Awake craniotomy anesthetic management using dexmedetomidine, propofol, and remifentanil

PubMed Central

Prontera, Andrea; Baroni, Stefano; Marudi, Andrea; Valzania, Franco; Feletti, Alberto; Benuzzi, Francesca; Bertellini, Elisabetta; Pavesi, Giacomo

2017-01-01

Introduction Awake craniotomy allows continuous monitoring of patients’ neurological functions during open surgery. Anesthesiologists have to sedate patients in a way so that they are compliant throughout the whole surgical procedure, nevertheless maintaining adequate analgesia and anxiolysis. Currently, the use of α2-receptor agonist dexmedetomidine as the primary hypnotic–sedative medication is increasing. Methods Nine patients undergoing awake craniotomy were treated with refined monitored anesthesia care (MAC) protocol consisting of a combination of local anesthesia without scalp block, low-dose infusion of dexmedetomidine, propofol, and remifentanil, without the need of airways management. Results The anesthetic protocol applied in our study has the advantage of decreasing the dose of each drug and thus reducing the occurrence of side effects. All patients had smooth and rapid awakenings. The brain remained relaxed during the entire procedure. Conclusion In our experience, this protocol is safe and effective during awake brain surgery. Nevertheless, prospective randomized trials are necessary to confirm the optimal anesthetic technique to be used. PMID:28424537

Awake craniotomy anesthetic management using dexmedetomidine, propofol, and remifentanil.

PubMed

Prontera, Andrea; Baroni, Stefano; Marudi, Andrea; Valzania, Franco; Feletti, Alberto; Benuzzi, Francesca; Bertellini, Elisabetta; Pavesi, Giacomo

2017-01-01

Awake craniotomy allows continuous monitoring of patients' neurological functions during open surgery. Anesthesiologists have to sedate patients in a way so that they are compliant throughout the whole surgical procedure, nevertheless maintaining adequate analgesia and anxiolysis. Currently, the use of α2-receptor agonist dexmedetomidine as the primary hypnotic-sedative medication is increasing. Nine patients undergoing awake craniotomy were treated with refined monitored anesthesia care (MAC) protocol consisting of a combination of local anesthesia without scalp block, low-dose infusion of dexmedetomidine, propofol, and remifentanil, without the need of airways management. The anesthetic protocol applied in our study has the advantage of decreasing the dose of each drug and thus reducing the occurrence of side effects. All patients had smooth and rapid awakenings. The brain remained relaxed during the entire procedure. In our experience, this protocol is safe and effective during awake brain surgery. Nevertheless, prospective randomized trials are necessary to confirm the optimal anesthetic technique to be used.

Protocol for determining bull trout presence

Treesearch

James Peterson; Jason B. Dunham; Philip Howell; Russell Thurow; Scott Bonar

2002-01-01

The Western Division of the American Fisheries Society was requested to develop protocols for determining presence/absence and potential habitat suitability for bull trout. The general approach adopted is similar to the process for the marbled murrelet, whereby interim guidelines are initially used, and the protocols are subsequently refined as data are collected....

An automated system for positive reinforcement training of group-housed macaque monkeys at breeding and research facilities.

PubMed

Tulip, Jennifer; Zimmermann, Jonas B; Farningham, David; Jackson, Andrew

2017-06-15

Behavioural training through positive reinforcement techniques is a well-recognised refinement to laboratory animal welfare. Behavioural neuroscience research requires subjects to be trained to perform repetitions of specific behaviours for food/fluid reward. Some animals fail to perform at a sufficient level, limiting the amount of data that can be collected and increasing the number of animals required for each study. We have implemented automated positive reinforcement training systems (comprising a button press task with variable levels of difficulty using LED cues and a fluid reward) at the breeding facility and research facility, to compare performance across these different settings, to pre-screen animals for selection and refine training protocols. Animals learned 1- and 4-choice button tasks within weeks of home enclosure training, with some inter-individual differences. High performance levels (∼200-300 trials per 60min session at ∼80% correct) were obtained without food or fluid restriction. Moreover, training quickly transferred to a laboratory version of the task. Animals that acquired the task at the breeding facility subsequently performed better both in early home enclosure sessions upon arrival at the research facility, and also in laboratory sessions. Automated systems at the breeding facility may be used to pre-screen animals for suitability for behavioural neuroscience research. In combination with conventional training, both the breeding and research facility systems facilitate acquisition and transference of learning. Automated systems have the potential to refine training protocols and minimise requirements for food/fluid control. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome.

PubMed

Lamm, Ayelet T; Stadler, Michael R; Zhang, Huibin; Gent, Jonathan I; Fire, Andrew Z

2011-02-01

We have used a combination of three high-throughput RNA capture and sequencing methods to refine and augment the transcriptome map of a well-studied genetic model, Caenorhabditis elegans. The three methods include a standard (non-directional) library preparation protocol relying on cDNA priming and foldback that has been used in several previous studies for transcriptome characterization in this species, and two directional protocols, one involving direct capture of single-stranded RNA fragments and one involving circular-template PCR (CircLigase). We find that each RNA-seq approach shows specific limitations and biases, with the application of multiple methods providing a more complete map than was obtained from any single method. Of particular note in the analysis were substantial advantages of CircLigase-based and ssRNA-based capture for defining sequences and structures of the precise 5' ends (which were lost using the double-strand cDNA capture method). Of the three methods, ssRNA capture was most effective in defining sequences to the poly(A) junction. Using data sets from a spectrum of C. elegans strains and stages and the UCSC Genome Browser, we provide a series of tools, which facilitate rapid visualization and assignment of gene structures.

Dry Starch Powders Modified Teabag Method

EPA Pesticide Factsheets

The following is a test protocol for a “tea bag analysis” that was conducted on PMN starches by the Corn Refiners Association. This protocol is one approach to providing information on swellability of high molecular weight polymers.

KoBaMIN: a knowledge-based minimization web server for protein structure refinement.

PubMed

Rodrigues, João P G L M; Levitt, Michael; Chopra, Gaurav

2012-07-01

The KoBaMIN web server provides an online interface to a simple, consistent and computationally efficient protein structure refinement protocol based on minimization of a knowledge-based potential of mean force. The server can be used to refine either a single protein structure or an ensemble of proteins starting from their unrefined coordinates in PDB format. The refinement method is particularly fast and accurate due to the underlying knowledge-based potential derived from structures deposited in the PDB; as such, the energy function implicitly includes the effects of solvent and the crystal environment. Our server allows for an optional but recommended step that optimizes stereochemistry using the MESHI software. The KoBaMIN server also allows comparison of the refined structures with a provided reference structure to assess the changes brought about by the refinement protocol. The performance of KoBaMIN has been benchmarked widely on a large set of decoys, all models generated at the seventh worldwide experiments on critical assessment of techniques for protein structure prediction (CASP7) and it was also shown to produce top-ranking predictions in the refinement category at both CASP8 and CASP9, yielding consistently good results across a broad range of model quality values. The web server is fully functional and freely available at http://csb.stanford.edu/kobamin.

Role Delineation Refinement and Verification. The Comprehensive Report. Final Report, October 1, 1978-July 31, 1980.

ERIC Educational Resources Information Center

Garrett, Gary L.; Zinsmeister, Joanne T.

This document reports research focusing on physical therapists and physical therapist assistant role delineation refinement and verification; entry-level role determinations; and translation of these roles into an examination development protocol and examination blueprint specifications. Following an introduction, section 2 describes the survey…

Field validation of protocols developed to evaluate in-line mastitis detection systems.

PubMed

Kamphuis, C; Dela Rue, B T; Eastwood, C R

2016-02-01

This paper reports on a field validation of previously developed protocols for evaluating the performance of in-line mastitis-detection systems. The protocols outlined 2 requirements of these systems: (1) to detect cows with clinical mastitis (CM) promptly and accurately to enable timely and appropriate treatment and (2) to identify cows with high somatic cell count (SCC) to manage bulk milk SCC levels. Gold standard measures, evaluation tests, performance measures, and performance targets were proposed. The current study validated the protocols on commercial dairy farms with automated in-line mastitis-detection systems using both electrical conductivity (EC) and SCC sensor systems that both monitor at whole-udder level. The protocol for requirement 1 was applied on 3 commercial farms. For requirement 2, the protocol was applied on 6 farms; 3 of them had low bulk milk SCC (128×10(3) cells/mL) and were the same farms as used for field evaluation of requirement 1. Three farms with high bulk milk SCC (270×10(3) cells/mL) were additionally enrolled. The field evaluation methodology and results were presented at a workshop including representation from 7 international suppliers of in-line mastitis-detection systems. Feedback was sought on the acceptance of standardized performance evaluation protocols and recommended refinements to the protocols. Although the methodology for requirement 1 was relatively labor intensive and required organizational skills over an extended period, no major issues were encountered during the field validation of both protocols. The validation, thus, proved the protocols to be practical. Also, no changes to the data collection process were recommended by the technology supplier representatives. However, 4 recommendations were made to refine the protocols: inclusion of an additional analysis that ignores small (low-density) clot observations in the definition of CM, extension of the time window from 4 to 5 milkings for timely alerts for CM, setting a maximum number of 10 milkings for the time window to detect a CM episode, and presentation of sensitivity for a larger range of false alerts per 1,000 milkings replacing minimum performance targets. The recommended refinements are discussed with suggested changes to the original protocols. The information presented is intended to inform further debate toward achieving international agreement on standard protocols to evaluate performance of in-line mastitis-detection systems. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Developing a service user informed intervention to improve participation and ability to perform daily activities in primary Sjögren's syndrome: a mixed-methods study protocol

PubMed Central

Hackett, Katie L; Newton, Julia L; Deane, Katherine H O; Rapley, Tim; Deary, Vincent; Kolehmainen, Niina; Lendrem, Dennis; Ng, Wan-Fai

2014-01-01

Introduction A significant proportion of patients with primary Sjögren's syndrome (PSS) is functionally impaired and experience difficulties participating in various aspects of everyday life. There is currently no evidence of efficacy for non-pharmacological interventions aimed specifically at supporting the patients with PSS to improve their participation and ability to perform daily activities. This paper describes a research protocol for a mixed-methods study to develop an intervention to improve these outcomes. The protocol follows the Medical Research Council framework for complex interventions. Methods and analysis We will use group concept mapping with the patients, adults who live with them and healthcare professionals to identify factors which prevent people with PSS from participating in daily life and performing daily activities. The factors will be prioritised by participants for importance and feasibility and will inform an intervention to be delivered within a National Health Service (NHS) setting. Evidence-based intervention techniques will be identified for the prioritised factors and combined into a deliverable intervention package. Key stakeholders will comment on the intervention content and mode of delivery through focus groups, and the data will be used to refine the intervention. The acceptability and feasibility of the refined intervention will be evaluated in a future study. Ethics and dissemination The study has been approved by an NHS Research Ethics Committee, REC Reference: 13/NI/0190. The findings of this study will be disseminated in peer-reviewed journals and through presentation at national and international conferences. Trial registration number UKCRN Study ID: 15939. PMID:25146718

Developing a service user informed intervention to improve participation and ability to perform daily activities in primary Sjögren's syndrome: a mixed-methods study protocol.

PubMed

Hackett, Katie L; Newton, Julia L; Deane, Katherine H O; Rapley, Tim; Deary, Vincent; Kolehmainen, Niina; Lendrem, Dennis; Ng, Wan-Fai

2014-08-21

A significant proportion of patients with primary Sjögren's syndrome (PSS) is functionally impaired and experience difficulties participating in various aspects of everyday life. There is currently no evidence of efficacy for non-pharmacological interventions aimed specifically at supporting the patients with PSS to improve their participation and ability to perform daily activities. This paper describes a research protocol for a mixed-methods study to develop an intervention to improve these outcomes. The protocol follows the Medical Research Council framework for complex interventions. We will use group concept mapping with the patients, adults who live with them and healthcare professionals to identify factors which prevent people with PSS from participating in daily life and performing daily activities. The factors will be prioritised by participants for importance and feasibility and will inform an intervention to be delivered within a National Health Service (NHS) setting. Evidence-based intervention techniques will be identified for the prioritised factors and combined into a deliverable intervention package. Key stakeholders will comment on the intervention content and mode of delivery through focus groups, and the data will be used to refine the intervention. The acceptability and feasibility of the refined intervention will be evaluated in a future study. The study has been approved by an NHS Research Ethics Committee, REC Reference: 13/NI/0190. The findings of this study will be disseminated in peer-reviewed journals and through presentation at national and international conferences. UKCRN Study ID: 15939. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Conformational Analysis of Free and Bound Retinoic Acid

PubMed Central

Fu, Zheng; Li, Xue; Merz, Kenneth M.

2012-01-01

The conformational profiles of unbound all-trans and 9-cis retinoic acid (RA) have been determined using classical and quantum mechanical calculations. Sixty-six all-trans-RA (ATRA) and forty-eight 9-cis-RA energy minimum conformers were identified via HF/6-31G* geometry optimizations in vacuo. Their relative conformational energies were estimated utilizing the M06, M06-2x and MP2 methods combined with the 6-311+G(d,p), aug-cc-pVDZ and aug-cc-pVTZ basis sets, as well as complete basis set MP2 extrapolations using the latter two basis sets. Single-point energy calculations performed with the M06-2x density functional were found to yield similar results to MP2/CBS for the low-energy retinoic acid conformations. Not unexpectedly, the conformational propensities of retinoic acid were governed by the orientation and arrangement of the torsion angles associated with the polyene tail. We also used previously reported QM/MM X-ray refinement results on four ATRA-protein crystal structures plus one newly refined 9-cis-RA complex (PDB ID 1XDK) in order to investigate the conformational preferences of bound retinoic acid. In the re-refined RA conformers the conjugated double bonds are nearly coplanar, which is consistent with the global minimum identified by the Omega/QM method rather than the corresponding crystallographically determined conformations given in the PDB. Consequently, a 91.3% average reduction of the local strain energy in the gas phase, as well as 92.1% in PCM solvent, was observed using the QM/MM refined structures versus the PDB deposited RA conformations. These results thus demonstrate that our QM/MM X-ray refinement approach can significantly enhance the quality of X-ray crystal structures refined by conventional refinement protocols, thereby providing reliable drug-target structural information for use in structure-based drug discovery applications. PMID:22844234

Diurnal Soil Temperature Effects within the Globe[R] Program Dataset

ERIC Educational Resources Information Center

Witter, Jason D.; Spongberg, Alison L.; Czajkowski, Kevin P.

2007-01-01

Long-term collection of soil temperature with depth is important when studying climate change. The international program GLOBE[R] provides an excellent opportunity to collect such data, although currently endorsed temperature collection protocols need to be refined. To enhance data quality, protocol-based methodology and automated data logging,…

PREFMD: a web server for protein structure refinement via molecular dynamics simulations.

PubMed

Heo, Lim; Feig, Michael

2018-03-15

Refinement of protein structure models is a long-standing problem in structural bioinformatics. Molecular dynamics-based methods have emerged as an avenue to achieve consistent refinement. The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in global structure accuracy over other state-of-the-art servers. PREFMD is freely available as a web server at http://feiglab.org/prefmd. Scripts for running PREFMD as a stand-alone package are available at https://github.com/feiglab/prefmd.git. feig@msu.edu. Supplementary data are available at Bioinformatics online.

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.

Computational prediction of atomic structures of helical membrane proteins aided by EM maps.

PubMed

Kovacs, Julio A; Yeager, Mark; Abagyan, Ruben

2007-09-15

Integral membrane proteins pose a major challenge for protein-structure prediction because only approximately 100 high-resolution structures are available currently, thereby impeding the development of rules or empirical potentials to predict the packing of transmembrane alpha-helices. However, when an intermediate-resolution electron microscopy (EM) map is available, it can be used to provide restraints which, in combination with a suitable computational protocol, make structure prediction feasible. In this work we present such a protocol, which proceeds in three stages: 1), generation of an ensemble of alpha-helices by flexible fitting into each of the density rods in the low-resolution EM map, spanning a range of rotational angles around the main helical axes and translational shifts along the density rods; 2), fast optimization of side chains and scoring of the resulting conformations; and 3), refinement of the lowest-scoring conformations with internal coordinate mechanics, by optimizing the van der Waals, electrostatics, hydrogen bonding, torsional, and solvation energy contributions. In addition, our method implements a penalty term through a so-called tethering map, derived from the EM map, which restrains the positions of the alpha-helices. The protocol was validated on three test cases: GpA, KcsA, and MscL.

Evaluation of anaesthetic protocols for laboratory adult zebrafish (Danio rerio).

PubMed

Martins, Tânia; Diniz, Enoque; Félix, Luís M; Antunes, Luís

2018-01-01

In the last decades, the use of zebrafish (Danio rerio) in biomedical research has increased. Anaesthesia is daily used in fish during experimental procedures to avoid discomfort, stress or pain. Also, fish welfare and the reliability of results can be compromised if an unsuitable anaesthetic protocol is used. Therefore, we aimed to refine anaesthetic protocols to be used in adult zebrafish by evaluating the efficacy of different anaesthetics, used alone or in combination. For that, zebrafish were randomly assigned to 8 different groups: 100 μg/mLMS-222 (MS); 0.2 μg/mL etomidate (E); 0.2 μg/mL etomidate + 100 μg/mL lidocaine (E+L); 1.25 μg/mL propofol (P); 1.25 μg/mL propofol + 100 μg/mL lidocaine (P+L); 100 μg/mL ketamine (K); 100 μg/mL ketamine + 1.25 μg/mL medetomidine (K+M); and 100 μg/mL ketamine + 1.25 μg/mL medetomidine/3.125 μg/mL atipamezole (K+M/A). The animals were placed in an anaesthetic water bath, then, the following parameters were registered: time for equilibrium loss and anaesthesia induction, loss of sensitivity to soft and painful stimuli, respiratory rate, recovery time, and activity after recovery. The combined forms of E+L, P+L and K+M were the fastest to induce a surgical anaesthetic stage. Nevertheless, E+L induced respiratory depression, while K+M was shown to have the longer recovery time compared to MS-222, even when atipamezole was added. In conclusion, the P+L combination was shown to provide good anaesthesia with analgesia, without causing a major respiratory depression, providing as well a quick recovery, similar to MS-222.

Combining Techniques to Refine Item to Skills Q-Matrices with a Partition Tree

ERIC Educational Resources Information Center

Desmarais, Michel C.; Xu, Peng; Beheshti, Behzad

2015-01-01

The problem of mapping items to skills is gaining interest with the emergence of recent techniques that can use data for both defining this mapping, and for refining mappings given by experts. We investigate the problem of refining mapping from an expert by combining the output of different techniques. The combination is based on a partition tree…

Imputing Observed Blood Pressure for Antihypertensive Treatment: Impact on Population and Genetic Analyses

PubMed Central

2014-01-01

BACKGROUND Elevated blood pressure (BP), a heritable risk factor for many age-related disorders, is commonly investigated in population and genetic studies, but antihypertensive use can confound study results. Routine methods to adjust for antihypertensives may not sufficiently account for newer treatment protocols (i.e., combination or multiple drug therapy) found in contemporary cohorts. METHODS We refined an existing method to impute unmedicated BP in individuals on antihypertensives by incorporating new treatment trends. We assessed BP and antihypertensive use in male twins (n = 1,237) from the Vietnam Era Twin Study of Aging: 36% reported antihypertensive use; 52% of those treated were on multiple drugs. RESULTS Estimated heritability was 0.43 (95% confidence interval (CI) = 0.20–0.50) and 0.44 (95% CI = 0.22–0.61) for measured systolic BP (SBP) and diastolic BP (DBP), respectively. We imputed BP for antihypertensives by 3 approaches: (i) addition of a fixed value of 10/5mm Hg to measured SBP/DBP; (ii) incremented addition of mm Hg to BP based on number of medications; and (iii) a refined approach adding mm Hg based on antihypertensive drug class and ethnicity. The imputations did not significantly affect estimated heritability of BP. However, use of our most refined imputation method and other methods resulted in significantly increased phenotypic correlations between BP and body mass index, a trait known to be correlated with BP. CONCLUSIONS This study highlights the potential usefulness of applying a representative adjustment for medication use, such as by considering drug class, ethnicity, and the combination of drugs when assessing the relationship between BP and risk factors. PMID:24532572

Optimized open-flow mixing: insights from microbubble streaming

NASA Astrophysics Data System (ADS)

Rallabandi, Bhargav; Wang, Cheng; Guo, Lin; Hilgenfeldt, Sascha

2015-11-01

Microbubble streaming has been developed into a robust and powerful flow actuation technique in microfluidics. Here, we study it as a paradigmatic system for microfluidic mixing under a continuous throughput of fluid (open-flow mixing), providing a systematic optimization of the device parameters in this practically important situation. Focusing on two-dimensional advective stirring (neglecting diffusion), we show through numerical simulation and analytical theory that mixing in steady streaming vortices becomes ineffective beyond a characteristic time scale, necessitating the introduction of unsteadiness. By duty cycling the streaming, such unsteadiness is introduced in a controlled fashion, leading to exponential refinement of the advection structures. The rate of refinement is then optimized for particular parameters of the time modulation, i.e. a particular combination of times for which the streaming is turned ``on'' and ``off''. The optimized protocol can be understood theoretically using the properties of the streaming vortices and the throughput Poiseuille flow. We can thus infer simple design principles for practical open flow micromixing applications, consistent with experiments. Current Address: Mechanical and Aerospace Engineering, Princeton University.

NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.

PubMed

Ryu, Hyojung; Lim, GyuTae; Sung, Bong Hyun; Lee, Jinhyuk

2016-02-15

Protein structure refinement is a necessary step for the study of protein function. In particular, some nuclear magnetic resonance (NMR) structures are of lower quality than X-ray crystallographic structures. Here, we present NMRe, a web-based server for NMR structure refinement. The previously developed knowledge-based energy function STAP (Statistical Torsion Angle Potential) was used for NMRe refinement. With STAP, NMRe provides two refinement protocols using two types of distance restraints. If a user provides NOE (Nuclear Overhauser Effect) data, the refinement is performed with the NOE distance restraints as a conventional NMR structure refinement. Additionally, NMRe generates NOE-like distance restraints based on the inter-hydrogen distances derived from the input structure. The efficiency of NMRe refinement was validated on 20 NMR structures. Most of the quality assessment scores of the refined NMR structures were better than those of the original structures. The refinement results are provided as a three-dimensional structure view, a secondary structure scheme, and numerical and graphical structure validation scores. NMRe is available at http://psb.kobic.re.kr/nmre/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Development of an acquisition protocol and a segmentation algortihm for wounds of cutaneous Leishmaniasis in digital images

NASA Astrophysics Data System (ADS)

Diaz, Kristians; Castañeda, Benjamín; Miranda, César; Lavarello, Roberto; Llanos, Alejandro

2010-03-01

We developed a protocol for the acquisition of digital images and an algorithm for a color-based automatic segmentation of cutaneous lesions of Leishmaniasis. The protocol for image acquisition provides control over the working environment to manipulate brightness, lighting and undesirable shadows on the injury using indirect lighting. Also, this protocol was used to accurately calculate the area of the lesion expressed in mm2 even in curved surfaces by combining the information from two consecutive images. Different color spaces were analyzed and compared using ROC curves in order to determine the color layer with the highest contrast between the background and the wound. The proposed algorithm is composed of three stages: (1) Location of the wound determined by threshold and mathematical morphology techniques to the H layer of the HSV color space, (2) Determination of the boundaries of the wound by analyzing the color characteristics in the YIQ space based on masks (for the wound and the background) estimated from the first stage, and (3) Refinement of the calculations obtained on the previous stages by using the discrete dynamic contours algorithm. The segmented regions obtained with the algorithm were compared with manual segmentations made by a medical specialist. Broadly speaking, our results support that color provides useful information during segmentation and measurement of wounds of cutaneous Leishmaniasis. Results from ten images showed 99% specificity, 89% sensitivity, and 98% accuracy.

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.

Refining dosing by oral gavage in the dog: A protocol to harmonise welfare

PubMed Central

Hall, Laura E.; Robinson, Sally; Buchanan-Smith, Hannah M.

2015-01-01

Introduction The dog is a frequently-used, non-rodent species in the safety assessment of new chemical entities. We have a scientific and ethical obligation to ensure that the best quality of data is achieved from their use. Oral gavage is a technique frequently used to deliver a compound directly into the stomach. As with other animals, in the dog, gavage is aversive and the frequency of its use is a cause for welfare concern but little research has been published on the technique nor how to Refine it. A Welfare Assessment Framework (Hall, 2014) was previously developed for use with the laboratory-housed dog and a contrasting pattern of behaviour, cardiovascular and affective measures were found in dogs with positive and negative welfare. Methods Using the framework, this study compared the effects of sham dosing (used to attempt to habituate dogs to dosing) and a Refined training protocol against a control, no-training group to determine the benefit to welfare and scientific output of each technique. Results Our findings show that sham dosing is ineffective as a habituation technique and ‘primes’ rather than desensitises dogs to dosing. Dogs in the control group showed few changes in parameters across the duration of the study, with some undesirable changes during dosing, while dogs in the Refined treatment group showed improvements in many parameters. Discussion It is recommended that if there is no time allocated for pre-study training a no-sham dosing protocol is used. However, brief training periods show a considerable benefit for welfare and quality of data to be obtained from the dogs' use. PMID:25575806

Computational Enzyme Design: Advances, hurdles and possible ways forward

PubMed Central

Linder, Mats

2012-01-01

This mini review addresses recent developments in computational enzyme design. Successful protocols as well as known issues and limitations are discussed from an energetic perspective. It will be argued that improved results can be obtained by including a dynamic treatment in the design protocol. Finally, a molecular dynamics-based approach for evaluating and refining computational designs is presented. PMID:24688650

Highly Efficient Training, Refinement, and Validation of a Knowledge-based Planning Quality-Control System for Radiation Therapy Clinical Trials

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

Li, Nan; Carmona, Ruben; Sirak, Igor

Purpose: To demonstrate an efficient method for training and validation of a knowledge-based planning (KBP) system as a radiation therapy clinical trial plan quality-control system. Methods and Materials: We analyzed 86 patients with stage IB through IVA cervical cancer treated with intensity modulated radiation therapy at 2 institutions according to the standards of the INTERTECC (International Evaluation of Radiotherapy Technology Effectiveness in Cervical Cancer, National Clinical Trials Network identifier: 01554397) protocol. The protocol used a planning target volume and 2 primary organs at risk: pelvic bone marrow (PBM) and bowel. Secondary organs at risk were rectum and bladder. Initial unfiltered dose-volumemore » histogram (DVH) estimation models were trained using all 86 plans. Refined training sets were created by removing sub-optimal plans from the unfiltered sample, and DVH estimation models… and DVH estimation models were constructed by identifying 30 of 86 plans emphasizing PBM sparing (comparing protocol-specified dosimetric cutpoints V{sub 10} (percentage volume of PBM receiving at least 10 Gy dose) and V{sub 20} (percentage volume of PBM receiving at least 20 Gy dose) with unfiltered predictions) and another 30 of 86 plans emphasizing bowel sparing (comparing V{sub 40} (absolute volume of bowel receiving at least 40 Gy dose) and V{sub 45} (absolute volume of bowel receiving at least 45 Gy dose), 9 in common with the PBM set). To obtain deliverable KBP plans, refined models must inform patient-specific optimization objectives and/or priorities (an auto-planning “routine”). Four candidate routines emphasizing different tradeoffs were composed, and a script was developed to automatically re-plan multiple patients with each routine. After selection of the routine that best met protocol objectives in the 51-patient training sample (KBP{sub FINAL}), protocol-specific DVH metrics and normal tissue complication probability were compared for original versus KBP{sub FINAL} plans across the 35-patient validation set. Paired t tests were used to test differences between planning sets. Results: KBP{sub FINAL} plans outperformed manual planning across the validation set in all protocol-specific DVH cutpoints. The mean normal tissue complication probability for gastrointestinal toxicity was lower for KBP{sub FINAL} versus validation-set plans (48.7% vs 53.8%, P<.001). Similarly, the estimated mean white blood cell count nadir was higher (2.77 vs 2.49 k/mL, P<.001) with KBP{sub FINAL} plans, indicating lowered probability of hematologic toxicity. Conclusions: This work demonstrates that a KBP system can be efficiently trained and refined for use in radiation therapy clinical trials with minimal effort. This patient-specific plan quality control resulted in improvements on protocol-specific dosimetric endpoints.« less

National Football League Head, Neck and Spine Committee's Concussion Diagnosis and Management Protocol: 2017-18 season.

PubMed

Ellenbogen, Richard G; Batjer, Hunt; Cardenas, Javier; Berger, Mitchel; Bailes, Julian; Pieroth, Elizabeth; Heyer, Robert; Theodore, Nicholas; Hsu, Wellington; Nabel, Elizabeth; Maroon, Joe; Cantu, Robert; Barnes, Ronnie; Collins, James; Putukian, Margot; Lonser, Russell; Solomon, Gary; Sills, Allen

2018-03-16

One of the National Football League's (NFL) Head, Neck and Spine Committee's principal goals is to create a 'best practice' protocol for concussion diagnosis and management for its players. The science related to concussion diagnosis and management continues to evolve, thus the protocol has evolved contemporaneously. The Fifth International Conference on Concussion in Sport was held in Berlin in 2016, and guidelines for sports concussion diagnosis and management were revised and refined. The NFL Head, Neck and Spine Committee has synthesised the most recent empirical evidence for sports concussion diagnosis and management including the Berlin consensus statement and tailored it to the game played in the NFL. One of the goals of the Committee is to provide a standardised, reliable, efficient and evidence-based protocol for concussion diagnosis and management that can be applied in this professional sport during practice and game day. In this article, the end-of-season version of the 2017-18 NFL Concussion Diagnosis and Management Protocol is described along with its clinical rationale. Immediate actions for concussion programme enhancement and research are reviewed. It is the Committee's expectation that the protocol will undergo refinement and revision over time as the science and clinical practice related to concussion in sports crystallise. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Photodynamic therapy as a local therapeutic adjunct for the treatment of vertebral metastases

NASA Astrophysics Data System (ADS)

Yee, Albert; Burch, Shane; Akens, Margarete; Won, Emily; Lo, Victor; Wise-Milestone, Lisa; Bisland, Stuart; Theriault, Aimee; Niu, Carolyn; Wilson, Brian C.; Whyne, Cari

2013-03-01

Metastatic cancer causes the majority of tumors in bone, most frequently detected in the spinal column. Skeletal complications cause pain and neurologic impairment. Photodynamic therapy (PDT) has been used to treat a variety of cancers. Minimally invasive surgical (MIS) strategies may allow targeted light application essential for PDT within bone structures. The purpose of this manuscript is to provide an update on pre-clinical status as well as early clinical experience of a Phase I clinical trial on vertebral PDT. A pre-clinical (rnu/rnu rat) vertebral metastasis model of osteolytic (MT-1 breast cancer) was optimized and used to evaluate the effect of vertebral PDT. PDT alone and in combination with other standard local (radiation therapy, RT) and systemic (bisphosphonates, BP) therapies was evaluated through bioluminescence imaging, micro-CT based stereology, histology, and biomechanical testing. Single PDT treatment (photosensitizer BPD-MA, 690nm light) ablated tumor tissue in targeted vertebrae. PDT led to significant increases in bone structural properties, with greatest benefits observed from combined BP+PDT therapy: 76% and 19% increases in bone volume fraction in treated tumor-bearing and healthy untreated controls, respectively. Similar synergistic improvements (but of lesser magnitude) were found in combined PDT+RT treatments. The safety and feasibility of MIS+PDT were evaluated in scale-up animal studies, refining surgical technique for clinical translation. Following appropriate institutional review board as well as Health Canada approval, 5 patients (light only control group) have undergone protocoled treatment to date. These patients have guided further refinement of human therapeutic application from a laser delivery and vertebral bone access perspective.

Improving the accuracy of macromolecular structure refinement at 7 Å resolution.

PubMed

Brunger, Axel T; Adams, Paul D; Fromme, Petra; Fromme, Raimund; Levitt, Michael; Schröder, Gunnar F

2012-06-06

In X-ray crystallography, molecular replacement and subsequent refinement is challenging at low resolution. We compared refinement methods using synchrotron diffraction data of photosystem I at 7.4 Å resolution, starting from different initial models with increasing deviations from the known high-resolution structure. Standard refinement spoiled the initial models, moving them further away from the true structure and leading to high R(free)-values. In contrast, DEN refinement improved even the most distant starting model as judged by R(free), atomic root-mean-square differences to the true structure, significance of features not included in the initial model, and connectivity of electron density. The best protocol was DEN refinement with initial segmented rigid-body refinement. For the most distant initial model, the fraction of atoms within 2 Å of the true structure improved from 24% to 60%. We also found a significant correlation between R(free) values and the accuracy of the model, suggesting that R(free) is useful even at low resolution. Copyright © 2012 Elsevier Ltd. All rights reserved.

Optimizing radiotherapy protocols using computer automata to model tumour cell death as a function of oxygen diffusion processes.

PubMed

Paul-Gilloteaux, Perrine; Potiron, Vincent; Delpon, Grégory; Supiot, Stéphane; Chiavassa, Sophie; Paris, François; Costes, Sylvain V

2017-05-23

The concept of hypofractionation is gaining momentum in radiation oncology centres, enabled by recent advances in radiotherapy apparatus. The gain of efficacy of this innovative treatment must be defined. We present a computer model based on translational murine data for in silico testing and optimization of various radiotherapy protocols with respect to tumour resistance and the microenvironment heterogeneity. This model combines automata approaches with image processing algorithms to simulate the cellular response of tumours exposed to ionizing radiation, modelling the alteration of oxygen permeabilization in blood vessels against repeated doses, and introducing mitotic catastrophe (as opposed to arbitrary delayed cell-death) as a means of modelling radiation-induced cell death. Published data describing cell death in vitro as well as tumour oxygenation in vivo are used to inform parameters. Our model is validated by comparing simulations to in vivo data obtained from the radiation treatment of mice transplanted with human prostate tumours. We then predict the efficacy of untested hypofractionation protocols, hypothesizing that tumour control can be optimized by adjusting daily radiation dosage as a function of the degree of hypoxia in the tumour environment. Further biological refinement of this tool will permit the rapid development of more sophisticated strategies for radiotherapy.

Computational Prediction of Atomic Structures of Helical Membrane Proteins Aided by EM Maps

PubMed Central

Kovacs, Julio A.; Yeager, Mark; Abagyan, Ruben

2007-01-01

Integral membrane proteins pose a major challenge for protein-structure prediction because only ≈100 high-resolution structures are available currently, thereby impeding the development of rules or empirical potentials to predict the packing of transmembrane α-helices. However, when an intermediate-resolution electron microscopy (EM) map is available, it can be used to provide restraints which, in combination with a suitable computational protocol, make structure prediction feasible. In this work we present such a protocol, which proceeds in three stages: 1), generation of an ensemble of α-helices by flexible fitting into each of the density rods in the low-resolution EM map, spanning a range of rotational angles around the main helical axes and translational shifts along the density rods; 2), fast optimization of side chains and scoring of the resulting conformations; and 3), refinement of the lowest-scoring conformations with internal coordinate mechanics, by optimizing the van der Waals, electrostatics, hydrogen bonding, torsional, and solvation energy contributions. In addition, our method implements a penalty term through a so-called tethering map, derived from the EM map, which restrains the positions of the α-helices. The protocol was validated on three test cases: GpA, KcsA, and MscL. PMID:17496035

A Distance Bounding Protocol for Location-Cloaked Applications

PubMed Central

Molina-Martínez, Cristián; Galdames, Patricio

2018-01-01

Location-based services (LBSs) assume that users are willing to release trustworthy and useful details about their whereabouts. However, many location privacy concerns have arisen. For location privacy protection, several algorithms build a cloaking region to hide a user’s location. However, many applications may not operate adequately on cloaked locations. For example, a traditional distance bounding protocol (DBP)—which is run by two nodes called the prover and the verifier—may conclude an untight and useless distance between these two entities. An LBS (verifier) may use this distance as a metric of usefulness and trustworthiness of the location claimed by the user (prover). However, we show that if a tight distance is desired, traditional DBP can refine a user’s cloaked location and compromise its location privacy. To find a proper balance, we propose a location-privacy-aware DBP protocol. Our solution consists of adding some small delays before submitting any user’s response. We show that several issues arise when a certain delay is chosen, and we propose some solutions. The effectiveness of our techniques in balancing location refinement and utility is demonstrated through simulation. PMID:29701641

Comparison of in vivo 3D cone-beam computed tomography tooth volume measurement protocols.

PubMed

Forst, Darren; Nijjar, Simrit; Flores-Mir, Carlos; Carey, Jason; Secanell, Marc; Lagravere, Manuel

2014-12-23

The objective of this study is to analyze a set of previously developed and proposed image segmentation protocols for precision in both intra- and inter-rater reliability for in vivo tooth volume measurements using cone-beam computed tomography (CBCT) images. Six 3D volume segmentation procedures were proposed and tested for intra- and inter-rater reliability to quantify maxillary first molar volumes. Ten randomly selected maxillary first molars were measured in vivo in random order three times with 10 days separation between measurements. Intra- and inter-rater agreement for all segmentation procedures was attained using intra-class correlation coefficient (ICC). The highest precision was for automated thresholding with manual refinements. A tooth volume measurement protocol for CBCT images employing automated segmentation with manual human refinement on a 2D slice-by-slice basis in all three planes of space possessed excellent intra- and inter-rater reliability. Three-dimensional volume measurements of the entire tooth structure are more precise than 3D volume measurements of only the dental roots apical to the cemento-enamel junction (CEJ).

Isolation of a furan fatty acid from Hevea brasiliensis latex employing the combined use of pH-zone-refining and conventional countercurrent chromatography.

PubMed

Englert, Michael; Ulms, Kerstin; Wendlinger, Christine; Vetter, Walter

2016-02-01

Furan fatty acids are valuable and bioactive minor fatty acids that usually contribute <0.1% to the fatty acid content of food samples. Their biological role still remains unclear as authentic furan fatty acid standards are not readily available and thorough experimental studies verifying the relevance of furan fatty acids are thus virtually impossible. An efficient protocol for the isolation of the furan fatty acid 9-(3-methyl-5-pentylfuran-2-yl)-nonanoic acid from hydrolyzed and centrifuged latex of Hevea brasiliensis was developed using countercurrent chromatography. A first run using pH-zone-refining countercurrent chromatography provided 48.4 mg of 9-(3-methyl-5-pentylfuran-2-yl)-nonanoic acid from 210 mg latex extract in a purity of 95%. The purity was increased to 99% by means of one second run in conventional countercurrent chromatography mode. The Structure and purity of 9-(3-methyl-5-pentylfuran-2-yl)-nonanoic acid were determined by gas chromatography coupled to mass spectrometry and (1)H and (13)C NMR spectroscopy. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Deformable complex network for refining low-resolution X-ray structures

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

Zhang, Chong; Wang, Qinghua; Ma, Jianpeng, E-mail: jpma@bcm.edu

2015-10-27

A new refinement algorithm called the deformable complex network that combines a novel angular network-based restraint with a deformable elastic network model in the target function has been developed to aid in structural refinement in macromolecular X-ray crystallography. In macromolecular X-ray crystallography, building more accurate atomic models based on lower resolution experimental diffraction data remains a great challenge. Previous studies have used a deformable elastic network (DEN) model to aid in low-resolution structural refinement. In this study, the development of a new refinement algorithm called the deformable complex network (DCN) is reported that combines a novel angular network-based restraint withmore » the DEN model in the target function. Testing of DCN on a wide range of low-resolution structures demonstrated that it constantly leads to significantly improved structural models as judged by multiple refinement criteria, thus representing a new effective refinement tool for low-resolution structural determination.« less

Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling

NASA Astrophysics Data System (ADS)

Bhakat, Soumendranath; Åberg, Emil; Söderhjelm, Pär

2018-01-01

Advanced molecular docking methods often aim at capturing the flexibility of the protein upon binding to the ligand. In this study, we investigate whether instead a simple rigid docking method can be applied, if combined with multiple target structures to model the backbone flexibility and molecular dynamics simulations to model the sidechain and ligand flexibility. The methods are tested for the binding of 35 ligands to FXR as part of the first stage of the Drug Design Data Resource (D3R) Grand Challenge 2 blind challenge. The results show that the multiple-target docking protocol performs surprisingly well, with correct poses found for 21 of the ligands. MD simulations started on the docked structures are remarkably stable, but show almost no tendency of refining the structure closer to the experimentally found binding pose. Reconnaissance metadynamics enhances the exploration of new binding poses, but additional collective variables involving the protein are needed to exploit the full potential of the method.

Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling.

PubMed

Bhakat, Soumendranath; Åberg, Emil; Söderhjelm, Pär

2018-01-01

Advanced molecular docking methods often aim at capturing the flexibility of the protein upon binding to the ligand. In this study, we investigate whether instead a simple rigid docking method can be applied, if combined with multiple target structures to model the backbone flexibility and molecular dynamics simulations to model the sidechain and ligand flexibility. The methods are tested for the binding of 35 ligands to FXR as part of the first stage of the Drug Design Data Resource (D3R) Grand Challenge 2 blind challenge. The results show that the multiple-target docking protocol performs surprisingly well, with correct poses found for 21 of the ligands. MD simulations started on the docked structures are remarkably stable, but show almost no tendency of refining the structure closer to the experimentally found binding pose. Reconnaissance metadynamics enhances the exploration of new binding poses, but additional collective variables involving the protein are needed to exploit the full potential of the method.

Combining visual rehabilitative training and noninvasive brain stimulation to enhance visual function in patients with hemianopia: a comparative case study.

PubMed

Plow, Ela B; Obretenova, Souzana N; Halko, Mark A; Kenkel, Sigrid; Jackson, Mary Lou; Pascual-Leone, Alvaro; Merabet, Lotfi B

2011-09-01

To standardize a protocol for promoting visual rehabilitative outcomes in post-stroke hemianopia by combining occipital cortical transcranial direct current stimulation (tDCS) with Vision Restoration Therapy (VRT). A comparative case study assessing feasibility and safety. A controlled laboratory setting. Two patients, both with right hemianopia after occipital stroke damage. METHODS AND OUTCOME MEASUREMENTS: Both patients underwent an identical VRT protocol that lasted 3 months (30 minutes, twice a day, 3 days per week). In patient 1, anodal tDCS was delivered to the occipital cortex during VRT training, whereas in patient 2 sham tDCS with VRT was performed. The primary outcome, visual field border, was defined objectively by using high-resolution perimetry. Secondary outcomes included subjective characterization of visual deficit and functional surveys that assessed performance on activities of daily living. For patient 1, the neural correlates of visual recovery were also investigated, by using functional magnetic resonance imaging. Delivery of combined tDCS with VRT was feasible and safe. High-resolution perimetry revealed a greater shift in visual field border for patient 1 versus patient 2. Patient 1 also showed greater recovery of function in activities of daily living. Contrary to the expectation, patient 2 perceived greater subjective improvement in visual field despite objective high-resolution perimetry results that indicated otherwise. In patient 1, visual function recovery was associated with functional magnetic resonance imaging activity in surviving peri-lesional and bilateral higher-order visual areas. Results of preliminary case comparisons suggest that occipital cortical tDCS may enhance recovery of visual function associated with concurrent VRT through visual cortical reorganization. Future studies may benefit from incorporating protocol refinements such as those described here, which include global capture of function, control for potential confounds, and investigation of underlying neural substrates of recovery. Copyright © 2011 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

A Pilot Study of Common Bile Duct Reconstruction with CorMatrix Extracellular Matrix in Swine (Sus scrofa)

DTIC Science & Technology

2015-02-06

additional pages if necessary.) PROTOCOL#: FDG20140008A DATE: 6 February 2015 PROTOCOL TITLE: A Pilot Study of Common Bile Duct Reconstruction with...obstruction or bile peritonitis. This was reported to the IACUC chair. 9. REDUCTION, REFINEMENT, OR REPLACEMENT OF ANIMAL USE; REPLACEMENT...benefit the DoD/USAF? We developed a porcine model of common bile duct injury and interposition grafting, gained experience managing these patients

FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A.

PubMed

Michino, Mayako; Chen, Jianhan; Stevens, Raymond C; Brooks, Charles L

2010-08-01

Building reliable structural models of G protein-coupled receptors (GPCRs) is a difficult task because of the paucity of suitable templates, low sequence identity, and the wide variety of ligand specificities within the superfamily. Template-based modeling is known to be the most successful method for protein structure prediction. However, refinement of homology models within 1-3 A C alpha RMSD of the native structure remains a major challenge. Here, we address this problem by developing a novel protocol (foldGPCR) for modeling the transmembrane (TM) region of GPCRs in complex with a ligand, aimed to accurately model the structural divergence between the template and target in the TM helices. The protocol is based on predicted conserved inter-residue contacts between the template and target, and exploits an all-atom implicit membrane force field. The placement of the ligand in the binding pocket is guided by biochemical data. The foldGPCR protocol is implemented by a stepwise hierarchical approach, in which the TM helical bundle and the ligand are assembled by simulated annealing trials in the first step, and the receptor-ligand complex is refined with replica exchange sampling in the second step. The protocol is applied to model the human beta(2)-adrenergic receptor (beta(2)AR) bound to carazolol, using contacts derived from the template structure of bovine rhodopsin. Comparison with the X-ray crystal structure of the beta(2)AR shows that our protocol is particularly successful in accurately capturing helix backbone irregularities and helix-helix packing interactions that distinguish rhodopsin from beta(2)AR. (c) 2010 Wiley-Liss, Inc.

77 FR 52021 - Proposed CERCLA Administrative Settlement Agreement and Order on Consent for the Mercury Refining...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-28

... and Order on Consent for the Mercury Refining Superfund Site, Towns of Guilderland and Colonie, Albany... Management of Michigan, Inc. (hereafter ``Settling Parties'') pertaining to the Mercury Refining Superfund... Superfund Mercury Refining Superfund Site Special Account, which combined total $79,028.49. Each Settling...

Magnesium Recycling of Partially Oxidized, Mixed Magnesium-Aluminum Scrap through Combined Refining and Solid Oxide Membrane Electrolysis Processes

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

Xiaofei Guan; Peter A. Zink; Uday B. Pal

2012-01-01

Pure magnesium (Mg) is recycled from 19g of partially oxidized 50.5wt.% Mg-Aluminum (Al) alloy. During the refining process, potentiodynamic scans (PDS) were performed to determine the electrorefining potential for magnesium. The PDS show that the electrorefining potential increases over time as the magnesium content inside the Mg-Al scrap decreases. Up to 100% percent of magnesium is refined from the Mg-Al scrap by a novel refining process of dissolving magnesium and its oxide into a flux followed by vapor phase removal of dissolved magnesium and subsequently condensing the magnesium vapor. The solid oxide membrane (SOM) electrolysis process is employed in themore » refining system to enable additional recycling of magnesium from magnesium oxide (MgO) in the partially oxidized Mg-Al scrap. The combination of the refining and SOM processes yields 7.4g of pure magnesium.« less

The use of preferred social stimuli as rewards for rhesus macaques in behavioural neuroscience

PubMed Central

Pearce, Bradley; Thiele, Alexander; Rowe, Candy

2017-01-01

Macaques are often motivated to perform in neuroscientific experiments by implementing fluid restriction protocols. Daily access to water is controlled and the monkeys are rewarded with droplets of fluid for performing correct trials in the laboratory. Although these protocols are widely used and highly effective, it is important from a 3Rs perspective to investigate refinements that may help to lessen the severity of the fluid restriction applied. We assessed the use of social stimuli (images of conspecifics) as rewards for four rhesus macaques performing simple cognitive tasks. We found that individual preferences for images of male faces, female perinea and control stimuli could be identified in each monkey. However, using preferred images did not translate into effective motivators on a trial-by-trial basis: animals preferred fluid rewards, even when fluid restriction was relaxed. There was no difference in the monkeys’ performance of a task when using greyscale versus colour images. Based on our findings, we cannot recommend the use of social stimuli, in this form, as a refinement to current fluid restriction protocols. We discuss the potential alternatives and possibilities for future research. PMID:28542356

A Distance Bounding Protocol for Location-Cloaked Applications.

PubMed

Molina-Martínez, Cristián; Galdames, Patricio; Duran-Faundez, Cristian

2018-04-26

Location-based services (LBSs) assume that users are willing to release trustworthy and useful details about their whereabouts. However, many location privacy concerns have arisen. For location privacy protection, several algorithms build a cloaking region to hide a user’s location. However, many applications may not operate adequately on cloaked locations. For example, a traditional distance bounding protocol (DBP)—which is run by two nodes called the prover and the verifier—may conclude an untight and useless distance between these two entities. An LBS (verifier) may use this distance as a metric of usefulness and trustworthiness of the location claimed by the user (prover). However, we show that if a tight distance is desired, traditional DBP can refine a user’s cloaked location and compromise its location privacy. To find a proper balance, we propose a location-privacy-aware DBP protocol. Our solution consists of adding some small delays before submitting any user’s response. We show that several issues arise when a certain delay is chosen, and we propose some solutions. The effectiveness of our techniques in balancing location refinement and utility is demonstrated through simulation.

Promoting communication with older adults: protocols for resolving interpersonal conflicts and for enhancing interactions with doctors.

PubMed

Weitzman, Patricia Flynn; Weitzman, Eben A

2003-07-01

In this paper, we review the importance of effective communication in older adulthood, and ideas for promoting it. We focus on theoretical and applied work in two communicative encounters that have particular relevance for older adult health, i.e., interpersonal conflict and visits with a healthcare provider. Little applied work has aimed to adapt training protocols for older adults in these two areas. We will present training protocols we have developed in constructive conflict resolution for older adults, and on enhancing doctor-patient communication. We present these protocols to stimulate ideas on the part of the reader on how to further develop and refine training efforts for older adults in effective communication.

Minimization of Hypoglycemia as an Adverse Event During Insulin Infusion: Further Refinement of the Yale Protocol.

PubMed

Marvin, Michael R; Inzucchi, Silvio E; Besterman, Brian J

2016-08-01

The management of hyperglycemia in the intensive care unit has been a controversial topic for more than a decade, with target ranges varying from 80-110 mg/dL to <200 mg/dL. Multiple insulin infusion protocols exist, including several computerized protocols, which have attempted to achieve these targets. Importantly, compliance with these protocols has not been a focus of clinical studies. GlucoCare™, a Food and Drug Administration (FDA)-cleared insulin-dosing calculator, was originally designed based on the Yale Insulin Infusion Protocol to target 100-140 mg/dL and has undergone several modifications to reduce hypoglycemia. The original Yale protocol was modified from 100-140 mg/dL to a range of 120-140 mg/dL (GlucoCare 120-140) and then to 140 mg/dL (GlucoCare 140, not a range but a single blood glucose [BG] level target) in an iterative and evidence-based manner to eliminate hypoglycemia <70 mg/dL. The final modification [GlucoCare 140(B)] includes the addition of bolus insulin "midprotocol" during an insulin infusion to reduce peak insulin rates for insulin-resistant patients. This study examined the results of these protocol modifications and evaluated the role of compliance with the protocol in the incidence of hypoglycemia <70 mg/dL. Protocol modifications resulted in mean BG levels of 133.4, 136.4, 143.8, and 146.4 mg/dL and hypoglycemic BG readings <70 mg/dL of 0.998%, 0.367%, 0.256%, and 0.04% for the 100-140, 120-140, 140, and 140(B) protocols, respectively (P < 0.001). Adherence to the glucose check interval significantly reduced the incidence of hypoglycemia (P < 0.001). Protocol modifications led to a reduction in peak insulin infusion rates (P < 0.001) and the need for dextrose-containing boluses (P < 0.001). This study demonstrates that refinements in protocol design can improve glucose control in critically ill patients and that the use of GlucoCare 140(B) can eliminate all significant hypoglycemia while achieving mean glucose levels between 140 and 150 mg/dL. In addition, attention to the timely performance of glucose levels can also reduce hypoglycemic events.

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

PubMed

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

2015-12-28

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

Integrated RF/Optical Interplanetary Networking Preliminary Explorations and Empirical Results

NASA Technical Reports Server (NTRS)

Raible, Daniel E.; Hylton, Alan G.

2012-01-01

Over the last decade interplanetary telecommunication capabilities have been significantly expanded--specifically in support of the Mars exploration rover and lander missions. NASA is continuing to drive advances in new, high payoff optical communications technologies to enhance the network to Gbps performance from Mars, and the transition from technology demonstration to operational system is examined through a hybrid RF/optical approach. Such a system combines the best features of RF and optical communications considering availability and performance to realize a dual band trunk line operating within characteristic constraints. Disconnection due to planetary obscuration and solar conjunction, link delays, timing, ground terminal mission congestion and scheduling policy along with space and atmospheric weather disruptions all imply the need for network protocol solutions to ultimately manage the physical layer in a transparent manner to the end user. Delay Tolerant Networking (DTN) is an approach under evaluation which addresses these challenges. A multi-hop multi-path hybrid RF and optical test bed has been constructed to emulate the integrated deep space network and to support protocol and hardware refinement. Initial experimental results characterize several of these challenges and evaluate the effectiveness of DTN as a solution to mitigate them.

Electronic trigger for capacitive touchscreen and extension of ISO 15781 standard time lag measurements to smartphones

NASA Astrophysics Data System (ADS)

Bucher, François-Xavier; Cao, Frédéric; Viard, Clément; Guichard, Frédéric

2014-03-01

We present in this paper a novel capacitive device that stimulates the touchscreen interface of a smartphone (or of any imaging device equipped with a capacitive touchscreen) and synchronizes triggering with the DxO LED Universal Timer to measure shooting time lag and shutter lag according to ISO 15781:2013. The device and protocol extend the time lag measurement beyond the standard by including negative shutter lag, a phenomenon that is more and more commonly found in smartphones. The device is computer-controlled, and this feature, combined with measurement algorithms, makes it possible to automatize a large series of captures so as to provide more refined statistical analyses when, for example, the shutter lag of "zero shutter lag" devices is limited by the frame time as our measurements confirm.

[Cardiac Anaesthesia: Anaesthesiological Management].

PubMed

Renner, Jochen; Bein, Berthold; Broch, Ole

2018-05-01

The anaesthesiological management of patients scheduled for cardiac surgery has been refined distinctively over the last decade due to different reasons. The continuing growth of the elderly patient population and the increasing number of combined cardiac surgery procedures in octogenarians on the one hand are one aspect. The rapid development of minimally invasive cardiac surgery and the enhancements in mechanical, artificial heart assist devices on the other hand can be seen as additional decisive factors. All of these innovations in the field of cardiac surgery implicate further enhancements regarding the anaesthesiological management. This review article addresses the following subareas of cardiac anaesthesia: significance of pharmacological myocardial protection, anaesthetic management during cardiopulmonary bypass, importance of "Enhanced Recovery After Cardiac Surgery"-protocols as well as innovations in the field of minimally invasive cardiac surgery like transcatheter aortic valve implantation. Georg Thieme Verlag KG Stuttgart · New York.

CONCEPTS AND APPROACHES FOR THE BIOASSESSMENT OF NON-WADEABLE STREAMS AND RIVERS

EPA Science Inventory

This document is intended to assist users in establishing or refining protocols, including the specific methods related to field sampling, laboratory sample processing, taxonomy, data entry, management and analysis, and final assessment and reporting. It also reviews and provide...

Travel behavior of blind individuals before and after receiving orientation and mobility training.

DOT National Transportation Integrated Search

2016-09-08

In this pilot study, we devised, tested, and refined a protocol for evaluating the travel behavior of blind individuals. Preliminary analyses of our pilot study data suggest that our new method involving Global Positioning Systems (GPS), acceleromete...

Combined Heat and Power Protocol for Uniform Methods Project | Advanced

Science.gov Websites

Manufacturing Research | NREL Combined Heat and Power Protocol for Uniform Methods Project Combined Heat and Power Protocol for Uniform Methods Project NREL developed a protocol that provides a ; is consistent with the scope and other protocols developed for the Uniform Methods Project (UMP

High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB-REDO strategies

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

Rimsa, Vadim; Eadsforth, Thomas C.; Joosten, Robbie P.

2014-02-01

The structure of a bacterial M14-family carboxypeptidase determined exploiting microfocus synchrotron radiation and highly automated refinement protocols reveals its potential to act as a polyglutamylase. A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high-throughput automated protocols embedded in PDB-REDO were coupled with model–map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N-terminal domain has previouslymore » only been observed in cytosolic carboxypeptidase (CCP) proteins. The C-terminal domain, which carries the Zn{sup 2+}-containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide-bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn{sup 2+}, where an acetate ion is identified, suggests recognition of the carboxy-terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1′ recognition subsite that suggests specificity towards an acidic substrate.« less

Magnesium Recycling of Partially Oxidized, Mixed Magnesium-Aluminum Scrap Through Combined Refining and Solid Oxide Membrane (SOM) Electrolysis Processes

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

Guan, Xiaofei; Zink, Peter; Pal, Uday

2012-03-11

Pure magnesium (Mg) is recycled from 19g of partially oxidized 50.5wt.%Mg-Aluminum (Al) alloy. During the refining process, potentiodynamic scans (PDS) were performed to determine the electrorefining potential for magnesium. The PDS show that the electrorefining potential increases over time as the Mg content inside the Mg-Al scrap decreases. Up to 100% percent of magnesium is refined from the Mg-Al scrap by a novel refining process of dissolving magnesium and its oxide into a flux followed by vapor phase removal of dissolved magnesium and subsequently condensing the magnesium vapors in a separate condenser. The solid oxide membrane (SOM) electrolysis process ismore » employed in the refining system to enable additional recycling of magnesium from magnesium oxide (MgO) in the partially oxidized Mg-Al scrap. The combination of the refining and SOM processes yields 7.4g of pure magnesium; could not collect and weigh all of the magnesium recovered.« less

Process and Outcome of Fecal Microbiota Transplants in Patients With Recurrent Clostridium difficile Infection: A Prospective Study.

PubMed

Walton, Janice; Burns, Denise; Gaehle, Kay E

The incidence of Clostridium difficile infection is on the rise worldwide, causing high mortality rates and costing patients, hospitals, and insurance companies millions of dollars annually. Fecal microbiota transplants successfully treat recurrent C. difficile infections unresponsive to standard pharmacologic treatment such as flagyl, vancomycin, or rifaximin. Evidence in the literature provided the foundation for the development and refinement of this fecal microbiota transplant protocol. During the initial phase of the project, the protocol included patient selection criteria, donor screening/selection, infection control, fecal processing and delivery, and patient pre and postprocedure education. This article highlights the second phase of prospective testing of a nurse-driven protocol to implement fecal microbiota transplantation in patients with recurrent C. difficile infection. All stages of the protocol are explained as well as rationale for component parts to achieve successful patient outcomes when the protocol is carefully followed.

Exploiting the Brachypodium Tool Box in cereal and grass research

USDA-ARS?s Scientific Manuscript database

It is now a decade since Brachypodium distachyon was suggested as a model species for temperate grasses and cereals. Since then transformation protocols, large expressed sequence tag (EST) populations, tools for forward and reverse genetic screens, highly refined cytogenetic probes, germplasm coll...

Structure Refinement of Protein Low Resolution Models Using the GNEIMO Constrained Dynamics Method

PubMed Central

Park, In-Hee; Gangupomu, Vamshi; Wagner, Jeffrey; Jain, Abhinandan; Vaidehi, Nagara-jan

2012-01-01

The challenge in protein structure prediction using homology modeling is the lack of reliable methods to refine the low resolution homology models. Unconstrained all-atom molecular dynamics (MD) does not serve well for structure refinement due to its limited conformational search. We have developed and tested the constrained MD method, based on the Generalized Newton-Euler Inverse Mass Operator (GNEIMO) algorithm for protein structure refinement. In this method, the high-frequency degrees of freedom are replaced with hard holonomic constraints and a protein is modeled as a collection of rigid body clusters connected by flexible torsional hinges. This allows larger integration time steps and enhances the conformational search space. In this work, we have demonstrated the use of a constraint free GNEIMO method for protein structure refinement that starts from low-resolution decoy sets derived from homology methods. In the eight proteins with three decoys for each, we observed an improvement of ~2 Å in the RMSD to the known experimental structures of these proteins. The GNEIMO method also showed enrichment in the population density of native-like conformations. In addition, we demonstrated structural refinement using a “Freeze and Thaw” clustering scheme with the GNEIMO framework as a viable tool for enhancing localized conformational search. We have derived a robust protocol based on the GNEIMO replica exchange method for protein structure refinement that can be readily extended to other proteins and possibly applicable for high throughput protein structure refinement. PMID:22260550

7 CFR 58.905 - Meaning of words.

Code of Federal Regulations, 2013 CFR

2013-01-01

... food made by evaporating a mixture of sweet milk and refined sugar (sucrose) or any combination of refined sugar (sucrose) and refined corn sugar (dextrose) to such point that the finished sweetened... liquid food made by evaporating sweet milk to such point that it contains not less than 6.5 percent of...

7 CFR 58.905 - Meaning of words.

Code of Federal Regulations, 2012 CFR

2012-01-01

... food made by evaporating a mixture of sweet milk and refined sugar (sucrose) or any combination of refined sugar (sucrose) and refined corn sugar (dextrose) to such point that the finished sweetened... liquid food made by evaporating sweet milk to such point that it contains not less than 6.5 percent of...

7 CFR 58.905 - Meaning of words.

Code of Federal Regulations, 2011 CFR

2011-01-01

... food made by evaporating a mixture of sweet milk and refined sugar (sucrose) or any combination of refined sugar (sucrose) and refined corn sugar (dextrose) to such point that the finished sweetened... liquid food made by evaporating sweet milk to such point that it contains not less than 6.5 percent of...

7 CFR 58.905 - Meaning of words.

Code of Federal Regulations, 2010 CFR

2010-01-01

... food made by evaporating a mixture of sweet milk and refined sugar (sucrose) or any combination of refined sugar (sucrose) and refined corn sugar (dextrose) to such point that the finished sweetened... liquid food made by evaporating sweet milk to such point that it contains not less than 6.5 percent of...

7 CFR 58.905 - Meaning of words.

Code of Federal Regulations, 2014 CFR

2014-01-01

... food made by evaporating a mixture of sweet milk and refined sugar (sucrose) or any combination of refined sugar (sucrose) and refined corn sugar (dextrose) to such point that the finished sweetened... liquid food made by evaporating sweet milk to such point that it contains not less than 6.5 percent of...

Evaluating the Feasibility of RESCUE: An Adjunctive HAI-Based Intervention for Veterans with PTSD

DTIC Science & Technology

This report documents accomplishment of the following tasks: a) Completed case series, conducted qualitative interviews, and refined the protocol...Continued active recruitment of participants; currently on track with our projected recruitment targets. As of April 2018, 76 participants have been

PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

PubMed

Joosten, Robbie P; Salzemann, Jean; Bloch, Vincent; Stockinger, Heinz; Berglund, Ann-Charlott; Blanchet, Christophe; Bongcam-Rudloff, Erik; Combet, Christophe; Da Costa, Ana L; Deleage, Gilbert; Diarena, Matteo; Fabbretti, Roberto; Fettahi, Géraldine; Flegel, Volker; Gisel, Andreas; Kasam, Vinod; Kervinen, Timo; Korpelainen, Eija; Mattila, Kimmo; Pagni, Marco; Reichstadt, Matthieu; Breton, Vincent; Tickle, Ian J; Vriend, Gert

2009-06-01

Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.

Marine Vehicle Sensor Network Architecture and Protocol Designs for Ocean Observation

PubMed Central

Zhang, Shaowei; Yu, Jiancheng; Zhang, Aiqun; Yang, Lei; Shu, Yeqiang

2012-01-01

The micro-scale and meso-scale ocean dynamic processes which are nonlinear and have large variability, have a significant impact on the fisheries, natural resources, and marine climatology. A rapid, refined and sophisticated observation system is therefore needed in marine scientific research. The maneuverability and controllability of mobile sensor platforms make them a preferred choice to establish ocean observing networks, compared to the static sensor observing platform. In this study, marine vehicles are utilized as the nodes of mobile sensor networks for coverage sampling of a regional ocean area and ocean feature tracking. A synoptic analysis about marine vehicle dynamic control, multi vehicles mission assignment and path planning methods, and ocean feature tracking and observing techniques is given. Combined with the observation plan in the South China Sea, we provide an overview of the mobile sensor networks established with marine vehicles, and the corresponding simulation results. PMID:22368475

Refining the application of direct embryogenesis in sugarcane: Effect of the developmental phase of leaf disc explants and the timing of DNA transfer on transformation efficiency.

PubMed

Snyman, S J; Meyer, G M; Richards, J M; Haricharan, N; Ramgareeb, S; Huckett, B I

2006-10-01

A rapid in vitro protocol using direct somatic embryogenesis and microprojectile bombardment was investigated to establish the developmental phases most suitable for efficient sugarcane transformation. Immature leaf roll disc explants with and without pre-emergent inflorescence tissue were compared. It was shown that for effective transformation to occur, explants should be cultured for several days to allow initiation of embryo development prior to bombardment. Leaf roll discs with pre-emergent inflorescences showed a higher degree of embryogenic competence than non-flowering explants, and transformation efficiency was higher when explants containing floral initials were bombarded. Despite the occurrence of high numbers of phenotypically negative plants, combining the use of inflorescent leaf roll discs with direct embryogenic regeneration has the potential to improve the speed and efficiency of transgenesis in sugarcane.

Efficient utilization of crude glycerol as fermentation substrate in the synthesis of poly(3-hydroxybutyrate) biopolymers

USDA-ARS?s Scientific Manuscript database

One refined and 2 crude glycerol samples were utilized to produce poly(3-hydroxybutyrate) (PHB) by Pseudomonas oleovorans NRRL B-14682. Fermentation conditions were determined to efficiently utilize glycerol while maintaining PHB yields. A batch culture protocol including 1% glycerol and an aerati...

Usability and Instructional Design Heuristics for E-Learning Evaluation.

ERIC Educational Resources Information Center

Reeves, Thomas C.; Benson, Lisa; Elliott, Dean; Grant, Michael; Holschuh, Doug; Kim, Beaumie; Kim, Hyeonjin; Lauber, Erick; Loh, Sebastian

Heuristic evaluation is a methodology for investigating the usability of software originally developed by Nielsen (1993, 2000). Nielsen's protocol was modified and refined for evaluating e-learning programs by participants in a doctoral seminar held at the University of Georgia in 2001. The modifications primarily involved expanding Nielsen's…

75 FR 23775 - Agency Information Collection Activities; Proposed Collection; Comment Request; Experimental...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-04

... for research entitled ``Experimental Study of Patient Information Prototypes.'' This study is designed..., the working group refined several prototypes and designed a study to investigate the usefulness of... Design and Protocol The study is experimental and will have two independent variables in a 3 x 2 design...

Compact Modbus TCP/IP protocol for data acquisition systems based on limited hardware resources

NASA Astrophysics Data System (ADS)

Bai, Q.; Jin, B.; Wang, D.; Wang, Y.; Liu, X.

