System and methods for predicting transmembrane domains in membrane proteins and mining the genome for recognizing G-protein coupled receptors

DOEpatents

Trabanino, Rene J; Vaidehi, Nagarajan; Hall, Spencer E; Goddard, William A; Floriano, Wely

2013-02-05

The invention provides computer-implemented methods and apparatus implementing a hierarchical protocol using multiscale molecular dynamics and molecular modeling methods to predict the presence of transmembrane regions in proteins, such as G-Protein Coupled Receptors (GPCR), and protein structural models generated according to the protocol. The protocol features a coarse grain sampling method, such as hydrophobicity analysis, to provide a fast and accurate procedure for predicting transmembrane regions. Methods and apparatus of the invention are useful to screen protein or polynucleotide databases for encoded proteins with transmembrane regions, such as GPCRs.

Broken symmetry in a two-qubit quantum control landscape

NASA Astrophysics Data System (ADS)

Bukov, Marin; Day, Alexandre G. R.; Weinberg, Phillip; Polkovnikov, Anatoli; Mehta, Pankaj; Sels, Dries

2018-05-01

We analyze the physics of optimal protocols to prepare a target state with high fidelity in a symmetrically coupled two-qubit system. By varying the protocol duration, we find a discontinuous phase transition, which is characterized by a spontaneous breaking of a Z2 symmetry in the functional form of the optimal protocol, and occurs below the quantum speed limit. We study in detail this phase and demonstrate that even though high-fidelity protocols come degenerate with respect to their fidelity, they lead to final states of different entanglement entropy shared between the qubits. Consequently, while globally both optimal protocols are equally far away from the target state, one is locally closer than the other. An approximate variational mean-field theory which captures the physics of the different phases is developed.

Quantifying interactions between real oscillators with information theory and phase models: application to cardiorespiratory coupling.

PubMed

Zhu, Yenan; Hsieh, Yee-Hsee; Dhingra, Rishi R; Dick, Thomas E; Jacono, Frank J; Galán, Roberto F

2013-02-01

Interactions between oscillators can be investigated with standard tools of time series analysis. However, these methods are insensitive to the directionality of the coupling, i.e., the asymmetry of the interactions. An elegant alternative was proposed by Rosenblum and collaborators [M. G. Rosenblum, L. Cimponeriu, A. Bezerianos, A. Patzak, and R. Mrowka, Phys. Rev. E 65, 041909 (2002); M. G. Rosenblum and A. S. Pikovsky, Phys. Rev. E 64, 045202 (2001)] which consists in fitting the empirical phases to a generic model of two weakly coupled phase oscillators. This allows one to obtain the interaction functions defining the coupling and its directionality. A limitation of this approach is that a solution always exists in the least-squares sense, even in the absence of coupling. To preclude spurious results, we propose a three-step protocol: (1) Determine if a statistical dependency exists in the data by evaluating the mutual information of the phases; (2) if so, compute the interaction functions of the oscillators; and (3) validate the empirical oscillator model by comparing the joint probability of the phases obtained from simulating the model with that of the empirical phases. We apply this protocol to a model of two coupled Stuart-Landau oscillators and show that it reliably detects genuine coupling. We also apply this protocol to investigate cardiorespiratory coupling in anesthetized rats. We observe reciprocal coupling between respiration and heartbeat and that the influence of respiration on the heartbeat is generally much stronger than vice versa. In addition, we find that the vagus nerve mediates coupling in both directions.

Cessation of oscillations in a chemo-mechanical oscillator

NASA Astrophysics Data System (ADS)

Phogat, Richa; Tiwari, Ishant; Kumar, Pawan; Rivera, Marco; Parmananda, Punit

2018-06-01

In this paper, different methods for cessation of oscillations in a chemo-mechanical oscillator [mercury beating heart (MBH)] are presented. The first set of experiments were carried out on a single MBH oscillator. To achieve cessation of oscillations, two protocols, namely, inverted feedback and delayed feedback were employed. In the second set of experiments, two quasi-identical MBH oscillators are considered. They are first synchronized via a bidirectional attractive coupling. These two synchronized oscillators are thereafter coupled with a unidirectional repulsive coupling and the system dynamics were observed. Subsequently, in the next protocol, the effect of a unidirectional delay coupling on the two synchronized oscillators was explored. The cessation of oscillations in all the above experimental setups was observed as the feedback/coupling was switched on at a suitable strength. Oscillatory dynamics of the system were restored when the feedback/coupling was switched off.

Noninvasive measurement of dynamic correlation functions

NASA Astrophysics Data System (ADS)

Uhrich, Philipp; Castrignano, Salvatore; Uys, Hermann; Kastner, Michael

2017-08-01

The measurement of dynamic correlation functions of quantum systems is complicated by measurement backaction. To facilitate such measurements we introduce a protocol, based on weak ancilla-system couplings, that is applicable to arbitrary (pseudo)spin systems and arbitrary equilibrium or nonequilibrium initial states. Different choices of the coupling operator give access to the real and imaginary parts of the dynamic correlation function. This protocol reduces disturbances due to the early-time measurements to a minimum, and we quantify the deviation of the measured correlation functions from the theoretical, unitarily evolved ones. Implementations of the protocol in trapped ions and other experimental platforms are discussed. For spin-1 /2 models and single-site observables we prove that measurement backaction can be avoided altogether, allowing for the use of ancilla-free protocols.

Quantifying interactions between real oscillators with information theory and phase models: Application to cardiorespiratory coupling

NASA Astrophysics Data System (ADS)

Zhu, Yenan; Hsieh, Yee-Hsee; Dhingra, Rishi R.; Dick, Thomas E.; Jacono, Frank J.; Galán, Roberto F.

2013-02-01

Interactions between oscillators can be investigated with standard tools of time series analysis. However, these methods are insensitive to the directionality of the coupling, i.e., the asymmetry of the interactions. An elegant alternative was proposed by Rosenblum and collaborators [M. G. Rosenblum, L. Cimponeriu, A. Bezerianos, A. Patzak, and R. Mrowka, Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.65.041909 65, 041909 (2002); M. G. Rosenblum and A. S. Pikovsky, Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.64.045202 64, 045202 (2001)] which consists in fitting the empirical phases to a generic model of two weakly coupled phase oscillators. This allows one to obtain the interaction functions defining the coupling and its directionality. A limitation of this approach is that a solution always exists in the least-squares sense, even in the absence of coupling. To preclude spurious results, we propose a three-step protocol: (1) Determine if a statistical dependency exists in the data by evaluating the mutual information of the phases; (2) if so, compute the interaction functions of the oscillators; and (3) validate the empirical oscillator model by comparing the joint probability of the phases obtained from simulating the model with that of the empirical phases. We apply this protocol to a model of two coupled Stuart-Landau oscillators and show that it reliably detects genuine coupling. We also apply this protocol to investigate cardiorespiratory coupling in anesthetized rats. We observe reciprocal coupling between respiration and heartbeat and that the influence of respiration on the heartbeat is generally much stronger than vice versa. In addition, we find that the vagus nerve mediates coupling in both directions.

In situ Compressive Loading and Correlative Noninvasive Imaging of the Bone-periodontal Ligament-tooth Fibrous Joint

PubMed Central

Jang, Andrew T.; Lin, Jeremy D.; Seo, Youngho; Etchin, Sergey; Merkle, Arno; Fahey, Kevin; Ho, Sunita P.

2014-01-01

This study demonstrates a novel biomechanics testing protocol. The advantage of this protocol includes the use of an in situ loading device coupled to a high resolution X-ray microscope, thus enabling visualization of internal structural elements under simulated physiological loads and wet conditions. Experimental specimens will include intact bone-periodontal ligament (PDL)-tooth fibrous joints. Results will illustrate three important features of the protocol as they can be applied to organ level biomechanics: 1) reactionary force vs. displacement: tooth displacement within the alveolar socket and its reactionary response to loading, 2) three-dimensional (3D) spatial configuration and morphometrics: geometric relationship of the tooth with the alveolar socket, and 3) changes in readouts 1 and 2 due to a change in loading axis, i.e. from concentric to eccentric loads. Efficacy of the proposed protocol will be evaluated by coupling mechanical testing readouts to 3D morphometrics and overall biomechanics of the joint. In addition, this technique will emphasize on the need to equilibrate experimental conditions, specifically reactionary loads prior to acquiring tomograms of fibrous joints. It should be noted that the proposed protocol is limited to testing specimens under ex vivo conditions, and that use of contrast agents to visualize soft tissue mechanical response could lead to erroneous conclusions about tissue and organ-level biomechanics. PMID:24638035

Unexplained infertility: overall ongoing pregnancy rate and mode of conception.

PubMed

Brandes, M; Hamilton, C J C M; van der Steen, J O M; de Bruin, J P; Bots, R S G M; Nelen, W L D M; Kremer, J A M

2011-02-01

Unexplained infertility is one of the most common diagnoses in fertility care. The aim of this study was to evaluate the outcome of current fertility management in unexplained infertility. In an observational, longitudinal, multicentre cohort study, 437 couples were diagnosed with unexplained infertility and were available for analysis. They were treated according to their prognosis using standing national treatment protocols: (i) expectant management-IUI-IVF (main treatment route), (ii) IUI-IVF and (iii) directly IVF. Primary outcome measures were: ongoing pregnancy rate, patient flow over the strategies, numbers of protocol violation and drop out rates. A secondary outcome measure was the prediction of ongoing pregnancy and mode of conception. Of all couples 81.5% (356/437) achieved an ongoing pregnancy and 73.9% (263/356) of the pregnancies were conceived spontaneously. There were 408 couples (93.4%) in strategy-1, 21 (5.0%) in strategy-2 and 8 (1.8%) in strategy-3. In total, 33 (7.6%) couples entered the wrong strategy. There were 104 couples (23.8%) who discontinued fertility treatment prematurely: 26 on doctor's advice (with 4 still becoming pregnant) and 78 on their own initiative (with 33 still achieving a pregnancy). Predictors for overall pregnancy chance and mode of conception were duration of infertility, female age and obstetrical history. Overall success rate in couples with unexplained infertility is high. Most pregnancies are conceived spontaneously. We recommend that if the pregnancy prognosis is good, expectant management should be suggested. The prognosis criteria for treatment with IUI or IVF needs to be investigated in randomized controlled trials.

Detection of DNA Methylation by Whole-Genome Bisulfite Sequencing.

PubMed

Li, Qing; Hermanson, Peter J; Springer, Nathan M

2018-01-01

DNA methylation plays an important role in the regulation of the expression of transposons and genes. Various methods have been developed to assay DNA methylation levels. Bisulfite sequencing is considered to be the "gold standard" for single-base resolution measurement of DNA methylation levels. Coupled with next-generation sequencing, whole-genome bisulfite sequencing (WGBS) allows DNA methylation to be evaluated at a genome-wide scale. Here, we described a protocol for WGBS in plant species with large genomes. This protocol has been successfully applied to assay genome-wide DNA methylation levels in maize and barley. This protocol has also been successfully coupled with sequence capture technology to assay DNA methylation levels in a targeted set of genomic regions.

GnRH antagonist versus long agonist protocols in IVF: a systematic review and meta-analysis accounting for patient type.

PubMed

Lambalk, C B; Banga, F R; Huirne, J A; Toftager, M; Pinborg, A; Homburg, R; van der Veen, F; van Wely, M

2017-09-01

Most reviews of IVF ovarian stimulation protocols have insufficiently accounted for various patient populations, such as ovulatory women, women with polycystic ovary syndrome (PCOS) or women with poor ovarian response, and have included studies in which the agonist or antagonist was not the only variable between the compared study arms. The aim of the current study was to compare GnRH antagonist protocols versus standard long agonist protocols in couples undergoing IVF or ICSI, while accounting for various patient populations and treatment schedules. The Cochrane Menstrual Disorders and Subfertility Review Group specialized register of controlled trials and Pubmed and Embase databases were searched from inception until June 2016. Eligible trials were those that compared GnRH antagonist protocols and standard long GnRH agonist protocols in couples undergoing IVF or ICSI. The primary outcome was ongoing pregnancy rate. Secondary outcomes were: live birth rate, clinical pregnancy rate, number of oocytes retrieved and safety with regard to ovarian hyperstimulation syndrome (OHSS). Separate comparisons were performed for the general IVF population, women with PCOS and women with poor ovarian response. Pre-planned subgroup analyses were performed for various antagonist treatment schedules. We included 50 studies. Of these, 34 studies reported on general IVF patients, 10 studies reported on PCOS patients and 6 studies reported on poor responders. In general IVF patients, ongoing pregnancy rate was significantly lower in the antagonist group compared with the agonist group (RR 0.89, 95% CI 0.82-0.96). In women with PCOS and in women with poor ovarian response, there was no evidence of a difference in ongoing pregnancy between the antagonist and agonist groups (RR 0.97, 95% CI 0.84-1.11 and RR 0.87, 95% CI 0.65-1.17, respectively). Subgroup analyses for various antagonist treatment schedules compared to the long protocol GnRH agonist showed a significantly lower ongoing pregnancy rate when the oral hormonal programming pill (OHP) pretreatment was combined with a flexible protocol (RR 0.74, 95% CI 0.59-0.91) while without OHP, the RR was 0.84, 95% CI 0.71-1.0. Subgroup analysis for the fixed antagonist schedule demonstrated no evidence of a significant difference with or without OHP (RR 0.94, 95% CI 0.79-1.12 and RR 0.94, 95% CI 0.83-1.05, respectively). Antagonists resulted in significantly lower OHSS rates both in the general IVF patients and in women with PCOS (RR 0.63, 95% CI 0.50-0.81 and RR 0.53, 95% CI 0.30-0.95, respectively). No data on OHSS was available from trials in poor responders. In a general IVF population, GnRH antagonists are associated with lower ongoing pregnancy rates when compared to long protocol agonists, but also with lower OHSS rates. Within this population, antagonist treatment prevents one case of OHSS in 40 patients but results in one less ongoing pregnancy out of every 28 women treated. Thus standard use of the long GnRH agonist treatment is perhaps still the approach of choice for prevention of premature luteinization. In couples with PCOS and poor responders, GnRH antagonists do not seem to compromise ongoing pregnancy rates and are associated with less OHSS and therefore could be considered as standard treatment. © The Author 2017. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Fragment Couplings via CO2 Extrusion-Recombination: Expansion of a Classic Bond-Forming Strategy via Metallaphotoredox.

PubMed

Le, Chi Chip; MacMillan, David W C

2015-09-23

In this study we demonstrate that molecular fragments, which can be readily coupled via a simple, in situ RO-C═OR bond-forming reaction, can subsequently undergo metal insertion-decarboxylation-recombination to generate Csp(2)-Csp(3) bonds when subjected to metallaphotoredox catalysis. In this embodiment the conversion of a wide variety of mixed anhydrides (formed in situ from carboxylic acids and acyl chlorides) to fragment-coupled ketones is accomplished in good to high yield. A three-step synthesis of the medicinal agent edivoxetine is also described using this new decarboxylation-recombination protocol.

Design, Synthesis, and Validation of an Effective, Reusable Silicon-Based Transfer Agent for Room-Temperature Pd-Catalyzed Cross-Coupling Reactions of Aryl and Heteroaryl Chlorides with Readily Available Aryl Lithium Reagents

PubMed Central

Martinez-Solorio, Dionicio; Melillo, Bruno; Sanchez, Luis; Liang, Yong; Lam, Erwin; Houk, K. N.; Smith, Amos B.

2016-01-01

A reusable silicon-based transfer agent (1) has been designed, synthesized, and validated for effective room-temperature palladium-catalyzed cross-coupling reactions (CCRs) of aryl and heteroaryl chlorides with readily accessible aryl lithium reagents. The crystalline, bench-stable siloxane transfer agent (1) is easily prepared via a one-step protocol. Importantly, this “green” CCR protocol circumvents prefunctionalization, isolation of organometallic cross-coupling partners, and/or stoichiometric waste aside from LiCl. DFT calculations support a σ-bond metathesis mechanism during transmetalation and lead to insights on the importance of the CF3 groups. PMID:26835838

Spin-Orbit-Coupled Interferometry with Ring-Trapped Bose-Einstein Condensates

NASA Astrophysics Data System (ADS)

Helm, J. L.; Billam, T. P.; Rakonjac, A.; Cornish, S. L.; Gardiner, S. A.

2018-02-01

We propose a method of atom interferometry using a spinor Bose-Einstein condensate with a time-varying magnetic field acting as a coherent beam splitter. Our protocol creates long-lived superpositional counterflow states, which are of fundamental interest and can be made sensitive to both the Sagnac effect and magnetic fields on the sub-μ G scale. We split a ring-trapped condensate, initially in the mf=0 hyperfine state, into superpositions of internal mf=±1 states and condensate superflow, which are spin-orbit coupled. After interrogation, the relative phase accumulation can be inferred from a population transfer to the mf=±1 states. The counterflow generation protocol is adiabatically deterministic and does not rely on coupling to additional optical fields or mechanical stirring techniques. Our protocol can maximize the classical Fisher information for any rotation, magnetic field, or interrogation time and so has the maximum sensitivity available to uncorrelated particles. Precision can increase with the interrogation time and so is limited only by the lifetime of the condensate.

Evaluation of a Brief Marriage Intervention for Internal Behavioral Health Consultants in Primary Care

DTIC Science & Technology

2016-09-01

couples at risk for marital deterioration who would otherwise be unlikely to seek traditional couple counseling . The randomized trial is being...protocol to better assess (1) ability to involve couples who otherwise would not seek marriage counseling , and (2) whether participating in Marriage

Improving the gate fidelity of capacitively coupled spin qubits

NASA Astrophysics Data System (ADS)

Wang, Xin; Barnes, Edwin

2015-03-01

Precise execution of quantum gates acting on two or multiple qubits is essential to quantum computation. For semiconductor spin qubits coupled via capacitive interaction, the best fidelity for a two-qubit gate demonstrated so far is around 70%, insufficient for fault-tolerant quantum computation. In this talk we present control protocols that may substantially improve the robustness of two-qubit gates against both nuclear noise and charge noise. Our pulse sequences incorporate simultaneous dynamical decoupling protocols and are simple enough for immediate experimental realization. Together with existing control protocols for single-qubit gates, our results constitute an important step toward scalable quantum computation using spin qubits. This work is done in collaboration with Sankar Das Sarma and supported by LPS-NSA-CMTC and IARPA-MQCO.

Regioselective Cu(I)-catalyzed tandem A3-coupling/decarboxylative coupling to 3-amino-1,4-enynes.

PubMed

Feng, Huangdi; Ermolat'ev, Denis S; Song, Gonghua; Van der Eycken, Erik V

2012-04-06

An efficient and novel copper-mediated protocol for the synthesis of 3-amino-1,4-enynes from glyoxylic acid, an amine, and an alkyne was developed. This new reaction involving two sequential C-C bond formations is air and moisture tolerant and proceeds via a tandem A(3)-coupling and a selective decarboxylative coupling.

Methods for the preparation of protein-oligonucleotide-lipid constructs.

PubMed

Takasaki, Jennifer; Raney, Sameersingh G; Chikh, Ghania; Sekirov, Laura; Brodsky, Irina; Tam, Ying; Ansell, Steven M

2006-01-01

A mixture of ionizable cationic lipids, steric barrier lipids, and colipids is used to encapsulate oligonucleotide DNA in lipidic particles called SALP. This material is under development as an adjuvant for vaccines. Previously we have shown that coupling the antigen directly to the surface of SALP can lead to enhanced immunological responses in vivo. Two different methods for preparing ovalbumin-SALP were assessed in this work. Originally the conjugates were prepared by treating SALP containing a maleimide-derivatized lipid with thiolated ovalbumin, a method we refer to as active coupling. This reaction was found to be difficult to control and generally resulted in low coupling efficiencies. The issues relating to this approach were characterized. We have recently developed alternative techniques based on first coupling ovalbumin to a micelle and then incubating the resultant product with SALP, methods we refer to as passive coupling. We have shown that this method allows accurate control of the levels of protein associated SALP and does not suffer from surface saturation effects seen with the active coupling method that places maximum limits on the amount of protein that can be coupled to the SALP surface. The products from the passive coupling protocol are shown to have activity comparable to those derived from the active coupling protocol in investigations of in vivo immune responses.

Synthesis of stilbene derivatives via visible-light-induced cross-coupling of aryl diazonium salts with nitroalkenes using -NO2 as a leaving group.

PubMed

Zhang, Na; Quan, Zheng-Jun; Zhang, Zhang; Da, Yu-Xia; Wang, Xi-Cun

2016-12-06

The straightforward visible-light-induced synthesis of stilbene compounds via the cross-coupling of nitroalkenes and diazonium tetrafluoroborates under transition-metal-free conditions is described. The protocol uses green LEDs as light sources and eosin Y as an organophotoredox catalyst. Broad substrate scope and exclusive selectivity for the (E)-configuration of stilbenes are observed. This protocol proceeds via a radical pathway, with nitroalkenes serving as the radical acceptor, and the nitro group is cleaved during the process.

Feasibility of Providing Safe Mouth Care and Collecting Oral and Fecal Microbiome Samples from Nursing Home Residents with Dysphagia: Proof of Concept Study.

PubMed

Jablonski, Rita A; Winstead, Vicki; Azuero, Andres; Ptacek, Travis; Jones-Townsend, Corteza; Byrd, Elizabeth; Geisinger, Maria L; Morrow, Casey

2017-09-01

Individuals with dysphagia who reside in nursing homes often receive inadequate mouth care and experience poor oral health. From a policy perspective, the combination of absent evidence-based mouth care protocols coupled with insufficient dental coverage create a pool of individuals at great risk for preventable infectious illnesses that contribute to high health care costs. The purpose of the current study was to determine (a) the safety of a mouth care protocol tailored for individuals with dysphagia residing in nursing homes without access to suction equipment, and (b) the feasibility of collecting oral and fecal samples for microbiota analyses. The mouth care protocol resulted in improved oral hygiene without aspiration, and oral and fecal samples were safely collected from participants. Policies supporting ongoing testing of evidence-based mouth care protocols for individuals with dysphagia are important to improve quality, demonstrate efficacy, and save health care costs. [Journal of Gerontological Nursing, 43(9), 9-15.]. Copyright 2017, SLACK Incorporated.

Fragment Couplings via CO2 Extrusion–Recombination: Expansion of a Classic Bond-Forming Strategy via Metallaphotoredox

PubMed Central

Le, Chi “Chip”; MacMillan, David W. C.

2015-01-01

In this study we demonstrate that molecular fragments, which can be readily coupled via a simple, in situ RO—C=OR bond-forming reaction, can subsequently undergo metal insertion–decarboxylation–recombination to generate Csp2–Csp3 bonds when subjected to metallaphotoredox catalysis. In this embodiment the conversion of a wide variety of mixed anhydrides (formed in situ from carboxylic acids and acyl chlorides) to fragment-coupled ketones is accomplished in good to high yield. A three-step synthesis of the medicinal agent edivoxetine is also described using this new decarboxylation–recombination protocol. PMID:26333771

Robustness of quantum key distribution with discrete and continuous variables to channel noise

NASA Astrophysics Data System (ADS)

Lasota, Mikołaj; Filip, Radim; Usenko, Vladyslav C.

2017-06-01

We study the robustness of quantum key distribution protocols using discrete or continuous variables to the channel noise. We introduce the model of such noise based on coupling of the signal to a thermal reservoir, typical for continuous-variable quantum key distribution, to the discrete-variable case. Then we perform a comparison of the bounds on the tolerable channel noise between these two kinds of protocols using the same noise parametrization, in the case of implementation which is perfect otherwise. Obtained results show that continuous-variable protocols can exhibit similar robustness to the channel noise when the transmittance of the channel is relatively high. However, for strong loss discrete-variable protocols are superior and can overcome even the infinite-squeezing continuous-variable protocol while using limited nonclassical resources. The requirement on the probability of a single-photon production which would have to be fulfilled by a practical source of photons in order to demonstrate such superiority is feasible thanks to the recent rapid development in this field.

Feasibility study for a numerical aerodynamic simulation facility. Volume 2: Hardware specifications/descriptions

NASA Technical Reports Server (NTRS)

Green, F. M.; Resnick, D. R.

1979-01-01

An FMP (Flow Model Processor) was designed for use in the Numerical Aerodynamic Simulation Facility (NASF). The NASF was developed to simulate fluid flow over three-dimensional bodies in wind tunnel environments and in free space. The facility is applicable to studying aerodynamic and aircraft body designs. The following general topics are discussed in this volume: (1) FMP functional computer specifications; (2) FMP instruction specification; (3) standard product system components; (4) loosely coupled network (LCN) specifications/description; and (5) three appendices: performance of trunk allocation contention elimination (trace) method, LCN channel protocol and proposed LCN unified second level protocol.

Open Source Cybersecurity for the 21st Century

DTIC Science & Technology

2013-03-01

would eventually develop into Transmission Control Protocol/Internet Protocol ( TCP /IP) based on the following ground rules:12  Each distinct...The internet’s design permits any device conforming to modern day protocol standards ( TCP /IP being the most prevalent) to communicate across the... factors , coupled with the internet’s global reach and low cost of entry, are what make securing the cyber domain one of the most complex challenges we

Synthesis of (+)-Antroquinonol: An Antihyperglycemic Agent.

PubMed

Sulake, Rohidas S; Lin, Hsiao-Han; Hsu, Chia-Yu; Weng, Ching-Feng; Chen, Chinpiao

2015-06-19

The total synthesis of antroquinonol has been accomplished through Suzuki-Miyaura cross-coupling and Barton-McCombie reaction, and the α,β-unsaturation was achieved through selenylation and oxidation protocols. In vitro and in vivo studies on the glucose-lowering properties of antroquinonol indicate that it is a potential antidiabetic agent.

A One-Pot Synthesis of Dibenzofurans from 6-Diazo-2-cyclohexenones.

PubMed

Zhao, Hua; Yang, Ke; Zheng, Hongyan; Ding, Ruichao; Yin, Fangjie; Wang, Ning; Li, Yun; Cheng, Bin; Wang, Huifei; Zhai, Hongbin

2015-12-04

A novel and efficient protocol for the rapid construction of dibenzofuran motifs from 6-diazo-2-cyclohexenone and ortho-haloiodobenzene has been developed. The process involves one-pot Pd-catalyzed cross-coupling/aromatization and Cu-catalyzed Ullmann coupling.

Multicomponent, flow diazotization/Mizoroki-Heck coupling protocol: dispelling myths about working with diazonium salts.

PubMed

Nalivela, Kumara S; Tilley, Michael; McGuire, Michael A; Organ, Michael G

2014-05-26

A single pass flow diazotization/Mizoroki-Heck protocol has been developed for the production of cinnimoyl and styryl products. The factors that govern aryl diazonium salt stability have been examined in detail leading to the development of a MeOH/DMF co-solvent system in which the diazonium salts can be generated in the presence of all other reaction components and then coupled selectively to give the desired products. Finally the key role of the reaction quench for flow reactions has been demonstrated. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Competitive Binding Assay for the G-Protein-Coupled Receptor 30 (GPR30) or G-Protein-Coupled Estrogen Receptor (GPER).

PubMed

Thekkumkara, Thomas; Snyder, Russell; Karamyan, Vardan T

2016-01-01

The role of 2-methoxyestradiol is becoming a major area of investigation because of its therapeutic utility, though its mechanism is not fully explored. Recent studies have identified the G-protein-coupled receptor 30 (GPR30, GPER) as a high-affinity membrane receptor for 2-methoxyestradiol. However, studies aimed at establishing the binding affinities of steroid compounds for specific targets are difficult, as the tracers are highly lipophilic and often result in nonspecific binding in lipid-rich membrane preparations with low-level target receptor expression. 2-Methoxyestradiol binding studies are essential to elucidate the underlying effects of this novel estrogen metabolite and to validate its targets; therefore, this competitive receptor-binding assay protocol was developed in order to assess the membrane receptor binding and affinity of 2-methyoxyestradiol.

Synthesis of disulfides and diselenides by copper-catalyzed coupling reactions in water.

PubMed

Li, Zhengkai; Ke, Fang; Deng, Hang; Xu, Hualong; Xiang, Haifeng; Zhou, Xiangge

2013-05-14

A simple and efficient protocol for copper-catalyzed coupling reactions between aryl halides and elemental sulfur or selenium has been developed. A variety of disulfides and diselenides can be obtained in moderate to excellent yields up to 96%.

Preparation, structural characterization, and catalytic performance of Pd(II) and Pt(II) complexes derived from cellulose Schiff base

NASA Astrophysics Data System (ADS)

Baran, Talat; Yılmaz Baran, Nuray; Menteş, Ayfer

2018-05-01

In this study, we reported production, characterization, and catalytic behavior of two novel heterogeneous palladium(II) and platinum(II) catalysts derived from cellulose biopolymer. In order to eliminate the use of toxic organic or inorganic solvents and to reduce the use of excess energy in the coupling reactions, we have developed a very simple, rapid, and eco-friendly microwave irradiation protocol. The developed microwave-assisted method of Suzuki cross coupling reactions produced excellent reaction yields in the presence of cellulose supported palladium and platinum (II) catalysts. Moreover, the catalysts easily regenerated after simple filtration, and they gave good reusability. This study revealed that the designed catalysts and method provide clean, simple, rapid, and impressive catalytic performance for Suzuki coupling reactions.

Sampled-data synchronisation of coupled harmonic oscillators with communication and input delays subject to controller failure

NASA Astrophysics Data System (ADS)

Zhao, Liyun; Zhou, Jin; Wu, Quanjun

2016-01-01

This paper considers the sampled-data synchronisation problems of coupled harmonic oscillators with communication and input delays subject to controller failure. A synchronisation protocol is proposed for such oscillator systems over directed network topology, and then some general algebraic criteria on exponential convergence for the proposed protocol are established. The main features of the present investigation include: (1) both the communication and input delays are simultaneously addressed, and the directed network topology is firstly considered and (2) the effects of time delays on synchronisation performance are theoretically and numerically investigated. It is shown that in the absence of communication delays, coupled harmonic oscillators can achieve synchronisation oscillatory motion. Whereas if communication delays are nonzero at infinite multiple sampled-data instants, its synchronisation (or consensus) state is zero. This conclusion can be used as an effective control strategy to stabilise coupled harmonic oscillators in practical applications. Furthermore, it is interesting to find that increasing either communication or input delays will enhance the synchronisation performance of coupled harmonic oscillators. Subsequently, numerical examples illustrate and visualise theoretical results.

Diaphorase Coupling Protocols for Red-Shifting Dehydrogenase Assays

PubMed Central

Davis, Mindy I.; Shen, Min; Simeonov, Anton

2016-01-01

Abstract Dehydrogenases are an important target for the development of cancer therapeutics. Dehydrogenases either produce or consume NAD(P)H, which is fluorescent but at a wavelength where many compounds found in chemical libraries are also fluorescent. By coupling dehydrogenases to diaphorase, which utilizes NAD(P)H to produce the fluorescent molecule resorufin from resazurin, the assay can be red-shifted into a spectral region that reduces interference from compound libraries. Dehydrogenases that produce NAD(P)H, such as isocitrate dehydrogenase 1 (IDH1), can be read in kinetic mode. Dehydrogenases that consume NAD(P)H, such as mutant IDH1 R132H, can be read in endpoint mode. Here, we report protocols for robust and miniaturized 1,536-well assays for WT IDH1 and IDH1 R132H coupled to diaphorase, and the counterassays used to further detect compound interference with the coupling reagents. This coupling technique is applicable to dehydrogenases that either produce or consume NAD(P)H, and the examples provided here can act as guidelines for the development of high-throughput screens against this enzyme class. PMID:27078681

Childhood trauma, attachment style, and a couple's experience of terminal cancer: case study.

PubMed

McLean, Linda M; Hales, Sarah

2010-06-01

The primary objective of this article is to elucidate the significance of psychosocial distress and risk in a sub-population of end-stage cancer patients and their spouse caregivers who present with an especially challenging attachment style and histories of childhood trauma. The case study presented highlights the need to both identify and offer an empirically validated couple-based intervention, along with a multi-disciplinary team approach over the trajectory of the illness and at end of life. A validated marital protocol (emotionally focused couple therapy [EFT]) is modified for this population and conducted by an EFT-trained psychologist as part of a pilot investigation as to the feasibility and effectiveness of EFT for the terminal cancer population. Measures of marital distress, depression, hopelessness, and attachment security are completed at baseline and subsequent intervals, as reported in another publication. Attachment insecurity and the exquisitely intimate relationship with caregiving and care receiving are underscored, given the couple's traumatic childhood history. The couple described herein, followed from diagnosis of metastatic disease to end of life illuminates the potential effectiveness of a modified EFT protocol, and underscores the need to both identify and intervene with a population potentially at significantly high risk for marital distress, suicidality, depression, and hopelessness. The benefits of a multidisciplinary team is evident as the patient's symptoms of physical distress increased toward end of life and she returned to earlier behaviors, namely suicidal ideation and an attempt to alleviate her experience of suffering. The strength of the marital bond, possibly as a result of the intervention, and the efforts of the multidisciplinary team approach, demonstrate potential to mitigate a catastrophic end of life and a complicated spousal bereavement. This case study adds to the current empirical literature in an area that is currently under-studied and under-reported.

Optimal and secure measurement protocols for quantum sensor networks

NASA Astrophysics Data System (ADS)

Eldredge, Zachary; Foss-Feig, Michael; Gross, Jonathan A.; Rolston, S. L.; Gorshkov, Alexey V.

2018-04-01

Studies of quantum metrology have shown that the use of many-body entangled states can lead to an enhancement in sensitivity when compared with unentangled states. In this paper, we quantify the metrological advantage of entanglement in a setting where the measured quantity is a linear function of parameters individually coupled to each qubit. We first generalize the Heisenberg limit to the measurement of nonlocal observables in a quantum network, deriving a bound based on the multiparameter quantum Fisher information. We then propose measurement protocols that can make use of Greenberger-Horne-Zeilinger (GHZ) states or spin-squeezed states and show that in the case of GHZ states the protocol is optimal, i.e., it saturates our bound. We also identify nanoscale magnetic resonance imaging as a promising setting for this technology.

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

PubMed

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

2015-01-01

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

An adaptive transmission protocol for managing dynamic shared states in collaborative surgical simulation.

PubMed

Qin, J; Choi, K S; Ho, Simon S M; Heng, P A

2008-01-01

A force prediction algorithm is proposed to facilitate virtual-reality (VR) based collaborative surgical simulation by reducing the effect of network latencies. State regeneration is used to correct the estimated prediction. This algorithm is incorporated into an adaptive transmission protocol in which auxiliary features such as view synchronization and coupling control are equipped to ensure the system consistency. We implemented this protocol using multi-threaded technique on a cluster-based network architecture.

Harmonic generation with an ultra-strongly coupled cavity polariton

NASA Astrophysics Data System (ADS)

Crescimanno, Michael; Singer, Kenneth; Liu, Bin; McMaster, Michael

2017-04-01

The large dipole density in a new class of glassy organic dyes results in ultrastrong exciton-cavity field coupling leading to polariton splittings of over an eV. We describe the theoretical model and experimental protocol used to understand third harmonic generation (THG) in this system. We quantify the THG enhancement at the polariton branches through its dependence on coupling, cavity-exciton detuning and cavity finesse.

Synthesis of alkyl- and aryl-amino-substituted anthraquinone derivatives by microwave-assisted copper(0)-catalyzed Ullmann coupling reactions.

PubMed

Baqi, Younis; Müller, Christa E

2010-05-01

This protocol describes the efficient, generally applicable Ullmann coupling reaction of bromaminic acid with alkyl- or aryl-amines in phosphate buffer under microwave irradiation using elemental copper as a catalyst. The reaction leads to a number of biologically active compounds. As a prototypical example, the synthesis of a new, potent antagonist of human platelet P2Y(12) receptors, which has potential as an antithrombotic drug, is described in detail. The optimized protocol includes a description of an appropriate reaction setup, thin layer chromatography for monitoring the reaction and a procedure for the isolation, purification and characterization of the anticipated product. The reaction is performed without the use of a glove box and there is no requirement for an inert atmosphere. The reaction typically proceeds within 2-30 min, the protocol, including workup, generally takes 1-3 h to complete.

New Application of the Comet Assay

PubMed Central

Cortés-Gutiérrez, Elva I.; Dávila-Rodríguez, Martha I.; Fernández, José Luís; López-Fernández, Carmen; Gosálbez, Altea; Gosálvez, Jaime

2011-01-01

The comet assay is a well-established, simple, versatile, visual, rapid, and sensitive tool used extensively to assess DNA damage and DNA repair quantitatively and qualitatively in single cells. The comet assay is most frequently used to analyze white blood cells or lymphocytes in human biomonitoring studies, although other cell types have been examined, including buccal, nasal, epithelial, and placental cells and even spermatozoa. This study was conducted to design a protocol that can be used to generate comets in subnuclear units, such as chromosomes. The new technique is based on the chromosome isolation protocols currently used for whole chromosome mounting in electron microscopy, coupled to the alkaline variant of the comet assay, to detect DNA damage. The results show that migrant DNA fragments can be visualized in whole nuclei and isolated chromosomes and that they exhibit patterns of DNA migration that depend on the level of DNA damage produced. This protocol has great potential for the highly reproducible study of DNA damage and repair in specific chromosomal domains. PMID:21540337

How to personalize ovarian stimulation in clinical practice.

PubMed

Sighinolfi, Giovanna; Grisendi, Valentina; La Marca, Antonio

2017-09-01

Controlled ovarian stimulation (COS) in in vitro fertilization (IVF) cycles is the starting point from which couple's prognosis depends. Individualization in follicle-stimulating hormone (FSH) starting dose and protocol used is based on ovarian response prediction, which depends on ovarian reserve. Anti-Müllerian hormone levels and the antral follicle count are considered the most accurate and reliable markers of ovarian reserve. A literature search was performed for studies that addressed the ability of ovarian reserve markers to predict poor and high ovarian response in assisted reproductive technology cycles. According to the predicted response to ovarian stimulation (poor- normal- or high- response), it is possible to counsel couples before treatment about the prognosis, and also to individualize ovarian stimulation protocols, choosing among GnRH-agonists or antagonists for endogenous FSH suppression, and the FSH starting dose in order to decrease the risk of cycle cancellation and ovarian hyperstimulation syndrome. In this review we discuss how to choose the best COS therapy, based on ovarian reserve markers, in order to enhance chances in IVF.

A Practical Method for the Vinylation of Aromatic Halides using Inexpensive Organosilicon Reagents

PubMed Central

Denmark, Scott E.; Butler, Christopher R.

2009-01-01

The preparation of styrenes by palladium-catalyzed cross-coupling of aromatic iodides and bromides with divinyltetramethyldisiloxane (DVDS) in the presence of inexpensive silanolate activators has been developed. To facilitate the discovery of optimal reaction conditions, Design of Experiment protocols were used. By the guided selection of reagents, stoichiometries, temperatures, and solvents the vinylation reaction was rapidly optimized with three stages consisting of ca. 175 experiments (of a possible 1440 combinations). A variety of aromatic iodides undergo cross-coupling at room temperature in the presence of potassium trimethylsilanoate using Pd(dba)2 in DMF in good yields. Triphenylphosphine oxide is needed to extend catalyst lifetime. Application of these conditions to aryl bromides was accomplished by the development of two complementary protocols. First, the direct implementation of the successful reaction conditions using aryl iodides at elevated temperature in THF provided the corresponding styrenes in good to excellent yields. Alternatively, the use of potassium triethylsilanolate and a bulky “Buchwald-type” ligand allows for the vinylation reactions to occur at or just above room temperature. A wide range of bromides underwent coupling in good yields for each of the protocols described. PMID:18303892

A highly sensitive protocol for microscopy of alkyne lipids and fluorescently tagged or immunostained proteins[S

PubMed Central

Gaebler, Anne; Penno, Anke; Kuerschner, Lars; Thiele, Christoph

2016-01-01

The demand to study the cellular localization of specific lipids has led to recent advances in lipid probes and microscopy. Alkyne lipids bear a small, noninterfering tag and can be detected upon click reaction with an azide-coupled reporter. Fluorescent alkyne lipid imaging crucially depends on appropriate azide reporters and labeling protocols that allow for an efficient click reaction and therefore a sensitive detection. We synthesized several azide reporters with different spacer components and tested their suitability for alkyne lipid imaging in fixed cells. The implementation of a copper-chelating picolyl moiety into fluorescent or biotin-based azide reagents strongly increased the sensitivity of the imaging routine. We demonstrate the applicability and evaluate the performance of this approach using different lipid classes and experimental setups. As azide picolyl reporters allow for reduced copper catalyst concentrations, they also enable coimaging of alkyne lipids with multiple fluorescent proteins including enhanced green fluorescent protein. Alternatively, and as we also show, microscopy of alkyne lipids can be combined with protein detection by immunocytochemistry. In summary, we present a robust, sensitive, and highly versatile protocol for the labeling of alkyne lipids with azide-coupled reporters for fluorescence microscopy that can be combined with different protein detection and imaging techniques. PMID:27565170

An FEC Adaptive Multicast MAC Protocol for Providing Reliability in WLANs

NASA Astrophysics Data System (ADS)

Basalamah, Anas; Sato, Takuro

For wireless multicast applications like multimedia conferencing, voice over IP and video/audio streaming, a reliable transmission of packets within short delivery delay is needed. Moreover, reliability is crucial to the performance of error intolerant applications like file transfer, distributed computing, chat and whiteboard sharing. Forward Error Correction (FEC) is frequently used in wireless multicast to enhance Packet Error Rate (PER) performance, but cannot assure full reliability unless coupled with Automatic Repeat Request forming what is knows as Hybrid-ARQ. While reliable FEC can be deployed at different levels of the protocol stack, it cannot be deployed on the MAC layer of the unreliable IEEE802.11 WLAN due to its inability to exchange ACKs with multiple recipients. In this paper, we propose a Multicast MAC protocol that enhances WLAN reliability by using Adaptive FEC and study it's performance through mathematical analysis and simulation. Our results show that our protocol can deliver high reliability and throughput performance.

Quantum State Transfer via Noisy Photonic and Phononic Waveguides

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

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

PubMed

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

2014-07-14

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

Domino-Fluorination-Protodefluorination Enables Decarboxylative Cross-Coupling of α-Oxocarboxylic Acids with Styrene via Photoredox Catalysis.

PubMed

Zhang, Muliang; Xi, Junwei; Ruzi, Rehanguli; Li, Nan; Wu, Zhongkai; Li, Weipeng; Zhu, Chengjian

2017-09-15

Domino-fluorination-protodefluorination decarboxylative cross-coupling of α-keto acids with styrene has been developed via photoredox catalysis. The critical part of this strategy is the formation of the carbon-fluorine (C-F) bond by the capture of a carbon-centered radical intermediate, which will overcome side reactions during the styrene radical functionalization process. Experimental studies have provided evidence indicating a domino-fluorination-protodefluorination pathway with α-keto acid initiating the photoredox cycle. The present catalytic protocol also affords a novel approach for the construction of α,β-unsaturated ketones under mild conditions.

Palladium-catalyzed cross-coupling of aryl chlorides and triflates with sodium cyanate: A practical synthesis of unsymmetrical ureas

PubMed Central

Vinogradova, Ekaterina V.; Fors, Brett P.; Buchwald, Stephen L.

2012-01-01

An efficient method for palladium-catalyzed cross-coupling of aryl chlorides and triflates with sodium cyanate is reported. The protocol allows for the synthesis of unsymmetrical N,N'-di- and N,N,N'-trisubstituted ureas in one pot, and is tolerant of a wide range of functional groups. Insight into the mechanism of aryl isocyanate formation is gleaned through studies of the transmetallation and reductive elimination steps of the reaction, including the first demonstration of reductive elimination from an arylpalladium isocyanate complex to produce an aryl isocyanate. PMID:22716197

Management of vaginal penetration phobia in Arab women: a retrospective study.

PubMed

Muammar, Tarfah; McWalter, Patricia; Alkhenizan, Abdullah; Shoukri, Mohamed; Gabr, Alia; Bin, Abdulaziz AlDanah

2015-01-01

Vaginal penetration phobia is a common and distressing problem world.wide. It interferes with vaginal penetrative sexual relations, and leads to unconsummated marriage (UCM). This problem may be heightened in Arab women, due to cultural taboos about pain and bleeding, that may be associated with the first coital experience after marriage. Data about this problem is scarce in Arab societies. The aim of this study was to evaluate the response of these women and their husbands to an individualized, psychotherapeutic assessment and treatment to resolve this problem. Retrospective descriptive in a general gynecology community setting over a 6-year period. The study involved a retrospective sequential cohort of 100 Arab couples with UCM due to the woman's VPP. They were evaluated by a female gynecologist in out patient clinics. Data was collected through chart review, and telephone interviews. Final analysis was performed on 100 Arab couples, who satisfied the inclusion criteria. They were followed up to assess their response to an individualized, structured treatment protocol. The treatment combined sex education with systematic desensitization, targeting fear and anxiety as.sociated with vaginal penetration. A total of 96% of the studied group had a successful outcome after an average of 4 sessions. Penetrative intercourse was reported by the tolerance of these women; further pregnancy was achieved in 77.8 % of the infertile couples. Insufficient knowledge of sexual intercourse is a major contributor to the development of VPP in the sampled population. It appears that they respond well to an individualized, structured treatment protocol as described by Hawten 1985 (regardless of other risk factors associated with vaginismus).

Silyl Radical Activation of Alkyl Halides in Metallaphotoredox Catalysis: A Unique Pathway for Cross-Electrophile Coupling.

PubMed

Zhang, Patricia; Le, Chi Chip; MacMillan, David W C

2016-07-06

A strategy for cross-electrophile coupling has been developed via the merger of photoredox and transition metal catalysis. In this report, we demonstrate the use of commercially available tris(trimethylsilyl)silane with metallaphotoredox catalysis to efficiently couple alkyl bromides with aryl or heteroaryl bromides in excellent yields. We hypothesize that a photocatalytically generated silyl radical species can perform halogen-atom abstraction to activate alkyl halides as nucleophilic cross-coupling partners. This protocol allows the use of mild yet robust conditions to construct Csp(3)-Csp(2) bonds generically via a unique cross-coupling pathway.

Home-Based HIV Testing and Counseling for Male Couples (Project Nexus): A Protocol for a Randomized Controlled Trial.

PubMed

Stephenson, Rob; Freeland, Ryan; Sullivan, Stephen P; Riley, Erin; Johnson, Brent A; Mitchell, Jason; McFarland, Deborah; Sullivan, Patrick S

2017-05-30

HIV prevalence remains high among men who have sex with men (MSM) in the United States, yet the majority of research has focused on MSM as individuals, not as dyads, and has discussed HIV risks primarily in the context of casual sex. Nexus is an online prevention program that combines home-based HIV testing and couples HIV testing and counseling (CHTC). It allows partners in dyadic MSM relationships to receive HIV testing and care in the comfort of their designated residence, via video-based chat. By using video-based technologies (eg, VSee video chat), male couples receive counseling and support from a remote online counselor, while testing for HIV at home. This randomized control trial (RCT) aims to examine the effects of video-based counseling combined with home-based HIV testing on couples' management of HIV risk, formation and adherence to explicit sexual agreements, and sexual risk-taking. The research implements a prospective RCT of 400 online-recruited male couples: 200 self-reported concordant-negative couples and 200 self-reported discordant couples. Couples in the control arm will receive one or two home-based HIV self-testing kits and will be asked to report their results via the study's website. Couples in the experimental arm will receive one or two home-based HIV self-testing kits and will conduct these tests together under the facilitation of a remotely located counselor during a prescheduled VSee-based video CHTC session. Study assessments are taken at baseline, as well as at 3- and 6-month follow-up sessions. Project Nexus was launched in April 2016 and is ongoing. To date, 219 eligible couples have been enrolled and randomized. Combining home-based HIV testing with video-based counseling creates an opportunity to expand CHTC to male couples who (1) live outside metro areas, (2) live in rural areas without access to testing services or LGBTQ resources, or (3) feel that current clinic-based testing is not for them (eg, due to fears of discrimination associated with HIV and/or sexuality). ClinicalTrials.gov NCT02335138; https://clinicaltrials.gov/ct2/show/NCT02335138 (Archived by WebCite at http://www.webcitation.org/6qHxtNIdW). ©Rob Stephenson, Ryan Freeland, Stephen P Sullivan, Erin Riley, Brent A Johnson, Jason Mitchell, Deborah McFarland, Patrick S Sullivan. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 30.05.2017.

Alkyne–Aldehyde Reductive C–C Coupling through Ruthenium-Catalyzed Transfer Hydrogenation: Direct Regio- and Stereoselective Carbonyl Vinylation to Form Trisubstituted Allylic Alcohols in the Absence of Premetallated Reagents

PubMed Central

Leung, Joyce C.; Patman, Ryan L.; Sam, Brannon

2011-01-01

Nonsymmetric 1,2-disubstituted alkynes engage in reductive coupling to a variety of aldehydes under the conditions of ruthenium-catalyzed transfer hydrogenation by employing formic acid as the terminal reductant and delivering the products of carbonyl vinylation with good to excellent levels of regioselectivity and with complete control of olefin stereochemistry. As revealed in an assessment of the ruthenium counterion, iodide plays an essential role in directing the regioselectivity of C–C bond formation. Isotopic labeling studies corroborate reversible catalytic propargyl C–H oxidative addition in advance of the C–C coupling, and demonstrate that the C–C coupling products do not experience reversible dehydrogenation by way of enone intermediates. This transfer hydrogenation protocol enables carbonyl vinylation in the absence of stoichiometric metallic reagents. PMID:21953608

Asian couples in negotiation: a mixed-method observational study of cultural variations across five Asian regions.

PubMed

Lee, Wai-Yung; Nakamura, Shin-Ichi; Chung, Moon Ja; Chun, Young Ju; Fu, Meng; Liang, Shu-Chuan; Liu, Cui-Lian

2013-09-01

The purpose of this study was to explore variations in how contemporary couples from five different Asian regions negotiate disagreements. Video recordings of 50 couples (10 each from Japan, Korea, Mainland China, Taiwan, and Hong Kong) discussing unresolved disagreements provided raw data for quantitative and qualitative analyses. First, teams of coders from each region used a common protocol to make quantitative ratings of content themes and interaction patterns for couples from their own region. An interregional panel of investigators then performed in-depth qualitative reviews for half of these cases, noting cultural differences not only in observed patterns of couple behavior but also in their own perceptions of these patterns. Both quantitative and qualitative analyses revealed clear regional differences on dimensions such as overt negativity, demand-withdraw interaction, and collaboration. The qualitative results also provided a richer, more nuanced view of other (e.g., gender-linked) conflict management patterns that the quantitative analyses did not capture. Inconsistencies between qualitative and quantitative data and between the qualitative observations of investigators from different regions were most pronounced for couples from Korea and Japan, whose conflict styles were subtler and less direct than those of couples from the other regions. © FPI, Inc.

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

PubMed

Yang, Haile; Chen, Jiakuan

2018-01-01

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

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

PubMed Central

Chen, Jiakuan

2018-01-01

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

Use of sonic tomography to detect and quantify wood decay in living trees1

PubMed Central

Gilbert, Gregory S.; Ballesteros, Javier O.; Barrios-Rodriguez, Cesar A.; Bonadies, Ernesto F.; Cedeño-Sánchez, Marjorie L.; Fossatti-Caballero, Nohely J.; Trejos-Rodríguez, Mariam M.; Pérez-Suñiga, José Moises; Holub-Young, Katharine S.; Henn, Laura A. W.; Thompson, Jennifer B.; García-López, Cesar G.; Romo, Amanda C.; Johnston, Daniel C.; Barrick, Pablo P.; Jordan, Fulvia A.; Hershcovich, Shiran; Russo, Natalie; Sánchez, Juan David; Fábrega, Juan Pablo; Lumpkin, Raleigh; McWilliams, Hunter A.; Chester, Kathleen N.; Burgos, Alana C.; Wong, E. Beatriz; Diab, Jonathan H.; Renteria, Sonia A.; Harrower, Jennifer T.; Hooton, Douglas A.; Glenn, Travis C.; Faircloth, Brant C.; Hubbell, Stephen P.

2016-01-01

Premise of the study: Field methodology and image analysis protocols using acoustic tomography were developed and evaluated as a tool to estimate the amount of internal decay and damage of living trees, with special attention to tropical rainforest trees with irregular trunk shapes. Methods and Results: Living trunks of a diversity of tree species in tropical rainforests in the Republic of Panama were scanned using an Argus Electronic PiCUS 3 Sonic Tomograph and evaluated for the amount and patterns of internal decay. A protocol using ImageJ analysis software was used to quantify the proportions of intact and compromised wood. The protocols provide replicable estimates of internal decay and cavities for trees of varying shapes, wood density, and bark thickness. Conclusions: Sonic tomography, coupled with image analysis, provides an efficient, noninvasive approach to evaluate decay patterns and structural integrity of even irregularly shaped living trees. PMID:28101433

Accelerating Pediatric Cancer Drug Development: Challenges and Opportunities for Pediatric Master Protocols.

PubMed

Khan, Tahira; Stewart, Mark; Blackman, Samuel; Rousseau, Raphaël; Donoghue, Martha; Cohen, Kenneth; Seibel, Nita; Fleury, Mark; Benettaib, Bouchra; Malik, Raleigh; Vassal, Gilles; Reaman, Gregory

2018-01-01

Although outcomes for children with cancer have significantly improved over the past 40 years, there has been little progress in the treatment of some pediatric cancers, particularly when advanced. Additionally, clinical trial options and availability are often insufficient. Improved genomic and immunologic understanding of pediatric cancers, combined with innovative clinical trial designs, may provide an enhanced opportunity to study childhood cancers. Master protocols, which incorporate the use of precision medicine approaches, coupled with the ability to quickly assess the safety and effectiveness of new therapies, have the potential to accelerate early-phase clinical testing of novel therapeutics and which may result in more rapid approval of new drugs for children with cancer. Designing and conducting master protocols for children requires addressing similar principles and requirements as traditional adult oncology trials, but there are also unique considerations for master protocols conducted in children with cancer. The purpose of this paper is to define the key challenges and opportunities associated with this approach in order to ensure that master protocols can be adapted to benefit children and adolescents and ensure that adequate data are captured to advance, in parallel, the clinical development of investigational agents for children with cancer.

Optimizing Variational Quantum Algorithms Using Pontryagin’s Minimum Principle

DOE PAGES

Yang, Zhi -Cheng; Rahmani, Armin; Shabani, Alireza; ...

2017-05-18

We use Pontryagin’s minimum principle to optimize variational quantum algorithms. We show that for a fixed computation time, the optimal evolution has a bang-bang (square pulse) form, both for closed and open quantum systems with Markovian decoherence. Our findings support the choice of evolution ansatz in the recently proposed quantum approximate optimization algorithm. Focusing on the Sherrington-Kirkpatrick spin glass as an example, we find a system-size independent distribution of the duration of pulses, with characteristic time scale set by the inverse of the coupling constants in the Hamiltonian. The optimality of the bang-bang protocols and the characteristic time scale ofmore » the pulses provide an efficient parametrization of the protocol and inform the search for effective hybrid (classical and quantum) schemes for tackling combinatorial optimization problems. Moreover, we find that the success rates of our optimal bang-bang protocols remain high even in the presence of weak external noise and coupling to a thermal bath.« less

Optimizing Variational Quantum Algorithms Using Pontryagin’s Minimum Principle

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

Yang, Zhi -Cheng; Rahmani, Armin; Shabani, Alireza

We use Pontryagin’s minimum principle to optimize variational quantum algorithms. We show that for a fixed computation time, the optimal evolution has a bang-bang (square pulse) form, both for closed and open quantum systems with Markovian decoherence. Our findings support the choice of evolution ansatz in the recently proposed quantum approximate optimization algorithm. Focusing on the Sherrington-Kirkpatrick spin glass as an example, we find a system-size independent distribution of the duration of pulses, with characteristic time scale set by the inverse of the coupling constants in the Hamiltonian. The optimality of the bang-bang protocols and the characteristic time scale ofmore » the pulses provide an efficient parametrization of the protocol and inform the search for effective hybrid (classical and quantum) schemes for tackling combinatorial optimization problems. Moreover, we find that the success rates of our optimal bang-bang protocols remain high even in the presence of weak external noise and coupling to a thermal bath.« less

Protocol for sortase-mediated construction of DNA-protein hybrids and functional nanostructures.

PubMed

Koussa, Mounir A; Sotomayor, Marcos; Wong, Wesley P

2014-05-15

Recent methods in DNA nanotechnology are enabling the creation of intricate nanostructures through the use of programmable, bottom-up self-assembly. However, structures consisting only of DNA are limited in their ability to act on other biomolecules. Proteins, on the other hand, perform a variety of functions on biological materials, but directed control of the self-assembly process remains a challenge. While DNA-protein hybrids have the potential to provide the best-of-both-worlds, they can be difficult to create as many of the conventional techniques for linking proteins to DNA render proteins dysfunctional. We present here a sortase-based protocol for covalently coupling proteins to DNA with minimal disturbance to protein function. To accomplish this we have developed a two-step process. First, a small synthetic peptide is bioorthogonally and covalently coupled to a DNA oligo using click chemistry. Next, the DNA-peptide chimera is covalently linked to a protein of interest under protein-compatible conditions using the enzyme sortase. Our protocol allows for the simple coupling and purification of a functional DNA-protein hybrid. We use this technique to form oligos bearing cadherin-23 and protocadherin-15 protein fragments. Upon incorporation into a linear M13 scaffold, these protein-DNA hybrids serve as the gate to a binary nanoswitch. The outlined protocol is reliable and modular, facilitating the construction of libraries of oligos and proteins that can be combined to form functional DNA-protein nanostructures. These structures will enable a new class of functional nanostructures, which could be used for therapeutic and industrial processes. Copyright © 2014. Published by Elsevier Inc.

Protocol for sortase-mediated construction of DNA-protein hybrids and functional nanostructures

PubMed Central

Koussa, Mounir A.; Sotomayor, Marcos; Wong, Wesley P.

2014-01-01

Recent methods in DNA nanotechnology are enabling the creation of intricate nanostructures through the use of programmable, bottom-up self-assembly. However, structures consisting only of DNA are limited in their ability to act on other biomolecules. Proteins, on the other hand, perform a variety of functions on biological materials, but directed control of the self-assembly process remains a challenge. While DNA-protein hybrids have the potential to provide the best-of-both-worlds, they can be difficult to create as many of the conventional techniques for linking proteins to DNA render proteins dysfunctional. We present here a sortase-based protocol for covalently coupling proteins to DNA with minimal disturbance to protein function. To accomplish this we have developed a two-step process. First, a small synthetic peptide is bioorthogonally and covalently coupled to a DNA oligo using click chemistry. Next, the DNA-peptide chimera is covalently linked to a protein of interest under protein-compatible conditions using the enzyme sortase. Our protocol allows for the simple coupling and purification of a functional DNA-protein hybrid. We use this technique to form oligos bearing cadherin-23 and protocadherin-15 protein fragments. Upon incorporation into a linear M13 scaffold, these protein-DNA hybrids serve as the gate to a binary nanoswitch. The outlined protocol is reliable and modular, facilitating the construction of libraries of oligos and proteins that can be combined to form functional DNA-protein nanostructures. These structures will enable a new class of functional nanostructures, which could be used for therapeutic and industrial processes. PMID:24568941

¹J(CH) couplings in Group 14/IVA tetramethyls from the gas-phase NMR and DFT structural study: a search for the best computational protocol.

PubMed

Nazarski, Ryszard B; Makulski, Włodzimierz

2014-08-07

Four tetramethyl compounds EMe4 (E = C, Si, Ge, and Pb) were studied by high-resolution NMR spectroscopy in gaseous and liquid states at 300 K. Extrapolation of experimental vapor-phase C-H J-couplings to a zero-pressure limit permitted determining the (1)J(0,CH)s in methyl groups of their nearly isolated molecules. Theoretical predictions of the latter NMR parameters were also performed in a locally dense basis sets/pseudopotential (Sn, Pb) approach, by applying a few DFT methods pre-selected in calculations of other gas-phase molecular properties of all these species and SnMe4 (bond lengths, C-H stretching IR vibrations). A very good agreement theory vs. experiment was achieved with some computational protocols for all five systems. The trends observed in their geometry and associated coupling constants ((1)J(CH)s, (2)J(HH)s) are discussed and rationalized in terms of the substituent-induced rehybridization of the methyl group (treated as a ligand) carbon, by using Bent's rule and the newly proposed, theoretically derived values of the Mulliken electronegativity (χ) of related atoms and groups. All these χ data for the Group-14/IVA entities were under a lot of controversy for a very long time. As a result, the recommended χ values are semi-experimentally confirmed for the first time and only a small correction is suggested for χ(Ge) and χ(GeMe3).

A highly sensitive protocol for microscopy of alkyne lipids and fluorescently tagged or immunostained proteins.

PubMed

Gaebler, Anne; Penno, Anke; Kuerschner, Lars; Thiele, Christoph

2016-10-01

The demand to study the cellular localization of specific lipids has led to recent advances in lipid probes and microscopy. Alkyne lipids bear a small, noninterfering tag and can be detected upon click reaction with an azide-coupled reporter. Fluorescent alkyne lipid imaging crucially depends on appropriate azide reporters and labeling protocols that allow for an efficient click reaction and therefore a sensitive detection. We synthesized several azide reporters with different spacer components and tested their suitability for alkyne lipid imaging in fixed cells. The implementation of a copper-chelating picolyl moiety into fluorescent or biotin-based azide reagents strongly increased the sensitivity of the imaging routine. We demonstrate the applicability and evaluate the performance of this approach using different lipid classes and experimental setups. As azide picolyl reporters allow for reduced copper catalyst concentrations, they also enable coimaging of alkyne lipids with multiple fluorescent proteins including enhanced green fluorescent protein. Alternatively, and as we also show, microscopy of alkyne lipids can be combined with protein detection by immunocytochemistry. In summary, we present a robust, sensitive, and highly versatile protocol for the labeling of alkyne lipids with azide-coupled reporters for fluorescence microscopy that can be combined with different protein detection and imaging techniques. Copyright © 2016 by the American Society for Biochemistry and Molecular Biology, Inc.

Dual trigger of triptorelin and HCG optimizes clinical outcome for high ovarian responder in GnRH-antagonist protocols.

PubMed

Li, Saijiao; Zhou, Danni; Yin, Tailang; Xu, Wangming; Xie, Qingzhen; Cheng, Dan; Yang, Jing

2018-01-12

In this paper, a retrospective cohort study was conducted to the high ovarian responders in GnRH-antagonist protocols of IVF/ICSI cycles. The purpose of the study is to investigate whether dual triggering of final oocyte maturation with a combination of gonadotropin-releasing hormone (GnRH) agonist and human chorionic gonadotropin (HCG) can improve the clinical outcome compared with traditional dose (10000IU) HCG trigger and low-dose (8000IU) HCG trigger for high ovarian responders in GnRH-antagonist in vitro fertilization/intracytoplasmic sperm injection (IVF-ICSI) cycles. Our study included 226 couples with high ovarian responders in GnRH-antagonist protocols of IVF/ICSI cycles. Standard dosage of HCG trigger (10000 IU of recombinant HCG) versus dual trigger (0.2 mg of triptorelin and 2000 IU of recombinant HCG) and low-dose HCG trigger (8000IU of recombinant HCG) were used for final oocyte maturation. Our main outcome measures were high quality embryo rate, the number of usable embryos, the risk of OHSS, duration of hospitalization and incidence rate of complications. Our evidence demonstrated that dual trigger is capable of preventing severe OHSS while still maintaining excellent high quality embryo rate in in high ovarian responders of GnRH-antagonist protocols.

Using Colored Stochastic Petri Net (CS-PN) software for protocol specification, validation, and evaluation

NASA Technical Reports Server (NTRS)

Zenie, Alexandre; Luguern, Jean-Pierre

1987-01-01

The specification, verification, validation, and evaluation, which make up the different steps of the CS-PN software are outlined. The colored stochastic Petri net software is applied to a Wound/Wait protocol decomposable into two principal modules: request or couple (transaction, granule) treatment module and wound treatment module. Each module is specified, verified, validated, and then evaluated separately, to deduce a verification, validation and evaluation of the complete protocol. The colored stochastic Petri nets tool is shown to be a natural extension of the stochastic tool, adapted to distributed systems and protocols, because the color conveniently takes into account the numerous sites, transactions, granules and messages.

Radiation dose reduction in thoracic and lumbar spine instrumentation using navigation based on an intraoperative cone beam CT imaging system: a prospective randomized clinical trial.

PubMed

Pireau, Nathalie; Cordemans, Virginie; Banse, Xavier; Irda, Nadia; Lichtherte, Sébastien; Kaminski, Ludovic

2017-11-01

Spine surgery still remains a challenge for every spine surgeon, aware of the potential serious outcomes of misplaced instrumentation. Though many studies have highlighted that using intraoperative cone beam CT imaging and navigation systems provides higher accuracy than conventional freehand methods for placement of pedicle screws in spine surgery, few studies are concerned about how to reduce radiation exposure for patients with the use of such technology. One of the main focuses of this study is based on the ALARA principle (as low as reasonably achievable). A prospective randomized trial was conducted in the hybrid operating room between December 2015 and December 2016, including 50 patients operated on for posterior instrumented thoracic and/or lumbar spinal fusion. Patients were randomized to intraoperative 3D acquisition high-dose (standard dose) or low-dose protocol, and a total of 216 pedicle screws were analyzed in terms of screw position. Two different methods were used to measure ionizing radiation: the total skin dose (derived from the dose-area product) and the radiation dose evaluated by thermoluminescent dosimeters on the surgical field. According to Gertzbein and Heary classifications, low-dose protocol provided a significant higher accuracy of pedicle screw placement than the high-dose protocol (96.1 versus 92%, respectively). Seven screws (3.2%), all implanted with the high-dose protocol, needed to be revised intraoperatively. The use of low-dose acquisition protocols reduced patient exposure by a factor of five. This study emphasizes the paramount importance of using low-dose protocols for intraoperative cone beam CT imaging coupled with the navigation system, as it at least does not affect the accuracy of pedicle screw placement and irradiates drastically less.

Thermally coupled moving boundary model for charge-discharge of LiFePO4/C cells

NASA Astrophysics Data System (ADS)

Khandelwal, Ashish; Hariharan, Krishnan S.; Gambhire, Priya; Kolake, Subramanya Mayya; Yeo, Taejung; Doo, Seokgwang

2015-04-01

Optimal thermal management is a key requirement in commercial utilization of lithium ion battery comprising of phase change electrodes. In order to facilitate design of battery packs, thermal management systems and fast charging profiles, a thermally coupled electrochemical model that takes into account the phase change phenomenon is required. In the present work, an electrochemical thermal model is proposed which includes the biphasic nature of phase change electrodes, such as lithium iron phosphate (LFP), via a generalized moving boundary model. The contribution of phase change to the heat released during the cell operation is modeled using an equivalent enthalpy approach. The heat released due to phase transformation is analyzed in comparison with other sources of heat such as reversible, irreversible and ohmic. Detailed study of the thermal behavior of the individual cell components with changing ambient temperature, rate of operation and heat transfer coefficient is carried out. Analysis of heat generation in the various regimes is used to develop cell design and operating guidelines. Further, different charging protocols are analyzed and a model based methodology is suggested to design an efficient quick charging protocol.

Total synthesis of Ivorenolide A following a base-induced elimination protocol.

PubMed

Mohapatra, Debendra K; Umamaheshwar, Gonela; Rao, R Nageshwar; Rao, T Srinivasa; R, Sudheer Kumar; Yadav, Jhillu S

2015-02-20

A concise and stereocontrolled first total synthesis of Ivorenolide A (1) is reported in 16 longest linear steps with a 13.4% overall yield starting from (+)-diethyl tartrate (DET). Key features are base-induced elimination protocol for the construction of chiral propargyl alcohols in both fragments, Pd-catalyzed cross-coupling of terminal acetylenes, and Shiina's 2-methyl-6-nitrobezoic anhydride (MNBA) mediated macrolactonization.

Displacemon Electromechanics: How to Detect Quantum Interference in a Nanomechanical Resonator

NASA Astrophysics Data System (ADS)

Khosla, K. E.; Vanner, M. R.; Ares, N.; Laird, E. A.

2018-04-01

We introduce the "displacemon" electromechanical architecture that comprises a vibrating nanobeam, e.g., a carbon nanotube, flux coupled to a superconducting qubit. This platform can achieve strong and even ultrastrong coupling, enabling a variety of quantum protocols. We use this system to describe a protocol for generating and measuring quantum interference between trajectories of a nanomechanical resonator. The scheme uses a sequence of qubit manipulations and measurements to cool the resonator, to apply two effective diffraction gratings, and then to measure the resulting interference pattern. We demonstrate the feasibility of generating a spatially distinct quantum superposition state of motion containing more than 1 06 nucleons using a vibrating nanotube acting as a junction in this new superconducting qubit configuration.

Noise-Resilient Quantum Computing with a Nitrogen-Vacancy Center and Nuclear Spins.

PubMed

Casanova, J; Wang, Z-Y; Plenio, M B

2016-09-23

Selective control of qubits in a quantum register for the purposes of quantum information processing represents a critical challenge for dense spin ensembles in solid-state systems. Here we present a protocol that achieves a complete set of selective electron-nuclear gates and single nuclear rotations in such an ensemble in diamond facilitated by a nearby nitrogen-vacancy (NV) center. The protocol suppresses internuclear interactions as well as unwanted coupling between the NV center and other spins of the ensemble to achieve quantum gate fidelities well exceeding 99%. Notably, our method can be applied to weakly coupled, distant spins representing a scalable procedure that exploits the exceptional properties of nuclear spins in diamond as robust quantum memories.

Validation of the A&D UM-211 device for office blood pressure measurement according to the European Society of Hypertension International Protocol revision 2010.

PubMed

Fania, Claudio; Albertini, Federica; Palatini, Paolo

2017-10-01

The aim of this study was to define the accuracy of UM-211, an automated oscillometric device for office use coupled to several cuffs for different arm sizes, according to the International Protocol of the European Society of Hypertension. The validation was performed in 33 individuals. Their mean age was 59.6±12.9 years, systolic blood pressure (BP) was 144.3±21.5 mmHg (range: 96-184 mmHg), diastolic BP was 86.8±18.5 mmHg (range: 48-124 mmHg), and arm circumference was 30.2±4.3 cm (range: 23-39 cm). Four sequential readings were taken by observers 1 and 2 using a double-headed stethoscope and a mercury sphygmomanometer, whereas three BP readings were taken by the supervisor using the test instrument. The differences between the readings provided by the device and the mean observer measurements were calculated. Therefore, each device measurement was compared with the previous and the next mean observer measurement. The validation results fulfilled all the 2010 European Society of Hypertension revision Protocol criteria for the general population and passed all validation grades. On average, the device overestimated systolic BP by 1.7±2.4 mmHg and diastolic BP by 1.7±2.5 mmHg. These data show that the UM-211 device coupled to several cuffs for different ranges of arm circumference met the requirements for validation according to the International Protocol and can be recommended for clinical use in the adult population. However, these results mainly apply to the use of the 22-32 and the 31-45 cm cuffs.

