HaloTag technology for specific and covalent labeling of fusion proteins.

PubMed

Benink, Hélène A; Urh, Marjeta

2015-01-01

Appending proteins of interest to fluorescent protein tags such as GFP has revolutionized how proteins are studied in the cellular environment. Over the last few decades many varieties of fluorescent proteins have been generated, each bringing new capability to research. However, taking full advantage of standard fluorescent proteins with advanced and differential features requires significant effort on the part of the researcher. This approach necessitates that many genetic fusions be generated and confirmed to function properly in cells with the same protein of interest. To lessen this burden, a newer category of protein fusion tags termed "self-labeling protein tags" has been developed. This approach utilizes a single protein tag, the function of which can be altered by attaching various chemical moieties (fluorescent labels, affinity handles, etc.). In this way a single genetically encoded protein fusion can easily be given functional diversity and adaptability as supplied by synthetic chemistry. Here we present protein labeling methods using HaloTag technology; comprised of HaloTag protein and the collection of small molecules designed to bind it specifically and provide it with varied functionalities. For imaging purposes these small molecules, termed HaloTag ligands, contain distinct fluorophores. Due to covalent and rapid binding between HaloTag protein and its ligands, labeling is permanent and efficient. Many of these ligands have been optimized for permeability across cellular membranes allowing for live cell labeling and imaging analysis. Nonpermeable ligands have also been developed for specific labeling of surface proteins. Overall, HaloTag is a versatile technology that empowers the end user to label a protein of interest with the choice of different fluorophores while alleviating the need for generation of multiple genetic fusions.

Research on segmentation based on multi-atlas in brain MR image

NASA Astrophysics Data System (ADS)

Qian, Yuejing

2018-03-01

Accurate segmentation of specific tissues in brain MR image can be effectively achieved with the multi-atlas-based segmentation method, and the accuracy mainly depends on the image registration accuracy and fusion scheme. This paper proposes an automatic segmentation method based on the multi-atlas for brain MR image. Firstly, to improve the registration accuracy in the area to be segmented, we employ a target-oriented image registration method for the refinement. Then In the label fusion, we proposed a new algorithm to detect the abnormal sparse patch and simultaneously abandon the corresponding abnormal sparse coefficients, this method is made based on the remaining sparse coefficients combined with the multipoint label estimator strategy. The performance of the proposed method was compared with those of the nonlocal patch-based label fusion method (Nonlocal-PBM), the sparse patch-based label fusion method (Sparse-PBM) and majority voting method (MV). Based on our experimental results, the proposed method is efficient in the brain MR images segmentation compared with MV, Nonlocal-PBM, and Sparse-PBM methods.

Detection of normal and chimeric nucleophosmin in human cells.

PubMed

Cordell, J L; Pulford, K A; Bigerna, B; Roncador, G; Banham, A; Colombo, E; Pelicci, P G; Mason, D Y; Falini, B

1999-01-15

In anaplastic large-cell lymphoma (ALCL), the (2;5) chromosomal translocation creates a fusion gene encoding the 80-kD NPM-ALK hybrid protein. This report describes three new monoclonal antibodies, two of which recognize, by Western blotting, the N-terminal portion of NPM present in the NPM-ALK fusion protein and also in two other NPM fusion proteins (NPM-RARalpha and NPM-MLF1). The third antibody recognizes the C-terminal portion (deleted in NPM-ALK) and reacts only with wild-type NPM. The three antibodies immunostain wild-type NPM (in paraffin-embedded normal tissue samples) in cell nuclei and in the cytoplasm of mitotic cells. Cerebral neurones, exceptionally, show diffuse cytoplasmic labeling. In contrast to normal tissues, the two antibodies against the N-terminal portion of NPM labeled the cytoplasm of neoplastic cells, in four ALK-positive ALCL, reflecting their reactivity with NPM-ALK fusion protein, whereas the antibody to the C-terminal NPM epitope labeled only cell nuclei. Immunocytochemical labeling with these antibodies can therefore confirm that an ALK-positive lymphoma expresses NPM-ALK (rather than a variant ALK-fusion protein) and may also provide evidence for chromosomal anomalies involving the NPM gene other than the classical (2;5) translocation.

A general approach for chemical labeling and rapid, spatially controlled protein inactivation

PubMed Central

Marks, Kevin M.; Braun, Patrick D.; Nolan, Garry P.

2004-01-01

Chemical labeling of proteins inside of living cells can enable studies of the location, movement, and function of proteins in vivo. Here we demonstrate an approach for chemical labeling of proteins that uses the high-affinity interaction between an FKBP12 mutant (F36V) and a synthetic, engineered ligand (SLF′). A fluorescein conjugate to the engineered ligand (FL-SLF′) retained binding to FKBP12(F36V) and possessed similar fluorescence properties as parental fluorescein. FL-SLF′ labeled FKBP12(F36V) fusion proteins in live mammalian cells, and was used to monitor the subcellular localization of a membrane targeted FKBP12(F36V) construct. Chemical labeling of FKBP12(F36V) fusion proteins with FL-SLF′ was readily detectable at low expression levels of the FKBP12(F36V) fusion, and the level of fluorescent staining with FL-SLF′ was proportional to the FKBP12(F36V) expression level. This FL-SLF′-FKBP12(F36V) labeling technique was tested in fluorophore assisted laser inactivation (FALI), a light-mediated technique to rapidly inactivate fluorophore-labeled target proteins. FL-SLF′ mediated FALI of a β-galactosidase-FKBP12(F36V) fusion protein, causing rapid inactivation of >90% of enzyme activity upon irradiation in vitro. FL-SLF′ also mediated FALI of a β-galactosidase fusion expressed in living NIH 3T3 cells, where β-galactosidase activity was reduced in 15 s. Thus, FL-SLF′ can be used to monitor proteins in vivo and to target rapid, spatially and temporally defined inactivation of target proteins in living cells in a process that we call FK-FALI. PMID:15218100

Early steps of supported bilayer formation probed by single vesicle fluorescence assays.

PubMed Central

Johnson, Joseph M; Ha, Taekjip; Chu, Steve; Boxer, Steven G

2002-01-01

We have developed a single vesicle assay to study the mechanisms of supported bilayer formation. Fluorescently labeled, unilamellar vesicles (30-100 nm diameter) were first adsorbed to a quartz surface at low enough surface concentrations to visualize single vesicles. Fusion and rupture events during the bilayer formation, induced by the subsequent addition of unlabeled vesicles, were detected by measuring two-color fluorescence signals simultaneously. Lipid-conjugated dyes monitored the membrane fusion while encapsulated dyes reported on the vesicle rupture. Four dominant pathways were observed, each exhibiting characteristic two-color fluorescence signatures: 1) primary fusion, in which an unlabeled vesicle fuses with a labeled vesicle on the surface, is signified by the dequenching of the lipid-conjugated dyes followed by rupture and final merging into the bilayer; 2) simultaneous fusion and rupture, in which a labeled vesicle on the surface ruptures simultaneously upon fusion with an unlabeled vesicle; 3) no dequenching, in which loss of fluorescence signal from both dyes occur simultaneously with the final merger into the bilayer; and 4) isolated rupture (pre-ruptured vesicles), in which a labeled vesicle on the surface spontaneously undergoes content loss, a process that occurs with high efficiency in the presence of a high concentration of Texas Red-labeled lipids. Vesicles that have undergone content loss appear to be more fusogenic than intact vesicles. PMID:12496104

Chromophore-assisted laser inactivation of alpha- and gamma-tubulin SNAP-tag fusion proteins inside living cells.

PubMed

Keppler, Antje; Ellenberg, Jan

2009-02-20

Chromophore-assisted laser inactivation (CALI) can help to unravel localized activities of target proteins at defined times and locations within living cells. Covalent SNAP-tag labeling of fusion proteins with fluorophores such as fluorescein is a fast and highly specific tool to attach the photosensitizer to its target protein in vivo for selective inactivation of the fusion protein. Here, we demonstrate the effectiveness and specificity of SNAP-tag-based CALI by acute inactivation of alpha-tubulin and gamma-tubulin SNAP-tag fusions during live imaging assays of cell division. Singlet oxygen is confirmed as the reactive oxygen species that leads to loss of fusion protein function. The major advantage of SNAP-tag CALI is the ease, reliability, and high flexibility in labeling: the genetically encoded protein tag can be covalently labeled with various dyes matching the experimental requirements. This makes SNAP-tag CALI a very useful tool for rapid inactivation of tagged proteins in living cells.

Statistical fusion of continuous labels: identification of cardiac landmarks

NASA Astrophysics Data System (ADS)

Xing, Fangxu; Soleimanifard, Sahar; Prince, Jerry L.; Landman, Bennett A.

2011-03-01

Image labeling is an essential task for evaluating and analyzing morphometric features in medical imaging data. Labels can be obtained by either human interaction or automated segmentation algorithms. However, both approaches for labeling suffer from inevitable error due to noise and artifact in the acquired data. The Simultaneous Truth And Performance Level Estimation (STAPLE) algorithm was developed to combine multiple rater decisions and simultaneously estimate unobserved true labels as well as each rater's level of performance (i.e., reliability). A generalization of STAPLE for the case of continuous-valued labels has also been proposed. In this paper, we first show that with the proposed Gaussian distribution assumption, this continuous STAPLE formulation yields equivalent likelihoods for the bias parameter, meaning that the bias parameter-one of the key performance indices-is actually indeterminate. We resolve this ambiguity by augmenting the STAPLE expectation maximization formulation to include a priori probabilities on the performance level parameters, which enables simultaneous, meaningful estimation of both the rater bias and variance performance measures. We evaluate and demonstrate the efficacy of this approach in simulations and also through a human rater experiment involving the identification the intersection points of the right ventricle to the left ventricle in CINE cardiac data.

Statistical Fusion of Continuous Labels: Identification of Cardiac Landmarks.

PubMed

Xing, Fangxu; Soleimanifard, Sahar; Prince, Jerry L; Landman, Bennett A

2011-01-01

Image labeling is an essential task for evaluating and analyzing morphometric features in medical imaging data. Labels can be obtained by either human interaction or automated segmentation algorithms. However, both approaches for labeling suffer from inevitable error due to noise and artifact in the acquired data. The Simultaneous Truth And Performance Level Estimation (STAPLE) algorithm was developed to combine multiple rater decisions and simultaneously estimate unobserved true labels as well as each rater's level of performance (i.e., reliability). A generalization of STAPLE for the case of continuous-valued labels has also been proposed. In this paper, we first show that with the proposed Gaussian distribution assumption, this continuous STAPLE formulation yields equivalent likelihoods for the bias parameter, meaning that the bias parameter-one of the key performance indices-is actually indeterminate. We resolve this ambiguity by augmenting the STAPLE expectation maximization formulation to include a priori probabilities on the performance level parameters, which enables simultaneous, meaningful estimation of both the rater bias and variance performance measures. We evaluate and demonstrate the efficacy of this approach in simulations and also through a human rater experiment involving the identification the intersection points of the right ventricle to the left ventricle in CINE cardiac data.

Multi-Atlas Based Segmentation of Brainstem Nuclei from MR Images by Deep Hyper-Graph Learning.

PubMed

Dong, Pei; Guo, Yangrong; Gao, Yue; Liang, Peipeng; Shi, Yonghong; Wang, Qian; Shen, Dinggang; Wu, Guorong

2016-10-01

Accurate segmentation of brainstem nuclei (red nucleus and substantia nigra) is very important in various neuroimaging applications such as deep brain stimulation and the investigation of imaging biomarkers for Parkinson's disease (PD). Due to iron deposition during aging, image contrast in the brainstem is very low in Magnetic Resonance (MR) images. Hence, the ambiguity of patch-wise similarity makes the recently successful multi-atlas patch-based label fusion methods have difficulty to perform as competitive as segmenting cortical and sub-cortical regions from MR images. To address this challenge, we propose a novel multi-atlas brainstem nuclei segmentation method using deep hyper-graph learning. Specifically, we achieve this goal in three-fold. First , we employ hyper-graph to combine the advantage of maintaining spatial coherence from graph-based segmentation approaches and the benefit of harnessing population priors from multi-atlas based framework. Second , besides using low-level image appearance, we also extract high-level context features to measure the complex patch-wise relationship. Since the context features are calculated on a tentatively estimated label probability map, we eventually turn our hyper-graph learning based label propagation into a deep and self-refining model. Third , since anatomical labels on some voxels (usually located in uniform regions) can be identified much more reliably than other voxels (usually located at the boundary between two regions), we allow these reliable voxels to propagate their labels to the nearby difficult-to-label voxels. Such hierarchical strategy makes our proposed label fusion method deep and dynamic. We evaluate our proposed label fusion method in segmenting substantia nigra (SN) and red nucleus (RN) from 3.0 T MR images, where our proposed method achieves significant improvement over the state-of-the-art label fusion methods.

Multiatlas whole heart segmentation of CT data using conditional entropy for atlas ranking and selection.

PubMed

Zhuang, Xiahai; Bai, Wenjia; Song, Jingjing; Zhan, Songhua; Qian, Xiaohua; Shi, Wenzhe; Lian, Yanyun; Rueckert, Daniel

2015-07-01

Cardiac computed tomography (CT) is widely used in clinical diagnosis of cardiovascular diseases. Whole heart segmentation (WHS) plays a vital role in developing new clinical applications of cardiac CT. However, the shape and appearance of the heart can vary greatly across different scans, making the automatic segmentation particularly challenging. The objective of this work is to develop and evaluate a multiatlas segmentation (MAS) scheme using a new atlas ranking and selection algorithm for automatic WHS of CT data. Research on different MAS strategies and their influence on WHS performance are limited. This work provides a detailed comparison study evaluating the impacts of label fusion, atlas ranking, and sizes of the atlas database on the segmentation performance. Atlases in a database were registered to the target image using a hierarchical registration scheme specifically designed for cardiac images. A subset of the atlases were selected for label fusion, according to the authors' proposed atlas ranking criterion which evaluated the performance of each atlas by computing the conditional entropy of the target image given the propagated atlas labeling. Joint label fusion was used to combine multiple label estimates to obtain the final segmentation. The authors used 30 clinical cardiac CT angiography (CTA) images to evaluate the proposed MAS scheme and to investigate different segmentation strategies. The mean WHS Dice score of the proposed MAS method was 0.918 ± 0.021, and the mean runtime for one case was 13.2 min on a workstation. This MAS scheme using joint label fusion generated significantly better Dice scores than the other label fusion strategies, including majority voting (0.901 ± 0.276, p < 0.01), locally weighted voting (0.905 ± 0.0247, p < 0.01), and probabilistic patch-based fusion (0.909 ± 0.0249, p < 0.01). In the atlas ranking study, the proposed criterion based on conditional entropy yielded a performance curve with higher WHS Dice scores compared to the conventional schemes (p < 0.03). In the atlas database study, the authors showed that the MAS using larger atlas databases generated better performance curves than the MAS using smaller ones, indicating larger atlas databases could produce more accurate segmentation. The authors have developed a new MAS framework for automatic WHS of CTA and investigated alternative implementations of MAS. With the proposed atlas ranking algorithm and joint label fusion, the MAS scheme is able to generate accurate segmentation within practically acceptable computation time. This method can be useful for the development of new clinical applications of cardiac CT.

SNARE-mediated Fusion of Single Proteoliposomes with Tethered Supported Bilayers in a Microfluidic Flow Cell Monitored by Polarized TIRF Microscopy

PubMed Central

Nikolaus, Joerg; Karatekin, Erdem

2016-01-01

In the ubiquitous process of membrane fusion the opening of a fusion pore establishes the first connection between two formerly separate compartments. During neurotransmitter or hormone release via exocytosis, the fusion pore can transiently open and close repeatedly, regulating cargo release kinetics. Pore dynamics also determine the mode of vesicle recycling; irreversible resealing results in transient, "kiss-and-run" fusion, whereas dilation leads to full fusion. To better understand what factors govern pore dynamics, we developed an assay to monitor membrane fusion using polarized total internal reflection fluorescence (TIRF) microscopy with single molecule sensitivity and ~15 msec time resolution in a biochemically well-defined in vitro system. Fusion of fluorescently labeled small unilamellar vesicles containing v-SNARE proteins (v-SUVs) with a planar bilayer bearing t-SNAREs, supported on a soft polymer cushion (t-SBL, t-supported bilayer), is monitored. The assay uses microfluidic flow channels that ensure minimal sample consumption while supplying a constant density of SUVs. Exploiting the rapid signal enhancement upon transfer of lipid labels from the SUV to the SBL during fusion, kinetics of lipid dye transfer is monitored. The sensitivity of TIRF microscopy allows tracking single fluorescent lipid labels, from which lipid diffusivity and SUV size can be deduced for every fusion event. Lipid dye release times can be much longer than expected for unimpeded passage through permanently open pores. Using a model that assumes retardation of lipid release is due to pore flickering, a pore "openness", the fraction of time the pore remains open during fusion, can be estimated. A soluble marker can be encapsulated in the SUVs for simultaneous monitoring of lipid and soluble cargo release. Such measurements indicate some pores may reseal after losing a fraction of the soluble cargo. PMID:27585113

Fluorescent Labeling of COS-7 Expressing SNAP-tag Fusion Proteins for Live Cell Imaging

PubMed Central

Provost, Christopher R.; Sun, Luo

2010-01-01

SNAP-tag and CLIP-tag protein labeling systems enable the specific, covalent attachment of molecules, including fluorescent dyes, to a protein of interest in live cells. These systems offer a broad selection of fluorescent substrates optimized for a range of imaging instrumentation. Once cloned and expressed, the tagged protein can be used with a variety of substrates for numerous downstream applications without having to clone again. There are two steps to using this system: cloning and expression of the protein of interest as a SNAP-tag fusion, and labeling of the fusion with the SNAP-tag substrate of choice. The SNAP-tag is a small protein based on human O6-alkylguanine-DNA-alkyltransferase (hAGT), a DNA repair protein. SNAP-tag labels are dyes conjugated to guanine or chloropyrimidine leaving groups via a benzyl linker. In the labeling reaction, the substituted benzyl group of the substrate is covalently attached to the SNAP-tag. CLIP-tag is a modified version of SNAP-tag, engineered to react with benzylcytosine rather than benzylguanine derivatives. When used in conjunction with SNAP-tag, CLIP-tag enables the orthogonal and complementary labeling of two proteins simultaneously in the same cells. PMID:20485262

Core labeling of adenovirus with EGFP

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

Le, Long P.; Le, Helen N.; Nelson, Amy R.

2006-08-01

The study of adenovirus could greatly benefit from diverse methods of virus detection. Recently, it has been demonstrated that carboxy-terminal EGFP fusions of adenovirus core proteins Mu, V, and VII properly localize to the nucleus and display novel function in the cell. Based on these observations, we hypothesized that the core proteins may serve as targets for labeling the adenovirus core with fluorescent proteins. To this end, we constructed various chimeric expression vectors with fusion core genes (Mu-EGFP, V-EGFP, preVII-EGFP, and matVII-EGFP) while maintaining expression of the native proteins. Expression of the fusion core proteins was suboptimal using E1 expressionmore » vectors with both conventional CMV and modified (with adenovirus tripartite leader sequence) CMV5 promoters, resulting in non-labeled viral particles. However, robust expression equivalent to the native protein was observed when the fusion genes were placed in the deleted E3 region. The efficient Ad-wt-E3-V-EGFP and Ad-wt-E3-preVII-EGFP expression vectors were labeled allowing visualization of purified virus and tracking of the viral core during early infection. The vectors maintained their viral function, including viral DNA replication, viral DNA encapsidation, cytopathic effect, and thermostability. Core labeling offers a means to track the adenovirus core in vector targeting studies as well as basic adenovirus virology.« less

Live-cell imaging of conidial anastomosis tube fusion during colony initiation in Fusarium oxysporum

PubMed Central

Kurian, Smija M.; Di Pietro, Antonio

2018-01-01

Fusarium oxysporum exhibits conidial anastomosis tube (CAT) fusion during colony initiation to form networks of conidial germlings. Here we determined the optimal culture conditions for this fungus to undergo CAT fusion between microconidia in liquid medium. Extensive high resolution, confocal live-cell imaging was performed to characterise the different stages of CAT fusion, using genetically encoded fluorescent labelling and vital fluorescent organelle stains. CAT homing and fusion were found to be dependent on adhesion to the surface, in contrast to germ tube development which occurs in the absence of adhesion. Staining with fluorescently labelled concanavalin A indicated that the cell wall composition of CATs differs from that of microconidia and germ tubes. The movement of nuclei, mitochondria, vacuoles and lipid droplets through fused germlings was observed by live-cell imaging. PMID:29734342

Live-cell imaging of conidial anastomosis tube fusion during colony initiation in Fusarium oxysporum.

PubMed

Kurian, Smija M; Di Pietro, Antonio; Read, Nick D

2018-01-01

Fusarium oxysporum exhibits conidial anastomosis tube (CAT) fusion during colony initiation to form networks of conidial germlings. Here we determined the optimal culture conditions for this fungus to undergo CAT fusion between microconidia in liquid medium. Extensive high resolution, confocal live-cell imaging was performed to characterise the different stages of CAT fusion, using genetically encoded fluorescent labelling and vital fluorescent organelle stains. CAT homing and fusion were found to be dependent on adhesion to the surface, in contrast to germ tube development which occurs in the absence of adhesion. Staining with fluorescently labelled concanavalin A indicated that the cell wall composition of CATs differs from that of microconidia and germ tubes. The movement of nuclei, mitochondria, vacuoles and lipid droplets through fused germlings was observed by live-cell imaging.

Multiatlas whole heart segmentation of CT data using conditional entropy for atlas ranking and selection

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

Zhuang, Xiahai, E-mail: zhuangxiahai@sjtu.edu.cn; Qian, Xiaohua; Bai, Wenjia

Purpose: Cardiac computed tomography (CT) is widely used in clinical diagnosis of cardiovascular diseases. Whole heart segmentation (WHS) plays a vital role in developing new clinical applications of cardiac CT. However, the shape and appearance of the heart can vary greatly across different scans, making the automatic segmentation particularly challenging. The objective of this work is to develop and evaluate a multiatlas segmentation (MAS) scheme using a new atlas ranking and selection algorithm for automatic WHS of CT data. Research on different MAS strategies and their influence on WHS performance are limited. This work provides a detailed comparison study evaluatingmore » the impacts of label fusion, atlas ranking, and sizes of the atlas database on the segmentation performance. Methods: Atlases in a database were registered to the target image using a hierarchical registration scheme specifically designed for cardiac images. A subset of the atlases were selected for label fusion, according to the authors’ proposed atlas ranking criterion which evaluated the performance of each atlas by computing the conditional entropy of the target image given the propagated atlas labeling. Joint label fusion was used to combine multiple label estimates to obtain the final segmentation. The authors used 30 clinical cardiac CT angiography (CTA) images to evaluate the proposed MAS scheme and to investigate different segmentation strategies. Results: The mean WHS Dice score of the proposed MAS method was 0.918 ± 0.021, and the mean runtime for one case was 13.2 min on a workstation. This MAS scheme using joint label fusion generated significantly better Dice scores than the other label fusion strategies, including majority voting (0.901 ± 0.276, p < 0.01), locally weighted voting (0.905 ± 0.0247, p < 0.01), and probabilistic patch-based fusion (0.909 ± 0.0249, p < 0.01). In the atlas ranking study, the proposed criterion based on conditional entropy yielded a performance curve with higher WHS Dice scores compared to the conventional schemes (p < 0.03). In the atlas database study, the authors showed that the MAS using larger atlas databases generated better performance curves than the MAS using smaller ones, indicating larger atlas databases could produce more accurate segmentation. Conclusions: The authors have developed a new MAS framework for automatic WHS of CTA and investigated alternative implementations of MAS. With the proposed atlas ranking algorithm and joint label fusion, the MAS scheme is able to generate accurate segmentation within practically acceptable computation time. This method can be useful for the development of new clinical applications of cardiac CT.« less

Drug-related webpages classification based on multi-modal local decision fusion

NASA Astrophysics Data System (ADS)

Hu, Ruiguang; Su, Xiaojing; Liu, Yanxin

2018-03-01

In this paper, multi-modal local decision fusion is used for drug-related webpages classification. First, meaningful text are extracted through HTML parsing, and effective images are chosen by the FOCARSS algorithm. Second, six SVM classifiers are trained for six kinds of drug-taking instruments, which are represented by PHOG. One SVM classifier is trained for the cannabis, which is represented by the mid-feature of BOW model. For each instance in a webpage, seven SVMs give seven labels for its image, and other seven labels are given by searching the names of drug-taking instruments and cannabis in its related text. Concatenating seven labels of image and seven labels of text, the representation of those instances in webpages are generated. Last, Multi-Instance Learning is used to classify those drugrelated webpages. Experimental results demonstrate that the classification accuracy of multi-instance learning with multi-modal local decision fusion is much higher than those of single-modal classification.

Automatic Structural Parcellation of Mouse Brain MRI Using Multi-Atlas Label Fusion

PubMed Central

Ma, Da; Cardoso, Manuel J.; Modat, Marc; Powell, Nick; Wells, Jack; Holmes, Holly; Wiseman, Frances; Tybulewicz, Victor; Fisher, Elizabeth; Lythgoe, Mark F.; Ourselin, Sébastien

2014-01-01

Multi-atlas segmentation propagation has evolved quickly in recent years, becoming a state-of-the-art methodology for automatic parcellation of structural images. However, few studies have applied these methods to preclinical research. In this study, we present a fully automatic framework for mouse brain MRI structural parcellation using multi-atlas segmentation propagation. The framework adopts the similarity and truth estimation for propagated segmentations (STEPS) algorithm, which utilises a locally normalised cross correlation similarity metric for atlas selection and an extended simultaneous truth and performance level estimation (STAPLE) framework for multi-label fusion. The segmentation accuracy of the multi-atlas framework was evaluated using publicly available mouse brain atlas databases with pre-segmented manually labelled anatomical structures as the gold standard, and optimised parameters were obtained for the STEPS algorithm in the label fusion to achieve the best segmentation accuracy. We showed that our multi-atlas framework resulted in significantly higher segmentation accuracy compared to single-atlas based segmentation, as well as to the original STAPLE framework. PMID:24475148

Improving cerebellar segmentation with statistical fusion

NASA Astrophysics Data System (ADS)

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

2016-03-01

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

A label field fusion bayesian model and its penalized maximum rand estimator for image segmentation.

PubMed

Mignotte, Max

2010-06-01

This paper presents a novel segmentation approach based on a Markov random field (MRF) fusion model which aims at combining several segmentation results associated with simpler clustering models in order to achieve a more reliable and accurate segmentation result. The proposed fusion model is derived from the recently introduced probabilistic Rand measure for comparing one segmentation result to one or more manual segmentations of the same image. This non-parametric measure allows us to easily derive an appealing fusion model of label fields, easily expressed as a Gibbs distribution, or as a nonstationary MRF model defined on a complete graph. Concretely, this Gibbs energy model encodes the set of binary constraints, in terms of pairs of pixel labels, provided by each segmentation results to be fused. Combined with a prior distribution, this energy-based Gibbs model also allows for definition of an interesting penalized maximum probabilistic rand estimator with which the fusion of simple, quickly estimated, segmentation results appears as an interesting alternative to complex segmentation models existing in the literature. This fusion framework has been successfully applied on the Berkeley image database. The experiments reported in this paper demonstrate that the proposed method is efficient in terms of visual evaluation and quantitative performance measures and performs well compared to the best existing state-of-the-art segmentation methods recently proposed in the literature.

A real-time monitoring platform of myogenesis regulators using double fluorescent labeling

PubMed Central

Sapoznik, Etai; Niu, Guoguang; Zhou, Yu; Prim, Peter M.; Criswell, Tracy L.

2018-01-01

Real-time, quantitative measurement of muscle progenitor cell (myoblast) differentiation is an important tool for skeletal muscle research and identification of drugs that support skeletal muscle regeneration. While most quantitative tools rely on sacrificial approach, we developed a double fluorescent tagging approach, which allows for dynamic monitoring of myoblast differentiation through assessment of fusion index and nuclei count. Fluorescent tagging of both the cell cytoplasm and nucleus enables monitoring of cell fusion and the formation of new myotube fibers, similar to immunostaining results. This labeling approach allowed monitoring the effects of Myf5 overexpression, TNFα, and Wnt agonist on myoblast differentiation. It also enabled testing the effects of surface coating on the fusion levels of scaffold-seeded myoblasts. The double fluorescent labeling of myoblasts is a promising technique to visualize even minor changes in myogenesis of myoblasts in order to support applications such as tissue engineering and drug screening. PMID:29444187

Solid-state nuclear magnetic resonance measurements of HIV fusion peptide 13CO to lipid 31P proximities support similar partially inserted membrane locations of the α helical and β sheet peptide structures.

PubMed

Gabrys, Charles M; Qiang, Wei; Sun, Yan; Xie, Li; Schmick, Scott D; Weliky, David P

2013-10-03

Fusion of the human immunodeficiency virus (HIV) membrane and the host cell membrane is an initial step of infection of the host cell. Fusion is catalyzed by gp41, which is an integral membrane protein of HIV. The fusion peptide (FP) is the ∼25 N-terminal residues of gp41 and is a domain of gp41 that plays a key role in fusion catalysis likely through interaction with the host cell membrane. Much of our understanding of the FP domain has been accomplished with studies of "HFP", i.e., a ∼25-residue peptide composed of the FP sequence but lacking the rest of gp41. HFP catalyzes fusion between membrane vesicles and serves as a model system to understand fusion catalysis. HFP binds to membranes and the membrane location of HFP is likely a significant determinant of fusion catalysis perhaps because the consequent membrane perturbation reduces the fusion activation energy. In the present study, many HFPs were synthesized and differed in the residue position that was (13)CO backbone labeled. Samples were then prepared that each contained a singly (13)CO labeled HFP incorporated into membranes that lacked cholesterol. HFP had distinct molecular populations with either α helical or oligomeric β sheet structure. Proximity between the HFP (13)CO nuclei and (31)P nuclei in the membrane headgroups was probed by solid-state NMR (SSNMR) rotational-echo double-resonance (REDOR) measurements. For many samples, there were distinct (13)CO shifts for the α helical and β sheet structures so that the proximities to (31)P nuclei could be determined for each structure. Data from several differently labeled HFPs were then incorporated into a membrane location model for the particular structure. In addition to the (13)CO labeled residue position, the HFPs also differed in sequence and/or chemical structure. "HFPmn" was a linear peptide that contained the 23 N-terminal residues of gp41. "HFPmn_V2E" contained the V2E mutation that for HIV leads to greatly reduced extent of fusion and infection. The present study shows that HFPmn_V2E induces much less vesicle fusion than HFPmn. "HFPtr" contained three strands with HFPmn sequence that were chemically cross-linked near their C-termini. HFPtr mimics the trimeric topology of gp41 and induces much more rapid and extensive vesicle fusion than HFPmn. For HFPmn and HFPtr, well-resolved α and β peaks were observed for A6-, L9-, and L12-labeled samples. For each of these samples, there were similar HFP (13)CO to lipid (31)P proximities in the α and β structures, which evidenced comparable membrane locations of the HFP in either structure including insertion into a single membrane leaflet. The data were also consistent with deeper insertion of HFPtr relative to HFPmn in both the α and β structures. The results supported a strong correlation between the membrane insertion depth of the HFP and its fusogenicity. More generally, the results supported membrane location of the HFP as an important determinant of its fusogenicity. The deep insertion of HFPtr in both the α and β structures provides the most relevant membrane location of the FP for HIV gp41-catalyzed membrane fusion because HIV gp41 is natively trimeric. Well-resolved α and β signals were observed in the HFPmn_V2E samples with L9- and L12- but not A6-labeling. The α signals were much more dominant for L9- and L12-labeled HFPmn_V2E than the corresponding HFPmn or HFPtr. The structural model for the less fusogenic HFPmn_V2E includes a shorter helix and less membrane insertion than either HFPmn or HFPtr. This greater helical population and different helical structure and membrane location could result in less membrane perturbation and lower fusogenicity of HFPmn_V2E and suggest that the β sheet fusion peptide is the most functionally relevant structure of HFPmn, HFPtr, and gp41.

Fusion of GFP to the M.EcoKI DNA methyltransferase produces a new probe of Type I DNA restriction and modification enzymes

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

Chen, Kai; Roberts, Gareth A.; Stephanou, Augoustinos S.

2010-07-23

Research highlights: {yields} Successful fusion of GFP to M.EcoKI DNA methyltransferase. {yields} GFP located at C-terminal of sequence specificity subunit does not later enzyme activity. {yields} FRET confirms structural model of M.EcoKI bound to DNA. -- Abstract: We describe the fusion of enhanced green fluorescent protein to the C-terminus of the HsdS DNA sequence-specificity subunit of the Type I DNA modification methyltransferase M.EcoKI. The fusion expresses well in vivo and assembles with the two HsdM modification subunits. The fusion protein functions as a sequence-specific DNA methyltransferase protecting DNA against digestion by the EcoKI restriction endonuclease. The purified enzyme shows Foerstermore » resonance energy transfer to fluorescently-labelled DNA duplexes containing the target sequence and to fluorescently-labelled ocr protein, a DNA mimic that binds to the M.EcoKI enzyme. Distances determined from the energy transfer experiments corroborate the structural model of M.EcoKI.« less

Efficient Multi-Atlas Registration using an Intermediate Template Image

PubMed Central

Dewey, Blake E.; Carass, Aaron; Blitz, Ari M.; Prince, Jerry L.

2017-01-01

Multi-atlas label fusion is an accurate but time-consuming method of labeling the human brain. Using an intermediate image as a registration target can allow researchers to reduce time constraints by storing the deformations required of the atlas images. In this paper, we investigate the effect of registration through an intermediate template image on multi-atlas label fusion and propose a novel registration technique to counteract the negative effects of through-template registration. We show that overall computation time can be decreased dramatically with minimal impact on final label accuracy and time can be exchanged for improved results in a predictable manner. We see almost complete recovery of Dice similarity over a simple through-template registration using the corrected method and still maintain a 3–4 times speed increase. Further, we evaluate the effectiveness of this method on brains of patients with normal-pressure hydrocephalus, where abnormal brain shape presents labeling difficulties, specifically the ventricular labels. Our correction method creates substantially better ventricular labeling than traditional methods and maintains the speed increase seen in healthy subjects. PMID:28943702

Efficient multi-atlas registration using an intermediate template image

NASA Astrophysics Data System (ADS)

Dewey, Blake E.; Carass, Aaron; Blitz, Ari M.; Prince, Jerry L.

2017-03-01

Multi-atlas label fusion is an accurate but time-consuming method of labeling the human brain. Using an intermediate image as a registration target can allow researchers to reduce time constraints by storing the deformations required of the atlas images. In this paper, we investigate the effect of registration through an intermediate template image on multi-atlas label fusion and propose a novel registration technique to counteract the negative effects of through-template registration. We show that overall computation time can be decreased dramatically with minimal impact on final label accuracy and time can be exchanged for improved results in a predictable manner. We see almost complete recovery of Dice similarity over a simple through-template registration using the corrected method and still maintain a 3-4 times speed increase. Further, we evaluate the effectiveness of this method on brains of patients with normal-pressure hydrocephalus, where abnormal brain shape presents labeling difficulties, specifically the ventricular labels. Our correction method creates substantially better ventricular labeling than traditional methods and maintains the speed increase seen in healthy subjects.

Machinery running state identification based on discriminant semi-supervised local tangent space alignment for feature fusion and extraction

NASA Astrophysics Data System (ADS)

Su, Zuqiang; Xiao, Hong; Zhang, Yi; Tang, Baoping; Jiang, Yonghua

2017-04-01

Extraction of sensitive features is a challenging but key task in data-driven machinery running state identification. Aimed at solving this problem, a method for machinery running state identification that applies discriminant semi-supervised local tangent space alignment (DSS-LTSA) for feature fusion and extraction is proposed. Firstly, in order to extract more distinct features, the vibration signals are decomposed by wavelet packet decomposition WPD, and a mixed-domain feature set consisted of statistical features, autoregressive (AR) model coefficients, instantaneous amplitude Shannon entropy and WPD energy spectrum is extracted to comprehensively characterize the properties of machinery running state(s). Then, the mixed-dimension feature set is inputted into DSS-LTSA for feature fusion and extraction to eliminate redundant information and interference noise. The proposed DSS-LTSA can extract intrinsic structure information of both labeled and unlabeled state samples, and as a result the over-fitting problem of supervised manifold learning and blindness problem of unsupervised manifold learning are overcome. Simultaneously, class discrimination information is integrated within the dimension reduction process in a semi-supervised manner to improve sensitivity of the extracted fusion features. Lastly, the extracted fusion features are inputted into a pattern recognition algorithm to achieve the running state identification. The effectiveness of the proposed method is verified by a running state identification case in a gearbox, and the results confirm the improved accuracy of the running state identification.

Rapid optical imaging of EGF receptor expression with a single-chain antibody SNAP-tag fusion protein.

PubMed

Kampmeier, Florian; Niesen, Judith; Koers, Alexander; Ribbert, Markus; Brecht, Andreas; Fischer, Rainer; Kiessling, Fabian; Barth, Stefan; Thepen, Theo

2010-10-01

The epidermal growth factor receptor (EGFR) is overexpressed in several types of cancer and its inhibition can effectively inhibit tumour progression. The purpose of this study was to design an EGFR-specific imaging probe that combines efficient tumour targeting with rapid systemic clearance to facilitate non-invasive assessment of EGFR expression. Genetic fusion of a single-chain antibody fragment with the SNAP-tag produced a 48-kDa antibody derivative that can be covalently and site-specifically labelled with substrates containing 0 (6)-benzylguanine. The EGFR-specific single-chain variable fragment (scFv) fusion protein 425(scFv)SNAP was labelled with the near infrared (NIR) dye BG-747, and its accumulation, specificity and kinetics were monitored using NIR fluorescence imaging in a subcutaneous pancreatic carcinoma xenograft model. The 425(scFv)SNAP fusion protein accumulates rapidly and specifically at the tumour site. Its small size allows efficient renal clearance and a high tumour to background ratio (TBR) of 33.2 +/- 6.3 (n = 4) 10 h after injection. Binding of the labelled antibody was efficiently competed with a 20-fold excess of unlabelled probe, resulting in an average TBR of 6 +/- 1.35 (n = 4), which is similar to that obtained with a non-tumour-specific probe (5.44 +/- 1.92, n = 4). When compared with a full-length antibody against EGFR (cetuximab), 425(scFv)SNAP-747 showed significantly higher TBRs and complete clearance 72 h post-injection. The 425(scFv)SNAP fusion protein combines rapid and specific targeting of EGFR-positive tumours with a versatile and robust labelling technique that facilitates the attachment of fluorophores for use in optical imaging. The same approach could be used to couple a chelating agent for use in nuclear imaging.

Fully automatic multi-atlas segmentation of CTA for partial volume correction in cardiac SPECT/CT

NASA Astrophysics Data System (ADS)

Liu, Qingyi; Mohy-ud-Din, Hassan; Boutagy, Nabil E.; Jiang, Mingyan; Ren, Silin; Stendahl, John C.; Sinusas, Albert J.; Liu, Chi

2017-05-01

Anatomical-based partial volume correction (PVC) has been shown to improve image quality and quantitative accuracy in cardiac SPECT/CT. However, this method requires manual segmentation of various organs from contrast-enhanced computed tomography angiography (CTA) data. In order to achieve fully automatic CTA segmentation for clinical translation, we investigated the most common multi-atlas segmentation methods. We also modified the multi-atlas segmentation method by introducing a novel label fusion algorithm for multiple organ segmentation to eliminate overlap and gap voxels. To evaluate our proposed automatic segmentation, eight canine 99mTc-labeled red blood cell SPECT/CT datasets that incorporated PVC were analyzed, using the leave-one-out approach. The Dice similarity coefficient of each organ was computed. Compared to the conventional label fusion method, our proposed label fusion method effectively eliminated gaps and overlaps and improved the CTA segmentation accuracy. The anatomical-based PVC of cardiac SPECT images with automatic multi-atlas segmentation provided consistent image quality and quantitative estimation of intramyocardial blood volume, as compared to those derived using manual segmentation. In conclusion, our proposed automatic multi-atlas segmentation method of CTAs is feasible, practical, and facilitates anatomical-based PVC of cardiac SPECT/CT images.

A pretargeted nanoparticle system for tumor cell labeling

PubMed Central

Gunn, Jonathan; Park, Steven I.; Veiseh, Omid; Press, Oliver W.; Zhang, Miqin

2011-01-01

Nanoparticle-based cancer diagnostics and therapeutics can be significantly enhanced by selective tissue localization, but the strategy can be complicated by the requirement of a targeting ligand conjugated on nanoparticles, that is specific to only one or a limited few types of neoplastic cells, necessitating the development of multiple nanoparticle systems for different diseases. Here, we present a new nanoparticle system that capitalizes on a targeting pretreatment strategy, where a circulating fusion protein (FP) selectively prelabels the targeted cellular epitope, and a biotinylated iron oxide nanoparticle serves as a secondary label that binds to the FP on the target cell. This approach enables a single nanoparticle formulation to be used with any one of existing fusion proteins to bind a variety of target cells. We demonstrated this approach with two fusion proteins against two model cancer cell lines: lymphoma (Ramos) and leukemia (Jurkat), which showed 72.2% and 91.1% positive labeling, respectively. Notably, TEM analysis showed that a large nanoparticle population was endocytosed via attachment to the non-internalizing CD20 epitope. PMID:21107453

A pretargeted nanoparticle system for tumor cell labeling.

PubMed

Gunn, Jonathan; Park, Steven I; Veiseh, Omid; Press, Oliver W; Zhang, Miqin

2011-03-01

Nanoparticle-based cancer diagnostics and therapeutics can be significantly enhanced by selective tissue localization, but the strategy can be complicated by the requirement of a targeting ligand conjugated on nanoparticles, that is specific to only one or a limited few types of neoplastic cells, necessitating the development of multiple nanoparticle systems for different diseases. Here, we present a new nanoparticle system that capitalizes on a targeting pretreatment strategy, where a circulating fusion protein (FP) selectively prelabels the targeted cellular epitope, and a biotinylated iron oxide nanoparticle serves as a secondary label that binds to the FP on the target cell. This approach enables a single nanoparticle formulation to be used with any one of existing fusion proteins to bind a variety of target cells. We demonstrated this approach with two fusion proteins against two model cancer cell lines: lymphoma (Ramos) and leukemia (Jurkat), which showed 72.2% and 91.1% positive labeling, respectively. Notably, TEM analysis showed that a large nanoparticle population was endocytosed via attachment to the non-internalizing CD20 epitope.

Differential pH-dependent cellular uptake pathways among foamy viruses elucidated using dual-colored fluorescent particles

PubMed Central

2012-01-01

Background It is thought that foamy viruses (FVs) enter host cells via endocytosis because all FV glycoproteins examined display pH-dependent fusion activities. Only the prototype FV (PFV) glycoprotein has also significant fusion activity at neutral pH, suggesting that its uptake mechanism may deviate from other FVs. To gain new insights into the uptake processes of FV in individual live host cells, we developed fluorescently labeled infectious FVs. Results N-terminal tagging of the FV envelope leader peptide domain with a fluorescent protein resulted in efficient incorporation of the fluorescently labeled glycoprotein into secreted virions without interfering with their infectivity. Double-tagged viruses consisting of an eGFP-tagged PFV capsid (Gag-eGFP) and mCherry-tagged Env (Ch-Env) from either PFV or macaque simian FV (SFVmac) were observed during early stages of the infection pathway. PFV Env, but not SFVmac Env, containing particles induced strong syncytia formation on target cells. Both virus types showed trafficking of double-tagged virions towards the cell center. Upon fusion and subsequent capsid release into the cytosol, accumulation of naked capsid proteins was observed within four hours in the perinuclear region, presumably representing the centrosomes. Interestingly, virions harboring fusion-defective glycoproteins still promoted virus attachment and uptake, but failed to show syncytia formation and perinuclear capsid accumulation. Biochemical and initial imaging analysis indicated that productive fusion events occur predominantly within 4–6 h after virus attachment. Non-fused or non-fusogenic viruses are rapidly cleared from the cells by putative lysosomal degradation. Quantitative monitoring of the fraction of individual viruses containing both Env and capsid signals as a function of time demonstrated that PFV virions fused within the first few minutes, whereas fusion of SFVmac virions was less pronounced and observed over the entire 90 minutes measured. Conclusions The characterized double-labeled FVs described here provide new mechanistic insights into FV early entry steps, demonstrating that productive viral fusion occurs early after target cell attachment and uptake. The analysis highlights apparent differences in the uptake pathways of individual FV species. Furthermore, the infectious double-labeled FVs promise to provide important tools for future detailed analyses on individual FV fusion events in real time using advanced imaging techniques. PMID:22935135

Combined NMR and EPR Spectroscopy to Determine Structures of Viral Fusion Domains in Membranes

PubMed Central

Tamm, Lukas K.; Lai, Alex L.; Li, Yinling

2008-01-01

Methods are described to determine the structures of viral membrane fusion domains in detergent micelles by NMR and in lipid bilayers by site-directed spin labeling and EPR spectroscopy. Since in favorable cases, the lower-resolution spin label data obtained in lipid bilayers fully support the higher-resolution structures obtained by solution NMR, it is possible to graft the NMR structural coordinates into membranes using the EPR-derived distance restraints to the lipid bilayer. Electron paramagnetic dynamics and distance measurements in bilayers support conclusions drawn from NMR in detergent micelles. When these methods are applied to a structure determination of the influenza virus fusion domain and four point mutations with different functional phenotypes, it is evident that a fixed-angle boomerang structure with a glycine edge on the outside of the N-terminal arm is both necessary and sufficient to support membrane fusion. The human immunodeficiency virus fusion domain forms a straight helix with a flexible C-terminus. While EPR data for this fusion domain are not yet available, it is tentatively speculated that, because of its higher hydrophobicity, a critically tilted insertion may occur even in the absence of a kinked boomerang structure in this case. PMID:17963720

Multifunctional recombinant phycobiliprotein-based fluorescent constructs and phycobilisome display

DOEpatents

Glazer, Alexander N.; Cai, Yuping

2007-01-30

The invention provides multifunctional fusion constructs which are rapidly incorporated into a macromolecular structure such as a phycobilisome such that the fusion proteins are separated from one another and unable to self-associate. The invention provides methods and compositions for displaying a functional polypeptide domain on an oligomeric phycobiliprotein, including fusion proteins comprising a functional displayed domain and a functional phycobiliprotein domain incorporated in a functional oligomeric phycobiliprotein. The fusion proteins provide novel specific labeling reagents.

Multifunctional recombinant phycobiliprotein-based fluorescent constructs and phycobilisome display

DOEpatents

Glazer, Alexander N.; Cai, Yuping

2007-02-13

The invention provides multifunctional fusion constructs which are rapidly incorporated into a macromolecular structure such as a phycobilisome such that the fusion proteins are separated from one another and unable to self-associate. The invention provides methods and compositions for displaying a functional polypeptide domain on an oligomeric phycobiliprotein. including fusion proteins comprising a functional displayed domain and a functional phycobiliprotein domain incorporated in a functional oligomeric phycobiliprotein. The fusion proteins provide novel specific labeling reagents.

Multifunctional recombinant phycobiliprotein-based fluorescent constructs and phycobilisome display

DOEpatents

Glazer, Alexander N.; Cai, Yuping

2003-11-18

The invention provides multifunctional fusion constructs which are rapidly incorporated into a macromolecular structure such as a phycobilisome such that the fusion proteins are separated from one another and unable to self-associate. The invention provides methods and compositions for displaying a functional polypeptide domain on an oligomeric phycobiliprotein, including fusion proteins comprising a functional displayed domain and a functional phycobiliprotein domain incorporated in a functional oligomeric phycobiliprotein. The fusion proteins provide novel specific labeling reagents.

Nonlocal atlas-guided multi-channel forest learning for human brain labeling

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

Ma, Guangkai; Gao, Yaozong; Wu, Guorong

Purpose: It is important for many quantitative brain studies to label meaningful anatomical regions in MR brain images. However, due to high complexity of brain structures and ambiguous boundaries between different anatomical regions, the anatomical labeling of MR brain images is still quite a challenging task. In many existing label fusion methods, appearance information is widely used. However, since local anatomy in the human brain is often complex, the appearance information alone is limited in characterizing each image point, especially for identifying the same anatomical structure across different subjects. Recent progress in computer vision suggests that the context features canmore » be very useful in identifying an object from a complex scene. In light of this, the authors propose a novel learning-based label fusion method by using both low-level appearance features (computed from the target image) and high-level context features (computed from warped atlases or tentative labeling maps of the target image). Methods: In particular, the authors employ a multi-channel random forest to learn the nonlinear relationship between these hybrid features and target labels (i.e., corresponding to certain anatomical structures). Specifically, at each of the iterations, the random forest will output tentative labeling maps of the target image, from which the authors compute spatial label context features and then use in combination with original appearance features of the target image to refine the labeling. Moreover, to accommodate the high inter-subject variations, the authors further extend their learning-based label fusion to a multi-atlas scenario, i.e., they train a random forest for each atlas and then obtain the final labeling result according to the consensus of results from all atlases. Results: The authors have comprehensively evaluated their method on both public LONI-LBPA40 and IXI datasets. To quantitatively evaluate the labeling accuracy, the authors use the dice similarity coefficient to measure the overlap degree. Their method achieves average overlaps of 82.56% on 54 regions of interest (ROIs) and 79.78% on 80 ROIs, respectively, which significantly outperform the baseline method (random forests), with the average overlaps of 72.48% on 54 ROIs and 72.09% on 80 ROIs, respectively. Conclusions: The proposed methods have achieved the highest labeling accuracy, compared to several state-of-the-art methods in the literature.« less

Nonlocal atlas-guided multi-channel forest learning for human brain labeling

PubMed Central

Ma, Guangkai; Gao, Yaozong; Wu, Guorong; Wu, Ligang; Shen, Dinggang

2016-01-01

Purpose: It is important for many quantitative brain studies to label meaningful anatomical regions in MR brain images. However, due to high complexity of brain structures and ambiguous boundaries between different anatomical regions, the anatomical labeling of MR brain images is still quite a challenging task. In many existing label fusion methods, appearance information is widely used. However, since local anatomy in the human brain is often complex, the appearance information alone is limited in characterizing each image point, especially for identifying the same anatomical structure across different subjects. Recent progress in computer vision suggests that the context features can be very useful in identifying an object from a complex scene. In light of this, the authors propose a novel learning-based label fusion method by using both low-level appearance features (computed from the target image) and high-level context features (computed from warped atlases or tentative labeling maps of the target image). Methods: In particular, the authors employ a multi-channel random forest to learn the nonlinear relationship between these hybrid features and target labels (i.e., corresponding to certain anatomical structures). Specifically, at each of the iterations, the random forest will output tentative labeling maps of the target image, from which the authors compute spatial label context features and then use in combination with original appearance features of the target image to refine the labeling. Moreover, to accommodate the high inter-subject variations, the authors further extend their learning-based label fusion to a multi-atlas scenario, i.e., they train a random forest for each atlas and then obtain the final labeling result according to the consensus of results from all atlases. Results: The authors have comprehensively evaluated their method on both public LONI_LBPA40 and IXI datasets. To quantitatively evaluate the labeling accuracy, the authors use the dice similarity coefficient to measure the overlap degree. Their method achieves average overlaps of 82.56% on 54 regions of interest (ROIs) and 79.78% on 80 ROIs, respectively, which significantly outperform the baseline method (random forests), with the average overlaps of 72.48% on 54 ROIs and 72.09% on 80 ROIs, respectively. Conclusions: The proposed methods have achieved the highest labeling accuracy, compared to several state-of-the-art methods in the literature. PMID:26843260

A generic screening platform for inhibitors of virus induced cell fusion using cellular electrical impedance

PubMed Central

Watterson, Daniel; Robinson, Jodie; Chappell, Keith J.; Butler, Mark S.; Edwards, David J.; Fry, Scott R.; Bermingham, Imogen M.; Cooper, Matthew A.; Young, Paul R.

2016-01-01

Fusion of the viral envelope with host cell membranes is an essential step in the life cycle of all enveloped viruses. Despite such a clear target for antiviral drug development, few anti-fusion drugs have progressed to market. One significant hurdle is the absence of a generic, high-throughput, reproducible fusion assay. Here we report that real time, label-free measurement of cellular electrical impedance can quantify cell-cell fusion mediated by either individually expressed recombinant viral fusion proteins, or native virus infection. We validated this approach for all three classes of viral fusion and demonstrated utility in quantifying fusion inhibition using antibodies and small molecule inhibitors specific for dengue virus and respiratory syncytial virus. PMID:26976324

A novel geometry-dosimetry label fusion method in multi-atlas segmentation for radiotherapy: a proof-of-concept study

NASA Astrophysics Data System (ADS)

Chang, Jina; Tian, Zhen; Lu, Weiguo; Gu, Xuejun; Chen, Mingli; Jiang, Steve B.

