomical objects of interest without leaking them. Cryptographers have long known such protocols; astronomers and other scientists may benefit from them also. We describe some latent opportunities that would be enabled by this protocol. Consider the following scenario: Alice has a set of stars that are candidate hosts of transiting planets. Bob has a similar set. Alice and Bob have a mutual desire to know the intersection of their two lists without revealing them to each other. Alice and Bob can recruit a trusted third party, Josephine, to make the comparison, report the results, and then destroy each list. Limitations of that approach are that 1) Josephine must devote time to make each comparison, 2) Alice and Bob may not know a Josephine that they both can trust, especially if Alice and Bob are from different communities, 3) Josephine may not indeed be trustworthy, 4) a fourth person may wittingly or unwittingly intercept one or both of the lists in Josephine's care, and 5) anticipating those limitations, Alice and Bob may elect not to recruit a Josephine and hence not compare their lists. We describe a variant that overcomes those limitations by A) encrypting the lists prior to transmitting them to Josephine, and B) replacing a human Josephine with a computer website.

Refining animal models in fracture research: seeking consensus in optimising both animal welfare and scientific validity for appropriate biomedical use.

PubMed

Auer, Jorg A; Goodship, Allen; Arnoczky, Steven; Pearce, Simon; Price, Jill; Claes, Lutz; von Rechenberg, Brigitte; Hofmann-Amtenbrinck, Margarethe; Schneider, Erich; Müller-Terpitz, R; Thiele, F; Rippe, Klaus-Peter; Grainger, David W

2007-08-01

In an attempt to establish some consensus on the proper use and design of experimental animal models in musculoskeletal research, AOVET (the veterinary specialty group of the AO Foundation) in concert with the AO Research Institute (ARI), and the European Academy for the Study of Scientific and Technological Advance, convened a group of musculoskeletal researchers, veterinarians, legal experts, and ethicists to discuss, in a frank and open forum, the use of animals in musculoskeletal research. The group narrowed the field to fracture research. The consensus opinion resulting from this workshop can be summarized as follows: Anaesthesia and pain management protocols for research animals should follow standard protocols applied in clinical work for the species involved. This will improve morbidity and mortality outcomes. A database should be established to facilitate selection of anaesthesia and pain management protocols for specific experimental surgical procedures and adopted as an International Standard (IS) according to animal species selected. A list of 10 golden rules and requirements for conduction of animal experiments in musculoskeletal research was drawn up comprising 1) Intelligent study designs to receive appropriate answers; 2) Minimal complication rates (5 to max. 10%); 3) Defined end-points for both welfare and scientific outputs analogous to quality assessment (QA) audit of protocols in GLP studies; 4) Sufficient details for materials and methods applied; 5) Potentially confounding variables (genetic background, seasonal, hormonal, size, histological, and biomechanical differences); 6) Post-operative management with emphasis on analgesia and follow-up examinations; 7) Study protocols to satisfy criteria established for a "justified animal study"; 8) Surgical expertise to conduct surgery on animals; 9) Pilot studies as a critical part of model validation and powering of the definitive study design; 10) Criteria for funding agencies to include requirements related to animal experiments as part of the overall scientific proposal review protocols. Such agencies are also encouraged to seriously consider and adopt the recommendations described here when awarding funds for specific projects. Specific new requirements and mandates related both to improving the welfare and scientific rigour of animal-based research models are urgently needed as part of international harmonization of standards.

Abbreviated breast magnetic resonance protocol: Value of high-resolution temporal dynamic sequence to improve lesion characterization.