Ligand- and base-free copper(II)-catalyzed C-N bond formation: cross-coupling reactions of organoboron compounds with aliphatic amines and anilines.

PubMed

Quach, Tan D; Batey, Robert A

2003-11-13

[reaction: see text] A ligandless and base-free Cu-catalyzed protocol for the cross-coupling of arylboronic acids and potassium aryltrifluoroborate salts with primary and secondary aliphatic amines and anilines is described. The process utilizes catalytic copper(II) acetate monohydrate and 4 A molecular sieves in dichloromethane at slightly elevated temperatures under an atmosphere of oxygen. A broad range of functional groups are tolerated on both of the cross-coupling partners.

Two-qubit gates and coupling with low-impedance flux qubits

NASA Astrophysics Data System (ADS)

Chow, Jerry; Corcoles, Antonio; Rigetti, Chad; Rozen, Jim; Keefe, George; Rothwell, Mary-Beth; Rohrs, John; Borstelmann, Mark; Divincenzo, David; Ketchen, Mark; Steffen, Matthias

2011-03-01

We experimentally demonstrate the coupling of two low-impedance flux qubits mediated via a transmission line resonator. We explore the viability of experimental coupling protocols which involve selective microwave driving on the qubits independently as well as fast frequency tuning through on-chip flux-bias. Pulse-shaping techniques for single-qubit and two-qubit gates are employed for reducing unwanted leakage and phase errors. A joint readout through the transmission line resonator is used for characterizing single-qubit and two-qubit states.

Ni-Catalyzed Dehydrogenative Cross-Coupling: Direct Transformation of Aldehydes to Esters and Amides

PubMed Central

Whittaker, Aaron M.; Dong, Vy M.

2015-01-01

By exploring a new mode of Ni-catalyzed cross-coupling, we have developed a protocol to transform both aromatic and aliphatic aldehydes into either esters or amides directly. The success of this oxidative coupling depends on the appropriate choice of catalyst and organic oxidant, including the use of either α,α,α-trifluoroacetophenone or excess aldehyde. We present mechanistic data that supports a catalytic cycle involving oxidative addition into the aldehyde C–H bond. PMID:25424967

Remarkable co-catalysis by copper(I) oxide in the palladium catalyzed cross-coupling of arylboronic acids with ethyl bromoacetate.

PubMed

Liu, Xing-xin; Deng, Min-zhi

2002-03-21

Copper(I) oxide can effectively co-catalyze the Suzuki type cross-coupling reactions of arylboronic acids with ethyl bromoacetate. As an alternative protocol for introducing the methylenecarboxy group into functionalized molecules, this reaction occurs in the absence of highly toxic thallium compounds or special ligands and should be convenient and practical.

Stereoselective Synthesis of Tetrasubstituted Furylalkenes via Gold-Catalyzed Cross-Coupling of Enynones with Diazo Compounds.

PubMed

Liu, Pei; Sun, Jiangtao

2017-07-07

A stereoselective, gold-catalyzed, cross-coupling reaction of enynones with diazo compounds has been developed, affording 2-alkenylfurans in moderate to good yields with excellent E-stereoselectivity. Upon using diazo compounds as nucleophiles to trap the in situ formed gold furyl carbene, this protocol provides a novel path toward the formation of unsymmetrical tetrasubstituted alkenes.

Minimizing irreversible losses in quantum systems by local counterdiabatic driving

PubMed Central

Sels, Dries; Polkovnikov, Anatoli

2017-01-01

Counterdiabatic driving protocols have been proposed [Demirplak M, Rice SA (2003) J Chem Phys A 107:9937–9945; Berry M (2009) J Phys A Math Theor 42:365303] as a means to make fast changes in the Hamiltonian without exciting transitions. Such driving in principle allows one to realize arbitrarily fast annealing protocols or implement fast dissipationless driving, circumventing standard adiabatic limitations requiring infinitesimally slow rates. These ideas were tested and used both experimentally and theoretically in small systems, but in larger chaotic systems, it is known that exact counterdiabatic protocols do not exist. In this work, we develop a simple variational approach allowing one to find the best possible counterdiabatic protocols given physical constraints, like locality. These protocols are easy to derive and implement both experimentally and numerically. We show that, using these approximate protocols, one can drastically suppress heating and increase fidelity of quantum annealing protocols in complex many-particle systems. In the fast limit, these protocols provide an effective dual description of adiabatic dynamics, where the coupling constant plays the role of time and the counterdiabatic term plays the role of the Hamiltonian. PMID:28461472

A cooled CCD camera-based protocol provides an effective solution for in vitro monitoring of luciferase.

PubMed

Afshari, Amirali; Uhde-Stone, Claudia; Lu, Biao

2015-03-13

Luciferase assay has become an increasingly important technique to monitor a wide range of biological processes. However, the mainstay protocols require a luminometer to acquire and process the data, therefore limiting its application to specialized research labs. To overcome this limitation, we have developed an alternative protocol that utilizes a commonly available cooled charge-coupled device (CCCD), instead of a luminometer for data acquiring and processing. By measuring activities of different luciferases, we characterized their substrate specificity, assay linearity, signal-to-noise levels, and fold-changes via CCCD. Next, we defined the assay parameters that are critical for appropriate use of CCCD for different luciferases. To demonstrate the usefulness in cultured mammalian cells, we conducted a case study to examine NFκB gene activation in response to inflammatory signals in human embryonic kidney cells (HEK293 cells). We found that data collected by CCCD camera was equivalent to those acquired by luminometer, thus validating the assay protocol. In comparison, The CCCD-based protocol is readily amenable to live-cell and high-throughput applications, offering fast simultaneous data acquisition and visual and quantitative data presentation. In conclusion, the CCCD-based protocol provides a useful alternative for monitoring luciferase reporters. The wide availability of CCCD will enable more researchers to use luciferases to monitor and quantify biological processes. Copyright © 2015 Elsevier Inc. All rights reserved.

Automated Solid-Phase Protein Modification with Integrated Enzymatic Digest for Reaction Validation: Application of a Compartmented Microfluidic Reactor for Rapid Optimization and Analysis of Protein Biotinylation

PubMed Central

Fraas, Regina; Diehm, Juliane; Franzreb, Matthias

2017-01-01

Protein modification by covalent coupling of small ligands or markers is an important prerequisite for the use of proteins in many applications. Well-known examples are the use of proteins with fluorescent markers in many in vivo experiments or the binding of biotinylated antibodies via biotin–streptavidin coupling in the frame of numerous bioassays. Multiple protocols were established for the coupling of the respective molecules, e.g., via the C and N-terminus, or via cysteines and lysines exposed at the protein surface. Still, in most cases the conditions of these standard protocols are only an initial guess. Optimization of the coupling parameters like reagent concentrations, pH, or temperature may strongly increase coupling yield and the biological activity of the modified protein. In order to facilitate the process of optimizing coupling conditions, a method was developed which uses a compartmented microfluidic reactor for the rapid screening of different coupling conditions. In addition, the system allows for the integration of an enzymatic digest of the modified protein directly after modification. In combination with a subsequent MALDI-TOF analysis of the resulting fragments, this gives a fast and detailed picture not only of the number and extent of the generated modifications but also of their position within the protein sequence. The described process was demonstrated for biotinylation of green fluorescent protein. Different biotin-excesses and different pH-values were tested in order to elucidate the influence on the modification extent and pattern. In addition, the results of solid-phase based modifications within the microfluidic reactor were compared to modification patterns resulting from coupling trials with unbound protein. As expected, modification patterns of immobilized proteins showed clear differences to the ones of dissolved proteins. PMID:29181376

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

PubMed Central

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

2017-01-01

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

Cooling a Mechanical Resonator with Nitrogen-Vacancy Centres Using a Room Temperature Excited State Spin-Strain Interaction

DOE PAGES

MacQuarrie, E. R.; Otten, M.; Gray, S. K.; ...

2017-02-06

Cooling a mechanical resonator mode to a sub-thermal state has been a long-standing challenge in physics. This pursuit has recently found traction in the field of optomechanics in which a mechanical mode is coupled to an optical cavity. An alternate method is to couple the resonator to a well-controlled two-level system. Here we propose a protocol to dissipatively cool a room temperature mechanical resonator using a nitrogen-vacancy centre ensemble. The spin ensemble is coupled to the resonator through its orbitally-averaged excited state, which has a spin-strain interaction that has not been previously studied. We experimentally demonstrate that the spin-strain couplingmore » in the excited state is 13.5 ± 0.5 times stronger than the ground state spin-strain coupling. Lastly, we then theoretically show that this interaction, combined with a high-density spin ensemble, enables the cooling of a mechanical resonator from room temperature to a fraction of its thermal phonon occupancy.« less

Cooling a Mechanical Resonator with Nitrogen-Vacancy Centres Using a Room Temperature Excited State Spin-Strain Interaction

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

MacQuarrie, E. R.; Otten, M.; Gray, S. K.

Cooling a mechanical resonator mode to a sub-thermal state has been a long-standing challenge in physics. This pursuit has recently found traction in the field of optomechanics in which a mechanical mode is coupled to an optical cavity. An alternate method is to couple the resonator to a well-controlled two-level system. Here we propose a protocol to dissipatively cool a room temperature mechanical resonator using a nitrogen-vacancy centre ensemble. The spin ensemble is coupled to the resonator through its orbitally-averaged excited state, which has a spin-strain interaction that has not been previously studied. We experimentally demonstrate that the spin-strain couplingmore » in the excited state is 13.5 ± 0.5 times stronger than the ground state spin-strain coupling. Lastly, we then theoretically show that this interaction, combined with a high-density spin ensemble, enables the cooling of a mechanical resonator from room temperature to a fraction of its thermal phonon occupancy.« less

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.

Ecto-Fc MS identifies ligand-receptor interactions through extracellular domain Fc fusion protein baits and shotgun proteomic analysis

PubMed Central

Savas, Jeffrey N.; De Wit, Joris; Comoletti, Davide; Zemla, Roland; Ghosh, Anirvan

2015-01-01

Ligand-receptor interactions represent essential biological triggers which regulate many diverse and important cellular processes. We have developed a discovery-based proteomic biochemical protocol which couples affinity purification with multidimensional liquid chromatographic tandem mass spectrometry (LCLC-MS/MS) and bioinformatic analysis. Compared to previous approaches, our analysis increases sensitivity, shortens analysis duration, and boosts comprehensiveness. In this protocol, receptor extracellular domains are fused with the Fc region of IgG to generate fusion proteins that are purified from transfected HEK293T cells. These “ecto-Fcs” are coupled to protein A beads and serve as baits for binding assays with prey proteins extracted from rodent brain. After capture, the affinity purified proteins are digested into peptides and comprehensively analyzed by LCLC-MS/MS with ion trap mass spectrometers. In four working days, this protocol can generate shortlists of candidate ligand-receptor protein-protein interactions. Our “Ecto-Fc MS” approach outperforms antibody-based approaches and provides a reproducible and robust framework to identify extracellular ligand – receptor interactions. PMID:25101821

Non-invasive prenatal diagnosis of paternally inherited disorders from maternal plasma: detection of NF1 and CFTR mutations using droplet digital PCR.

PubMed

Gruber, Aurélia; Pacault, Mathilde; El Khattabi, Laila Allach; Vaucouleur, Nicolas; Orhant, Lucie; Bienvenu, Thierry; Girodon, Emmanuelle; Vidaud, Dominique; Leturcq, France; Costa, Catherine; Letourneur, Franck; Anselem, Olivia; Tsatsaris, Vassilis; Goffinet, François; Viot, Géraldine; Vidaud, Michel; Nectoux, Juliette

2018-04-25

To limit risks of miscarriages associated with invasive procedures of current prenatal diagnosis practice, we aim to develop a personalized medicine-based protocol for non-invasive prenatal diagnosis (NIPD) of monogenic disorders relying on the detection of paternally inherited mutations in maternal blood using droplet digital PCR (ddPCR). This study included four couples at risk of transmitting paternal neurofibromatosis type 1 (NF1) mutations and four couples at risk of transmitting compound heterozygous CFTR mutations. NIPD was performed between 8 and 15 weeks of gestation, in parallel to conventional invasive diagnosis. We designed specific hydrolysis probes to detect the paternal mutation and to assess the presence of cell-free fetal DNA by ddPCR. Analytical performances of each assay were determined from paternal sample, an then fetal genotype was inferred from maternal plasma sample. Presence or absence of the paternal mutant allele was correctly determined in all the studied plasma DNA samples. We report an NIPD protocol suitable for implementation in an experienced laboratory of molecular genetics. Our proof-of-principle results point out a high accuracy for early detection of paternal NF1 and CFTR mutations in cell-free DNA, and open new perspectives for extending the technology to NIPD of many other monogenic diseases.

ARO - Terrestrial Research Program, Methodologies and Protocols for Characterization of Geomaterials

DTIC Science & Technology

2015-05-14

of ice involves melting, digestion, and analysis using inductively coupled plasma – mass spectrometry (ICPMS). ICP-MS analysis established elemental...4] have distinct chemical compositions. Knowledge of the chemical composition of the mineral assemblage present in a rock is critical to...activation analysis (INAA), to inductively-coupled plasma analysis and mass spectrometry (ICP & ICP-MS), mass spectrometry (MS), and laser-ablation

One-Step Synthesis of Aliphatic Potassium Acyltrifluoroborates (KATs) from Organocuprates.

PubMed

Liu, Sizhou M; Wu, Dino; Bode, Jeffrey W

2018-04-20

A one-step synthesis of aliphatic KATs from organocuprates is reported. Organolithium and organomagnesium reagents were readily transmetalated onto Cu(I) and coupled with a KAT-forming reagent to yield the respective aliphatic KAT. The protocol is suitable for primary, secondary and-for the first time-tertiary alkyl substrates. These protocols considerably expand the range of KATs that can be readily accessed in one step from commercially available starting materials.

Copper-catalyzed oxidative C-O bond formation of 2-acyl phenols and 1,3-dicarbonyl compounds with ethers: direct access to phenol esters and enol esters.

PubMed

Park, Jihye; Han, Sang Hoon; Sharma, Satyasheel; Han, Sangil; Shin, Youngmi; Mishra, Neeraj Kumar; Kwak, Jong Hwan; Lee, Cheong Hoon; Lee, Jeongmi; Kim, In Su

2014-05-16

A copper-catalyzed oxidative coupling of 2-carbonyl-substituted phenols and 1,3-dicarbonyl compounds with a wide range of dibenzyl or dialkyl ethers is described. This protocol provides an efficient preparation of phenol esters and enol esters in good yields with high chemoselectivity. This method represents an alternative protocol for classical esterification reactions.

HIV knowledge and sexual risk behavior among pregnant couples in South Africa: the PartnerPlus project.

PubMed

Villar-Loubet, Olga M; Cook, Ryan; Chakhtoura, Nahida; Peltzer, Karl; Weiss, Stephen M; Shikwane, Molatelo Elisa; Jones, Deborah L

2013-02-01

In sub-Saharan Africa, 60 % of people living with HIV are women and most are of childbearing age. Alarmingly, seroconversion rates during pregnancy are high and increase as pregnancy progresses, highlighting the importance of increasing HIV-knowledge among pregnant women and their partners. This study compared sexual risk behavior, HIV knowledge and condom use pre- to post-partum among South African couples (n = 239 couples) randomly assigned to an intervention or an enhanced standard of care with the PMTCT protocol at rural community health antenatal clinics. Consistent condom use and HIV-related knowledge increased baseline to post-intervention and was maintained at long term follow up post-partum among participants in the intervention condition. HIV knowledge mediated the relationship between the intervention and consistent condom use. Results from this pilot study provide support for the integration of HIV risk reduction interventions for both women and men into existing PMTCT services during and following pregnancy.

A two-step dilution tris-egg yolk extender containing Equex STM significantly improves sperm cryopreservation in the African wild dog (Lycaon pictus).

PubMed

Van den Berghe, Femke; Paris, Monique Christina Johanna; Briggs, Michael Brent; Farstad, Wenche Kristin; Paris, Damien Boyd Bertrand Paul

2018-02-01

Conservation management of endangered African wild dogs (AWD; Lycaon pictus) can benefit greatly from development of sperm freezing and artificial insemination. Previous freezing attempts yielded nearly 0% motile sperm within 2 h of thawing. In this study, two canine freezing protocols were tested: Protocol 1: a one-step dilution in TRIS-20% egg yolk containing 8% glycerol; and Protocol 2: a two-step dilution in TRIS-20% egg yolk containing a final extender concentration of 5% glycerol and 0.5% Equex STM, coupled with a TRIS-citrate-fructose thawing solution. Semen was collected by electroejaculation from n = 24 AWDs, of which eight ejaculates of sufficient quality (four good quality with initial sperm motility of 75.0 ± 4.4% and four poor quality; showing rapid decrease in sperm motility to 3.3 ± 3.3% prior to freezing) were frozen. For good quality samples, motility and sperm motility index persisted for up to 8 h for Protocol 2, and was higher between 2 and 6 h after thawing with a decrease from 4 h of incubation. Motility dropped to nearly 0% after 2 h incubation for Protocol 1. Viability was higher for Protocol 2 throughout the 8 h of incubation, with a decrease after 6 h, compared to 4 h for Protocol 1. Acrosome integrity was higher for Protocol 2 throughout post-thaw incubation, with a decrease after 2 h for both protocols. Protocols did not differ in normal sperm morphology or DNA integrity. Poor quality samples yielded similar results, except for acrosome integrity, which declined for Protocol 2. In conclusion, a two-step dilution in TRIS-egg yolk-glycerol extender containing Equex STM yields significantly improved post-thaw quality and longevity of AWD spermatozoa, making it suitable for sperm banking and artificial insemination initiatives. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Large Volume, Behaviorally-relevant Illumination for Optogenetics in Non-human Primates.

PubMed

Acker, Leah C; Pino, Erica N; Boyden, Edward S; Desimone, Robert

2017-10-03

This protocol describes a large-volume illuminator, which was developed for optogenetic manipulations in the non-human primate brain. The illuminator is a modified plastic optical fiber with etched tip, such that the light emitting surface area is > 100x that of a conventional fiber. In addition to describing the construction of the large-volume illuminator, this protocol details the quality-control calibration used to ensure even light distribution. Further, this protocol describes techniques for inserting and removing the large volume illuminator. Both superficial and deep structures may be illuminated. This large volume illuminator does not need to be physically coupled to an electrode, and because the illuminator is made of plastic, not glass, it will simply bend in circumstances when traditional optical fibers would shatter. Because this illuminator delivers light over behaviorally-relevant tissue volumes (≈ 10 mm 3 ) with no greater penetration damage than a conventional optical fiber, it facilitates behavioral studies using optogenetics in non-human primates.

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

PubMed

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

2017-11-27

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

A post-Kyoto partner: Considering the Montreal Protocol as a tool to manage nitrous oxide

NASA Astrophysics Data System (ADS)

Mauzerall, D. L.; Kanter, D.; Ravishankara, A. R.; Daniel, J. S.; Portmann, R. W.; Grabiel, P.; Moomaw, W.; Galloway, J. N.

2012-12-01

While nitrous oxide (N2O) was recently identified as the largest remaining anthropogenic threat to the stratospheric ozone layer, it is currently regulated under the 1997 Kyoto Protocol due to its simultaneous ability to warm the climate. The threat N2O poses to the stratospheric ozone layer, coupled with the uncertain future of the international climate regime, motivates our exploration of issues that could be relevant to the Parties to the 1987 Montreal Protocol if they decide to take measures to manage N2O in the future. There are clear legal avenues for the Montreal Protocol and its parent treaty, the 1985 Vienna Convention, to regulate N2O, as well as several ways to share authority with the existing and future international climate treaties. N2O mitigation strategies exist to address its most significant anthropogenic sources, including agriculture, where behavioral practices and new technologies could contribute significantly to mitigation efforts. Existing policies managing N2O and other forms of reactive nitrogen could be harnessed and built upon by the Montreal Protocol's existing bodies to implement N2O controls. Given the tight coupling of the nitrogen cycle, such controls would likely simultaneously reduce emissions of reactive nitrogen and hence have co-benefits for ecosystems and public health. Nevertheless, there are at least three major regulatory challenges that are unique and central to N2O control: food security, equity, and the nitrogen cascade. The possible inclusion of N2O in the Montreal Protocol need not be viewed as a sign of the Kyoto Protocol's failure to adequately deal with climate change, given the complexity of the issue. Rather, it could represent an additional tool in the field of sustainable development diplomacy.lt;img border=0 src="images/B43K-06_B.jpg">

Optimal protocols for slowly driven quantum systems.

PubMed

Zulkowski, Patrick R; DeWeese, Michael R

2015-09-01

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

An impurity-induced gap system as a quantum data bus for quantum state transfer

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

Chen, Bing, E-mail: chenbingphys@gmail.com; Li, Yong; Song, Z.

2014-09-15

We introduce a tight-binding chain with a single impurity to act as a quantum data bus for perfect quantum state transfer. Our proposal is based on the weak coupling limit of the two outermost quantum dots to the data bus, which is a gapped system induced by the impurity. By connecting two quantum dots to two sites of the data bus, the system can accomplish a high-fidelity and long-distance quantum state transfer. Numerical simulations for finite system show that the numerical and analytical results of the effective coupling strength agree well with each other. Moreover, we study the robustness ofmore » this quantum communication protocol in the presence of disorder in the couplings between the nearest-neighbor quantum dots. We find that the gap of the system plays an important role in robust quantum state transfer.« less

An Ultra-low-power Medium Access Control Protocol for Body Sensor Network.

PubMed

Li, Huaming; Tan, Jindong

2005-01-01

In this paper, a medium access control (MAC) protocol designed for Body Sensor Network (BSN-MAC) is proposed. BSN-MAC is an adaptive, feedback-based and IEEE 802.15.4-compatible MAC protocol. Due to the traffic coupling and sensor diversity characteristics of BSNs, common MAC protocols can not satisfy the unique requirements of the biomedical sensors in BSN. BSN-MAC exploits the feedback information from the deployed sensors to form a closed-loop control of the MAC parameters. A control algorithm is proposed to enable the BSN coordinator to adjust parameters of the IEEE 802.15.4 superframe to achieve both energy efficiency and low latency on energy critical nodes. We evaluate the performance of BSN-MAC using energy efficiency as the primary metric.

Validation of the Artsana CSI 610 automated blood pressure monitor in adults according to the International Protocol of the European Society of Hypertension.

PubMed

Pini, Claudio; Pastori, Marco; Baccheschi, Jordan; Omboni, Stefano; Parati, Gianfranco

2007-06-01

There is evidence that blood pressure measurement outside the doctor's office can provide valuable information for the diagnostic evaluation of hypertensive patients and for monitoring their response to treatment. Home blood pressure monitoring devices have a major role in this setting, provided that their accuracy in measuring blood pressure is demonstrated by validation studies. This study aimed at verifying whether the automatic electronic oscillometric blood pressure measuring device Artsana CSI 610 complied with the standard of accuracy indicated by the ESH International Protocol. Sequential measurements of systolic and diastolic blood pressure were obtained in 33 participants using the mercury sphygmomanometer (two observers) and the test device (one supervisor). A standard adult cuff was always employed during the study. According to the ESH validation protocol, 99 couples of test device and reference blood pressure measurements were obtained during the two phases of the study (three pairs for each of the 33 participants). The Artsana CSI 610 device successfully passed phase 1 of study validation with the number of absolute differences between test and reference device never <35 within 5 mmHg and never <40 within 10 and 15 mmHg. The test device also passed phase 2 of the validation study with a mean (+/-SD) device-observer difference of -1.4+/-4.8 mmHg for systolic and -0.9+/-3.5 mmHg for diastolic blood pressure. According to the results of the validation study on the basis of the ESH International Protocol, the Artsana CSI 610 can be recommended for clinical use in adults.

Construction of a single atom trap for quantum information protocols

NASA Astrophysics Data System (ADS)

Shea, Margaret E.; Baker, Paul M.; Gauthier, Daniel J.; Duke Physics Department Team

2016-05-01

The field of quantum information science addresses outstanding problems such as achieving fundamentally secure communication and solving computationally hard problems. Great progress has been made in the field, particularly using photons coupled to ions and super conducting qubits. Neutral atoms are also interesting for these applications and though the technology for control of neutrals lags behind that of trapped ions, they offer some key advantages: primarily coupling to optical frequencies closer to the telecom band than trapped ions or superconducting qubits. Here we report progress on constructing a single atom trap for 87 Rb. This system is a promising platform for studying the technical problems facing neutral atom quantum computing. For example, most protocols destroy the trap when reading out the neutral atom's state; we will investigate an alternative non-destructive state detection scheme. We detail the experimental systems involved and the challenges addressed in trapping a single atom. All of our hardware components are off the shelf and relatively inexpensive. Unlike many other systems, we place a high numerical aperture lens inside our vacuum system to increase photon collection efficiency. We gratefully acknowledge the financial support of the ARO through Grant # W911NF1520047.

Soil Sample Dissolution Development by Ultrawave Digester, Followed by Isotopic Separation and Analysis

DTIC Science & Technology

2017-01-09

uranium, americium, and thorium were analyzed, along with other transition and rare earth metals, utilizing inductively coupled plasma- mass spectrometry...inductively coupled plasma- mass spectrometry and/or alpha spectrometry, following digestion. For validation of the microwave protocol, radioactive... actinide elements. HF is a hazardous acid to work with and it is highly toxic. In this evaluation and validation, the actinides are of particular

Free-breathing imaging of the heart using 2D cine-GRICS (generalized reconstruction by inversion of coupled systems) with assessment of ventricular volumes and function.

PubMed

Vuissoz, Pierre-André; Odille, Freddy; Fernandez, Brice; Lohezic, Maelene; Benhadid, Adnane; Mandry, Damien; Felblinger, Jacques

2012-02-01

To assess cardiac function by means of a novel free-breathing cardiac magnetic resonance imaging (MRI) strategy. A stack of ungated 2D steady-state free precession (SSFP) slices was acquired during free breathing and reconstructed as cardiac cine imaging based on the generalized reconstruction by inversion of coupled systems (GRICS). A motion-compensated sliding window approach allows reconstructing cine movies with most motion artifacts cancelled. The proposed reconstruction uses prior knowledge from respiratory belts and electrocardiogram recordings and features a piecewise linear model that relates the electrocardiogram signal to cardiac displacements. The free-breathing protocol was validated in six subjects against a standard breath-held protocol. Image sharpness, as assessed by the image gradient entropy, was comparable to that of breath-held images and significantly better than in uncorrected images. Volumetric parameters of cardiac function in the left ventricle (LV) and right ventricle (RV) were similar, including end-systolic volumes, end-diastolic volumes and mass, stroke volumes, and ejection fractions (with differences of 3% ± 2.4 in the LV and 2.9% ± 4.4 in the RV). The duration of the free-breathing protocol was nearly the same as the breath-held protocol. Free-breathing cine-GRICS enables accurate assessment of volumetric parameters of cardiac function with efficient correction of motion. Copyright © 2011 Wiley Periodicals, Inc.

Evaluation of a physical activity intervention for new parents: protocol paper for a randomized trial.

PubMed

Quinlan, Alison; Rhodes, Ryan E; Beauchamp, Mark R; Symons Downs, Danielle; Warburton, Darren E R; Blanchard, Chris M

2017-11-09

Identifying critical life transitions in people's physical activity behaviors may illuminate the most opportune intervention apertures for chronic disease prevention. A substantive evidence base now indicates that parenthood is one of these critical transition points for physical activity decline. This study will examine whether a brief theory-based intervention can prevent a decline in physical activity among new parents over 6 months following intervention. This study protocol represents the first dyad-based physical activity initiative in the parenthood literature involving both mothers and fathers; prior research has focused on only mothers or only fathers (albeit limited), and has shown only short-term changes in physical activity. This study will be investigating whether a theory-based physical activity intervention can maintain or improve moderate to vigorous intensity physical activity measured via accelerometry of new parents over a 6 month period following intervention compared to a control group. This study is a 6-month longitudinal randomized controlled trial. Parents are measured at baseline (2 months postpartum) with two assessment points at 6 weeks (3.5 months postpartum) and 3 months (5 months postpartum) and a final follow-up assessment at 6 months (8 months postpartum). The content of the theory-based intervention was derived from the results of our prior longitudinal trial of new parents using an adapted theory of planned behavior framework to predict changes in physical activity. A total of 152 couples have been recruited to date. Sixteen couples dropped out after baseline and a total of 88 couples have completed their 6-month measures. If the intervention proves successful, couple-based physical activity promotion efforts among parents could be a promising avenue to pursue to help mitigate the declines of physical activity levels during parenthood. These findings could inform public health materials and practitioners. This trial has been registered with the Clinical Trials Registry maintained by the National Library of Medicine at the National Institutes of Health on April 19, 2014. The registration ID is NCT02290808 .

Resting-state functional MRI as a tool for evaluating brain hemodynamic responsiveness to external stimuli in rats.

PubMed

Paasonen, Jaakko; Salo, Raimo A; Huttunen, Joanna K; Gröhn, Olli

2017-09-01

Anesthesia is a major confounding factor in functional MRI (fMRI) experiments attributed to its effects on brain function. Recent evidence suggests that parameters obtained with resting-state fMRI (rs-fMRI) are coupled with anesthetic depth. Therefore, we investigated whether parameters obtained with rs-fMRI, such as functional connectivity (FC), are also directly related to blood-oxygen-level-dependent (BOLD) responses. A simple rs-fMRI protocol was implemented in a pharmacological fMRI study to evaluate the coupling between hemodynamic responses and FC under five anesthetics (α-chloralose, isoflurane, medetomidine, thiobutabarbital, and urethane). Temporal change in the FC was evaluated at 1-hour interval. Supplementary forepaw stimulation experiments were also conducted. Under thiobutabarbital anesthesia, FC was clearly coupled with nicotine-induced BOLD responses. Good correlation values were also obtained under isoflurane and medetomidine anesthesia. The observations in the thiobutabarbital group were supported by forepaw stimulation experiments. Additionally, the rs-fMRI protocol revealed significant temporal changes in the FC in the α-chloralose, thiobutabarbital, and urethane groups. Our results suggest that FC can be used to estimate brain hemodynamic responsiveness to stimuli and evaluate the level and temporal changes of anesthesia. Therefore, analysis of the fMRI baseline signal may be highly valuable tool for controlling the outcome of preclinical fMRI experiments. Magn Reson Med 78:1136-1146, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Middleware Trade Study for NASA Domain

NASA Technical Reports Server (NTRS)

Bowman, Dan

2007-01-01

This presentation presents preliminary results of a trade study designed to assess three distributed simulation middleware technologies for support of the NASA Constellation Distributed Space Exploration Simulation (DSES) project and Test and Verification Distributed System Integration Laboratory (DSIL). The technologies are: the High Level Architecture (HLA), the Test and Training Enabling Architecture (TENA), and an XML-based variant of Distributed Interactive Simulation (DIS-XML) coupled with the Extensible Messaging and Presence Protocol (XMPP). According to the criteria and weights determined in this study, HLA scores better than the other two for DSES as well as the DSIL

The Home Observation of Periconceptional Exposures (HOPE) study, a prospective cohort: aims, design, recruitment and compliance.

PubMed

Porucznik, Christina A; Cox, Kyley J; Schliep, Karen C; Wilkins, Diana G; Stanford, Joseph B

2016-06-08

To examine transient environmental exposures and their relationship with human fecundity, exposure assessment should occur optimally at the time of conception in both members of the couple. We performed an observational, prospective cohort study with biomonitoring in both members of a heterosexual couple trying to conceive. Couples collected urine, saliva, and semen specimens for up to two menstrual cycles on days corresponding to the time windows of fertilization, implantation, and early pregnancy, identified based on the woman's observations of her cervical fluid. Three hundred nine eligible couples were screened between 2011 and 2015, of which 183 enrolled. Eleven couples (6.0 %) withdrew or were lost to follow up. The most successful and cost effective recruiting strategies were word of mouth (40 % of participating couples), posters and flyers (37 %), and targeted Facebook advertising (13 %) with an overall investment of $37.35 spent on recruitment per couple. Both men and women collected ≥97.2 % of requested saliva samples, and men collected ≥89.9 % of requested semen samples. Within the periovulatory days (±3 days), there was at least one urine specimen collected by women in 97.1 % of cycles, and at least one by men in 91.7 % of cycles. Daily compliance with periovulatory urine specimens ranged from 66.5 to 92.4 % for women and from 55.7 to 75.0 % for men. Compliance was ≥88 % for questionnaire completion at specified time points. Couples planning to conceive can be recruited successfully for periconceptional monitoring, and will comply with intensive study protocols involving home collection of biospecimens and questionnaire data.

Considerations in establishing a post-mortem brain and tissue bank for the study of myalgic encephalomyelitis/chronic fatigue syndrome: a proposed protocol.

PubMed

Nacul, Luis; O'Donovan, Dominic G; Lacerda, Eliana M; Gveric, Djordje; Goldring, Kirstin; Hall, Alison; Bowman, Erinna; Pheby, Derek

2014-06-18

Our aim, having previously investigated through a qualitative study involving extensive discussions with experts and patients the issues involved in establishing and maintaining a disease specific brain and tissue bank for myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), was to develop a protocol for a UK ME/CFS repository of high quality human tissue from well characterised subjects with ME/CFS and controls suitable for a broad range of research applications. This would involve a specific donor program coupled with rapid tissue collection and processing, supplemented by comprehensive prospectively collected clinical, laboratory and self-assessment data from cases and controls. We reviewed the operations of existing tissue banks from published literature and from their internal protocols and standard operating procedures (SOPs). On this basis, we developed the protocol presented here, which was designed to meet high technical and ethical standards and legal requirements and was based on recommendations of the MRC UK Brain Banks Network. The facility would be most efficient and cost-effective if incorporated into an existing tissue bank. Tissue collection would be rapid and follow robust protocols to ensure preservation sufficient for a wide range of research uses. A central tissue bank would have resources both for wide-scale donor recruitment and rapid response to donor death for prompt harvesting and processing of tissue. An ME/CFS brain and tissue bank could be established using this protocol. Success would depend on careful consideration of logistic, technical, legal and ethical issues, continuous consultation with patients and the donor population, and a sustainable model of funding ideally involving research councils, health services, and patient charities. This initiative could revolutionise the understanding of this still poorly-understood disease and enhance development of diagnostic biomarkers and treatments.

Microplastics in seafood: Benchmark protocol for their extraction and characterization.

PubMed

Dehaut, Alexandre; Cassone, Anne-Laure; Frère, Laura; Hermabessiere, Ludovic; Himber, Charlotte; Rinnert, Emmanuel; Rivière, Gilles; Lambert, Christophe; Soudant, Philippe; Huvet, Arnaud; Duflos, Guillaume; Paul-Pont, Ika

2016-08-01

Pollution of the oceans by microplastics (<5 mm) represents a major environmental problem. To date, a limited number of studies have investigated the level of contamination of marine organisms collected in situ. For extraction and characterization of microplastics in biological samples, the crucial step is the identification of solvent(s) or chemical(s) that efficiently dissolve organic matter without degrading plastic polymers for their identification in a time and cost effective way. Most published papers, as well as OSPAR recommendations for the development of a common monitoring protocol for plastic particles in fish and shellfish at the European level, use protocols containing nitric acid to digest the biological tissues, despite reports of polyamide degradation with this chemical. In the present study, six existing approaches were tested and their effects were compared on up to 15 different plastic polymers, as well as their efficiency in digesting biological matrices. Plastic integrity was evaluated through microscopic inspection, weighing, pyrolysis coupled with gas chromatography and mass spectrometry, and Raman spectrometry before and after digestion. Tissues from mussels, crabs and fish were digested before being filtered on glass fibre filters. Digestion efficiency was evaluated through microscopical inspection of the filters and determination of the relative removal of organic matter content after digestion. Five out of the six tested protocols led to significant degradation of plastic particles and/or insufficient tissue digestion. The protocol using a KOH 10% solution and incubation at 60 °C during a 24 h period led to an efficient digestion of biological tissues with no significant degradation on all tested polymers, except for cellulose acetate. This protocol appeared to be the best compromise for extraction and later identification of microplastics in biological samples and should be implemented in further monitoring studies to ensure relevance and comparison of environmental and seafood product quality studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Role of UV photolysis in accelerating the biodegradation of 2,4,6-TCP.

PubMed

Wang, Wenbing; Kirumba, George; Zhang, Yongming; Wu, Yanqing; Rittmann, Bruce E

2015-09-18

2,4,6-TCP, a kind of chlorinated aromatic and aliphatic compound, is difficult to be biodegraded by ordinary microorganisms. UV photolysis and biodegradation of 2,4,6-TCP by Bacillus amyloliquefaciens intimate coupling is a potential means to accelerate its biotransformation. The initial steps of 2,4,6-TCP biodegradation involve mono-oxygenation reactions that have molecular oxygen and an intracellular electron carrier as cosubstrates. It was demonstrated that B. amyloliquefaciens has the 2,4,6-TCP monooxygenase gene tcpA which could encode 2,4,6-TCP monooxygenase (TCP-MO). TCP-MO would catalytically decompose 2,4,6-TCP into 2,6-DCHQ. We employed an internal loop photolytic biofilm reactor for 2,4,6-TCP degradation. Sequentially coupled photolysis and biodegradation experimental results suggested that 2,4,6-TCP removal rate in P + B (TCP(UV) + phenol) protocol was higher by 77 and 103 % when compared to B (TCP + phenol) and B (TCP-only) protocols respectively. The corresponding loss rate coefficient (k) values were 0.069, 0.039, 0.034 mg/L·min -1 respectively. This is because UV photolysis converted 2,4,6-TCP into its intermediates: 2,4-dichlorophenol (2,4-DCP), 4-monochlorophenol (4-MCP), phenol, 2,6-dichloro-p-hydroquinone (2,6-DCHQ), with all displaying less inhibition to bacterial action. In addition, phenol was the crucial UV-photolysis product from 2,4,6-TCP, its catabolic oxidation generating internal electron carriers that may accelerate the initial steps of 2,4,6-TCP biodegradation. Intimately coupled photolysis and biodegradation experimental results suggested that 2,4,6-TCP removal rate in P&B (TCP + phenol) protocol was higher by 166 and 681 % when compared to P&B (TCP-only) and P + B protocols respectively. The corresponding loss rate coefficient (k) values were 0.539, 0.203, 0.069 mg/L·min -1 respectively. It provided sufficient evidence to demonstrate that intimately coupled photolysis and biodegradation accelerated 2,4,6-TCP removal much faster than sequentially coupled photolysis and biodegradation. In addition, oxidation of phenol was the mechanism by which intimately coupled photolysis and biodegradation accelerated rapid 2,4,6-TCP removal producing electron equivalents that stimulated the initial mono-oxygenation reactions for 2,4,6-TCP biodegradation. It is important to note that 2,6-DCHQ (produced from UV-photolysis products or initial mono-oxygenation reactions) would be catalytically decomposed into 6-chlorohydroxyquinol (6-CHQ). Based on this, a tentative reaction mechanism for the photo-biodegradation 2,4,6-TCP was proposed.

Inductively-Coupled RF Powered O2 Plasma as a Sterilization Source

NASA Technical Reports Server (NTRS)

Sharma, S. P.; Rao, M. V. V. S.; Cruden, B. A.; Meyyappan, M.; Mogul, R.; Khare, B.; Chan, S. L.; Arnold, James O. (Technical Monitor)

2001-01-01

Low-temperature or cold plasmas have been shown to be effective for the sterilization of sensitive medical devices and electronic equipment. Low-temperature plasma sterilization procedures possess certain advantages over other protocols such as ethylene oxide, gamma radiation, and heat due to the use of inexpensive reagents, the insignificant environmental impacts and the low energy requirements. In addition, plasmas may also be more efficacious in the removal of robust microorganisms due to their higher chemical reactivity. Together, these attributes render cold plasma sterilization as ideal for the surface decontamination requirements for NASA Planetary Protection. Hence, the work described in this study involves the construction, characterization, and application of an inductively-coupled, RF powered oxygen (O2) plasma.

CHARM, a gender equity and family planning intervention for men and couples in rural India: protocol for the cluster randomized controlled trial evaluation.

PubMed

Yore, Jennifer; Dasgupta, Anindita; Ghule, Mohan; Battala, Madhusadana; Nair, Saritha; Silverman, Jay; Saggurti, Niranjan; Balaiah, Donta; Raj, Anita

2016-02-20

Globally, 41% of all pregnancies are unintended, increasing risk for unsafe abortion, miscarriage and maternal and child morbidities and mortality. One in four pregnancies in India (3.3 million pregnancies, annually) are unintended; 2/3 of these occur in the context of no modern contraceptive use. In addition, no contraceptive use until desired number and sex composition of children is achieved remains a norm in India. Research shows that globally and in India, the youngest and most newly married wives are least likely to use contraception and most likely to report husband's exclusive family planning decision-making control, suggesting that male engagement and family planning support is important for this group. Thus, the Counseling Husbands to Achieve Reproductive Health and Marital Equity (CHARM) intervention was developed in recognition of the need for more male engagement family planning models that include gender equity counseling and focus on spacing contraception use in rural India. For this study, a multi-session intervention delivered to men but inclusive of their wives was developed and evaluated as a two-armed cluster randomized controlled design study conducted across 50 mapped clusters in rural Maharashtra, India. Eligible rural young husbands and their wives (N = 1081) participated in a three session gender-equity focused family planning program delivered to the men (Sessions 1 and 2) and their wives (Session 3) by village health providers in rural India. Survey assessments were conducted at baseline and 9&18 month follow-ups with eligible men and their wives, and pregnancy tests were obtained from wives at baseline and 18-month follow-up. Additional in-depth understanding of how intervention impact occurred was assessed via in-depth interviews at 18 month follow-up with VHPs and a subsample of couples (n = 50, 2 couples per intervention cluster). Process evaluation was conducted to collect feedback from husbands, wives, and VHPs on program quality and to ascertain whether program elements were implemented according to curriculum protocols. Fidelity to intervention protocol was assessed via review of clinical records. All study procedures were completed in February 2015. Findings from this work offer important contributions to the growing field of male engagement in family planning, globally. ClinicalTrial.gov, NCT01593943.

A network architecture for precision formation flying using the IEEE 802.11 MAC Protocol

NASA Technical Reports Server (NTRS)

Clare, Loren P.; Gao, Jay L.; Jennings, Esther H.; Okino, Clayton

2005-01-01

Precision Formation Flying missions involve the tracking and maintenance of spacecraft in a desired geometric formation. The strong coupling of spacecraft in formation flying control requires inter-spacecraft communication to exchange information. In this paper, we present a network architecture that supports PFF control, from the initial random deployment phase to the final formation. We show that a suitable MAC layer for the application protocol is IEEE's 802.11 MAC protocol. IEEE 802.11 MAC has two modes of operations: DCF and PCF. We show that DCF is suitable for the initial deployment phase while switching to PCF when the spacecraft are in formation improves jitter and throughput. We also consider the effect of routing on protocol performance and suggest when it is profitable to turn off route discovery to achieve better network performance.

A combined experimental and theoretical spectroscopic protocol for determination of the structure of heterogeneous catalysts: developing the information content of the resonance Raman spectra of M1 MoVO x .

PubMed

Kubas, Adam; Noak, Johannes; Trunschke, Annette; Schlögl, Robert; Neese, Frank; Maganas, Dimitrios

2017-09-01

Absorption and multiwavelength resonance Raman spectroscopy are widely used to investigate the electronic structure of transition metal centers in coordination compounds and extended solid systems. In combination with computational methodologies that have predictive accuracy, they define powerful protocols to study the spectroscopic response of catalytic materials. In this work, we study the absorption and resonance Raman spectra of the M1 MoVO x catalyst. The spectra were calculated by time-dependent density functional theory (TD-DFT) in conjunction with the independent mode displaced harmonic oscillator model (IMDHO), which allows for detailed bandshape predictions. For this purpose cluster models with up to 9 Mo and V metallic centers are considered to represent the bulk structure of MoVO x . Capping hydrogens were used to achieve valence saturation at the edges of the cluster models. The construction of model structures was based on a thorough bonding analysis which involved conventional DFT and local coupled cluster (DLPNO-CCSD(T)) methods. Furthermore the relationship of cluster topology to the computed spectral features is discussed in detail. It is shown that due to the local nature of the involved electronic transitions, band assignment protocols developed for molecular systems can be applied to describe the calculated spectral features of the cluster models as well. The present study serves as a reference for future applications of combined experimental and computational protocols in the field of solid-state heterogeneous catalysis.

Synthesis of 1,1-diarylethylenes via efficient iron/copper co-catalyzed coupling of 1-arylvinyl halides with Grignard reagents.

PubMed

Hamze, Abdallah; Brion, Jean-Daniel; Alami, Mouad

2012-06-01

An efficient access to 1,1-diarylethylenes of biological interest by coupling functionalized aryl Grignard reagents and 1-arylvinyl halides in the presence of FeCl(3)/CuTC is described. This bimetallic system proved to be superior to the use of Fe or Cu catalyst alone. The synthetic utility of this protocol is illustrated in the field of steroid chemistry.

Pyrrole-Imidazole Polyamides: Manual Solid-Phase Synthesis.

PubMed

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

2015-12-01

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

Benchmarking a quantum teleportation protocol in superconducting circuits using tomography and an entanglement witness.

PubMed

Baur, M; Fedorov, A; Steffen, L; Filipp, S; da Silva, M P; Wallraff, A

2012-01-27

Teleportation of a quantum state may be used for distributing entanglement between distant qubits in quantum communication and for quantum computation. Here we demonstrate the implementation of a teleportation protocol, up to the single-shot measurement step, with superconducting qubits coupled to a microwave resonator. Using full quantum state tomography and evaluating an entanglement witness, we show that the protocol generates a genuine tripartite entangled state of all three qubits. Calculating the projection of the measured density matrix onto the basis states of two qubits allows us to reconstruct the teleported state. Repeating this procedure for a complete set of input states we find an average output state fidelity of 86%.

In situ measurement of the rheological properties and agglomeration on cementitious pastes

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

Kim, Jae Hong; Yim, Hong Jae, E-mail: yimhj@knu.ac.kr; Ferron, Raissa Douglas

2016-07-15

Various factors influence the rheology of cementitious pastes, with the most important being the mixing protocol, mixture proportions, and mixture composition. This study investigated the influence of ground-granulated blast-furnace slag, on the rheological behavior of cementitious pastes. In tandem with the rheological measurements, fresh state microstructural measurements were conducted using three different techniques: A coupled stroboscope-rheometer, a coupled laser backscattering-rheometer, and a conventional laser diffraction technique. Laser diffraction and the coupled stroboscope-rheometer were not good measures of the in situ state of flocculation of a sample. Rather, only the laser backscattering technique allowed for in situ measurement on a highlymore » concentrated suspension (cementitious paste). Using the coupled laser backscattering-rheometer technique, a link between the particle system and rheological behavior was determined through a modeling approach that takes into account agglomeration properties. A higher degree of agglomeration was seen in the ordinary Portland cement paste than pastes containing the slag and this was related to the degree of capillary pressure in the paste systems.« less

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

PubMed Central

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

2013-01-01

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

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

PubMed Central

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

2015-01-01

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

Olfactory Cued Learning Paradigm.

PubMed

Liu, Gary; McClard, Cynthia K; Tepe, Burak; Swanson, Jessica; Pekarek, Brandon; Panneerselvam, Sugi; Arenkiel, Benjamin R

2017-05-05

Sensory stimulation leads to structural changes within the CNS (Central Nervous System), thus providing the fundamental mechanism for learning and memory. The olfactory circuit offers a unique model for studying experience-dependent plasticity, partly due to a continuous supply of integrating adult born neurons. Our lab has recently implemented an olfactory cued learning paradigm in which specific odor pairs are coupled to either a reward or punishment to study downstream circuit changes. The following protocol outlines the basic set up for our learning paradigm. Here, we describe the equipment setup, programming of software, and method of behavioral training.

OMIP contribution to CMIP6: experimental and diagnostic protocol for the physical component of the Ocean Model Intercomparison Project

NASA Astrophysics Data System (ADS)

Griffies, Stephen M.; Danabasoglu, Gokhan; Durack, Paul J.; Adcroft, Alistair J.; Balaji, V.; Böning, Claus W.; Chassignet, Eric P.; Curchitser, Enrique; Deshayes, Julie; Drange, Helge; Fox-Kemper, Baylor; Gleckler, Peter J.; Gregory, Jonathan M.; Haak, Helmuth; Hallberg, Robert W.; Heimbach, Patrick; Hewitt, Helene T.; Holland, David M.; Ilyina, Tatiana; Jungclaus, Johann H.; Komuro, Yoshiki; Krasting, John P.; Large, William G.; Marsland, Simon J.; Masina, Simona; McDougall, Trevor J.; Nurser, A. J. George; Orr, James C.; Pirani, Anna; Qiao, Fangli; Stouffer, Ronald J.; Taylor, Karl E.; Treguier, Anne Marie; Tsujino, Hiroyuki; Uotila, Petteri; Valdivieso, Maria; Wang, Qiang; Winton, Michael; Yeager, Stephen G.

2016-09-01

The Ocean Model Intercomparison Project (OMIP) is an endorsed project in the Coupled Model Intercomparison Project Phase 6 (CMIP6). OMIP addresses CMIP6 science questions, investigating the origins and consequences of systematic model biases. It does so by providing a framework for evaluating (including assessment of systematic biases), understanding, and improving ocean, sea-ice, tracer, and biogeochemical components of climate and earth system models contributing to CMIP6. Among the WCRP Grand Challenges in climate science (GCs), OMIP primarily contributes to the regional sea level change and near-term (climate/decadal) prediction GCs.OMIP provides (a) an experimental protocol for global ocean/sea-ice models run with a prescribed atmospheric forcing; and (b) a protocol for ocean diagnostics to be saved as part of CMIP6. We focus here on the physical component of OMIP, with a companion paper (Orr et al., 2016) detailing methods for the inert chemistry and interactive biogeochemistry. The physical portion of the OMIP experimental protocol follows the interannual Coordinated Ocean-ice Reference Experiments (CORE-II). Since 2009, CORE-I (Normal Year Forcing) and CORE-II (Interannual Forcing) have become the standard methods to evaluate global ocean/sea-ice simulations and to examine mechanisms for forced ocean climate variability. The OMIP diagnostic protocol is relevant for any ocean model component of CMIP6, including the DECK (Diagnostic, Evaluation and Characterization of Klima experiments), historical simulations, FAFMIP (Flux Anomaly Forced MIP), C4MIP (Coupled Carbon Cycle Climate MIP), DAMIP (Detection and Attribution MIP), DCPP (Decadal Climate Prediction Project), ScenarioMIP, HighResMIP (High Resolution MIP), as well as the ocean/sea-ice OMIP simulations.

Should HCV discordant couples with a seropositive male partner be treated with assisted reproduction techniques (ART)?

PubMed

Savasi, Valeria; Oneta, Monica; Parrilla, Bina; Cetin, Irene

2013-04-01

The debate on HCV discordant couples requiring assisted reproduction is still open today, and specific guidelines have not yet been established on whether or not physicians should treat HCV discordant couples who require ART. We studied the results of our reproductive assistance with sperm washing in HCV discordant couples, all treated in a single center, including the serological status of mothers and babies, and the outcome of the pregnancies. Prospective study conducted between January 2008 and December 2010 in our Reproductive Center in Sacco Hospital, University of Milan. Thirty-five HCV serodiscordant infertile couples with an HCV viremic positive male partner were enrolled. All of them completed the immuno-virological and fertility triage, and were treated according to our clinical protocols. Forty-seven superovulation and IUI and 38 second-level ART procedures are reported. The pregnancy rates for IUI and ICSI are similar to those reported by the Italian ART register. All the 85 sperm samples were treated with sperm washing technique to reduce HCV in semen and the possible risk of transmission. We did not observe any preterm delivery or negative perinatal outcome. No mothers or babies are infected by HCV. This is the biggest prospective study conducted in a single center involving HCV discordant infertile couples in an ART program. Although sexual transmission of HCV is very low, in subfertile or infertile couples sperm washing should be used to treat HCV positive semen before ART. We suggest that it is not necessary to perform nested PCR to detect HCV RNA in the final swim-up. Since the presence of HCV in semen implies a possible risk of nosocomial contamination, safety regulations must be strictly applied in assisted reproduction laboratories. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Modeling Two-Oscillator Circadian Systems Entrained by Two Environmental Cycles

PubMed Central

Oda, Gisele A.; Friesen, W. Otto

2011-01-01

Several experimental studies have altered the phase relationship between photic and non-photic environmental, 24 h cycles (zeitgebers) in order to assess their role in the synchronization of circadian rhythms. To assist in the interpretation of the complex activity patterns that emerge from these “conflicting zeitgeber” protocols, we present computer simulations of coupled circadian oscillators forced by two independent zeitgebers. This circadian system configuration was first employed by Pittendrigh and Bruce (1959), to model their studies of the light and temperature entrainment of the eclosion oscillator in Drosophila. Whereas most of the recent experiments have restricted conflicting zeitgeber experiments to two experimental conditions, by comparing circadian oscillator phases under two distinct phase relationships between zeitgebers (usually 0 and 12 h), Pittendrigh and Bruce compared eclosion phase under 12 distinct phase relationships, spanning the 24 h interval. Our simulations using non-linear differential equations replicated complex non-linear phenomena, such as “phase jumps” and sudden switches in zeitgeber preferences, which had previously been difficult to interpret. Our simulations reveal that these phenomena generally arise when inter-oscillator coupling is high in relation to the zeitgeber strength. Manipulations in the structural symmetry of the model indicated that these results can be expected to apply to a wide range of system configurations. Finally, our studies recommend the use of the complete protocol employed by Pittendrigh and Bruce, because different system configurations can generate similar results when a “conflicting zeitgeber experiment” incorporates only two phase relationships between zeitgebers. PMID:21886835

Perception of nursing students about couples' violence: knowledge, beliefs and professional role 1

PubMed Central

Rigol-Cuadra, Assumpció; Galbany-Estragué, Paola; Fuentes-Pumarola, Concepció; Burjales-Martí, Maria Dolors; Rodríguez-Martín, Dolors; Ballester-Ferrando, David

2015-01-01

OBJECTIVES: to analyse the knowledge, beliefs and perception of the professional role that nursing students have, about exerted violence against women in relationships. METHOD: a descriptive qualitative study following the ecological model through 16 focus groups realized with 112 students from four nursing courses of four Spanish universities. RESULTS: the analytical categories were: knowledge, professional role, and beliefs about ones behaviour before the victim and the abuser. Students are unfamiliar with the characteristics of abuse, guidelines, protocols and screening questions and demand patterns for specific intervention. They do not identify their own professional role, be it delegated or specialized. Beliefs regarding their behaviour with the victim, not guided by professional criteria, perceive violence as a specific situation and disassociate the prevention of health care. They perceive the abuser as mentally ill, justifying the tolerance or delegation of performances. CONCLUSIONS: students define preconceived ideas about couples' violence. Speeches reproduce and reinforce stereotypical myths, values indicative of inadequate training for nursing studies which raises the need to fortify the competencies in relation to intimate couples' violence in the curriculum. PMID:26312637

Entangled state teleportation through a couple of quantum channels composed of XXZ dimers in an Ising- XXZ diamond chain

NASA Astrophysics Data System (ADS)

Rojas, M.; de Souza, S. M.; Rojas, Onofre

2017-02-01

The quantum teleportation plays an important role in quantum information process, in this sense, the quantum entanglement properties involving an infinite chain structure is quite remarkable because real materials could be well represented by an infinite chain. We study the teleportation of an entangled state through a couple of quantum channels, composed by Heisenberg dimers in an infinite Ising-Heisenberg diamond chain, the couple of chains are considered sufficiently far away from each other to be ignored the any interaction between them. To teleporting a couple of qubits through the quantum channel, we need to find the average density operator for Heisenberg spin dimers, which will be used as quantum channels. Assuming the input state as a pure state, we can apply the concept of fidelity as a useful measurement of teleportation performance of a quantum channel. Using the standard teleportation protocol, we have derived an analytical expression for the output concurrence, fidelity, and average fidelity. We study in detail the effects of coupling parameters, external magnetic field and temperature dependence of quantum teleportation. Finally, we explore the relations between entanglement of the quantum channel, the output entanglement and the average fidelity of the system. Through a kind of phase diagram as a function of Ising-Heisenberg diamond chain model parameters, we illustrate where the quantum teleportation will succeed and a region where the quantum teleportation could fail.

Iodine-Mediated Intramolecular Dehydrogenative Coupling: Synthesis of N-Alkylindolo[3,2-c]- and -[2,3-c]quinoline Iodides.

PubMed

Volvoikar, Prajesh S; Tilve, Santosh G

2016-03-04

An I2/TBHP-mediated intramolecular dehydrogenative coupling reaction is developed for the synthesis of a library of medicinally important 5,11-dialkylindolo[3,2-c]quinoline salts and 5,7-dimethylindolo[2,3-c]quinoline salts. The annulation reaction is followed by aromatization to yield tetracycles in good yield. This protocol is also demonstrated for the synthesis of the naturally occurring isocryptolepine in salt form.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

The Model Intercomparison Project on the Climatic Response to Volcanic Forcing (VolMIP): Experimental Design and Forcing Input Data for CMIP6

NASA Technical Reports Server (NTRS)

Zanchettin, Davide; Khodri, Myriam; Timmreck, Claudia; Toohey, Matthew; Schmidt, Anja; Gerber, Edwin P.; Hegerl, Gabriele; Robock, Alan; Pausata, Francesco; Ball, William T.;

The effectiveness of Korean medicine treatment in male patients with infertility: a study protocol for a prospective observational pilot study.

PubMed

Kim, Kwan-Ii; Jo, Junyoung

2018-01-01

Male factor subfertility has increasingly been considered the cause of infertility in couples. Many men with male infertility have sperm problems such as oligozoospermia, asthenozoospermia, or teratozoospermia. Because abnormal semen parameters are idiopathic to some extent, no standard therapy has been established to date. Herbal medicine has been reported to have beneficial properties in the treatment of subfertility, especially in improving semen quality both in vivo and in human studies. Therefore, we intend to investigate the effectiveness and safety of treatment using Korean medicine (KM) for infertile male patients with poor semen quality.This will be a single-center, prospective, case-only observational pilot study. About 20 male patients with infertility who visit Conmaul Hospital of Korean Medicine will be recruited. We will follow the standard treatment protocol, which has shown good results in the treatment of male infertility. The protocol is composed mainly of a 10-week herbal decoction treatment; acupuncture and/or pharmacopuncture are added when needed. Semen samples, quality of life, and the scrotal temperatures of infertile men will be observed before and after the 10-week treatment with KM.The study has received ethical approval from the Public Institutional Review Board (approval number: P01-201708-21-008). The findings will be disseminated to appropriate audiences via peer-reviewed publication and conference presentations. Korean Clinical Trial Registry (CRIS), Republic of Korea: KCT0002611.

Construction of 1-Heteroaryl-3-azabicyclo[3.1.0]hexanes by sp3-sp2 Suzuki-Miyaura and Chan-Evans-Lam Coupling Reactions of Tertiary Trifluoroborates.

PubMed

Harris, Michael R; Li, Qifang; Lian, Yajing; Xiao, Jun; Londregan, Allyn T

2017-05-05

Compounds that contain the 1-heteroaryl-3-azabicyclo[3.1.0]hexane architecture are of particular interest to the pharmaceutical industry yet remain a challenge to synthesize. We report herein an expedient and modular approach to the synthesis of 1-heteroaryl-3-azabicyclo[3.1.0]hexanes by Suzuki-Miyaura and Chan-Evans-Lam coupling reactions of tertiary trifluoroborate salts. Our Suzuki-Miyaura cross-coupling protocol is compatible with a broad range of aryl and heteroaryl bromides and chlorides. The unprecedented Chan-Evans-Lam coupling of tertiary trifluoroborates allows the facile construction of 1-heteroaryl-3-azabicyclo[3.1.0]hexanes containing C-tertiary arylamines at the ring juncture.

Nickel-Catalyzed Suzuki-Miyaura Cross-Coupling in a Green Alcohol Solvent for an Undergraduate Organic Chemistry Laboratory.

PubMed

Hie, Liana; Chang, Jonah J; Garg, Neil K

2015-03-10

A modern undergraduate organic chemistry laboratory experiment involving the Suzuki-Miyaura coupling is reported. Although Suzuki-Miyaura couplings typically employ palladium catalysts in environmentally harmful solvents, this experiment features the use of inexpensive nickel catalysis, in addition to a "green" alcohol solvent. The experiment employs heterocyclic substrates, which are important pharmaceutical building blocks. Thus, this laboratory procedure exposes students to a variety of contemporary topics in organic chemistry, including transition metal-catalyzed cross-couplings, green chemistry, and the importance of heterocycles in drug discovery, none of which are well represented in typical undergraduate organic chemistry curricula. The experimental protocol uses commercially available reagents and is useful in both organic and inorganic instructional laboratories.

Single-Electron Transmetalation via Photoredox/Nickel Dual Catalysis: Unlocking a New Paradigm for sp(3)-sp(2) Cross-Coupling.

PubMed

Tellis, John C; Kelly, Christopher B; Primer, David N; Jouffroy, Matthieu; Patel, Niki R; Molander, Gary A

2016-07-19

The important role of transition metal-catalyzed cross-coupling in expanding the frontiers of accessible chemical territory is unquestionable. Despite empowering chemists with Herculean capabilities in complex molecule construction, contemporary protocols are not without their Achilles' heel: Csp(3)-Csp(2)/sp(3) coupling. The underlying challenge in sp(3) cross-couplings is 2-fold: (i) methods employing conventional, bench-stable precursors are universally reliant on extreme reaction conditions because of the high activation barrier of transmetalation; (ii) circumvention of this barrier invariably relies on use of more reactive precursors, thereby sacrificing functional group tolerance, operational simplicity, and broad applicability. Despite the ubiquity of this problem, the nature of the transmetalation step has remained unchanged from the seminal reports of Negishi, Suzuki, Kumada, and Stille, thus suggesting that the challenges in Csp(3)-Csp(2)/sp(3) coupling result from inherent mechanistic constraints in the traditional cross-coupling paradigm. Rather than submitting to the limitations of this conventional approach, we envisioned that a process rooted in single-electron reactivity could furnish the same key metalated intermediate posited in two-electron transmetalation, while demonstrating entirely complementary reactivity patterns. Inspired by literature reports on the susceptibility of organoboron reagents toward photochemical, single-electron oxidative fragmentation, realization of a conceptually novel open shell transmetalation framework was achieved in the facile coupling of benzylic trifluoroborates with aryl halides via cooperative visible-light activated photoredox and Ni cross-coupling catalysis. Following this seminal study, we disclosed a suite of protocols for the cross-coupling of secondary alkyl, α-alkoxy, α-amino, and α-trifluoromethylbenzyltrifluoroborates. Furthermore, the selective cross-coupling of Csp(3) organoboron moieties in the presence of Csp(2) organoboron motifs was also demonstrated, highlighting the nuances of this approach to transmetalation. Computational modeling of the reaction mechanism uncovered useful details about the intermediates and transition-state structures involved in the nickel catalytic cycle. Most notably, a unique dynamic kinetic resolution process, characterized by radical homolysis/recombination equilibrium of a Ni(III) intermediate, was discovered. This process was ultimately found to be responsible for stereoselectivity in an enantioselective variant of these cross-couplings. Prompted by the intrinsic limitations of organotrifluoroborates, we sought other radical feedstocks and quickly identified alkylbis(catecholato)silicates as viable radical precursors for Ni/photoredox dual catalysis. These hypervalent silicate species have several notable benefits, including more favorable redox potentials that allow extension to primary alkyl systems incorporating unprotected amines as well as compatibility with less expensive Ru-based photocatalysts. Additionally, these reagents exhibit an amenability to alkenyl halide cross-coupling while simultaneously expanding the aryl halide scope. In the process of exploring these reagents, we serendipitously discovered a method to effect thioetherification of aryl halides via a H atom transfer mechanism. This latter discovery emphasizes that this robust cross-coupling paradigm is "blind" to the origins of the radical, opening opportunities for a wealth of new discoveries. Taken together, our studies in the area of photoredox/nickel dual catalysis have validated single-electron transmetalation as a powerful platform for enabling conventionally challenging Csp(3)-Csp(2) cross-couplings. More broadly, these findings represent the power of rational design in catalysis and the strategic use of mechanistic knowledge and manipulation for the development of new synthetic methods.

Imaging malaria sporozoites in the dermis of the mammalian host.

PubMed

Amino, Rogerio; Thiberge, Sabine; Blazquez, Samantha; Baldacci, Patricia; Renaud, Olivier; Shorte, Spencer; Ménard, Robert

2007-01-01

The initial phase of malaria infection is the pre-erythrocytic phase, which begins when parasites are injected by the mosquito into the dermis and ends when parasites are released from hepatocytes into the blood. We present here a protocol for the in vivo imaging of GFP-expressing sporozoites in the dermis of rodents, using the combination of a high-speed spinning-disk confocal microscope and a high-speed charge-coupled device (CCD) camera permitting rapid in vivo acquisitions. The steps of this protocol indicate how to infect mice through the bite of infected Anopheles stephensi mosquitoes, record the sporozoites' fate in the mouse ear and to present the data as maximum-fluorescence-intensity projections, time-lapse representations and movie clips. This protocol permits investigating the various aspects of sporozoite behavior in a quantitative manner, such as motility in the matrix, cell traversal, crossing the endothelial barrier of both blood and lymphatic vessels and intravascular gliding. Applied to genetically modified parasites and/or mice, these imaging techniques should be useful for studying the cellular and molecular bases of Plasmodium sporozoite infection in vivo.

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

PubMed

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

2011-01-01

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

Protocol for chromosome-specific probe construction using PRINS, micromanipulation and DOP-PCR techniques.

PubMed

Passamani, Paulo Z; Carvalho, Carlos R; Soares, Fernanda A F

2018-01-01

Chromosome-specific probes have been widely used in molecular cytogenetics, being obtained with different methods. In this study, a reproducible protocol for construction of chromosome-specific probes is proposed which associates in situ amplification (PRINS), micromanipulation and degenerate oligonucleotide-primed PCR (DOP-PCR). Human lymphocyte cultures were used to obtain metaphases from male and female individuals. The chromosomes were amplified via PRINS, and subcentromeric fragments of the X chromosome were microdissected using microneedles coupled to a phase contrast microscope. The fragments were amplified by DOP-PCR and labeled with tetramethyl-rhodamine-5-dUTP. The probes were used in fluorescent in situ hybridization (FISH) procedure to highlight these specific regions in the metaphases. The results show one fluorescent red spot in male and two in female X chromosomes and interphase nuclei.

Rigidity and retention of ceramic root canal posts.

PubMed

Purton, D G; Love, R M; Chandler, N P

2000-01-01

Ceramic root-canal posts offer potential advantages over other types with respect to aesthetics and biocompatibility. Any post must be sufficiently rigid and retentive to withstand functional forces. Ceraposts (1.2 mm coronal diameter, ceramic, tapering, smooth posts) and Paraposts (1.25 mm, stainless-steel, parallel, serrated posts) were tested for rigidity by means of a three-point bending test. To test retention in roots, ceramic posts were cemented using one of three protocols: (1) glass-ionomer cement, (2) silane coupling agent and resin cement, or (3) sandblasted post surface, silane coupling agent, and resin cement. Stainless-steel posts were cemented with resin. The tensile force required to dislodge the posts, following four weeks of storage in water, was recorded. Data were compared using Student's t-test and Mann-Whitney U analysis. Ceraposts were significantly more rigid than Paraposts (p < 0.001). Paraposts cemented with resin were significantly more strongly retained than Ceraposts following any cementation protocol (p < 0.001). Retention of the ceramic posts was significantly greater with a silane coupling agent and resin cement than with glass-ionomer cement (p < 0.001). Sandblasting the ceramic posts produced variable results and needs further investigation before it could be recommended.

NASA Constellation Distributed Simulation Middleware Trade Study

NASA Technical Reports Server (NTRS)

Hasan, David; Bowman, James D.; Fisher, Nancy; Cutts, Dannie; Cures, Edwin Z.

2008-01-01

This paper presents the results of a trade study designed to assess three distributed simulation middleware technologies for support of the NASA Constellation Distributed Space Exploration Simulation (DSES) project and Test and Verification Distributed System Integration Laboratory (DSIL). The technologies are the High Level Architecture (HLA), the Test and Training Enabling Architecture (TENA), and an XML-based variant of Distributed Interactive Simulation (DIS-XML) coupled with the Extensible Messaging and Presence Protocol (XMPP). According to the criteria and weights determined in this study, HLA scores better than the other two for DSES as well as the DSIL.

Systems, methods, and products for graphically illustrating and controlling a droplet actuator

NASA Technical Reports Server (NTRS)

Brafford, Keith R. (Inventor); Pamula, Vamsee K. (Inventor); Paik, Philip Y. (Inventor); Pollack, Michael G. (Inventor); Sturmer, Ryan A. (Inventor); Smith, Gregory F. (Inventor)

2010-01-01

Systems for controlling a droplet microactuator are provided. According to one embodiment, a system is provided and includes a controller, a droplet microactuator electronically coupled to the controller, and a display device displaying a user interface electronically coupled to the controller, wherein the system is programmed and configured to permit a user to effect a droplet manipulation by interacting with the user interface. According to another embodiment, a system is provided and includes a processor, a display device electronically coupled to the processor, and software loaded and/or stored in a storage device electronically coupled to the controller, a memory device electronically coupled to the controller, and/or the controller and programmed to display an interactive map of a droplet microactuator. According to yet another embodiment, a system is provided and includes a controller, a droplet microactuator electronically coupled to the controller, a display device displaying a user interface electronically coupled to the controller, and software for executing a protocol loaded and/or stored in a storage device electronically coupled to the controller, a memory device electronically coupled to the controller, and/or the controller.

Thermostabilisation of membrane proteins for structural studies

PubMed Central

Magnani, Francesca; Serrano-Vega, Maria J.; Shibata, Yoko; Abdul-Hussein, Saba; Lebon, Guillaume; Miller-Gallacher, Jennifer; Singhal, Ankita; Strege, Annette; Thomas, Jennifer A.; Tate, Christopher G.