2017-05-01

Multi-atlas segmentation (MAS) has been widely used to automate the delineation of organs at risk (OARs) for radiotherapy. Label fusion is a crucial step in MAS to cope with the segmentation variabilities among multiple atlases. However, most existing label fusion methods do not consider the potential dosimetric impact of the segmentation result. In this proof-of-concept study, we propose a novel geometry-dosimetry label fusion method for MAS-based OAR auto-contouring, which evaluates the segmentation performance in terms of both geometric accuracy and the dosimetric impact of the segmentation accuracy on the resulting treatment plan. Differently from the original selective and iterative method for performance level estimation (SIMPLE), we evaluated and rejected the atlases based on both Dice similarity coefficient and the predicted error of the dosimetric endpoints. The dosimetric error was predicted using our previously developed geometry-dosimetry model. We tested our method in MAS-based rectum auto-contouring on 20 prostate cancer patients. The accuracy in the rectum sub-volume close to the planning tumor volume (PTV), which was found to be a dosimetric sensitive region of the rectum, was greatly improved. The mean absolute distance between the obtained contour and the physician-drawn contour in the rectum sub-volume 2 mm away from PTV was reduced from 3.96 mm to 3.36 mm on average for the 20 patients, with the maximum decrease found to be from 9.22 mm to 3.75 mm. We also compared the dosimetric endpoints predicted for the obtained contours with those predicted for the physician-drawn contours. Our method led to smaller dosimetric endpoint errors than the SIMPLE method in 15 patients, comparable errors in 2 patients, and slightly larger errors in 3 patients. These results indicated the efficacy of our method in terms of considering both geometric accuracy and dosimetric impact during label fusion. Our algorithm can be applied to different tumor sites and radiation treatments, given a specifically trained geometry-dosimetry model.

A novel geometry-dosimetry label fusion method in multi-atlas segmentation for radiotherapy: a proof-of-concept study.

PubMed

Chang, Jina; Tian, Zhen; Lu, Weiguo; Gu, Xuejun; Chen, Mingli; Jiang, Steve B

2017-05-07

Multi-atlas segmentation (MAS) has been widely used to automate the delineation of organs at risk (OARs) for radiotherapy. Label fusion is a crucial step in MAS to cope with the segmentation variabilities among multiple atlases. However, most existing label fusion methods do not consider the potential dosimetric impact of the segmentation result. In this proof-of-concept study, we propose a novel geometry-dosimetry label fusion method for MAS-based OAR auto-contouring, which evaluates the segmentation performance in terms of both geometric accuracy and the dosimetric impact of the segmentation accuracy on the resulting treatment plan. Differently from the original selective and iterative method for performance level estimation (SIMPLE), we evaluated and rejected the atlases based on both Dice similarity coefficient and the predicted error of the dosimetric endpoints. The dosimetric error was predicted using our previously developed geometry-dosimetry model. We tested our method in MAS-based rectum auto-contouring on 20 prostate cancer patients. The accuracy in the rectum sub-volume close to the planning tumor volume (PTV), which was found to be a dosimetric sensitive region of the rectum, was greatly improved. The mean absolute distance between the obtained contour and the physician-drawn contour in the rectum sub-volume 2 mm away from PTV was reduced from 3.96 mm to 3.36 mm on average for the 20 patients, with the maximum decrease found to be from 9.22 mm to 3.75 mm. We also compared the dosimetric endpoints predicted for the obtained contours with those predicted for the physician-drawn contours. Our method led to smaller dosimetric endpoint errors than the SIMPLE method in 15 patients, comparable errors in 2 patients, and slightly larger errors in 3 patients. These results indicated the efficacy of our method in terms of considering both geometric accuracy and dosimetric impact during label fusion. Our algorithm can be applied to different tumor sites and radiation treatments, given a specifically trained geometry-dosimetry model.

Quenched substrates for live-cell labeling of SNAP-tagged fusion proteins with improved fluorescent background.

PubMed

Stöhr, Katharina; Siegberg, Daniel; Ehrhard, Tanja; Lymperopoulos, Konstantinos; Öz, Simin; Schulmeister, Sonja; Pfeifer, Andrea C; Bachmann, Julie; Klingmüller, Ursula; Sourjik, Victor; Herten, Dirk-Peter

2010-10-01

Recent developments in fluorescence microscopy raise the demands for bright and photostable fluorescent tags for specific and background free labeling in living cells. Aside from fluorescent proteins and other tagging methods, labeling of SNAP-tagged proteins has become available thereby increasing the pool of potentially applicable fluorescent dyes for specific labeling of proteins. Here, we report on novel conjugates of benzylguanine (BG) which are quenched in their fluorescence and become highly fluorescent upon labeling of the SNAP-tag, the commercial variant of the human O(6)-alkylguanosyltransferase (hAGT). We identified four conjugates showing a strong increase, i.e., >10-fold, in fluorescence intensity upon labeling of SNAP-tag in vitro. Moreover, we screened a subset of nine BG-dye conjugates in living Escherichia coli and found them all suited for labeling of the SNAP-tag. Here, quenched BG-dye conjugates yield a higher specificity due to reduced contribution from excess conjugate to the fluorescence signal. We further extended the application of these conjugates by labeling a SNAP-tag fusion of the Tar chemoreceptor in live E. coli cells and the eukaryotic transcription factor STAT5b in NIH 3T3 mouse fibroblast cells. Aside from the labeling efficiency and specificity in living cells, we discuss possible mechanisms that might be responsible for the changes in fluorescence emission upon labeling of the SNAP-tag, as well as problems we encountered with nonspecific labeling with certain conjugates in eukaryotic cells.

Segmentation by fusion of histogram-based k-means clusters in different color spaces.

PubMed

Mignotte, Max

2008-05-01

This paper presents a new, simple, and efficient segmentation approach, based on a fusion procedure which aims at combining several segmentation maps associated to simpler partition models in order to finally get a more reliable and accurate segmentation result. The different label fields to be fused in our application are given by the same and simple (K-means based) clustering technique on an input image expressed in different color spaces. Our fusion strategy aims at combining these segmentation maps with a final clustering procedure using as input features, the local histogram of the class labels, previously estimated and associated to each site and for all these initial partitions. This fusion framework remains simple to implement, fast, general enough to be applied to various computer vision applications (e.g., motion detection and segmentation), and has been successfully applied on the Berkeley image database. The experiments herein reported in this paper illustrate the potential of this approach compared to the state-of-the-art segmentation methods recently proposed in the literature.

Dual wavelength imaging allows analysis of membrane fusion of influenza virus inside cells.

PubMed

Sakai, Tatsuya; Ohuchi, Masanobu; Imai, Masaki; Mizuno, Takafumi; Kawasaki, Kazunori; Kuroda, Kazumichi; Yamashina, Shohei

2006-02-01

Influenza virus hemagglutinin (HA) is a determinant of virus infectivity. Therefore, it is important to determine whether HA of a new influenza virus, which can potentially cause pandemics, is functional against human cells. The novel imaging technique reported here allows rapid analysis of HA function by visualizing viral fusion inside cells. This imaging was designed to detect fusion changing the spectrum of the fluorescence-labeled virus. Using this imaging, we detected the fusion between a virus and a very small endosome that could not be detected previously, indicating that the imaging allows highly sensitive detection of viral fusion.

Transformation of general binary MRF minimization to the first-order case.

PubMed

Ishikawa, Hiroshi

2011-06-01

We introduce a transformation of general higher-order Markov random field with binary labels into a first-order one that has the same minima as the original. Moreover, we formalize a framework for approximately minimizing higher-order multi-label MRF energies that combines the new reduction with the fusion-move and QPBO algorithms. While many computer vision problems today are formulated as energy minimization problems, they have mostly been limited to using first-order energies, which consist of unary and pairwise clique potentials, with a few exceptions that consider triples. This is because of the lack of efficient algorithms to optimize energies with higher-order interactions. Our algorithm challenges this restriction that limits the representational power of the models so that higher-order energies can be used to capture the rich statistics of natural scenes. We also show that some minimization methods can be considered special cases of the present framework, as well as comparing the new method experimentally with other such techniques.

Human adipose tissue-derived stem cells exhibit proliferation potential and spontaneous rhythmic contraction after fusion with neonatal rat cardiomyocytes.

PubMed

Metzele, Roxana; Alt, Christopher; Bai, Xiaowen; Yan, Yasheng; Zhang, Zhi; Pan, Zhizhong; Coleman, Michael; Vykoukal, Jody; Song, Yao-Hua; Alt, Eckhard

2011-03-01

Various types of stem cells have been shown to have beneficial effects on cardiac function. It is still debated whether fusion of injected stem cells with local resident cardiomyocytes is one of the mechanisms. To better understand the role of fusion in stem cell-based myocardial regeneration, the present study was designed to investigate the fate of human adipose tissue-derived stem cells (hASCs) fused with neonatal rat cardiomyocytes in vitro. hASCs labeled with the green fluorescent probe Vybrant DiO were cocultured with neonatal rat cardiomyocytes labeled with the red fluorescent probe Vybrant DiI and then treated with fusion-inducing hemagglutinating virus of Japan (HVJ). Cells that incorporated both red and green fluorescent signals were considered to be hASCs that had fused with rat cardiomyocytes. Fusion efficiency was 19.86 ± 4.84% at 5 d after treatment with HVJ. Most fused cells displayed cardiomyocyte-like morphology and exhibited spontaneous rhythmic contraction. Both immunofluorescence staining and lentiviral vector labeling showed that fused cells contained separate rat cardiomyocyte and hASC nuclei. Immunofluorescence staining assays demonstrated that human nuclei in fused cells still expressed the proliferation marker Ki67. In addition, hASCs fused with rat cardiomyocytes were positive for troponin I. Whole-cell voltage-clamp analysis demonstrated action potentials in beating fused cells. RT-PCR analysis using rat- or human-specific myosin heavy chain primers revealed that the myosin heavy-chain expression in fused cells was derived from rat cardiomyocytes. Real-time PCR identified expression of human troponin T in fused cells and the presence of rat cardiomyocytes induced a cardiomyogenic protein expression of troponin T in human ASCs. This study illustrates that hASCs exhibit both stem cell (proliferation) and cardiomyocyte properties (action potential and spontaneous rhythmic beating) after fusion with rat cardiomyocytes, supporting the theory that fusion, even if artificially induced in our study, could indeed be a mechanism for cardiomyocyte renewal in the heart.

Statistical algorithms improve accuracy of gene fusion detection

PubMed Central

Hsieh, Gillian; Bierman, Rob; Szabo, Linda; Lee, Alex Gia; Freeman, Donald E.; Watson, Nathaniel; Sweet-Cordero, E. Alejandro

2017-01-01

Abstract Gene fusions are known to play critical roles in tumor pathogenesis. Yet, sensitive and specific algorithms to detect gene fusions in cancer do not currently exist. In this paper, we present a new statistical algorithm, MACHETE (Mismatched Alignment CHimEra Tracking Engine), which achieves highly sensitive and specific detection of gene fusions from RNA-Seq data, including the highest Positive Predictive Value (PPV) compared to the current state-of-the-art, as assessed in simulated data. We show that the best performing published algorithms either find large numbers of fusions in negative control data or suffer from low sensitivity detecting known driving fusions in gold standard settings, such as EWSR1-FLI1. As proof of principle that MACHETE discovers novel gene fusions with high accuracy in vivo, we mined public data to discover and subsequently PCR validate novel gene fusions missed by other algorithms in the ovarian cancer cell line OVCAR3. These results highlight the gains in accuracy achieved by introducing statistical models into fusion detection, and pave the way for unbiased discovery of potentially driving and druggable gene fusions in primary tumors. PMID:28541529

Beyond RGB: Very high resolution urban remote sensing with multimodal deep networks

NASA Astrophysics Data System (ADS)

Audebert, Nicolas; Le Saux, Bertrand; Lefèvre, Sébastien

2018-06-01

In this work, we investigate various methods to deal with semantic labeling of very high resolution multi-modal remote sensing data. Especially, we study how deep fully convolutional networks can be adapted to deal with multi-modal and multi-scale remote sensing data for semantic labeling. Our contributions are threefold: (a) we present an efficient multi-scale approach to leverage both a large spatial context and the high resolution data, (b) we investigate early and late fusion of Lidar and multispectral data, (c) we validate our methods on two public datasets with state-of-the-art results. Our results indicate that late fusion make it possible to recover errors steaming from ambiguous data, while early fusion allows for better joint-feature learning but at the cost of higher sensitivity to missing data.

Fusion activity of influenza virus PR8/34 correlates with a temperature-induced conformational change within the hemagglutinin ectodomain detected by photochemical labeling

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

Brunner, J.; Zugliani, C.; Mischler, R.

1991-03-05

Fusion of influenza viruses with membranes is catalyzed by the viral spike protein hemagglutinin (HA). Under mildly acidic conditions ({approximately}pH 5) this protein undergoes a conformational change that triggers the exposure of the fusion peptide, the hydrophobic N-terminal segment of the HA2 polypeptide chain. Insertion of this segment into the target membrane (or viral membrane ) is likely to represent a key step along the fusion pathway, but the details are far from being clear. The photoreactive phospholipid 1-palmitoyl-2-(11-(4-(3-(trifluoromethyl)diazirinyl)phenyl)(2-{sup 3}H)undecanoyl)-sn-glycero-3-phosphocholine (({sup 3}H)PTPC/11), inserted into the bilayer of large unilamellar vesicles (LUVs), allowed the authors to investigate both the interaction ofmore » viruses with the vesicles under perfusion conditions and the fusion process itself occurring at elevated temperatures only. Despite the observed binding of viruses to LUVs at pH 5 and 0C, labeling of HA2 was very weak. They have studied also the effect of temperature on the acid-induced (pH 5) interaction of bromelain-solubilized HA (BHA) with vesicles.« less

Effects of selective serotonin reuptake inhibitors on thought-action fusion, metacognitions, and thought suppression in obsessive-compulsive disorder.

PubMed

Besiroglu, Lutfullah; Çetinkaya, Nuralay; Selvi, Yavuz; Atli, Abdullah

2011-01-01

We aimed to assess whether cognitive processes change over time in patients with obsessive-compulsive disorder (OCD) receiving selective serotonin reuptake inhibitors without cognitive behavioral therapy and to investigate the factors associated with probable cognitive changes. During the 16 weeks of the study, 55 patients who met the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, criteria for OCD received open-label treatment with sertraline (100-200 mg/d) or fluoxetine (40-80 mg/d) and were assessed using the Yale-Brown Obsessive-Compulsive Scale, Beck Depression Inventory (BDI), Thought-Action Fusion Scale (TAFS), Metacognitions Questionnaire (MCQ-30), and White Bear Suppression Inventory (WBSI). The Yale-Brown Obsessive-Compulsive Scale (P < .001), BDI (P < .001), TAFS morality (P < .005), MCQ-30 (P < .01), and WBSI (P < .005) scores at follow-up were significantly lower than baseline scores. When we excluded OCD patients with depressive disorder (n = 12), statistical significance in paired comparisons for MCQ and WBSI disappeared. Similarly, when OCD patients with religious obsessions (n = 16) were excluded, paired comparisons for MCQ and TAF morality were not statistically significant. Changes in BDI, TAFS morality, MCQ-30, and WBSI (P < .005) were significantly correlated with changes in severity of obsessions, but not that of compulsions. After controlling for the change in depression severity, significant correlations between changes in obsessive and cognitive scales did not continue to have statistical significance. The BDI changes (P < .05) significantly explained the changes in symptom severity in a linear regression model. Our findings suggest that selective serotonin reuptake inhibitors can change appraisals of obsessive intrusions via their effects on negative emotions. Copyright © 2011 Elsevier Inc. All rights reserved.

F-18 Labeled Diabody-Luciferase Fusion Proteins for Optical-ImmunoPET

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

Wu, Anna M.

2013-01-18

The goal of the proposed work is to develop novel dual-labeled molecular imaging probes for multimodality imaging. Based on small, engineered antibodies called diabodies, these probes will be radioactively tagged with Fluorine-18 for PET imaging, and fused to luciferases for optical (bioluminescence) detection. Performance will be evaluated and validated using a prototype integrated optical-PET imaging system, OPET. Multimodality probes for optical-PET imaging will be based on diabodies that are dually labeled with 18F for PET detection and fused to luciferases for optical imaging. 1) Two sets of fusion proteins will be built, targeting the cell surface markers CEA or HER2.more » Coelenterazine-based luciferases and variant forms will be evaluated in combination with native substrate and analogs, in order to obtain two distinct probes recognizing different targets with different spectral signatures. 2) Diabody-luciferase fusion proteins will be labeled with 18F using amine reactive [18F]-SFB produced using a novel microwave-assisted, one-pot method. 3) Sitespecific, chemoselective radiolabeling methods will be devised, to reduce the chance that radiolabeling will inactivate either the target-binding properties or the bioluminescence properties of the diabody-luciferase fusion proteins. 4) Combined optical and PET imaging of these dual modality probes will be evaluated and validated in vitro and in vivo using a prototype integrated optical-PET imaging system, OPET. Each imaging modality has its strengths and weaknesses. Development and use of dual modality probes allows optical imaging to benefit from the localization and quantitation offered by the PET mode, and enhances the PET imaging by enabling simultaneous detection of more than one probe.« less

Progress in understanding the neuronal SNARE function and its regulation.

PubMed

Yoon, T-Y; Shin, Y-K

2009-02-01

Vesicle budding and fusion underlies many essential biochemical deliveries in eukaryotic cells, and its core fusion machinery is thought to be built on one protein family named soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE). Recent technical advances based on site-directed fluorescence labelling and nano-scale detection down to the single-molecule level rapidly unveiled the protein and the lipid intermediates along the fusion pathway as well as the molecular actions of fusion effectors. Here we summarize these new exciting findings in context with a new mechanistic model that reconciles two existing fusion models: the proteinaceous pore model and the hemifusion model. Further, we attempt to locate the points of action for the fusion effectors along the fusion pathway and to delineate the energetic interplay between the SNARE complexes and the fusion effectors.

Strong expression of the neuronal transcription factor FOXP2 is linked to an increased risk of early PSA recurrence in ERG fusion-negative cancers.

PubMed

Stumm, Laura; Burkhardt, Lia; Steurer, Stefan; Simon, Ronald; Adam, Meike; Becker, Andreas; Sauter, Guido; Minner, Sarah; Schlomm, Thorsten; Sirma, Hüseyin; Michl, Uwe

2013-07-01

Transcription factors of the forkhead box P (FOXP1-4) family have been implicated in various human cancer types before. The relevance and role of neuronal transcription factor FOXP2 in prostate cancer is unknown. A tissue microarray containing samples from more than 11 000 prostate cancers from radical prostatectomy specimens with clinical follow-up data was analysed for FOXP2 expression by immunohistochemistry. FOXP2 data were also compared with pre-existing ERG fusion (by fluorescence in situ hybridisation and immunohistochemistry) and cell proliferation (Ki67 labelling index) data. There was a moderate to strong FOXP2 protein expression in basal and secretory cells of normal prostatic glands. As compared with normal cells, FOXP2 expression was lost or reduced in 25% of cancers. Strong FOXP2 expression was linked to advanced tumour stage, high Gleason score, presence of lymph node metastases and early tumour recurrence (p<0.0001; each) in ERG fusion-negative, but not in ERG fusion-positive cancers. High FOXP2 expression was linked to high Ki67 labelling index (p<0.0001) in all cancers irrespective of ERG fusion status. These data demonstrate that similar high FOXP2 protein levels as in normal prostate epithelium exert a 'paradoxical' oncogenic role in 'non fusion-type' prostate cancer. It may be speculated that interaction of FOXP2 with members of pathways that are specifically activated in 'non fusion-type' cancers may be responsible for this phenomenon.

Near infrared and visible face recognition based on decision fusion of LBP and DCT features

NASA Astrophysics Data System (ADS)

Xie, Zhihua; Zhang, Shuai; Liu, Guodong; Xiong, Jinquan

2018-03-01

Visible face recognition systems, being vulnerable to illumination, expression, and pose, can not achieve robust performance in unconstrained situations. Meanwhile, near infrared face images, being light- independent, can avoid or limit the drawbacks of face recognition in visible light, but its main challenges are low resolution and signal noise ratio (SNR). Therefore, near infrared and visible fusion face recognition has become an important direction in the field of unconstrained face recognition research. In order to extract the discriminative complementary features between near infrared and visible images, in this paper, we proposed a novel near infrared and visible face fusion recognition algorithm based on DCT and LBP features. Firstly, the effective features in near-infrared face image are extracted by the low frequency part of DCT coefficients and the partition histograms of LBP operator. Secondly, the LBP features of visible-light face image are extracted to compensate for the lacking detail features of the near-infrared face image. Then, the LBP features of visible-light face image, the DCT and LBP features of near-infrared face image are sent to each classifier for labeling. Finally, decision level fusion strategy is used to obtain the final recognition result. The visible and near infrared face recognition is tested on HITSZ Lab2 visible and near infrared face database. The experiment results show that the proposed method extracts the complementary features of near-infrared and visible face images and improves the robustness of unconstrained face recognition. Especially for the circumstance of small training samples, the recognition rate of proposed method can reach 96.13%, which has improved significantly than 92.75 % of the method based on statistical feature fusion.

Paramyxovirus fusion: Real-time measurement of parainfluenza virus 5 virus-cell fusion

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

Connolly, Sarah A.; Lamb, Robert A.

2006-11-25

Although cell-cell fusion assays are useful surrogate methods for studying virus fusion, differences between cell-cell and virus-cell fusion exist. To examine paramyxovirus fusion in real time, we labeled viruses with fluorescent lipid probes and monitored virus-cell fusion by fluorimetry. Two parainfluenza virus 5 (PIV5) isolates (W3A and SER) and PIV5 containing mutations within the fusion protein (F) were studied. Fusion was specific and temperature-dependent. Compared to many low pH-dependent viruses, the kinetics of PIV5 fusion was slow, approaching completion within several minutes. As predicted from cell-cell fusion assays, virus containing an F protein with an extended cytoplasmic tail (rSV5 F551)more » had reduced fusion compared to wild-type virus (W3A). In contrast, virus-cell fusion for SER occurred at near wild-type levels, despite the fact that this isolate exhibits a severely reduced cell-cell fusion phenotype. These results support the notion that virus-cell and cell-cell fusion have significant differences.« less

The dynamics and regulation of mesenchymal cell fusion in the sea urchin embryo.

PubMed

Hodor, P G; Ettensohn, C A

1998-07-01

Cell-cell fusion occurs in a wide variety of developmental contexts, yet the mechanisms involved are just beginning to be elucidated. In the sea urchin embryo, primary mesenchyme cells (PMCs) fuse to form syncytial filopodial cables within which skeletal spicules are deposited. Taking advantage of the optical transparency and ease of micromanipulation of sea urchin embryos, we have developed methods for directly observing the dynamics of PMC fusion in vivo. A fraction of the PMCs was labeled with fluorescent dextran and transfer of the dye to unlabeled PMCs was followed by time-lapse, fluorescence microscopy. Fusion was first detected about 2 h after PMCs began to migrate within the blastocoel. Fusion proceeded in parallel with the assembly of the PMC ring pattern and was complete by the early gastrula stage. The formation of a single, extensive PMC syncytium was confirmed by DiI labeling of fixed embryos. When single micromeres were isolated and cultured in unsupplemented seawater, they divided and their progeny underwent fusion. This shows that the capacity to fuse is autonomously programmed in the micromere-PMC lineage by the 16-cell stage. PMC transplantations at late embryonic stages revealed that these cells remain fusion-competent long after their fusion is complete. At late stages, other mesenchyme cells (blastocoelar cells) are also present within the blastocoel and are migrating and fusing with one another. Fusion-competent blastocoelar cells and PMCs come into contact but do not fuse with one another, indicating that these two cell types fuse by distinct mechanisms. When secondary mesenchyme cells convert to a skeletogenic fate they alter their fusogenic properties and join the PMC syncytium, as shown by transfer of fluorescent dextran. Our analysis has provided a detailed picture of the cellular basis and regulation of mesodermal cell fusion and has important implications regarding molecular mechanisms that underlie fusion.

Affimer proteins for F-actin: novel affinity reagents that label F-actin in live and fixed cells.

PubMed

Lopata, Anna; Hughes, Ruth; Tiede, Christian; Heissler, Sarah M; Sellers, James R; Knight, Peter J; Tomlinson, Darren; Peckham, Michelle

2018-04-26

Imaging the actin cytoskeleton in cells uses a wide range of approaches. Typically, a fluorescent derivative of the small cyclic peptide phalloidin is used to image F-actin in fixed cells. Lifeact and F-tractin are popular for imaging the cytoskeleton in live cells. Here we characterised novel affinity reagents called Affimers that specifically bind to F-actin in vitro to determine if they are suitable alternatives as eGFP-fusion proteins, to label actin in live cells, or for labeling F-actin in fixed cells. In vitro experiments showed that 3 out of the 4 Affimers (Affimers 6, 14 and 24) tested bind tightly to purified F-actin, and appear to have overlapping binding sites. As eGFP-fusion proteins, the same 3 Affimers label F-actin in live cells. FRAP experiments suggest that eGFP-Affimer 6 behaves most similarly to F-tractin and Lifeact. However, it does not colocalise with mCherry-actin in dynamic ruffles, and may preferentially bind stable actin filaments. All 4 Affimers label F-actin in methanol fixed cells, while only Affimer 14 labels F-actin after paraformaldehyde fixation. eGFP-Affimer 6 has potential for use in selectively imaging the stable actin cytoskeleton in live cells, while all 4 Affimers are strong alternatives to phalloidin for labelling F-actin in fixed cells.

Blob-level active-passive data fusion for Benthic classification

NASA Astrophysics Data System (ADS)

Park, Joong Yong; Kalluri, Hemanth; Mathur, Abhinav; Ramnath, Vinod; Kim, Minsu; Aitken, Jennifer; Tuell, Grady

2012-06-01

We extend the data fusion pixel level to the more semantically meaningful blob level, using the mean-shift algorithm to form labeled blobs having high similarity in the feature domain, and connectivity in the spatial domain. We have also developed Bhattacharyya Distance (BD) and rule-based classifiers, and have implemented these higher-level data fusion algorithms into the CZMIL Data Processing System. Applying these new algorithms to recent SHOALS and CASI data at Plymouth Harbor, Massachusetts, we achieved improved benthic classification accuracies over those produced with either single sensor, or pixel-level fusion strategies. These results appear to validate the hypothesis that classification accuracy may be generally improved by adopting higher spatial and semantic levels of fusion.

A hexahistidine-Zn2+-dye label reveals STIM1 surface exposure

PubMed Central

Hauser, Christina T.; Tsien, Roger Y.

2007-01-01

Site-specific fluorescent labeling of proteins in vivo remains one of the most powerful techniques for imaging complex processes in live cells. Although fluorescent proteins in many colors are useful tools for tracking expression and localization of fusion proteins in cells, these relatively large tags (>220 aa) can perturb protein folding, trafficking and function. Much smaller genetically encodable domains (<15 aa) offer complementary advantages. We introduce a small fluorescent chelator whose membrane-impermeant complex with nontoxic Zn2+ ions binds tightly but reversibly to hexahistidine (His6) motifs on surface-exposed proteins. This live-cell label helps to resolve a current controversy concerning externalization of the stromal interaction molecule STIM1 upon depletion of Ca2+ from the endoplasmic reticulum. Whereas N-terminal fluorescent protein fusions interfere with surface exposure of STIM1, short His6 tags are accessible to the dye or antibodies, demonstrating externalization. PMID:17360414

Membrane-spanning lipids for an uncompromised monitoring of membrane fusion and intermembrane lipid transfer

PubMed Central

Schwarzmann, Günter; Breiden, Bernadette; Sandhoff, Konrad

2015-01-01

A Förster resonance energy transfer-based fusion and transfer assay was developed to study, in model membranes, protein-mediated membrane fusion and intermembrane lipid transfer of fluorescent sphingolipid analogs. For this assay, it became necessary to apply labeled reporter molecules that are resistant to spontaneous as well as protein-mediated intermembrane transfer. The novelty of this assay is the use of nonextractable fluorescent membrane-spanning bipolar lipids. Starting from the tetraether lipid caldarchaeol, we synthesized fluorescent analogs with fluorophores at both polar ends. In addition, we synthesized radioactive glycosylated caldarchaeols. These labeled lipids were shown to stretch through bilayer membranes rather than to loop within a single lipid layer of liposomes. More important, the membrane-spanning lipids (MSLs) in contrast to phosphoglycerides proved to be nonextractable by proteins. We could show that the GM2 activator protein (GM2AP) is promiscuous with respect to glycero- and sphingolipid transfer. Saposin (Sap) B also transferred sphingolipids albeit with kinetics different from GM2AP. In addition, we could unambiguously show that the recombinant activator protein Sap C x His6 induced membrane fusion rather than intermembrane lipid transfer. These findings showed that these novel MSLs, in contrast with fluorescent phosphoglycerolipids, are well suited for an uncompromised monitoring of membrane fusion and intermembrane lipid transfer. PMID:26269359

Expression and isotopic labelling of the potassium channel blocker ShK toxin as a thioredoxin fusion protein in bacteria.

PubMed

Chang, Shih Chieh; Galea, Charles A; Leung, Eleanor W W; Tajhya, Rajeev B; Beeton, Christine; Pennington, Michael W; Norton, Raymond S

2012-10-01

The polypeptide toxin ShK is a potent blocker of Kv1.3 potassium channels, which play a crucial role in the activation of human effector memory T-cells (T(EM)). Selective blockers constitute valuable therapeutic leads for the treatment of autoimmune diseases mediated by T(EM) cells, such as multiple sclerosis, rheumatoid arthritis, and type-1 diabetes. We have established a recombinant peptide expression system in order to generate isotopically-labelled ShK and various ShK analogues for in-depth biophysical and pharmacological studies. ShK was expressed as a thioredoxin fusion protein in Escherichia coli BL21 (DE3) cells and purified initially by Ni²⁺ iminodiacetic acid affinity chromatography. The fusion protein was cleaved with enterokinase and purified to homogeneity by reverse-phase HPLC. NMR spectra of ¹⁵N-labelled ShK were similar to those reported previously for the unlabelled synthetic peptide, confirming that recombinant ShK was correctly folded. Recombinant ShK blocked Kv1.3 channels with a K(d) of 25 pM and inhibited the proliferation of human and rat T lymphocytes with a preference for T(EM) cells, with similar potency to synthetic ShK in all assays. This expression system also enables the efficient production of ¹⁵N-labelled ShK for NMR studies of peptide dynamics and of the interaction of ShK with Kv1.3 channels. Copyright © 2012 Elsevier Ltd. All rights reserved.

Oral cancer/endothelial cell fusion experiences nuclear fusion and acquisition of enhanced survival potential.

PubMed

Song, Kai; Song, Yong; Zhao, Xiao-Ping; Shen, Hui; Wang, Meng; Yan, Ting-Lin; Liu, Ke; Shang, Zheng-Jun

2014-10-15

Most previous studies have linked cancer-macrophage fusion with tumor progression and metastasis. However, the characteristics of hybrid cells derived from oral cancer and endothelial cells and their involvement in cancer remained unknown. Double-immunofluorescent staining and fluorescent in situ hybridization (FISH) were performed to confirm spontaneous cell fusion between eGFP-labeled human umbilical vein endothelial cells (HUVECs) and RFP-labeled SCC9, and to detect the expression of vementin and cytokeratin 18 in the hybrids. The property of chemo-resistance of such hybrids was examined by TUNEL assay. The hybrid cells in xenografted tumor were identified by FISH and GFP/RFP dual-immunofluoresence staining. We showed that SCC9 cells spontaneously fused with cocultured endothelial cells, and the resultant hybrid cells maintained the division and proliferation activity after re-plating and thawing. Such hybrids expressed markers of both parental cells and became more resistant to chemotherapeutic drug cisplatin as compared to the parental SCC9 cells. Our in vivo data indicated that the hybrid cells contributed to tumor composition by using of immunostaining and FISH analysis, even though the hybrid cells and SCC9 cells were mixed with 1:10,000, according to the FACS data. Our study suggested that the fusion events between oral cancer and endothelial cells undergo nuclear fusion and acquire a new property of drug resistance and consequently enhanced survival potential. These experimental findings provide further supportive evidence for the theory that cell fusion is involved in cancer progression. Copyright © 2014 Elsevier Inc. All rights reserved.

RFP tags for labeling secretory pathway proteins

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

Han, Liyang; Zhao, Yanhua; Zhang, Xi

2014-05-09

Highlights: • Membrane protein Orai1 can be used to report the fusion properties of RFPs. • Artificial puncta are affected by dissociation constant as well as pKa of RFPs. • Among tested RFPs mOrange2 is the best choice for secretory protein labeling. - Abstract: Red fluorescent proteins (RFPs) are useful tools for live cell and multi-color imaging in biological studies. However, when labeling proteins in secretory pathway, many RFPs are prone to form artificial puncta, which may severely impede their further uses. Here we report a fast and easy method to evaluate RFPs fusion properties by attaching RFPs to anmore » environment sensitive membrane protein Orai1. In addition, we revealed that intracellular artificial puncta are actually colocalized with lysosome, thus besides monomeric properties, pKa value of RFPs is also a key factor for forming intracellular artificial puncta. In summary, our current study provides a useful guide for choosing appropriate RFP for labeling secretory membrane proteins. Among RFPs tested, mOrange2 is highly recommended based on excellent monomeric property, appropriate pKa and high brightness.« less

Neurologic impairment from ectopic bone in the lumbar canal: a potential complication of off-label PLIF/TLIF use of bone morphogenetic protein-2 (BMP-2).

PubMed

Wong, David A; Kumar, Anant; Jatana, Sanjay; Ghiselli, Gary; Wong, Katherine

2008-01-01

Bone morphogenetic protein-2 (BMP-2) (Infuse) has been approved for use in anterior lumbar fusion in conjunction with an LT cage. However, off-label use is seen with anterior cervical fusion, posterior lumbar interbody fusion (PLIF), and transforaminal lumbar interbody fusion (TLIF). The Federal Food and Drug Administration trial of BMP-2 in a PLIF application was halted because of a high incidence of ectopic bone forming in the neural canal (75%). The authors did not find a correlation between ectopic bone and increased leg pain. They concluded that the ectopic bone was a radiographic phenomenon and not associated with clinical findings. Complications using BMP in the cervical spine have been reported. Heretofore, there has not been a similar warning voiced for use of BMP in a lumbar PLIF or TLIF. The purpose was to report five cases of ectopic bone in the canal associated with PLIF/TLIF off-label use of BMP-2 potentially contributing to abnormal neurologic findings. This is an observational cohort study of patients referred to a tertiary care private medical center. This was a retrospective chart review of patients referred to a tertiary spine institute with complications after surgery where BMP-2 had been used in an off-label PLIF or TLIF application. Patient demographics, operating room (OR) notes from the index BMP surgery, imaging studies, and current clinical status were reviewed. Five cases of ectopic bone in the spinal canal with potential neurologic compromise were identified. It does appear that ectopic bone in the spinal canal associated with BMP-2 use in PLIF or TLIF may contribute to symptomatic neurologic findings in rare cases. Revision surgeries are difficult. This article challenges a previous publication, which concluded that the high incidence of ectopic bone was of no clinical significance. Isolating BMP anteriorly in the disc space using layered barriers of bone graft between the BMP and the annular defect may reduce the incidence of ectopic bone in the spinal canal. Surgeons need to weigh the benefits versus risks of any technology used off label when making treatment decisions with their patients.

G protein betagamma-subunits activated by serotonin mediate presynaptic inhibition by regulating vesicle fusion properties.

PubMed

Photowala, Huzefa; Blackmer, Trillium; Schwartz, Eric; Hamm, Heidi E; Alford, Simon

2006-03-14

Neurotransmitters are thought to be released as quanta, where synaptic vesicles deliver packets of neurotransmitter to the synaptic cleft by fusion with the plasma membrane. However, synaptic vesicles may undergo incomplete fusion. We provide evidence that G protein-coupled receptors inhibit release by causing such incomplete fusion. 5-hydroxytryptamine (5-HT) receptor signaling potently inhibits excitatory postsynaptic currents (EPSCs) between lamprey reticulospinal axons and their postsynaptic targets by a direct action on the vesicle fusion machinery. We show that 5-HT receptor-mediated presynaptic inhibition, at this synapse, involves a reduction in EPSC quantal size. Quantal size was measured directly by comparing unitary quantal amplitudes of paired EPSCs before and during 5-HT application and indirectly by determining the effect of 5-HT on the relationship between mean-evoked EPSC amplitude and variance. Results from FM dye-labeling experiments indicate that 5-HT prevents full fusion of vesicles. 5-HT reduces FM1-43 staining of vesicles with a similar efficacy to its effect on the EPSC. However, destaining of FM1-43-labeled vesicles is abolished by lower concentrations of 5-HT that leave a substantial EPSC. The use of a water-soluble membrane impermeant quenching agent in the extracellular space reduced FM1-43 fluorescence during stimulation in 5-HT. Thus vesicles contact the extracellular space during inhibition of synaptic transmission by 5-HT. We conclude that 5-HT, via free Gbetagamma, prevents the collapse of synaptic vesicles into the presynaptic membrane.

Statistically significant performance results of a mine detector and fusion algorithm from an x-band high-resolution SAR

NASA Astrophysics Data System (ADS)

Williams, Arnold C.; Pachowicz, Peter W.

2004-09-01

Current mine detection research indicates that no single sensor or single look from a sensor will detect mines/minefields in a real-time manner at a performance level suitable for a forward maneuver unit. Hence, the integrated development of detectors and fusion algorithms are of primary importance. A problem in this development process has been the evaluation of these algorithms with relatively small data sets, leading to anecdotal and frequently over trained results. These anecdotal results are often unreliable and conflicting among various sensors and algorithms. Consequently, the physical phenomena that ought to be exploited and the performance benefits of this exploitation are often ambiguous. The Army RDECOM CERDEC Night Vision Laboratory and Electron Sensors Directorate has collected large amounts of multisensor data such that statistically significant evaluations of detection and fusion algorithms can be obtained. Even with these large data sets care must be taken in algorithm design and data processing to achieve statistically significant performance results for combined detectors and fusion algorithms. This paper discusses statistically significant detection and combined multilook fusion results for the Ellipse Detector (ED) and the Piecewise Level Fusion Algorithm (PLFA). These statistically significant performance results are characterized by ROC curves that have been obtained through processing this multilook data for the high resolution SAR data of the Veridian X-Band radar. We discuss the implications of these results on mine detection and the importance of statistical significance, sample size, ground truth, and algorithm design in performance evaluation.

Programming Post-Translational Control over the Metabolic Labeling of Cellular Proteins with a Noncanonical Amino Acid.

PubMed

Thomas, Emily E; Pandey, Naresh; Knudsen, Sarah; Ball, Zachary T; Silberg, Jonathan J

2017-08-18

Transcriptional control can be used to program cells to label proteins with noncanonical amino acids by regulating the expression of orthogonal aminoacyl tRNA synthetases (aaRSs). However, we cannot yet program cells to control labeling in response to aaRS and ligand binding. To identify aaRSs whose activities can be regulated by interactions with ligands, we used a combinatorial approach to discover fragmented variants of Escherichia coli methionyl tRNA synthetase (MetRS) that require fusion to associating proteins for maximal activity. We found that these split proteins could be leveraged to create ligand-dependent MetRS using two approaches. When a pair of MetRS fragments was fused to FKBP12 and the FKBP-rapamycin binding domain (FRB) of mTOR and mutations were introduced that direct substrate specificity toward azidonorleucine (Anl), Anl metabolic labeling was significantly enhanced in growth medium containing rapamycin, which stabilizes the FKBP12-FRB complex. In addition, fusion of MetRS fragments to the termini of the ligand-binding domain of the estrogen receptor yielded proteins whose Anl metabolic labeling was significantly enhanced when 4-hydroxytamoxifen (4-HT) was added to the growth medium. These findings suggest that split MetRS can be fused to a range of ligand-binding proteins to create aaRSs whose metabolic labeling activities depend upon post-translational interactions with ligands.

Adjoint affine fusion and tadpoles

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

Urichuk, Andrew, E-mail: andrew.urichuk@uleth.ca; Walton, Mark A., E-mail: walton@uleth.ca; International School for Advanced Studies

2016-06-15

We study affine fusion with the adjoint representation. For simple Lie algebras, elementary and universal formulas determine the decomposition of a tensor product of an integrable highest-weight representation with the adjoint representation. Using the (refined) affine depth rule, we prove that equally striking results apply to adjoint affine fusion. For diagonal fusion, a coefficient equals the number of nonzero Dynkin labels of the relevant affine highest weight, minus 1. A nice lattice-polytope interpretation follows and allows the straightforward calculation of the genus-1 1-point adjoint Verlinde dimension, the adjoint affine fusion tadpole. Explicit formulas, (piecewise) polynomial in the level, are writtenmore » for the adjoint tadpoles of all classical Lie algebras. We show that off-diagonal adjoint affine fusion is obtained from the corresponding tensor product by simply dropping non-dominant representations.« less

Oral cancer/endothelial cell fusion experiences nuclear fusion and acquisition of enhanced survival potential

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

Song, Kai; The State Key Laboratory Breeding Base of Basic Science of Stomatology; Song, Yong

Most previous studies have linked cancer–macrophage fusion with tumor progression and metastasis. However, the characteristics of hybrid cells derived from oral cancer and endothelial cells and their involvement in cancer remained unknown. Double-immunofluorescent staining and fluorescent in situ hybridization (FISH) were performed to confirm spontaneous cell fusion between eGFP-labeled human umbilical vein endothelial cells (HUVECs) and RFP-labeled SCC9, and to detect the expression of vementin and cytokeratin 18 in the hybrids. The property of chemo-resistance of such hybrids was examined by TUNEL assay. The hybrid cells in xenografted tumor were identified by FISH and GFP/RFP dual-immunofluoresence staining. We showed thatmore » SCC9 cells spontaneously fused with cocultured endothelial cells, and the resultant hybrid cells maintained the division and proliferation activity after re-plating and thawing. Such hybrids expressed markers of both parental cells and became more resistant to chemotherapeutic drug cisplatin as compared to the parental SCC9 cells. Our in vivo data indicated that the hybrid cells contributed to tumor composition by using of immunostaining and FISH analysis, even though the hybrid cells and SCC9 cells were mixed with 1:10,000, according to the FACS data. Our study suggested that the fusion events between oral cancer and endothelial cells undergo nuclear fusion and acquire a new property of drug resistance and consequently enhanced survival potential. These experimental findings provide further supportive evidence for the theory that cell fusion is involved in cancer progression. - Highlights: • The fusion events between oral cancer and endothelial cells undergo nuclear fusion. • The resulting hybrid cells acquire a new property of drug resistance. • The resulting hybrid cells express the markers of both parental cells (i.e. vimentin and cytokeratin 18). • The hybrid cells contribute to tumor repopulation in vivo.« less

Fluorescent protein-tagged Vpr dissociates from HIV-1 core after viral fusion and rapidly enters the cell nucleus.

PubMed

Desai, Tanay M; Marin, Mariana; Sood, Chetan; Shi, Jiong; Nawaz, Fatima; Aiken, Christopher; Melikyan, Gregory B

2015-10-29

HIV-1 Vpr is recruited into virions during assembly and appears to remain associated with the viral core after the reverse transcription and uncoating steps of entry. This feature has prompted the use of fluorescently labeled Vpr to visualize viral particles and to follow trafficking of post-fusion HIV-1 cores in the cytoplasm. Here, we tracked single pseudovirus entry and fusion and observed that fluorescently tagged Vpr gradually dissociates from post-fusion viral cores over the course of several minutes and accumulates in the nucleus. Kinetics measurements showed that fluorescent Vpr released from the cores very rapidly entered the cell nucleus. More than 10,000 Vpr molecules can be delivered into the cell nucleus within 45 min of infection by HIV-1 particles pseudotyped with the avian sarcoma and leukosis virus envelope glycoprotein. The fraction of Vpr from cell-bound viruses that accumulated in the nucleus was proportional to the extent of virus-cell fusion and was fully blocked by viral fusion inhibitors. Entry of virus-derived Vpr into the nucleus occurred independently of envelope glycoproteins or target cells. Fluorescence correlation spectroscopy revealed two forms of nuclear Vpr-monomers and very large complexes, likely involving host factors. The kinetics of viral Vpr entering the nucleus after fusion was not affected by point mutations in the capsid protein that alter the stability of the viral core. The independence of Vpr shedding of capsid stability and its relatively rapid dissociation from post-fusion cores suggest that this process may precede capsid uncoating, which appears to occur on a slower time scale. Our results thus demonstrate that a bulk of fluorescently labeled Vpr incorporated into HIV-1 particles is released shortly after fusion. Future studies will address the question whether the quick and efficient nuclear delivery of Vpr derived from incoming viruses can regulate subsequent steps of HIV-1 infection.

Membrane-spanning lipids for an uncompromised monitoring of membrane fusion and intermembrane lipid transfer.

PubMed

Schwarzmann, Günter; Breiden, Bernadette; Sandhoff, Konrad

2015-10-01

A Förster resonance energy transfer-based fusion and transfer assay was developed to study, in model membranes, protein-mediated membrane fusion and intermembrane lipid transfer of fluorescent sphingolipid analogs. For this assay, it became necessary to apply labeled reporter molecules that are resistant to spontaneous as well as protein-mediated intermembrane transfer. The novelty of this assay is the use of nonextractable fluorescent membrane-spanning bipolar lipids. Starting from the tetraether lipid caldarchaeol, we synthesized fluorescent analogs with fluorophores at both polar ends. In addition, we synthesized radioactive glycosylated caldarchaeols. These labeled lipids were shown to stretch through bilayer membranes rather than to loop within a single lipid layer of liposomes. More important, the membrane-spanning lipids (MSLs) in contrast to phosphoglycerides proved to be nonextractable by proteins. We could show that the GM2 activator protein (GM2AP) is promiscuous with respect to glycero- and sphingolipid transfer. Saposin (Sap) B also transferred sphingolipids albeit with kinetics different from GM2AP. In addition, we could unambiguously show that the recombinant activator protein Sap C x His6 induced membrane fusion rather than intermembrane lipid transfer. These findings showed that these novel MSLs, in contrast with fluorescent phosphoglycerolipids, are well suited for an uncompromised monitoring of membrane fusion and intermembrane lipid transfer. Copyright © 2015 by the American Society for Biochemistry and Molecular Biology, Inc.

Enhancing vector shoreline data using a data fusion approach

NASA Astrophysics Data System (ADS)

Carlotto, Mark; Nebrich, Mark; DeMichele, David

2017-05-01

Vector shoreline (VSL) data is potentially useful in ATR systems that distinguish between objects on land or water. Unfortunately available data such as the NOAA 1:250,000 World Vector Shoreline and NGA Prototype Global Shoreline data cannot be used by themselves to make a land/water determination because of the manner in which the data are compiled. We describe a data fusion approach for creating labeled VSL data using test points from Global 30 Arc-Second Elevation (GTOPO30) data to determine the direction of vector segments; i.e., whether they are in clockwise or counterclockwise order. We show consistently labeled VSL data be used to easily determine whether a point is on land or water using a vector cross product test.

Multiclassifier fusion in human brain MR segmentation: modelling convergence.

PubMed

Heckemann, Rolf A; Hajnal, Joseph V; Aljabar, Paul; Rueckert, Daniel; Hammers, Alexander

2006-01-01

Segmentations of MR images of the human brain can be generated by propagating an existing atlas label volume to the target image. By fusing multiple propagated label volumes, the segmentation can be improved. We developed a model that predicts the improvement of labelling accuracy and precision based on the number of segmentations used as input. Using a cross-validation study on brain image data as well as numerical simulations, we verified the model. Fit parameters of this model are potential indicators of the quality of a given label propagation method or the consistency of the input segmentations used.

Construction and Analysis of High-Ethanol-Producing Fusants with Co-Fermentation Ability through Protoplast Fusion and Double Labeling Technology

PubMed Central

Ge, Jingping; Zhao, Jingwen; Zhang, Luyan; Zhang, Mengyun; Ping, Wenxiang

2014-01-01

Double labeling of resistance markers and report genes can be used to breed engineered Saccharomyces cerevisiae strains that can assimilate xylose and glucose as a mixed carbon source for ethanol fermentation and increased ethanol production. In this study Saccharomyces cerevisiae W5 and Candida shehatae 20335 were used as parent strains to conduct protoplast fusion and the resulting fusants were screened by double labeling. High performance liquid chromatography (HPLC) was used to assess the ethanol yield following the fermentation of xylose and glucose, as both single and mixed carbon sources, by the fusants. Interestingly, one fusant (ZLYRHZ7) was demonstrated to have an excellent fermentation performance, with an ethanol yield using the mixed carbon source of 0.424 g g−1, which compares with 0.240 g g−1 (W5) and 0.353 g g−1 (20335) for the parent strains. This indicates an improvement in the ethanol yield of 43.4% and 16.7%, respectively. PMID:25268957

Antigen Binding and Site-Directed Labeling of Biosilica-Immobilized Fusion Proteins Expressed in Diatoms

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

Ford, Nicole R.; Hecht, Karen A.; Hu, Dehong

2016-01-08

The diatom Thalassiosira pseudonana was genetically modified to express biosilica-targeted fusion proteins incorporating a tetracysteine tag for site-directed labeling with biarsenical affinity probes and either EGFP or single chain antibody to test colocalization of probes with the EGFP-tagged recombinant protein or binding of biosilica-immobilized antibodies to large and small molecule antigens, respectively. Site-directed labeling with the biarsenical probes demonstrated colocalization with EGFP-encoded proteins in nascent and mature biosilica, supporting their use in studying biosilica maturation. Isolated biosilica transformed with a single chain antibody against either the Bacillus anthracis surface layer protein EA1 or small molecule explosive trinitrotoluene (TNT) effectively boundmore » the respective antigens. A marked increase in fluorescence lifetime of the TNT surrogate Alexa Fluor 555-trinitrobenzene reflected the high binding specificity of the transformed isolated biosilica. These results demonstrated the potential use of biosilica-immobilized single chain antibodies as binders for large and small molecule antigens in sensing and therapeutics.« less

Construction and analysis of high-ethanol-producing fusants with co-fermentation ability through protoplast fusion and double labeling technology.

PubMed

Ge, Jingping; Zhao, Jingwen; Zhang, Luyan; Zhang, Mengyun; Ping, Wenxiang

2014-01-01

Double labeling of resistance markers and report genes can be used to breed engineered Saccharomyces cerevisiae strains that can assimilate xylose and glucose as a mixed carbon source for ethanol fermentation and increased ethanol production. In this study Saccharomyces cerevisiae W5 and Candida shehatae 20335 were used as parent strains to conduct protoplast fusion and the resulting fusants were screened by double labeling. High performance liquid chromatography (HPLC) was used to assess the ethanol yield following the fermentation of xylose and glucose, as both single and mixed carbon sources, by the fusants. Interestingly, one fusant (ZLYRHZ7) was demonstrated to have an excellent fermentation performance, with an ethanol yield using the mixed carbon source of 0.424 g g-1, which compares with 0.240 g g-1 (W5) and 0.353 g g-1 (20335) for the parent strains. This indicates an improvement in the ethanol yield of 43.4% and 16.7%, respectively.

The biomechanics of a multilevel lumbar spine hybrid using nucleus replacement in conjunction with fusion.

PubMed

Dahl, Michael C; Ellingson, Arin M; Mehta, Hitesh P; Huelman, Justin H; Nuckley, David J

2013-02-01

Degenerative disc disease is commonly a multilevel pathology with varying deterioration severity. The use of fusion on multiple levels can significantly affect functionality and has been linked to persistent adjacent disc degeneration. A hybrid approach of fusion and nucleus replacement (NR) has been suggested as a solution for mildly degenerated yet painful levels adjacent to fusion. To compare the biomechanical metrics of different hybrid implant constructs, hypothesizing that an NR+fusion hybrid would be similar to a single-level fusion and perform more naturally compared with a two-level fusion. A cadaveric in vitro repeated-measures study was performed to evaluate a multilevel lumbar NR+fusion hybrid. Eight cadaveric spines (L3-S1) were tested in a Spine Kinetic Simulator (Instron, Norwood, MA, USA). Pure moments of 8 Nm were applied in flexion/extension, lateral bending, and axial rotation as well as compression loading. Specimens were tested intact; fused (using transforaminal lumbar interbody fusion instrumentation with posterior rods) at L5-S1; with a nuclectomy at L4-L5 including fusion at L5-S1; with NR at L4-L5 including fusion at L5-S1; and finally with a two-level fusion spanning L4-S1. Repeated-measures analysis of variance and corrected t tests were used to statistically compare outcomes. The NR+fusion hybrid and single-level fusion exhibited no statistical differences for range of motion (ROM), stiffness, neutral zone, and intradiscal pressure in all loading directions. Compared with two-level fusion, the hybrid affords the construct 41.9% more ROM on average. Two-level fusion stiffness was statistically higher than all other constructs and resulted in significantly lower ROM in flexion, extension, and lateral bending. The hybrid construct produced approximately half of the L3-L4 adjacent-level pressures as the two-level fusion case while generating similar pressures to the single-level fusion case. These data portend more natural functional outcomes and fewer adjacent disc complications for a multilevel NR+fusion hybrid compared with the classical two-level fusion. Copyright © 2013 Elsevier Inc. All rights reserved.

Green fluorescent protein fusions to Arabidopsis fimbrin 1 for spatio-temporal imaging of F-actin dynamics in roots.

PubMed

Wang, Yuh-Shuh; Motes, Christy M; Mohamalawari, Deepti R; Blancaflor, Elison B

2004-10-01

The visualization of green fluorescent protein (GFP) fusions with microtubule or actin filament (F-actin) binding proteins has provided new insights into the function of the cytoskeleton during plant development. For studies on actin, GFP fusions to talin have been the most generally used reporters. Although GFP-Talin has allowed in vivo F-actin imaging in a variety of plant cells, its utility in monitoring F-actin in stably transformed plants is limited particularly in developing roots where interesting actin dependent cell processes are occurring. In this study, we created a variety of GFP fusions to Arabidopsis Fimbrin 1 (AtFim1) to explore their utility for in vivo F-actin imaging in root cells and to better understand the actin binding properties of AtFim1 in living plant cells. Translational fusions of GFP to full-length AtFim1 or to some truncated variants of AtFim1 showed filamentous labeling in transient expression assays. One truncated fimbrin-GFP fusion was capable of labeling distinct filaments in stably transformed Arabidopsis roots. The filaments decorated by this construct were highly dynamic in growing root hairs and elongating root cells and were sensitive to actin disrupting drugs. Therefore, the fimbrin-GFP reporters we describe in this study provide additional tools for studying the actin cytoskeleton during root cell development. Moreover, the localization of AtFim1-GFP offers insights into the regulation of actin organization in developing roots by this class of actin cross-linking proteins. Copyright 2004 Wiley-Liss, Inc.