PubMed

Oldrini, Guillaume; Fedida, Benjamin; Poujol, Julie; Felblinger, Jacques; Trop, Isabelle; Henrot, Philippe; Darai, Emile; Thomassin-Naggara, Isabelle

2017-10-01

To evaluate the added value of ULTRAFAST-MR sequence to an abbreviated FAST protocol in comparison with FULL protocol to distinguish benign from malignant lesions in a population of women, regardless of breast MR imaging indication. From March 10th to September 22th, 2014, we retrospectively included a total of 70 consecutive patients with 106 histologically proven lesions (58 malignant and 48 benign) who underwent breast MR imaging for preoperative breast staging (n=38), high-risk screening (n=7), problem solving (n=18), and nipple discharge (n=4) with 12 time resolved imaging of contrast kinetics (TRICKS) acquisitions during contrast inflow interleaved in a regular high-resolution dynamic MRI protocol (FULL protocol). Two readers scored MR exams as either positive or negative and described significant lesions according to Bi-RADS lexicon with a TRICKS images (ULTRAFAST), an abbreviated protocol (FAST) and all images (FULL protocol). Sensitivity, specificity, positive and negative predictive values, and accuracy were calculated for each protocol and compared with McNemar's test. For all readers, the combined FAST-ULTRAFAST protocol significantly improved the reading with a specificity of 83.3% and 70.8% in comparison with FAST protocol or FULL protocol, respectively, without change in sensitivity. By adding ULTRAFAST protocol to FAST protocol, readers 1 and 2 were able to correctly change the diagnosis in 22.9% (11/48) and 10.4% (5/48) of benign lesions, without missing any malignancy, respectively. Both interpretation and image acquisition times for combined FAST-ULTRAFAST protocol and FAST protocol were shorter compared to FULL protocol (p<0.001). Compared to FULL protocol, adding ULTRAFAST to FAST protocol improves specificity, mainly in correctly reclassifying benign masses and reducing interpretation and acquisition time, without decreasing sensitivity. Copyright © 2017 Elsevier B.V. All rights reserved.

The time-adjusted gradual replacement injection method enables better visualization of the right heart.

PubMed

Nakahara, Takehiro; Jinzaki, Masahiro; Niwamae, Nogiku; Saito, Yuuichirou; Arai, Masashi; Tsushima, Yoshito; Kuribayashi, Sachio; Kurabayashi, Masahiko

2014-01-01

Despite the improvement of cardiac CT, right heart visualization remains challenging. We herein describe a new method, called the time-adjusted gradual replacement injection protocol. The aim of this study was to compare this protocol with the split-bolus injection protocol. Fifty-two patients who had undergone dual-source cardiac CT were retrospectively recruited. Twenty-six patients were injected by using the split-bolus injection protocol, and 26 patients were injected by using the time-adjusted gradual replacement injection protocol. For this method, we injected contrast medium for 10 seconds at a flow rate of 0.07 × body weight mL/s, then gradually replaced the contrast material with saline until 2 seconds before finishing the scans. The CT attenuation was measured in 4 chambers, the aorta, and the coronary arteries. The visualization of the anatomic structures and the occurrence and severity of streak artifacts were scored for the cardiac structures in the heart. For the analyses, either Welch t-test or Student t-test was performed. In the right heart, the CT values and visualization scores were significantly higher in the time-adjusted replacement injection group than in the split-bolus injection group, whereas the artifact scores were comparable between the 2 groups. The CT values, visualization scores, and artifact scores of the left heart were not significantly different between the 2 groups. In this study, the time-adjusted gradual replacement injection protocol provided excellent attenuation for visualization of the right heart. This method may help to accurately evaluate the right cardiac anatomy and thereby identify any potential diseases. Copyright © 2014 Society of Cardiovascular Computed Tomography. Published by Elsevier Inc. All rights reserved.

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.

Implementing a Pro-forma for Multidisciplinary Management of an Enterocutaneous Fistula: A Case Study.