2017-01-01

The thermostability of an integral membrane protein in detergent solution is a key parameter that dictates the likelihood of obtaining well-diffracting crystals suitable for structure determination. However, many mammalian membrane proteins are too unstable for crystallisation. We developed a thermostabilisation strategy based on systematic mutagenesis coupled to a radioligand-binding thermostability assay that can be applied to receptors, ion channels and transporters. It takes approximately 6-12 months to thermostabilise a G protein-coupled receptor (GPCR) containing 300 amino acid residues. The resulting thermostabilised membrane proteins are more easily crystallised and result in high-quality structures. This methodology has facilitated structure-based drug design applied to GPCRs, because it is possible to determine multiple structures of the thermostabilised receptors bound to low affinity ligands. Protocols and advice are given on how to develop thermostability assays for membrane proteins and how to combine mutations to make an optimally stable mutant suitable for structural studies. PMID:27466713

Cardiovascular Deconditioning in Humans: Alteration in Cardiovascular Regulation and Function During Simulated Microgravity

NASA Technical Reports Server (NTRS)

Cohen, Richard

1999-01-01

Alterations in cardiovascular regulation and function that occur during and after space flight have been reported. These alterations are manifested, for example, by reduced orthostatic tolerance upon reentry to the earth's gravity from space. However, the precise physiologic mechanisms responsible for these alterations remain to be fully elucidated. Perhaps, as a result, effective countermeasures have yet to be developed. In this project we apply a powerful, new method - cardiovascular system identification (CSI) - for the study of the effects of space flight on the cardiovascular system so that effective countermeasures can be developed. CSI involves the mathematical analysis of second-to-second fluctuations in non-invasively measured heart rate, arterial blood pressure (ABP), and instantaneous lung volume (ILV - respiratory activity) in order to characterize quantitatively the physiologic mechanisms responsible for the couplings between these signals. Through the characterization of all the physiologic mechanisms coupling these signals, CSI provides a model of the closed-loop cardiovascular regulatory state in an individual subject. The model includes quantitative descriptions of the heart rate baroreflex, autonomic function, as well as other important physiologic mechanisms. We are in the process of incorporating beat-to-beat fluctuations of stroke volume into the CSI technique in order to quantify additional physiologic mechanisms such as those involved in control of peripheral vascular resistance and alterations in cardiac contractility. We apply CSI in conjunction with the two general protocols of the Human Studies Core project. The first protocol involves ground-based, human head down tilt bed rest to simulate microgravity and acute stressors - upright tilt, standing and bicycle exercise - to provide orthostatic and exercise challenges. The second protocol is intended to be the same as the first but with the addition of sleep deprivation to determine whether this contributes to cardiovascular alterations. In these studies, we focus on the basic physiologic mechanisms responsible for the alterations in cardiovascular regulation and function during the simulated microgravity in order to formulate hypotheses regarding what countermeasures are likely to be most effective. Compared to our original proposal, the protocol we are using has been slightly modified to lengthen the bed rest period to 16 days and streamline the data collection. These modifications provide us data on a longer bed rest period and have enabled us to increase our subject throughput. Based on review of our preliminary data we have decided to test a countermeasure which is applied the very end of the bed rest period. We will use the same bed rest protocol to test this countermeasure. We anticipate completing the baseline data collection in our first protocol plus testing of the countermeasure in an additional eight subjects, at which time we plan to initiate the second protocol which includes sleep deprivation. In future studies, we plan to apply CSI to test other potential countermeasures in conjunction with the same bed rest, sleep deprivation and acute stressor models. We also anticipate applying CSI for studying astronauts before and after space flight and ultimately, during space flight. The application of CSI is providing information relevant to the development and evaluation of effective countermeasures allowing humans to adapt appropriately upon re-exposure to a gravity field, and to live and work for longer periods of time in microgravity.

Stimulated Raman signals at conical intersections: Ab initio surface hopping simulation protocol with direct propagation of the nuclear wave function

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

Kowalewski, Markus, E-mail: mkowalew@uci.edu; Mukamel, Shaul, E-mail: smukamel@uci.edu

2015-07-28

Femtosecond Stimulated Raman Spectroscopy (FSRS) signals that monitor the excited state conical intersections dynamics of acrolein are simulated. An effective time dependent Hamiltonian for two C—H vibrational marker bands is constructed on the fly using a local mode expansion combined with a semi-classical surface hopping simulation protocol. The signals are obtained by a direct forward and backward propagation of the vibrational wave function on a numerical grid. Earlier work is extended to fully incorporate the anharmonicities and intermode couplings.

Couple characteristics and outcome of therapy in vaginismus.

PubMed

Munasinghe, Thiloma; Goonaratna, Colvin; de Silva, Padmal

2004-06-01

To describe couple characteristics and outcome of therapy in vaginismus. A prospective before-after intervention descriptive study. Department of Physiology, Faculty of Medicine, Colombo, Sri Lanka. Fifty six couples with vaginismus, mostly self referrals and referrals from gynaecologists and general practitioners, were treated with a standard cognitive behaviour therapy protocol with before-after assessments of the degree of vaginismus and individual partner self-ratings of the relationship and psychological status (GHQ-30). Success at the end of the therapy was equated to the absence of or only mild vaginismus and, improvement in the couple relationship and psychological status scores. Twenty seven (48%) of the 52 (93%) couples with non-consummation reported failure of coitus following previous non-surgical and surgical interventions. Love marriages (70%), frequent attempts at sex (75%, 3 or 4 times/week) and sexual arousal (women = 86%, men = 89%) characterised couples. Ten men developed sexual problems, mostly erectile failure and premature ejaculation secondarily. Couple therapy enabled penetrative sex in 45 (80.3%). The single prognostic indicator of outcome was the degree of vaginismus at first visit, those with mild and moderate vaginismus (77%) being significantly more likely to establish coitus (p<0.001) and complete the therapy (p<0.001). The couple relationship improved marginally (women p<0.01, men 0.025

0.01) but the psychological status remained unchanged. Dropouts and referrals for psychiatric and marital counselling failed to complete therapy. Couple sex therapy is effective in the management of vaginismus. Health professionals, especially gynaecologists and general practitioners, need to be aware of the problem and the satisfactory outcome of sex therapy.

Bidirectional private key exchange using delay-coupled semiconductor lasers.

PubMed

Porte, Xavier; Soriano, Miguel C; Brunner, Daniel; Fischer, Ingo

2016-06-15

We experimentally demonstrate a key exchange cryptosystem based on the phenomenon of identical chaos synchronization. In our protocol, the private key is symmetrically generated by the two communicating partners. It is built up from the synchronized bits occurring between two current-modulated bidirectionally coupled semiconductor lasers with additional self-feedback. We analyze the security of the exchanged key and discuss the amplification of its privacy. We demonstrate private key generation rates up to 11  Mbit/s over a public channel.

Substrate-Directed Hydroacylation: Rh-Catalyzed Coupling of Vinyl Phenols and Non-Chelating Aldehydes

PubMed Central

Murphy, Stephen K.; Bruch, Achim

2014-01-01

We report a protocol for branched-selective hydroacylation of vinylphenols with aryl, alkenyl and alkyl aldehydes. This cross-coupling yields α-aryl ketones that can be cyclized to benzofurans, and it enables access to eupomatenoid natural products in four steps or less from eugenol. Excellent reactivity and high levels of branched regioselectivity are obtained. We propose that aldehyde decarbonylation is overcome by using an anionic directing group on the olefin and a small bite-angle diphosphine ligand. PMID:24478146

First intention IVF protocol for polycystic ovaries: does oral contraceptive pill pretreatment influence COH outcome?

PubMed

Decanter, Christine; Robin, Geoffroy; Thomas, Patricia; Leroy, Maryse; Lefebvre, Catherine; Soudan, Benoit; Lefebvre-Khalil, Valerie; Leroy-Martin, Brigitte; Dewailly, Didier

2013-06-19

Morphological aspect of polycystic ovaries (PCO) is a very common finding in an IVF center population: this includes PCOS patients identified in 18-25% of the couples presenting with infertility and so called "sonographic PCO only" the prevalence of which has been estimated as high as 33% in asymptomatic patients. Finding the optimal first intention IVF protocol for polycystic ovaries patients is still challenging in order to improve the controlled ovarian hyperstimulation (COH) outcome while avoiding ovarian hyperstimulation syndrome (OHSS). It has been suggested that women with PCO would benefit from a longer period of pituitary down-regulation. The purpose of this study was to compare an extended duration of OCP pretreatment with a classic GnRH agonist protocol. A single center prospective non-randomized study was performed from January 2009 to December 2010 in the Lille University Hospital including 113 women diagnosed with PCO(S) according to the Rotterdam ultrasonographic criteria and undergoing their first IVF attempt. Comprehensive hormonal and ultra-sonographic assessments were collected during COH in these patients. LH and androgen suppression and dynamics of follicular growth were compared between the two protocols as well as the COH outcome in terms of oocyte/embryo number and quality, implantation and pregnancy rates. No significant difference was observed between the two groups concerning dynamics of follicular growth and hormonal values. Clinical and ongoing pregnancy rates were significantly lower in the OCP group despite same oocyte and embryo quality. Nevertheless, the cumulative pregnancy rate did not differ between the two groups. The incidence of OHSS was not statistically significant. Extended duration of OCP pretreatment, as a first intention IVF protocol for PCO patients, does not improve the pattern of follicular growth nor the oocyte and embryo quality.

Matching initial torque with different stimulation parameters influences skeletal muscle fatigue.

PubMed

Bickel, C Scott; Gregory, Chris M; Azuero, Andres

2012-01-01

A fundamental barrier to using electrical stimulation in the clinical setting is an inability to maintain torque production secondary to muscle fatigue. Electrical stimulation parameters are manipulated to influence muscle torque production, and they may also influence fatigability during repetitive stimulation. Our purpose was to determine the response of the quadriceps femoris to three different fatigue protocols using the same initial torque obtained by altering stimulator parameter settings. Participants underwent fatigue protocols in which either pulse frequency (lowHz), pulse duration (lowPD), or voltage (lowV) was manipulated to obtain an initial torque that equaled 25% of maximum voluntary isometric contraction. Muscle soreness was reported on a visual analog scale 48 h after each fatigue test. The lowHz protocol resulted in the least fatigue (25% +/- 14%); the lowPD (50% +/- 13%) and lowV (48% +/- 14%) protocols had similar levels of fatigue. The lowHz protocol resulted in significantly less muscle soreness than the higher frequency protocols. Stimulation protocols that use a lower frequency coupled with long pulse durations and high voltages result in lesser amounts of muscle fatigue and perceived soreness. The identification of optimal stimulation patterns to maximize muscle performance will reduce the effect of muscle fatigue and potentially improve clinical efficacy.

Robust quantum entanglement generation and generation-plus-storage protocols with spin chains

NASA Astrophysics Data System (ADS)

Estarellas, Marta P.; D'Amico, Irene; Spiller, Timothy P.

2017-04-01

Reliable quantum communication and/or processing links between modules are a necessary building block for various quantum processing architectures. Here we consider a spin-chain system with alternating strength couplings and containing three defects, which impose three domain walls between topologically distinct regions of the chain. We show that—in addition to its useful, high-fidelity, quantum state transfer properties—an entangling protocol can be implemented in this system, with optional localization and storage of the entangled states. We demonstrate both numerically and analytically that, given a suitable initial product-state injection, the natural dynamics of the system produces a maximally entangled state at a given time. We present detailed investigations of the effects of fabrication errors, analyzing random static disorder both in the diagonal and off-diagonal terms of the system Hamiltonian. Our results show that the entangled state formation is very robust against perturbations of up to ˜10 % the weaker chain coupling, and also robust against timing injection errors. We propose a further protocol, which manipulates the chain in order to localize and store each of the entangled qubits. The engineering of a system with such characteristics would thus provide a useful device for quantum information processing tasks involving the creation and storage of entangled resources.

Pilot studies for the North American Soil Geochemical Landscapes Project - Site selection, sampling protocols, analytical methods, and quality control protocols

USGS Publications Warehouse

Smith, D.B.; Woodruff, L.G.; O'Leary, R. M.; Cannon, W.F.; Garrett, R.G.; Kilburn, J.E.; Goldhaber, M.B.

2009-01-01

In 2004, the US Geological Survey (USGS) and the Geological Survey of Canada sampled and chemically analyzed soils along two transects across Canada and the USA in preparation for a planned soil geochemical survey of North America. This effort was a pilot study to test and refine sampling protocols, analytical methods, quality control protocols, and field logistics for the continental survey. A total of 220 sample sites were selected at approximately 40-km intervals along the two transects. The ideal sampling protocol at each site called for a sample from a depth of 0-5 cm and a composite of each of the O, A, and C horizons. The <2-mm fraction of each sample was analyzed for Al, Ca, Fe, K, Mg, Na, S, Ti, Ag, As, Ba, Be, Bi, Cd, Ce, Co, Cr, Cs, Cu, Ga, In, La, Li, Mn, Mo, Nb, Ni, P, Pb, Rb, Sb, Sc, Sn, Sr, Te, Th, Tl, U, V, W, Y, and Zn by inductively coupled plasma-mass spectrometry and inductively coupled plasma-atomic emission spectrometry following a near-total digestion in a mixture of HCl, HNO3, HClO4, and HF. Separate methods were used for Hg, Se, total C, and carbonate-C on this same size fraction. Only Ag, In, and Te had a large percentage of concentrations below the detection limit. Quality control (QC) of the analyses was monitored at three levels: the laboratory performing the analysis, the USGS QC officer, and the principal investigator for the study. This level of review resulted in an average of one QC sample for every 20 field samples, which proved to be minimally adequate for such a large-scale survey. Additional QC samples should be added to monitor within-batch quality to the extent that no more than 10 samples are analyzed between a QC sample. Only Cr (77%), Y (82%), and Sb (80%) fell outside the acceptable limits of accuracy (% recovery between 85 and 115%) because of likely residence in mineral phases resistant to the acid digestion. A separate sample of 0-5-cm material was collected at each site for determination of organic compounds. A subset of 73 of these samples was analyzed for a suite of 19 organochlorine pesticides by gas chromatography. Only three of these samples had detectable pesticide concentrations. A separate sample of A-horizon soil was collected for microbial characterization by phospholipid fatty acid analysis (PLFA), soil enzyme assays, and determination of selected human and agricultural pathogens. Collection, preservation and analysis of samples for both organic compounds and microbial characterization add a great degree of complication to the sampling and preservation protocols and a significant increase to the cost for a continental-scale survey. Both these issues must be considered carefully prior to adopting these parameters as part of the soil geochemical survey of North America.

Coupling of ultrasound-assisted extraction and expanded bed adsorption for simplified medicinal plant processing and its theoretical model: extraction and enrichment of ginsenosides from Radix Ginseng as a case study.

PubMed

Mi, Jianing; Zhang, Min; Zhang, Hongyang; Wang, Yuerong; Wu, Shikun; Hu, Ping

2013-02-01

A high-efficient and environmental-friendly method for the preparation of ginsenosides from Radix Ginseng using the method of coupling of ultrasound-assisted extraction with expanded bed adsorption is described. Based on the optimal extraction conditions screened by surface response methodology, ginsenosides were extracted and adsorbed, then eluted by the two-step elution protocol. The comparison results between the coupling of ultrasound-assisted extraction with expanded bed adsorption method and conventional method showed that the former was better than the latter in both process efficiency and greenness. The process efficiency and energy efficiency of the coupling of ultrasound-assisted extraction with expanded bed adsorption method rapidly increased by 1.4-fold and 18.5-fold of the conventional method, while the environmental cost and CO(2) emission of the conventional method were 12.9-fold and 17.0-fold of the new method. Furthermore, the theoretical model for the extraction of targets was derived. The results revealed that the theoretical model suitably described the process of preparing ginsenosides by the coupling of ultrasound-assisted extraction with expanded bed adsorption system. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Predicting the Coupling Properties of Axially-Textured Materials.

PubMed

Fuentes-Cobas, Luis E; Muñoz-Romero, Alejandro; Montero-Cabrera, María E; Fuentes-Montero, Luis; Fuentes-Montero, María E

2013-10-30

A description of methods and computer programs for the prediction of "coupling properties" in axially-textured polycrystals is presented. Starting data are the single-crystal properties, texture and stereography. The validity and proper protocols for applying the Voigt, Reuss and Hill approximations to estimate coupling properties effective values is analyzed. Working algorithms for predicting mentioned averages are given. Bunge's symmetrized spherical harmonics expansion of orientation distribution functions, inverse pole figures and (single and polycrystals) physical properties is applied in all stages of the proposed methodology. The established mathematical route has been systematized in a working computer program. The discussion of piezoelectricity in a representative textured ferro-piezoelectric ceramic illustrates the application of the proposed methodology. Polycrystal coupling properties, predicted by the suggested route, are fairly close to experimentally measured ones.

Predicting the Coupling Properties of Axially-Textured Materials

PubMed Central

Fuentes-Cobas, Luis E.; Muñoz-Romero, Alejandro; Montero-Cabrera, María E.; Fuentes-Montero, Luis; Fuentes-Montero, María E.

2013-01-01

A description of methods and computer programs for the prediction of “coupling properties” in axially-textured polycrystals is presented. Starting data are the single-crystal properties, texture and stereography. The validity and proper protocols for applying the Voigt, Reuss and Hill approximations to estimate coupling properties effective values is analyzed. Working algorithms for predicting mentioned averages are given. Bunge’s symmetrized spherical harmonics expansion of orientation distribution functions, inverse pole figures and (single and polycrystals) physical properties is applied in all stages of the proposed methodology. The established mathematical route has been systematized in a working computer program. The discussion of piezoelectricity in a representative textured ferro-piezoelectric ceramic illustrates the application of the proposed methodology. Polycrystal coupling properties, predicted by the suggested route, are fairly close to experimentally measured ones. PMID:28788370

Modern bioanalysis of proteins by electrophoretic techniques.

PubMed

Krizkova, Sona; Ryvolova, Marketa; Masarik, Michal; Zitka, Ondrej; Adam, Vojtech; Hubalek, Jaromir; Eckschlager, Tomas; Kizek, Rene

2014-01-01

In 1957, protein rich in cysteine able to bind cadmium was isolated from horse kidney and named as metallothionein according to its structural properties. Further, this protein and metallothionein-like proteins have been found in tissues of other animal species, yeasts, fungi and plants. MT is as a potential cancer marker in the focus of interest, and its properties, functions, and behavior under various conditions are intensively studied. Our protocol describes separation of two major mammalian isoforms of MT (MT-1 and MT-2) using capillary electrophoresis (CE) coupled with UV detector. This protocol enables separation of MT isoforms and studying of their basic behavior as well as their quantification with detection limit in units of ng per μL. Sodium borate buffer (20 mM, pH 9.5) was optimized as a background electrolyte, and the separation was carried out in fused silica capillary with internal diameter of 75 μm and electric field intensity of 350 V/cm. Optimal detection wavelength was 254 nm.

Inverse engineering for fast transport and spin control of spin-orbit-coupled Bose-Einstein condensates in moving harmonic traps

NASA Astrophysics Data System (ADS)

Chen, Xi; Jiang, Ruan-Lei; Li, Jing; Ban, Yue; Sherman, E. Ya.

2018-01-01

We investigate fast transport and spin manipulation of tunable spin-orbit-coupled Bose-Einstein condensates in a moving harmonic trap. Motivated by the concept of shortcuts to adiabaticity, we design inversely the time-dependent trap position and spin-orbit-coupling strength. By choosing appropriate boundary conditions we obtain fast transport and spin flip simultaneously. The nonadiabatic transport and relevant spin dynamics are illustrated with numerical examples and compared with the adiabatic transport with constant spin-orbit-coupling strength and velocity. Moreover, the influence of nonlinearity induced by interatomic interaction is discussed in terms of the Gross-Pitaevskii approach, showing the robustness of the proposed protocols. With the state-of-the-art experiments, such an inverse engineering technique paves the way for coherent control of spin-orbit-coupled Bose-Einstein condensates in harmonic traps.

Considerations in establishing a post-mortem brain and tissue bank for the study of myalgic encephalomyelitis/chronic fatigue syndrome: a proposed protocol

PubMed Central

2014-01-01

Background Our aim, having previously investigated through a qualitative study involving extensive discussions with experts and patients the issues involved in establishing and maintaining a disease specific brain and tissue bank for myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), was to develop a protocol for a UK ME/CFS repository of high quality human tissue from well characterised subjects with ME/CFS and controls suitable for a broad range of research applications. This would involve a specific donor program coupled with rapid tissue collection and processing, supplemented by comprehensive prospectively collected clinical, laboratory and self-assessment data from cases and controls. Findings We reviewed the operations of existing tissue banks from published literature and from their internal protocols and standard operating procedures (SOPs). On this basis, we developed the protocol presented here, which was designed to meet high technical and ethical standards and legal requirements and was based on recommendations of the MRC UK Brain Banks Network. The facility would be most efficient and cost-effective if incorporated into an existing tissue bank. Tissue collection would be rapid and follow robust protocols to ensure preservation sufficient for a wide range of research uses. A central tissue bank would have resources both for wide-scale donor recruitment and rapid response to donor death for prompt harvesting and processing of tissue. Conclusion An ME/CFS brain and tissue bank could be established using this protocol. Success would depend on careful consideration of logistic, technical, legal and ethical issues, continuous consultation with patients and the donor population, and a sustainable model of funding ideally involving research councils, health services, and patient charities. This initiative could revolutionise the understanding of this still poorly-understood disease and enhance development of diagnostic biomarkers and treatments. PMID:24938650

A Retrospective, Multicenter Study of the Tolerance of Induction Chemotherapy With Docetaxel, Cisplatin, and 5-Fluorouracil Followed by Radiotherapy With Concomitant Cetuximab in 46 Cases of Squamous Cell Carcinoma of the Head and Neck

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

Buiret, Guillaume, E-mail: guillaume.buiret@laposte.ne; Service de biostatistique, Hospices Civils de Lyon, Lyon; Combe, Claire

2010-06-01

Purpose: To investigate, in a multicenter study, the tolerance of induction chemotherapy (ICT) and external radiotherapy (ERT) with concomitant cetuximab in the treatment of patients with squamous cell carcinoma of the head and neck (SCCHN). Patients and Methods: Clinical data from 46 patients with Stage III or IV nonmetastatic SCCHN who received docetaxel, cisplatin, and 5-fluorouracil as ICT, followed by ERT with concomitant cetuximab, were retrospectively analyzed. Clinical safety (weight, allergy, mucositis, and dermatitis) and paraclinical safety (levels of hemoglobin, polynuclear neutrophils, and creatinine clearance) were studied. The primary objective was the proportion of patients who completed the protocol. Results:more » The percentage of patients completing ICT was 73.9%, ERT 93.5%, and cetuximab 69.6%. Induction chemotherapy was better tolerated than that previously reported. The rates of temporary suspensions of radiation (39.1%, mean duration of 13 days) and hospitalization (26.1%) during ERT with concomitant cetuximab were high. Weight loss during treatment (21.4% of patients lost >10% of their body weight), radiodermatitis, and radiomucositis were the main causes of temporary suspension of treatment, although Grade 4 dermatitis was not experienced. There were no allergic reactions to cetuximab. Conclusion: The completed protocol rate for SCCHN patients receiving ICT and ERT with concomitant cetuximab is high and the toxicity acceptable. Future improvements to protocol will be possible through early action and systematic implementation of nutritional support coupled with antibiotic treatment upon the first signs of radiodermatitis. These data could be useful for prospective studies on the safety and efficacy of this protocol.« less

Long-term ongoing pregnancy rate and mode of conception after a positive and negative post-coital test.

PubMed

Hessel, Marloes; Brandes, Monique; de Bruin, Jan Peter; Bots, Rob S G M; Kremer, Jan A M; Nelen, Willianne L D M; Hamilton, Carl J C M

2014-09-01

Many fertility clinics have decided to abolish the post-coital test. Yet, it is a significant factor in prognostic models that predict the spontaneous pregnancy rate within one year. The aim of this study was to evaluate (1) the long-term outcome of infertile couples with a positive or a negative post-coital test during their fertility work-up and (2) the contribution of the different modes of conception. Retrospective cohort study. Three fertility clinics in the Netherlands, of which two are secondary care training hospitals and is a one tertiary care academic training hospital. 2476 newly referred infertile couples, where a post-coital test was performed in 1624 couples. After basic fertility work-up, couples were treated according to the national treatment protocols. Spontaneous and overall ongoing pregnancy rate. The spontaneous and overall ongoing pregnancy rates after three years were 37.7 and 77.5% after a positive post-coital test compared with 26.9 and 68.8% after a negative test (p < 0.001). Even in couples with severe male factor infertility (total motile sperm count <3) (p = 0.005) and mild male factor infertility (total motile sperm count 3-20) (p < 0.001), there was a significantly higher spontaneous ongoing pregnancy rate, justifying expectant management. After a follow-up of three years a positive post-coital test is still associated with a higher spontaneous and a higher overall ongoing pregnancy rate, even in couples with severe male factor infertility. © 2014 Nordic Federation of Societies of Obstetrics and Gynecology.

Quantum cloning disturbed by thermal Davies environment

NASA Astrophysics Data System (ADS)

Dajka, Jerzy; Łuczka, Jerzy

2016-06-01

A network of quantum gates designed to implement universal quantum cloning machine is studied. We analyze how thermal environment coupled to auxiliary qubits, `blank paper' and `toner' required at the preparation stage of copying, modifies an output fidelity of the cloner. Thermal environment is described in terms of the Markovian Davies theory. We show that such a cloning machine is not universal any more but its output is independent of at least a part of parameters of the environment. As a case study, we consider cloning of states in a six-state cryptography's protocol. We also briefly discuss cloning of arbitrary input states.

Respiratory analysis of coupled mitochondria in cryopreserved liver biopsies.

PubMed

García-Roche, Mercedes; Casal, Alberto; Carriquiry, Mariana; Radi, Rafael; Quijano, Celia; Cassina, Adriana

2018-07-01

The aim of this work was to develop a cryopreservation method of small liver biopsies for in situ mitochondrial function assessment. Herein we describe a detailed protocol for tissue collection, cryopreservation, high-resolution respirometry using complex I and II substrates, calculation and interpretation of respiratory parameters. Liver biopsies from cow and rat were sequentially frozen in a medium containing dimethylsulfoxide as cryoprotectant and stored for up to 3 months at -80 °C. Oxygen consumption rate studies of fresh and cryopreserved samples revealed that most respiratory parameters remained unchanged. Additionally, outer mitochondrial membrane integrity was assessed adding cytochrome c, proving that our cryopreservation method does not harm mitochondrial structure. In sum, we present a reliable way to cryopreserve small liver biopsies without affecting mitochondrial function. Our protocol will enable the transport and storage of samples, extending and facilitating mitochondrial function analysis of liver biopsies. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

On the Control of Consensus Networks: Theory and Applications

NASA Astrophysics Data System (ADS)

Hudoba de Badyn, Mathias

Signed networks allow the study of positive and negative interactions between agents. In this thesis, three papers are presented that address controllability of networked dynamics. First, controllability of signed consensus networks is approached from a symmetry perspective, for both linear and nonlinear consensus protocols. It is shown that the graph-theoretic property of signed networks known as structural balance renders the consensus protocol uncontrollable when coupled with a certain type of symmetry. Stabilizability and output controllability of signed linear consensus is also examined, as well as a data-driven approach to finding bipartite consensus stemming from structural balance for signed nonlinear consensus. Second, an algorithm is constructed that allows one to grow a network while preserving controllability, and some generalizations of this algorithm are presented. Submodular optimization is used to analyze a second algorithm that adds nodes to a network to maximize the network connectivity.

Local quantum uncertainty guarantees the measurement precision for two coupled two-level systems in non-Markovian environment

NASA Astrophysics Data System (ADS)

Wu, Shao-xiong; Zhang, Yang; Yu, Chang-shui

2018-03-01

Quantum Fisher information (QFI) is an important feature for the precision of quantum parameter estimation based on the quantum Cramér-Rao inequality. When the quantum state satisfies the von Neumann-Landau equation, the local quantum uncertainty (LQU), as a kind of quantum correlation, present in a bipartite mixed state guarantees a lower bound on QFI in the optimal phase estimation protocol (Girolami et al., 2013). However, in the open quantum systems, there is not an explicit relation between LQU and QFI generally. In this paper, we study the relation between LQU and QFI in open systems which is composed of two interacting two-level systems coupled to independent non-Markovian environments with the entangled initial state embedded by a phase parameter θ. The analytical calculations show that the QFI does not depend on the phase parameter θ, and its decay can be restrained through enhancing the coupling strength or non-Markovianity. Meanwhile, the LQU is related to the phase parameter θ and shows plentiful phenomena. In particular, we find that the LQU can well bound the QFI when the coupling between the two systems is switched off or the initial state is Bell state.

Efficient functionalization of alginate biomaterials.

PubMed

Dalheim, Marianne Ø; Vanacker, Julie; Najmi, Maryam A; Aachmann, Finn L; Strand, Berit L; Christensen, Bjørn E

2016-02-01

Peptide coupled alginates obtained by chemical functionalization of alginates are commonly used as scaffold materials for cells in regenerative medicine and tissue engineering. We here present an alternative to the commonly used carbodiimide chemistry, using partial periodate oxidation followed by reductive amination. High and precise degrees of substitution were obtained with high reproducibility, and without formation of by-products. A protocol was established using l-Tyrosine methyl ester as a model compound and the non-toxic pic-BH3 as the reducing agent. DOSY was used to indirectly verify covalent binding and the structure of the product was further elucidated using NMR spectroscopy. The coupling efficiency was to some extent dependent on alginate composition, being most efficient on mannuronan. Three different bioactive peptide sequences (GRGDYP, GRGDSP and KHIFSDDSSE) were coupled to 8% periodate oxidized alginate resulting in degrees of substitution between 3.9 and 6.9%. Cell adhesion studies of mouse myoblasts (C2C12) and human dental stem cells (RP89) to gels containing various amounts of GRGDSP coupled alginate demonstrated the bioactivity of the material where RP89 cells needed higher peptide concentrations to adhere. Copyright © 2015 Elsevier Ltd. All rights reserved.

Natural Language Processing-Enabled and Conventional Data Capture Methods for Input to Electronic Health Records: A Comparative Usability Study.

PubMed

Kaufman, David R; Sheehan, Barbara; Stetson, Peter; Bhatt, Ashish R; Field, Adele I; Patel, Chirag; Maisel, James Mark

2016-10-28

The process of documentation in electronic health records (EHRs) is known to be time consuming, inefficient, and cumbersome. The use of dictation coupled with manual transcription has become an increasingly common practice. In recent years, natural language processing (NLP)-enabled data capture has become a viable alternative for data entry. It enables the clinician to maintain control of the process and potentially reduce the documentation burden. The question remains how this NLP-enabled workflow will impact EHR usability and whether it can meet the structured data and other EHR requirements while enhancing the user's experience. The objective of this study is evaluate the comparative effectiveness of an NLP-enabled data capture method using dictation and data extraction from transcribed documents (NLP Entry) in terms of documentation time, documentation quality, and usability versus standard EHR keyboard-and-mouse data entry. This formative study investigated the results of using 4 combinations of NLP Entry and Standard Entry methods ("protocols") of EHR data capture. We compared a novel dictation-based protocol using MediSapien NLP (NLP-NLP) for structured data capture against a standard structured data capture protocol (Standard-Standard) as well as 2 novel hybrid protocols (NLP-Standard and Standard-NLP). The 31 participants included neurologists, cardiologists, and nephrologists. Participants generated 4 consultation or admission notes using 4 documentation protocols. We recorded the time on task, documentation quality (using the Physician Documentation Quality Instrument, PDQI-9), and usability of the documentation processes. A total of 118 notes were documented across the 3 subject areas. The NLP-NLP protocol required a median of 5.2 minutes per cardiology note, 7.3 minutes per nephrology note, and 8.5 minutes per neurology note compared with 16.9, 20.7, and 21.2 minutes, respectively, using the Standard-Standard protocol and 13.8, 21.3, and 18.7 minutes using the Standard-NLP protocol (1 of 2 hybrid methods). Using 8 out of 9 characteristics measured by the PDQI-9 instrument, the NLP-NLP protocol received a median quality score sum of 24.5; the Standard-Standard protocol received a median sum of 29; and the Standard-NLP protocol received a median sum of 29.5. The mean total score of the usability measure was 36.7 when the participants used the NLP-NLP protocol compared with 30.3 when they used the Standard-Standard protocol. In this study, the feasibility of an approach to EHR data capture involving the application of NLP to transcribed dictation was demonstrated. This novel dictation-based approach has the potential to reduce the time required for documentation and improve usability while maintaining documentation quality. Future research will evaluate the NLP-based EHR data capture approach in a clinical setting. It is reasonable to assert that EHRs will increasingly use NLP-enabled data entry tools such as MediSapien NLP because they hold promise for enhancing the documentation process and end-user experience. ©David R. Kaufman, Barbara Sheehan, Peter Stetson, Ashish R. Bhatt, Adele I. Field, Chirag Patel, James Mark Maisel. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 28.10.2016.

Braids and phase gates through high-frequency virtual tunneling of Majorana zero modes

NASA Astrophysics Data System (ADS)

Gorantla, Pranay; Sensarma, Rajdeep

2018-05-01

Braiding of non-Abelian Majorana anyons is a first step towards using them in quantum computing. We propose a protocol for braiding Majorana zero modes formed at the edges of nanowires with strong spin-orbit coupling and proximity-induced superconductivity. Our protocol uses high-frequency virtual tunneling between the ends of the nanowires in a trijunction, which leads to an effective low-frequency coarse-grained dynamics for the system, to perform the braid. The braiding operation is immune to amplitude noise in the drives and depends only on relative phase between the drives, which can be controlled by the usual phase-locking techniques. We also show how a phase gate, which is necessary for universal quantum computation, can be implemented with our protocol.

Application of Strep-Tactin XT for affinity purification of Twin-Strep-tagged CB2, a G protein-coupled cannabinoid receptor

PubMed Central

Yeliseev, Alexei; Zoubak, Lioudmila; Schmidt, Thomas G.M.

2017-01-01

Human cannabinoid receptor CB2 belongs to the class A of G protein-coupled receptor (GPCR). High resolution structural studies of CB2 require milligram quantities of purified, structurally intact protein. Here we describe an efficient protocol for purification of this protein using the Twin-Strep-tag/Strep-Tactin XT system. To improve the affinity of interaction of the recombinant CB2 with the resin, the double repeat of the Strep-tag was attached either to the N- or C-terminus of CB2 via a short linker. The CB2 was isolated at high purity from dilute solutions containing high concentrations of detergents, glycerol and salts, by capturing onto the Strep-Tactin XT resin, and was eluted from the resin under mild conditions upon addition of biotin. Surface plasmon resonance studies performed demonstrate the high affinity of interaction between the Twin-Strep-tag fused to the CB2 and Strep-Tactin XT with an estimated Kd in the low nanomolar range. The affinity of binding did not vary significantly in response to the position of the tag at either N- or C-termini of the fusion. The variation in the length of the linker between the double repeats of the Strep-tag from 6 to 12 amino acid residues did not significantly affect the binding. The novel purification protocol reported here enables efficient isolation of a recombinant GPCR expressed at low titers in host cells. This procedure is suitable for preparation of milligram quantities of stable isotope-labelled receptor for high-resolution NMR studies. PMID:27867058

A synergic simulation-optimization approach for analyzing biomolecular dynamics in living organisms.

PubMed

Sadegh Zadeh, Kouroush

2011-01-01

A synergic duo simulation-optimization approach was developed and implemented to study protein-substrate dynamics and binding kinetics in living organisms. The forward problem is a system of several coupled nonlinear partial differential equations which, with a given set of kinetics and diffusion parameters, can provide not only the commonly used bleached area-averaged time series in fluorescence microscopy experiments but more informative full biomolecular/drug space-time series and can be successfully used to study dynamics of both Dirac and Gaussian fluorescence-labeled biomacromolecules in vivo. The incomplete Cholesky preconditioner was coupled with the finite difference discretization scheme and an adaptive time-stepping strategy to solve the forward problem. The proposed approach was validated with analytical as well as reference solutions and used to simulate dynamics of GFP-tagged glucocorticoid receptor (GFP-GR) in mouse cancer cell during a fluorescence recovery after photobleaching experiment. Model analysis indicates that the commonly practiced bleach spot-averaged time series is not an efficient approach to extract physiological information from the fluorescence microscopy protocols. It was recommended that experimental biophysicists should use full space-time series, resulting from experimental protocols, to study dynamics of biomacromolecules and drugs in living organisms. It was also concluded that in parameterization of biological mass transfer processes, setting the norm of the gradient of the penalty function at the solution to zero is not an efficient stopping rule to end the inverse algorithm. Theoreticians should use multi-criteria stopping rules to quantify model parameters by optimization. Copyright © 2010 Elsevier Ltd. All rights reserved.

Mental Health Trainees' Explicit and Implicit Attitudes Toward Transracial Adoptive Families Headed by Lesbian, Gay, and Heterosexual Couples.

PubMed

Tan, Tony Xing; Jordan-Arthur, Brittany; Garafano, Jeffrey S; Curran, Laura

2017-01-01

We investigated 109 (79.8% female; 76% White, and 83.5% Heterosexual) mental health trainees' explicit and implicit attitudes toward heterosexual, lesbian, and gay White couples adopting and raising Black children. To determine explicit attitudes, we used a vignette depicting a Black child ready for adoption and three types of equally qualified White families who were headed by a heterosexual couple, gay couple, or lesbian couple. The trainees were asked to indicate which type of family they preferred to adopt the child. To determine implicit attitudes, we used the computer programed latency-based multifactor implicit association test (IAT) protocol. The IAT data were collected from each participant individually. Explicit data showed that over 80% of the participants indicated no strong preference in terms of which type of family should adopted the child. However, IAT data showed that the trainees implicitly preferred lesbian couples. Overall, the degree of congruence between explicit and implicit was very low. Implications for training were discussed.

Remote entanglement stabilization for modular quantum computing

NASA Astrophysics Data System (ADS)

Didier, Nicolas; Shankar, S.; Mirrahimi, M.

Quantum information processing in a modular architecture requires to distribute and stabilize entanglement in a qubit network. We present autonomous entanglement stabilization protocols between two qubits that are coupled to distant cavities. The cavities coupling is mediated and controlled via a three-wave mixing device that generates either a delocalized mode or a two-mode squeezed state between the remote cavities depending on the pump frequency. Local drives on the qubits and the cavities steer and maintain the system to the desired qubit Bell state. We show that these reservoir-engineering based protocols stabilize entanglement in presence of qubit-cavity asymmetries and losses. Most spectacularly, even a weakly-squeezed state can stabilize a maximally entangled Bell state of two distant qubits through entanglement accumulation. This research was supported by the Agence Nationale de la Recherche under Grant ANR-14-CE26-0018, by Inria's DPEI under the TAQUILLA associated team and by ARO under Grant No. W911NF-14-1-0011.

Continuous wave protocol for simultaneous polarization and optical detection of P1-center electron spin resonance

NASA Astrophysics Data System (ADS)

Kamp, E. J.; Carvajal, B.; Samarth, N.

2018-01-01

The ready optical detection and manipulation of bright nitrogen vacancy center spins in diamond plays a key role in contemporary quantum information science and quantum metrology. Other optically dark defects such as substitutional nitrogen atoms (`P1 centers') could also become potentially useful in this context if they could be as easily optically detected and manipulated. We develop a relatively straightforward continuous wave protocol that takes advantage of the dipolar coupling between nitrogen vacancy and P1 centers in type 1b diamond to detect and polarize the dark P1 spins. By combining mutual spin flip transitions with radio frequency driving, we demonstrate the simultaneous optical polarization and detection of the electron spin resonance of the P1 center. This technique should be applicable to detecting and manipulating a broad range of dark spin populations that couple to the nitrogen vacancy center via dipolar fields, allowing for quantum metrology using these spin populations.

General hyperconcentration of photonic polarization-time-bin hyperentanglement assisted by nitrogen-vacancy centers coupled to resonators

NASA Astrophysics Data System (ADS)

Du, Fang-Fang; Deng, Fu-Guo; Long, Gui-Lu

2016-11-01

Entanglement concentration protocol (ECP) is used to extract the maximally entangled states from less entangled pure states. Here we present a general hyperconcentration protocol for two-photon systems in partially hyperentangled Bell states that decay with the interrelation between the time-bin and the polarization degrees of freedom (DOFs), resorting to an input-output process with respect to diamond nitrogen-vacancy centers coupled to resonators. We show that the resource can be utilized sufficiently and the success probability is largely improved by iteration of the hyper-ECP process. Besides, our hyper-ECP can be directly extended to concentrate nonlocal partially hyperentangled N-photon Greenberger-Horne-Zeilinger states, and the success probability remains unchanged with the growth of the number of photons. Moreover, the time-bin entanglement is a useful DOF and it only requires one path for transmission, which means it not only economizes on a large amount of quantum resources but also relaxes from the path-length dispersion in long-distance quantum communication.

Heralded quantum controlled-phase gates with dissipative dynamics in macroscopically distant resonators

NASA Astrophysics Data System (ADS)

Qin, Wei; Wang, Xin; Miranowicz, Adam; Zhong, Zhirong; Nori, Franco

2017-07-01

Heralded near-deterministic multiqubit controlled-phase gates with integrated error detection have recently been proposed by Borregaard et al. [Phys. Rev. Lett. 114, 110502 (2015), 10.1103/PhysRevLett.114.110502]. This protocol is based on a single four-level atom (a heralding quartit) and N three-level atoms (operational qutrits) coupled to a single-resonator mode acting as a cavity bus. Here we generalize this method for two distant resonators without the cavity bus between the heralding and operational atoms. Specifically, we analyze the two-qubit controlled-Z gate and its multiqubit-controlled generalization (i.e., a Toffoli-like gate) acting on the two-lowest levels of N qutrits inside one resonator, with their successful actions being heralded by an auxiliary microwave-driven quartit inside the other resonator. Moreover, we propose a circuit-quantum-electrodynamics realization of the protocol with flux and phase qudits in linearly coupled transmission-line resonators with dissipation. These methods offer a quadratic fidelity improvement compared to cavity-assisted deterministic gates.

GPCR-I-TASSER: A hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome

PubMed Central

Zhang, Jian; Yang, Jianyi; Jang, Richard; Zhang, Yang

2015-01-01

SUMMARY Experimental structure determination remains very difficult for G protein-coupled receptors (GPCRs). We propose a new hybrid protocol to construct GPCR structure models that integrates experimental mutagenesis data with ab initio transmembrane (TM) helix assembly simulations. The method was tested on 24 known GPCRs where the ab initio TM-helix assembly procedure constructed the correct fold for 20 cases. When combined with weak-homology and sparse mutagenesis restraints, the method generated correct folds for all the tested cases with an average C-alpha RMSD 2.4 Å in the TM-regions. The new hybrid protocol was applied to model all 1026 GPCRs in the human genome, where 923 have a high confidence score that are expected to have correct folds; these contain many pharmaceutically important families with no previously solved structures, including Trace amine, Prostanoids, Releasing hormones, Melanocortins, Vasopressin and Neuropeptide Y receptors. The results demonstrate new progress on genome-wide structure modeling of transmembrane proteins. PMID:26190572

gem-Difluoroolefination of Diazo Compounds with TMSCF3 or TMSCF2Br: Transition-Metal-Free Cross-Coupling of Two Carbene Precursors.

PubMed

Hu, Mingyou; Ni, Chuanfa; Li, Lingchun; Han, Yongxin; Hu, Jinbo

2015-11-18

A new olefination protocol for transition-metal-free cross-coupling of two carbene fragments arising from two different sources, namely, a nonfluorinated carbene fragment resulting from a diazo compound and a difluorocarbene fragment derived from Ruppert-Prakash reagent (TMSCF3) or TMSCF2Br, has been developed. This gem-difluoroolefination proceeds through the direct nucleophilic addition of diazo compounds to difluorocarbene followed by elimination of N2. Compared to previously reported Cu-catalyzed gem-difluoroolefination of diazo compounds with TMSCF3, which possesses a narrow substrate scope due to a demanding requirement on the reactivity of diazo compounds and in-situ-generated CuCF3, this transition-metal-free protocol affords a general and efficient approach to various disubstituted 1,1-difluoroalkenes, including difluoroacrylates, diaryldifluoroolefins, as well as arylalkyldifluoroolefins. In view of the ready availability of diazo compounds and difluorocarbene reagents and versatile transformations of 1,1-difluoroalkenes, this new gem-difluoroolefination method is expected to find wide applications in organic synthesis.

General hyperconcentration of photonic polarization-time-bin hyperentanglement assisted by nitrogen-vacancy centers coupled to resonators

PubMed Central

Du, Fang-Fang; Deng, Fu-Guo; Long, Gui-Lu

2016-01-01

Entanglement concentration protocol (ECP) is used to extract the maximally entangled states from less entangled pure states. Here we present a general hyperconcentration protocol for two-photon systems in partially hyperentangled Bell states that decay with the interrelation between the time-bin and the polarization degrees of freedom (DOFs), resorting to an input-output process with respect to diamond nitrogen-vacancy centers coupled to resonators. We show that the resource can be utilized sufficiently and the success probability is largely improved by iteration of the hyper-ECP process. Besides, our hyper-ECP can be directly extended to concentrate nonlocal partially hyperentangled N-photon Greenberger-Horne-Zeilinger states, and the success probability remains unchanged with the growth of the number of photons. Moreover, the time-bin entanglement is a useful DOF and it only requires one path for transmission, which means it not only economizes on a large amount of quantum resources but also relaxes from the path-length dispersion in long-distance quantum communication. PMID:27804973

Metal- and Reagent-Free Anodic C-C Cross-Coupling of Phenols with Benzofurans leading to a Furan Metathesis.

PubMed

Lips, Sebastian; Frontana-Uribe, Bernardo Antonio; Dörr, Maurice; Schollmeyer, Dieter; Franke, Robert; Waldvogel, Siegfried R

2018-04-20

Heterobiaryls consisting of a phenol and a benzofuran motif are of significant importance for pharmaceutical applications. An attractive sustainable, metal- and reagent-free, electrosynthetic, and highly efficient method, that allows access to (2-hydroxyphenyl)benzofurans is presented. Upon the electrochemical dehydrogenative C-C cross-coupling reaction, a metathesis of the benzo moiety at the benzofuran occurs. This gives rise to a substitution pattern at the hydroxyphenyl moiety which would not be compatible by a direct coupling process. The single-step protocol is easy to conduct in an undivided electrolysis cell, therefore scalable, and inherently safe. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

An efficient coupling of N-tosylhydrazones with 2-halopyridines: synthesis of 2-α-styrylpyridines endowed with antitumor activity.

PubMed

Lawson, Marie; Hamze, Abdallah; Peyrat, Jean-François; Bignon, Jérôme; Dubois, Joelle; Brion, Jean-Daniel; Alami, Mouad

2013-06-14

The synthesis of 2-α-styrylpyridines has been carried out by using the coupling of polyoxygenated N-tosylhydrazones with various 2-halopyridines. We demonstrated that the use of a catalytic amount of PdCl2(MeCN)2 in combination with a bidentate ferrocene DPPF or a monodentate alkyl phosphine (t)Bu2MeP-HBF4 constitutes an efficient protocol for this coupling, providing 2-α-styrylpyridines 2 in satisfactory to good yields. Among several polyoxygenated derivatives 2 evaluated, compound 2aa was found to exhibit excellent antiproliferative and antimitotic activities comparable to that of the reference compound isoCA-4.

Uthando Lwethu ('our love'): a protocol for a couples-based intervention to increase testing for HIV: a randomized controlled trial in rural KwaZulu-Natal, South Africa.

PubMed

Darbes, Lynae A; van Rooyen, Heidi; Hosegood, Victoria; Ngubane, Thulani; Johnson, Mallory O; Fritz, Katherine; McGrath, Nuala

2014-02-20

Couples-based HIV counseling and testing (CHCT) is a proven strategy to reduce the risk of HIV transmission between partners, but uptake of CHCT is low. We describe the study design of a randomized controlled trial (RCT) aimed to increase participation in CHCT and reduce sexual risk behavior for HIV among heterosexual couples in rural KwaZulu-Natal, South Africa. We hypothesize that the rate of participation in CHCT will be higher and sexual risk behavior will be lower in the intervention group as compared to the control. Heterosexual couples (N=350 couples, 700 individuals) are being recruited to participate in a randomized trial of a couples-based intervention comprising two group sessions (one mixed gender, one single gender) and four couples' counseling sessions. Couples must have been in a relationship together for at least 6 months. Quantitative assessments are conducted via mobile phones by gender-matched interviewers at baseline, 3, 6, and 9 months post-randomization. Intervention content is aimed to improve relationship dynamics, and includes communication skills and setting goals regarding CHCT. The Uthando Lwethu ('our love') intervention is the first couples-based intervention to have CHCT as its outcome. We are also targeting reductions in unprotected sex. CHCT necessitates the testing and mutual disclosure of both partners, conditions that are essential for improving subsequent outcomes such as disclosure of HIV status, sexual risk reduction, and improving treatment outcomes. Thus, improving rates of CHCT has the potential to improve health outcomes for heterosexual couples in a rural area of South Africa that is highly impacted by HIV. The results of our ongoing clinical trial will provide much needed information regarding whether a relationship-focused approach is effective in increasing rates of participation in CHCT. Our intervention represents an attempt to move away from individual-level conceptualizations, to a more integrated approach for HIV prevention. Study Name: Couples in Context: An RCT of a Couples-based HIV Prevention InterventionClinicalTrials.gov identifier: NCT01953133.South African clinical trial registration number: DOH-27-0212-3937.

Development of a head impact monitoring "Intelligent Mouthguard".

PubMed

Hedin, Daniel S; Gibson, Paul L; Bartsch, Adam J; Samorezov, Sergey

2016-08-01

The authors present the development and laboratory system-level testing of an impact monitoring "Intelligent Mouthguard" intended to help with identification of potentially concussive head impacts and cumulative head impact dosage. The goal of Intelligent Mouthguard is to provide an indicator of potential concussion risk, and help caregiver identify athletes needing sideline concussion protocol testing. Intelligent Mouthguard may also help identify individuals who are at higher risk based on historical dosage. Intelligent Mouthguard integrates inertial sensors to provide 3-degree of freedom linear and rotational kinematics. The electronics are fully integrated into a custom mouthguard that couples tightly to the upper teeth. The combination of tight coupling and highly accurate sensor data means the Intelligent Mouthguard meets the National Football League (NFL) Level I validity specification based on laboratory system-level test data presented in this study.

Catalytic alkylation of remote C-H bonds enabled by proton-coupled electron transfer

NASA Astrophysics Data System (ADS)

Choi, Gilbert J.; Zhu, Qilei; Miller, David C.; Gu, Carol J.; Knowles, Robert R.

2016-11-01

Despite advances in hydrogen atom transfer (HAT) catalysis, there are currently no molecular HAT catalysts that are capable of homolysing the strong nitrogen-hydrogen (N-H) bonds of N-alkyl amides. The motivation to develop amide homolysis protocols stems from the utility of the resultant amidyl radicals, which are involved in various synthetically useful transformations, including olefin amination and directed carbon-hydrogen (C-H) bond functionalization. In the latter process—a subset of the classical Hofmann-Löffler-Freytag reaction—amidyl radicals remove hydrogen atoms from unactivated aliphatic C-H bonds. Although powerful, these transformations typically require oxidative N-prefunctionalization of the amide starting materials to achieve efficient amidyl generation. Moreover, because these N-activating groups are often incorporated into the final products, these methods are generally not amenable to the direct construction of carbon-carbon (C-C) bonds. Here we report an approach that overcomes these limitations by homolysing the N-H bonds of N-alkyl amides via proton-coupled electron transfer. In this protocol, an excited-state iridium photocatalyst and a weak phosphate base cooperatively serve to remove both a proton and an electron from an amide substrate in a concerted elementary step. The resultant amidyl radical intermediates are shown to promote subsequent C-H abstraction and radical alkylation steps. This C-H alkylation represents a catalytic variant of the Hofmann-Löffler-Freytag reaction, using simple, unfunctionalized amides to direct the formation of new C-C bonds. Given the prevalence of amides in pharmaceuticals and natural products, we anticipate that this method will simplify the synthesis and structural elaboration of amine-containing targets. Moreover, this study demonstrates that concerted proton-coupled electron transfer can enable homolytic activation of common organic functional groups that are energetically inaccessible using traditional HAT-based approaches.

Catalytic alkylation of remote C-H bonds enabled by proton-coupled electron transfer.

PubMed

Choi, Gilbert J; Zhu, Qilei; Miller, David C; Gu, Carol J; Knowles, Robert R

2016-11-10

Despite advances in hydrogen atom transfer (HAT) catalysis, there are currently no molecular HAT catalysts that are capable of homolysing the strong nitrogen-hydrogen (N-H) bonds of N-alkyl amides. The motivation to develop amide homolysis protocols stems from the utility of the resultant amidyl radicals, which are involved in various synthetically useful transformations, including olefin amination and directed carbon-hydrogen (C-H) bond functionalization. In the latter process-a subset of the classical Hofmann-Löffler-Freytag reaction-amidyl radicals remove hydrogen atoms from unactivated aliphatic C-H bonds. Although powerful, these transformations typically require oxidative N-prefunctionalization of the amide starting materials to achieve efficient amidyl generation. Moreover, because these N-activating groups are often incorporated into the final products, these methods are generally not amenable to the direct construction of carbon-carbon (C-C) bonds. Here we report an approach that overcomes these limitations by homolysing the N-H bonds of N-alkyl amides via proton-coupled electron transfer. In this protocol, an excited-state iridium photocatalyst and a weak phosphate base cooperatively serve to remove both a proton and an electron from an amide substrate in a concerted elementary step. The resultant amidyl radical intermediates are shown to promote subsequent C-H abstraction and radical alkylation steps. This C-H alkylation represents a catalytic variant of the Hofmann-Löffler-Freytag reaction, using simple, unfunctionalized amides to direct the formation of new C-C bonds. Given the prevalence of amides in pharmaceuticals and natural products, we anticipate that this method will simplify the synthesis and structural elaboration of amine-containing targets. Moreover, this study demonstrates that concerted proton-coupled electron transfer can enable homolytic activation of common organic functional groups that are energetically inaccessible using traditional HAT-based approaches.

Cancer prevention trial of a synergistic mixture of green tea concentrate plus Capsicum (CAPSOL-T) in a random population of subjects ages 40-84

PubMed Central

2014-01-01

Background Experts agree that one of the more promising strategies in cancer management is early detection coupled with early intervention. In this study, we evaluated an early cancer detection strategy of cancer presence based on serum levels of the cancer-specific transcript variants of ENOX2 in serum coupled with an ENOX2-targeted nutraceutical preparation of green tea concentrate plus Capsicum (Capsol-T®) as a strategy of Curative Prevention® involving early detection coupled with early intervention in early stage cancer when in its most susceptible and manageable stages. Experimental design One hundred ten (110) subjects were tested for cancer presence using the ONCOblot® Tissue of Origin 2-D gel/western blot protocol for detection of serum presence of transcript variants of the ENOX2 protein. Subjects testing positive for ENOX2 received 350 mg of Capsol-T® in capsule form every 4 h including during the night for periods of at least 3 to 6 months or longer after which they were again tested for ENOX2 presence using the ONCOblot® Tissue of Origin Cancer Test protocol. Results Of the 110 subjects, both male and female, ages 40 to 84, with no evidence of clinical symptoms of cancer, 40% were positive for ENOX2 presence in the ONCOblot® Tissue of Origin Cancer Test. After completion of 3 to 17 months of Capsol-T® use, 94% of subjects subsequently tested negative for ENOX2 presence. Conclusions Oral Capsol-T® is well tolerated and, for ENOX2 presence in serum in the absence of clinical cancer symptoms, is consistently effective in reducing the serum ENOX2 levels to below detectable limits. PMID:24393573

Biogeochemical Protocols and Diagnostics for the CMIP6 Ocean Model Intercomparison Project (OMIP)

NASA Technical Reports Server (NTRS)

Orr, James C.; Najjar, Raymond G.; Aumont, Olivier; Bopp, Laurent; Bullister, John L.; Danabasoglu, Gokhan; Doney, Scott C.; Dunne, John P.; Dutay, Jean-Claude; Graven, Heather;

Biogeochemical protocols and diagnostics for the CMIP6 Ocean Model Intercomparison Project (OMIP)

NASA Astrophysics Data System (ADS)

Orr, James C.; Najjar, Raymond G.; Aumont, Olivier; Bopp, Laurent; Bullister, John L.; Danabasoglu, Gokhan; Doney, Scott C.; Dunne, John P.; Dutay, Jean-Claude; Graven, Heather; Griffies, Stephen M.; John, Jasmin G.; Joos, Fortunat; Levin, Ingeborg; Lindsay, Keith; Matear, Richard J.; McKinley, Galen A.; Mouchet, Anne; Oschlies, Andreas; Romanou, Anastasia; Schlitzer, Reiner; Tagliabue, Alessandro; Tanhua, Toste; Yool, Andrew

2017-06-01

The Ocean Model Intercomparison Project (OMIP) focuses on the physics and biogeochemistry of the ocean component of Earth system models participating in the sixth phase of the Coupled Model Intercomparison Project (CMIP6). OMIP aims to provide standard protocols and diagnostics for ocean models, while offering a forum to promote their common assessment and improvement. It also offers to compare solutions of the same ocean models when forced with reanalysis data (OMIP simulations) vs. when integrated within fully coupled Earth system models (CMIP6). Here we detail simulation protocols and diagnostics for OMIP's biogeochemical and inert chemical tracers. These passive-tracer simulations will be coupled to ocean circulation models, initialized with observational data or output from a model spin-up, and forced by repeating the 1948-2009 surface fluxes of heat, fresh water, and momentum. These so-called OMIP-BGC simulations include three inert chemical tracers (CFC-11, CFC-12, SF6) and biogeochemical tracers (e.g., dissolved inorganic carbon, carbon isotopes, alkalinity, nutrients, and oxygen). Modelers will use their preferred prognostic BGC model but should follow common guidelines for gas exchange and carbonate chemistry. Simulations include both natural and total carbon tracers. The required forced simulation (omip1) will be initialized with gridded observational climatologies. An optional forced simulation (omip1-spunup) will be initialized instead with BGC fields from a long model spin-up, preferably for 2000 years or more, and forced by repeating the same 62-year meteorological forcing. That optional run will also include abiotic tracers of total dissolved inorganic carbon and radiocarbon, CTabio and 14CTabio, to assess deep-ocean ventilation and distinguish the role of physics vs. biology. These simulations will be forced by observed atmospheric histories of the three inert gases and CO2 as well as carbon isotope ratios of CO2. OMIP-BGC simulation protocols are founded on those from previous phases of the Ocean Carbon-Cycle Model Intercomparison Project. They have been merged and updated to reflect improvements concerning gas exchange, carbonate chemistry, and new data for initial conditions and atmospheric gas histories. Code is provided to facilitate their implementation.

Enantioselective synthesis of chiral isotopomers of 1-alkanols by a ZACA-Cu-catalyzed cross-coupling protocol.

PubMed

Xu, Shiqing; Oda, Akimichi; Negishi, Ei-ichi

2014-12-01

Chiral compounds arising from the replacement of hydrogen atoms by deuterium are very important in organic chemistry and biochemistry. Some of these chiral compounds have a non-measurable specific rotation, owing to very small differences between the isotopomeric groups, and exhibit cryptochirality. This particular class of compounds is difficult to synthesize and characterize. Herein, we present a catalytic and highly enantioselective conversion of terminal alkenes to various β and more remote chiral isotopomers of 1-alkanols, with ≥99 % enantiomeric excess (ee), by the Zr-catalyzed asymmetric carboalumination of alkenes (ZACA) and Cu-catalyzed cross-coupling reactions. ZACA-in situ iodinolysis of allyl alcohol and ZACA-in situ oxidation of TBS-protected ω-alkene-1-ols protocols were applied to the synthesis of both (R)- and (S)-difunctional intermediates with 80-90 % ee. These intermediates were readily purified to provide enantiomerically pure (≥99 % ee) compounds by lipase-catalyzed acetylation. These functionally rich intermediates serve as very useful synthons for the construction of various chiral isotopomers of 1-alkanols in excellent enantiomeric purity (≥99 % ee) by introducing deuterium-labeled groups by Cu-catalyzed cross-coupling reactions without epimerization. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Monitoring dediazoniation product formation by high-performance liquid chromatography after derivatization.

PubMed

Bravo-Díaz, Carlos; González-Romero, Elisa

2003-03-14

A derivatization protocol that exploits the rapid reaction between arenediazonium ions and a suitable coupling agent followed by high-performance liquid chromatography analyses of the reaction mixture was employed to determine the product distribution, the rate constants for product formation and the association constant of 4-nitrobenzenediazonium, PNBD, ion with beta-cyclodextrin, beta-CD. The derivatization of PNBD with the coupling agent leads to the formation of a stable azo dye that prevents by-side reactions of PNBD with the solvents of the mobile phase, including water, or the metallic parts of the chromatographic system that would eventually lead to erroneous identification and quantification of dediazoniation products. The results show that in the presence of beta-CD, nitrobenzene is formed at the expense of 4-nitrophenol, which is the major product in its absence. The observed rate constants for the interaction between PNBD and beta-CD increase upon increasing [beta-CD] showing a saturation profile indicative of the formation of an inclusion complex between PNBD and beta-CD. By fitting the experimental data to a simplified Lineaweaver-Burk equation, the corresponding association constant and the maximum acceleration rate of beta-CD towards PNBD were estimated. The protocol is applicable under a variety of experimental conditions provided that the rate of the coupling reaction is much faster than that of dediazoniation.

The management of Convulsive Refractory Status Epilepticus in adults in the UK: No consistency in practice and little access to continuous EEG monitoring.

PubMed

Patel, Mitesh; Bagary, Manny; McCorry, Dougall

2015-01-01

Convulsive Status Epilepticus (CSE) is a common neurological emergency with patients presenting with prolonged epileptic activity. Sub-optimal management is coupled with high morbidity and mortality. Continuous electroencephalogram (EEG) monitoring is considered essential by the National Institute for Health and Care Excellence (NICE) in the management of Convulsive Refractory Status Epilepticus (CRSE). The aim of this research was to determine current clinical practice in the management of CRSE amongst adults in intensive care units (ICU) in the UK and establish if the use of a standardised protocol requires re-enforcement within trusts. 75 randomly selected UK NHS Trusts were contacted and asked to complete a questionnaire in addition to providing their protocol for CRSE management in ICU. 55 (73%) trusts responded. While 31 (56% of responders) had a protocol available in ICU for early stages of CSE, just 21 (38%) trusts had specific guidelines if CRSE occurred. Only 23 (42%) trusts involved neurologists at any stage of management and just 18 (33%) have access to continuous EEG monitoring. This study identifies significant inconsistency in the management of CSE in ICU's across the UK. A minority of ICU units have a protocol for CRSE or access to continuous EEG monitoring despite it being considered fundamental for management and supported by NICE guidance. Copyright © 2014 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

Long-term seafloor monitoring at an open ocean aquaculture site in the western Gulf of Maine, USA: development of an adaptive protocol.

PubMed

Grizzle, R E; Ward, L G; Fredriksson, D W; Irish, J D; Langan, R; Heinig, C S; Greene, J K; Abeels, H A; Peter, C R; Eberhardt, A L

2014-11-15

The seafloor at an open ocean finfish aquaculture facility in the western Gulf of Maine, USA was monitored from 1999 to 2008 by sampling sites inside a predicted impact area modeled by oceanographic conditions and fecal and food settling characteristics, and nearby reference sites. Univariate and multivariate analyses of benthic community measures from box core samples indicated minimal or no significant differences between impact and reference areas. These findings resulted in development of an adaptive monitoring protocol involving initial low-cost methods that required more intensive and costly efforts only when negative impacts were initially indicated. The continued growth of marine aquaculture is dependent on further development of farming methods that minimize negative environmental impacts, as well as effective monitoring protocols. Adaptive monitoring protocols, such as the one described herein, coupled with mathematical modeling approaches, have the potential to provide effective protection of the environment while minimize monitoring effort and costs. Copyright © 2014 Elsevier Ltd. All rights reserved.

Strep-Tagged Protein Purification.

PubMed

Maertens, Barbara; Spriestersbach, Anne; Kubicek, Jan; Schäfer, Frank

2015-01-01

The Strep-tag system can be used to purify recombinant proteins from any expression system. Here, protocols for lysis and affinity purification of Strep-tagged proteins from E. coli, baculovirus-infected insect cells, and transfected mammalian cells are given. Depending on the amount of Strep-tagged protein in the lysate, a protocol for batch binding and subsequent washing and eluting by gravity flow can be used. Agarose-based matrices with the coupled Strep-Tactin ligand are the resins of choice, with a binding capacity of up to 9 mg ml(-1). For purification of lower amounts of Strep-tagged proteins, the use of Strep-Tactin magnetic beads is suitable. In addition, Strep-tagged protein purification can also be automated using prepacked columns for FPLC or other liquid-handling chromatography instrumentation, but automated purification is not discussed in this protocol. The protocols described here can be regarded as an update of the Strep-Tag Protein Handbook (Qiagen, 2009). © 2015 Elsevier Inc. All rights reserved.

Catalytic Carbonyl Allylation, Propargylation and Vinylation from the Alcohol or Aldehyde Oxidation Level via C-C Bond Forming Hydrogenation and Transfer Hydrogenation: A Departure from Preformed Organometallic Reagents**

PubMed Central

Bower, John F.; Kim, In Su; Patman, Ryan L.; Krische, Michael J.

2009-01-01

Classical protocols for carbonyl allylation, propargylation and vinylation typically rely upon the use of preformed allyl metal, allenyl metal and vinyl metal reagents, respectively, mandating stoichiometric generation of metallic byproducts. Through transfer hydrogenative C-C coupling, carbonyl addition may be achieved from the aldehyde or alcohol oxidation level in the absence of stoichiometric organometallic reagents or metallic reductants. Here, we review transfer hydrogenative methods for carbonyl addition, which encompass the first cataltyic protocols enabling direct C–H functionalization of alcohols. PMID:19040235

Influence of different luting protocols on shear bond strength of computer aided design/computer aided manufacturing resin nanoceramic material to dentin

PubMed Central

Poggio, Claudio; Pigozzo, Marco; Ceci, Matteo; Scribante, Andrea; Beltrami, Riccardo; Chiesa, Marco

2016-01-01

Background: The purpose of this study was to evaluate the influence of three different luting protocols on shear bond strength of computer aided design/computer aided manufacturing (CAD/CAM) resin nanoceramic (RNC) material to dentin. Materials and Methods: In this in vitro study, 30 disks were milled from RNC blocks (Lava Ultimate/3M ESPE) with CAD/CAM technology. The disks were subsequently cemented to the exposed dentin of 30 recently extracted bovine permanent mandibular incisors. The specimens were randomly assigned into 3 groups of 10 teeth each. In Group 1, disks were cemented using a total-etch protocol (Scotchbond™ Universal Etchant phosphoric acid + Scotchbond Universal Adhesive + RelyX™ Ultimate conventional resin cement); in Group 2, disks were cemented using a self-etch protocol (Scotchbond Universal Adhesive + RelyX™ Ultimate conventional resin cement); in Group 3, disks were cemented using a self-adhesive protocol (RelyX™ Unicem 2 Automix self-adhesive resin cement). All cemented specimens were placed in a universal testing machine (Instron Universal Testing Machine 3343) and submitted to a shear bond strength test to check the strength of adhesion between the two substrates, dentin, and RNC disks. Specimens were stressed at a crosshead speed of 1 mm/min. Data were analyzed with analysis of variance and post-hoc Tukey's test at a level of significance of 0.05. Results: Post-hoc Tukey testing showed that the highest shear strength values (P < 0.001) were reported in Group 2. The lowest data (P < 0.001) were recorded in Group 3. Conclusion: Within the limitations of this in vitro study, conventional resin cements (coupled with etch and rinse or self-etch adhesives) showed better shear strength values compared to self-adhesive resin cements. Furthermore, conventional resin cements used together with a self-etch adhesive reported the highest values of adhesion. PMID:27076822

Influence of different luting protocols on shear bond strength of computer aided design/computer aided manufacturing resin nanoceramic material to dentin.

PubMed

Poggio, Claudio; Pigozzo, Marco; Ceci, Matteo; Scribante, Andrea; Beltrami, Riccardo; Chiesa, Marco

2016-01-01

The purpose of this study was to evaluate the influence of three different luting protocols on shear bond strength of computer aided design/computer aided manufacturing (CAD/CAM) resin nanoceramic (RNC) material to dentin. In this in vitro study, 30 disks were milled from RNC blocks (Lava Ultimate/3M ESPE) with CAD/CAM technology. The disks were subsequently cemented to the exposed dentin of 30 recently extracted bovine permanent mandibular incisors. The specimens were randomly assigned into 3 groups of 10 teeth each. In Group 1, disks were cemented using a total-etch protocol (Scotchbond™ Universal Etchant phosphoric acid + Scotchbond Universal Adhesive + RelyX™ Ultimate conventional resin cement); in Group 2, disks were cemented using a self-etch protocol (Scotchbond Universal Adhesive + RelyX™ Ultimate conventional resin cement); in Group 3, disks were cemented using a self-adhesive protocol (RelyX™ Unicem 2 Automix self-adhesive resin cement). All cemented specimens were placed in a universal testing machine (Instron Universal Testing Machine 3343) and submitted to a shear bond strength test to check the strength of adhesion between the two substrates, dentin, and RNC disks. Specimens were stressed at a crosshead speed of 1 mm/min. Data were analyzed with analysis of variance and post-hoc Tukey's test at a level of significance of 0.05. Post-hoc Tukey testing showed that the highest shear strength values (P < 0.001) were reported in Group 2. The lowest data (P < 0.001) were recorded in Group 3. Within the limitations of this in vitro study, conventional resin cements (coupled with etch and rinse or self-etch adhesives) showed better shear strength values compared to self-adhesive resin cements. Furthermore, conventional resin cements used together with a self-etch adhesive reported the highest values of adhesion.

Ultrasensitive Electrochemical Detection of mRNA Using Branched DNA Amplifiers

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

Mao, Xun; Liu, Guodong; Wang, Shengfu

2008-11-01

We describe here an ultrasensitive electrochemical detection of m RNA protocol without RNA purification and PCR amplification. The new m RNA electrical detection capability is coupled to the amplification feature of branched DNA (bDNA) technology and with the nagnetic beads based electrochemical bioassay.

Fluorescent nanoaggregates of pentacenequinone derivative for selective sensing of picric acid in aqueous media.