Bidirectional Fusion of the Heart-forming Fields in the Developing Chick Embryo

PubMed Central

Moreno-Rodriguez, R.A.; Krug, E.L.; Reyes, L.; Villavicencio, L.; Mjaatvedt, C.H.; Markwald, R.R.

2007-01-01

It is generally thought that the early pre-tubular chick heart is formed by fusion of the anterior or cephalic limits of the paired cardiogenic fields. However, this study shows that the heart fields initially fuse at their midpoint to form a transitory “butterfly”-shaped, cardiogenic structure. Fusion then progresses bi-directionally along the longitudinal axis in both cranial and caudal directions. Using in vivo labeling, we demonstrate that cells along the ventral fusion line are highly motile, crossing future primitive segments. We found that mesoderm cells migrated cephalically from the unfused tips of the anterior/cephalic wings into the head mesenchyme in the region that has been called the secondary heart field. Perturbing the anterior/cranial fusion results in formation of a biconal heart. A theoretical role of the ventral fusion line acting as a “heart organizer” and its role in cardia bifida is discussed. PMID:16252277

Site-specific labeling of proteins by using biotin protein ligase conjugated with fluorophores.

PubMed

Sueda, Shinji; Yoneda, Sawako; Hayashi, Hideki

2011-06-14

Biotin protein ligase (BPL) mediates the covalent attachment of biotin to a specific lysine residue of biotin carboxyl carrier protein (BCCP). This biotinylation in Sulfolobus tokodaii is unique in that BPL forms a tight complex with the product, biotinylated BCCP, and this property was exploited for fluorescent labeling of a membrane protein. Thus, the truncated form of BCCP (BCCPΔ100, 69 residues) was fused to either the N or C terminus of the bradykinin B2 receptor (B2R). The resulting fusion proteins, BCCPΔ100-B2R and B2R-BCCPΔ100, respectively, were separately expressed in mammalian HEK293 cells, and labeled with BPL conjugated with a fluorophore: either fluorescein, DyLight549 or green fluorescent protein. The fusion proteins were biotinylated and bound to BPL, thereby giving rise to strong fluorescence along the periphery of the cell. Some were capable of binding bradykinin and an antagonist. When stimulated with the former, the receptor translocated to the cytosol; this suggests that the labeled receptor retains its integrity in terms of ligand-binding and translocation. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

pH-induced conformational changes of AcrA, the membrane fusion protein of Escherichia coli multidrug efflux system.

PubMed

Ip, Hermia; Stratton, Kelly; Zgurskaya, Helen; Liu, Jun

2003-12-12

The multidrug efflux system AcrA-AcrB-TolC of Escherichia coli expels a wide range of drugs directly into the external medium from the bacterial cell. The mechanism of the efflux process is not fully understood. Of an elongated shape, AcrA is thought to span the periplasmic space coordinating the concerted operation of the inner and outer membrane proteins AcrB and TolC. In this study, we used site-directed spin labeling (SDSL) EPR (electron paramagnetic resonance) spectroscopy to investigate the molecular conformations of AcrA in solution. Ten AcrA mutants, each with an alanine to cysteine substitution, were engineered, purified, and labeled with a nitroxide spin label. EPR analysis of spin-labeled AcrA variants indicates that the side chain mobilities are consistent with the predicted secondary structure of AcrA. We further demonstrated that acidic pH induces oligomerization and conformational change of AcrA, and that the structural changes are reversible. These results suggest that the mechanism of action of AcrA in drug efflux is similar to the viral membrane fusion proteins, and that AcrA actively mediates the efflux of substrates.

Fusion peptide of influenza hemagglutinin requires a fixed angle boomerang structure for activity.

PubMed

Lai, Alex L; Park, Heather; White, Judith M; Tamm, Lukas K

2006-03-03

The fusion peptide of influenza hemagglutinin is crucial for cell entry of this virus. Previous studies showed that this peptide adopts a boomerang-shaped structure in lipid model membranes at the pH of membrane fusion. To examine the role of the boomerang in fusion, we changed several residues proposed to stabilize the kink in this structure and measured fusion. Among these, mutants E11A and W14A expressed hemagglutinins with hemifusion and no fusion activities, and F9A and N12A had no effect on fusion, respectively. Binding enthalpies and free energies of mutant peptides to model membranes and their ability to perturb lipid bilayer structures correlated well with the fusion activities of the parent full-length molecules. The structure of W14A determined by NMR and site-directed spin labeling features a flexible kink that points out of the membrane, in sharp contrast to the more ordered boomerang of the wild-type, which points into the membrane. A specific fixed angle boomerang structure is thus required to support membrane fusion.

Trafficking of astrocytic vesicles in hippocampal slices

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

Potokar, Maja; Kreft, Marko; Celica Biomedical Center, Technology Park 24, 1000 Ljubljana

2009-12-25

The increasingly appreciated role of astrocytes in neurophysiology dictates a thorough understanding of the mechanisms underlying the communication between astrocytes and neurons. In particular, the uptake and release of signaling substances into/from astrocytes is considered as crucial. The release of different gliotransmitters involves regulated exocytosis, consisting of the fusion between the vesicle and the plasma membranes. After fusion with the plasma membrane vesicles may be retrieved into the cytoplasm and may continue to recycle. To study the mobility implicated in the retrieval of secretory vesicles, these structures have been previously efficiently and specifically labeled in cultured astrocytes, by exposing livemore » cells to primary and secondary antibodies. Since the vesicle labeling and the vesicle mobility properties may be an artifact of cell culture conditions, we here asked whether the retrieving exocytotic vesicles can be labeled in brain tissue slices and whether their mobility differs to that observed in cell cultures. We labeled astrocytic vesicles and recorded their mobility with two-photon microscopy in hippocampal slices from transgenic mice with fluorescently tagged astrocytes (GFP mice) and in wild-type mice with astrocytes labeled by Fluo4 fluorescence indicator. Glutamatergic vesicles and peptidergic granules were labeled by the anti-vesicular glutamate transporter 1 (vGlut1) and anti-atrial natriuretic peptide (ANP) antibodies, respectively. We report that the vesicle mobility parameters (velocity, maximal displacement and track length) recorded in astrocytes from tissue slices are similar to those reported previously in cultured astrocytes.« less

Cell-penetrating anti-GFAP VHH and corresponding fluorescent fusion protein VHH-GFP spontaneously cross the blood-brain barrier and specifically recognize astrocytes: application to brain imaging.

PubMed

Li, Tengfei; Bourgeois, Jean-Pierre; Celli, Susanna; Glacial, Fabienne; Le Sourd, Anne-Marie; Mecheri, Salah; Weksler, Babette; Romero, Ignacio; Couraud, Pierre-Olivier; Rougeon, François; Lafaye, Pierre

2012-10-01

Antibodies normally do not cross the blood-brain barrier (BBB) and cannot bind an intracellular cerebral antigen. We demonstrate here for the first time that a new class of antibodies can cross the BBB without treatment. Camelids produce native homodimeric heavy-chain antibodies, the paratope being composed of a single-variable domain called VHH. Here, we used recombinant VHH directed against human glial fibrillary acidic protein (GFAP), a specific marker of astrocytes. Only basic VHHs (e.g., pI=9.4) were able to cross the BBB in vitro (7.8 vs. 0% for VHH with pI=7.7). By intracarotid and intravenous injections into live mice, we showed that these basic VHHs are able to cross the BBB in vivo, diffuse into the brain tissue, penetrate into astrocytes, and specifically label GFAP. To analyze their ability to be used as a specific transporter, we then expressed a recombinant fusion protein VHH-green fluorescent protein (GFP). These "fluobodies" specifically labeled GFAP on murine brain sections, and a basic variant (pI=9.3) of the fusion protein VHH-GFP was able to cross the BBB and to label astrocytes in vivo. The potential of VHHs as diagnostic or therapeutic agents in the central nervous system now deserves attention.

Multi-atlas and label fusion approach for patient-specific MRI based skull estimation.

PubMed

Torrado-Carvajal, Angel; Herraiz, Joaquin L; Hernandez-Tamames, Juan A; San Jose-Estepar, Raul; Eryaman, Yigitcan; Rozenholc, Yves; Adalsteinsson, Elfar; Wald, Lawrence L; Malpica, Norberto

2016-04-01

MRI-based skull segmentation is a useful procedure for many imaging applications. This study describes a methodology for automatic segmentation of the complete skull from a single T1-weighted volume. The skull is estimated using a multi-atlas segmentation approach. Using a whole head computed tomography (CT) scan database, the skull in a new MRI volume is detected by nonrigid image registration of the volume to every CT, and combination of the individual segmentations by label-fusion. We have compared Majority Voting, Simultaneous Truth and Performance Level Estimation (STAPLE), Shape Based Averaging (SBA), and the Selective and Iterative Method for Performance Level Estimation (SIMPLE) algorithms. The pipeline has been evaluated quantitatively using images from the Retrospective Image Registration Evaluation database (reaching an overlap of 72.46 ± 6.99%), a clinical CT-MR dataset (maximum overlap of 78.31 ± 6.97%), and a whole head CT-MRI pair (maximum overlap 78.68%). A qualitative evaluation has also been performed on MRI acquisition of volunteers. It is possible to automatically segment the complete skull from MRI data using a multi-atlas and label fusion approach. This will allow the creation of complete MRI-based tissue models that can be used in electromagnetic dosimetry applications and attenuation correction in PET/MR. © 2015 Wiley Periodicals, Inc.

Light- and transmission-electron-microscopic investigations on distribution of CD44, connexin 43 and actin cytoskeleton during the foreign body reaction to a nanoparticular hydroxyapatite in mini-pigs.

PubMed

Wenisch, Sabine; Cavalcanti-Adam, E Ada; Tryankowski, Eva; Raabe, Oksana; Kilian, Olaf; Heiss, Christian; Alt, Volker; Arnhold, Stefan; Schnettler, Reinhard

2012-07-01

Foreign body giant cells (FBGCs) are formed by fusion of mononucleated macrophages during the foreign body response to a nanoparticulate hydroxyapatite (HA) implanted in defects of mini-pig femura. The molecular mechanisms underlying the formation of FBGCs are still largely obscure. Here we propose connexin 43 (cx43) and CD44 as candidate molecules involved in the fusion process. Immunohistochemistry and ultrastructural immunogold labeling indicated that cx43 is present within the ruffled border of FBGCs and is the main component of gap junctions formed between fusing macrophages. CD44 was strongly expressed during clustering and fusion of mononucleated macrophages. FBGCs adhering apically at the implanted HA showed CD44 reactivity only along the basolateral aspects of the plasma membranes, while podosome formation was observed within the sealing zone and ruffled border. Taken together, these findings demonstrate that cx43 and CD44 are part of the fusion machinery responsible for the formation of FBGCs. Furthermore, the results of microfilament and cx43 labeling suggest a functional role for podosomes and hemi-channels in biomaterial degradation. Copyright © 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Sea Ice Concentration Estimation Using Active and Passive Remote Sensing Data Fusion

NASA Astrophysics Data System (ADS)

Zhang, Y.; Li, F.; Zhang, S.; Zhu, T.

2017-12-01

In this abstract, a decision-level fusion method by utilizing SAR and passive microwave remote sensing data for sea ice concentration estimation is investigated. Sea ice concentration product from passive microwave concentration retrieval methods has large uncertainty within thin ice zone. Passive microwave data including SSM/I, AMSR-E, and AMSR-2 provide daily and long time series observations covering whole polar sea ice scene, and SAR images provide rich sea ice details with high spatial resolution including deformation and polarimetric features. In the proposed method, the merits from passive microwave data and SAR data are considered. Sea ice concentration products from ASI and sea ice category label derived from CRF framework in SAR imagery are calibrated under least distance protocol. For SAR imagery, incident angle and azimuth angle were used to correct backscattering values from slant range to ground range in order to improve geocoding accuracy. The posterior probability distribution between category label from SAR imagery and passive microwave sea ice concentration product is modeled and integrated under Bayesian network, where Gaussian statistical distribution from ASI sea ice concentration products serves as the prior term, which represented as an uncertainty of sea ice concentration. Empirical model based likelihood term is constructed under Bernoulli theory, which meets the non-negative and monotonically increasing conditions. In the posterior probability estimation procedure, final sea ice concentration is obtained using MAP criterion, which equals to minimize the cost function and it can be calculated with nonlinear iteration method. The proposed algorithm is tested on multiple satellite SAR data sets including GF-3, Sentinel-1A, RADARSAT-2 and Envisat ASAR. Results show that the proposed algorithm can improve the accuracy of ASI sea ice concentration products and reduce the uncertainty along the ice edge.

3D-SIFT-Flow for atlas-based CT liver image segmentation

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

Xu, Yan, E-mail: xuyan04@gmail.com; Xu, Chenchao, E-mail: chenchaoxu33@gmail.com; Kuang, Xiao, E-mail: kuangxiao.ace@gmail.com

Purpose: In this paper, the authors proposed a new 3D registration algorithm, 3D-scale invariant feature transform (SIFT)-Flow, for multiatlas-based liver segmentation in computed tomography (CT) images. Methods: In the registration work, the authors developed a new registration method that takes advantage of dense correspondence using the informative and robust SIFT feature. The authors computed the dense SIFT features for the source image and the target image and designed an objective function to obtain the correspondence between these two images. Labeling of the source image was then mapped to the target image according to the former correspondence, resulting in accurate segmentation.more » In the fusion work, the 2D-based nonparametric label transfer method was extended to 3D for fusing the registered 3D atlases. Results: Compared with existing registration algorithms, 3D-SIFT-Flow has its particular advantage in matching anatomical structures (such as the liver) that observe large variation/deformation. The authors observed consistent improvement over widely adopted state-of-the-art registration methods such as ELASTIX, ANTS, and multiatlas fusion methods such as joint label fusion. Experimental results of liver segmentation on the MICCAI 2007 Grand Challenge are encouraging, e.g., Dice overlap ratio 96.27% ± 0.96% by our method compared with the previous state-of-the-art result of 94.90% ± 2.86%. Conclusions: Experimental results show that 3D-SIFT-Flow is robust for segmenting the liver from CT images, which has large tissue deformation and blurry boundary, and 3D label transfer is effective and efficient for improving the registration accuracy.« less

Selective cell-surface labeling of the molecular motor protein prestin

PubMed Central

McGuire, Ryan M.; Silberg, Jonathan J.; Pereira, Fred A.; Raphael, Robert M.

2011-01-01

Prestin, a multipass transmembrane protein whose N- an C-termini are localized to the cytoplasm, must be trafficked to the plasma membrane to fulfill its cellular function as a molecular motor. One challenge in studying prestin sequence-function relationships within living cells is separating the effects of amino acid substitutions on prestin trafficking, plasma membrane localization and function. To develop an approach for directly assessing prestin levels at the plasma membrane, we have investigated whether fusion of prestin to a single pass transmembrane protein results in a functional fusion protein with a surface-exposed N-terminal tag that can be detected in living cells. We find that fusion of the biotin-acceptor peptide (BAP) and transmembrane domain of the platelet-derived growth factor receptor (PDGFR) to the N-terminus of prestin-GFP yields a membrane protein that can be metabolically-labeled with biotin, trafficked to the plasma membrane, and selectively detected at the plasma membrane using fluorescently-tagged streptavidin. Furthermore, we show that the addition of a surface detectable tag and a single-pass transmembrane domain to prestin does not disrupt its voltage-sensitive activity. PMID:21651892

Learning Object Names at Different Hierarchical Levels Using Cross-Situational Statistics.

PubMed

Chen, Chi-Hsin; Zhang, Yayun; Yu, Chen

2018-05-01

Objects in the world usually have names at different hierarchical levels (e.g., beagle, dog, animal). This research investigates adults' ability to use cross-situational statistics to simultaneously learn object labels at individual and category levels. The results revealed that adults were able to use co-occurrence information to learn hierarchical labels in contexts where the labels for individual objects and labels for categories were presented in completely separated blocks, in interleaved blocks, or mixed in the same trial. Temporal presentation schedules significantly affected the learning of individual object labels, but not the learning of category labels. Learners' subsequent generalization of category labels indicated sensitivity to the structure of statistical input. Copyright © 2017 Cognitive Science Society, Inc.

Weber-aware weighted mutual information evaluation for infrared-visible image fusion

NASA Astrophysics Data System (ADS)

Luo, Xiaoyan; Wang, Shining; Yuan, Ding

2016-10-01

A performance metric for infrared and visible image fusion is proposed based on Weber's law. To indicate the stimulus of source images, two Weber components are provided. One is differential excitation to reflect the spectral signal of visible and infrared images, and the other is orientation to capture the scene structure feature. By comparing the corresponding Weber component in infrared and visible images, the source pixels can be marked with different dominant properties in intensity or structure. If the pixels have the same dominant property label, the pixels are grouped to calculate the mutual information (MI) on the corresponding Weber components between dominant source and fused images. Then, the final fusion metric is obtained via weighting the group-wise MI values according to the number of pixels in different groups. Experimental results demonstrate that the proposed metric performs well on popular image fusion cases and outperforms other image fusion metrics.

Visualization of Content Release from Cell Surface-Attached Single HIV-1 Particles Carrying an Extra-Viral Fluorescent pH-Sensor.

PubMed

Sood, Chetan; Marin, Mariana; Mason, Caleb S; Melikyan, Gregory B

2016-01-01

HIV-1 fusion leading to productive entry has long been thought to occur at the plasma membrane. However, our previous single virus imaging data imply that, after Env engagement of CD4 and coreceptors at the cell surface, the virus enters into and fuses with intracellular compartments. We were unable to reliably detect viral fusion at the plasma membrane. Here, we implement a novel virus labeling strategy that biases towards detection of virus fusion that occurs in a pH-neutral environment-at the plasma membrane or, possibly, in early pH-neutral vesicles. Virus particles are co-labeled with an intra-viral content marker, which is released upon fusion, and an extra-viral pH sensor consisting of ecliptic pHluorin fused to the transmembrane domain of ICAM-1. This sensor fully quenches upon virus trafficking to a mildly acidic compartment, thus precluding subsequent detection of viral content release. As an interesting secondary observation, the incorporation of the pH-sensor revealed that HIV-1 particles occasionally shuttle between neutral and acidic compartments in target cells expressing CD4, suggesting a small fraction of viral particles is recycled to the plasma membrane and re-internalized. By imaging viruses bound to living cells, we found that HIV-1 content release in neutral-pH environment was a rare event (~0.4% particles). Surprisingly, viral content release was not significantly reduced by fusion inhibitors, implying that content release was due to spontaneous formation of viral membrane defects occurring at the cell surface. We did not measure a significant occurrence of HIV-1 fusion at neutral pH above this defect-mediated background loss of content, suggesting that the pH sensor may destabilize the membrane of the HIV-1 pseudovirus and, thus, preclude reliable detection of single virus fusion events at neutral pH.

StarD7 behaves as a fusogenic protein in model and cell membrane bilayers.

PubMed

Angeletti, Sofía; Sanchez, Julieta M; Chamley, Larry W; Genti-Raimondi, Susana; Perillo, María A

2012-03-01

StarD7 is a surface active protein, structurally related with the START lipid transport family. So, the present work was aimed at elucidating a potential mechanism of action for StarD7 that could be related to its interaction with a lipid-membrane interface. We applied an assay based on the fluorescence de-quenching of BD-HPC-labeled DMPC-DMPS 4:1 mol/mol SUVs (donor liposomes) induced by the dilution with non-labeled DMPC-DMPS 4:1 mol/mol LUVs (acceptor liposomes). Recombinant StarD7 accelerated the dilution of BD-HPC in a concentration-dependent manner. This result could have been explained by either a bilayer fusion or monomeric transport of the labeled lipid between donor and acceptor liposomes. Further experiments (fluorescence energy transfer between DPH-HPC/BD-HPC, liposome size distribution analysis by dynamic light scattering, and the multinuclear giant cell formation induced by recombinant StarD7) strongly indicated that bilayer fusion was the mechanism responsible for the StarD7-induced lipid dilution. The efficiency of lipid dilution was dependent on StarD7 electrostatic interactions with the lipid-water interface, as shown by the pH- and salt-induced modulation. Moreover, this process was favored by phosphatidylethanolamine which is known to stabilize non-lamellar phases considered as intermediary in the fusion process. Altogether these findings allow postulate StarD7 as a fusogenic protein. Copyright © 2011 Elsevier B.V. All rights reserved.

BiFCROS: A Low-Background Fluorescence Repressor Operator System for Labeling of Genomic Loci.

PubMed

Milbredt, Sarah; Waldminghaus, Torsten

2017-06-07

Fluorescence-based methods are widely used to analyze elementary cell processes such as DNA replication or chromosomal folding and segregation. Labeling DNA with a fluorescent protein allows the visualization of its temporal and spatial organization. One popular approach is FROS (fluorescence repressor operator system). This method specifically labels DNA in vivo through binding of a fusion of a fluorescent protein and a repressor protein to an operator array, which contains numerous copies of the repressor binding site integrated into the genomic site of interest. Bound fluorescent proteins are then visible as foci in microscopic analyses and can be distinguished from the background fluorescence caused by unbound fusion proteins. Even though this method is widely used, no attempt has been made so far to decrease the background fluorescence to facilitate analysis of the actual signal of interest. Here, we present a new method that greatly reduces the background signal of FROS. BiFCROS (Bimolecular Fluorescence Complementation and Repressor Operator System) is based on fusions of repressor proteins to halves of a split fluorescent protein. Binding to a hybrid FROS array results in fluorescence signals due to bimolecular fluorescence complementation. Only proteins bound to the hybrid FROS array fluoresce, greatly improving the signal to noise ratio compared to conventional FROS. We present the development of BiFCROS and discuss its potential to be used as a fast and single-cell readout for copy numbers of genetic loci. Copyright © 2017 Milbredt and Waldminghaus.

BiFCROS: A Low-Background Fluorescence Repressor Operator System for Labeling of Genomic Loci

PubMed Central

Milbredt, Sarah; Waldminghaus, Torsten

2017-01-01

Fluorescence-based methods are widely used to analyze elementary cell processes such as DNA replication or chromosomal folding and segregation. Labeling DNA with a fluorescent protein allows the visualization of its temporal and spatial organization. One popular approach is FROS (fluorescence repressor operator system). This method specifically labels DNA in vivo through binding of a fusion of a fluorescent protein and a repressor protein to an operator array, which contains numerous copies of the repressor binding site integrated into the genomic site of interest. Bound fluorescent proteins are then visible as foci in microscopic analyses and can be distinguished from the background fluorescence caused by unbound fusion proteins. Even though this method is widely used, no attempt has been made so far to decrease the background fluorescence to facilitate analysis of the actual signal of interest. Here, we present a new method that greatly reduces the background signal of FROS. BiFCROS (Bimolecular Fluorescence Complementation and Repressor Operator System) is based on fusions of repressor proteins to halves of a split fluorescent protein. Binding to a hybrid FROS array results in fluorescence signals due to bimolecular fluorescence complementation. Only proteins bound to the hybrid FROS array fluoresce, greatly improving the signal to noise ratio compared to conventional FROS. We present the development of BiFCROS and discuss its potential to be used as a fast and single-cell readout for copy numbers of genetic loci. PMID:28450375

Changes in lipid bilayer structure caused by the helix-to-sheet transition of an HIV-1 gp41 fusion peptide derivative

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

Heller, William T.; Rai, Durgesh K.

HIV-1, like other enveloped viruses, undergoes fusion with the cell membrane to infect it. Viral coat proteins are thought to bind the virus to the membrane and actively fuse the viral and cellular membranes together. The actual molecular mechanism of fusion is challenging to visualize, resulting in the use of model systems. In this paper, the bilayer curvature modifying properties of a synthetic variant of the HIV-1 gp41 fusion peptide with lipid bilayer vesicles composed of a mixture of dimyristoyl phosphatidylcholine (DMPC) and dimyristoyl phosphatidylserine (DMPS) were studied. In 7:3 DMPC:DMPS vesicles made with deuterium-labeled DMPC, the peptide was observedmore » to undergo a concentration-dependent conformational transition between an α-helix and an antiparallel β-sheet. Through the use of small-angle neutron scattering (SANS) and selective deuterium labeling, it was revealed that conformational transition of the peptide is also accompanied by a transition in the structure of the lipid bilayer. In addition to changes in the distribution of the lipid between the leaflets of the vesicle, the SANS data are consistent with two regions having different thicknesses. Finally, of the two different bilayer structures, the one corresponding to the smaller area fraction, being ~8% of the vesicle area, is much thicker than the remainder of the vesicle, which suggests that there are regions of localized negative curvature similar to what takes place at the point of contact between two membranes immediately preceding fusion.« less

Changes in lipid bilayer structure caused by the helix-to-sheet transition of an HIV-1 gp41 fusion peptide derivative

DOE PAGES

Heller, William T.; Rai, Durgesh K.

2017-01-16

HIV-1, like other enveloped viruses, undergoes fusion with the cell membrane to infect it. Viral coat proteins are thought to bind the virus to the membrane and actively fuse the viral and cellular membranes together. The actual molecular mechanism of fusion is challenging to visualize, resulting in the use of model systems. In this paper, the bilayer curvature modifying properties of a synthetic variant of the HIV-1 gp41 fusion peptide with lipid bilayer vesicles composed of a mixture of dimyristoyl phosphatidylcholine (DMPC) and dimyristoyl phosphatidylserine (DMPS) were studied. In 7:3 DMPC:DMPS vesicles made with deuterium-labeled DMPC, the peptide was observedmore » to undergo a concentration-dependent conformational transition between an α-helix and an antiparallel β-sheet. Through the use of small-angle neutron scattering (SANS) and selective deuterium labeling, it was revealed that conformational transition of the peptide is also accompanied by a transition in the structure of the lipid bilayer. In addition to changes in the distribution of the lipid between the leaflets of the vesicle, the SANS data are consistent with two regions having different thicknesses. Finally, of the two different bilayer structures, the one corresponding to the smaller area fraction, being ~8% of the vesicle area, is much thicker than the remainder of the vesicle, which suggests that there are regions of localized negative curvature similar to what takes place at the point of contact between two membranes immediately preceding fusion.« less

Novel infectivity-enhanced oncolytic adenovirus with a capsid-incorporated dual-imaging moiety for monitoring virotherapy in ovarian cancer.

PubMed

Kimball, Kristopher J; Rivera, Angel A; Zinn, Kurt R; Icyuz, Mert; Saini, Vaibhav; Li, Jing; Zhu, Zeng B; Siegal, Gene P; Douglas, Joanne T; Curiel, David T; Alvarez, Ronald D; Borovjagin, Anton V

2009-01-01

We sought to develop a cancer-targeted, infectivity-enhanced oncolytic adenovirus that embodies a capsid-labeling fusion for noninvasive dual-modality imaging of ovarian cancer virotherapy. A functional fusion protein composed of fluorescent and nuclear imaging tags was genetically incorporated into the capsid of an infectivity-enhanced conditionally replicative adenovirus. Incorporation of herpes simplex virus thymidine kinase (HSV-tk) and monomeric red fluorescent protein 1 (mRFP1) into the viral capsid and its genomic stability were verified by molecular analyses. Replication and oncolysis were evaluated in ovarian cancer cells. Fusion functionality was confirmed by in vitro gamma camera and fluorescent microscopy imaging. Comparison of tk-mRFP virus to single-modality controls revealed similar replication efficiency and oncolytic potency. Molecular fusion did not abolish enzymatic activity of HSV-tk as the virus effectively phosphorylated thymidine both ex vivo and in vitro. In vitro fluorescence imaging demonstrated a strong correlation between the intensity of fluorescent signal and cytopathic effect in infected ovarian cancer cells, suggesting that fluorescence can be used to monitor viral replication. We have in vitro validated a new infectivity-enhanced oncolytic adenovirus with a dual-imaging modality-labeled capsid, optimized for ovarian cancer virotherapy. The new agent could provide incremental gains toward climbing the barriers for achieving conditionally replicated adenovirus efficacy in human trials.

Fusion activity of HIV gp41 fusion domain is related to its secondary structure and depth of membrane insertion in a cholesterol-dependent fashion.

PubMed

Lai, Alex L; Moorthy, Anna Eswara; Li, Yinling; Tamm, Lukas K

2012-04-20

The human immunodeficiency virus (HIV) gp41 fusion domain plays a critical role in membrane fusion during viral entry. A thorough understanding of the relationship between the structure and the activity of the fusion domain in different lipid environments helps to formulate mechanistic models on how it might function in mediating membrane fusion. The secondary structure of the fusion domain in small liposomes composed of different lipid mixtures was investigated by circular dichroism spectroscopy.  The fusion domain formed an α-helix in membranes containing less than 30 mol% cholesterol and  formed β-sheet secondary structure in membranes containing ≥30 mol% cholesterol. EPR spectra of spin-labeled fusion domains also indicated different conformations in membranes with and without cholesterol. Power saturation EPR data were further used to determine the orientation and depth of α-helical fusion domains in lipid bilayers. Fusion and membrane perturbation activities of the gp41 fusion domain were measured by lipid mixing and contents leakage. The fusion domain fused membranes in both its helical form and its β-sheet form. High cholesterol, which induced β-sheets, promoted fusion; however, acidic lipids, which promoted relatively deep membrane insertion as an α-helix, also induced fusion. The results indicate that the structure of the HIV gp41 fusion domain is plastic and depends critically on the lipid environment. Provided that their membrane insertion is deep, α-helical and β-sheet conformations contribute to membrane fusion. Copyright © 2012 Elsevier Ltd. All rights reserved.

Statistical Relational Learning (SRL) as an Enabling Technology for Data Acquisition and Data Fusion in Video

DTIC Science & Technology

2013-05-02

REPORT Statistical Relational Learning ( SRL ) as an Enabling Technology for Data Acquisition and Data Fusion in Video 14. ABSTRACT 16. SECURITY...particular, it is important to reason about which portions of video require expensive analysis and storage. This project aims to make these...inferences using new and existing tools from Statistical Relational Learning ( SRL ). SRL is a recently emerging technology that enables the effective 1

Correlative Microscopy Combining Secondary Ion Mass Spectrometry and Electron Microscopy: Comparison of Intensity-Hue-Saturation and Laplacian Pyramid Methods for Image Fusion.

PubMed

Vollnhals, Florian; Audinot, Jean-Nicolas; Wirtz, Tom; Mercier-Bonin, Muriel; Fourquaux, Isabelle; Schroeppel, Birgit; Kraushaar, Udo; Lev-Ram, Varda; Ellisman, Mark H; Eswara, Santhana

2017-10-17

Correlative microscopy combining various imaging modalities offers powerful insights into obtaining a comprehensive understanding of physical, chemical, and biological phenomena. In this article, we investigate two approaches for image fusion in the context of combining the inherently lower-resolution chemical images obtained using secondary ion mass spectrometry (SIMS) with the high-resolution ultrastructural images obtained using electron microscopy (EM). We evaluate the image fusion methods with three different case studies selected to broadly represent the typical samples in life science research: (i) histology (unlabeled tissue), (ii) nanotoxicology, and (iii) metabolism (isotopically labeled tissue). We show that the intensity-hue-saturation fusion method often applied for EM-sharpening can result in serious image artifacts, especially in cases where different contrast mechanisms interplay. Here, we introduce and demonstrate Laplacian pyramid fusion as a powerful and more robust alternative method for image fusion. Both physical and technical aspects of correlative image overlay and image fusion specific to SIMS-based correlative microscopy are discussed in detail alongside the advantages, limitations, and the potential artifacts. Quantitative metrics to evaluate the results of image fusion are also discussed.

[Detection of ALK, ROS1 and RET fusion genes in non-small cell lung cancer patients and its clinicopathologic correlation].

PubMed

Zhong, Shan; Zhang, Haiping; Bai, Dongyu; Gao, Dehong; Zheng, Jie; Ding, Yi

2015-09-01

To study the prevalence of ALK, ROS1 and RET fusion genes in non-small cell lung cancer (NSCLC), and its correlation with clinicopathologic features. Formalin-fixed and paraffin-embedded tissue sections from samples of 302 patients with NSCLC were screened for ALK, ROS1, RET fusions by real-time polymerase chain reaction (PCR). All of the cases were validated by Sanger DNA sequencing. The relationship between ALK, ROS1, RET fusion genes and clinicopathologic features were analyzed. In the cohort of 302 NSCLC samples, 3.97% (12/302) were found to contain ALK fusion genes, including 3 cases with E13; A20 gene fusion, 3 cases with E6; A20 gene fusion and 3 cases with E20; A20 gene fusion. There was no statistically significant difference in patient's gender, age, smoking history and histologic type. Moreover, in the 302 NSCLC samples studied, 3.97% (12/302) were found to contain ROS1 fusion genes, with CD74-ROS1 fusion identified in 9 cases. There was no statistically significant difference in patients' gender, age, smoking history and histologic type. One non-smoking elderly female patient with pulmonary adenocarcinoma had RET gene fusion. None of the cases studied had concurrent ALK, ROS1 and RET mutations. The ALK, ROS1 and RET fusion gene mutation rates in NSCLC are low, they represent some specific molecular subtypes of NSCLC. Genetic testing has significant meaning to guide clinical targeted therapy.

Selective cell-surface labeling of the molecular motor protein prestin.

PubMed

McGuire, Ryan M; Silberg, Jonathan J; Pereira, Fred A; Raphael, Robert M

2011-06-24

Prestin, a multipass transmembrane protein whose N- and C-termini are localized to the cytoplasm, must be trafficked to the plasma membrane to fulfill its cellular function as a molecular motor. One challenge in studying prestin sequence-function relationships within living cells is separating the effects of amino acid substitutions on prestin trafficking, plasma membrane localization and function. To develop an approach for directly assessing prestin levels at the plasma membrane, we have investigated whether fusion of prestin to a single pass transmembrane protein results in a functional fusion protein with a surface-exposed N-terminal tag that can be detected in living cells. We find that fusion of the biotin-acceptor peptide (BAP) and transmembrane domain of the platelet-derived growth factor receptor (PDGFR) to the N-terminus of prestin-GFP yields a membrane protein that can be metabolically-labeled with biotin, trafficked to the plasma membrane, and selectively detected at the plasma membrane using fluorescently-tagged streptavidin. Furthermore, we show that the addition of a surface detectable tag and a single-pass transmembrane domain to prestin does not disrupt its voltage-sensitive activity. Copyright © 2011 Elsevier Inc. All rights reserved.

Less label, more free: approaches in label-free quantitative mass spectrometry.

PubMed

Neilson, Karlie A; Ali, Naveid A; Muralidharan, Sridevi; Mirzaei, Mehdi; Mariani, Michael; Assadourian, Gariné; Lee, Albert; van Sluyter, Steven C; Haynes, Paul A

2011-02-01

In this review we examine techniques, software, and statistical analyses used in label-free quantitative proteomics studies for area under the curve and spectral counting approaches. Recent advances in the field are discussed in an order that reflects a logical workflow design. Examples of studies that follow this design are presented to highlight the requirement for statistical assessment and further experiments to validate results from label-free quantitation. Limitations of label-free approaches are considered, label-free approaches are compared with labelling techniques, and forward-looking applications for label-free quantitative data are presented. We conclude that label-free quantitative proteomics is a reliable, versatile, and cost-effective alternative to labelled quantitation. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparison of clinical outcomes in decompression and fusion versus decompression only in patients with ossification of the posterior longitudinal ligament: a meta-analysis.

PubMed

Mehdi, Syed K; Alentado, Vincent J; Lee, Bryan S; Mroz, Thomas E; Benzel, Edward C; Steinmetz, Michael P

2016-06-01

OBJECTIVE Ossification of the posterior longitudinal ligament (OPLL) is a pathological calcification or ossification of the PLL, predominantly occurring in the cervical spine. Although surgery is often necessary for patients with symptomatic neurological deterioration, there remains controversy with regard to the optimal surgical treatment. In this systematic review and meta-analysis, the authors identified differences in complications and outcomes after anterior or posterior decompression and fusion versus after decompression alone for the treatment of cervical myelopathy due to OPLL. METHODS A MEDLINE, SCOPUS, and Web of Science search was performed for studies reporting complications and outcomes after decompression and fusion or after decompression alone for patients with OPLL. A meta-analysis was performed to calculate effect summary mean values, 95% CIs, Q statistics, and I(2) values. Forest plots were constructed for each analysis group. RESULTS Of the 2630 retrieved articles, 32 met the inclusion criteria. There was no statistically significant difference in the incidence of excellent and good outcomes and of fair and poor outcomes between the decompression and fusion and the decompression-only cohorts. However, the decompression and fusion cohort had a statistically significantly higher recovery rate (63.2% vs 53.9%; p < 0.0001), a higher final Japanese Orthopaedic Association score (14.0 vs 13.5; p < 0.0001), and a lower incidence of OPLL progression (< 1% vs 6.3%; p < 0.0001) compared with the decompression-only cohort. There was no statistically significant difference in the incidence of complications between the 2 cohorts. CONCLUSIONS This study represents the only comprehensive review of outcomes and complications after decompression and fusion or after decompression alone for OPLL across a heterogeneous group of surgeons and patients. Based on these results, decompression and fusion is a superior surgical technique compared with posterior decompression alone in patients with OPLL. These results indicate that surgical decompression and fusion lead to a faster recovery, improved postoperative neurological functioning, and a lower incidence of OPLL progression compared with posterior decompression only. Furthermore, decompression and fusion did not lead to a greater incidence of complications compared with posterior decompression only.

volBrain: An Online MRI Brain Volumetry System

PubMed Central

Manjón, José V.; Coupé, Pierrick

2016-01-01

The amount of medical image data produced in clinical and research settings is rapidly growing resulting in vast amount of data to analyze. Automatic and reliable quantitative analysis tools, including segmentation, allow to analyze brain development and to understand specific patterns of many neurological diseases. This field has recently experienced many advances with successful techniques based on non-linear warping and label fusion. In this work we present a novel and fully automatic pipeline for volumetric brain analysis based on multi-atlas label fusion technology that is able to provide accurate volumetric information at different levels of detail in a short time. This method is available through the volBrain online web interface (http://volbrain.upv.es), which is publically and freely accessible to the scientific community. Our new framework has been compared with current state-of-the-art methods showing very competitive results. PMID:27512372

volBrain: An Online MRI Brain Volumetry System.

PubMed

Manjón, José V; Coupé, Pierrick

2016-01-01

The amount of medical image data produced in clinical and research settings is rapidly growing resulting in vast amount of data to analyze. Automatic and reliable quantitative analysis tools, including segmentation, allow to analyze brain development and to understand specific patterns of many neurological diseases. This field has recently experienced many advances with successful techniques based on non-linear warping and label fusion. In this work we present a novel and fully automatic pipeline for volumetric brain analysis based on multi-atlas label fusion technology that is able to provide accurate volumetric information at different levels of detail in a short time. This method is available through the volBrain online web interface (http://volbrain.upv.es), which is publically and freely accessible to the scientific community. Our new framework has been compared with current state-of-the-art methods showing very competitive results.

Outcome of transforaminal lumbar interbody fusion in spondylolisthesis-A clinico-radiological correlation.

PubMed

Balasubramanian, Vijay Anand; Douraiswami, Balaji; Subramani, Suresh

2018-06-01

Lumbar spondylolisthesis is a common cause of morbidity in middle aged individuals. Spinal fusion with instrumentation has become the gold standard for lumbar segmental instability. Studies which correlate the improvement in radiology postoperatively with functional outcome show contrasting reports. This study is aimed at finding the correlation between clinical and radiological outcomes after surgery with transforaminal lumbar interbody fusion. A retrospective study in 35 patients who underwent transforaminal lumbar interbody fusion in a period of 1 year was done. Preoperative pain (VAS Score), functional ability (ODI), radiological parameters (slip angle, slip grade, disc height, foraminal height, lumbar lordosis) were compared with postoperative recordings at the last followup. Functional improvement (Macnab's criteria) and fusion (Lee's fusion criteria) were assessed. Statistical analysis was done with student's paired t -test and Pearson's correlation coefficient. VAS score, ODI improved from 8 to 2 and 70 to 15 respectively. Slip angle improved from 23°to 5° on an average. 80% patients showed fusion and 85% showed good clinical outcome at 1 year followup. Analyzing with Pearson correlation coefficient showed no significant relation between pain scores and radiological parameters. But there was statistically significant relation between radiological fusion and the final clinical outcome. TLIF produces spinal fusion in most individuals. Strong spinal fusion is essential for good clinical outcome in spondylolisthesis patients who undergo TLIF. Reduction in slip is not necessary for all patients with listhesis.

Integrating Multilevel Command and Control into a Service Oriented Architecture to Provide Cross Domain Capability

DTIC Science & Technology

2006-06-01

Horizontal Fusion, the JCDX team developed two web services, a Classification Policy Decision Service (cPDS), and a Federated Search Provider (FSP...The cPDS web service primarily provides other systems with methods for handling labeled data such as label comparison. The federated search provider...level domains. To provide defense-in-depth, cPDS and the Federated Search Provider are implemented on a separate server known as the JCDX Web

Biodistribution, pharmacokinetics, and nuclear imaging studies of 111In-labeled rGel/BLyS fusion toxin in SCID mice bearing B cell lymphoma.

PubMed

Wen, Xiaoxia; Lyu, Mi-Ae; Zhang, Rui; Lu, Wei; Huang, Qian; Liang, Dong; Rosenblum, Michael G; Li, Chun

2011-08-01

We examined the biodistribution and pharmacokinetics of (111)In-labeled rGel/BLyS, a gelonin toxin (rGel)-B lymphocyte stimulator (BLyS) fusion protein. rGel/BLyS was labeled with In-111 through DTPA with a labeling efficiency >95%. Biodistribution/imaging studies were obtained in severe-combined immunodeficiency mice bearing diffuse large B cell lymphoma OCI-Ly10. Pharmacokinetic studies were performed in BALB/c mice. In vitro, DTPA-conjugated rGel/BLyS displayed selective cytotoxicity against OCI-Ly10 cells and mantle cell lymphoma JeKo cells. In vivo, rGel/BLyS exhibited a tri-exponential disposition with a rapid initial mean distribution followed by an extensive mean distribution and a long terminal elimination phase. At 48 h after injection, uptake of the radiotracer in tumors was 1.25 %ID/g, with a tumor-to-blood ratio of 13. Tumors were clearly visualized at 24-72 h post-injection. Micro-SPECT-CT images and ex vivo analyses confirmed the accumulation of rGel/BLyS in OCI-Ly10 tumors. (111)In-DTPA-rGel/BLyS are distributed to B cell tumors and induce apoptosis in tumors. Preclinical antitumor studies using rGel/BLyS should use a twice-per-week treatment schedule.

The transition zone above a lumbosacral fusion.

PubMed

Hambly, M F; Wiltse, L L; Raghavan, N; Schneiderman, G; Koenig, C

1998-08-15

The clinical and radiographic effect of a lumbar or lumbosacral fusion was studied in 42 patients who had undergone a posterolateral fusion with an average follow-up of 22.6 years. To examine the long-term effects of posterolateral lumbar or lumbosacral fusion on the cephalad two motion segments (transition zone). It is commonly held that accelerated degeneration occurs in the motion segments adjacent to a fusion. Most studies are of short-term, anecdotal, uncontrolled reports that pay particular attention only to the first motion segment immediately cephalad to the fusion. Forty-two patients who had previously undergone a posterolateral lumbar or lumbosacral fusion underwent radiographic and clinical evaluation. Rate of fusion, range of motion, osteophytes, degenerative spondylolisthesis, retrolisthesis, facet arthrosis, disc ossification, dynamic instability, and disc space height were all studied and statistically compared with an age- and gender-matched control group. The patient's self-reported clinical outcome was also recorded. Degenerative changes occurred at the second level above the fused levels with a frequency equal to those occurring in the first level. There was no statistical difference between the study group and the cohort group in the presence of radiographic changes within the transition zone. In those patients undergoing fusion for degenerative processes, 75% reported a good to excellent outcome, whereas 84% of those undergoing fusion for spondylolysis or spondylolisthesis reported a good to excellent outcome. Radiographic changes occur within the transition zone cephalad to a lumbar or lumbosacral fusion. However, these changes are also seen in control subjects who have had no surgery.

Purification and antibacterial activity of recombinant warnericin RK expressed in Escherichia coli.

PubMed

Verdon, Julien; Girardin, Nicolas; Marchand, Adrienne; Héchard, Yann; Berjeaud, Jean-Marc

2013-06-01

Warnericin RK is a small cationic peptide produced by Staphylococcus warneri RK. This peptide has an antimicrobial spectrum of activity almost restricted to the Legionella genus. It is a membrane-active peptide with a proposed detergent-like mechanism of action at high concentration. Moreover, the fatty acids content of Legionella was shown to modulate the peptide activity. In order to decipher the mode of action in details using solid-state NMR spectroscopy, large amount of an isotopic labeled peptide is required. Since it is less expensive to obtain such a peptide biologically, we report here methods to express warnericin RK in Escherichia coli with or without a fusion partner and to purify resulting recombinant peptides. The cDNA fragment encoding warnericin RK was synthesized and ligated into three expression vectors. Two fusion peptides, carrying polyhistidine tag in N- or C-terminal and a native peptide, without tag, were expressed in E. coli cells. Fusion peptides were purified, with a yield of 3 mg/l, by affinity chromatography and reverse-phase HPLC. The recombinant native peptide was purified using a two-step purification method consisting of a hydrophobic chromatography followed by a reverse-phase HPLC step with a yield of 1.4 mg/l. However, the anti-Legionella activity was lower for both tagged peptide probably because of structural modifications. So, the native recombinant peptide was preferentially chosen for (15)N-labeling experiments. Our results suggest that the developed production and purification procedures will be useful in obtaining a large quantity of recombinant isotope-labeled warnericin RK for further studies.

Single molecule super-resolution imaging of proteins in living Salmonella enterica using self-labelling enzymes

PubMed Central

Barlag, Britta; Beutel, Oliver; Janning, Dennis; Czarniak, Frederik; Richter, Christian P.; Kommnick, Carina; Göser, Vera; Kurre, Rainer; Fabiani, Florian; Erhardt, Marc; Piehler, Jacob; Hensel, Michael

2016-01-01

The investigation of the subcellular localization, dynamics and interaction of proteins and protein complexes in prokaryotes is complicated by the small size of the cells. Super-resolution microscopy (SRM) comprise various new techniques that allow light microscopy with a resolution that can be up to ten-fold higher than conventional light microscopy. Application of SRM techniques to living prokaryotes demands the introduction of suitable fluorescent probes, usually by fusion of proteins of interest to fluorescent proteins with properties compatible to SRM. Here we describe an approach that is based on the genetically encoded self-labelling enzymes HaloTag and SNAP-tag. Proteins of interest are fused to HaloTag or SNAP-tag and cell permeable substrates can be labelled with various SRM-compatible fluorochromes. Fusions of the enzyme tags to subunits of a type I secretion system (T1SS), a T3SS, the flagellar rotor and a transcription factor were generated and analysed in living Salmonella enterica. The new approach is versatile in tagging proteins of interest in bacterial cells and allows to determine the number, relative subcellular localization and dynamics of protein complexes in living cells. PMID:27534893

Nuclear dynamics during germination, conidiation, and hyphal fusion of Fusarium oxysporum.

PubMed

Ruiz-Roldán, M Carmen; Köhli, Michael; Roncero, M Isabel G; Philippsen, Peter; Di Pietro, Antonio; Espeso, Eduardo A

2010-08-01

In many fungal pathogens, infection is initiated by conidial germination. Subsequent stages involve germ tube elongation, conidiation, and vegetative hyphal fusion (anastomosis). Here, we used live-cell fluorescence to study the dynamics of green fluorescent protein (GFP)- and cherry fluorescent protein (ChFP)-labeled nuclei in the plant pathogen Fusarium oxysporum. Hyphae of F. oxysporum have uninucleated cells and exhibit an acropetal nuclear pedigree, where only the nucleus in the apical compartment is mitotically active. In contrast, conidiation follows a basopetal pattern, whereby mononucleated microconidia are generated by repeated mitotic cycles of the subapical nucleus in the phialide, followed by septation and cell abscission. Vegetative hyphal fusion is preceded by directed growth of the fusion hypha toward the receptor hypha and followed by a series of postfusion nuclear events, including mitosis of the apical nucleus of the fusion hypha, migration of a daughter nucleus into the receptor hypha, and degradation of the resident nucleus. These previously unreported patterns of nuclear dynamics in F. oxysporum could be intimately related to its pathogenic lifestyle.

Fusion of single proteoliposomes with planar, cushioned bilayers in microfluidic flow cells

PubMed Central

Karatekin, Erdem; Rothman, James E.

2013-01-01

Many biological processes rely on membrane fusion, therefore assays to study its mechanisms are necessary. Here we report an assay with sensitivity to single-vesicle, even to single-molecule events using fluorescently labeled vesicle-associated v-SNARE liposomes and target-membrane-associated t-SNARE-reconstituted planar, supported bilayers (SBLs). Docking and fusion events can be detected using conventional far-field epifluorescence or total internal reflection fluorsecence microscopy. Unlike most previous attempts, fusion here is dependent on SNAP25, one of the t-SNARE subunits that is required for fusion in vivo. The success of the assay is due to the use of (i) bilayers covered with a thin layer of poly(ethylene glycol) to control bilayer-bilayer and bilayer-substrate interactions, (ii) microfluidic flow channels which presents many advantages such as the removal of non-specifically bound liposomes by flow. The protocol takes 6–8 days to complete. Analysis can take up to two weeks. PMID:22517259

Statistical methods for quantitative mass spectrometry proteomic experiments with labeling.

PubMed

Oberg, Ann L; Mahoney, Douglas W

2012-01-01

Mass Spectrometry utilizing labeling allows multiple specimens to be subjected to mass spectrometry simultaneously. As a result, between-experiment variability is reduced. Here we describe use of fundamental concepts of statistical experimental design in the labeling framework in order to minimize variability and avoid biases. We demonstrate how to export data in the format that is most efficient for statistical analysis. We demonstrate how to assess the need for normalization, perform normalization, and check whether it worked. We describe how to build a model explaining the observed values and test for differential protein abundance along with descriptive statistics and measures of reliability of the findings. Concepts are illustrated through the use of three case studies utilizing the iTRAQ 4-plex labeling protocol.

Image segmentation with a novel regularized composite shape prior based on surrogate study

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

Zhao, Tingting, E-mail: tingtingzhao@mednet.ucla.edu; Ruan, Dan, E-mail: druan@mednet.ucla.edu

Purpose: Incorporating training into image segmentation is a good approach to achieve additional robustness. This work aims to develop an effective strategy to utilize shape prior knowledge, so that the segmentation label evolution can be driven toward the desired global optimum. Methods: In the variational image segmentation framework, a regularization for the composite shape prior is designed to incorporate the geometric relevance of individual training data to the target, which is inferred by an image-based surrogate relevance metric. Specifically, this regularization is imposed on the linear weights of composite shapes and serves as a hyperprior. The overall problem is formulatedmore » in a unified optimization setting and a variational block-descent algorithm is derived. Results: The performance of the proposed scheme is assessed in both corpus callosum segmentation from an MR image set and clavicle segmentation based on CT images. The resulted shape composition provides a proper preference for the geometrically relevant training data. A paired Wilcoxon signed rank test demonstrates statistically significant improvement of image segmentation accuracy, when compared to multiatlas label fusion method and three other benchmark active contour schemes. Conclusions: This work has developed a novel composite shape prior regularization, which achieves superior segmentation performance than typical benchmark schemes.« less

Detection and tracking of dual-labeled HIV particles using wide-field live cell imaging to follow viral core integrity

PubMed Central

Mamede, Joao I.; Hope, Thomas J.

2016-01-01

Summary Live cell imaging is a valuable technique that allows the characterization of the dynamic processes of the HIV-1 life-cycle. Here, we present a method of production and imaging of dual-labeled HIV viral particles that allows the visualization of two events. Varying release of the intravirion fluid phase marker reveals virion fusion and the loss of the integrity of HIV viral cores with the use of live wide-field fluorescent microscopy. PMID:26714704

Fluorescent Proteins: A Cell Biologist's User Guide

PubMed Central

Snapp, Erik Lee

2009-01-01

Fluorescent Proteins (FPs) have revolutionized cell biology. The value of labeling and visualizing proteins in living cells is evident from thousands of publications since the cloning of Green Fluorescent Protein (GFP). Biologists have been flooded with a cornucopia of FPs; however, the FP toolbox has not necessarily been optimized for cell biologists. Common FP plasmids are suboptimal for FP-fusion protein construction. More problematic are commercial and investigator-constructed FP-fusion proteins that disrupt important cellular targeting information. Even when cell biologists correctly construct FP-fusion proteins, it is rarely self-evident which FP should be used. Important FP information, such as oligomer formation or photostability, is often unsearchable or anecdotal. This brief guide is offered to assist in correctly exploiting FPs in cells. PMID:19819147

Recombinant production, isotope labeling and purification of ENOD40B: a plant peptide hormone.