2018-04-01

The Modbus TCP/IP has been a standard industry communication protocol and widely utilized for establishing sensor-cloud platforms on the Internet. However, numerous existing data acquisition systems built on traditional single-chip microcontrollers without sufficient resources cannot support it, because the complete Modbus TCP/IP protocol always works dependent on a full operating system which occupies abundant hardware resources. Hence, a compact Modbus TCP/IP protocol is proposed in this work to make it run efficiently and stably even on a resource-limited hardware platform. Firstly, the Modbus TCP/IP protocol stack is analyzed and the refined protocol suite is rebuilt by streamlining the typical TCP/IP suite. Then, specific implementation of every hierarchical layer is respectively presented in detail according to the protocol structure. Besides, the compact protocol is implemented in a traditional microprocessor to validate the feasibility of the scheme. Finally, the performance of the proposed scenario is assessed. The experimental results demonstrate that message packets match the frame format of Modbus TCP/IP protocol and the average bandwidth reaches to 1.15 Mbps. The compact protocol operates stably even based on a traditional microcontroller with only 4-kB RAM and 12-MHz system clock, and no communication congestion or frequent packet loss occurs.

Geographic variation in lumbar diskectomy: a protocol for evaluation.

PubMed

Barron, M; Kazandjian, V A

1992-03-01

In 1989 the Maryland Hospital Association (MHA) began developing a protocol related to lumbar diskectomy, a procedure with widely reported geographic variation in its use. The MHA's Laminectomy Advisory Committee drafted three criteria for performance of lumbar diskectomy and also developed a data-collection instrument with which the eight hospitals participating in a pilot study could abstract the necessary data from medical records. Both individual hospital and aggregate results showed wide variation in compliance with the criteria. These findings suggest research and development activities such as refinement of the data-collection instrument, use of the protocol for bench-marking, further investigation of clinical and other determinants of rate variation, and study of the effect of new diagnostic technology on utilization rates for this procedure.

Combination of dynamic transformation and dynamic recrystallization for realizing ultrafine-grained steels with superior mechanical properties

PubMed Central

Zhao, Lijia; Park, Nokeun; Tian, Yanzhong; Shibata, Akinobu; Tsuji, Nobuhiro

2016-01-01

Dynamic recrystallization (DRX) is an important grain refinement mechanism to fabricate steels with high strength and high ductility (toughness). The conventional DRX mechanism has reached the limitation of refining grains to several microns even though employing high-strain deformation. Here we show a DRX phenomenon occurring in the dynamically transformed (DT) ferrite, by which the required strain for the operation of DRX and the formation of ultrafine grains is significantly reduced. The DRX of DT ferrite shows an unconventional temperature dependence, which suggests an optimal condition for grain refinement. We further show that new strategies for ultra grain refinement can be evoked by combining DT and DRX mechanisms, based on which fully ultrafine microstructures having a mean grain size down to 0.35 microns can be obtained without high-strain deformation and exhibit superior mechanical properties. This study will open the door to achieving optimal grain refinement to nanoscale in a variety of steels requiring no high-strain deformation in practical industrial application. PMID:27966603

Recent refinements to cranial implants for rhesus macaques (Macaca mulatta)

PubMed Central

Johnston, Jessica M.; Cohen, Yale E.; Shirley, Harry; Tsunada, Joji; Bennur, Sharath; Christison-Lagay, Kate; Veeder, Christin L.

2017-01-01

The advent of cranial implants revolutionized primate neurophysiological research because they allow researchers to stably record neural activity from monkeys during active behavior. Cranial implants have improved over the years since their introduction, but chronic implants still increase the risk for medical complications including bacterial contamination and resultant infection, chronic inflammation, bone and tissue loss and complications related to the use of dental acrylic. These complications can lead to implant failure and early termination of study protocols. In an effort to reduce complications, we describe several refinements that have helped us improve cranial implants and the wellbeing of implanted primates. PMID:27096188

An Integrated Framework Advancing Membrane Protein Modeling and Design

PubMed Central

Weitzner, Brian D.; Duran, Amanda M.; Tilley, Drew C.; Elazar, Assaf; Gray, Jeffrey J.

2015-01-01

Membrane proteins are critical functional molecules in the human body, constituting more than 30% of open reading frames in the human genome. Unfortunately, a myriad of difficulties in overexpression and reconstitution into membrane mimetics severely limit our ability to determine their structures. Computational tools are therefore instrumental to membrane protein structure prediction, consequently increasing our understanding of membrane protein function and their role in disease. Here, we describe a general framework facilitating membrane protein modeling and design that combines the scientific principles for membrane protein modeling with the flexible software architecture of Rosetta3. This new framework, called RosettaMP, provides a general membrane representation that interfaces with scoring, conformational sampling, and mutation routines that can be easily combined to create new protocols. To demonstrate the capabilities of this implementation, we developed four proof-of-concept applications for (1) prediction of free energy changes upon mutation; (2) high-resolution structural refinement; (3) protein-protein docking; and (4) assembly of symmetric protein complexes, all in the membrane environment. Preliminary data show that these algorithms can produce meaningful scores and structures. The data also suggest needed improvements to both sampling routines and score functions. Importantly, the applications collectively demonstrate the potential of combining the flexible nature of RosettaMP with the power of Rosetta algorithms to facilitate membrane protein modeling and design. PMID:26325167

Comparison of Haloperidol Alone and in Combination with Midazolam for the Treatment of Acute Agitation in an Inpatient Palliative Care Service.

PubMed

Ferraz Gonçalves, José António; Almeida, Ana; Costa, Isabel; Silva, Paula; Carneiro, Rui

2016-12-01

Agitation is a very distressing problem that must be controlled as quickly as possible, but using a safe method. The authors conducted a comparison of two protocols: a combination of haloperidol and midazolam and haloperidol alone. The combination drug protocol controlled 101 out of 121 (84%) episodes of agitation with only the first dose, whereas the haloperidol alone protocol controlled 47 out of 74 (64%) episodes. This difference is statistically significant (P =.002), with a post hoc analyzed power of 0.88. The median time from the first dose to the control of agitation was 15 minutes (range: 5-210) with the combination and 60 minutes (range: 10-430) with the other protocol, P <.001. There were no complications other than some transient somnolence, mainly with the combination protocol. The authors conclude that the combination of haloperidol and midazolam is effective and safe for the control of agitation in palliative care and it is more effective than haloperidol alone. Therefore, the combination should be adopted as the preferred protocol. It would be helpful if the usefulness of this protocol is confirmed by others.

The effect of scandium addition on microstructure and mechanical properties of Al–Si–Mg alloy: A multi-refinement modifier

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

Xu, Cong, E-mail: xucong55555@gmail.com; Xiao, Wenlong, E-mail: wlxiao@buaa.edu.cn; Hanada, Shuji

2015-12-15

Effect of scandium (Sc) additions on the microstructure, mechanical properties and fracture behavior of Al–Si–Mg casting alloy (F357) were systematically investigated. It was found that Sc addition caused a multi-refining efficiency on the microstructure of as-cast F357 alloy, including refinement of grains and secondary dendrite arm spacing (SDAS), modification of eutectic Si and harmless disposal of β-Al{sub 5}FeSi phase. Subsequent T6 heat treatment had further induced the complete spheroidization of eutectic Si and precipitation of fine secondary Al{sub 3}Sc dispersoids in the Sc modified alloys. Thus the mechanical properties, especially the ductility, were significantly enhanced by the addition of Scmore » combined with the heat treatment. The highest ultimate tensile strength, yield strength and elongation were achieved in 0.8 wt.% Sc modified F357 alloy combined with T6 heat treatment. Furthermore, fractographic examinations indicated that the ductile fracture mechanism served as a dominate role in the modified alloys due to the formation of fine, deep and uniformly distributed dimples. - Highlights: • Detailed characterization of the multi-refining microstructure of Sc modified F357 alloy was performed. • The multi-refinement was proposed to refine grain and SDAS, modify eutectic Si and β-phase. • Sc modifier combined with T6 treatment is effective in improving tensile properties. • Modification of eutectic Si in F357 alloy with Sc is consistent with the IIT mechanism.« less

Trauma Quality Improvement: Reducing Triage Errors by Automating the Level Assignment Process.

PubMed

Stonko, David P; O Neill, Dillon C; Dennis, Bradley M; Smith, Melissa; Gray, Jeffrey; Guillamondegui, Oscar D

2018-04-12

Trauma patients are triaged by the severity of their injury or need for intervention while en route to the trauma center according to trauma activation protocols that are institution specific. Significant research has been aimed at improving these protocols in order to optimize patient outcomes while striving for efficiency in care. However, it is known that patients are often undertriaged or overtriaged because protocol adherence remains imperfect. The goal of this quality improvement (QI) project was to improve this adherence, and thereby reduce the triage error. It was conducted as part of the formal undergraduate medical education curriculum at this institution. A QI team was assembled and baseline data were collected, then 2 Plan-Do-Study-Act (PDSA) cycles were implemented sequentially. During the first cycle, a novel web tool was developed and implemented in order to automate the level assignment process (it takes EMS-provided data and automatically determines the level); the tool was based on the existing trauma activation protocol. The second PDSA cycle focused on improving triage accuracy in isolated, less than 10% total body surface area burns, which we identified to be a point of common error. Traumas were reviewed and tabulated at the end of each PDSA cycle, and triage accuracy was followed with a run chart. This study was performed at Vanderbilt University Medical Center and Medical School, which has a large level 1 trauma center covering over 75,000 square miles, and which sees urban, suburban, and rural trauma. The baseline assessment period and each PDSA cycle lasted 2 weeks. During this time, all activated, adult, direct traumas were reviewed. There were 180 patients during the baseline period, 189 after the first test of change, and 150 after the second test of change. All were included in analysis. Of 180 patients, 30 were inappropriately triaged during baseline analysis (3 undertriaged and 27 overtriaged) versus 16 of 189 (3 undertriaged and 13 overtriaged) following implementation of the web tool (p = 0.017 for combined errors). Overtriage dropped further from baseline to 10/150 after the second test of change (p = 0.005). The total number of triaged patients dropped from 92.3/week to 75.5/week after the second test of change. There was no statistically significant change in the undertriage rate. The combination of web tool implementation and protocol refinement decreased the combined triage error rate by over 50% (from 16.7%-7.9%). We developed and tested a web tool that improved triage accuracy, and provided a sustainable method to enact future quality improvement. This web tool and QI framework would be easily expandable to other hospitals. Copyright © 2018 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

The use of a photoionization detector to detect harmful volatile chemicals by emergency personnel

PubMed Central

Patel, Neil D; Fales, William D; Farrell, Robert N

2009-01-01

Objective The objective of this investigation was to determine if a photoionization detector (PID) could be used to detect the presence of a simulated harmful chemical on simulated casualties of a chemical release. Methods A screening protocol, based on existing radiation screening protocols, was developed for the purposes of the investigation. Three simulated casualties were contaminated with a simulated chemical agent and two groups of emergency responders were involved in the trials. The success–failure ratio of the participants was used to judge the performance of the PID in this application. Results A high success rate was observed when the screening protocol was properly adhered to (97.67%). Conversely, the success rate suffered when participants deviated from the protocol (86.31%). With one exception, all failures were noted to have been the result of a failure to correctly observe the established screening protocol. Conclusions The results of this investigation indicate that the PID may be an effective screening tool for emergency responders. However, additional study is necessary to both confirm the effectiveness of the PID and refine the screening protocol if necessary. PMID:27147829

Interactive simulations for quantum key distribution

NASA Astrophysics Data System (ADS)

Kohnle, Antje; Rizzoli, Aluna

2017-05-01

Secure communication protocols are becoming increasingly important, e.g. for internet-based communication. Quantum key distribution (QKD) allows two parties, commonly called Alice and Bob, to generate a secret sequence of 0s and 1s called a key that is only known to themselves. Classically, Alice and Bob could never be certain that their communication was not compromised by a malicious eavesdropper. Quantum mechanics however makes secure communication possible. The fundamental principle of quantum mechanics that taking a measurement perturbs the system (unless the measurement is compatible with the quantum state) also applies to an eavesdropper. Using appropriate protocols to create the key, Alice and Bob can detect the presence of an eavesdropper by errors in their measurements. As part of the QuVis Quantum Mechanics Visualisation Project, we have developed a suite of four interactive simulations that demonstrate the basic principles of three different QKD protocols. The simulations use either polarised photons or spin 1/2 particles as physical realisations. The simulations and accompanying activities are freely available for use online or download, and run on a wide range of devices including tablets and PCs. Evaluation with students over three years was used to refine the simulations and activities. Preliminary studies show that the refined simulations and activities help students learn the basic principles of QKD at both the introductory and advanced undergraduate levels.

The Varied Circumstances Prompting Requests for Emergency Contraception at School-Based Clinics

ERIC Educational Resources Information Center

Sidebottom, Abbey; Harrison, Patricia A.; Amidon, Donna; Finnegan, Katie

2008-01-01

Background: Little is known about the circumstances that prompt teenagers to request emergency contraception (EC). This evaluation was designed to refine the EC clinical protocol and improve pregnancy prevention efforts in high school-based clinics by analyzing information on EC use and subsequent contraception use of EC patients. Methods: Sites…

Early Campus Response to Disruptive Behavior

ERIC Educational Resources Information Center

Stump, Linda J.; Zdziarski, Eugene L.

2008-01-01

As major events define generations and tragedies define and refine protocol response to significant incidents, a sense of comfort and confidence is attained as the authors train individually and organizationally to respond to extreme events, and yet those who have experienced them know that no plan goes as it should. There are, however, steps or…

Protein structure modeling and refinement by global optimization in CASP12.

PubMed

Hong, Seung Hwan; Joung, InSuk; Flores-Canales, Jose C; Manavalan, Balachandran; Cheng, Qianyi; Heo, Seungryong; Kim, Jong Yun; Lee, Sun Young; Nam, Mikyung; Joo, Keehyoung; Lee, In-Ho; Lee, Sung Jong; Lee, Jooyoung

2018-03-01

For protein structure modeling in the CASP12 experiment, we have developed a new protocol based on our previous CASP11 approach. The global optimization method of conformational space annealing (CSA) was applied to 3 stages of modeling: multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain re-modeling. For better template selection and model selection, we updated our model quality assessment (QA) method with the newly developed SVMQA (support vector machine for quality assessment). For 3D chain building, we updated our energy function by including restraints generated from predicted residue-residue contacts. New energy terms for the predicted secondary structure and predicted solvent accessible surface area were also introduced. For difficult targets, we proposed a new method, LEEab, where the template term played a less significant role than it did in LEE, complemented by increased contributions from other terms such as the predicted contact term. For TBM (template-based modeling) targets, LEE performed better than LEEab, but for FM targets, LEEab was better. For model refinement, we modified our CASP11 molecular dynamics (MD) based protocol by using explicit solvents and tuning down restraint weights. Refinement results from MD simulations that used a new augmented statistical energy term in the force field were quite promising. Finally, when using inaccurate information (such as the predicted contacts), it was important to use the Lorentzian function for which the maximal penalty arising from wrong information is always bounded. © 2017 Wiley Periodicals, Inc.

Geochemical and mineralogical data for soils of the conterminous United States

USGS Publications Warehouse

Smith, David B.; Cannon, William F.; Woodruff, Laurel G.; Solano, Federico; Kilburn, James E.; Fey, David L.

2013-01-01

In 2007, the U.S. Geological Survey initiated a low-density (1 site per 1,600 square kilometers, 4,857 sites) geochemical and mineralogical survey of soils of the conterminous United States as part of the North American Soil Geochemical Landscapes Project. Sampling and analytical protocols were developed at a workshop in 2003, and pilot studies were conducted from 2004 to 2007 to test and refine these recommended protocols. The final sampling protocol for the national-scale survey included, at each site, a sample from a depth of 0 to 5 centimeters, a composite of the soil A horizon, and a deeper sample from the soil C horizon or, if the top of the C horizon was at a depth greater than 1 meter, from a depth of approximately 80–100 centimeters. The <2-millimeter fraction of each sample was analyzed for a suite of 45 major and trace elements by methods that yield the total or near-total elemental content. The major mineralogical components in the samples from the soil A and C horizons were determined by a quantitative X-ray diffraction method using Rietveld refinement. Sampling in the conterminous United States was completed in 2010, with chemical and mineralogical analyses completed in May 2013. The resulting dataset provides an estimate of the abundance and spatial distribution of chemical elements and minerals in soils of the conterminous United States and represents a baseline for soil geochemistry and mineralogy against which future changes may be recognized and quantified. This report (1) describes the sampling, sample preparation, and analytical methods used; (2) gives details of the quality control protocols used to monitor the quality of chemical and mineralogical analyses over approximately six years; and (3) makes available the soil geochemical and mineralogical data in downloadable tables.

Towards optimized anesthesia protocols for stereotactic surgery in rats: Analgesic, stress and general health effects of injectable anesthetics. A comparison of a recommended complete reversal anesthesia with traditional chloral hydrate monoanesthesia.

PubMed

Hüske, Christin; Sander, Svenja Esther; Hamann, Melanie; Kershaw, Olivia; Richter, Franziska; Richter, Angelika

2016-07-01

Although injectable anesthetics are still widely used in laboratory rodents, scientific data concerning pain and distress during and after stereotactic surgery are rare. However, optimal anesthesia protocols have a high impact on the quality of the derived data. We therefore investigated the suitability of recommended injectable anesthesia with a traditionally used monoanesthesia for stereotactic surgery in view of optimization and refinement in rats. The influence of the recommended complete reversal anesthesia (MMF; 0.15mg/kg medetomidine, 2mg/kg midazolam, 0.005mg/kg fentanyl; i.m.) with or without reversal and of chloral hydrate (430mg/kg, 3.6%, i.p.) on various physiological, biochemical and behavioral parameters (before, during, after surgery) was analyzed. Isoflurane was also included in stress parameter analysis. In all groups, depth of anesthesia was sufficient for stereotactic surgery with no animal losses. MMF caused transient exophthalmos, myositis at the injection site and increased early postoperative pain scores. Reversal induced agitation, restlessness and hypothermia. Even the low concentrated chloral hydrate led to peritonitis and multifocal liver necrosis, corresponding to increased stress hormone levels and loss in body weight. Increased stress response was also exerted by isoflurane anesthesia. Pronounced systemic toxicity of chloral hydrate strongly questions its further use in rodent anesthesia. In view of undesired effects of MMF and isoflurane, thorough consideration of anesthesia protocols for particular research projects is indispensable. Reversal should be restricted to emergency situations. Our data support further refinement of the current protocols and the importance of sham operated controls. Copyright © 2016 Elsevier B.V. All rights reserved.

Nursing Outcomes for Patients with Risk of Perioperative Positioning Injury.

PubMed

de Lima, Luciana Bjorklund; E Cardozo, Michelle Cardoso; Bernardes, Daniela de Souza; Rabelo-Silva, Eneida Rejane

2018-04-16

To select and refine the outcomes and indicators of Nursing Outcomes Classification for the diagnosis of risk for perioperative positioning injury. Validation study on expert consensus and refinement through pilot study. Eight outcomes and 35 indicators were selected in consensus. After clinical testing was performed, in which 10 patients were assessed at five different times. Eight outcomes and 33 indicators remained in the protocol. This study made it possible to select the most relevant outcomes and indicators to be measured for this diagnosis in clinical practice. Validation studies by consensus and clinical testing are important to promote the accuracy, creating opportunities to legitimize, and improve the concepts of taxonomies. © 2018 NANDA International, Inc.

Refining of metallurgical-grade silicon

NASA Technical Reports Server (NTRS)

Dietl, J.

1986-01-01

A basic requirement of large scale solar cell fabrication is to provide low cost base material. Unconventional refining of metallurical grade silicon represents one of the most promising ways of silicon meltstock processing. The refining concept is based on an optimized combination of metallurgical treatments. Commercially available crude silicon, in this sequence, requires a first pyrometallurgical step by slagging, or, alternatively, solvent extraction by aluminum. After grinding and leaching, high purity qualtiy is gained as an advanced stage of refinement. To reach solar grade quality a final pyrometallurgical step is needed: liquid-gas extraction.

Relationship Factors Contributing to the Progression of Combat Related PTSD and Suiciality Over Time

DTIC Science & Technology

2015-04-01

6 Table 1. Hiring and orientation of project staff, purchasing and installing equipment...continues to refine and maintain detailed protocols for data checking and downloading, and ethics training for all study personnel (e.g., general...human subjects certification, documented agreement to specific ethical practices regarding this study). Five University of Colorado Institutional Review

Mobile technology intervention to improve care coordination between HIV and substance use treatment providers: development, training, and evaluation protocol.

PubMed

Claborn, Kasey; Becker, Sara; Ramsey, Susan; Rich, Josiah; Friedmann, Peter D

2017-03-14

People living with HIV (PLWH) with a substance use disorder (SUD) tend to receive inadequate medical care in part because of a siloed healthcare system in which HIV and substance use services are delivered separately. Ideal treatment requires an interdisciplinary, team-based coordinated care approach, but many structural and systemic barriers impede the integration of HIV and SUD services. The current protocol describes the development and preliminary evaluation of a care coordination intervention (CCI), consisting of a tablet-based mobile platform for HIV and SUD treatment providers, an interagency communication protocol, and a training protocol. We hypothesize that HIV and SUD treatment providers will find the CCI to be acceptable, and that after receipt of the CCI, providers will: exhibit higher retention in dual care among patients, report increased frequency and quality of communication, and report increased rates of relational coordination. A three phase approach is used to refine and evaluate the CCI. Phase 1 consists of in-depth qualitative interviews with 8 key stakeholders as well as clinical audits of participating HIV and SUD treatment agencies. Phase 2 contains functionality testing of the mobile platform with frontline HIV and SUD treatment providers, followed by refinement of the CCI. Phase 3 consists of a pre-, post-test trial with 30 SUD and 30 HIV treatment providers. Data will be collected at the provider, organization, and patient levels. Providers will complete assessments at baseline, immediately post-training, and at 1-, 3-, and 6-months post-training. Organizational data will be collected at baseline, 1-, 3-, and 6-months post training, while patient data will be collected at baseline and 6-months post training. This study will develop and evaluate a CCI consisting of a tablet-based mobile platform for treatment providers, an interagency communication protocol, and a training protocol as a means of improving the integration of care for PLWH who have a SUD. Results have the potential to advance the field by bridging gaps in a fragmented healthcare system, and improving treatment efficiency, work flow, and communication among interdisciplinary providers from different treatment settings. NCT02906215.

Integrated decontamination process for metals

DOEpatents

Snyder, Thomas S.; Whitlow, Graham A.

1991-01-01

An integrated process for decontamination of metals, particularly metals that are used in the nuclear energy industry contaminated with radioactive material. The process combines the processes of electrorefining and melt refining to purify metals that can be decontaminated using either electrorefining or melt refining processes.

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

PubMed Central

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

2017-01-01

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

A framework for solving ill-structured community problems

NASA Astrophysics Data System (ADS)

Keller, William Cotesworth

A multifaceted protocol for solving ill-structured community problems has been developed. It embodies the lessons learned from the past by refining and extending features of previous models from the systems thinkers, and the fields of behavioral decision making and creative problem solving. The protocol also embraces additional features needed to address the unique aspects of community decision situations. The essential elements of the protocol are participants from the community, a problem-solving process, a systems picture, a facilitator, a modified Delphi method of communications, and technical expertise. This interdisciplinary framework has been tested by a quasi experiment with a real world community problem (the high cost of electrical power on Long Island, NY). Results indicate the protocol can enable members of the community to understand a complicated, ill-structured problem and guide them to action to solve the issue. However, the framework takes time (over one year in the test case) and will be inappropriate for crises where quick action is needed.

SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

PubMed

Tong, Jing; Pei, Jimin; Grishin, Nick V

2015-09-03

Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

Combining global and local approximations

NASA Technical Reports Server (NTRS)

Haftka, Raphael T.

1991-01-01

A method based on a linear approximation to a scaling factor, designated the 'global-local approximation' (GLA) method, is presented and shown capable of extending the range of usefulness of derivative-based approximations to a more refined model. The GLA approach refines the conventional scaling factor by means of a linearly varying, rather than constant, scaling factor. The capabilities of the method are demonstrated for a simple beam example with a crude and more refined FEM model.

A land classification protocol for pollinator ecology research: An urbanization case study.

PubMed

Samuelson, Ash E; Leadbeater, Ellouise

2018-06-01

Land-use change is one of the most important drivers of widespread declines in pollinator populations. Comprehensive quantitative methods for land classification are critical to understanding these effects, but co-option of existing human-focussed land classifications is often inappropriate for pollinator research. Here, we present a flexible GIS-based land classification protocol for pollinator research using a bottom-up approach driven by reference to pollinator ecology, with urbanization as a case study. Our multistep method involves manually generating land cover maps at multiple biologically relevant radii surrounding study sites using GIS, with a focus on identifying land cover types that have a specific relevance to pollinators. This is followed by a three-step refinement process using statistical tools: (i) definition of land-use categories, (ii) principal components analysis on the categories, and (iii) cluster analysis to generate a categorical land-use variable for use in subsequent analysis. Model selection is then used to determine the appropriate spatial scale for analysis. We demonstrate an application of our protocol using a case study of 38 sites across a gradient of urbanization in South-East England. In our case study, the land classification generated a categorical land-use variable at each of four radii based on the clustering of sites with different degrees of urbanization, open land, and flower-rich habitat. Studies of land-use effects on pollinators have historically employed a wide array of land classification techniques from descriptive and qualitative to complex and quantitative. We suggest that land-use studies in pollinator ecology should broadly adopt GIS-based multistep land classification techniques to enable robust analysis and aid comparative research. Our protocol offers a customizable approach that combines specific relevance to pollinator research with the potential for application to a wide range of ecological questions, including agroecological studies of pest control.

Contexts, Mechanisms, and Outcomes That Matter in Dutch Community-Based Physical Activity Programs Targeting Socially Vulnerable Groups.

PubMed

Herens, Marion; Wagemakers, Annemarie; Vaandrager, Lenneke; van Ophem, Johan; Koelen, Maria

2017-09-01

This article presents a practitioner-based approach to identify key combinations of contextual factors (C) and mechanisms (M) that trigger outcomes (O) in Dutch community-based health-enhancing physical activity (CBHEPA) programs targeting socially vulnerable groups. Data were collected in six programs using semi-structured interviews and focus groups using a timeline technique. Sessions were recorded, anonymized, and transcribed. A realist synthesis protocol was used for data-driven and thematic analysis of CMO configurations. CMO configurations related to community outreach, program sustainability, intersectoral collaboration, and enhancing participants' active lifestyles. We have refined the CBHEPA program theory by showing that actors' passion for, and past experiences with, physical activity programs trigger outcomes, alongside their commitment to socially vulnerable target groups. Project discontinuity, limited access to resources, and a trainer's stand-alone position were negative configurations. The authors conclude that local governance structures appear often to lack adaptive capacity to accommodate multilevel processes to sustain programs.

SURVIVAL OF CAPTIVE-REARED PUERTO RICAN PARROTS RELEASED IN THE CARIBBEAN NATIONAL FOREST

Treesearch

THOMAS H. WHITE; JAIME A. COLLAZO; FRANCISCO J. VILELLA

2005-01-01

We report first-year survival for 34 captive-reared Puerto Rican Parrots (Amazona vittata) released in the Caribbean National Forest, Puerto Rico between 2000 and 2002. The purpose of the releases were to increase population size and the potential number of breeding individuals of the sole extant wild population, and to refine release protocols for eventual...

Universal Blind Quantum Computation

NASA Astrophysics Data System (ADS)

Fitzsimons, Joseph; Kashefi, Elham

2012-02-01

Blind Quantum Computing (BQC) allows a client to have a server carry out a quantum computation for them such that the client's inputs, outputs and computation remain private. Recently we proposed a universal unconditionally secure BQC scheme, based on the conceptual framework of the measurement-based quantum computing model, where the client only needs to be able to prepare single qubits in separable states randomly chosen from a finite set and send them to the server, who has the balance of the required quantum computational resources. Here we present a refinement of the scheme which vastly expands the class of quantum circuits which can be directly implemented as a blind computation, by introducing a new class of resource states which we term dotted-complete graph states and expanding the set of single qubit states the client is required to prepare. These two modifications significantly simplify the overall protocol and remove the previously present restriction that only nearest-neighbor circuits could be implemented as blind computations directly. As an added benefit, the refined protocol admits a substantially more intuitive and simplified verification mechanism, allowing the correctness of a blind computation to be verified with arbitrarily small probability of error.

Refining and validating a two-stage and web-based cancer risk assessment tool for village doctors in China.

PubMed

Shen, Xing-Rong; Chai, Jing; Feng, Rui; Liu, Tong-Zhu; Tong, Gui-Xian; Cheng, Jing; Li, Kai-Chun; Xie, Shao-Yu; Shi, Yong; Wang, De-Bin

2014-01-01

The big gap between efficacy of population level prevention and expectations due to heterogeneity and complexity of cancer etiologic factors calls for selective yet personalized interventions based on effective risk assessment. This paper documents our research protocol aimed at refining and validating a two-stage and web- based cancer risk assessment tool, from a tentative one in use by an ongoing project, capable of identifying individuals at elevated risk for one or more types of the 80% leading cancers in rural China with adequate sensitivity and specificity and featuring low cost, easy application and cultural and technical sensitivity for farmers and village doctors. The protocol adopted a modified population-based case control design using 72, 000 non-patients as controls, 2, 200 cancer patients as cases, and another 600 patients as cases for external validation. Factors taken into account comprised 8 domains including diet and nutrition, risk behaviors, family history, precancerous diseases, related medical procedures, exposure to environment hazards, mood and feelings, physical activities and anthropologic and biologic factors. Modeling stresses explored various methodologies like empirical analysis, logistic regression, neuro-network analysis, decision theory and both internal and external validation using concordance statistics, predictive values, etc..

Radiogenetic therapy: strategies to overcome tumor resistance.

PubMed

Marples, B; Greco, O; Joiner, M C; Scott, S D

2003-01-01

The aim of cancer gene therapy is to selectively kill malignant cells at the tumor site, by exploiting traits specific to cancer cells and/or solid tumors. Strategies that take advantage of biological features common to different tumor types are particularly promising, since they have wide clinical applicability. Much attention has focused on genetic methods that complement radiotherapy, the principal treatment modality, or that exploit hypoxia, the most ubiquitous characteristic of most solid cancers. The goal of this review is to highlight two promising gene therapy methods developed specifically to target the tumor volume that can be readily used in combination with radiotherapy. The first approach uses radiation-responsive gene promoters to control the selective expression of a suicide gene (e.g., herpes simplex virus thymidine kinase) to irradiated tissue only, leading to targeted cell killing in the presence of a prodrug (e.g., ganciclovir). The second method utilizes oxygen-dependent promoters to produce selective therapeutic gene expression and prodrug activation in hypoxic cells, which are refractive to conventional radiotherapy. Further refining of tumor targeting can be achieved by combining radiation and hypoxia responsive elements in chimeric promoters activated by either and dual stimuli. The in vitro and in vivo studies described in this review suggest that the combination of gene therapy and radiotherapy protocols has potential for use in cancer care, particularly in cases currently refractory to treatment as a result of inherent or hypoxia-mediated radioresistance.

The "ComPAS Trial" combined treatment model for acute malnutrition: study protocol for the economic evaluation.

PubMed

Lelijveld, Natasha; Bailey, Jeanette; Mayberry, Amy; Trenouth, Lani; N'Diaye, Dieynaba S; Haghparast-Bidgoli, Hassan; Puett, Chloe

2018-04-24

Acute malnutrition is currently divided into severe (SAM) and moderate (MAM) based on level of wasting. SAM and MAM currently have separate treatment protocols and products, managed by separate international agencies. For SAM, the dose of treatment is allocated by the child's weight. A combined and simplified protocol for SAM and MAM, with a standardised dose of ready-to-use therapeutic food (RUTF), is being trialled for non-inferior recovery rates and may be more cost-effective than the current standard protocols for treating SAM and MAM. This is the protocol for the economic evaluation of the ComPAS trial, a cluster-randomised controlled, non-inferiority trial that compares a novel combined protocol for treating uncomplicated acute malnutrition compared to the current standard protocol in South Sudan and Kenya. We will calculate the total economic costs of both protocols from a societal perspective, using accounting data, interviews and survey questionnaires. The incremental cost of implementing the combined protocol will be estimated, and all costs and outcomes will be presented as a cost-consequence analysis. Incremental cost-effectiveness ratio will be calculated for primary and secondary outcome, if statistically significant. We hypothesise that implementing the combined protocol will be cost-effective due to streamlined logistics at clinic level, reduced length of treatment, especially for MAM, and reduced dosages of RUTF. The findings of this economic evaluation will be important for policymakers, especially given the hypothesised non-inferiority of the main health outcomes. The publication of this protocol aims to improve rigour of conduct and transparency of data collection and analysis. It is also intended to promote inclusion of economic evaluation in other nutrition intervention studies, especially for MAM, and improve comparability with other studies. ISRCTN 30393230 , date: 16/03/2017.

The combination of activated natural zeolite-bentonite to reduce Fe and Cu in refined bleached palm oil (RBPO) by using atomic absorption spectrophotometer method

NASA Astrophysics Data System (ADS)

Zakwan; Raja, PM; Giyanto

2018-02-01

Indonesia is one of the crude palm oil (CPO) production country in the world. As many products are derivated from the CPO, the quality must be increased continuously. One of the things that influence the quality of palm oil is the Fe and Cu content. The objective of this research was to reduce Fe and Cu content in Refined Bleached Palm Oil (RBPO). In processing CPO or Refined Bleachead Palm Oil (RBPO) may be contaminated by Fe and Cu from metal tank and pipe in the factory. The zeolite and bentonite was activated by maceration method using hydrochloric acid (0,1 N). Four batch reactions consisting of refined palm oil (RPO), activated natural zeolite-bentonite (ANZB) was bleached by heating and stirring them at about 105°C and 1200 rpm for 30 minutes. The results showed that all combinations of ANZB can reduce the Fe content. Thereafter, the optimal combination of ANZB was obtained in K1, K2 and K4 with Cu content 0.02 ppm. In the future, it is needed to study on the reduction of the Fe and Cu content in palm oil with the other adsorbent.

Ventricular fractional shortening in 108 dogs with malignant lymphoma undergoing chemotherapy with a cyclic combination protocol including doxorubicin.

PubMed

Tater, G; Eberle, N; Hungerbuehler, S; Joetzke, A; Nolte, I; Wess, G; Betz, D

2012-01-01

The aim of this study was to evaluate whether changes in the left ventricular fractional shortening (LVFS) can be detected in dogs with malignant lymphoma undergoing a cyclic combination chemotherapy protocol including doxorubicin. Left ventricular fractional shortening as a stand-alone measurement will not show a significant change during the cyclic combination protocol. In this retrospective study, the records of dogs with malignant lymphoma treated between April 2001 and October 2010 were reviewed. Inclusion criteria comprised: a diagnosis of malignant lymphoma, a cyclic combination chemotherapy (including L-asparaginase, vincristine, cyclophosphamide, doxorubicin and prednisolone), and an echocardiographic examination by an experienced examiner before treatment and after each doxorubicin administration. One hundred and eight dogs were included and a total of 446 LVFS measurements had been performed. Patients were divided into four groups according to the number of doxorubicin administrations. Median LVFS did not change significantly during the cyclic combination protocol in all groups. All median LVFS values remained above the lower reference value of 25%. The measurement of LVFS did not show a significant change during the cyclic combination protocol treatment including doxorubicin in this population of dogs. Therefore either this cyclic combination protocol does not cause a systolic dysfunction or LVFS is not sensitive enough to detect early changes. Newer methods that are more sensitive then LVFS might be necessary to detect such changes.

Combined Protocol for Acute Malnutrition Study (ComPAS) in rural South Sudan and urban Kenya: study protocol for a randomized controlled trial.

PubMed

Bailey, Jeanette; Lelijveld, Natasha; Marron, Bethany; Onyoo, Pamela; Ho, Lara S; Manary, Mark; Briend, André; Opondo, Charles; Kerac, Marko

2018-04-24

Acute malnutrition is a continuum condition, but severe and moderate forms are treated separately, with different protocols and therapeutic products, managed by separate United Nations agencies. The Combined Protocol for Acute Malnutrition Study (ComPAS) aims to simplify and unify the treatment of uncomplicated severe and moderate acute malnutrition (SAM and MAM) for children 6-59 months into one protocol in order to improve the global coverage, quality, continuity of care and cost-effectiveness of acute malnutrition treatment in resource-constrained settings. This study is a multi-site, cluster randomized non-inferiority trial with 12 clusters in Kenya and 12 clusters in South Sudan. Participants are 3600 children aged 6-59 months with uncomplicated acute malnutrition. This study will evaluate the impact of a simplified and combined protocol for the treatment of SAM and MAM compared to the standard protocol, which is the national treatment protocol in each country. We will assess recovery rate as a primary outcome and coverage, defaulting, death, length of stay, average weekly weight gain and average weekly mid-upper arm circumference (MUAC) gain as secondary outcomes. Recovery rate is defined across both treatment arms as MUAC ≥125 mm and no oedema for two consecutive visits. Per-protocol and intention-to-treat analyses will be conducted. If the combined protocol is shown to be non-inferior to the standard protocol, updating guidelines to use the combined protocol would eliminate the need for separate products, resources and procedures for MAM treatment. This would likely be more cost-effective, increase availability of services, enable earlier case finding and treatment before deterioration of MAM into SAM, promote better continuity of care and improve community perceptions of the programme. ISRCTN, ISRCTN30393230 . Registered on 16 March 2017.

Refining the Eye: Dermatology and Visual Literacy

ERIC Educational Resources Information Center

Zimmermann, Corinne; Huang, Jennifer T.; Buzney, Elizabeth A.

2016-01-01

In 2014 the Museum of Fine Arts Boston and Harvard Medical School began a partnership focused on building visual literacy skills for dermatology residents in the Harvard Combined Dermatology Residency Program. "Refining the Eye: Art and Dermatology", a four session workshop, took place in the museum's galleries and utilized the Visual…

76 FR 36103 - Combined Notice of Filings #1

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-21

...-2077-005. Applicants: Delaware City Refining Company LLC, PBF Power Marketing LLC. Desciption: Delaware City Refining Company LLC, Triennial Market Power Analysis and Notice of Change in Status. Filed Date..., 2011. Docket Numbers: ER10-2074-001; ER10-2097-003. Applicants: Kansas City Power & Light Company, KCP...

Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in double-blind predictions during the CASP11 experiment.

PubMed

Khoury, George A; Smadbeck, James; Kieslich, Chris A; Koskosidis, Alexandra J; Guzman, Yannis A; Tamamis, Phanourios; Floudas, Christodoulos A

2017-06-01

Protein structure refinement is the challenging problem of operating on any protein structure prediction to improve its accuracy with respect to the native structure in a blind fashion. Although many approaches have been developed and tested during the last four CASP experiments, a majority of the methods continue to degrade models rather than improve them. Princeton_TIGRESS (Khoury et al., Proteins 2014;82:794-814) was developed previously and utilizes separate sampling and selection stages involving Monte Carlo and molecular dynamics simulations and classification using an SVM predictor. The initial implementation was shown to consistently refine protein structures 76% of the time in our own internal benchmarking on CASP 7-10 targets. In this work, we improved the sampling and selection stages and tested the method in blind predictions during CASP11. We added a decomposition of physics-based and hybrid energy functions, as well as a coordinate-free representation of the protein structure through distance-binning Cα-Cα distances to capture fine-grained movements. We performed parameter estimation to optimize the adjustable SVM parameters to maximize precision while balancing sensitivity and specificity across all cross-validated data sets, finding enrichment in our ability to select models from the populations of similar decoys generated for targets in CASPs 7-10. The MD stage was enhanced such that larger structures could be further refined. Among refinement methods that are currently implemented as web-servers, Princeton_TIGRESS 2.0 demonstrated the most consistent and most substantial net refinement in blind predictions during CASP11. The enhanced refinement protocol Princeton_TIGRESS 2.0 is freely available as a web server at http://atlas.engr.tamu.edu/refinement/. Proteins 2017; 85:1078-1098. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

An adaptive multiblock high-order finite-volume method for solving the shallow-water equations on the sphere

DOE PAGES

McCorquodale, Peter; Ullrich, Paul; Johansen, Hans; ...

2015-09-04

We present a high-order finite-volume approach for solving the shallow-water equations on the sphere, using multiblock grids on the cubed-sphere. This approach combines a Runge--Kutta time discretization with a fourth-order accurate spatial discretization, and includes adaptive mesh refinement and refinement in time. Results of tests show fourth-order convergence for the shallow-water equations as well as for advection in a highly deformational flow. Hierarchical adaptive mesh refinement allows solution error to be achieved that is comparable to that obtained with uniform resolution of the most refined level of the hierarchy, but with many fewer operations.

Refined numerical solution of the transonic flow past a wedge

NASA Technical Reports Server (NTRS)

Liang, S.-M.; Fung, K.-Y.

1985-01-01

A numerical procedure combining the ideas of solving a modified difference equation and of adaptive mesh refinement is introduced. The numerical solution on a fixed grid is improved by using better approximations of the truncation error computed from local subdomain grid refinements. This technique is used to obtain refined solutions of steady, inviscid, transonic flow past a wedge. The effects of truncation error on the pressure distribution, wave drag, sonic line, and shock position are investigated. By comparing the pressure drag on the wedge and wave drag due to the shocks, a supersonic-to-supersonic shock originating from the wedge shoulder is confirmed.

Consideration and Checkboxes: Incorporating Ethics and Science into the 3Rs

PubMed Central

Landi, Margaret S; Shriver, Adam J; Mueller, Anne

2015-01-01

Members of the research community aim to both produce high-quality research and ensure that harm is minimized in animals. The primary means of ensuring these goals are both met is the 3Rs framework of replacement, reduction, and refinement. However, some approaches to the 3Rs may result in a ‘check box mentality’ in which IACUC members, researchers, administrators, and caretakers check off a list of tasks to evaluate a protocol. We provide reasons for thinking that the 3Rs approach could be enhanced with more explicit discussion of the ethical assumptions used to arrive at an approved research protocol during IACUC review. Here we suggest that the notion of moral considerability, and all of the related issues it gives rise to, should be incorporated into IACUC discussions of 3Rs deliberations during protocol review to ensure that animal wellbeing is enhanced within the constraints of scientific investigation. PMID:25836970

Department of Defense picture archiving and communication system acceptance testing: results and identification of problem components.

PubMed

Allison, Scott A; Sweet, Clifford F; Beall, Douglas P; Lewis, Thomas E; Monroe, Thomas

2005-09-01

The PACS implementation process is complicated requiring a tremendous amount of time, resources, and planning. The Department of Defense (DOD) has significant experience in developing and refining PACS acceptance testing (AT) protocols that assure contract compliance, clinical safety, and functionality. The DOD's AT experience under the initial Medical Diagnostic Imaging Support System contract led to the current Digital Imaging Network-Picture Archiving and Communications Systems (DIN-PACS) contract AT protocol. To identify the most common system and component deficiencies under the current DIN-PACS AT protocol, 14 tri-service sites were evaluated during 1998-2000. Sixteen system deficiency citations with 154 separate types of limitations were noted with problems involving the workstation, interfaces, and the Radiology Information System comprising more than 50% of the citations. Larger PACS deployments were associated with a higher number of deficiencies. The most commonly cited systems deficiencies were among the most expensive components of the PACS.

A Comparison of the Behaviour of AlTiB and AlTiC Grain Refiners

NASA Astrophysics Data System (ADS)

Schneider, W.; Kearns, M. A.; McGarry, M. J.; Whitehead, A. J.

AlTiC master alloys present a new alternative to AlTiB grain refiners which have enjoyed pre-eminence in cast houses for several decades. Recent investigations have shown that, under defined casting conditions, AlTiC is a more efficient grain refiner than AlTiB, is less prone to agglomeration and is more resistant to poisoning by Zr, Cr. Moreover it is observed that there are differences in the mechanism of grain refinement for the different alloys. This paper describes the influence of melt temperature and addition rate on the performance of both types of grain refiner in DC casting tests on different wrought alloys. Furthermore the effects of combined additions of the grain refiners and the recycling behaviour of the treated alloys are presented. Results are compared with laboratory test data. Finally, mechanisms of grain refinement are discussed which are consistent with the observed differences in behaviour with AlTiC and AlTiB.

A grid-enabled web service for low-resolution crystal structure refinement.

PubMed

O'Donovan, Daniel J; Stokes-Rees, Ian; Nam, Yunsun; Blacklow, Stephen C; Schröder, Gunnar F; Brunger, Axel T; Sliz, Piotr

2012-03-01

Deformable elastic network (DEN) restraints have proved to be a powerful tool for refining structures from low-resolution X-ray crystallographic data sets. Unfortunately, optimal refinement using DEN restraints requires extensive calculations and is often hindered by a lack of access to sufficient computational resources. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements in parallel on the Open Science Grid, the US cyberinfrastructure. Access to the grid is provided through a simple and intuitive web interface integrated into the SBGrid Science Portal. Using this portal, refinements combined with full parameter optimization that would take many thousands of hours on standard computational resources can now be completed in several hours. An example of the successful application of DEN restraints to the human Notch1 transcriptional complex using the grid resource, and summaries of all submitted refinements, are presented as justification.

Crystal structure of hemoglobin from the maned wolf (Chrysocyon brachyurus) using synchrotron radiation.

PubMed

Fadel, Valmir; Canduri, Fernanda; Olivieri, Johnny R; Smarra, André L S; Colombo, Marcio F; Bonilla-Rodriguez, Gustavo O; de Azevedo, Walter F

2003-12-01

Crystal structure of hemoglobin isolated from the Brazilian maned wolf (Chrysocyon brachyurus) was determined using standard molecular replacement technique and refined using maximum-likelihood and simulated annealing protocols to 1.87A resolution. Structural and functional comparisons between hemoglobins from the Chrysocyon brachyurus and Homo sapiens are discussed, in order to provide further insights in the comparative biochemistry of vertebrate hemoglobins.

Defense Logistics: DOD Has Addressed Most Reporting Requirements and Continues to Refine Its Asset Visibility Strategy

DTIC Science & Technology

2015-12-01

Development, Test, and Evaluation RFID Radio Frequency Identification SEP Supporting Execution Plan Strategy Strategy to Improve Asset...migration of active Radio Frequency Identification ( RFID )19 from a proprietary communication standard protocol to an international standard to...technologies enabling hands-off processing of materiel deploying through the Defense Transportation System. Materiel marked with RFID tags may be remotely

Extremity Regeneration of Soft Tissue Injury Using Growth Factor-Impregnated Gels

DTIC Science & Technology

2017-10-01

required repeated refinements. Four swine surgeries were performed, modifying the procedure after the first two and now with a successful and...post-operative pain management. Under the modified protocol, two swine surgeries have been successfully performed. Ongoing studies to determine the...Significant changes in use or care of human subjects, vertebrate animals, biohazards, and/or select agents Following the initial surgeries on two

Portable Language-Independent Adaptive Translation from OCR. Phase 1

DTIC Science & Technology

2009-04-01

including brute-force k-Nearest Neighbors ( kNN ), fast approximate kNN using hashed k-d trees, classification and regression trees, and locality...achieved by refinements in ground-truthing protocols. Recent algorithmic improvements to our approximate kNN classifier using hashed k-D trees allows...recent years discriminative training has been shown to outperform phonetic HMMs estimated using ML for speech recognition. Standard ML estimation

Immunohistochemical Analysis in the Rat Central Nervous System and Peripheral Lymph Node Tissue Sections.

PubMed

Adzemovic, Milena Z; Zeitelhofer, Manuel; Leisser, Marianne; Köck, Ulricke; Kury, Angela; Olsson, Tomas

2016-11-14

Immunohistochemistry (IHC) provides highly specific, reliable and attractive protein visualization. Correct performance and interpretation of an IHC-based multicolor labeling is challenging, especially when utilized for assessing interrelations between target proteins in the tissue with a high fat content such as the central nervous system (CNS). Our protocol represents a refinement of the standard immunolabeling technique particularly adjusted for detection of both structural and soluble proteins in the rat CNS and peripheral lymph nodes (LN) affected by neuroinflammation. Nonetheless, with or without further modifications, our protocol could likely be used for detection of other related protein targets, even in other organs and species than here presented.

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

PubMed

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

2013-05-01

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

A protocol for the development of Mediterranean climate services based on the experiences of the CLIM-RUN case studies

NASA Astrophysics Data System (ADS)

Goodess, Clare; Ruti, Paolo; Rousset, Nathalie

2014-05-01

During the closing stages of the CLIM-RUN EU FP7 project on Climate Local Information in the Mediterranean region Responding to User Needs, the real-world experiences encountered by the case-study teams are being assessed and synthesised to identify examples of good practice and, in particular, to produce the CLIM-RUN protocol for the development of Mediterranean climate services. The specific case studies have focused on renewable energy (Morocco, Spain, Croatia, Cyprus), tourism (Savoie, Tunisia, Croatia, Cyprus) and wild fires (Greece) as well as one cross-cutting case study (Veneto region). They have been implemented following a common programme of local workshops, questionnaires and interviews, with Climate Expert Team and Stakeholder Expert Team members collaborating to identify and translate user needs and subsequently develop climate products and information. Feedback from stakeholders has been essential in assessing and refining these products. The protocol covers the following issues: the overall process and methodological key stages; identification and selection of stakeholders; communication with stakeholders; identification of user needs; translation of needs; producing products; assessing and refining products; methodologies for evaluating the economic value of climate services; and beyond CLIM-RUN - the lessons learnt. Particular emphasis is given to stakeholder analysis in the context of the participatory, bottom-up approach promoted by CLIM-RUN and to the iterative approach taken in the development of climate products. Recommendations are also made for an envisioned three-tier business model for the development of climate services involving climate, intermediary and stakeholder tiers.

Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors.

PubMed

Raveh, Barak; London, Nir; Zimmerman, Lior; Schueler-Furman, Ora

2011-04-29

Flexible peptides that fold upon binding to another protein molecule mediate a large number of regulatory interactions in the living cell and may provide highly specific recognition modules. We present Rosetta FlexPepDock ab-initio, a protocol for simultaneous docking and de-novo folding of peptides, starting from an approximate specification of the peptide binding site. Using the Rosetta fragments library and a coarse-grained structural representation of the peptide and the receptor, FlexPepDock ab-initio samples efficiently and simultaneously the space of possible peptide backbone conformations and rigid-body orientations over the receptor surface of a given binding site. The subsequent all-atom refinement of the coarse-grained models includes full side-chain modeling of both the receptor and the peptide, resulting in high-resolution models in which key side-chain interactions are recapitulated. The protocol was applied to a benchmark in which peptides were modeled over receptors in either their bound backbone conformations or in their free, unbound form. Near-native peptide conformations were identified in 18/26 of the bound cases and 7/14 of the unbound cases. The protocol performs well on peptides from various classes of secondary structures, including coiled peptides with unusual turns and kinks. The results presented here significantly extend the scope of state-of-the-art methods for high-resolution peptide modeling, which can now be applied to a wide variety of peptide-protein interactions where no prior information about the peptide backbone conformation is available, enabling detailed structure-based studies and manipulation of those interactions. © 2011 Raveh et al.

Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors

PubMed Central

Raveh, Barak; London, Nir; Zimmerman, Lior; Schueler-Furman, Ora

2011-01-01

Flexible peptides that fold upon binding to another protein molecule mediate a large number of regulatory interactions in the living cell and may provide highly specific recognition modules. We present Rosetta FlexPepDock ab-initio, a protocol for simultaneous docking and de-novo folding of peptides, starting from an approximate specification of the peptide binding site. Using the Rosetta fragments library and a coarse-grained structural representation of the peptide and the receptor, FlexPepDock ab-initio samples efficiently and simultaneously the space of possible peptide backbone conformations and rigid-body orientations over the receptor surface of a given binding site. The subsequent all-atom refinement of the coarse-grained models includes full side-chain modeling of both the receptor and the peptide, resulting in high-resolution models in which key side-chain interactions are recapitulated. The protocol was applied to a benchmark in which peptides were modeled over receptors in either their bound backbone conformations or in their free, unbound form. Near-native peptide conformations were identified in 18/26 of the bound cases and 7/14 of the unbound cases. The protocol performs well on peptides from various classes of secondary structures, including coiled peptides with unusual turns and kinks. The results presented here significantly extend the scope of state-of-the-art methods for high-resolution peptide modeling, which can now be applied to a wide variety of peptide-protein interactions where no prior information about the peptide backbone conformation is available, enabling detailed structure-based studies and manipulation of those interactions. PMID:21572516

Solution structure of a DNA decamer containing the antiviral drug ganciclovir: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement.

PubMed

Foti, M; Marshalko, S; Schurter, E; Kumar, S; Beardsley, G P; Schweitzer, B I

1997-05-06

The nucleoside analog 9-[(1,3-dihydroxy-2-propoxy)methyl]guanine (ganciclovir, DHPG) is an antiviral drug that is used in the treatment of a variety of herpes viruses in immunocompromised patients and in a gene therapy protocol that has shown promising activity for the treatment of cancer. To probe the structural effects of ganciclovir when incorporated into DNA, we determined and compared the solution structure of a modified ganciclovir-containing decamer duplex [d(CTG)(ganciclovir)d(ATCCAG)]2 and a control duplex d[(CTGGATCCAG)]2 using nuclear magnetic resonance techniques. 1H and 31P resonances in both duplexes were assigned using a combination of 2-D 1H and 31P NMR experiments. Proton-proton distances determined from NOESY data and dihedral angles determined from DQF-COSY data were used in restrained molecular dynamics simulations starting from canonical A- and B-form DNA models. Both the control and ganciclovir sets of simulations converged to B-type structures. These structures were subjected to full relaxation matrix refinement to produce final structures that were in excellent agreement with the observed NOE intensities. Examination of the final ganciclovir-containing structures reveals that the base of the ganciclovir residue is hydrogen bonded to its complementary dC and is stacked in the helix; in fact, the base of ganciclovir exhibits increased stacking with the 5' base relative to the control. Interestingly, some of the most significant distortions in the structures occur 3' to the lesion site, including a noticeable kink in the sugar-phosphate backbone at this position. Further examination reveals that the backbone conformation, sugar pucker, and glycosidic torsion angle of the residue 3' to the lesion site all indicate an A-type conformation at this position. A possible correlation of these structural findings with results obtained from earlier biochemical studies will be discussed.

Decision Making and the IACUC: Part 1—Protocol Information Discussed at Full-Committee Reviews

PubMed Central

Silverman, Jerald; Lidz, Charles W; Clayfield, Jonathan C; Murray, Alexandra; Simon, Lorna J; Rondeau, Richard G

2015-01-01

IACUC protocols can be reviewed by either the full committee or designated members. Both review methods use the principles of the 3 Rs (reduce, refine, replace) as the overarching paradigm, with federal regulations and policies providing more detailed guidance. The primary goal of this study was to determine the frequency of topics discussed by IACUC during full-committee reviews and whether the topics included those required for consideration by IACUC (for example, pain and distress, number of animals used, availability of alternatives, skill and experience of researchers). We recorded and transcribed 87 protocol discussions undergoing full-committee review at 10 academic institutions. Each transcript was coded to capture the key concepts of the discussion and analyzed for the frequency of the codes mentioned. Pain and distress was the code mentioned most often, followed by the specific procedures performed, the study design, and the completeness of the protocol form. Infrequently mentioned topics were alternatives to animal use or painful or distressful procedures, the importance of the research, and preliminary data. Not all of the topics required to be considered by the IACUC were openly discussed for all protocols, and many of the discussions were limited in their depth. PMID:26224439

Homology Modeling of Dopamine D2 and D3 Receptors: Molecular Dynamics Refinement and Docking Evaluation

PubMed Central

Platania, Chiara Bianca Maria; Salomone, Salvatore; Leggio, Gian Marco; Drago, Filippo; Bucolo, Claudio

2012-01-01

Dopamine (DA) receptors, a class of G-protein coupled receptors (GPCRs), have been targeted for drug development for the treatment of neurological, psychiatric and ocular disorders. The lack of structural information about GPCRs and their ligand complexes has prompted the development of homology models of these proteins aimed at structure-based drug design. Crystal structure of human dopamine D3 (hD3) receptor has been recently solved. Based on the hD3 receptor crystal structure we generated dopamine D2 and D3 receptor models and refined them with molecular dynamics (MD) protocol. Refined structures, obtained from the MD simulations in membrane environment, were subsequently used in molecular docking studies in order to investigate potential sites of interaction. The structure of hD3 and hD2L receptors was differentiated by means of MD simulations and D3 selective ligands were discriminated, in terms of binding energy, by docking calculation. Robust correlation of computed and experimental Ki was obtained for hD3 and hD2L receptor ligands. In conclusion, the present computational approach seems suitable to build and refine structure models of homologous dopamine receptors that may be of value for structure-based drug discovery of selective dopaminergic ligands. PMID:22970199

Differentiation of whole grain and refined wheat (T. aestivum) flour using a fuzzy mass spectrometric fingerprinting and chemometric approaches

USDA-ARS?s Scientific Manuscript database

A fuzzy mass spectrometric (MS) fingerprinting method combined with chemometric analysis was established to provide rapid discrimination between whole grain and refined wheat flour. Twenty one samples, including thirteen samples from three cultivars and eight from local grocery store, were studied....

Prospects for the U.S. energy and refining industries: Markets, profitability and key drivers for change

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

Burke, B.F.

The US refining industry has experienced an extended period of change covering the past 20 years. Growing regulatory requirements, combined with shifting market characteristics, have resulted in massive investments and significant and ongoing structural change. Despite excellent capacity utilization, recent profitability has been poor. Industry psychology can be described as depressed, with honest concern about the long-term attractiveness of domestic refining as an area for continued participation and investment. This paper provides an overview of how the industry arrived at these levels of poor profitability, examines the current situation and future drivers, and presents Chem Systems` views on the outlookmore » for domestic refining.« less

Implementing Rapid Bioassessment Protocols (RBP’s) for Watershed Monitoring

DTIC Science & Technology

2010-08-01

rare taxa (Cao et al . 1998, 2001; Marchant 2002 ; and Cao and Williams 1999) may have on subsequent results and conclusions. However, the most recent...investigating abiotic and biotic properties of streams (Plafkin et al . 1989). Subsequent refinement of RBP has resulted in a simple and flexible set of...standard methods for evaluating environmental, biological, and physical habitat characteristics of streams (Barbour et al . 1999). This report discusses

The Efficacy of Exposure Therapy for Anxiety-Related Disorders and Its Underlying Mechanisms: The Case of OCD and PTSD.

PubMed

Foa, Edna B; McLean, Carmen P

2016-01-01

In this review we describe the intricate interrelationship among basic research, conceptualization of psychopathology, treatment development, treatment outcome research, and treatment mechanism research and how the interactions among these areas of study further our knowledge about psychopathology and its treatment. In describing the work of Edna Foa and her colleagues in anxiety disorders, we demonstrate how emotional processing theory of anxiety-related disorders and their treatment using exposure therapy have generated hypotheses about the psychopathology of posttraumatic stress disorder and obsessive-compulsive anxiety disorder that have informed the development and refinement of specific treatment protocols for these disorders: prolonged exposure and exposure and response (ritual) prevention. Further, we have shown that the next step after the development of theoretically driven treatment protocols is to evaluate their efficacy. Once evidence for a treatment's efficacy has accumulated, studies of the mechanisms involved in the reduction of the targeted psychopathology are conducted, which in turn inform the theory and further refine the treatments. We conclude our review with a discussion of how the knowledge derived from Foa and colleagues' programmatic research together with knowledge emerging from basic research on extinction learning can inform future research on the psychopathology of anxiety disorders and their treatments.

GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors

PubMed Central

Esguerra, Mauricio; Siretskiy, Alexey; Bello, Xabier; Sallander, Jessica; Gutiérrez-de-Terán, Hugo

2016-01-01

GPCR-ModSim (http://open.gpcr-modsim.org) is a centralized and easy to use service dedicated to the structural modeling of G-protein Coupled Receptors (GPCRs). 3D molecular models can be generated from amino acid sequence by homology-modeling techniques, considering different receptor conformations. GPCR-ModSim includes a membrane insertion and molecular dynamics (MD) equilibration protocol, which can be used to refine the generated model or any GPCR structure uploaded to the server, including if desired non-protein elements such as orthosteric or allosteric ligands, structural waters or ions. We herein revise the main characteristics of GPCR-ModSim and present new functionalities. The templates used for homology modeling have been updated considering the latest structural data, with separate profile structural alignments built for inactive, partially-active and active groups of templates. We have also added the possibility to perform multiple-template homology modeling in a unique and flexible way. Finally, our new MD protocol considers a series of distance restraints derived from a recently identified conserved network of helical contacts, allowing for a smoother refinement of the generated models which is particularly advised when there is low homology to the available templates. GPCR- ModSim has been tested on the GPCR Dock 2013 competition with satisfactory results. PMID:27166369

A new 3D reconstituted human corneal epithelium model as an alternative method for the eye irritation test.

PubMed

Jung, Kyoung-Mi; Lee, Su-Hyon; Ryu, Yang-Hwan; Jang, Won-Hee; Jung, Haeng-Sun; Han, Ju-Hee; Seok, Seung-Hyeok; Park, Jae-Hak; Son, Youngsook; Park, Young-Ho; Lim, Kyung-Min

2011-02-01

Many efforts are being made to develop new alternative in vitro test methods for the eye irritation test. Here we report a new reconstructed human corneal epithelial model (MCTT HCE model) prepared from primary-cultured human limbal epithelial cells as a new alternative in vitro eye irritation test method. In histological and immunohistochemical observation, MCTT HCE model displayed a morphology and biomarker expressions similar to intact human cornea. Moreover, the barrier function was well preserved as measured by high transepithelial electrical resistance, effective time-50 for Triton X-100, and corneal thickness. To employ the model as a new alternative method for eye irritation test, protocol refinement was performed and optimum assay condition was determined including treatment time, treatment volume, post-incubation time and rinsing method. Using the refined protocol, 25 reference chemicals with known eye irritation potentials were tested. With the viability cut-off value at 50%, chemicals were classified to irritant or non-irritant. When compared with GHS classification, the MCTT HCE model showed the accuracy of 88%, sensitivity of 100% and specificity of 77%. These results suggest that the MCTT HCE model might be useful as a new alternative eye irritation test method. Copyright © 2010 Elsevier Ltd. All rights reserved.

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.

Movement towards transdiagnostic psychotherapeutic practices for the affective disorders.

PubMed

Gros, Daniel F; Allan, Nicholas P; Szafranski, Derek D

2016-08-01

Evidence-based cognitive behavioural therapy (CBT) practices were first developed in the 1960s. Over the decades, refinements and alternative symptom foci resulted in the development of several CBT protocols/manuals for each of the many disorders, especially in the affective disorders. Although shown to be effective in highly trained providers, the proliferation of CBT protocols also has shown to demonstrate challenges in dissemination and implementation efforts due to the sheer number of CBT protocols and their related training requirements (eg, 6 months per protocol) and their related cost (eg, over US$2000 each; lost days/hours at work). To address these concerns, newer transdiagnostic CBT protocols have been developed to reduce the number of disorder-specific CBT protocols needed to treat patients with affective disorders. Transdiagnostic treatments are based on the notion that various disorder-specific CBT protocols contain important but overlapping treatment components that can be distilled into a single treatment and therefore address the symptoms and comorbidities across all of the disorders at once. 3 examples of transdiagnostic treatments include group CBT of anxiety, unified protocol for transdiagnostic treatment for emotional disorders and transdiagnostic behaviour therapy. Each transdiagnostic protocol is designed for a different set of disorders, contains a varied amount of CBT treatment components and is tested in different types of samples. However, together, these 3 transdiagnostic psychotherapies represent the future of CBT practice. 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/

Bridging the Gap Between Validation and Implementation of Non-Animal Veterinary Vaccine Potency Testing Methods.

PubMed

Dozier, Samantha; Brown, Jeffrey; Currie, Alistair

2011-11-29

In recent years, technologically advanced high-throughput techniques have been developed that replace, reduce or refine animal use in vaccine quality control tests. Following validation, these tests are slowly being accepted for use by international regulatory authorities. Because regulatory acceptance itself has not guaranteed that approved humane methods are adopted by manufacturers, various organizations have sought to foster the preferential use of validated non-animal methods by interfacing with industry and regulatory authorities. After noticing this gap between regulation and uptake by industry, we began developing a paradigm that seeks to narrow the gap and quicken implementation of new replacement, refinement or reduction guidance. A systematic analysis of our experience in promoting the transparent implementation of validated non-animal vaccine potency assays has led to the refinement of our paradigmatic process, presented here, by which interested parties can assess the local regulatory acceptance of methods that reduce animal use and integrate them into quality control testing protocols, or ensure the elimination of peripheral barriers to their use, particularly for potency and other tests carried out on production batches.

Comparative study of the physicochemical, nutritional, and antioxidant properties of some commercial refined and non-centrifugal sugars.

PubMed

Lee, Jong Suk; Ramalingam, Srinivasan; Jo, Il Guk; Kwon, Ye Som; Bahuguna, Ashutosh; Oh, Young Sook; Kwon, O-Jun; Kim, Myunghee

2018-07-01

Three refined and four unrefined branded commercial sugars available in Korea were investigated in terms of pH, soluble solids, moisture, ash content, turbidity, color values, microbial profile, reducing power, 2,2-diphenyl-1-picrylhydrazyl and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical scavenging activities, cellular antioxidant activity, and total phytoconstituent (i.e. phenolic, flavonoid, mineral, sucrose, glucose, and fructose) contents using standard analytical protocols such as high-performance liquid chromatography, gas chromatography-flame ionization detector/mass spectrometry, and inductively coupled plasma atomic emission spectroscopy. All tested physicochemical parameters were within the recommended standard levels. Significantly high nutritional and antioxidant properties were observed for the unrefined sugars, especially AUNO® sugar, whereas a high sucrose content was detected for the refined sugars. Hence, this study revealed that the degree of purification affects the nutritional values and antioxidant potentials of sugars. The present findings also indicate that unrefined sugars can be used as sweeteners in sugar-based cuisine to obtain nutritional and antioxidant-rich foodstuff. Copyright © 2018 Elsevier Ltd. All rights reserved.

An international road map to improve pain assessment in people with impaired cognition: the development of the Pain Assessment in Impaired Cognition (PAIC) meta-tool.

PubMed

Corbett, Anne; Achterberg, Wilco; Husebo, Bettina; Lobbezoo, Frank; de Vet, Henrica; Kunz, Miriam; Strand, Liv; Constantinou, Marios; Tudose, Catalina; Kappesser, Judith; de Waal, Margot; Lautenbacher, Stefan

2014-12-10

Pain is common in people with dementia, yet identification is challenging. A number of pain assessment tools exist, utilizing observation of pain-related behaviours, vocalizations and facial expressions. Whilst they have been developed robustly, these often lack sufficient evidence of psychometric properties, like reliability, face and construct validity, responsiveness and usability, and are not internationally implemented. The EU-COST initiative "Pain in impaired cognition, especially dementia" aims to combine the expertise of clinicians and researchers to address this important issue by building on previous research in the area, identifying existing pain assessment tools for dementia, and developing consensus for items for a new universal meta-tool for use in research and clinical settings. This paper reports on the initial phase of this collaboration task. All existing observational pain behaviour tools were identified and elements categorised using a three-step reduction process. Selection and refinement of items for the draft Pain Assessment in Impaired Cognition (PAIC) meta-tool was achieved through scrutiny of the evidence, consensus of expert opinion, frequency of use and alignment with the American Geriatric Society guidelines. The main aim of this process was to identify key items with potential empirical, rather than theoretical value to take forward for testing. 12 eligible assessment tools were identified, and pain items categorised according to behaviour, facial expression and vocalisation according to the AGS guidelines (Domains 1 - 3). This has been refined to create the PAIC meta-tool for validation and further refinement. A decision was made to create a supporting comprehensive toolkit to support the core assessment tool to provide additional resources for the assessment of overlapping symptoms in dementia, including AGS domains four to six, identification of specific types of pain and assessment of duration and location of pain. This multidisciplinary, cross-cultural initiative has created a draft meta-tool for capturing pain behaviour to be used across languages and culture, based on the most promising items used in existing tools. The draft PAIC meta-tool will now be taken forward for evaluation according to COSMIN guidelines and the EU-COST protocol in order to exclude invalid items, refine included items and optimise the meta-tool.