PubMed

Samad, Sohel; Anele, Chukwuemeka; Akhtar, Mansoor; Doughan, Samer

2015-06-01

Optimal management of patients with an entercocutaneous fistula (ECF) requires utilization of the sepsis, nutrition, anatomy, and surgical procedure (SNAP) protocol. The protocol includes early detection and treatment of sepsis, optimizing patient nutrition through oral and parenteral routes, identifying the fistula anatomy, optimal fistula management, and proceeding to corrective surgery when appropriate. The protocol requires multidisciplinary team (MDT) coordination among surgeons, nurses, dietitians, stoma nurses, and physiotherapists. This case study describes a 70-year-old man who developed an ECF subsequent to a laparotomy for a small bowel obstruction. Following a period of ileus, 16 days post laparotomy the patient developed a high-output (2,000 mL per day) fistula. The patient also became pyrexial with raised inflammatory markers, requiring antibiotic treatment. Following development of his ECF, he was managed using the SNAP protocol for the duration of his admission; however, in implementing this protocol with this patient, clinicians noted fluid charts were inadequate to allow effective management of the variables. Thus, a new pro-forma was created that encompassed fluid balance, nutritional status, and pertinent blood test results, as well as perifistular skin condition, medication, and documentation of management plans from the MDT team. The pro-forma was recorded daily in the patient notes. Following implementation of the pro-forma and the SNAP protocol, the patient recovered well clinically over a period of 4 weeks with a decrease in his fistula output to 300-500 mL per day, and he was discharged with plans for further corrective surgery to resect the fistula and for bowel re-anastomoses. Although fluid charts are readily available, they do not include all pertinent variables for optimal management of patients with an ECF. Further research is needed to validate the pro-forma and evaluate its effect on patient outcomes.

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.

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.

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).

Plasmid fermentation process for DNA immunization applications.

PubMed

Carnes, Aaron E; Williams, James A

2014-01-01

Plasmid DNA for immunization applications must be of the highest purity and quality. The ability of downstream purification to efficiently produce a pure final product is directly influenced by the performance of the upstream fermentation process. While several clinical manufacturing facilities already have validated fermentation processes in place to manufacture plasmid DNA for use in humans, a simple and inexpensive laboratory-scale fermentation process can be valuable for in-house production of plasmid DNA for use in animal efficacy studies. This chapter describes a simple fed-batch fermentation process for producing bacterial cell paste enriched with high-quality plasmid DNA. A constant feeding strategy results in a medium cell density culture with continuously increasing plasmid amplification towards the end of the process. Cell banking and seed culture preparation protocols, which can dramatically influence final product yield and quality, are also described. These protocols are suitable for production of research-grade plasmid DNA at the 100 mg-to-1.5 g scale from a typical 10 L laboratory benchtop fermentor.

A safe and accurate method to perform esthetic mandibular contouring surgery for Far Eastern Asians.

PubMed

Hsieh, A M-C; Huon, L-K; Jiang, H-R; Liu, S Y-C

2017-05-01

A tapered mandibular contour is popular with Far Eastern Asians. This study describes a safe and accurate method of using preoperative virtual surgical planning (VSP) and an intraoperative ostectomy guide to maximize the esthetic outcomes of mandibular symmetry and tapering while mitigating injury to the inferior alveolar nerve (IAN). Twelve subjects with chief complaints of a wide and square lower face underwent this protocol from January to June 2015. VSP was used to confirm symmetry and preserve the IAN while maximizing the surgeon's ability to taper the lower face via mandibular inferior border ostectomy. The accuracy of this method was confirmed by superimposition of the perioperative computed tomography scans in all subjects. No subjects complained of prolonged paresthesia after 3 months. A safe and accurate protocol for achieving an esthetic lower face in indicated Far Eastern individuals is described. Copyright © 2016 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

CRISPR/Cas-Mediated Knockin in Human Pluripotent Stem Cells.

PubMed

Verma, Nipun; Zhu, Zengrong; Huangfu, Danwei

2017-01-01

Fluorescent reporter and epitope-tagged human pluripotent stem cells (hPSCs) greatly facilitate studies on the pluripotency and differentiation characteristics of these cells. Unfortunately traditional procedures to generate such lines are hampered by a low targeting efficiency that necessitates a lengthy process of selection followed by the removal of the selection cassette. Here we describe a procedure to generate fluorescent reporter and epitope tagged hPSCs in an efficient one-step process using the CRISPR/Cas technology. Although the method described uses our recently developed iCRISPR platform, the protocols can be adapted for general use with CRISPR/Cas or other engineered nucleases. The transfection procedures described could also be used for additional applications, such as overexpression or lineage tracing studies.

Handling and restraint.