PubMed

Chae, Young Kee; Tonneli, Marco; Markley, John L

2012-08-01

The plant peptide hormone ENOD40B was produced in a protein production strain of Escherichia coli harboring an induction controller plasmid (Rosetta(DE3)pLysS) as a His6-tagged ubiquitin fusion protein. The fusion protein product was denatured and refolded as part of the isolation procedure and purified by immobilized metal ion chromatography. The peptide hormone was released from its fusion partner by adding yeast ubiquitin hydrolase (YUH) and subsequently purified by reversed phase chromatography. The purity of the resulting peptide fragment was assayed by MALDITOF mass spectrometry and NMR spectroscopy. The final yields of the target peptide were 7.0 mg per liter of LB medium and 3.4 mg per liter of minimal medium.

Surgical Treatment for Discogenic Low-Back Pain: Lumbar Arthroplasty Results in Superior Pain Reduction and Disability Level Improvement Compared With Lumbar Fusion

PubMed Central

2007-01-01

Background The US Food and Drug Administration approved the Charité artificial disc on October 26, 2004. This approval was based on an extensive analysis and review process; 20 years of disc usage worldwide; and the results of a prospective, randomized, controlled clinical trial that compared lumbar artificial disc replacement to fusion. The results of the investigational device exemption (IDE) study led to a conclusion that clinical outcomes following lumbar arthroplasty were at least as good as outcomes from fusion. Methods The author performed a new analysis of the Visual Analog Scale pain scores and the Oswestry Disability Index scores from the Charité artificial disc IDE study and used a nonparametric statistical test, because observed data distributions were not normal. The analysis included all of the enrolled subjects in both the nonrandomized and randomized phases of the study. Results Subjects from both the treatment and control groups improved from the baseline situation (P < .001) at all follow-up times (6 weeks to 24 months). Additionally, these pain and disability levels with artificial disc replacement were superior (P < .05) to the fusion treatment at all follow-up times including 2 years. Conclusions The a priori statistical plan for an IDE study may not adequately address the final distribution of the data. Therefore, statistical analyses more appropriate to the distribution may be necessary to develop meaningful statistical conclusions from the study. A nonparametric statistical analysis of the Charité artificial disc IDE outcomes scores demonstrates superiority for lumbar arthroplasty versus fusion at all follow-up time points to 24 months. PMID:25802574

Binary patterns encoded convolutional neural networks for texture recognition and remote sensing scene classification

NASA Astrophysics Data System (ADS)

Anwer, Rao Muhammad; Khan, Fahad Shahbaz; van de Weijer, Joost; Molinier, Matthieu; Laaksonen, Jorma

2018-04-01

Designing discriminative powerful texture features robust to realistic imaging conditions is a challenging computer vision problem with many applications, including material recognition and analysis of satellite or aerial imagery. In the past, most texture description approaches were based on dense orderless statistical distribution of local features. However, most recent approaches to texture recognition and remote sensing scene classification are based on Convolutional Neural Networks (CNNs). The de facto practice when learning these CNN models is to use RGB patches as input with training performed on large amounts of labeled data (ImageNet). In this paper, we show that Local Binary Patterns (LBP) encoded CNN models, codenamed TEX-Nets, trained using mapped coded images with explicit LBP based texture information provide complementary information to the standard RGB deep models. Additionally, two deep architectures, namely early and late fusion, are investigated to combine the texture and color information. To the best of our knowledge, we are the first to investigate Binary Patterns encoded CNNs and different deep network fusion architectures for texture recognition and remote sensing scene classification. We perform comprehensive experiments on four texture recognition datasets and four remote sensing scene classification benchmarks: UC-Merced with 21 scene categories, WHU-RS19 with 19 scene classes, RSSCN7 with 7 categories and the recently introduced large scale aerial image dataset (AID) with 30 aerial scene types. We demonstrate that TEX-Nets provide complementary information to standard RGB deep model of the same network architecture. Our late fusion TEX-Net architecture always improves the overall performance compared to the standard RGB network on both recognition problems. Furthermore, our final combination leads to consistent improvement over the state-of-the-art for remote sensing scene classification.

Mapping irrigated areas of Ghana using fusion of 30 m and 250 m resolution remote-sensing data

USGS Publications Warehouse

Gumma, M.K.; Thenkabail, P.S.; Hideto, F.; Nelson, A.; Dheeravath, V.; Busia, D.; Rala, A.

2011-01-01

Maps of irrigated areas are essential for Ghana's agricultural development. The goal of this research was to map irrigated agricultural areas and explain methods and protocols using remote sensing. Landsat Enhanced Thematic Mapper (ETM+) data and time-series Moderate Resolution Imaging Spectroradiometer (MODIS) data were used to map irrigated agricultural areas as well as other land use/land cover (LULC) classes, for Ghana. Temporal variations in the normalized difference vegetation index (NDVI) pattern obtained in the LULC class were used to identify irrigated and non-irrigated areas. First, the temporal variations in NDVI pattern were found to be more consistent in long-duration irrigated crops than with short-duration rainfed crops due to more assured water supply for irrigated areas. Second, surface water availability for irrigated areas is dependent on shallow dug-wells (on river banks) and dug-outs (in river bottoms) that affect the timing of crop sowing and growth stages, which was in turn reflected in the seasonal NDVI pattern. A decision tree approach using Landsat 30 m one time data fusion with MODIS 250 m time-series data was adopted to classify, group, and label classes. Finally, classes were tested and verified using ground truth data and national statistics. Fuzzy classification accuracy assessment for the irrigated classes varied between 67 and 93%. An irrigated area derived from remote sensing (32,421 ha) was 20-57% higher than irrigated areas reported by Ghana's Irrigation Development Authority (GIDA). This was because of the uncertainties involved in factors such as: (a) absence of shallow irrigated area statistics in GIDA statistics, (b) non-clarity in the irrigated areas in its use, under-development, and potential for development in GIDA statistics, (c) errors of omissions and commissions in the remote sensing approach, and (d) comparison involving widely varying data types, methods, and approaches used in determining irrigated area statistics using GIDA and remote sensing. Extensive field campaigns to help in better classification and validation of irrigated areas using high (30 m ) to very high (<5 m) resolution remote sensing data that are fused with multi temporal data like MODIS are the way forward. This is especially true in accounting for small yet contiguous patches of irrigated areas from dug-wells and dug-outs. ?? 2011 by the authors.

C7 pars fracture subadjacent to C7 pedicle screw instrumentation at the caudal end of a posterior cervical instrumentation construct.

PubMed

Halim, Andrea; Grauer, Jonathan

2014-07-01

We report a case of a C7 pars fracture subadjacent to C7 pedicle screw instrumentation at the caudal end of posterior cervical instrumentation construct. To date, posterior cervical instrumentation has been "off label"; however, the US Food and Drug Administration is considering approving label indication of such instrumentation for this common surgical practice. Complications related to the techniques are reported to be relatively low. We know of no previous reports of pars fractures occurring subadjacent to such instrumentation. A 43-year-old man underwent posterior C5-C7 instrumented fusion. Postoperatively, the patient experienced cervical spine injury after a mechanical fall down stairs. Work-up detected bilateral C7 pars fractures subadjacent to the posterior instrumentation construct. After we treated the pars fracture with distal extension of the posterior fusion to the level of T2, the patient progressed to union and marked improvement of initial clinical symptoms that was maintained 2.5 years after posterior instrumentation. To our knowledge, a C7 pars fracture subadjacent to posterior cervical instrumentation construct has not been reported. We hypothesize that the pars may have been vulnerable to fracture because of excessive bone resection during foraminotomy or decortication. This complication was successfully treated by extending the fusion caudally.

Far Western: probing membranes.

PubMed

Einarson, Margret B; Pugacheva, Elena N; Orlinick, Jason R

2007-08-01

INTRODUCTIONThe far-Western technique described in this protocol is fundamentally similar to Western blotting. In Western blots, an antibody is used to detect a query protein on a membrane. In contrast, in a far-Western blot (also known as an overlay assay) the antibody is replaced by a recombinant GST fusion protein (produced and purified from bacteria), and the assay detects the interaction of this protein with target proteins on a membrane. The membranes are washed and blocked, incubated with probe protein, washed again, and subjected to autoradiography. The GST fusion (probe) proteins are often labeled with (32)P; alternatively, the membrane can be probed with unlabeled GST fusion protein, followed by detection using commercially available GST antibodies. The nonradioactive approach is substantially more expensive (due to the purchase of antibody and detection reagents) than using radioactively labeled proteins. In addition, care must be taken to control for nonspecific interactions with GST alone and a signal resulting from antibody cross-reactivity. In some instances, proteins on the membrane are not able to interact after transfer. This may be due to improper folding, particularly in the case of proteins expressed from a phage expression library. This protocol describes a way to overcome this by washing the membrane in denaturation buffer, which is then serially diluted to permit slow renaturation of the proteins.

MUSE: MUlti-atlas region Segmentation utilizing Ensembles of registration algorithms and parameters, and locally optimal atlas selection

PubMed Central

Ou, Yangming; Resnick, Susan M.; Gur, Ruben C.; Gur, Raquel E.; Satterthwaite, Theodore D.; Furth, Susan; Davatzikos, Christos

2016-01-01

Atlas-based automated anatomical labeling is a fundamental tool in medical image segmentation, as it defines regions of interest for subsequent analysis of structural and functional image data. The extensive investigation of multi-atlas warping and fusion techniques over the past 5 or more years has clearly demonstrated the advantages of consensus-based segmentation. However, the common approach is to use multiple atlases with a single registration method and parameter set, which is not necessarily optimal for every individual scan, anatomical region, and problem/data-type. Different registration criteria and parameter sets yield different solutions, each providing complementary information. Herein, we present a consensus labeling framework that generates a broad ensemble of labeled atlases in target image space via the use of several warping algorithms, regularization parameters, and atlases. The label fusion integrates two complementary sources of information: a local similarity ranking to select locally optimal atlases and a boundary modulation term to refine the segmentation consistently with the target image's intensity profile. The ensemble approach consistently outperforms segmentations using individual warping methods alone, achieving high accuracy on several benchmark datasets. The MUSE methodology has been used for processing thousands of scans from various datasets, producing robust and consistent results. MUSE is publicly available both as a downloadable software package, and as an application that can be run on the CBICA Image Processing Portal (https://ipp.cbica.upenn.edu), a web based platform for remote processing of medical images. PMID:26679328

[Experimental study of glioma stem cell-mediated immune tolerance in tumor microenvironment].

PubMed

Xie, T; Ma, J W; Liu, B; Dong, J; Huang, Q

2017-11-23

Objective: To investigate the tumor microenvironment of immune tolerance induced by glioma stem cells (GSC). Methods: Human GSC SU3 cells transfected with red fluorescent protein (SU3-RFP) gene were implanted into the brain, subcutis (armpit and foot), liver and abdominal cavity of transgenic green fluorescence protein (GFP) nude mice to establish RFP(+) /GFP(+) dual fluorescence solid tumor model. The re-cultured cells derived from implanted tumor tissues, SU3-RFP cells co-cultured with peritoneal fluid of transgenic GFP nude mice and malignant ascites of tumor-bearing mice were observed by fluorescence microscopy and real-time video image tracing to analyze the microenvironment of immune tolerance mediated by RFP(+) /GFP(+) implanted tumor. Results: Dual fluorescence labeled frozen section showed that all of cells in the tumor microenvironment were GFP(+) , while the pressed tissue-patch showed that the tumor blood vessels exhibited a RFP(+) /GFP(+) double-positioning yellow. In the GFP single fluorescence labeled tumor tissue, all of cells in the microenvironment were green, including tumor edge, necrotic foci and blood vessel. Among them, CD68(+) , F4/80(+) , CD11c(+) , CD11b(+) and CD80(+) cells were observed. In the dual fluorescence labeled co-cultured cells, the phagocytosis and fusion between green host cells and red tumor cells were also observed, and these fusion cells might transfer to the malignant dendritic cells and macrophages. Conclusions: The tumor microenvironment of immune tolerance induced by GSC is not affected by the tissue types of tumor-inoculated sites, and the immune tolerance mediated by inflammatory cells is associated with the inducible malignant transformation, which may be driven by cell fusion.

Performing label-fusion-based segmentation using multiple automatically generated templates.

PubMed

Chakravarty, M Mallar; Steadman, Patrick; van Eede, Matthijs C; Calcott, Rebecca D; Gu, Victoria; Shaw, Philip; Raznahan, Armin; Collins, D Louis; Lerch, Jason P

2013-10-01

Classically, model-based segmentation procedures match magnetic resonance imaging (MRI) volumes to an expertly labeled atlas using nonlinear registration. The accuracy of these techniques are limited due to atlas biases, misregistration, and resampling error. Multi-atlas-based approaches are used as a remedy and involve matching each subject to a number of manually labeled templates. This approach yields numerous independent segmentations that are fused using a voxel-by-voxel label-voting procedure. In this article, we demonstrate how the multi-atlas approach can be extended to work with input atlases that are unique and extremely time consuming to construct by generating a library of multiple automatically generated templates of different brains (MAGeT Brain). We demonstrate the efficacy of our method for the mouse and human using two different nonlinear registration algorithms (ANIMAL and ANTs). The input atlases consist a high-resolution mouse brain atlas and an atlas of the human basal ganglia and thalamus derived from serial histological data. MAGeT Brain segmentation improves the identification of the mouse anterior commissure (mean Dice Kappa values (κ = 0.801), but may be encountering a ceiling effect for hippocampal segmentations. Applying MAGeT Brain to human subcortical structures improves segmentation accuracy for all structures compared to regular model-based techniques (κ = 0.845, 0.752, and 0.861 for the striatum, globus pallidus, and thalamus, respectively). Experiments performed with three manually derived input templates suggest that MAGeT Brain can approach or exceed the accuracy of multi-atlas label-fusion segmentation (κ = 0.894, 0.815, and 0.895 for the striatum, globus pallidus, and thalamus, respectively). Copyright © 2012 Wiley Periodicals, Inc.

Fusion of small unilamellar vesicles induced by bovine serum albumin fragments.

PubMed

Garcia, L A; Schenkman, S; Araujo, P S; Chaimovich, H

1983-07-01

The limited pepsin proteolysis products of bovine serum albumin, fragment A (residues 307-586) and fragment B (residues 1-306), induced the fusion of small unilamellar vesicles of egg phosphatidyl choline at concentrations near 5 microM. Fusion was demonstrated and analyzed on the basis of: a) time-dependent changes in absorbance; b) dilution of the fluorescent label 2-(10-(1-pyrene)decanoyl) phosphatidyl choline, incorporated into a small percentage of the vesicles, as measured by the decrease in the excimer to monomer (E/M) ratio; c) increase of the average hydrodynamic radius of the liposomes, estimated by Sepharose 4B filtration, and d) the strict inverse relationship between the size of the liposomes and their E/M ratios. Albumin fragment B, like albumin, induced the formation of large aggregates in which rapid cooperative fusion produced vesicles having a large hydrodynamic radius. Fragment A did not produce large aggregates and the initial fusion products exhibited a hydrodynamic radius. Fragment A did not produce large aggregates and the initial fusion products exhibited a hydrodynamic radius smaller than those obtained with fragment B. Albumin and fragments A and B are fusogenic only at pH below 4.0. These data discussed in terms of a general model for a signal-dependent protein-induced membrane fusion.

A genetically encoded fluorescent tRNA is active in live-cell protein synthesis

PubMed Central

Masuda, Isao; Igarashi, Takao; Sakaguchi, Reiko; Nitharwal, Ram G.; Takase, Ryuichi; Han, Kyu Young; Leslie, Benjamin J.; Liu, Cuiping; Gamper, Howard; Ha, Taekjip; Sanyal, Suparna

2017-01-01

Abstract Transfer RNAs (tRNAs) perform essential tasks for all living cells. They are major components of the ribosomal machinery for protein synthesis and they also serve in non-ribosomal pathways for regulation and signaling metabolism. We describe the development of a genetically encoded fluorescent tRNA fusion with the potential for imaging in live Escherichia coli cells. This tRNA fusion carries a Spinach aptamer that becomes fluorescent upon binding of a cell-permeable and non-toxic fluorophore. We show that, despite having a structural framework significantly larger than any natural tRNA species, this fusion is a viable probe for monitoring tRNA stability in a cellular quality control mechanism that degrades structurally damaged tRNA. Importantly, this fusion is active in E. coli live-cell protein synthesis allowing peptidyl transfer at a rate sufficient to support cell growth, indicating that it is accommodated by translating ribosomes. Imaging analysis shows that this fusion and ribosomes are both excluded from the nucleoid, indicating that the fusion and ribosomes are in the cytosol together possibly engaged in protein synthesis. This fusion methodology has the potential for developing new tools for live-cell imaging of tRNA with the unique advantage of both stoichiometric labeling and broader application to all cells amenable to genetic engineering. PMID:27956502

Spatiotemporal dynamics of membrane remodeling and fusion proteins during endocytic transport

PubMed Central

Arlt, Henning; Auffarth, Kathrin; Kurre, Rainer; Lisse, Dominik; Piehler, Jacob; Ungermann, Christian

2015-01-01

Organelles of the endolysosomal system undergo multiple fission and fusion events to combine sorting of selected proteins to the vacuole with endosomal recycling. This sorting requires a consecutive remodeling of the organelle surface in the course of endosomal maturation. Here we dissect the remodeling and fusion machinery on endosomes during the process of endocytosis. We traced selected GFP-tagged endosomal proteins relative to exogenously added fluorescently labeled α-factor on its way from the plasma membrane to the vacuole. Our data reveal that the machinery of endosomal fusion and ESCRT proteins has similar temporal localization on endosomes, whereas they precede the retromer cargo recognition complex. Neither deletion of retromer nor the fusion machinery with the vacuole affects this maturation process, although the kinetics seems to be delayed due to ESCRT deletion. Of importance, in strains lacking the active Rab7-like Ypt7 or the vacuolar SNARE fusion machinery, α-factor still proceeds to late endosomes with the same kinetics. This indicates that endosomal maturation is mainly controlled by the early endosomal fusion and remodeling machinery but not the downstream Rab Ypt7 or the SNARE machinery. Our data thus provide important further understanding of endosomal biogenesis in the context of cargo sorting. PMID:25657322

Effects of Local Administration of Boric Acid on Posterolateral Spinal Fusion with Autogenous Bone Grafting in a Rodent Model.

PubMed

Kömürcü, Erkam; Özyalvaçlı, Gülzade; Kaymaz, Burak; Gölge, Umut Hatay; Göksel, Ferdi; Cevizci, Sibel; Adam, Gürhan; Ozden, Raif

2015-09-01

Spinal fusion is among the most frequently applied spinal surgical procedures. The goal of the present study was to evaluate whether the local administration of boric acid (BA) improves spinal fusion in an experimental spinal fusion model in rats. Currently, there is no published data that evaluates the possible positive effects if the local administration of BA on posterolateral spinal fusion. Thirty-two rats were randomly divided into four independent groups: no material was added at the fusion area for group 1; an autogenous morselized corticocancellous bone graft was used for group 2; an autogenous morselized corticocancellous bone graft with boric acid (8.7 mg/kg) for group 3; and only boric acid was placed into the fusion area for group 4. The L4-L6 spinal segments were collected at week 6, and the assessments included radiography, manual palpation, and histomorphometry. A statistically significant difference was determined between the groups with regard to the mean histopathological scores (p = 0.002), and a paired comparison was made with the Mann-Whitney U test to detect the group/groups from which the difference originated. It was determined that only the graft + BA practice increased the histopathological score significantly with regard to the control group (p = 0.002). Whereas, there was no statistically significant difference between the groups in terms of the manual assessment of fusion and radiographic analysis (respectively p = 0.328 and p = 0.196). This preliminary study suggests that BA may clearly be useful as a therapeutic agent in spinal fusion. However, further research is required to show the most effective dosage of BA on spinal fusion, and should indicate whether BA effects spinal fusion in the human body.

The Nonsubsampled Contourlet Transform Based Statistical Medical Image Fusion Using Generalized Gaussian Density

PubMed Central

Yang, Guocheng; Li, Meiling; Chen, Leiting; Yu, Jie

2015-01-01

We propose a novel medical image fusion scheme based on the statistical dependencies between coefficients in the nonsubsampled contourlet transform (NSCT) domain, in which the probability density function of the NSCT coefficients is concisely fitted using generalized Gaussian density (GGD), as well as the similarity measurement of two subbands is accurately computed by Jensen-Shannon divergence of two GGDs. To preserve more useful information from source images, the new fusion rules are developed to combine the subbands with the varied frequencies. That is, the low frequency subbands are fused by utilizing two activity measures based on the regional standard deviation and Shannon entropy and the high frequency subbands are merged together via weight maps which are determined by the saliency values of pixels. The experimental results demonstrate that the proposed method significantly outperforms the conventional NSCT based medical image fusion approaches in both visual perception and evaluation indices. PMID:26557871

Live imaging of mouse secondary palate fusion

PubMed Central

Kim, Seungil; Prochazka, Jan; Bush, Jeffrey O.

2017-01-01

LONG ABSTRACT The fusion of the secondary palatal shelves to form the intact secondary palate is a key process in mammalian development and its disruption can lead to cleft secondary palate, a common congenital anomaly in humans. Secondary palate fusion has been extensively studied leading to several proposed cellular mechanisms that may mediate this process. However, these studies have been mostly performed on fixed embryonic tissues at progressive timepoints during development or in fixed explant cultures analyzed at static timepoints. Static analysis is limited for the analysis of dynamic morphogenetic processes such a palate fusion and what types of dynamic cellular behaviors mediate palatal fusion is incompletely understood. Here we describe a protocol for live imaging of ex vivo secondary palate fusion in mouse embryos. To examine cellular behaviors of palate fusion, epithelial-specific Keratin14-cre was used to label palate epithelial cells in ROSA26-mTmGflox reporter embryos. To visualize filamentous actin, Lifeact-mRFPruby reporter mice were used. Live imaging of secondary palate fusion was performed by dissecting recently-adhered secondary palatal shelves of embryonic day (E) 14.5 stage embryos and culturing in agarose-containing media on a glass bottom dish to enable imaging with an inverted confocal microscope. Using this method, we have detected a variety of novel cellular behaviors during secondary palate fusion. An appreciation of how distinct cell behaviors are coordinated in space and time greatly contributes to our understanding of this dynamic morphogenetic process. This protocol can be applied to mutant mouse lines, or cultures treated with pharmacological inhibitors to further advance understanding of how secondary palate fusion is controlled. PMID:28784960

Selective targeting of a TNFR decoy receptor pharmaceutical to the primate brain as a receptor-specific IgG fusion protein.

PubMed

Boado, Ruben J; Hui, Eric Ka-Wai; Lu, Jeff Zhiqiang; Zhou, Qing-Hui; Pardridge, William M

2010-03-01

Decoy receptors, such as the human tumor necrosis factor receptor (TNFR), are potential new therapies for brain disorders. However, decoy receptors are large molecule drugs that are not transported across the blood-brain barrier (BBB). To enable BBB transport of a TNFR decoy receptor, the human TNFR-II extracellular domain was re-engineered as a fusion protein with a chimeric monoclonal antibody (MAb) against the human insulin receptor (HIR). The HIRMAb acts as a molecular Trojan horse to ferry the TNFR therapeutic decoy receptor across the BBB. The HIRMAb-TNFR fusion protein was expressed in stably transfected CHO cells, and was analyzed with electrophoresis, Western blotting, size exclusion chromatography, and binding assays for the HIR and TNFalpha. The HIRMAb-TNFR fusion protein was radio-labeled by trititation, in parallel with the radio-iodination of recombinant TNFR:Fc fusion protein, and the proteins were co-injected in the adult Rhesus monkey. The TNFR:Fc fusion protein did not cross the primate BBB in vivo, but the uptake of the HIRMAb-TNFR fusion protein was high and 3% of the injected dose was taken up by the primate brain. The TNFR was selectively targeted to brain, relative to peripheral organs, following fusion to the HIRMAb. This study demonstrates that decoy receptors may be re-engineered as IgG fusion proteins with a BBB molecular Trojan horse that selectively targets the brain, and enables penetration of the BBB in vivo. IgG-decoy receptor fusion proteins represent a new class of human neurotherapeutics. Copyright 2010 Elsevier B.V. All rights reserved.

A data fusion framework for meta-evaluation of intelligent transportation system effectiveness

DOT National Transportation Integrated Search

This study presents a framework for the meta-evaluation of Intelligent Transportation System effectiveness. The framework is based on data fusion approaches that adjust for data biases and violations of other standard statistical assumptions. Operati...

Sensor fusion III: 3-D perception and recognition; Proceedings of the Meeting, Boston, MA, Nov. 5-8, 1990

NASA Technical Reports Server (NTRS)

Schenker, Paul S. (Editor)

1991-01-01

The volume on data fusion from multiple sources discusses fusing multiple views, temporal analysis and 3D motion interpretation, sensor fusion and eye-to-hand coordination, and integration in human shape perception. Attention is given to surface reconstruction, statistical methods in sensor fusion, fusing sensor data with environmental knowledge, computational models for sensor fusion, and evaluation and selection of sensor fusion techniques. Topics addressed include the structure of a scene from two and three projections, optical flow techniques for moving target detection, tactical sensor-based exploration in a robotic environment, and the fusion of human and machine skills for remote robotic operations. Also discussed are K-nearest-neighbor concepts for sensor fusion, surface reconstruction with discontinuities, a sensor-knowledge-command fusion paradigm for man-machine systems, coordinating sensing and local navigation, and terrain map matching using multisensing techniques for applications to autonomous vehicle navigation.

Titanium vs. polyetheretherketone (PEEK) interbody fusion: Meta-analysis and review of the literature.

PubMed

Seaman, Scott; Kerezoudis, Panagiotis; Bydon, Mohamad; Torner, James C; Hitchon, Patrick W

2017-10-01

Spinal interbody fusion is a standard and accepted method for spinal fusion. Interbody fusion devices include titanium (Ti) and polyetheretherketone (PEEK) cages with distinct biomechanical properties. Titanium and PEEK cages have been evaluated in the cervical and lumbar spine, with conflicting results in bony fusion and subsidence. Using Preferred Reporting Items for Systematic reviews and Meta-analyses (PRISMA) guidelines, we reviewed the available literature evaluating Ti and PEEK cages to assess subsidence and fusion rates. Six studies were included in the analysis, 3 of which were class IV evidence, 2 were class III, and 1 was class II. A total of 410 patients (Ti-228, PEEK-182) and 587 levels (Ti-327, PEEK-260) were studied. Pooled mean age was 50.8years in the Ti group, and 53.1years in the PEEK group. Anterior cervical discectomy was performed in 4 studies (395 levels) and transforaminal interbody fusion in 2 studies (192 levels). No statistically significant difference was found between groups with fusion (OR 1.16, 95% C.I 0.59-2.89, p=0.686, I 2 =49.7%) but there was a statistically significant the rate of subsidence with titanium (OR 3.59, 95% C.I 1.28-10.07, p=0.015, I 2 =56.9%) at last follow-up. Titanium and PEEK cages are associated with a similar rate of fusion, but there is an increased rate of subsidence with titanium cage. Future prospective randomized controlled trials are needed to further evaluate these cages using surgical and patient-reported outcomes. Copyright © 2017 Elsevier Ltd. All rights reserved.

One Cold Fusion Speaker is One Too Many for a Future Energy Conference

NASA Astrophysics Data System (ADS)

Vallone, Thomas

2001-04-01

In 1998, a Conference on Future Energy (COFE) was scheduled to take place at the State Department Open Forum in April, 1999. Only one speaker, Ed Storms (formerly with Los Alamos Lab), was scheduled to talk about cold fusion as part of fourteen plenary lectures over a two-day period. However, the entire meeting was labeled a "cold fusion" conference by APS Spokesperson Bob Park who repeated the words four times in one 1999 What's New column. What transpired afterwards has become a part of the cold fusion suppression history, including several APS ``pseudoscience" presentations mocking COFE scientists. A review of the actual COFE contents reveals the rational side of emerging energy technologies normally associated with the scientific process. The Park-related events display an opposite pattern of behavior ultimately designed to discredit the COFE organizer and deprive him of his livelihood (see APS News, March, 2000). The compiled record shows how the communication of scientific information becomes distorted by undue prejudice and unethical lobbying.

Correlated fluorescence-atomic force microscopy studies of the clathrin mediated endocytosis in SKMEL cells

NASA Astrophysics Data System (ADS)

Hor, Amy; Luu, Anh; Kang, Lin; Scott, Brandon; Bailey, Elizabeth; Hoppe, Adam; Smith, Steve

2017-02-01

Clathrin-mediated endocytosis (CME) is one of the central pathways for cargo transport into cells, and plays a major role in the maintenance of cellular functions, such as intercellular signaling, nutrient intake, and turnover of plasma membrane in cells. The clathrin-mediated endocytosis process involves invagination and formation of clathrin-coated vesicles. However, the biophysical mechanisms of vesicle formation are still debated. Currently, there are two models describing membrane bending during the formation of clathrin cages: the first involves the deposition of all clathrin molecules to the plasma membrane, forming a flat lattice prior to membrane bending, whereas in the second model, membrane bending happens simultaneously as the clathrin arrives to the site to form a clathrin-coated cage. We investigate clathrin vesicle formation mechanisms through the utilization of tapping-mode atomic force microscopy for high resolution topographical imaging in neutral buffer solution of unroofed cells exposing the inner membrane, combined with fluorescence imaging to definitively label intracellular constituents with specific fluorophores (actin filaments labeled with green phalloidin and clathrin coated vesicles with the fusion protein Tq2) in SKMEL (Human Melanoma) cells. An extensive statistical survey of many hundreds of CME events, at various stages of progression, are observed via this method, allowing inferences about the dominant mechanisms active in CME in SKMEL cells. Results indicate a mixed model incorporating aspects of both the aforementioned mechanisms for CME.

An optimal set of landmarks for metopic craniosynostosis diagnosis from shape analysis of pediatric CT scans of the head

NASA Astrophysics Data System (ADS)

Mendoza, Carlos S.; Safdar, Nabile; Myers, Emmarie; Kittisarapong, Tanakorn; Rogers, Gary F.; Linguraru, Marius George

2013-02-01

Craniosynostosis (premature fusion of skull sutures) is a severe condition present in one of every 2000 newborns. Metopic craniosynostosis, accounting for 20-27% of cases, is diagnosed qualitatively in terms of skull shape abnormality, a subjective call of the surgeon. In this paper we introduce a new quantitative diagnostic feature for metopic craniosynostosis derived optimally from shape analysis of CT scans of the skull. We built a robust shape analysis pipeline that is capable of obtaining local shape differences in comparison to normal anatomy. Spatial normalization using 7-degree-of-freedom registration of the base of the skull is followed by a novel bone labeling strategy based on graph-cuts according to labeling priors. The statistical shape model built from 94 normal subjects allows matching a patient's anatomy to its most similar normal subject. Subsequently, the computation of local malformations from a normal subject allows characterization of the points of maximum malformation on each of the frontal bones adjacent to the metopic suture, and on the suture itself. Our results show that the malformations at these locations vary significantly (p<0.001) between abnormal/normal subjects and that an accurate diagnosis can be achieved using linear regression from these automatic measurements with an area under the curve for the receiver operating characteristic of 0.97.

A Global Approach for Quantitative Super Resolution and Electron Microscopy on Cryo and Epoxy Sections Using Self-labeling Protein Tags.

PubMed

Müller, Andreas; Neukam, Martin; Ivanova, Anna; Sönmez, Anke; Münster, Carla; Kretschmar, Susanne; Kalaidzidis, Yannis; Kurth, Thomas; Verbavatz, Jean-Marc; Solimena, Michele

2017-02-02

Correlative light and electron microscopy (CLEM) is a powerful approach to investigate the molecular ultrastructure of labeled cell compartments. However, quantitative CLEM studies are rare, mainly due to small sample sizes and the sensitivity of fluorescent proteins to strong fixatives and contrasting reagents for EM. Here, we show that fusion of a self-labeling protein to insulin allows for the quantification of age-distinct insulin granule pools in pancreatic beta cells by a combination of super resolution and transmission electron microscopy on Tokuyasu cryosections. In contrast to fluorescent proteins like GFP organic dyes covalently bound to self-labeling proteins retain their fluorescence also in epoxy resin following high pressure freezing and freeze substitution, or remarkably even after strong chemical fixation. This enables for the assessment of age-defined granule morphology and degradation. Finally, we demonstrate that this CLEM protocol is highly versatile, being suitable for single and dual fluorescent labeling and detection of different proteins with optimal ultrastructure preservation and contrast.

Rational design of a monomeric and photostable far-red fluorescent protein for fluorescence imaging in vivo.

PubMed

Yu, Dan; Dong, Zhiqiang; Gustafson, William Clay; Ruiz-González, Rubén; Signor, Luca; Marzocca, Fanny; Borel, Franck; Klassen, Matthew P; Makhijani, Kalpana; Royant, Antoine; Jan, Yuh-Nung; Weiss, William A; Guo, Su; Shu, Xiaokun

2016-02-01

Fluorescent proteins (FPs) are powerful tools for cell and molecular biology. Here based on structural analysis, a blue-shifted mutant of a recently engineered monomeric infrared fluorescent protein (mIFP) has been rationally designed. This variant, named iBlueberry, bears a single mutation that shifts both excitation and emission spectra by approximately 40 nm. Furthermore, iBlueberry is four times more photostable than mIFP, rendering it more advantageous for imaging protein dynamics. By tagging iBlueberry to centrin, it has been demonstrated that the fusion protein labels the centrosome in the developing zebrafish embryo. Together with GFP-labeled nucleus and tdTomato-labeled plasma membrane, time-lapse imaging to visualize the dynamics of centrosomes in radial glia neural progenitors in the intact zebrafish brain has been demonstrated. It is further shown that iBlueberry can be used together with mIFP in two-color protein labeling in living cells and in two-color tumor labeling in mice. © 2015 The Protein Society.

Multimodality imaging using SPECT/CT and MRI and ligand functionalized 99mTc-labeled magnetic microbubbles

PubMed Central

2013-01-01

Background In the present study, we used multimodal imaging to investigate biodistribution in rats after intravenous administration of a new 99mTc-labeled delivery system consisting of polymer-shelled microbubbles (MBs) functionalized with diethylenetriaminepentaacetic acid (DTPA), thiolated poly(methacrylic acid) (PMAA), chitosan, 1,4,7-triacyclononane-1,4,7-triacetic acid (NOTA), NOTA-super paramagnetic iron oxide nanoparticles (SPION), or DTPA-SPION. Methods Examinations utilizing planar dynamic scintigraphy and hybrid imaging were performed using a commercially available single-photon emission computed tomography (SPECT)/computed tomography (CT) system. For SPION containing MBs, the biodistribution pattern of 99mTc-labeled NOTA-SPION and DTPA-SPION MBs was investigated and co-registered using fusion SPECT/CT and magnetic resonance imaging (MRI). Moreover, to evaluate the biodistribution, organs were removed and radioactivity was measured and calculated as percentage of injected dose. Results SPECT/CT and MRI showed that the distribution of 99mTc-labeled ligand-functionalized MBs varied with the type of ligand as well as with the presence of SPION. The highest uptake was observed in the lungs 1 h post injection of 99mTc-labeled DTPA and chitosan MBs, while a similar distribution to the lungs and the liver was seen after the administration of PMAA MBs. The highest counts of 99mTc-labeled NOTA-SPION and DTPA-SPION MBs were observed in the lungs, liver, and kidneys 1 h post injection. The highest counts were observed in the liver, spleen, and kidneys as confirmed by MRI 24 h post injection. Furthermore, the results obtained from organ measurements were in good agreement with those obtained from SPECT/CT. Conclusions In conclusion, microbubbles functionalized by different ligands can be labeled with radiotracers and utilized for SPECT/CT imaging, while the incorporation of SPION in MB shells enables imaging using MR. Our investigation revealed that biodistribution may be modified using different ligands. Furthermore, using a single contrast agent with fusion SPECT/CT/MR multimodal imaging enables visualization of functional and anatomical information in one image, thus improving the diagnostic benefit for patients. PMID:23442550

Inhibition of Sendai virus fusion with phospholipid vesicles and human erythrocyte membranes by hydrophobic peptides

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

Kelsey, D.R.; Flanagan, T.D.; Young, J.E.

1991-06-01

Hydrophobic di- and tripeptides which are capable of inhibiting enveloped virus infection of cells are also capable of inhibiting at least three different types of membrane fusion events. Large unilamellar vesicles (LUV) of N-methyl dioleoylphosphatidylethanolamine (N-methyl DOPE), containing encapsulated 1-aminonaphthalene-3,6,8-trisulfonic acid (ANTS) and/or p-xylene bis(pyridinium bromide) (DPX), were formed by extrusion. Vesicle fusion and leakage were then monitored with the ANTS/DPX fluorescence assay. Sendai virus fusion with lipid vesicles and Sendai virus fusion with human erythrocyte membranes were measured by following the relief of fluorescence quenching of virus labeled with octadecylrhodamine B chloride (R18). This study found that the effectivenessmore » of the peptides carbobenzoxy-L-Phe-L-Phe (Z-L-Phe-L-Phe), Z-L-Phe, Z-D-Phe, and Z-Gly-L-Phe-L-Phe in inhibiting N-methyl DOPE LUV fusion or fusion of virus with N-methyl DOPE LUV also paralleled their reported ability to block viral infectivity. Furthermore, Z-D-Phe-L-PheGly and Z-Gly-L-Phe inhibited Sendai virus fusion with human erythrocyte membranes with the same relative potency with which they inhibited vesicle-vesicle and virus-vesicle fusion. The evidence suggests a mechanism by which these peptides exert their inhibition of plaque formation by enveloped viruses. This class of inhibitors apparently acts by inhibiting fusion of the viral envelope with the target cell membrane, thereby preventing viral infection. The physical pathway by which these peptides inhibit membrane fusion was investigated. {sup 31}P nuclear magnetic resonance (NMR) of proposed intermediates in the pathway for membrane fusion in LUV revealed that the potent fusion inhibitor Z-D-Phe-L-PheGly selectively altered the structure (or dynamics) of the hypothesized fusion intermediates and that the poor inhibitor Z-Gly-L-Phe did not.« less

Snap-, CLIP- and Halo-Tag Labelling of Budding Yeast Cells

PubMed Central

Stagge, Franziska; Mitronova, Gyuzel Y.; Belov, Vladimir N.; Wurm, Christian A.; Jakobs, Stefan

2013-01-01

Fluorescence microscopy of the localization and the spatial and temporal dynamics of specifically labelled proteins is an indispensable tool in cell biology. Besides fluorescent proteins as tags, tag-mediated labelling utilizing self-labelling proteins as the SNAP-, CLIP-, or the Halo-tag are widely used, flexible labelling systems relying on exogenously supplied fluorophores. Unfortunately, labelling of live budding yeast cells proved to be challenging with these approaches because of the limited accessibility of the cell interior to the dyes. In this study we developed a fast and reliable electroporation-based labelling protocol for living budding yeast cells expressing SNAP-, CLIP-, or Halo-tagged fusion proteins. For the Halo-tag, we demonstrate that it is crucial to use the 6′-carboxy isomers and not the 5′-carboxy isomers of important dyes to ensure cell viability. We report on a simple rule for the analysis of 1H NMR spectra to discriminate between 6′- and 5′-carboxy isomers of fluorescein and rhodamine derivatives. We demonstrate the usability of the labelling protocol by imaging yeast cells with STED super-resolution microscopy and dual colour live cell microscopy. The large number of available fluorophores for these self-labelling proteins and the simplicity of the protocol described here expands the available toolbox for the model organism Saccharomyces cerevisiae. PMID:24205303

An enzyme-free and label-free surface plasmon resonance biosensor for ultrasensitive detection of fusion gene based on DNA self-assembly hydrogel with streptavidin encapsulation.

PubMed

Guo, Bin; Wen, Bo; Cheng, Wei; Zhou, Xiaoyan; Duan, Xiaolei; Zhao, Min; Xia, Qianfeng; Ding, Shijia

2018-07-30

In this research, an enzyme-free and label-free surface plasmon resonance (SPR) biosensing strategy has been developed for ultrasensitive detection of fusion gene based on the heterogeneous target-triggered DNA self-assembly aptamer-based hydrogel with streptavidin (SA) encapsulation. In the presence of target, the capture probes (Cp) immobilized on the chip surface can capture the PML/RARα, forming a Cp-PML/RARα duplex. After that, the aptamer-based network hydrogel nanostructure is formed on the gold surface via target-triggered self-assembly of X shaped polymers. Subsequently, the SA can be encapsulated into hydrogel by the specific binding of SA aptamer, forming the complex with super molecular weight. Thus, the developed strategy achieves dramatic enhancement of the SPR signal. Using PML/RARα "S" subtype as model analyte, the developed biosensing method can detect target down to 45.22 fM with a wide linear range from 100 fM to 10 nM. Moreover, the high efficiency biosensing method shows excellent practical ability to identify the clinical PCR products of PML/RARα. Thus, this proposed strategy presents a powerful platform for ultrasensitive detection of fusion gene and early diagnosis and monitoring of disease. Copyright © 2018 Elsevier B.V. All rights reserved.

Desensitized Optimal Filtering and Sensor Fusion Toolkit

NASA Technical Reports Server (NTRS)

Karlgaard, Christopher D.

2015-01-01

Analytical Mechanics Associates, Inc., has developed a software toolkit that filters and processes navigational data from multiple sensor sources. A key component of the toolkit is a trajectory optimization technique that reduces the sensitivity of Kalman filters with respect to model parameter uncertainties. The sensor fusion toolkit also integrates recent advances in adaptive Kalman and sigma-point filters for non-Gaussian problems with error statistics. This Phase II effort provides new filtering and sensor fusion techniques in a convenient package that can be used as a stand-alone application for ground support and/or onboard use. Its modular architecture enables ready integration with existing tools. A suite of sensor models and noise distribution as well as Monte Carlo analysis capability are included to enable statistical performance evaluations.

Spatial Statistical Data Fusion for Remote Sensing Applications

NASA Technical Reports Server (NTRS)

Nguyen, Hai

2010-01-01

Data fusion is the process of combining information from heterogeneous sources into a single composite picture of the relevant process, such that the composite picture is generally more accurate and complete than that derived from any single source alone. Data collection is often incomplete, sparse, and yields incompatible information. Fusion techniques can make optimal use of such data. When investment in data collection is high, fusion gives the best return. Our study uses data from two satellites: (1) Multiangle Imaging SpectroRadiometer (MISR), (2) Moderate Resolution Imaging Spectroradiometer (MODIS).

Imaging exocytosis of single glucagon-like peptide-1 containing granules in a murine enteroendocrine cell line with total internal reflection fluorescent microscopy

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

Ohara-Imaizumi, Mica; Aoyagi, Kyota; Akimoto, Yoshihiro

To analyze the exocytosis of glucagon-like peptide-1 (GLP-1) granules, we imaged the motion of GLP-1 granules labeled with enhanced yellow fluorescent protein (Venus) fused to human growth hormone (hGH-Venus) in an enteroendocrine cell line, STC-1 cells, by total internal reflection fluorescent (TIRF) microscopy. We found glucose stimulation caused biphasic GLP-1 granule exocytosis: during the first phase, fusion events occurred from two types of granules (previously docked granules and newcomers), and thereafter continuous fusion was observed mostly from newcomers during the second phase. Closely similar to the insulin granule fusion from pancreatic {beta} cells, the regulated biphasic exocytosis from two typesmore » of granules may be a common mechanism in glucose-evoked hormone release from endocrine cells.« less

Number-Theory in Nuclear-Physics in Number-Theory: Non-Primality Factorization As Fission VS. Primality As Fusion; Composites' Islands of INstability: Feshbach-Resonances?

NASA Astrophysics Data System (ADS)

Smith, A.; Siegel, Edward Carl-Ludwig

2011-03-01

Numbers: primality/indivisibility/non-factorization versus compositeness/divisibility/ factorization, often in tandem but not always, provocatively close analogy to nuclear-physics: (2 + 1)=(fusion)=3; (3+1)=(fission)=4[=2 x 2]; (4+1)=(fusion)=5; (5 +1)=(fission)=6[=2 x 3]; (6 + 1)=(fusion)=7; (7+1)=(fission)=8[= 2 x 4 = 2 x 2 x 2]; (8 + 1) =(non: fission nor fusion)= 9[=3 x 3]; then ONLY composites' Islands of fusion-INstability: 8, 9, 10; then 14, 15, 16, ... Could inter-digit Feshbach-resonances exist??? Possible applications to: quantum-information/ computing non-Shore factorization, millennium-problem Riemann-hypotheses proof as Goodkin BEC intersection with graph-theory "short-cut" method: Rayleigh(1870)-Polya(1922)-"Anderson"(1958)-localization, Goldbach-conjecture, financial auditing/accounting as quantum-statistical-physics; ...abound!!! Watkins [www.secamlocal.ex.ac.uk/people/staff/mrwatkin/] "Number-Theory in Physics" many interconnections: "pure"-maths number-theory to physics including Siegel [AMS Joint Mtg.(2002)-Abs.# 973-60-124] inversion of statistics on-average digits' Newcomb(1881)-Weyl(14-16)-Benford(38)-law to reveal both the quantum and BEQS (digits = bosons = digits:"spinEless-boZos"). 1881 1885 1901 1905 1925 < 1927, altering quantum-theory history!!!

Photoactivatable protein labeling by singlet oxygen mediated reactions.

PubMed

To, Tsz-Leung; Medzihradszky, Katalin F; Burlingame, Alma L; DeGrado, William F; Jo, Hyunil; Shu, Xiaokun

2016-07-15

Protein-protein interactions regulate many biological processes. Identification of interacting proteins is thus an important step toward molecular understanding of cell signaling. The aim of this study was to investigate the use of photo-generated singlet oxygen and a small molecule for proximity labeling of interacting proteins in cellular environment. The protein of interest (POI) was fused with a small singlet oxygen photosensitizer (miniSOG), which generates singlet oxygen ((1)O2) upon irradiation. The locally generated singlet oxygen then activated a biotin-conjugated thiol molecule to form a covalent bond with the proteins nearby. The labeled proteins can then be separated and subsequently identified by mass spectrometry. To demonstrate the applicability of this labeling technology, we fused the miniSOG to Skp2, an F-box protein of the SCF ubiquitin ligase, and expressed the fusion protein in mammalian cells and identified that the surface cysteine of its interacting partner Skp1 was labeled by the biotin-thiol molecule. This photoactivatable protein labeling method may find important applications including identification of weak and transient protein-protein interactions in the native cellular context, as well as spatial and temporal control of protein labeling. Copyright © 2016 Elsevier Ltd. All rights reserved.

Optimized labeling of membrane proteins for applications to super-resolution imaging in confined cellular environments using monomeric streptavidin.

PubMed

Chamma, Ingrid; Rossier, Olivier; Giannone, Grégory; Thoumine, Olivier; Sainlos, Matthieu

2017-04-01

Recent progress in super-resolution imaging (SRI) has created a strong need to improve protein labeling with probes of small size that minimize the target-to-label distance, increase labeling density, and efficiently penetrate thick biological tissues. This protocol describes a method for labeling genetically modified proteins incorporating a small biotin acceptor peptide with a 3-nm fluorescent probe, monomeric streptavidin. We show how to express, purify, and conjugate the probe to organic dyes with different fluorescent properties, and how to label selectively biotinylated membrane proteins for SRI techniques (point accumulation in nanoscale topography (PAINT), stimulated emission depletion (STED), stochastic optical reconstruction microscopy (STORM)). This method is complementary to the previously described anti-GFP-nanobody/SNAP-tag strategies, with the main advantage being that it requires only a short 15-amino-acid tag, and can thus be used with proteins resistant to fusion with large tags and for multicolor imaging. The protocol requires standard molecular biology/biochemistry equipment, making it easily accessible for laboratories with only basic skills in cell biology and biochemistry. The production/purification/conjugation steps take ∼5 d, and labeling takes a few minutes to an hour.

Return to golf after spine surgery.

PubMed

Abla, Adib A; Maroon, Joseph C; Lochhead, Richard; Sonntag, Volker K H; Maroon, Adara; Field, Melvin

2011-01-01

no published evidence indicates when patients can resume golfing after spine surgery. The objective of this study is to provide data from surveys sent to spine surgeons. a survey of North American Spine Society members was undertaken querying the suggested timing of return to golf. Of 1000 spine surgeons surveyed, 523 responded (52.3%). The timing of recommended return to golf and the reasons were questioned for college/professional athletes and avid and recreational golfers of both sexes. Responses were tallied for lumbar laminectomy, lumbar microdiscectomy, lumbar fusion, and anterior cervical discectomy with fusion. the most common recommended time for return to golf was 4-8 weeks after lumbar laminectomy and lumbar microdiscectomy, 2-3 months after anterior cervical fusion, and 6 months after lumbar fusion. The results showed a statistically significant increase in the recommended time to resume golf after lumbar fusion than after cervical fusion in all patients (p < 0.01). The same holds true for the return to play after cervical fusion compared with either lumbar laminectomy or lumbar microdiscectomy for all golfer types (p < 0.01). There was a statistically significant shorter recommended time for professional and college golfers compared with noncompetitive golfers after lumbar fusion (p < 0.01), anterior cervical discectomy and fusion (p < 0.01), and lumbar microdiscectomy (p < 0.01). the return to golf after spine surgery depends on many variables, including the general well-being of patients in terms of pain control and comfort when golfing. This survey serves as a guide that can assist medical practitioners in telling patients the average times recommended by surgeons across North America regarding return to golf after spine surgery.

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

Beavin, P. Jr.

A rapid direct dilution procedure for the estimation of soluble zirconium and a fusion procedure for the determination of total zirconium (soluble and insoluble forms) in cream base concentrates prepared from antiperspirant aerosols are described. The direct dilution procedure involves extraction of soluble zirconium with HCl (55 + 45). The filtered extract is reacted with alizarin red S to form a stable colored complex which is measured spectrophotometrically. The fusion procedure involves ashing the aerosol concentrate followed by fusion of the ash with potassium pyrosulfate to form an acid-soluble melt. Zirconium is precipitated from solution as the hydroxide and washedmore » to eliminate interfering ions, particularly sulfate. After redissolving in HCl (55 + 45) and reacting with alizarin red S, total zirconium is measured. Zirconyl chloride octahydrate, assayed gravimetrically by hydroxide precipitation and conversion to the oxide, is used as the zirconium reference standard. Concentration range of zirconium measured was 200 to 500 ..mu..g/100 ml. Recoveries of standard zirconium added to commercial aerosols labeled to contain aluminum and zirconyl hydroxychlorides ranged from 97 to 101 percent by the fusion procedure. Analysis of these aerosols by direct dilution gave generally slightly lower results than by fusion.« less

Fusion, rupture, and degeneration: the fate of in vivo-labelled PSVs in developing barley endosperm *

PubMed Central

Ibl, Verena; Kapusi, Eszter; Arcalis, Elsa; Kawagoe, Yasushi; Stoger, Eva

2014-01-01

Cereal endosperm is a highly differentiated tissue containing specialized organelles for the accumulation of storage proteins. The endosperm of barley contains hordeins, which are ultimately deposited within protein storage vacuoles (PSVs). These organelles have been characterized predominantly by the histochemical analysis of fixed immature tissue samples. However, little is known about the fate of PSVs during barley endosperm development, and in vivo imaging has not been attempted in order to gain further insight. In this report, young seeds were followed through development to characterize the dynamic morphology of PSVs from aleurone, subaleurone, and central starchy endosperm cells. TIP3-GFP was used as a PSV membrane marker and several fluorescent tracers were used to identify membranes and monitor endomembrane organelles in real time. Whereas the spherical appearance of strongly labelled TIP3-GFP PSVs in the aleurone remained constant, those in the subaleurone and central starchy endosperm underwent substantial morphological changes. Fusion and rupture events were observed in the subaleurone, and internal membranes derived from both the tonoplast and endoplasmic reticulum were identified within these PSVs. TIP3-GFP-labelled PSVs in the starchy endosperm cells underwent a dramatic reduction in size, so that finally the protein bodies were tightly enclosed. Potential desiccation-related membrane-altering processes that may be causally linked to these dynamic endomembrane events in the barley endosperm are discussed. PMID:24803499

Face-iris multimodal biometric scheme based on feature level fusion

NASA Astrophysics Data System (ADS)

Huo, Guang; Liu, Yuanning; Zhu, Xiaodong; Dong, Hongxing; He, Fei

2015-11-01

Unlike score level fusion, feature level fusion demands all the features extracted from unimodal traits with high distinguishability, as well as homogeneity and compatibility, which is difficult to achieve. Therefore, most multimodal biometric research focuses on score level fusion, whereas few investigate feature level fusion. We propose a face-iris recognition method based on feature level fusion. We build a special two-dimensional-Gabor filter bank to extract local texture features from face and iris images, and then transform them by histogram statistics into an energy-orientation variance histogram feature with lower dimensions and higher distinguishability. Finally, through a fusion-recognition strategy based on principal components analysis and support vector machine (FRSPS), feature level fusion and one-to-n identification are accomplished. The experimental results demonstrate that this method can not only effectively extract face and iris features but also provide higher recognition accuracy. Compared with some state-of-the-art fusion methods, the proposed method has a significant performance advantage.

/sup 18/O + /sup 12/C fusion-evaporation reaction

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

Heusch, B; Beck, C; Coffin, J P

1980-01-01

A study of the /sup 18/O + /sup 12/C fusion evaporation reaction has been undertaken for 2 reasons: to make a systematic study of the formation cross section for each individual evaporation residue over a broad excitation energy region in the compound nucleus /sup 30/Si:30 to 62 MeV; and to compare all results to fusion-evaporation calculations done in the framework of the Hauser-Feschbach statistical model.