Optimized DNA extraction from neonatal dried blood spots: application in methylome profiling

PubMed Central

2014-01-01

Background Neonatal dried blood spots (DBS) represent an inexpensive method for long-term biobanking worldwide and are considered gold mines for research for several human diseases, including those of metabolic, infectious, genetic and epigenetic origin. However, the utility of DBS is restricted by the limited amount and quality of extractable biomolecules (including DNA), especially for genome wide profiling. Degradation of DNA in DBS often occurs during storage and extraction. Moreover, amplifying small quantities of DNA often leads to a bias in subsequent data, particularly in methylome profiles. Thus it is important to develop methodologies that maximize both the yield and quality of DNA from DBS for downstream analyses. Results Using combinations of in-house-derived and modified commercial extraction kits, we developed a robust and efficient protocol, compatible with methylome studies, many of which require stringent bisulfite conversion steps. Several parameters were tested in a step-wise manner, including blood extraction, cell lysis, protein digestion, and DNA precipitation, purification and elution. DNA quality was assessed based on spectrophotometric measurements, DNA detectability by PCR, and DNA integrity by gel electrophoresis and bioanalyzer analyses. Genome scale Infinium HumanMethylation450 and locus-specific pyrosequencing data generated using the refined DBS extraction protocol were of high quality, reproducible and consistent. Conclusions This study may prove useful to meet the increased demand for research on prenatal, particularly epigenetic, origins of human diseases and for newborn screening programs, all of which are often based on DNA extracted from DBS. PMID:24980254

Using realist evaluation to assess primary healthcare teams' responses to intimate partner violence in Spain.

PubMed

Goicolea, Isabel; Hurtig, Anna-Karin; San Sebastian, Miguel; Marchal, Bruno; Vives-Cases, Carmen

2015-01-01

Few evaluations have assessed the factors triggering an adequate health care response to intimate partner violence. This article aimed to: 1) describe a realist evaluation carried out in Spain to ascertain why, how and under what circumstances primary health care teams respond to intimate partner violence, and 2) discuss the strengths and challenges of its application. We carried out a series of case studies in four steps. First, we developed an initial programme theory (PT1), based on interviews with managers. Second, we refined PT1 into PT2 by testing it in a primary healthcare team that was actively responding to violence. Third, we tested the refined PT2 by incorporating three other cases located in the same region. Qualitative and quantitative data were collected and thick descriptions were produced and analysed using a retroduction approach. Fourth, we analysed a total of 15 cases, and identified combinations of contextual factors and mechanisms that triggered an adequate response to violence by using qualitative comparative analysis. There were several key mechanisms -the teams' self-efficacy, perceived preparation, women-centred care-, and contextual factors -an enabling team environment and managerial style, the presence of motivated professionals, the use of the protocol and accumulated experience in primary health care- that should be considered to develop adequate primary health-care responses to violence. The full application of this realist evaluation was demanding, but also well suited to explore a complex intervention reflecting the situation in natural settings. Copyright © 2015 SESPAS. Published by Elsevier Espana. All rights reserved.

Efficacy of monitoring and empirical predictive modeling at improving public health protection at Chicago beaches

USGS Publications Warehouse

Nevers, Meredith B.; Whitman, Richard L.

2011-01-01

Efforts to improve public health protection in recreational swimming waters have focused on obtaining real-time estimates of water quality. Current monitoring techniques rely on the time-intensive culturing of fecal indicator bacteria (FIB) from water samples, but rapidly changing FIB concentrations result in management errors that lead to the public being exposed to high FIB concentrations (type II error) or beaches being closed despite acceptable water quality (type I error). Empirical predictive models may provide a rapid solution, but their effectiveness at improving health protection has not been adequately assessed. We sought to determine if emerging monitoring approaches could effectively reduce risk of illness exposure by minimizing management errors. We examined four monitoring approaches (inactive, current protocol, a single predictive model for all beaches, and individual models for each beach) with increasing refinement at 14 Chicago beaches using historical monitoring and hydrometeorological data and compared management outcomes using different standards for decision-making. Predictability (R2) of FIB concentration improved with model refinement at all beaches but one. Predictive models did not always reduce the number of management errors and therefore the overall illness burden. Use of a Chicago-specific single-sample standard-rather than the default 235 E. coli CFU/100 ml widely used-together with predictive modeling resulted in the greatest number of open beach days without any increase in public health risk. These results emphasize that emerging monitoring approaches such as empirical models are not equally applicable at all beaches, and combining monitoring approaches may expand beach access.

Associations of whole and refined grain intakes with adiposity-related cancer risk in the Framingham Offspring Cohort (1991-2013)

USDA-ARS?s Scientific Manuscript database

Objective: The objective of this prospective cohort study is to evaluate associations between whole and refined grains and their food sources in relation to risk of adiposity-related cancers combined and three of the most commonly diagnosed site-specific cancers in the US: breast, prostate, and colo...

Differentiation of Bread Made with Whole Grain and Refined Wheat (T. aestivum) Flour Using LC/MS-based chromatographic Fingerprinting and Chemometric Approaches

USDA-ARS?s Scientific Manuscript database

A fuzzy chromatography mass spectrometric (FCMS) fingerprinting method combined with chemometric analysis was established to diffrentiate between whole wheat (WW) flours and refined wheat (RW) flour, and the breads made from them. The chemical compositions of the bread samples were profiled using h...

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

The administration of a high refined carbohydrate diet promoted an increase in pulmonary inflammation and oxidative stress in mice exposed to cigarette smoke

PubMed Central

Pena, Karina Braga; Ramos, Camila de Oliveira; Soares, Nícia Pedreira; da Silva, Pamela Félix; Bandeira, Ana Carla Balthar; Costa, Guilherme de Paula; Cangussú, Sílvia Dantas; Talvani, André; Bezerra, Frank Silva

2016-01-01

This study aimed to evaluate the effects of a high refined carbohydrate diet and pulmonary inflammatory response in C57BL/6 mice exposed to cigarette smoke (CS). Twenty-four male mice were divided into four groups: control group (CG), which received a standard diet; cigarette smoke group (CSG), which was exposed to CS; a high refined carbohydrate diet group (RG), which received a high refined carbohydrate diet; and a high refined carbohydrates diet and cigarette smoke group (RCSG), which received a high refined carbohydrate diet and was exposed to CS. The animals were monitored for food intake and body weight gain for 12 weeks. After this period, the CSG and RCSG were exposed to CS for five consecutive days. At the end of the experimental protocol, all animals were euthanized for subsequent analyses. There was an increase of inflammatory cells in the bronchoalveolar lavage fluid (BALF) of CSG compared to CG and RCSG compared to CG, CSG, and RG. In addition, in the BALF, there was an increase of tumor necrosis factor alpha in RCSG compared to CG, CSG, and RG; interferon gamma increase in RCSG compared to the CSG; and increase in interleukin-10 in RCSG compared to CG and RG. Lipid peroxidation increased in RCSG compared to CG, CSG, and RG. Furthermore, the oxidation of proteins increased in CSG compared to CG. The analysis of oxidative stress showed an increase in superoxide dismutase in RCSG compared to CG, CSG, and RG and an increase in the catalase activity in RCSG compared with CG. In addition, there was a decrease in the glutathione reduced/glutathione total ratio of CSG, RG, and RCSG compared to CG. Therefore, the administration of a high refined carbohydrate diet promoted an increase in pulmonary inflammation and oxidative stress in mice exposed to CS. PMID:28008246

Advanced Computational Methods for High-accuracy Refinement of Protein Low-quality Models

NASA Astrophysics Data System (ADS)

Zang, Tianwu

Predicting the 3-dimentional structure of protein has been a major interest in the modern computational biology. While lots of successful methods can generate models with 3˜5A root-mean-square deviation (RMSD) from the solution, the progress of refining these models is quite slow. It is therefore urgently needed to develop effective methods to bring low-quality models to higher-accuracy ranges (e.g., less than 2 A RMSD). In this thesis, I present several novel computational methods to address the high-accuracy refinement problem. First, an enhanced sampling method, named parallel continuous simulated tempering (PCST), is developed to accelerate the molecular dynamics (MD) simulation. Second, two energy biasing methods, Structure-Based Model (SBM) and Ensemble-Based Model (EBM), are introduced to perform targeted sampling around important conformations. Third, a three-step method is developed to blindly select high-quality models along the MD simulation. These methods work together to make significant refinement of low-quality models without any knowledge of the solution. The effectiveness of these methods is examined in different applications. Using the PCST-SBM method, models with higher global distance test scores (GDT_TS) are generated and selected in the MD simulation of 18 targets from the refinement category of the 10th Critical Assessment of Structure Prediction (CASP10). In addition, in the refinement test of two CASP10 targets using the PCST-EBM method, it is indicated that EBM may bring the initial model to even higher-quality levels. Furthermore, a multi-round refinement protocol of PCST-SBM improves the model quality of a protein to the level that is sufficient high for the molecular replacement in X-ray crystallography. Our results justify the crucial position of enhanced sampling in the protein structure prediction and demonstrate that a considerable improvement of low-accuracy structures is still achievable with current force fields.

Acute Effect of Different Combined Stretching Methods on Acceleration and Speed in Soccer Players.

PubMed

Amiri-Khorasani, Mohammadtaghi; Calleja-Gonzalez, Julio; Mogharabi-Manzari, Mansooreh

2016-04-01

The purpose of this study was to investigate the acute effect of different stretching methods, during a warm-up, on the acceleration and speed of soccer players. The acceleration performance of 20 collegiate soccer players (body height: 177.25 ± 5.31 cm; body mass: 65.10 ± 5.62 kg; age: 16.85 ± 0.87 years; BMI: 20.70 ± 5.54; experience: 8.46 ± 1.49 years) was evaluated after different warm-up procedures, using 10 and 20 m tests. Subjects performed five types of a warm-up: static, dynamic, combined static + dynamic, combined dynamic + static, and no-stretching. Subjects were divided into five groups. Each group performed five different warm-up protocols in five non-consecutive days. The warm-up protocol used for each group was randomly assigned. The protocols consisted of 4 min jogging, a 1 min stretching program (except for the no-stretching protocol), and 2 min rest periods, followed by the 10 and 20 m sprint test, on the same day. The current findings showed significant differences in the 10 and 20 m tests after dynamic stretching compared with static, combined, and no-stretching protocols. There were also significant differences between the combined stretching compared with static and no-stretching protocols. We concluded that soccer players performed better with respect to acceleration and speed, after dynamic and combined stretching, as they were able to produce more force for a faster execution.

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.

Adaptive mesh refinement and front-tracking for shear bands in an antiplane shear model

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

Garaizar, F.X.; Trangenstein, J.

1998-09-01

In this paper the authors describe a numerical algorithm for the study of hear-band formation and growth in a two-dimensional antiplane shear of granular materials. The algorithm combines front-tracking techniques and adaptive mesh refinement. Tracking provides a more careful evolution of the band when coupled with special techniques to advance the ends of the shear band in the presence of a loss of hyperbolicity. The adaptive mesh refinement allows the computational effort to be concentrated in important areas of the deformation, such as the shear band and the elastic relief wave. The main challenges are the problems related to shearmore » bands that extend across several grid patches and the effects that a nonhyperbolic growth rate of the shear bands has in the refinement process. They give examples of the success of the algorithm for various levels of refinement.« less

Orthogonal polynomials for refinable linear functionals

NASA Astrophysics Data System (ADS)

Laurie, Dirk; de Villiers, Johan

2006-12-01

A refinable linear functional is one that can be expressed as a convex combination and defined by a finite number of mask coefficients of certain stretched and shifted replicas of itself. The notion generalizes an integral weighted by a refinable function. The key to calculating a Gaussian quadrature formula for such a functional is to find the three-term recursion coefficients for the polynomials orthogonal with respect to that functional. We show how to obtain the recursion coefficients by using only the mask coefficients, and without the aid of modified moments. Our result implies the existence of the corresponding refinable functional whenever the mask coefficients are nonnegative, even when the same mask does not define a refinable function. The algorithm requires O(n^2) rational operations and, thus, can in principle deliver exact results. Numerical evidence suggests that it is also effective in floating-point arithmetic.

Determination of the optimal level for combining area and yield estimates

NASA Technical Reports Server (NTRS)

Bauer, M. E. (Principal Investigator); Hixson, M. M.; Jobusch, C. D.

1981-01-01

Several levels of obtaining both area and yield estimates of corn and soybeans in Iowa were considered: county, refined strata, refined/split strata, crop reporting district, and state. Using the CCEA model form and smoothed weather data, regression coefficients at each level were derived to compute yield and its variance. Variances were also computed with stratum level. The variance of the yield estimates was largest at the state and smallest at the county level for both crops. The refined strata had somewhat larger variances than those associated with the refined/split strata and CRD. For production estimates, the difference in standard deviations among levels was not large for corn, but for soybeans the standard deviation at the state level was more than 50% greater than for the other levels. The refined strata had the smallest standard deviations. The county level was not considered in evaluation of production estimates due to lack of county area variances.

Development of a comprehensive performance-testing protocol for competitive surfers.

PubMed

Sheppard, Jeremy M; Nimphius, Sophia; Haff, Greg G; Tran, Tai T; Spiteri, Tania; Brooks, Hedda; Slater, Gary; Newton, Robert U

2013-09-01

Appropriate and valid testing protocols for evaluating the physical performances of surfing athletes are not well refined. The purpose of this project was to develop, refine, and evaluate a testing protocol for use with elite surfers, including measures of anthropometry, strength and power, and endurance. After pilot testing and consultation with athletes, coaches, and sport scientists, a specific suite of tests was developed. Forty-four competitive junior surfers (16.2 ± 1.3 y, 166.3 ± 7.3 cm, 57.9 ± 8.5 kg) participated in this study involving a within-day repeated-measures analysis, using an elite junior group of 22 international competitors (EJG), to establish reliability of the measures. To reflect validity of the testing measures, a comparison of performance results was then undertaken between the EJG and an age-matched competitive junior group of 22 nationally competitive surfers (CJG). Percent typical error of measurement (%TEM) for primary variables gained from the assessments ranged from 1.1% to 3.0%, with intraclass correlation coefficients ranging from .96 to .99. One-way analysis of variance revealed that the EJG had lower skinfolds (P = .005, d = 0.9) than the CJG, despite no difference in stature (P = .102) or body mass (P = .827). The EJG were faster in 15-m sprint-paddle velocity (P < .001, d = 1.3) and had higher lower-body isometric peak force (P = .04, d = 0.7) and superior endurance-paddling velocity (P = .008, d = 0.9). The relatively low %TEM of these tests in this population allows for high sensitivity to detect change. The results of this study suggest that competitively superior junior surfers are leaner and possess superior strength, paddling power, and paddling endurance.

Deposition and Characterization of Thin Films on Metallic Substrates

NASA Technical Reports Server (NTRS)

Gatica, Jorge E.

2005-01-01

A CVD method was successfully developed to produce conversion coatings on aluminum alloys surfaces with reproducible results with a variety of precursors. A well defined protocol to prepare the precursor solutions formulated in a previous research was extended to other additives. It was demonstrated that solutions prepared following such a protocol could be used to systematically generate protective coatings onto aluminum surfaces. Experiments with a variety of formulations revealed that a refined deposition protocol yields reproducible conversion coatings of controlled composition. A preliminary correlation between solution formulations and successful precursors was derived. Coatings were tested for adhesion properties enhancement for commercial paints. A standard testing method was followed and clear trends were identified. Only one precursors was tested systematically. Anticipated work on other precursors should allow a better characterization of the effect of intermetallics on the production of conversion/protective coatings on metals and ceramics. The significance of this work was the practical demonstration that chemical vapor deposition (CVD) techniques can be used to systematically generate protective/conversion coating on non-ferrous surfaces. In order to become an effective approach to replace chromate-based pre- treatment processes, namely in the aerospace or automobile industry, the process parameters must be defined more precisely. Moreover, the feasibility of scale-up designs necessitates a more comprehensive characterization of the fluid flow, transport phenomena, and chemical kinetics interacting in the process. Kinetic characterization showed a significantly different effect of magnesium-based precursors when compared to iron-based precursors. Future work will concentrate on refining the process through computer simulations and further experimental studies on the effect of other transition metals to induce deposition of conversion/protective films on aluminum and other metallic substrates.

The noninvasive mouse ear swelling assay. I. Refinements for detecting weak contact sensitizers.

PubMed

Thorne, P S; Hawk, C; Kaliszewski, S D; Guiney, P D

1991-11-01

The noninvasive mouse ear swelling assay (MESA) is a model for delayed-type hypersensitivity that holds promise as a testing protocol for allergic contact dermatitis (ACD). The MESA employs only topical sensitization on the abdomen and does not use injections, adjuvants, anesthesia, occlusion, or disruption of the stratum corneum. Five days after induction, the ears are challenged topically and ear swelling measurements taken at 24, 48, and 72 hr indicate the extent of ACD. In this study, refinements of the assay were explored in BALB/cBy mice using dinitrofluorobenzene (DNFB) and dinitrochlorobenzene (DNCB). A complete dose-response curve was developed for DNFB and the dose which sensitized half the mice in a group (SD50, 0.001%, w/v) was used to test noninvasive enhancement protocols. Several triple-dose protocols tested produced no increase in responsiveness and daily dosing showed a trend toward tolerance induction yielding 20% positive responses. Dietary vitamin A supplementation produced a dramatic enhancement of the responses: ear thickness increase was doubled and the SD50 sensitized 94 to 100% of the mice in the vitamin A groups. We conclude that the MESA allowed identification of ACD potency for known sensitizers at very low concentrations which do not produce ACD with other techniques. The importance of dose-response studies for avoiding the high-dose reduced-response region was also shown. Based on the observation that the vitamin A-augmented MESA was considerably more sensitive than with regular feed, a companion study (P.S. Thorne. C. Hawk, S.D. Kaliszewski, P.D. Guiney, Fundam. Appl. Tox. 17, 807-820, 1991) presents tests of the enhancements to the MESA developed in this work, using weak sensitizers and complex mixtures.

Complementary and Alternative Medicine Use Among US Navy and Marine Corps Personnel

DTIC Science & Technology

2007-05-16

protection of human subjects in research (Protocol NHRC.2001.0001). Postal survey The choice of questions and question layouts for the sur- vey instrument were...specific health problems within the past 12 months. The optically scanned 10-page survey instrument was designed to take approximately 30 minutes to...suggestions, the survey instrument was refined before the initial mailing. Additionally, a random sample of 33% of individuals who completed the

Complementary and Alternative Medicine Use Among US Navy and Marine Corps Personnel

DTIC Science & Technology

2007-05-16

subjects in research (Protocol NHRC.2001.0001). Postal survey The choice of questions and question layouts for the sur- vey instrument were modeled...health problems within the past 12 months. The optically scanned 10-page survey instrument was designed to take approximately 30 minutes to com- plete...the survey instrument was refined before the initial mailing. Additionally, a random sample of 33% of individuals who completed the initial

CONCEPTS AND APPROACHES FOR THE ...

EPA Pesticide Factsheets

This document is intended to assist users in establishing or refining protocols, including the specific methods related to field sampling, laboratory sample processing, taxonomy, data entry, management and analysis, and final assessment and reporting. It also reviews and provides information on development of monitoring designs to address certain types of environmental questions and approaches for documenting and reporting data quality and performance characteristics for large river biological monitoring. The approaches presented are not intended to replace existing program components but may in some cases be useful for refining them. The goal of this research is to develop methods and indicators that are useful for evaluating the condition of aquatic communities, for assessing the restoration of aquatic communities in response to mitigation and best management practices, and for determining the exposure of aquatic communities to different classes of stressors (i.e., pesticides, sedimentation, habitat alteration).

The Quality and Validation of Structures from Structural Genomics

PubMed Central

Domagalski, Marcin J.; Zheng, Heping; Zimmerman, Matthew D.; Dauter, Zbigniew; Wlodawer, Alexander; Minor, Wladek

2014-01-01

Quality control of three-dimensional structures of macromolecules is a critical step to ensure the integrity of structural biology data, especially those produced by structural genomics centers. Whereas the Protein Data Bank (PDB) has proven to be a remarkable success overall, the inconsistent quality of structures reveals a lack of universal standards for structure/deposit validation. Here, we review the state-of-the-art methods used in macromolecular structure validation, focusing on validation of structures determined by X-ray crystallography. We describe some general protocols used in the rebuilding and re-refinement of problematic structural models. We also briefly discuss some frontier areas of structure validation, including refinement of protein–ligand complexes, automation of structure redetermination, and the use of NMR structures and computational models to solve X-ray crystal structures by molecular replacement. PMID:24203341

The slip-and-slide algorithm: a refinement protocol for detector geometry

PubMed Central

Ginn, Helen Mary; Stuart, David Ian

2017-01-01

Geometry correction is traditionally plagued by mis-fitting of correlated parameters, leading to local minima which prevent further improvements. Segmented detectors pose an enhanced risk of mis-fitting: even a minor confusion of detector distance and panel separation can prevent improvement in data quality. The slip-and-slide algorithm breaks down effects of the correlated parameters and their associated target functions in a fundamental shift in the approach to the problem. Parameters are never refined against the components of the data to which they are insensitive, providing a dramatic boost in the exploitation of information from a very small number of diffraction patterns. This algorithm can be applied to exploit the adherence of the spot-finding results prior to indexing to a given lattice using unit-cell dimensions as a restraint. Alternatively, it can be applied to the predicted spot locations and the observed reflection positions after indexing from a smaller number of images. Thus, the indexing rate can be boosted by 5.8% using geometry refinement from only 125 indexed patterns or 500 unindexed patterns. In one example of cypovirus type 17 polyhedrin diffraction at the Linac Coherent Light Source, this geometry refinement reveals a detector tilt of 0.3° (resulting in a maximal Z-axis error of ∼0.5 mm from an average detector distance of ∼90 mm) whilst treating all panels independently. Re-indexing and integrating with updated detector geometry reduces systematic errors providing a boost in anomalous signal of sulfur atoms by 20%. Due to the refinement of decoupled parameters, this geometry method also reaches convergence. PMID:29091058

A refined methodology for modeling volume quantification performance in CT

NASA Astrophysics Data System (ADS)

Chen, Baiyu; Wilson, Joshua; Samei, Ehsan

2014-03-01

The utility of CT lung nodule volume quantification technique depends on the precision of the quantification. To enable the evaluation of quantification precision, we previously developed a mathematical model that related precision to image resolution and noise properties in uniform backgrounds in terms of an estimability index (e'). The e' was shown to predict empirical precision across 54 imaging and reconstruction protocols, but with different correlation qualities for FBP and iterative reconstruction (IR) due to the non-linearity of IR impacted by anatomical structure. To better account for the non-linearity of IR, this study aimed to refine the noise characterization of the model in the presence of textured backgrounds. Repeated scans of an anthropomorphic lung phantom were acquired. Subtracted images were used to measure the image quantum noise, which was then used to adjust the noise component of the e' calculation measured from a uniform region. In addition to the model refinement, the validation of the model was further extended to 2 nodule sizes (5 and 10 mm) and 2 segmentation algorithms. Results showed that the magnitude of IR's quantum noise was significantly higher in structured backgrounds than in uniform backgrounds (ASiR, 30-50%; MBIR, 100-200%). With the refined model, the correlation between e' values and empirical precision no longer depended on reconstruction algorithm. In conclusion, the model with refined noise characterization relfected the nonlinearity of iterative reconstruction in structured background, and further showed successful prediction of quantification precision across a variety of nodule sizes, dose levels, slice thickness, reconstruction algorithms, and segmentation software.

Development and worldwide use of non-lethal, and minimal population-level impact, protocols for the isolation of amphibian chytrid fungi.

PubMed

Fisher, Matthew C; Ghosh, Pria; Shelton, Jennifer M G; Bates, Kieran; Brookes, Lola; Wierzbicki, Claudia; Rosa, Gonçalo M; Farrer, Rhys A; Aanensen, David M; Alvarado-Rybak, Mario; Bataille, Arnaud; Berger, Lee; Böll, Susanne; Bosch, Jaime; Clare, Frances C; A Courtois, Elodie; Crottini, Angelica; Cunningham, Andrew A; Doherty-Bone, Thomas M; Gebresenbet, Fikirte; Gower, David J; Höglund, Jacob; James, Timothy Y; Jenkinson, Thomas S; Kosch, Tiffany A; Lambertini, Carolina; Laurila, Anssi; Lin, Chun-Fu; Loyau, Adeline; Martel, An; Meurling, Sara; Miaud, Claude; Minting, Pete; Ndriantsoa, Serge; O'Hanlon, Simon J; Pasmans, Frank; Rakotonanahary, Tsanta; Rabemananjara, Falitiana C E; Ribeiro, Luisa P; Schmeller, Dirk S; Schmidt, Benedikt R; Skerratt, Lee; Smith, Freya; Soto-Azat, Claudio; Tessa, Giulia; Toledo, Luís Felipe; Valenzuela-Sánchez, Andrés; Verster, Ruhan; Vörös, Judit; Waldman, Bruce; Webb, Rebecca J; Weldon, Che; Wombwell, Emma; Zamudio, Kelly R; Longcore, Joyce E; Garner, Trenton W J

2018-05-17

Parasitic chytrid fungi have emerged as a significant threat to amphibian species worldwide, necessitating the development of techniques to isolate these pathogens into culture for research purposes. However, early methods of isolating chytrids from their hosts relied on killing amphibians. We modified a pre-existing protocol for isolating chytrids from infected animals to use toe clips and biopsies from toe webbing rather than euthanizing hosts, and distributed the protocol to researchers as part of the BiodivERsA project RACE; here called the RML protocol. In tandem, we developed a lethal procedure for isolating chytrids from tadpole mouthparts. Reviewing a database of use a decade after their inception, we find that these methods have been applied across 5 continents, 23 countries and in 62 amphibian species. Isolation of chytrids by the non-lethal RML protocol occured in 18% of attempts with 207 fungal isolates and three species of chytrid being recovered. Isolation of chytrids from tadpoles occured in 43% of attempts with 334 fungal isolates of one species (Batrachochytrium dendrobatidis) being recovered. Together, these methods have resulted in a significant reduction and refinement of our use of threatened amphibian species and have improved our ability to work with this group of emerging pathogens.

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

USGS Publications Warehouse

Marion, Jeffrey L.; Wimpey, Jeremy F.

2011-01-01

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

Modeling and docking antibody structures with Rosetta

PubMed Central

Weitzner, Brian D.; Jeliazkov, Jeliazko R.; Lyskov, Sergey; Marze, Nicholas; Kuroda, Daisuke; Frick, Rahel; Adolf-Bryfogle, Jared; Biswas, Naireeta; Dunbrack, Roland L.; Gray, Jeffrey J.

2017-01-01

We describe Rosetta-based computational protocols for predicting the three-dimensional structure of an antibody from sequence (RosettaAntibody) and then docking the antibody to protein antigens (SnugDock). Antibody modeling leverages canonical loop conformations to graft large segments from experimentally-determined structures as well as (1) energetic calculations to minimize loops, (2) docking methodology to refine the VL–VH relative orientation, and (3) de novo prediction of the elusive complementarity determining region (CDR) H3 loop. To alleviate model uncertainty, antibody–antigen docking resamples CDR loop conformations and can use multiple models to represent an ensemble of conformations for the antibody, the antigen or both. These protocols can be run fully-automated via the ROSIE web server (http://rosie.rosettacommons.org/) or manually on a computer with user control of individual steps. For best results, the protocol requires roughly 1,000 CPU-hours for antibody modeling and 250 CPU-hours for antibody–antigen docking. Tasks can be completed in under a day by using public supercomputers. PMID:28125104

Space-based Networking Technology Developments in the Interplanetary Network Directorate Information Technology Program

NASA Technical Reports Server (NTRS)

Clare, Loren; Clement, B.; Gao, J.; Hutcherson, J.; Jennings, E.

2006-01-01

Described recent development of communications protocols, services, and associated tools targeted to reduce risk, reduce cost and increase efficiency of IND infrastructure and supported mission operations. Space-based networking technologies developed were: a) Provide differentiated quality of service (QoS) that will give precedence to traffic that users have selected as having the greatest importance and/or time-criticality; b) Improve the total value of information to users through the use of QoS prioritization techniques; c) Increase operational flexibility and improve command-response turnaround; d) Enable new class of networked and collaborative science missions; e) Simplify applications interfaces to communications services; and f) Reduce risk and cost from a common object model and automated scheduling and communications protocols. Technologies are described in three general areas: communications scheduling, middleware, and protocols. Additionally developed simulation environment, which provides comprehensive, quantitative understanding of the technologies performance within overall, evolving architecture, as well as ability to refine & optimize specific components.

Protocol vulnerability detection based on network traffic analysis and binary reverse engineering.

PubMed

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

2017-01-01

Network protocol vulnerability detection plays an important role in many domains, including protocol security analysis, application security, and network intrusion detection. In this study, by analyzing the general fuzzing method of network protocols, we propose a novel approach that combines network traffic analysis with the binary reverse engineering method. For network traffic analysis, the block-based protocol description language is introduced to construct test scripts, while the binary reverse engineering method employs the genetic algorithm with a fitness function designed to focus on code coverage. This combination leads to a substantial improvement in fuzz testing for network protocols. We build a prototype system and use it to test several real-world network protocol implementations. The experimental results show that the proposed approach detects vulnerabilities more efficiently and effectively than general fuzzing methods such as SPIKE.

Chapter 23: Combined Heat and Power 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.; Simons, George; Barsun, Stephan

The main focus of most evaluations is to determine the energy-savings impacts of the installed measure. This protocol defines a combined heat and power (CHP) measure as a system that sequentially generates both electrical energy and useful thermal energy from one fuel source at a host customer's facility or residence. This protocol is aimed primarily at regulators and administrators of ratepayer-funded CHP programs; however, project developers may find the protocol useful to understand how CHP projects are evaluated.

Knowledge-based versus experimentally acquired distance and angle constraints for NMR structure refinement.

PubMed

Cui, Feng; Jernigan, Robert; Wu, Zhijun

2008-04-01

Nuclear Overhauser effects (NOE) distance constraints and torsion angle constraints are major conformational constraints for nuclear magnetic resonance (NMR) structure refinement. In particular, the number of NOE constraints has been considered as an important determinant for the quality of NMR structures. Of course, the availability of torsion angle constraints is also critical for the formation of correct local conformations. In our recent work, we have shown how a set of knowledge-based short-range distance constraints can also be utilized for NMR structure refinement, as a complementary set of conformational constraints to the NOE and torsion angle constraints. In this paper, we show the results from a series of structure refinement experiments by using different types of conformational constraints--NOE, torsion angle, or knowledge-based constraints--or their combinations, and make a quantitative assessment on how the experimentally acquired constraints contribute to the quality of structural models and whether or not they can be combined with or substituted by the knowledge-based constraints. We have carried out the experiments on a small set of NMR structures. Our preliminary calculations have revealed that the torsion angle constraints contribute substantially to the quality of the structures, but require to be combined with the NOE constraints to be fully effective. The knowledge-based constraints can be functionally as crucial as the torsion angle constraints, although they are statistical constraints after all and are not meant to be able to replace the latter.

An adaptive mesh-moving and refinement procedure for one-dimensional conservation laws

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Flaherty, Joseph E.; Arney, David C.

1993-01-01

We examine the performance of an adaptive mesh-moving and /or local mesh refinement procedure for the finite difference solution of one-dimensional hyperbolic systems of conservation laws. Adaptive motion of a base mesh is designed to isolate spatially distinct phenomena, and recursive local refinement of the time step and cells of the stationary or moving base mesh is performed in regions where a refinement indicator exceeds a prescribed tolerance. These adaptive procedures are incorporated into a computer code that includes a MacCormack finite difference scheme wih Davis' artificial viscosity model and a discretization error estimate based on Richardson's extrapolation. Experiments are conducted on three problems in order to qualify the advantages of adaptive techniques relative to uniform mesh computations and the relative benefits of mesh moving and refinement. Key results indicate that local mesh refinement, with and without mesh moving, can provide reliable solutions at much lower computational cost than possible on uniform meshes; that mesh motion can be used to improve the results of uniform mesh solutions for a modest computational effort; that the cost of managing the tree data structure associated with refinement is small; and that a combination of mesh motion and refinement reliably produces solutions for the least cost per unit accuracy.

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum.

PubMed

Brunger, Axel T; Das, Debanu; Deacon, Ashley M; Grant, Joanna; Terwilliger, Thomas C; Read, Randy J; Adams, Paul D; Levitt, Michael; Schröder, Gunnar F

2012-04-01

Phasing by molecular replacement remains difficult for targets that are far from the search model or in situations where the crystal diffracts only weakly or to low resolution. Here, the process of determining and refining the structure of Cgl1109, a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum, at ∼3 Å resolution is described using a combination of homology modeling with MODELLER, molecular-replacement phasing with Phaser, deformable elastic network (DEN) refinement and automated model building using AutoBuild in a semi-automated fashion, followed by final refinement cycles with phenix.refine and Coot. This difficult molecular-replacement case illustrates the power of including DEN restraints derived from a starting model to guide the movements of the model during refinement. The resulting improved model phases provide better starting points for automated model building and produce more significant difference peaks in anomalous difference Fourier maps to locate anomalous scatterers than does standard refinement. This example also illustrates a current limitation of automated procedures that require manual adjustment of local sequence misalignments between the homology model and the target sequence.

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum

PubMed Central

Brunger, Axel T.; Das, Debanu; Deacon, Ashley M.; Grant, Joanna; Terwilliger, Thomas C.; Read, Randy J.; Adams, Paul D.; Levitt, Michael; Schröder, Gunnar F.

2012-01-01

Phasing by molecular replacement remains difficult for targets that are far from the search model or in situations where the crystal diffracts only weakly or to low resolution. Here, the process of determining and refining the structure of Cgl1109, a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum, at ∼3 Å resolution is described using a combination of homology modeling with MODELLER, molecular-replacement phasing with Phaser, deformable elastic network (DEN) refinement and automated model building using AutoBuild in a semi-automated fashion, followed by final refinement cycles with phenix.refine and Coot. This difficult molecular-replacement case illustrates the power of including DEN restraints derived from a starting model to guide the movements of the model during refinement. The resulting improved model phases provide better starting points for automated model building and produce more significant difference peaks in anomalous difference Fourier maps to locate anomalous scatterers than does standard refinement. This example also illustrates a current limitation of automated procedures that require manual adjustment of local sequence misalignments between the homology model and the target sequence. PMID:22505259

Solution of free-boundary problems using finite-element/Newton methods and locally refined grids - Application to analysis of solidification microstructure

NASA Technical Reports Server (NTRS)

Tsiveriotis, K.; Brown, R. A.

1993-01-01

A new method is presented for the solution of free-boundary problems using Lagrangian finite element approximations defined on locally refined grids. The formulation allows for direct transition from coarse to fine grids without introducing non-conforming basis functions. The calculation of elemental stiffness matrices and residual vectors are unaffected by changes in the refinement level, which are accounted for in the loading of elemental data to the global stiffness matrix and residual vector. This technique for local mesh refinement is combined with recently developed mapping methods and Newton's method to form an efficient algorithm for the solution of free-boundary problems, as demonstrated here by sample calculations of cellular interfacial microstructure during directional solidification of a binary alloy.

Refining MARGINS Mini-Lessons Using Classroom Observations

NASA Astrophysics Data System (ADS)

Iverson, E. A.; Manduca, C. A.; McDaris, J. R.; Lee, S.

2009-12-01

One of the challenges that we face in developing teaching materials or activities from research findings is testing the materials to determine that they work as intended. Traditionally faculty develop material for their own class, notice what worked and didn’t, and improve them the next year. However, as we move to a community process of creating and sharing teaching materials, a community-based process for testing materials is appropriate. The MARGINS project has piloted such a process for testing teaching materials and activities developed as part of its mini-lesson project (http://serc.carleton.edu/margins/index.html). Building on prior work developing mechanisms for community review of teaching resources (e.g. Kastens, 2002; Hancock and Manduca, 2005; Mayhew and Hall, 2007), the MARGINS evaluation team developed a structured classroom observation protocol. The goals of field testing are to a) gather structured, consistent feedback for the lesson authors based on classroom use; b) guide reviewers of these lessons to reflect on research-based educational practice as a framework for their comments; c) collect information on the data and observations that the reviewer used to underpin their review; d) determine which mini-lessons are ready to be made widely available on the website. The protocol guides faculty observations on why they used the activity, the effectiveness of the activity in their classroom, the success of the activity in leading to the desired learning, and what other faculty need to successfully use the activity. Available online (http://serc.carleton.edu/margins/protocol.html), the protocol can be downloaded and completed during instruction with the activity. In order to encourage review of mini-lessons using the protocol, a workshop focused on review and revision of activities was held in May 2009. In preparation for the workshop, 13 of the 28 participants chose to field test a mini-lesson prior to the workshop and reported that they found this process instructive. Activity authors found the observations very helpful and the first mini-lessons have now been revised using feedback from testers. Initial results show that the tested mini-lessons give students hands-on experience with scientific data and help students make connections between geologic phenomena and data. Productive feedback ranged from suggestions for improving activity design, adaptations for other audiences, suggestions for clearer presentation, and tips for using the materials. The team plans to broaden the use of the protocol to test and refine all of the mini-lessons in the MARGINS collection.

Formal Logic and Flowchart for Diagnosis Validity Verification and Inclusion in Clinical Decision Support Systems

NASA Astrophysics Data System (ADS)

Sosa, M.; Grundel, L.; Simini, F.

2016-04-01

Logical reasoning is part of medical practice since its origins. Modern Medicine has included information-intensive tools to refine diagnostics and treatment protocols. We are introducing formal logic teaching in Medical School prior to Clinical Internship, to foster medical practice. Two simple examples (Acute Myocardial Infarction and Diabetes Mellitus) are given in terms of formal logic expression and truth tables. Flowcharts of both diagnostic processes help understand the procedures and to validate them logically. The particularity of medical information is that it is often accompanied by “missing data” which suggests to adapt formal logic to a “three state” logic in the future. Medical Education must include formal logic to understand complex protocols and best practices, prone to mutual interactions.

Global polar geospatial information service retrieval based on search engine and ontology reasoning

USGS Publications Warehouse

Chen, Nengcheng; E, Dongcheng; Di, Liping; Gong, Jianya; Chen, Zeqiang

2007-01-01

In order to improve the access precision of polar geospatial information service on web, a new methodology for retrieving global spatial information services based on geospatial service search and ontology reasoning is proposed, the geospatial service search is implemented to find the coarse service from web, the ontology reasoning is designed to find the refined service from the coarse service. The proposed framework includes standardized distributed geospatial web services, a geospatial service search engine, an extended UDDI registry, and a multi-protocol geospatial information service client. Some key technologies addressed include service discovery based on search engine and service ontology modeling and reasoning in the Antarctic geospatial context. Finally, an Antarctica multi protocol OWS portal prototype based on the proposed methodology is introduced.

A holistic approach to ZigBee performance enhancement for home automation networks.

PubMed

Betzler, August; Gomez, Carles; Demirkol, Ilker; Paradells, Josep

2014-08-14

Wireless home automation networks are gaining importance for smart homes. In this ambit, ZigBee networks play an important role. The ZigBee specification defines a default set of protocol stack parameters and mechanisms that is further refined by the ZigBee Home Automation application profile. In a holistic approach, we analyze how the network performance is affected with the tuning of parameters and mechanisms across multiple layers of the ZigBee protocol stack and investigate possible performance gains by implementing and testing alternative settings. The evaluations are carried out in a testbed of 57 TelosB motes. The results show that considerable performance improvements can be achieved by using alternative protocol stack configurations. From these results, we derive two improved protocol stack configurations for ZigBee wireless home automation networks that are validated in various network scenarios. In our experiments, these improved configurations yield a relative packet delivery ratio increase of up to 33.6%, a delay decrease of up to 66.6% and an improvement of the energy efficiency for battery powered devices of up to 48.7%, obtainable without incurring any overhead to the network.

A Holistic Approach to ZigBee Performance Enhancement for Home Automation Networks

PubMed Central

Betzler, August; Gomez, Carles; Demirkol, Ilker; Paradells, Josep

2014-01-01

Wireless home automation networks are gaining importance for smart homes. In this ambit, ZigBee networks play an important role. The ZigBee specification defines a default set of protocol stack parameters and mechanisms that is further refined by the ZigBee Home Automation application profile. In a holistic approach, we analyze how the network performance is affected with the tuning of parameters and mechanisms across multiple layers of the ZigBee protocol stack and investigate possible performance gains by implementing and testing alternative settings. The evaluations are carried out in a testbed of 57 TelosB motes. The results show that considerable performance improvements can be achieved by using alternative protocol stack configurations. From these results, we derive two improved protocol stack configurations for ZigBee wireless home automation networks that are validated in various network scenarios. In our experiments, these improved configurations yield a relative packet delivery ratio increase of up to 33.6%, a delay decrease of up to 66.6% and an improvement of the energy efficiency for battery powered devices of up to 48.7%, obtainable without incurring any overhead to the network. PMID:25196004

Defining Hand Stereotypies in Rett Syndrome: A Movement Disorders Perspective.

PubMed

Dy, Marisela E; Waugh, Jeff L; Sharma, Nutan; O'Leary, Heather; Kapur, Kush; D'Gama, Alissa M; Sahin, Mustafa; Urion, David K; Kaufmann, Walter E

2017-10-01

Hand stereotypies (HS) are a primary diagnostic criterion for Rett syndrome (RTT) but are difficult to characterize and quantify systematically. We collected video on 27 girls (2-12 years of age) with classic RTT who participated in a mecasermin trial. The present study focused exclusively on video analyses, by reviewing two five-minute windows per subject to identify the two most common HS. Three raters with expertise in movement disorders independently rated the five-minute windows using standardized terminology to determine the level of agreement. We iteratively refined the protocol in three stages to improve descriptive accuracy, categorizing HS as "central" or "peripheral," "simple" or "complex," scoring each hand separately. Inter-rater agreement was analyzed using Kappa statistics. In the initial protocol evaluating HS by video, inter-rater agreement was 20.7%. In the final protocol, inter-rater agreement for the two most frequent HS was higher than the initial protocol at 50%. Phenotypic variability makes standardized evaluation of HS in RTT a challenge; we achieved only 50% level of agreement and only for the most frequent HS. Therefore, objective measures are needed to evaluate HS. Copyright © 2017 Elsevier Inc. All rights reserved.

GENERIC VERIFICATION PROTOCOL: DISTRIBUTED GENERATION AND COMBINED HEAT AND POWER FIELD TESTING PROTOCOL

EPA Science Inventory

This report is a generic verification protocol by which EPA’s Environmental Technology Verification program tests newly developed equipment for distributed generation of electric power, usually micro-turbine generators and internal combustion engine generators. The protocol will ...

Fiscal Year 2011 United States Army Annual Financial Report. America’s Army: At a Strategic Crossroads

DTIC Science & Technology

2011-01-01

successful in any operational scenario. In FY 2011, the Army updated the Cost of the Doctrinal Army Model using improved and refined methods and the...8,100 severely wounded Soldiers and veterans with cases spanning from Post- Traumatic Stress Disorder to double amputees. This population is supported... method dubbed “EoIP” (Everything over Internet Protocol). Getting the right information at the right time requires universal accessibility

Effectiveness of Acupressure Treatment for Pain Management and Fatigue Relief in Gulf War Veterans

DTIC Science & Technology

2015-10-01

acupressure for fatigue relief and pain management in veterans with GWI. The study staffs have gained valuable knowledge related to acupressure and its...potential for fatigue relief and pain management in veterans with GWI. This knowledge may lead to further refinement of the protocol as well as...1 TITLE: Effectiveness of Acupressure Treatment in Pain Management and Fatigue Relief for Gulf War Veterans AWARD #: W81XWH-12-1-0567 REPORT

An Environmentally Friendly Process Involving Refining and Membrane-Based Electrolysis for Magnesium Recovery from Partially Oxidized Scrap Alloy

NASA Astrophysics Data System (ADS)

Guan, Xiaofei; Pal, Uday B.; Powell, Adam C.

2013-10-01

Magnesium is recovered from partially oxidized scrap alloy by combining refining and solid oxide membrane (SOM) electrolysis. In this combined process, a molten salt eutectic flux (45 wt.% MgF2-55 wt.% CaF2) containing 10 wt.% MgO and 2 wt.% YF3 was used as the medium for magnesium recovery. During refining, magnesium and its oxide are dissolved from the scrap into the molten flux. Forming gas is bubbled through the flux and the dissolved magnesium is removed via the gas phase and condensed in a separate condenser at a lower temperature. The molten flux has a finite solubility for magnesium and acts as a selective medium for magnesium dissolution, but not aluminum or iron, and therefore the magnesium recovered has high purity. After refining, SOM electrolysis is performed in the same reactor to enable electrolysis of the dissolved magnesium oxide in the molten flux producing magnesium at the cathode and oxygen at the SOM anode. During SOM electrolysis, it is necessary to decrease the concentration of the dissolved magnesium in the flux to improve the faradaic current efficiency and prevent degradation of the SOM. Thus, for both refining and SOM electrolysis, it is very important to measure and control the magnesium solubility in the molten flux. High magnesium solubility facilitates refining whereas lower solubility benefits the SOM electrolysis process. Computational fluid dynamics modeling was employed to simulate the flow behavior of the flux stirred by the forming gas. Based on the modeling results, an optimized design of the stirring tubes and its placement in the flux are determined for efficiently removing the dissolved magnesium and also increasing the efficiency of the SOM electrolysis process.

Long Term Resource Monitoring Program procedures: fish monitoring

USGS Publications Warehouse

Ratcliff, Eric N.; Glittinger, Eric J.; O'Hara, T. Matt; Ickes, Brian S.

2014-01-01

This manual constitutes the second revision of the U.S. Army Corps of Engineers’ Upper Mississippi River Restoration-Environmental Management Program (UMRR-EMP) Long Term Resource Monitoring Program (LTRMP) element Fish Procedures Manual. The original (1988) manual merged and expanded on ideas and recommendations related to Upper Mississippi River fish sampling presented in several early documents. The first revision to the manual was made in 1995 reflecting important protocol changes, such as the adoption of a stratified random sampling design. The 1995 procedures manual has been an important document through the years and has been cited in many reports and scientific manuscripts. The resulting data collected by the LTRMP fish component represent the largest dataset on fish within the Upper Mississippi River System (UMRS) with more than 44,000 collections of approximately 5.7 million fish. The goal of this revision of the procedures manual is to document changes in LTRMP fish sampling procedures since 1995. Refinements to sampling methods become necessary as monitoring programs mature. Possible refinements are identified through field experiences (e.g., sampling techniques and safety protocols), data analysis (e.g., planned and studied gear efficiencies and reallocations of effort), and technological advances (e.g., electronic data entry). Other changes may be required because of financial necessity (i.e., unplanned effort reductions). This version of the LTRMP fish monitoring manual describes the most current (2014) procedures of the LTRMP fish component.

NASA Extreme Environment Mission Operations: Science Operations Development for Human Exploration

NASA Technical Reports Server (NTRS)

Bell, Mary S.

2014-01-01

The purpose of NASA Extreme Environment Mission Operations (NEEMO) mission 16 in 2012 was to evaluate and compare the performance of a defined series of representative near-Earth asteroid (NEA) extravehicular activity (EVA) tasks under different conditions and combinations of work systems, constraints, and assumptions considered for future human NEA exploration missions. NEEMO 16 followed NASA's 2011 Desert Research and Technology Studies (D-RATS), the primary focus of which was understanding the implications of communication latency, crew size, and work system combinations with respect to scientific data quality, data management, crew workload, and crew/mission control interactions. The 1-g environment precluded meaningful evaluation of NEA EVA translation, worksite stabilization, sampling, or instrument deployment techniques. Thus, NEEMO missions were designed to provide an opportunity to perform a preliminary evaluation of these important factors for each of the conditions being considered. NEEMO 15 also took place in 2011 and provided a first look at many of the factors, but the mission was cut short due to a hurricane threat before all objectives were completed. ARES Directorate (KX) personnel consulted with JSC engineers to ensure that high-fidelity planetary science protocols were incorporated into NEEMO mission architectures. ARES has been collaborating with NEEMO mission planners since NEEMO 9 in 2006, successively building upon previous developments to refine science operations concepts within engineering constraints; it is expected to continue the collaboration as NASA's human exploration mission plans evolve.

Improved ethanol yield and reduced minimum ethanol selling price (MESP) by modifying low severity dilute acid pretreatment with deacetylation and mechanical refining: 2) Techno-economic analysis

PubMed Central

2012-01-01

Background Our companion paper discussed the yield benefits achieved by integrating deacetylation, mechanical refining, and washing with low acid and low temperature pretreatment. To evaluate the impact of the modified process on the economic feasibility, a techno-economic analysis (TEA) was performed based on the experimental data presented in the companion paper. Results The cost benefits of dilute acid pretreatment technology combined with the process alternatives of deacetylation, mechanical refining, and pretreated solids washing were evaluated using cost benefit analysis within a conceptual modeling framework. Control cases were pretreated at much lower acid loadings and temperatures than used those in the NREL 2011 design case, resulting in much lower annual ethanol production. Therefore, the minimum ethanol selling prices (MESP) of the control cases were $0.41-$0.77 higher than the $2.15/gallon MESP of the design case. This increment is highly dependent on the carbohydrate content in the corn stover. However, if pretreatment was employed with either deacetylation or mechanical refining, the MESPs were reduced by $0.23-$0.30/gallon. Combing both steps could lower the MESP further by $0.44 ~ $0.54. Washing of the pretreated solids could also greatly improve the final ethanol yields. However, the large capital cost of the solid–liquid separation unit negatively influences the process economics. Finally, sensitivity analysis was performed to study the effect of the cost of the pretreatment reactor and the energy input for mechanical refining. A 50% cost reduction in the pretreatment reactor cost reduced the MESP of the entire conversion process by $0.11-$0.14/gallon, while a 10-fold increase in energy input for mechanical refining will increase the MESP by $0.07/gallon. Conclusion Deacetylation and mechanical refining process options combined with low acid, low severity pretreatments show improvements in ethanol yields and calculated MESP for cellulosic ethanol production. PMID:22967479

Effective and Safe Anesthesia for Yorkshire and Yucatan Swine with and without Cardiovascular Injury and Intervention

PubMed Central

Linkenhoker, Jan R; Burkholder, Tanya H; Linton, CG Garry; Walden, April; Abusakran-Monday, Kim A; Rosero, Ana P; Foltz, Charmaine J

2010-01-01

The goal of this study was to identify an injectable anesthetic protocol that provides sedation sufficient for peripheral vascular catheterization, intubation, and transport while minimizing cardiovascular changes in Yorkshire and Yucatan pigs with and without cardiovascular injury and intervention (CI). Phase 1 examined the safety and efficacy of acepromazine–ketamine, diazepam–ketamine, midazolam–ketamine, and medetomidine–ketamine in 5 healthy Yorkshire pigs. For each drug combination, we obtained multiple measurements of heart rate, blood pressure, respiratory rate, temperature, sedation score, ability to catheterize and intubate, and recovery score. Phase 2 evaluated and refined the dose of the most effective Phase 1 anesthetic combination (midazolam–ketamine) in healthy and CI Yorkshire pigs (n = 53 trials). Phase 3 mirrored Phase 2 but tested midazolam–ketamine in healthy and CI Yucatan pigs (n = 34 trials). Midazolam (0.5 mg/kg)–ketamine (25 to 27 mg/kg) was the most effective anesthetic combination in healthy Yorkshire pigs, but this dose was less effective in healthy Yucatan pigs and CI Yorkshire and Yucatan pigs. Midazolam–ketamine resulted in tachycardia and apnea more frequently in CI pigs than healthy pigs. This combination also caused vomiting in one CI Yucatan pig. Overall, midazolam–ketamine provided safe and effective sedation for catheterization and intubation of both healthy and CI pigs. This study suggests Yucatan pigs may require a higher dose midazolam–ketamine to achieve the same level of sedation as that in Yorkshire pigs. Although anesthetic complication rates were higher in CI pigs, our results indicate that midazolam–ketamine can be safely used for sedation of both pig breeds with and without CI. PMID:20587167

A refined method for calculating equivalent effective stratospheric chlorine

NASA Astrophysics Data System (ADS)

Engel, Andreas; Bönisch, Harald; Ostermöller, Jennifer; Chipperfield, Martyn P.; Dhomse, Sandip; Jöckel, Patrick

2018-01-01

Chlorine and bromine atoms lead to catalytic depletion of ozone in the stratosphere. Therefore the use and production of ozone-depleting substances (ODSs) containing chlorine and bromine is regulated by the Montreal Protocol to protect the ozone layer. Equivalent effective stratospheric chlorine (EESC) has been adopted as an appropriate metric to describe the combined effects of chlorine and bromine released from halocarbons on stratospheric ozone. Here we revisit the concept of calculating EESC. We derive a refined formulation of EESC based on an advanced concept of ODS propagation into the stratosphere and reactive halogen release. A new transit time distribution is introduced in which the age spectrum for an inert tracer is weighted with the release function for inorganic halogen from the source gases. This distribution is termed the release time distribution. We show that a much better agreement with inorganic halogen loading from the chemistry transport model TOMCAT is achieved compared with using the current formulation. The refined formulation shows EESC levels in the year 1980 for the mid-latitude lower stratosphere, which are significantly lower than previously calculated. The year 1980 is commonly used as a benchmark to which EESC must return in order to reach significant progress towards halogen and ozone recovery. Assuming that - under otherwise unchanged conditions - the EESC value must return to the same level in order for ozone to fully recover, we show that it will take more than 10 years longer than estimated in this region of the stratosphere with the current method for calculation of EESC. We also present a range of sensitivity studies to investigate the effect of changes and uncertainties in the fractional release factors and in the assumptions on the shape of the release time distributions. We further discuss the value of EESC as a proxy for future evolution of inorganic halogen loading under changing atmospheric dynamics using simulations from the EMAC model. We show that while the expected changes in stratospheric transport lead to significant differences between EESC and modelled inorganic halogen loading at constant mean age, EESC is a reasonable proxy for modelled inorganic halogen on a constant pressure level.

Refined hyperentanglement purification of two-photon systems for high-capacity quantum communication with cavity-assisted interaction

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

Du, Fang-Fang; Li, Tao; Long, Gui-Lu, E-mail: gllong@tsinghua.edu.cn

Hyperentanglement, defined as the entanglement in multiple degrees of freedom (DOFs) of a photonic quantum system, has attracted much attention recently as it can improve the channel capacity of quantum communication largely. Here we present a refined hyperentanglement purification protocol (hyper-EPP) for two-photon systems in mixed hyperentangled states in both the spatial-mode and polarization DOFs, assisted by cavity quantum electrodynamics. By means of the spatial (polarization) quantum state transfer process, the quantum states that are discarded in the previous hyper-EPPs can be preserved. That is, the spatial (polarization) state of a four-photon system with high fidelity can be transformed intomore » another four-photon system with low fidelity, not disturbing its polarization (spatial) state, which makes this hyper-EPP take the advantage of possessing a higher efficiency.« less

Refinement of habituation procedures in diet-induced obese mice.

PubMed

Kärrberg, L; Andersson, L; Kastenmayer, R J; Ploj, K

2016-10-01

Orogastric gavage, while a common method for delivering experimental substances in mice, has been shown to induce stress. To minimize the associated stress with this procedure, sham gavage prior to the start of experiment is a common method for habiutating mice. We investigated whether handling and restraint could replace sham treatment in the acclimatization protocol. Mice were either undisturbed, hand-restrained for 10 s or sham-gavaged daily for six days prior to eight days of twice daily gavage. The results showed that repetitive restraint and gavage had no differences in body weight after eight days of treatment compared with the body weights at the start of treatment, whereas animals left undisturbed lost significant weight once treatment began. These data suggest that procedure refinement by replacing sham treatment with hand restraint is sufficient to acclimatize mice to the stress associated with gavage. © The Author(s) 2016.

REVIEW OF THE NEGOTIATION OF THE MODEL PROTOCOL ADDITIONAL TO THE AGREEMENT(S) BETWEEN STATE(S) AND THE INTERNATIONAL ATOMIC ENERGY AGENCY FOR THE APPLICATION OF SAFEGUARDS, INFCIRC/540 (Corrected) VOLUME II/III IAEA COMMITTEE 24, Major Issues Underlying the Model Additional Protocol (1996-1997).

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

Rosenthal, M.D.; Saum-Manning, L.; Houck, F.

Volume I of this Review traces the origins of the Model Additional Protocol. It covers the period from 1991, when events in Iraq triggered an intensive review of the safeguards system, until 1996, when the IAEA Board of Governors established Committee 24 to negotiate a new protocol to safeguards agreement. The period from 1991-1996 set the stage for this negotiation and shaped its outcome in important ways. During this 5-year period, many proposals for strengthening safeguards were suggested and reviewed. Some proposals were dropped, for example, the suggestion by the IAEA Secretariat to verify certain imports, and others were refined.more » A rough consensus was established about the directions in which the international community wanted to go, and this was reflected in the draft of an additional protocol that was submitted to the IAEA Board of Governors on May 6, 1996 in document GOV/2863, Strengthening the Effectiveness and Improving the Efficiency of the Safeguards System - Proposals For Implementation Under Complementary Legal Authority, A Report by the Director General. This document ended with a recommendation that, 'the Board, through an appropriate mechanism, finalize the required legal instrument taking as a basis the draft protocol proposed by the Secretariat and the explanation of the measures contained in this document.'« less

Protocol for determining bull trout presence

USGS Publications Warehouse

Peterson, James; Dunham, Jason B.; Howell, Philip; Thurow, Russell; Bonar, Scott

2002-01-01

The Western Division of the American Fisheries Society was requested to develop protocols for determining presence/absence and potential habitat suitability for bull trout. The general approach adopted is similar to the process for the marbled murrelet, whereby interim guidelines are initially used, and the protocols are subsequently refined as data are collected. Current data were considered inadequate to precisely identify suitable habitat but could be useful in stratifying sampling units for presence/absence surveys. The presence/absence protocol builds on previous approaches (Hillman and Platts 1993; Bonar et al. 1997), except it uses the variation in observed bull trout densities instead of a minimum threshold density and adjusts for measured differences in sampling efficiency due to gear types and habitat characteristics. The protocol consists of: 1. recommended sample sizes with 80% and 95% detection probabilities for juvenile and resident adult bull trout for day and night snorkeling and electrofishing adjusted for varying habitat characteristics for 50m and 100m sampling units, 2. sampling design considerations, including possible habitat characteristics for stratification, 3. habitat variables to be measured in the sampling units, and 3. guidelines for training sampling crews. Criteria for habitat strata consist of coarse, watershed-scale characteristics (e.g., mean annual air temperature) and fine-scale, reach and habitat-specific features (e.g., water temperature, channel width). The protocols will be revised in the future using data from ongoing presence/absence surveys, additional research on sampling efficiencies, and development of models of habitat/species occurrence.

Grain Refinement of Al-Si Hypoeutectic Alloys by Al3Ti1B Master Alloy and Ultrasonic Treatment

NASA Astrophysics Data System (ADS)

Wang, Gui; Wang, Eric Qiang; Prasad, Arvind; Dargusch, Matthew; StJohn, David H.

Al-Si alloys are widely used in automotive and aerospace industries due to their excellent castability, high strength to weight ratio and good corrosion resistance. However, Si poisoning severely limits the degree of grain refinement with the grain size becoming larger as the Si content increases. Generally the effect of Si poisoning is reduced by increasing the amount of master alloy added to the melt during casting. However, an alternative approach is physical grain refinement through the application of an external force (e.g. mechanical or electromagnetic stirring, intensive shearing and ultrasonic irradiation). This work compares the grain refining efficiency of three approaches to the grain refinement of a range of hypoeutectic Al-Si alloys by (i) the addition of A13Ti1B master alloy, (ii) the application of Ultrasonic Treatment (UT) and (iii) the combined addition of A13Ti1B master alloy and the application of UT.

A multi-block adaptive solving technique based on lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Zhang, Yang; Xie, Jiahua; Li, Xiaoyue; Ma, Zhenghai; Zou, Jianfeng; Zheng, Yao

2018-05-01

In this paper, a CFD parallel adaptive algorithm is self-developed by combining the multi-block Lattice Boltzmann Method (LBM) with Adaptive Mesh Refinement (AMR). The mesh refinement criterion of this algorithm is based on the density, velocity and vortices of the flow field. The refined grid boundary is obtained by extending outward half a ghost cell from the coarse grid boundary, which makes the adaptive mesh more compact and the boundary treatment more convenient. Two numerical examples of the backward step flow separation and the unsteady flow around circular cylinder demonstrate the vortex structure of the cold flow field accurately and specifically.

Assume-Guarantee Abstraction Refinement Meets Hybrid Systems

NASA Technical Reports Server (NTRS)

Bogomolov, Sergiy; Frehse, Goran; Greitschus, Marius; Grosu, Radu; Pasareanu, Corina S.; Podelski, Andreas; Strump, Thomas

2014-01-01

Compositional verification techniques in the assume- guarantee style have been successfully applied to transition systems to efficiently reduce the search space by leveraging the compositional nature of the systems under consideration. We adapt these techniques to the domain of hybrid systems with affine dynamics. To build assumptions we introduce an abstraction based on location merging. We integrate the assume-guarantee style analysis with automatic abstraction refinement. We have implemented our approach in the symbolic hybrid model checker SpaceEx. The evaluation shows its practical potential. To the best of our knowledge, this is the first work combining assume-guarantee reasoning with automatic abstraction-refinement in the context of hybrid automata.

New advances in scanning microscopy and its application to study parasitic protozoa.

PubMed

de Souza, Wanderley; Attias, Marcia

2018-07-01

Scanning electron microscopy has been used to observe and study parasitic protozoa for at least 40 years. However, field emission electron sources, as well as improvements in lenses and detectors, brought the resolution power of scanning electron microscopes (SEM) to a new level. Parallel to the refinement of instruments, protocols for preservation of the ultrastructure, immunolabeling, exposure of cytoskeleton and inner structures of parasites and host cells were developed. This review is focused on protozoan parasites of medical and veterinary relevance, e.g., Toxoplasma gondii, Tritrichomonas foetus, Giardia intestinalis, and Trypanosoma cruzi, compilating the main achievements in describing the fine ultrastructure of their surface, cytoskeleton and interaction with host cells. Two new resources, namely, Helium Ion Microscopy (HIM) and Slice and View, using either Focused Ion Beam (FIB) abrasion or Microtome Serial Sectioning (MSS) within the microscope chamber, combined to backscattered electron imaging of fixed (chemically or by quick freezing followed by freeze substitution and resin embedded samples is bringing an exponential amount of valuable information. In HIM there is no need of conductive coating and the depth of field is much higher than in any field emission SEM. As for FIB- and MSS-SEM, high resolution 3-D models of areas and volumes larger than any other technique allows can be obtained. The main results achieved with all these technological tools and some protocols for sample preparation are included in this review. In addition, we included some results obtained with environmental/low vacuum scanning microscopy and cryo-scanning electron microscopy, both promising, but not yet largely employed SEM modalities. Copyright © 2018. Published by Elsevier Inc.

Biomechanical Comparison of Robotically Applied Pure Moment, Ideal Follower Load, and Novel Trunk Weight Loading Protocols on L4-L5 Cadaveric Segments during Flexion-Extension.

PubMed

Bennett, Charles R; DiAngelo, Denis J; Kelly, Brian P

2015-01-01

Extremely few in-vitro biomechanical studies have incorporated shear loads leaving a gap for investigation, especially when applied in combination with compression and bending under dynamic conditions. The objective of this study was to biomechanically compare sagittal plane application of two standard protocols, pure moment (PM) and follower load (FL), with a novel trunk weight (TW) loading protocol designed to induce shear in combination with compression and dynamic bending in a neutrally potted human cadaveric L4-L5 motion segment unit (MSU) model. A secondary objective and novelty of the current study was the application of all three protocols within the same testing system serving to reduce artifacts due to testing system variability. Six L4-L5 segments were tested in a Cartesian load controlled system in flexion-extension to 8Nm under PM, simulated ideal 400N FL, and vertically oriented 400N TW loading protocols. Comparison metrics used were rotational range of motion (RROM), flexibility, neutral zone (NZ) range of motion, and L4 vertebral body displacements. Significant differences in vertebral body translations were observed with different initial force applications but not with subsequent bending moment application. Significant reductions were observed in combined flexion-extension RROM, in flexibility during extension, and in NZ region flexibility with the TW loading protocol as compared to PM loading. Neutral zone ranges of motion were not different between all protocols. The combined compression and shear forces applied across the spinal joint in the trunk weight protocol may have a small but significantly increased stabilizing effect on segment flexibility and kinematics during sagittal plane flexion and extension.

Biomechanical Comparison of Robotically Applied Pure Moment, Ideal Follower Load, and Novel Trunk Weight Loading Protocols on L4-L5 Cadaveric Segments during Flexion-Extension

PubMed Central

Bennett, Charles R.; DiAngelo, Denis J.

2015-01-01

Background Extremely few in-vitro biomechanical studies have incorporated shear loads leaving a gap for investigation, especially when applied in combination with compression and bending under dynamic conditions. The objective of this study was to biomechanically compare sagittal plane application of two standard protocols, pure moment (PM) and follower load (FL), with a novel trunk weight (TW) loading protocol designed to induce shear in combination with compression and dynamic bending in a neutrally potted human cadaveric L4-L5 motion segment unit (MSU) model. A secondary objective and novelty of the current study was the application of all three protocols within the same testing system serving to reduce artifacts due to testing system variability. Methods Six L4-L5 segments were tested in a Cartesian load controlled system in flexion-extension to 8Nm under PM, simulated ideal 400N FL, and vertically oriented 400N TW loading protocols. Comparison metrics used were rotational range of motion (RROM), flexibility, neutral zone (NZ) range of motion, and L4 vertebral body displacements. Results Significant differences in vertebral body translations were observed with different initial force applications but not with subsequent bending moment application. Significant reductions were observed in combined flexion-extension RROM, in flexibility during extension, and in NZ region flexibility with the TW loading protocol as compared to PM loading. Neutral zone ranges of motion were not different between all protocols. Conclusions The combined compression and shear forces applied across the spinal joint in the trunk weight protocol may have a small but significantly increased stabilizing effect on segment flexibility and kinematics during sagittal plane flexion and extension. PMID:26273551

Combining accuracy assessment of land-cover maps with environmental monitoring programs

USGS Publications Warehouse

Stehman, S.V.; Czaplewski, R.L.; Nusser, S.M.; Yang, L.; Zhu, Z.