PubMed

Donovan, John; Brown, Patricia

2006-07-01

For the safety of the handler and the animal, proper methods for handling and restraining laboratory animals should be followed. Improper handling can result in increased stress and injury to the animal. In addition, the handler risks injury from bite wounds or scratches inflicted when the animal becomes fearful or anxious. By using sure, direct movements with a determined attitude, the animal can be easily handled and restrained. Animals can be restrained either manually or in a plastic restrainer. The protocols in this unit describe handling and manual restraint of mice, rats, hamsters, and rabbits. Alternate protocols describe restraint using the plastic restrainer.

Handling and restraint.

PubMed

Donovan, John; Brown, Patricia

2004-09-01

For the safety of the handler and the animal, proper methods for handling and restraining laboratory animals should be followed. Improper handling can result in increased stress and injury to the animal. In addition, the handler risks injury from bite wounds or scratches inflicted when the animal becomes fearful or anxious. By using sure, direct movements with a determined attitude, the animal can be easily handled and restrained. Animals can be restrained either manually or in a plastic restrainer. The protocols in this unit describe handling and manual restraint of mice, rats, hamsters, and rabbits. Alternate protocols describe restraint using the plastic restrainer.

[Giant hernias with loss of domain: what is the best way to prepare patients?].

PubMed

Balaphas, Alexandre; Morel, Philippe; Breguet, Romain; Assalino, Michela

2016-06-15

Giant hernias with loss of domain induce physiological modifications that impair quality of life and make more complex their surgical management. A good preparation of patients before surgery is the key to an eventless postoperative course. The progressive pre-operative pneumoperitoneum (PPP) is one of the described abdominal augmentation protocols which can help patients to tolerate hernia content reintegration and avoid components separation technique during hernia repair. This article describes the management of these complex patients. We also report the case of a patient who follows successfully a PPP protocol.

Combining fluorescence imaging with Hi-C to study 3D genome architecture of the same single cell.

PubMed

Lando, David; Basu, Srinjan; Stevens, Tim J; Riddell, Andy; Wohlfahrt, Kai J; Cao, Yang; Boucher, Wayne; Leeb, Martin; Atkinson, Liam P; Lee, Steven F; Hendrich, Brian; Klenerman, Dave; Laue, Ernest D

2018-05-01

Fluorescence imaging and chromosome conformation capture assays such as Hi-C are key tools for studying genome organization. However, traditionally, they have been carried out independently, making integration of the two types of data difficult to perform. By trapping individual cell nuclei inside a well of a 384-well glass-bottom plate with an agarose pad, we have established a protocol that allows both fluorescence imaging and Hi-C processing to be carried out on the same single cell. The protocol identifies 30,000-100,000 chromosome contacts per single haploid genome in parallel with fluorescence images. Contacts can be used to calculate intact genome structures to better than 100-kb resolution, which can then be directly compared with the images. Preparation of 20 single-cell Hi-C libraries using this protocol takes 5 d of bench work by researchers experienced in molecular biology techniques. Image acquisition and analysis require basic understanding of fluorescence microscopy, and some bioinformatics knowledge is required to run the sequence-processing tools described here.

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

Heat acclimation: Gold mines and genes

PubMed Central

Schneider, Suzanne M.

2016-01-01

ABSTRACT The underground gold mines of South Africa offer a unique historical setting to study heat acclimation. The early heat stress research was conducted and described by a young medical officer, Dr. Aldo Dreosti. He developed practical and specific protocols to first assess the heat tolerance of thousands of new mining recruits, and then used the screening results as the basis for assigning a heat acclimation protocol. The mines provide an interesting paradigm where the prevention of heat stroke evolved from genetic selection, where only Black natives were recruited due to a false assumption of their intrinsic tolerance to heat, to our current appreciation of the epigenetic and other molecular adaptations that occur with exposure to heat. PMID:28090556

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

Organoid culture systems for prostate epithelial tissue and prostate cancer tissue

PubMed Central

Drost, Jarno; Karthaus, Wouter R.; Gao, Dong; Driehuis, Else; Sawyers, Charles L.; Chen, Yu; Clevers, Hans

2016-01-01

Summary This protocol describes a recently developed strategy to generate 3D prostate organoid cultures from healthy mouse and human prostate (either bulk or FAC-sorted single luminal and basal cells), metastatic prostate cancer lesions and circulating tumour cells. Organoids derived from healthy material contain the differentiated luminal and basal cell types, whereas organoids derived from prostate cancer tissue mimic the histology of the tumour. The stepwise establishment of these cultures and the fully defined serum-free conditioned medium that is required to sustain organoid growth are outlined. Organoids established using this protocol can be used to study many different aspects of prostate biology, including homeostasis, tumorigenesis and drug discovery. PMID:26797458

Isolation of Eosinophils from the Lamina Propria of the Murine Small Intestine.