Deep learning and texture-based semantic label fusion for brain tumor segmentation

NASA Astrophysics Data System (ADS)

Vidyaratne, L.; Alam, M.; Shboul, Z.; Iftekharuddin, K. M.

2018-02-01

Brain tumor segmentation is a fundamental step in surgical treatment and therapy. Many hand-crafted and learning based methods have been proposed for automatic brain tumor segmentation from MRI. Studies have shown that these approaches have their inherent advantages and limitations. This work proposes a semantic label fusion algorithm by combining two representative state-of-the-art segmentation algorithms: texture based hand-crafted, and deep learning based methods to obtain robust tumor segmentation. We evaluate the proposed method using publicly available BRATS 2017 brain tumor segmentation challenge dataset. The results show that the proposed method offers improved segmentation by alleviating inherent weaknesses: extensive false positives in texture based method, and the false tumor tissue classification problem in deep learning method, respectively. Furthermore, we investigate the effect of patient's gender on the segmentation performance using a subset of validation dataset. Note the substantial improvement in brain tumor segmentation performance proposed in this work has recently enabled us to secure the first place by our group in overall patient survival prediction task at the BRATS 2017 challenge.

Deep Learning and Texture-Based Semantic Label Fusion for Brain Tumor Segmentation.

PubMed

Vidyaratne, L; Alam, M; Shboul, Z; Iftekharuddin, K M

2018-01-01

Brain tumor segmentation is a fundamental step in surgical treatment and therapy. Many hand-crafted and learning based methods have been proposed for automatic brain tumor segmentation from MRI. Studies have shown that these approaches have their inherent advantages and limitations. This work proposes a semantic label fusion algorithm by combining two representative state-of-the-art segmentation algorithms: texture based hand-crafted, and deep learning based methods to obtain robust tumor segmentation. We evaluate the proposed method using publicly available BRATS 2017 brain tumor segmentation challenge dataset. The results show that the proposed method offers improved segmentation by alleviating inherent weaknesses: extensive false positives in texture based method, and the false tumor tissue classification problem in deep learning method, respectively. Furthermore, we investigate the effect of patient's gender on the segmentation performance using a subset of validation dataset. Note the substantial improvement in brain tumor segmentation performance proposed in this work has recently enabled us to secure the first place by our group in overall patient survival prediction task at the BRATS 2017 challenge.

An SH2 domain-based tyrosine kinase assay using biotin ligase modified with a terbium(III) complex.

PubMed

Sueda, Shinji; Shinboku, Yuki; Kusaba, Takeshi

2013-01-01

Src homology 2 (SH2) domains are modules of approximately 100 amino acids and are known to bind phosphotyrosine-containing sequences with high affinity and specificity. In the present work, we developed an SH2 domain-based assay for Src tyrosine kinase using a unique biotinylation reaction from archaeon Sulfolobus tokodaii. S. tokodaii biotinylation has a unique property that biotin protein ligase (BPL) forms a stable complex with its biotinylated substrate protein (BCCP). Here, an SH2 domain from lymphocyte-specific tyrosine kinase was genetically fused to a truncated BCCP, and the resulting fusion protein was labeled through biotinylation with BPL carrying multiple copies of a luminescent Tb(3+) complex. The labeled SH2 fusion proteins were employed to detect a phosphorylated peptide immobilized on the surface of the microtiter plate, where the phosphorylated peptide was produced by phosphorylation to the substrate peptide by Src tyrosine kinase. Our assay allows for a reliable determination of the activity of Src kinase lower than 10 pg/μL by a simple procedure.

Correlated Fluorescence-Atomic Force Microscopy Studies of the Clathrin Mediated Endocytosis in SKMEL Cells

NASA Astrophysics Data System (ADS)

Smith, Steve; Hor, Amy; Luu, Anh; Kang, Lin; Scott, Brandon; Bailey, Elizabeth; Hoppe, Adam

Clathrin-mediated endocytosis is one of the central pathways for cargo transport into cells, and plays a major role in the maintenance of cellular functions, such as intercellular signaling, nutrient intake, and turnover of plasma membrane in cells. The clathrin-mediated endocytosis process involves invagination and formation of clathrin-coated vesicles. However, the biophysical mechanisms of vesicle formation are still debated. We investigate clathrin vesicle formation mechanisms through the utilization of tapping-mode atomic force microscopy for high resolution topographical imaging in neutral buffer solution of unroofed cells exposing the inner membrane, combined with fluorescence imaging to definitively label intracellular constituents with specific fluorescent fusion proteins (actin filaments labeled with green phalloidin-antibody and clathrin coated vesicles with the fusion protein Tq2) in SKMEL (Human Melanoma) cells. Results from our work are compared against dynamical polarized total internal fluorescence (TIRF), super-resolution photo-activated localization microscopy (PALM) and transmission electron microscopy (TEM) to draw conclusions regarding the prominent model of vesicle formation in clathrin-mediated endocytosis. Funding provided by NSF MPS/DMR/BMAT award # 1206908.

A global map of rainfed cropland areas (GMRCA) at the end of last millennium using remote sensing

USGS Publications Warehouse

Biradar, C.M.; Thenkabail, P.S.; Noojipady, P.; Li, Y.; Dheeravath, V.; Turral, H.; Velpuri, M.; Gumma, M.K.; Gangalakunta, O.R.P.; Cai, X.L.; Xiao, X.; Schull, M.A.; Alankara, R.D.; Gunasinghe, S.; Mohideen, S.

2009-01-01

The overarching goal of this study was to produce a global map of rainfed cropland areas (GMRCA) and calculate country-by-country rainfed area statistics using remote sensing data. A suite of spatial datasets, methods and protocols for mapping GMRCA were described. These consist of: (a) data fusion and composition of multi-resolution time-series mega-file data-cube (MFDC), (b) image segmentation based on precipitation, temperature, and elevation zones, (c) spectral correlation similarity (SCS), (d) protocols for class identification and labeling through uses of SCS R2-values, bi-spectral plots, space-time spiral curves (ST-SCs), rich source of field-plot data, and zoom-in-views of Google Earth (GE), and (e) techniques for resolving mixed classes by decision tree algorithms, and spatial modeling. The outcome was a 9-class GMRCA from which country-by-country rainfed area statistics were computed for the end of the last millennium. The global rainfed cropland area estimate from the GMRCA 9-class map was 1.13 billion hectares (Bha). The total global cropland areas (rainfed plus irrigated) was 1.53 Bha which was close to national statistics compiled by FAOSTAT (1.51 Bha). The accuracies and errors of GMRCA were assessed using field-plot and Google Earth data points. The accuracy varied between 92 and 98% with kappa value of about 0.76, errors of omission of 2-8%, and the errors of commission of 19-36%. ?? 2008 Elsevier B.V.

Fluorescent labeling of SNAP-tagged proteins in cells.

PubMed

Lukinavičius, Gražvydas; Reymond, Luc; Johnsson, Kai

2015-01-01

One of the most prominent self-labeling tags is SNAP-tag. It is an in vitro evolution product of the human DNA repair protein O (6)-alkylguanine-DNA alkyltransferase (hAGT) that reacts specifically with benzylguanine (BG) and benzylchloropyrimidine (CP) derivatives, leading to covalent labeling of SNAP-tag with a synthetic probe (Gronemeyer et al., Protein Eng Des Sel 19:309-316, 2006; Curr Opin Biotechnol 16:453-458, 2005; Keppler et al., Nat Biotechnol 21:86-89, 2003; Proc Natl Acad Sci U S A 101:9955-9959, 2004). SNAP-tag is well suited for the analysis and quantification of fused target protein using fluorescence microscopy techniques. It provides a simple, robust, and versatile approach to the imaging of fusion proteins under a wide range of experimental conditions.

Bacterial Expression and Purification of the Amyloidogenic Peptide PAPf39 for Multidimensional NMR Spectroscopy

PubMed Central

Shanmuganathan, Aranganathan; Bishop, Anthony C.; French, Kinsley C.; McCallum, Scott A.; Makhatadze, George I.

2013-01-01

PAPf39 is a 39 residue peptide fragment from human prostatic acidic phosphatase that forms amyloid fibrils in semen. These fibrils have been implicated in facilitating HIV transmission. To enable structural studies of PAPf39 by NMR spectroscopy, efficient methods allowing the production of milligram quantities of isotopically labeled peptide are essential. Here, we report the high-yield expression, as a fusion to ubiquitin at the N-terminus and an intein at the C-terminus, and purification of uniformly labeled 13C- and 15N-labeled PAPf39 peptide. This allows the study of the PAPf39 monomer conformational ensemble by NMR spectroscopy. To this end, we performed the NMR chemical shift assignment of the PAPf39 peptide in the monomeric state at low pH. PMID:23314347

Consumer knowledge and attitudes toward nutritional labels.

PubMed

Cannoosamy, Komeela; Pugo-Gunsam, Prity; Jeewon, Rajesh

2014-01-01

To determine Mauritian consumers' attitudes toward nutritional labels based on the Kano model and to identify determinants of the use and understanding of nutrition labels. The researchers also used a Kano model questionnaire to determine consumers' attitudes toward nutrition labeling. Four hundred consumers residing in Mauritius. Information was elicited via a questionnaire that assessed nutritional knowledge and information about the use and understanding of nutritional labels and demographic factors. Nutritional label use and understanding, nutrition knowledge, and association of demographic factors with label use. Statistical tests performed included 1-way ANOVA and independent samples t tests. Statistically significant relationships (P < .05) were found for nutritional knowledge and nutritional label usage with demographic factors. All demographic factors with the exception of gender were significantly associated (P < .05) with nutritional label understanding. Based on the outcome of the Kano survey, calorie content, trans fat content, protein content, and cholesterol content were found to be must-be attributes: that is, attributes that, when not present, result in consumer dissatisfaction. Age, education, income, household size, and nutrition knowledge had an impact on nutritional label use. Health promoters should aim to increase the use of nutritional labels. Copyright © 2014 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.

[Analyses of segment motor function in patients with degenerative lumbar disease on the treatment of WavefleX dynamic stabilization system].

PubMed

Wu, Junsong; Du, Junhua; Jiang, Xiangyun; Wang, Quan; Li, Xigong; Du, Jingyu; Lin, Xiangjin

2014-06-17

To explore the changes of range-of-motion (ROM) in patients with degenerative lumbar disease on the treatment of WavefleX dynamic stabilization system and examine the postoperative lumbar regularity and tendency of ROM. Nine patients with degenerative lumbar disease on the treatment of WavefleX dynamic stabilization system were followed up with respect to ROMs at 5 timepoints within 12 months. Records of ROM were made for instrumented segments, adjacent segments and total lumbar. Compared with preoperation, ROMs in non-fusional segments with WavefleX dynamic stabilization system decreased statistical significantly (P < 0.05 or P < 0.01) at different timepoints; ROMs in adjacent segments increased at some levels without wide statistical significance. The exception was single L3/4 at Month 12 (P < 0.05) versus control group simultaneously at the levels of L3/4, L4/5 and L5/S1, ROMs decreased at Months 6 and 12 with wide statistical significance (P < 0.05 or P < 0.01). ROMs in total lumbar had statistical significant decrease (P < 0.01) in both group of non-fusional segments and hybrid group of non-fusion and fusion. The trends of continuous augments were observed during follow-ups. Statistically significant augments were also acquired at 4 timepoints as compared to control group (P < 0.01). The treatment of degenerative lumbar diseases with WavefleX dynamic stabilization system may limit excessive extension/inflexion and preserve some motor functions. Moreover, it can sustain physiological lordosis, decrease and transfer disc load in adjacent segments to prevent early degeneration of adjacent segment. Trends of motor function augment in total lumbar need to be confirmed during future long-term follow-ups.

Endo-β-Glucosidase Tag Allows Dual Detection of Fusion Proteins by Fluorescent Mechanism-Based Probes and Activity Measurement.

PubMed

Kallemeijn, Wouter W; Scheij, Saskia; Voorn-Brouwer, Tineke M; Witte, Martin D; Verhoek, Marri; Overkleeft, Hermen S; Boot, Rolf G; Aerts, Johannes M F G

2016-09-15

β-Glucoside-configured cyclophellitols are activity-based probes (ABPs) that allow sensitive detection of β-glucosidases. Their applicability to detect proteins fused with β-glucosidase was investigated in the cellular context. The tag was Rhodococcus sp. M-777 endoglycoceramidase II (EGCaseII), based on its lack of glycans and ability to hydrolyze fluorogenic 4-methylumbelliferyl β-d-lactoside (an activity absent in mammalian cells). Specific dual detection of fusion proteins was possible in vitro and in situ by using fluorescent ABPs and a fluorogenic substrate. Pre-blocking with conduritol β-epoxide (a poor inhibitor of EGCaseII) eliminated ABP labeling of endogenous β-glucosidases. ABPs equipped with biotin allowed convenient purification of the fusion proteins. Diversification of ABPs (distinct fluorophores, fluorogenic high-resolution detection moieties) should assist further research in living cells and organisms. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A new microcolumn-type microchip for examining the expression of chimeric fusion genes using a nucleic acid sandwich hybridization technique.

PubMed

Ohnishi, Michihiro; Sasaki, Naoyuki; Kishimoto, Takuya; Watanabe, Hidetoshi; Takagi, Masatoshi; Mizutani, Shuki; Kishii, Noriyuki; Yasuda, Akio

2014-11-01

We report a new type of microcolumn installed in a microchip. The architecture allows use of a nucleic acid sandwich hybridization technique to detect a messenger RNA (mRNA) chain as a target. Data are presented that demonstrate that the expression of a chimeric fusion gene can be detected. The microcolumn was filled with semi-transparent microbeads made of agarose gel that acted as carriers, allowing increased efficiency of the optical detection of fluorescence from the microcolumn. The hybrid between the target trapped on the microbeads and a probe DNA labeled with a fluorescent dye was detected by measuring the intensity of the fluorescence from the microcolumn directly. These results demonstrate an easy and simple method for determining the expression of chimeric fusion genes with no preamplification. Copyright © 2014 Elsevier B.V. All rights reserved.

Allorecognition triggers autophagy and subsequent necrosis in the cnidarian Hydractinia symbiolongicarpus.

PubMed

Buss, Leo W; Anderson, Christopher; Westerman, Erica; Kritzberger, Chad; Poudyal, Monita; Moreno, Maria A; Lakkis, Fadi G

2012-01-01

Transitory fusion is an allorecognition phenotype displayed by the colonial hydroid Hydractinia symbiolongicarpus when interacting colonies share some, but not all, loci within the allorecognition gene complex (ARC). The phenotype is characterized by an initial fusion followed by subsequent cell death resulting in separation of the two incompatible colonies. We here characterize this cell death process using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and continuous in vivo digital microscopy. These techniques reveal widespread autophagy and subsequent necrosis in both colony and grafted polyp assays. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assays and ultrastructural observations revealed no evidence of apoptosis. Pharmacological inhibition of autophagy using 3-methyladenine (3-MA) completely suppressed transitory fusion in vivo in colony assays. Rapamycin did not have a significant effect in the same assays. These results establish the hydroid allorecognition system as a novel model for the study of cell death.

TH-CD-206-02: BEST IN PHYSICS (IMAGING): 3D Prostate Segmentation in MR Images Using Patch-Based Anatomical Signature

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

Yang, X; Jani, A; Rossi, P

Purpose: MRI has shown promise in identifying prostate tumors with high sensitivity and specificity for the detection of prostate cancer. Accurate segmentation of the prostate plays a key role various tasks: to accurately localize prostate boundaries for biopsy needle placement and radiotherapy, to initialize multi-modal registration algorithms or to obtain the region of interest for computer-aided detection of prostate cancer. However, manual segmentation during biopsy or radiation therapy can be time consuming and subject to inter- and intra-observer variation. This study’s purpose it to develop an automated method to address this technical challenge. Methods: We present an automated multi-atlas segmentationmore » for MR prostate segmentation using patch-based label fusion. After an initial preprocessing for all images, all the atlases are non-rigidly registered to a target image. And then, the resulting transformation is used to propagate the anatomical structure labels of the atlas into the space of the target image. The top L similar atlases are further chosen by measuring intensity and structure difference in the region of interest around prostate. Finally, using voxel weighting based on patch-based anatomical signature, the label that the majority of all warped labels predict for each voxel is used for the final segmentation of the target image. Results: This segmentation technique was validated with a clinical study of 13 patients. The accuracy of our approach was assessed using the manual segmentation (gold standard). The mean volume Dice Overlap Coefficient was 89.5±2.9% between our and manual segmentation, which indicate that the automatic segmentation method works well and could be used for 3D MRI-guided prostate intervention. Conclusion: We have developed a new prostate segmentation approach based on the optimal feature learning label fusion framework, demonstrated its clinical feasibility, and validated its accuracy. This segmentation technique could be a useful tool in image-guided interventions for prostate-cancer diagnosis and treatment.« less

Fusion between Intestinal epithelial cells and macrophages in a cancer context results in nuclear reprogramming.

PubMed

Powell, Anne E; Anderson, Eric C; Davies, Paige S; Silk, Alain D; Pelz, Carl; Impey, Soren; Wong, Melissa H

2011-02-15

The most deadly phase in cancer progression is attributed to the inappropriate acquisition of molecular machinery leading to metastatic transformation and spread of disease to distant organs. Although it is appreciated that metastasis involves epithelial-mesenchymal interplay, the underlying mechanism defining this process is poorly understood. Specifically, how cancer cells evade immune surveillance and gain the ability to navigate the circulatory system remains a focus. One possible mechanism underlying metastatic conversion is fusion between blood-derived immune cells and cancer cells. While this notion is a century old, in vivo evidence that cell fusion occurs within tumors and imparts genetic or physiologic changes remains controversial. We have previously demonstrated in vivo cell fusion between blood cells and intestinal epithelial cells in an injury setting. Here, we hypothesize that immune cells, such as macrophages, fuse with tumor cells imparting metastatic capabilities by transferring their cellular identity. We used parabiosis to introduce fluorescent-labeled bone marrow-derived cells to mice with intestinal tumors, finding that fusion between circulating blood-derived cells and tumor epithelium occurs during the natural course of tumorigenesis. Moreover, we identify the macrophage as a key cellular partner for this process. Interestingly, cell fusion hybrids retain a transcriptome identity characteristic of both parental derivatives, while also expressing a unique subset of transcripts. Our data supports the novel possibility that tumorigenic cell fusion may impart physical behavior attributed to migratory macrophages, including navigation of circulation and immune evasion. As such, cell fusion may represent a promising novel mechanism underlying the metastatic conversion of cancer cells. ©2011 AACR.

Bone Morphogenetic Proteins in Anterior Cervical Fusion: A Systematic Review and Meta-Analysis.

PubMed

Zadegan, Shayan Abdollah; Abedi, Aidin; Jazayeri, Seyed Behnam; Nasiri Bonaki, Hirbod; Jazayeri, Seyed Behzad; Vaccaro, Alexander R; Rahimi-Movaghar, Vafa

2017-08-01

Bone morphogenetic proteins (BMPs) have been commonly used as a graft substitute in spinal fusion. Although the U.S. Food and Drug Administration issued a warning on life-threatening complications of recombinant human BMPs (rhBMPs) in cervical spine fusion in 2008, their off-label use has been continued. This investigation aimed to review the evidence for the use of rhBMP-2 and rhBMP-7 in anterior cervical spine fusions. A comprehensive search was performed through Ovid (MEDLINE), PubMed, and Embase. The risk of bias assessment was according to the recommended criteria by the Cochrane Back and Neck group and MINORS (Methodological Index for Non-Randomized Studies). A wide array of radiographic and clinical outcomes including the adverse events were collated. Eighteen articles (1 randomized and 17 nonrandomized) were eligible for inclusion. The fusion rate was higher with use of rhBMP in most studies and our meta-analysis of the pooled data from 4782 patients confirmed this finding (odds ratio, 5.45; P < 0.00001). Altogether, the rhBMP and control groups were comparable in patient-reported outcomes. However, most studies tended to show a significantly higher incidence of overall complication rate, dysphagia/dysphonia, cervical swelling, readmission, wound complications, neurologic complications, and ossification. Application of rhBMPs in cervical spine fusion yields a significantly higher fusion rate with similar patient-reported outcomes, yet increased risk of life-threatening complications. Thus, we do not recommend the use of rhBMP in anterior cervical fusions. Copyright © 2017 Elsevier Inc. All rights reserved.

Granule mobility, fusion frequency and insulin secretion are differentially affected by insulinotropic stimuli.

PubMed

Schumacher, Kirstin; Matz, Magnus; Brüning, Dennis; Baumann, Knut; Rustenbeck, Ingo

2015-05-01

The pre-exocytotic behavior of insulin granules was studied against the background of the entirety of submembrane granules in MIN6 cells, and the characteristics were compared with the macroscopic secretion pattern and the cytosolic Ca(2+) concentration of MIN6 pseudo-islets at 22°C, 32°C and 37°C. The mobility of granules labeled by insulin-EGFP and the fusion events were assessed by TIRF microscopy utilizing an observer-independent algorithm. In the z-dimension, 40 mm K(+) or 30 mm glucose increased the granule turnover. The effect of high K(+) was quickly reversible. The increase by glucose was more sustained and modified the efficacy of a subsequent K(+) stimulus. The effect size of glucose increased with physiological temperature whereas that of high K(+) did not. The mobility in the x/y-dimension and the fusion rates were little affected by the stimuli, in contrast to secretion. Fusion and secretion, however, had the same temperature dependence. Granules that appeared and fused within one image sequence had significantly larger caging diameters than pre-existent granules that underwent fusion. These in turn had a different mobility than residence-matched non-fusing granules. In conclusion, delivery to the membrane, tethering and fusion of granules are differently affected by insulinotropic stimuli. Fusion rates and secretion do not appear to be tightly coupled. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Recoil-Implantation Of Multiple Radioisotopes Towards Wear Rate Measurements And Particle Tracing In Prosthetic Joints

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

Warner, Jacob A.; Timmers, Heiko; Smith, Paul N.

2011-06-01

This study demonstrates a new method of radioisotope labeling of ultra-high molecular weight polyethylene inserts in prosthetic joints for wear studies. The radioisotopes {sup 97}Ru, {sup 100}Pd, {sup 100}Rh, and {sup 101m}Rh are produced in fusion evaporation reactions induced by {sup 12}C ions in a {sup 92}Zr target foil. The fusion products recoil-implant into ultra-high molecular weight polyethylene plugs, machined to fit into the surface of the inserts. During laboratory simulations of the joint motion, a wear rate of the labeled polyethylene may be measured and the pathways of wear debris particles can be traced by detecting characteristic gamma-rays. Themore » concentration profiles of the radioisotopes extend effectively uniformly from the polyethylene surface to a depth of about 4 {mu}m. The multiplicity of labeling and the use of several gamma-ray lines aids with avoiding systematic measurement uncertainties. Two polyethylene plugs were labeled and one was fitted into the surface of the tibial insert of a knee prosthesis, which had been worn in. Actuation over close to 100,000 cycles with a 900 N axial load and a 24 deg. flexion angle removed (14{+-}1)% of the gamma-ray activity from the plug. Most of this activity dispersed into the serum lubricant identifying this as the important debris pathway. Less than 1% activity was transferred to the femoral component of the prosthesis and the measured activity on the tibial tray was insignificant. Assuming uniform wear across the superior surface of the insert, a wear rate of (12{+-}3) mm{sup 3}/Megacycle was determined. This is consistent with wear rate measurements under similar conditions using other techniques.« less

The C. elegans Excretory Canal as a Model for Intracellular Lumen Morphogenesis and In Vivo Polarized Membrane Biogenesis in a Single Cell: labeling by GFP-fusions, RNAi Interaction Screen and Imaging.

PubMed

Zhang, Nan; Membreno, Edward; Raj, Susan; Zhang, Hongjie; Khan, Liakot A; Gobel, Verena

2017-10-03

The four C. elegans excretory canals are narrow tubes extended through the length of the animal from a single cell, with almost equally far extended intracellular endotubes that build and stabilize the lumen with a membrane and submembraneous cytoskeleton of apical character. The excretory cell expands its length approximately 2,000 times to generate these canals, making this model unique for the in vivo assessment of de novo polarized membrane biogenesis, intracellular lumen morphogenesis and unicellular tubulogenesis. The protocol presented here shows how to combine standard labeling, gain- and loss-of-function genetic or RNA interference (RNAi)-, and microscopic approaches to use this model to visually dissect and functionally analyze these processes on a molecular level. As an example of a labeling approach, the protocol outlines the generation of transgenic animals with fluorescent fusion proteins for live analysis of tubulogenesis. As an example of a genetic approach, it highlights key points of a visual RNAi-based interaction screen designed to modify a gain-of-function cystic canal phenotype. The specific methods described are how to: label and visualize the canals by expressing fluorescent proteins; construct a targeted RNAi library and strategize RNAi screening for the molecular analysis of canal morphogenesis; visually assess modifications of canal phenotypes; score them by dissecting fluorescence microscopy; characterize subcellular canal components at higher resolution by confocal microscopy; and quantify visual parameters. The approach is useful for the investigator who is interested in taking advantage of the C. elegans excretory canal for identifying and characterizing genes involved in the phylogenetically conserved processes of intracellular lumen and unicellular tube morphogenesis.

Evidence for biphasic uncoating during HIV-1 infection from a novel imaging assay

PubMed Central

2013-01-01

Background Uncoating of the HIV-1 core plays a critical role during early post-fusion stages of infection but is poorly understood. Microscopy-based assays are unable to easily distinguish between intact and partially uncoated viral cores. Results In this study, we used 5-ethynyl uridine (EU) to label viral-associated RNA during HIV production. At early time points after infection with EU-labeled virions, the viral-associated RNA was stained with an EU-specific dye and was detected by confocal microscopy together with viral proteins. We observed that detection of the viral-associated RNA was specific for EU-labeled virions, was detected only after viral fusion with target cells, and occurred after an initial opening of the core. In vitro staining of cores showed that the opening of the core allowed the small molecule dye, but not RNase A or antibodies, inside. Also, staining of the viral-associated RNA, which is co-localized with nucleocapsid, decays over time after viral infection. The decay rate of RNA staining is dependent on capsid (CA) stability, which was altered by CA mutations or a small molecule inducer of HIV-1 uncoating. While the staining of EU-labeled RNA was not affected by inhibition of reverse transcription, the kinetics of core opening of different CA mutants correlated with initiation of reverse transcription. Analysis of the E45A CA mutant suggests that initial core opening is independent of complete capsid disassembly. Conclusions Taken together, our results establish a novel RNA accessibility-based assay that detects an early event in HIV-1 uncoating and can be used to further define this process. PMID:23835323

Characterization of MCSF-induced proliferation and subsequent osteoclast formation in murine marrow culture.

PubMed

Biskobing, D M; Fan, X; Rubin, J

1995-07-01

To clarify events involved in 1,25(OH)2D3-stimulated osteoclast-like cell (OCLC) formation in primary murine marrow culture, we have characterized kinetics of precursor proliferation and fusion and their dependence on macrophage colony-stimulating factor (MCSF). 3H-thymidine nuclear incorporation in tartrate-resistant acid phosphatase positive multinucleated cells (TRAP+ MNCs) was assessed: 3H-thymidine incorporation was greatest when tracer was added during day 4 or 5, with labeled nuclei in 81% (day 4) and 90% (day 5) of the TRAP+ MNCs counted at the end of day 7. The percentage of total nuclei labeled was highest when 3H-thymidine was dosed on day 4 (58%), decreasing to 2% by day 7. Final TRAP+ MNC numbers were depleted by 80% when treated for 24 h with hydroxyurea on either day 3 or 4; this inhibition dropped to 57% and 12% when hydroxyurea was pulsed during days 5 or 6, respectively. The absence of 1,25(OH)2D3 during days 1-4 caused 70% attenuation of TRAP+ MNC formation; however, exposure to 3H-thymidine during day 4 in this experiment resulted in subsequent labeling of 81% of the TRAP+ MNCs formed, indicating that precursor proliferation occurred in the absence of 1,25(OH)2D3. To demonstrate that proliferation required MCSF, cultures were exposed to a monoclonal anti-MCSF antibody during days 3, 4, 5, 6, or 7. Inhibition of TRAP+ MNC formation was 85% when antibody was added during day 3. Antibody treatment after day 5 had little effect on the OCLC number. Fusion of precursors showed steady progression with OCLCs containing 4.8 +/- 0.3 nuclei at the end of day 4, 8.3 +/- 0.5 nuclei after day 5, 12.0 +/- 1.3 after day 6, and 13.7 +/- 1.5 at the end of day 7. This steady accretion of nuclei was unaffected by doses of MCSF antibody which blocked proliferation. In conclusion, we have shown that OCLCs arise from an MCSF-dependent expansion of the precursor pool occurring during days 3 and 4. Fusion of these precursors, which begins as proliferation diminishes, is able to progress in the presence of anti-MCSF antibody. These results should help refine the analysis of factors affecting proliferation and fusion of osteoclasts in murine marrow culture.

Enhanced metastatic capacity of breast cancer cells after interaction and hybrid formation with mesenchymal stroma/stem cells (MSC).

PubMed

Melzer, Catharina; von der Ohe, Juliane; Hass, Ralf

2018-01-05

Fusion of breast cancer cells with tumor-associated populations of the microenvironment including mesenchymal stroma/stem-like cells (MSC) represents a rare event in cell communication whereby the metastatic capacity of those hybrid cells remains unclear. Functional changes were investigated in vitro and in vivo following spontaneous fusion and hybrid cell formation between primary human MSC and human MDA-MB-231 breast cancer cells. Thus, lentiviral eGFP-labeled MSC and breast cancer cells labeled with mcherry resulted in dual-fluorescing hybrid cells after co-culture. Double FACS sorting and single cell cloning revealed two different aneuploid male hybrid populations (MDA-hyb1 and MDA-hyb2) with different STR profiles, pronounced telomerase activities, and enhanced proliferative capacities as compared to the parental cells. Microarray-based mRNA profiling demonstrated marked regulation of genes involved in epithelial-mesenchymal transition and increased expression of metastasis-associated genes including S100A4. In vivo studies following subcutaneous injection of the breast cancer and the two hybrid populations substantiated the in vitro findings by a significantly elevated tumor growth of the hybrid cells. Moreover, both hybrid populations developed various distant organ metastases in a much shorter period of time than the parental breast cancer cells. Together, these data demonstrate spontaneous development of new tumor cell populations exhibiting different parental properties after close interaction and subsequent fusion of MSC with breast cancer cells. This formation of tumor hybrids contributes to continuously increasing tumor heterogeneity and elevated metastatic capacities.

SAFE Software and FED Database to Uncover Protein-Protein Interactions using Gene Fusion Analysis.

PubMed

Tsagrasoulis, Dimosthenis; Danos, Vasilis; Kissa, Maria; Trimpalis, Philip; Koumandou, V Lila; Karagouni, Amalia D; Tsakalidis, Athanasios; Kossida, Sophia

2012-01-01

Domain Fusion Analysis takes advantage of the fact that certain proteins in a given proteome A, are found to have statistically significant similarity with two separate proteins in another proteome B. In other words, the result of a fusion event between two separate proteins in proteome B is a specific full-length protein in proteome A. In such a case, it can be safely concluded that the protein pair has a common biological function or even interacts physically. In this paper, we present the Fusion Events Database (FED), a database for the maintenance and retrieval of fusion data both in prokaryotic and eukaryotic organisms and the Software for the Analysis of Fusion Events (SAFE), a computational platform implemented for the automated detection, filtering and visualization of fusion events (both available at: http://www.bioacademy.gr/bioinformatics/projects/ProteinFusion/index.htm). Finally, we analyze the proteomes of three microorganisms using these tools in order to demonstrate their functionality.

SAFE Software and FED Database to Uncover Protein-Protein Interactions using Gene Fusion Analysis

PubMed Central

Tsagrasoulis, Dimosthenis; Danos, Vasilis; Kissa, Maria; Trimpalis, Philip; Koumandou, V. Lila; Karagouni, Amalia D.; Tsakalidis, Athanasios; Kossida, Sophia

2012-01-01

Domain Fusion Analysis takes advantage of the fact that certain proteins in a given proteome A, are found to have statistically significant similarity with two separate proteins in another proteome B. In other words, the result of a fusion event between two separate proteins in proteome B is a specific full-length protein in proteome A. In such a case, it can be safely concluded that the protein pair has a common biological function or even interacts physically. In this paper, we present the Fusion Events Database (FED), a database for the maintenance and retrieval of fusion data both in prokaryotic and eukaryotic organisms and the Software for the Analysis of Fusion Events (SAFE), a computational platform implemented for the automated detection, filtering and visualization of fusion events (both available at: http://www.bioacademy.gr/bioinformatics/projects/ProteinFusion/index.htm). Finally, we analyze the proteomes of three microorganisms using these tools in order to demonstrate their functionality. PMID:22267904

Effect of lateral mobility of fluorescent probes in lipid mixing assays of cell fusion.

PubMed

Huang, S K; Cheng, M; Hui, S W

1990-11-01

Monolayers of human erythrocytes, immobilized on a cover slip, were induced to fuse by polyethylene glycol (mol wt 8,000). The mobility of fluorescent probes, 1-oleoyl-2-[12-[(7-nitro-2,1,3-benzoxadizol-4-yl)amino]dodecanoyl] phosphatidyl-choline (C12-NBD-PC), from labeled cells to unlabeled cells was monitored by video-enhanced fluorescence microscopy. A dequenching curve was obtained from the measurement of fluorescence intensities of pairs of fused cells over time. The dequenching curve and the curve obtained from macroscopic measurements of a cell monolayer (described in the preceding article) were compared and discussed. The slow probe transfer rate between a pair of fused cells was explained by a diffusion model based on membrane area conservation and the geometry of the fusion lumen. An equivalent lumen between two fused cells, thought to be the main rate limitation of probe mobility after fusion, was calculated to be approximately 130 nm in diameter. Lumens of 75 nm in diameter were observed by electron microscopy. Thus, the rate of macroscopic fluorescence dequenching depends not only upon the fusion efficiency, but also upon the number of simultaneous fusion partners, the geometry of their contact points, and the lateral mobility of the fluorescent probes through these points. The relative fusion efficiency can be derived only from the saturation dequenching values.

HIV gp41 fusion peptide increases membrane ordering in a cholesterol-dependent fashion.

PubMed

Lai, Alex L; Freed, Jack H

2014-01-07

Fusion between viral envelopes and host cell membranes, which is mediated by special glycoproteins anchored on the viral membrane, is required for HIV viral entry and infection. The HIV gp41 fusion peptide (FP), which initiates membrane fusion, adopts either an α-helical or β-sheeted structure depending on the cholesterol concentration. We used phosphocholine spin labels on the lipid headgroup and different positions on the acyl chain to detect its perturbation on lipid bilayers containing different cholesterol concentrations by electron-spin resonance. Our findings were as follows. 1), gp41 FP affects the lipid order in the same manner as previously shown for influenza hemagglutinin FP, i.e., it has a cooperative effect versus the peptide/lipid ratio, supporting our hypothesis that membrane ordering is a common prerequisite for viral membrane fusion. 2), gp41 FP induces membrane ordering in all lipid compositions studied, whereas a nonfusion mutant FP perturbs lipid order to a significantly smaller extent. 3), In high-cholesterol-containing lipid bilayers, where gp41 FP is in the β-aggregation conformation, its effect on the lipid ordering reaches deeper into the bilayer. The different extent to which the two conformers perturb is correlated with their fusogenicity. The possible role of the two conformers in membrane fusion is discussed. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Rapid fusion between mesenchymal stem cells and cardiomyocytes yields electrically active, non-contractile hybrid cells.

PubMed

Shadrin, Ilya Y; Yoon, Woohyun; Li, Liqing; Shepherd, Neal; Bursac, Nenad

2015-07-10

Cardiac cell therapies involving bone marrow-derived human mesenchymal stem cells (hMSCs) have shown promising results, although their mechanisms of action are still poorly understood. Here, we investigated direct interactions between hMSCs and cardiomyocytes in vitro. Using a genetic Ca(2+) indicator gCaMP3 to efficiently label hMSCs in co-cultures with neonatal rat ventricular myocytes (NRVMs), we determined that 25-40% of hMSCs (from 4 independent donors) acquired periodic Ca(2+) transients and cardiac markers through spontaneous fusion with NRVMs. Sharp electrode and voltage-clamp recordings in fused cells showed action potential properties and Ca(2+) current amplitudes in between those of non-fused hMSCs and NRVMs. Time-lapse video-microscopy revealed the first direct evidence of active fusion between hMSCs and NRVMs within several hours of co-culture. Application of blebbistatin, nifedipine or verapamil caused complete and reversible inhibition of fusion, suggesting potential roles for actomyosin bridging and Ca(2+) channels in the fusion process. Immunostaining for Cx43, Ki67, and sarcomeric α-actinin showed that fused cells remain strongly coupled to surrounding NRVMs, but downregulate sarcomeric structures over time, acquiring a non-proliferative and non-contractile phenotype. Overall, these results describe the phenotype and mechanisms of hybrid cell formation via fusion of hMSCs and cardiomyocytes with potential implications for cardiac cell therapy.

The Habc Domain of the SNARE Vam3 Interacts with the HOPS Tethering Complex to Facilitate Vacuole Fusion*

PubMed Central

Lürick, Anna; Kuhlee, Anne; Bröcker, Cornelia; Kümmel, Daniel; Raunser, Stefan; Ungermann, Christian

2015-01-01

Membrane fusion at vacuoles requires a consecutive action of the HOPS tethering complex, which is recruited by the Rab GTPase Ypt7, and vacuolar SNAREs to drive membrane fusion. It is assumed that the Sec1/Munc18-like Vps33 within the HOPS complex is largely responsible for SNARE chaperoning. Here, we present direct evidence for HOPS binding to SNAREs and the Habc domain of the Vam3 SNARE protein, which may explain its function during fusion. We show that HOPS interacts strongly with the Vam3 Habc domain, assembled Q-SNAREs, and the R-SNARE Ykt6, but not the Q-SNARE Vti1 or the Vam3 SNARE domain. Electron microscopy combined with Nanogold labeling reveals that the binding sites for vacuolar SNAREs and the Habc domain are located in the large head of the HOPS complex, where Vps16 and Vps33 have been identified before. Competition experiments suggest that HOPS bound to the Habc domain can still interact with assembled Q-SNAREs, whereas Q-SNARE binding prevents recognition of the Habc domain. In agreement, membranes carrying Vam3ΔHabc fuse poorly unless an excess of HOPS is provided. These data suggest that the Habc domain of Vam3 facilitates the assembly of the HOPS/SNARE machinery at fusion sites and thus supports efficient membrane fusion. PMID:25564619

Load-sharing through elastic micro-motion accelerates bone formation and interbody fusion.

PubMed

Ledet, Eric H; Sanders, Glenn P; DiRisio, Darryl J; Glennon, Joseph C

2018-02-13

Achieving a successful spinal fusion requires the proper biological and biomechanical environment. Optimizing load-sharing in the interbody space can enhance bone formation. For anterior cervical discectomy and fusion (ACDF), loading and motion are largely dictated by the stiffness of the plate, which can facilitate a balance between stability and load-sharing. The advantages of load-sharing may be substantial for patients with comorbidities and in multilevel procedures where pseudarthrosis rates are significant. We aimed to evaluate the efficacy of a novel elastically deformable, continuously load-sharing anterior cervical spinal plate for promotion of bone formation and interbody fusion relative to a translationally dynamic plate. An in vivo animal model was used to evaluate the effects of an elastically deformable spinal plate on bone formation and spine fusion. Fourteen goats underwent an ACDF and received either a translationally dynamic or elastically deformable plate. Animals were followed up until 18 weeks and were evaluated by plain x-ray, computed tomography scan, and undecalcified histology to evaluate the rate and quality of bone formation and interbody fusion. Animals treated with the elastically deformable plate demonstrated statistically significantly superior early bone formation relative to the translationally dynamic plate. Trends in the data from 8 to 18 weeks postoperatively suggest that the elastically deformable implant enhanced bony bridging and fusion, but these enhancements were not statistically significant. Load-sharing through elastic micro-motion accelerates bone formation in the challenging goat ACDF model. The elastically deformable implant used in this study may promote early bony bridging and increased rates of fusion, but future studies will be necessary to comprehensively characterize the advantages of load-sharing through micro-motion. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

IFITM Proteins Restrict Viral Membrane Hemifusion

PubMed Central

Golfetto, Ottavia; Bungart, Brittani; Li, Minghua; Ding, Shilei; He, Yuxian; Liang, Chen; Lee, James C.; Gratton, Enrico; Cohen, Fredric S.; Liu, Shan-Lu

2013-01-01

The interferon-inducible transmembrane (IFITM) protein family represents a new class of cellular restriction factors that block early stages of viral replication; the underlying mechanism is currently not known. Here we provide evidence that IFITM proteins restrict membrane fusion induced by representatives of all three classes of viral membrane fusion proteins. IFITM1 profoundly suppressed syncytia formation and cell-cell fusion induced by almost all viral fusion proteins examined; IFITM2 and IFITM3 also strongly inhibited their fusion, with efficiency somewhat dependent on cell types. Furthermore, treatment of cells with IFN also markedly inhibited viral membrane fusion and entry. By using the Jaagsiekte sheep retrovirus envelope and influenza A virus hemagglutinin as models for study, we showed that IFITM-mediated restriction on membrane fusion is not at the steps of receptor- and/or low pH-mediated triggering; instead, the creation of hemifusion was essentially blocked by IFITMs. Chlorpromazine (CPZ), a chemical known to promote the transition from hemifusion to full fusion, was unable to rescue the IFITM-mediated restriction on fusion. In contrast, oleic acid (OA), a lipid analog that generates negative spontaneous curvature and thereby promotes hemifusion, virtually overcame the restriction. To explore the possible effect of IFITM proteins on membrane molecular order and fluidity, we performed fluorescence labeling with Laurdan, in conjunction with two-photon laser scanning and fluorescence-lifetime imaging microscopy (FLIM). We observed that the generalized polarizations (GPs) and fluorescence lifetimes of cell membranes expressing IFITM proteins were greatly enhanced, indicating higher molecularly ordered and less fluidized membranes. Collectively, our data demonstrated that IFITM proteins suppress viral membrane fusion before the creation of hemifusion, and suggested that they may do so by reducing membrane fluidity and conferring a positive spontaneous curvature in the outer leaflets of cell membranes. Our study provides novel insight into the understanding of how IFITM protein family restricts viral membrane fusion and infection. PMID:23358889

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

Shi, Xin, E-mail: xinshih86029@gmail.com; Zhao, Xiangmo, E-mail: xinshih86029@gmail.com; Hui, Fei, E-mail: xinshih86029@gmail.com

Clock synchronization in wireless sensor networks (WSNs) has been studied extensively in recent years and many protocols are put forward based on the point of statistical signal processing, which is an effective way to optimize accuracy. However, the accuracy derived from the statistical data can be improved mainly by sufficient packets exchange, which will consume the limited power resources greatly. In this paper, a reliable clock estimation using linear weighted fusion based on pairwise broadcast synchronization is proposed to optimize sync accuracy without expending additional sync packets. As a contribution, a linear weighted fusion scheme for multiple clock deviations ismore » constructed with the collaborative sensing of clock timestamp. And the fusion weight is defined by the covariance of sync errors for different clock deviations. Extensive simulation results show that the proposed approach can achieve better performance in terms of sync overhead and sync accuracy.« less

Circumferential fusion is dominant over posterolateral fusion in a long-term perspective: cost-utility evaluation of a randomized controlled trial in severe, chronic low back pain.

PubMed

Soegaard, Rikke; Bünger, Cody E; Christiansen, Terkel; Høy, Kristian; Eiskjaer, Søren P; Christensen, Finn B

2007-10-15

Cost-utility evaluation of a randomized, controlled trial with a 4- to 8-year follow-up. To investigate the incremental cost per quality-adjusted-life-year (QALY) when comparing circumferential fusion to posterolateral fusion in a long-term, societal perspective. The cost-effectiveness of circumferential fusion in a long-term perspective is uncertain but nonetheless highly relevant as the ISSLS prize winner 2006 in clinical studies reported the effect of circumferential fusion superior to the effect of posterolateral fusion. A recent trial found no significant difference between posterolateral and circumferential fusion reporting cost-effectiveness from a 2-year viewpoint. A total of 146 patients were randomized to posterolateral or circumferential fusion and followed 4 to 8 years after surgery. The mean age of the cohort was 46 years (range, 20-65 years); 61% were females, 49% were smokers, 30% had primary diagnosis of isthmic spondylolisthesis, 35% had disc degeneration and no previous surgery, and 35% had disc degeneration and previous surgery. Eighty-two percent of patients have had symptoms for more than 2 years and 50% were out of the labor market due to sickness. The EQ-5D instrument was applied for the measurement of health-related quality of life and costs (2004 U.S. dollars) were measured in a full-scale societal perspective. Productivity costs were valued by the Friction Cost method, and both costs and effects were discounted. Arithmetic means and 95% bias-corrected, bootstrapped confidence intervals were reported. Nonparametric statistics were used for tests of statistical significance. Comprehensive sensitivity analysis was conducted and reported using cost-effectiveness acceptability curves. The circumferential group demonstrated clinical superiority over the posterolateral fusion group in functional outcome (P < 0.01), fusion rate (P < 0.04), and number of reoperations (P < 0.01) among others. Cost-utility analysis demonstrated circumferential fusion dominant over posterolateral fusion, that is, for each QALY gained performing circumferential fusion, the incremental saving was estimated at U.S. $49,306 (95% confidence interval, $27,183-$2,735,712). Results proved to be strong to various sensitivity analyses; only a differentiated underestimation of patients' need for postoperative household help against the circumferential approach could alter the dominance; however, still the probability of cost-effectiveness was >0.85 given a threshold for willingness to pay of U.S. $50,000 per QALY. Circumferential fusion is dominant over instrumented posterolateral fusion, that is, both being significantly cheaper and significantly better in a long-term, societal perspective.

Semantic Labelling of Ultra Dense Mls Point Clouds in Urban Road Corridors Based on Fusing Crf with Shape Priors

NASA Astrophysics Data System (ADS)

Yao, W.; Polewski, P.; Krzystek, P.

2017-09-01

In this paper, a labelling method for the semantic analysis of ultra-high point density MLS data (up to 4000 points/m2) in urban road corridors is developed based on combining a conditional random field (CRF) for the context-based classification of 3D point clouds with shape priors. The CRF uses a Random Forest (RF) for generating the unary potentials of nodes and a variant of the contrastsensitive Potts model for the pair-wise potentials of node edges. The foundations of the classification are various geometric features derived by means of co-variance matrices and local accumulation map of spatial coordinates based on local neighbourhoods. Meanwhile, in order to cope with the ultra-high point density, a plane-based region growing method combined with a rule-based classifier is applied to first fix semantic labels for man-made objects. Once such kind of points that usually account for majority of entire data amount are pre-labeled; the CRF classifier can be solved by optimizing the discriminative probability for nodes within a subgraph structure excluded from pre-labeled nodes. The process can be viewed as an evidence fusion step inferring a degree of belief for point labelling from different sources. The MLS data used for this study were acquired by vehicle-borne Z+F phase-based laser scanner measurement, which permits the generation of a point cloud with an ultra-high sampling rate and accuracy. The test sites are parts of Munich City which is assumed to consist of seven object classes including impervious surfaces, tree, building roof/facade, low vegetation, vehicle and pole. The competitive classification performance can be explained by the diverse factors: e.g. the above ground height highlights the vertical dimension of houses, trees even cars, but also attributed to decision-level fusion of graph-based contextual classification approach with shape priors. The use of context-based classification methods mainly contributed to smoothing of labelling by removing outliers and the improvement in underrepresented object classes. In addition, the routine operation of a context-based classification for such high density MLS data becomes much more efficient being comparable to non-contextual classification schemes.

a Comparative Analysis of Spatiotemporal Data Fusion Models for Landsat and Modis Data

NASA Astrophysics Data System (ADS)

Hazaymeh, K.; Almagbile, A.

2018-04-01

In this study, three documented spatiotemporal data fusion models were applied to Landsat-7 and MODIS surface reflectance, and NDVI. The algorithms included the spatial and temporal adaptive reflectance fusion model (STARFM), sparse representation based on a spatiotemporal reflectance fusion model (SPSTFM), and spatiotemporal image-fusion model (STI-FM). The objectives of this study were to (i) compare the performance of these three fusion models using a one Landsat-MODIS spectral reflectance image pairs using time-series datasets from the Coleambally irrigation area in Australia, and (ii) quantitatively evaluate the accuracy of the synthetic images generated from each fusion model using statistical measurements. Results showed that the three fusion models predicted the synthetic Landsat-7 image with adequate agreements. The STI-FM produced more accurate reconstructions of both Landsat-7 spectral bands and NDVI. Furthermore, it produced surface reflectance images having the highest correlation with the actual Landsat-7 images. This study indicated that STI-FM would be more suitable for spatiotemporal data fusion applications such as vegetation monitoring, drought monitoring, and evapotranspiration.

Statistical sensor fusion analysis of near-IR polarimetric and thermal imagery for the detection of minelike targets

NASA Astrophysics Data System (ADS)

Weisenseel, Robert A.; Karl, William C.; Castanon, David A.; DiMarzio, Charles A.

1999-02-01

We present an analysis of statistical model based data-level fusion for near-IR polarimetric and thermal data, particularly for the detection of mines and mine-like targets. Typical detection-level data fusion methods, approaches that fuse detections from individual sensors rather than fusing at the level of the raw data, do not account rationally for the relative reliability of different sensors, nor the redundancy often inherent in multiple sensors. Representative examples of such detection-level techniques include logical AND/OR operations on detections from individual sensors and majority vote methods. In this work, we exploit a statistical data model for the detection of mines and mine-like targets to compare and fuse multiple sensor channels. Our purpose is to quantify the amount of knowledge that each polarimetric or thermal channel supplies to the detection process. With this information, we can make reasonable decisions about the usefulness of each channel. We can use this information to improve the detection process, or we can use it to reduce the number of required channels.

Label-free and amplified quantitation of proteins in complex mixtures using diffractive optics technology.

PubMed

Cleverley, Steve; Chen, Irene; Houle, Jean-François

2010-01-15

Immunoaffinity approaches remain invaluable tools for characterization and quantitation of biopolymers. Their application in separation science is often limited due to the challenges of immunoassay development. Typical end-point immunoassays require time consuming and labor-intensive approaches for optimization. Real-time label-free analysis using diffractive optics technology (dot) helps guide a very effective iterative process for rapid immunoassay development. Both label-free and amplified approaches can be used throughout feasibility testing and ultimately in the final assay, providing a robust platform for biopolymer analysis over a very broad dynamic range. We demonstrate the use of dot in rapidly developing assays for quantitating (1) human IgG in complex media, (2) a fusion protein in production media and (3) protein A contamination in purified immunoglobulin preparations. 2009 Elsevier B.V. All rights reserved.

PSF/SFPQ is a very common gene fusion partner in TFE3 rearrangement-associated perivascular epithelioid cell tumors (PEComas) and melanotic Xp11 translocation renal cancers: clinicopathologic, immunohistochemical, and molecular characteristics suggesting classification as a distinct entity.

PubMed

Rao, Qiu; Shen, Qin; Xia, Qiu-yuan; Wang, Zi-yu; Liu, Biao; Shi, Shan-shan; Shi, Qun-li; Yin, Hong-lin; Wu, Bo; Ye, Sheng-bing; Li, Li; Chen, Jie-Yu; Pan, Min-hong; Li, Qing; Li, Rui; Wang, Xuan; Zhang, Ru-song; Yu, Bo; Ma, Heng-hui; Lu, Zhen-feng; Zhou, Xiao-jun

2015-09-01

An increasing number of TFE3 rearrangement-associated tumors, such as TFE3 rearrangement-associated perivascular epithelioid cell tumors (PEComas), melanotic Xp11 translocation renal cancers, and melanotic Xp11 neoplasms, have recently been reported. We examined 12 such cases, including 5 TFE3 rearrangement-associated PEComas located in the pancreas, cervix, or pelvis and 7 melanotic Xp11 translocation renal cancers, using clinicopathologic, immunohistochemical, and molecular analyses. All the tumors shared a similar morphology, including a purely nested or sheet-like architecture separated by a delicate vascular network, purely epithelioid cells displaying a clear or granular eosinophilic cytoplasm, a lack of papillary structures and spindle cell or fat components, uniform round or oval nuclei containing small visible nucleoli, and, in most cases (11/12), melanin pigmentation. The levels of mitotic activity and necrosis varied. All 12 cases displayed moderately (2+) or strongly (3+) positive immunoreactivity for TFE3 and cathepsin K. One case labeled focally for HMB45 and Melan-A, whereas the others typically labeled moderately (2+) or strongly (3+) for 1 of these markers. None of the cases were immunoreactive for smooth muscle actin, desmin, CKpan, S100, or PAX8. PSF-TFE3 fusion genes were confirmed by reverse transcription polymerase chain reaction in cases (7/7) in which a novel PSF-TFE3 fusion point was identified. All of the cases displayed TFE3 rearrangement associated with Xp11 translocation. Furthermore, we developed a PSF-TFE3 fusion fluorescence in situ hybridization assay for the detection of the PSF-TFE3 fusion gene and detected it in all 12 cases. Clinical follow-up data were available for 7 patients. Three patients died, and 2 patients (cases 1 and 3) remained alive with no evidence of disease after initial resection. Case 2 experienced recurrence and remained alive with disease. Case 5, a recent case, remained alive with extensive abdominal cavity metastases. Our data suggest that these tumors belong to a single clinicopathologic spectrum and expand the known characteristics of TFE3 rearrangement-associated tumors.