PubMed

Bhalla, Vandana; Gupta, Ankush; Kumar, Manoj

2012-06-15

Novel pentacenequinone derivative 3 has been synthesized using the Suzuki-Miyaura coupling protocol which forms fluorescent nanoaggregates in aqueous media due to its aggregation-induced emission enhancement attributes and selectively senses picric acid with a detection limit of 500 ppb.

Allene formation by gold catalyzed cross-coupling of masked carbenes and vinylidenes

PubMed Central

Lavallo, Vincent; Frey, Guido D.; Kousar, Shazia; Donnadieu, Bruno; Bertrand, Guy

2007-01-01

Addition of a sterically demanding cyclic (alkyl)(amino)carbene (CAAC) to AuCl(SMe2) followed by treatment with [Et3Si(Tol)]+[B(C6F5)4]− in toluene affords the isolable [(CAAC)Au(η2-toluene)]+[B(C6F5)4]− complex. This cationic Au(I) complex efficiently mediates the catalytic coupling of enamines and terminal alkynes to yield allenes and not propargyl amines as observed with other catalysts. Mono-, di-, and tri-substituted enamines can be used, as well as aryl-, alkyl-, and trimethylsilyl-substituted terminal alkynes. The reaction tolerates sterically hindered substrates and is diastereoselective. This general catalytic protocol directly couples two unsaturated carbon centers to form the three-carbon allenic core. The reaction most probably proceeds through an unprecedented “carbene/vinylidene cross-coupling.” PMID:17698808

Continuous flow room temperature reductive aqueous homo-coupling of aryl halides using supported Pd catalysts

PubMed Central

Feiz, Afsaneh; Bazgir, Ayoob; Balu, Alina M.; Luque, Rafael

2016-01-01

A convenient and environmentally friendly protocol for the preparation of biaryls at room temperature under continuous flow conditions is reported. A simple reductive homo-coupling Ullmann-type reaction was performed in an H-Cube mini using commercially available supported Pd catalysts under mild reaction conditions, with quantitative conversion to target products. Commercial Pd catalysts were found to be highly stable under the investigated reaction conditions, with a minimum Pd leaching into solution after several reaction runs (ca. 20 h on stream). PMID:27600989

Silver-catalyzed double-decarboxylative cross-coupling of α-keto acids with cinnamic acids in water: a strategy for the preparation of chalcones.

PubMed

Zhang, Ning; Yang, Daoshan; Wei, Wei; Yuan, Li; Nie, Fafa; Tian, Laijin; Wang, Hua

2015-03-20

A silver-catalyzed double-decarboxylative protocol has been proposed for the construction of chalcone derivatives via cascade coupling of substituted α-keto acids with cinnamic acids under the mild aqueous conditions. The developed method for constructing C-C bonds via double-decarboxylative reactions is efficient, practical, and environmentally benign by using the readily available starting materials. It should provide a promising synthesis candidate for the formation of diverse and useful chalcone derivatives in the fields of synthetic and pharmaceutical chemistry.

2,2'-Biphenols via protecting group-free thermal or microwave-accelerated Suzuki-Miyaura coupling in water.

PubMed

Schmidt, Bernd; Riemer, Martin; Karras, Manfred

2013-09-06

User-friendly protocols for the protecting group-free synthesis of 2,2'-biphenols via Suzuki-Miyaura coupling of o-halophenols and o-boronophenol are presented. The reactions proceed in water in the presence of simple additives such as K2CO3, KOH, KF, or TBAF and with commercially available Pd/C as precatalyst. Expensive or laboriously synthesized ligands or other additives are not required. In the case of bromophenols, efficient rate acceleration and short reaction times were accomplished by microwave irradiation.

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

NASA Astrophysics Data System (ADS)

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

2014-02-01

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

Natural Language Processing–Enabled and Conventional Data Capture Methods for Input to Electronic Health Records: A Comparative Usability Study

PubMed Central

Sheehan, Barbara; Stetson, Peter; Bhatt, Ashish R; Field, Adele I; Patel, Chirag; Maisel, James Mark

2016-01-01

Background The process of documentation in electronic health records (EHRs) is known to be time consuming, inefficient, and cumbersome. The use of dictation coupled with manual transcription has become an increasingly common practice. In recent years, natural language processing (NLP)–enabled data capture has become a viable alternative for data entry. It enables the clinician to maintain control of the process and potentially reduce the documentation burden. The question remains how this NLP-enabled workflow will impact EHR usability and whether it can meet the structured data and other EHR requirements while enhancing the user’s experience. Objective The objective of this study is evaluate the comparative effectiveness of an NLP-enabled data capture method using dictation and data extraction from transcribed documents (NLP Entry) in terms of documentation time, documentation quality, and usability versus standard EHR keyboard-and-mouse data entry. Methods This formative study investigated the results of using 4 combinations of NLP Entry and Standard Entry methods (“protocols”) of EHR data capture. We compared a novel dictation-based protocol using MediSapien NLP (NLP-NLP) for structured data capture against a standard structured data capture protocol (Standard-Standard) as well as 2 novel hybrid protocols (NLP-Standard and Standard-NLP). The 31 participants included neurologists, cardiologists, and nephrologists. Participants generated 4 consultation or admission notes using 4 documentation protocols. We recorded the time on task, documentation quality (using the Physician Documentation Quality Instrument, PDQI-9), and usability of the documentation processes. Results A total of 118 notes were documented across the 3 subject areas. The NLP-NLP protocol required a median of 5.2 minutes per cardiology note, 7.3 minutes per nephrology note, and 8.5 minutes per neurology note compared with 16.9, 20.7, and 21.2 minutes, respectively, using the Standard-Standard protocol and 13.8, 21.3, and 18.7 minutes using the Standard-NLP protocol (1 of 2 hybrid methods). Using 8 out of 9 characteristics measured by the PDQI-9 instrument, the NLP-NLP protocol received a median quality score sum of 24.5; the Standard-Standard protocol received a median sum of 29; and the Standard-NLP protocol received a median sum of 29.5. The mean total score of the usability measure was 36.7 when the participants used the NLP-NLP protocol compared with 30.3 when they used the Standard-Standard protocol. Conclusions In this study, the feasibility of an approach to EHR data capture involving the application of NLP to transcribed dictation was demonstrated. This novel dictation-based approach has the potential to reduce the time required for documentation and improve usability while maintaining documentation quality. Future research will evaluate the NLP-based EHR data capture approach in a clinical setting. It is reasonable to assert that EHRs will increasingly use NLP-enabled data entry tools such as MediSapien NLP because they hold promise for enhancing the documentation process and end-user experience. PMID:27793791

A combined experimental and theoretical spectroscopic protocol for determination of the structure of heterogeneous catalysts: developing the information content of the resonance Raman spectra of M1 MoVOx † †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc01771e Click here for additional data file.

PubMed Central

Kubas, Adam; Noak, Johannes

2017-01-01

Absorption and multiwavelength resonance Raman spectroscopy are widely used to investigate the electronic structure of transition metal centers in coordination compounds and extended solid systems. In combination with computational methodologies that have predictive accuracy, they define powerful protocols to study the spectroscopic response of catalytic materials. In this work, we study the absorption and resonance Raman spectra of the M1 MoVOx catalyst. The spectra were calculated by time-dependent density functional theory (TD-DFT) in conjunction with the independent mode displaced harmonic oscillator model (IMDHO), which allows for detailed bandshape predictions. For this purpose cluster models with up to 9 Mo and V metallic centers are considered to represent the bulk structure of MoVOx. Capping hydrogens were used to achieve valence saturation at the edges of the cluster models. The construction of model structures was based on a thorough bonding analysis which involved conventional DFT and local coupled cluster (DLPNO-CCSD(T)) methods. Furthermore the relationship of cluster topology to the computed spectral features is discussed in detail. It is shown that due to the local nature of the involved electronic transitions, band assignment protocols developed for molecular systems can be applied to describe the calculated spectral features of the cluster models as well. The present study serves as a reference for future applications of combined experimental and computational protocols in the field of solid-state heterogeneous catalysis. PMID:28989667

Protocol for Uniformly Measuring and Expressing the Performance of Energy Storage Systems

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

Conover, David R.; Crawford, Alasdair J.; Fuller, Jason

This Protocol provides a set of “best practices” for characterizing energy storage systems (ESSs) and measuring and reporting their performance. It serves as a basis for assessing how an ESS will perform with respect to key performance attributes relevant to different applications. It is intended to provide a valid and accurate basis for the comparison of different ESSs. By achieving the stated purpose, the Protocol will enable more informed decision-making in the selection of ESSs for various stationary applications. The Protocol identifies general information and technical specifications relevant in describing an ESS and also defines a set of test, measurement,more » and evaluation criteria with which to express the performance of ESSs that are intended for energy-intensive and/or power-intensive stationary applications. An ESS includes a storage device, battery management system, and any power conversion systems installed with the storage device. The Protocol is agnostic with respect to the storage technology and the size and rating of the ESS. The Protocol does not apply to single-use storage devices and storage devices that are not coupled with power conversion systems, nor does it address safety, security, or operations and maintenance of ESSs, or provide any pass/fail criteria.« less

Methodology for the specification of communication activities within the framework of a multi-layered architecture: Toward the definition of a knowledge base

NASA Astrophysics Data System (ADS)

Amyay, Omar

A method defined in terms of synthesis and verification steps is presented. The specification of the services and protocols of communication within a multilayered architecture of the Open Systems Interconnection (OSI) type is an essential issue for the design of computer networks. The aim is to obtain an operational specification of the protocol service couple of a given layer. Planning synthesis and verification steps constitute a specification trajectory. The latter is based on the progressive integration of the 'initial data' constraints and verification of the specification originating from each synthesis step, through validity constraints that characterize an admissible solution. Two types of trajectories are proposed according to the style of the initial specification of the service protocol couple: operational type and service supplier viewpoint; knowledge property oriented type and service viewpoint. Synthesis and verification activities were developed and formalized in terms of labeled transition systems, temporal logic and epistemic logic. The originality of the second specification trajectory and the use of the epistemic logic are shown. An 'artificial intelligence' approach enables a conceptual model to be defined for a knowledge base system for implementing the method proposed. It is structured in three levels of representation of the knowledge relating to the domain, the reasoning characterizing synthesis and verification activities and the planning of the steps of a specification trajectory.

Performance Analysis of Modified Accelerative Preallocation MAC Protocol for Passive Star-Coupled WDMA Networks

NASA Astrophysics Data System (ADS)

Yun, Changho; Kim, Kiseon

2006-04-01

For the passive star-coupled wavelength-division multiple-access (WDMA) network, a modified accelerative preallocation WDMA (MAP-WDMA) media access control (MAC) protocol is proposed, which is based on AP-WDMA. To show the advantages of MAP-WDMA as an adequate MAC protocol for the network over AP-WDMA, the channel utilization, the channel-access delay, and the latency of MAP-WDMA are investigated and compared with those of AP-WDMA under various data traffic patterns, including uniform, quasi-uniform type, disconnected type, mesh type, and ring type data traffics, as well as the assumption that a given number of network stations is equal to that of channels, in other words, without channel sharing. As a result, the channel utilization of MAP-WDMA can be competitive with respect to that of AP-WDMA at the expense of insignificantly higher latency. Namely, if the number of network stations is small, MAP-WDMA provides better channel utilization for uniform, quasi-uniform-type, and disconnected-type data traffics at all data traffic loads, as well as for mesh and ring-type data traffics at low data traffic loads. Otherwise, MAP-WDMA only outperforms AP-WDMA for the first three data traffics at higher data traffic loads. In the aspect of channel-access delay, MAP-WDMA gives better performance than AP-WDMA, regardless of data traffic patterns and the number of network stations.

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

PubMed

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

2017-01-01

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

Thermodynamic geometry of minimum-dissipation driven barrier crossing

NASA Astrophysics Data System (ADS)

Sivak, David A.; Crooks, Gavin E.

2016-11-01

We explore the thermodynamic geometry of a simple system that models the bistable dynamics of nucleic acid hairpins in single molecule force-extension experiments. Near equilibrium, optimal (minimum-dissipation) driving protocols are governed by a generalized linear response friction coefficient. Our analysis demonstrates that the friction coefficient of the driving protocols is sharply peaked at the interface between metastable regions, which leads to minimum-dissipation protocols that drive rapidly within a metastable basin, but then linger longest at the interface, giving thermal fluctuations maximal time to kick the system over the barrier. Intuitively, the same principle applies generically in free energy estimation (both in steered molecular dynamics simulations and in single-molecule experiments), provides a design principle for the construction of thermodynamically efficient coupling between stochastic objects, and makes a prediction regarding the construction of evolved biomolecular motors.

Thermodynamic geometry of minimum-dissipation driven barrier crossing

NASA Astrophysics Data System (ADS)

Sivak, David; Crooks, Gavin

We explore the thermodynamic geometry of a simple system that models the bistable dynamics of nucleic acid hairpins in single molecule force-extension experiments. Near equilibrium, optimal (minimum-dissipation) driving protocols are governed by a generalized linear response friction coefficient. Our analysis demonstrates that the friction coefficient of the driving protocols is sharply peaked at the interface between metastable regions, which leads to minimum-dissipation protocols that drive rapidly within a metastable basin, but then linger longest at the interface, giving thermal fluctuations maximal time to kick the system over the barrier. Intuitively, the same principle applies generically in free energy estimation (both in steered molecular dynamics simulations and in single-molecule experiments), provides a design principle for the construction of thermodynamically efficient coupling between stochastic objects, and makes a prediction regarding the construction of evolved biomolecular motors.

Progress towards a microwave-based high-fidelity Toffoli gate with superconducting qubits

NASA Astrophysics Data System (ADS)

Rigetti, Chad; Chow, Jerry; Corcoles, Antonio; Rozen, Jim; Keefe, George; Rothwell, Mary Beth; Rohrs, Jack; Borstelmann, Mark; Divincenzo, David; Ketchen, Mark; Steffen, Matthias

2011-03-01

We describe recent progress at IBM towards a microwave-based implementation of the Toffoli gate using three capacitively shunted flux qubits dispersively coupled to a resonator. We discuss the device architecture and the microwave protocol, along with expected limits to gate fidelity and scaling.

Decarbonylative Phosphorylation of Amides by Palladium and Nickel Catalysis: The Hirao Cross-Coupling of Amide Derivatives.

PubMed

Liu, Chengwei; Szostak, Michal

2017-10-02

Considering the ubiquity of organophosphorus compounds in organic synthesis, pharmaceutical discovery agrochemical crop protection and materials chemistry, new methods for their construction hold particular significance. A conventional method for the synthesis of C-P bonds involves cross-coupling of aryl halides and dialkyl phosphites (the Hirao reaction). We report a catalytic deamidative phosphorylation of a wide range of amides using a palladium or nickel catalyst giving aryl phosphonates in good to excellent yields. The present method tolerates a wide range of functional groups. The reaction constitutes the first example of a transition-metal-catalyzed generation of C-P bonds from amides. This redox-neutral protocol can be combined with site-selective conventional cross-coupling for the regioselective synthesis of potential pharmacophores. Mechanistic studies suggest an oxidative addition/transmetallation pathway. In light of the importance of amides and phosphonates as synthetic intermediates, we envision that this Pd and Ni-catalyzed C-P bond forming method will find broad application. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Breast dosimetry in clinical mammography

NASA Astrophysics Data System (ADS)

Benevides, Luis Alberto Do Rego

The objective of this study was show that a clinical dosimetry protocol that utilizes a dosimetric breast phantom series based on population anthropometric measurements can reliably predict the average glandular dose (AGD) imparted to the patient during a routine screening mammogram. In the study, AGD was calculated using entrance skin exposure and dose conversion factors based on fibroglandular content, compressed breast thickness, mammography unit parameters and modifying parameters for homogeneous phantom (phantom factor), compressed breast lateral dimensions (volume factor) and anatomical features (anatomical factor). The protocol proposes the use of a fiber-optic coupled (FOCD) or Metal Oxide Semiconductor Field Effect Transistor (MOSFET) dosimeter to measure the entrance skin exposure at the time of the mammogram without interfering with diagnostic information of the mammogram. The study showed that FOCD had sensitivity with less than 7% energy dependence, linear in all tube current-time product stations, and was reproducible within 2%. FOCD was superior to MOSFET dosimeter in sensitivity, reusability, and reproducibility. The patient fibroglandular content was evaluated using a calibrated modified breast tissue equivalent homogeneous phantom series (BRTES-MOD) designed from anthropomorphic measurements of a screening mammography population and whose elemental composition was referenced to International Commission on Radiation Units and Measurements Report 44 tissues. The patient fibroglandular content, compressed breast thickness along with unit parameters and spectrum half-value layer were used to derive the currently used dose conversion factor (DgN). The study showed that the use of a homogeneous phantom, patient compressed breast lateral dimensions and patient anatomical features can affect AGD by as much as 12%, 3% and 1%, respectively. The protocol was found to be superior to existing methodologies. In addition, the study population anthropometric measurements enabled the development of analytical equations to calculate the whole breast area, estimate for the skin layer thickness and optimal location for automatic exposure control ionization chamber. The clinical dosimetry protocol developed in this study can reliably predict the AGD imparted to an individual patient during a routine screening mammogram.

Coupling a single nitrogen-vacancy center with a superconducting qubit via the electro-optic effect

NASA Astrophysics Data System (ADS)

Li, Chang-Hao; Li, Peng-Bo

2018-05-01

We propose an efficient scheme for transferring quantum states and generating entangled states between two qubits of different nature. The hybrid system consists of a single nitrogen-vacancy (NV) center and a superconducting (SC) qubit, which couple to an optical cavity and a microwave resonator, respectively. Meanwhile, the optical cavity and the microwave resonator are coupled via the electro-optic effect. By adjusting the relative parameters, we can achieve high-fidelity quantum state transfer as well as highly entangled states between the NV center and the SC qubit. This protocol is within the reach of currently available techniques, and may provide interesting applications in quantum communication and computation with single NV centers and SC qubits.

Prior to Conception: The Role of an Acupuncture Protocol in Improving Women's Reproductive Functioning Assessed by a Pilot Pragmatic Randomised Controlled Trial

PubMed Central

Cochrane, Suzanne; Smith, Caroline A.; Possamai-Inesedy, Alphia; Bensoussan, Alan

2016-01-01

The global average of couples with fertility problems is 9%. Assisted reproductive technologies are often inaccessible. Evidence points to acupuncture offering an opportunity to promote natural fertility. This study asked whether providing a multiphasic fertility acupuncture protocol to women with sub/infertility would increase their awareness of fertility and achieve normalisation of their menstrual cycle compared with a lifestyle control. In a pragmatic randomised controlled trial sub/infertile women were offered an intervention of acupuncture and lifestyle modification or lifestyle modification only. There was a statistically significant increase in fertility awareness in the acupuncture group (86.4%, 19) compared to 40% (n = 8) of the lifestyle only participants (Relative Risk (RR) 2.38, 95% confidence interval (CI) of 1.25, 4.50), with an adjusted p value of 0.011. Changes in menstrual regularity were not statistically significant. There was no statistical difference in the pregnancy rate with seven women (adjusted p = 0.992) achieving pregnancy during the course of the study intervention. Those receiving the acupuncture conceived within an average of 5.5 weeks compared to 10.67 weeks for the lifestyle only group (p = 0.422). The acupuncture protocol tested influenced women who received it compared to women who used lifestyle modification alone: their fertility awareness and wellbeing increased, and those who conceived did so in half the time. PMID:27242910

Total Synthesis of Acremoauxin A and Oxazinin 3: Scope and Mechanism of Direct Indole and Pyrrole Couplings Adjacent to Carbonyl Compounds

PubMed Central

Richter, Jeremy M.; Whitefield, Brandon W.; Maimone, Thomas J.; Lin, David W.; Castroviejo, M. Pilar; Baran, Phil S.

2008-01-01

Full details are provided for a recently invented method to couple indoles and pyrroles to carbonyl compounds. The reaction is ideally suited for structurally complex substrates and exhibits high levels of chemoselectivity (functional group tolerability), regioselectivity (coupling occurs exclusively at C–3 of indole or C–2 of pyrrole), stereoselectivity (substrate control), and practicality (amenable to scale-up). In addition, quaternary stereocenters are easily and predictably generated. The reaction has been applied to a number of synthetic problems including total syntheses of members of the hapalindole family of natural products, ketorolac, acremoauxin A, and oxazinin 3. Mechanistically, this coupling protocol appears to operate by a single electron transfer process requiring generation of an electron-deficient radical adjacent to a carbonyl which is then intercepted by an indole or pyrrole anion. PMID:17900115

Crosstalk error correction through dynamical decoupling of single-qubit gates in capacitively coupled singlet-triplet semiconductor spin qubits

NASA Astrophysics Data System (ADS)

Buterakos, Donovan; Throckmorton, Robert E.; Das Sarma, S.

2018-01-01

In addition to magnetic field and electric charge noise adversely affecting spin-qubit operations, performing single-qubit gates on one of multiple coupled singlet-triplet qubits presents a new challenge: crosstalk, which is inevitable (and must be minimized) in any multiqubit quantum computing architecture. We develop a set of dynamically corrected pulse sequences that are designed to cancel the effects of both types of noise (i.e., field and charge) as well as crosstalk to leading order, and provide parameters for these corrected sequences for all 24 of the single-qubit Clifford gates. We then provide an estimate of the error as a function of the noise and capacitive coupling to compare the fidelity of our corrected gates to their uncorrected versions. Dynamical error correction protocols presented in this work are important for the next generation of singlet-triplet qubit devices where coupling among many qubits will become relevant.

A Simple Bioconjugate Attachment Protocol for Use in Single Molecule Force Spectroscopy Experiments Based on Mixed Self-Assembled Monolayers

PubMed Central

Attwood, Simon J.; Simpson, Anna M. C.; Stone, Rachael; Hamaia, SamirW.; Roy, Debdulal; Farndale, RichardW.; Ouberai, Myriam; Welland, Mark E.

2012-01-01

Single molecule force spectroscopy is a technique that can be used to probe the interaction force between individual biomolecular species. We focus our attention on the tip and sample coupling chemistry, which is crucial to these experiments. We utilised a novel approach of mixed self-assembled monolayers of alkanethiols in conjunction with a heterobifunctional crosslinker. The effectiveness of the protocol is demonstrated by probing the biotin-avidin interaction. We measured unbinding forces comparable to previously reported values measured at similar loading rates. Specificity tests also demonstrated a significant decrease in recognition after blocking with free avidin. PMID:23202965

Use of the 2-chlorotrityl chloride resin for microwave-assisted solid phase peptide synthesis.

PubMed

Ieronymaki, Matthaia; Androutsou, Maria Eleni; Pantelia, Anna; Friligou, Irene; Crisp, Molly; High, Kirsty; Penkman, Kirsty; Gatos, Dimitrios; Tselios, Theodore

2015-09-01

A fast and efficient microwave (MW)-assisted solid-phase peptide synthesis protocol using the 2-chlorotrityl chloride resin and the Fmoc/tBu methodology, has been developed. The established protocol combines the advantages of MW irradiation and the acid labile 2-chlorotrityl chloride resin. The effect of temperature during the MW irradiation, the degree of resin substitution during the coupling of the first amino acids and the rate of racemization for each amino acid were evaluated. The suggested solid phase methodology is applicable for orthogonal peptide synthesis and for the synthesis of cyclic peptides. © 2015 Wiley Periodicals, Inc.

Validation of the iHealth BP3 upper-arm blood pressure monitor, for clinic use and self-measurement, according to the European Society of Hypertension International Protocol revision 2010.

PubMed

Chen, Can; Shang, Fujun; Wang, Jiepin; Chen, Jianghong; Ji, Na; Wan, Yi

2012-12-01

This study aimed to evaluate the performance of the iHealth BP3 upper-arm blood pressure monitor, which is designed for clinic use and self-measurement of blood pressure using Apple touch devices as an interface. The European Society of Hypertension International Protocol (ESH-IP) revision 2010 for the validation of blood pressure measuring devices in adults was followed precisely. Ninty-nine couples of test device and reference blood pressure measurements were obtained during the study (three pairs for each of the 33 participants). The 33 participants, age 47.1±12.3 years (age range 27-69 years) and arm circumference 30.0±4.4 cm, had a mean systolic blood pressure (SBP) of 143.9±27.4 mmHg and a mean diastolic blood pressure (DBP) of 90.1±18.3 mmHg. The device passed all of the requirements fulfilling the standards of the protocol, and the mean±SD device-observer difference was 2.8±4.2 mmHg for SBP and -0.4±3.5 mmHg for DBP. According to the results of the validation study on the basis of the ESH-IP revision 2010, the iHealth BP3 can be recommended for clinic use and self-measurement in an adult population. © 2012 Wolters Kluwer Health | Lippincott Williams & Wilkins.

Energetics and kinetics of primary charge separation in bacterial photosynthesis.

PubMed

LeBard, David N; Kapko, Vitaliy; Matyushov, Dmitry V

2008-08-21

We report the results of molecular dynamics (MD) simulations and formal modeling of the free-energy surfaces and reaction rates of primary charge separation in the reaction center of Rhodobacter sphaeroides. Two simulation protocols were used to produce MD trajectories. Standard force-field potentials were employed in the first protocol. In the second protocol, the special pair was made polarizable to reproduce a high polarizability of its photoexcited state observed by Stark spectroscopy. The charge distribution between covalent and charge-transfer states of the special pair was dynamically adjusted during the simulation run. We found from both protocols that the breadth of electrostatic fluctuations of the protein/water environment far exceeds previous estimates, resulting in about 1.6 eV reorganization energy of electron transfer in the first protocol and 2.5 eV in the second protocol. Most of these electrostatic fluctuations become dynamically frozen on the time scale of primary charge separation, resulting in much smaller solvation contributions to the activation barrier. While water dominates solvation thermodynamics on long observation times, protein emerges as the major thermal bath coupled to electron transfer on the picosecond time of the reaction. Marcus parabolas were obtained for the free-energy surfaces of electron transfer by using the first protocol, while a highly asymmetric surface was obtained in the second protocol. A nonergodic formulation of the diffusion-reaction electron-transfer kinetics has allowed us to reproduce the experimental results for both the temperature dependence of the rate and the nonexponential decay of the population of the photoexcited special pair.

Exploring the feasibility and acceptability of couple-based psychosexual support following prostate cancer surgery: study protocol for a pilot randomised controlled trial

PubMed Central

2014-01-01

Background Men who undergo surgery for prostate cancer frequently experience significant side-effects including urinary and sexual dysfunction. These difficulties can lead to anxiety, depression and reduced quality of life. Many partners also experience psychological distress. An additional impact can be on the couple relationship, with changes to intimacy, and unmet psychosexual supportive needs in relation to sexual recovery and rehabilitation. The aim of this exploratory randomised controlled trial pilot study is to determine the feasibility and acceptability of a novel family-relational-psychosexual intervention to support intimacy and reduce distress among couples following prostate cancer surgery and to estimate the efficacy of this intervention. Methods/Design The intervention will comprise six sessions of psychosexual and relationship support delivered by experienced couple-support practitioners. Specialist training in delivering the intervention will be provided to practitioners and they will be guided by a detailed treatment manual based on systemic principles. Sixty-eight couples will be randomised to receive either the intervention or standard care (comprising usual follow-up hospital appointments). A pre-test, post-test design will be used to test the feasibility of the intervention (baseline, end of intervention and six-month follow-up) and its acceptability to couples and healthcare professionals (qualitative interviews). Both individual and relational outcome measures will assess sexual functioning, anxiety and depression, couple relationship, use of health services and erectile dysfunction medication/technologies. An economic analysis will estimate population costs of the intervention, compared to usual care, using simple modelling to evaluate the affordability of the intervention. Discussion Given the increasing incidence and survival of post-operative men with prostate cancer, it is timely and appropriate to determine the feasibility of a definitive trial through a pilot randomised controlled trial of a family-relational-psychosexual intervention for couples. The study will provide evidence about the components of a couple-based intervention, its acceptability to patients and healthcare professionals, and its influence on sexual and relational functioning. Data from this study will be used to calculate sample sizes required for any definitive trial. Trial registration ClinicalTrials.gov Identifier: NCT01842438. Registration date: 24 April 2013; Randomisation of first patient: 13 May 2013 PMID:24886676

Isolation of 1E4 IgM Anti-Fasciola hepatica Rediae Monoclonal Antibody from Ascites: Comparison of Two Purification Protocols.

PubMed

Alba, Annia; Marcet, Ricardo; Otero, Oscar; Hernández, Hilda M; Figueredo, Mabel; Sarracent, Jorge

2016-02-01

Purification of immunoglobulin M (IgM) antibodies could be challenging, and is often characterized by the optimization of the purification protocol to best suit the particular features of the molecule. Here, two different schemes were compared to purify, from ascites, the 1E4 IgM monoclonal antibody (mAb) previously raised against the stage of redia of the trematode Fasciola hepatica. This immunoglobulin is used as capture antibody in an immunoenzymatic assay to detect parasite ongoing infection in its intermediate hosts. The first purification protocol of the 1E4 mAb involved two chromatographic steps: an affinity chromatography on a Concanavalin A matrix followed by size exclusion chromatography. An immunoaffinity chromatography was selected as the second protocol for one-step purification of the antibody using the crude extract of adult parasites coupled to a commercial matrix. Immunoreactivity of the fractions during purification schemes was assessed by indirect immunoenzymatic assays against the crude extract of F. hepatica rediae, while purity was estimated by protein electrophoresis. Losses on the recovery of the antibody isolated by the first purification protocol occurred due to protein precipitation during the concentration of the sample and to low resolution of the size exclusion molecular chromatography step regarding this particular immunoglobulin. The immunoaffinity chromatography using F. hepatica antigens as ligands proved to be the most suitable protocol yielding a pure and immunoreactive antibody. The purification protocols used are discussed regarding efficiency and difficulties.

Metal-free TEMPO-promoted C(sp³)-H amination to afford multisubstituted benzimidazoles.

PubMed

Xue, Ding; Long, Ya-Qiu

2014-05-16

An efficient TEMPO-air/cat. TEMPO-O2 oxidative protocol was developed to synthesize multisubstituted or fused tetracyclic benzimidazoles via a metal-free oxidative C-N coupling between the sp(3) C-H and free N-H of readily available N(1)-benzyl/alkyl-1,2-phenylenediamines.

Constructing the Components of a Lab Report Using Peer Review

ERIC Educational Resources Information Center

Berry, David E.; Fawkes, Kelli L.

2010-01-01

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

GPCR-I-TASSER: A Hybrid Approach to G Protein-Coupled Receptor Structure Modeling and the Application to the Human Genome.

PubMed

Zhang, Jian; Yang, Jianyi; Jang, Richard; Zhang, Yang

2015-08-04

Experimental structure determination remains difficult for G protein-coupled receptors (GPCRs). We propose a new hybrid protocol to construct GPCR structure models that integrates experimental mutagenesis data with ab initio transmembrane (TM) helix assembly simulations. The method was tested on 24 known GPCRs where the ab initio TM-helix assembly procedure constructed the correct fold for 20 cases. When combined with weak homology and sparse mutagenesis restraints, the method generated correct folds for all the tested cases with an average Cα root-mean-square deviation 2.4 Å in the TM regions. The new hybrid protocol was applied to model all 1,026 GPCRs in the human genome, where 923 have a high confidence score and are expected to have correct folds; these contain many pharmaceutically important families with no previously solved structures, including Trace amine, Prostanoids, Releasing hormones, Melanocortins, Vasopressin, and Neuropeptide Y receptors. The results demonstrate new progress on genome-wide structure modeling of TM proteins. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dynamical characterization of inactivation path in voltage-gated Na+ ion channel by non-equilibrium response spectroscopy

PubMed Central

Pal, Krishnendu; Gangopadhyay, Gautam

2016-01-01

ABSTRACT Inactivation path of voltage gated sodium channel has been studied here under various voltage protocols as it is the main governing factor for the periodic occurrence and shape of the action potential. These voltage protocols actually serve as non-equilibrium response spectroscopic tools to study the ion channel in non-equilibrium environment. In contrast to a lot of effort in finding the crystal structure based molecular mechanism of closed-state(CSI) and open-state inactivation(OSI); here our approach is to understand the dynamical characterization of inactivation. The kinetic flux as well as energetic contribution of the closed and open- state inactivation path is compared here for voltage protocols, namely constant, pulsed and oscillating. The non-equilibrium thermodynamic quantities used in response to these voltage protocols serve as improved characterization tools for theoretical understanding which not only agrees with the previously known kinetic measurements but also predict the energetically optimum processes to sustain the auto-regulatory mechanism of action potential and the consequent inactivation steps needed. The time dependent voltage pattern governs the population of the conformational states which when couple with characteristic rate parameters, the CSI and OSI selectivity arise dynamically to control the inactivation path. Using constant, pulsed and continuous oscillating voltage protocols we have shown that during depolarization the OSI path is more favored path of inactivation however, in the hyper-polarized situation the CSI is favored. It is also shown that the re-factorisation of inactivated sodium channel to resting state occurs via CSI path. Here we have shown how the subtle energetic and entropic cost due to the change in the depolarization magnitude determines the optimum path of inactivation. It is shown that an efficient CSI and OSI dynamical profile in principle can characterize the open-state drug blocking phenomena. PMID:27367642

Differential Effects of HRAS Mutation on LTP-Like Activity Induced by Different Protocols of Repetitive Transcranial Magnetic Stimulation.

PubMed

Dileone, Michele; Ranieri, Federico; Florio, Lucia; Capone, Fioravante; Musumeci, Gabriella; Leoni, Chiara; Mordillo-Mateos, Laura; Tartaglia, Marco; Zampino, Giuseppe; Di Lazzaro, Vincenzo

2016-01-01

Costello syndrome (CS) is a rare congenital disorder due to a G12S amino acid substitution in HRAS protoncogene. Previous studies have shown that Paired Associative Stimulation (PAS), a repetitive brain stimulation protocol inducing motor cortex plasticity by coupling peripheral nerve stimulation with brain stimulation, leads to an extremely pronounced motor cortex excitability increase in CS patients. Intermittent Theta Burst Stimulation (iTBS) represents a protocol able to induce motor cortex plasticity by trains of stimuli at 50 Hz. In healthy subjects PAS and iTBS produce similar after-effects in motor cortex excitability. Experimental models showed that HRAS-dependent signalling pathways differently affect LTP induced by different patterns of repetitive synaptic stimulation. We aimed to compare iTBS-induced after-effects on motor cortex excitability with those produced by PAS in CS patients and to observe whether HRAS mutation differentially affects two different forms of neuromodulation protocols. We evaluated in vivo after-effects induced by PAS and iTBS applied over the right motor cortex in 4 CS patients and in 21 healthy age-matched controls. Our findings confirmed HRAS-dependent extremely pronounced PAS-induced after-effects and showed for the first time that iTBS induces no change in MEP amplitude in CS patients whereas both protocols lead to an increase of about 50% in controls. CS patients are characterized by an impairment of iTBS-related LTP-like phenomena besides enhanced PAS-induced after-effects, suggesting that HRAS-dependent signalling pathways have a differential influence on PAS- and iTBS-induced plasticity in humans. Copyright © 2015 Elsevier Inc. All rights reserved.

Implementation of a Publish-Subscribe Protocol in Microgrid Islanding and Resynchronization with Self-Discovery

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

Starke, M.; Herron, A.; King, D.

Communications systems and protocols are becoming second nature to utilities operating distribution systems. Traditionally, centralized communication approaches are often used, while recently in microgrid applications, distributed communication and control schema emerge offering several advantages such as improved system reliability, plug-and-play operation and distributed intelligence. Still, operation and control of microgrids including distributed communication schema have been less of a discussion in the literature. To address the challenge of multiple-inverter microgrid synchronization, a publish-subscribe protocol based, Data Distribution Service (DDS), communication schema for microgrids is proposed in this paper. The communication schema is discussed in details for individual devices such asmore » generators, photovoltaic systems, energy storage systems, microgrid point of common coupling switch, and supporting applications. In conclusion, islanding and resynchronization of a microgrid are demonstrated on a test-bed utilizing this schema.« less

Implementation of a Publish-Subscribe Protocol in Microgrid Islanding and Resynchronization with Self-Discovery

DOE PAGES

Starke, M.; Herron, A.; King, D.; ...

2017-08-24

Communications systems and protocols are becoming second nature to utilities operating distribution systems. Traditionally, centralized communication approaches are often used, while recently in microgrid applications, distributed communication and control schema emerge offering several advantages such as improved system reliability, plug-and-play operation and distributed intelligence. Still, operation and control of microgrids including distributed communication schema have been less of a discussion in the literature. To address the challenge of multiple-inverter microgrid synchronization, a publish-subscribe protocol based, Data Distribution Service (DDS), communication schema for microgrids is proposed in this paper. The communication schema is discussed in details for individual devices such asmore » generators, photovoltaic systems, energy storage systems, microgrid point of common coupling switch, and supporting applications. In conclusion, islanding and resynchronization of a microgrid are demonstrated on a test-bed utilizing this schema.« less

Ploidy Manipulation of Zebrafish Embryos with Heat Shock 2 Treatment

PubMed Central

Baars, Destiny L.; Pelegri, Francisco

2016-01-01

Manipulation of ploidy allows for useful transformations, such as diploids to tetraploids, or haploids to diploids. In the zebrafish Danio rerio, specifically the generation of homozygous gynogenetic diploids is useful in genetic analysis because it allows the direct production of homozygotes from a single heterozygous mother. This article describes a modified protocol for ploidy duplication based on a heat pulse during the first cell cycle, Heat Shock 2 (HS2). Through inhibition of centriole duplication, this method results in a precise cell division stall during the second cell cycle. The precise one-cycle division stall, coupled to unaffected DNA duplication, results in whole genome duplication. Protocols associated with this method include egg and sperm collection, UV treatment of sperm, in vitro fertilization and heat pulse to cause a one-cell cycle division delay and ploidy duplication. A modified version of this protocol could be applied to induce ploidy changes in other animal species. PMID:28060351

Assisted reproductive technology: an overview of Cochrane Reviews.

PubMed

Farquhar, Cindy; Rishworth, Josephine R; Brown, Julie; Nelen, Willianne L D M; Marjoribanks, Jane

2015-07-15

As many as one in six couples will encounter problems with fertility, defined as failure to achieve a clinical pregnancy after regular intercourse for 12 months. Increasingly, couples are turning to assisted reproductive technology (ART) for help with conceiving and ultimately giving birth to a healthy live baby of their own. Fertility treatments are complex, and each ART cycle consists of several steps. If one of the steps is incorrectly applied, the stakes are high as conception may not occur. With this in mind, it is important that each step of the ART cycle is supported by good evidence from well-designed studies. To summarise the evidence from Cochrane systematic reviews on procedures and treatment options available to couples with subfertility undergoing assisted reproductive technology (ART). Published Cochrane systematic reviews of couples undergoing ART (in vitro fertilisation or intracytoplasmic sperm injection) were eligible for inclusion in the overview. We also identified Cochrane reviews in preparation, for future inclusion.The outcomes of the overview were live birth (primary outcome), clinical pregnancy, multiple pregnancy, miscarriage and ovarian hyperstimulation syndrome (secondary outcomes). Studies of intrauterine insemination and ovulation induction were excluded.Selection of systematic reviews, data extraction and quality assessment were undertaken in duplicate. Review quality was assessed by using the AMSTAR tool. Reviews were organised by their relevance to specific stages in the ART cycle. Their findings were summarised in the text and data for each outcome were reported in 'Additional tables'. Fifty-nine systematic reviews published in The Cochrane Library up to July 2015 were included. All were high quality. Thirty-two reviews identified interventions that were effective (n = 19) or promising (n = 13), 14 reviews identified interventions that were either ineffective (n = 2) or possibly ineffective (n = 12), and 13 reviews were unable to draw conclusions due to lack of evidence.An additional 11 protocols and five titles were identified for future inclusion in this overview. This overview provides the most up to date evidence on ART cycles from systematic reviews of randomised controlled trials. Fertility treatments are costly and the stakes are high. Using the best available evidence to optimise outcomes is best practice. The evidence from this overview could be used to develop clinical practice guidelines and protocols for use in daily clinical practice, in order to improve live birth rates and reduce rates of multiple pregnancy, cycle cancellation and ovarian hyperstimulation syndrome.

Assisted reproductive technology: an overview of Cochrane reviews.

PubMed

Farquhar, Cindy; Rishworth, Josephine R; Brown, Julie; Nelen, Willianne L D M; Marjoribanks, Jane

2014-12-23

As many as one in six couples will encounter problems with fertility, defined as failure to achieve a clinical pregnancy after regular intercourse for 12 months. Increasingly, couples are turning to assisted reproductive technology (ART) for help with conceiving and ultimately giving birth to a healthy live baby of their own. Fertility treatments are complex, and each ART cycle consists of several steps. If one of the steps is incorrectly applied, the stakes are high as conception may not occur. With this in mind, it is important that each step of the ART cycle is supported by good evidence from well-designed studies. To summarise the evidence from Cochrane systematic reviews on procedures and treatment options available to couples with subfertility undergoing assisted reproductive technology (ART). Published Cochrane systematic reviews of couples undergoing ART (in vitro fertilisation or intracytoplasmic sperm injection) were eligible for inclusion in the overview. We also identified Cochrane reviews in preparation, for future inclusion.The outcomes of the overview were live birth (primary outcome), clinical pregnancy, multiple pregnancy, miscarriage and ovarian hyperstimulation syndrome (secondary outcomes). Studies of intrauterine insemination and ovulation induction were excluded.Selection of systematic reviews, data extraction and quality assessment were undertaken in duplicate. Review quality was assessed by using the AMSTAR tool. Reviews were organised by their relevance to specific stages in the ART cycle. Their findings were summarised in the text and data for each outcome were reported in 'Additional tables'. Fifty-eight systematic reviews published in The Cochrane Library were included. All were high quality. Thirty-two reviews identified interventions that were effective (n = 19) or promising (n = 13), 14 reviews identified interventions that were either ineffective (n = 3) or possibly ineffective (n=11), and 12 reviews were unable to draw conclusions due to lack of evidence.An additional 11 protocols and one title were identified for future inclusion in this overview. This overview provides the most up to date evidence on ART cycles from systematic reviews of randomised controlled trials. Fertility treatments are costly and the stakes are high. Using the best available evidence to optimise outcomes is best practice. The evidence from this overview could be used to develop clinical practice guidelines and protocols for use in daily clinical practice, in order to improve live birth rates and reduce rates of multiple pregnancy, cycle cancellation and ovarian hyperstimulation syndrome.

Assisted reproductive technology: an overview of Cochrane Reviews.

PubMed

Farquhar, Cindy; Rishworth, Josephine R; Brown, Julie; Nelen, Willianne L D M; Marjoribanks, Jane

2013-08-22

As many as one in six couples will encounter problems with fertility, defined as failure to achieve a clinical pregnancy after regular intercourse for 12 months. Increasingly, couples are turning to assisted reproductive technology (ART) for help with conceiving and ultimately giving birth to a healthy live baby of their own. Fertility treatments are complex, and each ART cycle consists of several steps. If one of the steps is incorrectly applied, the stakes are high as conception may not occur. With this in mind, it is important that each step of the ART cycle is supported by good evidence from well-designed studies. To summarise the evidence from Cochrane systematic reviews on procedures and treatment options available to couples with subfertility undergoing assisted reproductive technology (ART). Published Cochrane systematic reviews of couples undergoing ART (in vitro fertilisation or intracytoplasmic sperm injection) were eligible for inclusion in the overview. We also identified Cochrane reviews in preparation, for future inclusion.The outcomes of the overview were live birth (primary outcome), clinical pregnancy, multiple pregnancy, miscarriage and ovarian hyperstimulation syndrome (secondary outcomes). Studies of intrauterine insemination and ovulation induction were excluded.Selection of systematic reviews, data extraction and quality assessment were undertaken in duplicate. Review quality was assessed by using the AMSTAR tool. Reviews were organised by their relevance to specific stages in the ART cycle. Their findings were summarised in the text and data for each outcome were reported in 'Additional tables'. Fifty-four systematic reviews published in The Cochrane Library were included. All were high quality. Thirty reviews identified interventions that were effective (n = 18) or promising (n = 12), 13 reviews identified interventions that were either ineffective (n = 3) or possibly ineffective (n=10), and 11 reviews were unable to draw conclusions due to lack of evidence.An additional 15 protocols and two titles were identified for future inclusion in this overview. This overview provides the most up to date evidence on ART cycles from systematic reviews of randomised controlled trials. Fertility treatments are costly and the stakes are high. Using the best available evidence to optimise outcomes is best practice. The evidence from this overview could be used to develop clinical practice guidelines and protocols for use in daily clinical practice, in order to improve live birth rates and reduce rates of multiple pregnancy, cycle cancellation and ovarian hyperstimulation syndrome.

Studying the Stoichiometry of Epidermal Growth Factor Receptor in Intact Cells using Correlative Microscopy.

PubMed

Peckys, Diana B; de Jonge, Niels

2015-09-11

This protocol describes the labeling of epidermal growth factor receptor (EGFR) on COS7 fibroblast cells, and subsequent correlative fluorescence microscopy and environmental scanning electron microscopy (ESEM) of whole cells in hydrated state. Fluorescent quantum dots (QDs) were coupled to EGFR via a two-step labeling protocol, providing an efficient and specific protein labeling, while avoiding label-induced clustering of the receptor. Fluorescence microscopy provided overview images of the cellular locations of the EGFR. The scanning transmission electron microscopy (STEM) detector was used to detect the QD labels with nanoscale resolution. The resulting correlative images provide data of the cellular EGFR distribution, and the stoichiometry at the single molecular level in the natural context of the hydrated intact cell. ESEM-STEM images revealed the receptor to be present as monomer, as homodimer, and in small clusters. Labeling with two different QDs, i.e., one emitting at 655 nm and at 800 revealed similar characteristic results.

Mitochondrial Respiration in Insulin-Producing β-Cells: General Characteristics and Adaptive Effects of Hypoxia

PubMed Central

Ma, Zuheng; Scholz, Hanne; Björklund, Anneli; Grill, Valdemar

2015-01-01

Objective To provide novel insights on mitochondrial respiration in β-cells and the adaptive effects of hypoxia. Methods and Design Insulin-producing INS-1 832/13 cells were exposed to 18 hours of hypoxia followed by 20–22 hours re-oxygenation. Mitochondrial respiration was measured by high-resolution respirometry in both intact and permeabilized cells, in the latter after establishing three functional substrate-uncoupler-inhibitor titration (SUIT) protocols. Concomitant measurements included proteins of mitochondrial complexes (Western blotting), ATP and insulin secretion. Results Intact cells exhibited a high degree of intrinsic uncoupling, comprising about 50% of oxygen consumption in the basal respiratory state. Hypoxia followed by re-oxygenation increased maximal overall respiration. Exploratory experiments in peremabilized cells could not show induction of respiration by malate or pyruvate as reducing substrates, thus glutamate and succinate were used as mitochondrial substrates in SUIT protocols. Permeabilized cells displayed a high capacity for oxidative phosphorylation for both complex I- and II-linked substrates in relation to maximum capacity of electron transfer. Previous hypoxia decreased phosphorylation control of complex I-linked respiration, but not in complex II-linked respiration. Coupling control ratios showed increased coupling efficiency for both complex I- and II-linked substrates in hypoxia-exposed cells. Respiratory rates overall were increased. Also previous hypoxia increased proteins of mitochondrial complexes I and II (Western blotting) in INS-1 cells as well as in rat and human islets. Mitochondrial effects were accompanied by unchanged levels of ATP, increased basal and preserved glucose-induced insulin secretion. Conclusions Exposure of INS-1 832/13 cells to hypoxia, followed by a re-oxygenation period increases substrate-stimulated respiratory capacity and coupling efficiency. Such effects are accompanied by up-regulation of mitochondrial complexes also in pancreatic islets, highlighting adaptive capacities of possible importance in an islet transplantation setting. Results also indicate idiosyncrasies of β-cells that do not respire in response to a standard inclusion of malate in SUIT protocols. PMID:26401848

Mitochondrial Respiration in Insulin-Producing β-Cells: General Characteristics and Adaptive Effects of Hypoxia.

PubMed

Hals, Ingrid K; Bruerberg, Simon Gustafson; Ma, Zuheng; Scholz, Hanne; Björklund, Anneli; Grill, Valdemar

2015-01-01

To provide novel insights on mitochondrial respiration in β-cells and the adaptive effects of hypoxia. Insulin-producing INS-1 832/13 cells were exposed to 18 hours of hypoxia followed by 20-22 hours re-oxygenation. Mitochondrial respiration was measured by high-resolution respirometry in both intact and permeabilized cells, in the latter after establishing three functional substrate-uncoupler-inhibitor titration (SUIT) protocols. Concomitant measurements included proteins of mitochondrial complexes (Western blotting), ATP and insulin secretion. Intact cells exhibited a high degree of intrinsic uncoupling, comprising about 50% of oxygen consumption in the basal respiratory state. Hypoxia followed by re-oxygenation increased maximal overall respiration. Exploratory experiments in peremabilized cells could not show induction of respiration by malate or pyruvate as reducing substrates, thus glutamate and succinate were used as mitochondrial substrates in SUIT protocols. Permeabilized cells displayed a high capacity for oxidative phosphorylation for both complex I- and II-linked substrates in relation to maximum capacity of electron transfer. Previous hypoxia decreased phosphorylation control of complex I-linked respiration, but not in complex II-linked respiration. Coupling control ratios showed increased coupling efficiency for both complex I- and II-linked substrates in hypoxia-exposed cells. Respiratory rates overall were increased. Also previous hypoxia increased proteins of mitochondrial complexes I and II (Western blotting) in INS-1 cells as well as in rat and human islets. Mitochondrial effects were accompanied by unchanged levels of ATP, increased basal and preserved glucose-induced insulin secretion. Exposure of INS-1 832/13 cells to hypoxia, followed by a re-oxygenation period increases substrate-stimulated respiratory capacity and coupling efficiency. Such effects are accompanied by up-regulation of mitochondrial complexes also in pancreatic islets, highlighting adaptive capacities of possible importance in an islet transplantation setting. Results also indicate idiosyncrasies of β-cells that do not respire in response to a standard inclusion of malate in SUIT protocols.

Analytic few-photon scattering in waveguide QED

NASA Astrophysics Data System (ADS)

Hurst, David L.; Kok, Pieter

2018-04-01

We develop an approach to light-matter coupling in waveguide QED based upon scattering amplitudes evaluated via Dyson series. For optical states containing more than single photons, terms in this series become increasingly complex, and we provide a diagrammatic recipe for their evaluation, which is capable of yielding analytic results. Our method fully specifies a combined emitter-optical state that permits investigation of light-matter entanglement generation protocols. We use our expressions to study two-photon scattering from a Λ -system and find that the pole structure of the transition amplitude is dramatically altered as the two ground states are tuned from degeneracy.

Bioluminescence resonance energy transfer (BRET) to detect the interactions between kappa opioid receptor and non visual arrestins.

PubMed

Bedini, Andrea

2015-01-01

Bioluminescence resonance energy transfer (BRET) is a very sensitive technique employed to study protein-protein interactions, including G-protein-coupled receptors (GPCRs) hetero- and homo-dimerization. Recently, BRET has also been used to investigate the interaction between GPCRs (e.g., β2 adrenergic receptor, muscarinic M2 receptor, dopaminergic D2 receptor) and non-visual arrestins. Here a BRET protocol is described to investigate interactions between the kappa opioid receptor (KOR) and non visual arrestins (arrestin-2 and arrestin-3) in HEK-293 cells, both under basal conditions and after exposure to KOR ligands.

Pulsed source of spectrally uncorrelated and indistinguishable photons at telecom wavelengths.

PubMed

Bruno, N; Martin, A; Guerreiro, T; Sanguinetti, B; Thew, R T

2014-07-14

We report on the generation of indistinguishable photon pairs at telecom wavelengths based on a type-II parametric down conversion process in a periodically poled potassium titanyl phosphate (PPKTP) crystal. The phase matching, pump laser characteristics and coupling geometry are optimised to obtain spectrally uncorrelated photons with high coupling efficiencies. Four photons are generated by a counter-propagating pump in the same crystal and anlysed via two photon interference experiments between photons from each pair source as well as joint spectral and g((2)) measurements. We obtain a spectral purity of 0.91 and coupling efficiencies around 90% for all four photons without any filtering. These pure indistinguishable photon sources at telecom wavelengths are perfectly adapted for quantum network demonstrations and other multi-photon protocols.

An effective placental cotyledons proteins extraction method for 2D gel electrophoresis.

PubMed

Tan, Niu J; Daim, Leona D J; Jamil, Amilia A M; Mohtarrudin, Norhafizah; Thilakavathy, Karuppiah

2017-03-01

Effective protein extraction is essential especially in producing a well-resolved proteome on 2D gels. A well-resolved placental cotyledon proteome, with good reproducibility, have allowed researchers to study the proteins underlying the physiology and pathophysiology of pregnancy. The aim of this study is to determine the best protein extraction protocol for the extraction of protein from placental cotyledons tissues for a two-dimensional gel electrophoresis (2D-GE). Based on widely used protein extraction strategies, 12 different extraction methodologies were carefully selected, which included one chemical extraction, two mechanical extraction coupled protein precipitations, and nine chemical extraction coupled protein precipitations. Extracted proteins were resolved in a one-dimensional gel electrophoresis and 2D-GE; then, it was compared with set criteria: extraction efficacy, protein resolution, reproducibility, and recovery efficiency. Our results revealed that a better profile was obtained by chemical extraction in comparison to mechanical extraction. We further compared chemical extraction coupled protein precipitation methodologies, where the DNase/lithium chloride-dense sucrose homogenization coupled dichloromethane-methanol precipitation (DNase/LiCl-DSH-D/MPE) method showed good protein extraction efficiency. This, however, was carried out with the best protein resolution and proteome reproducibility on 2D-gels. DNase/LiCl-DSH-D/MPE was efficient in the extraction of proteins from placental cotyledons tissues. In addition, this methodology could hypothetically allow the protein extraction of any tissue that contains highly abundant lipid and glycogen. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multiscale Universal Interface: A concurrent framework for coupling heterogeneous solvers

NASA Astrophysics Data System (ADS)

Tang, Yu-Hang; Kudo, Shuhei; Bian, Xin; Li, Zhen; Karniadakis, George Em

2015-09-01

Concurrently coupled numerical simulations using heterogeneous solvers are powerful tools for modeling multiscale phenomena. However, major modifications to existing codes are often required to enable such simulations, posing significant difficulties in practice. In this paper we present a C++ library, i.e. the Multiscale Universal Interface (MUI), which is capable of facilitating the coupling effort for a wide range of multiscale simulations. The library adopts a header-only form with minimal external dependency and hence can be easily dropped into existing codes. A data sampler concept is introduced, combined with a hybrid dynamic/static typing mechanism, to create an easily customizable framework for solver-independent data interpretation. The library integrates MPI MPMD support and an asynchronous communication protocol to handle inter-solver information exchange irrespective of the solvers' own MPI awareness. Template metaprogramming is heavily employed to simultaneously improve runtime performance and code flexibility. We validated the library by solving three different multiscale problems, which also serve to demonstrate the flexibility of the framework in handling heterogeneous models and solvers. In the first example, a Couette flow was simulated using two concurrently coupled Smoothed Particle Hydrodynamics (SPH) simulations of different spatial resolutions. In the second example, we coupled the deterministic SPH method with the stochastic Dissipative Particle Dynamics (DPD) method to study the effect of surface grafting on the hydrodynamics properties on the surface. In the third example, we consider conjugate heat transfer between a solid domain and a fluid domain by coupling the particle-based energy-conserving DPD (eDPD) method with the Finite Element Method (FEM).

Forskolin-free cAMP assay for Gi-coupled receptors.

PubMed

Gilissen, Julie; Geubelle, Pierre; Dupuis, Nadine; Laschet, Céline; Pirotte, Bernard; Hanson, Julien

2015-12-01

G protein-coupled receptors (GPCRs) represent the most successful receptor family for treating human diseases. Many are poorly characterized with few ligands reported or remain completely orphans. Therefore, there is a growing need for screening-compatible and sensitive assays. Measurement of intracellular cyclic AMP (cAMP) levels is a validated strategy for measuring GPCRs activation. However, agonist ligands for Gi-coupled receptors are difficult to track because inducers such as forskolin (FSK) must be used and are sources of variations and errors. We developed a method based on the GloSensor system, a kinetic assay that consists in a luciferase fused with cAMP binding domain. As a proof of concept, we selected the succinate receptor 1 (SUCNR1 or GPR91) which could be an attractive drug target. It has never been validated as such because very few ligands have been described. Following analyses of SUCNR1 signaling pathways, we show that the GloSensor system allows real time, FSK-free detection of an agonist effect. This FSK-free agonist signal was confirmed on other Gi-coupled receptors such as CXCR4. In a test screening on SUCNR1, we compared the results obtained with a FSK vs FSK-free protocol and were able to identify agonists with both methods but with fewer false positives when measuring the basal levels. In this report, we validate a cAMP-inducer free method for the detection of Gi-coupled receptors agonists compatible with high-throughput screening. This method will facilitate the study and screening of Gi-coupled receptors for active ligands. Copyright © 2015 Elsevier Inc. All rights reserved.

Multiscale Universal Interface: A concurrent framework for coupling heterogeneous solvers

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

Tang, Yu-Hang, E-mail: yuhang_tang@brown.edu; Kudo, Shuhei, E-mail: shuhei-kudo@outlook.jp; Bian, Xin, E-mail: xin_bian@brown.edu

2015-09-15

Graphical abstract: - Abstract: Concurrently coupled numerical simulations using heterogeneous solvers are powerful tools for modeling multiscale phenomena. However, major modifications to existing codes are often required to enable such simulations, posing significant difficulties in practice. In this paper we present a C++ library, i.e. the Multiscale Universal Interface (MUI), which is capable of facilitating the coupling effort for a wide range of multiscale simulations. The library adopts a header-only form with minimal external dependency and hence can be easily dropped into existing codes. A data sampler concept is introduced, combined with a hybrid dynamic/static typing mechanism, to create anmore » easily customizable framework for solver-independent data interpretation. The library integrates MPI MPMD support and an asynchronous communication protocol to handle inter-solver information exchange irrespective of the solvers' own MPI awareness. Template metaprogramming is heavily employed to simultaneously improve runtime performance and code flexibility. We validated the library by solving three different multiscale problems, which also serve to demonstrate the flexibility of the framework in handling heterogeneous models and solvers. In the first example, a Couette flow was simulated using two concurrently coupled Smoothed Particle Hydrodynamics (SPH) simulations of different spatial resolutions. In the second example, we coupled the deterministic SPH method with the stochastic Dissipative Particle Dynamics (DPD) method to study the effect of surface grafting on the hydrodynamics properties on the surface. In the third example, we consider conjugate heat transfer between a solid domain and a fluid domain by coupling the particle-based energy-conserving DPD (eDPD) method with the Finite Element Method (FEM)« less

Biofilm coupled with UV irradiation for phenol degradation and change of its community structure.

PubMed

Xia, Siqing; Yan, Ning; Zhu, Jun; Zhang, Yongming

2011-06-01

The extensive use of phenol compounds and the inability to remove these compounds during wastewater treatment have resulted in the widespread occurrence of phenols in the natural environment. Phenols have been linked to serious risks to human and environmental health. Hence, the need to develop technologies that can effectively remove phenols from wastewater and source waters is a pressing challenge. In this study, light ceramic particles were immersed in activated sludge acclimated to degrade phenol, and microorganisms were allowed to attach to the particles surface to form biofilm. Then the ceramic particles with biofilm were moved into the photolytic circulating-bed biofilm reactor made of quartz glass, which was used for the degradation of phenol by three protocols: photolysis with UV light alone (P), biodegradation alone (B), and the two mechanisms operating simultaneously (photobiodegradation, P&B). The experimental results indicated that phenol removal rate was quickest by B experiment. However, P&B experiment gave more complete mineralization of phenol than that by other protocols. During P&B experiment, the microorganisms grown on porous ceramic carrier still kept the bioactivity degrading phenol, even under UV light irradiation. However, the dominant members of the bacterial community changed dramatically after the intimately coupled photobiodegradation, according to molecular biological analysis to the biofilm. Whereas Beijerinckia sp. was the dominant strain in the inoculum, it was replaced by Thauera sp. MZ1T that played a main role on degrading phenol during P&B experiment.

Deterministic quantum state transfer between remote qubits in cavities

NASA Astrophysics Data System (ADS)

Vogell, B.; Vermersch, B.; Northup, T. E.; Lanyon, B. P.; Muschik, C. A.

2017-12-01

Performing a faithful transfer of an unknown quantum state is a key challenge for enabling quantum networks. The realization of networks with a small number of quantum links is now actively pursued, which calls for an assessment of different state transfer methods to guide future design decisions. Here, we theoretically investigate quantum state transfer between two distant qubits, each in a cavity, connected by a waveguide, e.g., an optical fiber. We evaluate the achievable success probabilities of state transfer for two different protocols: standard wave packet shaping and adiabatic passage. The main loss sources are transmission losses in the waveguide and absorption losses in the cavities. While special cases studied in the literature indicate that adiabatic passages may be beneficial in this context, it remained an open question under which conditions this is the case and whether their use will be advantageous in practice. We answer these questions by providing a full analysis, showing that state transfer by adiabatic passage—in contrast to wave packet shaping—can mitigate the effects of undesired cavity losses, far beyond the regime of coupling to a single waveguide mode and the regime of lossless waveguides, as was proposed so far. Furthermore, we show that the photon arrival probability is in fact bounded in a trade-off between losses due to non-adiabaticity and due to coupling to off-resonant waveguide modes. We clarify that neither protocol can avoid transmission losses and discuss how the cavity parameters should be chosen to achieve an optimal state transfer.

Boeing's STAR-FODB test results

NASA Astrophysics Data System (ADS)

Fritz, Martin E.; de la Chapelle, Michael; Van Ausdal, Arthur W.

1995-05-01

Boeing has successfully concluded a 2 1/2 year, two phase developmental contract for the STAR-Fiber Optic Data Bus (FODB) that is intended for future space-based applications. The first phase included system analysis, trade studies, behavior modeling, and architecture and protocal selection. During this phase we selected AS4074 Linear Token Passing Bus (LTPB) protocol operating at 200 Mbps, along with the passive, star-coupled fiber media. The second phase involved design, build, integration, and performance and environmental test of brassboard hardware. The resulting brassboard hardware successfully passed performance testing, providing 200 Mbps operation with a 32 X 32 star-coupled medium. This hardware is suitable for a spaceflight experiment to validate ground testing and analysis and to demonstrate performace in the intended environment. The fiber bus interface unit (FBIU) is a multichip module containing transceiver, protocol, and data formatting chips, buffer memory, and a station management controller. The FBIU has been designed for low power, high reliability, and radiation tolerance. Nine FBIUs were built and integrated with the fiber optic physical layer consisting of the fiber cable plant (FCP) and star coupler assembly (SCA). Performance and environmental testing, including radiation exposure, was performed on selected FBIUs and the physical layer. The integrated system was demonstrated with a full motion color video image transfer across the bus while simultaneously performing utility functions with a fiber bus control module (FBCM) over a telemetry and control (T&C) bus, in this case AS1773.

Two coupled, driven Ising spin systems working as an engine.

PubMed

Basu, Debarshi; Nandi, Joydip; Jayannavar, A M; Marathe, Rahul

2017-05-01

Miniaturized heat engines constitute a fascinating field of current research. Many theoretical and experimental studies are being conducted that involve colloidal particles in harmonic traps as well as bacterial baths acting like thermal baths. These systems are micron-sized and are subjected to large thermal fluctuations. Hence, for these systems average thermodynamic quantities, such as work done, heat exchanged, and efficiency, lose meaning unless otherwise supported by their full probability distributions. Earlier studies on microengines are concerned with applying Carnot or Stirling engine protocols to miniaturized systems, where system undergoes typical two isothermal and two adiabatic changes. Unlike these models we study a prototype system of two classical Ising spins driven by time-dependent, phase-different, external magnetic fields. These spins are simultaneously in contact with two heat reservoirs at different temperatures for the full duration of the driving protocol. Performance of the model as an engine or a refrigerator depends only on a single parameter, namely the phase between two external drivings. We study this system in terms of fluctuations in efficiency and coefficient of performance (COP). We find full distributions of these quantities numerically and study the tails of these distributions. We also study reliability of the engine. We find the fluctuations dominate mean values of efficiency and COP, and their probability distributions are broad with power law tails.

Two coupled, driven Ising spin systems working as an engine

NASA Astrophysics Data System (ADS)

Basu, Debarshi; Nandi, Joydip; Jayannavar, A. M.; Marathe, Rahul

2017-05-01

Miniaturized heat engines constitute a fascinating field of current research. Many theoretical and experimental studies are being conducted that involve colloidal particles in harmonic traps as well as bacterial baths acting like thermal baths. These systems are micron-sized and are subjected to large thermal fluctuations. Hence, for these systems average thermodynamic quantities, such as work done, heat exchanged, and efficiency, lose meaning unless otherwise supported by their full probability distributions. Earlier studies on microengines are concerned with applying Carnot or Stirling engine protocols to miniaturized systems, where system undergoes typical two isothermal and two adiabatic changes. Unlike these models we study a prototype system of two classical Ising spins driven by time-dependent, phase-different, external magnetic fields. These spins are simultaneously in contact with two heat reservoirs at different temperatures for the full duration of the driving protocol. Performance of the model as an engine or a refrigerator depends only on a single parameter, namely the phase between two external drivings. We study this system in terms of fluctuations in efficiency and coefficient of performance (COP). We find full distributions of these quantities numerically and study the tails of these distributions. We also study reliability of the engine. We find the fluctuations dominate mean values of efficiency and COP, and their probability distributions are broad with power law tails.

Groundwater economics: An object-oriented foundation for integrated studies of irrigated agricultural systems

NASA Astrophysics Data System (ADS)

Steward, David R.; Peterson, Jeffrey M.; Yang, Xiaoying; Bulatewicz, Tom; Herrera-Rodriguez, Mauricio; Mao, Dazhi; Hendricks, Nathan

2009-05-01

An integrated foundation is presented to study the impacts of external forcings on irrigated agricultural systems. Individually, models are presented that simulate groundwater hydrogeology and econometric farm level crop choices and irrigated water use. The natural association between groundwater wells and agricultural parcels is employed to couple these models using geographic information science technology and open modeling interface protocols. This approach is used to study the collective action problem of the common pool. Three different policies (existing, regulation, and incentive based) are studied in the semiarid grasslands overlying the Ogallala Aquifer in the central United States. Results show that while regulation using the prior appropriation doctrine and incentives using a water buy-back program may each achieve the same level of water savings across the study region, each policy has a different impact on spatial patterns of groundwater declines and farm level economic activity. This represents the first time that groundwater and econometric models of irrigated agriculture have been integrated at the well-parcel level and provides methods for scientific investigation of this coupled natural-human system. Results are useful for science to inform decision making and public policy debate.

Uthando Lwethu (‘our love’): a protocol for a couples-based intervention to increase testing for HIV: a randomized controlled trial in rural KwaZulu-Natal, South Africa

PubMed Central

2014-01-01

Background Couples-based HIV counseling and testing (CHCT) is a proven strategy to reduce the risk of HIV transmission between partners, but uptake of CHCT is low. We describe the study design of a randomized controlled trial (RCT) aimed to increase participation in CHCT and reduce sexual risk behavior for HIV among heterosexual couples in rural KwaZulu-Natal, South Africa. We hypothesize that the rate of participation in CHCT will be higher and sexual risk behavior will be lower in the intervention group as compared to the control. Methods/design Heterosexual couples (N = 350 couples, 700 individuals) are being recruited to participate in a randomized trial of a couples-based intervention comprising two group sessions (one mixed gender, one single gender) and four couples’ counseling sessions. Couples must have been in a relationship together for at least 6 months. Quantitative assessments are conducted via mobile phones by gender-matched interviewers at baseline, 3, 6, and 9 months post-randomization. Intervention content is aimed to improve relationship dynamics, and includes communication skills and setting goals regarding CHCT. Discussion The Uthando Lwethu (‘our love’) intervention is the first couples-based intervention to have CHCT as its outcome. We are also targeting reductions in unprotected sex. CHCT necessitates the testing and mutual disclosure of both partners, conditions that are essential for improving subsequent outcomes such as disclosure of HIV status, sexual risk reduction, and improving treatment outcomes. Thus, improving rates of CHCT has the potential to improve health outcomes for heterosexual couples in a rural area of South Africa that is highly impacted by HIV. The results of our ongoing clinical trial will provide much needed information regarding whether a relationship-focused approach is effective in increasing rates of participation in CHCT. Our intervention represents an attempt to move away from individual-level conceptualizations, to a more integrated approach for HIV prevention. Trial registration Study Name: Couples in Context: An RCT of a Couples-based HIV Prevention Intervention ClinicalTrials.gov identifier: NCT01953133. South African clinical trial registration number: DOH-27-0212-3937 PMID:24552199

Still a hard-to-reach population? Using social media to recruit Latino gay couples for an HIV intervention adaptation study.

PubMed

Martinez, Omar; Wu, Elwin; Shultz, Andrew Z; Capote, Jonathan; López Rios, Javier; Sandfort, Theo; Manusov, Justin; Ovejero, Hugo; Carballo-Dieguez, Alex; Chavez Baray, Silvia; Moya, Eva; López Matos, Jonathan; DelaCruz, Juan J; Remien, Robert H; Rhodes, Scott D

2014-04-24

Online social networking use has increased rapidly among African American and Latino men who have sex with men (MSM), making it important to understand how these technologies can be used to reach, retain, and maintain individuals in care and promote health wellness. In particular, the Internet is increasingly recognized as a platform for health communication and education. However, little is known about how primarily Spanish-speaking populations use and engage with each other through social media platforms. We aimed to recruit eligible couples for a study to adapt "Connect 'n Unite" (an HIV prevention intervention initially created for black gay couples) for Spanish-speaking Latino gay couples living in New York City. In order to successfully design and implement an effective social media recruitment campaign to reach Spanish-speaking Latino gay couples for our ongoing "Latinos en Pareja" study, our community stakeholders and research team used McGuire's communication/persuasion matrix. The matrix guided our research, specifically each marketing "channel", targeted "message", and target population or "receiver". We developed a social media recruitment protocol and trained our research staff and stakeholders to conduct social media recruitment. As a result, in just 1 month, we recruited all of our subjects (N=14 couples, that is, N=28 participants) and reached more than 35,658 participants through different channels. One of the major successes of our social media recruitment campaign was to build a strong stakeholder base that became involved early on in all aspects of the research process-from pilot study writing and development to recruitment and retention. In addition, the variety of "messages" used across different social media platforms (including Facebook, the "Latinos en Pareja" study website, Craigslist, and various smartphone applications such as Grindr, SCRUFF, and Jack'd) helped recruit Latino gay couples. We also relied on a wide range of community-based organizations across New York City to promote the study and build in the social media components. Our findings highlight the importance of incorporating communication technologies into the recruitment and engagement of participants in HIV interventions. Particularly, the success of our social media recruitment strategy with Spanish-speaking Latino MSM shows that this population is not particularly "hard to reach", as it is often characterized within public health literature.