2000-01-01

A scientifically valid accuracy assessment of a large-area, land-cover map is expensive. Environmental monitoring programs offer a potential source of data to partially defray the cost of accuracy assessment while still maintaining the statistical validity. In this article, three general strategies for combining accuracy assessment and environmental monitoring protocols are described. These strategies range from a fully integrated accuracy assessment and environmental monitoring protocol, to one in which the protocols operate nearly independently. For all three strategies, features critical to using monitoring data for accuracy assessment include compatibility of the land-cover classification schemes, precisely co-registered sample data, and spatial and temporal compatibility of the map and reference data. Two monitoring programs, the National Resources Inventory (NRI) and the Forest Inventory and Monitoring (FIM), are used to illustrate important features for implementing a combined protocol.

Brain Consequences of Spinal Cord Injury with and without Neuropathic Pain: Translating Animal Models of Neuroinflammation onto Human Neural Networks and Back

DTIC Science & Technology

2016-10-01

During year one , we have: Obtained IRB and HRPO approval for the human studies , obtained IACUC and ACURO approval for the animal studies , refined the...human study protocol and collected PET-MR data on healthy individuals and spinal cord injured subjects, developed the rodent imaging procedures...qualtiative synthesis of the current state of the field, and 6 studies can be included in a quantitative meta-analysis. The studies eligible for inclusion in

Quantum processing by remote quantum control

NASA Astrophysics Data System (ADS)

Qiang, Xiaogang; Zhou, Xiaoqi; Aungskunsiri, Kanin; Cable, Hugo; O'Brien, Jeremy L.

2017-12-01

Client-server models enable computations to be hosted remotely on quantum servers. We present a novel protocol for realizing this task, with practical advantages when using technology feasible in the near term. Client tasks are realized as linear combinations of operations implemented by the server, where the linear coefficients are hidden from the server. We report on an experimental demonstration of our protocol using linear optics, which realizes linear combination of two single-qubit operations by a remote single-qubit control. In addition, we explain when our protocol can remain efficient for larger computations, as well as some ways in which privacy can be maintained using our protocol.

Non-native Speech Perception Training Using Vowel Subsets: Effects of Vowels in Sets and Order of Training

PubMed Central

Nishi, Kanae; Kewley-Port, Diane

2008-01-01

Purpose Nishi and Kewley-Port (2007) trained Japanese listeners to perceive nine American English monophthongs and showed that a protocol using all nine vowels (fullset) produced better results than the one using only the three more difficult vowels (subset). The present study extended the target population to Koreans and examined whether protocols combining the two stimulus sets would provide more effective training. Method Three groups of five Korean listeners were trained on American English vowels for nine days using one of the three protocols: fullset only, first three days on subset then six days on fullset, or first six days on fullset then three days on subset. Participants' performance was assessed by pre- and post-training tests, as well as by a mid-training test. Results 1) Fullset training was also effective for Koreans; 2) no advantage was found for the two combined protocols over the fullset only protocol, and 3) sustained “non-improvement” was observed for training using one of the combined protocols. Conclusions In using subsets for training American English vowels, care should be taken not only in the selection of subset vowels, but also for the training orders of subsets. PMID:18664694

Protocols for Copying and Proofreading in Template-Assisted Polymerization

NASA Astrophysics Data System (ADS)

Pigolotti, Simone; Sartori, Pablo

2016-03-01

We discuss how information encoded in a template polymer can be stochastically copied into a copy polymer. We consider four different stochastic copy protocols of increasing complexity, inspired by building blocks of the mRNA translation pathway. In the first protocol, monomer incorporation occurs in a single stochastic transition. We then move to a more elaborate protocol in which an intermediate step can be used for error correction. Finally, we discuss the operating regimes of two kinetic proofreading protocols: one in which proofreading acts from the final copying step, and one in which it acts from an intermediate step. We review known results for these models and, in some cases, extend them to analyze all possible combinations of energetic and kinetic discrimination. We show that, in each of these protocols, only a limited number of these combinations leads to an improvement of the overall copying accuracy.

Combination Protocol of Low-Frequency rTMS and Intensive Occupational Therapy for Post-stroke Upper Limb Hemiparesis: a 6-year Experience of More Than 1700 Japanese Patients.

PubMed

Kakuda, Wataru; Abo, Masahiro; Sasanuma, Jinichi; Shimizu, Masato; Okamoto, Takatsugu; Kimura, Chikou; Kakita, Kiyohito; Hara, Hiroyoshi

2016-06-01

Several years ago, we proposed a combination protocol of repetitive transcranial magnetic stimulation (rTMS) and intensive occupational therapy (OT) for upper limb hemiparesis after stroke. Subsequently, the number of patients treated with the protocol has increased in Japan. We aimed to present the latest data on our proposed combination protocol for post-stroke upper limb hemiparesis as a result of a multi-institutional study. After confirming that a patient met the inclusion criteria for the protocol, they were scheduled to receive the 15-day inpatient protocol. In the protocol, two sessions of 20-min rTMS and 120-min occupational therapy were provided daily, except for Sundays and the days of admission/discharge. Motor function of the affected upper limb was evaluated by the Fugl-Meyer assessment (FMA) and Wolf motor function test (WMFT) at admission/discharge and at 4 weeks after discharge if possible. A total of 1725 post-stroke patients were studied (mean age at admission 61.4 ± 13.0 years). The scheduled 15-day protocol was completed by all patients. At discharge, the increase in FMA score, shortening in performance time of WMFT, and increase in functional ability scale (FAS) score of WMFT were significant (FMA score 46.8 ± 12.2 to 50.9 ± 11.4 points, p < 0.001; performance time of WMFT 2.57 ± 1.32 to 2.21 ± 1.33, p < 0.001; FAS score of WMFT 47.4 ± 14. to 51.4 ± 14.3 points, p < 0.001). Our proposed combination protocol can be a potentially safe and useful therapeutic intervention for upper limb hemiparesis after stroke, although its efficacy should be confirmed in a randomized controlled study.

Increasing access to kidney transplantation for sensitized recipient through three-way kidney paired donation with desensitization: The first Indian report

PubMed Central

Kute, Vivek B; Patel, Himanshu V; Shah, Pankaj R; Modi, Pranjal R; Shah, Veena R; Rizvi, Sayyed J; Pal, Bipin C; Modi, Manisha P; Shah, Priya S; Varyani, Umesh T; Wakhare, Pavan S; Shinde, Saiprasad G; Ghodela, Viajay A; Patel, Minaxi H; Trivedi, Varsha B; Trivedi, Hargovind L

2016-01-01

The combination of kidney paired donation (KPD) with desensitization represents a promising method of increasing the rate of living donor kidney transplantation (LDKT) in immunologically challenging patients. Patients who are difficult to match and desensitize due to strong donor specific antibody are may be transplanted by a combination of desensitization and KPD protocol with more immunologically favorable donor. We present our experience of combination of desensitization protocol with three-way KPD which contributed to successful LDKT in highly sensitized end stage renal disease patient. All recipients were discharged with normal and stable allograft function at 24 mo follow up. We believe that this is first report from India where three-way KPD exchange was performed with the combination of KPD and desensitization. The combination of desensitization protocol with KPD improves access and outcomes of LDKT. PMID:27803919

Protein Structure and Function Prediction Using I-TASSER

PubMed Central

Yang, Jianyi; Zhang, Yang

2016-01-01

I-TASSER is a hierarchical protocol for automated protein structure prediction and structure-based function annotation. Starting from the amino acid sequence of target proteins, I-TASSER first generates full-length atomic structural models from multiple threading alignments and iterative structural assembly simulations followed by atomic-level structure refinement. The biological functions of the protein, including ligand-binding sites, enzyme commission number, and gene ontology terms, are then inferred from known protein function databases based on sequence and structure profile comparisons. I-TASSER is freely available as both an on-line server and a stand-alone package. This unit describes how to use the I-TASSER protocol to generate structure and function prediction and how to interpret the prediction results, as well as alternative approaches for further improving the I-TASSER modeling quality for distant-homologous and multi-domain protein targets. PMID:26678386

Accomplishing much in a short time: use of a rapid improvement event to redesign the assessment and treatment of patients with alcohol withdrawal.

PubMed

Sankoff, Jeffrey; Taub, Julie; Mintzer, David

2013-01-01

The use of Lean tools for quality improvement and process refinement is gaining acceptance in many health care institutions. Traditionally, these tools are used to apply incremental changes to established processes in order to reduce waste and improve quality. In this article, the authors describe a novel Lean methodology, the Rapid Improvement Event (RIE), used in a unique way to develop a new treatment protocol for a specific medical condition: alcohol withdrawal. The RIE allowed for the collaboration of a multidisciplinary group of providers invested in the success of a new protocol for alcohol withdrawal that spans areas from the emergency department to the inpatient ward at an inner-city safety net hospital. It also allowed for the definition of measures for its success once it is implemented.

Effect of Grain Refinement and Cooling Rate on the Microstructure and Mechanical Properties of Secondary Al-Si-Cu Alloys

NASA Astrophysics Data System (ADS)

Timelli, Giulio; Camicia, Giordano; Ferraro, Stefano

2014-02-01

The effect of AlTi5B1 grain refinement and different solidification rates on metallurgical and mechanical properties of a secondary AlSi7Cu3Mg alloy is reported. While the Ti content ranges from 0.04 up to 0.225 wt.%, the cooling rate varies between 0.1 and 5.5 °C/s. Metallographic and thermal analysis techniques have been used to quantitatively examine the macro- and microstructural changes occurring with grain refiner addition at various cooling rates. The results indicate that a small AlTi5B1 addition produces the greatest refinement, while no significant reduction of grain size is obtained with a great amount of grain refiner. On increasing the cooling rate, a lower amount of AlTi5B1 master alloy is necessary to produce a uniform grain size throughout the casting. The combined addition of AlTi5B1 and Sr does not produce any reciprocal interaction or effect on primary α-Al and eutectic solidification. The grain refinement improves the plastic behavior of the alloy and increases the reliability of castings, as evidenced by the Weibull statistics.

Analyzing the effect of routing protocols on media access control protocols in radio networks

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

Barrett, C. L.; Drozda, M.; Marathe, A.

2002-01-01

We study the effect of routing protocols on the performance of media access control (MAC) protocols in wireless radio networks. Three well known MAC protocols: 802.11, CSMA, and MACA are considered. Similarly three recently proposed routing protocols: AODV, DSR and LAR scheme 1 are considered. The experimental analysis was carried out using GloMoSim: a tool for simulating wireless networks. The main focus of our experiments was to study how the routing protocols affect the performance of the MAC protocols when the underlying network and traffic parameters are varied. The performance of the protocols was measured w.r.t. five important parameters: (i)more » number of received packets, (ii) average latency of each packet, (iii) throughput (iv) long term fairness and (v) number of control packets at the MAC layer level. Our results show that combinations of routing and MAC protocols yield varying performance under varying network topology and traffic situations. The result has an important implication; no combination of routing protocol and MAC protocol is the best over all situations. Also, the performance analysis of protocols at a given level in the protocol stack needs to be studied not locally in isolation but as a part of the complete protocol stack. A novel aspect of our work is the use of statistical technique, ANOVA (Analysis of Variance) to characterize the effect of routing protocols on MAC protocols. This technique is of independent interest and can be utilized in several other simulation and empirical studies.« less

Two-Step Vapor/Liquid/Solid Purification

NASA Technical Reports Server (NTRS)

Holland, L. R.

1986-01-01

Vertical distillation system combines in single operation advantages of multiple zone refining with those of distillation. Developed specifically to load Bridgman-Stockbarger (vertical-solidification) growth ampoules with ultrapure tellurium and cadmium, system, with suitable modifications, serves as material refiner. In first phase of purification process, ampoule heated to drive off absorbed volatiles. Second phase, evaporator heated to drive off volatiles in charge. Third phase, slowly descending heater causes distillation from evaporator to growing crystal in ampoule.

Abbreviated Combined MR Protocol: A New Faster Strategy for Characterizing Breast Lesions.

PubMed

Moschetta, Marco; Telegrafo, Michele; Rella, Leonarda; Stabile Ianora, Amato Antonio; Angelelli, Giuseppe

2016-06-01

The use of an abbreviated magnetic resonance (MR) protocol has been recently proposed for cancer screening. The aim of our study is to evaluate the diagnostic accuracy of an abbreviated MR protocol combining short TI inversion recovery (STIR), turbo-spin-echo (TSE)-T2 sequences, a pre-contrast T1, and a single intermediate (3 minutes after contrast injection) post-contrast T1 sequence for characterizing breast lesions. A total of 470 patients underwent breast MR examination for screening, problem solving, or preoperative staging. Two experienced radiologists evaluated both standard and abbreviated protocols in consensus. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and diagnostic accuracy for both protocols were calculated (with the histological findings and 6-month ultrasound follow-up as the reference standard) and compared with the McNemar test. The post-processing and interpretation times for the MR images were compared with the paired t test. In 177 of 470 (38%) patients, the MR sequences detected 185 breast lesions. Standard and abbreviated protocols obtained sensitivity, specificity, diagnostic accuracy, PPV, and NPV values respectively of 92%, 92%, 92%, 68%, and 98% and of 89%, 91%, 91%, 64%, and 98% with no statistically significant difference (P < .0001). The mean post-processing and interpretation time were, respectively, 7 ± 1 minutes and 6 ± 3.2 minutes for the standard protocol and 1 ± 1.2 minutes and 2 ± 1.2 minutes for the abbreviated protocol, with a statistically significant difference (P < .01). An abbreviated combined MR protocol represents a time-saving tool for radiologists and patients with the same diagnostic potential as the standard protocol in patients undergoing breast MRI for screening, problem solving, or preoperative staging. Copyright © 2016 Elsevier Inc. All rights reserved.

Adaptive Mesh Refinement for Microelectronic Device Design

NASA Technical Reports Server (NTRS)

Cwik, Tom; Lou, John; Norton, Charles

1999-01-01

Finite element and finite volume methods are used in a variety of design simulations when it is necessary to compute fields throughout regions that contain varying materials or geometry. Convergence of the simulation can be assessed by uniformly increasing the mesh density until an observable quantity stabilizes. Depending on the electrical size of the problem, uniform refinement of the mesh may be computationally infeasible due to memory limitations. Similarly, depending on the geometric complexity of the object being modeled, uniform refinement can be inefficient since regions that do not need refinement add to the computational expense. In either case, convergence to the correct (measured) solution is not guaranteed. Adaptive mesh refinement methods attempt to selectively refine the region of the mesh that is estimated to contain proportionally higher solution errors. The refinement may be obtained by decreasing the element size (h-refinement), by increasing the order of the element (p-refinement) or by a combination of the two (h-p refinement). A successful adaptive strategy refines the mesh to produce an accurate solution measured against the correct fields without undue computational expense. This is accomplished by the use of a) reliable a posteriori error estimates, b) hierarchal elements, and c) automatic adaptive mesh generation. Adaptive methods are also useful when problems with multi-scale field variations are encountered. These occur in active electronic devices that have thin doped layers and also when mixed physics is used in the calculation. The mesh needs to be fine at and near the thin layer to capture rapid field or charge variations, but can coarsen away from these layers where field variations smoothen and charge densities are uniform. This poster will present an adaptive mesh refinement package that runs on parallel computers and is applied to specific microelectronic device simulations. Passive sensors that operate in the infrared portion of the spectrum as well as active device simulations that model charge transport and Maxwell's equations will be presented.

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

PubMed

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

2017-11-21

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

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

PubMed Central

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

2017-01-01

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

Enhanced service zone architecture for multiservices over IP

NASA Astrophysics Data System (ADS)

Michaely, Boaz; Mohan, Seshadri

2001-07-01

Recently, the field of IP Telephony has been experienced considerable evolution through the specification of new protocols and introduction of products implementing these protocols. We visualize IP Telephony evolving to soon offer multiservices encompassing not only voice, but also data, video and multimedia. While the progress has focused on refining protocols and architectures, very little attention has been given to business models for offering these services. This paper introduces the concept of a Service Zone, which from a service provider/network operator perspective fits within the operator's administrative domain, but is viewed as an independent zone with its own management and services, requiring minimal integration with the core network services. Besides its own management, the Enhanced Services Zone may also provide provisioning and maintenance features needed to provide the customer services and availability that subscribers expect from a telephony service providers. The platform must provide reliable service over time, be scalable to meet increased capacity demands, and be upgradeable to incorporate advanced services and features as they become available. Signaling flows are illustrated using SIP and H.323.

Database integration of protocol-specific neurological imaging datasets

PubMed Central

Pacurar, Emil E.; Sethi, Sean K.; Habib, Charbel; Laze, Marius O.; Martis-Laze, Rachel; Haacke, E. Mark

2016-01-01

For many years now, Magnetic Resonance Innovations (MR Innovations), a magnetic resonance imaging (MRI) software development, technology, and research company, has been aggregating a multitude of MRI data from different scanning sites through its collaborations and research contracts. The majority of the data has adhered to neuroimaging protocols developed by our group which has helped ensure its quality and consistency. The protocols involved include the study of: traumatic brain injury, extracranial venous imaging for multiple sclerosis and Parkinson's disease, and stroke. The database has proven invaluable in helping to establish disease biomarkers, validate findings across multiple data sets, develop and refine signal processing algorithms, and establish both public and private research collaborations. Myriad Masters and PhD dissertations have been possible thanks to the availability of this database. As an example of a project that cuts across diseases, we have used the data and specialized software to develop new guidelines for detecting cerebral microbleeds. Ultimately, the database has been vital in our ability to provide tools and information for researchers and radiologists in diagnosing their patients, and we encourage collaborations and welcome sharing of similar data in this database. PMID:25959660

Robust Multi-unit Auction Protocol against False-name Bids

NASA Astrophysics Data System (ADS)

Yokoo, Makoto; Sakurai, Yuko; Matsubara, Shigeo

This paper presents a new multi-unit auction protocol (IR protocol) that is robust against false-name bids. Internet auctions have become an integral part of Electronic Commerce and a promising field for applying agent and Artificial Intelligence technologies. Although the Internet provides an excellent infrastructure for executing auctions, the possibility of a new type of cheating called false-name bids has been pointed out. A false-name bid is a bid submitted under a fictitious name. A protocol called LDS has been developed for combinatorial auctions of multiple different items and has proven to be robust against false-name bids. Although we can modify the LDS protocol to handle multi-unit auctions, in which multiple units of an identical item are auctioned, the protocol is complicated and requires the auctioneer to carefully pre-determine the combination of bundles to obtain a high social surplus or revenue. For the auctioneer, our newly developed IR protocol is easier to use than the LDS, since the combination of bundles is automatically determined in a flexible manner according to the declared evaluation values of agents. The evaluation results show that the IR protocol can obtain a better social surplus than that obtained by the LDS protocol.

Experimental determination of spin-dependent electron density by joint refinement of X-ray and polarized neutron diffraction data.

PubMed

Deutsch, Maxime; Claiser, Nicolas; Pillet, Sébastien; Chumakov, Yurii; Becker, Pierre; Gillet, Jean Michel; Gillon, Béatrice; Lecomte, Claude; Souhassou, Mohamed

2012-11-01

New crystallographic tools were developed to access a more precise description of the spin-dependent electron density of magnetic crystals. The method combines experimental information coming from high-resolution X-ray diffraction (XRD) and polarized neutron diffraction (PND) in a unified model. A new algorithm that allows for a simultaneous refinement of the charge- and spin-density parameters against XRD and PND data is described. The resulting software MOLLYNX is based on the well known Hansen-Coppens multipolar model, and makes it possible to differentiate the electron spins. This algorithm is validated and demonstrated with a molecular crystal formed by a bimetallic chain, MnCu(pba)(H(2)O)(3)·2H(2)O, for which XRD and PND data are available. The joint refinement provides a more detailed description of the spin density than the refinement from PND data alone.

Combining Heterogeneous Correlation Matrices: Simulation Analysis of Fixed-Effects Methods

ERIC Educational Resources Information Center

Hafdahl, Adam R.

2008-01-01

Monte Carlo studies of several fixed-effects methods for combining and comparing correlation matrices have shown that two refinements improve estimation and inference substantially. With rare exception, however, these simulations have involved homogeneous data analyzed using conditional meta-analytic procedures. The present study builds on…

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.

Analysis of the Impact of Rosuvastatin on Bacterial Mevalonate Production Using a UPLC-Mass Spectrometry Approach.

PubMed

Nolan, J A; Kinsella, M; Hill, C; Joyce, S A; Gahan, C G M

2016-07-01

Statins are widely prescribed cholesterol-lowering medications and act through inhibition of the human enzyme 3-methylglutaryl coenzyme A reductase (HMG-R) which produces mevalonate (MVAL), a key substrate for cholesterol biosynthesis. Some important microbial species also express an isoform of HMG-R; however, the nature of the interaction between statins and bacteria is currently unclear and studies would benefit from protocols to quantify MVAL in complex microbial environments. The objective of this study was to develop a protocol for the analytical quantification of MVAL in bacterial systems and to utilise this approach to analyse the effects of Rosuvastatin (RSV) on bacterial MVAL formation. To determine the effective concentration range of RSV, we examined the dose-dependent inhibition of growth in the HMG-R(+) bacterial pathogens Listeria monocytogenes, Staphylococcus aureus and Enterococcus faecium at various concentrations of pure RSV. Growth inhibition generally correlated with a reduction in bacterial MVAL levels, particularly in culture supernatants at high RSV concentrations, as determined using our ultra-performance liquid chromatography mass spectrometry protocol. This work therefore outlines a refined protocol for the analysis of MVAL in microbial cultures and provides evidence for statin-mediated inhibition of bacterial HMG-R. Furthermore, we show that MVAL is readily transported and secreted from bacterial cells into the growth media.

Multidisciplinary effort in treating children with hepatoblastoma in China.

PubMed

Yuan, Xiao-Jun; Wang, Huan-Min; Jiang, Hui; Tang, Meng-Jie; Li, Zhang-Lin; Zou, Xiang; Fang, Yong-Jun; Pan, Ci; Tou, Jin-Fa; Zhang, Ke-Ren; Liu, Xiang; Li, Wei-Song; Li, Yang; Lu, Jun; Wu, Ye-Ming

2016-05-28

The purpose of this study is to report the first nationwide protocol (Wuhan Protocol) developed by Chinese Children's Cancer Group and the results of multidisciplinary effort in treating hepatoblastoma. In this study, we reported the final analysis, which includes 153 hepatoblastoma patients in 13 hospitals from January 2006 to December 2013. The 6-year overall survival and event-free survival rates were 83.3 ± 3.1% and 71.0 ± 3.7%, respectively, in this cohort. The univariate analysis revealed that female (P = 0.027), under 5 years of age (P = 0.039), complete surgical resection (P = 0.000), no metastases (P = 0.000), and delayed surgery following neoadjuvant chemotherapy (P = 0.000) had better prognosis. In multivariate analysis, male, 5 years of age or above, stage PRETEXT III or IV, and incomplete surgical resection were among the some adverse factors contributing to poor prognosis. The preliminary results from this study showed that patients who underwent treatment following Wuhan Protocol had similar OS and EFS rates compared to those in developed countries. However, the protocol remains to be further optimized in standardizing surgical resection (including liver transplantation), refining risk stratification and risk-based chemotherapy. Copyright © 2016 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Development of a multilocus-based approach for sponge (phylum Porifera) identification: refinement and limitations.

PubMed

Yang, Qi; Franco, Christopher M M; Sorokin, Shirley J; Zhang, Wei

2017-02-02

For sponges (phylum Porifera), there is no reliable molecular protocol available for species identification. To address this gap, we developed a multilocus-based Sponge Identification Protocol (SIP) validated by a sample of 37 sponge species belonging to 10 orders from South Australia. The universal barcode COI mtDNA, 28S rRNA gene (D3-D5), and the nuclear ITS1-5.8S-ITS2 region were evaluated for their suitability and capacity for sponge identification. The highest Bit Score was applied to infer the identity. The reliability of SIP was validated by phylogenetic analysis. The 28S rRNA gene and COI mtDNA performed better than the ITS region in classifying sponges at various taxonomic levels. A major limitation is that the databases are not well populated and possess low diversity, making it difficult to conduct the molecular identification protocol. The identification is also impacted by the accuracy of the morphological classification of the sponges whose sequences have been submitted to the database. Re-examination of the morphological identification further demonstrated and improved the reliability of sponge identification by SIP. Integrated with morphological identification, the multilocus-based SIP offers an improved protocol for more reliable and effective sponge identification, by coupling the accuracy of different DNA markers.

Development of a multilocus-based approach for sponge (phylum Porifera) identification: refinement and limitations

PubMed Central

Yang, Qi; Franco, Christopher M. M.; Sorokin, Shirley J.; Zhang, Wei

2017-01-01

For sponges (phylum Porifera), there is no reliable molecular protocol available for species identification. To address this gap, we developed a multilocus-based Sponge Identification Protocol (SIP) validated by a sample of 37 sponge species belonging to 10 orders from South Australia. The universal barcode COI mtDNA, 28S rRNA gene (D3–D5), and the nuclear ITS1-5.8S-ITS2 region were evaluated for their suitability and capacity for sponge identification. The highest Bit Score was applied to infer the identity. The reliability of SIP was validated by phylogenetic analysis. The 28S rRNA gene and COI mtDNA performed better than the ITS region in classifying sponges at various taxonomic levels. A major limitation is that the databases are not well populated and possess low diversity, making it difficult to conduct the molecular identification protocol. The identification is also impacted by the accuracy of the morphological classification of the sponges whose sequences have been submitted to the database. Re-examination of the morphological identification further demonstrated and improved the reliability of sponge identification by SIP. Integrated with morphological identification, the multilocus-based SIP offers an improved protocol for more reliable and effective sponge identification, by coupling the accuracy of different DNA markers. PMID:28150727

Gender-Specific Combination HIV Prevention for Youth in High-Burden Settings: The MP3 Youth Observational Pilot Study Protocol

PubMed Central

Agot, Kawango

2017-01-01

Background Nearly three decades into the epidemic, sub-Saharan Africa (SSA) remains the region most heavily affected by human immunodeficiency virus (HIV), with nearly 70% of the 34 million people living with HIV globally residing in the region. In SSA, female and male youth (15 to 24 years) are at a disproportionately high risk of HIV infection compared to adults. As such, there is a need to target HIV prevention strategies to youth and to tailor them to a gender-specific context. This protocol describes the process for the multi-staged approach in the design of the MP3 Youth pilot study, a gender-specific, combination, HIV prevention intervention for youth in Kenya. Objective The objective of this multi-method protocol is to outline a rigorous and replicable methodology for a gender-specific combination HIV prevention pilot study for youth in high-burden settings, illustrating the triangulated methods undertaken to ensure that age, sex, and context are integral in the design of the intervention. Methods The mixed-methods, cross-sectional, longitudinal cohort pilot study protocol was developed by first conducting a systematic review of the literature, which shaped focus group discussions around prevention package and delivery options, and that also informed age- and sex- stratified mathematical modeling. The review, qualitative data, and mathematical modeling created a triangulated evidence base of interventions to be included in the pilot study protocol. To design the pilot study protocol, we convened an expert panel to select HIV prevention interventions effective for youth in SSA, which will be offered in a mobile health setting. The goal of the pilot study implementation and evaluation is to apply lessons learned to more effective HIV prevention evidence and programming. Results The combination HIV prevention package in this protocol includes (1) offering HIV testing and counseling for all youth; (2) voluntary medical circumcision and condoms for males; (3) pre-exposure prophylaxis (PrEP), conditional cash transfer (CCT), and contraceptives for females; and (4) referrals for HIV care among those identified as HIV-positive. The combination package platform selected is mobile health teams in an integrated services delivery model. A cross-sectional analysis will be conducted to determine the uptake of the interventions. To determine long-term impact, the protocol outlines enrolling selected participants in mutually exclusive longitudinal cohorts (HIV-positive, PrEP, CCT, and HIV-negative) followed by using mobile phone text messages (short message service, SMS) and in-person surveys to prospectively assess prevention method uptake, adherence, and risk compensation behaviors. Cross-sectional and sub-cohort analyses will be conducted to determine intervention packages uptake. Conclusions The literature review, focus groups, and modeling indicate that offering age- and gender- specific combination HIV prevention interventions that include biomedical, behavioral, and structural interventions can have an impact on HIV risk reduction. Implementing this protocol will show the feasibility of delivering these services at scale. The MP3 Youth study is one of the few combination HIV prevention intervention protocols incorporating youth- and gender-specific interventions in one delivery setting. Lessons learned from the design of the protocol can be incorporated into the national guidance for combination HIV prevention for youth in Kenya and other high-burden SSA settings. Trial Registration ClinicalTrials.gov NCT01571128; http://clinicaltrials.gov/ct2/show/NCT01571128?term=MP3+youth&rank=1 (Archived by WebCite at http://www.webcitation.org/6nmioPd54) PMID:28274904

Combinative application of pH-zone-refining and conventional high-speed counter-current chromatography for preparative separation of caged polyprenylated xanthones from gamboge.

PubMed

Xu, Min; Fu, Wenwei; Zhang, Baojun; Tan, Hongsheng; Xiu, Yanfeng; Xu, Hongxi

2016-02-01

An efficient method for the preparative separation of four structurally similar caged xanthones from the crude extracts of gamboge was established, which involves the combination of pH-zone-refining counter-current chromatography and conventional high-speed counter-current chromatography for the first time. pH-zone-refining counter-current chromatography was performed with the solvent system composed of n-hexane/ethyl acetate/methanol/water (7:3:8:2, v/v/v/v), where 0.1% trifluoroacetic acid was added to the upper organic stationary phase as a retainer and 0.03% triethylamine was added to the aqueous mobile phase as an eluter. From 3.157 g of the crude extract, 1.134 g of gambogic acid, 180.5 mg of gambogenic acid and 572.9 mg of a mixture of two other caged polyprenylated xanthones were obtained. The mixture was further separated by conventional high-speed counter-current chromatography with a solvent system composed of n-hexane/ethyl acetate/methanol/water (5:5:10:5, v/v/v/v) and n-hexane/methyl tert-butyl ether/acetonitrile/water (8:2:6:4,v/v/v/v), yielding 11.6 mg of isogambogenic acid and 10.4 mg of β-morellic acid from 218.0 mg of the mixture, respectively. The purities of all four of the compounds were over 95%, as determined by high-performance liquid chromatography, and the chemical structures of the four compounds were confirmed by electrospray ionization mass spectrometry and NMR spectroscopy. The combinative application of pH-zone-refining counter-current chromatography and conventional high-speed counter-current chromatography shows great advantages in isolating and enriching the caged polyprenylated xanthones. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nitric oxide contributes to the augmented vasodilatation during hypoxic exercise

PubMed Central

Casey, Darren P; Madery, Brandon D; Curry, Timothy B; Eisenach, John H; Wilkins, Brad W; Joyner, Michael J

2010-01-01

We tested the hypotheses that (1) nitric oxide (NO) contributes to augmented skeletal muscle vasodilatation during hypoxic exercise and (2) the combined inhibition of NO production and adenosine receptor activation would attenuate the augmented vasodilatation during hypoxic exercise more than NO inhibition alone. In separate protocols subjects performed forearm exercise (10% and 20% of maximum) during normoxia and normocapnic hypoxia (80% arterial O2 saturation). In protocol 1 (n= 12), subjects received intra-arterial administration of saline (control) and the NO synthase inhibitor NG-monomethyl-l-arginine (l-NMMA). In protocol 2 (n= 10), subjects received intra-arterial saline (control) and combined l-NMMA–aminophylline (adenosine receptor antagonist) administration. Forearm vascular conductance (FVC; ml min−1 (100 mmHg)−1) was calculated from forearm blood flow (ml min−1) and blood pressure (mmHg). In protocol 1, the change in FVC (Δ from normoxic baseline) due to hypoxia under resting conditions and during hypoxic exercise was substantially lower with l-NMMA administration compared to saline (control; P < 0.01). In protocol 2, administration of combined l-NMMA–aminophylline reduced the ΔFVC due to hypoxic exercise compared to saline (control; P < 0.01). However, the relative reduction in ΔFVC compared to the respective control (saline) conditions was similar between l-NMMA only (protocol 1) and combined l-NMMA–aminophylline (protocol 2) at 10% (−17.5 ± 3.7 vs.−21.4 ± 5.2%; P= 0.28) and 20% (−13.4 ± 3.5 vs.−18.8 ± 4.5%; P= 0.18) hypoxic exercise. These findings suggest that NO contributes to the augmented vasodilatation observed during hypoxic exercise independent of adenosine. PMID:19948661

Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand

PubMed Central

DeLuca, Samuel; Khar, Karen; Meiler, Jens

2015-01-01

RosettaLigand has been successfully used to predict binding poses in protein-small molecule complexes. However, the RosettaLigand docking protocol is comparatively slow in identifying an initial starting pose for the small molecule (ligand) making it unfeasible for use in virtual High Throughput Screening (vHTS). To overcome this limitation, we developed a new sampling approach for placing the ligand in the protein binding site during the initial ‘low-resolution’ docking step. It combines the translational and rotational adjustments to the ligand pose in a single transformation step. The new algorithm is both more accurate and more time-efficient. The docking success rate is improved by 10–15% in a benchmark set of 43 protein/ligand complexes, reducing the number of models that typically need to be generated from 1000 to 150. The average time to generate a model is reduced from 50 seconds to 10 seconds. As a result we observe an effective 30-fold speed increase, making RosettaLigand appropriate for docking medium sized ligand libraries. We demonstrate that this improved initial placement of the ligand is critical for successful prediction of an accurate binding position in the ‘high-resolution’ full atom refinement step. PMID:26207742

Age-related clinical and biological features of PTEN abnormalities in T-cell acute lymphoblastic leukaemia.

PubMed

Tesio, M; Trinquand, A; Ballerini, P; Hypolite, G; Lhermitte, L; Petit, A; Ifrah, N; Baruchel, A; Dombret, H; Macintyre, E; Asnafi, V

2017-12-01

The tumour suppressor gene PTEN is commonly altered in T-cell acute lymphoblastic leukaemia but its prognostic impact is still debated. We screened a cohort of 573 fully characterised adult and paediatric T-cell acute lymphoblastic leukaemia (T-ALL) patients for genomic PTEN abnormalities. PTEN-inactivating mutations and/or deletions were identified in 91 cases (16%), including 18% of paediatric (49/277) and 14% of adult cases (42/296). Thirty-four patients harboured only mutations, 12 cases demonstrated only large deletions and 9 only microdeletions. About 36 patients had combined alterations. Different mechanisms of PTEN inactivation predicted differences in the clinical outcome for both adult and paediatric patients treated according to the GRAALL03/05 and FRALLE2000 protocols. Whereas large deletions predicted lower 5-year overall survival (P=0.0053 in adults, P=0.001 in children) and disease-free survival (P=0.0009 in adults, P=0.0002 in children), mutations were not associated with a worse prognosis. The prognostic impact of PTEN loss is therefore linked to the underlying type of genomic abnormality, both in adult and paediatric T-ALLs, demonstrating that detailed analysis of the type of abnormality type would be useful to refine risk stratification.

A Systematic Review of Acquired Uterine Arteriovenous Malformations: Pathophysiology, Diagnosis, and Transcatheter Treatment

PubMed Central

Yoon, Daniel J.; Jones, Megan; Taani, Jamal Al; Buhimschi, Catalin; Dowell, Joshua D.

2015-01-01

Objective An acquired uterine arteriovenous malformation (AVM) is a rare cause of vaginal bleeding and, although hysterectomy is the definitive therapy, transcatheter embolization (TCE) provides an alternative treatment option. This systematic review presents the indications, technique, and outcomes for transcatheter treatment of the acquired uterine AVMs. Study Design Literature databases were searched from 2003 to 2013 for eligible clinical studies, including the patient characteristics, procedural indication, results, complications, as well as descriptions on laterality and embolic agents utilized. Results A total of 40 studies were included comprising of 54 patients (average age of 33.4 years). TCE had a primary success rate with symptomatic control of 61% (31 patients) and secondary success rate of 91% after repeated embolization. When combined with medical therapy, symptom resolution was noted in 48 (85%) patients without more invasive surgical procedures. Conclusion Low-level evidence supports the role of TCE, including in the event of persistent bleeding following initial embolization, for the treatment of acquired uterine AVMs. The variety of embolic agents and laterality of approach delineate the importance of refining procedural protocols in the treatment of the acquired uterine AVM. Condensation A review on the management of patients with acquired uterine AVMs. PMID:26929872

A novel protocol for dispatcher assisted CPR improves CPR quality and motivation among rescuers-A randomized controlled simulation study.

PubMed

Rasmussen, Stinne Eika; Nebsbjerg, Mette Amalie; Krogh, Lise Qvirin; Bjørnshave, Katrine; Krogh, Kristian; Povlsen, Jonas Agerlund; Riddervold, Ingunn Skogstad; Grøfte, Thorbjørn; Kirkegaard, Hans; Løfgren, Bo

2017-01-01

Emergency dispatchers use protocols to instruct bystanders in cardiopulmonary resuscitation (CPR). Studies changing one element in the dispatcher's protocol report improved CPR quality. Whether several changes interact is unknown and the effect of combining multiple changes previously reported to improve CPR quality into one protocol remains to be investigated. We hypothesize that a novel dispatch protocol, combining multiple beneficial elements improves CPR quality compared with a standard protocol. A novel dispatch protocol was designed including wording on chest compressions, using a metronome, regular encouragements and a 10-s rest each minute. In a simulated cardiac arrest scenario, laypersons were randomized to perform single-rescuer CPR guided with the novel or the standard protocol. a composite endpoint of time to first compression, hand position, compression depth and rate and hands-off time (maximum score: 22 points). Afterwards participants answered a questionnaire evaluating the dispatcher assistance. The novel protocol (n=61) improved CPR quality score compared with the standard protocol (n=64) (mean (SD): 18.6 (1.4)) points vs. 17.5 (1.7) points, p<0.001. The novel protocol resulted in deeper chest compressions (mean (SD): 58 (12)mm vs. 52 (13)mm, p=0.02) and improved rate of correct hand position (61% vs. 36%, p=0.01) compared with the standard protocol. In both protocols hands-off time was short. The novel protocol improved motivation among rescuers compared with the standard protocol (p=0.002). Participants guided with a standard dispatch protocol performed high quality CPR. A novel bundle of care protocol improved CPR quality score and motivation among rescuers. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Refining Ovarian Cancer Test accuracy Scores (ROCkeTS): protocol for a prospective longitudinal test accuracy study to validate new risk scores in women with symptoms of suspected ovarian cancer

PubMed Central

Sundar, Sudha; Rick, Caroline; Dowling, Francis; Au, Pui; Rai, Nirmala; Champaneria, Rita; Stobart, Hilary; Neal, Richard; Davenport, Clare; Mallett, Susan; Sutton, Andrew; Kehoe, Sean; Timmerman, Dirk; Bourne, Tom; Van Calster, Ben; Gentry-Maharaj, Aleksandra; Deeks, Jon

2016-01-01

Introduction Ovarian cancer (OC) is associated with non-specific symptoms such as bloating, making accurate diagnosis challenging: only 1 in 3 women with OC presents through primary care referral. National Institute for Health and Care Excellence guidelines recommends sequential testing with CA125 and routine ultrasound in primary care. However, these diagnostic tests have limited sensitivity or specificity. Improving accurate triage in women with vague symptoms is likely to improve mortality by streamlining referral and care pathways. The Refining Ovarian Cancer Test Accuracy Scores (ROCkeTS; HTA 13/13/01) project will derive and validate new tests/risk prediction models that estimate the probability of having OC in women with symptoms. This protocol refers to the prospective study only (phase III). Methods and analysis ROCkeTS comprises four parallel phases. The full ROCkeTS protocol can be found at http://www.birmingham.ac.uk/ROCKETS. Phase III is a prospective test accuracy study. The study will recruit 2450 patients from 15 UK sites. Recruited patients complete symptom and anxiety questionnaires, donate a serum sample and undergo ultrasound scored as per International Ovarian Tumour Analysis (IOTA) criteria. Recruitment is at rapid access clinics, emergency departments and elective clinics. Models to be evaluated include those based on ultrasound derived by the IOTA group and novel models derived from analysis of existing data sets. Estimates of sensitivity, specificity, c-statistic (area under receiver operating curve), positive predictive value and negative predictive value of diagnostic tests are evaluated and a calibration plot for models will be presented. ROCkeTS has received ethical approval from the NHS West Midlands REC (14/WM/1241) and is registered on the controlled trials website (ISRCTN17160843) and the National Institute of Health Research Cancer and Reproductive Health portfolios. PMID:27507231

A refined protocol for coding nursing home residents' comments during satisfaction interviews.

PubMed

Levy-Storms, Lené; Simmons, Sandra F; Gutierrez, Veronica F; Miller-Martinez, Dana; Hickey, Kelly; Schnelle, John F

2005-11-01

This study's objective was to refine a method for coding nursing home (NH) residents' comments about their perceptions of care into unmet needs specific to the manner and frequency of care delivery. NH residents (N=69) were interviewed with both closed-ended (i.e., forced-choice) and open-ended (i.e., residents' own words) questions about their perceptions of care across eight care domains. Unmet needs included comments indicating that residents desired a change in staff- and non-staff-related care. Staff-related unmet needs were further coded into unmet emotional support (i.e., emotional support or manner of care delivery) and instrumental (i.e., instrumental support or frequency of care) needs. Of 66 residents who commented, 66% expressed at least one unmet need across eight care domains. Among these 44 residents, 52% and 84% had unmet emotional support and instrumental support needs, respectively (kappa=68 and.92). An additional 18% expressed both unmet emotional support and instrumental support needs. The refined method offers a systematic way to code residents' comments about their care into unmet needs related to the manner and frequency of care delivery. The findings have direct implications for the identification of care areas in need of improvement from the resident's perspective and the evaluation of improvement efforts.

A comparison of maximal bioenergetic enzyme activities obtained with commonly used homogenization techniques.

PubMed

Grace, M; Fletcher, L; Powers, S K; Hughes, M; Coombes, J

1996-12-01

Homogenization of tissue for analysis of bioenergetic enzyme activities is a common practice in studies examining metabolic properties of skeletal muscle adaptation to disease, aging, inactivity or exercise. While numerous homogenization techniques are in use today, limited information exists concerning the efficacy of specific homogenization protocols. Therefore, the purpose of this study was to compare the efficacy of four commonly used approaches to homogenizing skeletal muscle for analysis of bioenergetic enzyme activity. The maximal enzyme activity (Vmax) of citrate synthase (CS) and lactate dehydrogenase (LDH) were measured from homogenous muscle samples (N = 48 per homogenization technique) and used as indicators to determine which protocol had the highest efficacy. The homogenization techniques were: (1) glass-on-glass pestle; (2) a combination of a mechanical blender and a teflon pestle (Potter-Elvehjem); (3) a combination of the mechanical blender and a biological detergent; and (4) the combined use of a mechanical blender and a sonicator. The glass-on-glass pestle homogenization protocol produced significantly higher (P < 0.05) enzyme activities compared to all other protocols for both enzymes. Of the four protocols examined, the data demonstrate that the glass-on-glass pestle homogenization protocol is the technique of choice for studying bioenergetic enzyme activity in skeletal muscle.

Mars Sample Handling Protocol Workshop Series: Workshop 4

NASA Technical Reports Server (NTRS)

Race Margaret S. (Editor); DeVincenzi, Donald L. (Editor); Rummel, John D. (Editor); Acevedo, Sara E. (Editor)

2001-01-01

In preparation for missions to Mars that will involve the return of samples to Earth, it will be necessary to prepare for the receiving, handling, testing, distributing, and archiving of martian materials here on Earth. Previous groups and committees have studied selected aspects of sample return activities, but specific detailed protocols for the handling and testing of returned samples must still be developed. To further refine the requirements for sample hazard testing and to develop the criteria for subsequent release of sample materials from quarantine, the NASA Planetary Protection Officer convened a series of workshops in 2000-2001. The overall objective of the Workshop Series was to produce a Draft Protocol by which returned martian sample materials can be assessed for biological hazards and examined for evidence of life (extant or extinct) while safeguarding the purity of the samples from possible terrestrial contamination. This report also provides a record of the proceedings of Workshop 4, the final Workshop of the Series, which was held in Arlington, Virginia, June 5-7, 2001. During Workshop 4, the sub-groups were provided with a draft of the protocol compiled in May 2001 from the work done at prior Workshops in the Series. Then eight sub-groups were formed to discuss the following assigned topics: Review and Assess the Draft Protocol for Physical/Chemical Testing Review and Assess the Draft Protocol for Life Detection Testing Review and Assess the Draft Protocol for Biohazard Testing Environmental and Health/Monitoring and Safety Issues Requirements of the Draft Protocol for Facilities and Equipment Contingency Planning for Different Outcomes of the Draft Protocol Personnel Management Considerations in Implementation of the Draft Protocol Draft Protocol Implementation Process and Update Concepts This report provides the first complete presentation of the Draft Protocol for Mars Sample Handling to meet planetary protection needs. This Draft Protocol, which was compiled from deliberations and recommendations from earlier Workshops in the Series, represents a consensus that emerged from the discussions of all the sub-groups assembled over the course of the five Workshops of the Series. These discussions converged on a conceptual approach to sample handling, as well as on specific analytical requirements. Discussions also identified important issues requiring attention, as well as research and development needed for protocol implementation.

Heme oxygenase-1, carbon monoxide, and bilirubin induce tolerance in recipients toward islet allografts by modulating T regulatory cells.

PubMed

Lee, Soo Sun; Gao, Wenda; Mazzola, Silvia; Thomas, Michael N; Csizmadia, Eva; Otterbein, Leo E; Bach, Fritz H; Wang, Hongjun

2007-11-01

Heme oxygenase-1 (HO-1) induction in, or carbon monoxide (CO), or bilirubin administration to, donors and/or recipients frequently lead to long-term survival (>100 days) of DBA/2 islets into B6AF1 recipients. We tested here whether similar treatments show value in a stronger immunogenetic combination, i.e., BALB/c to C57BL/6, and attempted to elucidate the mechanism accounting for tolerance. Induction of HO-1, administering CO or bilirubin to the donor, the islets or the recipient, prolonged islet allograft survival to different extents. Combining all the above treatments (the "combined" protocol) led to survival for >100 days and antigen-specific tolerance to 60% of the transplanted grafts. A high level of forkhead box P3 (Foxp3) and transforming growth factor beta (TGF-beta) expression was detected in the long-term surviving grafts. With the combined protocol, significantly more T regulatory cells (Tregs) were observed surrounding islets 7 days following transplantation. No prolongation of graft survival was observed using the combined protocol when CD4+ CD25+ T cells were predepleted from the recipients before transplantation. In conclusion, our combined protocol led to long-term survival and tolerance to islets in the BALB/c to C57BL/6 combination by promoting Foxp3+ Tregs; these cells played a critical role in the induction and maintenance of tolerance in the recipient.

Bayesian ensemble refinement by replica simulations and reweighting.

PubMed

Hummer, Gerhard; Köfinger, Jürgen

2015-12-28

We describe different Bayesian ensemble refinement methods, examine their interrelation, and discuss their practical application. With ensemble refinement, the properties of dynamic and partially disordered (bio)molecular structures can be characterized by integrating a wide range of experimental data, including measurements of ensemble-averaged observables. We start from a Bayesian formulation in which the posterior is a functional that ranks different configuration space distributions. By maximizing this posterior, we derive an optimal Bayesian ensemble distribution. For discrete configurations, this optimal distribution is identical to that obtained by the maximum entropy "ensemble refinement of SAXS" (EROS) formulation. Bayesian replica ensemble refinement enhances the sampling of relevant configurations by imposing restraints on averages of observables in coupled replica molecular dynamics simulations. We show that the strength of the restraints should scale linearly with the number of replicas to ensure convergence to the optimal Bayesian result in the limit of infinitely many replicas. In the "Bayesian inference of ensembles" method, we combine the replica and EROS approaches to accelerate the convergence. An adaptive algorithm can be used to sample directly from the optimal ensemble, without replicas. We discuss the incorporation of single-molecule measurements and dynamic observables such as relaxation parameters. The theoretical analysis of different Bayesian ensemble refinement approaches provides a basis for practical applications and a starting point for further investigations.

Bayesian ensemble refinement by replica simulations and reweighting

NASA Astrophysics Data System (ADS)

Hummer, Gerhard; Köfinger, Jürgen

2015-12-01

We describe different Bayesian ensemble refinement methods, examine their interrelation, and discuss their practical application. With ensemble refinement, the properties of dynamic and partially disordered (bio)molecular structures can be characterized by integrating a wide range of experimental data, including measurements of ensemble-averaged observables. We start from a Bayesian formulation in which the posterior is a functional that ranks different configuration space distributions. By maximizing this posterior, we derive an optimal Bayesian ensemble distribution. For discrete configurations, this optimal distribution is identical to that obtained by the maximum entropy "ensemble refinement of SAXS" (EROS) formulation. Bayesian replica ensemble refinement enhances the sampling of relevant configurations by imposing restraints on averages of observables in coupled replica molecular dynamics simulations. We show that the strength of the restraints should scale linearly with the number of replicas to ensure convergence to the optimal Bayesian result in the limit of infinitely many replicas. In the "Bayesian inference of ensembles" method, we combine the replica and EROS approaches to accelerate the convergence. An adaptive algorithm can be used to sample directly from the optimal ensemble, without replicas. We discuss the incorporation of single-molecule measurements and dynamic observables such as relaxation parameters. The theoretical analysis of different Bayesian ensemble refinement approaches provides a basis for practical applications and a starting point for further investigations.

Multidataset Refinement Resonant Diffraction, and Magnetic Structures

PubMed Central

Attfield, J. Paul

2004-01-01

The scope of Rietveld and other powder diffraction refinements continues to expand, driven by improvements in instrumentation, methodology and software. This will be illustrated by examples from our research in recent years. Multidataset refinement is now commonplace; the datasets may be from different detectors, e.g., in a time-of-flight experiment, or from separate experiments, such as at several x-ray energies giving resonant information. The complementary use of x rays and neutrons is exemplified by a recent combined refinement of the monoclinic superstructure of magnetite, Fe3O4, below the 122 K Verwey transition, which reveals evidence for Fe2+/Fe3+ charge ordering. Powder neutron diffraction data continue to be used for the solution and Rietveld refinement of magnetic structures. Time-of-flight instruments on cold neutron sources can produce data that have a high intensity and good resolution at high d-spacings. Such profiles have been used to study incommensurate magnetic structures such as FeAsO4 and β–CrPO4. A multiphase, multidataset refinement of the phase-separated perovskite (Pr0.35Y0.07Th0.04Ca0.04Sr0.5)MnO3 has been used to fit three components with different crystal and magnetic structures at low temperatures. PMID:27366599

Interdisciplinary cognitive task analysis: a strategy to develop a comprehensive endoscopic retrograde cholangiopancreatography protocol for use in fellowship training.

PubMed

Canopy, Erin; Evans, Matt; Boehler, Margaret; Roberts, Nicole; Sanfey, Hilary; Mellinger, John

2015-10-01

Endoscopic retrograde cholangiopancreatography is a challenging procedure performed by surgeons and gastroenterologists. We employed cognitive task analysis to identify steps and decision points for this procedure. Standardized interviews were conducted with expert gastroenterologists (7) and surgeons (4) from 4 institutions. A procedural step and cognitive decision point protocol was created from audio-taped transcriptions and was refined by 5 additional surgeons. Conceptual elements, sequential actions, and decision points were iterated for 5 tasks: patient preparation, duodenal intubation, selective cannulation, imaging interpretation with related therapeutic intervention, and complication management. A total of 180 steps were identified. Gastroenterologists identified 34 steps not identified by surgeons, and surgeons identified 20 steps not identified by gastroenterologists. The findings suggest that for complex procedures performed by diverse practitioners, more experts may help delineate distinctive emphases differentiated by training background and type of practice. Copyright © 2015 Elsevier Inc. All rights reserved.

Effects of Annular Electromagnetic Stirring Coupled with Intercooling on Grain Refinement and Homogeneity During Direct Chill Casting of Large-Sized 7005 Alloy Billet

NASA Astrophysics Data System (ADS)

Luo, Yajun; Zhang, Zhifeng; Li, Bao; Gao, Mingwei; Qiu, Yang; He, Min

2017-12-01

To obtain a large-sized, high-quality aluminum alloy billet, an advanced uniform direct chill (UDC) casting method was developed by combining annular electromagnetic stirring (A-EMS) with intercooling in the sump. The 7005 alloy was chosen to investigate the effect of UDC on grain refinement and homogeneity during normal direct chill (NDC) casting. It was concluded that the microstructure consisting of both primary α-Al phase and secondary phases becomes finer and more homogeneous for the billets prepared with UDC casting compared to those prepared with NDC casting, and the forced cooling from both the inner and outer melt under A-EMS has a measurable effect on grain refinement and homogeneity.

A Flexible Multidose GnRH Antagonist versus a Microdose Flare-Up GnRH Agonist Combined with a Flexible Multidose GnRH Antagonist Protocol in Poor Responders to IVF.

PubMed

Çelik, Gayem İnayet Turgay; Sütçü, Havva Kömür; Akpak, Yaşam Kemal; Akar, Münire Erman

2015-01-01

To compare the effectiveness of a flexible multidose gonadotropin-releasing hormone (GnRH) antagonist against the effectiveness of a microdose flare-up GnRH agonist combined with a flexible multidose GnRH antagonist protocol in poor responders to in vitro fertilization (IVF). A retrospective study in Akdeniz University, Faculty of Medicine, Department of Obstetrics and Gynecology, IVF Center, for 131 poor responders in the intracytoplasmic sperm injection-embryo transfer (ICSI-ET) program between January 2006 and November 2012. The groups were compared to the patients' characteristics, controlled ovarian stimulation (COH) results, and laboratory results. Combination protocol was applied to 46 patients (group 1), and a single protocol was applied to 85 patients (group 2). In group 1, the duration of the treatment was longer and the dose of FSH was higher. The cycle cancellation rate was significantly higher in group 2 (26.1% versus 38.8%). A significant difference was not observed with respect to the number and quality of oocytes and embryos or to the number of embryos transferred. There were no statistically significant differences in the hCG positivity (9.5% versus 9.4%) or the clinical pregnancy rates (7.1% versus 10.6%). The combination protocol does not provide additional efficacy.

A Flexible Multidose GnRH Antagonist versus a Microdose Flare-Up GnRH Agonist Combined with a Flexible Multidose GnRH Antagonist Protocol in Poor Responders to IVF

PubMed Central

Turgay Çelik, Gayem İnayet; Sütçü, Havva Kömür; Akpak, Yaşam Kemal; Akar, Münire Erman

2015-01-01

Objective. To compare the effectiveness of a flexible multidose gonadotropin-releasing hormone (GnRH) antagonist against the effectiveness of a microdose flare-up GnRH agonist combined with a flexible multidose GnRH antagonist protocol in poor responders to in vitro fertilization (IVF). Study Design. A retrospective study in Akdeniz University, Faculty of Medicine, Department of Obstetrics and Gynecology, IVF Center, for 131 poor responders in the intracytoplasmic sperm injection-embryo transfer (ICSI-ET) program between January 2006 and November 2012. The groups were compared to the patients' characteristics, controlled ovarian stimulation (COH) results, and laboratory results. Results. Combination protocol was applied to 46 patients (group 1), and a single protocol was applied to 85 patients (group 2). In group 1, the duration of the treatment was longer and the dose of FSH was higher. The cycle cancellation rate was significantly higher in group 2 (26.1% versus 38.8%). A significant difference was not observed with respect to the number and quality of oocytes and embryos or to the number of embryos transferred. There were no statistically significant differences in the hCG positivity (9.5% versus 9.4%) or the clinical pregnancy rates (7.1% versus 10.6%). Conclusion. The combination protocol does not provide additional efficacy. PMID:26161425

Clinical review: Reunification of acid–base physiology

PubMed Central

Kellum, John A

2005-01-01

Recent advances in acid–base physiology and in the epidemiology of acid–base disorders have refined our understanding of the basic control mechanisms that determine blood pH in health and disease. These refinements have also brought parity between the newer, quantitative and older, descriptive approaches to acid–base physiology. This review explores how the new and older approaches to acid–base physiology can be reconciled and combined to result in a powerful bedside tool. A case based tutorial is also provided. PMID:16277739

Refinements to the Graves and Pitarka (2010) Broadband Ground-Motion Simulation Method

DOE PAGES

Graves, Robert; Pitarka, Arben

2014-12-17

This brief article describes refinements to the Graves and Pitarka (2010) broadband ground-motion simulation methodology (GP2010 hereafter) that have been implemented in version 14.3 of the Southern California Earthquake Center (SCEC) Broadband Platform (BBP). The updated version of our method on the current SCEC BBP is referred to as GP14.3. Here, our simulation technique is a hybrid approach that combines low- and high-frequency motions computed with different methods into a single broadband response.

Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design.

PubMed

Smith, Colin A; Kortemme, Tanja

2011-01-01

Predicting the set of sequences that are tolerated by a protein or protein interface, while maintaining a desired function, is useful for characterizing protein interaction specificity and for computationally designing sequence libraries to engineer proteins with new functions. Here we provide a general method, a detailed set of protocols, and several benchmarks and analyses for estimating tolerated sequences using flexible backbone protein design implemented in the Rosetta molecular modeling software suite. The input to the method is at least one experimentally determined three-dimensional protein structure or high-quality model. The starting structure(s) are expanded or refined into a conformational ensemble using Monte Carlo simulations consisting of backrub backbone and side chain moves in Rosetta. The method then uses a combination of simulated annealing and genetic algorithm optimization methods to enrich for low-energy sequences for the individual members of the ensemble. To emphasize certain functional requirements (e.g. forming a binding interface), interactions between and within parts of the structure (e.g. domains) can be reweighted in the scoring function. Results from each backbone structure are merged together to create a single estimate for the tolerated sequence space. We provide an extensive description of the protocol and its parameters, all source code, example analysis scripts and three tests applying this method to finding sequences predicted to stabilize proteins or protein interfaces. The generality of this method makes many other applications possible, for example stabilizing interactions with small molecules, DNA, or RNA. Through the use of within-domain reweighting and/or multistate design, it may also be possible to use this method to find sequences that stabilize particular protein conformations or binding interactions over others.

Light attenuation versus evolved carbon (AVEC) - A new way to look at elemental and organic carbon analysis

NASA Astrophysics Data System (ADS)

Nicolosi, E. M. G.; Quincey, P.; Font, A.; Fuller, G. W.

2018-02-01

The Attenuation Versus Evolved Carbon (AVEC) plot is a new way to represent thermal-optical organic carbon/elemental carbon (OC/EC) analysis data. The accumulated carbon concentration is plotted against the attenuation (ln (I0/I)). Unlike the thermogram, it provides information about the sample properties rather than the instantaneous instrument sensor status. The plot can be used to refine the determination of OC and EC split point, either from consideration of laser instability or transit time within the instrument; to investigate the optical properties of the particles; and to spot the early evolution of pyrolysed carbon (PC) and/or EC during the inert phase. 168 samples from three sites were studied. The gradient of the AVEC plot curve in the oxygenated phase provides information about the mass absorption cross section (σ) of the particles leaving the filter. The σ of the PC generated in the higher temperature Quartz protocol was greater than the PC generated in the lower temperature EUSAAR_2 protocol. Also, in both cases the PC evolved at a lower temperature in the oxygenated phase than the native EC. To minimise the shadowing effect, σ was also measured for the particles leaving the filter at the end of the analysis. These σ values, which are expected to be a combination of inherent σ together with fixed instrumental factors, were consistent between the different sites (45 ± 10 m2 g-1 in rural samples, 42 ± 8 m2 g-1 in urban samples and 35 ± 14 m2 g-1 in roadside samples). The AVEC plot can be generated from the data routinely produced by the analytical instrument using the R-code supplied in the supplementary material.

Technology platform development for targeted plasma metabolites in human heart failure.

PubMed

Chan, Cy X'avia; Khan, Anjum A; Choi, Jh Howard; Ng, Cm Dominic; Cadeiras, Martin; Deng, Mario; Ping, Peipei

2013-01-01

Heart failure is a multifactorial disease associated with staggeringly high morbidity and motility. Recently, alterations of multiple metabolites have been implicated in heart failure; however, the lack of an effective technology platform to assess these metabolites has limited our understanding on how they contribute to this disease phenotype. We have successfully developed a new workflow combining specific sample preparation with tandem mass spectrometry that enables us to extract most of the targeted metabolites. 19 metabolites were chosen ascribing to their biological relevance to heart failure, including extracellular matrix remodeling, inflammation, insulin resistance, renal dysfunction, and cardioprotection against ischemic injury. In this report, we systematically engineered, optimized and refined a protocol applicable to human plasma samples; this study contributes to the methodology development with respect to deproteinization, incubation, reconstitution, and detection with mass spectrometry. The deproteinization step was optimized with 20% methanol/ethanol at a plasma:solvent ratio of 1:3. Subsequently, an incubation step was implemented which remarkably enhanced the metabolite signals and the number of metabolite peaks detected by mass spectrometry in both positive and negative modes. With respect to the step of reconstitution, 0.1% formic acid was designated as the reconstitution solvent vs. 6.5 mM ammonium bicarbonate, based on the comparable number of metabolite peaks detected in both solvents, and yet the signal detected in the former was higher. By adapting this finalized protocol, we were able to retrieve 13 out of 19 targeted metabolites from human plasma. We have successfully devised a simple albeit effective workflow for the targeted plasma metabolites relevant to human heart failure. This will be employed in tandem with high throughput liquid chromatography mass spectrometry platform to validate and characterize these potential metabolic biomarkers for diagnostic and therapeutic development of heart failure patients.

Evolution of the MIDTAL microarray: the adaption and testing of oligonucleotide 18S and 28S rDNA probes and evaluation of subsequent microarray generations with Prymnesium spp. cultures and field samples.

PubMed

McCoy, Gary R; Touzet, Nicolas; Fleming, Gerard T A; Raine, Robin

2015-07-01

The toxic microalgal species Prymnesium parvum and Prymnesium polylepis are responsible for numerous fish kills causing economic stress on the aquaculture industry and, through the consumption of contaminated shellfish, can potentially impact on human health. Monitoring of toxic phytoplankton is traditionally carried out by light microscopy. However, molecular methods of identification and quantification are becoming more common place. This study documents the optimisation of the novel Microarrays for the Detection of Toxic Algae (MIDTAL) microarray from its initial stages to the final commercial version now available from Microbia Environnement (France). Existing oligonucleotide probes used in whole-cell fluorescent in situ hybridisation (FISH) for Prymnesium species from higher group probes to species-level probes were adapted and tested on the first-generation microarray. The combination and interaction of numerous other probes specific for a whole range of phytoplankton taxa also spotted on the chip surface caused high cross reactivity, resulting in false-positive results on the microarray. The probe sequences were extended for the subsequent second-generation microarray, and further adaptations of the hybridisation protocol and incubation temperatures significantly reduced false-positive readings from the first to the second-generation chip, thereby increasing the specificity of the MIDTAL microarray. Additional refinement of the subsequent third-generation microarray protocols with the addition of a poly-T amino linker to the 5' end of each probe further enhanced the microarray performance but also highlighted the importance of optimising RNA labelling efficiency when testing with natural seawater samples from Killary Harbour, Ireland.

FF12MC: A revised AMBER forcefield and new protein simulation protocol

PubMed Central

2016-01-01

ABSTRACT Specialized to simulate proteins in molecular dynamics (MD) simulations with explicit solvation, FF12MC is a combination of a new protein simulation protocol employing uniformly reduced atomic masses by tenfold and a revised AMBER forcefield FF99 with (i) shortened C—H bonds, (ii) removal of torsions involving a nonperipheral sp3 atom, and (iii) reduced 1–4 interaction scaling factors of torsions ϕ and ψ. This article reports that in multiple, distinct, independent, unrestricted, unbiased, isobaric–isothermal, and classical MD simulations FF12MC can (i) simulate the experimentally observed flipping between left‐ and right‐handed configurations for C14–C38 of BPTI in solution, (ii) autonomously fold chignolin, CLN025, and Trp‐cage with folding times that agree with the experimental values, (iii) simulate subsequent unfolding and refolding of these miniproteins, and (iv) achieve a robust Z score of 1.33 for refining protein models TMR01, TMR04, and TMR07. By comparison, the latest general‐purpose AMBER forcefield FF14SB locks the C14–C38 bond to the right‐handed configuration in solution under the same protein simulation conditions. Statistical survival analysis shows that FF12MC folds chignolin and CLN025 in isobaric–isothermal MD simulations 2–4 times faster than FF14SB under the same protein simulation conditions. These results suggest that FF12MC may be used for protein simulations to study kinetics and thermodynamics of miniprotein folding as well as protein structure and dynamics. Proteins 2016; 84:1490–1516. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:27348292

Mars Micro-Meteorology Station Electronic Design, Assembly and Test Project

NASA Technical Reports Server (NTRS)

Twiggs, Robert J.; Merrihew, Seven; Engberg, Brian; Hicks, Michael; Tillier, Clemens

1996-01-01

The Micro-Met mission is a micro-meteorological experiment for Mars designed to take globally distributed pressure measurements for at least one martian year. A series of 16 landers equally spaced over the planet's surface will take pressure and temperature data and relay it to investigators on Earth. Measurements will be logged once every hour and transmitted to an orbiter once every thirty days using Mars Balloon Relay protocol. Micro-Met data will aid tremendously in the development and refinement of a global model of Martian weather.

Report of a Meeting on Contemporary Topics in Zebrafish Husbandry and Care

PubMed Central

Osborne, Nikki; Paull, Gregory; Grierson, Adam; Dunford, Karen; Busch-Nentwich, Elisabeth M.; Sneddon, Lynne U.; Wren, Natalie; Higgins, Joe

2016-01-01

Abstract A meeting on Contemporary Topics in Zebrafish Husbandry and Care was held in the United Kingdom in 2014, with the aim of providing a discussion forum for researchers, animal technologists, and veterinarians from academia and industry to share good practice and exchange ideas. Presentation topics included protocols for optimal larval rearing, implementing the 3Rs (replacement, reduction, and refinement) in large-scale colony management, and environmental enrichment. The audience also participated in a survey of current practice relating to practical husbandry, cryopreservation, and the provision of enrichment. PMID:27537782

Report of a Meeting on Contemporary Topics in Zebrafish Husbandry and Care.

PubMed

Osborne, Nikki; Paull, Gregory; Grierson, Adam; Dunford, Karen; Busch-Nentwich, Elisabeth M; Sneddon, Lynne U; Wren, Natalie; Higgins, Joe; Hawkins, Penny

2016-12-01

A meeting on Contemporary Topics in Zebrafish Husbandry and Care was held in the United Kingdom in 2014, with the aim of providing a discussion forum for researchers, animal technologists, and veterinarians from academia and industry to share good practice and exchange ideas. Presentation topics included protocols for optimal larval rearing, implementing the 3Rs (replacement, reduction, and refinement) in large-scale colony management, and environmental enrichment. The audience also participated in a survey of current practice relating to practical husbandry, cryopreservation, and the provision of enrichment.