REDOR solid-state NMR as a probe of the membrane locations of membrane-associated peptides and proteins

NASA Astrophysics Data System (ADS)

Jia, Lihui; Liang, Shuang; Sackett, Kelly; Xie, Li; Ghosh, Ujjayini; Weliky, David P.

2015-04-01

Rotational-echo double-resonance (REDOR) solid-state NMR is applied to probe the membrane locations of specific residues of membrane proteins. Couplings are measured between protein 13CO nuclei and membrane lipid or cholesterol 2H and 31P nuclei. Specific 13CO labeling is used to enable unambiguous assignment and 2H labeling covers a small region of the lipid or cholesterol molecule. The 13CO-31P and 13CO-2H REDOR respectively probe proximity to the membrane headgroup region and proximity to specific insertion depths within the membrane hydrocarbon core. One strength of the REDOR approach is use of chemically-native proteins and membrane components. The conventional REDOR pulse sequence with 100 kHz 2H π pulses is robust with respect to the 2H quadrupolar anisotropy. The 2H T1's are comparable to the longer dephasing times (τ's) and this leads to exponential rather than sigmoidal REDOR buildups. The 13CO-2H buildups are well-fitted to A × (1 - e-γτ) where A and γ are fitting parameters that are correlated as the fraction of molecules (A) with effective 13CO-2H coupling d = 3γ/2. The REDOR approach is applied to probe the membrane locations of the "fusion peptide" regions of the HIV gp41 and influenza virus hemagglutinin proteins which both catalyze joining of the viral and host cell membranes during initial infection of the cell. The HIV fusion peptide forms an intermolecular antiparallel β sheet and the REDOR data support major deeply-inserted and minor shallowly-inserted molecular populations. A significant fraction of the influenza fusion peptide molecules form a tight hairpin with antiparallel N- and C-α helices and the REDOR data support a single peptide population with a deeply-inserted N-helix. The shared feature of deep insertion of the β and α fusion peptide structures may be relevant for fusion catalysis via the resultant local perturbation of the membrane bilayer. Future applications of the REDOR approach may include samples that contain cell membrane extracts and use of lower temperatures and dynamic nuclear polarization to reduce data acquisition times.

HCP: A Flexible CNN Framework for Multi-label Image Classification.

PubMed

Wei, Yunchao; Xia, Wei; Lin, Min; Huang, Junshi; Ni, Bingbing; Dong, Jian; Zhao, Yao; Yan, Shuicheng

2015-10-26

Convolutional Neural Network (CNN) has demonstrated promising performance in single-label image classification tasks. However, how CNN best copes with multi-label images still remains an open problem, mainly due to the complex underlying object layouts and insufficient multi-label training images. In this work, we propose a flexible deep CNN infrastructure, called Hypotheses-CNN-Pooling (HCP), where an arbitrary number of object segment hypotheses are taken as the inputs, then a shared CNN is connected with each hypothesis, and finally the CNN output results from different hypotheses are aggregated with max pooling to produce the ultimate multi-label predictions. Some unique characteristics of this flexible deep CNN infrastructure include: 1) no ground-truth bounding box information is required for training; 2) the whole HCP infrastructure is robust to possibly noisy and/or redundant hypotheses; 3) the shared CNN is flexible and can be well pre-trained with a large-scale single-label image dataset, e.g., ImageNet; and 4) it may naturally output multi-label prediction results. Experimental results on Pascal VOC 2007 and VOC 2012 multi-label image datasets well demonstrate the superiority of the proposed HCP infrastructure over other state-of-the-arts. In particular, the mAP reaches 90.5% by HCP only and 93.2% after the fusion with our complementary result in [44] based on hand-crafted features on the VOC 2012 dataset.

Tumor or abnormality identification from magnetic resonance images using statistical region fusion based segmentation.

PubMed

Subudhi, Badri Narayan; Thangaraj, Veerakumar; Sankaralingam, Esakkirajan; Ghosh, Ashish

2016-11-01

In this article, a statistical fusion based segmentation technique is proposed to identify different abnormality in magnetic resonance images (MRI). The proposed scheme follows seed selection, region growing-merging and fusion of multiple image segments. In this process initially, an image is divided into a number of blocks and for each block we compute the phase component of the Fourier transform. The phase component of each block reflects the gray level variation among the block but contains a large correlation among them. Hence a singular value decomposition (SVD) technique is adhered to generate a singular value of each block. Then a thresholding procedure is applied on these singular values to identify edgy and smooth regions and some seed points are selected for segmentation. By considering each seed point we perform a binary segmentation of the complete MRI and hence with all seed points we get an equal number of binary images. A parcel based statistical fusion process is used to fuse all the binary images into multiple segments. Effectiveness of the proposed scheme is tested on identifying different abnormalities: prostatic carcinoma detection, tuberculous granulomas identification and intracranial neoplasm or brain tumor detection. The proposed technique is established by comparing its results against seven state-of-the-art techniques with six performance evaluation measures. Copyright © 2016 Elsevier Inc. All rights reserved.

Ricin A chain reaches the endoplasmic reticulum after endocytosis

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

Liu Qiong; Department of Biochemistry and Molecular Biology, Ningbo University Medical School, Ningbo 315211; Zhan Jinbiao

Ricin is a potent ribosome inactivating protein and now has been widely used for synthesis of immunotoxins. To target ribosome in the mammalian cytosol, ricin must firstly retrograde transport from the endomembrane system to reach the endoplasmic reticulum (ER) where the ricin A chain (RTA) is recognized by ER components that facilitate its membrane translocation to the cytosol. In the study, the fusion gene of enhanced green fluorescent protein (EGFP)-RTA was expressed with the pET-28a (+) system in Escherichia coli under the control of a T7 promoter. The fusion protein showed a green fluorescence. The recombinant protein can be purifiedmore » by metal chelated affinity chromatography on a column of NTA. The rabbit anti-GFP antibody can recognize the fusion protein of EGFP-RTA just like the EGFP protein. The cytotoxicity of EGFP-RTA and RTA was evaluated by the MTT assay in HeLa and HEP-G2 cells following fluid-phase endocytosis. The fusion protein had a similar cytotoxicity of RTA. After endocytosis, the subcellular location of the fusion protein can be observed with the laser scanning confocal microscopy and the immuno-gold labeling Electro Microscopy. This study provided important evidence by a visualized way to prove that RTA does reach the endoplasmic reticulum.« less

A conserved role for calpains during myoblast fusion.

PubMed

Buffolo, Marcio; Batista Possidonio, Ana Claudia; Mermelstein, Claudia; Araujo, Helena

2015-07-01

Myoblast fusion is a key step during skeletal muscle differentiation as it enables the formation of contractile fibers. Calpains have been implicated in some aspects of myogenesis in mammals, but whether they exert a conserved function during myoblast fusion has not been investigated. Here, we studied Calpain function in two models of myogenesis: in vitro analysis of chick myogenic cultures and in vivo analysis of Drosophila melanogaster muscle development. First we showed that Calpain A is important for fly muscle function. In addition, Calpain A knockdown reduced lateral body wall muscle length and width, as well as the number of nuclei in dorsal oblique muscles, consistent with fewer cells fusing to form fibers. Treatment of chick cultures with a selective Calpain inhibitor led to the formation of thinner myotubes containing a reduced number of nuclei, consistent with decreased myoblast fusion. Dynamic changes in IκBα labeling and transfection with a dominant-negative IκBα suggest a role for the NFκB pathway during chick myogenesis and a possible role of Calpains in attenuating NFκB signals that restrict myoblast fusion. Our data suggest that different model organisms may be used to study the role of Calpains in regular myogenesis and Calpain-related muscular degenerative disorders. © 2015 Wiley Periodicals, Inc.

Local SIMPLE multi-atlas-based segmentation applied to lung lobe detection on chest CT

NASA Astrophysics Data System (ADS)

Agarwal, M.; Hendriks, E. A.; Stoel, B. C.; Bakker, M. E.; Reiber, J. H. C.; Staring, M.

2012-02-01

For multi atlas-based segmentation approaches, a segmentation fusion scheme which considers local performance measures may be more accurate than a method which uses a global performance measure. We improve upon an existing segmentation fusion method called SIMPLE and extend it to be localized and suitable for multi-labeled segmentations. We demonstrate the algorithm performance on 23 CT scans of COPD patients using a leave-one- out experiment. Our algorithm performs significantly better (p < 0.01) than majority voting, STAPLE, and SIMPLE, with a median overlap of the fissure of 0.45, 0.48, 0.55 and 0.6 for majority voting, STAPLE, SIMPLE, and the proposed algorithm, respectively.

Visualization and in vivo tracking of the exosomes of murine melanoma B16-BL6 cells in mice after intravenous injection.

PubMed

Takahashi, Yuki; Nishikawa, Makiya; Shinotsuka, Haruka; Matsui, Yuriko; Ohara, Saori; Imai, Takafumi; Takakura, Yoshinobu

2013-05-20

The development of exosomes as delivery vehicles requires understanding how and where exogenously administered exosomes are distributed in vivo. In the present study, we designed a fusion protein consisting of Gaussia luciferase and a truncated lactadherin, gLuc-lactadherin, and constructed a plasmid expressing the fusion protein. B16-BL6 murine melanoma cells were transfected with the plasmid, and exosomes released from the cells were collected by ultracentrifugation. Strong luciferase activity was detected in the fraction containing exosomes, indicating their efficient labeling with gLuc-lactadherin. Then, the labeled B16-BL6 exosomes were intravenously injected into mice, and their tissue distribution was evaluated. Pharmacokinetic analysis of the exosome blood concentration-time profile revealed that B16-BL6 exosomes disappeared very quickly from the blood circulation with a half-life of approximately 2min. Little luciferase activity was detected in the serum at 4h after exosome injection, suggesting rapid clearance of B16-BL6 exosomes in vivo. Moreover, sequential in vivo imaging revealed that the B16-BL6 exosome-derived signals distributed first to the liver and then to the lungs. These results indicate that gLuc-lactadherin labeling is useful for tracing exosomes in vivo and that B16-BL6 exosomes are rapidly cleared from the blood circulation after systemic administration. Copyright © 2013 Elsevier B.V. All rights reserved.

Subcellular Localization Screening of Colletotrichum higginsianum Effector Candidates Identifies Fungal Proteins Targeted to Plant Peroxisomes, Golgi Bodies, and Microtubules.

PubMed

Robin, Guillaume P; Kleemann, Jochen; Neumann, Ulla; Cabre, Lisa; Dallery, Jean-Félix; Lapalu, Nicolas; O'Connell, Richard J

2018-01-01

The genome of the hemibiotrophic anthracnose fungus, Colletotrichum higginsianum , encodes a large inventory of putative secreted effector proteins that are sequentially expressed at different stages of plant infection, namely appressorium-mediated penetration, biotrophy and necrotrophy. However, the destinations to which these proteins are addressed inside plant cells are unknown. In the present study, we selected 61 putative effector genes that are highly induced in appressoria and/or biotrophic hyphae. We then used Agrobacterium -mediated transformation to transiently express them as N -terminal fusions with fluorescent proteins in cells of Nicotiana benthamiana for imaging by confocal microscopy. Plant compartments labeled by the fusion proteins in N. benthamiana were validated by co-localization with specific organelle markers, by transient expression of the proteins in the true host plant, Arabidopsis thaliana , and by transmission electron microscopy-immunogold labeling. Among those proteins for which specific subcellular localizations could be verified, nine were imported into plant nuclei, three were imported into the matrix of peroxisomes, three decorated cortical microtubule arrays and one labeled Golgi stacks. Two peroxisome-targeted proteins harbored canonical C -terminal tripeptide signals for peroxisome import via the PTS1 (peroxisomal targeting signal 1) pathway, and we showed that these signals are essential for their peroxisome localization. Our findings provide valuable information about which host processes are potentially manipulated by this pathogen, and also reveal plant peroxisomes, microtubules, and Golgi as novel targets for fungal effectors.

Fusion, rupture, and degeneration: the fate of in vivo-labelled PSVs in developing barley endosperm.

PubMed

Ibl, Verena; Kapusi, Eszter; Arcalis, Elsa; Kawagoe, Yasushi; Stoger, Eva

2014-07-01

Cereal endosperm is a highly differentiated tissue containing specialized organelles for the accumulation of storage proteins. The endosperm of barley contains hordeins, which are ultimately deposited within protein storage vacuoles (PSVs). These organelles have been characterized predominantly by the histochemical analysis of fixed immature tissue samples. However, little is known about the fate of PSVs during barley endosperm development, and in vivo imaging has not been attempted in order to gain further insight. In this report, young seeds were followed through development to characterize the dynamic morphology of PSVs from aleurone, subaleurone, and central starchy endosperm cells. TIP3-GFP was used as a PSV membrane marker and several fluorescent tracers were used to identify membranes and monitor endomembrane organelles in real time. Whereas the spherical appearance of strongly labelled TIP3-GFP PSVs in the aleurone remained constant, those in the subaleurone and central starchy endosperm underwent substantial morphological changes. Fusion and rupture events were observed in the subaleurone, and internal membranes derived from both the tonoplast and endoplasmic reticulum were identified within these PSVs. TIP3-GFP-labelled PSVs in the starchy endosperm cells underwent a dramatic reduction in size, so that finally the protein bodies were tightly enclosed. Potential desiccation-related membrane-altering processes that may be causally linked to these dynamic endomembrane events in the barley endosperm are discussed. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

2.5-Year-Olds Use Cross-Situational Consistency to Learn Verbs under Referential Uncertainty

ERIC Educational Resources Information Center

Scott, Rose M.; Fisher, Cynthia

2012-01-01

Recent evidence shows that children can use cross-situational statistics to learn new object labels under referential ambiguity (e.g., Smith & Yu, 2008). Such evidence has been interpreted as support for proposals that statistical information about word-referent co-occurrence plays a powerful role in word learning. But object labels represent only…

Impact of Lumbar Fusion on Health Care Resource Utilization.

PubMed

Mina, Curtis; Carreon, Leah Y; Glassman, Steven D

2016-02-01

A longitudinal cohort. The aim of this study was to determine the extent of health care resource utilization decrease 2 years after lumbar spinal fusion. Despite the assumption that surgery will minimize the need for ongoing nonsurgical treatment, the impact of lumbar fusion on subsequent health care resource utilization has not been effectively studied. Patients who had continuous coverage by a major insurer during the year before decompression and posterolateral instrumented spinal fusion, and the 2 and a half years following were identified. All charges processed during this time-period were collected. Charges associated with the index surgery, the 90-day postoperative period, and those unrelated to spinal care were excluded. Associations with Oswestry Disability Index (ODI) score improvement at 2 years after surgery and health care resource utilization were determined. Sixty-six patients were included in the analysis. The mean age was 59 years and 39% were males. There was a decrease in health care utilization costs 1 year after surgery ($3267.59) compared with pre-op ($4246.32), but this was not statistically significant (P = 0.197). There was a statistically significant decrease in costs during the second year after surgery ($1420.97) compared with either pre-op (P = 0.000) or 1-year costs (P = 0.001). No statistically significant correlations could be found between change in ODI scores and costs incurred at either year post-op. Health care utilization decreased at 1 year and significantly at 2 years after lumbar fusion. However, there was no correlation between use of nonsurgical resources and clinical outcome based on ODI scores. This raises the question as to whether these resources were used in a rational manner. This cooperative study between a major insurer and a tertiary spine center provides improved insight into the cost profile of lumbar fusion surgery. Further study is needed to determine whether ongoing post-op treatment is necessary or simply established practice. 2.

Fusion of Local Statistical Parameters for Buried Underwater Mine Detection in Sonar Imaging

NASA Astrophysics Data System (ADS)

Maussang, F.; Rombaut, M.; Chanussot, J.; Hétet, A.; Amate, M.

2008-12-01

Detection of buried underwater objects, and especially mines, is a current crucial strategic task. Images provided by sonar systems allowing to penetrate in the sea floor, such as the synthetic aperture sonars (SASs), are of great interest for the detection and classification of such objects. However, the signal-to-noise ratio is fairly low and advanced information processing is required for a correct and reliable detection of the echoes generated by the objects. The detection method proposed in this paper is based on a data-fusion architecture using the belief theory. The input data of this architecture are local statistical characteristics extracted from SAS data corresponding to the first-, second-, third-, and fourth-order statistical properties of the sonar images, respectively. The interest of these parameters is derived from a statistical model of the sonar data. Numerical criteria are also proposed to estimate the detection performances and to validate the method.

Number-Theory in Nuclear-Physics in Number-Theory: Non-Primality Factorization As Fission VS. Primality As Fusion; Composites' Islands of INstability: Feshbach-Resonances?

NASA Astrophysics Data System (ADS)

Siegel, Edward

2011-10-01

Numbers: primality/indivisibility/non-factorization versus compositeness/divisibility /factor-ization, often in tandem but not always, provocatively close analogy to nuclear-physics: (2 + 1)=(fusion)=3; (3+1)=(fission)=4[=2 × 2]; (4+1)=(fusion)=5; (5 +1)=(fission)=6[=2 × 3]; (6 + 1)=(fusion)=7; (7+1)=(fission)=8[= 2 × 4 = 2 × 2 × 2]; (8 + 1) =(non: fission nor fusion)= 9[=3 × 3]; then ONLY composites' Islands of fusion-INstability: 8, 9, 10; then 14, 15, 16,... Could inter-digit Feshbach-resonances exist??? Applications to: quantum-information/computing non-Shore factorization, millennium-problem Riemann-hypotheses proof as Goodkin BEC intersection with graph-theory ``short-cut'' method: Rayleigh(1870)-Polya(1922)-``Anderson'' (1958)-localization, Goldbach-conjecture, financial auditing/accounting as quantum-statistical-physics;... abound!!!

Number-Theory in Nuclear-Physics in Number-Theory: Non-Primality Factorization As Fission VS. Primality As Fusion; Composites' Islands of INstability: Feshbach-Resonances?

NASA Astrophysics Data System (ADS)

Siegel, Edward

2011-04-01

Numbers: primality/indivisibility/non-factorization versus compositeness/divisibility /factor-ization, often in tandem but not always, provocatively close analogy to nuclear-physics: (2 + 1)=(fusion)=3; (3+1)=(fission)=4[=2 x 2]; (4+1)=(fusion)=5; (5+1)=(fission)=6[=2 x 3]; (6 + 1)=(fusion)=7; (7+1)=(fission)=8[= 2 x 4 = 2 x 2 x 2]; (8 + 1) =(non: fission nor fusion)= 9[=3 x 3]; then ONLY composites' Islands of fusion-INstability: 8, 9, 10; then 14, 15, 16,... Could inter-digit Feshbach-resonances exist??? Applications to: quantum-information and computing non-Shore factorization, millennium-problem Riemann-hypotheses physics-proof as numbers/digits Goodkin Bose-Einstein Condensation intersection with graph-theory ``short-cut'' method: Rayleigh(1870)-Polya(1922)-``Anderson'' (1958)-localization, Goldbach-conjecture, financial auditing/accounting as quantum-statistical-physics;... abound!!!

Improving vertebra segmentation through joint vertebra-rib atlases

NASA Astrophysics Data System (ADS)

Wang, Yinong; Yao, Jianhua; Roth, Holger R.; Burns, Joseph E.; Summers, Ronald M.

2016-03-01

Accurate spine segmentation allows for improved identification and quantitative characterization of abnormalities of the vertebra, such as vertebral fractures. However, in existing automated vertebra segmentation methods on computed tomography (CT) images, leakage into nearby bones such as ribs occurs due to the close proximity of these visibly intense structures in a 3D CT volume. To reduce this error, we propose the use of joint vertebra-rib atlases to improve the segmentation of vertebrae via multi-atlas joint label fusion. Segmentation was performed and evaluated on CTs containing 106 thoracic and lumbar vertebrae from 10 pathological and traumatic spine patients on an individual vertebra level basis. Vertebra atlases produced errors where the segmentation leaked into the ribs. The use of joint vertebra-rib atlases produced a statistically significant increase in the Dice coefficient from 92.5 +/- 3.1% to 93.8 +/- 2.1% for the left and right transverse processes and a decrease in the mean and max surface distance from 0.75 +/- 0.60mm and 8.63 +/- 4.44mm to 0.30 +/- 0.27mm and 3.65 +/- 2.87mm, respectively.

Whole abdominal wall segmentation using augmented active shape models (AASM) with multi-atlas label fusion and level set

NASA Astrophysics Data System (ADS)

Xu, Zhoubing; Baucom, Rebeccah B.; Abramson, Richard G.; Poulose, Benjamin K.; Landman, Bennett A.

2016-03-01

The abdominal wall is an important structure differentiating subcutaneous and visceral compartments and intimately involved with maintaining abdominal structure. Segmentation of the whole abdominal wall on routinely acquired computed tomography (CT) scans remains challenging due to variations and complexities of the wall and surrounding tissues. In this study, we propose a slice-wise augmented active shape model (AASM) approach to robustly segment both the outer and inner surfaces of the abdominal wall. Multi-atlas label fusion (MALF) and level set (LS) techniques are integrated into the traditional ASM framework. The AASM approach globally optimizes the landmark updates in the presence of complicated underlying local anatomical contexts. The proposed approach was validated on 184 axial slices of 20 CT scans. The Hausdorff distance against the manual segmentation was significantly reduced using proposed approach compared to that using ASM, MALF, and LS individually. Our segmentation of the whole abdominal wall enables the subcutaneous and visceral fat measurement, with high correlation to the measurement derived from manual segmentation. This study presents the first generic algorithm that combines ASM, MALF, and LS, and demonstrates practical application for automatically capturing visceral and subcutaneous fat volumes.

Aequorin fusion proteins as bioluminescent tracers for competitive immunoassays

NASA Astrophysics Data System (ADS)

Mirasoli, Mara; Michelini, Elisa; Deo, Sapna K.; Dikici, Emre; Roda, Aldo; Daunert, Sylvia

2004-06-01

The use of bio- and chemiluminescence for the development of quantitative binding assays offers undoubted advantages over other detection systems, such as spectrophotometry, fluorescence, or radioactivity. Indeed, bio- and chemiluminescence detection provides similar, or even better, sensitivity and detectability than radioisotopes, while avoiding the problems of health hazards, waste disposal, and instability associated with the use of radioisotopes. Among bioluminescent labels, the calcium-activated photoprotein aequorin, originally isolated from Aequorea victoria and today available as a recombinant product, is characterized by very high detectability, down to attomole levels. It has been used as a bioluminescent label for developing a variety of highly sensitive immunoassays, using various analyte-aequorin conjugation strategies. When the analyte is a protein or a peptide, genetic engineering techniques can be used to produce protein fusions where the analyte is in-frame fused with aequorin, thus producing homogeneous one-to-one conjugation products, available in virtually unlimited amount. Various assays were developed using this strategy: a short review of the most interesting applications is presented, as well as the cloning, purification and initial characterization of an endothelin-1-aequorin conjugate suitable for developing a competitive immunoassay for endothelin-1, a potent vasoconstrictor peptide, involved in hypertension.

Spinal Fusion for Chronic Low Back Pain: A ‘Magic Bullet’ or Wishful Thinking?

PubMed Central

2016-01-01

Chronic low back pain is a common, disabling and costly health problem. The treatment of chronic low back is difficult and is often ineffective. For treatment to be effective the cause of the pain has to be established but unfortunately in 80% to 95% of the patients the cause cannot be determined despite the existence of modern imaging techniques. A pathoanatomical diagnosis which fits into a classical disease model where successful treatment can be carried out, can only be made in 5% to 7% of the patients. The back pain in the rest of the patients where no pathoanatomical diagnosis can be made is often labelled, unscientifically, as chronic low back pain. Despite the existence of sophisticated imaging techniques and a plethora of diagnostic test the source of pain in patients with nonspecific back pain cannot be established. There exist no causal relationship between imaging findings of degenerated disc, lumbar facet arthritis, spondylosis, spondylolysis and spondylolisthesis, to the pain in these patients. Surgical treatment of non-specific back pain where no pathoanatomical diagnosis has been established is bound to fail. Therefore the outcome of spinal fusion in these patients can be no better than nonsurgical treatment. Spinal fusion is a major surgery which can be associated with significant morbidity and occasionally with mortality. Yet there is rapid rise in the rates of spinal fusion. There is a growing tension between ethics and conflicts of interest for surgeons. The spine, unfortunately, has been labelled as a profit centre and there are allegations of conflicts of interest in the relationship of doctors with the multi-billion dollar spinal devices industry. The devices industry has a significant influence on not only research publications in peer review journals but also on decisions made by doctors which can have a detrimental effect on the welfare of the patient. PMID:28435551

The interaction between Pseudomonas aeruginosa cells and cationic PC:Chol:DOTAP liposomal vesicles versus outer-membrane structure and envelope properties of bacterial cell.

PubMed

Drulis-Kawa, Zuzanna; Dorotkiewicz-Jach, Agata; Gubernator, Jerzy; Gula, Grzegorz; Bocer, Tomasz; Doroszkiewicz, Wlodzimierz

2009-02-09

The interactions between cationic liposomal formulations (PC:Chol:DOTAP 3:4:3) and 23 Pseudomonas aeruginosa strains were tested. The study was undertaken because different antimicrobial results had been obtained by the authors for Pseudomonas aeruginosa strains and liposomal antibiotics (Drulis-Kawa, Z., Gubernator, J., Dorotkiewicz-Jach, A., Doroszkiewicz, W., Kozubek, A., 2006. The comparison of in vitro antimicrobial activity of liposomes containing meropenem and gentamicin. Cell. Mol. Biol. Lett., 11, 360-375; Drulis-Kawa, Z., Gubernator, J., Dorotkiewicz-Jach, A., Doroszkiewicz W., Kozubek, A., 2006. In vitro antimicrobial activity of liposomal meropenem against Pseudomonas aeruginosa strains. Int. J. Pharm., 315, 59-66). The experiments evaluate the roles of the bacterial outer-membrane structure, especially outer-membrane proteins and LPS, and envelope properties (hydrophobicity and electrostatic potential) in the interactions/fusion process between cells and lipid vesicles. The interactions were examined by fluorescent microscopy using PE-rhodamine-labelled liposomes. Some of the strains exhibited red-light emission (fusion with vesicles or vesicles surrounding the cell) and some showed negative reaction (no red-light emission). The main aim of the study was to determine what kinds of bacterial structure or envelope properties have a major influence on the fusion process. Negatively charged cells and hydrophobic properties promote interaction with cationic lipid vesicles, but no specific correlation was noted for the tested strains. A similar situation concerned LPS structure, where parent strains and their mutants possessing identical ladder-like band patterns in SDS-PAGE analysis exhibited totally different results with fluorescent microscopy. Outer-membrane protein analysis showed that an 18-kDA protein occurred in the isolates showing fusion with rhodamine-labelled vesicles and, conversely, strains lacking the 18-kDA protein exhibited no positive reaction (red emission). This suggests that even one protein may be responsible for favouring stronger interactions between Pseudomonas aeruginosa cells and cationic liposomal formulations (PC:Chol:DOTAP 3:4:3).

Medicare payment data for spine reimbursement; important but flawed data for evaluating utilization of resources.

PubMed

Menger, Richard P; Wolf, Michael E; Kukreja, Sunil; Sin, Anthony; Nanda, Anil

2015-01-01

Medicare data showing physician-specific reimbursement for 2012 were recently made public in the mainstream media. Given the ongoing interest in containing healthcare costs, we analyze these data in the context of the delivery of spinal surgery. Demographics of 206 leading surgeons were extracted including state, geographic area, residency training program, fellowship training, and academic affiliation. Using current procedural terminology (CPT) codes, information was evaluated regarding the number of lumbar laminectomies, lumbar fusions, add-on laminectomy levels, and anterior cervical fusions reimbursed by Medicare in 2012. In 2012 Medicare reimbursed the average neurosurgeon slightly more than an orthopedic surgeon for all procedures ($142,075 vs. $110,920), but this was not found to be statistically significant (P = 0.218). Orthopedic surgeons had a statistical trend illustrating increased reimbursement for lumbar fusions specifically, $1187 versus $1073 (P = 0.07). Fellowship trained spinal surgeons also, on average, received more from Medicare ($125,407 vs. $76,551), but again this was not statistically significant (P = 0.112). A surgeon in private practice, on average, was reimbursed $137,495 while their academic counterparts were reimbursed $103,144 (P = 0.127). Surgeons performing cervical fusions in the Centers for Disease Control West Region did receive statistically significantly less reimbursement for that procedure then those surgeons in other parts of the country (P = 0.015). Surgeons in the West were reimbursed on average $849 for CPT code 22,551 while those in the Midwest received $1475 per procedure. Medicare reimbursement data are fundamentally flawed in determining healthcare expenditure as it shows a bias toward delivery of care in specific patient demographics. However, neurosurgeons, not just policy makers, must take ownership to analyze, investigate, and interpret these data as it will affect healthcare reimbursement and delivery moving forward.

Linking sounds to meanings: infant statistical learning in a natural language.

PubMed

Hay, Jessica F; Pelucchi, Bruna; Graf Estes, Katharine; Saffran, Jenny R

2011-09-01

The processes of infant word segmentation and infant word learning have largely been studied separately. However, the ease with which potential word forms are segmented from fluent speech seems likely to influence subsequent mappings between words and their referents. To explore this process, we tested the link between the statistical coherence of sequences presented in fluent speech and infants' subsequent use of those sequences as labels for novel objects. Notably, the materials were drawn from a natural language unfamiliar to the infants (Italian). The results of three experiments suggest that there is a close relationship between the statistics of the speech stream and subsequent mapping of labels to referents. Mapping was facilitated when the labels contained high transitional probabilities in the forward and/or backward direction (Experiment 1). When no transitional probability information was available (Experiment 2), or when the internal transitional probabilities of the labels were low in both directions (Experiment 3), infants failed to link the labels to their referents. Word learning appears to be strongly influenced by infants' prior experience with the distribution of sounds that make up words in natural languages. Copyright © 2011 Elsevier Inc. All rights reserved.

Quantification of spheno-occipital synchondrosis fusion in a contemporary Malaysian population.

PubMed

Hisham, Salina; Flavel, Ambika; Abdullah, Nurliza; Noor, Mohamad Helmee Mohamad; Franklin, Daniel

2018-03-01

Timing of fusion of the spheno-occipital synchondrosis (SOS) is correlated with age. Previous research, however, has demonstrated variation in the timing of closure among different global populations. The present study aims to quantify the timing of SOS fusion in Malaysian individuals as visualised in multi-detector computed tomography (CT) scans and to thereafter formulate age estimation models based on fusion status. Anonymised cranial CT scans of 336 males and 164 females, aged 5-25 years, were acquired from the National Institute of Forensic Medicine, Hospital Kuala Lumpur and Department of Diagnostic Imaging, Hospital Sultanah Aminah. The scans were received in DICOM format and reconstructed into three-dimensional images using OsiriX. The SOS is scored as open, fusing endocranially, fusing ectocranially or completely fused. Statistical analyses are performed using IBM SPSS Statistics version 24. Transition analysis (Nphases2) is then utilised to calculate age ranges for each stage. To assess the reliability of an observation, intra- and inter-observer agreement is quantified using Fleiss Kappa and was found to be excellent (κ=0.785-0.907 and 0.812). The mean (SD) age for complete fusion is 20.84 (2.84) years in males and 19.78 (3.35) years in females. Transition ages between Stages 0 and 1, 1 and 2, and 2 and 3 in males are 12.52, 13.98 and 15.52 years, respectively (SD 1.37); in females, the corresponding data are 10.47, 12.26 and 13.80 years (SD 1.72). Complete fusion of the SOS was observed in all individuals above the age of 18 years. SOS fusion status provides upper and lower age boundaries for forensic age estimation in the Malaysian sample. Copyright © 2018 Elsevier B.V. All rights reserved.

The effect of recombinant bone morphogenetic protein-2 in revision tibiotalocalcaneal arthrodesis: utilization of the Retrograde Arthrodesis Intramedullary Nail database.

PubMed

DeVries, J George; Nguyen, Minh; Berlet, Gregory C; Hyer, Christopher F

2012-01-01

The use of bone morphogenetic protein-2 (BMP-2) has been recommended for high-risk fusions and nonunion. Patients undergoing revisional tibiotalocalcaneal (TTC) arthrodesis via a retrograde arthrodesis nail to evaluate the influence of BMP-2 on rate of fusion in this high-risk population are presented. A retrospective chart and radiographic review were performed on 23 patients with failed prior fusion attempts at the ankle treated with retrograde intramedullary nailing. Sixteen patients were treated without BMP-2 (None group) and 7 were treated with BMP-2 (BMP group). The primary and secondary end-points were successful fusion, and time to fusion, respectively, with a variety of variables evaluated for influence. Other than the use of BMP-2, there were no statistical differences in the patient population. Overall, 11 of 16 ankles (68.8%) in the None group and 5 of 7 ankles (71.4%) in the BMP group resulted in a stable, functional limb. Rate of complication was similar between the 2 groups (p > .05). Time to radiographic ankle union was 115.2 and 184.0 days in the None and BMP groups (p > .05). The effect of BMP-2 on revisional TTC fusions with retrograde nails is reported here. The overall result as a stable, functional limb was 69.6%, which suggests that revision surgery in this high-risk population is a reasonable consideration. Even though this study was unable to demonstrate statistically significant differences, biologic augmentation with BMP-2 did not increase the complication rate and showed a slightly enhanced salvage rate for revision TTC fusions with an intramedullary nail. Copyright © 2012 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

Association of insurance status and spinal fusion usage in the United States during two decades.

PubMed

John, Jason; Mirahmadizadeh, Alireza; Seifi, Ali

2018-05-01

This study examined the distribution of spinal fusion usage among payer groups in the United States. Using the National Inpatient Sample (NIS) database, total discharges, length of stay, and mean hospital charges of patients who underwent spinal fusion from 1997 to 2014 in the United States were determined and analyzed. 5,715,625 total discharges with spinal fusion were reported. Among them, 2,875,188 (50.3%) were covered by private insurance, 1,710,182 by Medicare (29.9%), 342,638 (6.0%) by Medicaid, and 91,990 (1.6%) were uninsured. A statistically significant increase in spinal fusion usage occurred within each payer group over the study period (P < 0.001). For every year of the study period, private insurance patients had the most number and uninsured patients had the least number of total discharges with spinal fusion. Furthermore, annual growth in spinal fusion usage was greatest among private insurance patients, and smallest among uninsured patients. Total discharges with spinal fusion increased significantly across all payer groups between 1997 and 2014, but not equally. Further inquiry is indicated to determine the etiology of spinal fusion usage discrepancies between payer groups. Copyright © 2018 Elsevier Ltd. All rights reserved.

Engineering streptokinase for generation of active site-labeled plasminogen analogs*

PubMed Central

Laha, Malabika; Panizzi, Peter; Nahrendorf, Matthias; Bock, Paul E.

2011-01-01

We previously demonstrated that streptokinase (SK) can be used to generate active site-labeled fluorescent analogs of plasminogen (Pg) by virtue of its non-proteolytic activation of the zymogen. The method is versatile and allows for stoichiometric and active site-specific incorporation of any one of many molecular probes. The limitation of the labeling approach is that it is both time-consuming and low yield. Here we demonstrate an improved method for the preparation of labeled Pg analogs by the use of an engineered SK mutant fusion protein with both COOH- and NH2-terminal His6-tags. The NH2-terminal tag is followed by a tobacco etch virus proteinase cleavage site to ensure that the SK Ile1 residue, essential for conformational activation of Pg, is preserved. The SK COOH-terminal Lys414 residue and residues Arg253-Leu260 in the SK β-domain were deleted to prevent cleavage by plasmin (Pm), and to disable Pg substrate binding to the SK·Pg*/Pm catalytic complexes, respectively. Near-elimination of Pm generation with the SKΔ(R253-L260)ΔK414-His6 mutant increased the yield of labeled Pg 2.6-fold and reduced the time required >2-fold. The versatility of the labeling method was extended to the application of Pg labeled with a near-infrared probe to quantitate Pg receptors on immune cells by flow cytometry. PMID:21570944

Scaffold-free, label-free and nozzle-free biofabrication technology using magnetic levitational assembly.

PubMed

Parfenov, Vladislav A; Koudan, Elizaveta V; Bulanova, Elena A; Karalkin, Pavel A; Pereira, Frederico DAS; Norkin, Nikita E; Knyazeva, Alisa D; Gryadunova, Anna A; Petrov, Oleg F; Vasiliev, M M; Myasnikov, Maxim; Chernikov, Valery P; Kasyanov, Vladimir A; Marchenkov, Artem Yu; Brakke, Kenneth A; Khesuani, Yusef D; Demirci, Utkan; Mironov, Vladimir A

2018-05-31

Tissue spheroids have been proposed as building blocks in 3D biofabrication. Conventional magnetic force-driven 2D patterning of tissue spheroids requires prior cell labeling by magnetic nanoparticles, meanwhile a label-free approach for 3D magnetic levitational assembly has been introduced. Here we present first-time report on rapid assembly of 3D tissue construct using scaffold-free, nozzle-free and label-free magnetic levitation of tissue spheroids. Chondrospheres of standard size, shape and capable to fusion have been biofabricated from primary sheep chondrocytes using non-adhesive technology. Label-free magnetic levitation was performed using a prototype device equipped with permanent magnets in presence of gadolinium (Gd3+) in culture media, which enables magnetic levitation. Mathematical modeling and computer simulations were used for prediction of magnetic field and kinetics of tissue spheroids assembly into 3D tissue constructs. First, we used polystyrene beads to simulate the assembly of tissue spheroids and to determine the optimal settings for magnetic levitation in presence of Gd3+. Second, we proved the ability of chondrospheres to assemble rapidly into 3D tissue construct in the permanent magnetic field in the presence of Gd3+. Thus, scaffold- and label-free magnetic levitation of tissue spheroids is a promising approach for rapid 3D biofabrication and attractive alternative to label-based magnetic force-driven tissue engineering. . © 2018 IOP Publishing Ltd.

Resource-constrained Data Collection and Fusion for Identifying Weak Distributed Patterns in Networks

DTIC Science & Technology

2013-10-15

statistic,” in Artifical Intelligence and Statistics (AISTATS), 2013. [6] ——, “Detecting activity in graphs via the Graph Ellipsoid Scan Statistic... Artifical Intelligence and Statistics (AISTATS), 2013. [8] ——, “Near-optimal anomaly detection in graphs using Lovász Extended Scan Statistic,” in Neural...networks,” in Artificial Intelligence and Statistics (AISTATS), 2010. 11 [11] D. Aldous, “The random walk construction of uniform spanning trees and

Fusion set selection with surrogate metric in multi-atlas based image segmentation

NASA Astrophysics Data System (ADS)

Zhao, Tingting; Ruan, Dan

2016-02-01

Multi-atlas based image segmentation sees unprecedented opportunities but also demanding challenges in the big data era. Relevant atlas selection before label fusion plays a crucial role in reducing potential performance loss from heterogeneous data quality and high computation cost from extensive data. This paper starts with investigating the image similarity metric (termed ‘surrogate’), an alternative to the inaccessible geometric agreement metric (termed ‘oracle’) in atlas relevance assessment, and probes into the problem of how to select the ‘most-relevant’ atlases and how many such atlases to incorporate. We propose an inference model to relate the surrogates and the oracle geometric agreement metrics. Based on this model, we quantify the behavior of the surrogates in mimicking oracle metrics for atlas relevance ordering. Finally, analytical insights on the choice of fusion set size are presented from a probabilistic perspective, with the integrated goal of including the most relevant atlases and excluding the irrelevant ones. Empirical evidence and performance assessment are provided based on prostate and corpus callosum segmentation.

Fatty acid trafficking in starved cells: regulation by lipid droplet lipolysis, autophagy, and mitochondrial fusion dynamics.

PubMed

Rambold, Angelika S; Cohen, Sarah; Lippincott-Schwartz, Jennifer

2015-03-23

Fatty acids (FAs) provide cellular energy under starvation, yet how they mobilize and move into mitochondria in starved cells, driving oxidative respiration, is unclear. Here, we clarify this process by visualizing FA trafficking with a fluorescent FA probe. The labeled FA accumulated in lipid droplets (LDs) in well-fed cells but moved from LDs into mitochondria when cells were starved. Autophagy in starved cells replenished LDs with FAs, increasing LD number over time. Cytoplasmic lipases removed FAs from LDs, enabling their transfer into mitochondria. This required mitochondria to be highly fused and localized near LDs. When mitochondrial fusion was prevented in starved cells, FAs neither homogeneously distributed within mitochondria nor became efficiently metabolized. Instead, FAs reassociated with LDs and fluxed into neighboring cells. Thus, FAs engage in complex trafficking itineraries regulated by cytoplasmic lipases, autophagy, and mitochondrial fusion dynamics, ensuring maximum oxidative metabolism and avoidance of FA toxicity in starved cells. Copyright © 2015 Elsevier Inc. All rights reserved.

Genetic Encoding of bicyclononynes and trans-cyclooctenes for site-specific protein labeling in vitro and in live mammalian cells via rapid fluorogenic Diels-Alder reactions.

PubMed

Lang, Kathrin; Davis, Lloyd; Wallace, Stephen; Mahesh, Mohan; Cox, Daniel J; Blackman, Melissa L; Fox, Joseph M; Chin, Jason W

2012-06-27

Rapid, site-specific labeling of proteins with diverse probes remains an outstanding challenge for chemical biologists. Enzyme-mediated labeling approaches may be rapid but use protein or peptide fusions that introduce perturbations into the protein under study and may limit the sites that can be labeled, while many "bioorthogonal" reactions for which a component can be genetically encoded are too slow to effect quantitative site-specific labeling of proteins on a time scale that is useful for studying many biological processes. We report a fluorogenic reaction between bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) and tetrazines that is 3-7 orders of magnitude faster than many bioorthogonal reactions. Unlike the reactions of strained alkenes, including trans-cyclooctenes and norbornenes, with tetrazines, the BCN-tetrazine reaction gives a single product of defined stereochemistry. We have discovered aminoacyl-tRNA synthetase/tRNA pairs for the efficient site-specific incorporation of a BCN-containing amino acid, 1, and a trans-cyclooctene-containing amino acid 2 (which also reacts extremely rapidly with tetrazines) into proteins expressed in Escherichia coli and mammalian cells. We demonstrate the rapid fluorogenic labeling of proteins containing 1 and 2 in vitro, in E. coli , and in live mammalian cells. These approaches may be extended to site-specific protein labeling in animals, and we anticipate that they will have a broad impact on labeling and imaging studies.

Small-molecule-based protein-labeling technology in live cell studies: probe-design concepts and applications.

PubMed

Mizukami, Shin; Hori, Yuichiro; Kikuchi, Kazuya

2014-01-21

The use of genetic engineering techniques allows researchers to combine functional proteins with fluorescent proteins (FPs) to produce fusion proteins that can be visualized in living cells, tissues, and animals. However, several limitations of FPs, such as slow maturation kinetics or issues with photostability under laser illumination, have led researchers to examine new technologies beyond FP-based imaging. Recently, new protein-labeling technologies using protein/peptide tags and tag-specific probes have attracted increasing attention. Although several protein-labeling systems are com mercially available, researchers continue to work on addressing some of the limitations of this technology. To reduce the level of background fluorescence from unlabeled probes, researchers have pursued fluorogenic labeling, in which the labeling probes do not fluoresce until the target proteins are labeled. In this Account, we review two different fluorogenic protein-labeling systems that we have recently developed. First we give a brief history of protein labeling technologies and describe the challenges involved in protein labeling. In the second section, we discuss a fluorogenic labeling system based on a noncatalytic mutant of β-lactamase, which forms specific covalent bonds with β-lactam antibiotics such as ampicillin or cephalosporin. Based on fluorescence (or Förster) resonance energy transfer and other physicochemical principles, we have developed several types of fluorogenic labeling probes. To extend the utility of this labeling system, we took advantage of a hydrophobic β-lactam prodrug structure to achieve intracellular protein labeling. We also describe a small protein tag, photoactive yellow protein (PYP)-tag, and its probes. By utilizing a quenching mechanism based on close intramolecular contact, we incorporated a turn-on switch into the probes for fluorogenic protein labeling. One of these probes allowed us to rapidly image a protein while avoiding washout. In the future, we expect that protein-labeling systems with finely designed probes will lead to novel methodologies that allow researchers to image biomolecules and to perturb protein functions.

Fusion of deformed nuclei in the reactions of 76Ge+150Nd and 28Si+198Pt at the Coulomb barrier region

NASA Astrophysics Data System (ADS)

Nishio, K.; Ikezoe, H.; Mitsuoka, S.; Lu, J.

2000-07-01

Evaporation residue cross sections for 28Si+198Pt and 76Ge+150Nd, both of which form a compound nucleus 226U, were measured in the vicinity of the Coulomb barrier. The measurement gives direct evidence that the system really fuses together to form a fully equilibrated compound nucleus. For the 28Si+198Pt reaction, we have measured the fission fragments to determine the fusion cross section by taking advantage of the highly fissile character of 226U. The evaporation residue cross section and the fusion cross section for 28Si+198Pt allowed us to investigate the deexcitation process (exit channel) of the compound nucleus 226U, and the parameters entering in a statistical model calculation could be determined. By estimating the deexcitation of the compound nucleus 226U with the statistical model, the effect of the deformed nucleus 150Nd on the fusion reaction 76Ge+150Nd was extracted. The experimental data indicated that there is more than 13 MeV extra-extra-push energy for the system to fuse together when the projectile 76Ge collides at the tip of the deformed 150Nd nucleus. On the contrary, for the side collision which is more compact in configuration than the tip collision, no fusion hindrance is suggested.

Failure analysis of knee arthrodesis with the WichitaFusion Nail.

PubMed

Parcel, Ted W; Levering, Melissa; Polikandriotis, John A; Gustke, Kenneth A; Bernasek, Thomas L

2013-11-01

Arthrodesis is a salvage procedure for failed total knee arthroplasty with the intent to create a stable, pain-free limb on which to ambulate or transfer. For many patients, the alternative to arthrodesis may be an above-knee amputation. Available techniques for knee arthrodesis include compression plating, external fixators, and intramedullary fixation. The purpose of this study was to report the knee fusion rate of consecutive patients at 1 institution using an intramedullary fusion nail and to identify patient risk factors for fusion failure. Between November 1998 and November 2008, twenty-eight patients undergoing knee arthrodesis with an average follow-up of 18 months (range, 3-64 months) were retrospectively studied. Demographic information, presence of fusion, clinical function, pain level, and bone defect data were collected and analyzed. Eighty-two percent (23/28) of patients had radiographic evidence of successful fusion with an average time to fusion of 21 weeks (range, 10-58 weeks). When examining patient variables that could correlate with fusion rates, patients with an Anderson Orthopaedic Research Institute type 3 femoral or type 3 tibial defect had a statistically significant lower fusion rate. The intramedullary fusion nail is an effective device for knee arthrodesis that offers ease of insertion through the knee wound with the advantages of initial bone compression and rigid fixation. Although the use of intramedullary fusion nails leads to a high fusion rate, significant bone deficiency limits successful fusion. Copyright 2013, SLACK Incorporated.

Non-ad-hoc decision rule for the Dempster-Shafer method of evidential reasoning

NASA Astrophysics Data System (ADS)

Cheaito, Ali; Lecours, Michael; Bosse, Eloi

1998-03-01

This paper is concerned with the fusion of identity information through the use of statistical analysis rooted in Dempster-Shafer theory of evidence to provide automatic identification aboard a platform. An identity information process for a baseline Multi-Source Data Fusion (MSDF) system is defined. The MSDF system is applied to information sources which include a number of radars, IFF systems, an ESM system, and a remote track source. We use a comprehensive Platform Data Base (PDB) containing all the possible identity values that the potential target may take, and we use the fuzzy logic strategies which enable the fusion of subjective attribute information from sensor and the PDB to make the derivation of target identity more quickly, more precisely, and with statistically quantifiable measures of confidence. The conventional Dempster-Shafer lacks a formal basis upon which decision can be made in the face of ambiguity. We define a non-ad hoc decision rule based on the expected utility interval for pruning the `unessential' propositions which would otherwise overload the real-time data fusion systems. An example has been selected to demonstrate the implementation of our modified Dempster-Shafer method of evidential reasoning.

Quantifying Performance Bias in Label Fusion

DTIC Science & Technology

2012-08-21

detect ), may provide the end-user with the means to appropriately adjust the performance and optimal thresholds for performance by fusing legacy systems...boolean combination of classification systems in ROC space: An application to anomaly detection with HMMs. Pattern Recognition, 43(8), 2732-2752. 10...Shamsuddin, S. (2009). An overview of neural networks use in anomaly intrusion detection systems. Paper presented at the Research and Development (SCOReD

[Analysis and Control of in Vivo Kinetics of Exosomes for the Development of Exosome-based DDS].

PubMed

Takahashi, Yuki; Nishikawa, Makiya; Takakura, Yoshinobu

2016-01-01

  Exosomes are secretory membrane vesicles containing lipids, proteins, and nucleic acids. They act as intercellular transporters by delivering their components to exosome recipient cells. Based on their endogenous delivery system properties, exosomes are expected to become drug delivery systems (DDS) for various molecules such as nucleic acid-based drugs. Important factors such as drug loading to exosomes, production, and pharmacokinetics of exosomes need to be considered for the development of exosome-based DDS. Of these, the pharmacokinetics of exosomes have rarely been studied, probably because of the lack of quantitative evaluation methods of in vivo exosomal pharmacokinetics. We selected lactadherin as an exosome tropic protein and developed it as a fusion protein with Gaussia luciferase to label exosomes for in vivo imaging. In addition, a fusion protein of lactadherin and streptavidin was developed, and the tissue distribution of exosomes was quantitatively evaluated by radiolabeling the exosomes using (125)I-labeled biotin. Using labeled exosomes, we found that intravenously injected exosomes were rapidly cleared from the systemic circulation by macrophages. In addition, the exosomes were mainly distributed to the liver, lung, and spleen. We also examined the effect of exosome isolation methods on their physicochemical and pharmacokinetic properties. We found that exosomes collected by the ultracentrifugation-based density-gradient method were more dispersed than exosomes collected by other methods, including the ultracentrifugation-based pelleting method. The gradient method is more time-consuming than others; therefore the development of a more efficient method for exosome isolation will advance the development of exosome-based DDS.

The significance of calcified fibrocartilage on the cortical endplate of the translational sheep spine model.

PubMed

Sinclair, Sarina K; Bell, Spencer; Epperson, Richard Tyler; Bloebaum, Roy D

2013-05-01

To gain an understanding of the vertebral cortical endplate and factors that may affect the ability to achieve skeletal attachment to intervertebral implants and fusion, this study aimed to characterize the hypermineralized tissue on the cortical endplate of the vertebral body on a commonly used animal model. Skeletally mature sheep were injected with tetracycline prior to euthanasia and the C2-C3, T5-T6, and L2-L3 spinal motion segments were excised and prepared. Vertebral tissues were imaged using backscatter electron (BSE) imaging, histology, and tetracycline labeling was used to assess bone remodeling within different tissue layers. It was determined that the hypermineralized tissue layer was calcified fibrocartilage (CFC). No tetracycline labels were identified in the CFC layer, in contrast to single and double labels that were present in the underlying bone, indicating the CFC present on the cortical endplate was not being actively remodeled. The average thickness of the CFC layer was 146.3 ± 70.53 µm in the cervical region, 98.2 ± 40.29 µm in the thoracic region, and 150.89 ± 69.25 µm in the lumbar region. This difference in thickness may be attributed to the regional biomechanical properties of the spine. Results from this investigation indicate the presence of a nonremodeling tissue on the cortical endplate of the vertebral body in sheep spines, which attaches the intervertebral disc to the vertebrae. This tissue, if not removed, would likely prevent successful bony attachment to an intervertebral device in spinal fusion studies and total disc replacement surgeries. Copyright © 2013 Wiley Periodicals, Inc.

Pharmacokinetics and brain uptake in the rhesus monkey of a fusion protein of arylsulfatase a and a monoclonal antibody against the human insulin receptor.

PubMed

Boado, Ruben J; Lu, Jeff Zhiqiang; Hui, Eric K-W; Sumbria, Rachita K; Pardridge, William M

2013-05-01

Metachromatic leukodystrophy (MLD) is a lysosomal storage disorder of the brain caused by mutations in the gene encoding the lysosomal sulfatase, arylsulfatase A (ASA). It is not possible to treat the brain in MLD with recombinant ASA, because the enzyme does not cross the blood-brain barrier (BBB). In the present investigation, a BBB-penetrating IgG-ASA fusion protein is engineered and expressed, where the ASA monomer is fused to the carboxyl terminus of each heavy chain of an engineered monoclonal antibody (MAb) against the human insulin receptor (HIR). The HIRMAb crosses the BBB via receptor-mediated transport on the endogenous BBB insulin receptor, and acts as a molecular Trojan horse to ferry the ASA into brain from blood. The HIRMAb-ASA is expressed in stably transfected Chinese hamster ovary cells grown in serum free medium, and purified by protein A affinity chromatography. The fusion protein retains high affinity binding to the HIR, EC50 = 0.34 ± 0.11 nM, and retains high ASA enzyme activity, 20 ± 1 units/mg. The HIRMAb-ASA fusion protein is endocytosed and triaged to the lysosomal compartment in MLD fibroblasts. The fusion protein was radio-labeled with the Bolton-Hunter reagent, and the [(125) I]-HIRMAb-ASA rapidly penetrates the brain in the Rhesus monkey following intravenous administration. Film and emulsion autoradiography of primate brain shows global distribution of the fusion protein throughout the monkey brain. These studies describe a new biological entity that is designed to treat the brain of humans with MLD following non-invasive, intravenous infusion of an IgG-ASA fusion protein. Copyright © 2012 Wiley Periodicals, Inc.