DServO: A Peer-to-Peer-based Approach to Biomedical Ontology Repositories.

PubMed

Mambone, Zakaria; Savadogo, Mahamadi; Some, Borlli Michel Jonas; Diallo, Gayo

2015-01-01

We present in this poster an extension of the ServO ontology server system, which adopts a decentralized Peer-To-Peer approach for managing multiple heterogeneous knowledge organization systems. It relies on the use of the JXTA protocol coupled with information retrieval techniques to provide a decentralized infrastructure for managing multiples instances of Ontology Repositories.

Copper-Catalyzed C(sp2)-S Coupling Reactions for the Synthesis of Aryl Dithiocarbamates with Thiuram Disulfide Reagents.

PubMed

Dong, Zhi-Bing; Liu, Xing; Bolm, Carsten

2017-11-03

An efficient protocol for the copper-catalyzed preparation of aryl dithiocarbamates from aryl iodides and inexpensive, environmentally benign tetraalkylthiuram disulfides was developed. The features of mild reaction conditions, high yields, and broad substrate scope render this new approach synthetically attractive for the preparation of potentially biologically active compounds.

A Failure to Communicate

ERIC Educational Resources Information Center

Fredette, Michelle

2011-01-01

In April, Asia officially ran out of Internet Protocol (IP) version 4 addresses--the computer equivalent of running out of telephone numbers. Over the next couple of years, the rest of the world will also run dry. Yet, unlike the Y2K bug that had some people convinced the sky would fall, this particular problem is generating little more than tired…

Gonadotrophin-releasing hormone antagonists for assisted conception.

PubMed

Al-Inany, H G; Abou-Setta, A M; Aboulghar, M

2006-07-19

Gonadotrophin-releasing hormone antagonists produce immediate suppression of gonadotrophin secretion, hence, they can be given after starting gonadotrophin administration. This has resulted in dramatic reduction in the duration of treatment cycle. Two different regimes have been described. The multiple-dose protocol involves the administration of 0.25 mg cetrorelix (or ganirelix) daily from day six to seven of stimulation, or when the leading follicle is 14 to15 mm, until human chorionic gonadotrophin (HCG) administration and the single-dose protocol involves the single administration of 3 mg cetrorelix on day seven to eight of stimulation. Assuming comparable clinical outcome, these benefits would justify a change from the standard long protocol of GnRH agonists to the new GnRH antagonist regimens. To evaluate the evidence regarding the efficacy of gonadotrophin-releasing hormone (GnRH) antagonists with the standard long protocol of GnRH agonists for controlled ovarian hyperstimulation in assisted conception. We searched Cochrane Menstrual Disorders and Subfertility Group's Specialised Register, MEDLINE and EMBASE databases from 1987 to February 2006, and handsearched bibliographies of relevant publications and reviews, and abstracts of scientific meetings. We also contacted manufacturers in the field. Randomized controlled studies comparing different protocols of GnRH antagonists with GnRH agonists in assisted conception cycles were included in this review. Two authors independently assessed trial quality and extracted data. If relevant data were missing or unclear, the authors have been consulted Twenty seven RCTs comparing the GnRH antagonist to the long protocol of GnRH agonist fulfilled the inclusion criteria. Clinical pregnancy rate was significantly lower in the antagonist group. (OR = 0.84, 95% CI = 0.72 - 0.97). The ongoing pregnancy/ live-birth rate showed the same significant lower pregnancy in the antagonist group (P = 0.03; OR 0.82, 95% CI 0.69 to 0.98).However, there was statistically significant reduction in incidence of severe OHSS with antagonist protocol. The relative risk ratio was (P = 0.01; RR 0.61, 95% CI 0.42 to 0.89). In addition, interventions to prevent OHSS (e.g. coasting, cycle cancellation) were administered more frequently in the agonist group (P = 0.03; OR 0.44, 95% CI 0.21 to 0.93). GnRH antagonist protocol is a short and simple protocol with good clinical outcome with significant reduction in incidence of severe ovarian hyperstimulation syndrome and amount of gonadotrophins but the lower pregnancy rate compared to the GnRH agonist long protocol necessitates counseling subfertile couples before recommending change from GnRH agonist to antagonist..

A mapping variable ring polymer molecular dynamics study of condensed phase proton-coupled electron transfer

NASA Astrophysics Data System (ADS)

Pierre, Sadrach; Duke, Jessica R.; Hele, Timothy J. H.; Ananth, Nandini

2017-12-01

We investigate the mechanisms of condensed phase proton-coupled electron transfer (PCET) using Mapping-Variable Ring Polymer Molecular Dynamics (MV-RPMD), a recently developed method that employs an ensemble of classical trajectories to simulate nonadiabatic excited state dynamics. Here, we construct a series of system-bath model Hamiltonians for the PCET, where four localized electron-proton states are coupled to a thermal bath via a single solvent mode, and we employ MV-RPMD to simulate state population dynamics. Specifically, for each model, we identify the dominant PCET mechanism, and by comparing against rate theory calculations, we verify that our simulations correctly distinguish between concerted PCET, where the electron and proton transfer together, and sequential PCET, where either the electron or the proton transfers first. This work represents a first application of MV-RPMD to multi-level condensed phase systems; we introduce a modified MV-RPMD expression that is derived using a symmetric rather than asymmetric Trotter discretization scheme and an initialization protocol that uses a recently derived population estimator to constrain trajectories to a dividing surface. We also demonstrate that, as expected, the PCET mechanisms predicted by our simulations are robust to an arbitrary choice of the initial dividing surface.

Sterilization of beehive material with a double inductively coupled low pressure plasma

NASA Astrophysics Data System (ADS)

Priehn, M.; Denis, B.; Aumeier, P.; Kirchner, W. H.; Awakowicz, P.; Leichert, L. I.

2016-09-01

American Foulbrood is a severe, notifiable disease of the honey bee. It is caused by infection of bee larvae with spores of the gram-positive bacterium Paenibacillus larvae. Spores of this organism are found in high numbers in an infected hive and are highly resistant to physical and chemical inactivation methods. The procedures to rehabilitate affected apiaries often result in the destruction of beehive material. In this study we assess the suitability of a double inductively coupled low pressure plasma as a non-destructive, yet effective alternative inactivation method for bacterial spores of the model organism Bacillus subtilis on beehive material. Plasma treatment was able to effectively remove spores from wax, which, under protocols currently established in veterinary practice, normally is destroyed by ignition or autoclaved for sterilization. Spores were removed from wooden surfaces with efficacies significantly higher than methods currently used in veterinary practice, such as scorching by flame treatment. In addition, we were able to non-destructively remove spores from the highly delicate honeycomb wax structures, potentially making treatment of beehive material with double inductively coupled low pressure plasma part of a fast and reliable method to rehabilitate infected bee colonies with the potential to re-use honeycombs.

Thermodynamics of coupled protein adsorption and stability using hybrid Monte Carlo simulations.

PubMed

Zhong, Ellen D; Shirts, Michael R

2014-05-06

A better understanding of changes in protein stability upon adsorption can improve the design of protein separation processes. In this study, we examine the coupling of the folding and the adsorption of a model protein, the B1 domain of streptococcal protein G, as a function of surface attraction using a hybrid Monte Carlo (HMC) approach with temperature replica exchange and umbrella sampling. In our HMC implementation, we are able to use a molecular dynamics (MD) time step that is an order of magnitude larger than in a traditional MD simulation protocol and observe a factor of 2 enhancement in the folding and unfolding rate. To demonstrate the convergence of our systems, we measure the travel of our order parameter the fraction of native contacts between folded and unfolded states throughout the length of our simulations. Thermodynamic quantities are extracted with minimum statistical variance using multistate reweighting between simulations at different temperatures and harmonic distance restraints from the surface. The resultant free energies, enthalpies, and entropies of the coupled unfolding and absorption processes are in qualitative agreement with previous experimental and computational observations, including entropic stabilization of the adsorbed, folded state relative to the bulk on surfaces with low attraction.

Matrix effects of calcium on high-precision sulfur isotope measurement by multiple-collector inductively coupled plasma mass spectrometry.

PubMed

Liu, Chenhui; Bian, Xiao-Peng; Yang, Tao; Lin, An-Jun; Jiang, Shao-Yong

2016-05-01

Multiple-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) has been successfully applied in the rapid and high-precision measurement for sulfur isotope ratios in recent years. During the measurement, the presence of matrix elements would affect the instrumental mass bias for sulfur and these matrix-induced effects have aroused a lot of researchers' interest. However, these studies have placed more weight on highlighting the necessity for their proposed correction protocols (e.g., chemical purification and matrix-matching) while less attention on the key property of the matrix element gives rise to the matrix effects. In this study, four groups of sulfate solutions, which have different concentrations of sulfur (0.05-0.60mM) but a constant sequence of atomic calcium/sulfur ratios (0.1-50), are investigated under wet (solution) and dry (desolvation) plasma conditions to make a detailed evaluation on the matrix effects from calcium on sulfur isotope measurement. Based on a series of comparative analyses, we indicated that, the matrix effects of calcium on both measured sulfur isotope ratios and detected (32)S signal intensities are dependent mainly on the absolute calcium concentration rather than its relative concentration ratio to sulfur (i.e., atomic calcium/sulfur ratio). Also, for the same group of samples, the matrix effects of calcium under dry plasma condition are much more significant than that of wet plasma. This research affords the opportunity to realize direct and relatively precise sulfur isotope measurement for evaporite gypsum, and further provides some suggestions with regard to sulfur isotope analytical protocols for sedimentary pore water. Copyright © 2016 Elsevier B.V. All rights reserved.

Purification and switching protocols for dissipatively stabilized entangled qubit states

NASA Astrophysics Data System (ADS)

Hein, Sven M.; Aron, Camille; Türeci, Hakan E.

2016-06-01

Pure dephasing processes limit the fidelities achievable in driven-dissipative schemes for stabilization of entangled states of qubits. We propose a scheme which, combined with already existing entangling methods, purifies the desired entangled state by driving out of equilibrium auxiliary dissipative cavity modes coupled to the qubits. We lay out the specifics of our scheme and compute its efficiency in the particular context of two superconducting qubits in a cavity-QED architecture, where the strongly coupled auxiliary modes provided by collective cavity excitations can drive and sustain the qubits in maximally entangled Bell states with fidelities reaching 90% for experimentally accessible parameters.

Hybrid quantum processors: molecular ensembles as quantum memory for solid state circuits.

PubMed

Rabl, P; DeMille, D; Doyle, J M; Lukin, M D; Schoelkopf, R J; Zoller, P

2006-07-21

We investigate a hybrid quantum circuit where ensembles of cold polar molecules serve as long-lived quantum memories and optical interfaces for solid state quantum processors. The quantum memory realized by collective spin states (ensemble qubit) is coupled to a high-Q stripline cavity via microwave Raman processes. We show that, for convenient trap-surface distances of a few microm, strong coupling between the cavity and ensemble qubit can be achieved. We discuss basic quantum information protocols, including a swap from the cavity photon bus to the molecular quantum memory, and a deterministic two qubit gate. Finally, we investigate coherence properties of molecular ensemble quantum bits.

On chaos synchronization and secure communication.

PubMed

Kinzel, W; Englert, A; Kanter, I

2010-01-28

Chaos synchronization, in particular isochronal synchronization of two chaotic trajectories to each other, may be used to build a means of secure communication over a public channel. In this paper, we give an overview of coupling schemes of Bernoulli units deduced from chaotic laser systems, different ways to transmit information by chaos synchronization and the advantage of bidirectional over unidirectional coupling with respect to secure communication. We present the protocol for using dynamical private commutative filters for tap-proof transmission of information that maps the task of a passive attacker to the class of non-deterministic polynomial time-complete problems. This journal is © 2010 The Royal Society

Detecting Circular RNAs by RNA Fluorescence In Situ Hybridization.

PubMed

Zirkel, Anne; Papantonis, Argyris

2018-01-01

Fluorescence in situ hybridization (FISH) coupled to high-resolution microscopy is a powerful method for analyzing the subcellular localization of RNA. However, the detection of circular RNAs (circRNAs) using microscopy is challenging because the only feature of a circRNA that can be used for the probe design is its junction. Circular RNAs are expressed at varying levels, and for their efficient monitoring by FISH, background fluorescence levels need to be kept low. Here, we describe a FISH protocol coupled to high-precision localizations using a single fluorescently labeled probe spanning the circRNA junction; this allows circRNA detection in mammalian cells with high signal-to-noise ratios.

Electronic Maxwell demon in the coherent strong-coupling regime

NASA Astrophysics Data System (ADS)

Schaller, Gernot; Cerrillo, Javier; Engelhardt, Georg; Strasberg, Philipp

2018-05-01

We consider an external feedback control loop implementing the action of a Maxwell demon. Applying control actions that are conditioned on measurement outcomes, the demon may transport electrons against a bias voltage and thereby effectively converts information into electric power. While the underlying model—a feedback-controlled quantum dot that is coupled to two electronic leads—is well explored in the limit of small tunnel couplings, we can address the strong-coupling regime with a fermionic reaction-coordinate mapping. This exact mapping transforms the setup into a serial triple quantum dot coupled to two leads. We find that a continuous projective measurement of the central dot occupation would lead to a complete suppression of electronic transport due to the quantum Zeno effect. In contrast, by using a microscopic detector model we can implement a weak measurement, which allows for closure of the control loop without transport blockade. Then, in the weak-coupling regime, the energy flows associated with the feedback loop are negligible, and dominantly the information gained in the measurement induces a bound for the generated electric power. In the strong coupling limit, the protocol may require more energy for operating the control loop than electric power produced, such that the whole device is no longer information dominated and can thus not be interpreted as a Maxwell demon.

Community-based implementation and effectiveness in a randomized trial of a risk reduction intervention for HIV-serodiscordant couples: study protocol

PubMed Central

2014-01-01

Background The HIV/AIDS epidemic continues to disproportionately affect African American communities in the US, particularly those located in urban areas. Despite the fact that HIV is often transmitted from one sexual partner to another, most HIV prevention interventions have focused only on individuals, rather than couples. This five-year study investigates community-based implementation, effectiveness, and sustainability of ‘Eban II,’ an evidence-based risk reduction intervention for African-American heterosexual, serodiscordant couples. Methods/design This hybrid implementation/effectiveness implementation study is guided by organizational change theory as conceptualized in the Texas Christian University Program Change Model (PCM), a model of phased organizational change from exposure to adoption, implementation, and sustainability. The primary implementation aims are to assist 10 community-based organizations (CBOs) to implement and sustain Eban II; specifically, to partner with CBOs to expose providers to the intervention; facilitate its adoption, implementation and sustainment; and to evaluate processes and determinants of implementation, effectiveness, fidelity, and sustainment. The primary effectiveness aim is to evaluate the effect of Eban II on participant (n = 200 couples) outcomes, specifically incidents of protected sex and proportion of condom use. We will also determine the cost-effectiveness of implementation, as measured by implementation costs and potential cost savings. A mixed methods evaluation will examine implementation at the agency level; staff members from the CBOs will complete baseline measures of organizational context and climate, while key stakeholders will be interviewed periodically throughout implementation. Effectiveness of Eban II will be assessed using a randomized delayed enrollment (waitlist) control design to evaluate the impact of treatment on outcomes at posttest and three-month follow-up. Multi-level hierarchical modeling with a multi-level nested structure will be used to evaluate the effects of agency- and couples-level characteristics on couples-level outcomes (e.g., condom use). Discussion This study will produce important information regarding the value of the Eban II program and a theory-guided implementation process and tools designed for use in implementing Eban II and other evidence-based programs in demographically diverse, resource-constrained treatment settings. Trial registration NCT00644163 PMID:24950708

Community-based implementation and effectiveness in a randomized trial of a risk reduction intervention for HIV-serodiscordant couples: study protocol.

PubMed

Hamilton, Alison B; Mittman, Brian S; Williams, John K; Liu, Honghu H; Eccles, Alicia M; Hutchinson, Craig S; Wyatt, Gail E

2014-06-20

The HIV/AIDS epidemic continues to disproportionately affect African American communities in the US, particularly those located in urban areas. Despite the fact that HIV is often transmitted from one sexual partner to another, most HIV prevention interventions have focused only on individuals, rather than couples. This five-year study investigates community-based implementation, effectiveness, and sustainability of 'Eban II,' an evidence-based risk reduction intervention for African-American heterosexual, serodiscordant couples. This hybrid implementation/effectiveness implementation study is guided by organizational change theory as conceptualized in the Texas Christian University Program Change Model (PCM), a model of phased organizational change from exposure to adoption, implementation, and sustainability. The primary implementation aims are to assist 10 community-based organizations (CBOs) to implement and sustain Eban II; specifically, to partner with CBOs to expose providers to the intervention; facilitate its adoption, implementation and sustainment; and to evaluate processes and determinants of implementation, effectiveness, fidelity, and sustainment. The primary effectiveness aim is to evaluate the effect of Eban II on participant (n = 200 couples) outcomes, specifically incidents of protected sex and proportion of condom use. We will also determine the cost-effectiveness of implementation, as measured by implementation costs and potential cost savings. A mixed methods evaluation will examine implementation at the agency level; staff members from the CBOs will complete baseline measures of organizational context and climate, while key stakeholders will be interviewed periodically throughout implementation. Effectiveness of Eban II will be assessed using a randomized delayed enrollment (waitlist) control design to evaluate the impact of treatment on outcomes at posttest and three-month follow-up. Multi-level hierarchical modeling with a multi-level nested structure will be used to evaluate the effects of agency- and couples-level characteristics on couples-level outcomes (e.g., condom use). This study will produce important information regarding the value of the Eban II program and a theory-guided implementation process and tools designed for use in implementing Eban II and other evidence-based programs in demographically diverse, resource-constrained treatment settings. NCT00644163.

A Convenient Method for Extraction and Analysis with High-Pressure Liquid Chromatography of Catecholamine Neurotransmitters and Their Metabolites.

PubMed

Xie, Li; Chen, Liqin; Gu, Pan; Wei, Lanlan; Kang, Xuejun

2018-03-01

The extraction and analysis of catecholamine neurotransmitters in biological fluids is of great importance in assessing nervous system function and related diseases, but their precise measurement is still a challenge. Many protocols have been described for neurotransmitter measurement by a variety of instruments, including high-pressure liquid chromatography (HPLC). However, there are shortcomings, such as complicated operation or hard-to-detect multiple targets, which cannot be avoided, and presently, the dominant analysis technique is still HPLC coupled with sensitive electrochemical or fluorimetric detection, due to its high sensitivity and good selectivity. Here, a detailed protocol is described for the pretreatment and detection of catecholamines with high pressure liquid chromatography with electrochemical detection (HPLC-ECD) in real urine samples of infants, using electrospun composite nanofibers composed of polymeric crown ether with polystyrene as adsorbent, also known as the packed-fiber solid phase extraction (PFSPE) method. We show how urine samples can be easily precleaned by a nanofiber-packed solid phase column, and how the analytes in the sample can be rapidly enriched, desorbed, and detected on an ECD system. PFSPE greatly simplifies the pretreatment procedures for biological samples, allowing for decreased time, expense, and reduction of the loss of targets. Overall, this work illustrates a simple and convenient protocol for solid-phase extraction coupled to an HPLC-ECD system for simultaneous determination of three monoamine neurotransmitters (norepinephrine (NE), epinephrine (E), dopamine (DA)) and two of their metabolites (3-methoxy-4-hydroxyphenylglycol (MHPG) and 3,4-dihydroxy-phenylacetic acid (DOPAC)) in infants' urine. The established protocol was applied to assess the differences of urinary catecholamines and their metabolites between high-risk infants with perinatal brain damage and healthy controls. Comparative analysis revealed a significant difference in urinary MHPG between the two groups, indicating that the catecholamine metabolites may be an important candidate marker for early diagnosis of cases at risk for brain damage in infants.

Bearer channel control protocol for the dynamic VB5.2 interface in ATM access networks

NASA Astrophysics Data System (ADS)

Fragoulopoulos, Stratos K.; Mavrommatis, K. I.; Venieris, Iakovos S.

1996-12-01

In the multi-vendor systems, a customer connected to an Access network (AN) must be capable of selecting a specific Service Node (SN) according to the services the SN provides. The multiplicity of technologically varying AN calls for the definition of a standard reference point between the AN and the SN widely known as the VB interface. Two versions are currently offered. The VB5.1 is simpler to implement but is not as flexible as the VB5.2, which supports switched connections. The VB5.2 functionality is closely coupled to the Broadband Bearer Channel Connection Protocol (B-BCCP). The B-BCCP is used for conveying the necessary information for dynamic resource allocation, traffic policing and routing in the AN as well as for information exchange concerning the status of the AN before a new call is established by the SN. By relying on such a protocol for the exchange of information instead of intercepting and interpreting signalling messages in the AN, the architecture of the AN is simplified because the functionality related to processing is not duplicated. In this paper a prominent B- BCCP candidate is defined, called the Service node Access network Interaction Protocol.

An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands.

PubMed

Saleh, Noureldin; Ibrahim, Passainte; Saladino, Giorgio; Gervasio, Francesco Luigi; Clark, Timothy

2017-05-22

A generally applicable metadynamics scheme for predicting the free energy profile of ligand binding to G-protein-coupled receptors (GPCRs) is described. A common and effective collective variable (CV) has been defined using the ideally placed and highly conserved Trp6.48 as a reference point for ligand-GPCR distance measurement and the common orientation of GPCRs in the cell membrane. Using this single CV together with well-tempered multiple-walker metadynamics with a funnel-like boundary allows an efficient exploration of the entire ligand binding path from the extracellular medium to the orthosteric binding site, including vestibule and intermediate sites. The protocol can be used with X-ray structures or high-quality homology models (based on a high-quality template and after thorough refinement) for the receptor and is universally applicable to agonists, antagonists, and partial and reverse agonists. The root-mean-square error (RMSE) in predicted binding free energies for 12 diverse ligands in five receptors (a total of 23 data points) is surprisingly small (less than 1 kcal mol -1 ). The RMSEs for simulations that use receptor X-ray structures and homology models are very similar.

Modeling of coupled differential equations for cellular chemical signaling pathways: Implications for assay protocols utilized in cellular engineering.

PubMed

O'Clock, George D

2016-08-01

Cellular engineering involves modification and control of cell properties, and requires an understanding of fundamentals and mechanisms of action for cellular derived product development. One of the keys to success in cellular engineering involves the quality and validity of results obtained from cell chemical signaling pathway assays. The accuracy of the assay data cannot be verified or assured if the effect of positive feedback, nonlinearities, and interrelationships between cell chemical signaling pathway elements are not understood, modeled, and simulated. Nonlinearities and positive feedback in the cell chemical signaling pathway can produce significant aberrations in assay data collection. Simulating the pathway can reveal potential instability problems that will affect assay results. A simulation, using an electrical analog for the coupled differential equations representing each segment of the pathway, provides an excellent tool for assay validation purposes. With this approach, voltages represent pathway enzyme concentrations and operational amplifier feedback resistance and input resistance values determine pathway gain and rate constants. The understanding provided by pathway modeling and simulation is strategically important in order to establish experimental controls for assay protocol structure, time frames specified between assays, and assay concentration variation limits; to ensure accuracy and reproducibility of results.

Efficient excitation of nonlinear phonons via chirped pulses: Induced structural phase transitions

NASA Astrophysics Data System (ADS)

Itin, A. P.; Katsnelson, M. I.

2018-05-01

Nonlinear phononics play important role in strong laser-solid interactions. We discuss a dynamical protocol for efficient phonon excitation, considering recent inspiring proposals: inducing ferroelectricity in paraelectric perovskites, and inducing structural deformations in cuprates [Subedi et al., Phys. Rev. B 89, 220301(R) (2014), 10.1103/PhysRevB.89.220301; Phys. Rev. B 95, 134113 (2017), 10.1103/PhysRevB.95.134113]. High-frequency phonon modes are driven by midinfrared pulses, and coupled to lower-frequency modes those indirect excitations cause structural deformations. We study in more detail the case of KTaO3 without strain, where it was not possible to excite the needed low-frequency phonon mode by resonant driving of the higher frequency one. Behavior of the system is explained using a reduced model of coupled driven nonlinear oscillators. We find a dynamical mechanism which prevents effective excitation at resonance driving. To induce ferroelectricity, we employ driving with sweeping frequency, realizing so-called capture into resonance. The method can be applied to many other related systems.

A method of chemiluminescence coupled with ultrafiltration for investigating the interaction between ibuprofen and human serum albumin.

PubMed

Xiong, Xunyu; Zhang, Qunzheng; Nan, Yefei; Gu, Xuefan

2013-01-01

In acidic media, ibuprofen substantially enhanced the weak chemiluminescence (CL) produced by sodium sulfite and potassium permanganate. The increased signals were linearly correlated with ibuprofen concentrations ranging from 1.2 × 10(-3) to 4.8 μM, with a detection limit of 4.8 × 10(-4) μM. Two ultrafiltration (UF) membranes were used to construct a unit for trapping 0.15 and 0.75 μM human serum albumin (HSA) and coupled online with the CL system. At low HSA concentrations, the numbers of bound molecules per binding site were calculated to be 0.9 for Sudlow site I and 6.2 for Sudlow site II. The association constants on these binding sites were 5.9 × 10(5) and 3.4 × 10(4) M(-1), respectively. Our CL-UF protocol presents a rapid and sensitive method for studies on drug-protein interaction. Copyright © 2012 John Wiley & Sons, Ltd.

Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry

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

Zhou, Mowei; Wu, Si; Stenoien, David L.

Top-down mass spectrometry is a valuable tool for charactering post-translational modifications on histones for understanding of gene control and expression. In this protocol, we describe a top-down workflow using liquid chromatography coupled to mass spectrometry for fast global profiling of changes in histone proteoforms between a wild-type and a mutant of a fungal species. The proteoforms exhibiting different abundances can be subjected to further targeted studies by other mass spectrometric or biochemical assays. This method can be generally adapted for preliminary screening for changes in histone modifications between samples such as wild-type vs. mutant, and control vs. disease.

Enhancing point of care vigilance using computers.

PubMed

St Jacques, Paul; Rothman, Brian

2011-09-01

Information technology has the potential to provide a tremendous step forward in perioperative patient safety. Through automated delivery of information through fixed and portable computer resources, clinicians may achieve improved situational awareness of the overall operation of the operating room suite and the state of individual patients in various stages of surgical care. Coupling the raw, but integrated, information with decision support and alerting algorithms enables clinicians to achieve high reliability in documentation compliance and response to care protocols. Future studies and outcomes analysis are needed to quantify the degree of benefit of these new components of perioperative information systems. Copyright © 2011 Elsevier Inc. All rights reserved.

DAISY-DAMP: A distributed AI system for the dynamic allocation and management of power

NASA Technical Reports Server (NTRS)

Hall, Steven B.; Ohler, Peter C.

1988-01-01

One of the critical parameters that must be addressed when designing a loosely coupled Distributed AI SYstem (DAISY) has to do with the degree to which authority is centralized or decentralized. The decision to implement the Dynamic Allocation and Management of Power (DAMP) system as a network of cooperating agents mandated this study. The DAISY-DAMP problem is described; the component agents of the system are characterized; and the communication protocols system elucidated. The motivations and advantages in designing the system with authority decentralized is discussed. Progress in the area of Speech Act theory is proposed as playing a role in constructing decentralized systems.

Global Effects of SuperParameterization on Hydro-Thermal Land-Atmosphere Coupling on Multiple Timescales and an Amplification of the Bowen Ratio

NASA Astrophysics Data System (ADS)

Qin, H.; Pritchard, M. S.; Kooperman, G. J.; Parishani, H.

2017-12-01

Conventional General Circulation Models (GCMs) in the Global Land-Atmosphere Coupling Experiment (GLACE) tend to produce overly strong Land-Atmosphere coupling (L-A coupling) strength. We investigate the effects of cloud SuperParameterization (SP) on L-A coupling on timescales longer than the diurnal where it has been previously shown to have a strong effect. Using the Community Atmosphere Model v3.5 (CAM3.5) and its SuperParameterized counterpart SPCAM3.5, we conducted experiments following the GLACE and Atmospheric Model Intercomparison Project (AMIP) protocols. On synoptic-to-subseasonal timescales, SP significantly mutes hydrologic L-A coupling on a global scale, through the atmospheric segment. But on longer seasonal timescales, SP does not exhibit detectable effects on hydrologic L-A coupling. Two regional effects of SP on thermal L-A coupling are also discovered and explored. Over the Arabian Peninsula, SP strikingly reduces thermal L-A coupling due to a control by mean regional rainfall reduction. Over the Southwestern US and Northern Mexico, however, SP remarkably enhances the thermal L-A coupling independent of rainfall or soil moisture. We argue that the cause may be a previously unrecognized effect of SP to amplify the simulated Bowen ratio. Not only does this help reconcile a puzzling local enhancement of thermal L-A coupling over the Southwestern US, but it is also demonstrated to be a robust, global effect of SP over land that is independent of model version and experiment design, and that has important consequences for climate change prediction.

Simultaneous diffuse near-infrared imaging of hemodynamic and oxygenation changes and electroencephalographic measurements of neuronal activity in the human brain

NASA Astrophysics Data System (ADS)

Noponen, Tommi; Kicic, Dubravko; Kotilahti, Kalle; Kajava, Timo; Kahkonen, Seppo; Nissila, Ilkka; Merilainen, Pekka; Katila, Toivo

2005-04-01

Visually evoked hemodynamic responses and potentials were simultaneously measured using a 16-channel optical imaging instrument and a 60-channel electroencephalography instrument during normo-, hypo- and hypercapnia from three subjects. Flashing and pattern-reversed checkerboard stimuli were used. The study protocol included two counterbalanced measurements during both normo- and hypocapnia and normo- and hypercapnia. Hypocapnia was produced by controlled hyperventilation and hypercapnia by breathing carbon dioxide enriched air. Near-infrared imaging was also used to monitor the concentration changes of oxy- and deoxyhaemoglobin due to hypo- and hypercapnia. Hemodynamic responses and evoked potentials were successfully detected for each subject above the visual cortex. The latencies of the hemodynamic responses during hypocapnia were shorter whereas during hypercapnia they were longer when compared to the latencies during normocapnia. Hypocapnia tended to decrease the latencies of visually evoked potentials compared to those during normocapnia while hypercapnia did not show any consistent effect to the potentials. The developed measurement setup and the study protocol provide the opportunity to investigate the neurovascular coupling and the links between the baseline level of blood flow, electrical activity and hemodynamic responses in the human brain.

Use of optokinetics based OKCSIB protocol in restoring mobility in primary progressive MS.

PubMed

Chitambira, Benjamin; McConaghy, Ciara

2017-10-04

The case is of a mid-40s patient who developed progressive muscle weakness and loss of mobility over 6 weeks due to primary progressive multiple sclerosis. 2.5 days before admission, she became bed bound with weakness of 1/5 on the Oxford scale. She normally rested for a couple of days after similar periods of worsening symptoms and then got back on her feet although with worse balance. She was treated with optokinetic chart stimulation and sensory interaction for balance (OKCSIB) protocol. Within 2 days of intervention, she was mobile with a delta frame and supervision of one. By the end of a week, she was independently mobile with her delta frame. It is recommended that instead of just practising function, the OKCSIB protocol be used to regain antigravity extensor control loss of which leads to deteriorating function in neurological conditions. © BMJ Publishing Group Ltd (unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Clock Scan Protocol for Image Analysis: ImageJ Plugins.

PubMed

Dobretsov, Maxim; Petkau, Georg; Hayar, Abdallah; Petkau, Eugen

2017-06-19

The clock scan protocol for image analysis is an efficient tool to quantify the average pixel intensity within, at the border, and outside (background) a closed or segmented convex-shaped region of interest, leading to the generation of an averaged integral radial pixel-intensity profile. This protocol was originally developed in 2006, as a visual basic 6 script, but as such, it had limited distribution. To address this problem and to join similar recent efforts by others, we converted the original clock scan protocol code into two Java-based plugins compatible with NIH-sponsored and freely available image analysis programs like ImageJ or Fiji ImageJ. Furthermore, these plugins have several new functions, further expanding the range of capabilities of the original protocol, such as analysis of multiple regions of interest and image stacks. The latter feature of the program is especially useful in applications in which it is important to determine changes related to time and location. Thus, the clock scan analysis of stacks of biological images may potentially be applied to spreading of Na + or Ca ++ within a single cell, as well as to the analysis of spreading activity (e.g., Ca ++ waves) in populations of synaptically-connected or gap junction-coupled cells. Here, we describe these new clock scan plugins and show some examples of their applications in image analysis.

Optimized protocol for quantitative multiple reaction monitoring-based proteomic analysis of formalin-fixed, paraffin embedded tissues

PubMed Central

Kennedy, Jacob J.; Whiteaker, Jeffrey R.; Schoenherr, Regine M.; Yan, Ping; Allison, Kimberly; Shipley, Melissa; Lerch, Melissa; Hoofnagle, Andrew N.; Baird, Geoffrey Stuart; Paulovich, Amanda G.

2016-01-01

Despite a clinical, economic, and regulatory imperative to develop companion diagnostics, precious few new biomarkers have been successfully translated into clinical use, due in part to inadequate protein assay technologies to support large-scale testing of hundreds of candidate biomarkers in formalin-fixed paraffin embedded (FFPE) tissues. While the feasibility of using targeted, multiple reaction monitoring-mass spectrometry (MRM-MS) for quantitative analyses of FFPE tissues has been demonstrated, protocols have not been systematically optimized for robust quantification across a large number of analytes, nor has the performance of peptide immuno-MRM been evaluated. To address this gap, we used a test battery approach coupled to MRM-MS with the addition of stable isotope labeled standard peptides (targeting 512 analytes) to quantitatively evaluate the performance of three extraction protocols in combination with three trypsin digestion protocols (i.e. 9 processes). A process based on RapiGest buffer extraction and urea-based digestion was identified to enable similar quantitation results from FFPE and frozen tissues. Using the optimized protocols for MRM-based analysis of FFPE tissues, median precision was 11.4% (across 249 analytes). There was excellent correlation between measurements made on matched FFPE and frozen tissues, both for direct MRM analysis (R2 = 0.94) and immuno-MRM (R2 = 0.89). The optimized process enables highly reproducible, multiplex, standardizable, quantitative MRM in archival tissue specimens. PMID:27462933

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

PubMed

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

2018-02-26

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

A pilot randomized controlled trial of the feasibility of a self-directed coping skills intervention for couples facing prostate cancer: Rationale and design

PubMed Central

2012-01-01

Background Although it is known both patients’ and partners’ reactions to a prostate cancer diagnosis include fear, uncertainty, anxiety and depression with patients’ partners’ reactions mutually determining how they cope with and adjust to the illness, few psychosocial interventions target couples. Those that are available tend to be led by highly trained professionals, limiting their accessibility and long-term sustainability. In addition, it is recognised that patients who might benefit from conventional face-to-face psychosocial interventions do not access these, either by preference or because of geographical or mobility barriers. Self-directed interventions can overcome some of these limitations and have been shown to contribute to patient well-being. This study will examine the feasibility of a self-directed, coping skills intervention for couples affected by cancer, called Coping-Together, and begin to explore its potential impact on couples’ illness adjustment. The pilot version of Coping-Together includes a series of four booklets, a DVD, and a relaxation audio CD. Methods/design In this double-blind, two-group, parallel, randomized controlled trial, 70 couples will be recruited within 4 months of a prostate cancer diagnosis through urology private practices and randomized to: 1) Coping-Together or 2) a minimal ethical care condition. Minimal ethical care condition couples will be mailed information booklets available at the Cancer Council New South Wales and a brochure for the Cancer Council Helpline. The primary outcome (anxiety) and additional secondary outcomes (distress, depression, dyadic adjustment, quality of life, illness or caregiving appraisal, self-efficacy, and dyadic and individual coping) will be assessed at baseline (before receiving study material) and 2 months post-baseline. Intention-to-treat and per protocol analysis will be conducted. Discussion As partners’ distress rates exceed not only population norms, but also those reported by patients themselves, it is imperative that coping skills interventions target the couple as a unit and enhance both partners’ ability to overcome cancer challenges. This pilot study will examine the feasibility and potential efficacy of Coping-Together in optimising couples’ illness adjustment. This is one of the first feasibility studies to test this innovative coping intervention, which in turn will contribute to the larger literature advocating for psychosocial care of couples affected by prostate cancer. Trial registration Australian New Zealand Clinical Trials Registry ACTRN12611000438954 PMID:23013404

Mathematical Model Formulation And Validation Of Water And Solute Transport In Whole Hamster Pancreatic Islets

PubMed Central

Benson, Charles T.; Critser, John K.

2014-01-01

Optimization of cryopreservation protocols for cells and tissues requires accurate models of heat and mass transport. Model selection often depends on the configuration of the tissue. Here, a mathematical and conceptual model of water and solute transport for whole hamster pancreatic islets has been developed and experimentally validated incorporating fundamental biophysical data from previous studies on individual hamster islet cells while retaining whole-islet structural information. It describes coupled transport of water and solutes through the islet by three methods: intracellularly, intercellularly, and in combination. In particular we use domain decomposition techniques to couple a transmembrane flux model with an interstitial mass transfer model. The only significant undetermined variable is the cellular surface area which is in contact with the intercellularly transported solutes, Ais. The model was validated and Ais determined using a 3 × 3 factorial experimental design blocked for experimental day. Whole islet physical experiments were compared with model predictions at three temperatures, three perfusing solutions, and three islet size groups. A mean of 4.4 islets were compared at each of the 27 experimental conditions and found to correlate with a coefficient of determination of 0.87 ± 0.06 (mean ± S.D.). Only the treatment variable of perfusing solution was found to be significant (p < 0.05). We have devised a model that retains much of the intrinsic geometric configuration of the system, and thus fewer laboratory experiments are needed to determine model parameters and thus to develop new optimized cryopreservation protocols. Additionally, extensions to ovarian follicles and other concentric tissue structures may be made. PMID:24950195

Multi-Element Bioimaging of Arabidopsis thaliana Roots.

PubMed

Persson, Daniel Pergament; Chen, Anle; Aarts, Mark G M; Salt, David E; Schjoerring, Jan K; Husted, Søren

2016-10-01

Better understanding of root function is central for the development of plants with more efficient nutrient uptake and translocation. We here present a method for multielement bioimaging at the cellular level in roots of the genetic model system Arabidopsis (Arabidopsis thaliana). Using conventional protocols for microscopy, we observed that diffusible ions such as potassium and sodium were lost during sample dehydration. Thus, we developed a protocol that preserves ions in their native, cellular environment. Briefly, fresh roots are encapsulated in paraffin, cryo-sectioned, and freeze dried. Samples are finally analyzed by laser ablation-inductively coupled plasma-mass spectrometry, utilizing a specially designed internal standard procedure. The method can be further developed to maintain the native composition of proteins, enzymes, RNA, and DNA, making it attractive in combination with other omics techniques. To demonstrate the potential of the method, we analyzed a mutant of Arabidopsis unable to synthesize the metal chelator nicotianamine. The mutant accumulated substantially more zinc and manganese than the wild type in the tissues surrounding the vascular cylinder. For iron, the images looked completely different, with iron bound mainly in the epidermis of the wild-type plants but confined to the cortical cell walls of the mutant. The method offers the power of inductively coupled plasma-mass spectrometry to be fully employed, thereby providing a basis for detailed studies of ion transport in roots. Being applicable to Arabidopsis, the molecular and genetic approaches available in this system can now be fully exploited in order to gain a better mechanistic understanding of these processes. © 2016 American Society of Plant Biologists. All Rights Reserved.

Multi-Element Bioimaging of Arabidopsis thaliana Roots1[OPEN

PubMed Central

Salt, David E.

2016-01-01

Better understanding of root function is central for the development of plants with more efficient nutrient uptake and translocation. We here present a method for multielement bioimaging at the cellular level in roots of the genetic model system Arabidopsis (Arabidopsis thaliana). Using conventional protocols for microscopy, we observed that diffusible ions such as potassium and sodium were lost during sample dehydration. Thus, we developed a protocol that preserves ions in their native, cellular environment. Briefly, fresh roots are encapsulated in paraffin, cryo-sectioned, and freeze dried. Samples are finally analyzed by laser ablation-inductively coupled plasma-mass spectrometry, utilizing a specially designed internal standard procedure. The method can be further developed to maintain the native composition of proteins, enzymes, RNA, and DNA, making it attractive in combination with other omics techniques. To demonstrate the potential of the method, we analyzed a mutant of Arabidopsis unable to synthesize the metal chelator nicotianamine. The mutant accumulated substantially more zinc and manganese than the wild type in the tissues surrounding the vascular cylinder. For iron, the images looked completely different, with iron bound mainly in the epidermis of the wild-type plants but confined to the cortical cell walls of the mutant. The method offers the power of inductively coupled plasma-mass spectrometry to be fully employed, thereby providing a basis for detailed studies of ion transport in roots. Being applicable to Arabidopsis, the molecular and genetic approaches available in this system can now be fully exploited in order to gain a better mechanistic understanding of these processes. PMID:27566167

Beyond the Compositional Threshold of Nanoparticle-Based Materials.

PubMed

Portehault, David; Delacroix, Simon; Gouget, Guillaume; Grosjean, Rémi; Chan-Chang, Tsou-Hsi-Camille

2018-04-17

The design of inorganic nanoparticles relies strongly on the knowledge from solid-state chemistry not only for characterization techniques, but also and primarily for choosing the systems that will yield the desired properties. The range of inorganic solids reported and studied as nanoparticles is however strikingly narrow when compared to the solid-state chemistry portfolio of bulk materials. Efforts to enlarge the collection of inorganic particles are becoming increasingly important for three reasons. First, they can yield materials more performing than current ones for a range of fields including biomedicine, optics, catalysis, and energy. Second, looking outside the box of common compositions is a way to target original properties or to discover genuinely new behaviors. The third reason lies in the path followed to reach these novel nano-objects: exploration and setup of new synthetic approaches. Indeed, willingness to access original nanoparticles faces a synthetic challenge: how to reach nanoparticles of solids that originally belong to the realm of solid-state chemistry and its typical protocols at high temperature? To answer this question, alternative reaction pathways must be sought, which may in turn provide tracks for new, untargeted materials. The corresponding strategies require limiting particle growth by confinement at high temperatures or by decreasing the synthesis temperature. Both approaches, especially the latter, provide a nice playground to discover metastable solids never reported before. The aim of this Account is to raise attention to the topic of the design of new inorganic nanoparticles. To do so, we take the perspective of our own work in the field, by first describing synthetic challenges and how they are addressed by current protocols. We then use our achievements to highlight the possibilities offered by new nanomaterials and to introduce synthetic approaches that are not in the focus of recent literature but hold, in our opinion, great promise. We will span methods of low temperature "chimie douce" aqueous synthesis coupled to microwave heating, sol-gel chemistry and processing coupled to solid state reactions, and then molten salt synthesis. These protocols pave the way to metastable low valence oxyhydroxides, vanadates, perovskite oxides, boron carbon nitrides, and metal borides, all obtained at the nanoscale with structural and morphological features differing from "usual" nanomaterials. These nano-objects show original properties, from sensing, thermoelectricity, charge and spin transports, photoluminescence, and catalysis, which require advanced characterization of surface states. We then identify future trends of synthetic methodologies that will merit further attention in this burgeoning field, by emphasizing the importance of unveiling reaction mechanisms and coupling experiments with modeling.

Characterization of addressability by simultaneous randomized benchmarking.

PubMed

Gambetta, Jay M; Córcoles, A D; Merkel, S T; Johnson, B R; Smolin, John A; Chow, Jerry M; Ryan, Colm A; Rigetti, Chad; Poletto, S; Ohki, Thomas A; Ketchen, Mark B; Steffen, M

2012-12-14

The control and handling of errors arising from cross talk and unwanted interactions in multiqubit systems is an important issue in quantum information processing architectures. We introduce a benchmarking protocol that provides information about the amount of addressability present in the system and implement it on coupled superconducting qubits. The protocol consists of randomized benchmarking experiments run both individually and simultaneously on pairs of qubits. A relevant figure of merit for the addressability is then related to the differences in the measured average gate fidelities in the two experiments. We present results from two similar samples with differing cross talk and unwanted qubit-qubit interactions. The results agree with predictions based on simple models of the classical cross talk and Stark shifts.

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

PubMed

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

2003-04-01

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

Quantum sensing of the phase-space-displacement parameters using a single trapped ion

NASA Astrophysics Data System (ADS)

Ivanov, Peter A.; Vitanov, Nikolay V.

2018-03-01

We introduce a quantum sensing protocol for detecting the parameters characterizing the phase-space displacement by using a single trapped ion as a quantum probe. We show that, thanks to the laser-induced coupling between the ion's internal states and the motion mode, the estimation of the two conjugated parameters describing the displacement can be efficiently performed by a set of measurements of the atomic state populations. Furthermore, we introduce a three-parameter protocol capable of detecting the magnitude, the transverse direction, and the phase of the displacement. We characterize the uncertainty of the two- and three-parameter problems in terms of the Fisher information and show that state projective measurement saturates the fundamental quantum Cramér-Rao bound.

Investigating the Effects of the Interaction Intensity in a Weak Measurement.

PubMed

Piacentini, Fabrizio; Avella, Alessio; Gramegna, Marco; Lussana, Rudi; Villa, Federica; Tosi, Alberto; Brida, Giorgio; Degiovanni, Ivo Pietro; Genovese, Marco

2018-05-03

Measurements are crucial in quantum mechanics, for fundamental research as well as for applicative fields like quantum metrology, quantum-enhanced measurements and other quantum technologies. In the recent years, weak-interaction-based protocols like Weak Measurements and Protective Measurements have been experimentally realized, showing peculiar features leading to surprising advantages in several different applications. In this work we analyze the validity range for such measurement protocols, that is, how the interaction strength affects the weak value extraction, by measuring different polarization weak values on heralded single photons. We show that, even in the weak interaction regime, the coupling intensity limits the range of weak values achievable, setting a threshold on the signal amplification effect exploited in many weak measurement based experiments.

Calibration and energy measurement of optically levitated nanoparticle sensors

NASA Astrophysics Data System (ADS)

Hebestreit, Erik; Frimmer, Martin; Reimann, René; Dellago, Christoph; Ricci, Francesco; Novotny, Lukas

2018-03-01

Optically levitated nanoparticles offer enormous potential for precision sensing. However, as for any other metrology device, the absolute measurement performance of a levitated-particle sensor is limited by the accuracy of the calibration relating the measured signal to an absolute displacement of the particle. Here, we suggest and demonstrate calibration protocols for levitated-nanoparticle sensors. Our calibration procedures include the treatment of anharmonicities in the trapping potential, as well as a protocol using a harmonic driving force, which is applicable if the sensor is coupled to a heat bath of unknown temperature. Finally, using the calibration, we determine the center-of-mass temperature of an optically levitated particle in thermal equilibrium from its motion and discuss the optimal measurement time required to determine the said temperature.

Enantioselective Synthesis of All-Carbon Quaternary Centers Structurally Related to Amaryllidaceae Alkaloids.

PubMed

Mikušek, Jiří; Jansa, Petr; Jagtap, Pratap R; Vašíček, Tomáš; Císařová, Ivana; Matoušová, Eliška

2018-05-18

Enantioselective synthesis of all-carbon quaternary centers remains a considerable challenge for synthetic organic chemists. Here, we report a two-step protocol to synthesize such centers including tandem cyclization/Suzuki cross-coupling followed by halocarbocyclization. During this process, two rings, three new C-C bonds and a stereochemically defined all-carbon quaternary center are formed. The absolute configuration of this center is controlled by the stereochemistry of the adjacent stereocenter, which derives from an appropriate enantioenriched starting material. Using this method, we synthesized polycyclic compounds structurally similar to Amaryllidaceae alkaloids in high enantiomeric excesses. Because these products resemble naturally occurring compounds, our protocol can be used to synthesize various potentially bioactive compounds. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Asymmetries in the spectral density of an interaction-quenched Luttinger liquid

NASA Astrophysics Data System (ADS)

Calzona, A.; Gambetta, F. M.; Carrega, M.; Cavaliere, F.; Sassetti, M.

2018-03-01

The spectral density of an interaction-quenched one-dimensional system is investigated. Both direct and inverse quench protocols are considered and it is found that the former leads to stronger effects on the spectral density with respect to the latter. Such asymmetry is directly reflected on transport properties of the system, namely the charge and energy current flowing to the system from a tunnel coupled biased probe. In particular, the injection of particles from the probe to the right-moving channel of the system is considered. The resulting fractionalization phenomena are strongly affected by the quench protocol and display asymmetries in the case of direct and inverse quench. Transport properties therefore emerge as natural probes for the observation of this quench-induced behavior.

Dried Blood Spots - Preparing and Processing for Use in Immunoassays and in Molecular Techniques

PubMed Central

Grüner, Nico; Stambouli, Oumaima; Ross, R. Stefan

2015-01-01

The idea of collecting blood on a paper card and subsequently using the dried blood spots (DBS) for diagnostic purposes originated a century ago. Since then, DBS testing for decades has remained predominantly focused on the diagnosis of infectious diseases especially in resource-limited settings or the systematic screening of newborns for inherited metabolic disorders and only recently have a variety of new and innovative DBS applications begun to emerge. For many years, pre-analytical variables were only inappropriately considered in the field of DBS testing and even today, with the exception of newborn screening, the entire pre-analytical phase, which comprises the preparation and processing of DBS for their final analysis has not been standardized. Given this background, a comprehensive step-by-step protocol, which covers al the essential phases, is proposed, i.e., collection of blood; preparation of blood spots; drying of blood spots; storage and transportation of DBS; elution of DBS, and finally analyses of DBS eluates. The effectiveness of this protocol was first evaluated with 1,762 coupled serum/DBS pairs for detecting markers of hepatitis B virus, hepatitis C virus, and human immunodeficiency virus infections on an automated analytical platform. In a second step, the protocol was utilized during a pilot study, which was conducted on active drug users in the German cities of Berlin and Essen. PMID:25867233

Synchronization of hybrid coupled reaction-diffusion neural networks with time delays via generalized intermittent control with spacial sampled-data.

PubMed

Lu, Binglong; Jiang, Haijun; Hu, Cheng; Abdurahman, Abdujelil

2018-05-04

The exponential synchronization of hybrid coupled reaction-diffusion neural networks with time delays is discussed in this article. At first, a generalized intermittent control with spacial sampled-data is introduced, which is intermittent in time and data sampling in space. This type of control strategy not only can unify the traditional periodic intermittent control and the aperiodic case, but also can lower the update rate of the controller in both temporal and spatial domains. Next, based on the designed control protocol and the Lyapunov-Krasovskii functional approach, some novel and readily verified criteria are established to guarantee the exponential synchronization of the considered networks. These criteria depend on the diffusion coefficients, coupled strengths, time delays as well as control parameters. Finally, the effectiveness of the proposed control strategy is shown by a numerical example. Copyright © 2018 Elsevier Ltd. All rights reserved.

Optomechanical proposal for monitoring microtubule mechanical vibrations

NASA Astrophysics Data System (ADS)

Barzanjeh, Sh.; Salari, V.; Tuszynski, J. A.; Cifra, M.; Simon, C.

2017-07-01

Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs.

Interaction of charge carriers with lattice and molecular phonons in crystalline pentacene

NASA Astrophysics Data System (ADS)

Girlando, Alberto; Grisanti, Luca; Masino, Matteo; Brillante, Aldo; Della Valle, Raffaele G.; Venuti, Elisabetta

2011-08-01

The computational protocol we have developed for the calculation of local (Holstein) and non-local (Peierls) carrier-phonon coupling in molecular organic semiconductors is applied to both the low temperature and high temperature bulk crystalline phases of pentacene. The electronic structure is calculated by the semimpirical INDO/S (Intermediate Neglect of Differential Overlap with Spectroscopic parametrization) method. In the phonon description, the rigid molecule approximation is removed, allowing mixing of low-frequency intra-molecular modes with inter-molecular (lattice) phonons. A clear distinction remains between the low-frequency phonons, which essentially modulate the transfer integral from a molecule to another (Peierls coupling), and the high-frequency intra-molecular phonons, which modulate the on-site energy (Holstein coupling). The results of calculation agree well with the values extracted from experiment. The comparison with similar calculations made for rubrene allows us to discuss the implications for the current models of mobility.

Respiratory flows during early childhood: Computational models to examine therapeutic aerosols in the developing airways

NASA Astrophysics Data System (ADS)

Tenenbaum-Katan, Janna; Hofemeier, Philipp; Sznitman, Josué; Janna Tenenbaum-Katan Team

2015-11-01

Inhalation therapy is the cornerstone of early-childhood respiratory treatments, as well as a rising potential for systemic drug delivery and pulmonary vaccination. As such, indispensable understanding of respiratory flow phenomena, coupled with particle transport at the deep regions of children's lungs is necessary to attain efficient targeting of aerosol therapy. However, fundamental research of pulmonary transport is overwhelmingly focused on adults. In our study, we have developed an anatomically-inspired computational model of representing pulmonary acinar regions at several age points during a child's development. Our numerical simulations examine respiratory flows and particle deposition maps within the acinar model, accounting for varying age dependant anatomical considerations and ventilation patterns. Resulting deposition maps of aerosols alter with age, such findings might suggest that medication protocols of inhalation therapy in young children should be considered to be accordingly amended with the child's development. Additionally to understanding basic scientific concepts of age effects on aerosol deposition, our research can potentially contribute practical guidelines to therapy protocols, and its' necessary modifications with age. We acknowledge the support of the ISF and the Israeli ministry of Science.

Phonon Networks with Silicon-Vacancy Centers in Diamond Waveguides

NASA Astrophysics Data System (ADS)

Lemonde, M.-A.; Meesala, S.; Sipahigil, A.; Schuetz, M. J. A.; Lukin, M. D.; Loncar, M.; Rabl, P.

2018-05-01

We propose and analyze a novel realization of a solid-state quantum network, where separated silicon-vacancy centers are coupled via the phonon modes of a quasi-one-dimensional diamond waveguide. In our approach, quantum states encoded in long-lived electronic spin states can be converted into propagating phonon wave packets and be reabsorbed efficiently by a distant defect center. Our analysis shows that under realistic conditions, this approach enables the implementation of high-fidelity, scalable quantum communication protocols within chip-scale spin-qubit networks. Apart from quantum information processing, this setup constitutes a novel waveguide QED platform, where strong-coupling effects between solid-state defects and individual propagating phonons can be explored at the quantum level.

Imaging of Selenium by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) in 2-D Electrophoresis Gels and Biological Tissues.

PubMed

Cruz, Elisa Castañeda Santa; Susanne Becker, J; Sabine Becker, J; Sussulini, Alessandra

2018-01-01

Selenium and selenoproteins are important components of living organisms that play a role in different biological processes. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is a powerful analytical technique that has been employed to obtain distribution maps of selenium in biological tissues in a direct manner, as well as in selenoproteins, previously separated by their molecular masses and isoelectric points using two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). In this chapter, we present the protocols to perform LA-ICP-MS imaging experiments, allowing the distribution visualization and determination of selenium and/or selenoproteins in biological systems.

Synthesis of aryl thioethers through the N-chlorosuccinimide-promoted cross-coupling reaction of thiols with Grignard reagents.

PubMed

Cheng, Jun-Hao; Ramesh, Chintakunta; Kao, Hsin-Lun; Wang, Yu-Jen; Chan, Chien-Ching; Lee, Chin-Fa

2012-11-16

A convenient one-pot approach for the synthesis of aryl sulfides through the coupling of thiols with Grignard reagents in the presence of N-chlorosuccinimide is described. The sulfenylchlorides were formed when thiols were treated with N-chlorosuccinimide, and the resulting sulfenylchlorides were then directly reacted with Grignard reagents to provide aryl sulfides in good to excellent yields under mild reaction conditions. Functional groups including ester, fluoro, and chloro are tolerated by the reaction conditions employed. It is important to note that this method has a short reaction time (30 min in total) and represents an alternative approach for the synthesis of aryl sulfides over the existing protocols.

Phonon Networks with Silicon-Vacancy Centers in Diamond Waveguides.

PubMed

Lemonde, M-A; Meesala, S; Sipahigil, A; Schuetz, M J A; Lukin, M D; Loncar, M; Rabl, P

2018-05-25

We propose and analyze a novel realization of a solid-state quantum network, where separated silicon-vacancy centers are coupled via the phonon modes of a quasi-one-dimensional diamond waveguide. In our approach, quantum states encoded in long-lived electronic spin states can be converted into propagating phonon wave packets and be reabsorbed efficiently by a distant defect center. Our analysis shows that under realistic conditions, this approach enables the implementation of high-fidelity, scalable quantum communication protocols within chip-scale spin-qubit networks. Apart from quantum information processing, this setup constitutes a novel waveguide QED platform, where strong-coupling effects between solid-state defects and individual propagating phonons can be explored at the quantum level.

Development of analytical methods for multiplex bio-assay with inductively coupled plasma mass spectrometry.

PubMed

Ornatsky, Olga I; Kinach, Robert; Bandura, Dmitry R; Lou, Xudong; Tanner, Scott D; Baranov, Vladimir I; Nitz, Mark; Winnik, Mitchell A

2008-01-01

Advances in the development of highly multiplexed bio-analytical assays with inductively coupled plasma mass spectrometry (ICP-MS) detection are discussed. Use of novel reagents specifically designed for immunological methods utilizing elemental analysis is presented. The major steps of method development, including selection of elements for tags, validation of tagged reagents, and examples of multiplexed assays, are considered in detail. The paper further describes experimental protocols for elemental tagging of antibodies, immunostaining of live and fixed human leukemia cells, and preparation of samples for ICP-MS analysis. Quantitative analysis of surface antigens on model cell lines using a cocktail of seven lanthanide labeled antibodies demonstrated high specificity and concordance with conventional immunophenotyping.

Camphyl-based α-diimine palladium complexes: highly efficient precatalysts for direct arylation of thiazoles in open-air.

PubMed

Chen, Fu-Min; Lu, Dong-Dong; Hu, Li-Qun; Huang, Ju; Liu, Feng-Shou

2017-07-21

Based on the strategy of the development of phosphine-free palladium-catalyzed direct C-H arylation, a series of camphyl-based α-diimine palladium complexes bearing sterically bulky substituents were synthesized and characterized. The palladium complexes were applied for the cross-coupling of thiazole derivatives with aryl bromides. The effect of the sterically bulky substituent on the N-aryl moiety as well as the reaction conditions was screened. Under the optimal protocols, a wide range of aryl bromides can be smoothly coupled with thiazoles in good to excellent yields in the presence of a low palladium loading of 0.2 mol% under open-air conditions.

Pure spin current manipulation in antiferromagnetically exchange coupled heterostructures

NASA Astrophysics Data System (ADS)

Avilés-Félix, L.; Butera, A.; González-Chávez, D. E.; Sommer, R. L.; Gómez, J. E.

2018-03-01

We present a model to describe the spin currents generated by ferromagnet/spacer/ferromagnet exchange coupled trilayer systems and heavy metal layers with strong spin-orbit coupling. By exploiting the magnitude of the exchange coupling (oscillatory RKKY-like coupling) and the spin-flop transition in the magnetization process, it has been possible to produce spin currents polarized in arbitrary directions. The spin-flop transition of the trilayer system originates pure spin currents whose polarization vector depends on the exchange field and the magnetization equilibrium angles. We also discuss a protocol to control the polarization sign of the pure spin current injected into the metallic layer by changing the initial conditions of magnetization of the ferromagnetic layers previously to the spin pumping and inverse spin Hall effect experiments. The small differences in the ferromagnetic layers lead to a change in the magnetization vector rotation that permits the control of the sign of the induced voltage components due to the inverse spin Hall effect. Our results can lead to important advances in hybrid spintronic devices with new functionalities, particularly, the ability to control microscopic parameters such as the polarization direction and the sign of the pure spin current through the variation of macroscopic parameters, such as the external magnetic field or the thickness of the spacer in antiferromagnetic exchange coupled systems.

Comparison of the Liaison® Calprotectin kit with a well established point of care test (Quantum Blue - Bühlmann-Alere®) in terms of analytical performances and ability to detect relapses amongst a Crohn population in follow-up.

PubMed

Delefortrie, Quentin; Schatt, Patricia; Grimmelprez, Alexandre; Gohy, Patrick; Deltour, Didier; Collard, Geneviève; Vankerkhoven, Patrick

2016-02-01

Although colonoscopy associated with histopathological sampling remains the gold standard in the diagnostic and follow-up of inflammatory bowel disease (IBD), calprotectin is becoming an essential biomarker in gastroenterology. The aim of this work is to compare a newly developed kit (Liaison® Calprotectin - Diasorin®) and its two distinct extraction protocols (weighing and extraction device protocol) with a well established point of care test (Quantum Blue® - Bühlmann-Alere®) in terms of analytical performances and ability to detect relapses amongst a Crohn's population in follow-up. Stool specimens were collected over a six month period and were composed of control and Crohn's patients. Amongst the Crohn's population disease activity (active vs quiescent) was evaluated by gastroenterologists. A significant difference was found between all three procedures in terms of calprotectin measurements (weighing protocol=30.3μg/g (median); stool extraction device protocol=36.9μg/g (median); Quantum Blue® (median)=63; Friedman test, P value=0.05). However, a good correlation was found between both extraction methods coupled with the Liaison® analyzer and between the Quantum Blue® (weighing protocol/extraction device protocol Rs=0.844, P=0.01; Quantum Blue®/extraction device protocol Rs=0.708, P=0.01; Quantum Blue®/weighing protocol, Rs=0.808, P=0.01). Finally, optimal cut-offs (and associated negative predictive values - NPV) for detecting relapses were in accordance with above results (Quantum Blue® 183.5μg/g and NPV of 100%>extraction device protocol+Liaison® analyzer 124.5μg/g and NPV of 93.5%>weighing protocol+Liaison® analyzer 106.5μg/g and NPV of 95%). Although all three methods correlated well and had relatively good NPV in terms of detecting relapses amongst a Crohn's population in follow-up, the lack of any international standard is the origin of different optimal cut-offs between the three procedures. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Enantioselective Decarboxylative Arylation of α-Amino Acids via the Merger of Photoredox and Nickel Catalysis.

PubMed

Zuo, Zhiwei; Cong, Huan; Li, Wei; Choi, Junwon; Fu, Gregory C; MacMillan, David W C

2016-02-17

An asymmetric decarboxylative Csp(3)-Csp(2) cross-coupling has been achieved via the synergistic merger of photoredox and nickel catalysis. This mild, operationally simple protocol transforms a wide variety of naturally abundant α-amino acids and readily available aryl halides into valuable chiral benzylic amines in high enantiomeric excess, thereby producing motifs found in pharmacologically active agents.

Coupled Physical and Digital Cadaver Dissection Followed by a Visual Test Protocol Provides Insights into the Nature of Anatomical Knowledge and Its Evaluation

ERIC Educational Resources Information Center

Hisley, Kenneth C.; Anderson, Larry D.; Smith, Stacy E.; Kavic, Stephen M.; Tracy, J. Kathleen

2008-01-01

This research effort compared and contrasted two conceptually different methods for the exploration of human anatomy in the first-year dissection laboratory by accomplished students: "physical" dissection using an embalmed cadaver and "digital" dissection using three-dimensional volume modeling of whole-body CT and MRI image sets acquired using…

Selective sp3 C-H alkylation via polarity-match-based cross-coupling.

PubMed

Le, Chip; Liang, Yufan; Evans, Ryan W; Li, Ximing; MacMillan, David W C

2017-07-06

The functionalization of carbon-hydrogen (C-H) bonds is one of the most attractive strategies for molecular construction in organic chemistry. The hydrogen atom is considered to be an ideal coupling handle, owing to its relative abundance in organic molecules and its availability for functionalization at almost any stage in a synthetic sequence. Although many C-H functionalization reactions involve C(sp 3 )-C(sp 2 ) coupling, there is a growing demand for C-H alkylation reactions, wherein sp 3 C-H bonds are replaced with sp 3 C-alkyl groups. Here we describe a polarity-match-based selective sp 3 C-H alkylation via the combination of photoredox, nickel and hydrogen-atom transfer catalysis. This methodology simultaneously uses three catalytic cycles to achieve hydridic C-H bond abstraction (enabled by polarity matching), alkyl halide oxidative addition, and reductive elimination to enable alkyl-alkyl fragment coupling. The sp 3 C-H alkylation is highly selective for the α-C-H of amines, ethers and sulphides, which are commonly found in pharmaceutically relevant architectures. This cross-coupling protocol should enable broad synthetic applications in de novo synthesis and late-stage functionalization chemistry.

Selective sp3 C–H alkylation via polarity-match-based cross-coupling

PubMed Central

Le, Chip; Liang, Yufan; Evans, Ryan W.; Li, Ximing; MacMillan, David W. C.

2017-01-01

The functionalization of carbon–hydrogen (C–H) bonds is one of the most attractive strategies for molecular construction in organic chemistry. The hydrogen atom is considered to be an ideal coupling handle, owing to its relative abundance in organic molecules and its availability for functionalization at almost any stage in a synthetic sequence1. Although many C–H functionalization reactions involve C(sp3)–C(sp2) coupling, there is a growing demand for C–H alkylation reactions, wherein sp3 C–H bonds are replaced with sp3 C–alkyl groups. Here we describe a polarity-match-based selective sp3 C–H alkylation via the combination of photoredox, nickel and hydrogen-atom transfer catalysis. This methodology simultaneously uses three catalytic cycles to achieve hydridic C–H bond abstraction (enabled by polarity matching), alkyl halide oxidative addition, and reductive elimination to enable alkyl–alkyl fragment coupling. The sp3 C–H alkylation is highly selective for the α-C–H of amines, ethers and sulphides, which are commonly found in pharmaceutically relevant architectures. This cross-coupling protocol should enable broad synthetic applications in de novo synthesis and late-stage functionalization chemistry. PMID:28636596

Selective sp3 C-H alkylation via polarity-match-based cross-coupling

NASA Astrophysics Data System (ADS)

Le, Chip; Liang, Yufan; Evans, Ryan W.; Li, Ximing; MacMillan, David W. C.

2017-07-01

The functionalization of carbon-hydrogen (C-H) bonds is one of the most attractive strategies for molecular construction in organic chemistry. The hydrogen atom is considered to be an ideal coupling handle, owing to its relative abundance in organic molecules and its availability for functionalization at almost any stage in a synthetic sequence. Although many C-H functionalization reactions involve C(sp3)-C(sp2) coupling, there is a growing demand for C-H alkylation reactions, wherein sp3 C-H bonds are replaced with sp3 C-alkyl groups. Here we describe a polarity-match-based selective sp3 C-H alkylation via the combination of photoredox, nickel and hydrogen-atom transfer catalysis. This methodology simultaneously uses three catalytic cycles to achieve hydridic C-H bond abstraction (enabled by polarity matching), alkyl halide oxidative addition, and reductive elimination to enable alkyl-alkyl fragment coupling. The sp3 C-H alkylation is highly selective for the α-C-H of amines, ethers and sulphides, which are commonly found in pharmaceutically relevant architectures. This cross-coupling protocol should enable broad synthetic applications in de novo synthesis and late-stage functionalization chemistry.

Estimating national crop yield potential and the relevance of weather data sources

NASA Astrophysics Data System (ADS)

Van Wart, Justin

2011-12-01

To determine where, when, and how to increase yields, researchers often analyze the yield gap (Yg), the difference between actual current farm yields and crop yield potential. Crop yield potential (Yp) is the yield of a crop cultivar grown under specific management limited only by temperature and solar radiation and also by precipitation for water limited yield potential (Yw). Yp and Yw are critical components of Yg estimations, but are very difficult to quantify, especially at larger scales because management data and especially daily weather data are scarce. A protocol was developed to estimate Yp and Yw at national scales using site-specific weather, soils and management data. Protocol procedures and inputs were evaluated to determine how to improve accuracy of Yp, Yw and Yg estimates. The protocol was also used to evaluate raw, site-specific and gridded weather database sources for use in simulations of Yp or Yw. The protocol was applied to estimate crop Yp in US irrigated maize and Chinese irrigated rice and Yw in US rainfed maize and German rainfed wheat. These crops and countries account for >20% of global cereal production. The results have significant implications for past and future studies of Yp, Yw and Yg. Accuracy of national long-term average Yp and Yw estimates was significantly improved if (i) > 7 years of simulations were performed for irrigated and > 15 years for rainfed sites, (ii) > 40% of nationally harvested area was within 100 km of all simulation sites, (iii) observed weather data coupled with satellite derived solar radiation data were used in simulations, and (iv) planting and harvesting dates were specified within +/- 7 days of farmers actual practices. These are much higher standards than have been applied in national estimates of Yp and Yw and this protocol is a substantial step in making such estimates more transparent, robust, and straightforward. Finally, this protocol may be a useful tool for understanding yield trends and directing research and development efforts aimed at providing for a secure and stable future food supply.

Effectiveness of the 'Home-but not Alone' mobile health application educational programme on parental outcomes: a randomized controlled trial, study protocol.

PubMed

Shorey, Shefaly; Ng, Yvonne Peng Mei; Danbjørg, Dorthe Boe; Dennis, Cindy-Lee; Morelius, Evalotte

2017-01-01

The aim of this study was to describe a study protocol that evaluates the effectiveness of the 'Home-but not Alone' educational programme delivered via a mobile health application in improving parenting outcomes. The development in mobile-based technology gives us the opportunity to develop an accessible educational programme that can be potentially beneficial to new parents. However, there is a scarcity of theory-based educational programmes that have incorporated technology such as a mobile health application in the early postpartum period. A randomized controlled trial with a two-group pre-test and post-test design. The data will be collected from 118 couples. Eligible parents will be randomly allocated to either a control group (receiving routine care) or an intervention group (routine care plus access to the 'Home-but not Alone' mobile health application. Outcome measures comprise of parenting self-efficacy, social support, parenting satisfaction and postnatal depression. Data will be collected at the baseline (on the day of discharge) and at four weeks postpartum. This will be an empirical study that evaluates a theory-based educational programme delivered via an innovative mobile health application on parental outcomes. Results from this study will enhance parenting self-efficacy, social support and parenting satisfaction, which may then reduce parental risks of postnatal depression. © 2016 John Wiley & Sons Ltd.