Adaptive Reliable Routing Protocol Using Combined Link Stability Estimation for Mobile Ad hoc Networks

NASA Astrophysics Data System (ADS)

Vadivel, R.; Bhaskaran, V. Murali

2010-10-01

The main reason for packet loss in ad hoc networks is the link failure or node failure. In order to increase the path stability, it is essential to distinguish and moderate the failures. By knowing individual link stability along a path, path stability can be identified. In this paper, we develop an adaptive reliable routing protocol using combined link stability estimation for mobile ad hoc networks. The main objective of this protocol is to determine a Quality of Service (QoS) path along with prolonging the network life time and to reduce the packet loss. We calculate a combined metric for a path based on the parameters Link Expiration Time, Node Remaining Energy and Node Velocity and received signal strength to predict the link stability or lifetime. Then, a bypass route is established to retransmit the lost data, when a link failure occurs. By simulation results, we show that the proposed reliable routing protocol achieves high delivery ratio with reduced delay and packet drop.

Child maltreatment: a review of key literature in 2015.

PubMed

Newton, Alice W

2016-06-01

This review addresses some of the more salient articles in the field of child maltreatment published in 2015, with a goal of helping the general practitioner understand the evolution of research in the field of child abuse pediatrics (a board-certified specialty since 2009). Researchers continue to refine the database for child abuse pediatrics. Several articles focus on the inconsistencies in approach to the evaluation of possible physical child abuse between hospitals and practitioners. Multiple researchers aim to develop a protocol that standardizes the response to findings of a sentinel injury, such as a rib fracture, abdominal trauma, or unexplained bruising in a nonambulatory infant. Professionals are also working to improve our understanding about the impact of trauma on children and how best to ameliorate its effects. With solid, evidence-based literature published on various topics in the field of child abuse pediatrics, experts work to refine and unify the clinician's approach to the evaluation of possible physical abuse.

Replica Exchange Improves Sampling in Low-Resolution Docking Stage of RosettaDock

PubMed Central

Zhang, Zhe; Lange, Oliver F.

2013-01-01

Many protein-protein docking protocols are based on a shotgun approach, in which thousands of independent random-start trajectories minimize the rigid-body degrees of freedom. Another strategy is enumerative sampling as used in ZDOCK. Here, we introduce an alternative strategy, ReplicaDock, using a small number of long trajectories of temperature replica exchange. We compare replica exchange sampling as low-resolution stage of RosettaDock with RosettaDock's original shotgun sampling as well as with ZDOCK. A benchmark of 30 complexes starting from structures of the unbound binding partners shows improved performance for ReplicaDock and ZDOCK when compared to shotgun sampling at equal or less computational expense. ReplicaDock and ZDOCK consistently reach lower energies and generate significantly more near-native conformations than shotgun sampling. Accordingly, they both improve typical metrics of prediction quality of complex structures after refinement. Additionally, the refined ReplicaDock ensembles reach significantly lower interface energies and many previously hidden features of the docking energy landscape become visible when ReplicaDock is applied. PMID:24009670

Gender-Specific Combination HIV Prevention for Youth in High-Burden Settings: The MP3 Youth Observational Pilot Study Protocol.

PubMed

Buttolph, Jasmine; Inwani, Irene; Agot, Kawango; Cleland, Charles M; Cherutich, Peter; Kiarie, James N; Osoti, Alfred; Celum, Connie L; Baeten, Jared M; Nduati, Ruth; Kinuthia, John; Hallett, Timothy B; Alsallaq, Ramzi; Kurth, Ann E

2017-03-08

Nearly three decades into the epidemic, sub-Saharan Africa (SSA) remains the region most heavily affected by human immunodeficiency virus (HIV), with nearly 70% of the 34 million people living with HIV globally residing in the region. In SSA, female and male youth (15 to 24 years) are at a disproportionately high risk of HIV infection compared to adults. As such, there is a need to target HIV prevention strategies to youth and to tailor them to a gender-specific context. This protocol describes the process for the multi-staged approach in the design of the MP3 Youth pilot study, a gender-specific, combination, HIV prevention intervention for youth in Kenya. The objective of this multi-method protocol is to outline a rigorous and replicable methodology for a gender-specific combination HIV prevention pilot study for youth in high-burden settings, illustrating the triangulated methods undertaken to ensure that age, sex, and context are integral in the design of the intervention. The mixed-methods, cross-sectional, longitudinal cohort pilot study protocol was developed by first conducting a systematic review of the literature, which shaped focus group discussions around prevention package and delivery options, and that also informed age- and sex- stratified mathematical modeling. The review, qualitative data, and mathematical modeling created a triangulated evidence base of interventions to be included in the pilot study protocol. To design the pilot study protocol, we convened an expert panel to select HIV prevention interventions effective for youth in SSA, which will be offered in a mobile health setting. The goal of the pilot study implementation and evaluation is to apply lessons learned to more effective HIV prevention evidence and programming. The combination HIV prevention package in this protocol includes (1) offering HIV testing and counseling for all youth; (2) voluntary medical circumcision and condoms for males; (3) pre-exposure prophylaxis (PrEP), conditional cash transfer (CCT), and contraceptives for females; and (4) referrals for HIV care among those identified as HIV-positive. The combination package platform selected is mobile health teams in an integrated services delivery model. A cross-sectional analysis will be conducted to determine the uptake of the interventions. To determine long-term impact, the protocol outlines enrolling selected participants in mutually exclusive longitudinal cohorts (HIV-positive, PrEP, CCT, and HIV-negative) followed by using mobile phone text messages (short message service, SMS) and in-person surveys to prospectively assess prevention method uptake, adherence, and risk compensation behaviors. Cross-sectional and sub-cohort analyses will be conducted to determine intervention packages uptake. The literature review, focus groups, and modeling indicate that offering age- and gender- specific combination HIV prevention interventions that include biomedical, behavioral, and structural interventions can have an impact on HIV risk reduction. Implementing this protocol will show the feasibility of delivering these services at scale. The MP3 Youth study is one of the few combination HIV prevention intervention protocols incorporating youth- and gender-specific interventions in one delivery setting. Lessons learned from the design of the protocol can be incorporated into the national guidance for combination HIV prevention for youth in Kenya and other high-burden SSA settings. ClinicalTrials.gov NCT01571128; http://clinicaltrials.gov/ct2/show/NCT01571128?term=MP3+youth&rank=1 (Archived by WebCite at http://www.webcitation.org/6nmioPd54). ©Jasmine Buttolph, Irene Inwani, Kawango Agot, Charles M Cleland, Peter Cherutich, James N Kiarie, Alfred Osoti, Connie L Celum, Jared M Baeten, Ruth Nduati, John Kinuthia, Timothy B Hallett, Ramzi Alsallaq, Ann E Kurth. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 08.03.2017.

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.

Clinically Practical Magnetic Resonance Protocol for Improved Specificity in Breast Cancer Diagnosis

DTIC Science & Technology

2007-06-01

Protocol for Improved Specificity in Breast Cancer Diagnosis PRINCIPAL INVESTIGATOR: Luminita Alina Tudorica, Ph.D. CONTRACTING...TITLE AND SUBTITLE 5a. CONTRACT NUMBER Clinically Practical Magnetic Resonance Protocol for Improved Specificity in Breast Cancer Diagnosis 5b... breast cancer study in a clinical setting. This study aims to improve specificity of breast cancer detection by using a combined MRI/MRS protocol. In

Permutation Entropy and Signal Energy Increase the Accuracy of Neuropathic Change Detection in Needle EMG

PubMed Central

2018-01-01

Background and Objective. Needle electromyography can be used to detect the number of changes and morphological changes in motor unit potentials of patients with axonal neuropathy. General mathematical methods of pattern recognition and signal analysis were applied to recognize neuropathic changes. This study validates the possibility of extending and refining turns-amplitude analysis using permutation entropy and signal energy. Methods. In this study, we examined needle electromyography in 40 neuropathic individuals and 40 controls. The number of turns, amplitude between turns, signal energy, and “permutation entropy” were used as features for support vector machine classification. Results. The obtained results proved the superior classification performance of the combinations of all of the above-mentioned features compared to the combinations of fewer features. The lowest accuracy from the tested combinations of features had peak-ratio analysis. Conclusion. Using the combination of permutation entropy with signal energy, number of turns and mean amplitude in SVM classification can be used to refine the diagnosis of polyneuropathies examined by needle electromyography. PMID:29606959

Combination therapy for radiation-induced bone marrow aplasia in nonhuman primates using synthokine SC-55494 and recombinant human granulocyte colony-stimulating factor.

PubMed

MacVittie, T J; Farese, A M; Herodin, F; Grab, L B; Baum, C M; McKearn, J P

1996-05-15

Combination cytokine therapy continues to be evaluated in an effort to stimulate multilineage hematopoietic reconstitution after bone marrow myelosuppression. This study evaluated the efficacy of combination therapy with the synthetic interleukin-3 receptor agonist, Synthokine-SC55494, and recombinant methionyl human granulocyte colony-stimulating factor (rhG-CSF) on platelet and neutrophil recovery in nonhuman primates exposed to total body 700 cGy 60Co gamma radiation. After irradiation on day (d) 0, cohorts of animals subcutaneously received single-agent protocols of either human serum albumin (HSA; every day [QD], 15 micrograms/kg/d, n = 10), Synthokine (twice daily [BID], 100, micrograms/kg/d, n = 15), rhG-CSF (QD, 10 micrograms/kg/d, n = 5), or a combination of Synthokine and rhG-CSF (BID, 100 and 10 micrograms/kg/d, respectively, n = 5) for 23 days beginning on d1. Complete blood counts were monitored for 60 days postirradiation and the durations of neutropenia (absolute neutrophil count < 500/microL) and thrombocytopenia (platelet count < 20,000/microL) were assessed. Animals were provided clinical support in the form of antibiotics, fresh irradiated whole blood, and fluids. All cytokine protocols significantly (P < .05) reduced the duration thrombocytopenia versus the HSA-treated animals. Only the combination protocol of Synthokine + rhG-CSF and rhG-CSF alone significantly shortened the period neutropenia (P < .05). The combined Synthokine/rhG-CSF protocol significantly improved platelet nadir versus Synthokine alone and HSA controls and neutrophil nadir versus rhG-CSF alone and HSA controls. All cytokine protocols decreased the time to recovery to preirradiation neutrophil and platelet values. The Synthokine/rhG-CSF protocol also reduced the transfusion requirements per treatment group to 0 among 5 animals as compared with 2 among 5 animals for Synthokine alone, 8 among 5 animals for rhG-CSF, and 17 among 10 animals for HSA. These data showed that the combination of Synthokine, SC-55494, and rhG-CSF further decreased the cytopenic periods and nadirs for both platelets and neutrophils relative to Synthokine and rhG-CSF monotherapy and suggest that this combination therapy would be effective against both neutropenia and thrombocytopenia consequent to drug- or radiation- induced myelosuppression.

Animal welfare and the refinement of neuroscience research methods--a case study of Huntington's disease models.

PubMed

Olsson, I Anna S; Hansen, Axel K; Sandøe, Peter

2008-07-01

The use of animals in biomedical and other research presents an ethical dilemma: we do not want to lose scientific benefits, nor do we want to cause laboratory animals to suffer. Scientists often refer to the potential human benefits of animal models to justify their use. However, even if this is accepted, it still needs to be argued that the same benefits could not have been achieved with a mitigated impact on animal welfare. Reducing the adverse effects of scientific protocols ('refinement') is therefore crucial in animal-based research. It is especially important that researchers share knowledge on how to avoid causing unnecessary suffering. We have previously demonstrated that even in studies in which animal use leads to spontaneous death, scientists often fail to report measures to minimize animal distress (Olsson et al. 2007). In this paper, we present the full results of a case study examining reports, published in peer-reviewed journals between 2003 and 2004, of experiments employing animal models to study the neurodegenerative disorder Huntington's disease. In 51 references, experiments in which animals were expected to develop motor deficits so severe that they would have difficulty eating and drinking normally were conducted, yet only three references were made to housing adaptation to facilitate food and water intake. Experiments including end-stages of the disease were reported in 14 papers, yet of these only six referred to the euthanasia of moribund animals. If the reference in scientific publications reflects the actual application of refinement, researchers do not follow the 3Rs (replacement, reduction, refinement) principle. While in some cases, it is clear that less-than-optimal techniques were used, we recognize that scientists may apply refinement without referring to it; however, if they do not include such information in publications, it suggests they find it less relevant. Journal publishing policy could play an important role: first, in ensuring that referees seriously consider whether submitted studies were indeed carried out with the smallest achievable negative impact on the animals and, secondly, in encouraging scientists to share refinements through the inclusion of a 3Rs section in papers publishing the results of animal-based research.

Combining Static Analysis and Model Checking for Software Analysis

NASA Technical Reports Server (NTRS)

Brat, Guillaume; Visser, Willem; Clancy, Daniel (Technical Monitor)

2003-01-01

We present an iterative technique in which model checking and static analysis are combined to verify large software systems. The role of the static analysis is to compute partial order information which the model checker uses to reduce the state space. During exploration, the model checker also computes aliasing information that it gives to the static analyzer which can then refine its analysis. The result of this refined analysis is then fed back to the model checker which updates its partial order reduction. At each step of this iterative process, the static analysis computes optimistic information which results in an unsafe reduction of the state space. However we show that the process converges to a fired point at which time the partial order information is safe and the whole state space is explored.

Acute effects of warm-up stretch protocols on balance, vertical jump height, and range of motion in dancers.

PubMed

Morrin, Niamh; Redding, Emma

2013-01-01

The aim of this study was to examine the acute effects of static stretching (SS), dynamic stretching (DS), and a combined (static and dynamic) stretch protocol on vertical jump (VJ) height, balance, and range of motion (ROM) in dancers. A no-stretch (NS) intervention acted as the control condition. It was hypothesized that the DS and combination stretch protocols would have more positive effects on performance indicators than SS and NS, and SS would have negative effects as compared to the NS condition. Ten trained female dancers (27 ± 5 years of age) were tested on four occasions. Each session began with initial measurements of hamstring ROM on the dominant leg. The participants subsequently carried out a cardiovascular (CV) warm-up, which was followed by one of the four randomly selected stretch conditions. Immediately after the stretch intervention the participants were tested on VJ performance, hamstring ROM, and balance. The data showed that DS (p < 0.05) and the combination stretch (p < .05) produced significantly greater VJ height scores as compared to SS, and the combination stretch demonstrated significantly enhanced balance performance as compared to SS (p < 0.05). With regard to ROM, a one-way ANOVA indicated that SS and the combination stretch displayed significantly greater changes in ROM than DS (p < 0.05). From comparison of the stretch protocols used in the current study, it can be concluded that SS does not appear to be detrimental to a dancer's performance, and DS has some benefits but not in all three key area's tested, namely lower body power (VJ height), balance, and range of motion. However, combination stretching showed significantly enhanced balance and vertical jump height scores and significantly improved pre-stretch and post-stretch ROM values. It is therefore suggested that a combined warm-up protocol consisting of SS and DS should be promoted as an effective warm-up for dancers.

The effect of different exercise protocols and regression-based algorithms on the assessment of the anaerobic threshold.

PubMed

Zuniga, Jorge M; Housh, Terry J; Camic, Clayton L; Bergstrom, Haley C; Schmidt, Richard J; Johnson, Glen O

2014-09-01

The purpose of this study was to examine the effect of ramp and step incremental cycle ergometer tests on the assessment of the anaerobic threshold (AT) using 3 different computerized regression-based algorithms. Thirteen healthy adults (mean age and body mass [SD] = 23.4 [3.3] years and body mass = 71.7 [11.1] kg) visited the laboratory on separate occasions. Two-way repeated measures analyses of variance with appropriate follow-up procedures were used to analyze the data. The step protocol resulted in greater mean values across algorithms than the ramp protocol for the V[Combining Dot Above]O2 (step = 1.7 [0.6] L·min and ramp = 1.5 [0.4] L·min) and heart rate (HR) (step = 133 [21] b·min and ramp = 124 [15] b·min) at the AT. There were no significant mean differences, however, in power outputs at the AT between the step (115.2 [44.3] W) and the ramp (112.2 [31.2] W) protocols. Furthermore, there were no significant mean differences for V[Combining Dot Above]O2, HR, or power output across protocols among the 3 computerized regression-based algorithms used to estimate the AT. The current findings suggested that the protocol selection, but not the regression-based algorithms can affect the assessment of the V[Combining Dot Above]O2 and HR at the AT.

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

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.

Refined estimates of local recurrence risks by DCIS score adjusting for clinicopathological features: a combined analysis of ECOG-ACRIN E5194 and Ontario DCIS cohort studies.

PubMed

Rakovitch, E; Gray, R; Baehner, F L; Sutradhar, R; Crager, M; Gu, S; Nofech-Mozes, S; Badve, S S; Hanna, W; Hughes, L L; Wood, W C; Davidson, N E; Paszat, L; Shak, S; Sparano, J A; Solin, L J

2018-06-01

Better tools are needed to estimate local recurrence (LR) risk after breast-conserving surgery (BCS) for DCIS. The DCIS score (DS) was validated as a predictor of LR in E5194 and Ontario DCIS cohort (ODC) after BCS. We combined data from E5194 and ODC adjusting for clinicopathological factors to provide refined estimates of the 10-year risk of LR after treatment by BCS alone. Data from E5194 and ODC were combined. Patients with positive margins or multifocality were excluded. Identical Cox regression models were fit for each study. Patient-specific meta-analysis was used to calculate precision-weighted estimates of 10-year LR risk by DS, age, tumor size and year of diagnosis. The combined cohort includes 773 patients. The DS and age at diagnosis, tumor size and year of diagnosis provided independent prognostic information on the 10-year LR risk (p ≤ 0.009). Hazard ratios from E5194 and ODC cohorts were similar for the DS (2.48, 1.95 per 50 units), tumor size ≤ 1 versus  > 1-2.5 cm (1.45, 1.47), age ≥ 50 versus < 50 year (0.61, 0.84) and year ≥ 2000 (0.67, 0.49). Utilization of DS combined with tumor size and age at diagnosis predicted more women with very low (≤ 8%) or higher (> 15%) 10-year LR risk after BCS alone compared to utilization of DS alone or clinicopathological factors alone. The combined analysis provides refined estimates of 10-year LR risk after BCS for DCIS. Adding information on tumor size and age at diagnosis to the DS adjusting for year of diagnosis provides improved LR risk estimates to guide treatment decision making.

Object-based change detection method using refined Markov random field

NASA Astrophysics Data System (ADS)

Peng, Daifeng; Zhang, Yongjun

2017-01-01

In order to fully consider the local spatial constraints between neighboring objects in object-based change detection (OBCD), an OBCD approach is presented by introducing a refined Markov random field (MRF). First, two periods of images are stacked and segmented to produce image objects. Second, object spectral and textual histogram features are extracted and G-statistic is implemented to measure the distance among different histogram distributions. Meanwhile, object heterogeneity is calculated by combining spectral and textual histogram distance using adaptive weight. Third, an expectation-maximization algorithm is applied for determining the change category of each object and the initial change map is then generated. Finally, a refined change map is produced by employing the proposed refined object-based MRF method. Three experiments were conducted and compared with some state-of-the-art unsupervised OBCD methods to evaluate the effectiveness of the proposed method. Experimental results demonstrate that the proposed method obtains the highest accuracy among the methods used in this paper, which confirms its validness and effectiveness in OBCD.

Evidence from mathematical modeling that carbonic anhydrase II and IV enhance CO2 fluxes across Xenopus oocyte plasma membranes

PubMed Central

Musa-Aziz, Raif; Boron, Walter F.

2014-01-01

Exposing an oocyte to CO2/HCO3− causes intracellular pH (pHi) to decline and extracellular-surface pH (pHS) to rise to a peak and decay. The two companion papers showed that oocytes injected with cytosolic carbonic anhydrase II (CA II) or expressing surface CA IV exhibit increased maximal rate of pHi change (dpHi/dt)max, increased maximal pHS changes (ΔpHS), and decreased time constants for pHi decline and pHS decay. Here we investigate these results using refinements of an earlier mathematical model of CO2 influx into a spherical cell. Refinements include 1) reduced cytosolic water content, 2) reduced cytosolic diffusion constants, 3) refined CA II activity, 4) layer of intracellular vesicles, 5) reduced membrane CO2 permeability, 6) microvilli, 7) refined CA IV activity, 8) a vitelline membrane, and 9) a new simulation protocol for delivering and removing the bulk extracellular CO2/HCO3− solution. We show how these features affect the simulated pHi and pHS transients and use the refined model with the experimental data for 1.5% CO2/10 mM HCO3− (pHo = 7.5) to find parameter values that approximate ΔpHS, the time to peak pHS, the time delay to the start of the pHi change, (dpHi/dt)max, and the change in steady-state pHi. We validate the revised model against data collected as we vary levels of CO2/HCO3− or of extracellular HEPES buffer. The model confirms the hypothesis that CA II and CA IV enhance transmembrane CO2 fluxes by maximizing CO2 gradients across the plasma membrane, and it predicts that the pH effects of simultaneously implementing intracellular and extracellular-surface CA are supra-additive. PMID:24965589

Refining Housing, Husbandry and Care for Animals Used in Studies Involving Biotelemetry

PubMed Central

Hawkins, Penny

2014-01-01

Simple Summary Biotelemetry, the remote detection and measurement of an animal function or activity, is widely used in animal research. Biotelemetry devices transmit physiological or behavioural data and may be surgically implanted into animals, or externally attached. This can help to reduce animal numbers and improve welfare, e.g., if animals can be group housed and move freely instead of being tethered to a recording device. However, biotelemetry can also cause pain and distress to animals due to surgery, attachment, single housing and long term laboratory housing. This article explains how welfare and science can be improved by avoiding or minimising these harms. Abstract Biotelemetry can contribute towards reducing animal numbers and suffering in disciplines including physiology, pharmacology and behavioural research. However, the technique can also cause harm to animals, making biotelemetry a ‘refinement that needs refining’. Current welfare issues relating to the housing and husbandry of animals used in biotelemetry studies are single vs. group housing, provision of environmental enrichment, long term laboratory housing and use of telemetered data to help assess welfare. Animals may be singly housed because more than one device transmits on the same wavelength; due to concerns regarding damage to surgical sites; because they are wearing exteriorised jackets; or if monitoring systems can only record from individually housed animals. Much of this can be overcome by thoughtful experimental design and surgery refinements. Similarly, if biotelemetry studies preclude certain enrichment items, husbandry refinement protocols can be adapted to permit some environmental stimulation. Nevertheless, long-term laboratory housing raises welfare concerns and maximum durations should be defined. Telemetered data can be used to help assess welfare, helping to determine endpoints and refine future studies. The above measures will help to improve data quality as well as welfare, because experimental confounds due to physiological and psychological stress will be minimised. PMID:26480045

Erratum: Development, appraisal, validation and implementation of a consensus protocol for the assessment of cerebral amyloid angiopathy in post-mortem brain tissue.

PubMed

Love, Seth; Chalmers, Katy; Ince, Paul; Esiri, Margaret; Attems, Johannes; Kalaria, Raj; Jellinger, Kurt; Yamada, Masahito; McCarron, Mark; Minett, Thais; Matthews, Fiona; Greenberg, Steven; Mann, David; Kehoe, Patrick Gavin

2015-01-01

In a collaboration involving 11 groups with research interests in cerebral amyloid angiopathy (CAA), we used a two-stage process to develop and in turn validate a new consensus protocol and scoring scheme for the assessment of CAA and associated vasculopathic abnormalities in post-mortem brain tissue. Stage one used an iterative Delphi-style survey to develop the consensus protocol. The resultant scoring scheme was tested on a series of digital images and paraffin sections that were circulated blind to a number of scorers. The scoring scheme and choice of staining methods were refined by open-forum discussion. The agreed protocol scored parenchymal and meningeal CAA on a 0-3 scale, capillary CAA as present/absent and vasculopathy on 0-2 scale, in the 4 cortical lobes that were scored separately. A further assessment involving three centres was then undertaken. Neuropathologists in three centres (Bristol, Oxford and Sheffield) independently scored sections from 75 cases (25 from each centre) and high inter-rater reliability was demonstrated. Stage two used the results of the three-centre assessment to validate the protocol by investigating previously described associations between APOE genotype (previously determined), and both CAA and vasculopathy. Association of capillary CAA with or without arteriolar CAA with APOE ε4 was confirmed. However APOE ε2 was also found to be a strong risk factor for the development of CAA, not only in AD but also in elderly non-demented controls. Further validation of this protocol and scoring scheme is encouraged, to aid its wider adoption to facilitate collaborative and replication studies of CAA.[This corrects the article on p. 19 in vol. 3, PMID: 24754000.].

Development, appraisal, validation and implementation of a consensus protocol for the assessment of cerebral amyloid angiopathy in post-mortem brain tissue

PubMed Central

Love, Seth; Chalmers, Katy; Ince, Paul; Esiri, Margaret; Attems, Johannes; Kalaria, Raj; Jellinger, Kurt; Yamada, Masahito; McCarron, Mark; Minett, Thais; Matthews, Fiona; Greenberg, Steven; Mann, David; Kehoe, Patrick Gavin

2015-01-01

In a collaboration involving 11 groups with research interests in cerebral amyloid angiopathy (CAA), we used a two-stage process to develop and in turn validate a new consensus protocol and scoring scheme for the assessment of CAA and associated vasculopathic abnormalities in post-mortem brain tissue. Stage one used an iterative Delphi-style survey to develop the consensus protocol. The resultant scoring scheme was tested on a series of digital images and paraffin sections that were circulated blind to a number of scorers. The scoring scheme and choice of staining methods were refined by open-forum discussion. The agreed protocol scored parenchymal and meningeal CAA on a 0-3 scale, capillary CAA as present/absent and vasculopathy on 0-2 scale, in the 4 cortical lobes that were scored separately. A further assessment involving three centres was then undertaken. Neuropathologists in three centres (Bristol, Oxford and Sheffield) independently scored sections from 75 cases (25 from each centre) and high inter-rater reliability was demonstrated. Stage two used the results of the three-centre assessment to validate the protocol by investigating previously described associations between APOE genotype (previously determined), and both CAA and vasculopathy. Association of capillary CAA with or without arteriolar CAA with APOE ε4 was confirmed. However APOE ε2 was also found to be a strong risk factor for the development of CAA, not only in AD but also in elderly non-demented controls. Further validation of this protocol and scoring scheme is encouraged, to aid its wider adoption to facilitate collaborative and replication studies of CAA. PMID:26807344

Development, appraisal, validation and implementation of a consensus protocol for the assessment of cerebral amyloid angiopathy in post-mortem brain tissue

PubMed Central

Love, Seth; Chalmers, Katy; Ince, Paul; Esiri, Margaret; Attems, Johannes; Jellinger, Kurt; Yamada, Masahito; McCarron, Mark; Minett, Thais; Matthews, Fiona; Greenberg, Steven; Mann, David; Kehoe, Patrick Gavin

2014-01-01

In a collaboration involving 11 groups with research interests in cerebral amyloid angiopathy (CAA), we used a two-stage process to develop and in turn validate a new consensus protocol and scoring scheme for the assessment of CAA and associated vasculopathic abnormalities in post-mortem brain tissue. Stage one used an iterative Delphi-style survey to develop the consensus protocol. The resultant scoring scheme was tested on a series of digital images and paraffin sections that were circulated blind to a number of scorers. The scoring scheme and choice of staining methods were refined by open-forum discussion. The agreed protocol scored parenchymal and meningeal CAA on a 0-3 scale, capillary CAA as present/absent and vasculopathy on 0-2 scale, in the 4 cortical lobes that were scored separately. A further assessment involving three centres was then undertaken. Neuropathologists in three centres (Bristol, Oxford and Sheffield) independently scored sections from 75 cases (25 from each centre) and high inter-rater reliability was demonstrated. Stage two used the results of the three-centre assessment to validate the protocol by investigating previously described associations between APOE genotype (previously determined), and both CAA and vasculopathy. Association of capillary CAA with or without arteriolar CAA with APOE ε4 was confirmed. However APOE ε2 was also found to be a strong risk factor for the development of CAA, not only in AD but also in elderly non-demented controls. Further validation of this protocol and scoring scheme is encouraged, to aid its wider adoption to facilitate collaborative and replication studies of CAA. PMID:24754000

Improving cardiac operating room to intensive care unit handover using a standardised handover process.

PubMed

Gleicher, Yehoshua; Mosko, Jeffrey David; McGhee, Irene

2017-01-01

Handovers from the cardiovascular operating room (CVOR) to the cardiovascular intensive care unit (CVICU) are complex processes involving the transfer of information, equipment and responsibility, at a time when the patient is most vulnerable. This transfer is typically variable in structure, content and execution. This variability can lead to the omission and miscommunication of critical information leading to patient harm. We set out to improve the quality of patient handover from the CVOR to the CVICU by introducing a standardised handover protocol. This study is an interventional time-series study over a 4-month period at an adult cardiac surgery centre. A standardised handover protocol was developed using quality improvement methodologies. The protocol included a handover content checklist and introduction of a formal 'sterile cockpit' timeout. Implementation of the protocol was refined using monthly iterative Plan-Do-Study-Act. The primary outcome was the quality of handovers, measured by a Handover Score, comprising handover content, teamwork and patient care planning indicators. Secondary outcomes included handover duration, adherence to the standardised handover protocol and handover team satisfaction surveys. 37 handovers were observed (6 pre intervention and 31 post intervention). The mean handover score increased from 6.5 to 14.0 (maximum 18 points). Specific improvements included fewer handover interruptions and more frequent postoperative patient care planning. Average handover duration increased slightly from 2:40 to 2:57 min. Caregivers noted improvements in teamwork, content received and patient care planning. The majority (>95%) agreed that the intervention was a valuable addition to the CVOR to CVICU handover process. Implementation of a standardised handover protocol for postcardiac surgery patients was associated with fewer interruptions during handover, more reliable transfer of critical content and improved patient care planning.

Estimating changes in urban land and urban population using refined areal interpolation techniques

NASA Astrophysics Data System (ADS)

Zoraghein, Hamidreza; Leyk, Stefan

2018-05-01

The analysis of changes in urban land and population is important because the majority of future population growth will take place in urban areas. U.S. Census historically classifies urban land using population density and various land-use criteria. This study analyzes the reliability of census-defined urban lands for delineating the spatial distribution of urban population and estimating its changes over time. To overcome the problem of incompatible enumeration units between censuses, regular areal interpolation methods including Areal Weighting (AW) and Target Density Weighting (TDW), with and without spatial refinement, are implemented. The goal in this study is to estimate urban population in Massachusetts in 1990 and 2000 (source zones), within tract boundaries of the 2010 census (target zones), respectively, to create a consistent time series of comparable urban population estimates from 1990 to 2010. Spatial refinement is done using ancillary variables such as census-defined urban areas, the National Land Cover Database (NLCD) and the Global Human Settlement Layer (GHSL) as well as different combinations of them. The study results suggest that census-defined urban areas alone are not necessarily the most meaningful delineation of urban land. Instead, it appears that alternative combinations of the above-mentioned ancillary variables can better depict the spatial distribution of urban land, and thus make it possible to reduce the estimation error in transferring the urban population from source zones to target zones when running spatially-refined temporal areal interpolation.

Changing Urbania: Estimating Changes in Urban Land and Urban Population Using Refined Areal Interpolation Techniques

NASA Astrophysics Data System (ADS)

Zoraghein, H.; Leyk, S.; Balk, D.

2017-12-01

The analysis of changes in urban land and population is important because the majority of future population growth will take place in urban areas. The U.S. Census historically classifies urban land using population density and various land-use criteria. This study analyzes the reliability of census-defined urban lands for delineating the spatial distribution of urban population and estimating its changes over time. To overcome the problem of incompatible enumeration units between censuses, regular areal interpolation methods including Areal Weighting (AW) and Target Density Weighting (TDW), with and without spatial refinement, are implemented. The goal in this study is to estimate urban population in Massachusetts in 1990 and 2000 (source zones), within tract boundaries of the 2010 census (target zones), respectively, to create a consistent time series of comparable urban population estimates from 1990 to 2010. Spatial refinement is done using ancillary variables such as census-defined urban areas, the National Land Cover Database (NLCD) and the Global Human Settlement Layer (GHSL) as well as different combinations of them. The study results suggest that census-defined urban areas alone are not necessarily the most meaningful delineation of urban land. Instead it appears that alternative combinations of the above-mentioned ancillary variables can better depict the spatial distribution of urban land, and thus make it possible to reduce the estimation error in transferring the urban population from source zones to target zones when running spatially-refined temporal areal interpolation.

Adaptive Probabilistic Protocols for Advanced Networks/Assuring the Integrity of Highly Decentralized Communications Systems

DTIC Science & Technology

2005-03-01

to obtain a protocol customized to the needs of a specific setting, under control of an automated theorem proving system that can guarantee...new “compositional” method for protocol design and implementation, in which small microprotocols are combined to obtain a protocol customized to the...and Network Centric Enterprise (NCES) visions. This final report documents a wide range of contributions and technology transitions, including: A

Communication-Gateway Software For NETEX, DECnet, And TCP/IP

NASA Technical Reports Server (NTRS)

Keith, B.; Ferry, D.; Fendler, E.

1990-01-01

Communications gateway software, GATEWAY, provides process-to-process communication between remote applications programs in different protocol domains. Communicating peer processes may be resident on any paired combination of NETEX, DECnet, or TCP/IP hosts. Provides necessary mapping from one protocol to another and facilitates practical intermachine communications in cost-effective manner by eliminating need to standardize on single protocol or to implement multiple protocols in host computers. Written in Ada.

Quantum cryptography: individual eavesdropping with the knowledge of the error-correcting protocol

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

Horoshko, D B

2007-12-31

The quantum key distribution protocol BB84 combined with the repetition protocol for error correction is analysed from the point of view of its security against individual eavesdropping relying on quantum memory. It is shown that the mere knowledge of the error-correcting protocol changes the optimal attack and provides the eavesdropper with additional information on the distributed key. (fifth seminar in memory of d.n. klyshko)

Optimisation of pharmacy content in clinical cancer research protocols: Experience of the United Kingdom Chemotherapy and Pharmacy Advisory Service.

PubMed

Debruyne, Philip R; Johnson, Philip J; Pottel, Lies; Daniels, Susanna; Greer, Rachel; Hodgkinson, Elizabeth; Kelly, Stephen; Lycke, Michelle; Samol, Jens; Mason, Julie; Kimber, Donna; Loucaides, Eileen; Parmar, Mahesh Kb; Harvey, Sally

2015-06-01

Clarity and accuracy of the pharmacy aspects of cancer clinical trial protocols is essential. Inconsistencies and ambiguities in such protocols have the potential to delay research and jeopardise both patient safety and collection of credible data. The Chemotherapy and Pharmacy Advisory Service was established by the UK National Cancer Research Network, currently known as National Institute for Health Research Clinical Research Network, to improve the quality of pharmacy-related content in cancer clinical research protocols. This article reports the scope of Chemotherapy and Pharmacy Advisory Service, its methodology of mandated protocol review and pharmacy-related guidance initiatives and its current impact. Over a 6-year period (2008-2013) since the inception of Chemotherapy and Pharmacy Advisory Service, cancer clinical trial protocols were reviewed by the service, prior to implementation at clinical trial sites. A customised Review Checklist was developed and used by a panel of experts to standardise the review process and report back queries and inconsistencies to chief investigators. Based on common queries, a Standard Protocol Template comprising specific guidance on drug-related content and a Pharmacy Manual Template were developed. In addition, a guidance framework was established to address 'ad hoc' pharmacy-related queries. The most common remarks made at protocol review have been summarised and categorised through retrospective analysis. In order to evaluate the impact of the service, chief investigators were asked to respond to queries made at protocol review and make appropriate changes to their protocols. Responses from chief investigators have been collated and acceptance rates determined. A total of 176 protocols were reviewed. The median number of remarks per protocol was 26, of which 20 were deemed clinically relevant and mainly concerned the drug regimen, support medication, frequency and type of monitoring and drug supply aspects. Further analysis revealed that 62% of chief investigators responded to the review. All responses were positive with an overall acceptance rate of 89% of the proposed protocol changes. Review of pharmacy content of cancer clinical trial protocols is feasible and exposes many undetected clinically relevant issues that could hinder efficient trial conduct. Our service audit revealed that the majority of suggestions were effectively incorporated in the final protocols. The refinement of existing and development of new pharmacy-related guidance documents by Chemotherapy and Pharmacy Advisory Service might aid in better and safer clinical research. © The Author(s) 2015.

Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking.

PubMed

Sasse, Alexander; de Vries, Sjoerd J; Schindler, Christina E M; de Beauchêne, Isaure Chauvot; Zacharias, Martin

2017-01-01

Protein-protein docking protocols aim to predict the structures of protein-protein complexes based on the structure of individual partners. Docking protocols usually include several steps of sampling, clustering, refinement and re-scoring. The scoring step is one of the bottlenecks in the performance of many state-of-the-art protocols. The performance of scoring functions depends on the quality of the generated structures and its coupling to the sampling algorithm. A tool kit, GRADSCOPT (GRid Accelerated Directly SCoring OPTimizing), was designed to allow rapid development and optimization of different knowledge-based scoring potentials for specific objectives in protein-protein docking. Different atomistic and coarse-grained potentials can be created by a grid-accelerated directly scoring dependent Monte-Carlo annealing or by a linear regression optimization. We demonstrate that the scoring functions generated by our approach are similar to or even outperform state-of-the-art scoring functions for predicting near-native solutions. Of additional importance, we find that potentials specifically trained to identify the native bound complex perform rather poorly on identifying acceptable or medium quality (near-native) solutions. In contrast, atomistic long-range contact potentials can increase the average fraction of near-native poses by up to a factor 2.5 in the best scored 1% decoys (compared to existing scoring), emphasizing the need of specific docking potentials for different steps in the docking protocol.

Introducing Clicker Training as a Cognitive Enrichment for Laboratory Mice.

PubMed

Leidinger, Charlotte; Herrmann, Felix; Thöne-Reineke, Christa; Baumgart, Nadine; Baumgart, Jan

2017-03-06

Establishing new refinement strategies in laboratory animal science is a central goal in fulfilling the requirements of Directive 2010/63/EU. Previous research determined a profound impact of gentle handling protocols on the well-being of laboratory mice. By introducing clicker training to the keeping of mice, not only do we promote the amicable treatment of mice, but we also enable them to experience cognitive enrichment. Clicker training is a form of positive reinforcement training using a conditioned secondary reinforcer, the "click" sound of a clicker, which serves as a time bridge between the strengthened behavior and an upcoming reward. The effective implementation of the clicker training protocol with a cohort of 12 BALB/c inbred mice of each sex proved to be uncomplicated. The mice learned rather quickly when challenged with tasks of the clicker training protocol, and almost all trained mice overcame the challenges they were given (100% of female mice and 83% of male mice). This study has identified that clicker training for mice strongly correlates with reduced fear in the mice during human-mice interactions, as shown by reduced anxiety-related behaviors (e.g., defecation, vocalization, and urination) and fewer depression-like behaviors (e.g., floating). By developing a reliable protocol that can be easily integrated into the daily routine of the keeping of laboratory mice, the lifetime experience of welfare in the mice can be improved substantially.

Clinically applied procedures for human ovarian tissue cryopreservation result in different levels of efficacy and efficiency.

PubMed

Bastings, Lobke; Westphal, Johan R; Beerendonk, Catharina C M; Bekkers, Ruud L M; Zusterzeel, Petra L M; Hendriks, Jan C M; Braat, Didi D M; Peek, Ronald

2016-12-01

Different protocols are being used worldwide for the cryopreservation of human ovarian tissue for fertility preservation purposes. The efficiency and efficacy of the majority of these protocols has not been extensively evaluated, possibly resulting in sub-optimally cryopreserved ovarian tissue. To address the impact of this issue, we assessed the effects of two clinically successful human ovarian tissue slow-freezing cryopreservation procedures on the quality of the cryopreserved tissue. To differentiate between cryopreservation ( C ) versus thawing ( T ) related effects, four combinations of these two (A and B) very different cryopreservation/thawing protocols (A C A T , A C B T , B C A T , B C B T ) were studied. Before and after cryopreservation and thawing, the percentage of living and morphologically normal follicles, as well as the overall tissue viability, was assessed. Our experiments revealed that the choice of the cryopreservation protocol noticeably affected the overall tissue viability and percentage of living follicles, with a higher viability after protocol B C when compared to A C . No statistically significant differences in tissue viability were observed between the two thawing protocols, but thawing protocol B T required considerably more human effort and materials than thawing protocol A T . Tissue morphology was best retained using the B C A T combination. Our results indicate that extensive and systematical evaluation of clinically used protocols is warranted.

Assessing Juvenile Salmonid Passage Through Culverts: Field Research in Support of Protocol Development

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

Williams, Greg D.; Evans, Nathan R.; Pearson, Walter H.

2001-10-30

The primary goal of our research this spring/ summer was to refine techniques and examine scenarios under which a standardized protocol could be applied to assess juvenile coho salmon (O. kisutch) passage through road culverts. Field evaluations focused on capture-mark- recapture methods that allowed analysis of fish movement patterns, estimates of culvert passability, and potential identification of cues inducing these movements. At this stage, 0+ age coho salmon fry 30 mm to 65 mm long (fork length) were the species and age class of interest. Ultimately, the protocol will provide rapid, statistically rigorous methods for trained personnel to perform standardizedmore » biological assessments of culvert passability to a number of juvenile salmon species. Questions to be addressed by the research include the following: ? Do hydraulic structures such as culverts restrict habitat for juvenile salmonids? ? How do existing culverts and retrofits perform relative to juvenile salmonid passage? ? Do some culvert characteristics and hydraulic conditions provide better passage than others? ? Does the culvert represent a barrier to certain size classes of fish? Recommendations addressed issues of study site selection, initial capture, marking, recapture/observations, and estimating movement.« less

Behavioral Screening for Toxicology | Science Inventory | US ...

EPA Pesticide Factsheets

Screening for behavioral toxicity, or neurotoxicity, has been in use for decades; however, only in the past 20 years has this become a standard practice in toxicology. Current screening batteries, such as the functional observational battery (FOB), are derived from protocols used in pharmacology, toxicology, and psychology. Although there is a range of protocols in use today, all focus on detailed observations and specific tests of reflexes and responses. Several neurological functions are typically assessed, including autonomic, neuromuscular, and sensory, as well as levels of activity and excitability. The tests have been shown to be valid in detecting expected effects of known neurotoxicants, and reliable and reproducible whn compared across laboratories. Regardless of the specific protocol used, proper conduct and statistical analyses of the data are critical. Interpretation is based on the information from individual end points as well as the profile, or pattern, of effects observed. As long as continual refinements are made, behavioral screening methods will continue to be important tools with which to protect human health in the future.autonomic function; behavior; behavioral phenotypes; behavioral toxicity; excitability; functional observational battery ; motor activity; mouse; neuromuscular function; positive controls; rat; screening battery ; sensory function Screening for behavioral toxicity, or neurotoxicity, has been in use for decades; how

High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB_REDO strategies.

PubMed

Rimsa, Vadim; Eadsforth, Thomas C; Joosten, Robbie P; Hunter, William N

2014-02-01

A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high-throughput automated protocols embedded in PDB_REDO were coupled with model-map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N-terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. The C-terminal domain, which carries the Zn2+-containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide-bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn2+, where an acetate ion is identified, suggests recognition of the carboxy-terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1' recognition subsite that suggests specificity towards an acidic substrate.

Template-based protein-protein docking exploiting pairwise interfacial residue restraints.

PubMed

Xue, Li C; Rodrigues, João P G L M; Dobbs, Drena; Honavar, Vasant; Bonvin, Alexandre M J J

2017-05-01

Although many advanced and sophisticated ab initio approaches for modeling protein-protein complexes have been proposed in past decades, template-based modeling (TBM) remains the most accurate and widely used approach, given a reliable template is available. However, there are many different ways to exploit template information in the modeling process. Here, we systematically evaluate and benchmark a TBM method that uses conserved interfacial residue pairs as docking distance restraints [referred to as alpha carbon-alpha carbon (CA-CA)-guided docking]. We compare it with two other template-based protein-protein modeling approaches, including a conserved non-pairwise interfacial residue restrained docking approach [referred to as the ambiguous interaction restraint (AIR)-guided docking] and a simple superposition-based modeling approach. Our results show that, for most cases, the CA-CA-guided docking method outperforms both superposition with refinement and the AIR-guided docking method. We emphasize the superiority of the CA-CA-guided docking on cases with medium to large conformational changes, and interactions mediated through loops, tails or disordered regions. Our results also underscore the importance of a proper refinement of superimposition models to reduce steric clashes. In summary, we provide a benchmarked TBM protocol that uses conserved pairwise interface distance as restraints in generating realistic 3D protein-protein interaction models, when reliable templates are available. The described CA-CA-guided docking protocol is based on the HADDOCK platform, which allows users to incorporate additional prior knowledge of the target system to further improve the quality of the resulting models. © The Author 2016. Published by Oxford University Press.

Evaluation of an Alcohol Withdrawal Protocol and a Preprinted Order Set at a Tertiary Care Hospital

PubMed Central

Ng, Karen; Dahri, Karen; Chow, Ivy; Legal, Michael

2011-01-01

Background: Alcohol withdrawal protocols involving symptom-triggered administration of benzodiazepine have been established to reduce the duration of treatment and the cumulative benzodiazepine dose (relative to usual care). However, the effects of a protocol combining fixed-schedule and symptom-triggered benzodiazepine dosing are less clear. Objective: To assess the efficacy and safety of a combination fixed-scheduled and symptom-triggered benzodiazepine dosing protocol for alcohol withdrawal, relative to usual care, for medical inpatients at a tertiary care hospital. Methods: A chart review of admissions to the internal medicine service for alcohol withdrawal was conducted to compare treatment outcomes before (October 2005 to April 2007) and after (October 2007 to April 2009) implementation of the combination protocol. The primary outcome was duration of benzodiazepine treatment for alcohol withdrawal. The secondary outcomes were cumulative benzodiazepine dose administered, safety implications, and use of adjunctive medications. Results: A total of 159 patients met the inclusion criteria. Assessable data were available for 71 charts from the pre-implementation period and 72 charts from the post-implementation period. The median duration of benzodiazepine treatment was 91 h before implementation and 57 h after implementation (p < 0.001). Use of the protocol was also associated with a significant reduction in severe complications of alcohol withdrawal (50% versus 33%, p = 0.019), median cumulative benzodiazepine dose (in lorazepam equivalents) (20.0 mg versus 15.5 mg, p = 0.026), and use of adjunctive medications (65% versus 38%, p = 0.001). The incidence of serious adverse outcomes of treatment with benzodiazepines was not significantly different between the 2 groups. Conclusions: Implementation of an alcohol withdrawal protocol with a combination of fixed-schedule and symptom-triggered benzodiazepine dosing in a medical ward was associated with a shorter duration of benzodiazepine use and a lower incidence of severe complications of alcohol withdrawal. PMID:22479099

Protocols | Office of Cancer Clinical Proteomics Research

Cancer.gov

Each reagent on the Antibody Portal has been characterized by a combination of methods specific for that antibody. To view the customized antibody methods and protocols (Standard Operating Procedures) used to generate and characterize each reagent, select an antibody of interest and open the protocols associated with their respective characterization methods along with characterization data.

A multigear protocol for sampling crayfish assemblages in Gulf of Mexico coastal streams

Treesearch

William R. Budnick; William E. Kelso; Susan B. Adams; Michael D. Kaller

2018-01-01

Identifying an effective protocol for sampling crayfish in streams that vary in habitat and physical/chemical characteristics has proven problematic. We evaluated an active, combined-gear (backpack electrofishing and dipnetting) sampling protocol in 20 Coastal Plain streams in Louisiana. Using generalized linear models and rarefaction curves, we evaluated environmental...

Enhanced Representation of Turbulent Flow Phenomena in Large-Eddy Simulations of the Atmospheric Boundary Layer using Grid Refinement with Pseudo-Spectral Numerics

NASA Astrophysics Data System (ADS)

Torkelson, G. Q.; Stoll, R., II

2017-12-01

Large Eddy Simulation (LES) is a tool commonly used to study the turbulent transport of momentum, heat, and moisture in the Atmospheric Boundary Layer (ABL). For a wide range of ABL LES applications, representing the full range of turbulent length scales in the flow field is a challenge. This is an acute problem in regions of the ABL with strong velocity or scalar gradients, which are typically poorly resolved by standard computational grids (e.g., near the ground surface, in the entrainment zone). Most efforts to address this problem have focused on advanced sub-grid scale (SGS) turbulence model development, or on the use of massive computational resources. While some work exists using embedded meshes, very little has been done on the use of grid refinement. Here, we explore the benefits of grid refinement in a pseudo-spectral LES numerical code. The code utilizes both uniform refinement of the grid in horizontal directions, and stretching of the grid in the vertical direction. Combining the two techniques allows us to refine areas of the flow while maintaining an acceptable grid aspect ratio. In tests that used only refinement of the vertical grid spacing, large grid aspect ratios were found to cause a significant unphysical spike in the stream-wise velocity variance near the ground surface. This was especially problematic in simulations of stably-stratified ABL flows. The use of advanced SGS models was not sufficient to alleviate this issue. The new refinement technique is evaluated using a series of idealized simulation test cases of neutrally and stably stratified ABLs. These test cases illustrate the ability of grid refinement to increase computational efficiency without loss in the representation of statistical features of the flow field.

A Variable Resolution Atmospheric General Circulation Model for a Megasite at the North Slope of Alaska

NASA Astrophysics Data System (ADS)

Dennis, L.; Roesler, E. L.; Guba, O.; Hillman, B. R.; McChesney, M.

2016-12-01

The Atmospheric Radiation Measurement (ARM) climate research facility has three siteslocated on the North Slope of Alaska (NSA): Barrrow, Oliktok, and Atqasuk. These sites, incombination with one other at Toolik Lake, have the potential to become a "megasite" whichwould combine observational data and high resolution modeling to produce high resolutiondata products for the climate community. Such a data product requires high resolutionmodeling over the area of the megasite. We present three variable resolution atmosphericgeneral circulation model (AGCM) configurations as potential alternatives to stand-alonehigh-resolution regional models. Each configuration is based on a global cubed-sphere gridwith effective resolution of 1 degree, with a refinement in resolution down to 1/8 degree overan area surrounding the ARM megasite. The three grids vary in the size of the refined areawith 13k, 9k, and 7k elements. SquadGen, NCL, and GIMP are used to create the grids.Grids vary based upon the selection of areas of refinement which capture climate andweather processes that may affect a proposed NSA megasite. A smaller area of highresolution may not fully resolve climate and weather processes before they reach the NSA,however grids with smaller areas of refinement have a significantly reduced computationalcost compared with grids with larger areas of refinement. Optimal size and shape of thearea of refinement for a variable resolution model at the NSA is investigated.

New Insights on Degumming and Bleaching Process Parameters on The Formation of 3-Monochloropropane-1,2-Diol Esters and Glycidyl Esters in Refined, Bleached, Deodorized Palm Oil.

PubMed

Sim, Biow Ing; Muhamad, Halimah; Lai, Oi Ming; Abas, Faridah; Yeoh, Chee Beng; Nehdi, Imededdine Arbi; Khor, Yih Phing; Tan, Chin Ping

2018-04-01

This paper examines the interactions of degumming and bleaching processes as well as their influences on the formation of 3-monochloropropane-1,2-diol esters (3-MCPDE) and glycidyl esters in refined, bleached and deodorized palm oil by using D-optimal design. Water degumming effectively reduced the 3-MCPDE content up to 50%. Acid activated bleaching earth had a greater effect on 3-MCPDE reduction compared to natural bleaching earth and acid activated bleaching earth with neutral pH, indicating that performance and adsorption capacities of bleaching earth are the predominant factors in the removal of esters, rather than its acidity profile. The combination of high dosage phosphoric acid during degumming with the use of acid activated bleaching earth eliminated almost all glycidyl esters during refining. Besides, the effects of crude palm oil quality was assessed and it was found that the quality of crude palm oil determines the level of formation of 3-MCPDE and glycidyl esters in palm oil during the high temperature deodorization step of physical refining process. Poor quality crude palm oil has strong impact towards 3-MCPDE and glycidyl esters formation due to the intrinsic components present within. The findings are useful to palm oil refining industry in choosing raw materials as an input during the refining process.

AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics.

PubMed

Labbé, Céline M; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O; Pajeva, Ilza; Miteva, Maria A

2017-07-03

AMMOS2 is an interactive web server for efficient computational refinement of protein-small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein-ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein-ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein-ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein-ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein-ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein-ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

AMMOS2: a web server for protein–ligand–water complexes refinement via molecular mechanics

PubMed Central

Labbé, Céline M.; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O.; Pajeva, Ilza

2017-01-01

Abstract AMMOS2 is an interactive web server for efficient computational refinement of protein–small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein–ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein–ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein–ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein–ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein–ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein–ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php. PMID:28486703

Transcranial magnetic stimulation with acepromazine or dexmedetomidine in combination with levomethadone/fenpipramide in healthy Beagle dogs.

PubMed

Amendt, H-L; Siedenburg, J S; Steffensen, N; Söbbeler, F J; Schütter, A; Tünsmeyer, J; Rohn, K; Kästner, S B R; Tipold, A; Stein, V M

2016-11-01

The aim of this study was to evaluate the influence of two sedation protocols on transcranial magnetic motor evoked potentials (TMMEPs) after transcranial magnetic stimulation in medium sized dogs. Onset latencies and peak-to-peak amplitudes, elicited in the extensor carpi radialis and cranial tibial muscles, were analysed in 10 healthy Beagles that received either acepromazine or dexmedetomidine in combination with levomethadone/fenpipramide, in a crossover design. Similar TMMEP recordings could be made using both sedation protocols at 80-90% stimulation intensity; however, there were significantly shorter onset latencies with the acepromazine-levomethadone/fenpipramide protocol at 100% stimulation intensity. Reference values were established and it was concluded that both drug combinations are feasible for measuring TMMEPs in medium sized dogs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Secure multi-party communication with quantum key distribution managed by trusted authority

DOEpatents

Nordholt, Jane Elizabeth; Hughes, Richard John; Peterson, Charles Glen

2013-07-09

Techniques and tools for implementing protocols for secure multi-party communication after quantum key distribution ("QKD") are described herein. In example implementations, a trusted authority facilitates secure communication between multiple user devices. The trusted authority distributes different quantum keys by QKD under trust relationships with different users. The trusted authority determines combination keys using the quantum keys and makes the combination keys available for distribution (e.g., for non-secret distribution over a public channel). The combination keys facilitate secure communication between two user devices even in the absence of QKD between the two user devices. With the protocols, benefits of QKD are extended to multi-party communication scenarios. In addition, the protocols can retain benefit of QKD even when a trusted authority is offline or a large group seeks to establish secure communication within the group.

Secure multi-party communication with quantum key distribution managed by trusted authority

DOEpatents

Hughes, Richard John; Nordholt, Jane Elizabeth; Peterson, Charles Glen

2015-01-06

Techniques and tools for implementing protocols for secure multi-party communication after quantum key distribution ("QKD") are described herein. In example implementations, a trusted authority facilitates secure communication between multiple user devices. The trusted authority distributes different quantum keys by QKD under trust relationships with different users. The trusted authority determines combination keys using the quantum keys and makes the combination keys available for distribution (e.g., for non-secret distribution over a public channel). The combination keys facilitate secure communication between two user devices even in the absence of QKD between the two user devices. With the protocols, benefits of QKD are extended to multi-party communication scenarios. In addition, the protocols can retain benefit of QKD even when a trusted authority is offline or a large group seeks to establish secure communication within the group.

TREATMENT OF PULMONICOLA COCHLEOTREMA INFECTION WITH IVERMECTIN-PRAZIQUANTEL COMBINATION IN AN ANTILLEAN MANATEE (TRICHECHUS MANATUS MANATUS).

PubMed

Borges, João Carlos Gomes; Jung, Larissa Molinari; Santos, Sebastião Silva Dos; Carvalho, Vitor Luz; Ramos, Rafael Antonio Nascimento; Alves, Leucio Câmara

2017-03-01

The aim of this study was to report the use of an oral combination of ivermectin plus praziquantel in the treatment of a Pulmonicola cochleotrema in an Antillean manatee ( Trichechus manatus manatus). A female manatee was found exhibiting respiratory changes and the presence of parasites in the nares. Based on clinical manifestations presented by the manatee, a symptomatic therapeutic protocol was employed, which included an anthelmintic treatment using a combination of ivermectin plus praziquantel. The parasites retrieved were identified as P. cochleotrema. The fourth day after the onset of the therapeutic protocol, the clinical signs declined and on the seventh day posttreatment no clinical signs were observed. This is the first time a therapeutic protocol of ivermectin plus praziquantel has been used in the treatment of P. cochleotrema in manatees.

[Immunocytochemical demonstration of astrocytes in brain sections combined with Nissl staining].

PubMed

Korzhevskiĭ, D E; Otellin, V A

2004-01-01

The aim of the present study was to develop an easy and reliable protocol of combined preparation staining, which would unite the advantages of immunocytochemical demonstration of astrocytes with the availability to evaluate functional state of neurons provided by Nissl technique. The presented protocol of paraffin sections processing allows to retain high quality of tissue structure and provides for selective demonstration of astrocytes using the monoclonal antibodies against glial fibrillary acidic protein and contrast Nissl staining of cells. The protocol can be used without any changes for processing of brain sections obtained from the humans and other mammals with the exception of mice and rabbits.

What is a clinical pathway? Refinement of an operational definition to identify clinical pathway studies for a Cochrane systematic review.

PubMed

Lawal, Adegboyega K; Rotter, Thomas; Kinsman, Leigh; Machotta, Andreas; Ronellenfitsch, Ulrich; Scott, Shannon D; Goodridge, Donna; Plishka, Christopher; Groot, Gary

2016-02-23

Clinical pathways (CPWs) are a common component in the quest to improve the quality of health. CPWs are used to reduce variation, improve quality of care, and maximize the outcomes for specific groups of patients. An ongoing challenge is the operationalization of a definition of CPW in healthcare. This may be attributable to both the differences in definition and a lack of conceptualization in the field of clinical pathways. This correspondence article describes a process of refinement of an operational definition for CPW research and proposes an operational definition for the future syntheses of CPWs literature. Following the approach proposed by Kinsman et al. (BMC Medicine 8(1):31, 2010) and Wieland et al. (Alternative Therapies in Health and Medicine 17(2):50, 2011), we used a four-stage process to generate a five criteria checklist for the definition of CPWs. We refined the operational definition, through consensus, merging two of the checklist's criteria, leading to a more inclusive criterion for accommodating CPW studies conducted in various healthcare settings. The following four criteria for CPW operational definition, derived from the refinement process described above, are (1) the intervention was a structured multidisciplinary plan of care; (2) the intervention was used to translate guidelines or evidence into local structures; (3) the intervention detailed the steps in a course of treatment or care in a plan, pathway, algorithm, guideline, protocol or other 'inventory of actions' (i.e. the intervention had time-frames or criteria-based progression); and (4) the intervention aimed to standardize care for a specific population. An intervention meeting all four criteria was considered to be a CPW. The development of operational definitions for complex interventions is a useful approach to appraise and synthesize evidence for policy development and quality improvement.

Solution NMR Refinement of a Metal Ion Bound Protein Using Metal Ion Inclusive Restrained Molecular Dynamics Methods

PubMed Central

Chakravorty, Dhruva K.; Wang, Bing; Lee, Chul Won; Guerra, Alfredo J.; Giedroc, David P.; Merz, Kenneth M.

2013-01-01

Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine the zinc coordination complex structure of the zinc sensing transcriptional repressor protein Staphylococcus aureus CzrA, generating over 130 ns of MD and QM/MM MD NMR-data compliant sampling. In addition to refining the first coordination shell structure of the Zn(II) ion, this protocol benefits from being performed in a periodically replicated solvation environment including long-range electrostatics. We determine that unrestrained (not based on NMR data) MD simulations correlated to the NMR data in a time-averaged ensemble. The accurate solution structure ensemble of the metal-bound protein accurately describes the role of conformational dynamics in allosteric regulation of DNA binding by zinc and serves to validate our previous unrestrained MD simulations of CzrA. This methodology has potentially broad applicability in the structure determination of metal ion bound proteins, protein folding and metal template protein-design studies. PMID:23609042

Crystal structure of human tooth enamel studied by neutron diffraction

NASA Astrophysics Data System (ADS)

Ouladdiaf, Bachir; Rodriguez-Carvajal, Juan; Goutaudier, Christelle; Ouladdiaf, Selma; Grosgogeat, Brigitte; Pradelle, Nelly; Colon, Pierre

2015-02-01

Crystal structure of human tooth enamel was investigated using high-resolution neutron powder diffraction. Excellent agreement between observed and refined patterns is obtained, using the hexagonal hydroxyapatite model for the tooth enamel, where a large hydroxyl deficiency ˜70% is found in the 4e site. Rietveld refinements method combined with the difference Fourier maps have revealed, however, that the hydroxyl ions are not only disordered along the c-axis but also within the basal plane. Additional H ions located at the 6h site and forming HPO42- anions were found.

Leveraging the trusted clinician: documenting disease management program enrollment.

PubMed

Frazee, Sharon Glave; Kirkpatrick, Patricia; Fabius, Raymond; Chimera, Joseph

2007-02-01

The objective of this study was to test the hypothesis that an integrated disease management (IDM) protocol (patent-pending), which combines telephonic-delivered disease management (TDM) with a worksite-based primary care center and pharmacy delivery, would yield higher contact and enrollment rates than traditional remote disease management alone. IDM is characterized by the combination of standard TDM with a worksite-based primary care and pharmacy delivery protocol led by trusted clinicians. This prospective cohort study tracks contact and enrollment rates for persons assigned to either IDM or traditional TDM protocols, and compares them on contact and enrollment efficiency. The IDM protocol showed a significant improvement in contact and enrollment rates over traditional TDM. Integrating a worksite-based primary care and pharmacy delivery system led by trusted clinicians with traditional TDM increases contact and enrollment rates, resulting in higher patient engagement. The IDM protocol should be adopted by employers seeking higher returns on their investment in disease management programming.

Modified CTAB and TRIzol protocols improve RNA extraction from chemically complex Embryophyta1

PubMed Central

Jordon-Thaden, Ingrid E.; Chanderbali, Andre S.; Gitzendanner, Matthew A.; Soltis, Douglas E.

2015-01-01

Premise of the study: Here we present a series of protocols for RNA extraction across a diverse array of plants; we focus on woody, aromatic, aquatic, and other chemically complex taxa. Methods and Results: Ninety-one taxa were subjected to RNA extraction with three methods presented here: (1) TRIzol/TURBO DNA-free kits using the manufacturer’s protocol with the addition of sarkosyl; (2) a combination method using cetyltrimethylammonium bromide (CTAB) and TRIzol/sarkosyl/TURBO DNA-free; and (3) a combination of CTAB and QIAGEN RNeasy Plant Mini Kit. Bench-ready protocols are given. Conclusions: After an iterative process of working with chemically complex taxa, we conclude that the use of TRIzol supplemented with sarkosyl and the TURBO DNA-free kit is an effective, efficient, and robust method for obtaining RNA from 100 mg of leaf tissue of land plant species (Embryophyta) examined. Our protocols can be used to provide RNA of suitable stability, quantity, and quality for transcriptome sequencing. PMID:25995975

Combination Chemotherapy and Donor Stem Cell Transplant in Treating Patients With Aplastic Anemia or Hematologic Cancer

ClinicalTrials.gov

2018-01-30

Chronic Myeloproliferative Disorders; Leukemia; Lymphoma; Myelodysplastic Syndromes; Myelodysplastic/Myeloproliferative Diseases; Nonmalignant Neoplasm; Unspecified Adult Solid Tumor, Protocol Specific; Unspecified Childhood Solid Tumor, Protocol Specific

SU-E-J-101: Improved CT to CBCT Deformable Registration Accuracy by Incorporating Multiple CBCTs

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

Godley, A; Stephans, K; Olsen, L Sheplan

2015-06-15

Purpose: Combining prior day CBCT contours with STAPLE was previously shown to improve automated prostate contouring. These accurate STAPLE contours are now used to guide the planning CT to pre-treatment CBCT deformable registration. Methods: Six IGRT prostate patients with daily kilovoltage CBCT had their original planning CT and 9 CBCTs contoured by the same physician. These physician contours for the planning CT and each prior CBCT are deformed to match the current CBCT anatomy, producing multiple contour sets. These sets are then combined using STAPLE into one optimal set (e.g. for day 3 CBCT, combine contours produced using the planmore » plus day 1 and 2 CBCTs). STAPLE computes a probabilistic estimate of the true contour from this collection of contours by maximizing sensitivity and specificity. The deformation field from planning CT to CBCT registration is then refined by matching its deformed contours to the STAPLE contours. ADMIRE (Elekta Inc.) was used for this. The refinement does not force perfect agreement of the contours, typically Dice’s Coefficient (DC) of > 0.9 is obtained, and the image difference metric remains in the optimization of the deformable registration. Results: The average DC between physician delineated CBCT contours and deformed planning CT contours for the bladder, rectum and prostate was 0.80, 0.79 and 0.75, respectively. The accuracy significantly improved to 0.89, 0.84 and 0.84 (P<0.001 for all) when using the refined deformation field. The average time to run STAPLE with five scans and refine the planning CT deformation was 66 seconds on a Telsa K20c GPU. Conclusion: Accurate contours generated from multiple CBCTs provided guidance for CT to CBCT deformable registration, significantly improving registration accuracy as measured by contour DC. A more accurate deformation field is now available for transferring dose or electron density to the CBCT for adaptive planning. Research grant from Elekta.« less

An Acupuncture Research Protocol Developed from Historical Writings by Mathematical Reflections: A Rational Individualized Acupoint Selection Method for Immediate Pain Relief

PubMed Central

Schroeder, Sven; Meyer-Hamme, Gesa; Zhang, Jianwei; Epplée, Susanne; Friedemann, Thomas; Hu, Weiguo

2013-01-01

While balancing yin and yang is one basic principle of Chinese medicine, balancing methods for combination of meridians and acupoints had been described throughout the history of Chinese medicine. We have identified six historical systems for combinations of acupuncture points in historical writings. All of them represent symmetrical combinations which are defined by the steps in the Chinese Clock. Taking the historical systems as a basis, we calculated the possible combinations that fit into these systems they revealed, leading to a total of 19 systems offering new balancing combinations. Merging the data of these 19 systems, there are 7 combinatorial options for every meridian. On the basis of this data, we calculated 4-meridian combinations with an ideal balance pattern, which is given when all meridians balance each other. We identified 5 of these patterns for every meridian, so we end up with 60 patterns for all the 12 meridians but we find multiple overlapping. Finally, 15 distinct patterns remain. By combining this theoretical concept with the Image and Mirror Concept, we developed an acupuncture research protocol. This protocol potentially solves some problems of acupuncture trials because it represents a rational reproducible procedure independent of examiner experience, but the resulting treatment is individualized. PMID:23431334

National protocol framework for the inventory and monitoring of bees

USGS Publications Warehouse

Droege, Sam; Engler, Joseph D.; Sellers, Elizabeth A.; Lee O'Brien,

2016-01-01

This national protocol framework is a standardized tool for the inventory and monitoring of the approximately 4,200 species of native and non-native bee species that may be found within the National Wildlife Refuge System (NWRS) administered by the U.S. Fish and Wildlife Service (USFWS). However, this protocol framework may also be used by other organizations and individuals to monitor bees in any given habitat or location. Our goal is to provide USFWS stations within the NWRS (NWRS stations are land units managed by the USFWS such as national wildlife refuges, national fish hatcheries, wetland management districts, conservation areas, leased lands, etc.) with techniques for developing an initial baseline inventory of what bee species are present on their lands and to provide an inexpensive, simple technique for monitoring bees continuously and for monitoring and evaluating long-term population trends and management impacts. The latter long-term monitoring technique requires a minimal time burden for the individual station, yet can provide a good statistical sample of changing populations that can be investigated at the station, regional, and national levels within the USFWS’ jurisdiction, and compared to other sites within the United States and Canada. This protocol framework was developed in cooperation with the United States Geological Survey (USGS), the USFWS, and a worldwide network of bee researchers who have investigated the techniques and methods for capturing bees and tracking population changes. The protocol framework evolved from field and lab-based investigations at the USGS Bee Inventory and Monitoring Laboratory at the Patuxent Wildlife Research Center in Beltsville, Maryland starting in 2002 and was refined by a large number of USFWS, academic, and state groups. It includes a Protocol Introduction and a set of 8 Standard Operating Procedures or SOPs and adheres to national standards of protocol content and organization. The Protocol Narrative describes the history and need for the protocol framework and summarizes the basic elements of objectives, sampling design, field methods, training, data management, analysis, and reporting. The SOPs provide more detail and specific instructions for implementing the protocol framework. A central database, for managing all the resulting data is under development. We welcome use of this protocol framework by our partners, as appropriate for their bee inventory and monitoring objectives.