Low-energy nuclear reaction of the 14N+169Tm system: Incomplete fusion

NASA Astrophysics Data System (ADS)

Kumar, R.; Sharma, Vijay R.; Yadav, Abhishek; Singh, Pushpendra P.; Agarwal, Avinash; Appannababu, S.; Mukherjee, S.; Singh, B. P.; Ali, R.; Bhowmik, R. K.

2017-11-01

Excitation functions of reaction residues produced in the 14N+169Tm system have been measured to high precision at energies above the fusion barrier, ranging from 1.04 VB to 1.30 VB , and analyzed in the framework of the statistical model code pace4. Analysis of α -emitting channels points toward the onset of incomplete fusion even at slightly above-barrier energies where complete fusion is supposed to be one of the dominant processes. The onset and strength of incomplete fusion have been deduced and studied in terms of various entrance channel parameters. Present results together with the reanalysis of existing data for various projectile-target combinations conclusively suggest strong influence of projectile structure on the onset of incomplete fusion. Also, a strong dependence on the Coulomb effect (ZPZT) has been observed for the present system along with different projectile-target combinations available in the literature. It is concluded that the fraction of incomplete fusion linearly increases with ZPZT and is found to be more for larger ZPZT values, indicating significantly important linear systematics.

Reliability of Measured Data for pH Sensor Arrays with Fault Diagnosis and Data Fusion Based on LabVIEW

PubMed Central

Liao, Yi-Hung; Chou, Jung-Chuan; Lin, Chin-Yi

2013-01-01

Fault diagnosis (FD) and data fusion (DF) technologies implemented in the LabVIEW program were used for a ruthenium dioxide pH sensor array. The purpose of the fault diagnosis and data fusion technologies is to increase the reliability of measured data. Data fusion is a very useful statistical method used for sensor arrays in many fields. Fault diagnosis is used to avoid sensor faults and to measure errors in the electrochemical measurement system, therefore, in this study, we use fault diagnosis to remove any faulty sensors in advance, and then proceed with data fusion in the sensor array. The average, self-adaptive and coefficient of variance data fusion methods are used in this study. The pH electrode is fabricated with ruthenium dioxide (RuO2) sensing membrane using a sputtering system to deposit it onto a silicon substrate, and eight RuO2 pH electrodes are fabricated to form a sensor array for this study. PMID:24351636

Reliability of measured data for pH sensor arrays with fault diagnosis and data fusion based on LabVIEW.

PubMed

Liao, Yi-Hung; Chou, Jung-Chuan; Lin, Chin-Yi

2013-12-13

Fault diagnosis (FD) and data fusion (DF) technologies implemented in the LabVIEW program were used for a ruthenium dioxide pH sensor array. The purpose of the fault diagnosis and data fusion technologies is to increase the reliability of measured data. Data fusion is a very useful statistical method used for sensor arrays in many fields. Fault diagnosis is used to avoid sensor faults and to measure errors in the electrochemical measurement system, therefore, in this study, we use fault diagnosis to remove any faulty sensors in advance, and then proceed with data fusion in the sensor array. The average, self-adaptive and coefficient of variance data fusion methods are used in this study. The pH electrode is fabricated with ruthenium dioxide (RuO2) sensing membrane using a sputtering system to deposit it onto a silicon substrate, and eight RuO2 pH electrodes are fabricated to form a sensor array for this study.

Cholesterol Facts and Statistics

MedlinePlus

... commit" type="submit" value="Submit" /> Related CDC Web Sites Division for Heart Disease and Stroke Prevention ... commit" type="submit" value="Submit" /> Related CDC Web Sites Division for Heart Disease and Stroke Prevention ...

Biomechanical Characteristics of an Integrated Lumbar Interbody Fusion Device

PubMed Central

Voronov, Leonard I.; Vastardis, Georgios; Zelenakova, Julia; Carandang, Gerard; Havey, Robert M.; Waldorff, Erik I.; Zindrick, Michael R.

2014-01-01

Introduction We hypothesized that an Integrated Lumbar Interbody Fusion Device (PILLAR SA, Orthofix, Lewisville, TX) will function biomechanically similar to a traditional anterior interbody spacer (PILLAR AL, Orthofix, Lewisville, TX) plus posterior instrumentation (FIREBIRD, Orthofix, Lewisville, TX). Purpose of this study was to determine if an Integrated Interbody Fusion Device (PILLAR SA) can stabilize single motion segments as well as an anterior interbody spacer (PILLAR AL) + pedicle screw construct (FIREBIRD). Methods Eight cadaveric lumbar spines (age: 43.9±4.3 years) were used. Each specimen's range of motion was tested in flexion-extension (FE), lateral bending (LB), and axial rotation (AR) under intact condition, after L4-L5 PILLAR SA with intervertebral screws and after L4-L5 360° fusion (PILLAR AL + Pedicle Screws and rods (FIREBIRD). Each specimen was tested in flexion (8Nm) and extension (6Nm) without preload (0 N) and under 400N of preload, in lateral bending (±6 Nm) and axial rotation (±5 Nm) without preload. Results Integrated fusion using the PILLAR SA device demonstrated statistically significant reductions in range of motion of the L4-L5 motion segment as compared to the intact condition for each test direction. PILLAR SA reduced ROM from 8.9±1.9 to 2.9±1.1° in FE with 400N follower preload (67.4%), 8.0±1.7 to 2.5±1.1° in LB, and 2.2±1.2 to 0.7±0.3° in AR. A comparison between the PILLAR SA integrated fusion device versus 360° fusion construct with spacer and bilateral pedicle screws was statistically significant in FE and LB. The 360° fusion yielded motion of 1.0±0.5° in FE, 1.0±0.8° in LB (p0.05). Conclusions The PILLAR SA resulted in motions of less than 3° in all modes of motion and was not as motion restricting as the traditional 360° using bilateral pedicle screws. The residual segmental motions compare very favorably with published biomechanical studies of other interbody integrated fusion devices. PMID:25694931

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

Chang, J; Gu, X; Lu, W

Purpose: A novel distance-dose weighting method for label fusion was developed to increase segmentation accuracy in dosimetrically important regions for prostate radiation therapy. Methods: Label fusion as implemented in the original SIMPLE (OS) for multi-atlas segmentation relies iteratively on the majority vote to generate an estimated ground truth and DICE similarity measure to screen candidates. The proposed distance-dose weighting puts more values on dosimetrically important regions when calculating similarity measure. Specifically, we introduced distance-to-dose error (DDE), which converts distance to dosimetric importance, in performance evaluation. The DDE calculates an estimated DE error derived from surface distance differences between the candidatemore » and estimated ground truth label by multiplying a regression coefficient. To determine the coefficient at each simulation point on the rectum, we fitted DE error with respect to simulated voxel shift. The DEs were calculated by the multi-OAR geometry-dosimetry training model previously developed in our research group. Results: For both the OS and the distance-dose weighted SIMPLE (WS) results, the evaluation metrics for twenty patients were calculated using the ground truth segmentation. The mean difference of DICE, Hausdorff distance, and mean absolute distance (MAD) between OS and WS have shown 0, 0.10, and 0.11, respectively. In partial MAD of WS which calculates MAD within a certain PTV expansion voxel distance, the lower MADs were observed at the closer distances from 1 to 8 than those of OS. The DE results showed that the segmentation from WS produced more accurate results than OS. The mean DE error of V75, V70, V65, and V60 were decreased by 1.16%, 1.17%, 1.14%, and 1.12%, respectively. Conclusion: We have demonstrated that the method can increase the segmentation accuracy in rectum regions adjacent to PTV. As a result, segmentation using WS have shown improved dosimetric accuracy than OS. The WS will provide dosimetrically important label selection strategy in multi-atlas segmentation. CPRIT grant RP150485.« less

Pedicle screw fixation for isthmic spondylolisthesis: does posterior lumbar interbody fusion improve outcome over posterolateral fusion?

PubMed

La Rosa, Giovanni; Conti, Alfredo; Cacciola, Fabio; Cardali, Salvatore; La Torre, Domenico; Gambadauro, Nicola Maria; Tomasello, Francesco

2003-09-01

Posterolateral fusion involving instrumentation-assisted segmental fixation represents a valid procedure in the treatment of lumbar instability. In cases of anterior column failure, such as in isthmic spondylolisthesis, supplemental posterior lumbar interbody fusion (PLIF) may improve the fusion rate and endurance of the construct. Posterior lumbar interbody fusion is, however, a more demanding procedure and increases costs and risks of the intervention. The advantages of this technique must, therefore, be weighed against those of a simple posterior lumbar fusion. Thirty-five consecutive patients underwent pedicle screw fixation for isthmic spondylolisthesis. In 18 patients posterior lumbar fusion was performed, and in 17 patients PLIF was added. Clinical, economic, functional, and radiographic data were assessed to determine differences in clinical and functional results and biomechanical properties. At 2-year follow-up examination, the correction of subluxation, disc height, and foraminal area were maintained in the group in which a PLIF procedure was performed, but not in the posterolateral fusion-only group (p < 0.05). Nevertheless, no statistical intergroup differences were demonstrated in terms of neurological improvement (p = 1), economic (p = 0.43), or functional (p = 0.95) outcome, nor in terms of fusion rate (p = 0.49). The authors' findings support the view that an interbody fusion confers superior mechanical strength to the spinal construct; when posterolateral fusion is the sole intervention, progressive loss of the extreme correction can be expected. Such mechanical insufficiency, however, did not influence clinical outcome.

Fusion yield: Guderley model and Tsallis statistics

NASA Astrophysics Data System (ADS)

Haubold, H. J.; Kumar, D.

2011-02-01

The reaction rate probability integral is extended from Maxwell-Boltzmann approach to a more general approach by using the pathway model introduced by Mathai in 2005 (A pathway to matrix-variate gamma and normal densities. Linear Algebr. Appl. 396, 317-328). The extended thermonuclear reaction rate is obtained in the closed form via a Meijer's G-function and the so-obtained G-function is represented as a solution of a homogeneous linear differential equation. A physical model for the hydrodynamical process in a fusion plasma-compressed and laser-driven spherical shock wave is used for evaluating the fusion energy integral by integrating the extended thermonuclear reaction rate integral over the temperature. The result obtained is compared with the standard fusion yield obtained by Haubold and John in 1981 (Analytical representation of the thermonuclear reaction rate and fusion energy production in a spherical plasma shock wave. Plasma Phys. 23, 399-411). An interpretation for the pathway parameter is also given.

Laser-induced tissue fluorescence in radiofrequency tissue-fusion characterization.

PubMed

Su, Lei; Fonseca, Martina B; Arya, Shobhit; Kudo, Hiromi; Goldin, Robert; Hanna, George B; Elson, Daniel S

2014-01-01

Heat-induced tissue fusion is an important procedure in modern surgery and can greatly reduce trauma, complications, and mortality during minimally invasive surgical blood vessel anastomosis, but it may also have further benefits if applied to other tissue types such as small and large intestine anastomoses. We present a tissue-fusion characterization technology using laser-induced fluorescence spectroscopy, which provides further insight into tissue constituent variations at the molecular level. In particular, an increase of fluorescence intensity in 450- to 550-nm range for 375- and 405-nm excitation suggests that the collagen cross-linking in fused tissues increased. Our experimental and statistical analyses showed that, by using fluorescence spectral data, good fusion could be differentiated from other cases with an accuracy of more than 95%. This suggests that the fluorescence spectroscopy could be potentially used as a feedback control method in online tissue-fusion monitoring.

The Effect of Multispectral Image Fusion Enhancement on Human Efficiency

DTIC Science & Technology

2017-03-20

performance of the ideal observer is indicative of the relative amount of informa- tion across various experimental manipulations. In our experimental design ...registration and fusion processes, and contributed strongly to the statistical analyses. LMB contributed to the experimental design and writing structure. All... designed to be innovative, low-cost, and (relatively) easy-to-implement, and to provide support across the spectrum of possible users including

Statistical rice yield modeling using blended MODIS-Landsat based crop phenology metrics in Taiwan

NASA Astrophysics Data System (ADS)

Chen, C. R.; Chen, C. F.; Nguyen, S. T.; Lau, K. V.

2015-12-01

Taiwan is a populated island with a majority of residents settled in the western plains where soils are suitable for rice cultivation. Rice is not only the most important commodity, but also plays a critical role for agricultural and food marketing. Information of rice production is thus important for policymakers to devise timely plans for ensuring sustainably socioeconomic development. Because rice fields in Taiwan are generally small and yet crop monitoring requires information of crop phenology associating with the spatiotemporal resolution of satellite data, this study used Landsat-MODIS fusion data for rice yield modeling in Taiwan. We processed the data for the first crop (Feb-Mar to Jun-Jul) and the second (Aug-Sep to Nov-Dec) in 2014 through five main steps: (1) data pre-processing to account for geometric and radiometric errors of Landsat data, (2) Landsat-MODIS data fusion using using the spatial-temporal adaptive reflectance fusion model, (3) construction of the smooth time-series enhanced vegetation index 2 (EVI2), (4) rice yield modeling using EVI2-based crop phenology metrics, and (5) error verification. The fusion results by a comparison bewteen EVI2 derived from the fusion image and that from the reference Landsat image indicated close agreement between the two datasets (R2 > 0.8). We analysed smooth EVI2 curves to extract phenology metrics or phenological variables for establishment of rice yield models. The results indicated that the established yield models significantly explained more than 70% variability in the data (p-value < 0.001). The comparison results between the estimated yields and the government's yield statistics for the first and second crops indicated a close significant relationship between the two datasets (R2 > 0.8), in both cases. The root mean square error (RMSE) and mean absolute error (MAE) used to measure the model accuracy revealed the consistency between the estimated yields and the government's yield statistics. This study demonstrates advantages of using EVI2-based phenology metrics (derived from Landsat-MODIS fusion data) for rice yield estimation in Taiwan prior to the harvest period.

Incorporating priors on expert performance parameters for segmentation validation and label fusion: a maximum a posteriori STAPLE

PubMed Central

Commowick, Olivier; Warfield, Simon K

2010-01-01

In order to evaluate the quality of segmentations of an image and assess intra- and inter-expert variability in segmentation performance, an Expectation Maximization (EM) algorithm for Simultaneous Truth And Performance Level Estimation (STAPLE) was recently developed. This algorithm, originally presented for segmentation validation, has since been used for many applications, such as atlas construction and decision fusion. However, the manual delineation of structures of interest is a very time consuming and burdensome task. Further, as the time required and burden of manual delineation increase, the accuracy of the delineation is decreased. Therefore, it may be desirable to ask the experts to delineate only a reduced number of structures or the segmentation of all structures by all experts may simply not be achieved. Fusion from data with some structures not segmented by each expert should be carried out in a manner that accounts for the missing information. In other applications, locally inconsistent segmentations may drive the STAPLE algorithm into an undesirable local optimum, leading to misclassifications or misleading experts performance parameters. We present a new algorithm that allows fusion with partial delineation and which can avoid convergence to undesirable local optima in the presence of strongly inconsistent segmentations. The algorithm extends STAPLE by incorporating prior probabilities for the expert performance parameters. This is achieved through a Maximum A Posteriori formulation, where the prior probabilities for the performance parameters are modeled by a beta distribution. We demonstrate that this new algorithm enables dramatically improved fusion from data with partial delineation by each expert in comparison to fusion with STAPLE. PMID:20879379

Incorporating priors on expert performance parameters for segmentation validation and label fusion: a maximum a posteriori STAPLE.

PubMed

Commowick, Olivier; Warfield, Simon K

2010-01-01

In order to evaluate the quality of segmentations of an image and assess intra- and inter-expert variability in segmentation performance, an Expectation Maximization (EM) algorithm for Simultaneous Truth And Performance Level Estimation (STAPLE) was recently developed. This algorithm, originally presented for segmentation validation, has since been used for many applications, such as atlas construction and decision fusion. However, the manual delineation of structures of interest is a very time consuming and burdensome task. Further, as the time required and burden of manual delineation increase, the accuracy of the delineation is decreased. Therefore, it may be desirable to ask the experts to delineate only a reduced number of structures or the segmentation of all structures by all experts may simply not be achieved. Fusion from data with some structures not segmented by each expert should be carried out in a manner that accounts for the missing information. In other applications, locally inconsistent segmentations may drive the STAPLE algorithm into an undesirable local optimum, leading to misclassifications or misleading experts performance parameters. We present a new algorithm that allows fusion with partial delineation and which can avoid convergence to undesirable local optima in the presence of strongly inconsistent segmentations. The algorithm extends STAPLE by incorporating prior probabilities for the expert performance parameters. This is achieved through a Maximum A Posteriori formulation, where the prior probabilities for the performance parameters are modeled by a beta distribution. We demonstrate that this new algorithm enables dramatically improved fusion from data with partial delineation by each expert in comparison to fusion with STAPLE.

Information Measures of Degree Distributions with an Application to Labeled Graphs

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

Joslyn, Cliff A.; Purvine, Emilie AH

2016-01-11

The problem of describing the distribution of labels over a set of objects is relevant to many domains. For example: cyber security, social media, and protein interactions all care about the manner in which labels are distributed among different objects. In this paper we present three interacting statistical measures on label distributions, inspired by entropy and information theory. Labeled graphs are discussed as a specific case of labels distributed over a set of edges. We describe a use case in cyber security using a labeled directed multi-graph of IPFLOW. Finally we show how these measures respond when labels are updatedmore » in certain ways.« less

The effects of doxorubicin (adriamycin) on spinal fusion: an experimental model of posterolateral lumbar spinal arthrodesis.

PubMed

Tortolani, P Justin; Park, Andrew E; Louis-Ugbo, John; Attallah-Wasef, Emad S; Kraiwattanapong, Chaiwat; Heller, John G; Boden, Scott D; Yoon, S Tim

2004-01-01

Malignant spinal lesions may require surgical excision and segmental stabilization. The decision to perform a concomitant fusion procedure is influenced in part by the need for adjunctive chemotherapy as well as the patient's anticipated survival. Although some evidence exists that suggests that chemotherapy may inhibit bony healing, no information exists regarding the effect of chemotherapy on spinal fusion healing. To determine the effect of a frequently used chemotherapeutic agent, doxorubicin, on posterolateral spinal fusion rates. Prospective animal model of posterolateral lumbar fusion. Determination of spinal fusion by manual palpation of excised spines. Plain radiographic evaluation of denuded spines to evaluate intertransverse bone formation. Thirty-two New Zealand White rabbits underwent posterior intertransverse process fusion at L5-L6 with the use of iliac autograft bone. Rabbits randomly received either intravenous doxorubicin (2.5 mg/kg) by means of the central vein of the ear at the time of surgery (16 animals) or no treatment (16 animals; the control group). The animals were euthanized at 5 weeks, and the lumbar spines were excised. Spine fusion was assessed by manually palpating (by observers blinded to the treatment group) at the level of arthrodesis, and at the adjacent levels proximal and distal. This provided similar information to surgical fusion assessment by palpation in humans. Fusion was defined as the absence of palpable motion. Posteroanterior radiographs of the excised spines were graded in a blinded fashion using a five-point scoring system (0 to 4) devised to describe the amount of bone observed between the L5-L6 transverse processes. Power analysis conducted before initiation of the study indicated that an allocation of 16 animals to each group would permit detection of at least a 20% difference in fusion rates with statistical significance at p=.05. Eleven of the 16 spines (69%) in the control group and 6 of the 16 spines (38%) in the doxorubicin group fused. This difference was statistically significant (=.038). There was no significant correlation (p>.05) between the radiographic grade of bone formation (0 to 4) and fusion as determined by palpation. There were four wound infections in the control group and four in the doxorubicin group. However, solid fusions were palpated in three of these four spines in both the control and treatment groups. No significant differences in wound complications were noted with doxorubicin administration. A single dose of doxorubicin administered intravenously at the time of surgery appears to play a significant inhibitory role in the process of spinal fusion. If similar effects occur in humans, these data suggest that doxorubicin may be harmful to bone healing in a spine fusion if given during the perioperative period. Further investigation will be necessary to determine the effect of time to aid at determining whether doxorubicin administered several weeks pre- or postoperatively results in improved fusion rate, and whether bone morphogenetic proteins can overcome these inhibitory effects.

Complications Related to the Recombinant Human Bone Morphogenetic Protein 2 Use in Posterior Cervical Fusion.

PubMed

Takahashi, Shinji; Buser, Zorica; Cohen, Jeremiah R; Roe, Allison; Myhre, Sue L; Meisel, Hans-Joerg; Brodke, Darrel S; Yoon, S Tim; Park, Jong-Beom; Wang, Jeffrey C; Youssef, Jim A

2017-11-01

A retrospective cohort study. To compare the complications between posterior cervical fusions with and without recombinant human bone morphogenetic protein 2 (rhBMP2). Use of rhBMP2 in anterior cervical spinal fusion procedures can lead to potential complications such as neck edema, resulting in airway complications or neurological compression. However, there are no data on the complications associated with the "off-label" use of rhBMP2 in upper and lower posterior cervical fusion approaches. Patients from the PearlDiver database who had a posterior cervical fusion between 2005 and 2011 were identified. We evaluated complications within 90 days after fusion and data was divided in 2 groups: (1) posterior cervical fusion including upper cervical spine O-C2 (upper group) and (2) posterior cervical fusion including lower cervical spine C3-C7 (lower group). Complications were divided into: any complication, neck-related complications, wound-related complications, and other complications. Of the 352 patients in the upper group, 73 patients (20.7%) received rhBMP2, and 279 patients (79.3%) did not. Likewise, in the lower group of 2372 patients, 378 patients (15.9%) had surgery with rhBMP2 and 1994 patients (84.1%) without. In the upper group, complications were observed in 7 patients (9.6%) with and 34 patients (12%) without rhBMP2. In the lower group, complications were observed in 42 patients (11%) with and 276 patients (14%) without rhBMP2. Furthermore, in the lower group the wound-related complications were significantly higher in the rhBMP2 group (23 patients, 6.1%) compared with the non-rhBMP2 group (75 patients, 3.8%). Our data showed that the use of rhBMP2 does not increase the risk of complications in upper cervical spine fusion procedures. However, in the lower cervical spine, rhBMP2 may elevate the risk of wound-related complications. Overall, there were no major complications associated with the use of rhBMP2 for posterior cervical fusion approaches. Level III.

Data and Statistics: Women and Heart Disease

MedlinePlus

... commit" type="submit" value="Submit" /> Related CDC Web Sites Heart Disease Stroke High Blood Pressure Salt ... commit" type="submit" value="Submit" /> Related CDC Web Sites Heart Disease Stroke High Blood Pressure Salt ...

Influence of Alendronate and Endplate Degeneration to Single Level Posterior Lumbar Spinal Interbody Fusion

PubMed Central

Rhee, Wootack; Ha, Seongil; Lim, Jae Hyeon; Jang, Il Tae

2014-01-01

Objective Using alendronate after spinal fusion is a controversial issue due to the inhibition of osteoclast mediated bone resorption. In addition, there are an increasing number of reports that the endplate degeneration influences the lumbar spinal fusion. The object of this retrospective controlled study was to evaluate how the endplate degeneration and the bisphosphonate medication influence the spinal fusion through radiographic evaluation. Methods In this study, 44 patients who underwent single-level posterior lumbar interbody fusion (PLIF) using cage were examined from April 2007 to March 2009. All patients had been diagnosed as osteoporosis and would be recommended for alendronate medication. Endplate degeneration is categorized by the Modic changes. The solid fusion is defined if there was bridging bone between the vertebral bodies, either within or external to the cage on the plain X-ray and if there is less than 5° of angular difference in dynamic X-ray. Results In alendronate group, fusion was achieved in 66.7% compared to 73.9% in control group (no medication). Alendronate did not influence the fusion rate of PLIF. However, there was the statistical difference of fusion rate between the endplate degeneration group and the group without endplate degeneration. A total of 52.4% of fusion rate was seen in the endplate degeneration group compared to 91.3% in the group without endplate degeneration. The endplate degeneration suppresses the fusion process of PLIF. Conclusion Alendronate does not influence the fusion process in osteoporotic patients. The endplate degeneration decreases the fusion rate. PMID:25620981

CXCR2 inverse agonism detected by arrestin redistribution.

PubMed

Kredel, Simone; Wolff, Michael; Wiedenmann, Jörg; Moepps, Barbara; Nienhaus, G Ulrich; Gierschik, Peter; Kistler, Barbara; Heilker, Ralf

2009-10-01

To study CXCR2 modulated arrestin redistribution, the authors employed arrestin as a fusion protein containing either the Aequorea victoria-derived enhanced green fluorescent protein (EGFP) or a recently developed mutant of eqFP611, a red fluorescent protein derived from Entacmaea quadricolor. This mutant, referred to as RFP611, had earlier been found to assume a dimeric quarternary structure. It was therefore employed in this work as a "tandem" (td) construct for pseudo-monomeric fusion protein labeling. Both arrestin fusion proteins, containing either td-RFP611 (Arr-td-RFP611) or enhanced green fluorescent protein (EGFP; Arr-EGFP), were found to colocalize with internalized fluorescently labeled Gro-alpha a few minutes after Gro-alpha addition. Intriguingly, however, Arr-td-RFP611 and Arr-EGFP displayed distinct cellular distribution patterns in the absence of any CXCR2-activating ligand. Under these conditions, Arr-td-RFP611 showed a largely homogeneous cytosolic distribution, whereas Arr-EGFP segregated, to a large degree, into granular spots. These observations indicate a higher sensitivity of Arr EGFP to the constitutive activity of CXCR2 and, accordingly, an increased arrestin redistribution to coated pits and endocytic vesicles. In support of this interpretation, the authors found the known CXCR2 antagonist Sch527123 to act as an inverse agonist with respect to Arr-EGFP redistribution. The inverse agonistic properties of Sch527123 were confirmed in vitro in a guanine nucleotide binding assay, revealing an IC(50) value similar to that observed for Arr-EGFP redistribution. Thus, the redistribution assay, when based on Arr-EGFP, enables the profiling of antagonistic test compounds with respect to inverse agonism. When based on Arr-td-RFP611, the assay may be employed to study CXCR2 agonism or neutral antagonism.

Preparation of stable isotope-labeled peripheral cannabinoid receptor CB2 by bacterial fermentation

PubMed Central

Berger, Christian; Ho, Jenny T.C.; Kimura, Tomohiro; Hess, Sonja; Gawrisch, Klaus; Yeliseev, Alexei

2010-01-01

We developed a bacterial fermentation protocol for production of a stable isotope-labeled cannabinoid receptor CB2 for subsequent structural studies of this protein by nuclear magnetic resonance spectroscopy. The human peripheral cannabinoid receptor was expressed in Escherichia coli as a fusion with maltose binding protein and two affinity tags. The fermentation was performed in defined media comprised of mineral salts, glucose and 15N2-L-tryptophan to afford incorporation of the labeled amino acid into the protein. Medium, growth and expression conditions were optimized so that the fermentation process produced about 2 mg of purified, labeled CB2 per liter of culture medium. By performing a mass spectroscopic characterization of the purified CB2, we determined that one of the two 15N atoms in tryptophan was incorporated into the recombinant protein. NMR analysis of 15N chemical shifts strongly suggests that the 15N atoms are located in Trp-indole rings. Importantly, analysis of the peptides derived from the CNBr cleavage of the purified protein confirmed a minimum of 95% incorporation of the labeled tryptophan into the CB2 sequence. The labeled CB2, purified and reconstituted into liposomes at a protein-to-lipid molar ratio of 1:500, was functional as confirmed by activation of cognate G proteins in an in vitro coupled assay. To our knowledge, this is the first reported production of a biologically active, stable isotope-labeled G protein-coupled receptor by bacterial fermentation. PMID:20044006

Multi-object model-based multi-atlas segmentation for rodent brains using dense discrete correspondences

NASA Astrophysics Data System (ADS)

Lee, Joohwi; Kim, Sun Hyung; Styner, Martin

2016-03-01

The delineation of rodent brain structures is challenging due to low-contrast multiple cortical and subcortical organs that are closely interfacing to each other. Atlas-based segmentation has been widely employed due to its ability to delineate multiple organs at the same time via image registration. The use of multiple atlases and subsequent label fusion techniques has further improved the robustness and accuracy of atlas-based segmentation. However, the accuracy of atlas-based segmentation is still prone to registration errors; for example, the segmentation of in vivo MR images can be less accurate and robust against image artifacts than the segmentation of post mortem images. In order to improve the accuracy and robustness of atlas-based segmentation, we propose a multi-object, model-based, multi-atlas segmentation method. We first establish spatial correspondences across atlases using a set of dense pseudo-landmark particles. We build a multi-object point distribution model using those particles in order to capture inter- and intra- subject variation among brain structures. The segmentation is obtained by fitting the model into a subject image, followed by label fusion process. Our result shows that the proposed method resulted in greater accuracy than comparable segmentation methods, including a widely used ANTs registration tool.

D Semantic Labeling of ALS Data Based on Domain Adaption by Transferring and Fusing Random Forest Models

NASA Astrophysics Data System (ADS)

Wu, J.; Yao, W.; Zhang, J.; Li, Y.

2018-04-01

Labeling 3D point cloud data with traditional supervised learning methods requires considerable labelled samples, the collection of which is cost and time expensive. This work focuses on adopting domain adaption concept to transfer existing trained random forest classifiers (based on source domain) to new data scenes (target domain), which aims at reducing the dependence of accurate 3D semantic labeling in point clouds on training samples from the new data scene. Firstly, two random forest classifiers were firstly trained with existing samples previously collected for other data. They were different from each other by using two different decision tree construction algorithms: C4.5 with information gain ratio and CART with Gini index. Secondly, four random forest classifiers adapted to the target domain are derived through transferring each tree in the source random forest models with two types of operations: structure expansion and reduction-SER and structure transfer-STRUT. Finally, points in target domain are labelled by fusing the four newly derived random forest classifiers using weights of evidence based fusion model. To validate our method, experimental analysis was conducted using 3 datasets: one is used as the source domain data (Vaihingen data for 3D Semantic Labelling); another two are used as the target domain data from two cities in China (Jinmen city and Dunhuang city). Overall accuracies of 85.5 % and 83.3 % for 3D labelling were achieved for Jinmen city and Dunhuang city data respectively, with only 1/3 newly labelled samples compared to the cases without domain adaption.

Embedding the results of focussed Bayesian fusion into a global context

NASA Astrophysics Data System (ADS)

Sander, Jennifer; Heizmann, Michael

2014-05-01

Bayesian statistics offers a well-founded and powerful fusion methodology also for the fusion of heterogeneous information sources. However, except in special cases, the needed posterior distribution is not analytically derivable. As consequence, Bayesian fusion may cause unacceptably high computational and storage costs in practice. Local Bayesian fusion approaches aim at reducing the complexity of the Bayesian fusion methodology significantly. This is done by concentrating the actual Bayesian fusion on the potentially most task relevant parts of the domain of the Properties of Interest. Our research on these approaches is motivated by an analogy to criminal investigations where criminalists pursue clues also only locally. This publication follows previous publications on a special local Bayesian fusion technique called focussed Bayesian fusion. Here, the actual calculation of the posterior distribution gets completely restricted to a suitably chosen local context. By this, the global posterior distribution is not completely determined. Strategies for using the results of a focussed Bayesian analysis appropriately are needed. In this publication, we primarily contrast different ways of embedding the results of focussed Bayesian fusion explicitly into a global context. To obtain a unique global posterior distribution, we analyze the application of the Maximum Entropy Principle that has been shown to be successfully applicable in metrology and in different other areas. To address the special need for making further decisions subsequently to the actual fusion task, we further analyze criteria for decision making under partial information.

Chromosomal inactivation of Bacillus subtilis exfusants: a prokaryotic model of epigenetic regulation.

PubMed

Grandjean, V; Hauck, Y; Beloin, C; Le Hégarat, F; Hirschbein, L

1998-01-01

Epigenetic mechanisms are not exclusively reserved to eukaryotic organisms. They are also observed in prokaryotes. As described first by Hotchkiss and Gabor, protoplast fusion between strains of Bacillus subtilis produces heterodiploid cells. Heterodiploidy is associated with the inactivation of one of the chromosomes. To study the physical structure of the fusion product and the molecular mechanisms of inactivation, we constructed heterodiploid clones containing two chromosomes labeled by a NotI restriction fragment length polymorphism. In the progeny, we identified haploid recombinant clones that contain a chromosome carrying large regions of inactivated DNA. Studies of both recombinants of the latter kind and heterodiploid cells indicated that chromosomal inactivation was not determined by alteration of the inactivated nucleotide sequence, but was probably due to a modification in the structure of the bacterial chromatin.

TU-AB-202-11: Tumor Segmentation by Fusion of Multi-Tracer PET Images Using Copula Based Statistical Methods

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

Lapuyade-Lahorgue, J; Ruan, S; Li, H

Purpose: Multi-tracer PET imaging is getting more attention in radiotherapy by providing additional tumor volume information such as glucose and oxygenation. However, automatic PET-based tumor segmentation is still a very challenging problem. We propose a statistical fusion approach to joint segment the sub-area of tumors from the two tracers FDG and FMISO PET images. Methods: Non-standardized Gamma distributions are convenient to model intensity distributions in PET. As a serious correlation exists in multi-tracer PET images, we proposed a new fusion method based on copula which is capable to represent dependency between different tracers. The Hidden Markov Field (HMF) model ismore » used to represent spatial relationship between PET image voxels and statistical dynamics of intensities for each modality. Real PET images of five patients with FDG and FMISO are used to evaluate quantitatively and qualitatively our method. A comparison between individual and multi-tracer segmentations was conducted to show advantages of the proposed fusion method. Results: The segmentation results show that fusion with Gaussian copula can receive high Dice coefficient of 0.84 compared to that of 0.54 and 0.3 of monomodal segmentation results based on individual segmentation of FDG and FMISO PET images. In addition, high correlation coefficients (0.75 to 0.91) for the Gaussian copula for all five testing patients indicates the dependency between tumor regions in the multi-tracer PET images. Conclusion: This study shows that using multi-tracer PET imaging can efficiently improve the segmentation of tumor region where hypoxia and glucidic consumption are present at the same time. Introduction of copulas for modeling the dependency between two tracers can simultaneously take into account information from both tracers and deal with two pathological phenomena. Future work will be to consider other families of copula such as spherical and archimedian copulas, and to eliminate partial volume effect by considering dependency between neighboring voxels.« less

Variability and trends in area, location, cloudiness and cloud top temperature of the ITCZ in the east to central Pacific over the past 30 years

NASA Astrophysics Data System (ADS)

Magnusdottir, G.; Bain, C.; Smyth, P.; Stern, H.; Knapp, K.

2010-12-01

A team of multidisciplinary scientists at the University of California Irvine has developed a novel spatial-temporal statistical model to detect the presence/absence of the ITCZ in high-resolution instantaneous satellite data. The Markov random field (MRF) statistical model is briefly introduced and compared to other automatic methods such as thresholding. The statistical model emulates human identification of the ITCZ as an envelope of convective activity (as seen in different fields) plus produces the same results given the same data, which may not be the case for human analysis. The MRF statistical model uses satellite data at a given location as well as information from its neighboring points (in time and space) to decide whether the given point is classified as ITCZ or non-ITCZ. Two different labels of ITCZ occurrence are produced. IR-only labels result from running the model with 3-hourly infrared data available for a 30 yr period, 1980--2009. Data-all labels result from running the model with additional satellite data (visible and total precipitable water), available from 1995--2008. IR-only labels detect less area of ITCZ than Data-all labels, especially where the ITCZ is shallower. Yet, qualitatively, the results for the two sets of labels are similar. Here, we focus on results from the IR-only labels over the east Pacific for the past 30 summer half-years (May to October). The IR data are from the HURSAT Basin data of NOAA’s National Climatic Data Center, which are derived from ISCCP B1 data. The data were collected from radiometers on different geostationary satellites. The IR channel data were recalibrated to reduce inter-satellite differences. The seasonal distribution of the ITCZ through the summer half year is presented, showing typical location and extent. The ITCZ is mostly confined to the eastern Pacific in May, and becomes more zonally distributed towards September and October each year. Northward and westward shifts in the location of the ITCZ occur in line with the seasonal cycle and warm sea surface temperatures. The ITCZ is quite variable on interannual time scales and highly correlated with ENSO variability. When we removed the ENSO signal from labels, interannual variability remained high. The resulting IR-only labels, showed no evidence of a trend in location, nor evidence of a trend in area for the 30 yr period. However, a trend in cloudiness within labels is observed and will be discussed.

Towards a new tool for the evaluation of the quality of ultrasound compressed images.

PubMed

Delgorge, Cécile; Rosenberger, Christophe; Poisson, Gérard; Vieyres, Pierre

2006-11-01

This paper presents a new tool for the evaluation of ultrasound image compression. The goal is to measure the image quality as easily as with a statistical criterion, and with the same reliability as the one provided by the medical assessment. An initial experiment is proposed to medical experts and represents our reference value for the comparison of evaluation criteria. Twenty-one statistical criteria are selected from the literature. A cumulative absolute similarity measure is defined as a distance between the criterion to evaluate and the reference value. A first fusion method based on a linear combination of criteria is proposed to improve the results obtained by each of them separately. The second proposed approach combines different statistical criteria and uses the medical assessment in a training phase with a support vector machine. Some experimental results are given and show the benefit of fusion.

The cost-effectiveness of interbody fusions versus posterolateral fusions in 137 patients with lumbar spondylolisthesis.

PubMed

Bydon, Mohamad; Macki, Mohamed; Abt, Nicholas B; Witham, Timothy F; Wolinsky, Jean-Paul; Gokaslan, Ziya L; Bydon, Ali; Sciubba, Daniel M

2015-03-01

Reimbursements for interbody fusions have declined recently because of their questionable cost-effectiveness. A Markov model was adopted to compare the cost-effectiveness of posterior lumbar interbody fusion (PLIF) or transforaminal lumbar interbody fusion (/TLIF) versus noninterbody fusion and posterolateral fusion (PLF) in patients with lumbar spondylolisthesis. Decision model analysis based on retrospective data from a single institutional series. One hundred thirty-seven patients underwent first-time instrumented lumbar fusions for degenerative or isthmic spondylolisthesis. Quality of life adjustments and expenditures were assigned to each short-term complication (durotomy, surgical site infection, and medical complication) and long-term outcome (bowel/bladder dysfunction and paraplegia, neurologic deficit, and chronic back pain). Patients were divided into a PLF cohort and a PLF plus PLIF/TLIF cohort. Anterior techniques and multilevel interbody fusions were excluded. Each short-term complication and long-term outcome was assigned a numerical quality-adjusted life-year (QALY), based on time trade-off values in the Beaver Dam Health Outcomes Study. The cost data for short-term complications were calculated from charges accrued by the institution's finance sector, and the cost data for long-term outcomes were estimated from the literature. The difference in cost of PLF plus PLIF/TLIF from the cost of PLF alone divided by the difference in QALY equals the cost-effectiveness ratio (CER). We do not report any study funding sources or any study-specific appraisal of potential conflict of interest-associated biases in this article. Of 137 first-time lumbar fusions for spondylolisthesis, 83 patients underwent PLF and 54 underwent PLIF/TLIF. The average time to reoperation was 3.5 years. The mean QALY over 3.5 years was 2.81 in the PLF cohort versus 2.66 in the PLIFo/TLIF cohort (p=.110). The mean 3.5-year costs of $54,827.05 after index interbody fusion were statistically higher than that of the $48,822.76 after PLF (p=.042). The CER of interbody fusion to PLF after the first operation was -$46,699.40 per QALY; however, of the 27 patients requiring reoperation, the incident (reoperation) rate ratio was 7.89 times higher after PLF (2.91, 26.67). The CER after the first reoperation was -$24,429.04 per QALY (relative to PLF). Two patients in the PLF cohort required a second reoperation, whereas none required a second reoperation in the PLIF/TLIF cohort. Taken collectively, the total CER for the interbody fusion is $9,883.97 per QALY. The reoperation rate was statistically higher for PLF, whereas the negative CER for the initial operation and first reoperation favors PLF. However, when second reoperations were included, the CER for the interbody fusion became $9,883.97 per QALY, suggesting moderate long-term cost savings and better functional outcomes with the interbody fusion. Copyright © 2015 Elsevier Inc. All rights reserved.

Statistical comparison of a hybrid approach with approximate and exact inference models for Fusion 2+

NASA Astrophysics Data System (ADS)

Lee, K. David; Wiesenfeld, Eric; Gelfand, Andrew

2007-04-01

One of the greatest challenges in modern combat is maintaining a high level of timely Situational Awareness (SA). In many situations, computational complexity and accuracy considerations make the development and deployment of real-time, high-level inference tools very difficult. An innovative hybrid framework that combines Bayesian inference, in the form of Bayesian Networks, and Possibility Theory, in the form of Fuzzy Logic systems, has recently been introduced to provide a rigorous framework for high-level inference. In previous research, the theoretical basis and benefits of the hybrid approach have been developed. However, lacking is a concrete experimental comparison of the hybrid framework with traditional fusion methods, to demonstrate and quantify this benefit. The goal of this research, therefore, is to provide a statistical analysis on the comparison of the accuracy and performance of hybrid network theory, with pure Bayesian and Fuzzy systems and an inexact Bayesian system approximated using Particle Filtering. To accomplish this task, domain specific models will be developed under these different theoretical approaches and then evaluated, via Monte Carlo Simulation, in comparison to situational ground truth to measure accuracy and fidelity. Following this, a rigorous statistical analysis of the performance results will be performed, to quantify the benefit of hybrid inference to other fusion tools.

Lentivirus-mediated bifunctional cell labeling for in vivo melanoma study

PubMed Central

Day, Chi-Ping; Carter, John; Bonomi, Carrie; Esposito, Dominic; Crise, Bruce; Ortiz-Conde, Betty; Hollingshead, Melinda; Merlino, Glenn

2009-01-01

SUMMARY Lentiviral vectors (LVs) are capable of labeling a broad spectrum of cell types, achieving stable expression of transgenes. However, for in vivo studies, the duration of marker gene expression has been highly variable. We have developed a series of LVs harboring different promoters for expressing reporter gene in mouse cells. Long-term culture and colony formation of several LV-labeled mouse melanoma cells showed that promoters derived from mammalian house-keeping genes, especially those encoding RNA polymerase II (Pol2) and ferritin (FerH), provided the highest consistency for reporter expression. For in vivo studies, primary B16BL6 mouse melanoma were infected with LVs whose luciferase-GFP fusion gene (Luc/GFP) was driven by either Pol2 or FerH promoters. When transplanted into syngeneic C57BL/6 mice, Luc/GFP-labeled B16BL6 mouse melanoma cells can be monitored by bioluminescence imaging in vivo, and GFP-positive cells can be isolated from the tumors by FACS. Pol2-Luc/GFP labeling, while lower in activity, was more sustainable than FerH-Luc/GFP labeling in B16BL6 over consecutive passages into mice. We conclude that Pol-2-Luc/GFP labeling allows long-term in vivo monitoring and tumor cell isolation in immunocompetent mouse melanoma models. SIGNIFICANCE In this study we have developed and identified lentiviral vectors that allow labeled mouse melanoma cells to maintain long-term and consistent expression of a bifunctional luciferase-GFP marker gene, even in syngeneic mice with an intact immune function. This cell-labeling system can be used to build immunocompetent mouse melanoma models that permit both tumor monitoring and FACS-based tumor cell isolation from tissues, greatly facilitating the in vivo study of melanoma. PMID:19175523

Further studies on the effect of chloroquine on the uptake, metabolism and intracellular translocation of [35S]cystine in cystinotic fibroblasts.

PubMed

Danpure, C J; Jennings, P R; Fyfe, D A

1986-03-14

The present study uses the lysosomotropic drug chloroquine to investigate the mechanisms by which exogenous [35S]cystine is able to label the intracellular (intralysosomal) cystine pool(s) in cystinotic fibroblasts. When cystinotic fibroblasts were labelled for short periods of time (8 h or less), chloroquine (20 microM) inhibited the labelling of the intracellular cystine pool(s). However, when the cells were labelled for longer periods of time (24 h or more) chloroquine stimulated the labelling of the intracellular cystine pool(s). The short-term effect was selectively abolished when the cells were washed free of chloroquine, while the long-term effect was selectively abolished when the medium was depleted of cystine. Two routes of translocation of exogenous cystine to the lysosomes could be defined. One route was fast, had a low capacity, was inhibited by chloroquine and increased with increasing medium pH, while the other route was slow, had a high capacity, was stimulated by chloroquine and was more active at low pH. The former pathway probably consisted of plasma membrane transport of cystine into the cytosol followed by direct or indirect transport into the lysosomes. The latter route possibly consisted of pinocytosis with fusion of the cystine-containing pinosomes with lysosomes.

Multi-layered nanoparticles for penetrating the endosome and nuclear membrane via a step-wise membrane fusion process.

PubMed

Akita, Hidetaka; Kudo, Asako; Minoura, Arisa; Yamaguti, Masaya; Khalil, Ikramy A; Moriguchi, Rumiko; Masuda, Tomoya; Danev, Radostin; Nagayama, Kuniaki; Kogure, Kentaro; Harashima, Hideyoshi

2009-05-01

Efficient targeting of DNA to the nucleus is a prerequisite for effective gene therapy. The gene-delivery vehicle must penetrate through the plasma membrane, and the DNA-impermeable double-membraned nuclear envelope, and deposit its DNA cargo in a form ready for transcription. Here we introduce a concept for overcoming intracellular membrane barriers that involves step-wise membrane fusion. To achieve this, a nanotechnology was developed that creates a multi-layered nanoparticle, which we refer to as a Tetra-lamellar Multi-functional Envelope-type Nano Device (T-MEND). The critical structural elements of the T-MEND are a DNA-polycation condensed core coated with two nuclear membrane-fusogenic inner envelopes and two endosome-fusogenic outer envelopes, which are shed in stepwise fashion. A double-lamellar membrane structure is required for nuclear delivery via the stepwise fusion of double layered nuclear membrane structure. Intracellular membrane fusions to endosomes and nuclear membranes were verified by spectral imaging of fluorescence resonance energy transfer (FRET) between donor and acceptor fluorophores that had been dually labeled on the liposome surface. Coating the core with the minimum number of nucleus-fusogenic lipid envelopes (i.e., 2) is essential to facilitate transcription. As a result, the T-MEND achieves dramatic levels of transgene expression in non-dividing cells.

Calculation of Formation and Decay of Heavy Compound Nuclei

NASA Astrophysics Data System (ADS)

Cherepanov, E. A.

2001-04-01

The report describes a method for calculating fusion and decay probabilities in reactions leading to the production of transfermium elements. The competition between quasi-fission and fussion is described on the basis of the Dinuclear System Concept (DNSC). The both competition between fusion and quasi-fission and statistical decay of heavy highly fissionable excited compound nuclei is described in an approach based on the Monte-Carlo method.

Multi-scale pixel-based image fusion using multivariate empirical mode decomposition.

PubMed

Rehman, Naveed ur; Ehsan, Shoaib; Abdullah, Syed Muhammad Umer; Akhtar, Muhammad Jehanzaib; Mandic, Danilo P; McDonald-Maier, Klaus D

2015-05-08

A novel scheme to perform the fusion of multiple images using the multivariate empirical mode decomposition (MEMD) algorithm is proposed. Standard multi-scale fusion techniques make a priori assumptions regarding input data, whereas standard univariate empirical mode decomposition (EMD)-based fusion techniques suffer from inherent mode mixing and mode misalignment issues, characterized respectively by either a single intrinsic mode function (IMF) containing multiple scales or the same indexed IMFs corresponding to multiple input images carrying different frequency information. We show that MEMD overcomes these problems by being fully data adaptive and by aligning common frequency scales from multiple channels, thus enabling their comparison at a pixel level and subsequent fusion at multiple data scales. We then demonstrate the potential of the proposed scheme on a large dataset of real-world multi-exposure and multi-focus images and compare the results against those obtained from standard fusion algorithms, including the principal component analysis (PCA), discrete wavelet transform (DWT) and non-subsampled contourlet transform (NCT). A variety of image fusion quality measures are employed for the objective evaluation of the proposed method. We also report the results of a hypothesis testing approach on our large image dataset to identify statistically-significant performance differences.

Multi-Scale Pixel-Based Image Fusion Using Multivariate Empirical Mode Decomposition

PubMed Central

Rehman, Naveed ur; Ehsan, Shoaib; Abdullah, Syed Muhammad Umer; Akhtar, Muhammad Jehanzaib; Mandic, Danilo P.; McDonald-Maier, Klaus D.

2015-01-01

A novel scheme to perform the fusion of multiple images using the multivariate empirical mode decomposition (MEMD) algorithm is proposed. Standard multi-scale fusion techniques make a priori assumptions regarding input data, whereas standard univariate empirical mode decomposition (EMD)-based fusion techniques suffer from inherent mode mixing and mode misalignment issues, characterized respectively by either a single intrinsic mode function (IMF) containing multiple scales or the same indexed IMFs corresponding to multiple input images carrying different frequency information. We show that MEMD overcomes these problems by being fully data adaptive and by aligning common frequency scales from multiple channels, thus enabling their comparison at a pixel level and subsequent fusion at multiple data scales. We then demonstrate the potential of the proposed scheme on a large dataset of real-world multi-exposure and multi-focus images and compare the results against those obtained from standard fusion algorithms, including the principal component analysis (PCA), discrete wavelet transform (DWT) and non-subsampled contourlet transform (NCT). A variety of image fusion quality measures are employed for the objective evaluation of the proposed method. We also report the results of a hypothesis testing approach on our large image dataset to identify statistically-significant performance differences. PMID:26007714

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

Osychenko, A A; Zalesskii, A D; Krivokharchenko, A S

Using the method of femtosecond laser surgery we study the fusion of two-cell mouse embryos under the action of tightly focused femtosecond laser radiation with the fusion efficiency reaching 60%. The detailed statistical analysis of the efficiency of blastomere fusion and development of the embryo up to the blastocyst stage after exposure of the embryos from different mice to a femtosecond pulse is presented. It is shown that the efficiency of blastocyst formation essentially depends on the biological characteristics of the embryo, namely, the strain and age of the donor mouse. The possibility of obtaining hexaploid embryonal cells using themore » methods of femtosecond laser surgery is demonstrated. (extreme light fields and their applications)« less

In-beam Fission Study at JAEA

NASA Astrophysics Data System (ADS)

Nishio, Katsuhisa

2013-12-01

Fission fragment mass distributions were measured in heavy-ion induced fissions using 238U target nucleus. The measured mass distributions changed drastically with incident energy. The results are explained by a change of the ratio between fusion and quasifission with nuclear orientation. A calculation based on a fluctuation dissipation model reproduced the mass distributions and their incident energy dependence. Fusion probability was determined in the analysis. Evaporation residue cross sections were calculated with a statistical model in the reactions of 30Si + 238U and 34S + 238U using the obtained fusion probability in the entrance channel. The results agree with the measured cross sections for seaborgium and hassium isotopes.

In-beam fission study for Heavy Element Synthesis

NASA Astrophysics Data System (ADS)

Nishio, Katsuhisa

2013-12-01

Fission fragment mass distributions were measured in heavy-ion induced fissions using 238U target nucleus. The measured mass distributions changed drastically with incident energy. The results are explained by a change of the ratio between fusion and qasifission with nuclear orientation. A calculation based on a fluctuation dissipation model reproduced the mass distributions and their incident energy dependence. Fusion probability was determined in the analysis. Evaporation residue cross sections were calculated with a statistical model in the reactions of 30Si + 238U and 34S + 238U using the obtained fusion probability in the entrance channel. The results agree with the measured cross sections for seaborgium and hassium isotopes.

Graded levels of FGF protein span the midbrain and can instruct graded induction and repression of neural mapping labels

PubMed Central

Chen, Yao; Mohammadi, Moosa; Flanagan, John G.

2009-01-01

Summary Graded guidance labels are widely used in neural map formation, but it is not well understood which potential strategy leads to their graded expression. In midbrain tectal map development, FGFs can induce an entire midbrain, but their protein distribution is unclear, nor is it known whether they may act instructively to produce graded gene expression. Using a receptor-alkaline phosphatase fusion probe, we find a long-range posterior>anterior FGF protein gradient spanning the midbrain. Heparan sulfate proteoglycan (HSPG) is required for this gradient. To test whether graded FGF concentrations can instruct graded gene expression, a quantitative tectal explant assay was developed. Engrailed-2 and ephrin-As, normally in posterior>anterior tectal gradients, showed graded upregulation. Moreover, EphAs, normally in anterior>posterior countergradients, showed coordinately graded downregulation. These results provide a mechanism to establish graded mapping labels, and more generally provide a developmental strategy to coordinately induce a structure and pattern its cell properties in gradients. PMID:19555646

Simultaneous skull-stripping and lateral ventricle segmentation via fast multi-atlas likelihood fusion

NASA Astrophysics Data System (ADS)

Tang, Xiaoying; Kutten, Kwame; Ceritoglu, Can; Mori, Susumu; Miller, Michael I.