Still a Hard-to-Reach Population? Using Social Media to Recruit Latino Gay Couples for an HIV Intervention Adaptation Study

PubMed Central

Wu, Elwin; Shultz, Andrew Z; Capote, Jonathan; López Rios, Javier; Sandfort, Theo; Manusov, Justin; Ovejero, Hugo; Carballo-Dieguez, Alex; Chavez Baray, Silvia; Moya, Eva; López Matos, Jonathan; DelaCruz, Juan J; Remien, Robert H; Rhodes, Scott D

2014-01-01

Background Online social networking use has increased rapidly among African American and Latino men who have sex with men (MSM), making it important to understand how these technologies can be used to reach, retain, and maintain individuals in care and promote health wellness. In particular, the Internet is increasingly recognized as a platform for health communication and education. However, little is known about how primarily Spanish-speaking populations use and engage with each other through social media platforms. Objective We aimed to recruit eligible couples for a study to adapt “Connect ‘n Unite” (an HIV prevention intervention initially created for black gay couples) for Spanish-speaking Latino gay couples living in New York City. Methods In order to successfully design and implement an effective social media recruitment campaign to reach Spanish-speaking Latino gay couples for our ongoing “Latinos en Pareja” study, our community stakeholders and research team used McGuire’s communication/persuasion matrix. The matrix guided our research, specifically each marketing “channel”, targeted “message”, and target population or “receiver”. We developed a social media recruitment protocol and trained our research staff and stakeholders to conduct social media recruitment. Results As a result, in just 1 month, we recruited all of our subjects (N=14 couples, that is, N=28 participants) and reached more than 35,658 participants through different channels. One of the major successes of our social media recruitment campaign was to build a strong stakeholder base that became involved early on in all aspects of the research process—from pilot study writing and development to recruitment and retention. In addition, the variety of “messages” used across different social media platforms (including Facebook, the “Latinos en Pareja” study website, Craigslist, and various smartphone applications such as Grindr, SCRUFF, and Jack’d) helped recruit Latino gay couples. We also relied on a wide range of community-based organizations across New York City to promote the study and build in the social media components. Conclusions Our findings highlight the importance of incorporating communication technologies into the recruitment and engagement of participants in HIV interventions. Particularly, the success of our social media recruitment strategy with Spanish-speaking Latino MSM shows that this population is not particularly “hard to reach”, as it is often characterized within public health literature. PMID:24763130

Rapid and simultaneous detection of Mycobacterium tuberculosis complex and Beijing/W genotype in sputum by an optimized DNA extraction protocol and a novel multiplex real-time PCR.

PubMed

Leung, Eric T Y; Zheng, L; Wong, Rity Y K; Chan, Edward W C; Au, T K; Chan, Raphael C Y; Lui, Grace; Lee, Nelson; Ip, Margaret

2011-07-01

Rapid diagnosis and genotyping of Mycobacterium tuberculosis by molecular methods are often limited by the amount and purity of DNA extracted from body fluids. In this study, we evaluated 12 DNA extraction methods and developed a highly sensitive protocol for mycobacterial DNA extraction directly from sputa using surface-coated magnetic particles. We have also developed a novel multiplex real-time PCR for simultaneous identification of M. tuberculosis complex and the Beijing/W genotype (a hypervirulent sublineage of M. tuberculosis) by using multiple fluorogenic probes targeting both the M. tuberculosis IS6110 and the Rv0927c-pstS3 intergenic region. With reference strains and clinical isolates, our real-time PCR accurately identified 20 non-Beijing/W and 20 Beijing/W M. tuberculosis strains from 17 different species of nontuberculosis Mycobacterium (NTM). Further assessment of our DNA extraction protocol and real-time PCR with 335 nonduplicate sputum specimens correctly identified all 74 M. tuberculosis culture-positive specimens. In addition, 15 culture-negative specimens from patients with confirmed tuberculosis were also identified. No cross-reactivity was detected with NTM specimens (n = 31). The detection limit of the assay is 10 M. tuberculosis bacilli, as determined by endpoint dilution analysis. In conclusion, an optimized DNA extraction protocol coupled with a novel multiprobe multiplex real-time PCR for the direct detection of M. tuberculosis, including Beijing/W M. tuberculosis, was found to confer high sensitivity and specificity. The combined procedure has the potential to compensate for the drawbacks of conventional mycobacterial culture in routine clinical laboratory setting, such as the lengthy incubation period and the limitation to viable organisms.

Temporal Organization of the Sleep-Wake Cycle under Food Entrainment in the Rat

PubMed Central

Castro-Faúndez, Javiera; Díaz, Javier; Ocampo-Garcés, Adrián

2016-01-01

Study Objectives: To analyze the temporal organization of the sleep-wake cycle under food entrainment in the rat. Methods: Eighteen male Sprague-Dawley rats were chronically implanted for polysomnographic recording. During the baseline (BL) protocol, rats were recorded under a 12:12 light-dark (LD) schedule in individual isolation chambers with food and water ad libitum. Food entrainment was performed by means of a 4-h food restriction (FR) protocol starting at photic zeitgeber time 5. Eight animals underwent a 3-h phase advance of the FR protocol (A-FR). We compared the mean curves and acrophases of wakefulness, NREM sleep, and REM sleep under photic and food entrainment and after a phase advance in scheduled food delivery. We further evaluated the dynamics of REM sleep homeostasis and the NREM sleep EEG delta wave profile. Results: A prominent food-anticipatory arousal interval was observed after nine or more days of FR, characterized by increased wakefulness and suppression of REM sleep propensity and dampening of NREM sleep EEG delta activity. REM sleep exhibited a robust nocturnal phase preference under FR that was not explained by a nocturnal REM sleep rebound. The mean curve of sleep-wake states and NREM sleep EEG delta activity remained phase-locked to the timing of meals during the A-FR protocol. Conclusions: Our results support the hypothesis that under food entrainment, the sleep-wake cycle is coupled to a food-entrainable oscillator (FEO). Our findings suggest an unexpected interaction between FEO output and NREM sleep EEG delta activity generators. Citation: Castro-Faúndez J, Díaz J, Ocampo-Garcés A. Temporal organization of the sleep-wake cycle under food entrainment in the rat. SLEEP 2016;39(7):1451–1465. PMID:27091526

Outcomes from a university-based low-cost in vitro fertilization program providing access to care for a low-resource socioculturally diverse urban community.

PubMed

Herndon, Christopher N; Anaya, Yanett; Noel, Martha; Cakmak, Hakan; Cedars, Marcelle I

2017-10-01

To report on outcomes from a university-based low-cost and low-complexity IVF program using mild stimulation approaches and simplified protocols to provide basic access to ART to a socioculturally diverse low-income urban population. Retrospective cohort study. Academic infertility center. Sixty-five infertile couples were enrolled from a county hospital serving a low-resource largely immigrant population. Patients were nonrandomly allocated to one of four mild stimulation protocols: clomiphene/letrozole alone, two clomiphene/letrozole-based protocols involving sequential or flare addition of low-dose gonadotropins, and low-dose gonadotropins alone. Clinical fellows managed all aspects of cycle preparation, monitoring, oocyte retrieval, and embryo transfer under an attending preceptor. Retrieval was undertaken without administration of deep anesthesia, and laboratory interventions were minimized. All embryo transfers were performed at the cleavage stage. Sociomedical demographics, treatment response, and pregnancy outcomes were recorded. From August 2010 to June 2016, 65 patients initiated 161 stimulation IVF cycles, which resulted in 107 retrievals, 91 fresh embryo transfers, and 40 frozen embryo transfer cycles. The mean age of patients was 33.3 years, and mean reported duration of infertility was 5.3 years; 33.5% (54/161) of cycles were cancelled before oocyte retrieval, with 13% due to premature ovulation. Overall, cumulative live birth rates per retrieval including subsequent use of frozen embryos was 29.0%; 44.6% (29/65) of patients enrolled in the program achieved pregnancy. Use of mild stimulation protocols, simplified monitoring, and minimized laboratory handling procedures enabled access to care in a low-resource socioculturally diverse infertile population. Copyright © 2017. Published by Elsevier Inc.

Inconsistent Strategies to Spin up Models in CMIP5: Implications for Ocean Biogeochemical Model Performance Assessment

NASA Technical Reports Server (NTRS)

Seferian, Roland; Gehlen, Marion; Bopp, Laurent; Resplandy, Laure; Orr, James C.; Marti, Olivier; Dunne, John P.; Christian, James R.; Doney, Scott C.; Ilyina, Tatiana;

Performance assessment of two lysis methods for direct identification of yeasts from clinical blood cultures using MALDI-TOF mass spectrometry.

PubMed

Jeddi, Fakhri; Yapo-Kouadio, Gisèle Cha; Normand, Anne-Cécile; Cassagne, Carole; Marty, Pierre; Piarroux, Renaud

2017-02-01

In cases of fungal infection of the bloodstream, rapid species identification is crucial to provide adapted therapy and thereby ameliorate patient outcome. Currently, the commercial Sepsityper kit and the sodium-dodecyl sulfate (SDS) method coupled with MALDI-TOF mass spectrometry are the most commonly reported lysis protocols for direct identification of fungi from positive blood culture vials. However, the performance of these two protocols has never been compared on clinical samples. Accordingly, we performed a two-step survey on two distinct panels of clinical positive blood culture vials to identify the most efficient protocol, establish an appropriate log score (LS) cut-off, and validate the best method. We first compared the performance of the Sepsityper and the SDS protocols on 71 clinical samples. For 69 monomicrobial samples, mass spectrometry LS values were significantly higher with the SDS protocol than with the Sepsityper method (P < .0001), especially when the best score of four deposited spots was considered. Next, we established the LS cut-off for accurate identification at 1.7, based on specimen DNA sequence data. Using this LS cut-off, 66 (95.6%) and 46 (66.6%) isolates were correctly identified at the species level with the SDS and the Sepsityper protocols, respectively. In the second arm of the survey, we validated the SDS protocol on an additional panel of 94 clinical samples. Ninety-two (98.9%) of 93 monomicrobial samples were correctly identified at the species level (median LS = 2.061). Overall, our data suggest that the SDS method yields more accurate species identification of yeasts, than the Sepsityper protocol. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A Dyadic Behavioral Intervention to Optimize Same Sex Male Couples' Engagement Across the HIV Care Continuum: Development of and Protocol for an Innovative Couples-based Approach (Partner Steps).

PubMed

Bazzi, Angela Robertson; Fergus, Kirkpatrick B; Stephenson, Rob; Finneran, Catherine A; Coffey-Esquivel, Julia; Hidalgo, Marco A; Hoehnle, Sam; Sullivan, Patrick S; Garofalo, Robert; Mimiaga, Matthew J

2016-08-25

An estimated one- to two-thirds of new human immunodeficiency virus (HIV) infections among US men who have sex with men (MSM) occur within the context of primary partnerships. Thus, HIV interventions that recognize and harness the power of relationships are needed. Increasingly, HIV prevention efforts are being directed toward improving engagement across the HIV care continuum from testing to linkage to care, antiretroviral therapy (ART) adherence, engagement in care, and viral suppression. However, to our knowledge, no behavioral interventions have attempted to address the HIV care continuum using a dyadic approach. The objective of this paper is to describe the development of and protocol for an innovative couples-based approach to improving treatment adherence and engagement in care among HIV serodiscordant and concordant HIV-positive same sex male couples in the United States. We developed the Partner Steps intervention by drawing from relationship-oriented theory, existing efficacious individual-level ART adherence interventions, couple-focused HIV prevention interventions, and expert consultation. We incorporated new content to address all aspects of the HIV care continuum (eg, linkage to and retention in care) and to draw on relationship strengths through interactive activities. The resulting theory-based Partner Steps intervention is delivered by a trained bachelors-level counselor (interventionist) over 2 in-person sessions with male-male dyads in which at least 1 partner has recent suboptimal engagement in HIV care. Each session is designed to use relationship strengths to increase motivation for HIV care and treatment, and cover sequential intervention "steps" relating to specific challenges in HIV care engagement and barriers to ART adherence. For each step, couples work with a trained interventionist to identify their unique challenges, actively problem-solve with the interventionist, and articulate and commit to working together to implement a plan in which each partner agrees to complete specific tasks. We drew on theory and evidence to develop novel intervention strategies that leverage strengths of relationships to address engagement across the entire HIV care continuum. We provide details on intervention development and content that may be of use to researchers as well as medical and mental health professionals for whom a dyadic approach to HIV prevention and care may best suit their patient population.

Factors Associated With Marital Satisfaction in Infertile Couple: A Comprehensive Literature Review

PubMed Central

Samadaee-Gelehkolaee, Keshvar; McCarthy, Barry W; Khalilian, Alireza; Hamzehgardeshi, Zeinab; Peyvandi, Sepideh; Elyasi, Forouza; Shahidi, Maryam

2016-01-01

Background: Many factors impact on marital satisfaction. Related factors include demographic factors, assisted reproductive techniques, psychological health, quality of life, psychological, socioeconomic and family support, and sexual function. Methods: This study is a literature review of research studies conducted on factors associated with marital satisfaction in infertile couples. The current literature review search was undertaken using multiple databases selected from articles pertinent to the study. The selection of subjects was undertaken from1990 through 2015. The methodological quality was analyzed based on a checklist adopted from a systematic review. Quality assessment of full text studies was finally carried out by two reviewers. Results: The initial search yielded a list of 445 papers, and then reviewers studied titles and abstracts. Thereafter, 69 papers were incorporated, and researchers reviewed summaries of all of the searched articles. Finally, the researchers utilized the data gained from 64 full articles so as to compile this review paper. Reviewing the studies conducted on marital satisfaction, they classified related findings into 6 categories: demographic factors, using fertility assisting methods, psychological health, life quality, economic, social, and family support, and sexual function. Conclusion: The results of this review article depicted that various factors play role in creating marriage life satisfaction in an infertile couple, so that paying attention to them can play an important role in continuing their treatment. Thus, to identify such factors is considered essential in their treatment protocol highly based on culture. Of the drawbacks of this research is that it has tried at best to employ the studies belonging to diverse countries with different cultures. Also, the number of the papers was considerably limited. PMID:26652079

Use of Standing Gold Nanorods for Detection of Malachite Green and Crystal Violet in Fish by SERS.

PubMed

Chen, Xiaowei; Nguyen, Trang H D; Gu, Liqun; Lin, Mengshi

2017-07-01

With growing consumption of aquaculture products, there is increasing demand on rapid and sensitive techniques that can detect prohibited substances in the seafood products. This study aimed to develop a novel surface-enhanced Raman spectroscopy (SERS) method coupled with simplified extraction protocol and novel gold nanorod (AuNR) substrates to detect banned aquaculture substances (malachite green [MG] and crystal violet [CV]) and their mixture (1:1) in aqueous solution and fish samples. Multivariate statistical tools such as principal component analysis (PCA) and partial least squares regression (PLSR) were used in data analysis. PCA results demonstrate that SERS can distinguish MG, CV and their mixture (1:1) in aqueous solution and in fish samples. The detection limit of SERS coupled with standing AuNR substrates is 1 ppb for both MG and CV in fish samples. A good linear relationship between the actual concentration and predicted concentration of analytes based on PLSR models with R 2 values from 0.87 to 0.99 were obtained, indicating satisfactory quantification results of this method. These results demonstrate that the SERS method coupled with AuNR substrates can be used for rapid and accurate detection of MG and CV in fish samples. © 2017 Institute of Food Technologists®.

Optimizing Adiabaticity in a Trapped-Ion Quantum Simulator

NASA Astrophysics Data System (ADS)

Richerme, Phil; Senko, Crystal; Korenblit, Simcha; Smith, Jacob; Lee, Aaron; Monroe, Christopher

2013-05-01

Trapped-ion quantum simulators are a leading platform for the study of interacting spin systems, such as fully-connected Ising models with transverse and axial fields. Phonon-mediated spin-dependent optical dipole forces act globally on a linear chain of trapped Yb-171+ ions to generate the spin-spin couplings, with the form and range of such couplings controlled by laser frequencies and trap voltages. The spins are initially prepared along an effective transverse magnetic field, which is large compared to the Ising couplings and slowly ramped down during the quantum simulation. The system remains in the ground state throughout the evolution if the ramp is adiabatic, and the spin ordering is directly measured by state-dependent fluorescence imaging of the ions onto a camera. Two techniques can improve the identification of the ground state at the end of simulations that are unavoidably diabatic. First, we show an optimized ramp protocol that gives a maximal probability of measuring the true ground state given a finite ramp time. Second, we show that no spin ordering is more prevalent than the ground state(s), even for non-adiabatic ramps. This work is supported by grants from the U.S. Army Research Office with funding from the DARPA OLE program, IARPA, and the MURI program; and the NSF Physics Frontier Center at JQI.

Inhibitory Effects of Hydroethanolic Leaf Extracts of Kalanchoe brasiliensis and Kalanchoe pinnata (Crassulaceae) against Local Effects Induced by Bothrops jararaca Snake Venom

PubMed Central

Fernandes, Júlia Morais; Félix-Silva, Juliana; da Cunha, Lorena Medeiros; Gomes, Jacyra Antunes dos Santos; Siqueira, Emerson Michell da Silva; Gimenes, Luisa Possamai; Lopes, Norberto Peporine; Soares, Luiz Alberto Lira; Fernandes-Pedrosa, Matheus de Freitas; Zucolotto, Silvana Maria

2016-01-01

The species Kalanchoe brasiliensis and Kalanchoe pinnata, both known popularly as “Saião,” are used interchangeably in traditional medicine for their antiophidic properties. Studies evaluating the anti-venom activity of these species are scarce. This study aims to characterize the chemical constituents and evaluate the inhibitory effects of hydroethanolic leaf extracts of K. brasiliensis and K. pinnata against local effects induced by Bothrops jararaca snake venom. Thin Layer Chromatography (TLC) and High Performance Liquid Chromatography coupled with Diode Array Detection and Electrospray Mass Spectrometry (HPLC-DAD-MS/MS) were performed for characterization of chemical markers of the extracts from these species. For antiophidic activity evaluation, B. jararaca venom-induced paw edema and skin hemorrhage in mice were evaluated. In both models, hydroethanolic extracts (125–500 mg/kg) were administered intraperitoneally in different protocols. Inhibition of phospholipase enzymatic activity of B. jararaca was evaluated. The HPLC-DAD-MS/MS chromatographic profile of extracts showed some particularities in the chemical profile of the two species. K. brasileinsis exhibited major peaks that have UV spectra similar to flavonoid glycosides derived from patuletin and eupafolin, while K. pinnata showed UV spectra similar to flavonoids glycosides derived from quercetin and kaempferol. Both extracts significantly reduced the hemorrhagic activity of B. jararaca venom in pre-treatment protocol, reaching about 40% of inhibition, while only K. pinnata was active in post-treatment protocol (about 30% of inhibition). In the antiedematogenic activity, only K. pinnata was active, inhibiting about 66% and 30% in pre and post-treatment protocols, respectively. Both extracts inhibited phospholipase activity; however, K. pinnata was more active. In conclusion, the results indicate the potential antiophidic activity of Kalanchoe species against local effects induced by B. jararaca snake venom, suggesting their potential use as a new source of bioactive molecules against bothropic venom. PMID:28033347

Inhibitory Effects of Hydroethanolic Leaf Extracts of Kalanchoe brasiliensis and Kalanchoe pinnata (Crassulaceae) against Local Effects Induced by Bothrops jararaca Snake Venom.

PubMed

Fernandes, Júlia Morais; Félix-Silva, Juliana; da Cunha, Lorena Medeiros; Gomes, Jacyra Antunes Dos Santos; Siqueira, Emerson Michell da Silva; Gimenes, Luisa Possamai; Lopes, Norberto Peporine; Soares, Luiz Alberto Lira; Fernandes-Pedrosa, Matheus de Freitas; Zucolotto, Silvana Maria

2016-01-01

The species Kalanchoe brasiliensis and Kalanchoe pinnata, both known popularly as "Saião," are used interchangeably in traditional medicine for their antiophidic properties. Studies evaluating the anti-venom activity of these species are scarce. This study aims to characterize the chemical constituents and evaluate the inhibitory effects of hydroethanolic leaf extracts of K. brasiliensis and K. pinnata against local effects induced by Bothrops jararaca snake venom. Thin Layer Chromatography (TLC) and High Performance Liquid Chromatography coupled with Diode Array Detection and Electrospray Mass Spectrometry (HPLC-DAD-MS/MS) were performed for characterization of chemical markers of the extracts from these species. For antiophidic activity evaluation, B. jararaca venom-induced paw edema and skin hemorrhage in mice were evaluated. In both models, hydroethanolic extracts (125-500 mg/kg) were administered intraperitoneally in different protocols. Inhibition of phospholipase enzymatic activity of B. jararaca was evaluated. The HPLC-DAD-MS/MS chromatographic profile of extracts showed some particularities in the chemical profile of the two species. K. brasileinsis exhibited major peaks that have UV spectra similar to flavonoid glycosides derived from patuletin and eupafolin, while K. pinnata showed UV spectra similar to flavonoids glycosides derived from quercetin and kaempferol. Both extracts significantly reduced the hemorrhagic activity of B. jararaca venom in pre-treatment protocol, reaching about 40% of inhibition, while only K. pinnata was active in post-treatment protocol (about 30% of inhibition). In the antiedematogenic activity, only K. pinnata was active, inhibiting about 66% and 30% in pre and post-treatment protocols, respectively. Both extracts inhibited phospholipase activity; however, K. pinnata was more active. In conclusion, the results indicate the potential antiophidic activity of Kalanchoe species against local effects induced by B. jararaca snake venom, suggesting their potential use as a new source of bioactive molecules against bothropic venom.

Virtual reality cue exposure for the relapse prevention of tobacco consumption: a study protocol for a randomized controlled trial.

PubMed

Giovancarli, Camille; Malbos, Eric; Baumstarck, Karine; Parola, Nathalie; Pélissier, Marie-Florence; Lançon, Christophe; Auquier, Pascal; Boyer, Laurent

2016-02-19

Successful interventions have been developed for smoking cessation, but the success of smoking relapse prevention interventions has been limited. In particular, cognitive behavioural therapy (CBT) has been hampered by a high relapse rate. Because relapses can be due to the presence of conditions associated with tobacco consumption (such as drinking in bars with friends), virtual reality exposure therapy (VRET) can generate synthetic environments that represent risk situations for the patient in the context of relapse prevention. The primary objective of this study is to evaluate the effectiveness of CBT coupled with VRET, in comparison to CBT alone, in the prevention of smoking relapse. The secondary objectives are to assess the impact of CBT coupled with VRET on anxiety, depression, quality of life, self-esteem and addictive comorbidities (such as alcohol, cannabis, and gambling). A third objective examines the feasibility and acceptability of VR use considering elements such as presence, cybersickness and number of patients who complete the VRET program. The present study is a 14-month (2 months of therapy followed by 12 months of follow-up), prospective, comparative, randomized and open clinical trial, involving two parallel groups (CBT coupled with VRET versus CBT alone). The primary outcome is the proportion of individuals with tobacco abstinence at 6 months after the end of the therapy. Abstinence is defined by the total absence of tobacco consumption assessed during a post-test interview and with an apparatus that measures the carbon monoxide levels expired. A total of 60 individuals per group will be included. This study is the first to examine the efficacy of CBT coupled with VRET in the prevention of smoking relapse. Because VRET is simple to use and has a low cost, this interactive therapeutic method might be easily implemented in clinical practice if the study confirms its efficacy. ClinicalTrials.gov Identifier: NCT02205060 (registered 25 July 2014).

Global Effects of Superparameterization on Hydrothermal Land-Atmosphere Coupling on Multiple Timescales

NASA Astrophysics Data System (ADS)

Qin, Hongchen; Pritchard, Michael S.; Kooperman, Gabriel J.; Parishani, Hossein

2018-02-01

Many conventional General Circulation Models (GCMs) in the Global Land-Atmosphere Coupling Experiment (GLACE) tend to produce what is now recognized as overly strong land-atmosphere (L-A) coupling. We investigate the effects of cloud Superparameterization (SP) on L-A coupling on timescales beyond diurnal where it has been recently shown to have a favorable muting effect hydrologically. Using the Community Atmosphere Model v3.5 (CAM3.5) and its Superparameterized counterpart SPCAM3.5, we conducted soil moisture interference experiments following the GLACE and Atmospheric Model Intercomparison Project (AMIP) protocols. The results show that, on weekly-to-subseasonal timescales, SP also mutes hydrologic L-A coupling. This is detectable globally, and happens through the evapotranspiration-precipitation segment. But on seasonal timescales, SP does not exhibit detectable effects on hydrologic L-A coupling. Two robust regional effects of SP on thermal L-A coupling have also been explored. Over the Arabian Peninsula, SP reduces thermal L-A coupling through a straightforward control by mean rainfall reduction. More counterintuitively, over the Southwestern US and Northern Mexico, SP enhances the thermal L-A coupling in a way that is independent of rainfall and soil moisture. This signal is associated with a systematic and previously unrecognized effect of SP that produces an amplified Bowen ratio, and is detectable in multiple SP model versions and experiment designs. In addition to amplifying the present-day Bowen ratio, SP is found to amplify the climate sensitivity of Bowen ratio as well, which likely plays a role in influencing climate change predictions at the L-A interface.

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

Use of bacteriophage cell wall-binding proteins for rapid diagnostics of Listeria.

PubMed

Schmelcher, Mathias; Loessner, Martin J

2014-01-01

Diagnostic protocols for food-borne bacterial pathogens such as Listeria need to be sensitive, specific, rapid, and inexpensive. Conventional culture methods are hampered by lengthy enrichment and incubation steps. Bacteriophage-derived high-affinity binding molecules (cell wall-binding domains, CBDs) specific for Listeria cells have recently been introduced as tools for detection and differentiation of this pathogen in foods. When coupled with magnetic separation, these proteins offer advantages in sensitivity and speed compared to the standard diagnostic methods. Furthermore, fusion of CBDs to differently colored fluorescent reporter proteins enables differentiation of Listeria strains in mixed cultures. This chapter provides protocols for detection of Listeria in food by CBD-based magnetic separation and subsequent multiplexed identification of strains of different serotypes with reporter-CBD fusion proteins.

Microwave-to-optical frequency conversion with a Rydberg atom coupled to a coplanar waveguide

NASA Astrophysics Data System (ADS)

Gard, Bryan; Jacobs, Kurt; McDermott, Robert; Saffman, Mark

2017-04-01

A primary candidate for converting quantum information from microwave to optical frequencies is the use of Rydberg states of a single atom trapped near a surface. The fact that the Rydberg states possess both large electric dipole moments and microwave transition frequencies allows them to interact with superconducting mesoscopic circuits. By considering a concrete example, that of a Cesium atom, and using numerical search methods to optimize the control protocols, we determine the fidelities and transmission rates that could be achievable with such a device. We show that while protocols that exploit the adiabatic STIRAP mechanism provide the best raw transfer fidelities, the fastest communication speeds can be obtained by using heralding, which allows one to remove the adiabatic constraint. Support from Oak Ridge Associated Universities.

Discrimination of almonds (Prunus dulcis) geographical origin by minerals and fatty acids profiling.

PubMed

Amorello, Diana; Orecchio, Santino; Pace, Andrea; Barreca, Salvatore

2016-09-01

Twenty-one almond samples from three different geographical origins (Sicily, Spain and California) were investigated by determining minerals and fatty acids compositions. Data were used to discriminate by chemometry almond origin by linear discriminant analysis. With respect to previous PCA profiling studies, this work provides a simpler analytical protocol for the identification of almonds geographical origin. Classification by using mineral contents data only was correct in 77% of the samples, while, by using fatty acid profiles, the percentages of samples correctly classified reached 82%. The coupling of mineral contents and fatty acid profiles lead to an increased efficiency of the classification with 87% of samples correctly classified.

Dispersive Readout of Adiabatic Phases

NASA Astrophysics Data System (ADS)

Kohler, Sigmund

2017-11-01

We propose a protocol for the measurement of adiabatic phases of periodically driven quantum systems coupled to an open cavity that enables dispersive readout. It turns out that the cavity transmission exhibits peaks at frequencies determined by a resonance condition that involves the dynamical and the geometric phase. Since these phases scale differently with the driving frequency, one can determine them by fitting the peak positions to the theoretically expected behavior. For the derivation of the resonance condition and for a numerical study, we develop a Floquet theory for the dispersive readout of ac driven quantum systems. The feasibility is demonstrated for two test cases that generalize Landau-Zener-Stückelberg-Majorana interference to two-parameter driving.

Inverse spin Hall and spin rectification effects in NiFe/FeMn exchange-biased thin films

NASA Astrophysics Data System (ADS)

Garcia, W. J. S.; Seeger, R. L.; da Silva, R. B.; Harres, A.

2017-11-01

Materials presenting high spin-orbit coupling are able to convert spin currents in charge currents. The phenomenon, known as inverse spin Hall effect, promises to revolutionize spintronic technology enabling the electrical detection of spin currents. It has been observed in a variety of systems, usually non-magnetic metals. We study the voltage emerging in exchange biased Ta/NiFe/FeMn/Ta thin films near the ferromagnetic resonance. Measured signals are related to both inverse spin Hall and spin rectification effects, and two distinct protocols were employed to separate their contributions.The curve shift due to the exchange bias effect may enable high frequency applications without an external applied magnetic field.

AN OBSERVATIONAL STUDY OF SOCIAL CONTROL, MOOD, AND SELF-EFFICACY IN COUPLES DURING TREATMENT FOR HEAD AND NECK CANCER

PubMed Central

BADR, HODA; YEUNG, CHI; LEWIS, MEGAN A.; MILBURY, KATHRIN; REDD, WILLIAM H.

2014-01-01

OBJECTIVE Head and neck cancer (HNC) patients experience debilitating side effects, including abnormally reduced salivation and difficulty swallowing. Intensive self-care protocols are prescribed to control side effects and minimize discomfort, but non-adherence rates are high. Although spouses are in a prime position to encourage adherence, studies have yet to examine how spouse social control (i.e., attempts to influence patient behavior to support adherence) affects HNC patient mood and self-efficacy for engaging in these self-care routines. METHODS One-hundred twenty-five HNC couples where the patient (86% male) was undergoing radiotherapy were recorded in the laboratory as they discussed a cancer-related issue that the patient identified as being a topic of concern. RESULTS Sixty-eight couples discussed side-effects and spouses engaged in social control in 61 of these discussions. Although oral complications and pain were frequently identified by patients as being topics of concern, dental/oral care and pain management were some of the least likely self-care behaviors to be targeted by spouses, who focused primarily on encouraging patients to maintain their weight and hydration. Although spouses engaged in an almost equal number of positive and negative control attempts, only positive control was significantly (p<.05) associated with patient positive mood and self-efficacy. CONCLUSION HNC couples may benefit from programs that emphasize the regular practice of self-care routines to control oral side effects, pain, and nutrition/hydration problems. Likewise, programs that encourage spouses to maximize their use of positive social control may also boost patients’ mood during treatment and empower them to engage in recommended self-care behaviors. PMID:25471820

Replacing Conventional Carbon Nucleophiles with Electrophiles: Nickel-Catalyzed Reductive Alkylation of Aryl Bromides and Chlorides

PubMed Central

2012-01-01

A general method is presented for the synthesis of alkylated arenes by the chemoselective combination of two electrophilic carbons. Under the optimized conditions, a variety of aryl and vinyl bromides are reductively coupled with alkyl bromides in high yields. Under similar conditions, activated aryl chlorides can also be coupled with bromoalkanes. The protocols are highly functional-group tolerant (−OH, −NHTs, −OAc, −OTs, −OTf, −COMe, −NHBoc, −NHCbz, −CN, −SO2Me), and the reactions are assembled on the benchtop with no special precautions to exclude air or moisture. The reaction displays different chemoselectivity than conventional cross-coupling reactions, such as the Suzuki–Miyaura, Stille, and Hiyama–Denmark reactions. Substrates bearing both an electrophilic and nucleophilic carbon result in selective coupling at the electrophilic carbon (R–X) and no reaction at the nucleophilic carbon (R–[M]) for organoboron (−Bpin), organotin (−SnMe3), and organosilicon (−SiMe2OH) containing organic halides (X–R–[M]). A Hammett study showed a linear correlation of σ and σ(−) parameters with the relative rate of reaction of substituted aryl bromides with bromoalkanes. The small ρ values for these correlations (1.2–1.7) indicate that oxidative addition of the bromoarene is not the turnover-frequency determining step. The rate of reaction has a positive dependence on the concentration of alkyl bromide and catalyst, no dependence upon the amount of zinc (reducing agent), and an inverse dependence upon aryl halide concentration. These results and studies with an organic reductant (TDAE) argue against the intermediacy of organozinc reagents. PMID:22463689

Multi-Family Group Intervention for OEF/OIF Traumatic Brain Injury Survivors and their Families

DTIC Science & Technology

2011-10-01

protocol. For example, due to a high degree of marital conflict observed in two couples in the initial Bronx group, the second group incorporated...veterans’ family members. Insufficient information can exacerbate marital or family conflict and lead to psychological distress and social isolation...disappointment, frustration, family conflict , and child distress (Collins & Kennedy, KRISTY STRAITS-TRÖSTER received her PhD in clinical psychology from the

Synthesis of aza-fused polycyclic quinolines through copper-catalyzed cascade reactions.

PubMed

Cai, Qian; Li, Zhengqiu; Wei, Jiajia; Fu, Liangbin; Ha, Chengyong; Pei, Duanqing; Ding, Ke

2010-04-02

A new and efficient method for the synthesis of aza-fused polycyclic quinolines (e.g., benzimidazo[1,2-a]quinolines) is described. This protocol includes an intermolecular condensation followed by a copper-catalyzed intramolecular C-N coupling reaction. The method is applied to a wide range of 2-iodo, 2-bromo, and 2-chloro aryl aldehyde substrates to yield the aza-fused polycyclic quinolines in good yields.

Computationally Aided Absolute Stereochemical Determination of Enantioenriched Amines.

PubMed

Zhang, Jun; Gholami, Hadi; Ding, Xinliang; Chun, Minji; Vasileiou, Chrysoula; Nehira, Tatsuo; Borhan, Babak

2017-03-17

A simple and efficient protocol for sensing the absolute stereochemistry and enantiomeric excess of chiral monoamines is reported. Preparation of the sample requires a single-step reaction of the 1,1'-(bromomethylene)dinaphthalene (BDN) with the chiral amine. Analysis of the exciton coupled circular dichroism generated from the BDN-derivatized chiral amine sample, along with comparison to conformational analysis performed computationally, yields the absolute stereochemistry of the parent chiral monoamine.

Enantioselective Decarboxylative Arylation of α-Amino Acids via the Merger of Photoredox and Nickel Catalysis

PubMed Central

Zuo, Zhiwei; Cong, Huan; Li, Wei; Choi, Junwon; Fu, Gregory C.; MacMillan, David W. C.

2016-01-01

An asymmetric decarboxylative Csp3–Csp2 cross-coupling has been achieved via the synergistic merger of photoredox and nickel catalysis. This mild, operationally simple protocol transforms a wide variety of naturally abundant α-amino acids and readily available aryl halides into valuable chiral benzylic amines in high enantiomeric excess, thereby producing motifs found in pharmacologically active agents. PMID:26849354

Synthesis of 2-aryl and 3-aryl benzo[b]furan thioethers using aryl sulfonyl hydrazides as sulfenylation reagents.

PubMed

Zhao, Xia; Zhang, Lipeng; Lu, Xiaoyu; Li, Tianjiao; Lu, Kui

2015-03-06

An efficient, metal-free protocol used to synthesize aryl benzo[b]furan thioethers based on the I2-catalyzed cross-coupling of benzo[b]furans as well as the electrophilic cyclization of 2-alkynylphenol derivatives with aryl sulfonyl hydrazides was developed. Various 2-aryl and 3-aryl benzo[b]furan thioethers were obtained in moderate to good yields.

Towards quantum networks of single spins: analysis of a quantum memory with an optical interface in diamond.

PubMed

Blok, M S; Kalb, N; Reiserer, A; Taminiau, T H; Hanson, R

2015-01-01

Single defect centers in diamond have emerged as a powerful platform for quantum optics experiments and quantum information processing tasks. Connecting spatially separated nodes via optical photons into a quantum network will enable distributed quantum computing and long-range quantum communication. Initial experiments on trapped atoms and ions as well as defects in diamond have demonstrated entanglement between two nodes over several meters. To realize multi-node networks, additional quantum bit systems that store quantum states while new entanglement links are established are highly desirable. Such memories allow for entanglement distillation, purification and quantum repeater protocols that extend the size, speed and distance of the network. However, to be effective, the memory must be robust against the entanglement generation protocol, which typically must be repeated many times. Here we evaluate the prospects of using carbon nuclear spins in diamond as quantum memories that are compatible with quantum networks based on single nitrogen vacancy (NV) defects in diamond. We present a theoretical framework to describe the dephasing of the nuclear spins under repeated generation of NV spin-photon entanglement and show that quantum states can be stored during hundreds of repetitions using typical experimental coupling parameters. This result demonstrates that nuclear spins with weak hyperfine couplings are promising quantum memories for quantum networks.

Identification of an 18 bp deletion in the TWIST1 gene by CO-amplification at lower denaturation temperature-PCR (COLD-PCR) for non-invasive prenatal diagnosis of craniosynostosis: first case report.

PubMed

Galbiati, Silvia; Stenirri, Stefania; Sbaiz, Luca; Barberis, Marco; Cremonesi, Laura; Restagno, Gabriella; Ferrari, Maurizio

2014-04-01

Non-invasive prenatal diagnosis has found application in a limited number of genetic diseases due to the difficulty in detecting a few copies of fetal mutated sequences in the presence of a large excess of wild-type maternal alleles, even in the case of single-base mutations. We developed conditions for the enrichment of fetal mutated alleles in maternal plasma based on CO-amplification at lower denaturation temperature-PCR (COLD-PCR). In particular, we applied a full COLD-PCR protocol to the identification of a p.A87_G92del mutation in the TWIST1 gene causing craniosynostosis in a couple at risk for the disease. The use of the COLD-PCR protocol coupled with direct sequencing enabled correct identification of the fetal paternally inherited mutated allele, in accordance with the result obtained on DNA extracted from chorionic villi. COLD-PCR proved to be a simple and powerful tool for the identification of minority mutated alleles even in the case of a moderately large deletion (18 bp) and confirmed to be very suitable for non-invasive prenatal diagnosis of a variety of genetic diseases.

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

Anthracenyl polar embedded stationary phases with enhanced aromatic selectivity. Part II: A density functional theory study.

PubMed

Mignot, Mélanie; Schammé, Benjamin; Tognetti, Vincent; Joubert, Laurent; Cardinael, Pascal; Peulon-Agasse, Valérie

2017-10-13

New polar embedded aromatic stationary phases (mono- and trifunctional versions) that contain an amide-embedded group coupled with a tricyclic aromatic moiety were developed for chromatographic applications and described in the first paper of this series. These phases offered better separation performance for PAHs than for alkylbenzene homologues, and an enhanced ability to differentiate aromatic planarity to aromatic tridimensional conformation, especially for the trifunctional version and when using methanol instead of acetonitrile. In this second paper, a density functional theory study of the retention process is reported. In particular, it was shown that the selection of the suitable computational protocol allowed for describing rigorously the interactions that could take place, the solvent effects, and the structural changes for the monofunctional and the trifunctional versions. For the first time, the experimental data coupled with these DFT results provided a better understanding of the interaction mechanisms and highlighted the importance of the multimodal character of the designed stationary phases: alkyl spacers for interactions with hydrophobic solutes, amide embedded groups for dipole-dipole and hydrogen-bond interactions, and aromatic terminal groups for π-π interactions. Copyright © 2017 Elsevier B.V. All rights reserved.

Cross-Shear Implementation in Sliding-Distance-Coupled Finite Element Analysis of Wear in Metal-on-Polyethylene Total Joint Arthroplasty: Intervertebral Total Disc Replacement as an Illustrative Application

PubMed Central

Goreham-Voss, Curtis M.; Hyde, Philip J.; Hall, Richard M.; Fisher, John; Brown, Thomas D.

2010-01-01

Computational simulations of wear of orthopaedic total joint replacement implants have proven to valuably complement laboratory physical simulators, for pre-clinical estimation of abrasive/adhesive wear propensity. This class of numerical formulations has primarily involved implementation of the Archard/Lancaster relationship, with local wear computed as the product of (finite element) contact stress, sliding speed, and a bearing-couple-dependent wear factor. The present study introduces an augmentation, whereby the influence of interface cross-shearing motion transverse to the prevailing molecular orientation of the polyethylene articular surface is taken into account in assigning the instantaneous local wear factor. The formulation augment is implemented within a widely-utilized commercial finite element software environment (ABAQUS). Using a contemporary metal-on-polyethylene total disc replacement (ProDisc-L) as an illustrative implant, physically validated computational results are presented to document the role of cross-shearing effects in alternative laboratory consensus testing protocols. Going forward, this formulation permits systematically accounting for cross-shear effects in parametric computational wear studies of metal-on-polyethylene joint replacements, heretofore a substantial limitation of such analyses. PMID:20399432

Diagnosis of autism through EEG processed by advanced computational algorithms: A pilot study.

PubMed

Grossi, Enzo; Olivieri, Chiara; Buscema, Massimo

2017-04-01

Multi-Scale Ranked Organizing Map coupled with Implicit Function as Squashing Time algorithm(MS-ROM/I-FAST) is a new, complex system based on Artificial Neural networks (ANNs) able to extract features of interest in computerized EEG through the analysis of few minutes of their EEG without any preliminary pre-processing. A proof of concept study previously published showed accuracy values ranging from 94%-98% in discerning subjects with Mild Cognitive Impairment and/or Alzheimer's Disease from healthy elderly people. The presence of deviant patterns in simple resting state EEG recordings in autism, consistent with the atypical organization of the cerebral cortex present, prompted us in applying this potent analytical systems in search of a EEG signature of the disease. The aim of the study is to assess how effectively this methodology distinguishes subjects with autism from typically developing ones. Fifteen definite ASD subjects (13 males; 2 females; age range 7-14; mean value = 10.4) and ten typically developing subjects (4 males; 6 females; age range 7-12; mean value 9.2) were included in the study. Patients received Autism diagnoses according to DSM-V criteria, subsequently confirmed by the ADOS scale. A segment of artefact-free EEG lasting 60 seconds was used to compute input values for subsequent analyses. MS-ROM/I-FAST coupled with a well-documented evolutionary system able to select predictive features (TWIST) created an invariant features vector input of EEG on which supervised machine learning systems acted as blind classifiers. The overall predictive capability of machine learning system in sorting out autistic cases from normal control amounted consistently to 100% with all kind of systems employed using training-testing protocol and to 84% - 92.8% using Leave One Out protocol. The similarities among the ANN weight matrixes measured with apposite algorithms were not affected by the age of the subjects. This suggests that the ANNs do not read age-related EEG patterns, but rather invariant features related to the brain's underlying disconnection signature. This pilot study seems to open up new avenues for the development of non-invasive diagnostic testing for the early detection of ASD. Copyright © 2017 Elsevier B.V. All rights reserved.

Solving iTOUGH2 simulation and optimization problems using the PEST protocol

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

Finsterle, S.A.; Zhang, Y.

2011-02-01

The PEST protocol has been implemented into the iTOUGH2 code, allowing the user to link any simulation program (with ASCII-based inputs and outputs) to iTOUGH2's sensitivity analysis, inverse modeling, and uncertainty quantification capabilities. These application models can be pre- or post-processors of the TOUGH2 non-isothermal multiphase flow and transport simulator, or programs that are unrelated to the TOUGH suite of codes. PEST-style template and instruction files are used, respectively, to pass input parameters updated by the iTOUGH2 optimization routines to the model, and to retrieve the model-calculated values that correspond to observable variables. We summarize the iTOUGH2 capabilities and demonstratemore » the flexibility added by the PEST protocol for the solution of a variety of simulation-optimization problems. In particular, the combination of loosely coupled and tightly integrated simulation and optimization routines provides both the flexibility and control needed to solve challenging inversion problems for the analysis of multiphase subsurface flow and transport systems.« less

Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples

PubMed Central

Snyder-Mackler, Noah; Majoros, William H.; Yuan, Michael L.; Shaver, Amanda O.; Gordon, Jacob B.; Kopp, Gisela H.; Schlebusch, Stephen A.; Wall, Jeffrey D.; Alberts, Susan C.; Mukherjee, Sayan; Zhou, Xiang; Tung, Jenny

2016-01-01

Research on the genetics of natural populations was revolutionized in the 1990s by methods for genotyping noninvasively collected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomics era. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA from noninvasively collected samples, coupled with a novel computational approach to reconstruct pedigree links from the resulting low-coverage data. We validated both methods using fecal samples from 62 wild baboons, including 48 from an independently constructed extended pedigree. We enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA and reconstructed near-perfect pedigree relationships even with extremely low-coverage sequencing. We anticipate that these methods will be broadly applicable to the many research systems for which only noninvasive samples are available. The lab protocol and software (“WHODAD”) are freely available at www.tung-lab.org/protocols-and-software.html and www.xzlab.org/software.html, respectively. PMID:27098910

Consensus for second-order multi-agent systems with position sampled data

NASA Astrophysics Data System (ADS)

Wang, Rusheng; Gao, Lixin; Chen, Wenhai; Dai, Dameng

2016-10-01

In this paper, the consensus problem with position sampled data for second-order multi-agent systems is investigated. The interaction topology among the agents is depicted by a directed graph. The full-order and reduced-order observers with position sampled data are proposed, by which two kinds of sampled data-based consensus protocols are constructed. With the provided sampled protocols, the consensus convergence analysis of a continuous-time multi-agent system is equivalently transformed into that of a discrete-time system. Then, by using matrix theory and a sampled control analysis method, some sufficient and necessary consensus conditions based on the coupling parameters, spectrum of the Laplacian matrix and sampling period are obtained. While the sampling period tends to zero, our established necessary and sufficient conditions are degenerated to the continuous-time protocol case, which are consistent with the existing result for the continuous-time case. Finally, the effectiveness of our established results is illustrated by a simple simulation example. Project supported by the Natural Science Foundation of Zhejiang Province, China (Grant No. LY13F030005) and the National Natural Science Foundation of China (Grant No. 61501331).

Metabolic profiling of body fluids and multivariate data analysis.

PubMed

Trezzi, Jean-Pierre; Jäger, Christian; Galozzi, Sara; Barkovits, Katalin; Marcus, Katrin; Mollenhauer, Brit; Hiller, Karsten

2017-01-01

Metabolome analyses of body fluids are challenging due pre-analytical variations, such as pre-processing delay and temperature, and constant dynamical changes of biochemical processes within the samples. Therefore, proper sample handling starting from the time of collection up to the analysis is crucial to obtain high quality samples and reproducible results. A metabolomics analysis is divided into 4 main steps: 1) Sample collection, 2) Metabolite extraction, 3) Data acquisition and 4) Data analysis. Here, we describe a protocol for gas chromatography coupled to mass spectrometry (GC-MS) based metabolic analysis for biological matrices, especially body fluids. This protocol can be applied on blood serum/plasma, saliva and cerebrospinal fluid (CSF) samples of humans and other vertebrates. It covers sample collection, sample pre-processing, metabolite extraction, GC-MS measurement and guidelines for the subsequent data analysis. Advantages of this protocol include: •Robust and reproducible metabolomics results, taking into account pre-analytical variations that may occur during the sampling process•Small sample volume required•Rapid and cost-effective processing of biological samples•Logistic regression based determination of biomarker signatures for in-depth data analysis.

Evolution of a Patient Information Management System in a Local Area Network Environment at Loyola University of Chicago Medical Center

PubMed Central

Price, Ronald N; Chandrasekhar, Arcot J; Tamirisa, Balaji

1990-01-01

The Department of Medicine at Loyola University Medical Center (LUMC) of Chicago has implemented a local area network (LAN) based Patient Information Management System (PIMS) as part of its integrated departmental database management system. PIMS consists of related database applications encompassing demographic information, current medications, problem lists, clinical data, prior events, and on-line procedure results. Integration into the existing departmental database system permits PIMS to capture and manipulate data in other departmental applications. Standardization of clinical data is accomplished through three data tables that verify diagnosis codes, procedures codes and a standardized set of clinical data elements. The modularity of the system, coupled with standardized data formats, allowed the development of a Patient Information Protocol System (PIPS). PIPS, a userdefinable protocol processor, provides physicians with individualized data entry or review screens customized for their specific research protocols or practice habits. Physician feedback indicates that the PIMS/PIPS combination enhances their ability to collect and review specific patient information by filtering large amount of clinical data.

Mathematical model formulation and validation of water and solute transport in whole hamster pancreatic islets.

PubMed

Benson, James D; Benson, Charles T; Critser, John K

2014-08-01

Optimization of cryopreservation protocols for cells and tissues requires accurate models of heat and mass transport. Model selection often depends on the configuration of the tissue. Here, a mathematical and conceptual model of water and solute transport for whole hamster pancreatic islets has been developed and experimentally validated incorporating fundamental biophysical data from previous studies on individual hamster islet cells while retaining whole-islet structural information. It describes coupled transport of water and solutes through the islet by three methods: intracellularly, intercellularly, and in combination. In particular we use domain decomposition techniques to couple a transmembrane flux model with an interstitial mass transfer model. The only significant undetermined variable is the cellular surface area which is in contact with the intercellularly transported solutes, Ais. The model was validated and Ais determined using a 3×3 factorial experimental design blocked for experimental day. Whole islet physical experiments were compared with model predictions at three temperatures, three perfusing solutions, and three islet size groups. A mean of 4.4 islets were compared at each of the 27 experimental conditions and found to correlate with a coefficient of determination of 0.87±0.06 (mean ± SD). Only the treatment variable of perfusing solution was found to be significant (p<0.05). We have devised a model that retains much of the intrinsic geometric configuration of the system, and thus fewer laboratory experiments are needed to determine model parameters and thus to develop new optimized cryopreservation protocols. Additionally, extensions to ovarian follicles and other concentric tissue structures may be made. Copyright © 2014 Elsevier Inc. All rights reserved.

On-chip human microvasculature assay for visualization and quantitation of tumor cell extravasation dynamics

PubMed Central

Chen, Michelle B.; Whisler, Jordan A.; Fröse, Julia; Yu, Cathy; Shin, Yoojin

2017-01-01

Distant metastasis, which results in >90% of cancer related deaths, is enabled by hematogenous dissemination of tumor cells via the circulation. This requires the completion of a sequence of complex steps including transit, initial arrest, extravasation, survival and proliferation. Increased understanding of the cellular and molecular players enabling each of these steps is key in uncovering new opportunities for therapeutic intervention during early metastatic dissemination. Here, we describe an in vitro model of the human microcirculation with the potential to recapitulate discrete steps of early metastatic seeding, including arrest, transendothelial migration and early micrometastases formation. The microdevice features self-organized human microvascular networks formed over 4–5 days, after which tumor can be perfused and extravasation events easily tracked over 72 hours, via standard confocal microscopy. Contrary to most in vivo and in vitro extravasation assays, robust and rapid scoring of extravascular cells combined with high-resolution imaging can be easily achieved due to the confinement of the vascular network to one plane close to the surface of the device. This renders extravascular cells clearly distinct and allows tumor cells of interest to be identified quickly compared to those in thick tissues. The ability to generate large numbers of devices (~36) per experiment coupled with fast quantitation further allows for highly parametric studies, which is required when testing multiple genetic or pharmacological perturbations. This is coupled with the capability for live tracking of single cell extravasation events allowing both tumor and endothelial morphological dynamics to be observed in high detail with a moderate number of data points. This Protocol Extension describes an adaptation of an existing Protocol describing a microfluidic platform that offers additional applications. PMID:28358393

High‐precision determination of lithium and magnesium isotopes utilising single column separation and multi‐collector inductively coupled plasma mass spectrometry

PubMed Central

Misra, Sambuddha; Lloyd, Nicholas; Elderfield, Henry; Bickle, Mike J.

2017-01-01

Rationale Li and Mg isotopes are increasingly used as a combined tool within the geosciences. However, established methods require separate sample purification protocols utilising several column separation procedures. This study presents a single‐step cation‐exchange method for quantitative separation of trace levels of Li and Mg from multiple sample matrices. Methods The column method utilises the macro‐porous AGMP‐50 resin and a high‐aspect ratio column, allowing quantitative separation of Li and Mg from natural waters, sediments, rocks and carbonate matrices following the same elution protocol. High‐precision isotope determination was conducted by multi‐collector inductively coupled plasma mass spectrometry (MC‐ICPMS) on the Thermo Scientific™ NEPTUNE Plus™ fitted with 1013 Ω amplifiers which allow accurate and precise measurements at ion beams ≤0.51 V. Results Sub‐nanogram Li samples (0.3–0.5 ng) were regularly separated (yielding Mg masses of 1–70 μg) using the presented column method. The total sample consumption during isotopic analysis is <0.5 ng Li and <115 ng Mg with long‐term external 2σ precisions of ±0.39‰ for δ7Li and ±0.07‰ for δ26Mg. The results for geological reference standards and seawater analysed by our method are in excellent agreement with published values despite the order of magnitude lower sample consumption. Conclusions The possibility of eluting small sample masses and the low analytical sample consumption make this method ideal for samples of limited mass or low Li concentration, such as foraminifera, mineral separates or dilute river waters. PMID:29078008

Direct Alkynylation of 3H-Imidazo[4,5-b]pyridines Using gem-Dibromoalkenes as Alkynes Source.

PubMed

Aziz, Jessy; Baladi, Tom; Piguel, Sandrine

2016-05-20

C2 direct alkynylation of 3H-imidazo[4,5-b]pyridine derivatives is explored for the first time. Stable and readily available 1,1-dibromo-1-alkenes, electrophilic alkyne precursors, are used as coupling partners. The simple reaction conditions include an inexpensive copper catalyst (CuBr·SMe2 or Cu(OAc)2), a phosphine ligand (DPEphos) and a base (LiOtBu) in 1,4-dioxane at 120 °C. This C-H alkynylation method revealed to be compatible with a variety of substitutions on both coupling partners: heteroarenes and gem-dibromoalkenes. This protocol allows the straightforward synthesis of various 2-alkynyl-3H-imidazo[4,5-b]pyridines, a valuable scaffold in drug design.

Catalyst-free activation of methylene chloride and alkynes by amines in a three-component coupling reaction to synthesize propargylamines.

PubMed

Rawat, Vikas S; Bathini, Thulasiram; Govardan, S; Sreedhar, Bojja

2014-09-14

Propargylamines are synthesized via metal-free activation of the C-halogen bond of dihalomethanes and the C-H bond of terminal alkynes in a three-component coupling without catalyst or additional base and under mild reaction conditions. The dihalomethanes are used both as solvents as well as precursors for the methylene fragment (C1) in the final product. The scope of the reaction and the influence of various reaction variables has been investigated. A plausible reaction mechanism is proposed and the involvement of various intermediates that can be generated in situ in the process is discussed. The metal-free conditions also make this protocol environmentally benign and atom economical.

Linear alkane polymerization on a gold surface.

PubMed

Zhong, Dingyong; Franke, Jörn-Holger; Podiyanachari, Santhosh Kumar; Blömker, Tobias; Zhang, Haiming; Kehr, Gerald; Erker, Gerhard; Fuchs, Harald; Chi, Lifeng

2011-10-14

In contrast to the many methods of selectively coupling olefins, few protocols catenate saturated hydrocarbons in a predictable manner. We report here the highly selective carbon-hydrogen (C-H) activation and subsequent dehydrogenative C-C coupling reaction of long-chain (>C(20)) linear alkanes on an anisotropic gold(110) surface, which undergoes an appropriate reconstruction by adsorption of the molecules and subsequent mild annealing, resulting in nanometer-sized channels (1.22 nanometers in width). Owing to the orientational constraint of the reactant molecules in these one-dimensional channels, the reaction takes place exclusively at specific sites (terminal CH(3) or penultimate CH(2) groups) in the chains at intermediate temperatures (420 to 470 kelvin) and selects for aliphatic over aromatic C-H activation.

Compact beam splitters in coupled waveguides using shortcuts to adiabaticity

NASA Astrophysics Data System (ADS)

Chen, Xi; Wen, Rui-Dan; Shi, Jie-Long; Tseng, Shuo-Yen

2018-04-01

There are various works on adiabatic (three) waveguide coupler devices but most are focused on the quantum optical analogies and the physics itself. We successfully apply shortcuts to adiabaticity techniques to the coupled waveguide system with a suitable length for integrated optics devices. Especially, the counter-diabatic driving protocol followed by unitary transformation overcomes the previously unrealistic implemention, and is used to design feasible and robust 1 × 2 and 1 × 3 beam splitters for symmetric and asymmetric three waveguide couplers. Numerical simulations with the beam propagation method demonstrate that these shortcut designs for beam splitters are shorter than the adiabatic ones, and also have a better tolerance than parallel waveguides resonant beam splitters with respect to spacing errors and wavelength variation.

Low-power, low-cost urinalysis system with integrated dipstick evaluation and microscopic analysis.

PubMed

Smith, Gennifer T; Li, Linkai; Zhu, Yue; Bowden, Audrey K

2018-06-21

We introduce a coupled dipstick and microscopy device for analyzing urine samples. The device is capable of accurately assessing urine dipstick results while simultaneously imaging the microscopic contents within the sample. We introduce a long working distance, cellphone-based microscope in combination with an oblique illumination scheme to accurately visualize and quantify particles within the urine sample. To facilitate accurate quantification, we couple the imaging set-up with a power-free filtration system. The proposed device is reusable, low-cost, and requires very little power. We show that results obtained with the proposed device and custom-built app are consistent with those obtained with the standard clinical protocol, suggesting the potential clinical utility of the device.

Quantum light in coupled interferometers for quantum gravity tests.

PubMed

Ruo Berchera, I; Degiovanni, I P; Olivares, S; Genovese, M

2013-05-24

In recent years quantum correlations have received a lot of attention as a key ingredient in advanced quantum metrology protocols. In this Letter we show that they provide even larger advantages when considering multiple-interferometer setups. In particular, we demonstrate that the use of quantum correlated light beams in coupled interferometers leads to substantial advantages with respect to classical light, up to a noise-free scenario for the ideal lossless case. On the one hand, our results prompt the possibility of testing quantum gravity in experimental configurations affordable in current quantum optics laboratories and strongly improve the precision in "larger size experiments" such as the Fermilab holometer; on the other hand, they pave the way for future applications to high precision measurements and quantum metrology.

Development of analytical methods for multiplex bio-assay with inductively coupled plasma mass spectrometry

PubMed Central

Ornatsky, Olga I.; Kinach, Robert; Bandura, Dmitry R.; Lou, Xudong; Tanner, Scott D.; Baranov, Vladimir I.; Nitz, Mark; Winnik, Mitchell A.

2008-01-01

Advances in the development of highly multiplexed bio-analytical assays with inductively coupled plasma mass spectrometry (ICP-MS) detection are discussed. Use of novel reagents specifically designed for immunological methods utilizing elemental analysis is presented. The major steps of method development, including selection of elements for tags, validation of tagged reagents, and examples of multiplexed assays, are considered in detail. The paper further describes experimental protocols for elemental tagging of antibodies, immunostaining of live and fixed human leukemia cells, and preparation of samples for ICP-MS analysis. Quantitative analysis of surface antigens on model cell lines using a cocktail of seven lanthanide labeled antibodies demonstrated high specificity and concordance with conventional immunophenotyping. PMID:19122859

Applying an Empirical Hydropathic Forcefield in Refinement May Improve Low-Resolution Protein X-Ray Crystal Structures

PubMed Central

Koparde, Vishal N.; Scarsdale, J. Neel; Kellogg, Glen E.

2011-01-01

Background The quality of X-ray crystallographic models for biomacromolecules refined from data obtained at high-resolution is assured by the data itself. However, at low-resolution, >3.0 Å, additional information is supplied by a forcefield coupled with an associated refinement protocol. These resulting structures are often of lower quality and thus unsuitable for downstream activities like structure-based drug discovery. Methodology An X-ray crystallography refinement protocol that enhances standard methodology by incorporating energy terms from the HINT (Hydropathic INTeractions) empirical forcefield is described. This protocol was tested by refining synthetic low-resolution structural data derived from 25 diverse high-resolution structures, and referencing the resulting models to these structures. The models were also evaluated with global structural quality metrics, e.g., Ramachandran score and MolProbity clashscore. Three additional structures, for which only low-resolution data are available, were also re-refined with this methodology. Results The enhanced refinement protocol is most beneficial for reflection data at resolutions of 3.0 Å or worse. At the low-resolution limit, ≥4.0 Å, the new protocol generated models with Cα positions that have RMSDs that are 0.18 Å more similar to the reference high-resolution structure, Ramachandran scores improved by 13%, and clashscores improved by 51%, all in comparison to models generated with the standard refinement protocol. The hydropathic forcefield terms are at least as effective as Coulombic electrostatic terms in maintaining polar interaction networks, and significantly more effective in maintaining hydrophobic networks, as synthetic resolution is decremented. Even at resolutions ≥4.0 Å, these latter networks are generally native-like, as measured with a hydropathic interactions scoring tool. PMID:21246043

Replacing the CCSDS Telecommand Protocol with the Next Generation Uplink (NGU)

NASA Technical Reports Server (NTRS)

Kazz, Greg J.; Greenberg, Ed; Burleigh, Scott C.

2012-01-01

The current CCSDS Telecommand (TC) Recommendations 1-3 have essentially been in use since the early 1960s. The purpose of this paper is to propose a successor protocol to TC. The current CCSDS recommendations can only accommodate telecommand rates up to approximately 1 mbit/s. However today's spacecraft are storehouses for software including software for Field Programmable Gate Arrays (FPGA) which are rapidly replacing unique hardware systems. Changes to flight software occasionally require uplinks to deliver very large volumes of data. In the opposite direction, high rate downlink missions that use acknowledged CCSDS File Delivery Protocol (CFDP)4 will increase the uplink data rate requirements. It is calculated that a 5 mbits/s downlink could saturate a 4 kbits/s uplink with CFDP downlink responses: negative acknowledgements (NAKs), FINISHs, End-of-File (EOF), Acknowledgements (ACKs). Moreover, it is anticipated that uplink rates of 10 to 20 mbits/s will be required to support manned missions. The current TC recommendations cannot meet these new demands. Specifically, they are very tightly coupled to the Bose-Chaudhuri-Hocquenghem (BCH) code in Ref. 2. This protocol requires that an uncorrectable BCH codeword delimit the TC frame and terminate the randomization process. This method greatly limits telecom performance since only the BCH code can support the protocol. More modern techniques such as the CCSDS Low Density Parity Check (LDPC)5 codes can provide a minimum performance gain of up to 6 times higher command data rates as long as sufficient power is available in the data. This paper will describe the proposed protocol format, trade-offs, and advantages offered, along with a discussion of how reliable communications takes place at higher nominal rates.

Evaluation of telomere length in human cardiac tissues using cardiac quantitative FISH.

PubMed

Sharifi-Sanjani, Maryam; Meeker, Alan K; Mourkioti, Foteini

2017-09-01

Telomere length has been correlated with various diseases, including cardiovascular disease and cancer. The use of currently available telomere-length measurement techniques is often restricted by the requirement of a large amount of cells (Southern-based techniques) or the lack of information on individual cells or telomeres (PCR-based methods). Although several methods have been used to measure telomere length in tissues as a whole, the assessment of cell-type-specific telomere length provides valuable information on individual cell types. The development of fluorescence in situ hybridization (FISH) technologies enables the quantification of telomeres in individual chromosomes, but the use of these methods is dependent on the availability of isolated cells, which prevents their use with fixed archival samples. Here we describe an optimized quantitative FISH (Q-FISH) protocol for measuring telomere length that bypasses the previous limitations by avoiding contributions from undesired cell types. We have used this protocol on small paraffin-embedded cardiac-tissue samples. This protocol describes step-by-step procedures for tissue preparation, permeabilization, cardiac-tissue pretreatment and hybridization with a Cy3-labeled telomeric repeat complementing (CCCTAA) 3 peptide nucleic acid (PNA) probe coupled with cardiac-specific antibody staining. We also describe how to quantify telomere length by means of the fluorescence intensity and area of each telomere within individual nuclei. This protocol provides comparative cell-type-specific telomere-length measurements in relatively small human cardiac samples and offers an attractive technique to test hypotheses implicating telomere length in various cardiac pathologies. The current protocol (from tissue collection to image procurement) takes ∼28 h along with three overnight incubations. We anticipate that the protocol could be easily adapted for use on different tissue types.

Theoretical Characterization of the Spectral Density of the Water-Soluble Chlorophyll-Binding Protein from Combined Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulations.

PubMed

Rosnik, Andreana M; Curutchet, Carles

2015-12-08

Over the past decade, both experimentalists and theorists have worked to develop methods to describe pigment-protein coupling in photosynthetic light-harvesting complexes in order to understand the molecular basis of quantum coherence effects observed in photosynthesis. Here we present an improved strategy based on the combination of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations and excited-state calculations to predict the spectral density of electronic-vibrational coupling. We study the water-soluble chlorophyll-binding protein (WSCP) reconstituted with Chl a or Chl b pigments as the system of interest and compare our work with data obtained by Pieper and co-workers from differential fluorescence line-narrowing spectra (Pieper et al. J. Phys. Chem. B 2011, 115 (14), 4042-4052). Our results demonstrate that the use of QM/MM MD simulations where the nuclear positions are still propagated at the classical level leads to a striking improvement of the predicted spectral densities in the middle- and high-frequency regions, where they nearly reach quantitative accuracy. This demonstrates that the so-called "geometry mismatch" problem related to the use of low-quality structures in QM calculations, not the quantum features of pigments high-frequency motions, causes the failure of previous studies relying on similar protocols. Thus, this work paves the way toward quantitative predictions of pigment-protein coupling and the comprehension of quantum coherence effects in photosynthesis.

Bayesian deconvolution and quantification of metabolites in complex 1D NMR spectra using BATMAN.

PubMed

Hao, Jie; Liebeke, Manuel; Astle, William; De Iorio, Maria; Bundy, Jacob G; Ebbels, Timothy M D

2014-01-01

Data processing for 1D NMR spectra is a key bottleneck for metabolomic and other complex-mixture studies, particularly where quantitative data on individual metabolites are required. We present a protocol for automated metabolite deconvolution and quantification from complex NMR spectra by using the Bayesian automated metabolite analyzer for NMR (BATMAN) R package. BATMAN models resonances on the basis of a user-controllable set of templates, each of which specifies the chemical shifts, J-couplings and relative peak intensities for a single metabolite. Peaks are allowed to shift position slightly between spectra, and peak widths are allowed to vary by user-specified amounts. NMR signals not captured by the templates are modeled non-parametrically by using wavelets. The protocol covers setting up user template libraries, optimizing algorithmic input parameters, improving prior information on peak positions, quality control and evaluation of outputs. The outputs include relative concentration estimates for named metabolites together with associated Bayesian uncertainty estimates, as well as the fit of the remainder of the spectrum using wavelets. Graphical diagnostics allow the user to examine the quality of the fit for multiple spectra simultaneously. This approach offers a workflow to analyze large numbers of spectra and is expected to be useful in a wide range of metabolomics studies.

Standardised surface electromyography allows effective submental muscles assessment.

PubMed

Musto, Federica; Rosati, Riccardo; Sforza, Chiarella; Toma, Marilisa; Dellavia, Claudia

2017-06-01

The aims of this pilot study were to evaluate: (i) the reproducibility and variability of an electromyographical protocol developed for the assessment of submental muscles (SM) (ii) to apply the new protocol to maximal teeth clenching, a simple and largely studied static task in order to quantify the relative contribution of submental muscles. In 20 healthy subjects, aged 19-35years, surface electromyography of SM, masseter (MM) and anterior temporalis (TA) muscles was performed during maximal voluntary clenching (MVC) with and without cotton rolls and the pushing of the tongue against the palate. Clenching on cotton rolls and pushing the tongue against the palate were used to standardise respectively MM and TA, and SM muscular potentials. The exercises were repeated in two appointments (T1-T2); submental muscles standardisation was also repeated twice (A-B) in each session to assess repeatability. Symmetry and activity were calculated for each couple of muscles. A two-way analysis of variance was computed for SM: no Factor 1 (T1 vs T2) or Factor 2 (A vs B) or F1×F2 significant effects were found. SM recruitment was 31% of the maximal activity, with symmetry values larger than 80%. In conclusion, standardised electromyography allows a reliable assessment of Submental muscles activity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Overview of Five-Years of Experience Performing Non-Invasive Fetal Sex Assessment in Maternal Blood

PubMed Central

Perlado-Marina, Sara; Bustamante-Aragones, Ana; Horcajada, Laura; Trujillo-Tiebas, Maria Jose; Lorda-Sanchez, Isabel; Ruiz Ramos, Marta; Plaza, Javier; Rodriguez de Alba, Marta

2013-01-01

Since the discovery of the presence of fetal DNA in maternal blood, non-invasive fetal sex determination has been the test most widely translated into clinical practice. To date there is no agreement between the different laboratories performing such tests in relation to which is the best protocol. As a consequence there are almost as many protocols as laboratories offering the service, using different methodologies and thus obtaining different diagnostic accuracies. By the end of 2007, after a validation study performed in 316 maternal samples collected between the 5th and 12th week of gestation, the fetal sex determination was incorporated into clinical practice in our Service. The test is performed in the first trimester of pregnancy, and it is offered as part of the genetic counseling process for couples at risk of X-linked disorders. As a general rule and in order to avoid misdiagnosis, two samples at different gestational ages are tested per patient. The analysis is performed by the study of the SRY gene by RT-PCR. Two hundred and twenty six pregnancies have been tested so far in these 5 years. Neither false positives nor false negatives diagnoses have been registered, thus giving a diagnostic accuracy of 100%. PMID:26835681

Scalable quantum information processing with photons and atoms

NASA Astrophysics Data System (ADS)

Pan, Jian-Wei

Over the past three decades, the promises of super-fast quantum computing and secure quantum cryptography have spurred a world-wide interest in quantum information, generating fascinating quantum technologies for coherent manipulation of individual quantum systems. However, the distance of fiber-based quantum communications is limited due to intrinsic fiber loss and decreasing of entanglement quality. Moreover, probabilistic single-photon source and entanglement source demand exponentially increased overheads for scalable quantum information processing. To overcome these problems, we are taking two paths in parallel: quantum repeaters and through satellite. We used the decoy-state QKD protocol to close the loophole of imperfect photon source, and used the measurement-device-independent QKD protocol to close the loophole of imperfect photon detectors--two main loopholes in quantum cryptograph. Based on these techniques, we are now building world's biggest quantum secure communication backbone, from Beijing to Shanghai, with a distance exceeding 2000 km. Meanwhile, we are developing practically useful quantum repeaters that combine entanglement swapping, entanglement purification, and quantum memory for the ultra-long distance quantum communication. The second line is satellite-based global quantum communication, taking advantage of the negligible photon loss and decoherence in the atmosphere. We realized teleportation and entanglement distribution over 100 km, and later on a rapidly moving platform. We are also making efforts toward the generation of multiphoton entanglement and its use in teleportation of multiple properties of a single quantum particle, topological error correction, quantum algorithms for solving systems of linear equations and machine learning. Finally, I will talk about our recent experiments on quantum simulations on ultracold atoms. On the one hand, by applying an optical Raman lattice technique, we realized a two-dimensional spin-obit (SO) coupling and topological bands with ultracold bosonic atoms. A controllable crossover between 2D and 1D SO couplings is studied, and the SO effects and nontrivial band topology are observe. On the other hand, utilizing a two-dimensional spin-dependent optical superlattice and a single layer of atom cloud, we directly observed the four-body ring-exchange coupling and the Anyonic fractional statistics.