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

PubMed

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

2018-01-22

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

Combining Nitrous Oxide with Carbon Dioxide Decreases the Time to Loss of Consciousness during Euthanasia in Mice — Refinement of Animal Welfare?

PubMed Central

Thomas, Aurelie A.; Flecknell, Paul A.; Golledge, Huw D. R.

2012-01-01

Carbon dioxide (CO2) is the most commonly used euthanasia agent for rodents despite potentially causing pain and distress. Nitrous oxide is used in man to speed induction of anaesthesia with volatile anaesthetics, via a mechanism referred to as the “second gas” effect. We therefore evaluated the addition of Nitrous Oxide (N2O) to a rising CO2 concentration could be used as a welfare refinement of the euthanasia process in mice, by shortening the duration of conscious exposure to CO2. Firstly, to assess the effect of N2O on the induction of anaesthesia in mice, 12 female C57Bl/6 mice were anaesthetized in a crossover protocol with the following combinations: Isoflurane (5%)+O2 (95%); Isoflurane (5%)+N2O (75%)+O2 (25%) and N2O (75%)+O2 (25%) with a total flow rate of 3l/min (into a 7l induction chamber). The addition of N2O to isoflurane reduced the time to loss of the righting reflex by 17.6%. Secondly, 18 C57Bl/6 and 18 CD1 mice were individually euthanized by gradually filling the induction chamber with either: CO2 (20% of the chamber volume.min−1); CO2+N2O (20 and 60% of the chamber volume.min−1 respectively); or CO2+Nitrogen (N2) (20 and 60% of the chamber volume.min−1). Arterial partial pressure (Pa) of O2 and CO2 were measured as well as blood pH and lactate. When compared to the gradually rising CO2 euthanasia, addition of a high concentration of N2O to CO2 lowered the time to loss of righting reflex by 10.3% (P<0.001), lead to a lower PaO2 (12.55±3.67 mmHg, P<0.001), a higher lactataemia (4.64±1.04 mmol.l−1, P = 0.026), without any behaviour indicative of distress. Nitrous oxide reduces the time of conscious exposure to gradually rising CO2 during euthanasia and hence may reduce the duration of any stress or distress to which mice are exposed during euthanasia. PMID:22438874

Combining nitrous oxide with carbon dioxide decreases the time to loss of consciousness during euthanasia in mice--refinement of animal welfare?

PubMed

Thomas, Aurelie A; Flecknell, Paul A; Golledge, Huw D R

2012-01-01

Carbon dioxide (CO(2)) is the most commonly used euthanasia agent for rodents despite potentially causing pain and distress. Nitrous oxide is used in man to speed induction of anaesthesia with volatile anaesthetics, via a mechanism referred to as the "second gas" effect. We therefore evaluated the addition of Nitrous Oxide (N(2)O) to a rising CO(2) concentration could be used as a welfare refinement of the euthanasia process in mice, by shortening the duration of conscious exposure to CO2. Firstly, to assess the effect of N(2)O on the induction of anaesthesia in mice, 12 female C57Bl/6 mice were anaesthetized in a crossover protocol with the following combinations: Isoflurane (5%)+O(2) (95%); Isoflurane (5%)+N(2)O (75%)+O(2) (25%) and N(2)O (75%)+O(2) (25%) with a total flow rate of 3 l/min (into a 7 l induction chamber). The addition of N(2)O to isoflurane reduced the time to loss of the righting reflex by 17.6%. Secondly, 18 C57Bl/6 and 18 CD1 mice were individually euthanized by gradually filling the induction chamber with either: CO(2) (20% of the chamber volume.min-1); CO(2)+N(2)O (20 and 60% of the chamber volume.min(-1) respectively); or CO(2)+Nitrogen (N(2)) (20 and 60% of the chamber volume.min-1). Arterial partial pressure (P(a)) of O(2) and CO(2) were measured as well as blood pH and lactate. When compared to the gradually rising CO(2) euthanasia, addition of a high concentration of N(2)O to CO(2) lowered the time to loss of righting reflex by 10.3% (P<0.001), lead to a lower P(a)O(2) (12.55 ± 3.67 mmHg, P<0.001), a higher lactataemia (4.64 ± 1.04 mmol.l(-1), P = 0.026), without any behaviour indicative of distress. Nitrous oxide reduces the time of conscious exposure to gradually rising CO(2) during euthanasia and hence may reduce the duration of any stress or distress to which mice are exposed during euthanasia.

HiCUP: pipeline for mapping and processing Hi-C data.

PubMed

Wingett, Steven; Ewels, Philip; Furlan-Magaril, Mayra; Nagano, Takashi; Schoenfelder, Stefan; Fraser, Peter; Andrews, Simon

2015-01-01

HiCUP is a pipeline for processing sequence data generated by Hi-C and Capture Hi-C (CHi-C) experiments, which are techniques used to investigate three-dimensional genomic organisation. The pipeline maps data to a specified reference genome and removes artefacts that would otherwise hinder subsequent analysis. HiCUP also produces an easy-to-interpret yet detailed quality control (QC) report that assists in refining experimental protocols for future studies. The software is freely available and has already been used for processing Hi-C and CHi-C data in several recently published peer-reviewed studies.

Clinical experience with a high-performance ATM-connected DICOM archive for cardiology

NASA Astrophysics Data System (ADS)

Solomon, Harry P.

1997-05-01

A system to archive large image sets, such as cardiac cine runs, with near realtime response must address several functional and performance issues, including efficient use of a high performance network connection with standard protocols, an architecture which effectively integrates both short- and long-term mass storage devices, and a flexible data management policy which allows optimization of image distribution and retrieval strategies based on modality and site-specific operational use. Clinical experience with such as archive has allowed evaluation of these systems issues and refinement of a traffic model for cardiac angiography.

One-step hydrothermal synthesis and electrochemical performance of sodium-manganese-iron phosphate as cathode material for Li-ion batteries

NASA Astrophysics Data System (ADS)

Karegeya, Claude; Mahmoud, Abdelfattah; Vertruyen, Bénédicte; Hatert, Frédéric; Hermann, Raphaël P.; Cloots, Rudi; Boschini, Frédéric

2017-09-01

The sodium-manganese-iron phosphate Na2Mn1.5Fe1.5(PO4)3 (NMFP) with alluaudite structure was obtained by a one-step hydrothermal synthesis route. The physical properties and structure of this material were obtained through XRD and Mössbauer analyses. X-ray diffraction Rietveld refinements confirm a cationic distribution of Na+ and presence of vacancies in A(2)', Na+ and small amounts of Mn2+ in A(1), Mn2+ in M(1), 0.5 Mn2+ and Fe cations (Mn2+,Fe2+ and Fe3+) in M(2), leading to the structural formula Na2Mn(Mn0.5Fe1.5)(PO4)3. The particles morphology was investigated by SEM. Several reactions with different hydrothermal reaction times were attempted to design a suitable synthesis protocol of NMFP compound. The time of reaction was varied from 6 to 48 h at 220 °C. The pure phase of NMFP particles was firstly obtained when the hydrothermal reaction of NMFP precursors mixture was maintained at 220 °C for 6 h. When the reaction time was increased from 6 to 12, 24 and 48 h, the dandelion structure was destroyed in favor of NMFP micro-rods. The combination of NMFP (NMFP-6H, NMFP-12H, NMFP-24H and NMFP-48H) structure refinement and Mössbauer characterizations shows that the increase of the reaction time leads to the progressive increment of Fe(III) and the decrease of the crystal size. The electrochemical tests indicated that NMFP is a 3 V sodium intercalating cathode. The comparison of the discharge capacity evolution of studied NMFP electrode materials at C/5 current density shows different capacities of 48, 40, 34 and 34 mA h g-1 for NMFP-6H, NMFP-12H, NMFP-24H and NMFP-48H respectively. Interestingly, all samples show excellent capacity retention of about 99% during 50 cycles.

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

Karegeya, Claude; Mahmoud, Abdelfattah; Vertruyen, Bénédicte

The sodium-manganese-iron phosphate Na 2Mn 1.5Fe 1.5(PO 4) 3 (NMFP) with alluaudite structure was obtained by a one-step hydrothermal synthesis route. The physical properties and structure of this material were obtained through XRD and Mössbauer analyses. X-ray diffraction Rietveld refinements confirm a cationic distribution of Na + and presence of vacancies in A(2)’, Na + and small amounts of Mn 2+ in A(1), Mn 2+ in M(1) , 0.5 Mn 2+ and Fe cations (Mn 2+,Fe 2+ and Fe 3+) in M(2), leading to the structural formula Na 2Mn(Mn 0.5Fe 1.5)(PO 4) 3. The particles morphology was investigated by SEM.more » Several reactions with different hydrothermal reaction times were attempted to design a suitable synthesis protocol of NMFP compound. The time of reaction was varied from 6 to 48 hours at 220°C. The pure phase of NMFP particles was firstly obtained when the hydrothermal reaction of NMFP precursors mixture was maintained at 220°C for 6 hours. When the reaction time was increased from 6 to 12, 24 and 48 hours, the dandelion structure was destroyed in favor of NMFP micro-rods. The combination of NMFP (NMFP-6H, NMFP-12H, NMFP-24H and NMFP-48H) structure refinement and Mössbauer characterizations shows that the increase of the reaction time leads to the progressive increment of Fe(III) and the decrease of the crystal size. The electrochemical tests indicated that NMFP is a 3 V sodium intercalating cathode. The comparison of the discharge capacity evolution of studied NMFP electrode materials at C/5 current density shows different capacities of 48, 40, 34 and 34 mAhg-1 for NMFP-6H, NMFP-12H, NMFP-24H and NMFP-48H respectively. Interestingly, all samples show excellent capacity retention of about 99 % during 50 cycles.« less

Mapping the Natchez Trace Parkway

USGS Publications Warehouse

Rangoonwala, Amina; Bannister, Terri; Ramsey, Elijah W.

2011-01-01

Based on a National Park Service (NPS) landcover classification, a landcover map of the 715-km (444-mile) NPS Natchez Trace Parkway (hereafter referred to as the "Parkway") was created. The NPS landcover classification followed National Vegetation Classification (NVC) protocols. The landcover map, which extended the initial landcover classification to the entire Parkway, was based on color-infrared photography converted to 1-m raster-based digital orthophoto quarter quadrangles, according to U.S. Geological Survey mapping standards. Our goal was to include as many alliance classes as possible in the Parkway landcover map. To reach this goal while maintaining a consistent and quantifiable map product throughout the Parkway extent, a mapping strategy was implemented based on the migration of class-based spectral textural signatures and the congruent progressive refinement of those class signatures along the Parkway. Progressive refinement provided consistent mapping by evaluating the spectral textural distinctiveness of the alliance-association classes, and where necessary, introducing new map classes along the Parkway. By following this mapping strategy, the use of raster-based image processing and geographic information system analyses for the map production provided a quantitative and reproducible product. Although field-site classification data were severely limited, the combination of spectral migration of class membership along the Parkway and the progressive classification strategy produced an organization of alliances that was internally highly consistent. The organization resulted from the natural patterns or alignments of spectral variance and the determination of those spectral patterns that were compositionally similar in the dominant species as NVC alliances. Overall, the mapped landcovers represented the existent spectral textural patterns that defined and encompassed the complex variety of compositional alliances and associations of the Parkway. Based on that mapped representation, forests dominate the Parkway landscape. Grass is the second largest Parkway land cover, followed by scrub-shrub and shrubland classes and pine plantations. The map provides a good representation of the landcover patterns and their changes over the extent of the Parkway, south to north.

Comparison of butorphanol-detomidine versus butorphanol-azaperone for the standing sedation of captive greater one-horned rhinoceroses (Rhinoceros unicornis).

PubMed

Bapodra, Priya; Cracknell, Jonathan; Wolfe, Barbara A

2014-03-01

Three adult and two subadult greater one-horned rhinoceroses (Rhinoceros unicornis) were sedated a total of nine times using two different intramuscular sedative combinations in order to compare the effectiveness of these combinations in inducing consistent standing sedation in this species. The sedation protocols compared were butorphanol tartrate (50-60 mg) and detomidine hydrochloride (20-30 mg; BD) versus butorphanol tartrate (80-120 mg) and azaperone (80-120 mg; BA). Specific doses were adjusted according to age and sex class, and based on previous experience. Parameters compared included time to achieve defined levels of sedation, time to recovery following antagonism, physiological parameters including heart rate, respiratory rate, indirect arterial blood pressure, and venous blood gas values. A hydraulic restraint chute was utilized to mechanically restrain animals during the procedures, and blood collection and ophthalmic examinations were conducted on all animals. Both protocols resulted in standing sedation for > or = 22.3 +/- 2.9 min or until antagonists were administered. The BD protocol resulted in deeper and more consistent sedation, compared to the BA protocol. Naltrexone hydrochloride (250-300 mg) and tolazoline hydrochloride (1,500-2,000 mg) were administered intramuscularly to antagonize protocol BD, whereas naltrexone alone (200-500 mg) was used to antagonize BA. Time to full antagonism, defined as normal mentation and ambulation following administration of antagonists, was prolonged in the BD protocol (132.3 +/- 17.2 min) compared with the BA protocol (7.5 +/- 2.5 min). Venous blood gas analysis did not reveal any significant blood gas deviations during sedation when compared with either conscious equine or white rhinoceros (Ceratotherium simum) venous reference ranges. In summary, both combinations resulted in adequate standing sedation for minimally invasive procedures, although BD resulted in more profound and consistent sedation.

A comparison of protocols and observer precision for measuring physical stream attributes

USGS Publications Warehouse

Whitacre, H.W.; Roper, B.B.; Kershner, J.L.

2007-01-01

Stream monitoring programs commonly measure physical attributes to assess the effect of land management on stream habitat. Variability associated with the measurement of these attributes has been linked to a number of factors, but few studies have evaluated variability due to differences in protocols. We compared six protocols, five used by the U.S. Department of Agriculture Forest Service and one by the U.S. Environmental Protection Agency, on six streams in Oregon and Idaho to determine whether differences in protocol affect values for 10 physical stream attributes. Results from Oregon and Idaho were combined for groups participating in both states, with significant differences in attribute means for 9 out of the 10 stream attributes. Significant differences occurred in 5 of 10 in Idaho, and 10 of 10 in Oregon. Coefficients of variation, signal-to-noise ratio, and root mean square error were used to evaluate measurement precision. There were differences among protocols for all attributes when states were analyzed separately and as a combined dataset. Measurement differences were influenced by choice of instruments, measurement method, measurement location, attribute definitions, and training approach. Comparison of data gathered by observers using different protocols will be difficult unless a core set of protocols for commonly measured stream attributes can be standardized among monitoring programs.

Design criteria monograph on turbopump gears

NASA Technical Reports Server (NTRS)

1975-01-01

Turbopump power gears were brought to acceptable levels of usefulness and reliability through refinements in interdependent areas of design, materials, processing, and quality control combined with extensive development testing that explored problem areas and evaluated potential solutions.

Aerobic exercise deconditioning and countermeasures during bed rest.

PubMed

Lee, Stuart M C; Moore, Alan D; Everett, Meghan E; Stenger, Michael B; Platts, Steven H

2010-01-01

Bed rest is a well-accepted model for spaceflight in which the physiologic adaptations, particularly in the cardiovascular system, are studied and potential countermeasures can be tested. Bed rest without countermeasures results in reduced aerobic capacity and altered submaximal exercise responses. Aerobic endurance and factors which may impact prolonged exercise, however, have not been well studied. The initial loss of aerobic capacity is rapid, occurring in parallel with the loss of plasma volume. Thereafter, the reduction in maximal aerobic capacity proceeds more slowly and is influenced by central and peripheral adaptation. Exercise capacity can be maintained during bed rest and may be improved during recovery with appropriate countermeasures. Plasma volume restoration, resistive exercise, orthostatic stress, aerobic exercise, and aerobic exercise plus orthostatic stress all have been tested with varying levels of success. However, the optimal combination of elements-exercise modality, intensity, duration, muscle groups exercised and frequency of aerobic exercise, orthostatic stress, and supplementary resistive or anaerobic exercise training-has not been systematically evaluated. Currently, frequent (at least 3 days per week) bouts of intense exercise (interval-style and near maximal) with orthostatic stress appears to be the most efficacious method to protect aerobic capacity during bed rest. Further refinement of protocols and countermeasure hardware may be necessary to insure the success of countermeasures in the unique environment of space.

Use (and abuse) of expert elicitation in support of decision making for public policy

PubMed Central

Morgan, M. Granger

2014-01-01

The elicitation of scientific and technical judgments from experts, in the form of subjective probability distributions, can be a valuable addition to other forms of evidence in support of public policy decision making. This paper explores when it is sensible to perform such elicitation and how that can best be done. A number of key issues are discussed, including topics on which there are, and are not, experts who have knowledge that provides a basis for making informed predictive judgments; the inadequacy of only using qualitative uncertainty language; the role of cognitive heuristics and of overconfidence; the choice of experts; the development, refinement, and iterative testing of elicitation protocols that are designed to help experts to consider systematically all relevant knowledge when they make their judgments; the treatment of uncertainty about model functional form; diversity of expert opinion; and when it does or does not make sense to combine judgments from different experts. Although it may be tempting to view expert elicitation as a low-cost, low-effort alternative to conducting serious research and analysis, it is neither. Rather, expert elicitation should build on and use the best available research and analysis and be undertaken only when, given those, the state of knowledge will remain insufficient to support timely informed assessment and decision making. PMID:24821779

Secure multi-party communication with quantum key distribution managed by trusted authority

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

Hughes, Richard John; Nordholt, Jane Elizabeth; Peterson, Charles Glen

Techniques and tools for implementing protocols for secure multi-party communication after quantum key distribution ("QKD") are described herein. In example implementations, a trusted authority facilitates secure communication between multiple user devices. The trusted authority distributes different quantum keys by QKD under trust relationships with different users. The trusted authority determines combination keys using the quantum keys and makes the combination keys available for distribution (e.g., for non-secret distribution over a public channel). The combination keys facilitate secure communication between two user devices even in the absence of QKD between the two user devices. With the protocols, benefits of QKD aremore » extended to multi-party communication scenarios. In addition, the protocols can retain benefit of QKD even when a trusted authority is offline or a large group seeks to establish secure communication within the group.« less

Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination.

PubMed

Millán, Claudia; Sammito, Massimo Domenico; McCoy, Airlie J; Nascimento, Andrey F Ziem; Petrillo, Giovanna; Oeffner, Robert D; Domínguez-Gil, Teresa; Hermoso, Juan A; Read, Randy J; Usón, Isabel

2018-04-01

Macromolecular structures can be solved by molecular replacement provided that suitable search models are available. Models from distant homologues may deviate too much from the target structure to succeed, notwithstanding an overall similar fold or even their featuring areas of very close geometry. Successful methods to make the most of such templates usually rely on the degree of conservation to select and improve search models. ARCIMBOLDO_SHREDDER uses fragments derived from distant homologues in a brute-force approach driven by the experimental data, instead of by sequence similarity. The new algorithms implemented in ARCIMBOLDO_SHREDDER are described in detail, illustrating its characteristic aspects in the solution of new and test structures. In an advance from the previously published algorithm, which was based on omitting or extracting contiguous polypeptide spans, model generation now uses three-dimensional volumes respecting structural units. The optimal fragment size is estimated from the expected log-likelihood gain (LLG) values computed assuming that a substructure can be found with a level of accuracy near that required for successful extension of the structure, typically below 0.6 Å root-mean-square deviation (r.m.s.d.) from the target. Better sampling is attempted through model trimming or decomposition into rigid groups and optimization through Phaser's gyre refinement. Also, after model translation, packing filtering and refinement, models are either disassembled into predetermined rigid groups and refined (gimble refinement) or Phaser's LLG-guided pruning is used to trim the model of residues that are not contributing signal to the LLG at the target r.m.s.d. value. Phase combination among consistent partial solutions is performed in reciprocal space with ALIXE. Finally, density modification and main-chain autotracing in SHELXE serve to expand to the full structure and identify successful solutions. The performance on test data and the solution of new structures are described.

Internet and Intranet Use with a PC: Effects of Adapter Cards, Windows Versions and TCP/IP Software on Networking Performance.

ERIC Educational Resources Information Center

Nieuwenhuysen, Paul

1997-01-01

Explores data transfer speeds obtained with various combinations of hardware and software components through a study of access to the Internet from a notebook computer connected to a local area network based on Ethernet and TCP/IP (transmission control protocol/Internet protocol) network protocols. Upgrading is recommended for higher transfer…

[Efficiency evaluation of capsaicinoids to discriminate bio-waste oils from edible vegetable oils].

PubMed

Mao, Lisha; Liu, Honghe; Kang, Li; Jiang, Jie; Liao, Shicheng; Liu, Guihua; Deng, Pingjian

2014-07-01

To evaluate the efficiency of capsaicinoids to discriminate bio-waste oil from edible vegetable oil. 14 raw vegetable oils, 24 fried waste oils, 34 kitchen-waste oils, 32 edible non-peanut vegetable oil, 32 edible peanuts oil, 16 edible oil add flavorand and 11 refined bio-waste oils were prepared and examined for capsaicinoids including capsaicin, dihydrocapsaicin and nonylic acid vanillylamide. The detection results of the above samples were statistically tested based on sample category to assessment identify the effectiveness of the bio-waste oils with capsaicinoids. As a indicator, capsaincin was possessed of high detection sensitivity and has the highest efficiency to discern kitchen-waste oils and refined bio-waste oils samples from edible non-peanut vegetable oil correctly. The accuracy rate of identification were 100% and 90.1% respectively. There is the background in peanut oil. CONCLUSION Capsaicin added in cooking process can be retained in the refining process and hardly be removed in the refining process. In the case of fully eliminating the background interference, capsaicinoids can effectively identify bio-waste oils and edible vegetable oil in combination.

Effect of zirconium addition on welding of aluminum grain refined by titanium plus boron

NASA Astrophysics Data System (ADS)

Zaid, A. I. O.

2014-06-01

Aluminum oxidizes freely in ordinary atmosphere which makes its welding difficult and weak, particularly it solidifies in columnar structure with large grains. Therefore, it is anticipated that the effect of addition of some grain refiners to its melt before solidification is worth while investigating as it may enhance its weldabilty and improve its mechanical strength. In this paper, the effect of addition of zirconium at a weight of 0.1% (which corresponds to the peretictic limit on the aluminum-zirconium base phase diagram) to commercially pure aluminum, grain refined by Ti+B on its weldability, using gas tungsten arc welding, GTAW, method which was formerly known as TIG. A constant current level of 30 AC Ampere was used because it removes the oxides during the welding process. Metallographic examination of the weldments of the different combinations of Al with Al and Al with its microalloys: in the heat affected zone, HAZ, and away from it was carried out and examined for HAZ width, porosity, cracks and microhardness. It was found that grain refining by Ti+B or Zr resulted in enhancement of the weldment.

Refining Ovarian Cancer Test accuracy Scores (ROCkeTS): protocol for a prospective longitudinal test accuracy study to validate new risk scores in women with symptoms of suspected ovarian cancer.

PubMed

Sundar, Sudha; Rick, Caroline; Dowling, Francis; Au, Pui; Snell, Kym; Rai, Nirmala; Champaneria, Rita; Stobart, Hilary; Neal, Richard; Davenport, Clare; Mallett, Susan; Sutton, Andrew; Kehoe, Sean; Timmerman, Dirk; Bourne, Tom; Van Calster, Ben; Gentry-Maharaj, Aleksandra; Menon, Usha; Deeks, Jon

2016-08-09

Ovarian cancer (OC) is associated with non-specific symptoms such as bloating, making accurate diagnosis challenging: only 1 in 3 women with OC presents through primary care referral. National Institute for Health and Care Excellence guidelines recommends sequential testing with CA125 and routine ultrasound in primary care. However, these diagnostic tests have limited sensitivity or specificity. Improving accurate triage in women with vague symptoms is likely to improve mortality by streamlining referral and care pathways. The Refining Ovarian Cancer Test Accuracy Scores (ROCkeTS; HTA 13/13/01) project will derive and validate new tests/risk prediction models that estimate the probability of having OC in women with symptoms. This protocol refers to the prospective study only (phase III). ROCkeTS comprises four parallel phases. The full ROCkeTS protocol can be found at http://www.birmingham.ac.uk/ROCKETS. Phase III is a prospective test accuracy study. The study will recruit 2450 patients from 15 UK sites. Recruited patients complete symptom and anxiety questionnaires, donate a serum sample and undergo ultrasound scored as per International Ovarian Tumour Analysis (IOTA) criteria. Recruitment is at rapid access clinics, emergency departments and elective clinics. Models to be evaluated include those based on ultrasound derived by the IOTA group and novel models derived from analysis of existing data sets. Estimates of sensitivity, specificity, c-statistic (area under receiver operating curve), positive predictive value and negative predictive value of diagnostic tests are evaluated and a calibration plot for models will be presented. ROCkeTS has received ethical approval from the NHS West Midlands REC (14/WM/1241) and is registered on the controlled trials website (ISRCTN17160843) and the National Institute of Health Research Cancer and Reproductive Health portfolios. 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/

Using generalizability theory to develop clinical assessment protocols.

PubMed

Preuss, Richard A

2013-04-01

Clinical assessment protocols must produce data that are reliable, with a clinically attainable minimal detectable change (MDC). In a reliability study, generalizability theory has 2 advantages over classical test theory. These advantages provide information that allows assessment protocols to be adjusted to match individual patient profiles. First, generalizability theory allows the user to simultaneously consider multiple sources of measurement error variance (facets). Second, it allows the user to generalize the findings of the main study across the different study facets and to recalculate the reliability and MDC based on different combinations of facet conditions. In doing so, clinical assessment protocols can be chosen based on minimizing the number of measures that must be taken to achieve a realistic MDC, using repeated measures to minimize the MDC, or simply based on the combination that best allows the clinician to monitor an individual patient's progress over a specified period of time.

Thiolation mediated pegylation platform to generate functional universal red blood cells.

PubMed

Nacharaju, Parimala; Manjula, Belur N; Acharya, Seetharama A

2007-01-01

The PEGylation that adds an extension arm on protein amino groups with the conservation of their positive charge masks the A and D antigens of erythrocytes efficiently. In the present study, the efficiency of masking the antigens of RBC by PEGylation protocols that do not conserve the charge with and without adding extension arms is compared. The conjugation of PEG-5000 to RBCs through the addition of extension arms masked the D antigen more efficiently than the other protocol. A combination of PEG-5 K and PEG-20 K is needed to mask the A antigen, irrespective of the PEGylation approach. The oxygen affinity of the PEGylated RBCs increased by the extension arm facilitated PEGylation. The protocol involving the conjugation of PEG-chains without adding extension arm did not alter the oxygen affinity of RBCs. A combination of PEGylation protocols is an alternate strategy to generate universal red blood cells with good levels of oxygen affinity.

Solar Power Satellite (SPS) solid-state antenna power combiner

NASA Technical Reports Server (NTRS)

1980-01-01

A low loss power-combining microstrip antenna suitable for solid state solar power satellite (SPS) application was developed. A unique approach for performing both the combining and radiating function in a single cavity-type circuit was verified, representing substantial refinements over previous demonstration models in terms of detailed geometry to obtain good matching and adequate bandwidth at the design frequency. The combiner circuit was designed, built, and tested and the overall results support the view that the solid state power-combining antenna approach is a viable candidate for a solid state SPS antenna building block.

A Secure and Efficient Handover Authentication Protocol for Wireless Networks

PubMed Central

Wang, Weijia; Hu, Lei

2014-01-01

Handover authentication protocol is a promising access control technology in the fields of WLANs and mobile wireless sensor networks. In this paper, we firstly review an efficient handover authentication protocol, named PairHand, and its existing security attacks and improvements. Then, we present an improved key recovery attack by using the linearly combining method and reanalyze its feasibility on the improved PairHand protocol. Finally, we present a new handover authentication protocol, which not only achieves the same desirable efficiency features of PairHand, but enjoys the provable security in the random oracle model. PMID:24971471

Working Memory Training in ADHD: Controlling for Engagement, Motivation, and Expectancy of Improvement (Pilot Study).

PubMed

Mawjee, Karizma; Woltering, Steven; Lai, Nathan; Gotlieb, Howell; Kronitz, Reena; Tannock, Rosemary

2017-09-01

The aim of this study was to evaluate whether a shortened-length session of CogMed Working Memory Training (CWMT) would be a suitable active control group and evaluate study protocol to aid in design refinements for a larger randomized controlled trial (RCT). Thirty-eight post-secondary students diagnosed with ADHD were randomized into 25 sessions of standard (45 min/session) or shortened (15 min/session) CWMT, or into a waitlist control group. There was no significant difference in completion rate or training index score between the standard- and shortened-length groups indicating that both groups showed improvement and put forth good effort during training. Preliminary findings suggest that shorter training sessions may induce similar levels of engagement, motivation, and expectancy of improvement in participants. We conclude that a larger scale RCT that utilizes shortened-length training as an active control group is warranted, but that a few modifications to the study protocol will be required.

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM.

PubMed

Tuncbag, Nurcan; Gursoy, Attila; Nussinov, Ruth; Keskin, Ozlem

2011-08-11

Prediction of protein-protein interactions at the structural level on the proteome scale is important because it allows prediction of protein function, helps drug discovery and takes steps toward genome-wide structural systems biology. We provide a protocol (termed PRISM, protein interactions by structural matching) for large-scale prediction of protein-protein interactions and assembly of protein complex structures. The method consists of two components: rigid-body structural comparisons of target proteins to known template protein-protein interfaces and flexible refinement using a docking energy function. The PRISM rationale follows our observation that globally different protein structures can interact via similar architectural motifs. PRISM predicts binding residues by using structural similarity and evolutionary conservation of putative binding residue 'hot spots'. Ultimately, PRISM could help to construct cellular pathways and functional, proteome-scale annotation. PRISM is implemented in Python and runs in a UNIX environment. The program accepts Protein Data Bank-formatted protein structures and is available at http://prism.ccbb.ku.edu.tr/prism_protocol/.

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.

How feasible is remote 3D dosimetry for MR guided Radiation Therapy (MRgRT)?

NASA Astrophysics Data System (ADS)

Mein, S.; Rankine, L.; Miles, D.; Juang, T.; Cai, B.; Curcuru, A.; Mutic, S.; Fenoli, J.; Adamovics, J.; Li, H.; Oldham, M.

2017-05-01

To develop and apply a remote dosimetry protocol with PRESAGE® radiochromic plastic and optical-CT readout in the validation of MRI guided radiation therapy (MRgRT) treatments (MRIdian® by ViewRay®). Through multi-institutional collaboration we performed PRESAGE® dosimetry studies in 4ml cuvettes to investigate dose-response linearity, MR-compatibility, and energy-independence. An open calibration field and symmetrical 3-field plans were delivered to 10cm diameter PRESAGE® to examine percent depth dose and response uniformity under a magnetic field. Evidence of non-linear dose response led to a large volume PRESAGE® study where small corrections were developed for temporally- and spatially-dependent behaviors observed between irradiation and delayed readout. TG-119 plans were created in the MRIdian® TPS and then delivered to 14.5cm 2kg PRESAGE® dosimeters. Through the domestic investigation of an off-site MRgRT system, a refined 3D remote dosimetry protocol is presented capable of validation of advanced MRgRT radiation treatments.

* Ethical Issues in the Use of Animal Models for Tissue Engineering: Reflections on Legal Aspects, Moral Theory, Three Rs Strategies, and Harm-Benefit Analysis.

PubMed

Liguori, Gabriel R; Jeronimus, Bertus F; de Aquinas Liguori, Tácia T; Moreira, Luiz Felipe P; Harmsen, Martin C

2017-12-01

Animal experimentation requires a solid and rational moral foundation. Objective and emphatic decision-making and protocol evaluation by researchers and ethics committees remain a difficult and sensitive matter. This article presents three perspectives that facilitate a consideration of the minimally acceptable standard for animal experiments, in particular, in tissue engineering (TE) and regenerative medicine. First, we review the boundaries provided by law and public opinion in America and Europe. Second, we review contemporary moral theory to introduce the Neo-Rawlsian contractarian theory to objectively evaluate the ethics of animal experiments. Third, we introduce the importance of available reduction, replacement, and refinement strategies, which should be accounted for in moral decision-making and protocol evaluation of animal experiments. The three perspectives are integrated into an algorithmic and graphic harm-benefit analysis tool based on the most relevant aspects of animal models in TE. We conclude with a consideration of future avenues to improve animal experiments.

Accelerator mass spectrometry of strontium-90 for homeland security, environmental monitoring and human health

NASA Astrophysics Data System (ADS)

Tumey, Scott J.; Brown, Thomas A.; Hamilton, Terry E.; Hillegonds, Darren J.

2008-05-01

Strontium-90 is one of the most hazardous materials managed by agencies charged with protecting the public from radiation. Traditional radiometric methods have been limited by low sample throughput and slow turnaround times. Mass spectrometry offers the advantage of shorter analysis times and the ability to measure samples immediately after processing, however conventional mass spectrometric techniques are susceptible to molecular isobaric interferences that limit their overall sensitivity. In contrast, accelerator mass spectrometry is insensitive to molecular interferences and we have therefore begun developing a method for determination of 90Sr by accelerator mass spectrometry. Despite a pervasive interference from 90Zr, our initial development has yielded an instrumental background of ∼108 atoms (75 mBq) per sample. Further refinement of our system (e.g. redesign of our detector, use of alternative target materials) is expected to push the background below 106 atoms, close to the theoretical limit for AMS. Once we have refined our system and developed suitable sample preparation protocols, we will utilize our capability in applications to homeland security, environmental monitoring and human health.

A Cartesian grid approach with hierarchical refinement for compressible flows

NASA Technical Reports Server (NTRS)

Quirk, James J.

1994-01-01

Many numerical studies of flows that involve complex geometries are limited by the difficulties in generating suitable grids. We present a Cartesian boundary scheme for two-dimensional, compressible flows that is unfettered by the need to generate a computational grid and so it may be used, routinely, even for the most awkward of geometries. In essence, an arbitrary-shaped body is allowed to blank out some region of a background Cartesian mesh and the resultant cut-cells are singled out for special treatment. This is done within a finite-volume framework and so, in principle, any explicit flux-based integration scheme can take advantage of this method for enforcing solid boundary conditions. For best effect, the present Cartesian boundary scheme has been combined with a sophisticated, local mesh refinement scheme, and a number of examples are shown in order to demonstrate the efficacy of the combined algorithm for simulations of shock interaction phenomena.

Arbitrary Lagrangian-Eulerian Method with Local Structured Adaptive Mesh Refinement for Modeling Shock Hydrodynamics

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

Anderson, R W; Pember, R B; Elliott, N S

2001-10-22

A new method that combines staggered grid Arbitrary Lagrangian-Eulerian (ALE) techniques with structured local adaptive mesh refinement (AMR) has been developed for solution of the Euler equations. This method facilitates the solution of problems currently at and beyond the boundary of soluble problems by traditional ALE methods by focusing computational resources where they are required through dynamic adaption. Many of the core issues involved in the development of the combined ALEAMR method hinge upon the integration of AMR with a staggered grid Lagrangian integration method. The novel components of the method are mainly driven by the need to reconcile traditionalmore » AMR techniques, which are typically employed on stationary meshes with cell-centered quantities, with the staggered grids and grid motion employed by Lagrangian methods. Numerical examples are presented which demonstrate the accuracy and efficiency of the method.« less

GLOBE Goes GO with Mosquitoes

NASA Astrophysics Data System (ADS)

Boger, R. A.; Low, R.

2016-12-01

The GLOBE Mosquito Larvae protocol and a new citizen science initiative, GLOBE Observers (GO), were both launched in Summer 2016. While the GLOBE Mosquito Larvae Protocol and associated educational materials target K-16 student inquiry and research, the GO protocol version is simplified to enable citizen scientists of all ages from all walks of life to participate. GO allows citizen scientists to collect and submit environmental data through an easy-to-use smart phone app available for both Apple and Android mobile devices. GO mosquito asks for photos of larvae mosquito genus or species, location, and type of water source (e.g., container or pond) where the larvae were found. To initiate the new mosquito GLOBE/GO opportunities, workshops have been held in Barbuda, Thailand, West Indies, US Gulf Coast, New York City, and at the GLOBE Annual Meeting in Colorado. Through these venues, the protocols have been refined and a field campaign has been initiated so that GO and GLOBE citizen scientists (K-16 students and all others) can contribute data. Quality assurance measures are taken through the online training required to participate and the validation of identification by other citizen sciences and mosquito experts. Furthermore, initial research is underway to develop optical recognition software starting with the species that carry the Zika virus (Aedes aegypti and A. albopictus). With this launch, we plan to move forward by providing opportunities throughout the world to engage people in meaningful environmental and public health data collection and to promote citizen scientists to become agents of change in their communities.

Effect of Fatigue Protocols on Lower Limb Neuromuscular Function and Implications for Anterior Cruciate Ligament Injury Prevention Training: A Systematic Review.

PubMed

Barber-Westin, Sue D; Noyes, Frank R

2017-12-01

Approximately two-thirds of anterior cruciate ligament (ACL) tears are sustained during noncontact situations when an athlete is cutting, pivoting, decelerating, or landing from a jump. Some investigators have postulated that fatigue may result in deleterious alterations in lower limb biomechanics during these activities that could increase the risk of noncontact ACL injuries. However, prior studies have noted a wide variation in fatigue protocols, athletic tasks studied, and effects of fatigue on lower limb kinetics and kinematics. First, to determine if fatigue uniformly alters lower limb biomechanics during athletic tasks that are associated with noncontact ACL injuries. Second, to determine if changes should be made in ACL injury prevention training programs to alter the deleterious effects of fatigue on lower limb kinetics and kinematics. Systematic review; Level of evidence, 4. A systematic review of the literature using MEDLINE was performed. Key terms were fatigue, neuromuscular, exercise, hop test, and single-legged function tests. Inclusion criteria were original research studies involving healthy participants, use of a fatigue protocol, study of at least 1 lower limb task that involved landing from a hop or jump or cutting, and analysis of at least 1 biomechanical variable. Thirty-seven studies involving 806 athletes (485 female, 321 male; mean age, 22.7 years) met the inclusion criteria. General fatigue protocols were used in 20 investigations, peripheral protocols were used in 17 studies, and 21 different athletic tasks were studied (13 single-legged, 8 double-legged). There was no consistency among investigations regarding the effects of fatigue on hip, knee, or ankle joint angles and moments or surface electromyography muscle activation patterns. The fatigue protocols typically did not produce statistically significant changes in ground-reaction forces. Published fatigue protocols did not uniformly produce alterations in lower limb neuromuscular factors that heighten the risk of noncontact ACL injuries. Therefore, justification does not currently exist for major changes in ACL injury prevention training programs to account for potential fatigue effects. However, the effect of fatigue related to ACL injuries is worthy of further investigation, including the refinement of protocols and methods of analysis.

Live birth in a 46-year-old woman using microdose GnRH agonist flare-up protocol combined with GnRH antagonist: a case report.

PubMed

Zhang, Hong; Liu, Ya-Qiong; Lu, Guang-Xiu; Gong, Fei

2016-12-01

Few successful pregnancies after age 45 years with low ovarian reserve have been reported. We report a 46-year-old woman with basal FSH 20.36 mIU/mL and an antral follicle count of four obtained two embryos and delivered a healthy infant with IVF using a microdose GnRH-a flare-up protocol combined with GnRH-ant.

Noise Analysis of Simultaneous Quantum Key Distribution and Classical Communication Scheme Using a True Local Oscillator

DOE PAGES

Qi, Bing; Lim, Charles Ci Wen

2018-05-07

Recently, we proposed a simultaneous quantum and classical communication (SQCC) protocol where random numbers for quantum key distribution and bits for classical communication are encoded on the same weak coherent pulse and decoded by the same coherent receiver. Such a scheme could be appealing in practice since a single coherent communication system can be used for multiple purposes. However, previous studies show that the SQCC protocol can tolerate only very small phase noise. This makes it incompatible with the coherent communication scheme using a true local oscillator (LO), which presents a relatively high phase noise due to the fact thatmore » the signal and the LO are generated from two independent lasers. We improve the phase noise tolerance of the SQCC scheme using a true LO by adopting a refined noise model where phase noises originating from different sources are treated differently: on the one hand, phase noise associated with the coherent receiver may be regarded as trusted noise since the detector can be calibrated locally and the photon statistics of the detected signals can be determined from the measurement results; on the other hand, phase noise due to the instability of fiber interferometers may be regarded as untrusted noise since its randomness (from the adversary’s point of view) is hard to justify. Simulation results show the tolerable phase noise in this refined noise model is significantly higher than that in the previous study, where all of the phase noises are assumed to be untrusted. In conclusion, we conduct an experiment to show that the required phase stability can be achieved in a coherent communication system using a true LO.« less

Noise Analysis of Simultaneous Quantum Key Distribution and Classical Communication Scheme Using a True Local Oscillator

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

Qi, Bing; Lim, Charles Ci Wen

Recently, we proposed a simultaneous quantum and classical communication (SQCC) protocol where random numbers for quantum key distribution and bits for classical communication are encoded on the same weak coherent pulse and decoded by the same coherent receiver. Such a scheme could be appealing in practice since a single coherent communication system can be used for multiple purposes. However, previous studies show that the SQCC protocol can tolerate only very small phase noise. This makes it incompatible with the coherent communication scheme using a true local oscillator (LO), which presents a relatively high phase noise due to the fact thatmore » the signal and the LO are generated from two independent lasers. We improve the phase noise tolerance of the SQCC scheme using a true LO by adopting a refined noise model where phase noises originating from different sources are treated differently: on the one hand, phase noise associated with the coherent receiver may be regarded as trusted noise since the detector can be calibrated locally and the photon statistics of the detected signals can be determined from the measurement results; on the other hand, phase noise due to the instability of fiber interferometers may be regarded as untrusted noise since its randomness (from the adversary’s point of view) is hard to justify. Simulation results show the tolerable phase noise in this refined noise model is significantly higher than that in the previous study, where all of the phase noises are assumed to be untrusted. In conclusion, we conduct an experiment to show that the required phase stability can be achieved in a coherent communication system using a true LO.« less

Identification and characterization of outcome measures reported in animal models of epilepsy: Protocol for a systematic review of the literature-A TASK2 report of the AES/ILAE Translational Task Force of the ILAE.

PubMed

Simonato, Michele; Iyengar, Sloka; Brooks-Kayal, Amy; Collins, Stephen; Depaulis, Antoine; Howells, David W; Jensen, Frances; Liao, Jing; Macleod, Malcolm R; Patel, Manisha; Potschka, Heidrun; Walker, Matthew; Whittemore, Vicky; Sena, Emily S

2017-11-01

Current antiseizure therapy is ineffective in approximately one third of people with epilepsy and is often associated with substantial side effects. In addition, most current therapeutic paradigms offer treatment, but not cure, and no therapies are able to modify the underlying disease, that is, can prevent or halt the process of epileptogenesis or alleviate the cognitive and psychiatric comorbidities. Preclinical research in the field of epilepsy has been extensive, but unfortunately, not all the animal models being used have been validated for their predictive value. The overall goal of TASK2 of the AES/ILAE Translational Task Force is to organize and coordinate systematic reviews on selected topics regarding animal research in epilepsy. Herein we describe our strategy. In the first part of the paper we provide an overview of the usefulness of systematic reviews and meta-analysis for preclinical research and explain the essentials for their conduct. Then we describe in detail the protocol for a first systematic review, which will focus on the identification and characterization of outcome measures reported in animal models of epilepsy. The specific goals of this study are to define systematically the phenotypic characteristics of the most commonly used animal models, and to effectively compare these with the manifestations of human epilepsy. This will provide epilepsy researchers with detailed information on the strengths and weaknesses of epilepsy models, facilitating their refinement and future research. Ultimately, this could lead to a refined use of relevant models for understanding the mechanism(s) of the epilepsies and developing novel therapies. Wiley Periodicals, Inc. © 2017 International League Against Epilepsy.

Noise Analysis of Simultaneous Quantum Key Distribution and Classical Communication Scheme Using a True Local Oscillator

NASA Astrophysics Data System (ADS)

Qi, Bing; Lim, Charles Ci Wen

2018-05-01

Recently, we proposed a simultaneous quantum and classical communication (SQCC) protocol where random numbers for quantum key distribution and bits for classical communication are encoded on the same weak coherent pulse and decoded by the same coherent receiver. Such a scheme could be appealing in practice since a single coherent communication system can be used for multiple purposes. However, previous studies show that the SQCC protocol can tolerate only very small phase noise. This makes it incompatible with the coherent communication scheme using a true local oscillator (LO), which presents a relatively high phase noise due to the fact that the signal and the LO are generated from two independent lasers. We improve the phase noise tolerance of the SQCC scheme using a true LO by adopting a refined noise model where phase noises originating from different sources are treated differently: on the one hand, phase noise associated with the coherent receiver may be regarded as trusted noise since the detector can be calibrated locally and the photon statistics of the detected signals can be determined from the measurement results; on the other hand, phase noise due to the instability of fiber interferometers may be regarded as untrusted noise since its randomness (from the adversary's point of view) is hard to justify. Simulation results show the tolerable phase noise in this refined noise model is significantly higher than that in the previous study, where all of the phase noises are assumed to be untrusted. We conduct an experiment to show that the required phase stability can be achieved in a coherent communication system using a true LO.

The use of animal models in homeopathic research--a review of 2010-2014 PubMed indexed papers.

PubMed

Bonamin, Leoni Villano; Cardoso, Thayná Neves; de Carvalho, Aloísio Cunha; Amaral, Juliana Gimenez

2015-10-01

In the 1990s, a study was performed on the effects of highly diluted thyroxine on frog metamorphosis. This model represented one of the most discussed examples of the biological effects of high dilutions over the next two decades. In 2010, another critical conceptual review of the use of animal models in homeopathy and high-dilution research was published. The main contribution of these studies was the elucidation of the biological features and phenomenology of the effects of high dilutions on living systems, representing an important step forward in our understanding of the mechanisms of action of homeopathic medicines. We performed a further review of this line of investigation using the same methods. Fifty-three articles that were indexed in the PubMed database and used 12 different animal species were systematically evaluated. Only a fraction of the studies (29/53) reported herein were performed with "ultra high" dilutions. The other studies were performed with dilutions in ranges below 10(-23) (14/53 articles) or commercial complexes (10/53 articles). Only two articles reported negative results; both used in vivo protocols to test commercial complexes, one in fish and one in bees. The quality of the employed techniques improved in 2010-2014 compared with the studies that were reviewed previously in 2010, with the inclusion of more ethically refined protocols, including in vitro primary cell cultures and ex vivo studies (10/53 articles), often with three or more replicates and analyses of epigenetic mechanisms that were previously unknown in 2010. In our updated review of the past 5 years, we found further demonstrations of the biological effects of homeopathy using more refined animal models and in vitro techniques. Copyright © 2015 The Faculty of Homeopathy. Published by Elsevier Ltd. All rights reserved.

Subthalamic nucleus deep brain stimulation for Parkinson's disease: evidence for effectiveness and limitations from 12 years' experience.

PubMed

Chan, Anne Y Y; Yeung, Jonas H M; Mok, Vincent C T; Ip, Vincent H L; Wong, Adrian; Kuo, S H; Chan, Danny T M; Zhu, X L; Wong, Edith; Lau, Claire K Y; Wong, Rosanna K M; Tang, Venus; Lau, Christine; Poon, W S

2014-12-01

To present the result and experience of subthalamic nucleus deep brain stimulation for Parkinson's disease. Case series. Prince of Wales Hospital, Hong Kong. A cohort of patients with Parkinson's disease received subthalamic nucleus deep brain stimulation from September 1998 to January 2010. Patient assessment data before and after the operation were collected prospectively. Forty-one patients (21 male and 20 female) with Parkinson's disease underwent bilateral subthalamic nucleus deep brain stimulation and were followed up for a median interval of 12 months. For the whole group, the mean improvements of Unified Parkinson's Disease Rating Scale (UPDRS) parts II and III were 32.5% and 31.5%, respectively (P<0.001). Throughout the years, a multidisciplinary team was gradually built. The deep brain stimulation protocol evolved and was substantiated by updated patient selection criteria and outcome assessment, integrated imaging and neurophysiological targeting, refinement of surgical technique as well as the accumulation of experience in deep brain stimulation programming. Most of the structural improvement occurred before mid-2005. Patients receiving the operation before June 2005 (19 cases) and after (22 cases) were compared; the improvements in UPDRS part III were 13.2% and 55.2%, respectively (P<0.001). There were three operative complications (one lead migration, one cerebral haematoma, and one infection) in the group operated on before 2005. There was no operative mortality. The functional state of Parkinson's disease patients with motor disabilities refractory to best medical treatment improved significantly after subthalamic nucleus deep brain stimulation. A dedicated multidisciplinary team building, refined protocol for patient selection and assessment, improvement of targeting methods, meticulous surgical technique, and experience in programming are the key factors contributing to the improved outcome.

Technical standards and guidelines: prenatal screening for Down syndrome that includes first-trimester biochemistry and/or ultrasound measurements.

PubMed

Palomaki, Glenn E; Lee, Jo Ellen S; Canick, Jacob A; McDowell, Geraldine A; Donnenfeld, Alan E

2009-09-01

This statement is intended to augment the current general ACMG Standards and Guidelines for Clinical Genetics Laboratories and to address guidelines specific to first-trimester screening for Down syndrome. The aim is to provide the laboratory the necessary information to ensure accurate and reliable Down syndrome screening results given a screening protocol (e.g., combined first trimester and integrated testing). Information about various test combinations and their expected performance are provided, but other issues such as availability of reagents, patient interest in early test results, access to open neural tube defect screening, and availability of chorionic villus sampling are all contextual factors in deciding which screening protocol(s) will be selected by individual health care providers. Individual laboratories are responsible for meeting the quality assurance standards described by the Clinical Laboratory Improvement Act, the College of American Pathologists, and other regulatory agencies, with respect to appropriate sample documentation, assay validation, general proficiency, and quality control measures. These guidelines address first-trimester screening that includes ultrasound measurement and interpretation of nuchal translucency thickness and protocols that combine markers from both the first and second trimesters. Laboratories can use their professional judgment to make modification or additions.

Enhancing Endosomal Escape of Transduced Proteins by Photochemical Internalisation

PubMed Central

Mellert, Kevin; Lamla, Markus; Scheffzek, Klaus; Wittig, Rainer; Kaufmann, Dieter

2012-01-01

Induced internalisation of functional proteins into cultured cells has become an important aspect in a rising number of in vitro and in vivo assays. The endo-lysosomal entrapment of the transduced proteins remains the major problem in all transduction protocols. In this study we compared the efficiency, cytotoxicity and protein targeting of different commercially available transduction reagents by transducing a well-studied fluorescently labelled protein (Atto488-bovine serum albumin) into cultured human sarcoma cells. The amount of internalised protein and toxicity differed between the different reagents, but the percentage of transduced cells was consistently high. Furthermore, in all protocols the signals of the transduced Atto488-BSA were predominantly punctual consistent with an endosomal localisation. To overcome the endosomal entrapment, the transduction protocols were combined with a photochemical internalisation (PCI) treatment. Using this combination revealed that an endosomal disruption is highly effective in cell penetrating peptide (CPP) mediated transduction, whereas lipid-mediated transductions lead to a lower signal spreading throughout the cytosol. No change in the signal distribution could be achieved in treatments using non-lipid polymers as a transduction reagent. Therefore, the combination of protein transduction protocols based on CPPs with the endosomolytic treatment PCI can facilitate protein transduction experiments in vitro. PMID:23285056

Enhancing endosomal escape of transduced proteins by photochemical internalisation.

PubMed

Mellert, Kevin; Lamla, Markus; Scheffzek, Klaus; Wittig, Rainer; Kaufmann, Dieter

2012-01-01

Induced internalisation of functional proteins into cultured cells has become an important aspect in a rising number of in vitro and in vivo assays. The endo-lysosomal entrapment of the transduced proteins remains the major problem in all transduction protocols. In this study we compared the efficiency, cytotoxicity and protein targeting of different commercially available transduction reagents by transducing a well-studied fluorescently labelled protein (Atto488-bovine serum albumin) into cultured human sarcoma cells. The amount of internalised protein and toxicity differed between the different reagents, but the percentage of transduced cells was consistently high. Furthermore, in all protocols the signals of the transduced Atto488-BSA were predominantly punctual consistent with an endosomal localisation. To overcome the endosomal entrapment, the transduction protocols were combined with a photochemical internalisation (PCI) treatment. Using this combination revealed that an endosomal disruption is highly effective in cell penetrating peptide (CPP) mediated transduction, whereas lipid-mediated transductions lead to a lower signal spreading throughout the cytosol. No change in the signal distribution could be achieved in treatments using non-lipid polymers as a transduction reagent. Therefore, the combination of protein transduction protocols based on CPPs with the endosomolytic treatment PCI can facilitate protein transduction experiments in vitro.

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.

A Draft Protocol for Detecting Possible Biohazards in Martian Samples Returned to Earth

NASA Technical Reports Server (NTRS)

Viso, M.; DeVincenzi, D. L.; Race, M. S.; Schad, P. J.; Stabekis, P. D.; Acevedo, S. E.; Rummel, J. D.

2002-01-01

In preparation for missions to Mars that will involve the return of samples, it is necessary to prepare for the safe receiving, handling, testing, distributing, and archiving of martian materials here on Earth. Previous groups and committees have studied selected aspects of sample return activities, but a specific protocol for handling and testing of returned -=1 samples from Mars remained to be developed. To refine the requirements for Mars sample hazard testing and to develop criteria for the subsequent release of sample materials from precautionary containment, NASA Planetary Protection Officer, working in collaboration with CNES, convened a series of workshops to produce a Protocol by which returned martian sample materials could be assessed for biological hazards and examined for evidence of life (extant or extinct), while safeguarding the samples from possible terrestrial contamination. The Draft Protocol was then reviewed by an Oversight and Review Committee formed specifically for that purpose and composed of senior scientists. In order to preserve the scientific value of returned martian samples under safe conditions, while avoiding false indications of life within the samples, the Sample Receiving Facility (SRF) is required to allow handling and processing of the Mars samples to prevent their terrestrial contamination while maintaining strict biological containment. It is anticipated that samples will be able to be shipped among appropriate containment facilities wherever necessary, under procedures developed in cooperation with international appropriate institutions. The SRF will need to provide different types of laboratory environments for carrying out, beyond sample description and curation, the various aspects of the protocol: Physical/Chemical analysis, Life Detection testing, and Biohazard testing. The main principle of these tests will be described and the criteria for release will be discussed, as well as the requirements for the SRF and its personnel.

Rethinking developmental toxicity testing: Evolution or revolution?

PubMed

Scialli, Anthony R; Daston, George; Chen, Connie; Coder, Prägati S; Euling, Susan Y; Foreman, Jennifer; Hoberman, Alan M; Hui, Julia; Knudsen, Thomas; Makris, Susan L; Morford, LaRonda; Piersma, Aldert H; Stanislaus, Dinesh; Thompson, Kary E

2018-06-01

Current developmental toxicity testing adheres largely to protocols suggested in 1966 involving the administration of test compound to pregnant laboratory animals. After more than 50 years of embryo-fetal development testing, are we ready to consider a different approach to human developmental toxicity testing? A workshop was held under the auspices of the Developmental and Reproductive Toxicology Technical Committee of the ILSI Health and Environmental Sciences Institute to consider how we might design developmental toxicity testing if we started over with 21st century knowledge and techniques (revolution). We first consider what changes to the current protocols might be recommended to make them more predictive for human risk (evolution). The evolutionary approach includes modifications of existing protocols and can include humanized models, disease models, more accurate assessment and testing of metabolites, and informed approaches to dose selection. The revolution could start with hypothesis-driven testing where we take what we know about a compound or close analog and answer specific questions using targeted experimental techniques rather than a one-protocol-fits-all approach. Central to the idea of hypothesis-driven testing is the concept that testing can be done at the level of mode of action. It might be feasible to identify a small number of key events at a molecular or cellular level that predict an adverse outcome and for which testing could be performed in vitro or in silico or, rarely, using limited in vivo models. Techniques for evaluating these key events exist today or are in development. Opportunities exist for refining and then replacing current developmental toxicity testing protocols using techniques that have already been developed or are within reach. © 2018 The Authors. Birth Defects Research Published by Wiley Periodicals, Inc.

Refined protocols of tamoxifen injection for inducible DNA recombination in mouse astroglia.

PubMed

Jahn, Hannah M; Kasakow, Carmen V; Helfer, Andreas; Michely, Julian; Verkhratsky, Alexei; Maurer, Hans H; Scheller, Anja; Kirchhoff, Frank

2018-04-12

Inducible DNA recombination of floxed alleles in vivo by liver metabolites of tamoxifen (TAM) is an important tool to study gene functions. Here, we describe protocols for optimal DNA recombination in astrocytes, based on the GLAST-Cre ERT2 /loxP system. In addition, we demonstrate that quantification of genomic recombination allows to determine the proportion of cell types in various brain regions. We analyzed the presence and clearance of TAM and its metabolites (N-desmethyl-tamoxifen, 4-hydroxytamoxifen and endoxifen) in brain and serum of mice by liquid chromatographic-high resolution-tandem mass spectrometry (LC-HR-MS/MS) and assessed optimal injection protocols by quantitative RT-PCR of several floxed target genes (p2ry1, gria1, gabbr1 and Rosa26-tdTomato locus). Maximal recombination could be achieved in cortex and cerebellum by single daily injections for five and three consecutive days, respectively. Furthermore, quantifying the loss of floxed alleles predicted the percentage of GLAST-positive cells (astroglia) per brain region. We found that astrocytes contributed 20 to 30% of the total cell number in cortex, hippocampus, brainstem and optic nerve, while in the cerebellum Bergmann glia, velate astrocytes and white matter astrocytes accounted only for 8% of all cells.

A pedagogical example of second-order arithmetic sequences applied to the construction of computer passwords by upper elementary grade students

NASA Astrophysics Data System (ADS)

Coggins, Porter E.

2015-04-01

The purpose of this paper is (1) to present how general education elementary school age students constructed computer passwords using digital root sums and second-order arithmetic sequences, (2) argue that computer password construction can be used as an engaging introduction to generate interest in elementary school students to study mathematics related to computer science, and (3) share additional mathematical ideas accessible to elementary school students that can be used to create computer passwords. This paper serves to fill a current gap in the literature regarding the integration of mathematical content accessible to upper elementary school students and aspects of computer science in general, and computer password construction in particular. In addition, the protocols presented here can serve as a hook to generate further interest in mathematics and computer science. Students learned to create a random-looking computer password by using biometric measurements of their shoe size, height, and age in months and to create a second-order arithmetic sequence, then converted the resulting numbers into characters that become their computer passwords. This password protocol can be used to introduce students to good computer password habits that can serve a foundation for a life-long awareness of data security. A refinement of the password protocol is also presented.

Cartesian Off-Body Grid Adaption for Viscous Time- Accurate Flow Simulation

NASA Technical Reports Server (NTRS)

Buning, Pieter G.; Pulliam, Thomas H.

2011-01-01

An improved solution adaption capability has been implemented in the OVERFLOW overset grid CFD code. Building on the Cartesian off-body approach inherent in OVERFLOW and the original adaptive refinement method developed by Meakin, the new scheme provides for automated creation of multiple levels of finer Cartesian grids. Refinement can be based on the undivided second-difference of the flow solution variables, or on a specific flow quantity such as vorticity. Coupled with load-balancing and an inmemory solution interpolation procedure, the adaption process provides very good performance for time-accurate simulations on parallel compute platforms. A method of using refined, thin body-fitted grids combined with adaption in the off-body grids is presented, which maximizes the part of the domain subject to adaption. Two- and three-dimensional examples are used to illustrate the effectiveness and performance of the adaption scheme.

The combined effects of action observation and passive proprioceptive training on adaptive motor learning.

PubMed

Lei, Yuming; Bao, Shancheng; Wang, Jinsung

2016-09-07

Sensorimotor adaptation can be induced by action observation, and also by passive training. Here, we investigated the effect of a protocol that combined action observation and passive training on visuomotor adaptation, by comparing it with the effect of action observation or passive training alone. Subjects were divided into five conditions during the training session: (1) action observation, in which the subjects watched a video of a model who adapted to a novel visuomotor rotation; (2) proprioceptive training, in which the subject's arm was moved passively to target locations that were associated with desired trajectories; (3) combined training, in which the subjects watched the video of a model during a half of the session and experienced passive movements during the other half; (4) active training, in which the subjects adapted actively to the rotation; and (5) a control condition, in which the subjects did not perform any task. Following that session, all subjects adapted to the same visuomotor rotation. Results showed that the subjects in the combined training condition adapted to the rotation significantly better than those in the observation or proprioceptive training condition, although their performance was not as good as that of those who adapted actively. These findings suggest that although a protocol that combines action observation and passive training consists of all the processes involved in active training (error detection and correction, effector-specific and proprioceptively based reaching movements), these processes in that protocol may work differently as compared to a protocol in which the same processes are engaged actively. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

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.

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.

Combining 27Al Solid-State NMR and First-Principles Simulations To Explore Crystal Structure in Disordered Aluminum Oxynitride.

PubMed

Tu, Bingtian; Liu, Xin; Wang, Hao; Wang, Weimin; Zhai, Pengcheng; Fu, Zhengyi

2016-12-19

The nuclear magnetic resonance (NMR) technique gives insight into the local information in a crystal structure, while Rietveld refinement of powder X-ray diffraction (PXRD) sketches out the framework of a crystal lattice. In this work, first-principles calculations were combined with the solid-state NMR technique and Rietveld refinement to explore the crystal structure of a disordered aluminum oxynitride (γ-alon). The theoretical NMR parameters (chemical shift, δ iso , quadrupolar coupling constants, C Q , and asymmetry parameter, η) of Al 22.5 O 28.5 N 3.5 , predicted by the gauge-including projector augmented wave (GIPAW) algorithm, were used to facilitate the analytical investigation of the 27 Al magic-angle spinning (MAS) NMR spectra of the as-prepared sample, whose formula was confirmed to be Al 2.811 O 3.565 N 0.435 by quantitative analysis. The experimental δ iso , C Q , and η of 27 Al showed a small discrepancy compared with theoretical models. The ratio of aluminum located at the 8a to 16d sites was calculated to be 0.531 from the relative integration of peaks in the 27 Al NMR spectra. The occupancies of aluminum at the 8a and 16d positions were determined through NMR investigations to be 0.9755 and 0.9178, respectively, and were used in the Rietveld refinement to obtain the lattice parameter and anion parameter of Al 2.811 O 3.565 N 0.435 . The results from 27 Al NMR investigations and PXRD structural refinement complemented each other. This work provides a powerful and accessible strategy to precisely understand the crystal structure of novel oxynitride materials with multiple disorder.

Electronic decision protocols for ART patient triaging to expand access to HIV treatment in South Africa: a cross sectional study for development and validation.

PubMed

Mitchell, Marc; Hedt, Bethany L; Eshun-Wilson, Ingrid; Fraser, Hamish; John, Melanie-Anne; Menezes, Colin; Grobusch, Martin P; Jackson, Jonathan; Taljaard, Jantjie; Lesh, Neal

2012-03-01

The shortage of doctors and nurses, along with future expansion into rural clinics, will require that the majority of clinic visits by HIV infected patients on antiretroviral therapy (ART) are managed by non-doctors. The goal of this study was to develop and evaluate a screening protocol to determine which patients needed a full clinical assessment and which patients were stable enough to receive their medications without a doctor's consultation. For this study, we developed an electronic, handheld tool to guide non-physician counselors through screening questions. Patients visiting two ART clinics in South Africa for routine follow-up visits between March 2007 and April 2008 were included in our study. Each patient was screened by non-physician counselors using the handheld device and then received a full clinical assessment. Clinicians' report on whether full clinical assessment had been necessary was used as the gold standard for determining "required referral". Observations were randomly divided into two datasets--989 for developing a referral protocol and 200 for validating protocol performance. A third of patients had at least one physical complaint, and 16% had five or more physical complaints. 38% of patients required referral for full clinical assessment. We identify a subset of questions which are 87% sensitive and 47% specific for recommended patient referral. The final screening protocol is highly sensitive and could reduce burden on ART clinicians by 30%. The uptake and acceptance of the handheld tool to support implementation of the protocol was high. Further examination of the data reveals several important questions to include in future referral algorithms to improve sensitivity and specificity. Based on these results, we identify a refined algorithm to explore in future evaluations. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Effects of different duration isometric contractions on tendon elasticity in human quadriceps muscles

PubMed Central

Kubo, Keitaro; Kanehisa, Hiroaki; Fukunaga, Tetsuo

2001-01-01

The present study aimed to investigate the influence of isometric training protocols with long- and short-duration contractions on the elasticity of human tendon structures in vivo. The elasticity was assessed through in vivo determination of the elongation (L) of the tendons and aponeuroses using ultrasonography, while the subjects performed ramp isometric exercise up to maximum voluntary contraction (MVC).Eight young males completed 12 weeks (4 days per week) of a unilateral isometric training programme on knee extensors, which consisted of two different combinations of contraction and relaxation times at 70 % MVC: one leg was trained using a short-duration protocol (3 sets of 50 repetitions of contraction for 1 s and relaxation for 2 s), and the other leg was trained using a long-duration protocol (4 sets of a combination of contraction for 20 s and relaxation for 1 min). The training volume per session, expressed as the integrated torque, was the same for the two protocols.Both protocols resulted in a significant increase in MVC: 31.8 ± 17.2 % for the short-duration protocol and 33.9 ± 14.4 % for the long-duration protocol. Moreover, the training produced significant increases in the muscle volume of the constituents of the quadriceps femoris, with similar relative gains for the two protocols: 7.4 ± 3.9 % for the short-duration protocol and 7.6 ± 4.3 % for the long-duration protocol.The short-duration protocol produced no significant change in L values at any of the force production levels. For the long-duration protocol, however, the L values above 550 N were significantly shorter after training. Analysis revealed that the group × test time interaction effect on tendon stiffness was significant. Stiffness increased significantly for the long-duration protocol, but not for the short-duration protocol.The present study demonstrates a greater increase in stiffness of human tendon structures following isometric training using longer duration contractions compared to shorter contractions. This suggests that the changes in the elasticity of the tendon structures after resistance training may be affected by the duration of muscle contraction. PMID:11600697

Mercury Production and Use in Colonial Andean Silver Production: Emissions and Health Implications

PubMed Central

Hagan, Nicole A.