PubMed

Berek, Claudia; Beller, Alexander; Chu, Van Trung

2016-01-01

Only recently has it become apparent that eosinophils play a crucial role in mucosal immune homeostasis. Although eosinophils are the main cellular component of the lamina propria of the gastrointestinal tract, they have often been overlooked because they express numerous markers, which are normally used to characterize macrophages and/or dendritic cells. To study their function in mucosal immunity, it is important to isolate them with high purity and viability. Here, we describe a protocol to purify eosinophils from the lamina propria of the murine small intestine. The method involves preparation of the small intestine, removal of epithelial cells and digestion of the lamina propria to release eosinophils. A protocol to sort eosinophils is included.

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--STANDARD OPERATING PROCEDURE FOR PREPARATION OF STANDARD OPERATING PROCEDURES (SOPS) (UA-G-1.0)

EPA Science Inventory

The purpose of this SOP is to establish a uniform format for the preparation of SOPs. Use of these protocols ensures consistent implementation of project tasks, documents the preparation and implementation of the procedures used, describes quality control measures and the limits...

DNA Fingerprinting Using PCR: A Practical Forensic Science Activity

ERIC Educational Resources Information Center

Choi, Hyun-Jung; Ahn, Jung Hoon; Ko, Minsu

2008-01-01

This paper describes a forensic science simulation programme applicable for use in colleges. Students were asked to find a putative suspect by DNA fingerprinting using a simple protocol developed in this study. DNA samples were obtained from a hair root and a drop of blood, common sources of DNA in forensic science. The DNA fingerprinting protocol…

Factors Contributing to Academic Success and Persistence in Female, Lower Socioeconomic College Students

ERIC Educational Resources Information Center

Huffman, Martisia Denise

2012-01-01

This qualitative research study looked at 13 students who because of their backgrounds and/or family environments were considered to be high risk of educational failure, but against the odds completed a 4-year degree with honors. Analysis of the open-ended interview protocol produced 5 emergent themes: (a) self-described individual attributes that…

Prolonged Exposure Therapy Following Awareness under Anesthesia: A Case Study

ERIC Educational Resources Information Center

Levinson, Cheri A.; Rodebaugh, Thomas L.; Bertelson, Amy D.

2013-01-01

Awareness during surgery is estimated to effect between 40,000 to 140,000 patients per year in the United States, and there is a growing literature suggesting that this event can lead to the development of posttraumatic stress disorder (PTSD). The current article describes treatment implemented from a manualized protocol of a woman diagnosed with…

Signaling Task Awareness in Think-Aloud Protocols from Students Selecting Relevant Information from Text

ERIC Educational Resources Information Center

Schellings, Gonny L. M.; Broekkamp, Hein

2011-01-01

Self-regulated learning has been described as an adaptive process: students adapt their learning strategies for attaining different learning goals. In order to be adaptive, students must have a clear notion of what the task requirements consist of. Both trace data and questionnaire data indicate that students adapt study strategies in limited ways…

Development of a redox-free Mitsunobu reaction exploiting phosphine oxides as precursors to dioxyphosphoranes.

PubMed

Tang, Xiaoping; Chapman, Charlotte; Whiting, Matthew; Denton, Ross

2014-07-14

The development of the first redox-free protocol for the Mitsunobu reaction is described. This has been achieved by exploiting triphenylphosphine oxide--the unwanted by-product in the conventional Mitsunobu reaction--as the precursor to the active P(V) coupling reagent. Multinuclear NMR studies are consistent with hydroxyl activation via an alkoxyphosphonium salt.

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.