Accurate structure, thermodynamics and spectroscopy of medium-sized radicals by hybrid Coupled Cluster/Density Functional Theory approaches: the case of phenyl radical

PubMed Central

Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Egidi, Franco; Puzzarini, Cristina

2015-01-01

The CCSD(T) model coupled with extrapolation to the complete basis-set limit and additive approaches represents the “golden standard” for the structural and spectroscopic characterization of building blocks of biomolecules and nanosystems. However, when open-shell systems are considered, additional problems related to both specific computational difficulties and the need of obtaining spin-dependent properties appear. In this contribution, we present a comprehensive study of the molecular structure and spectroscopic (IR, Raman, EPR) properties of the phenyl radical with the aim of validating an accurate computational protocol able to deal with conjugated open-shell species. We succeeded in obtaining reliable and accurate results, thus confirming and, partly, extending the available experimental data. The main issue to be pointed out is the need of going beyond the CCSD(T) level by including a full treatment of triple excitations in order to fulfil the accuracy requirements. On the other hand, the reliability of density functional theory in properly treating open-shell systems has been further confirmed. PMID:23802956

Use of the Wilkinson catalyst for the ortho-C-H heteroarylation of aromatic amines: facile access to highly extended π-conjugated heteroacenes for organic semiconductors.

PubMed

Huang, Yumin; Wu, Di; Huang, Jingsheng; Guo, Qiang; Li, Juan; You, Jingsong

2014-11-03

An unprecedented catalytic system composed of the Wilkinson catalyst [Rh(PPh3)3Cl] and CF3COOH enabled the highly regioselective cross-coupling of aromatic amines with a variety of heteroarenes through dual C-H bond cleavage. This protocol provided a facile and rapid route from readily available substrates to (2-aminophenyl)heteroaryl compounds, which may be conveniently transformed into highly extended π-conjugated heteroacenes. The experimental studies and calculations showed that thianaphtheno[3,2-b]indoles have large HOMO-LUMO energy gaps and low-lying HOMO levels, and could therefore potentially be high-performance organic semiconductors. Herein we report the first use of a rhodium(I) catalyst for oxidative C-H/C-H coupling reactions. The current innovative catalyst system is much less expensive than [RhCp*Cl2]2/AgSbF6 and could open the door for the application of this approach to other types of C-H activation processes. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Two-Dimensional Electronic Spectroscopy of Benzene, Phenol, and Their Dimer: An Efficient First-Principles Simulation Protocol.

PubMed

Nenov, Artur; Mukamel, Shaul; Garavelli, Marco; Rivalta, Ivan

2015-08-11

First-principles simulations of two-dimensional electronic spectroscopy in the ultraviolet region (2DUV) require computationally demanding multiconfigurational approaches that can resolve doubly excited and charge transfer states, the spectroscopic fingerprints of coupled UV-active chromophores. Here, we propose an efficient approach to reduce the computational cost of accurate simulations of 2DUV spectra of benzene, phenol, and their dimer (i.e., the minimal models for studying electronic coupling of UV-chromophores in proteins). We first establish the multiconfigurational recipe with the highest accuracy by comparison with experimental data, providing reference gas-phase transition energies and dipole moments that can be used to construct exciton Hamiltonians involving high-lying excited states. We show that by reducing the active spaces and the number of configuration state functions within restricted active space schemes, the computational cost can be significantly decreased without loss of accuracy in predicting 2DUV spectra. The proposed recipe has been successfully tested on a realistic model proteic system in water. Accounting for line broadening due to thermal and solvent-induced fluctuations allows for direct comparison with experiments.

Effects of dominant and non-dominant passive arm manoeuvres on the neurovascular coupling response.

PubMed

Llwyd, Osian; Panerai, Ronney B; Robinson, Thompson G

2017-11-01

Models designed to study neurovascular coupling (NVC) describe a possible cerebral hemisphere dominance dependent on task completed and preference in handedness. We investigated whether passive arm manoeuvre performed with dominant (Dom-Arm) or non-dominant arm (ND-Arm) stimulated haemodynamic differences in either contralateral (Cont-H) or ipsilateral (Ipsil-H) cerebral hemisphere. Healthy individuals lying in supine position, had measurements of beat-to-beat blood pressure (BP, mmHg), electrocardiogram (HR, bpm), end-tidal CO 2 (etCO 2 , mmHg), and bilateral insonation of the middle cerebral arteries (MCA, cm s -1 ). Arm movement was performed for 60 s with passive flexion and extension of the elbow (1 Hz), before manoeuvre was repeated on other arm. Data were normalised and effect of treatment was analysed for differences between manoeuvres and within each time period. Seventeen (eight males) healthy volunteers, aged 56 ± 7 years, were studied. Dom-Arm and ND-Arm manoeuvres stimulated a comparable temporal response in peripheral and cerebral haemodynamic parameters between Cont-H and Ipsil-H. Both manoeuvres can be used to evoke similar bilateral MCA responses in assessing NVC. This finding should lead to more efficient protocols when using passive arm movement for NVC studies in healthy subjects.

21 CFR 58.120 - Protocol.

Code of Federal Regulations, 2010 CFR

2010-04-01

... FOR NONCLINICAL LABORATORY STUDIES Protocol for and Conduct of a Nonclinical Laboratory Study § 58.120 Protocol. (a) Each study shall have an approved written protocol that clearly indicates the objectives and all methods for the conduct of the study. The protocol shall contain, as applicable, the following...

Validation of the Medipro MediCare 100f upper arm blood pressure monitor, for self-measurement, according to the European Society of Hypertension International Protocol revision 2010.

PubMed

Yi, Jun; Wan, Yi; Pan, Feng; Yu, Xiaorong; Zhao, Huadong; Shang, Fujun; Xu, Yongyong

2011-08-01

The validation of sphygmomanometer is important in accurate blood pressure measurement. This study presents the validation results by the Medipro MediCare 100f upper arm blood pressure monitor according to the European Society of Hypertension International Protocol (ESH-IP) revision 2010. The ESH-IP revision 2010 for the validation of blood pressure measuring devices in adults was followed precisely. A total of 99 couples of test device and reference blood pressure measurements were obtained during the study (three pairs for each of the 33 participants). The device produced 73, 93, and 98 measurements within 5, 10, and 15 mmHg for systolic blood pressure (SBP) and 79, 93, and 96 for diastolic blood pressure (DBP), respectively. The mean standard deviation device-observer difference was 1.4 ± 5.2 mmHg for SBP and 0.02±5.8 mmHg for DBP. The number of participants with two or three of the device-observer differences within 5 mmHg was 24 for SBP and 30 for DBP, whereas there was no participant with none of the device-observer differences within 5 mmHg. According to the results of the validation study based on the ESH-IP revision 2010, the Medipro MediCare 100f can be recommended for self-measurement in an adult population.

On-line separation and characterization of hyaluronan oligosaccharides derived from radical depolymerization

PubMed Central

Zhao, Xue; Yang, Bo; Li, Lingyun; Zhang, Fuming; Linhardt, Robert J.

2013-01-01

Hydroxyl radicals are widely implicated in the oxidation of carbohydrates in biological and industrial processes and are often responsible for their structural modification resulting in functional damage. In this study, the radical depolymerization of the polysaccharide hyaluronan was studied in a reaction with hydroxyl radicals generated by Fenton Chemistry. A simple method for isolation and identification of the resulting non-sulfated oligosaccharide products of oxidative depolymerization was established. Hyaluronan oligosaccharides were analyzed using ion-pairing reversed phase high performance liquid chromotography coupled with tandem electrospray mass spectrometry. The sequence of saturated hyaluronan oligosaccharides having even- and odd-numbers of saccharide units, afforded through oxidative depolymerization, were identified. This study represents a simple, effective ‘fingerprinting’ protocol for detecting the damage done to hyaluronan by oxidative radicals. This study should help reveal the potential biological outcome of reactive-oxygen radical-mediated depolymerization of hyaluronan. PMID:23768593

Pathogen Reduced, Plasmalyte Extended Stored Platelets

DTIC Science & Technology

2017-10-01

products of very different signal strengths . In May 2017 we modified the protocol to replace the chromium label with a second indium label of fresh...failing to comply with a collection of information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO...determine the efficacy of using a pathogen inactivation technique (Mirasol) coupled with a platelet additive solution (PAS) to extend the life of stored

Preparation of gold nanocluster bioconjugates for electron microscopy.

PubMed

Heinecke, Christine L; Ackerson, Christopher J

2013-01-01

In this chapter, we describe types of gold nanoparticle-biomolecule conjugates and their use in electron microscopy. Included are two detailed protocols for labeling an IgG antibody with gold monolayer protected clusters. The first approach is a direct bonding approach that utilizes the ligand place exchange reaction. The second approach describes NHS-EDC coupling of Au(144)(pMBA)(60) with IgG. Also included are various characterization techniques for determining labeling efficiency.

Diversity-oriented synthesis of dihydrobenzoxazepinones by coupling the Ugi multicomponent reaction with a Mitsunobu cyclization

PubMed Central

Moni, Lisa; Banfi, Luca; Basso, Andrea; Brambilla, Alice

2014-01-01

Summary An operationally simple protocol for the synthesis of 2,3-dihydrobenzo[f][1,4]oxazepin-3-ones, based on an Ugi reaction of an ortho-(benzyloxy)benzylamine, glycolic acid, an isocyanide and an aldehyde, followed by an intramolecular Mitsunobu substitution was developed. The required ortho-(benzyloxy)benzylamines have been in situ generated from the corresponding azides, in turn prepared in high yields from salicylic derivatives. PMID:24605140

Nickel-catalyzed sp2 C-H bonds arylation of N-aromatic heterocycles with Grignard reagents at room temperature.

PubMed

Qu, Gui-Rong; Xin, Peng-Yang; Niu, Hong-Ying; Wang, Dong-Chao; Ding, Rui-Fang; Guo, Hai-Ming

2011-10-21

A novel protocol for nickel-catalyzed direct sp(2) C-H bond arylation of purines has been developed. This new reaction proceeded efficiently at room temperature using Grignard reagent as the coupling partner within 5 hours in good to high yields. This approach provides a new access to a variety of C8-arylpurines which are potentially of great importance in medicinal chemistry.

Detection-enhanced steady state entanglement with ions.

PubMed

Bentley, C D B; Carvalho, A R R; Kielpinski, D; Hope, J J

2014-07-25

Driven dissipative steady state entanglement schemes take advantage of coupling to the environment to robustly prepare highly entangled states. We present a scheme for two trapped ions to generate a maximally entangled steady state with fidelity above 0.99, appropriate for use in quantum protocols. Furthermore, we extend the scheme by introducing detection of our dissipation process, significantly enhancing the fidelity. Our scheme is robust to anomalous heating and requires no sympathetic cooling.

Predictive Factors of Patients' and Their Partners' Sexual Function Improvement After Collagenase Clostridium Histolyticum Injection for Peyronie's Disease: Results From a Multi-Center Single-Arm Study.

PubMed

Cocci, Andrea; Russo, Giorgio Ivan; Salonia, Andrea; Cito, Gianmartin; Regis, Federica; Polloni, Gaia; Giubilei, Gianluca; Cacciamani, Giovanni; Capece, Marco; Falcone, Marco; Greco, Isabella; Timpano, Massimiliano; Minervini, Andrea; Gacci, Mauro; Cai, Tommaso; Garaffa, Giulio; Giammusso, Bruno; Arcaniolo, Davide; Mirone, Vincenzo; Mondaini, Nicola

2018-05-01

Collagenase Clostridium histolyticum (CCH; Xiapex) injections represent the only licensed medical treatment for Peyronie's disease (PD). To evaluate the efficacy and safety of CCH injections in men with stable PD, using a modified treatment protocol and to assess partners' bother improvement in a large cohort of White-European sexually active heterosexual men treated in a single tertiary-referral center. All the 135 patients enrolled underwent a thorough assessment, which included history taking, physical examination, and pharmacologically induced artificial erection test (intra-cavernous injection) to assess the degree of penile curvature (PC) at baseline and after the completion of the treatment. Patients with calcified plaque and/or ventral curvature were excluded. All patients underwent a modified treatment protocol, which consisted of 3 intra-lesional injections of 0.9 mg of CCH performed at 4-week intervals at the point of maximum curvature. After each injection, patients were instructed to follow a strict routine involving daily penile stretching in the intervals between injections. International Index of Erectile Function (IIEF)-15, Global Assessment of PD, PD questionnaires (PDQ), and Female Sexual Function Index (FSFI) questionnaire were performed at baseline and at the end of treatment. Overall, 135 patients completed the study protocol. Before treatment, 18 (13.33%) partners showed a degree of sexual dysfunction. Baseline median IIEF-15, FSFI, and PDQ scores were, respectively, 59.0, 35.0, and 23.0. Overall, both IIEF-total and all domains significantly improved after treatment (all P < .01). A PC mean change of 19.07 (P = .00) was measured. At the univariate linear regression analysis, IIEF-15, IIEF-erectile function, IIEF-sexual desire, and IIEF-intercourse satisfaction were positively associated with FSFI (all P ≤ .03); conversely, PDQ-penile pain, PDQ-symptom bother, and post-treament penile curvature (P ≤ .04) were associated with a decreased FSFI score. Furthermore, median change of PC was significantly associated with median change of FSFI (r = 0.25; 95% CI 0.02-0.11; P = .004). Global satisfaction after treatment was 89.6% (121/135). This modified CCH treatment protocol could improve both patients' and partner's sexual function. This was an open-label, single-arm clinical study, without placebo. where only heterosexual couples in stable relationships were included. Furthermore, no real assessment of female sexual distress was carried out and long-term sexual function in both patients and female partners were not taken into account. The modified treatment schedule with CCH injections for stable PD has a positive impact on both patients' and partners' sexual function in heterosexual couples with a stable sexual relationship. Cocci A, Russo GI, Salonia A, et al. Predictive Factors of Patients' and Their Partners' Sexual Function Improvement After Collagenase Clostridium Histolyticum Injection for Peyronie's Disease: Results From a Multi-Center Single-Arm Study. J Sex Med 2018;15:716-721. Copyright © 2018 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.

Stacking sequence and interlayer coupling in few-layer graphene revealed by in situ imaging

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

Wang, Zhu-Jun; Dong, Jichen; Cui, Yi

In the transition from graphene to graphite, the addition of each individual graphene layer modifies the electronic structure and produces a different material with unique properties. Controlled growth of few-layer graphene is therefore of fundamental interest and will provide access to materials with engineered electronic structure. Here we combine isothermal growth and etching experiments with in situ scanning electron microscopy to reveal the stacking sequence and interlayer coupling strength in few-layer graphene. The observed layer-dependent etching rates reveal the relative strength of the graphene graphene and graphene substrate interaction and the resulting mode of adlayer growth. Scanning tunnelling microscopy andmore » density functional theory calculations confirm a strong coupling between graphene edge atoms and platinum. Simulated etching confirms that etching can be viewed as reversed growth. This work demonstrates that real-time imaging under controlled atmosphere is a powerful method for designing synthesis protocols for sp2 carbon nanostructures in between graphene and graphite.« less

Stacking sequence and interlayer coupling in few-layer graphene revealed by in situ imaging

DOE PAGES

Wang, Zhu-Jun; Dong, Jichen; Cui, Yi; ...

2016-10-19

In the transition from graphene to graphite, the addition of each individual graphene layer modifies the electronic structure and produces a different material with unique properties. Controlled growth of few-layer graphene is therefore of fundamental interest and will provide access to materials with engineered electronic structure. Here we combine isothermal growth and etching experiments with in situ scanning electron microscopy to reveal the stacking sequence and interlayer coupling strength in few-layer graphene. The observed layer-dependent etching rates reveal the relative strength of the graphene graphene and graphene substrate interaction and the resulting mode of adlayer growth. Scanning tunnelling microscopy andmore » density functional theory calculations confirm a strong coupling between graphene edge atoms and platinum. Simulated etching confirms that etching can be viewed as reversed growth. This work demonstrates that real-time imaging under controlled atmosphere is a powerful method for designing synthesis protocols for sp2 carbon nanostructures in between graphene and graphite.« less

Oxidative C-H/C-H Cross-Coupling Reactions between N-Acylanilines and Benzamides Enabled by a Cp*-Free RhCl3/TFA Catalytic System.

PubMed

You, Jingsong; Shi, Yang; Zhang, Luoqiang; Lan, Jingbo; Zhang, Min; Zhou, Fulin; Wei, Wenlong

2018-06-03

Using the dual chelation-assisted strategy, a completely regiocontrolled oxidative C-H/C-H cross-coupling reaction between an N-acylaniline and a benzamide has been accomplished for the first time, which enables a step-economical and highly efficient pathway to 2-amino-2'-carboxybiaryl scaffolds from readily available substrates. A Cp*-free RhCl3/TFA catalytic system has been developed to replace the generally used [Cp*RhCl2]2/AgSbF6 (Cp* = pentamethyl cyclopentadienyl) in oxidative C-H/C-H cross-coupling reactions between two (hetero)arenes. The RhCl3/TFA system avoids the use of expensive Cp* ligand and AgSbF6. As an illustrative example, the protocol developed herein greatly streamlines access to naturally occurring benzo[c]phenanthridine alkaloid oxynitidine in an excellent overall yield. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stacking sequence and interlayer coupling in few-layer graphene revealed by in situ imaging

PubMed Central

Wang, Zhu-Jun; Dong, Jichen; Cui, Yi; Eres, Gyula; Timpe, Olaf; Fu, Qiang; Ding, Feng; Schloegl, R.; Willinger, Marc-Georg

2016-01-01

In the transition from graphene to graphite, the addition of each individual graphene layer modifies the electronic structure and produces a different material with unique properties. Controlled growth of few-layer graphene is therefore of fundamental interest and will provide access to materials with engineered electronic structure. Here we combine isothermal growth and etching experiments with in situ scanning electron microscopy to reveal the stacking sequence and interlayer coupling strength in few-layer graphene. The observed layer-dependent etching rates reveal the relative strength of the graphene–graphene and graphene–substrate interaction and the resulting mode of adlayer growth. Scanning tunnelling microscopy and density functional theory calculations confirm a strong coupling between graphene edge atoms and platinum. Simulated etching confirms that etching can be viewed as reversed growth. This work demonstrates that real-time imaging under controlled atmosphere is a powerful method for designing synthesis protocols for sp2 carbon nanostructures in between graphene and graphite. PMID:27759024

Quantum critical probing and simulation of colored quantum noise

NASA Astrophysics Data System (ADS)

Mascarenhas, Eduardo; de Vega, Inés

2017-12-01

We propose a protocol to simulate the evolution of a non-Markovian open quantum system by considering a collisional process with a many-body system, which plays the role of an environment. As a result of our protocol, the environment spatial correlations are mapped into the time correlations of a noise that drives the dynamics of the open system. Considering the weak coupling limit, the open system can also be considered as a probe of the environment properties. In this regard, when preparing the environment in its ground state, a measurement of the dynamics of the open system allows to determine the length of the environment spatial correlations and therefore its critical properties. To illustrate our proposal we simulate the full system dynamics with matrix-product-states and compare this to the reduced dynamics obtained with an approximated variational master equation.

A high-throughput microRNA expression profiling system.

PubMed

Guo, Yanwen; Mastriano, Stephen; Lu, Jun

2014-01-01

As small noncoding RNAs, microRNAs (miRNAs) regulate diverse biological functions, including physiological and pathological processes. The expression and deregulation of miRNA levels contain rich information with diagnostic and prognostic relevance and can reflect pharmacological responses. The increasing interest in miRNA-related research demands global miRNA expression profiling on large numbers of samples. We describe here a robust protocol that supports high-throughput sample labeling and detection on hundreds of samples simultaneously. This method employs 96-well-based miRNA capturing from total RNA samples and on-site biochemical reactions, coupled with bead-based detection in 96-well format for hundreds of miRNAs per sample. With low-cost, high-throughput, high detection specificity, and flexibility to profile both small and large numbers of samples, this protocol can be adapted in a wide range of laboratory settings.

An introduction to planar chromatography and its application to natural products isolation.

PubMed

Gibbons, Simon

2012-01-01

Thin-layer chromatography (TLC) is an easy, inexpensive, rapid, and the most widely used method for the analysis and isolation of small organic natural and synthetic products. It also has use in the biological evaluation of organic compounds, particularly in the areas of antimicrobial and antioxidant metabolites and for the evaluation of acetylcholinesterase inhibitors which have utility in the treatment of Alzheimer's disease. The ease and inexpensiveness of use of this technique, coupled with the ability to rapidly develop separation and bioassay protocols will ensure that TLC will be used for some considerable time alongside conventional instrumental methods. This chapter deals with the basic principles of TLC and describes methods for the analysis and isolation of natural products. Examples of methods for isolation of several classes of natural product are detailed and protocols for TLC bioassays are given.

An eco-compatible strategy for the diversity-oriented synthesis of macrocycles exploiting carbohydrate-derived building blocks.

PubMed

Maurya, Sushil K; Rana, Rohit

2017-01-01

An efficient, eco-compatible diversity-oriented synthesis (DOS) approach for the generation of library of sugar embedded macrocyclic compounds with various ring size containing 1,2,3-triazole has been developed. This concise strategy involves the iterative use of readily available sugar-derived alkyne/azide-alkene building blocks coupled through copper catalyzed azide-alkyne cycloaddition (CuAAC) reaction followed by pairing of the linear cyclo-adduct using greener reaction conditions. The eco-compatibility, mild reaction conditions, greener solvents, easy purification and avoidance of hazards and toxic solvents are advantages of this protocol to access this important structural class. The diversity of the macrocycles synthesized (in total we have synthesized 13 macrocycles) using a set of standard reaction protocols demonstrate the potential of the new eco-compatible approach for the macrocyclic library generation.

Role of AMPA and NMDA receptors and back-propagating action potentials in spike timing-dependent plasticity.

PubMed

Fuenzalida, Marco; Fernández de Sevilla, David; Couve, Alejandro; Buño, Washington

2010-01-01

The cellular mechanisms that mediate spike timing-dependent plasticity (STDP) are largely unknown. We studied in vitro in CA1 pyramidal neurons the contribution of AMPA and N-methyl-d-aspartate (NMDA) components of Schaffer collateral (SC) excitatory postsynaptic potentials (EPSPs; EPSP(AMPA) and EPSP(NMDA)) and of the back-propagating action potential (BAP) to the long-term potentiation (LTP) induced by a STDP protocol that consisted in pairing an EPSP and a BAP. Transient blockade of EPSP(AMPA) with 7-nitro-2,3-dioxo-1,4-dihydroquinoxaline-6-carbonitrile (CNQX) during the STDP protocol prevented LTP. Contrastingly LTP was induced under transient inhibition of EPSP(AMPA) by combining SC stimulation, an imposed EPSP(AMPA)-like depolarization, and BAP or by coupling the EPSP(NMDA) evoked under sustained depolarization (approximately -40 mV) and BAP. In Mg(2+)-free solution EPSP(NMDA) and BAP also produced LTP. Suppression of EPSP(NMDA) or BAP always prevented LTP. Thus activation of NMDA receptors and BAPs are needed but not sufficient because AMPA receptor activation is also obligatory for STDP. However, a transient depolarization of another origin that unblocks NMDA receptors and a BAP may also trigger LTP.

In Vitro Propagation and Conservation of Bacopa monnieri L.

PubMed

Sharma, Neelam; Singh, Rakesh; Pandey, Ruchira

2016-01-01

Bacopa monnieri L. (common name brahmi) is a traditional and renowned Indian medicinal plant with high commercial value for its memory revitalizer potential. Demand for this herb has further escalated due to popularization of various brahmi-based drugs coupled with reported anticancer property. Insufficient seed availability and problems associated with seed propagation including short seed viability are the major constraints of seed conservation in the gene banks. In vitro clonal propagation, a prerequisite for in vitro conservation by enhanced axillary branching was standardized. We have developed a simple, single step protocol for in vitro establishment, propagation and medium-term conservation of B. monnieri. Single node explants, cultured on Murashige and Skoog's medium supplemented with BA (0.2 mg/L), exhibited shoot proliferation without callus formation. Rooting was achieved on the same medium. The in vitro raised plants were successfully transferred to soil with ~80 % survival. On the same medium, shoots could also be conserved for 12 months with high survival and genetic stability was maintained as revealed by molecular markers. The protocol optimized in the present study has been applied for culture establishment, shoot multiplication and medium-term conservation of several Bacopa germplasm, procured from different agro-ecological regions of India.

Changes in long luteal protocol affects the number of days of stimulation: evolution of an assisted reproductive technology practice.

PubMed

Palmer, C Benjamin; Forstein, David A; Higdon, H Lee; Boone, William R

2011-01-01

To determine if the types of drugs used in controlled ovarian hyperstimulation influence the number of days of stimulation. This retrospective study of couples presenting at an assisted reproductive technology (ART) facility January 1997 through December 2007 included patients who were < 40 years of age, had a body mass index (BMI) of 20-35, used fresh sperm or oocytes, had > or = 3 embryos available on day 3, never had previous ART, and did not use a gestational carrier. Data analysis was limited to patients treated with long luteal stimulation. Data were separated into two groups: patients stimulated with urinary drugs and those stimulated with recombinant drugs. The groups were not different in age and day 3 follicle-stimulating hormone values, but were different in BMI, diagnoses, and fertilization methods. There were a significantly greater number of days of stimulation, total number of follicles produced, and peak estradiol level in the recombinant group. The recombinant group had less drug given per day, less endometrial thickness, and fewer embryos transferred. A change in our long luteal stimulation protocol appears to have lengthened the days of stimulation for our patients without altering pregnancy rate.

Using the Real-Ear-to-Coupler Difference within the American Academy of Audiology Pediatric Amplification Guideline: Protocols for Applying and Predicting Earmold RECDs.

PubMed

Moodie, Sheila; Pietrobon, Jonathan; Rall, Eileen; Lindley, George; Eiten, Leisha; Gordey, Dave; Davidson, Lisa; Moodie, K Shane; Bagatto, Marlene; Haluschak, Meredith Magathan; Folkeard, Paula; Scollie, Susan

2016-03-01

Real-ear-to-coupler difference (RECD) measurements are used for the purposes of estimating degree and configuration of hearing loss (in dB SPL ear canal) and predicting hearing aid output from coupler-based measures. Accurate measurements of hearing threshold, derivation of hearing aid fitting targets, and predictions of hearing aid output in the ear canal assume consistent matching of RECD coupling procedure (i.e., foam tip or earmold) with that used during assessment and in verification of the hearing aid fitting. When there is a mismatch between these coupling procedures, errors are introduced. The goal of this study was to quantify the systematic difference in measured RECD values obtained when using a foam tip versus an earmold with various tube lengths. Assuming that systematic errors exist, the second goal was to investigate the use of a foam tip to earmold correction for the purposes of improving fitting accuracy when mismatched RECD coupling conditions occur (e.g., foam tip at assessment, earmold at verification). Eighteen adults and 17 children (age range: 3-127 mo) participated in this study. Data were obtained using simulated ears of various volumes and earmold tubing lengths and from patients using their own earmolds. Derived RECD values based on simulated ear measurements were compared with RECD values obtained for adult and pediatric ears for foam tip and earmold coupling. Results indicate that differences between foam tip and earmold RECDs are consistent across test ears for adults and children which support the development of a correction between foam tip and earmold couplings for RECDs that can be applied across individuals. The foam tip to earmold correction values developed in this study can be used to provide improved estimations of earmold RECDs. This may support better accuracy in acoustic transforms related to transforming thresholds and/or hearing aid coupler responses to ear canal sound pressure level for the purposes of fitting behind-the-ear hearing aids. American Academy of Audiology.

Dynamic whole-body PET parametric imaging: I. Concept, acquisition protocol optimization and clinical application.

PubMed

Karakatsanis, Nicolas A; Lodge, Martin A; Tahari, Abdel K; Zhou, Y; Wahl, Richard L; Rahmim, Arman

2013-10-21

Static whole-body PET/CT, employing the standardized uptake value (SUV), is considered the standard clinical approach to diagnosis and treatment response monitoring for a wide range of oncologic malignancies. Alternative PET protocols involving dynamic acquisition of temporal images have been implemented in the research setting, allowing quantification of tracer dynamics, an important capability for tumor characterization and treatment response monitoring. Nonetheless, dynamic protocols have been confined to single-bed-coverage limiting the axial field-of-view to ~15-20 cm, and have not been translated to the routine clinical context of whole-body PET imaging for the inspection of disseminated disease. Here, we pursue a transition to dynamic whole-body PET parametric imaging, by presenting, within a unified framework, clinically feasible multi-bed dynamic PET acquisition protocols and parametric imaging methods. We investigate solutions to address the challenges of: (i) long acquisitions, (ii) small number of dynamic frames per bed, and (iii) non-invasive quantification of kinetics in the plasma. In the present study, a novel dynamic (4D) whole-body PET acquisition protocol of ~45 min total length is presented, composed of (i) an initial 6 min dynamic PET scan (24 frames) over the heart, followed by (ii) a sequence of multi-pass multi-bed PET scans (six passes × seven bed positions, each scanned for 45 s). Standard Patlak linear graphical analysis modeling was employed, coupled with image-derived plasma input function measurements. Ordinary least squares Patlak estimation was used as the baseline regression method to quantify the physiological parameters of tracer uptake rate Ki and total blood distribution volume V on an individual voxel basis. Extensive Monte Carlo simulation studies, using a wide set of published kinetic FDG parameters and GATE and XCAT platforms, were conducted to optimize the acquisition protocol from a range of ten different clinically acceptable sampling schedules examined. The framework was also applied to six FDG PET patient studies, demonstrating clinical feasibility. Both simulated and clinical results indicated enhanced contrast-to-noise ratios (CNRs) for Ki images in tumor regions with notable background FDG concentration, such as the liver, where SUV performed relatively poorly. Overall, the proposed framework enables enhanced quantification of physiological parameters across the whole body. In addition, the total acquisition length can be reduced from 45 to ~35 min and still achieve improved or equivalent CNR compared to SUV, provided the true Ki contrast is sufficiently high. In the follow-up companion paper, a set of advanced linear regression schemes is presented to particularly address the presence of noise, and attempt to achieve a better trade-off between the mean-squared error and the CNR metrics, resulting in enhanced task-based imaging.

Dynamic whole body PET parametric imaging: I. Concept, acquisition protocol optimization and clinical application

PubMed Central

Karakatsanis, Nicolas A.; Lodge, Martin A.; Tahari, Abdel K.; Zhou, Y.; Wahl, Richard L.; Rahmim, Arman

2013-01-01

Static whole body PET/CT, employing the standardized uptake value (SUV), is considered the standard clinical approach to diagnosis and treatment response monitoring for a wide range of oncologic malignancies. Alternative PET protocols involving dynamic acquisition of temporal images have been implemented in the research setting, allowing quantification of tracer dynamics, an important capability for tumor characterization and treatment response monitoring. Nonetheless, dynamic protocols have been confined to single bed-coverage limiting the axial field-of-view to ~15–20 cm, and have not been translated to the routine clinical context of whole-body PET imaging for the inspection of disseminated disease. Here, we pursue a transition to dynamic whole body PET parametric imaging, by presenting, within a unified framework, clinically feasible multi-bed dynamic PET acquisition protocols and parametric imaging methods. We investigate solutions to address the challenges of: (i) long acquisitions, (ii) small number of dynamic frames per bed, and (iii) non-invasive quantification of kinetics in the plasma. In the present study, a novel dynamic (4D) whole body PET acquisition protocol of ~45min total length is presented, composed of (i) an initial 6-min dynamic PET scan (24 frames) over the heart, followed by (ii) a sequence of multi-pass multi-bed PET scans (6 passes x 7 bed positions, each scanned for 45sec). Standard Patlak linear graphical analysis modeling was employed, coupled with image-derived plasma input function measurements. Ordinary least squares (OLS) Patlak estimation was used as the baseline regression method to quantify the physiological parameters of tracer uptake rate Ki and total blood distribution volume V on an individual voxel basis. Extensive Monte Carlo simulation studies, using a wide set of published kinetic FDG parameters and GATE and XCAT platforms, were conducted to optimize the acquisition protocol from a range of 10 different clinically acceptable sampling schedules examined. The framework was also applied to six FDG PET patient studies, demonstrating clinical feasibility. Both simulated and clinical results indicated enhanced contrast-to-noise ratios (CNRs) for Ki images in tumor regions with notable background FDG concentration, such as the liver, where SUV performed relatively poorly. Overall, the proposed framework enables enhanced quantification of physiological parameters across the whole-body. In addition, the total acquisition length can be reduced from 45min to ~35min and still achieve improved or equivalent CNR compared to SUV, provided the true Ki contrast is sufficiently high. In the follow-up companion paper, a set of advanced linear regression schemes is presented to particularly address the presence of noise, and attempt to achieve a better trade-off between the mean-squared error (MSE) and the CNR metrics, resulting in enhanced task-based imaging. PMID:24080962

Dynamic whole-body PET parametric imaging: I. Concept, acquisition protocol optimization and clinical application

NASA Astrophysics Data System (ADS)

Karakatsanis, Nicolas A.; Lodge, Martin A.; Tahari, Abdel K.; Zhou, Y.; Wahl, Richard L.; Rahmim, Arman

2013-10-01

Static whole-body PET/CT, employing the standardized uptake value (SUV), is considered the standard clinical approach to diagnosis and treatment response monitoring for a wide range of oncologic malignancies. Alternative PET protocols involving dynamic acquisition of temporal images have been implemented in the research setting, allowing quantification of tracer dynamics, an important capability for tumor characterization and treatment response monitoring. Nonetheless, dynamic protocols have been confined to single-bed-coverage limiting the axial field-of-view to ˜15-20 cm, and have not been translated to the routine clinical context of whole-body PET imaging for the inspection of disseminated disease. Here, we pursue a transition to dynamic whole-body PET parametric imaging, by presenting, within a unified framework, clinically feasible multi-bed dynamic PET acquisition protocols and parametric imaging methods. We investigate solutions to address the challenges of: (i) long acquisitions, (ii) small number of dynamic frames per bed, and (iii) non-invasive quantification of kinetics in the plasma. In the present study, a novel dynamic (4D) whole-body PET acquisition protocol of ˜45 min total length is presented, composed of (i) an initial 6 min dynamic PET scan (24 frames) over the heart, followed by (ii) a sequence of multi-pass multi-bed PET scans (six passes × seven bed positions, each scanned for 45 s). Standard Patlak linear graphical analysis modeling was employed, coupled with image-derived plasma input function measurements. Ordinary least squares Patlak estimation was used as the baseline regression method to quantify the physiological parameters of tracer uptake rate Ki and total blood distribution volume V on an individual voxel basis. Extensive Monte Carlo simulation studies, using a wide set of published kinetic FDG parameters and GATE and XCAT platforms, were conducted to optimize the acquisition protocol from a range of ten different clinically acceptable sampling schedules examined. The framework was also applied to six FDG PET patient studies, demonstrating clinical feasibility. Both simulated and clinical results indicated enhanced contrast-to-noise ratios (CNRs) for Ki images in tumor regions with notable background FDG concentration, such as the liver, where SUV performed relatively poorly. Overall, the proposed framework enables enhanced quantification of physiological parameters across the whole body. In addition, the total acquisition length can be reduced from 45 to ˜35 min and still achieve improved or equivalent CNR compared to SUV, provided the true Ki contrast is sufficiently high. In the follow-up companion paper, a set of advanced linear regression schemes is presented to particularly address the presence of noise, and attempt to achieve a better trade-off between the mean-squared error and the CNR metrics, resulting in enhanced task-based imaging.

Publication trends of study protocols in rehabilitation.

PubMed

Jesus, Tiago S; Colquhoun, Heather L

2017-09-04

Growing evidence points for the need to publish study protocols in the health field. To observe whether the growing interest in publishing study protocols in the broader health field has been translated into increased publications of rehabilitation study protocols. Observational study using publication data and its indexation in PubMed. Not applicable. Not applicable. PubMed was searched with appropriate combinations of Medical Subject Headings up to December 2014. The effective presence of study protocols was manually screened. Regression models analyzed the yearly growth of publications. Two-sample Z-tests analyzed whether the proportion of Systematic Reviews (SRs) and Randomized Controlled Trials (RCTs) among study protocols differed from that of the same designs for the broader rehabilitation research. Up to December 2014, 746 publications of rehabilitation study protocols were identified, with an exponential growth since 2005 (r2=0.981; p<0.001). RCT protocols were the most common among rehabilitation study protocols (83%), while RCTs were significantly more prevalent among study protocols than among the broader rehabilitation research (83% vs. 35.8%; p<0.001). For SRs, the picture was reversed: significantly less common among study protocols (2.8% vs. 9.3%; p<0.001). Funding was more often reported by rehabilitation study protocols than the broader rehabilitation research (90% vs. 53.1%; p<0.001). Rehabilitation journals published a significantly lower share of rehabilitation study protocols than they did for the broader rehabilitation research (1.8% vs.16.7%; p<0.001). Identifying the reasons for these discrepancies and reverting unwarranted disparities (e.g. low rate of publication for rehabilitation SR protocols) are likely new avenues for rehabilitation research and its publication. SRs, particularly those aggregating RCT results, are considered the best standard of evidence to guide rehabilitation clinical practice; however, that standard can be improved in rigor and/or transparency if the publications of rehabilitation SRs protocols become more common.

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.

MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations

NASA Astrophysics Data System (ADS)

Dibak, Manuel; del Razo, Mauricio J.; De Sancho, David; Schütte, Christof; Noé, Frank

2018-06-01

Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible to obtain long time-scale behavior of small to intermediate biomolecules and complexes. To model the interactions of many molecules at large length scales, particle-based reaction-diffusion (RD) simulations are more suitable but lack molecular detail. Thus, coupling MSMs and RD simulations (MSM/RD) would be highly desirable, as they could efficiently produce simulations at large time and length scales, while still conserving the characteristic features of the interactions observed at atomic detail. While such a coupling seems straightforward, fundamental questions are still open: Which definition of MSM states is suitable? Which protocol to merge and split RD particles in an association/dissociation reaction will conserve the correct bimolecular kinetics and thermodynamics? In this paper, we make the first step toward MSM/RD by laying out a general theory of coupling and proposing a first implementation for association/dissociation of a protein with a small ligand (A + B ⇌ C). Applications on a toy model and CO diffusion into the heme cavity of myoglobin are reported.

Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry.

PubMed

Zhou, Mowei; Wu, Si; Stenoien, David L; Zhang, Zhaorui; Connolly, Lanelle; Freitag, Michael; Paša-Tolić, Ljiljana

2017-01-01

Top-down mass spectrometry is a valuable tool for understanding gene expression through characterization of combinatorial histone post-translational modifications (i.e., histone code). In this protocol, we describe a top-down workflow that employs liquid chromatography (LC) coupled to mass spectrometry (MS), for fast global profiling of changes in histone proteoforms, and apply LCMS top-down approach for comparative analysis of a wild-type and a mutant fungal species. The proteoforms exhibiting differential abundances can be subjected to further targeted studies by other MS or orthogonal (e.g., biochemical) assays. This method can be generally adapted for screening of changes in histone modifications between samples such as wild type vs. mutant or healthy vs. diseased.

Superconducting Qubits as Mechanical Quantum Engines

NASA Astrophysics Data System (ADS)

Sachtleben, Kewin; Mazon, Kahio T.; Rego, Luis G. C.

2017-09-01

We propose the equivalence of superconducting qubits with a pistonlike mechanical quantum engine. The work reports a study on the nature of the nonequilibrium work exchanged with the quantum-nonadiabatic working medium, which is modeled as a multilevel coupled quantum well system subject to an external control parameter. The quantum dynamics is solved for arbitrary control protocols. It is shown that the work output has two components: one that depends instantaneously on the level populations and another that is due to the quantum coherences built in the system. The nonadiabatic coherent dynamics of the quantum engine gives rise to a resistance (friction) force that decreases the work output. We consider the functional equivalence of such a device and a rf-SQUID flux qubit.

One-step purification of assembly-competent tubulin from diverse eukaryotic sources

PubMed Central

Widlund, Per O.; Podolski, Marija; Reber, Simone; Alper, Joshua; Storch, Marko; Hyman, Anthony A.; Howard, Jonathon; Drechsel, David N.

2012-01-01

We have developed a protocol that allows rapid and efficient purification of native, active tubulin from a variety of species and tissue sources by affinity chromatography. The affinity matrix comprises a bacterially expressed, recombinant protein, the TOG1/2 domains from Saccharomyces cerevisiae Stu2, covalently coupled to a Sepharose support. The resin has a high capacity to specifically bind tubulin from clarified crude cell extracts, and, after washing, highly purified tubulin can be eluted under mild conditions. The eluted tubulin is fully functional and can be efficiently assembled into microtubules. The method eliminates the need to use heterologous systems for the study of microtubule-associated proteins and motor proteins, which has been a major issue in microtubule-related research. PMID:22993214

Nonadiabatic effects in periodically driven dissipative open quantum systems

NASA Astrophysics Data System (ADS)

Reimer, Viktor; Pedersen, Kim G. L.; Tanger, Niklas; Pletyukhov, Mikhail; Gritsev, Vladimir

2018-04-01

We present a general method to calculate the periodic steady state of a driven-dissipative system coupled to a transmission line (and more generally, to a reservoir) under periodic modulation of its parameters. Using Floquet's theorem, we formulate the differential equation for the system's density operator which has to be solved for a single period of modulation. On this basis we also provide systematic expansions in both the adiabatic and high-frequency regime. Applying our method to three different systems—two- and three-level models as well as the driven nonlinear cavity—we propose periodic modulation protocols of parameters leading to a temporary suppression of effective dissipation rates, and study the arising nonadiabatic features in the response of these systems.

Amplification of Angular Rotations Using Weak Measurements

NASA Astrophysics Data System (ADS)

Magaña-Loaiza, Omar S.; Mirhosseini, Mohammad; Rodenburg, Brandon; Boyd, Robert W.

2014-05-01

We present a weak measurement protocol that permits a sensitive estimation of angular rotations based on the concept of weak-value amplification. The shift in the state of a pointer, in both angular position and the conjugate orbital angular momentum bases, is used to estimate angular rotations. This is done by an amplification of both the real and imaginary parts of the weak-value of a polarization operator that has been coupled to the pointer, which is a spatial mode, via a spin-orbit coupling. Our experiment demonstrates the first realization of weak-value amplification in the azimuthal degree of freedom. We have achieved effective amplification factors as large as 100, providing a sensitivity that is on par with more complicated methods that employ quantum states of light or extremely large values of orbital angular momentum.

An oxidative cross-coupling reaction of 4-hydroxydithiocoumarin and amines/thiols using a combination of I2 and TBHP: access to lead molecules for biomedical applications.

PubMed

Mahato, Karuna; Arora, Neha; Ray Bagdi, Prasanta; Gattu, Radhakrishna; Ghosh, Siddhartha Sankar; Khan, Abu T

2018-02-06

A metal-free I 2 /TBHP induced highly atom economic and operationally simple oxidative cross-coupling reaction has been developed for the direct synthesis of sulfenamides/sulfanes/disulfides from the reaction of 4-hydroxydithiocoumarin and amines/thiols. The novelties of the present protocol are unprecedented S-C bond formation in addition to S-N and S-S bonds, shorter reaction time, mild and environmentally benign reaction conditions, functional group tolerance and moderate to excellent yields. Moreover, the four newly synthesized compounds namely 4q, 6d, 6e and 7a exhibit anti-proliferative activity against the breast cancer cell line MCF7, and may be lead molecules for future drug development.

Using Bioluminescence Resonance Energy Transfer (BRET) to Characterize Agonist-Induced Arrestin Recruitment to Modified and Unmodified G Protein-Coupled Receptors.

PubMed

Donthamsetti, Prashant; Quejada, Jose Rafael; Javitch, Jonathan A; Gurevich, Vsevolod V; Lambert, Nevin A

2015-09-01

G protein-coupled receptors (GPCRs) represent ∼25% of current drug targets. Ligand binding to these receptors activates G proteins and arrestins, which are involved in differential signaling pathways. Because functionally selective or biased ligands activate one of these two pathways, they may be superior medications for certain diseases states. The identification of such ligands requires robust drug screening assays for both G protein and arrestin activity. This unit describes protocols for two bioluminescence resonance energy transfer (BRET)-based assays used to monitor arrestin recruitment to GPCRs. One assay requires modification of GPCRs by fusion to a BRET donor or acceptor moiety, whereas the other can detect arrestin recruitment to unmodified GPCRs. Copyright © 2015 John Wiley & Sons, Inc.

Weak-value amplification as an optimal metrological protocol

NASA Astrophysics Data System (ADS)

Alves, G. Bié; Escher, B. M.; de Matos Filho, R. L.; Zagury, N.; Davidovich, L.

2015-06-01

The implementation of weak-value amplification requires the pre- and postselection of states of a quantum system, followed by the observation of the response of the meter, which interacts weakly with the system. Data acquisition from the meter is conditioned to successful postselection events. Here we derive an optimal postselection procedure for estimating the coupling constant between system and meter and show that it leads both to weak-value amplification and to the saturation of the quantum Fisher information, under conditions fulfilled by all previously reported experiments on the amplification of weak signals. For most of the preselected states, full information on the coupling constant can be extracted from the meter data set alone, while for a small fraction of the space of preselected states, it must be obtained from the postselection statistics.

Automated large-scale purification of a G protein-coupled receptor for neurotensin.

PubMed

White, Jim F; Trinh, Loc B; Shiloach, Joseph; Grisshammer, Reinhard

2004-04-30

Structure determination of integral membrane proteins requires milligram amounts of purified, functional protein on a regular basis. Here, we describe a protocol for the purification of a G protein-coupled neurotensin receptor fusion protein at the 3-mg or 10-mg level using immobilized metal affinity chromatography and a neurotensin column in a fully automated mode. Fermentation at a 200-l scale of Escherichia coli expressing functional receptors provides the material needed to feed into the purification routine. Constructs with tobacco etch virus protease recognition sites at either end of the receptor allow the isolation of neurotensin receptor devoid of its fusion partners. The presented expression and purification procedures are simple and robust, and provide the basis for crystallization experiments of receptors on a routine basis.

Outer synchronization of complex networks with internal delay and coupling delay via aperiodically intermittent pinning control

NASA Astrophysics Data System (ADS)

Zhang, Chuan; Wang, Xingyuan; Wang, Chunpeng; Xia, Zhiqiu

This paper concerns the outer synchronization problem between two complex delayed networks via the method of aperiodically intermittent pinning control. Apart from previous works, internal delay and coupling delay are both involved in this model, and the designed intermittent controllers can be aperiodic. The main work in this paper can be summarized as follows: First, two cases of aperiodically intermittent control with constant gain and adaptive gain are implemented, respectively. The intermittent control and pinning control are combined to reduce consumptions further. Then, based on the Lyapunov stability theory, synchronization protocols are given by strict derivation. Especially, the designed controllers are indeed simple and valid in application of theory to practice. Finally, numerical examples put the proposed control methods to the test.

A Dyadic Behavioral Intervention to Optimize Same Sex Male Couples’ Engagement Across the HIV Care Continuum: Development of and Protocol for an Innovative Couples-based Approach (Partner Steps)

PubMed Central

2016-01-01

Background An estimated one- to two-thirds of new human immunodeficiency virus (HIV) infections among US men who have sex with men (MSM) occur within the context of primary partnerships. Thus, HIV interventions that recognize and harness the power of relationships are needed. Increasingly, HIV prevention efforts are being directed toward improving engagement across the HIV care continuum from testing to linkage to care, antiretroviral therapy (ART) adherence, engagement in care, and viral suppression. However, to our knowledge, no behavioral interventions have attempted to address the HIV care continuum using a dyadic approach. Objective The objective of this paper is to describe the development of and protocol for an innovative couples-based approach to improving treatment adherence and engagement in care among HIV serodiscordant and concordant HIV-positive same sex male couples in the United States. Methods We developed the Partner Steps intervention by drawing from relationship-oriented theory, existing efficacious individual-level ART adherence interventions, couple-focused HIV prevention interventions, and expert consultation. We incorporated new content to address all aspects of the HIV care continuum (eg, linkage to and retention in care) and to draw on relationship strengths through interactive activities. Results The resulting theory-based Partner Steps intervention is delivered by a trained bachelors-level counselor (interventionist) over 2 in-person sessions with male-male dyads in which at least 1 partner has recent suboptimal engagement in HIV care. Each session is designed to use relationship strengths to increase motivation for HIV care and treatment, and cover sequential intervention “steps” relating to specific challenges in HIV care engagement and barriers to ART adherence. For each step, couples work with a trained interventionist to identify their unique challenges, actively problem-solve with the interventionist, and articulate and commit to working together to implement a plan in which each partner agrees to complete specific tasks. Conclusions We drew on theory and evidence to develop novel intervention strategies that leverage strengths of relationships to address engagement across the entire HIV care continuum. We provide details on intervention development and content that may be of use to researchers as well as medical and mental health professionals for whom a dyadic approach to HIV prevention and care may best suit their patient population. PMID:27562905

A research protocol for a pilot randomized controlled trial designed to examine the feasibility of a couple-based mind-body intervention for patients with metastatic lung cancer and their partners.

PubMed

Milbury, Kathrin; Tsao, Anne S; Liao, Zhongxing; Owns, April; Engle, Rosalinda; Gonzalez, Edrea A; Bruera, Eduardo; Cohen, Lorenzo

2018-01-01

Given the generally incurable nature of metastatic non-small cell lung cancer (mNSCLC), patients and their romantic partners are at risk for existential/spiritual distress. Although a handful of dyadic psychosocial interventions for lung cancer patients and their caregivers exist, none of them target spiritual well-being. Informed by the mindfulness-based intervention literature and our pilot work in couples affected by lung cancer, we developed a brief couple-based mind-body (CBMB) intervention. The primary aim of this research protocol is to determine the feasibility of implementing the CBMB intervention versus an active control (AC) or wait list control (WLC) group in patients with mNSCLC and their partners using a randomized controlled trial design. Seventy-five patients with mNSCLC receiving treatment and their partners are randomized to the CBMB intervention, an AC or a WLC group. Those in the CBMB intervention and AC groups receive four intervention sessions of 60 min each over 4 weeks and complete weekly homework assignments. The first session is delivered in person, and the remaining sessions are delivered via videoconference. The dyads in the AC group discuss cancer-related and personal growth concerns with the interventionist but are not taught coping skills. Patients and partners in all groups complete baseline assessments of quality of life (QOL) prior to randomization. Follow-up assessments are performed 4 weeks and then again 3 months later. The primary outcome is feasibility (i.e., ≥ 30% of eligible couples consent, ≥ 70% of enrolled couples are retained, and ≥ 50% of all CBMB and AC sessions are attended). We will also perform primarily descriptive analyses of the self-reported outcomes (e.g., spiritual well-being and psychological distress) and explore potential intervention mediators (i.e., compassion, communication, mindfulness, and closeness) to inform a larger, future trial. This trial will provide important information regarding the feasibility of a behavioral intervention in a vulnerable yet understudied population using videoconferencing and descriptive data regarding spiritual well-being and other indices of QOL in both mNSCLC patients and their partners. ClinicalTrials.gov NCT02596490.

Efficacy of four synchronization protocols on the estrus behavior and conception in native Korean cattle (Hanwoo).

PubMed

Lee, Myeung-Sik; Rahman, Md Saidur; Kwon, Woo-Sung; Chung, Hak-Jae; Yang, Boh-Suk; Pang, Myung-Geol

2013-11-01

Ineffective estrus detection is the foremost limiting factor in the fertility of farmed cattle worldwide. Failure to detect estrus or erroneous diagnosis of estrus results in great economic losses in Korea each year. This study was carried out in order to comprehensively describe the estrus behaviors and conception rates of different estrus synchronization protocols applied to 40 cycling native Korean cattle (Hanwoo). The cows were grouped into four (n = 10) and treated with the following protocols: (1) Day -15: controlled intravaginal drug-releasing device (CIDR) for 12 days; Day -5: prostaglandin F2α (PGF2α), (2) ovulation synchronization (OVS): Day -15: GnRH; Day -6: PGF2α; Day -4: GnRH, (3) Day -15: progesterone-releasing intravaginal device for 12 days; Day -5: PGF2α; and (4) Day -15: PGF2α; Day -4: PGF2α. Artificial insemination was performed 12 hours after the detection of estrus using frozen-thawed semen. Estrus signs were compared using a charge-coupled device camera (CCDC) and a control method (direct visual observation). The pregnancy of the cows was determined by transrectal ultrasonography at Days 25 to 30 postinsemination. The results indicated that the day of estrus return was significantly earlier using the CCDC method compared with direct visualization (P < 0.05). Mounting of other cows was the most predominant sign of estrus among the flock (P < 0.05), as analyzed using the CCDC. In the OVS group, a lower rate of mounting was observed than in the other three groups. Moreover, significantly fewer estrus behaviors were noticed in the OVS protocol group (P < 0.05). Both first service conception and overall conception rates were significantly higher (P < 0.05) in the CIDR and OVS treatment groups. In conclusion, the CIDR and OVS protocols appear to be the best practice for the synchronization of estrus for reproductive competence through the CCDC in Hanwoo cows. However, CIDR has a practical advantage over OVS with respect to estrus detection. Copyright © 2013 Elsevier Inc. All rights reserved.

Prevention of birth defects in the pre-conception period: knowledge and practice of health care professionals (nurses and doctors) in a city of Southern Brazil

PubMed Central

Ferreira, Flávia Romariz; Russo Akiba, Heloisa Regina; Júnior, Edward Araujo; Figueiredo, Elisabeth Niglio; Abrahão, Anelise Riedel

2015-01-01

Background: Some congenital defects can be prevented in the pregestational stage. However, many health professionals are not prepared to provide counselling to couples regarding the same. Objective: This study aimed to assess the performance of doctors and nurses from a primary health-care unit in Florianopolis, Brazil, in preventing birth defects in the preconception period based on the recommendations of the Control Center of Disease Prevention. Materials and Methods: This descriptive cross sectional study was performed at a tertiary referral center. In this study, a semi-structured questionnaire was provided to 160 health professionals comprising doctors and nurses who were actively involved in providing primary health care in family health programs. The non-parametric Chi-square (χ2) test was used to analyse the data obtained through multiple choice questions. Results: Our results showed that although 81.9% of health professionals provided health-care assistance based on protocols, and only 46.2% professionals were aware of the presence of the topic in the protocol. Of the recommendations provided by the Control Center of Disease Prevention, the use of folic acid was the most prescribed. However, this prescription was not statistically different between nurses and doctors (P=0.85). Conclusion: This study identified the fragile nature in these professional’s knowledge about the prevention of birth defects in pre-conception period, as evidenced by the inconsistency in their responses. PMID:26644794

Couple experiences of provider-initiated couple HIV testing in an antenatal clinic in Lusaka, Zambia: lessons for policy and practice.

PubMed

Musheke, Maurice; Bond, Virginia; Merten, Sonja

2013-03-14

Couple HIV testing has been recognized as critical to increase uptake of HIV testing, facilitate disclosure of HIV status to marital partner, improve access to treatment, care and support, and promote safe sex. The Zambia national protocol on integrated prevention of mother-to-child transmission of HIV (PMTCT) allows for the provision of couple testing in antenatal clinics. This paper examines couple experiences of provider-initiated couple HIV testing at a public antenatal clinic and discusses policy and practical lessons. Using a narrative approach, open-ended in-depth interviews were held with couples (n = 10) who underwent couple HIV testing; women (n = 5) and men (n = 2) who had undergone couple HIV testing but were later abandoned by their spouses; and key informant interviews with lay counsellors (n = 5) and nurses (n = 2). On-site observations were also conducted at the antenatal clinic and HIV support group meetings. Data collection was conducted between March 2010 and September 2011. Data was organised and managed using Atlas ti, and analysed and interpreted thematically using content analysis approach. Health workers sometimes used coercive and subtle strategies to enlist women's spouses for couple HIV testing resulting in some men feeling 'trapped' or 'forced' to test as part of their paternal responsibility. Couple testing had some positive outcomes, notably disclosure of HIV status to marital partner, renewed commitment to marital relationship, uptake of and adherence to treatment and formation of new social networks. However, there were also negative repercussions including abandonment, verbal abuse and cessation of sexual relations. Its promotion also did not always lead to safe sex as this was undermined by gendered power relationships and the desires for procreation and sexual intimacy. Couple HIV testing provides enormous bio-medical and social benefits and should be encouraged. However, testing strategies need to be non-coercive. Providers of couple HIV testing also need to be mindful of the intimate context of partner relationships including couples' childbearing aspirations and lived experiences. There is also need to make antenatal clinics more male-friendly and responsive to men's health needs, as well as being attentive and responsive to gender inequality during couselling sessions.

Direct Aldehyde C-H Arylation and Alkylation via the Combination of Nickel, Hydrogen Atom Transfer, and Photoredox Catalysis.

PubMed

Zhang, Xiaheng; MacMillan, David W C

2017-08-23

A mechanism that enables direct aldehyde C-H functionalization has been achieved via the synergistic merger of photoredox, nickel, and hydrogen atom transfer catalysis. This mild, operationally simple protocol transforms a wide variety of commercially available aldehydes, along with aryl or alkyl bromides, into the corresponding ketones in excellent yield. This C-H abstraction coupling technology has been successfully applied to the expedient synthesis of the medicinal agent haloperidol.

Using Reputation Systems and Non-Deterministic Routing to Secure Wireless Sensor Networks

PubMed Central

Moya, José M.; Vallejo, Juan Carlos; Fraga, David; Araujo, Álvaro; Villanueva, Daniel; de Goyeneche, Juan-Mariano

2009-01-01

Security in wireless sensor networks is difficult to achieve because of the resource limitations of the sensor nodes. We propose a trust-based decision framework for wireless sensor networks coupled with a non-deterministic routing protocol. Both provide a mechanism to effectively detect and confine common attacks, and, unlike previous approaches, allow bad reputation feedback to the network. This approach has been extensively simulated, obtaining good results, even for unrealistically complex attack scenarios. PMID:22412345

Enantioselective α-Alkylation of Aldehydes via Photoredox Organocatalysis: Rapid Access to Pharmacophore Fragments from β-Cyanoaldehydes**

PubMed Central

Welin, Eric R.; Warkentin, Alexander A.; Conrad, Jay C.

2015-01-01

The combination of photoredox catalysis and enamine catalysis has enabled the development of an enantioselective α-cyanoalkylation of aldehydes. This synergistic catalysis protocol allows for the coupling of two highly versatile yet orthogonal functionalities, allowing rapid diversification of the oxonitrile products to a wide array of medicinally relevant derivatives and heterocycles. This methodology has also been applied to the total synthesis of the lignan natural product (−)-bursehernin. PMID:26130043

Hydrodynamic size-based separation and characterization of protein aggregates from total cell lysates

PubMed Central

Tanase, Maya; Zolla, Valerio; Clement, Cristina C; Borghi, Francesco; Urbanska, Aleksandra M; Rodriguez-Navarro, Jose Antonio; Roda, Barbara; Zattoni, Andrea; Reschiglian, Pierluigi; Cuervo, Ana Maria; Santambrogio, Laura

2016-01-01

Herein we describe a protocol that uses hollow-fiber flow field-flow fractionation (FFF) coupled with multiangle light scattering (MALS) for hydrodynamic size-based separation and characterization of complex protein aggregates. The fractionation method, which requires 1.5 h to run, was successfully modified from the analysis of protein aggregates, as found in simple protein mixtures, to complex aggregates, as found in total cell lysates. In contrast to other related methods (filter assay, analytical ultracentrifugation, gel electrophoresis and size-exclusion chromatography), hollow-fiber flow FFF coupled with MALS allows a flow-based fractionation of highly purified protein aggregates and simultaneous measurement of their molecular weight, r.m.s. radius and molecular conformation (e.g., round, rod-shaped, compact or relaxed). The polyethersulfone hollow fibers used, which have a 0.8-mm inner diameter, allow separation of as little as 20 μg of total cell lysates. In addition, the ability to run the samples in different denaturing and nondenaturing buffer allows defining true aggregates from artifacts, which can form during sample preparation. The protocol was set up using Paraquat-induced carbonylation, a model that induces protein aggregation in cultured cells. This technique will advance the biochemical, proteomic and biophysical characterization of molecular-weight aggregates associated with protein mutations, as found in many CNS degenerative diseases, or chronic oxidative stress, as found in aging, and chronic metabolic and inflammatory conditions. PMID:25521790

Influence of land-atmosphere feedbacks on temperature and precipitation extremes in the GLACE-CMIP5 ensemble

NASA Astrophysics Data System (ADS)

Lorenz, Ruth; Argüeso, Daniel; Donat, Markus G.; Pitman, Andrew J.; van den Hurk, Bart; Berg, Alexis; Lawrence, David M.; Chéruy, Frédérique; Ducharne, Agnès.; Hagemann, Stefan; Meier, Arndt; Milly, P. C. D.; Seneviratne, Sonia I.

2016-01-01

We examine how soil moisture variability and trends affect the simulation of temperature and precipitation extremes in six global climate models using the experimental protocol of the Global Land-Atmosphere Coupling Experiment of the Coupled Model Intercomparison Project, Phase 5 (GLACE-CMIP5). This protocol enables separate examinations of the influences of soil moisture variability and trends on the intensity, frequency, and duration of climate extremes by the end of the 21st century under a business-as-usual (Representative Concentration Pathway 8.5) emission scenario. Removing soil moisture variability significantly reduces temperature extremes over most continental surfaces, while wet precipitation extremes are enhanced in the tropics. Projected drying trends in soil moisture lead to increases in intensity, frequency, and duration of temperature extremes by the end of the 21st century. Wet precipitation extremes are decreased in the tropics with soil moisture trends in the simulations, while dry extremes are enhanced in some regions, in particular the Mediterranean and Australia. However, the ensemble results mask considerable differences in the soil moisture trends simulated by the six climate models. We find that the large differences between the models in soil moisture trends, which are related to an unknown combination of differences in atmospheric forcing (precipitation, net radiation), flux partitioning at the land surface, and how soil moisture is parameterized, imply considerable uncertainty in future changes in climate extremes.

Dereplicating and spatial mapping of secondary metabolites from fungal cultures in situ

DOE PAGES

Kertesz, Vilmos; Van Berkel, Gary J.; Sica, Vincent P.; ...

2015-07-30

Ambient ionization techniques coupled to mass spectrometry have recently become prevalent in natural product research due to their ability to examine secondary metabolites in situ. Identifying, mapping, and monitoring secondary metabolites directly on an organism provides invaluable spatial and temporal details that are lost through traditional extraction processes. Most ambient ionization techniques do not collect mutually supportive data, such as chromatographic retention times and/or UV/VIS spectra, and this can limit the ability to identify certain metabolites, such as differentiating isomers. To overcome this, the droplet liquid microjunction surface sampling probe (droplet LMJ SSP) was coupled with UPLC PDA HRMS MS/MS,more » thus providing separation, retention times, and UV/VIS data used in traditional dereplication protocols. By capturing these mutually supportive data, the identity of secondary metabolites could be confidently and rapidly assigned in situ. Using the droplet LMJ SSP, a protocol was constructed to analyze the secondary metabolite profile of fungal cultures directly without any sample preparation. The results demonstrate that fungal cultures can be dereplicated from the Petri dish, thus identifying secondary metabolites, including isomers, and confirming them against reference standards. As a result, heat maps, similar to mass spectrometry imaging, can be used to ascertain the location and relative concentration of secondary metabolites directly on the surface and/or surroundings of a fungal culture.« less

Purification of family B G protein-coupled receptors using nanodiscs: Application to human glucagon-like peptide-1 receptor

PubMed Central

Cai, Yingying; Liu, Yuting; Culhane, Kelly J.; DeVree, Brian T.; Yang, Yang; Sunahara, Roger K.; Yan, Elsa C. Y.

2017-01-01

Family B G protein-coupled receptors (GPCRs) play vital roles in hormone-regulated homeostasis. They are drug targets for metabolic diseases, including type 2 diabetes and osteoporosis. Despite their importance, the signaling mechanisms for family B GPCRs at the molecular level remain largely unexplored due to the challenges in purification of functional receptors in sufficient amount for biophysical characterization. Here, we purified the family B GPCR human glucagon-like peptide-1 (GLP-1) receptor (GLP1R), whose agonists, e.g. exendin-4, are used for the treatment of type 2 diabetes mellitus. The receptor was expressed in HEK293S GnTl- cells using our recently developed protocol. The protocol incorporates the receptor into the native-like lipid environment of reconstituted high density lipoprotein (rHDL) particles, also known as nanodiscs, immediately after the membrane solubilization step followed by chromatographic purification, minimizing detergent contact with the target receptor to reduce denaturation and prolonging stabilization of receptor in lipid bilayers without extra steps of reconstitution. This method yielded purified GLP1R in nanodiscs that could bind to GLP-1 and exendin-4 and activate Gs protein. This nanodisc purification method can potentially be a general strategy to routinely obtain purified family B GPCRs in the 10s of microgram amounts useful for spectroscopic analysis of receptor functions and activation mechanisms. PMID:28609478

Purification of family B G protein-coupled receptors using nanodiscs: Application to human glucagon-like peptide-1 receptor.

PubMed

Cai, Yingying; Liu, Yuting; Culhane, Kelly J; DeVree, Brian T; Yang, Yang; Sunahara, Roger K; Yan, Elsa C Y

2017-01-01

Family B G protein-coupled receptors (GPCRs) play vital roles in hormone-regulated homeostasis. They are drug targets for metabolic diseases, including type 2 diabetes and osteoporosis. Despite their importance, the signaling mechanisms for family B GPCRs at the molecular level remain largely unexplored due to the challenges in purification of functional receptors in sufficient amount for biophysical characterization. Here, we purified the family B GPCR human glucagon-like peptide-1 (GLP-1) receptor (GLP1R), whose agonists, e.g. exendin-4, are used for the treatment of type 2 diabetes mellitus. The receptor was expressed in HEK293S GnTl- cells using our recently developed protocol. The protocol incorporates the receptor into the native-like lipid environment of reconstituted high density lipoprotein (rHDL) particles, also known as nanodiscs, immediately after the membrane solubilization step followed by chromatographic purification, minimizing detergent contact with the target receptor to reduce denaturation and prolonging stabilization of receptor in lipid bilayers without extra steps of reconstitution. This method yielded purified GLP1R in nanodiscs that could bind to GLP-1 and exendin-4 and activate Gs protein. This nanodisc purification method can potentially be a general strategy to routinely obtain purified family B GPCRs in the 10s of microgram amounts useful for spectroscopic analysis of receptor functions and activation mechanisms.

Nitrous Oxide-dependent Iron-catalyzed Coupling Reactions of Grignard Reagents.

PubMed

Döhlert, Peter; Weidauer, Maik; Enthaler, Stephan

2015-01-01

The formation of carbon-carbon bonds is one of the fundamental transformations in chemistry. In this regard the application of palladium-based catalysts has been extensively investigated during recent years, but nowadays research focuses on iron catalysis, due to sustainability, costs and toxicity issues; hence numerous examples for iron-catalyzed cross-coupling reactions have been established, based on the coupling of electrophiles (R(1)-X, X = halide) with nucleophiles (R(2)-MgX). Only a small number of protocols deals with the iron-catalyzed oxidative coupling of nucleophiles (R(1)-MgX + R(2)-MgX) with the aid of oxidants (1,2-dihaloethanes). However, some issues arise with these oxidants; hence more recently the potential of the industrial waste product nitrous oxide (N(2)O) was investigated, because the unproblematic side product N(2) is formed. Based on that, we demonstrate the catalytic potential of easily accessible iron complexes in the oxidative coupling of Grignard reagents. Importantly, nitrous oxide was essential to obtain yields up to >99% at mild conditions (e.g. 1 atm, ambient temperature) and low catalyst loadings (0.1 mol%) Excellent catalyst performance is realized with turnover numbers of up to 1000 and turnover frequencies of up to 12000 h(-1). Moreover, a good functional group tolerance is observed (e.g. amide, ester, nitrile, alkene, alkyne). Afterwards the reaction of different Grignard reagents revealed interesting results with respect to the selectivity of cross-coupling product formation.

Quantum sensing of weak radio-frequency signals by pulsed Mollow absorption spectroscopy.

PubMed

Joas, T; Waeber, A M; Braunbeck, G; Reinhard, F

2017-10-17

Quantum sensors-qubits sensitive to external fields-have become powerful detectors for various small acoustic and electromagnetic fields. A major key to their success have been dynamical decoupling protocols which enhance sensitivity to weak oscillating (AC) signals. Currently, those methods are limited to signal frequencies below a few MHz. Here we harness a quantum-optical effect, the Mollow triplet splitting of a strongly driven two-level system, to overcome this limitation. We microscopically understand this effect as a pulsed dynamical decoupling protocol and find that it enables sensitive detection of fields close to the driven transition. Employing a nitrogen-vacancy center, we detect GHz microwave fields with a signal strength (Rabi frequency) below the current detection limit, which is set by the center's spectral linewidth [Formula: see text]. Pushing detection sensitivity to the much lower 1/T 2 limit, this scheme could enable various applications, most prominently coherent coupling to single phonons and microwave photons.Dynamical decoupling protocols can enhance the sensitivity of quantum sensors but this is limited to signal frequencies below a few MHz. Here, Joas et al. use the Mollow triplet splitting in a nitrogen-vacancy centre to overcome this limitation, enabling sensitive detection of signals in the GHz range.

Systems oncology: towards patient-specific treatment regimes informed by multiscale mathematical modelling.