2012-01-01

Background: Colonial cinnabar mining and refining began in Huancavelica, Peru, in 1564. With a local source of mercury, the amalgamation process was adopted to refine silver in Potosí, Bolivia, in the early 1570s. As a result, large quantities of mercury were released into the environment. Objectives: We used archival, primary, and secondary sources to develop the first estimate of mercury emissions from cinnabar refining in Huancavelica and to revise previous estimates of emissions from silver refining in Potosí during the colonial period (1564–1810). Discussion: Although other estimates of historical mercury emissions have recognized Potosí as a significant source, Huancavelica has been overlooked. In addition, previous estimates of mercury emissions from silver refining under-estimated emissions because of unrecorded (contra-band) production and volatilization of mercury during processing and recovery. Archival descriptions document behavioral and health issues during the colonial period that are consistent with known effects of mercury intoxication. Conclusions: According to our calculations, between 1564 and 1810, an estimated 17,000 metric tons of mercury vapor were emitted from cinnabar smelting in Huancavelica, and an estimated 39,000 metric tons were released as vapor during silver refining operations in Potosí. Huancavelica and Potosí combined contributed > 25% of the 196,000 metric tons of mercury vapor emissions in all of Latin America between 1500 and 1800. The historical record is laden with evidence of mercury intoxication consistent with effects recognized today. Our estimates serve as the foundation of investigations of present-day contamination in Huancavelica and Potosí resulting from historical emissions of mercury. PMID:22334094

GWM-2005 - A Groundwater-Management Process for MODFLOW-2005 with Local Grid Refinement (LGR) Capability

USGS Publications Warehouse

Ahlfeld, David P.; Baker, Kristine M.; Barlow, Paul M.

2009-01-01

This report describes the Groundwater-Management (GWM) Process for MODFLOW-2005, the 2005 version of the U.S. Geological Survey modular three-dimensional groundwater model. GWM can solve a broad range of groundwater-management problems by combined use of simulation- and optimization-modeling techniques. These problems include limiting groundwater-level declines or streamflow depletions, managing groundwater withdrawals, and conjunctively using groundwater and surface-water resources. GWM was initially released for the 2000 version of MODFLOW. Several modifications and enhancements have been made to GWM since its initial release to increase the scope of the program's capabilities and to improve its operation and reporting of results. The new code, which is called GWM-2005, also was designed to support the local grid refinement capability of MODFLOW-2005. Local grid refinement allows for the simulation of one or more higher resolution local grids (referred to as child models) within a coarser grid parent model. Local grid refinement is often needed to improve simulation accuracy in regions where hydraulic gradients change substantially over short distances or in areas requiring detailed representation of aquifer heterogeneity. GWM-2005 can be used to formulate and solve groundwater-management problems that include components in both parent and child models. Although local grid refinement increases simulation accuracy, it can also substantially increase simulation run times.

Reframing Recovery: Developmental Considerations for Maintaining Change

ERIC Educational Resources Information Center

Lawson, Gerard; Lambert, Simone F.; Gressard, Charles F.

2011-01-01

Lasting recovery for clients can be challenging to establish in addictions counseling. Through the combination of 2 approaches, motivational interviewing and developmental counseling and therapy, client treatment can be refined to promote transformative change and long-lasting recovery. (Contains 2 tables.)

The Combined Utility of a Brief Functional Measure and Performance-Based Screening Test for Case Finding of Cognitive Impairment in Primary Healthcare.

PubMed

Chan, Qun Lin; Shaik, Muhammad Amin; Xu, Jing; Xu, Xin; Chen, Christopher Li-Hsian; Dong, YanHong

2016-04-01

Use of a total risk score (TRS) based on vascular and sociodemographic risk factors has been recommended to identify patients at risk of cognitive impairment. Moreover, combining screening tests has been reported to improve positive predictive values (PPV) for case finding of cognitive impairment. We investigated the utility of the conjunctive combination of the informant-based AD8 and the performance-based National Institute of Neurological Disorders and Stroke-Canadian Stroke Network (NINDS-CSN) 5-minute protocol for the detection of cognitive impairment, defined by a clinical dementia rating (CDR) score ≥0.5, in patients at risk of cognitive impairment (TRS ≥3). Participants were recruited from 2 primary healthcare centers in Singapore and received the AD8, Montreal Cognitive Assessment, Mini-Mental State Examination, CDR, and a formal neuropsychological test battery. The scores for NINDS-CSN 5-minute protocol were extracted from the Montreal Cognitive Assessment items. Area under the receiver operating characteristics curve analyses were conducted to determine the discriminant indices of the screening instruments, the conjunctive combination (ie, screened positive on both tests), and the compensatory combination (ie, screened positive in either of or both tests). A total of 309 participants were recruited of whom 78.7% (n = 243) had CDR = 0 and 21.3% (n = 66) had CDR ≥0.5. The conjunctive combination of AD8 and NINDS-CSN 5-minute protocol achieved excellent PPV and acceptable sensitivity (PPV 91.7%, sensitivity 73.3%). The conjunctive combination of the AD8 and NINDS-CSN 5-minute protocol is brief and accurate, and hence, suitable for case finding of cognitive impairment (CDR ≥0.5) in patients screened positive on the TRS in primary healthcare centers. Copyright © 2016. Published by Elsevier Inc.

Inflatable Antennas Support Emergency Communication

NASA Technical Reports Server (NTRS)

2010-01-01

Glenn Research Center awarded Small Business Innovation Research (SBIR) contracts to ManTech SRS Technologies, of Newport Beach, California, to develop thin film inflatable antennas for space communication. With additional funding, SRS modified the concepts for ground-based inflatable antennas. GATR (Ground Antenna Transmit and Receive) Technologies, of Huntsville, Alabama, licensed the technology and refined it to become the world s first inflatable antenna certified by the Federal Communications Commission. Capable of providing Internet access, voice over Internet protocol, e-mail, video teleconferencing, broadcast television, and other high-bandwidth communications, the systems have provided communication during the wildfires in California, after Hurricane Katrina in Mississippi, and following the 2010 Haiti earthquake.

Refined approach for quantification of in vivo ischemia-reperfusion injury in the mouse heart

PubMed Central

Medway, Debra J.; Schulz-Menger, Jeanette; Schneider, Jurgen E.; Neubauer, Stefan; Lygate, Craig A.

2009-01-01

Cardiac ischemia-reperfusion experiments in the mouse are important in vivo models of human disease. Infarct size is a particularly important scientific readout as virtually all cardiocirculatory pathways are affected by it. Therefore, such measurements must be exact and valid. The histological analysis, however, remains technically challenging, and the resulting quality is often unsatisfactory. For this report we have scrutinized each step involved in standard double-staining histology. We have tested published approaches and challenged their practicality. As a result, we propose an improved and streamlined protocol, which consistently yields high-quality histology, thereby minimizing experimental noise and group sizes. PMID:19820193

Improving Efficiency Using a Hybrid Approach: Revising an Intravenous/Blood Workshop in a Clinical Research Environment.

PubMed

Parchen, Debra A; Phelps, Sandra E; Johnson, Eunice M; Fisher, Cheryl A

2016-01-01

Orienting to a new job can be overwhelming, especially if the nurse is required to develop or refine new skills, such as intravenous (IV) therapy or blood administration. At the National Institutes of Health Clinical Center Nursing Department, a group of nurse educators redesigned their IV/Blood Workshop to prepare nurses with skills needed when caring for patients on protocol in a research intensive environment. Innovative teaching strategies and a hybrid instructional approach were used along with a preworkshop activity, skills lab practice, and follow-up skill validation at the unit level to provide a comprehensive curriculum while decreasing resource utilization.

Bragg projection ptychography on niobium phase domain

DOE PAGES

Burdet, Nicolas; Shi, Xiaowen; Huang, Xiaojing; ...

2016-08-10

Here, we demonstrate that the highly sensitive phase-contrast properties of Bragg coherent diffraction measurements combined with the translational diversity of ptychography can provide a Bragg “dark field” imaging method capable of revealing the finger print of domain structure in metallic thin films. Experimental diffraction data was taken from a epitaxially grown niobium metallic thin film on sapphire; and analyzed with the help of a careful combination of implemented refinement mechanisms.

QUANTIFYING HAZARDOUS SPECIES IN PARTICULATE MATTER DERIVED FROM FOSSIL-FUEL COMBUSTION

EPA Science Inventory

An analysis protocol that combines X-ray absorption near-edge structure spectroscopy with selective leaching has been developed to examine hazardous species in size- segregated particulate matter (PM) samples derived from the combustion of fossil fuels. The protocol has been used...

Extended high dose letrozole regimen versus short low dose letrozole regimen as an adjuvant to gonadotropin releasing hormone antagonist protocol in poor responders undergoing IVF-ET.

PubMed

Fouda, Usama M; Sayed, Ahmed M

2011-12-01

To compare the efficacy and cost-effectiveness of extended high dose letrozole regimen/HPuFSH-gonadotropin releasing hormone antagonist (GnRHant) protocol with short low dose letrozole regimen/HPuFSH-GnRHant protocol in poor responders undergoing IVF-ET. In this randomized controlled trial, 136 women who responded poorly to GnRH agonist long protocol in their first IVF cycle were randomized into two equal groups using computer generated list and were treated in the second IVF cycle by either extended letrozole regimen (5 mg/day during the first 5 days of cycle and 2.5 mg/day during the subsequent 3 days) combined with HPuFSH-GnRHant protocol or short letrozole regimen (2.5 mg/day from cycle day 3-7) combined with HPuFSH-GnRHant protocol. There were no significant differences between both groups with regard to number of oocytes retrieved and clinical pregnancy rate (5.39 ± 2.08 vs. 5.20 ± 1.88 and 22.06% vs. 16.18%, respectively).The total gonadotropins dose and medications cost per cycle were significantly lower in extended letrozole group (44.87 ± 9.16 vs. 59.97 ± 14.91 ampoules and 616.52 ± 94.97 vs. 746.84 ± 149.21 US Dollars ($), respectively).The cost-effectiveness ratio was 2794 $ in extended letrozole group and 4616 $ in short letrozole group. Extended letrozole regimen/HPuFSH-GnRHant protocol was more cost-effective than short letrozole regimen/HPuFSH-GnRHant protocol in poor responders undergoing IVF-ET.

A Secure Routing Protocol for Wireless Sensor Networks Considering Secure Data Aggregation.

PubMed

Rahayu, Triana Mugia; Lee, Sang-Gon; Lee, Hoon-Jae

2015-06-26

The commonly unattended and hostile deployments of WSNs and their resource-constrained sensor devices have led to an increasing demand for secure energy-efficient protocols. Routing and data aggregation receive the most attention since they are among the daily network routines. With the awareness of such demand, we found that so far there has been no work that lays out a secure routing protocol as the foundation for a secure data aggregation protocol. We argue that the secure routing role would be rendered useless if the data aggregation scheme built on it is not secure. Conversely, the secure data aggregation protocol needs a secure underlying routing protocol as its foundation in order to be effectively optimal. As an attempt for the solution, we devise an energy-aware protocol based on LEACH and ESPDA that combines secure routing protocol and secure data aggregation protocol. We then evaluate its security effectiveness and its energy-efficiency aspects, knowing that there are always trade-off between both.

A Secure Routing Protocol for Wireless Sensor Networks Considering Secure Data Aggregation

PubMed Central

Rahayu, Triana Mugia; Lee, Sang-Gon; Lee, Hoon-Jae

2015-01-01

The commonly unattended and hostile deployments of WSNs and their resource-constrained sensor devices have led to an increasing demand for secure energy-efficient protocols. Routing and data aggregation receive the most attention since they are among the daily network routines. With the awareness of such demand, we found that so far there has been no work that lays out a secure routing protocol as the foundation for a secure data aggregation protocol. We argue that the secure routing role would be rendered useless if the data aggregation scheme built on it is not secure. Conversely, the secure data aggregation protocol needs a secure underlying routing protocol as its foundation in order to be effectively optimal. As an attempt for the solution, we devise an energy-aware protocol based on LEACH and ESPDA that combines secure routing protocol and secure data aggregation protocol. We then evaluate its security effectiveness and its energy-efficiency aspects, knowing that there are always trade-off between both. PMID:26131669

Exponentially Decelerated Contrast Media Injection Rate Combined With a Novel Patient-Specific Contrast Formula Reduces Contrast Volume Administration and Radiation Dose During Computed Tomography Pulmonary Angiography.

PubMed

Saade, Charbel; Mayat, Ahmad; El-Merhi, Fadi

2016-01-01

Matching contrast injection timing with vessel dynamics significantly improves vessel opacification and reduces contrast dose in the assessment of pulmonary embolism during computed tomography (CT) pulmonary angiography. The aim of this study was to investigate opacification of the pulmonary vasculature (PV) during CT pulmonary angiography using a patient-specific contrast formula (PSCF) and exponentially decelerated contrast media (EDCM) injection rate. Institutional review board approved this retrospective study. Computed tomography pulmonary angiography was performed on 200 patients with suspected pulmonary embolism using a 64-channel CT scanner. Patient demographics were equally distributed. Patients were randomly assigned to 2 equal protocol groups: protocol A used a PSCF, and protocol B involved the use of a PSCF combined with EDCM. The mean cross-sectional opacification profile of 8 central and 11 peripheral PVs were measured for each patient, and arteriovenous contrast ratio was calculated. Protocols were compared using Mann-Whitney U nonparametric statistics. Jackknife alternative free-response receiver operating characteristic analyses were used to assess diagnostic efficacy. Interobserver variations were investigated using kappa methods. A number of pulmonary arteries demonstrated increases in opacification (P < 0.02) for protocol B compared with A, whereas opacification in all veins was reduced in protocol B (P < 0.03). Subsequently, increased arteriovenous contrast ratio in protocol B compared with A was observed at all anatomic locations (P < 0.0002). An increase in jackknife alternative free-response receiver operating characteristic figure of merit (P < 0.0002) and interobserver variation was observed with protocol B compared with protocol A (κ = 0.3-0.73). Mean contrast volume was reduced in protocol B (29 [4] mL) compared with protocol A (33 [9] mL). Mean effective radiation dose in protocol B (1.2 [0.4] mSv) was reduced by 14% compared with protocol A (1.4 [0.6] mSv). Significant improvements in visualization of the PV can be achieved with a low contrast volume using an EDCM and PSCF. The reduced risk of cancer induction is highlighted.

Structural analysis of glycoproteins: building N-linked glycans with Coot.

PubMed

Emsley, Paul; Crispin, Max

2018-04-01

Coot is a graphics application that is used to build or manipulate macromolecular models; its particular forte is manipulation of the model at the residue level. The model-building tools of Coot have been combined and extended to assist or automate the building of N-linked glycans. The model is built by the addition of monosaccharides, placed by variation of internal coordinates. The subsequent model is refined by real-space refinement, which is stabilized with modified and additional restraints. It is hoped that these enhanced building tools will help to reduce building errors of N-linked glycans and improve our knowledge of the structures of glycoproteins.

Microstructural Modeling of Dynamic Intergranular and Transgranular Fracture Modes in Zircaloys

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

Mohammed, I.; Zikry, M.A.; Ziaei, S.

2017-04-01

In this time period, we have continued to focus on (i) refining the thermo-mechanical fracture model for zirconium (Zr) alloys subjected to large deformations and high temperatures that accounts for the cracking of ZrH and ZrH2 hydrides, (ii) formulating a framework to account intergranular fracture due to iodine diffusion and pit formation in grain-boundaries (GBs). Our future objectives are focused on extending to a combined population of ZrH and ZrH2 populations and understanding how thermo-mechanical behavior affects hydride reorientation and cracking. We will also refine the intergranular failure mechanisms for grain boundaries with pits.

6-Aminopenicillanic acid revisited: A combined solid state NMR and in silico refinement

NASA Astrophysics Data System (ADS)

Aguiar, Daniel Lima Marques de; San Gil, Rosane Aguiar da Silva; Alencastro, Ricardo Bicca de; Souza, Eugenio Furtado de; Borré, Leandro Bandeira; Vaiss, Viviane da Silva; Leitão, Alexandre Amaral

2016-09-01

13C/15N (experimental and ab initio) solid-state NMR was used to achieve an affordable way to improve hydrogen refinement of 6-aminopenicillanic acid (6-APA) structure. The lattice effect on the isotropic chemical shifts was probed by using two different magnetic shielding calculations: isolated molecules and periodic crystal structure. The electron density difference maps of optimized and non-optimized structures were calculated in order to investigate the interactions inside the 6-APA unit cell. The 13C and 15N chemical shifts assignments were unambiguously stablished. In addition, some of the literature 13C resonances ambiguities could be properly solved.

Bell-Curve Genetic Algorithm for Mixed Continuous and Discrete Optimization Problems

NASA Technical Reports Server (NTRS)

Kincaid, Rex K.; Griffith, Michelle; Sykes, Ruth; Sobieszczanski-Sobieski, Jaroslaw

2002-01-01

In this manuscript we have examined an extension of BCB that encompasses a mix of continuous and quasi-discrete, as well as truly-discrete applications. FVe began by testing two refinements to the discrete version of BCB. The testing of midpoint versus fitness (Tables 1 and 2) proved inconclusive. The testing of discrete normal tails versus standard mutation showed was conclusive and demonstrated that the discrete normal tails are better. Next, we implemented these refinements in a combined continuous and discrete BCB and compared the performance of two discrete distance on the hub problem. Here we found when "order does matter" it pays to take it into account.

SNAr-Based, facile synthesis of a library of Benzothiaoxazepine-1,1’-dioxides

PubMed Central

Rolfe, Alan; Samarakoon, Thiwanka B.; Klimberg, Sarra V.; Brzozowski, Marek; Neuenswander, Benjamin; Lushington, Gerald H.

2011-01-01

The construction of a library of benzothiaoxazepine-1,1’-dioxides utilizing a one-pot, SNAr diversification – ODCT50 scavenging protocol is reported. This protocol combines microwave irradiation to facilitate the reaction, in conjunction with a soluble ROMP-derived scavenger (ODCT) to afford the desired products in good overall purity. Utilizing this protocol, a 78-member library was successfully synthesized and submitted for biological evaluation. PMID:20879738

Methodological accuracy of image-based electron density assessment using dual-energy computed tomography.

PubMed

Möhler, Christian; Wohlfahrt, Patrick; Richter, Christian; Greilich, Steffen

2017-06-01

Electron density is the most important tissue property influencing photon and ion dose distributions in radiotherapy patients. Dual-energy computed tomography (DECT) enables the determination of electron density by combining the information on photon attenuation obtained at two different effective x-ray energy spectra. Most algorithms suggested so far use the CT numbers provided after image reconstruction as input parameters, i.e., are imaged-based. To explore the accuracy that can be achieved with these approaches, we quantify the intrinsic methodological and calibration uncertainty of the seemingly simplest approach. In the studied approach, electron density is calculated with a one-parametric linear superposition ('alpha blending') of the two DECT images, which is shown to be equivalent to an affine relation between the photon attenuation cross sections of the two x-ray energy spectra. We propose to use the latter relation for empirical calibration of the spectrum-dependent blending parameter. For a conclusive assessment of the electron density uncertainty, we chose to isolate the purely methodological uncertainty component from CT-related effects such as noise and beam hardening. Analyzing calculated spectrally weighted attenuation coefficients, we find universal applicability of the investigated approach to arbitrary mixtures of human tissue with an upper limit of the methodological uncertainty component of 0.2%, excluding high-Z elements such as iodine. The proposed calibration procedure is bias-free and straightforward to perform using standard equipment. Testing the calibration on five published data sets, we obtain very small differences in the calibration result in spite of different experimental setups and CT protocols used. Employing a general calibration per scanner type and voltage combination is thus conceivable. Given the high suitability for clinical application of the alpha-blending approach in combination with a very small methodological uncertainty, we conclude that further refinement of image-based DECT-algorithms for electron density assessment is not advisable. © 2017 American Association of Physicists in Medicine.

Microdose GnRH Agonist Flare-Up versus Ultrashort GnRH Agonist Combined with Fixed GnRH Antagonist in Poor Responders of Assisted Reproductive Techniques Cycles.

PubMed

Eftekhar, Maryam; Mohammadian, Farnaz; Yousefnejad, Fariba; Khani, Parisa

2013-01-01

This study compares the microdose flare-up protocol to the ultrashort gonadotropinreleasing hormone (GnRH) agonist flare combined with the fixed multidose GnRH antagonist protocol in poor responders undergoing ovarian stimulation. In this randomized clinical trial, 120 women who were candidates for assisted reproductive techniques (ART) and had histories of one or more failed in vitro fertilization (IVF) cycles with three or fewer retrieved oocytes were prospectively randomized into two groups. Group I (60 patients) received the microdose flare-up regimen and group II (60 patients) received the ultrashort GnRH agonist combined with fixed GnRH antagonist. There were no significant differences between the groups in the number of used gonadotropin ampoules (p=0.591), duration of stimulation (p=0.610), number of retrieved oocytes (p=0.802), fertilization rate (p=0.456), and the number of transferred embryos (p=0.954). The clinical pregnancy rates were statistically similar in group I (10%) compared with group II (13.3%, p=0.389). According to our results, there is no significant difference between these protocols for improving the ART outcome in poor responders. Additional prospective, randomized studies with more patients is necessary to determine the best protocol (Registration Number: IRCT201105096420N1).

Combining Correlation Matrices: Simulation Analysis of Improved Fixed-Effects Methods

ERIC Educational Resources Information Center

Hafdahl, Adam R.

2007-01-01

The originally proposed multivariate meta-analysis approach for correlation matrices--analyze Pearson correlations, with each study's observed correlations replacing their population counterparts in its conditional-covariance matrix--performs poorly. Two refinements are considered: Analyze Fisher Z-transformed correlations, and substitute better…

Visual grading characteristics and ordinal regression analysis during optimisation of CT head examinations.

PubMed

Zarb, Francis; McEntee, Mark F; Rainford, Louise

2015-06-01

To evaluate visual grading characteristics (VGC) and ordinal regression analysis during head CT optimisation as a potential alternative to visual grading assessment (VGA), traditionally employed to score anatomical visualisation. Patient images (n = 66) were obtained using current and optimised imaging protocols from two CT suites: a 16-slice scanner at the national Maltese centre for trauma and a 64-slice scanner in a private centre. Local resident radiologists (n = 6) performed VGA followed by VGC and ordinal regression analysis. VGC alone indicated that optimised protocols had similar image quality as current protocols. Ordinal logistic regression analysis provided an in-depth evaluation, criterion by criterion allowing the selective implementation of the protocols. The local radiology review panel supported the implementation of optimised protocols for brain CT examinations (including trauma) in one centre, achieving radiation dose reductions ranging from 24 % to 36 %. In the second centre a 29 % reduction in radiation dose was achieved for follow-up cases. The combined use of VGC and ordinal logistic regression analysis led to clinical decisions being taken on the implementation of the optimised protocols. This improved method of image quality analysis provided the evidence to support imaging protocol optimisation, resulting in significant radiation dose savings. • There is need for scientifically based image quality evaluation during CT optimisation. • VGC and ordinal regression analysis in combination led to better informed clinical decisions. • VGC and ordinal regression analysis led to dose reductions without compromising diagnostic efficacy.

Direction-aware Slope Limiter for 3D Cubic Grids with Adaptive Mesh Refinement

DOE PAGES

Velechovsky, Jan; Francois, Marianne M.; Masser, Thomas

2018-06-07

In the context of finite volume methods for hyperbolic systems of conservation laws, slope limiters are an effective way to suppress creation of unphysical local extrema and/or oscillations near discontinuities. We investigate properties of these limiters as applied to piecewise linear reconstructions of conservative fluid quantities in three-dimensional simulations. In particular, we are interested in linear reconstructions on Cartesian adaptively refined meshes, where a reconstructed fluid quantity at a face center depends on more than a single gradient component of the quantity. We design a new slope limiter, which combines the robustness of a minmod limiter with the accuracy ofmore » a van Leer limiter. The limiter is called Direction-Aware Limiter (DAL), because the combination is based on a principal flow direction. In particular, DAL is useful in situations where the Barth–Jespersen limiter for general meshes fails to maintain global linear functions, such as on cubic computational meshes with stencils including only faceneighboring cells. Here, we verify the new slope limiter on a suite of standard hydrodynamic test problems on Cartesian adaptively refined meshes. Lastly, we demonstrate reduced mesh imprinting; for radially symmetric problems such as the Sedov blast wave or the Noh implosion test cases, the results with DAL show better preservation of radial symmetry compared to the other standard methods on Cartesian meshes.« less

Direction-aware Slope Limiter for 3D Cubic Grids with Adaptive Mesh Refinement

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

Velechovsky, Jan; Francois, Marianne M.; Masser, Thomas

In the context of finite volume methods for hyperbolic systems of conservation laws, slope limiters are an effective way to suppress creation of unphysical local extrema and/or oscillations near discontinuities. We investigate properties of these limiters as applied to piecewise linear reconstructions of conservative fluid quantities in three-dimensional simulations. In particular, we are interested in linear reconstructions on Cartesian adaptively refined meshes, where a reconstructed fluid quantity at a face center depends on more than a single gradient component of the quantity. We design a new slope limiter, which combines the robustness of a minmod limiter with the accuracy ofmore » a van Leer limiter. The limiter is called Direction-Aware Limiter (DAL), because the combination is based on a principal flow direction. In particular, DAL is useful in situations where the Barth–Jespersen limiter for general meshes fails to maintain global linear functions, such as on cubic computational meshes with stencils including only faceneighboring cells. Here, we verify the new slope limiter on a suite of standard hydrodynamic test problems on Cartesian adaptively refined meshes. Lastly, we demonstrate reduced mesh imprinting; for radially symmetric problems such as the Sedov blast wave or the Noh implosion test cases, the results with DAL show better preservation of radial symmetry compared to the other standard methods on Cartesian meshes.« less

Statistical Analysis of CFD Solutions from 2nd Drag Prediction Workshop

NASA Technical Reports Server (NTRS)

Hemsch, M. J.; Morrison, J. H.

2004-01-01

In June 2001, the first AIAA Drag Prediction Workshop was held to evaluate results obtained from extensive N-Version testing of a series of RANS CFD codes. The geometry used for the computations was the DLR-F4 wing-body combination which resembles a medium-range subsonic transport. The cases reported include the design cruise point, drag polars at eight Mach numbers, and drag rise at three values of lift. Although comparisons of the code-to-code medians with available experimental data were similar to those obtained in previous studies, the code-to-code scatter was more than an order-of-magnitude larger than expected and far larger than desired for design and for experimental validation. The second Drag Prediction Workshop was held in June 2003 with emphasis on the determination of installed pylon-nacelle drag increments and on grid refinement studies. The geometry used was the DLR-F6 wing-body-pylon-nacelle combination for which the design cruise point and the cases run were similar to the first workshop except for additional runs on coarse and fine grids to complement the runs on medium grids. The code-to-code scatter was significantly reduced for the wing-body configuration compared to the first workshop, although still much larger than desired. However, the grid refinement studies showed no sign$cant improvement in code-to-code scatter with increasing grid refinement.

CCSDS Advanced Orbiting Systems Virtual Channel Access Service for QoS MACHETE Model

NASA Technical Reports Server (NTRS)

Jennings, Esther H.; Segui, John S.

2011-01-01

To support various communications requirements imposed by different missions, interplanetary communication protocols need to be designed, validated, and evaluated carefully. Multimission Advanced Communications Hybrid Environment for Test and Evaluation (MACHETE), described in "Simulator of Space Communication Networks" (NPO-41373), NASA Tech Briefs, Vol. 29, No. 8 (August 2005), p. 44, combines various tools for simulation and performance analysis of space networks. The MACHETE environment supports orbital analysis, link budget analysis, communications network simulations, and hardware-in-the-loop testing. By building abstract behavioral models of network protocols, one can validate performance after identifying the appropriate metrics of interest. The innovators have extended the MACHETE model library to include a generic link-layer Virtual Channel (VC) model supporting quality-of-service (QoS) controls based on IP streams. The main purpose of this generic Virtual Channel model addition was to interface fine-grain flow-based QoS (quality of service) between the network and MAC layers of the QualNet simulator, a commercial component of MACHETE. This software model adds the capability of mapping IP streams, based on header fields, to virtual channel numbers, allowing extended QoS handling at link layer. This feature further refines the QoS v existing at the network layer. QoS at the network layer (e.g. diffserv) supports few QoS classes, so data from one class will be aggregated together; differentiating between flows internal to a class/priority is not supported. By adding QoS classification capability between network and MAC layers through VC, one maps multiple VCs onto the same physical link. Users then specify different VC weights, and different queuing and scheduling policies at the link layer. This VC model supports system performance analysis of various virtual channel link-layer QoS queuing schemes independent of the network-layer QoS systems.

Radionuclide-fluorescence Reporter Gene Imaging to Track Tumor Progression in Rodent Tumor Models

PubMed Central

Volpe, Alessia; Man, Francis; Lim, Lindsay; Khoshnevisan, Alex; Blower, Julia; Blower, Philip J.; Fruhwirth, Gilbert O.

2018-01-01

Metastasis is responsible for most cancer deaths. Despite extensive research, the mechanistic understanding of the complex processes governing metastasis remains incomplete. In vivo models are paramount for metastasis research, but require refinement. Tracking spontaneous metastasis by non-invasive in vivo imaging is now possible, but remains challenging as it requires long-time observation and high sensitivity. We describe a longitudinal combined radionuclide and fluorescence whole-body in vivo imaging approach for tracking tumor progression and spontaneous metastasis. This reporter gene methodology employs the sodium iodide symporter (NIS) fused to a fluorescent protein (FP). Cancer cells are engineered to stably express NIS-FP followed by selection based on fluorescence-activated cell sorting. Corresponding tumor models are established in mice. NIS-FP expressing cancer cells are tracked non-invasively in vivo at the whole-body level by positron emission tomography (PET) using the NIS radiotracer [18F]BF4-. PET is currently the most sensitive in vivo imaging technology available at this scale and enables reliable and absolute quantification. Current methods either rely on large cohorts of animals that are euthanized for metastasis assessment at varying time points, or rely on barely quantifiable 2D imaging. The advantages of the described method are: (i) highly sensitive non-invasive in vivo 3D PET imaging and quantification, (ii) automated PET tracer production, (iii) a significant reduction in required animal numbers due to repeat imaging options, (iv) the acquisition of paired data from subsequent imaging sessions providing better statistical data, and (v) the intrinsic option for ex vivo confirmation of cancer cells in tissues by fluorescence microscopy or cytometry. In this protocol, we describe all steps required for routine NIS-FP-afforded non-invasive in vivo cancer cell tracking using PET/CT and ex vivo confirmation of in vivo results. This protocol has applications beyond cancer research whenever in vivo localization, expansion and long-time monitoring of a cell population is of interest. PMID:29608157

Recording Brain Electromagnetic Activity During the Administration of the Gaseous Anesthetic Agents Xenon and Nitrous Oxide in Healthy Volunteers.

PubMed

Pelentritou, Andria; Kuhlmann, Levin; Cormack, John; Woods, Will; Sleigh, Jamie; Liley, David

2018-01-13

Anesthesia arguably provides one of the only systematic ways to study the neural correlates of global consciousness/unconsciousness. However to date most neuroimaging or neurophysiological investigations in humans have been confined to the study of γ-Amino-Butyric-Acid-(GABA)-receptor-agonist-based anesthetics, while the effects of dissociative N-Methyl-D-Aspartate-(NMDA)-receptor-antagonist-based anesthetics ketamine, nitrous oxide (N2O) and xenon (Xe) are largely unknown. This paper describes the methods underlying the simultaneous recording of magnetoencephalography (MEG) and electroencephalography (EEG) from healthy males during inhalation of the gaseous anesthetic agents N2O and Xe. Combining MEG and EEG data enables the assessment of electromagnetic brain activity during anesthesia at high temporal, and moderate spatial, resolution. Here we describe a detailed protocol, refined over multiple recording sessions, that includes subject recruitment, anesthesia equipment setup in the MEG scanner room, data collection and basic data analysis. In this protocol each participant is exposed to varying levels of Xe and N2O in a repeated measures cross-over design. Following relevant baseline recordings participants are exposed to step-wise increasing inspired concentrations of Xe and N2O of 8, 16, 24 and 42%, and 16, 32 and 47% respectively, during which their level of responsiveness is tracked with an auditory continuous performance task (aCPT). Results are presented for a number of recordings to highlight the sensor-level properties of the raw data, the spectral topography, the minimization of head movements, and the unequivocal level dependent effects on the auditory evoked responses. This paradigm describes a general approach to the recording of electromagnetic signals associated with the action of different kinds of gaseous anesthetics, which can be readily adapted to be used with volatile and intravenous anesthetic agents. It is expected that the method outlined can contribute to the understanding of the macro-scale mechanisms of anesthesia by enabling methodological extensions involving source space imaging and functional network analysis.

DNA electrotransfer into the skin using a combination of one high- and one low-voltage pulse.

PubMed

Pavselj, N; Préat, V

2005-09-02

Electroporation is an effective alternative to viral methods to significantly improve DNA transfection after intradermal and topical delivery. The aim of the study was to check whether a combination of a short high-voltage pulse (HV) to permeabilize the skin cells and a long low-voltage pulse (LV) to transfer DNA by electrophoresis was more efficient to enhance DNA expression than conventional repeated HV or LV pulses alone after intradermal injection of DNA plasmid. GFP and luciferase expressions in the skin were enhanced by HV+LV protocol as compared to HV or LV pulses alone. The expression lasted for up to 10 days. Consistently, HV+LV protocol induced a higher Th2 immune response against ovalbumin than HV or LV pulses. Standard methods were used to assess the effect of electric pulses on skin: the application of a combination of HV and LV pulses on rat skin fold delivered by plate electrodes was well tolerated. These data demonstrate that a combination of one HV (700 to 1000 V/cm; 100 micros) followed by one LV (140 to 200 V/cm; 400 ms) is an efficient electroporation protocol to enhance DNA expression in the skin.

42 CFR 493.1278 - Standard: Histocompatibility.

Code of Federal Regulations, 2013 CFR

2013-10-01

... screening, compatibility testing and crossmatching) to be performed for each type of cell, tissue or organ... protocols for cadaver donor, living, living-related, and combined organ and tissue transplants; (ii) Testing protocols for patients at high risk for allograft rejection; and (iii) The level of testing required to...

42 CFR 493.1278 - Standard: Histocompatibility.

Code of Federal Regulations, 2014 CFR

2014-10-01

... screening, compatibility testing and crossmatching) to be performed for each type of cell, tissue or organ... protocols for cadaver donor, living, living-related, and combined organ and tissue transplants; (ii) Testing protocols for patients at high risk for allograft rejection; and (iii) The level of testing required to...

Species and tissues specific differentiation of processed animal proteins in aquafeeds using proteomics tools.

PubMed

Rasinger, J D; Marbaix, H; Dieu, M; Fumière, O; Mauro, S; Palmblad, M; Raes, M; Berntssen, M H G

2016-09-16

The rapidly growing aquaculture industry drives the search for sustainable protein sources in fish feed. In the European Union (EU) since 2013 non-ruminant processed animal proteins (PAP) are again permitted to be used in aquafeeds. To ensure that commercial fish feeds do not contain PAP from prohibited species, EU reference methods were established. However, due to the heterogeneous and complex nature of PAP complementary methods are required to guarantee the safe use of this fish feed ingredient. In addition, there is a need for tissue specific PAP detection to identify the sources (i.e. bovine carcass, blood, or meat) of illegal PAP use. In the present study, we investigated and compared different protein extraction, solubilisation and digestion protocols on different proteomics platforms for the detection and differentiation of prohibited PAP. In addition, we assessed if tissue specific PAP detection was feasible using proteomics tools. All work was performed independently in two different laboratories. We found that irrespective of sample preparation gel-based proteomics tools were inappropriate when working with PAP. Gel-free shotgun proteomics approaches in combination with direct spectral comparison were able to provide quality species and tissue specific data to complement and refine current methods of PAP detection and identification. To guarantee the safe use of processed animal protein (PAP) in aquafeeds efficient PAP detection and monitoring tools are required. The present study investigated and compared various proteomics workflows and shows that the application of shotgun proteomics in combination with direct comparison of spectral libraries provides for the desired species and tissue specific classification of this heat sterilized and pressure treated (≥133°C, at 3bar for 20min) protein feed ingredient. Copyright © 2016 Elsevier B.V. All rights reserved.

Difficulties in controlling mobilization pain using a standardized patient-controlled analgesia protocol in burns.

PubMed

Nilsson, Andreas; Kalman, Sigga; Sonesson, Lena Karin; Arvidsson, Anders; Sjöberg, Folke

2011-01-01

The aim of this study was to evaluate pain relief for patients with burns during rest and mobilization with morphine according to a standard protocol for patient-controlled analgesia (PCA). Eighteen patients with a mean (SD) burned TBSA% of 26 (20) were studied for 10 days. Using a numeric rating scale (NRS, 0 = no pain and 10 = unbearable pain), patients were asked to estimate their acceptable and worst experienced pain by specifying a number on a scale and at what point they would like additional analgesics. Patients were allowed free access to morphine with a PCA pump device. Bolus doses were set according to age, (100 - age)/24 = bolus dose (mg), and 6 minutes lockout time. Degrees of pain, morphine requirements, doses delivered and demanded, oral intake of food, and antiemetics given were used as endpoints. Acceptable pain (mean [SD]) was estimated to be 3.8 (1.3) on the NRS, and additional treatment was considered necessary at scores of 4.3 (1.6) or more. NRS at rest was 2.7 (2.2) and during mobilization 4.7 (2.6). Required mean morphine per day was 81 (15) mg, and the number of doses requested increased during the first 6 days after the burn. The authors found no correlation between dose of morphine required and any other variables. Background pain can be controlled adequately with a standard PCA protocol. During mobilization, the pain experienced was too intense, despite having the already high doses of morphine increased. The present protocol must be refined further to provide analgesia adequate to cover mobilization as well.

Transmission fidelity is the key to the build-up of cumulative culture

PubMed Central

Lewis, Hannah M.; Laland, Kevin N.

2012-01-01

Many animals have socially transmitted behavioural traditions, but human culture appears unique in that it is cumulative, i.e. human cultural traits increase in diversity and complexity over time. It is often suggested that high-fidelity cultural transmission is necessary for cumulative culture to occur through refinement, a process known as ‘ratcheting’, but this hypothesis has never been formally evaluated. We discuss processes of information transmission and loss of traits from a cognitive viewpoint alongside other cultural processes of novel invention (generation of entirely new traits), modification (refinement of existing traits) and combination (bringing together two established traits to generate a new trait). We develop a simple cultural transmission model that does not assume major evolutionary changes (e.g. in brain architecture) and show that small changes in the fidelity with which information is passed between individuals can lead to cumulative culture. In comparison, modification and combination have a lesser influence on, and novel invention appears unimportant to, the ratcheting process. Our findings support the idea that high-fidelity transmission is the key driver of human cumulative culture, and that progress in cumulative culture depends more on trait combination than novel invention or trait modification. PMID:22734060

Transmission fidelity is the key to the build-up of cumulative culture.

PubMed

Lewis, Hannah M; Laland, Kevin N

2012-08-05

Many animals have socially transmitted behavioural traditions, but human culture appears unique in that it is cumulative, i.e. human cultural traits increase in diversity and complexity over time. It is often suggested that high-fidelity cultural transmission is necessary for cumulative culture to occur through refinement, a process known as 'ratcheting', but this hypothesis has never been formally evaluated. We discuss processes of information transmission and loss of traits from a cognitive viewpoint alongside other cultural processes of novel invention (generation of entirely new traits), modification (refinement of existing traits) and combination (bringing together two established traits to generate a new trait). We develop a simple cultural transmission model that does not assume major evolutionary changes (e.g. in brain architecture) and show that small changes in the fidelity with which information is passed between individuals can lead to cumulative culture. In comparison, modification and combination have a lesser influence on, and novel invention appears unimportant to, the ratcheting process. Our findings support the idea that high-fidelity transmission is the key driver of human cumulative culture, and that progress in cumulative culture depends more on trait combination than novel invention or trait modification.

MANEMO Routing in Practice: Protocol Selection, Expected Performance, and Experimental Evaluation

NASA Astrophysics Data System (ADS)

Tazaki, Hajime; van Meter, Rodney; Wakikawa, Ryuji; Wongsaardsakul, Thirapon; Kanchanasut, Kanchana; Dias de Amorim, Marcelo; Murai, Jun

Motivated by the deployment of post-disaster MANEMO (MANET for NEMO) composed of mobile routers and stations, we evaluate two candidate routing protocols through network simulation, theoretical performance analysis, and field experiments. The first protocol is the widely adopted Optimized Link State Routing protocol (OLSR) and the second is the combination of the Tree Discovery Protocol (TDP) with Network In Node Advertisement (NINA). To the best of our knowledge, this is the first time that these two protocols are compared in both theoretical and practical terms. We focus on the control overhead generated when mobile routers perform a handover. Our results confirm the correctness and operational robustness of both protocols. More interestingly, although in the general case OLSR leads to better results, TDP/NINA outperforms OLSR both in the case of sparse networks and in highly mobile networks, which correspond to the operation point of a large set of post-disaster scenarios.

Catalysts for coal liquefaction processes

DOEpatents

Garg, Diwakar

1986-01-01

Improved catalysts for catalytic solvent refining or hydroliquefaction of non-anthracitic coal at elevated temperatures under hydrogen pressure in a hydrogen donor solvent comprise a combination of zinc or copper, or a compound thereof, and a Group VI or non-ferrous Group VIII metal, or a compound thereof.

Catalysts for coal liquefaction processes

DOEpatents

Garg, D.

1986-10-14

Improved catalysts for catalytic solvent refining or hydroliquefaction of non-anthracitic coal at elevated temperatures under hydrogen pressure in a hydrogen donor solvent comprise a combination of zinc or copper, or a compound thereof, and a Group VI or non-ferrous Group VIII metal, or a compound thereof.

Identification of vegetable oil botanical speciation in refined vegetable oil blends using an innovative combination of chromatographic and spectroscopic techniques.

PubMed

Osorio, Maria Teresa; Haughey, Simon A; Elliott, Christopher T; Koidis, Anastasios

2015-12-15

European Regulation 1169/2011 requires producers of foods that contain refined vegetable oils to label the oil types. A novel rapid and staged methodology has been developed for the first time to identify common oil species in oil blends. The qualitative method consists of a combination of a Fourier Transform Infrared (FTIR) spectroscopy to profile the oils and fatty acid chromatographic analysis to confirm the composition of the oils when required. Calibration models and specific classification criteria were developed and all data were fused into a simple decision-making system. The single lab validation of the method demonstrated the very good performance (96% correct classification, 100% specificity, 4% false positive rate). Only a small fraction of the samples needed to be confirmed with the majority of oils identified rapidly using only the spectroscopic procedure. The results demonstrate the huge potential of the methodology for a wide range of oil authenticity work. Copyright © 2014 Elsevier Ltd. All rights reserved.

Improved Atomistic Monte Carlo Simulations Demonstrate that Poly-L-Proline Adopts Heterogeneous Ensembles of Conformations of Semi-Rigid Segments Interrupted by Kinks

PubMed Central

Radhakrishnan, Aditya; Vitalis, Andreas; Mao, Albert H.; Steffen, Adam T.; Pappu, Rohit V.

2012-01-01

Poly-L-proline (PLP) polymers are useful mimics of biologically relevant proline-rich sequences. Biophysical and computational studies of PLP polymers in aqueous solutions are challenging because of the diversity of length scales and the slow time scales for conformational conversions. We describe an atomistic simulation approach that combines an improved ABSINTH implicit solvation model, with conformational sampling based on standard and novel Metropolis Monte Carlo moves. Refinements to forcefield parameters were guided by published experimental data for proline-rich systems. We assessed the validity of our simulation results through quantitative comparisons to experimental data that were not used in refining the forcefield parameters. Our analysis shows that PLP polymers form heterogeneous ensembles of conformations characterized by semi-rigid, rod-like segments interrupted by kinks, which result from a combination of internal cis peptide bonds, flexible backbone ψ-angles, and the coupling between ring puckering and backbone degrees of freedom. PMID:22329658

Agrobacterium-mediated transformation of two Serbian potato cultivars (Solanum tuberosum L. cv. Dragacevka and cv. Jelica)

USDA-ARS?s Scientific Manuscript database

An efficient protocol for Agrobacterium-mediated transformation of Serbian potato cultivars Dragacevka and Jelica, enabling the introduction of oryzacystatin genes OCI and OCII, was established. Starting with leaf explants a two-stage transformation protocol combining procedures of Webb and Wenzler...

Combining Electrolysis and Electroporation for Tissue Ablation.

PubMed

Phillips, Mary; Rubinsky, Liel; Meir, Arie; Raju, Narayan; Rubinsky, Boris

2015-08-01

Electrolytic ablation is a method that operates by delivering low magnitude direct current to the target region over long periods of time, generating electrolytic products that destroy cells. This study was designed to explore the hypothesis stating that electrolytic ablation can be made more effective when the electrolysis-producing electric charges are delivered using electric pulses with field strength typical in reversible electroporation protocols. (For brevity we will refer to tissue ablation protocols that combine electroporation and electrolysis as E(2).) The mechanistic explanation of this hypothesis is related to the idea that products of electrolysis generated by E(2) protocols can gain access to the interior of the cell through the electroporation permeabilized cell membrane and therefore cause more effective cell death than from the exterior of an intact cell. The goal of this study is to provide a first-order examination of this hypothesis by comparing the charge dosage required to cause a comparable level of damage to a rat liver, in vivo, when using either conventional electrolysis or E(2) approaches. Our results show that E(2) protocols produce tissue damage that is consistent with electrolytic ablation. Furthermore, E(2) protocols cause damage comparable to that produced by conventional electrolytic protocols while delivering orders of magnitude less charge to the target tissue over much shorter periods of time. © The Author(s) 2014.

Bulk Nanolaminated Nickel: Preparation, Microstructure, Mechanical Property, and Thermal Stability

NASA Astrophysics Data System (ADS)

Liu, Fan; Yuan, Hao; Goel, Sunkulp; Liu, Ying; Wang, Jing Tao

2018-02-01

A bulk nanolaminated (NL) structure with distinctive fractions of low- and high-angle grain boundaries ( f LAGBs and f HAGBs) is produced in pure nickel, through a two-step process of primary grain refinement by equal-channel angular pressing (ECAP), followed by a secondary geometrical refinement via liquid nitrogen rolling (LNR). The lamellar boundary spacings of 2N and 4N nickel are refined to 40 and 70 nm, respectively, and the yield strength of the NL structure in 2N nickel reaches 1.5 GPa. The impacts of the deformation path, material purity, grain boundary (GB) misorientation, and energy on the microstructure, refinement ability, mechanical strength, and thermal stability are investigated to understand the inherent governing mechanisms. GB migration is the main restoration mechanism limiting the refinement of an NL structure in 4N nickel, while in 2N nickel, shear banding occurs and mediates one-fifth of the total true normal rolling strain at the mesoscale, restricting further refinement. Three typical structures [ultrafine grained (UFG), NL with low f LAGBs, and NL with high f LAGBs] obtained through three different combinations of ECAP and LNR were studied by isochronal annealing for 1 hour at temperatures ranging from 433 K to 973 K (160 °C to 700 °C). Higher thermal stability in the NL structure with high f LAGBs is shown by a 50 K (50 °C) delay in the initiation temperature of recrystallization. Based on calculations and analyses of the stored energies of deformed structures from strain distribution, as characterized by kernel average misorientation (KAM), and from GB misorientations, higher thermal stability is attributed to high f LAGBs in this type of NL structure. This is confirmed by a slower change in the microstructure, as revealed by characterizing its annealing kinetics using KAM maps.

Revisiting Cardiac Cellular Composition

PubMed Central

Pinto, Alexander R.; Ilinykh, Alexei; Ivey, Malina J.; Kuwabara, Jill T.; D'Antoni, Michelle L.; Debuque, Ryan; Chandran, Anjana; Wang, Lina; Arora, Komal; Rosenthal, Nadia; Tallquist, Michelle D.

2015-01-01

Rationale Accurate knowledge of the cellular composition of the heart is essential to fully understand the changes that occur during pathogenesis and to devise strategies for tissue engineering and regeneration. Objective To examine the relative frequency of cardiac endothelial cells, hematopoietic-derived cells and fibroblasts in the mouse and human heart. Methods and Results Using a combination of genetic tools and cellular markers, we examined the occurrence of the most prominent cell types in the adult mouse heart. Immunohistochemistry revealed that endothelial cells constitute over 60%, hematopoietic-derived cells 5–10%, and fibroblasts under 20% of the non-myocytes in the heart. A refined cell isolation protocol and an improved flow cytometry approach provided an independent means of determining the relative abundance of non-myocytes. High dimensional analysis and unsupervised clustering of cell populations confirmed that endothelial cells are the most abundant cell population. Interestingly, fibroblast numbers are smaller than previously estimated, and two commonly assigned fibroblast markers, Sca-1 and CD90, underrepresent fibroblast numbers. We also describe an alternative fibroblast surface marker that more accurately identifies the resident cardiac fibroblast population. Conclusions This new perspective on the abundance of different cell types in the heart demonstrates that fibroblasts comprise a relatively minor population. By contrast, endothelial cells constitute the majority of non-cardiomyocytes and are likely to play a greater role in physiologic function and response to injury than previously appreciated. PMID:26635390

Wayfinding the Live 5-2-1-0 Initiative-At the Intersection between Systems Thinking and Community-Based Childhood Obesity Prevention.

PubMed

Amed, Shazhan; Shea, Stephanie; Pinkney, Susan; Wharf Higgins, Joan; Naylor, Patti-Jean

2016-06-21

Childhood obesity is complex and requires a 'systems approach' that collectively engages across multiple community settings. Sustainable Childhood Obesity Prevention through Community Engagement (SCOPE) has implemented Live 5-2-1-0-a multi-sector, multi-component childhood obesity prevention initiative informed by systems thinking and participatory research via an innovative knowledge translation (KT) model (RE-FRAME). This paper describes the protocol for implementing and evaluating RE-FRAME in two 'existing' (>2 years of implementation) and two 'new' Live 5-2-1-0 communities to understand how to facilitate and sustain systems/community-level change. In this mixed-methods study, RE-FRAME was implemented via online resources, webinars, a backbone organization (SCOPE) coordinating the initiative, and a linking system supporting KT. Qualitative and quantitative data were collected using surveys and stakeholder interviews, analyzed using thematic analysis and descriptive statistics, respectively. Existing communities described the consistency of Live 5-2-1-0 and extensive local partnerships/champions as catalysts for synergistic community-wide action; new communities felt that the simplicity of the message combined with the transfer of experiential learning would inform their own strategies and policies/programs to broadly disseminate Live 5-2-1-0. RE-FRAME effectively guided the refinement of the initiative and provided a framework upon which evaluation results described how to implement a community-based systems approach to childhood obesity prevention.

Study on the interaction of artificial and natural food colorants with human serum albumin: A computational point of view.

PubMed

Masone, Diego; Chanforan, Céline

2015-06-01

Due to the high amount of artificial food colorants present in infants' diets, their adverse effects have been of major concern among the literature. Artificial food colorants have been suggested to affect children's behavior, being hyperactivity the most common disorder. In this study we compare binding affinities of a group of artificial colorants (sunset yellow, quinoline yellow, carmoisine, allura red and tartrazine) and their natural industrial equivalents (carminic acid, curcumin, peonidin-3-glucoside, cyanidin-3-glucoside) to human serum albumin (HSA) by a docking approach and further refinement through atomistic molecular dynamics simulations. Due to the protein-ligand conformational interface complexity, we used collective variable driven molecular dynamics to refine docking predictions and to score them according to a hydrogen-bond criterion. With this protocol, we were able to rank ligand affinities to HSA and to compare between the studied natural and artificial food additives. Our results show that the five artificial colorants studied bind better to HSA than their equivalent natural options, in terms of their H-bonding network, supporting the hypothesis of their potential risk to human health. Copyright © 2015 Elsevier Ltd. All rights reserved.

Spatiotemporal Local-Remote Senor Fusion (ST-LRSF) for Cooperative Vehicle Positioning.

PubMed

Jeong, Han-You; Nguyen, Hoa-Hung; Bhawiyuga, Adhitya

2018-04-04

Vehicle positioning plays an important role in the design of protocols, algorithms, and applications in the intelligent transport systems. In this paper, we present a new framework of spatiotemporal local-remote sensor fusion (ST-LRSF) that cooperatively improves the accuracy of absolute vehicle positioning based on two state estimates of a vehicle in the vicinity: a local sensing estimate, measured by the on-board exteroceptive sensors, and a remote sensing estimate, received from neighbor vehicles via vehicle-to-everything communications. Given both estimates of vehicle state, the ST-LRSF scheme identifies the set of vehicles in the vicinity, determines the reference vehicle state, proposes a spatiotemporal dissimilarity metric between two reference vehicle states, and presents a greedy algorithm to compute a minimal weighted matching (MWM) between them. Given the outcome of MWM, the theoretical position uncertainty of the proposed refinement algorithm is proven to be inversely proportional to the square root of matching size. To further reduce the positioning uncertainty, we also develop an extended Kalman filter model with the refined position of ST-LRSF as one of the measurement inputs. The numerical results demonstrate that the proposed ST-LRSF framework can achieve high positioning accuracy for many different scenarios of cooperative vehicle positioning.

Clinical evaluation of the Novacor totally implantable ventricular assist system. Current status.

PubMed

Daniel, M A; Lee, J; LaForge, D H; Chen, H; Billich, J; Miller, P J; Ramasamy, N; Strauss, L R; Jassawalla, J S; Portner, P M

1991-01-01

The totally implantable Novacor left ventricular assist system (LVAS) is currently approaching clinical evaluation. In vivo testing and production are underway with National Institutes of Health (NIH) support. Activity over the past year has focused on manufacturing engineering, preproduction quality assurance, and in vivo experiment completion. Subsequent to successful completion of the NIH-sponsored, 2-year preclinical device readiness test (DRT), a number of refinements were identified and approved by the NIH technical/data review board. Most of these were necessitated by obsolescence or unavailability of electronic components and the decision to use only high reliability military (MIL) qualified electronic components and processes. A few additional refinements were identified to increase design margins, all of which were qualified by accelerated testing. The development of production processes, automated test programs, and MIL compliant environmental stress screening procedures was completed. Production of LVAS subsystems, including core electronic components (hybrids, application-specific integrated circuits, and surface mount boards), was initiated. Animal studies are underway. The clinical trial, at Presbyterian-University Hospital of Pittsburgh and St. Louis University Medical Center, awaits completion of in vivo experiments, protocol development, and Food and Drug Administration approval.

Accelerator mass spectrometry of Strontium-90 for homeland security, environmental monitoring, and human health

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

Tumey, S J; Brown, T A; Hamilton, T F

2008-03-03

Strontium-90 is one of the most hazardous materials managed by agencies charged with protecting the public from radiation. Traditional radiometric methods have been limited by low sample throughput and slow turnaround times. Mass spectrometry offers the advantage of shorter analysis times and the ability to measure samples immediately after processing, however conventional mass spectrometric techniques are susceptible to molecular isobaric interferences that limit their overall sensitivity. In contrast, accelerator mass spectrometry is insensitive to molecular interferences and we have therefore begun developing a method for determination of {sup 90}Sr by accelerator mass spectrometry. Despite a pervasive interference from {sup 90}Zr,more » our initial development has yielded an instrumental background of {approx} 10{sup 8} atoms (75 mBq) per sample. Further refinement of our system (e.g., redesign of our detector, use of alternative target materials) is expected to push the background below 10{sup 6} atoms, close to the theoretical limit for AMS. Once we have refined our system and developed suitable sample preparation protocols, we will utilize our capability in applications to homeland security, environmental monitoring, and human health.« less

Viability and fertilizing capacity of cryopreserved sperm from three North American acipenseriform species: A retrospective study

USGS Publications Warehouse

Horvath, A.; Wayman, W.R.; Dean, J.C.; Urbanyi, B.; Tiersch, T.R.; Mims, S.D.; Johnson, D.; Jenkins, J.A.

2008-01-01

Populations of sturgeon across the globe are threatened due to unregulated harvest and habitat loss, and the status varies among species across North America. Ready access to viable and functional sperm would contribute to recovery programmes for these species. In this study, we examined the motility, viability (cell membrane integrity) of cryopreserved sperm from three North American acipenseriform species and fertilizing capacity. Milt samples were collected from captive shortnose sturgeon (Acipenser brevirostrum), wild paddlefish (Polyodon spathula) and pallid sturgeon (Scaphirhynchus albus) and cryopreserved using combinations of Modified Tsvetkova's (MT) extender, Original Tsvetkova's extender, and modified Hanks' balanced salt solution, along with the cryoprotectants methanol (MeOH) or dimethyl sulfoxide (DMSO). A dual-staining technique using the fluorescent stains SYBR-14 and propidium iodide was employed with flow cytometry to determine the percentages of spermatozoa that were viable by virtue of having intact membranes. The percentage of viable spermatozoa ranged from 5% to 12% in shortnose sturgeon, 30-59% in paddlefish, and 44-58% in pallid sturgeon. In the first experiment with shortnose sturgeon sperm, methanol allowed for higher values for dependent variables than did DMSO, and sperm viability generally correlated with post-thaw motility. However, fertilization rate, neurulation, or hatching rates were independent from these factors. In the second experiment with shortnose sturgeon, 5% MeOH combined with MT yielded higher values for all parameters tested than the other combinations: viability was correlated with motility, fertilization rate, and hatching rate. Overall, viability and post-thaw motility was not affected by the use of hyperosmotic extenders (OT) or cryoprotectants (DMSO), but their use decreased fertilization percentages. For paddlefish sperm (experiment 3), MT combined with 10% MeOH was clearly a good choice for cryopreservation; viability and motility results were correlated, but independent of fertilization. For pallid sturgeon sperm (experiment 4), MT with 5-10% MeOH showed significantly higher sperm quality and fertilization parameters. Membrane integrity can be used as a predictor of fertilization by cryopreserved sperm, however additional sperm quality parameters, supplementary to motility and membrane integrity, would be useful in the refining and optimizing cryopreservation protocols with acipenseriform sperm. ?? 2008 Blackwell Verlag, Berlin.

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).

Use of a deuterated internal standard with pyrolysis-GC/MS dimeric marker analysis to quantify tire tread particles in the environment.

PubMed

Unice, Kenneth M; Kreider, Marisa L; Panko, Julie M

2012-11-08

Pyrolysis(pyr)-GC/MS analysis of characteristic thermal decomposition fragments has been previously used for qualitative fingerprinting of organic sources in environmental samples. A quantitative pyr-GC/MS method based on characteristic tire polymer pyrolysis products was developed for tread particle quantification in environmental matrices including soil, sediment, and air. The feasibility of quantitative pyr-GC/MS analysis of tread was confirmed in a method evaluation study using artificial soil spiked with known amounts of cryogenically generated tread. Tread concentration determined by blinded analyses was highly correlated (r2 ≥ 0.88) with the known tread spike concentration. Two critical refinements to the initial pyrolysis protocol were identified including use of an internal standard and quantification by the dimeric markers vinylcyclohexene and dipentene, which have good specificity for rubber polymer with no other appreciable environmental sources. A novel use of deuterated internal standards of similar polymeric structure was developed to correct the variable analyte recovery caused by sample size, matrix effects, and ion source variability. The resultant quantitative pyr-GC/MS protocol is reliable and transferable between laboratories.

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

TH-CD-BRA-11: Implementation and Evaluation of a New 3D Dosimetry Protocol for Validating MRI Guided Radiation Therapy Treatments

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

Mein, S; Rankine, L; Department of Radiation Oncology, Washington University School of Medicine

Purpose: To develop, evaluate and apply a novel high-resolution 3D remote dosimetry protocol for validation of MRI guided radiation therapy treatments (MRIdian by ViewRay™). We demonstrate the first application of the protocol (including two small but required new correction terms) utilizing radiochromic 3D plastic PRESAGE™ with optical-CT readout. Methods: A detailed study of PRESAGE™ dosimeters (2kg) was conducted to investigate the temporal and spatial stability of radiation induced optical density change (ΔOD) over 8 days. Temporal stability was investigated on 3 dosimeters irradiated with four equally-spaced square 6MV fields delivering doses between 10cGy and 300cGy. Doses were imaged (read-out) bymore » optical-CT at multiple intervals. Spatial stability of ΔOD response was investigated on 3 other dosimeters irradiated uniformly with 15MV extended-SSD fields with doses of 15cGy, 30cGy and 60cGy. Temporal and spatial (radial) changes were investigated using CERR and MATLAB’s Curve Fitting Tool-box. A protocol was developed to extrapolate measured ΔOD readings at t=48hr (the typical shipment time in remote dosimetry) to time t=1hr. Results: All dosimeters were observed to gradually darken with time (<5% per day). Consistent intra-batch sensitivity (0.0930±0.002 ΔOD/cm/Gy) and linearity (R2=0.9996) was observed at t=1hr. A small radial effect (<3%) was observed, attributed to curing thermodynamics during manufacture. The refined remote dosimetry protocol (including polynomial correction terms for temporal and spatial effects, CT and CR) was then applied to independent dosimeters irradiated with MR-IGRT treatments. Excellent line profile agreement and 3D-gamma results for 3%/3mm, 10% threshold were observed, with an average passing rate 96.5%± 3.43%. Conclusion: A novel 3D remote dosimetry protocol is presented capable of validation of advanced radiation treatments (including MR-IGRT). The protocol uses 2kg radiochromic plastic dosimeters read-out by optical-CT within a week of treatment. The protocol requires small corrections for temporal and spatially-dependent behaviors observed between irradiation and readout.« less

Association between post-game recovery protocols, physical and perceived recovery, and performance in elite Australian Football League players.

PubMed

Bahnert, Andrew; Norton, Kevin; Lock, Phillip

2013-03-01

To determine the associations between post-game recovery protocols and physical and perceptual recovery, and game performance in Australian Football League players. A longitudinal quasi-experimental study design was used across a season. A full squad of 44 footballers was monitored weekly across a 23-game season. Players were required to choose from a number of recovery modalities available immediately post-game. These included floor stretching, pool stretching, bike active recovery, pool active recovery, cold-water immersion, contrast therapy and use of a compression garment. Perceptual measures of recovery were recorded throughout the week and a test of physical performance was conducted two days post-game. Game performance ratings were also recorded. The associations between the post-game recovery protocols chosen and players' perceived recovery, and physical and game performances were determined by the association rule data-mining strategy. Statistically significant associations were found between a number of post-game recovery protocols and perceptual recovery. In general, players who chose cold-water immersion, floor stretching, no active recovery (neither bike or pool) and the use of a compression garment post-game, had an increased probability of reporting greater perceptual recovery across the following week, relative to all other permutations of recovery protocols chosen. There were no associations found between post-game recovery protocol combinations and physical recovery. No associations were found between the post-game recovery methods and the next game performance. Perceptual recovery among players was enhanced through the selection of specific combinations of recovery protocols post game. However, no links were found between recovery protocols and physical or game performance measures. Copyright © 2012 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

Value of 100 kVp scan with sinogram-affirmed iterative reconstruction algorithm on a single-source CT system during whole-body CT for radiation and contrast medium dose reduction: an intra-individual feasibility study.

PubMed

Nagayama, Y; Nakaura, T; Oda, S; Tsuji, A; Urata, J; Furusawa, M; Tanoue, S; Utsunomiya, D; Yamashita, Y

2018-02-01

To perform an intra-individual investigation of the usefulness of a contrast medium (CM) and radiation dose-reduction protocol using single-source computed tomography (CT) combined with 100 kVp and sinogram-affirmed iterative reconstruction (SAFIRE) for whole-body CT (WBCT; chest-abdomen-pelvis CT) in oncology patients. Forty-three oncology patients who had undergone WBCT under both 120 and 100 kVp protocols at different time points (mean interscan intervals: 98 days) were included retrospectively. The CM doses for the 120 and 100 kVp protocols were 600 and 480 mg iodine/kg, respectively; 120 kVp images were reconstructed with filtered back-projection (FBP), whereas 100 kVp images were reconstructed with FBP (100 kVp-F) and the SAFIRE (100 kVp-S). The size-specific dose estimate (SSDE), iodine load and image quality of each protocol were compared. The SSDE and iodine load of 100 kVp protocol were 34% and 21%, respectively, lower than of 120 kVp protocol (SSDE: 10.6±1.1 versus 16.1±1.8 mGy; iodine load: 24.8±4versus 31.5±5.5 g iodine, p<0.01). Contrast enhancement, objective image noise, contrast-to-noise-ratio, and visual score of 100 kVp-S were similar to or better than of 120 kVp protocol. Compared with the 120 kVp protocol, the combined use of 100 kVp and SAFIRE in WBCT for oncology assessment with an SSCT facilitated substantial reduction in the CM and radiation dose while maintaining image quality. Copyright © 2017 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Physical and cognitive task analysis in interventional radiology.

PubMed

Johnson, S; Healey, A; Evans, J; Murphy, M; Crawshaw, M; Gould, D

2006-01-01

To identify, describe and detail the cognitive thought processes, decision-making, and physical actions involved in the preparation and successful performance of core interventional radiology procedures. Five commonly performed core interventional radiology procedures were selected for cognitive task analysis. Several examples of each procedure being performed by consultant interventional radiologists were videoed. The videos of those procedures, and the steps required for successful outcome, were analysed by a psychologist and an interventional radiologist. Once a skeleton algorithm of the procedures was defined, further refinement was achieved using individual interview techniques with consultant interventional radiologists. Additionally a critique of each iteration of the established algorithm was sought from non-participating independent consultant interventional radiologists. Detailed task descriptions and decision protocols were developed for five interventional radiology procedures (arterial puncture, nephrostomy, venous access, biopsy-using both ultrasound and computed tomography, and percutaneous transhepatic cholangiogram). Identical tasks performed within these procedures were identified and standardized within the protocols. Complex procedures were broken down and their constituent processes identified. This might be suitable for use as a training protocol to provide a universally acceptable safe practice at the most fundamental level. It is envisaged that data collected in this way can be used as an educational resource for trainees and could provide the basis for a training curriculum in interventional radiology. It will direct trainees towards safe practice of the highest standard. It will also provide performance objectives of a simulator model.