PubMed

Powathil, Gibin G; Swat, Maciej; Chaplain, Mark A J

2015-02-01

The multiscale complexity of cancer as a disease necessitates a corresponding multiscale modelling approach to produce truly predictive mathematical models capable of improving existing treatment protocols. To capture all the dynamics of solid tumour growth and its progression, mathematical modellers need to couple biological processes occurring at various spatial and temporal scales (from genes to tissues). Because effectiveness of cancer therapy is considerably affected by intracellular and extracellular heterogeneities as well as by the dynamical changes in the tissue microenvironment, any model attempt to optimise existing protocols must consider these factors ultimately leading to improved multimodal treatment regimes. By improving existing and building new mathematical models of cancer, modellers can play important role in preventing the use of potentially sub-optimal treatment combinations. In this paper, we analyse a multiscale computational mathematical model for cancer growth and spread, incorporating the multiple effects of radiation therapy and chemotherapy in the patient survival probability and implement the model using two different cell based modelling techniques. We show that the insights provided by such multiscale modelling approaches can ultimately help in designing optimal patient-specific multi-modality treatment protocols that may increase patients quality of life. Copyright © 2014 Elsevier Ltd. All rights reserved.

Polarization entanglement purification of nonlocal microwave photons based on the cross-Kerr effect in circuit QED

NASA Astrophysics Data System (ADS)

Zhang, Hao; Liu, Qian; Xu, Xu-Sheng; Xiong, Jun; Alsaedi, Ahmed; Hayat, Tasawar; Deng, Fu-Guo

2017-11-01

Microwave photons have become very important qubits in quantum communication, as the first quantum satellite has been launched successfully. Therefore, it is a necessary and meaningful task for ensuring the high security and efficiency of microwave-based quantum communication in practice. Here, we present an original polarization entanglement purification protocol for nonlocal microwave photons based on the cross-Kerr effect in circuit quantum electrodynamics (QED). Our protocol can solve the problem that the purity of maximally entangled states used for constructing quantum channels will decrease due to decoherence from environment noise. This task is accomplished by means of the polarization parity-check quantum nondemolition (QND) detector, the bit-flipping operation, and the linear microwave elements. The QND detector is composed of several cross-Kerr effect systems which can be realized by coupling two superconducting transmission line resonators to a superconducting molecule with the N -type level structure. We give the applicable experimental parameters of QND measurement system in circuit QED and analyze the fidelities. Our protocol has good applications in long-distance quantum communication assisted by microwave photons in the future, such as satellite quantum communication.

Megasessions: Efficacy of Fewer, Longer Treatment Sessions for Fat Reduction in Noninvasive Body Contouring Using a Radiofrequency Based Device.

PubMed

Duncan, Diane

2017-05-01

While the field of noninvasive body contouring is booming, many patients still note a lesser result than they might achieve with a single session of liposuction or dermolipectomy. The duration of a noninvasive fat reduction treatment series can be daunting. Patients have questioned the worth of these procedures when the expected benefit is modest and the time they devote to the project is significant. An eight-patient mini-study was performed to see if two or three "megasessions" could be substituted for eight weekly sessions of bipolar radiofrequency based fat reduction treatments. Patients were randomized into a two session or three session group by drawing straws. The device used was the BodyFX bipolar RF device by InMode. This device employs a suction coupled vacuum that heats a section of skin and soft tissue in the treatment region and delivers a high voltage pulse. Each patient was treated for 2 hours per session, using the Body FX, more superficial Mini FX, and the Deep FX device in an effort to treat on a multilevel basis. Preoperative 2D and 3D Vectra photos were taken, and were repeated at 1 month and 3 months post-treatment. Volumetric analysis and patient assessment showed similar results with a two or three treatment "megasession" protocol when compared with the traditional protocol of eight weekly sessions. While the cohort number was not statistically significant, the photographs and measurements are compelling enough to warrant further investigation into this treatment protocol.

J Drugs Dermatol. 2017;16(5):478-480.

Evaluation of training nurses to perform semi-automated three-dimensional left ventricular ejection fraction using a customised workstation-based training protocol.

PubMed

Guppy-Coles, Kristyan B; Prasad, Sandhir B; Smith, Kym C; Hillier, Samuel; Lo, Ada; Atherton, John J

2015-06-01

We aimed to determine the feasibility of training cardiac nurses to evaluate left ventricular function utilising a semi-automated, workstation-based protocol on three dimensional echocardiography images. Assessment of left ventricular function by nurses is an attractive concept. Recent developments in three dimensional echocardiography coupled with border detection assistance have reduced inter- and intra-observer variability and analysis time. This could allow abbreviated training of nurses to assess cardiac function. A comparative, diagnostic accuracy study evaluating left ventricular ejection fraction assessment utilising a semi-automated, workstation-based protocol performed by echocardiography-naïve nurses on previously acquired three dimensional echocardiography images. Nine cardiac nurses underwent two brief lectures about cardiac anatomy, physiology and three dimensional left ventricular ejection fraction assessment, before a hands-on demonstration in 20 cases. We then selected 50 cases from our three dimensional echocardiography library based on optimal image quality with a broad range of left ventricular ejection fractions, which was quantified by two experienced sonographers and the average used as the comparator for the nurses. Nurses independently measured three dimensional left ventricular ejection fraction using the Auto lvq package with semi-automated border detection. The left ventricular ejection fraction range was 25-72% (70% with a left ventricular ejection fraction <55%). All nurses showed excellent agreement with the sonographers. Minimal intra-observer variability was noted on both short-term (same day) and long-term (>2 weeks later) retest. It is feasible to train nurses to measure left ventricular ejection fraction utilising a semi-automated, workstation-based protocol on previously acquired three dimensional echocardiography images. Further study is needed to determine the feasibility of training nurses to acquire three dimensional echocardiography images on real-world patients to measure left ventricular ejection fraction. Nurse-performed evaluation of left ventricular function could facilitate the broader application of echocardiography to allow cost-effective screening and monitoring for left ventricular dysfunction in high-risk populations. © 2014 John Wiley & Sons Ltd.

Modelling energy costs for different operational strategies of a large water resource recovery facility.

PubMed

Póvoa, P; Oehmen, A; Inocêncio, P; Matos, J S; Frazão, A

2017-05-01

The main objective of this paper is to demonstrate the importance of applying dynamic modelling and real energy prices on a full scale water resource recovery facility (WRRF) for the evaluation of control strategies in terms of energy costs with aeration. The Activated Sludge Model No. 1 (ASM1) was coupled with real energy pricing and a power consumption model and applied as a dynamic simulation case study. The model calibration is based on the STOWA protocol. The case study investigates the importance of providing real energy pricing comparing (i) real energy pricing, (ii) weighted arithmetic mean energy pricing and (iii) arithmetic mean energy pricing. The operational strategies evaluated were (i) old versus new air diffusers, (ii) different DO set-points and (iii) implementation of a carbon removal controller based on nitrate sensor readings. The application in a full scale WRRF of the ASM1 model coupled with real energy costs was successful. Dynamic modelling with real energy pricing instead of constant energy pricing enables the wastewater utility to optimize energy consumption according to the real energy price structure. Specific energy cost allows the identification of time periods with potential for linking WRRF with the electric grid to optimize the treatment costs, satisfying operational goals.

Coupled Thermo-Mechanical and Photo-Chemical Degradation Mechanisms that determine the Reliability and Operational Lifetimes for CPV Technologies

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

Dauskardt, Reinhold H.

This project sought to identify and characterize the coupled intrinsic photo-chemo-mechanical degradation mechanisms that determine the reliability and operational lifetimes for CPV technologies. Over a three year period, we have completed a highly successful program which has developed quantitative metrologies and detailed physics-based degradation models, providing new insight into the fundamental reliability physics necessary for improving materials, creating accelerated testing protocols, and producing more accurate lifetime predictions. The tasks for the program were separated into two focus areas shown in the figure below. Focus Area 1, led by Reinhold Dauskardt and Warren Cai with a primary collaboration with David Millermore » of NREL, studied the degradation mechanisms present in encapsulant materials. Focus Area 2, led by Reinhold Dauskardt and Ryan Brock with a primary collaboration with James Ermer and Peter Hebert of Spectrolab, studied stress development and degradation within internal CPV device interfaces. Each focus area was productive, leading to several publications, including findings on the degradation of silicone encapsulant under terrestrial UV, a model for photodegradation of silicone encapsulant adhesion, quantification and process tuning of antireflective layers on CPV, and discovery of a thermal cycling degradation mechanism present in metal gridline structures.« less

Development of a fluorescence-activated cell sorting method coupled with whole genome amplification to analyze minority and trace Dehalococcoides genomes in microbial communities.

PubMed

Lee, Patrick K H; Men, Yujie; Wang, Shanquan; He, Jianzhong; Alvarez-Cohen, Lisa

2015-02-03

Dehalococcoides mccartyi are functionally important bacteria that catalyze the reductive dechlorination of chlorinated ethenes. However, these anaerobic bacteria are fastidious to isolate, making downstream genomic characterization challenging. In order to facilitate genomic analysis, a fluorescence-activated cell sorting (FACS) method was developed in this study to separate D. mccartyi cells from a microbial community, and the DNA of the isolated cells was processed by whole genome amplification (WGA) and hybridized onto a D. mccartyi microarray for comparative genomics against four sequenced strains. First, FACS was successfully applied to a D. mccartyi isolate as positive control, and then microarray results verified that WGA from 10(6) cells or ∼1 ng of genomic DNA yielded high-quality coverage detecting nearly all genes across the genome. As expected, some inter- and intrasample variability in WGA was observed, but these biases were minimized by performing multiple parallel amplifications. Subsequent application of the FACS and WGA protocols to two enrichment cultures containing ∼10% and ∼1% D. mccartyi cells successfully enabled genomic analysis. As proof of concept, this study demonstrates that coupling FACS with WGA and microarrays is a promising tool to expedite genomic characterization of target strains in environmental communities where the relative concentrations are low.

Enhancing a slow and weak optomechanical nonlinearity with delayed quantum feedback

PubMed Central

Wang, Zhaoyou; Safavi-Naeini, Amir H.

2017-01-01

A central goal of quantum optics is to generate large interactions between single photons so that one photon can strongly modify the state of another one. In cavity optomechanics, photons interact with the motional degrees of freedom of an optical resonator, for example, by imparting radiation pressure forces on a movable mirror or sensing minute fluctuations in the position of the mirror. Here, we show that the optical nonlinearity arising from these effects, typically too small to operate on single photons, can be sufficiently enhanced with feedback to generate large interactions between single photons. We propose a protocol that allows photons propagating in a waveguide to interact with each other through multiple bounces off an optomechanical system. The protocol is analysed by evolving the full many-body quantum state of the waveguide-coupled system, illustrating that large photon–photon interactions mediated by mechanical motion may be within experimental reach. PMID:28677674

Guiding lead optimization with GPCR structure modeling and molecular dynamics.

PubMed

Heifetz, Alexander; James, Tim; Morao, Inaki; Bodkin, Michael J; Biggin, Philip C

2016-10-01

G-protein coupled receptor (GPCR) modeling approaches are widely used in the hit-to-lead and lead optimization stages of drug discovery. Modern protocols that involve molecular dynamics simulation can address key issues such as the free energy of binding (affinity), ligand-induced GPCR flexibility, ligand binding kinetics, conserved water positions and their role in ligand binding and the effects of mutations. The goals of these calculations are to predict the structures of the complexes between existing ligands and their receptors, to understand the key interactions and to utilize these insights in the design of new molecules with improved binding, selectivity or other pharmacological properties. In this review we present a brief survey of various computational approaches illustrated through a hierarchical GPCR modeling protocol and its prospective application in three industrial drug discovery projects. Copyright © 2016 Elsevier Ltd. All rights reserved.

A new approach to entangling neutral atoms.

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

Lee, Jongmin; Martin, Michael J.; Jau, Yuan-Yu

2016-11-01

Our team has developed a new approach to entangling neutral atoms with a Rydberg-dressed interaction. Entangling neutral atoms is an essential key of quantum technologies such as quantum computation, many-body quantum simulation, and high-precision atomic sensors . The demonstrated Rydberg-dressed protocol involves adiabatically imposing a light shift on the ground state by coupling an excited Rydberg state with a tuned laser field. Using this technique, we have demonstrated a strong and tunable dipole - dipole interaction between two individually trapped atoms with energy shifts of order 1 MHz, which has been challenging to achieve in other protocols . During thismore » program, we experimentally demonstrated Bell-state entanglement and the isomorphism to the Jaynes - Cumming model of a Rydberg-dressed two-atom system. Our theoretical calculations of a CPHASE quantum logic gate and arbitrary Dicke state quantum control in this system encourage further work.« less

Phase-modulated decoupling and error suppression in qubit-oscillator systems.

PubMed

Green, Todd J; Biercuk, Michael J

2015-03-27

We present a scheme designed to suppress the dominant source of infidelity in entangling gates between quantum systems coupled through intermediate bosonic oscillator modes. Such systems are particularly susceptible to residual qubit-oscillator entanglement at the conclusion of a gate period that reduces the fidelity of the target entangling operation. We demonstrate how the exclusive use of discrete shifts in the phase of the field moderating the qubit-oscillator interaction is sufficient to both ensure multiple oscillator modes are decoupled and to suppress the effects of fluctuations in the driving field. This approach is amenable to a wide variety of technical implementations including geometric phase gates in superconducting qubits and the Molmer-Sorensen gate for trapped ions. We present detailed example protocols tailored to trapped-ion experiments and demonstrate that our approach has the potential to enable multiqubit gate implementation with a significant reduction in technical complexity relative to previously demonstrated protocols.

Effect of leg exercise training on vascular volumes during 30 days of 6 deg head-down bed rest

NASA Technical Reports Server (NTRS)

Greenleaf, J. E.; Vernikos, J.; Wade, C. E.; Barnes, P. R.

1992-01-01

In order to investigate the effects of leg exercise training on vascular volumes during 30 d of 6-deg head-down bed rest, plasma and red cell volumes, body density, and water balance were measured in 19 men confined to bed rest (BR). One group had no exercise training (NOE), another near-maximal variable-intensity isotonic exercise (ITE) for 60 min/d, and the third near-maximal intermittent isokinetic exercise (IKE) for 60 min/d. Mean energy costs for the NOE, IKE, and ITE regimens were determined. Body densities within groups and mean urine volumes between groups were unchanged during BR. Changes in red cell volume followed changes in plasma volume. There was close coupling between resting plasma volume and plasma protein and osmotic content. It is argued that the ITE training protocol is better than the IKE protocol for maintaining plasma volume during prolonged exposure to BR.

Microwave-assisted synthesis of triple-helical, collagen-mimetic lipopeptides

PubMed Central

Banerjee, Jayati; Hanson, Andrea J; Muhonen, Wallace W; Shabb, John B; Mallik, Sanku

2018-01-01

Collagen-mimetic peptides and lipopeptides are widely used as substrates for matrix degrading enzymes, as new biomaterials for tissue engineering, as drug delivery systems and so on. However, the preparation and subsequent purification of these peptides and their fatty-acid conjugates are really challenging. Herein, we report a rapid microwave-assisted, solid-phase synthetic protocol to prepare the fatty-acid conjugated, triple-helical peptides containing the cleavage site for the enzyme matrix metalloproteinase-9 (MMP-9). We employed a PEG-based resin as the solid support and the amino acids were protected with Fmoc- and tert-butyl groups. The amino acids were coupled at 50 °C (25 W of microwave power) for 5 min. The deprotection reactions were carried out at 75 °C (35 W of microwave power) for 3 min. Using this protocol, a peptide containing 23 amino acids was synthesized and then conjugated to stearic acid in 14 h. PMID:20057380

Total synthesis of mycobacterial arabinogalactan containing 92 monosaccharide units

NASA Astrophysics Data System (ADS)

Wu, Yong; Xiong, De-Cai; Chen, Si-Cong; Wang, Yong-Shi; Ye, Xin-Shan

2017-03-01

Carbohydrates are diverse bio-macromolecules with highly complex structures that are involved in numerous biological processes. Well-defined carbohydrates obtained by chemical synthesis are essential to the understanding of their functions. However, synthesis of carbohydrates is greatly hampered by its insufficient efficiency. So far, assembly of long carbohydrate chains remains one of the most challenging tasks for synthetic chemists. Here we describe a highly efficient assembly of a 92-mer polysaccharide by the preactivation-based one-pot glycosylation protocol. Several linear and branched oligosaccharide/polysaccharide fragments ranging from 5-mer to 31-mer in length have been rapidly constructed in one-pot manner, which enables the first total synthesis of a biologically important mycobacterial arabinogalactan through a highly convergent [31+31+30] coupling reaction. Our results show that the preactivation-based one-pot glycosylation protocol may provide access to the construction of long and complicated carbohydrate chains.

Microscale immobilized enzyme reactors in proteomics: latest developments.

PubMed

Safdar, Muhammad; Spross, Jens; Jänis, Janne

2014-01-10

Enzymatic digestion of proteins is one of the key steps in proteomic analyses. There has been a steady progress in the applied digestion protocols in the past, starting from conventional time-consuming in-solution or in-gel digestion protocols to rapid and efficient methods utilizing different types of microscale enzyme reactors. Application of such microreactors has been proven beneficial due to lower sample consumption, higher sensitivity and straightforward coupling with LC-MS set-ups. Novel stationary phases, immobilization techniques and device formats are being constantly developed and tested to optimize digestion efficiency of proteolytic enzymes. This review focuses on the latest developments associated with the preparation and application of microscale enzyme reactors for proteomics applications since 2008 onwards. A special attention has been paid to the discussion of different stationary phases applied for immobilization purposes. Copyright © 2013 Elsevier B.V. All rights reserved.

Physical key-protected one-time pad

PubMed Central

Horstmeyer, Roarke; Judkewitz, Benjamin; Vellekoop, Ivo M.; Assawaworrarit, Sid; Yang, Changhuei

2013-01-01

We describe an encrypted communication principle that forms a secure link between two parties without electronically saving either of their keys. Instead, random cryptographic bits are kept safe within the unique mesoscopic randomness of two volumetric scattering materials. We demonstrate how a shared set of patterned optical probes can generate 10 gigabits of statistically verified randomness between a pair of unique 2 mm3 scattering objects. This shared randomness is used to facilitate information-theoretically secure communication following a modified one-time pad protocol. Benefits of volumetric physical storage over electronic memory include the inability to probe, duplicate or selectively reset any bits without fundamentally altering the entire key space. Our ability to securely couple the randomness contained within two unique physical objects can extend to strengthen hardware required by a variety of cryptographic protocols, which is currently a critically weak link in the security pipeline of our increasingly mobile communication culture. PMID:24345925

Enhancing a slow and weak optomechanical nonlinearity with delayed quantum feedback

NASA Astrophysics Data System (ADS)

Wang, Zhaoyou; Safavi-Naeini, Amir H.

2017-07-01

A central goal of quantum optics is to generate large interactions between single photons so that one photon can strongly modify the state of another one. In cavity optomechanics, photons interact with the motional degrees of freedom of an optical resonator, for example, by imparting radiation pressure forces on a movable mirror or sensing minute fluctuations in the position of the mirror. Here, we show that the optical nonlinearity arising from these effects, typically too small to operate on single photons, can be sufficiently enhanced with feedback to generate large interactions between single photons. We propose a protocol that allows photons propagating in a waveguide to interact with each other through multiple bounces off an optomechanical system. The protocol is analysed by evolving the full many-body quantum state of the waveguide-coupled system, illustrating that large photon-photon interactions mediated by mechanical motion may be within experimental reach.

Wireless Multimedia Sensor Networks: Current Trends and Future Directions

PubMed Central

Almalkawi, Islam T.; Zapata, Manel Guerrero; Al-Karaki, Jamal N.; Morillo-Pozo, Julian

2010-01-01

Wireless Multimedia Sensor Networks (WMSNs) have emerged and shifted the focus from the typical scalar wireless sensor networks to networks with multimedia devices that are capable to retrieve video, audio, images, as well as scalar sensor data. WMSNs are able to deliver multimedia content due to the availability of inexpensive CMOS cameras and microphones coupled with the significant progress in distributed signal processing and multimedia source coding techniques. In this paper, we outline the design challenges of WMSNs, give a comprehensive discussion of the proposed architectures, algorithms and protocols for the different layers of the communication protocol stack for WMSNs, and evaluate the existing WMSN hardware and testbeds. The paper will give the reader a clear view of the state of the art at all aspects of this research area, and shed the light on its main current challenges and future trends. We also hope it will foster discussions and new research ideas among its researchers. PMID:22163571

Deterministic Generation of All-Photonic Quantum Repeaters from Solid-State Emitters

NASA Astrophysics Data System (ADS)

Buterakos, Donovan; Barnes, Edwin; Economou, Sophia E.

2017-10-01

Quantum repeaters are nodes in a quantum communication network that allow reliable transmission of entanglement over large distances. It was recently shown that highly entangled photons in so-called graph states can be used for all-photonic quantum repeaters, which require substantially fewer resources compared to atomic-memory-based repeaters. However, standard approaches to building multiphoton entangled states through pairwise probabilistic entanglement generation severely limit the size of the state that can be created. Here, we present a protocol for the deterministic generation of large photonic repeater states using quantum emitters such as semiconductor quantum dots and defect centers in solids. We show that arbitrarily large repeater states can be generated using only one emitter coupled to a single qubit, potentially reducing the necessary number of photon sources by many orders of magnitude. Our protocol includes a built-in redundancy, which makes it resilient to photon loss.

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

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

PubMed

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

2018-03-01

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

COLD-PCR and microarray: two independent highly sensitive approaches allowing the identification of fetal paternally inherited mutations in maternal plasma.

PubMed

Galbiati, Silvia; Monguzzi, Alessandra; Damin, Francesco; Soriani, Nadia; Passiu, Marianna; Castellani, Carlo; Natacci, Federica; Curcio, Cristina; Seia, Manuela; Lalatta, Faustina; Chiari, Marcella; Ferrari, Maurizio; Cremonesi, Laura

2016-07-01

Until now, non-invasive prenatal diagnosis of genetic diseases found only limited routine applications. In autosomal recessive diseases, it can be used to determine the carrier status of the fetus through the detection of a paternally inherited disease allele in cases where maternal and paternal mutated alleles differ. Conditions for non-invasive identification of fetal paternally inherited mutations in maternal plasma were developed by two independent approaches: coamplification at lower denaturation temperature-PCR (COLD-PCR) and highly sensitive microarrays. Assays were designed for identifying 14 mutations, 7 causing β-thalassaemia and 7 cystic fibrosis. In total, 87 non-invasive prenatal diagnoses were performed by COLD-PCR in 75 couples at risk for β-thalassaemia and 12 for cystic fibrosis. First, to identify the more appropriate methodology for the analysis of minority mutated fetal alleles in maternal plasma, both fast and full COLD-PCR protocols were developed for the most common Italian β-thalassaemia Cd39 and IVSI.110 mutations. In 5 out of 31 samples, no enrichment was obtained with the fast protocol, while full COLD-PCR provided the correct fetal genotypes. Thus, full COLD-PCR protocols were developed for all the remaining mutations and all analyses confirmed the fetal genotypes obtained by invasive prenatal diagnosis. Microarray analysis was performed on 40 samples from 28 couples at risk for β-thalassaemia and 12 for cystic fibrosis. Results were in complete concordance with those obtained by both COLD-PCR and invasive procedures. COLD-PCR and microarray approaches are not expensive, simple to handle, fast and can be easily set up in specialised clinical laboratories where prenatal diagnosis is routinely performed. 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/

Synthesis of photodegradable hydrogels as dynamically tunable cell culture platforms

PubMed Central

Kloxin, April M.; Tibbitt, Mark W.; Anseth, Kristi S.

2013-01-01

We describe a detailed procedure to create photolabile, poly(ethylene glycol)-based (PEG) hydrogels and manipulate material properties in situ. The cytocompatible chemistry and degradation process enable dynamic, tunable changes for applications in 2D or 3D cell culture. The materials are created by synthesizing an o-nitrobenzylether-based photodegradable monomer that can be coupled to primary amines. Here, we provide coupling procedures to PEG-bis-amine to form a photodegradable crosslinker or to the fibronectin-derived peptide RGDS to form a photoreleasable tether. Hydrogels are synthesized with the photodegradable crosslinker in the presence or absence of cells, allowing direct encapsulation or seeding on surfaces. Cell-material interactions can be probed in 2D or 3D by spatiotemporally controlling the gel microenvironment, which allows unique experiments to be performed to monitor cell response to changes in their niche. Degradation is readily achieved with cytocompatible wavelengths of low intensity flood irradiation (365 to 420 nm) in minutes or with highintensity laser irradiation (405 nm) in seconds. In this protocol, synthesis and purification of the photodegradable monomers take approximately 2 weeks, but can be substantially shortened by purchasing the o-nitrobenzylether precursor. Preparation of the sterile solutions for hydrogel fabrication takes hours, while the reaction to form the final hydrogel is complete in minutes. Hydrogel degradation occurs on-demand, in seconds to minutes, with user-directed light exposure. This comprehensive protocol is useful for controlling peptide presentation and substrate modulus during cell culture on or within an elastic matrix. These PEG-based materials are useful for probing the dynamic influence of cell-cell and cell-material interactions on cell function in 2D or 3D. While other protocols are available for controlling peptide presentation or modulus, few allow manipulation of material properties in situ and in the presence of cells down to the micrometer scale. PMID:21127482

Robust state preparation in quantum simulations of Dirac dynamics

NASA Astrophysics Data System (ADS)

Song, Xue-Ke; Deng, Fu-Guo; Lamata, Lucas; Muga, J. G.

2017-02-01

A nonrelativistic system such as an ultracold trapped ion may perform a quantum simulation of a Dirac equation dynamics under specific conditions. The resulting Hamiltonian and dynamics are highly controllable, but the coupling between momentum and internal levels poses some difficulties to manipulate the internal states accurately in wave packets. We use invariants of motion to inverse engineer robust population inversion processes with a homogeneous, time-dependent simulated electric field. This exemplifies the usefulness of inverse-engineering techniques to improve the performance of quantum simulation protocols.

Quantification of deep traps in nanocrystal solids, their electronic properties, and their influence on device behavior.

PubMed

Bozyigit, Deniz; Volk, Sebastian; Yarema, Olesya; Wood, Vanessa

2013-11-13

We implement three complementary techniques to quantify the number, energy, and electronic properties of trap states in nanocrystal (NC)-based devices. We demonstrate that, for a given technique, the ability to observe traps depends on the Fermi level position, highlighting the importance of a multitechnique approach that probes trap coupling to both the conduction and the valence bands. We then apply our protocol for characterizing traps to quantitatively explain the measured performances of PbS NC-based solar cells.

Copper-Catalyzed Synthesis of Tetrasubstituted Enynylboronates via Chemo-, Regio-, and Stereoselective Borylalkynylation.

PubMed

Han, Jung Tae; Yun, Jaesook

2018-04-06

An efficient, catalytic method for accessing tetrasubstituted enynylboronates has been established via copper-catalyzed chemo-, regio-, and stereoselective borylalkynylation of internal alkynes. In this protocol, a range of symmetrical and unsymmetrical internal alkynes with aryl, heteroaryl, and alkyl substituents afforded fully substituted enynylboron compounds in good yields and with high levels of regio- and stereoselectivity, up to a ratio of >20:1. The enynylboron products could be further utilized in transforming the C-B bond into C-C bonds by coupling reactions.

Storage and retrieval of quantum information with a hybrid optomechanics-spin system

NASA Astrophysics Data System (ADS)

Feng, Zhi-Bo; Zhang, Jian-Qi; Yang, Wan-Li; Feng, Mang

2016-08-01

We explore an efficient scheme for transferring the quantum state between an optomechanical cavity and an electron spin of diamond nitrogen-vacancy center. Assisted by a mechanical resonator, quantum information can be controllably stored (retrieved) into (from) the electron spin by adjusting the external field-induced detuning or coupling. Our scheme connects effectively the cavity photon and the electron spin and transfers quantum states between two regimes with large frequency difference. The experimental feasibility of our protocol is justified with accessible laboratory parameters.

Microwave-Assisted Condensation Reactions of Acetophenone Derivatives and Activated Methylene Compounds with Aldehydes Catalyzed by Boric Acid under Solvent-Free Conditions.

PubMed

Brun, Elodie; Safer, Abdelmounaim; Carreaux, François; Bourahla, Khadidja; L'helgoua'ch, Jean-Martial; Bazureau, Jean-Pierre; Villalgordo, Jose Manuel

2015-06-23

We here disclosed a new protocol for the condensation of acetophenone derivatives and active methylene compounds with aldehydes in the presence of boric acid under microwave conditions. Implementation of the reaction is simple, healthy and environmentally friendly owing to the use of a non-toxic catalyst coupled to a solvent-free procedure. A large variety of known or novel compounds have thus been prepared, including with substrates bearing acid or base-sensitive functional groups.

Rhodium-catalyzed redox-neutral coupling of phenidones with alkynes.

PubMed

Fan, Zhoulong; Lu, Heng; Li, Wei; Geng, Kaijun; Zhang, Ao

2017-07-21

A switchable synthesis of N-substituted indole derivatives from phenidones via rhodium-catalyzed redox-neutral C-H activation has been achieved. In this protocol, we firstly disclosed that the reactivity of Rh(iii) catalysis could be enhanced through employing palladium acetate as an additive. Some representative features include external oxidant-free, applicable to terminal alkynes, short reaction time and operational simplicity. The utility of this method is further showcased by the economical synthesis of potent anticancer PARP-1 inhibitors.

Synthesis of Natural and Unnatural Cyclooligomeric Depsipeptides Enabled by Flow Chemistry

PubMed Central

Lücke, Daniel; Dalton, Toryn; Ley, Steven V.

2016-01-01

Abstract Flow chemistry has been successfully integrated into the synthesis of a series of cyclooligomeric depsipeptides of three different ring sizes including the natural products beauvericin (1 a), bassianolide (2 b) and enniatin C (1 b). A reliable flow chemistry protocol was established for the coupling and macrocyclisation to form challenging N‐methylated amides. This flexible approach has allowed the rapid synthesis of both natural and unnatural depsipeptides in high yields, enabling further exploration of their promising biological activity. PMID:26844421

Enantioselective α-Alkylation of Aldehydes by Photoredox Organocatalysis: Rapid Access to Pharmacophore Fragments from β-Cyanoaldehydes.

PubMed

Welin, Eric R; Warkentin, Alexander A; Conrad, Jay C; MacMillan, David W C

2015-08-10

The combination of photoredox catalysis and enamine catalysis has enabled the development of an enantioselective α-cyanoalkylation of aldehydes. This synergistic catalysis protocol allows for the coupling of two highly versatile yet orthogonal functionalities, allowing rapid diversification of the oxonitrile products to a wide array of medicinally relevant derivatives and heterocycles. This methodology has also been applied to the total synthesis of the lignan natural product (-)-bursehernin. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A quality analysis of clinical anaesthesia study protocols from the Chinese clinical trials registry according to the SPIRIT statement.

PubMed

Yang, Lei; Chen, Shouming; Yang, Di; Li, Jiajin; Wu, Taixiang; Zuo, Yunxia

2018-05-15

To learn about the overall quality of clinical anaesthesia study protocols from the Chinese Clinical Trials Registry and to discuss the way to improve study protocol quality. We defined completeness of each sub-item in SPIRIT as N/A (not applicable) or with a score of 0, 1, or 2. For each protocol, we calculated the proportion of adequately reported items (score = 2 and N/A) and unreported items (score = 0). Protocol quality was determined according to the proportion of reported items, with values >50% indicating high quality. Protocol quality was determined according to the proportion of reported items. For each sub-item in SPIRIT, we calculated the adequately reported rate (percentage of all protocols with score 2 and NA on one sub-item) as well as the unreported rate (percentage of all protocols with score 0 on one sub-item). Total 126 study protocols were available for assessment. Among these, 88.1% were assessed as being of low quality. By comparison, the percentage of low-quality protocols was 88.9% after the publication of the SPIRIT statement. Among the 51 SPIRIT sub-items, 18 sub-items had an unreported rate above 90% while 16 had a higher adequately reported rate than an unreported rate. The overall quality of clinical anaesthesia study protocols registered in the ChiCTR was poor. A mandatory protocol upload and self-check based on the SPIRIT statement during the trial registration process may improve protocol quality in the future.

Compact 3D quantum memory

NASA Astrophysics Data System (ADS)

Xie, Edwar; Deppe, Frank; Renger, Michael; Repp, Daniel; Eder, Peter; Fischer, Michael; Goetz, Jan; Pogorzalek, Stefan; Fedorov, Kirill G.; Marx, Achim; Gross, Rudolf

2018-05-01

Superconducting 3D microwave cavities offer state-of-the-art coherence times and a well-controlled environment for superconducting qubits. In order to realize at the same time fast readout and long-lived quantum information storage, one can couple the qubit to both a low-quality readout and a high-quality storage cavity. However, such systems are bulky compared to their less coherent 2D counterparts. A more compact and scalable approach is achieved by making use of the multimode structure of a 3D cavity. In our work, we investigate such a device where a transmon qubit is capacitively coupled to two modes of a single 3D cavity. External coupling is engineered so that the memory mode has an about 100 times larger quality factor than the readout mode. Using an all-microwave second-order protocol, we realize a lifetime enhancement of the stored state over the qubit lifetime by a factor of 6 with a fidelity of approximately 80% determined via quantum process tomography. We also find that this enhancement is not limited by fundamental constraints.

Hamiltonian quantum simulation with bounded-strength controls

NASA Astrophysics Data System (ADS)

Bookatz, Adam D.; Wocjan, Pawel; Viola, Lorenza

2014-04-01

We propose dynamical control schemes for Hamiltonian simulation in many-body quantum systems that avoid instantaneous control operations and rely solely on realistic bounded-strength control Hamiltonians. Each simulation protocol consists of periodic repetitions of a basic control block, constructed as a modification of an ‘Eulerian decoupling cycle,’ that would otherwise implement a trivial (zero) target Hamiltonian. For an open quantum system coupled to an uncontrollable environment, our approach may be employed to engineer an effective evolution that simulates a target Hamiltonian on the system while suppressing unwanted decoherence to the leading order, thereby allowing for dynamically corrected simulation. We present illustrative applications to both closed- and open-system simulation settings, with emphasis on simulation of non-local (two-body) Hamiltonians using only local (one-body) controls. In particular, we provide simulation schemes applicable to Heisenberg-coupled spin chains exposed to general linear decoherence, and show how to simulate Kitaev's honeycomb lattice Hamiltonian starting from Ising-coupled qubits, as potentially relevant to the dynamical generation of a topologically protected quantum memory. Additional implications for quantum information processing are discussed.

ortho-Methoxyphenols as Convenient Oxidative Bioconjugation Reagents with Application to Site-Selective Heterobifunctional Cross-Linkers.

PubMed

ElSohly, Adel M; MacDonald, James I; Hentzen, Nina B; Aanei, Ioana L; El Muslemany, Kareem M; Francis, Matthew B

2017-03-15

The synthesis of complex protein-based bioconjugates has been facilitated greatly by recent developments in chemoselective methods for biomolecular modification. The oxidative coupling of o-aminophenols or catechols with aniline functional groups is chemoselective, mild, and rapid; however, the oxidatively sensitive nature of the electron-rich aromatics and the paucity of commercial sources pose some obstacles to the general use of these reactive strategies. Herein, we identify o-methoxyphenols as air-stable, commercially available derivatives that undergo efficient oxidative couplings with anilines in the presence of periodate as oxidant. Mechanistic considerations informed the development of a preoxidation protocol that can greatly reduce the amount of periodate necessary for effective coupling. The stability and versatility of these reagents was demonstrated through the synthesis of complex protein-protein bioconjugates using a site-selective heterobifunctional cross-linker comprising both o-methoxyphenol and 2-pyridinecarboxaldehyde moieties. This compound was used to link epidermal growth factor to genome-free MS2 viral capsids, affording nanoscale delivery vectors that can target a variety of cancer cell types.

Acceptance of vulvovaginal pain in women with provoked vestibulodynia and their partners: associations with pain, psychological, and sexual adjustment.

PubMed

Boerner, Katelynn E; Rosen, Natalie O

2015-06-01

Provoked vestibulodynia (PVD) is a common vulvovaginal pain condition associated with negative psychological and sexual consequences for affected women and their sexual partners. Greater pain acceptance has been found to be associated with better functional and psychological outcomes in individuals with chronic pain, and acceptance-based strategies are being increasingly incorporated into treatment protocols. The present study is a novel investigation of pain acceptance in PVD couples. The aim was to examine the associations between acceptance of vulvovaginal pain and women's pain during intercourse, as well as the psychological and sexual adjustment of both women with PVD and their partners. Sixty-one couples (M(age) for women = 27.95 years, SD = 5.87; M(age) for men = 30.48 years, SD = 6.70) in which the woman was diagnosed with PVD completed the Chronic Pain Acceptance Questionnaire, in reference to women's vulvovaginal pain. Women also rated their pain during intercourse, and couples completed measures of anxiety, depression, sexual function, and sexual satisfaction. Dependent measures were (i) women's self-reported pain during intercourse on a numerical rating scale; (ii) State-Trait Anxiety Inventory trait subscale; (iii) Beck Depression Inventory-II; (iv) Derogatis Interview for Sexual Functioning; and (v) Global Measure of Sexual Satisfaction Scale. Women's greater pain acceptance was associated with their lower self-reported pain during intercourse, controlling for partner's pain acceptance. Greater pain acceptance among women was associated with their own lower anxiety and depression, greater sexual functioning, as well as their own and their partner's greater sexual satisfaction, controlling for the partner's pain acceptance. Additionally, greater pain acceptance among male partners was associated with their own lower depression. Findings suggest that psychological interventions for PVD should target increasing couples' vulvovaginal pain acceptance in order to improve women's pain and the sexual and psychological functioning of both members of the couple. © 2015 International Society for Sexual Medicine.

Single Cell Gene Expression Profiling of Skeletal Muscle-Derived Cells.

PubMed

Gatto, Sole; Puri, Pier Lorenzo; Malecova, Barbora

2017-01-01

Single cell gene expression profiling is a fundamental tool for studying the heterogeneity of a cell population by addressing the phenotypic and functional characteristics of each cell. Technological advances that have coupled microfluidic technologies with high-throughput quantitative RT-PCR analyses have enabled detailed analyses of single cells in various biological contexts. In this chapter, we describe the procedure for isolating the skeletal muscle interstitial cells termed Fibro-Adipogenic Progenitors (FAPs ) and their gene expression profiling at the single cell level. Moreover, we accompany our bench protocol with bioinformatics analysis designed to process raw data as well as to visualize single cell gene expression data. Single cell gene expression profiling is therefore a useful tool in the investigation of FAPs heterogeneity and their contribution to muscle homeostasis.

Stroboscopic versus nonstroboscopic dynamics in the Floquet realization of the Harper-Hofstadter Hamiltonian

NASA Astrophysics Data System (ADS)

Bukov, Marin; Polkovnikov, Anatoli

2014-10-01

We study the stroboscopic and nonstroboscopic dynamics in the Floquet realization of the Harper-Hofstadter Hamiltonian. We show that the former produces the evolution expected in the high-frequency limit only for observables, which commute with the operator to which the driving protocol couples. On the contrary, nonstroboscopic dynamics is capable of capturing the evolution governed by the Floquet Hamiltonian of any observable associated with the effective high-frequency model. We provide exact numerical simulations for the dynamics of the number operator following a quantum cyclotron orbit on a 2×2 plaquette, as well as the chiral current operator flowing along the legs of a 2×20 ladder. The exact evolution is compared with its stroboscopic and nonstroboscopic counterparts, including finite-frequency corrections.

Real life experimental determination of platinum group metals content in automotive catalytic converters

NASA Astrophysics Data System (ADS)

Yakoumis, I.; Moschovi, A. M.; Giannopoulou, I.; Panias, D.

2018-03-01

The real life experimental protocol for the preparation of spent automobile catalyst samples for elemental analysis is thoroughly described in the following study. Collection, sorting and dismantling, homogenization and sample preparation for X-Ray fluorescence spectroscopy and Atomic Adsorption Spectroscopy combined with Inductive coupled plasma mass spectrometry are discussed in detail for both ceramic and metallic spent catalysts. The concentrations of Platinum Group Metals (PGMs) in spent catalytic converters are presented based on typical consignments of recycled converters (more than 45,000 pieces) from the Greek Market. The conclusions clearly denoted commercial metallic catalytic foil contains higher PGMs loading than ceramic honeycombs. On the other hand, the total PGMs loading in spent ceramic catalytic converters has been found higher than the corresponding value for the metallic ones.

Intracranial recordings and human memory.

PubMed

Johnson, Elizabeth L; Knight, Robert T

2015-04-01

Recent work involving intracranial recording during human memory performance provides superb spatiotemporal resolution on mnemonic processes. These data demonstrate that the cortical regions identified in neuroimaging studies of memory fall into temporally distinct networks and the hippocampal theta activity reported in animal memory literature also plays a central role in human memory. Memory is linked to activity at multiple interacting frequencies, ranging from 1 to 500Hz. High-frequency responses and coupling between different frequencies suggest that frontal cortex activity is critical to human memory processes, as well as a potential key role for the thalamus in neocortical oscillations. Future research will inform unresolved questions in the neuroscience of human memory and guide creation of stimulation protocols to facilitate function in the damaged brain. Copyright © 2014 Elsevier Ltd. All rights reserved.

Iron-Catalyzed C-O Bond Activation: Opportunity for Sustainable Catalysis.

PubMed

Bisz, Elwira; Szostak, Michal

2017-10-23

Oxygen-based electrophiles have emerged as some of the most valuable cross-coupling partners in organic synthesis due to several major strategic and environmental benefits, such as abundance and potential to avoid toxic halide waste. In this context, iron-catalyzed C-O activation/cross-coupling holds particular promise to achieve sustainable catalytic protocols due to its natural abundance, inherent low toxicity, and excellent economic and ecological profile. Recently, tremendous progress has been achieved in the development of new methods for functional-group-tolerant iron-catalyzed cross-coupling reactions by selective C-O cleavage. These methods establish highly attractive alternatives to traditional cross-coupling reactions by using halides as electrophilic partners. In particular, new easily accessible oxygen-based electrophiles have emerged as substrates in iron-catalyzed cross-coupling reactions, which significantly broaden the scope of this catalysis platform. New mechanistic manifolds involving iron catalysis have been established; thus opening up vistas for the development of a wide range of unprecedented reactions. The synthetic potential of this sustainable mode of reactivity has been highlighted by the development of new strategies in the construction of complex motifs, including in target synthesis. The most recent advances in sustainable iron-catalyzed cross-coupling of C-O-based electrophiles are reviewed, with a focus on both mechanistic aspects and synthetic utility. It should be noted that this catalytic manifold provides access to motifs that are often not easily available by other methods, such as the assembly of stereodefined dienes or C(sp 2 )-C(sp 3 ) cross-couplings, thus emphasizing the synthetic importance of this mode of reactivity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Metallaphotoredox-catalysed sp3-sp3 cross-coupling of carboxylic acids with alkyl halides

NASA Astrophysics Data System (ADS)

Johnston, Craig P.; Smith, Russell T.; Allmendinger, Simon; MacMillan, David W. C.

2016-08-01

In the past 50 years, cross-coupling reactions mediated by transition metals have changed the way in which complex organic molecules are synthesized. The predictable and chemoselective nature of these transformations has led to their widespread adoption across many areas of chemical research. However, the construction of a bond between two sp3-hybridized carbon atoms, a fundamental unit of organic chemistry, remains an important yet elusive objective for engineering cross-coupling reactions. In comparison to related procedures with sp2-hybridized species, the development of methods for sp3-sp3 bond formation via transition metal catalysis has been hampered historically by deleterious side-reactions, such as β-hydride elimination with palladium catalysis or the reluctance of alkyl halides to undergo oxidative addition. To address this issue, nickel-catalysed cross-coupling processes can be used to form sp3-sp3 bonds that utilize organometallic nucleophiles and alkyl electrophiles. In particular, the coupling of alkyl halides with pre-generated organozinc, Grignard and organoborane species has been used to furnish diverse molecular structures. However, the manipulations required to produce these activated structures is inefficient, leading to poor step- and atom-economies. Moreover, the operational difficulties associated with making and using these reactive coupling partners, and preserving them through a synthetic sequence, has hindered their widespread adoption. A generically useful sp3-sp3 coupling technology that uses bench-stable, native organic functional groups, without the need for pre-functionalization or substrate derivatization, would therefore be valuable. Here we demonstrate that the synergistic merger of photoredox and nickel catalysis enables the direct formation of sp3-sp3 bonds using only simple carboxylic acids and alkyl halides as the nucleophilic and electrophilic coupling partners, respectively. This metallaphotoredox protocol is suitable for many primary and secondary carboxylic acids. The merit of this coupling strategy is illustrated by the synthesis of the pharmaceutical tirofiban in four steps from commercially available starting materials.

Does adopting a prenatal substance use protocol reduce racial disparities in CPS reporting related to maternal drug use? A California case study.

PubMed

Roberts, S C M; Zahnd, E; Sufrin, C; Armstrong, M A

2015-02-01

This study examined whether adopting a standardized prenatal substance use protocol (protocol) in a hospital labor and delivery unit reduced racial disparities in reporting to child protective services (CPS) related to maternal drug use during pregnancy. This study used an interrupted time series design with a non-equivalent control. One hospital adopted a protocol and another hospital group serving a similar geographic population did not change protocols. Data on CPS reporting disparities from these hospitals over 3.5 years were analyzed using segmented regression. In the hospital that adopted the protocol, almost five times more black than white newborns were reported during the study period. Adopting the protocol was not associated with reduced disparities. Adopting a protocol cannot be assumed to reduce CPS reporting disparities. Efforts to encourage hospitals to adopt protocols as a strategy to reduce disparities may be misguided. Other strategies to reduce disparities are needed.

Ice-sheet modelling accelerated by graphics cards

NASA Astrophysics Data System (ADS)

Brædstrup, Christian Fredborg; Damsgaard, Anders; Egholm, David Lundbek

2014-11-01

Studies of glaciers and ice sheets have increased the demand for high performance numerical ice flow models over the past decades. When exploring the highly non-linear dynamics of fast flowing glaciers and ice streams, or when coupling multiple flow processes for ice, water, and sediment, researchers are often forced to use super-computing clusters. As an alternative to conventional high-performance computing hardware, the Graphical Processing Unit (GPU) is capable of massively parallel computing while retaining a compact design and low cost. In this study, we present a strategy for accelerating a higher-order ice flow model using a GPU. By applying the newest GPU hardware, we achieve up to 180× speedup compared to a similar but serial CPU implementation. Our results suggest that GPU acceleration is a competitive option for ice-flow modelling when compared to CPU-optimised algorithms parallelised by the OpenMP or Message Passing Interface (MPI) protocols.

GENERAL: Thermal entanglement and teleportation of a thermally mixed entangled state of a Heisenberg chain through a Werner state

NASA Astrophysics Data System (ADS)

Huang, Li-Yuan; Fang, Mao-Fa

2008-07-01

The thermal entanglement and teleportation of a thermally mixed entangled state of a two-qubit Heisenberg XXX chain under the Dzyaloshinski-Moriya (DM) anisotropic antisymmetric interaction through a noisy quantum channel given by a Werner state is investigated. The dependences of the thermal entanglement of the teleported state on the DM coupling constant, the temperature and the entanglement of the noisy quantum channel are studied in detail for both the ferromagnetic and the antiferromagnetic cases. The result shows that a minimum entanglement of the noisy quantum channel must be provided in order to realize the entanglement teleportation. The values of fidelity of the teleported state are also studied for these two cases. It is found that under certain conditions, we can transfer an initial state with a better fidelity than that for any classical communication protocol.

Resonance Raman spectroscopy in malaria research.

PubMed

Wood, Bayden R; McNaughton, Don

2006-10-01

In recent years, the field of Raman spectroscopy has witnessed a surge in technological development, with the incorporation of ultrasensitive, charge-coupled devices, improved laser sources and precision Rayleigh-filter systems. This has led to the development of sensitive confocal micro-Raman spectrometers and imaging spectrometers that are capable of obtaining high spatial-resolution spectra and images of subcellular components within single living cells. This review reports on the application of resonance micro-Raman spectroscopy to the study of malaria pigment (hemozoin), a by-product of hemoglobin catabolization by the malaria parasite, which is an important target site for antimalarial drugs. The review aims to briefly describe recent studies on the application of this technology, elucidate molecular and electronic properties of the malaria pigment and its synthetic analog beta-hematin, provide insight into the mechanism of hemozoin formation within the food vacuole of the parasite, and comment on developing strategies for using this technology in drug-screening protocols.

Evidence of CuI/CuII Redox Process by X-ray Absorption and EPR Spectroscopy: Direct Synthesis of Dihydrofurans from b-Ketocarbonyl Derivatives and Olefins

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

Yi, Hong; Liao, Zhixiong; Zhang, Guanghui

Abstract: The CuI/CuII and CuI/CuIII catalytic cycles have been subject to intense debate in the field of copper-catalyzed oxidative coupling reactions. A mechanistic study on the CuI/CuII redox process, by X-ray absorption (XAS) and electron paramagnetic resonance (EPR) spectroscopies, has elucidated the reduction mechanism of CuII to CuI by 1,3-diketone and detailed investigation revealed that the halide ion is important for the reduction process. The oxidative nature of the thereby-formed CuI has also been studied by XAS and EPR spectroscopy. This mechanistic information is applicable to the copper-catalyzed oxidative cyclization of b-ketocarbonyl derivatives to dihydrofurans. This protocol provides an idealmore » route to highly substituted dihydrofuran rings from easily available 1,3-dicarbonyls and olefins. Copper« less

Suppression of anomalous synchronization and nonstationary behavior of neural network under small-world topology

NASA Astrophysics Data System (ADS)

Boaretto, B. R. R.; Budzinski, R. C.; Prado, T. L.; Kurths, J.; Lopes, S. R.

2018-05-01

It is known that neural networks under small-world topology can present anomalous synchronization and nonstationary behavior for weak coupling regimes. Here, we propose methods to suppress the anomalous synchronization and also to diminish the nonstationary behavior occurring in weakly coupled neural network under small-world topology. We consider a network of 2000 thermally sensitive identical neurons, based on the model of Hodgkin-Huxley in a small-world topology, with the probability of adding non local connection equal to p = 0 . 001. Based on experimental protocols to suppress anomalous synchronization, as well as nonstationary behavior of the neural network dynamics, we make use of (i) external stimulus (pulsed current); (ii) biologic parameters changing (neuron membrane conductance changes); and (iii) body temperature changes. Quantification analysis to evaluate phase synchronization makes use of the Kuramoto's order parameter, while recurrence quantification analysis, particularly the determinism, computed over the easily accessible mean field of network, the local field potential (LFP), is used to evaluate nonstationary states. We show that the methods proposed can control the anomalous synchronization and nonstationarity occurring for weak coupling parameter without any effect on the individual neuron dynamics, neither in the expected asymptotic synchronized states occurring for large values of the coupling parameter.

Gold Nanomaterials in Consumer Cosmetics Nanoproducts: Analyses, Characterization, and Dermal Safety Assessment.

PubMed

Cao, Mingjing; Li, Jiayang; Tang, Jinglong; Chen, Chunying; Zhao, Yuliang

2016-10-01

Establishment of analytical methods of engineered nanomaterials in consumer products for their human and environmental risk assessment becomes urgent for both academic and industrial needs. Owing to the difficulties and challenges around nanomaterials in complex media, proper chemical separation and biological assays of nanomaterials from nanoproducts needs to be firstly developed. Herein, a facile and rapid method to separate and analyze gold nanomaterials in cosmetics is reported. Gold nanomaterials are successfully separated from different facial or eye creams and their physiochemical properties are analyzed by quantitative and qualitative state-of-the art techniques with high sensitivity or high spatial resolution. In turn, a protocol including quantification of gold by inductively coupled plasma mass spectrometry and thorough characterization of morphology, size distribution, and surface property by electron microscopes, atomic force microscope, and X-ray photoelectron spectroscope is developed. Subsequently, the preliminary toxicity assessment indicates that gold nanomaterials in cosmetic creams have no observable toxicity to human keratinocytes even after 24 h exposure up to a concentration of 200 μg mL -1 . The environmental scanning electron microscope reveals that gold nanomaterials are mostly attached on the cell membrane. Thus, the present study provides a full analysis protocol for toxicity assessment of gold nanomaterials in consumer products (cosmetic creams). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Increased Arctic Deposition of Persistent Compounds as a Result of the Montreal Protocol

NASA Astrophysics Data System (ADS)

Young, C.; Pickard, H. M.; De Silva, A. O.; Spencer, C.; Criscitiello, A. S.; Muir, D.; Sharp, M. J.

2017-12-01

Perfluorocarboxylic acids (PFCAs) are among the diverse groups of compounds characterized as persistent organic pollutants. They are toxic, resistant to environmental degradation, and adversely impact human and environmental health. PFCAs with four or fewer carbons, short-chain PFCAs (scPFCAs), are of particular interest because of their increasing levels in the environment, toxicity to plants, and potential for accumulation in some aquatic ecosystems, making them an emerging environmental concern. A minor source of scPFCAs to the Arctic has been shown to be atmospheric transformation of fluoropolymer precursors, followed by deposition. Additional potential sources of scPFCAs to the Arctic are chlorofluorocarbon (CFC)-replacement compounds. Through analysis of an ice core from the Canadian High Arctic, we show that Montreal Protocol-mandated introduction of CFC-replacement compounds for the heat-transfer industry has led to increasing inputs of these scPFCAs to the remote environment. Flux measurements for scPFCAs as a class of contaminants have only been reported in a couple studies to date. Here, we provide the first multi-decadal temporal record of scPFCA deposition, demonstrating a dramatic increase in deposition resulting from emission of CFC-replacements. These results bring to the forefront a need for a holistic approach to environmental risk assessment that considers impacts of replacement substances and degradation products.

Clinical Efficacy and Immune Regulation With Peanut Oral Immunotherapy

PubMed Central

Jones, Stacie M.; Pons, Laurent; Roberts, Joseph L.; Scurlock, Amy M.; Perry, Tamara T.; Kulis, Mike; Shreffler, Wayne G.; Steele, Pamela; Henry, Karen A.; Adair, Margaret; Francis, James M.; Durham, Stephen; Vickery, Brian P.; Zhong, Xiaoping; Burks, A. Wesley

2009-01-01

Background Oral immunotherapy (OIT) has been thought to induce clinical desensitization to allergenic foods, but trials coupling the clinical response and immunologic effects of peanut OIT have not been reported. Objective The study objective was to investigate the clinical efficacy and immunologic changes associated with OIT. Methods Peanut-allergic children underwent an OIT protocol including initial day escalation, build-up, and maintenance phases, and then oral food challenge. Clinical response and immunologic changes were evaluated. Results Of 29 subjects who completed the protocol, 27 ingested 3.9 g peanut protein during food challenge. Most symptoms noted during OIT resolved spontaneously or with antihistamines. By 6 months, titrated skin prick tests and activation of basophils significantly declined. Peanut-specific IgE decreased by 12–18 months, while IgG4 increased significantly. Serum factors inhibited IgE–peanut complex formation in an IgE-facilitated allergen binding assay. Secretion of IL-10, IL-5, IFN-γ, and TNF-α from PBMCs increased over 6–12 months. Peanut-specific FoxP3 T cells increased until 12 months and then decreased thereafter. Additionally, T cell microarrays showed downregulation of genes in apoptotic pathways. Conclusion OIT induces clinical desensitization to peanut, with significant longer term humoral and cellular changes. Microarray data suggest a novel role for apoptosis in OIT. PMID:19577283

A quality analysis of clinical anaesthesia study protocols from the Chinese clinical trials registry according to the SPIRIT statement

PubMed Central

Yang, Lei; Chen, Shouming; Yang, Di; Li, Jiajin; Wu, Taixiang; Zuo, Yunxia

2018-01-01

Objective To learn about the overall quality of clinical anaesthesia study protocols from the Chinese Clinical Trials Registry and to discuss the way to improve study protocol quality. Methods We defined completeness of each sub-item in SPIRIT as N/A (not applicable) or with a score of 0, 1, or 2. For each protocol, we calculated the proportion of adequately reported items (score = 2 and N/A) and unreported items (score = 0). Protocol quality was determined according to the proportion of reported items, with values >50% indicating high quality. Protocol quality was determined according to the proportion of reported items. For each sub-item in SPIRIT, we calculated the adequately reported rate (percentage of all protocols with score 2 and NA on one sub-item) as well as the unreported rate (percentage of all protocols with score 0 on one sub-item). Results Total 126 study protocols were available for assessment. Among these, 88.1% were assessed as being of low quality. By comparison, the percentage of low-quality protocols was 88.9% after the publication of the SPIRIT statement. Among the 51 SPIRIT sub-items, 18 sub-items had an unreported rate above 90% while 16 had a higher adequately reported rate than an unreported rate. Conclusions The overall quality of clinical anaesthesia study protocols registered in the ChiCTR was poor. A mandatory protocol upload and self-check based on the SPIRIT statement during the trial registration process may improve protocol quality in the future. PMID:29872509

Effectiveness of a Technology-Based Supportive Educational Parenting Program on Parental Outcomes in Singapore: Protocol for a Randomized Controlled Trial.

PubMed

Shorey, Shefaly; Ng, Yvonne Peng Mei; Siew, An Ling; Yoong, Joanne; Mörelius, Evalotte

2018-01-10

Supportive educational programs during the perinatal period are scarce in Singapore. There is no continuity of care available in terms of support from community care nurses in Singapore. Parents are left on their own most of the time, which results in a stressful transition to parenthood. There is a need for easily accessible technology-based educational programs that can support parents during this crucial perinatal period. The aim of this study was to describe the study protocol of a randomized controlled trial on a technology-based supportive educational parenting program. A randomized controlled two-group pretest and repeated posttest experimental design will be used. The study will recruit 118 parents (59 couples) from the antenatal clinics of a tertiary public hospital in Singapore. Eligible parents will be randomly allocated to receive either the supportive educational parenting program or routine perinatal care from the hospital. Outcome measures include parenting self-efficacy, parental bonding, postnatal depression, social support, parenting satisfaction, and cost evaluation. Data will be collected at the antenatal period, immediate postnatal period, and at 1 month and 3 months post childbirth. Recruitment of the study participants commenced in December 2016 and is still ongoing. Data collection is projected to finish within 12 months, by December 2017. This study will identify a potentially clinically useful, effective, and cost-effective supportive educational parenting program to improve parental self-efficacy and bonding in newborn care, which will then improve parents' social support-seeking behaviors, emotional well-being, and satisfaction with parenting. It is hoped that better supported and satisfied parents will consider having more children, which may in turn influence Singapore's ailing birth rate. International Standard Randomized Controlled Trial Number (ISRCTN): 48536064; https://www.isrctn.com/ISRCTN48536064 (Archived by WebCite at http://www.webcitation.org/6wMuEysiO). ©Shefaly Shorey, Yvonne Peng Mei Ng, An Ling Siew, Joanne Yoong, Evalotte Mörelius. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 10.01.2018.

Optimizing the high-resolution manometry (HRM) study protocol.

PubMed

Patel, A; Ding, A; Mirza, F; Gyawali, C P

2015-02-01

Intolerance of the esophageal manometry catheter may prolong high-resolution manometry (HRM) studies and increase patient distress. We assessed the impact of obtaining the landmark phase at the end of the study when the patient has acclimatized to the HRM catheter. 366 patients (mean age 55.4 ± 0.8 years, 62.0% female) undergoing esophageal HRM over a 1-year period were studied. The standard protocol consisted of the landmark phase, 10 5 mL water swallows 20-30 s apart, and multiple rapid swallows where 4-6 2 mL swallows were administered in rapid succession. The modified protocol consisted of the landmark phase at the end of the study after test swallows. Study duration, technical characteristics, indications, and motor findings were compared between standard and modified protocols. Of the 366 patients, 89.6% underwent the standard protocol (study duration 12.9 ± 0.3 min). In 10.4% with poor catheter tolerance undergoing the modified protocol, study duration was significantly longer (15.6 ± 1.0 min, p = 0.004) despite similar duration of study maneuvers. Only elevated upper esophageal sphincter basal pressures at the beginning of the study segregated modified protocol patients. The 95th percentile time to landmark phase in the standard protocol patients was 6.1 min; as many as 31.4% of modified protocol patients could not obtain their first study maneuver within this period (p = 0.0003). Interpretation was not impacted by shifting the landmark phase to the end of the study. Modification of the HRM study protocol with the landmark phase obtained at the end of the study optimizes study duration without compromising quality. © 2014 John Wiley & Sons Ltd.

Influence of land-atmosphere feedbacks on temperature and precipitation extremes in the GLACE-CMIP5 ensemble

USGS Publications Warehouse

Lorenz, Ruth; Argueso, Daniel; Donat, Markus G.; Pitman, Andrew J.; van den Hurk, Bart; Berg, Alexis; Lawrence, David M.; Cheruy, Frederique; Ducharne, Agnes; Hagemann, Stefan; Meier, Arndt; Milly, Paul C.D.; Seneviratne, Sonia I

2016-01-01

We examine how soil moisture variability and trends affect the simulation of temperature and precipitation extremes in six global climate models using the experimental protocol of the Global Land-Atmosphere Coupling Experiment of the Coupled Model Intercomparison Project, Phase 5 (GLACE-CMIP5). This protocol enables separate examinations of the influences of soil moisture variability and trends on the intensity, frequency, and duration of climate extremes by the end of the 21st century under a business-as-usual (Representative Concentration Pathway 8.5) emission scenario. Removing soil moisture variability significantly reduces temperature extremes over most continental surfaces, while wet precipitation extremes are enhanced in the tropics. Projected drying trends in soil moisture lead to increases in intensity, frequency, and duration of temperature extremes by the end of the 21st century. Wet precipitation extremes are decreased in the tropics with soil moisture trends in the simulations, while dry extremes are enhanced in some regions, in particular the Mediterranean and Australia. However, the ensemble results mask considerable differences in the soil moisture trends simulated by the six climate models. We find that the large differences between the models in soil moisture trends, which are related to an unknown combination of differences in atmospheric forcing (precipitation, net radiation), flux partitioning at the land surface, and how soil moisture is parameterized, imply considerable uncertainty in future changes in climate extremes.

Incorporating Aptamers in the Multiple Analyte Profiling Assays (xMAP): Detection of C-Reactive Protein.

PubMed

Bernard, Elyse D; Nguyen, Kathy C; DeRosa, Maria C; Tayabali, Azam F; Aranda-Rodriguez, Rocio

2017-01-01

Aptamers are short oligonucleotide sequences used in detection systems because of their high affinity binding to a variety of macromolecules. With the introduction of aptamers over 25 years ago came the exploration of their use in many different applications as a substitute for antibodies. Aptamers have several advantages; they are easy to synthesize, can bind to analytes for which it is difficult to obtain antibodies, and in some cases bind better than antibodies. As such, aptamer applications have significantly expanded as an adjunct to a variety of different immunoassay designs. The Multiple-Analyte Profiling (xMAP) technology developed by Luminex Corporation commonly uses antibodies for the detection of analytes in small sample volumes through the use of fluorescently coded microbeads. This technology permits the simultaneous detection of multiple analytes in each sample tested and hence could be applied in many research fields. Although little work has been performed adapting this technology for use with apatmers, optimizing aptamer-based xMAP assays would dramatically increase the versatility of analyte detection. We report herein on the development of an xMAP bead-based aptamer/antibody sandwich assay for a biomarker of inflammation (C-reactive protein or CRP). Protocols for the coupling of aptamers to xMAP beads, validation of coupling, and for an aptamer/antibody sandwich-type assay for CRP are detailed. The optimized conditions, protocols and findings described in this research could serve as a starting point for the development of new aptamer-based xMAP assays.

Quantification of Fatty Acid Oxidation Products Using On-line High Performance Liquid Chromatography Tandem Mass Spectrometry

PubMed Central

Levison, Bruce S.; Zhang, Renliang; Wang, Zeneng; Fu, Xiaoming; DiDonato, Joseph A.; Hazen, Stanley L.

2013-01-01

Oxidized fatty acids formed via lipid peroxidation are implicated in pathological processes such as inflammation and atherosclerosis. A number of methods may be used to detect specific oxidized fatty acids containing a single or multiple combinations of epoxide, hydroxyl, ketone and hydroperoxide moieties on varying carbon chain lengths from C8 up to C30. Some of these methods are nonspecific and their use in biological systems is fraught with difficulty. Measures of specific-oxidized fatty acid derivatives help in identifying oxidation pathways in pathological processes. We used liquid chromatography coupled with electrospray ionization tandem mass spectrometry (LC-MS/MS) as efficient, selective and sensitive methods for identifying and analyzing multiple specific fatty acid peroxidation products in human plasma and other biological matrices. We then distilled the essential components of a number of these analyses to provide an efficient protocol by which fatty acid oxidation products and their parent compounds can be determined. In this protocol, addition of synthetic internal standard to the sample, followed by base hydrolysis at elevated temperature, and liquid-liquid phase sample extraction with lighter than water solvents facilitates isolation of the oxidized fatty acid species. These species can be identified and accurately quantified using stable isotope dilution and multiple reaction monitoring. Use of a coupled multiplexed gradient HPLC system on the front end enables high-throughput chromatography and more efficient use of mass spectrometer time. PMID:23499838

Elucidating Molecular Motion through Structural and Dynamic Filters of Energy-Minimized Conformer Ensembles

PubMed Central

2015-01-01

Complex RNA structures are constructed from helical segments connected by flexible loops that move spontaneously and in response to binding of small molecule ligands and proteins. Understanding the conformational variability of RNA requires the characterization of the coupled time evolution of interconnected flexible domains. To elucidate the collective molecular motions and explore the conformational landscape of the HIV-1 TAR RNA, we describe a new methodology that utilizes energy-minimized structures generated by the program “Fragment Assembly of RNA with Full-Atom Refinement (FARFAR)”. We apply structural filters in the form of experimental residual dipolar couplings (RDCs) to select a subset of discrete energy-minimized conformers and carry out principal component analyses (PCA) to corroborate the choice of the filtered subset. We use this subset of structures to calculate solution T1 and T1ρ relaxation times for 13C spins in multiple residues in different domains of the molecule using two simulation protocols that we previously published. We match the experimental T1 times to within 2% and the T1ρ times to within less than 10% for helical residues. These results introduce a protocol to construct viable dynamic trajectories for RNA molecules that accord well with experimental NMR data and support the notion that the motions of the helical portions of this small RNA can be described by a relatively small number of discrete conformations exchanging over time scales longer than 1 μs. PMID:24479561

Preparation of Segmented Microtubules to Study Motions Driven by the Disassembling Microtubule Ends

PubMed Central

Volkov, Vladimir A.; Zaytsev, Anatoly V.; Grishchuk, Ekaterina L.

2014-01-01

Microtubule depolymerization can provide force to transport different protein complexes and protein-coated beads in vitro. The underlying mechanisms are thought to play a vital role in the microtubule-dependent chromosome motions during cell division, but the relevant proteins and their exact roles are ill-defined. Thus, there is a growing need to develop assays with which to study such motility in vitro using purified components and defined biochemical milieu. Microtubules, however, are inherently unstable polymers; their switching between growth and shortening is stochastic and difficult to control. The protocols we describe here take advantage of the segmented microtubules that are made with the photoablatable stabilizing caps. Depolymerization of such segmented microtubules can be triggered with high temporal and spatial resolution, thereby assisting studies of motility at the disassembling microtubule ends. This technique can be used to carry out a quantitative analysis of the number of molecules in the fluorescently-labeled protein complexes, which move processively with dynamic microtubule ends. To optimize a signal-to-noise ratio in this and other quantitative fluorescent assays, coverslips should be treated to reduce nonspecific absorption of soluble fluorescently-labeled proteins. Detailed protocols are provided to take into account the unevenness of fluorescent illumination, and determine the intensity of a single fluorophore using equidistant Gaussian fit. Finally, we describe the use of segmented microtubules to study microtubule-dependent motions of the protein-coated microbeads, providing insights into the ability of different motor and nonmotor proteins to couple microtubule depolymerization to processive cargo motion. PMID:24686554

The Behavior of TCP and Its Extensions in Space

NASA Technical Reports Server (NTRS)

Wang, Ruhai; Horan, Stephen

2001-01-01

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

Limitations and possibilities of low cell number ChIP-seq

PubMed Central

2012-01-01

Background Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq) offers high resolution, genome-wide analysis of DNA-protein interactions. However, current standard methods require abundant starting material in the range of 1–20 million cells per immunoprecipitation, and remain a bottleneck to the acquisition of biologically relevant epigenetic data. Using a ChIP-seq protocol optimised for low cell numbers (down to 100,000 cells / IP), we examined the performance of the ChIP-seq technique on a series of decreasing cell numbers. Results We present an enhanced native ChIP-seq method tailored to low cell numbers that represents a 200-fold reduction in input requirements over existing protocols. The protocol was tested over a range of starting cell numbers covering three orders of magnitude, enabling determination of the lower limit of the technique. At low input cell numbers, increased levels of unmapped and duplicate reads reduce the number of unique reads generated, and can drive up sequencing costs and affect sensitivity if ChIP is attempted from too few cells. Conclusions The optimised method presented here considerably reduces the input requirements for performing native ChIP-seq. It extends the applicability of the technique to isolated primary cells and rare cell populations (e.g. biobank samples, stem cells), and in many cases will alleviate the need for cell culture and any associated alteration of epigenetic marks. However, this study highlights a challenge inherent to ChIP-seq from low cell numbers: as cell input numbers fall, levels of unmapped sequence reads and PCR-generated duplicate reads rise. We discuss a number of solutions to overcome the effects of reducing cell number that may aid further improvements to ChIP performance. PMID:23171294

Shuttle Payload Ground Command and Control: An Experiment Implementation Combustion Module-2 Software Development, STS-107

NASA Technical Reports Server (NTRS)

Carek, David Andrew

2003-01-01

This presentation covers the design of a command and control architecture developed by the author for the Combustion Module-2 microgravity experiment, which flew aboard the STS-107 Shuttle mission, The design was implemented to satisfy a hybrid network that utilized TCP/IP for both the onboard segment and ground segment, with an intermediary unreliable transport for the space to ground segment. With the infusion of Internet networking technologies into Space Shuttle, Space Station, and spacecraft avionics systems, comes the need for robust methodologies for ground command and control. Considerations of high bit error links, and unreliable transport over intermittent links must be considered in such systems. Internet protocols applied to these systems, coupled with the appropriate application layer protections, can provide adequate communication architectures for command and control. However, there are inherent limitations and additional complexities added by the use of Internet protocols that must be considered during the design. This presentation will discuss the rationale for the: framework and protocol algorithms developed by the author. A summary of design considerations, implantation issues, and learned lessons will be will be presented. A summary of mission results using this communications architecture will be presented. Additionally, areas of further needed investigation will be identified.