Individualized music for dementia: Evolution and application of evidence-based protocol.

PubMed

Gerdner, Linda A

2012-04-22

The theory-based intervention of individualized music has been evaluated clinically and empirically leading to advancement and refinement of an evidence-based protocol, currently in its 5th edition. An expanded version of the protocol was written for professional health care providers with a consumer version tailored for family caregivers. The underlying mid-range theory is presented along with a seminal study that was followed by further research in the United States, Canada, Great Britain, France, Sweden, Norway, Japan and Taiwan. Key studies are summarized. Given its efficacy when implemented by research staff, studies have advanced to testing the intervention under real-life conditions when implemented and evaluated by trained nursing assistants in long-term care facilities and visiting family members. In addition, one study evaluated the implementation of music by family members in the home setting. Initial research focused on agitation as the dependent variable with subsequent research indicating a more holistic response such as positive affect, expressed satisfaction, and meaningful interaction with others. The article advances by describing on-line programs designed to train health care professionals in the assessment, implementation and evaluation of individualized music. In addition, Gerdner has written a story for a picture book intended for children and their families (in press). The story models principles of individualized music to elicit positive memories, reduce anxiety and agitation, and promote communication. The article concludes with implications for future research.

A detailed description of the implementation of inpatient insulin orders with a commercial electronic health record system.

PubMed

Neinstein, Aaron; MacMaster, Heidemarie Windham; Sullivan, Mary M; Rushakoff, Robert

2014-07-01

In the setting of Meaningful Use laws and professional society guidelines, hospitals are rapidly implementing electronic glycemic management order sets. There are a number of best practices established in the literature for glycemic management protocols and programs. We believe that this is the first published account of the detailed steps to be taken to design, implement, and optimize glycemic management protocols in a commercial computerized provider order entry (CPOE) system. Prior to CPOE implementation, our hospital already had a mature glycemic management program. To transition to CPOE, we underwent the following 4 steps: (1) preparation and requirements gathering, (2) design and build, (3) implementation and dissemination, and (4) optimization. These steps required more than 2 years of coordinated work between physicians, nurses, pharmacists, and programmers. With the move to CPOE, our complex glycemic management order sets were successfully implemented without any significant interruptions in care. With feedback from users, we have continued to refine the order sets, and this remains an ongoing process. Successful implementation of glycemic management protocols in CPOE is dependent on broad stakeholder input and buy-in. When using a commercial CPOE system, there may be limitations of the system, necessitating workarounds. There should be an upfront plan to apply resources for continuous process improvement and optimization after implementation. © 2014 Diabetes Technology Society.

Individualized music for dementia: Evolution and application of evidence-based protocol

PubMed Central

Gerdner, Linda A

2012-01-01

The theory-based intervention of individualized music has been evaluated clinically and empirically leading to advancement and refinement of an evidence-based protocol, currently in its 5th edition. An expanded version of the protocol was written for professional health care providers with a consumer version tailored for family caregivers. The underlying mid-range theory is presented along with a seminal study that was followed by further research in the United States, Canada, Great Britain, France, Sweden, Norway, Japan and Taiwan. Key studies are summarized. Given its efficacy when implemented by research staff, studies have advanced to testing the intervention under real-life conditions when implemented and evaluated by trained nursing assistants in long-term care facilities and visiting family members. In addition, one study evaluated the implementation of music by family members in the home setting. Initial research focused on agitation as the dependent variable with subsequent research indicating a more holistic response such as positive affect, expressed satisfaction, and meaningful interaction with others. The article advances by describing on-line programs designed to train health care professionals in the assessment, implementation and evaluation of individualized music. In addition, Gerdner has written a story for a picture book intended for children and their families (in press). The story models principles of individualized music to elicit positive memories, reduce anxiety and agitation, and promote communication. The article concludes with implications for future research. PMID:24175165

Large-scale production and isolation of Candida biofilm extracellular matrix.

PubMed

Zarnowski, Robert; Sanchez, Hiram; Andes, David R

2016-12-01

The extracellular matrix of biofilm is unique to the biofilm lifestyle, and it has key roles in community survival. A complete understanding of the biochemical nature of the matrix is integral to the understanding of the roles of matrix components. This knowledge is a first step toward the development of novel therapeutics and diagnostics to address persistent biofilm infections. Many of the assay methods needed for refined matrix composition analysis require milligram amounts of material that is separated from the cellular components of these complex communities. The protocol described here explains the large-scale production and isolation of the Candida biofilm extracellular matrix. To our knowledge, the proposed procedure is the only currently available approach in the field that yields milligram amounts of biofilm matrix. This procedure first requires biofilms to be seeded in large-surface-area roller bottles, followed by cell adhesion and biofilm maturation during continuous movement of the medium across the surface of the rotating bottle. The formed matrix is then separated from the entire biomass using sonication, which efficiently removes the matrix without perturbing the fungal cell wall. Subsequent filtration, dialysis and lyophilization steps result in a purified matrix product sufficient for biochemical, structural and functional assays. The overall protocol takes ∼11 d to complete. This protocol has been used for Candida species, but, using the troubleshooting guide provided, it could be adapted for other fungi or bacteria.

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

PubMed

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

2016-07-01

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

Doxycycline prevents and reverses schizophrenic-like behaviors induced by ketamine in mice via modulation of oxidative, nitrergic and cholinergic pathways.

PubMed

Ben-Azu, Benneth; Omogbiya, Itivere Adrian; Aderibigbe, Adegbuyi Oladele; Umukoro, Solomon; Ajayi, Abayomi Mayowa; Iwalewa, Ezekiel O

2018-05-01

The involvement of oxidative, nitrergic, cholinergic and inflammatory alterations have been reported to contribute to the pathophysiology of schizophrenia, a debilitating neuropsychiatric disorder. Our previous studies have shown that doxycycline (DOX), a notable member of tetracyclines with proven antioxidant and anti-inflammatory properties, attenuated psychotic-like behaviors induced by apomophine and ketamine (KET) in mice. This present study was designed to further evaluate in detail the ability of DOX and its combination with risperidone (RIS) to prevent and reverse KET-induced schizophrenic-like behaviors and the role of oxidative/nitrergic and cholinergic pathways in mice. In the prevention protocol, mice were treated orally with DOX (25, 50 or 100 mg/kg), RIS (0.5 mg/kg), DOX (50 mg/kg) in combination with RIS, or vehicle for 14 consecutive days. In addition, the animals received intraperitoneal injection of KET (20 mg/kg/day) from the 8th to the 14th day. In the reversal protocol, the animals received KET or vehicle for 14 days prior to DOX, RIS, DOX in-combination with RIS or vehicle treatments. Schizophrenic-like behaviors consisting of positive, negative and cognitive symptoms were evaluated using open field, social interaction, Y-maze and novel object recognition tests. Thereafter, the brain levels of biomarkers of oxidative stress, nitrite and acetylcholinesterase activity were determined. DOX given alone or in combination with RIS attenuated schizophrenic-like behaviors induced by chronic injection of KET in both preventive and reversal treatment protocols. DOX significantly increased glutathione, superoxide dismutase and catalase levels in the brain of chronic KET-treated mice. However, it decreased malonyladehyde, nitrite levels and acetylcholinesterase activity when given alone or in-combination with RIS in both protocols. Taken together, these findings showed that doxycycline ameliorated schizophrenic-like behaviors induced by ketamine in both preventive and reversal treatment protocols in mice via inhibition of oxidative and nitrergic alterations, and acetylcholinesterase activity. Our data further suggests that adjunctive oral administration of doxycycline may augment the therapeutic efficacy of risperidone particularly for the treatment of negative and cognitive symptoms associated with schizophrenia. Copyright © 2018 Elsevier Inc. All rights reserved.

Provider Expectations for Recovery Scale: Refining a measure of provider attitudes

PubMed Central

Salyers, Michelle P.; Brennan, Madeline; Kean, Jacob

2014-01-01

Objective The purpose of this study was to refine and test the psychometric properties of a scale to measure provider attitudes about recovery. Methods This was a secondary data analysis that combined survey data from 1,128 mental health providers from 3 state hospitals, 6 community mental health centers, and 1 VA Medical Center. Rasch analyses were used to examine item-level functioning to reduce the scale to a briefer, unidimensional construct. Convergent validity was assessed through correlations with related measures. Results The Provider Expectations for Recovery scale had strong internal consistency, was related to education and setting in expected ways, and was associated with lower levels of burnout and higher levels of job satisfaction. Conclusions and Implications for Practice A 10-item scale of Provider Expectations for Recovery appears to be a useful tool to measure an important construct in recovery-oriented care. The process of refining the measure also highlights potential factors in how providers view recovery. PMID:23834613

Crystallization in lactose refining-a review.

PubMed

Wong, Shin Yee; Hartel, Richard W

2014-03-01

In the dairy industry, crystallization is an important separation process used in the refining of lactose from whey solutions. In the refining operation, lactose crystals are separated from the whey solution through nucleation, growth, and/or aggregation. The rate of crystallization is determined by the combined effect of crystallizer design, processing parameters, and impurities on the kinetics of the process. This review summarizes studies on lactose crystallization, including the mechanism, theory of crystallization, and the impact of various factors affecting the crystallization kinetics. In addition, an overview of the industrial crystallization operation highlights the problems faced by the lactose manufacturer. The approaches that are beneficial to the lactose manufacturer for process optimization or improvement are summarized in this review. Over the years, much knowledge has been acquired through extensive research. However, the industrial crystallization process is still far from optimized. Therefore, future effort should focus on transferring the new knowledge and technology to the dairy industry. © 2014 Institute of Food Technologists®

Characteristics of ADC12/nano Al2O3composites with Addition of Ti Produced By Stir Casting Method

NASA Astrophysics Data System (ADS)

Zulfia, A.; Krisiphala; Ferdian, D.; Utomo, B. W.; Dhaneswara, D.

2018-03-01

The mechanical properties and microstructure of ADC12/nano Al2O3 matrix composites have been studied in this work. The composites were produced by stir casting method. ADC 12 as matrix composites was combined by Mg and Ti. The addition of Ti was varied from 0.02 to 0.08 wt-% as grain refinement wetting to improve mechanical properties such as tensile strength, hardness and wear resistance, while Mg addition was to promote wetting between ADC 12 and nano Al2O3. The optimum tensile strength was found at 0.04 wt-% addition of Ti with value of 132.5 MPa, further adding more Ti cause a poisoning mechanism that will hindered the grain refining process and reduce the tensile strength. The hardness and wear resistance of composites would also increase because of the refinement process. and the added Magnesium in the material that will form Mg2Si primary phases who have a high hardness value.

Evaluation of the University of Florida lomustine, vincristine, procarbazine, and prednisone chemotherapy protocol for the treatment of relapsed lymphoma in dogs: 33 cases (2003-2009).

PubMed

Fahey, Christine E; Milner, Rowan J; Barabas, Karri; Lurie, David; Kow, Kelvin; Parfitt, Shannon; Lyles, Sarah; Clemente, Monica

2011-07-15

To evaluate the toxicity and efficacy of a modification of a previously evaluated combination of lomustine, vincristine, procarbazine, and prednisone (LOPP) as a rescue protocol for refractory lymphoma in dogs. Retrospective case series. Animals-33 dogs with a cytologic or histologic diagnosis of lymphoma that developed resistance to their induction chemotherapy protocol. Lomustine was administered on day 0 of the protocol. Vincristine was administered on day 0 and again 1 time on day 14. Procarbazine and prednisone were administered on days 0 through 13 of the protocol. This cycle was repeated every 28 days. Median time from initiation to discontinuation of the University of Florida LOPP protocol was 84 days (range, 10 to 308 days). Overall median survival time was 290 days (range, 51 to 762 days). Overall response rate with this protocol was 61% (20/33), with 36% (12) having a complete response and 24% (8) having a partial response. Toxicosis rates were lower than for the previously published LOPP protocol. The University of Florida LOPP protocol may be an acceptable alternative to the mechlorethamine, vincristine, procarbazine, and prednisone protocol as a rescue protocol for dogs with lymphoma.

Virtual surgical planning for treatment of severe mandibular retrognathia with collapsed occlusion using contemporary surgical and prosthodontic protocols.

PubMed

Dhima, Matilda; Salinas, Thomas J; Rieck, Kevin L

2013-11-01

To meet functional and esthetic needs in an older adult for treatment of complex skeletal and dentoalveolar deformities using contemporary surgical and prosthodontic protocols. An older adult with dentoalveolar complex and skeletal deformity (mandibular retrognathia) was treated by a combination of virtual planning and current surgical and prosthodontic protocols. Treatment planning steps and sequencing are presented. Skeletal, soft tissue, and dental harmonies were attained without biological or mechanical complications. Definitive oral rehabilitation was completed with a maxillary complete denture and a mandibular metal ceramic fixed implant-retained prosthesis. A surgical and prosthodontic team approach in combination with technologic advances can predictably optimize esthetic and functional outcomes for patients with complex skeletal and dentoalveolar deformities. Copyright © 2013 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

Do emergency medical services dispatch nature and severity codes agree with paramedic field findings?

PubMed

Neely, K W; Eldurkar, J A; Drake, M E

2000-02-01

Emergency medical services (EMS) systems increasingly seek to triage patients to alternative EMS resources. Emergency medical services dispatchers may be asked to perform this triage. New protocols may be necessary. Alternatively, existing protocols may be sufficient for this task. For an existing dispatch protocol to be sufficient, it at least must accurately categorize patient condition and severity based on an external standard. To examine the extent to which nature codes (NCs), or patient condition codes, and severity codes (SCs) currently assigned in one urban 911 center agree with paramedic field findings. The null hypothesis was that there is no routine agreement (75%) between dispatcher-assigned NC or SC and paramedic-assigned NC or SC for the same patient using the same protocol. Emergency medical services dispatch nature and severity code data and matching out-of-hospital data were prospectively gathered over six months. Dispatch data included the NC: caller-identified problem, and the SC: dispatcher-assessed severity. Each NC is modified by one of three SCs (1, 3, or 9): 1 is emergent, 3 is urgent, and 9 is neither. Paramedics verified and/or corrected dispatcher-assigned NCs and SCs using the same dispatch protocol. One thousand forty usable cases fell into 33 unique NC/SC combinations. The designation of SC 1 was assigned 275 times, SC 3 was assigned 736 times, and SC 9 was assigned 24 times. The SC was missing five times. The overall NC agreement was 0.70 (95% CI = 0.697 to 0.703). The overall SC agreement was 0.65 (95% CI = 0.645 to 0.655). The NC agreement exceeded 75% for ten (59%) NC/SC combinations. The SC agreement exceeded 75% for five (29%) NC/SC combinations. There was both NC and SC agreement for four (24%) combinations: urgent breathing problems, urgent diabetic problems, urgent falls, and urgent overdoses. The greatest NC/SC disagreement occurred within emergent and urgent traffic crashes. Paramedics adjusted SC toward lower severity 29% of the time and toward higher severity 5.4% of the time. There was no upward SC adjustment for eight (47%) combinations. Certain dispatcher-assigned NC and SC codes and NC/SC combinations achieved the study threshold. Overall agreement failed to achieve the threshold. The lowest SC level was rarely assigned, preventing a meaningful analysis of all severity levels.

Industry and Education: A Winning Combination.

ERIC Educational Resources Information Center

Payne, John H.; Williams-Foster, Cathy

1997-01-01

Describes how the petrochemical employers of Texas City, Texas developed a fully accredited two-year associate degree program at the local community college tailored to train process operators for entry into the refining and chemical industry. Discusses planning; scholarship funds; vendor and community support; student population; outcomes of the…

In Situ/On-Site Biodegradation of Refined Oils and Fuels (A Technology Review). Volume 3. Appendices B to F.

DTIC Science & Technology

1992-06-01

streams (Oxitron system). The system combines the features of activated sludge and fixed-film biological processes (see Appendix F, Biotechnologies...contaminated aqueous streams. The system combines the features of activated sludge and fixed-film biological processes (see Appendix F, Biotechnologies in... marine oil spills have been estimated to average $6.50/gal of spilled oil (Bartha and Atlas, 1977). This translates to roughly $2000 per metric ton

A Review and Update of Treatment Options and Controversies in the Management of Hepatocellular Carcinoma.

PubMed

Dhir, Mashaal; Melin, Alyson A; Douaiher, Jeffrey; Lin, Chi; Zhen, Weining Ken; Hussain, Shahid M; Geschwind, Jean-Francois H; Doyle, Maria B Majella; Abou-Alfa, Ghassan K; Are, Chandrakanth

2016-06-01

To review the current management, outline recent advances and address controversies in the management of hepatocellular carcinoma (HCC). The treatment of HCC is multidisciplinary involving hepatologists, surgeons, medical oncologists, radiation oncologists, radiologists, interventional radiologists, and other disciplines. Each of these disciplines brings its unique perspective and differing opinions that add to controversies in the management of HCC. A focused literature review was performed to identify recent studies on the management of HCC and thereby summarize relevant information on the various therapeutic modalities and controversies involved in the treatment of HCC. The main treatment algorithms continue to rely on hepatic resection or transplantation with controversies involving patients harboring early stage disease and borderline hepatic function. The other treatment strategies include locoregional therapies, radiation, and systemic therapy used alone or in combination with other treatment modalities. Recent advances in locoregional therapies, radiation, and systemic therapies have provided better therapeutic options with curative intent potential for some locoregional therapies. Further refinements in combination therapies such as algorithms consisting of locoregional therapies and systemic or radiation therapies are likely to add additional options and improve survival. The management of HCC has witnessed significant strides with advances in existing options and introduction of several new treatment modalities of various combinations. Further refinements in these treatment options combined with enrollment in clinical trials are essential to improve the management and outcomes of patients with HCC.

Drought Stress Predominantly Endures Arabidopsis thaliana to Pseudomonas syringae Infection

PubMed Central

Gupta, Aarti; Dixit, Sandeep K.; Senthil-Kumar, Muthappa

2016-01-01

Plant responses to a combination of drought and bacterial pathogen infection, an agronomically important and altogether a new stress, are not well-studied. While occurring concurrently, these two stresses can lead to synergistic or antagonistic effects on plants due to stress-interaction. It is reported that plant responses to the stress combinations consist of both strategies, unique to combined stress and those shared between combined and individual stresses. However, the combined stress response mechanisms governing stress interaction and net impact are largely unknown. In order to study these adaptive strategies, an accurate and convenient methodology is lacking even in model plants like Arabidopsis thaliana. The gradual nature of drought stress imposition protocol poses a hindrance in simultaneously applying pathogen infection under laboratory conditions to achieve combined stress. In present study we aimed to establish systematic combined stress protocol and to study physiological responses of the plants to various degrees of combined stress. Here, we have comprehensively studied the impact of combined drought and Pseudomonas syringae pv. tomato DC3000 infection on A. thaliana. Further, by employing different permutations of drought and pathogen stress intensities, an attempt was made to dissect the contribution of each individual stress effects during their concurrence. We hereby present two main aspects of combined stress viz., stress interaction and net impact of the stress on plants. Mainly, this study established a systematic protocol to assess the impact of combined drought and bacterial pathogen stress. It was observed that as a result of net impact, some physiological responses under combined stress are tailored when compared to the plants exposed to individual stresses. We also infer that plant responses under combined stress in this study are predominantly influenced by the drought stress. Our results show that pathogen multiplication was reduced by drought stress in combined stressed plants. Combined stressed plants also displayed reduced ROS generation and declined cell death which could be attributed to activation of effective basal defense responses. We hypothesize a model on ABA mediated gene regulation to partly explain the possible mechanistic basis for reduced in planta bacterial numbers under combined stress over individual pathogen stress. PMID:27375661

Chelation protocols for the elimination and prevention of iron overload in thalassaemia.

PubMed

Kolnagou, Annita; Kontoghiorghes, George John

2018-01-01

Iron overload toxicity is the main cause of mortality and morbidity in thalassaemia patients. The complete elimination and prevention of iron overload is the main aim of chelation therapy, which can be achieved by chelation protocols that can effectively remove excess iron load and maintain body iron at normal levels. Deferiprone and selected combinations with deferoxamine can be designed, adjusted and used effectively for removing all excess stored iron and for maintaining normal iron stores (NIS) in different categories of thalassaemia patients. High doses of deferiprone (75-100 mg/kg/day) and deferoxamine (50-60 mg/kg, 1-7 days/week) combinations can be used for achieving and maintaining NIS in heavily iron loaded transfused patients. In contrast, deferiprone (75-100 mg/kg/day) can be used effectively and sometimes intermittently for maintaining NIS in non heavily transfused patients. Deferasirox can in particular be used in patients not tolerating deferoxamine and deferiprone. The design of tailored made personalised protocols using deferiprone and selected combinations with deferoxamine should be considered as optimum chelation therapies for the complete treatment and the prevention of iron overload in thalassaemia.

A round-robin gamma stereotactic radiosurgery dosimetry interinstitution comparison of calibration protocols

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

Drzymala, R. E., E-mail: drzymala@wustl.edu; Alvarez, P. E.; Bednarz, G.

2015-11-15

Purpose: Absorbed dose calibration for gamma stereotactic radiosurgery is challenging due to the unique geometric conditions, dosimetry characteristics, and nonstandard field size of these devices. Members of the American Association of Physicists in Medicine (AAPM) Task Group 178 on Gamma Stereotactic Radiosurgery Dosimetry and Quality Assurance have participated in a round-robin exchange of calibrated measurement instrumentation and phantoms exploring two approved and two proposed calibration protocols or formalisms on ten gamma radiosurgery units. The objectives of this study were to benchmark and compare new formalisms to existing calibration methods, while maintaining traceability to U.S. primary dosimetry calibration laboratory standards. Methods:more » Nine institutions made measurements using ten gamma stereotactic radiosurgery units in three different 160 mm diameter spherical phantoms [acrylonitrile butadiene styrene (ABS) plastic, Solid Water, and liquid water] and in air using a positioning jig. Two calibrated miniature ionization chambers and one calibrated electrometer were circulated for all measurements. Reference dose-rates at the phantom center were determined using the well-established AAPM TG-21 or TG-51 dose calibration protocols and using two proposed dose calibration protocols/formalisms: an in-air protocol and a formalism proposed by the International Atomic Energy Agency (IAEA) working group for small and nonstandard radiation fields. Each institution’s results were normalized to the dose-rate determined at that institution using the TG-21 protocol in the ABS phantom. Results: Percentages of dose-rates within 1.5% of the reference dose-rate (TG-21 + ABS phantom) for the eight chamber-protocol-phantom combinations were the following: 88% for TG-21, 70% for TG-51, 93% for the new IAEA nonstandard-field formalism, and 65% for the new in-air protocol. Averages and standard deviations for dose-rates over all measurements relative to the TG-21 + ABS dose-rate were 0.999 ± 0.009 (TG-21), 0.991 ± 0.013 (TG-51), 1.000 ± 0.009 (IAEA), and 1.009 ± 0.012 (in-air). There were no statistically significant differences (i.e., p > 0.05) between the two ionization chambers for the TG-21 protocol applied to all dosimetry phantoms. The mean results using the TG-51 protocol were notably lower than those for the other dosimetry protocols, with a standard deviation 2–3 times larger. The in-air protocol was not statistically different from TG-21 for the A16 chamber in the liquid water or ABS phantoms (p = 0.300 and p = 0.135) but was statistically different from TG-21 for the PTW chamber in all phantoms (p = 0.006 for Solid Water, 0.014 for liquid water, and 0.020 for ABS). Results of IAEA formalism were statistically different from TG-21 results only for the combination of the A16 chamber with the liquid water phantom (p = 0.017). In the latter case, dose-rates measured with the two protocols differed by only 0.4%. For other phantom-ionization-chamber combinations, the new IAEA formalism was not statistically different from TG-21. Conclusions: Although further investigation is needed to validate the new protocols for other ionization chambers, these results can serve as a reference to quantitatively compare different calibration protocols and ionization chambers if a particular method is chosen by a professional society to serve as a standardized calibration protocol.« less

Towards ethically improved animal experimentation in the study of animal reproduction.

PubMed

Blache, D; Martin, G B; Maloney, S K

2008-07-01

The ethics of animal-based research is a continuing area of debate, but ethical research protocols do not prevent scientific progress. In this paper, we argue that our current knowledge of the factors that affect reproductive processes provides researchers with a solid foundation upon which they can conduct more ethical research and simultaneously produce data of higher quality. We support this argument by showing how a deep understanding of the genetics, nutrition and temperament of our experimental animals can improve compliance with two of the '3 Rs', reduction and refinement, simply by offering better control over the variance in our experimental model. The outcome is a better experimental design, on both ethical and scientific grounds.

Fault tolerant architectures for integrated aircraft electronics systems, task 2

NASA Technical Reports Server (NTRS)

Levitt, K. N.; Melliar-Smith, P. M.; Schwartz, R. L.

1984-01-01

The architectural basis for an advanced fault tolerant on-board computer to succeed the current generation of fault tolerant computers is examined. The network error tolerant system architecture is studied with particular attention to intercluster configurations and communication protocols, and to refined reliability estimates. The diagnosis of faults, so that appropriate choices for reconfiguration can be made is discussed. The analysis relates particularly to the recognition of transient faults in a system with tasks at many levels of priority. The demand driven data-flow architecture, which appears to have possible application in fault tolerant systems is described and work investigating the feasibility of automatic generation of aircraft flight control programs from abstract specifications is reported.

Improving Efficiency using a Hybrid Approach: Revising an IV/Blood Workshop in a Clinical Research Environment

PubMed Central

Parchen, Debra A.; Phelps, Sandra E.; Johnson, Eunice M.; Fisher, Cheryl A.

2016-01-01

Orienting to a new job can be overwhelming, especially if the nurse is required to develop or refine new skills, such as intravenous (IV) therapy or blood administration. At the National Institutes of Health Clinical Center Nursing Department, a group of nurse educators redesigned the IV/Blood Workshop to prepare nurses with skills needed when caring for patients on protocol in a research intensive environment. Innovative teaching strategies and a hybrid instructional approach were utilized along with a pre-workshop activity, skills lab practice, and follow up skill validation at the unit level to provide a comprehensive curriculum while decreasing resource utilization. PMID:27187829

Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins.

PubMed

Emperador, Agustí; Orozco, Modesto

2017-03-14

We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems.

DIGITAL CARTOGRAPHY OF THE PLANETS: NEW METHODS, ITS STATUS, AND ITS FUTURE.

USGS Publications Warehouse

Batson, R.M.

1987-01-01

A system has been developed that establishes a standardized cartographic database for each of the 19 planets and major satellites that have been explored to date. Compilation of the databases involves both traditional and newly developed digital image processing and mosaicking techniques, including radiometric and geometric corrections of the images. Each database, or digital image model (DIM), is a digital mosaic of spacecraft images that have been radiometrically and geometrically corrected and photometrically modeled. During compilation, ancillary data files such as radiometric calibrations and refined photometric values for all camera lens and filter combinations and refined camera-orientation matrices for all images used in the mapping are produced.

Nonrigid synthetic aperture radar and optical image coregistration by combining local rigid transformations using a Kohonen network.

PubMed

Salehpour, Mehdi; Behrad, Alireza

2017-10-01

This study proposes a new algorithm for nonrigid coregistration of synthetic aperture radar (SAR) and optical images. The proposed algorithm employs point features extracted by the binary robust invariant scalable keypoints algorithm and a new method called weighted bidirectional matching for initial correspondence. To refine false matches, we assume that the transformation between SAR and optical images is locally rigid. This property is used to refine false matches by assigning scores to matched pairs and clustering local rigid transformations using a two-layer Kohonen network. Finally, the thin plate spline algorithm and mutual information are used for nonrigid coregistration of SAR and optical images.

VizieR Online Data Catalog: methoxy radical (CH3O) rotational spectrum (Laas+,

NASA Astrophysics Data System (ADS)

Laas, J. C.; Widicus Weaver, S. L.

2017-08-01

The methoxy radical (CH3O) has recently been detected interstellar medium and may be an important tracer of methanol-related chemistry in cold sources. Despite its importance, the spectral information needed to guide further astronomical searches is limited. We have therefore studied the low-temperature rotational spectrum in the laboratory within the spectral range of 246-303GHz. We have combined these new measurements with results from a number of literature reports to refine the molecular parameters and provide an updated and improved spectral line catalog. We present here the results of the laboratory studies and the refined analysis for the millimeter and submillimeter spectrum of methoxy. (1 data file).

Domain decomposition methods in computational fluid dynamics

NASA Technical Reports Server (NTRS)

Gropp, William D.; Keyes, David E.

1991-01-01

The divide-and-conquer paradigm of iterative domain decomposition, or substructuring, has become a practical tool in computational fluid dynamic applications because of its flexibility in accommodating adaptive refinement through locally uniform (or quasi-uniform) grids, its ability to exploit multiple discretizations of the operator equations, and the modular pathway it provides towards parallelism. These features are illustrated on the classic model problem of flow over a backstep using Newton's method as the nonlinear iteration. Multiple discretizations (second-order in the operator and first-order in the preconditioner) and locally uniform mesh refinement pay dividends separately, and they can be combined synergistically. Sample performance results are included from an Intel iPSC/860 hypercube implementation.

When combined X-ray and polarized neutron diffraction data challenge high-level calculations: spin-resolved electron density of an organic radical.

PubMed

Voufack, Ariste Bolivard; Claiser, Nicolas; Lecomte, Claude; Pillet, Sébastien; Pontillon, Yves; Gillon, Béatrice; Yan, Zeyin; Gillet, Jean Michel; Marazzi, Marco; Genoni, Alessandro; Souhassou, Mohamed

2017-08-01

Joint refinement of X-ray and polarized neutron diffraction data has been carried out in order to determine charge and spin density distributions simultaneously in the nitronyl nitroxide (NN) free radical Nit(SMe)Ph. For comparison purposes, density functional theory (DFT) and complete active-space self-consistent field (CASSCF) theoretical calculations were also performed. Experimentally derived charge and spin densities show significant differences between the two NO groups of the NN function that are not observed from DFT theoretical calculations. On the contrary, CASSCF calculations exhibit the same fine details as observed in spin-resolved joint refinement and a clear asymmetry between the two NO groups.

On two-point boundary correlations in the six-vertex model with domain wall boundary conditions

NASA Astrophysics Data System (ADS)

Colomo, F.; Pronko, A. G.

2005-05-01

The six-vertex model with domain wall boundary conditions on an N × N square lattice is considered. The two-point correlation function describing the probability of having two vertices in a given state at opposite (top and bottom) boundaries of the lattice is calculated. It is shown that this two-point boundary correlator is expressible in a very simple way in terms of the one-point boundary correlators of the model on N × N and (N - 1) × (N - 1) lattices. In alternating sign matrix (ASM) language this result implies that the doubly refined x-enumerations of ASMs are just appropriate combinations of the singly refined ones.

Microdose GnRH Agonist Flare-Up versus Ultrashort GnRH Agonist Combined with Fixed GnRH Antagonist in Poor Responders of Assisted Reproductive Techniques Cycles

PubMed Central

Eftekhar, Maryam; Mohammadian, Farnaz; Yousefnejad, Fariba; Khani, Parisa

2013-01-01

Background: This study compares the microdose flare-up protocol to the ultrashort gonadotropinreleasing hormone (GnRH) agonist flare combined with the fixed multidose GnRH antagonist protocol in poor responders undergoing ovarian stimulation. Materials and Methods: In this randomized clinical trial, 120 women who were candidates for assisted reproductive techniques (ART) and had histories of one or more failed in vitro fertilization (IVF) cycles with three or fewer retrieved oocytes were prospectively randomized into two groups. Group I (60 patients) received the microdose flare-up regimen and group II (60 patients) received the ultrashort GnRH agonist combined with fixed GnRH antagonist. Results: There were no significant differences between the groups in the number of used gonadotropin ampoules (p=0.591), duration of stimulation (p=0.610), number of retrieved oocytes (p=0.802), fertilization rate (p=0.456), and the number of transferred embryos (p=0.954). The clinical pregnancy rates were statistically similar in group I (10%) compared with group II (13.3%, p=0.389). Conclusion: According to our results, there is no significant difference between these protocols for improving the ART outcome in poor responders. Additional prospective, randomized studies with more patients is necessary to determine the best protocol (Registration Number: IRCT201105096420N1). PMID:24520450

PROFILE: Environmental Impact Assessment Under the National Environmental Policy Act and the Protocol on Environmental Protection to the Antarctic Treaty.

PubMed

Ensminger; McCold; Webb

1999-07-01

/ Antarctica has been set aside by the international community for protection as a natural reserve and a place for scientific research. Through the Antarctic Treaty of 1961, the signing nations agreed to cooperate in protecting the antarctic environment, in conducting scientific studies, and in abstaining from the exercise of territorial claims. The 1991 signing of the Protocol on Environmental Protection to the Antarctic Treaty (Protocol) by representatives of the 26 nations comprising the Antarctic Treaty Consultative Parties (Parties) significantly strengthened environmental protection measures for the continent. The Protocol required ratification by each of the governments individually prior to official implementation. The US government ratified the Protocol by passage of the Antarctic Science, Tourism, and Conservation Act of 1997. Japan completed the process by ratifying the Protocol on December 15, 1997. US government actions undertaken in Antarctica are subject to the requirements of both the Protocol and the US National Environmental Policy Act (NEPA). There are differences in the scope and intent of the Protocol and NEPA; however, both require environmental impact assessment (EIA) as part of the planning process for proposed actions that have the potential for environmental impacts. In this paper we describe the two instruments and highlight key similarities and differences with particular attention to EIA. Through this comparison of the EIA requirements of NEPA and the Protocol, we show how the requirements of each can be used in concert to provide enhanced environmental protection for the antarctic environment. NEPA applies only to actions of the US government; therefore, because NEPA includes certain desirable attributes that have been refined and clarified through numerous court cases, and because the Protocol is just entering implementation internationally, some recommendations are made for strengthening the procedural requirements of the Protocol for activities undertaken by all Parties in Antarctica. The Protocol gives clear and strong guidance for protection of specific, valued antarctic environmental resources including intrinsic wilderness and aesthetic values, and the value of Antarctica as an area for scientific research. That guidance requires a higher standard of environmental protection for Antarctica than is required in other parts of the world. This paper shows that taken together NEPA and the Protocol call for closer examination of proposed actions and a more rigorous consideration of environmental impacts than either would alone. Three areas are identified where the EIA provisions of the Protocol could be strengthened to improve its effectiveness. First, the thresholds defined by the Protocol need to be clarified. Specifically, the meanings of the terms "minor" and "transitory" are not clear in the context of the Protocol. The use of "or" in the phrase "minor or transitory" further confuses the meaning. Second, cumulative impact assessment is called for by the Protocol but is not defined. A clear definition could reduce the chance that cumulative impacts would be given inadequate consideration. Finally, the public has limited opportunities to comment on or influence the preparation of initial or comprehensive environmental evaluations. Experience has shown that public input to environmental documents has a considerable influence on agency decision making and the quality of EIA that agencies perform.KEY WORDS: Environment; Impact assessment; Antarctica; NEPA; Protocol; Antarctic Treatyhttp://link.springer-ny.com/link/service/journals/00267/bibs/24n1p13.html

Guidelines for Inclusion of Patient-Reported Outcomes in Clinical Trial Protocols: The SPIRIT-PRO Extension.

PubMed

Calvert, Melanie; Kyte, Derek; Mercieca-Bebber, Rebecca; Slade, Anita; Chan, An-Wen; King, Madeleine T; Hunn, Amanda; Bottomley, Andrew; Regnault, Antoine; Chan, An-Wen; Ells, Carolyn; O'Connor, Daniel; Revicki, Dennis; Patrick, Donald; Altman, Doug; Basch, Ethan; Velikova, Galina; Price, Gary; Draper, Heather; Blazeby, Jane; Scott, Jane; Coast, Joanna; Norquist, Josephine; Brown, Julia; Haywood, Kirstie; Johnson, Laura Lee; Campbell, Lisa; Frank, Lori; von Hildebrand, Maria; Brundage, Michael; Palmer, Michael; Kluetz, Paul; Stephens, Richard; Golub, Robert M; Mitchell, Sandra; Groves, Trish

2018-02-06

Patient-reported outcome (PRO) data from clinical trials can provide valuable evidence to inform shared decision making, labeling claims, clinical guidelines, and health policy; however, the PRO content of clinical trial protocols is often suboptimal. The SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) statement was published in 2013 and aims to improve the completeness of trial protocols by providing evidence-based recommendations for the minimum set of items to be addressed, but it does not provide PRO-specific guidance. To develop international, consensus-based, PRO-specific protocol guidance (the SPIRIT-PRO Extension). The SPIRIT-PRO Extension was developed following the Enhancing Quality and Transparency of Health Research (EQUATOR) Network's methodological framework for guideline development. This included (1) a systematic review of existing PRO-specific protocol guidance to generate a list of potential PRO-specific protocol items (published in 2014); (2) refinements to the list and removal of duplicate items by the International Society for Quality of Life Research (ISOQOL) Protocol Checklist Taskforce; (3) an international stakeholder survey of clinical trial research personnel, PRO methodologists, health economists, psychometricians, patient advocates, funders, industry representatives, journal editors, policy makers, ethicists, and researchers responsible for evidence synthesis (distributed by 38 international partner organizations in October 2016); (4) an international Delphi exercise (n = 137 invited; October 2016 to February 2017); and (5) consensus meeting (n = 30 invited; May 2017). Prior to voting, consensus meeting participants were informed of the results of the Delphi exercise and given data from structured reviews evaluating the PRO protocol content of 3 defined samples of trial protocols. The systematic review identified 162 PRO-specific protocol recommendations from 54 sources. The ISOQOL Taskforce (n = 21) reduced this to 56 items, which were considered by 138 international stakeholder survey participants and 99 Delphi panelists. The final wording of the SPIRIT-PRO Extension was agreed on at a consensus meeting (n = 29 participants) and reviewed by external group of experts during a consultation period. Eleven extensions and 5 elaborations to the SPIRIT 2013 checklist were recommended for inclusion in clinical trial protocols in which PROs are a primary or key secondary outcome. Extension items focused on PRO-specific issues relating to the trial rationale, objectives, eligibility criteria, concepts used to evaluate the intervention, time points for assessment, PRO instrument selection and measurement properties, data collection plan, translation to other languages, proxy completion, strategies to minimize missing data, and whether PRO data will be monitored during the study to inform clinical care. The SPIRIT-PRO guidelines provide recommendations for items that should be addressed and included in clinical trial protocols in which PROs are a primary or key secondary outcome. Improved design of clinical trials including PROs could help ensure high-quality data that may inform patient-centered care.

Fingerprinting Software Defined Networks and Controllers

DTIC Science & Technology

2015-03-01

24 2.5.3 Intrusion Prevention System with SDN . . . . . . . . . . . . . . . 25 2.5.4 Modular Security Services...Control Message Protocol IDS Intrusion Detection System IPS Intrusion Prevention System ISP Internet Service Provider LLDP Link Layer Discovery Protocol...layer functions (e.g., web proxies, firewalls, intrusion detection/prevention, load balancers, etc.). The increase in switch capabilities combined

Improving Internet Archive Service through Proxy Cache.

ERIC Educational Resources Information Center

Yu, Hsiang-Fu; Chen, Yi-Ming; Wang, Shih-Yong; Tseng, Li-Ming

2003-01-01

Discusses file transfer protocol (FTP) servers for downloading archives (files with particular file extensions), and the change to HTTP (Hypertext transfer protocol) with increased Web use. Topics include the Archie server; proxy cache servers; and how to improve the hit rate of archives by a combination of caching and better searching mechanisms.…

Unconditional security proof of long-distance continuous-variable quantum key distribution with discrete modulation.

PubMed

Leverrier, Anthony; Grangier, Philippe

2009-05-08

We present a continuous-variable quantum key distribution protocol combining a discrete modulation and reverse reconciliation. This protocol is proven unconditionally secure and allows the distribution of secret keys over long distances, thanks to a reverse reconciliation scheme efficient at very low signal-to-noise ratio.

Extracting similar terms from multiple EMR-based semantic embeddings to support chart reviews.

PubMed

Cheng Ye, M S; Fabbri, Daniel

2018-05-21

Word embeddings project semantically similar terms into nearby points in a vector space. When trained on clinical text, these embeddings can be leveraged to improve keyword search and text highlighting. In this paper, we present methods to refine the selection process of similar terms from multiple EMR-based word embeddings, and evaluate their performance quantitatively and qualitatively across multiple chart review tasks. Word embeddings were trained on each clinical note type in an EMR. These embeddings were then combined, weighted, and truncated to select a refined set of similar terms to be used in keyword search and text highlighting. To evaluate their quality, we measured the similar terms' information retrieval (IR) performance using precision-at-K (P@5, P@10). Additionally a user study evaluated users' search term preferences, while a timing study measured the time to answer a question from a clinical chart. The refined terms outperformed the baseline method's information retrieval performance (e.g., increasing the average P@5 from 0.48 to 0.60). Additionally, the refined terms were preferred by most users, and reduced the average time to answer a question. Clinical information can be more quickly retrieved and synthesized when using semantically similar term from multiple embeddings. Copyright © 2018. Published by Elsevier Inc.

Purifying, Separating, and Concentrating Cells From a Sample Low in Biomass

NASA Technical Reports Server (NTRS)

Benardini, James N.; LaDuc, Myron T.; Diamond, Rochelle

2012-01-01

Frequently there is an inability to process and analyze samples of low biomass due to limiting amounts of relevant biomaterial in the sample. Furthermore, molecular biological protocols geared towards increasing the density of recovered cells and biomolecules of interest, by their very nature, also concentrate unwanted inhibitory humic acids and other particulates that have an adversarial effect on downstream analysis. A novel and robust fluorescence-activated cell-sorting (FACS)-based technology has been developed for purifying (removing cells from sampling matrices), separating (based on size, density, morphology), and concentrating cells (spores, prokaryotic, eukaryotic) from a sample low in biomass. The technology capitalizes on fluorescent cell-sorting technologies to purify and concentrate bacterial cells from a low-biomass, high-volume sample. Over the past decade, cell-sorting detection systems have undergone enhancements and increased sensitivity, making bacterial cell sorting a feasible concept. Although there are many unknown limitations with regard to the applicability of this technology to environmental samples (smaller cells, few cells, mixed populations), dogmatic principles support the theoretical effectiveness of this technique upon thorough testing and proper optimization. Furthermore, the pilot study from which this report is based proved effective and demonstrated this technology capable of sorting and concentrating bacterial endospore and bacterial cells of varying size and morphology. Two commercial off-the-shelf bacterial counting kits were used to optimize a bacterial stain/dye FACS protocol. A LIVE/DEAD BacLight Viability and Counting Kit was used to distinguish between the live and dead cells. A Bacterial Counting Kit comprising SYTO BC (mixture of SYTO dyes) was employed as a broad-spectrum bacterial counting agent. Optimization using epifluorescence microscopy was performed with these two dye/stains. This refined protocol was further validated using varying ratios and mixtures of cells to ensure homogenous staining compared to that of individual cells, and were utilized for flow analyzer and FACS labeling. This technology focuses on the purification and concentration of cells from low-biomass spacecraft assembly facility samples. Currently, purification and concentration of low-biomass samples plague planetary protection downstream analyses. Having a capability to use flow cytometry to concentrate cells out of low-biomass, high-volume spacecraft/ facility sample extracts will be of extreme benefit to the fields of planetary protection and astrobiology. Successful research and development of this novel methodology will significantly increase the knowledge base for designing more effective cleaning protocols, and ultimately lead to a more empirical and true account of the microbial diversity present on spacecraft surfaces. Refined cleaning and an enhanced ability to resolve microbial diversity may decrease the overall cost of spacecraft assembly and/or provide a means to begin to assess challenging planetary protection missions.

Incorporating thyroid markers in Down syndrome screening protocols.

PubMed

Dhaifalah, Ishraq; Salek, Tomas; Langova, Dagmar; Cuckle, Howard

2017-05-01

The article aimed to assess the benefit of incorporating maternal serum thyroid disease marker levels (thyroid-stimulating hormone and free thyroxine) into first trimester Down syndrome screening protocols. Statistical modelling was used to predict performance with and without the thyroid markers. Two protocols were considered: the combined test and the contingent cell-free DNA (cfDNA) test, where 15-40% women are selected for cfDNA because of increased risk based on combined test results. Published parameters were used for the combined test, cfDNA and the Down syndrome means for thyroid-stimulating hormone and free thyroxine; other parameters were derived from a series of 5230 women screened for both thyroid disease and Down syndrome. Combined test: For a fixed 85% detection rate, the predicted false positive rate was reduced from 5.3% to 3.6% with the addition of the thyroid markers. Contingent cfDNA test: For a fixed 95% detection rate, the proportion of women selected for cfDNA was reduced from 25.6% to 20.2%. When screening simultaneously for maternal thyroid disease and Down syndrome, thyroid marker levels should be used in the calculation of Down syndrome risk. The benefit is modest but can be achieved with no additional cost. © 2017 John Wiley & Sons, Ltd. © 2017 John Wiley & Sons, Ltd.

Transcranial direct current stimulation improves neurorehabilitation of task-specific dystonia: a pilot study.

PubMed

Rosset-Llobet, Jaume; Fàbregas-Molas, Sílvia; Pascual-Leone, Alvaro

2014-03-01

Sensory-motor returning (SMR) can help the symptoms of task-specific focal hand dystonia. However, effects vary across patients and take many sessions. Here, we present proof of principle evidence that transcranial direct current stimulation (tDCS) can enhance these effects. We compared the effects of a combined tDCS-SMR protocol (n=4 patients) with the efficacy of SMR alone (n=30 patients). All 4 patients treated with the combined protocol showed greater improvement than those undergoing SMR alone. Results encourage a larger, parallel-group clinical trial with sham tDCS control.

Immunocytochemical detection of astrocytes in brain slices in combination with Nissl staining.

PubMed

Korzhevskii, D E; Otellin, V A

2005-07-01

The present study was performed to develop a simple and reliable method for the combined staining of specimens to allow the advantages of immunocytochemical detection of astrocytes and assessment of the functional state of neurons by the Nissl method to be assessed simultaneously. The protocol suggested for processing paraffin sections allows preservation of tissue structure at high quality and allows the selective identification of astrocytes with counterstaining of neurons by the Nissl method. The protocol can be used without modification for processing brain specimens from humans and various mammals--except mice and rabbits.

The Latest in Handheld Microscopes

ERIC Educational Resources Information Center

Wighting, Mervyn J.; Lucking, Robert A.; Christmann, Edwin P.

2004-01-01

Around 1590, Zacharias Jansenn of Holland invented the microscope. Jansenn, an eyeglass maker by trade, experimented with lenses and discovered that things appeared closer with combinations of lenses. Over the past 400 years, several refinements to microscopes have occurred, making it possible to magnify objects between 200 and 1,500 times their…

Terrain Models in Field Geology Courses.

ERIC Educational Resources Information Center

Whittecar, G. Richard

1984-01-01

Describes a terrain model for geologic mapping which, when combined with exercises in rock description, Brunton compass manipulation, orienteering, and geologic report writing, allows students to refine skills needed for summer field camp. Advantages and limitations of the model and its use in a field course are also discussed. (BC)

A comparative study of cellulose nanofibrils disintegrated via multiple processing approaches

Treesearch

Yan Qing; Ronald Sabo; J.Y. Zhu; Umesh Agarwal; Zhiyong Cai; Yiqiang Wu

2013-01-01

Various cellulose nanofibrils (CNFs) created by refining and microfluidization, in combination withenzymatic or 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) oxidized pretreatment were compared. Themorphological properties, degree of polymerization, and crystallinity for the obtained nanofibrils, aswell as physical and mechanical properties of the corresponding films...

Enhancing Air Pollution Exposure Assessment in the 21st Century by Measurement and Modeling

EPA Science Inventory

Exposure assessments may be conducted using measurement data, modeling results, or through a combination of measurements and models. Models are required to estimate exposure when measurement data is insufficient due to spatial or temporal gaps (e.g., for refined local scale asses...

A COMBINED MODELING AND MEASUREMENT TECHNIQUE FOR ESTIMATING WIND-BLOWN DUST EMISSIONS AT OWENS (DRY) LAKE, CA

EPA Science Inventory

A refined method of modeling atmospheric dust concentrations due to wind erosion was developed using real-time saltation flux measurements and ambient dust monitoring data at Owens Lake, California. This modeling method may have practical applications for modeling the atmospheric...

Prototype solar heating and combined heating and cooling systems

NASA Technical Reports Server (NTRS)

1977-01-01

System analysis activities were directed toward refining the heating system parameters. Trade studies were performed to support hardware selections for all systems and for the heating only operational test sites in particular. The heating system qualification tests were supported by predicting qualification test component performance prior to conducting the test.

Promise of combined hydrothermal/chemical and mechanical refining for pretreatment of woody and herbaceous biomass

USDA-ARS?s Scientific Manuscript database

Production of advanced biofuels from woody and herbaceous feedstocks is moving into commercialization. Biomass needs to be pretreated to overcome the physicochemical properties of biomass that hinder enzyme accessibility, impeding the conversion of the plant cell walls to fermentable sugars. Pretrea...

Language Arts Resource Guide K-12.

ERIC Educational Resources Information Center

Pitman, John C.

One of a series designed to help districts refine and upgrade their current curricular offerings, this resource guide deals with the development of a unified K-12 language arts curriculum that combines the four major language arts components of listening, speaking, reading, and writing. Following a brief foreword and list of acknowledgments, the…

Incorporating Retention Time to Refine Models Predicting Thermal Regimes of Stream Networks Across New England

EPA Science Inventory

Thermal regimes are a critical factor in models predicting effects of watershed management activities on fish habitat suitability. We have assembled a database of lotic temperature time series across New England (> 7000 station-year combinations) from state and Federal data s...

Crystallographic structure refinement with quadrupolar nuclei: a combined solid-state NMR and GIPAW DFT example using MgBr(2).

PubMed

Widdifield, Cory M; Bryce, David L

2009-09-07

Solid-state NMR spectroscopy and GIPAW DFT calculations reveal the pronounced sensitivity of (79/81)Br and (25)Mg quadrupolar coupling constants to subtle aspects of solid state structure which were not previously detected by pXRD methods.

An Instrument to Measure Anomia.

ERIC Educational Resources Information Center

Moore, Allen B.

1980-01-01

Four hundred and eighty-six disadvantaged adults from North Carolina were the subjects in a study that factor-analyzed three instruments designed to measure anomia, yielding a 12-item unidimensional scale. (The refined combination scale is presented as of potential usefulness for research on the effects of educational intervention on anomia.) (LRA)

Developing Awareness through Poetry.

ERIC Educational Resources Information Center

Roeming, Robert F., Ed.

This booklet contains the proceedings of a seminar in which poets demonstrated through readings and analysis of their works how poetry, combining appeals to both reason and emotion, can develop and refine individual awareness of the world and nature around us. The primary participants in the program were Bruce Cutler, Dolores Kendrick, and May…

How to Use the Marine Realms Information Bank (MRIB) Digital Libraries

USGS Publications Warehouse

Lightsom, Frances L.; Allwardt, Alan O.

2009-01-01

Marine Realms Information Bank (MRIB) digital libraries provide access to free online scientific resources about oceans, coasts, and coastal watersheds. MRIB allows category, geographic, and keyword searching, alone or in combination. Instructions for searching the three MRIB libraries and for refining the searches are explained in detail.

IMPlementation of A Relatives' Toolkit (IMPART study): an iterative case study to identify key factors impacting on the implementation of a web-based supported self-management intervention for relatives of people with psychosis or bipolar experiences in a National Health Service: a study protocol.

PubMed

Lobban, Fiona; Appleton, Victoria; Appelbe, Duncan; Barraclough, Johanna; Bowland, Julie; Fisher, Naomi R; Foster, Sheena; Johnson, Sonia; Lewis, Elizabeth; Mateus, Céu; Mezes, Barbara; Murray, Elizabeth; O'Hanlon, Puffin; Pinfold, Vanessa; Rycroft-Malone, Jo; Siddle, Ron; Smith, Jo; Sutton, Chris J; Walker, Andrew; Jones, Steven H

2017-12-28

Web-based interventions to support people to manage long-term health conditions are available and effective but rarely used in clinical services. The aim of this study is to identify critical factors impacting on the implementation of an online supported self-management intervention for relatives of people with recent onset psychosis or bipolar disorder into routine clinical care and to use this information to inform an implementation plan to facilitate widespread use and inform wider implementation of digital health interventions. A multiple case study design within six early intervention in psychosis (EIP) services in England, will be used to test and refine theory-driven hypotheses about factors impacting on implementation of the Relatives' Education And Coping Toolkit (REACT). Qualitative data including behavioural observation, document analysis, and in-depth interviews collected in the first two EIP services (wave 1) and analysed using framework analysis, combined with quantitative data describing levels of use by staff and relatives and impact on relatives' distress and wellbeing, will be used to identify factors impacting on implementation. Consultation via stakeholder workshops with staff and relatives and co-facilitated by relatives in the research team will inform development of an implementation plan to address these factors, which will be evaluated and refined in the four subsequent EIP services in waves 2 and 3. Transferability of the implementation plan to non-participating services will be explored. Observation of implementation in a real world clinical setting, across carefully sampled services, in real time provides a unique opportunity to understand factors impacting on implementation likely to be generalizable to other web-based interventions, as well as informing further development of implementation theories. However, there are inherent challenges in investigating implementation without influencing the process under observation. We outline our strategies to ensure our design is transparent, flexible, and responsive to the timescales and activities happening within each service whilst also meeting the aims of the project. ISCTRN 16267685 (09/03/2016).

One-step hydrothermal synthesis and electrochemical performance of sodium-manganese-iron phosphate as cathode material for Li-ion batteries

DOE PAGES

Karegeya, Claude; Mahmoud, Abdelfattah; Vertruyen, Bénédicte; ...

2017-06-23

The sodium-manganese-iron phosphate Na 2Mn 1.5Fe 1.5(PO 4) 3 (NMFP) with alluaudite structure was obtained by a one-step hydrothermal synthesis route. The physical properties and structure of this material were obtained through XRD and Mössbauer analyses. X-ray diffraction Rietveld refinements confirm a cationic distribution of Na + and presence of vacancies in A(2)’, Na + and small amounts of Mn 2+ in A(1), Mn 2+ in M(1) , 0.5 Mn 2+ and Fe cations (Mn 2+,Fe 2+ and Fe 3+) in M(2), leading to the structural formula Na 2Mn(Mn 0.5Fe 1.5)(PO 4) 3. The particles morphology was investigated by SEM.more » Several reactions with different hydrothermal reaction times were attempted to design a suitable synthesis protocol of NMFP compound. The time of reaction was varied from 6 to 48 hours at 220°C. The pure phase of NMFP particles was firstly obtained when the hydrothermal reaction of NMFP precursors mixture was maintained at 220°C for 6 hours. When the reaction time was increased from 6 to 12, 24 and 48 hours, the dandelion structure was destroyed in favor of NMFP micro-rods. The combination of NMFP (NMFP-6H, NMFP-12H, NMFP-24H and NMFP-48H) structure refinement and Mössbauer characterizations shows that the increase of the reaction time leads to the progressive increment of Fe(III) and the decrease of the crystal size. The electrochemical tests indicated that NMFP is a 3 V sodium intercalating cathode. The comparison of the discharge capacity evolution of studied NMFP electrode materials at C/5 current density shows different capacities of 48, 40, 34 and 34 mAhg-1 for NMFP-6H, NMFP-12H, NMFP-24H and NMFP-48H respectively. Interestingly, all samples show excellent capacity retention of about 99 % during 50 cycles.« less

One-step hydrothermal synthesis and electrochemical performance of sodium-manganese-iron phosphate as cathode material for Li-ion batteries

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

Karegeya, Claude; Mahmoud, Abdelfattah; Vertruyen, Bénédicte

The sodium-manganese-iron phosphate Na 2Mn 1.5Fe 1.5(PO 4) 3 (NMFP) with alluaudite structure was obtained by a one-step hydrothermal synthesis route. The physical properties and structure of this material were obtained through XRD and Mössbauer analyses. X-ray diffraction Rietveld refinements confirm a cationic distribution of Na + and presence of vacancies in A(2)’, Na + and small amounts of Mn 2+ in A(1), Mn 2+ in M(1) , 0.5 Mn 2+ and Fe cations (Mn 2+,Fe 2+ and Fe 3+) in M(2), leading to the structural formula Na 2Mn(Mn 0.5Fe 1.5)(PO 4) 3. The particles morphology was investigated by SEM.more » Several reactions with different hydrothermal reaction times were attempted to design a suitable synthesis protocol of NMFP compound. The time of reaction was varied from 6 to 48 hours at 220°C. The pure phase of NMFP particles was firstly obtained when the hydrothermal reaction of NMFP precursors mixture was maintained at 220°C for 6 hours. When the reaction time was increased from 6 to 12, 24 and 48 hours, the dandelion structure was destroyed in favor of NMFP micro-rods. The combination of NMFP (NMFP-6H, NMFP-12H, NMFP-24H and NMFP-48H) structure refinement and Mössbauer characterizations shows that the increase of the reaction time leads to the progressive increment of Fe(III) and the decrease of the crystal size. The electrochemical tests indicated that NMFP is a 3 V sodium intercalating cathode. The comparison of the discharge capacity evolution of studied NMFP electrode materials at C/5 current density shows different capacities of 48, 40, 34 and 34 mAhg-1 for NMFP-6H, NMFP-12H, NMFP-24H and NMFP-48H respectively. Interestingly, all samples show excellent capacity retention of about 99 % during 50 cycles.« less

The three stages of building and testing mid-level theories in a realist RCT: a theoretical and methodological case-example.

PubMed

Jamal, Farah; Fletcher, Adam; Shackleton, Nichola; Elbourne, Diana; Viner, Russell; Bonell, Chris

2015-10-15

Randomised controlled trials (RCTs) of social interventions are often criticised as failing to open the 'black box' whereby they only address questions about 'what works' without explaining the underlying processes of implementation and mechanisms of action, and how these vary by contextual characteristics of person and place. Realist RCTs are proposed as an approach to evaluation science that addresses these gaps while preserving the strengths of RCTs in providing evidence with strong internal validity in estimating effects. In the context of growing interest in designing and conducting realist trials, there is an urgent need to offer a worked example to provide guidance on how such an approach might be practically taken forward. The aim of this paper is to outline a three-staged theoretical and methodological process of undertaking a realist RCT using the example of the evaluation of a whole-school restorative intervention aiming to reduce aggression and bullying in English secondary schools. First, informed by the findings of our initial pilot trial and sociological theory, we elaborate our theory of change and specific a priori hypotheses about how intervention mechanisms interact with context to produce outcomes. Second, we describe how we will use emerging findings from the integral process evaluation within the RCT to refine, and add to, these a priori hypotheses before the collection of quantitative, follow-up data. Third, we will test our hypotheses using a combination of process and outcome data via quantitative analyses of effect mediation (examining mechanisms) and moderation (examining contextual contingencies). The results are then used to refine and further develop the theory of change. The aim of the realist RCT approach is thus not merely to assess whether the intervention is effective or not, but to develop empirically informed mid-range theory through a three-stage process. There are important implications for those involved with reporting and reviewing RCTs, including the use of new, iterative protocols. Current Controlled Trials ISRCTN10751359 (Registered 11 March 2014).

Landmark Image Retrieval by Jointing Feature Refinement and Multimodal Classifier Learning.

PubMed

Zhang, Xiaoming; Wang, Senzhang; Li, Zhoujun; Ma, Shuai; Xiaoming Zhang; Senzhang Wang; Zhoujun Li; Shuai Ma; Ma, Shuai; Zhang, Xiaoming; Wang, Senzhang; Li, Zhoujun

2018-06-01

Landmark retrieval is to return a set of images with their landmarks similar to those of the query images. Existing studies on landmark retrieval focus on exploiting the geometries of landmarks for visual similarity matches. However, the visual content of social images is of large diversity in many landmarks, and also some images share common patterns over different landmarks. On the other side, it has been observed that social images usually contain multimodal contents, i.e., visual content and text tags, and each landmark has the unique characteristic of both visual content and text content. Therefore, the approaches based on similarity matching may not be effective in this environment. In this paper, we investigate whether the geographical correlation among the visual content and the text content could be exploited for landmark retrieval. In particular, we propose an effective multimodal landmark classification paradigm to leverage the multimodal contents of social image for landmark retrieval, which integrates feature refinement and landmark classifier with multimodal contents by a joint model. The geo-tagged images are automatically labeled for classifier learning. Visual features are refined based on low rank matrix recovery, and multimodal classification combined with group sparse is learned from the automatically labeled images. Finally, candidate images are ranked by combining classification result and semantic consistence measuring between the visual content and text content. Experiments on real-world datasets demonstrate the superiority of the proposed approach as compared to existing methods.

Combined DNA-RNA Fluorescent In situ Hybridization (FISH) to Study X Chromosome Inactivation in Differentiated Female Mouse Embryonic Stem Cells

PubMed Central

Barakat, Tahsin Stefan; Gribnau, Joost

2014-01-01

Fluorescent in situ hybridization (FISH) is a molecular technique which enables the detection of nucleic acids in cells. DNA FISH is often used in cytogenetics and cancer diagnostics, and can detect aberrations of the genome, which often has important clinical implications. RNA FISH can be used to detect RNA molecules in cells and has provided important insights in regulation of gene expression. Combining DNA and RNA FISH within the same cell is technically challenging, as conditions suitable for DNA FISH might be too harsh for fragile, single stranded RNA molecules. We here present an easily applicable protocol which enables the combined, simultaneous detection of Xist RNA and DNA encoded by the X chromosomes. This combined DNA-RNA FISH protocol can likely be applied to other systems where both RNA and DNA need to be detected. PMID:24961515

Upgrading physical activity counselling in primary care in the Netherlands.

PubMed

Verwey, Renée; van der Weegen, Sanne; Spreeuwenberg, Marieke; Tange, Huibert; van der Weijden, Trudy; de Witte, Luc

2016-06-01

The systematic development of a counselling protocol in primary care combined with a monitoring and feedback tool to support chronically ill patients to achieve a more active lifestyle. An iterative user-centred design method was used to develop a counselling protocol: the Self-management Support Programme (SSP). The needs and preferences of future users of this protocol were identified by analysing the literature, through qualitative research, and by consulting an expert panel. The counselling protocol is based on the Five A's model. Practice nurses apply motivational interviewing, risk communication and goal setting to support self-management of patients in planning how to achieve a more active lifestyle. The protocol consists of a limited number of behaviour change consultations intertwined with interaction with and responses from the It's LiFe! monitoring and feedback tool. This tool provides feedback on patients' physical activity levels via an app on their smartphone. A summary of these levels is automatically sent to the general practice so that practice nurses can respond to this information. A SSP to stimulate physical activity was defined based on user requirements of care providers and patients, followed by a review by a panel of experts. By following this user-centred approach, the organization of care was carefully taken into account, which has led to a practical and affordable protocol for physical activity counselling combined with mobile technology. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

On the routing protocol influence on the resilience of wireless sensor networks to jamming attacks.

PubMed

Del-Valle-Soto, Carolina; Mex-Perera, Carlos; Monroy, Raul; Nolazco-Flores, Juan Arturo

2015-03-27

In this work, we compare a recently proposed routing protocol, the multi-parent hierarchical (MPH) protocol, with two well-known protocols, the ad hoc on-demand distance vector (AODV) and dynamic source routing (DSR). For this purpose, we have developed a simulator, which faithfully reifies the workings of a given protocol, considering a fixed, reconfigurable ad hoc network given by the number and location of participants, and general network conditions. We consider a scenario that can be found in a large number of wireless sensor network applications, a single sink node that collects all of the information generated by the sensors. The metrics used to compare the protocols were the number of packet retransmissions, carrier sense multiple access (CSMA) inner loop retries, the number of nodes answering the queries from the coordinator (sink) node and the energy consumption. We tested the network under ordinary (without attacks) conditions (and combinations thereof) and when it is subject to different types of jamming attacks (in particular, random and reactive jamming attacks), considering several positions for the jammer. Our results report that MPH has a greater ability to tolerate such attacks than DSR and AODV, since it minimizes and encapsulates the network segment under attack. The self-configuring capabilities of MPH derived from a combination of a proactive routes update, on a periodic-time basis, and a reactive behavior provide higher resilience while offering a better performance (overhead and energy consumption) than AODV and DSR, as shown in our simulation results.

Quantitative Assessment of In-solution Digestion Efficiency Identifies Optimal Protocols for Unbiased Protein Analysis*

PubMed Central

León, Ileana R.; Schwämmle, Veit; Jensen, Ole N.; Sprenger, Richard R.

2013-01-01

The majority of mass spectrometry-based protein quantification studies uses peptide-centric analytical methods and thus strongly relies on efficient and unbiased protein digestion protocols for sample preparation. We present a novel objective approach to assess protein digestion efficiency using a combination of qualitative and quantitative liquid chromatography-tandem MS methods and statistical data analysis. In contrast to previous studies we employed both standard qualitative as well as data-independent quantitative workflows to systematically assess trypsin digestion efficiency and bias using mitochondrial protein fractions. We evaluated nine trypsin-based digestion protocols, based on standard in-solution or on spin filter-aided digestion, including new optimized protocols. We investigated various reagents for protein solubilization and denaturation (dodecyl sulfate, deoxycholate, urea), several trypsin digestion conditions (buffer, RapiGest, deoxycholate, urea), and two methods for removal of detergents before analysis of peptides (acid precipitation or phase separation with ethyl acetate). Our data-independent quantitative liquid chromatography-tandem MS workflow quantified over 3700 distinct peptides with 96% completeness between all protocols and replicates, with an average 40% protein sequence coverage and an average of 11 peptides identified per protein. Systematic quantitative and statistical analysis of physicochemical parameters demonstrated that deoxycholate-assisted in-solution digestion combined with phase transfer allows for efficient, unbiased generation and recovery of peptides from all protein classes, including membrane proteins. This deoxycholate-assisted protocol was also optimal for spin filter-aided digestions as compared with existing methods. PMID:23792921

BFT replication resistant to MAC attacks

NASA Astrophysics Data System (ADS)

Zbierski, Maciej

2016-09-01

Over the last decade numerous Byzantine fault-tolerant (BFT) replication protocols have been proposed in the literature. However, the vast majority of these solutions reuse the same authentication scheme, which makes them susceptible to a so called MAC attack. Such vulnerability enables malicious clients to undetectably prevent the replicated service from processing incoming client requests, and consequently making it permanently unavailable. While some BFT protocols attempted to address this issue by using different authentication mechanisms, they at the same time significantly degraded the performance achieved in correct environments. This article presents a novel adaptive authentication mechanism which can be combined with practically any Byzantine fault-tolerant replication protocol. Unlike previous solutions, the proposed scheme dynamically switches between two operation modes to combine high performance in correct environments and liveness during MAC attacks. The experiment results presented in the article demonstrate that the proposed mechanism can sufficiently tolerate MAC attacks without introducing any observable overhead whenever no faults are present.