2015-03-01

In this paper, we propose and validate a fully automated pipeline for simultaneous skull-stripping and lateral ventricle segmentation using T1-weighted images. The pipeline is built upon a segmentation algorithm entitled fast multi-atlas likelihood-fusion (MALF) which utilizes multiple T1 atlases that have been pre-segmented into six whole-brain labels - the gray matter, the white matter, the cerebrospinal fluid, the lateral ventricles, the skull, and the background of the entire image. This algorithm, MALF, was designed for estimating brain anatomical structures in the framework of coordinate changes via large diffeomorphisms. In the proposed pipeline, we use a variant of MALF to estimate those six whole-brain labels in the test T1-weighted image. The three tissue labels (gray matter, white matter, and cerebrospinal fluid) and the lateral ventricles are then grouped together to form a binary brain mask to which we apply morphological smoothing so as to create the final mask for brain extraction. For computational purposes, all input images to MALF are down-sampled by a factor of two. In addition, small deformations are used for the changes of coordinates. This substantially reduces the computational complexity, hence we use the term "fast MALF". The skull-stripping performance is qualitatively evaluated on a total of 486 brain scans from a longitudinal study on Alzheimer dementia. Quantitative error analysis is carried out on 36 scans for evaluating the accuracy of the pipeline in segmenting the lateral ventricle. The volumes of the automated lateral ventricle segmentations, obtained from the proposed pipeline, are compared across three different clinical groups. The ventricle volumes from our pipeline are found to be sensitive to the diagnosis.

A SNAP-Tagged Derivative of HIV-1—A Versatile Tool to Study Virus-Cell Interactions

PubMed Central

Eckhardt, Manon; Anders, Maria; Muranyi, Walter; Heilemann, Mike; Krijnse-Locker, Jacomine; Müller, Barbara

2011-01-01

Fluorescently labeled human immunodeficiency virus (HIV) derivatives, combined with the use of advanced fluorescence microscopy techniques, allow the direct visualization of dynamic events and individual steps in the viral life cycle. HIV proteins tagged with fluorescent proteins (FPs) have been successfully used for live-cell imaging analyses of HIV-cell interactions. However, FPs display limitations with respect to their physicochemical properties, and their maturation kinetics. Furthermore, several independent FP-tagged constructs have to be cloned and characterized in order to obtain spectral variations suitable for multi-color imaging setups. In contrast, the so-called SNAP-tag represents a genetically encoded non-fluorescent tag which mediates specific covalent coupling to fluorescent substrate molecules in a self-labeling reaction. Fusion of the SNAP-tag to the protein of interest allows specific labeling of the fusion protein with a variety of synthetic dyes, thereby offering enhanced flexibility for fluorescence imaging approaches. Here we describe the construction and characterization of the HIV derivative HIVSNAP, which carries the SNAP-tag as an additional domain within the viral structural polyprotein Gag. Introduction of the tag close to the C-terminus of the matrix domain of Gag did not interfere with particle assembly, release or proteolytic virus maturation. The modified virions were infectious and could be propagated in tissue culture, albeit with reduced replication capacity. Insertion of the SNAP domain within Gag allowed specific staining of the viral polyprotein in the context of virus producing cells using a SNAP reactive dye as well as the visualization of individual virions and viral budding sites by stochastic optical reconstruction microscopy. Thus, HIVSNAP represents a versatile tool which expands the possibilities for the analysis of HIV-cell interactions using live cell imaging and sub-diffraction fluorescence microscopy. PMID:21799764

HybridGO-Loc: mining hybrid features on gene ontology for predicting subcellular localization of multi-location proteins.

PubMed

Wan, Shibiao; Mak, Man-Wai; Kung, Sun-Yuan

2014-01-01

Protein subcellular localization prediction, as an essential step to elucidate the functions in vivo of proteins and identify drugs targets, has been extensively studied in previous decades. Instead of only determining subcellular localization of single-label proteins, recent studies have focused on predicting both single- and multi-location proteins. Computational methods based on Gene Ontology (GO) have been demonstrated to be superior to methods based on other features. However, existing GO-based methods focus on the occurrences of GO terms and disregard their relationships. This paper proposes a multi-label subcellular-localization predictor, namely HybridGO-Loc, that leverages not only the GO term occurrences but also the inter-term relationships. This is achieved by hybridizing the GO frequencies of occurrences and the semantic similarity between GO terms. Given a protein, a set of GO terms are retrieved by searching against the gene ontology database, using the accession numbers of homologous proteins obtained via BLAST search as the keys. The frequency of GO occurrences and semantic similarity (SS) between GO terms are used to formulate frequency vectors and semantic similarity vectors, respectively, which are subsequently hybridized to construct fusion vectors. An adaptive-decision based multi-label support vector machine (SVM) classifier is proposed to classify the fusion vectors. Experimental results based on recent benchmark datasets and a new dataset containing novel proteins show that the proposed hybrid-feature predictor significantly outperforms predictors based on individual GO features as well as other state-of-the-art predictors. For readers' convenience, the HybridGO-Loc server, which is for predicting virus or plant proteins, is available online at http://bioinfo.eie.polyu.edu.hk/HybridGoServer/.

The Effect of Diagnostic Labels on the Affective Responses of College Students towards Peers with "Asperger's Syndrome" and "Autism Spectrum Disorder"

ERIC Educational Resources Information Center

Brosnan, Mark; Mills, Elizabeth

2016-01-01

Given the removal of Asperger's Syndrome label in "Diagnostic and Statistical Manual of Mental Disorders-Fifth Edition," the impact of clinical labels upon the affective responses of college students was explored. A total of 120 college students read two vignettes depicting social interactions typical of a person with autism spectrum…

Biosensing of BCR/ABL fusion gene using an intensity-interrogation surface plasmon resonance imaging system

NASA Astrophysics Data System (ADS)

Wu, Jiangling; Huang, Yu; Bian, Xintong; Li, DanDan; Cheng, Quan; Ding, Shijia

2016-10-01

In this work, a custom-made intensity-interrogation surface plasmon resonance imaging (SPRi) system has been developed to directly detect a specific sequence of BCR/ABL fusion gene in chronic myelogenous leukemia (CML). The variation in the reflected light intensity detected from the sensor chip composed of gold islands array is proportional to the change of refractive index due to the selective hybridization of surface-bound DNA probes with target ssDNA. SPRi measurements were performed with different concentrations of synthetic target DNA sequence. The calibration curve of synthetic target sequence shows a good relationship between the concentration of synthetic target and the change of reflected light intensity. The detection limit of this SPRi measurement could approach 10.29 nM. By comparing SPRi images, the target ssDNA and non-complementary DNA sequence are able to be distinguished. This SPRi system has been applied for assay of BCR/ABL fusion gene extracted from real samples. This nucleic acid-based SPRi biosensor therefore offers an alternative high-effective, high-throughput label-free tool for DNA detection in biomedical research and molecular diagnosis.

Enhanced EGFP-chromophore-assisted laser inactivation using deficient cells rescued with functional EGFP-fusion proteins.

PubMed

Vitriol, Eric A; Uetrecht, Andrea C; Shen, Feimo; Jacobson, Ken; Bear, James E

2007-04-17

Chromophore-assisted laser inactivation (CALI) is a light-mediated technique that offers precise spatiotemporal control of protein inactivation, enabling better understanding of the protein's role in cell function. EGFP has been used effectively as a CALI chromophore, and its cotranslational attachment to the target protein avoids having to use exogenously added labeling reagents. A potential drawback to EGFP-CALI is that the CALI phenotype can be obscured by the endogenous, unlabeled protein that is not susceptible to light inactivation. Performing EGFP-CALI experiments in deficient cells rescued with functional EGFP-fusion proteins permits more complete loss of function to be achieved. Here, we present a modified lentiviral system for rapid and efficient generation of knockdown cell lines complemented with physiological levels of EGFP-fusion proteins. We demonstrate that CALI of EGFP-CapZbeta increases uncapped actin filaments, resulting in enhanced filament growth and the formation of numerous protrusive structures. We show that these effects are completely dependent upon knocking down the endogenous protein. We also demonstrate that CALI of EGFP-Mena in Mena/VASP-deficient cells stabilizes lamellipodial protrusions.

Expression and purification of E. coli BirA biotin ligase for in vitro biotinylation.

PubMed

Li, Yifeng; Sousa, Rui

2012-03-01

The extremely tight binding between biotin and avidin or streptavidin makes labeling proteins with biotin a useful tool for many applications. BirA is the Escherichia coli biotin ligase that site-specifically biotinylates a lysine side chain within a 15-amino acid acceptor peptide (also known as Avi-tag). As a complementary approach to in vivo biotinylation of Avi-tag-bearing proteins, we developed a protocol for producing recombinant BirA ligase for in vitro biotinylation. The target protein was expressed as both thioredoxin and MBP fusions, and was released from the corresponding fusion by TEV protease. The liberated ligase was separated from its carrier using HisTrap HP column. We obtained 24.7 and 27.6 mg BirA ligase per liter of culture from thioredoxin and MBP fusion constructs, respectively. The recombinant enzyme was shown to be highly active in catalyzing in vitro biotinylation. The described protocol provides an effective means for making BirA ligase that can be used for biotinylation of different Avi-tag-bearing substrates. Copyright © 2011 Elsevier Inc. All rights reserved.

A resilient and efficient CFD framework: Statistical learning tools for multi-fidelity and heterogeneous information fusion

NASA Astrophysics Data System (ADS)

Lee, Seungjoon; Kevrekidis, Ioannis G.; Karniadakis, George Em

2017-09-01

Exascale-level simulations require fault-resilient algorithms that are robust against repeated and expected software and/or hardware failures during computations, which may render the simulation results unsatisfactory. If each processor can share some global information about the simulation from a coarse, limited accuracy but relatively costless auxiliary simulator we can effectively fill-in the missing spatial data at the required times by a statistical learning technique - multi-level Gaussian process regression, on the fly; this has been demonstrated in previous work [1]. Based on the previous work, we also employ another (nonlinear) statistical learning technique, Diffusion Maps, that detects computational redundancy in time and hence accelerate the simulation by projective time integration, giving the overall computation a "patch dynamics" flavor. Furthermore, we are now able to perform information fusion with multi-fidelity and heterogeneous data (including stochastic data). Finally, we set the foundations of a new framework in CFD, called patch simulation, that combines information fusion techniques from, in principle, multiple fidelity and resolution simulations (and even experiments) with a new adaptive timestep refinement technique. We present two benchmark problems (the heat equation and the Navier-Stokes equations) to demonstrate the new capability that statistical learning tools can bring to traditional scientific computing algorithms. For each problem, we rely on heterogeneous and multi-fidelity data, either from a coarse simulation of the same equation or from a stochastic, particle-based, more "microscopic" simulation. We consider, as such "auxiliary" models, a Monte Carlo random walk for the heat equation and a dissipative particle dynamics (DPD) model for the Navier-Stokes equations. More broadly, in this paper we demonstrate the symbiotic and synergistic combination of statistical learning, domain decomposition, and scientific computing in exascale simulations.

A study of carbobenzoxy-D-phenylalanine-L-phenylalanine-glycine, an inhibitor of membrane fusion, in phospholipid bilayers with multinuclear magnetic resonance.

PubMed

Dentino, A R; Westerman, P W; Yeagle, P L

1995-05-04

The anti-viral and membrane fusion inhibitor, carbobenzoxy-D-phenylalanine-L-phenylalanine-glycine (ZfFG), was studied in phospholipid bilayers, where earlier studies had indicated this peptide functioned. Multinuclear magnetic resonance (NMR) studies were performed with isotopically labeled peptide. A peptide labeled in the glycine carboxyl with 13C was synthesized, and the isotropic 13C-NMR chemical shift of that carbon was measured as a function of pH. A pKa of 3.6 for the carboxyl was determined from the peptide bound to a phosphatidylcholine bilayer. ZfFG inhibits the formation by sonication of highly curved, small unilamellar vesicles. Experiments as a function of pH revealed that this ability of ZfFG was governed by a pKa of 3.7. Therefore the protonation state of the carboxyl of ZfFG appeared to regulate the effectiveness of this anti-viral peptide at destabilizing highly curved phospholipid assemblies. Such destabilization had previously been discovered to be related to the mechanism of the anti-fusion and anti-viral activity of this peptide. The location of the carboxyl of ZfFG in the membrane was probed with paramagnetic relaxation enhancement of the 13C spin lattice relaxation of the carboxyl carbon in the glycine of ZfFG (enriched in 13C). Results suggested that this carboxyl is at or above the surface of the phospholipid bilayer. The dynamics of the molecule in the membrane were examined with 2H-NMR studies of ZfFG, deuterated in the alpha-carbon protons of the glycine. When ZfFG was bound to membranes of phosphatidylcholine, a sharp 2H-NMR spectral component was observed, consistent with a disordering of the glycine methylene segment of the peptide. When ZfFG was bound to N-methyl dioleoylphosphatidylethanolamine (N-methyl DOPE) bilayers at temperatures below 30 degrees C, a large quadrupole splitting was observed. These results suggest that ZfFG likely inhibits membrane fusion from the surface of the lipid bilayer, but not by forming a tight, stoichiometric complex with the phospholipids.

Automatic recognition of 3D GGO CT imaging signs through the fusion of hybrid resampling and layer-wise fine-tuning CNNs.

PubMed

Han, Guanghui; Liu, Xiabi; Zheng, Guangyuan; Wang, Murong; Huang, Shan

2018-06-06

Ground-glass opacity (GGO) is a common CT imaging sign on high-resolution CT, which means the lesion is more likely to be malignant compared to common solid lung nodules. The automatic recognition of GGO CT imaging signs is of great importance for early diagnosis and possible cure of lung cancers. The present GGO recognition methods employ traditional low-level features and system performance improves slowly. Considering the high-performance of CNN model in computer vision field, we proposed an automatic recognition method of 3D GGO CT imaging signs through the fusion of hybrid resampling and layer-wise fine-tuning CNN models in this paper. Our hybrid resampling is performed on multi-views and multi-receptive fields, which reduces the risk of missing small or large GGOs by adopting representative sampling panels and processing GGOs with multiple scales simultaneously. The layer-wise fine-tuning strategy has the ability to obtain the optimal fine-tuning model. Multi-CNN models fusion strategy obtains better performance than any single trained model. We evaluated our method on the GGO nodule samples in publicly available LIDC-IDRI dataset of chest CT scans. The experimental results show that our method yields excellent results with 96.64% sensitivity, 71.43% specificity, and 0.83 F1 score. Our method is a promising approach to apply deep learning method to computer-aided analysis of specific CT imaging signs with insufficient labeled images. Graphical abstract We proposed an automatic recognition method of 3D GGO CT imaging signs through the fusion of hybrid resampling and layer-wise fine-tuning CNN models in this paper. Our hybrid resampling reduces the risk of missing small or large GGOs by adopting representative sampling panels and processing GGOs with multiple scales simultaneously. The layer-wise fine-tuning strategy has ability to obtain the optimal fine-tuning model. Our method is a promising approach to apply deep learning method to computer-aided analysis of specific CT imaging signs with insufficient labeled images.

Analysis of clinically relevant values of Ki-67 labeling index in Japanese breast cancer patients.

PubMed

Tamaki, Kentaro; Ishida, Takanori; Tamaki, Nobumitsu; Kamada, Yoshihiko; Uehara, Kanou; Miyashita, Minoru; Amari, Masakazu; Tadano-Sato, Akiko; Takahashi, Yayoi; Watanabe, Mika; McNamara, Keely; Ohuchi, Noriaki; Sasano, Hironobu

2014-05-01

It has become important to standardize the methods of Ki-67 evaluation in breast cancer patients, especially those used in the interpretation and scoring of immunoreactivity. Therefore, in this study, we examined the Ki-67 immunoreactivity of breast cancer surgical specimens processed and stained in the same manner in one single Japanese institution by counting nuclear immunoreactivity in the same fashion. We examined 408 Japanese breast cancers with invasive ductal carcinoma and studied the correlation between Ki-67 labeling index and ER/HER2 status and histological grade of breast cancer. We also analyzed overall survival (OS) and disease-free survival (DFS) of these patients according to individual Ki-67 labeling index. There were statistically significant differences of Ki-67 labeling index between ER positive/HER2 negative and ER positive/HER2 positive, ER negative/HER2 positive or ER negative/HER2 negative, and ER positive/HER2 positive and ER negative/HER2 negative groups (all P < 0.001). There were also statistically significant differences of Ki-67 labeling index among each histological grade (P < 0.001, respectively). As for multivariate analyses, Ki-67 labeling index was strongly associated with OS (HR 39.12, P = 0.031) and DFS (HR 10.85, P = 0.011) in ER positive and HER2 negative breast cancer patients. In addition, a statistically significant difference was noted between classical luminal A group and "20 % luminal A" in DFS (P = 0.039) but not between classical luminal A group and "25 % luminal A" (P = 0.105). A significant positive correlation was detected between Ki-67 labeling index and ER/HER2 status and histological grades of the cases examined in our study. The suggested optimal cutoff point of Ki-67 labeling index is between 20 and 25 % in ER positive and HER2 negative breast cancer patients.

PAX3/7-FOXO1 fusion status in older rhabdomyosarcoma patient population by fluorescent in situ hybridization.

PubMed

Dumont, Sarah N; Lazar, Alexander J; Bridge, Julia A; Benjamin, Robert S; Trent, Jonathan C

2012-02-01

In pediatric alveolar rhabdomyosarcoma, the PAX3-FOXO1 and PAX7-FOXO1 gene fusions are prognostic indicators, while little is known concerning this disease in older patients. To determine whether PAX3/7-FOXO1 fusion gene status correlates with outcome in adolescent, young adult, and adult rhabdomyosarcoma patients, the histological, immunohistochemical, and clinical characteristics of 105 patients followed at The University of Texas MD Anderson Cancer Center from 1957 to 2001 were evaluated. The samples were assembled into a tissue microarray, and fusion gene status was determined by fluorescence in situ hybridization using PAX3, PAX7, and FOXO1 loci-specific probes. The disease characteristics and specific gene fusion were correlated with patient outcomes using the log-rank test. Fifty-two percent of the samples exhibited a PAX3-FOXO1 fusion, 15% the PAX7-FOXO1 fusion, and 33% were negative for a rearrangement of these loci. The presence of PAX3/7-FOXO1 translocation was significantly associated with a higher frequency of metastatic disease. Although a statistically significant correlation between the PAX3/7-FOXO1 fusion gene status and overall survival was not identified, there was a trend toward better outcomes for patients with fusion-negative RMS. Therefore, identification of a FOXO1 fusion appears to be an interesting tool for predicting outcomes in older rhabdomyosarcoma patients and is worth further investigations in this rare subgroup of RMS population.

Parameters optimization defined by statistical analysis for cysteine-dextran radiolabeling with technetium tricarbonyl core.

PubMed

Núñez, Eutimio Gustavo Fernández; Faintuch, Bluma Linkowski; Teodoro, Rodrigo; Wiecek, Danielle Pereira; da Silva, Natanael Gomes; Papadopoulos, Minas; Pelecanou, Maria; Pirmettis, Ioannis; de Oliveira Filho, Renato Santos; Duatti, Adriano; Pasqualini, Roberto

2011-04-01

The objective of this study was the development of a statistical approach for radiolabeling optimization of cysteine-dextran conjugates with Tc-99m tricarbonyl core. This strategy has been applied to the labeling of 2-propylene-S-cysteine-dextran in the attempt to prepare a new class of tracers for sentinel lymph node detection, and can be extended to other radiopharmaceuticals for different targets. The statistical routine was based on three-level factorial design. Best labeling conditions were achieved. The specific activity reached was 5 MBq/μg. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

Clinical application of 3D arterial spin-labeled brain perfusion imaging for Alzheimer disease: comparison with brain perfusion SPECT.

PubMed

Takahashi, H; Ishii, K; Hosokawa, C; Hyodo, T; Kashiwagi, N; Matsuki, M; Ashikaga, R; Murakami, T

2014-05-01

Alzheimer disease is the most common neurodegenerative disorder with dementia, and a practical and economic biomarker for diagnosis of Alzheimer disease is needed. Three-dimensional arterial spin-labeling, with its high signal-to-noise ratio, enables measurement of cerebral blood flow precisely without any extrinsic tracers. We evaluated the performance of 3D arterial spin-labeling compared with SPECT, and demonstrated the 3D arterial spin-labeled imaging characteristics in the diagnosis of Alzheimer disease. This study included 68 patients with clinically suspected Alzheimer disease who underwent both 3D arterial spin-labeling and SPECT imaging. Two readers independently assessed both images. Kendall W coefficients of concordance (K) were computed, and receiver operating characteristic analyses were performed for each reader. The differences between the images in regional perfusion distribution were evaluated by means of statistical parametric mapping, and the incidence of hypoperfusion of the cerebral watershed area, referred to as "borderzone sign" in the 3D arterial spin-labeled images, was determined. Readers showed K = 0.82/0.73 for SPECT/3D arterial spin-labeled imaging, and the respective areas under the receiver operating characteristic curve were 0.82/0.69 for reader 1 and 0.80/0.69 for reader 2. Statistical parametric mapping showed that the perisylvian and medial parieto-occipital perfusion in the arterial spin-labeled images was significantly higher than that in the SPECT images. Borderzone sign was observed on 3D arterial spin-labeling in 70% of patients misdiagnosed with Alzheimer disease. The diagnostic performance of 3D arterial spin-labeling and SPECT for Alzheimer disease was almost equivalent. Three-dimensional arterial spin-labeled imaging was more influenced by hemodynamic factors than was SPECT imaging. © 2014 by American Journal of Neuroradiology.

The role of image registration in brain mapping

PubMed Central

Toga, A.W.; Thompson, P.M.

2008-01-01

Image registration is a key step in a great variety of biomedical imaging applications. It provides the ability to geometrically align one dataset with another, and is a prerequisite for all imaging applications that compare datasets across subjects, imaging modalities, or across time. Registration algorithms also enable the pooling and comparison of experimental findings across laboratories, the construction of population-based brain atlases, and the creation of systems to detect group patterns in structural and functional imaging data. We review the major types of registration approaches used in brain imaging today. We focus on their conceptual basis, the underlying mathematics, and their strengths and weaknesses in different contexts. We describe the major goals of registration, including data fusion, quantification of change, automated image segmentation and labeling, shape measurement, and pathology detection. We indicate that registration algorithms have great potential when used in conjunction with a digital brain atlas, which acts as a reference system in which brain images can be compared for statistical analysis. The resulting armory of registration approaches is fundamental to medical image analysis, and in a brain mapping context provides a means to elucidate clinical, demographic, or functional trends in the anatomy or physiology of the brain. PMID:19890483

[Glossary of terms used by radiologists in image processing].

PubMed

Rolland, Y; Collorec, R; Bruno, A; Ramée, A; Morcet, N; Haigron, P

1995-01-01

We give the definition of 166 words used in image processing. Adaptivity, aliazing, analog-digital converter, analysis, approximation, arc, artifact, artificial intelligence, attribute, autocorrelation, bandwidth, boundary, brightness, calibration, class, classification, classify, centre, cluster, coding, color, compression, contrast, connectivity, convolution, correlation, data base, decision, decomposition, deconvolution, deduction, descriptor, detection, digitization, dilation, discontinuity, discretization, discrimination, disparity, display, distance, distorsion, distribution dynamic, edge, energy, enhancement, entropy, erosion, estimation, event, extrapolation, feature, file, filter, filter floaters, fitting, Fourier transform, frequency, fusion, fuzzy, Gaussian, gradient, graph, gray level, group, growing, histogram, Hough transform, Houndsfield, image, impulse response, inertia, intensity, interpolation, interpretation, invariance, isotropy, iterative, JPEG, knowledge base, label, laplacian, learning, least squares, likelihood, matching, Markov field, mask, matching, mathematical morphology, merge (to), MIP, median, minimization, model, moiré, moment, MPEG, neural network, neuron, node, noise, norm, normal, operator, optical system, optimization, orthogonal, parametric, pattern recognition, periodicity, photometry, pixel, polygon, polynomial, prediction, pulsation, pyramidal, quantization, raster, reconstruction, recursive, region, rendering, representation space, resolution, restoration, robustness, ROC, thinning, transform, sampling, saturation, scene analysis, segmentation, separable function, sequential, smoothing, spline, split (to), shape, threshold, tree, signal, speckle, spectrum, spline, stationarity, statistical, stochastic, structuring element, support, syntaxic, synthesis, texture, truncation, variance, vision, voxel, windowing.

Autophagy contributes to regulation of nuclear dynamics during vegetative growth and hyphal fusion in Fusarium oxysporum.

PubMed

Corral-Ramos, Cristina; Roca, M Gabriela; Di Pietro, Antonio; Roncero, M Isabel G; Ruiz-Roldán, Carmen

2015-01-01

In the fungal pathogen Fusarium oxysporum, vegetative hyphal fusion triggers nuclear mitotic division in the invading hypha followed by migration of a nucleus into the receptor hypha and degradation of the resident nucleus. Here we examined the role of autophagy in fusion-induced nuclear degradation. A search of the F. oxysporum genome database for autophagy pathway components identified putative orthologs of 16 core autophagy-related (ATG) genes in yeast, including the ubiquitin-like protein Atg8, which is required for the formation of autophagosomal membranes. F. oxysporum Foatg8Δ mutants were generated in a strain harboring H1-cherry fluorescent protein (ChFP)-labeled nuclei to facilitate analysis of nuclear dynamics. The Foatg8Δ mutants did not show MDC-positive staining in contrast to the wild type and the FoATG8-complemented (cFoATG8) strain, suggesting that FoAtg8 is required for autophagy in F. oxysporum. The Foatg8Δ strains displayed reduced rates of hyphal growth, conidiation, and fusion, and were significantly attenuated in virulence on tomato plants and in the nonvertebrate animal host Galleria mellonella. In contrast to wild-type hyphae, which are almost exclusively composed of uninucleated hyphal compartments, the hyphae of the Foatg8Δ mutants contained a significant fraction of hyphal compartments with 2 or more nuclei. The increase in the number of nuclei per hyphal compartment was particularly evident after hyphal fusion events. Time-lapse microscopy analyses revealed abnormal mitotic patterns during vegetative growth in the Foatg8Δ mutants. Our results suggest that autophagy mediates nuclear degradation after hyphal fusion and has a general function in the control of nuclear distribution in F. oxysporum.

Autophagy contributes to regulation of nuclear dynamics during vegetative growth and hyphal fusion in Fusarium oxysporum

PubMed Central

Corral-Ramos, Cristina; Roca, M Gabriela; Di Pietro, Antonio; Roncero, M Isabel G; Ruiz-Roldán, Carmen

2015-01-01

In the fungal pathogen Fusarium oxysporum, vegetative hyphal fusion triggers nuclear mitotic division in the invading hypha followed by migration of a nucleus into the receptor hypha and degradation of the resident nucleus. Here we examined the role of autophagy in fusion-induced nuclear degradation. A search of the F. oxysporum genome database for autophagy pathway components identified putative orthologs of 16 core autophagy-related (ATG) genes in yeast, including the ubiquitin-like protein Atg8, which is required for the formation of autophagosomal membranes. F. oxysporum Foatg8Δ mutants were generated in a strain harboring H1-cherry fluorescent protein (ChFP)-labeled nuclei to facilitate analysis of nuclear dynamics. The Foatg8Δ mutants did not show MDC-positive staining in contrast to the wild type and the FoATG8-complemented (cFoATG8) strain, suggesting that FoAtg8 is required for autophagy in F. oxysporum. The Foatg8Δ strains displayed reduced rates of hyphal growth, conidiation, and fusion, and were significantly attenuated in virulence on tomato plants and in the nonvertebrate animal host Galleria mellonella. In contrast to wild-type hyphae, which are almost exclusively composed of uninucleated hyphal compartments, the hyphae of the Foatg8Δ mutants contained a significant fraction of hyphal compartments with 2 or more nuclei. The increase in the number of nuclei per hyphal compartment was particularly evident after hyphal fusion events. Time-lapse microscopy analyses revealed abnormal mitotic patterns during vegetative growth in the Foatg8Δ mutants. Our results suggest that autophagy mediates nuclear degradation after hyphal fusion and has a general function in the control of nuclear distribution in F. oxysporum. PMID:25560310

Recombinant human bone morphogenetic protein-2-induced radiculitis in elective minimally invasive transforaminal lumbar interbody fusions: a series review.

PubMed

Mindea, Stefan A; Shih, Patrick; Song, John K

2009-06-15

Retrospective single center analysis. The purpose of our study is to quantify the development of a postoperative radiculitis in our minimally invasive transforaminal lumbar interbody fusion patient population. The application of recombinant human Bone Morphogenetic Protein-2 (BMP) in spinal surgery has allowed for greater success in spinal fusions. This has led to the FDA approving its use in anterior lumbar interbody fusion. However, its well-recognized benefits have generated its "off-label" use in the cervical, thoracic, and lumbar spine. Despite its benefits, the adverse effects of its inflammatory properties are just starting to get recognized. Some clear adverse reactions have been documented in the literature in the cervical spine. However, we feel that these inflammatory properties may be present in the lumbar spine as well. We performed a retrospective chart review of 43 patients who had undergone a minimally invasive transforaminal lumbar interbody fusions. Thirty-five of these patients had BMP and 8 patients did not have BMP. We documented whether there was a preoperative radiculopathy present and whether a radiculopathy was present postoperative. We reviewed radiographic postoperative imaging to establish a structural cause for any radiculopathy. If new or increasing radicular symptoms were present, we attempted to assess the duration of these symptoms. Our analysis, showed that 0 of the 8 patients of the non-BMP group had new radicular symptoms that were not attributed to structural causes. In the BMP group, 4 of the 35 patients (11.4%) had new radicular symptoms without structural etiology. Our analysis suggest that patients undergoing minimally invasive transforaminal lumbar interbody fusions procedures have a higher incidence of developing new radicular symptoms that could be attributed to BMP.

Chemical Ligation of Folded Recombinant Proteins: Segmental Isotopic Labeling of Domains for NMR Studies

NASA Astrophysics Data System (ADS)

Xu, Rong; Ayers, Brenda; Cowburn, David; Muir, Tom W.

1999-01-01

A convenient in vitro chemical ligation strategy has been developed that allows folded recombinant proteins to be joined together. This strategy permits segmental, selective isotopic labeling of the product. The src homology type 3 and 2 domains (SH3 and SH2) of Abelson protein tyrosine kinase, which constitute the regulatory apparatus of the protein, were individually prepared in reactive forms that can be ligated together under normal protein-folding conditions to form a normal peptide bond at the ligation junction. This strategy was used to prepare NMR sample quantities of the Abelson protein tyrosine kinase-SH(32) domain pair, in which only one of the domains was labeled with 15N Mass spectrometry and NMR analyses were used to confirm the structure of the ligated protein, which was also shown to have appropriate ligand-binding properties. The ability to prepare recombinant proteins with selectively labeled segments having a single-site mutation, by using a combination of expression of fusion proteins and chemical ligation in vitro, will increase the size limits for protein structural determination in solution with NMR methods. In vitro chemical ligation of expressed protein domains will also provide a combinatorial approach to the synthesis of linked protein domains.

Fluorogenic Green-Inside Red-Outside (GIRO) Labeling Approach Reveals Adenylyl Cyclase-Dependent Control of BKα Surface Expression

PubMed Central

2015-01-01

The regulation of surface levels of protein is critical for proper cell function and influences properties including cell adhesion, ion channel contributions to current flux, and the sensitivity of surface receptors to ligands. Here we demonstrate a two-color labeling system in live cells using a single fluorogen activating peptide (FAP) based fusion tag, which enables the rapid and simultaneous quantification of surface and internal proteins. In the nervous system, BK channels can regulate neural excitability and neurotransmitter release, and the surface trafficking of BK channels can be modulated by signaling cascades and assembly with accessory proteins. Using this labeling approach, we examine the dynamics of BK channel surface expression in HEK293 cells. Surface pools of the pore-forming BKα subunit were stable, exhibiting a plasma membrane half-life of >10 h. Long-term activation of adenylyl cyclase by forskolin reduced BKα surface levels by 30%, an effect that could not be attributed to increased bulk endocytosis of plasma membrane proteins. This labeling approach is compatible with microscopic imaging and flow cytometry, providing a solid platform for examining protein trafficking in living cells. PMID:26301573

Union rate of tibiotalocalcaneal nails with internal or external bone stimulation.

PubMed

De Vries, J George; Berlet, Gregory C; Hyer, Christopher F

2012-11-01

The use of bone growth stimulation has been reported in the application of hindfoot and ankle arthrodesis. Most studies have been retrospective case series with few patients. The authors present a comparative analysis of patients undergoing tibiotalocalcaneal (TTC) arthrodesis via a retrograde intramedullary arthrodesis nail to evaluate the influence of internal versus external bone stimulation in this population. One hundred fifty-four patients were treated with retrograde intramedullary nailing. A comprehensive chart and radiographic review was performed from a database of patients who underwent TTC fusion with or without bone stimulation. Ninety-one patients with retrograde TTC nailing were treated with direct current internal bone stimulation at the time of the index procedure (internal group) and 63 were treated with combined magnetic field external bone stimulation (external group). The primary end point was fusion with potential variables evaluated for influence on fusion rates. Demographically the cohorts were similar groups in age and comorbidities. Surgical and outcome data were examined, and there were few statistically significant differences between the two groups. There was no statistically significant difference in rate of union (52.7% and 57.1%, p = .63) or rate of complications between the internal and external groups. Overall, the success rate for achieving a stable, functional limb for the groups was 81.3% (74/91 patients) and 82.5% (52/63 patients) in the internal and external groups, respectively (p = .62). The authors demonstrated there were no statistically significant differences between the union and complication rate when comparing these types of internal and external bone stimulation in this patient population. Consideration of these results may help guide physicians when considering bone stimulation as an adjunct to TTC fusions with a retrograde intramedullary nail.

Practical considerations in Bayesian fusion of point sensors

NASA Astrophysics Data System (ADS)

Johnson, Kevin; Minor, Christian

2012-06-01

Sensor data fusion is and has been a topic of considerable research, but rigorous and quantitative understanding of the benefits of fusing specific types of sensor data remains elusive. Often, sensor fusion is performed on an ad hoc basis with the assumption that overall detection capabilities will improve, only to discover later, after expensive and time consuming laboratory and/or field testing that little advantage was gained. The work presented here will discuss these issues with theoretical and practical considerations in the context of fusing chemical sensors with binary outputs. Results are given for the potential performance gains one could expect with such systems, as well as the practical difficulties involved in implementing an optimal Bayesian fusion strategy with realistic scenarios. Finally, a discussion of the biases that inaccurate statistical estimates introduce into the results and their consequences is presented.

Anterior lumbar interbody fusion versus transforaminal lumbar interbody fusion--systematic review and meta-analysis.

PubMed

Phan, Kevin; Thayaparan, Ganesha K; Mobbs, Ralph J

2015-01-01

To assess the clinical and radiographic outcomes and complications of anterior lumbar interbody fusion (ALIF) versus transforaminal lumbar interbody fusion (TLIF). A systematic literature search was conducted from six electronic databases. The relative risk and weighted mean difference (WMD) were used as statistical summary effect sizes. Fusion rates (88.6% vs. 91.9%, P = 0.23) and clinical outcomes were comparable between ALIF and TLIF. ALIF was associated with restoration of disk height (WMD, 2.71 mm, P = 0.01), segmental lordosis (WMD, 2.35, P = 0.03), and whole lumbar lordosis (WMD, 6.33, P = 0.03). ALIF was also associated with longer hospitalization (WMD, 1.8 days, P = 0.01), lower dural injury (0.4% vs. 3.8%, P = 0.05) but higher blood vessel injury (2.6% vs. 0%, P = 0.04). ALIF and TLIF appear to have similar success and clinical outcomes, with different complication profiles. ALIF may be associated with superior restoration of disk height and lordosis, but requires further validation in future studies.

Traceless affinity labeling of endogenous proteins for functional analysis in living cells.

PubMed

Hayashi, Takahiro; Hamachi, Itaru

2012-09-18

Protein labeling and imaging techniques have provided tremendous opportunities to study the structure, function, dynamics, and localization of individual proteins in the complex environment of living cells. Molecular biology-based approaches, such as GFP-fusion tags and monoclonal antibodies, have served as important tools for the visualization of individual proteins in cells. Although these techniques continue to be valuable for live cell imaging, they have a number of limitations that have only been addressed by recent progress in chemistry-based approaches. These chemical approaches benefit greatly from the smaller probe sizes that should result in fewer perturbations to proteins and to biological systems as a whole. Despite the research in this area, so far none of these labeling techniques permit labeling and imaging of selected endogenous proteins in living cells. Researchers have widely used affinity labeling, in which the protein of interest is labeled by a reactive group attached to a ligand, to identify and characterize proteins. Since the first report of affinity labeling in the early 1960s, efforts to fine-tune the chemical structures of both the reactive group and ligand have led to protein labeling with excellent target selectivity in the whole proteome of living cells. Although the chemical probes used for affinity labeling generally inactivate target proteins, this strategy holds promise as a valuable tool for the labeling and imaging of endogenous proteins in living cells and by extension in living animals. In this Account, we summarize traceless affinity labeling, a technique explored mainly in our laboratory. In our overview of the different labeling techniques, we emphasize the challenge of designing chemical probes that allow for dissociation of the affinity module (often a ligand) after the labeling reaction so that the labeled protein retains its native function. This feature distinguishes the traceless labeling approach from the traditional affinity labeling method and allows for real-time monitoring of protein activity. With the high target specificity and biocompatibility of this technique, we have achieved individual labeling and imaging of endogenously expressed proteins in samples of high biological complexity. We also highlight applications in which our current approach enabled the monitoring of important biological events, such as ligand binding, in living cells. These novel chemical labeling techniques are expected to provide a molecular toolbox for studying a wide variety of proteins and beyond in living cells.

Classification without labels: learning from mixed samples in high energy physics

NASA Astrophysics Data System (ADS)

Metodiev, Eric M.; Nachman, Benjamin; Thaler, Jesse

2017-10-01

Modern machine learning techniques can be used to construct powerful models for difficult collider physics problems. In many applications, however, these models are trained on imperfect simulations due to a lack of truth-level information in the data, which risks the model learning artifacts of the simulation. In this paper, we introduce the paradigm of classification without labels (CWoLa) in which a classifier is trained to distinguish statistical mixtures of classes, which are common in collider physics. Crucially, neither individual labels nor class proportions are required, yet we prove that the optimal classifier in the CWoLa paradigm is also the optimal classifier in the traditional fully-supervised case where all label information is available. After demonstrating the power of this method in an analytical toy example, we consider a realistic benchmark for collider physics: distinguishing quark- versus gluon-initiated jets using mixed quark/gluon training samples. More generally, CWoLa can be applied to any classification problem where labels or class proportions are unknown or simulations are unreliable, but statistical mixtures of the classes are available.

Classification without labels: learning from mixed samples in high energy physics

DOE PAGES

Metodiev, Eric M.; Nachman, Benjamin; Thaler, Jesse

2017-10-25

Modern machine learning techniques can be used to construct powerful models for difficult collider physics problems. In many applications, however, these models are trained on imperfect simulations due to a lack of truth-level information in the data, which risks the model learning artifacts of the simulation. In this paper, we introduce the paradigm of classification without labels (CWoLa) in which a classifier is trained to distinguish statistical mixtures of classes, which are common in collider physics. Crucially, neither individual labels nor class proportions are required, yet we prove that the optimal classifier in the CWoLa paradigm is also the optimalmore » classifier in the traditional fully-supervised case where all label information is available. After demonstrating the power of this method in an analytical toy example, we consider a realistic benchmark for collider physics: distinguishing quark- versus gluon-initiated jets using mixed quark/gluon training samples. More generally, CWoLa can be applied to any classification problem where labels or class proportions are unknown or simulations are unreliable, but statistical mixtures of the classes are available.« less

Classification without labels: learning from mixed samples in high energy physics

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

Metodiev, Eric M.; Nachman, Benjamin; Thaler, Jesse

Modern machine learning techniques can be used to construct powerful models for difficult collider physics problems. In many applications, however, these models are trained on imperfect simulations due to a lack of truth-level information in the data, which risks the model learning artifacts of the simulation. In this paper, we introduce the paradigm of classification without labels (CWoLa) in which a classifier is trained to distinguish statistical mixtures of classes, which are common in collider physics. Crucially, neither individual labels nor class proportions are required, yet we prove that the optimal classifier in the CWoLa paradigm is also the optimalmore » classifier in the traditional fully-supervised case where all label information is available. After demonstrating the power of this method in an analytical toy example, we consider a realistic benchmark for collider physics: distinguishing quark- versus gluon-initiated jets using mixed quark/gluon training samples. More generally, CWoLa can be applied to any classification problem where labels or class proportions are unknown or simulations are unreliable, but statistical mixtures of the classes are available.« less

Tyrosine kinase fusion genes in pediatric BCR-ABL1-like acute lymphoblastic leukemia

PubMed Central

Boer, Judith M.; Steeghs, Elisabeth M.P.; Marchante, João R.M.; Boeree, Aurélie; Beaudoin, James J.; Berna Beverloo, H.; Kuiper, Roland P.; Escherich, Gabriele; van der Velden, Vincent H.J.; van der Schoot, C. Ellen; de Groot-Kruseman, Hester A.; Pieters, Rob; den Boer, Monique L.

2017-01-01

Approximately 15% of pediatric B cell precursor acute lymphoblastic leukemia (BCP-ALL) is characterized by gene expression similar to that of BCR-ABL1-positive disease and unfavorable prognosis. This BCR-ABL1-like subtype shows a high frequency of B-cell development gene aberrations and tyrosine kinase-activating lesions. To evaluate the clinical significance of tyrosine kinase gene fusions in children with BCP-ALL, we studied the frequency of recently identified tyrosine kinase fusions, associated genetic features, and prognosis in a representative Dutch/German cohort. We identified 14 tyrosine kinase fusions among 77 BCR-ABL1-like cases (18%) and none among 76 non-BCR-ABL1-like B-other cases. Novel exon fusions were identified for RCSD1-ABL2 and TERF2-JAK2. JAK2 mutation was mutually exclusive with tyrosine kinase fusions and only occurred in cases with high CRLF2 expression. The non/late response rate and levels of minimal residual disease in the fusion-positive BCR-ABL1-like group were higher than in the non-BCR-ABL1-like B-others (p<0.01), and also higher, albeit not statistically significant, compared with the fusion-negative BCR-ABL1-like group. The 8-year cumulative incidence of relapse in the fusion-positive BCR-ABL1-like group (35%) was comparable with that in the fusion-negative BCR-ABL1-like group (35%), and worse than in the non-BCR-ABL1-like B-other group (17%, p=0.07). IKZF1 deletions, predominantly other than the dominant-negative isoform and full deletion, co-occurred with tyrosine kinase fusions. This study shows that tyrosine kinase fusion-positive cases are a high-risk subtype of BCP-ALL, which warrants further studies with specific kinase inhibitors to improve outcome. PMID:27894077

The effect of excision of the posterior arch of C1 on C1/C2 fusion using transarticular screws.

PubMed

Chang, K C; Samartzis, D; Fuego, S M; Dhatt, S S; Wong, Y W; Cheung, W Y; Luk, K D K; Cheung, K M C

2013-07-01

Transarticular screw fixation with autograft is an established procedure for the surgical treatment of atlantoaxial instability. Removal of the posterior arch of C1 may affect the rate of fusion. This study assessed the rate of atlantoaxial fusion using transarticular screws with or without removal of the posterior arch of C1. We reviewed 30 consecutive patients who underwent atlantoaxial fusion with a minimum follow-up of two years. In 25 patients (group A) the posterior arch of C1 was not excised (group A) and in five it was (group B). Fusion was assessed on static and dynamic radiographs. In selected patients CT imaging was also used to assess fusion and the position of the screws. There were 15 men and 15 women with a mean age of 51.2 years (23 to 77) and a mean follow-up of 7.7 years (2 to 11.6). Stable union with a solid fusion or a stable fibrous union was achieved in 29 patients (97%). In Group A, 20 patients (80%) achieved a solid fusion, four (16%) a stable fibrous union and one (4%) a nonunion. In Group B, stable union was achieved in all patients, three having a solid fusion and two a stable fibrous union. There was no statistically significant difference between the status of fusion in the two groups. Complications were noted in 12 patients (40%); these were mainly related to the screws, and included malpositioning and breakage. The presence of an intact or removed posterior arch of C1 did not affect the rate of fusion in patients with atlantoaxial instability undergoing C1/C2 fusion using transarticular screws and autograft.

Hybrid Biosynthetic Autograft Extender for Use in Posterior Lumbar Interbody Fusion: Safety and Clinical Effectiveness.

PubMed

Chedid, Mokbel K; Tundo, Kelly M; Block, Jon E; Muir, Jeffrey M

2015-01-01

Autologous iliac crest bone graft is the preferred option for spinal fusion, but the morbidity associated with bone harvest and the need for graft augmentation in more demanding cases necessitates combining local bone with bone substitutes. The purpose of this study was to document the clinical effectiveness and safety of a novel hybrid biosynthetic scaffold material consisting of poly(D,L-lactide-co-glycolide) (PLGA, 75:25) combined by lyophilization with unmodified high molecular weight hyaluronic acid (10-12% wt:wt) as an extender for a broad range of spinal fusion procedures. We retrospectively evaluated all patients undergoing single- and multi-level posterior lumbar interbody fusion at an academic medical center over a 3-year period. A total of 108 patients underwent 109 procedures (245 individual vertebral levels). Patient-related outcomes included pain measured on a Visual Analog Scale. Radiographic outcomes were assessed at 6 weeks, 3-6 months, and 1 year postoperatively. Radiographic fusion or progression of fusion was documented in 221 of 236 index levels (93.6%) at a mean (±SD) time to fusion of 10.2+4.1 months. Single and multi-level fusions were not associated with significantly different success rates. Mean pain scores (+SD) for all patients improved from 6.8+2.5 at baseline to 3.6+2.9 at approximately 12 months. Improvements in VAS were greatest in patients undergoing one- or two-level fusion, with patients undergoing multi-level fusion demonstrating lesser but still statistically significant improvements. Overall, stable fusion was observed in 64.8% of vertebral levels; partial fusion was demonstrated in 28.8% of vertebral levels. Only 15 of 236 levels (6.4%) were non-fused at final follow-up.

Four-corner fusion: comparison of patient satisfaction and functional outcome of conventional K-wire technique vs. a new locking plate.

PubMed

Hernekamp, J F; Reinecke, A; Neubrech, F; Bickert, B; Kneser, U; Kremer, T

2016-04-01

Four-corner fusion is a standard procedure for advanced carpal collapse. Several operative techniques and numerous implants for osseous fixation have been described. Recently, a specially designed locking plate (Aptus©, Medartis, Basel, Switzerland) was introduced. The purpose of this study was to compare functional results after osseous fixation using K-wires (standard of care, SOC) with four-corner fusion and locking plate fixation. 21 patients who underwent four-corner fusion in our institution between 2008 and 2013 were included in a retrospective analysis. In 11 patients, osseous fixation was performed using locking plates whereas ten patients underwent bone fixation with conventional K-wires. Outcome parameters were functional outcome, osseous consolidation, patient satisfaction (DASH- and Krimmer Score), pain and perioperative morbidity and the time until patients returned to daily work. Patients were divided in two groups and paired t-tests were performed for statistical analysis. No implant related complications were observed. Osseous consolidation was achieved in all cases. Differences between groups were not significant regarding active range of motion (AROM), pain and function. Overall patient satisfaction was acceptable in all cases; differences in the DASH questionnaire and the Krimmer questionnaire were not significant. One patient of the plate group required conversion to total wrist arthrodesis without implant-related complications. Both techniques for four-corner fusion have similar healing rates. Using the more expensive locking implant avoids a second operation for K-wire removal, but no statistical differences were detected in functional outcome as well as in patient satisfaction when compared to SOC.

Statistical image quantification toward optimal scan fusion and change quantification

NASA Astrophysics Data System (ADS)

Potesil, Vaclav; Zhou, Xiang Sean

2007-03-01

Recent advance of imaging technology has brought new challenges and opportunities for automatic and quantitative analysis of medical images. With broader accessibility of more imaging modalities for more patients, fusion of modalities/scans from one time point and longitudinal analysis of changes across time points have become the two most critical differentiators to support more informed, more reliable and more reproducible diagnosis and therapy decisions. Unfortunately, scan fusion and longitudinal analysis are both inherently plagued with increased levels of statistical errors. A lack of comprehensive analysis by imaging scientists and a lack of full awareness by physicians pose potential risks in clinical practice. In this paper, we discuss several key error factors affecting imaging quantification, studying their interactions, and introducing a simulation strategy to establish general error bounds for change quantification across time. We quantitatively show that image resolution, voxel anisotropy, lesion size, eccentricity, and orientation are all contributing factors to quantification error; and there is an intricate relationship between voxel anisotropy and lesion shape in affecting quantification error. Specifically, when two or more scans are to be fused at feature level, optimal linear fusion analysis reveals that scans with voxel anisotropy aligned with lesion elongation should receive a higher weight than other scans. As a result of such optimal linear fusion, we will achieve a lower variance than naïve averaging. Simulated experiments are used to validate theoretical predictions. Future work based on the proposed simulation methods may lead to general guidelines and error lower bounds for quantitative image analysis and change detection.

Perianth organization and intra-specific floral variability.

PubMed

Herrera, J; Arista, M; Ortiz, P L

2008-11-01

Floral symmetry and fusion of perianth parts are factors that contribute to fine-tune the match between flowers and their animal pollination vectors. In the present study, we investigated whether the possession of a sympetalous (fused) corolla and bilateral symmetry of flowers translate into decreased intra-specific variability as a result of natural stabilizing selection exerted by pollinators. Average size of the corolla and intra-specific variability were determined in two sets of southern Spanish entomophilous plant species. In the first set, taxa were paired by family to control for the effect of phylogeny (phylogenetically independent contrasts), whereas in the second set species were selected at random. Flower size data from a previous study (with different species) were also used to test the hypothesis that petal fusion contributes to decrease intra-specific variability. In the phylogenetically independent contrasts, floral symmetry was a significant correlate of intra-specific variation, with bilaterally symmetrical flowers showing more constancy than radially symmetrical flowers (i.e. unsophisticated from a functional perspective). As regards petal fusion, species with fused petals were on average more constant than choripetalous species, but the difference was not statistically significant. The reanalysis of data from a previous study yielded largely similar results, with a distinct effect of symmetry on variability, but no effect of petal fusion. The randomly-chosen species sample, on the other hand, failed to reveal any significant effect of either symmetry or petal fusion on intra-specific variation. The problem of low-statistical power in this kind of analysis, and the difficulty of testing an evolutionary hypothesis that involves phenotypic traits with a high degree of morphological correlation is discussed.

In vivo Labeling of Constellations of Functionally Identified Neurons for Targeted in vitro Recordings

PubMed Central

Lien, Anthony D.; Scanziani, Massimo

2011-01-01

Relating the functional properties of neurons in an intact organism with their cellular and synaptic characteristics is necessary for a mechanistic understanding of brain function. However, while the functional properties of cortical neurons (e.g., tuning to sensory stimuli) are necessarily determined in vivo, detailed cellular and synaptic analysis relies on in vitro techniques. Here we describe an approach that combines in vivo calcium imaging (for functional characterization) with photo-activation of fluorescent proteins (for neuron labeling), thereby allowing targeted in vitro recording of multiple neurons with known functional properties. We expressed photo-activatable GFP rendered non-diffusible through fusion with a histone protein (H2B–PAGFP) in the mouse visual cortex to rapidly photo-label constellations of neurons in vivo at cellular and sub-cellular resolution using two-photon excitation. This photo-labeling method was compatible with two-photon calcium imaging of neuronal responses to visual stimuli, allowing us to label constellations of neurons with specific functional properties. Photo-labeled neurons were easily identified in vitro in acute brain slices and could be targeted for whole-cell recording. We also demonstrate that in vitro and in vivo image stacks of the same photo-labeled neurons could be registered to one another, allowing the exact in vivo response properties of individual neurons recorded in vitro to be known. The ability to perform in vitro recordings from neurons with known functional properties opens up exciting new possibilities for dissecting the cellular, synaptic, and circuit mechanisms that underlie neuronal function in vivo. PMID:22144948

MYB Labeling by Immunohistochemistry Is More Sensitive and Specific for Breast Adenoid Cystic Carcinoma than MYB Labeling by FISH.

PubMed

Poling, Justin S; Yonescu, Raluca; Subhawong, Andrea P; Sharma, Rajni; Argani, Pedram; Ning, Yi; Cimino-Mathews, Ashley

2017-07-01

Breast adenoid cystic carcinoma (ACC) is a primary breast carcinoma that, like salivary gland ACC, displays the t(6;9) translocation resulting in the MYB-NFIB gene fusion and immunopositivity for MYB by immunohistochemistry (IHC). However, it is not well established whether MYB immunoreactivity or rearrangement can be used to support a diagnosis of ACC in a malignant basaloid or benign cribriform breast lesion. Whole sections of primary breast ACC (n=11), collagenous spherulosis (CS; n=7), and microglandular adenosis (MGA; n=5) and tissue microarrays containing 16 basal-like, triple-negative breast carcinomas (TNBC) were labeled for MYB by IHC and underwent MYB fluorescence in situ hybridization using a break-apart probe. Strong, diffuse nuclear MYB labeling was seen in 100% ACC compared with no cases of basal-like TNBC, CS, or MGA (P=0.0001). Any degree of nuclear MYB labeling was seen in 100% ACC compared with 54% of all other cases (P=0.007), with any labeling seen in 71% CS, 63% basal-like TNBC, and 0% MGA. MYB rearrangement was detected in 89% (8/9) of evaluable ACC compared with 4% (1/26) of all other evaluable cases (P=0.0001), with a rearrangement detected in 1 (7%; n=1/15) evaluable basal-like TNBC. Strong, diffuse nuclear labeling for MYB is more sensitive than MYB fluorescence in situ hybridization for breast ACC and can be used to support a diagnosis of ACC in a cribriform or basaloid lesion in the breast. However, weak and focal labeling should be interpreted with caution as it can be seen in other benign cribriform and malignant basaloid lesions.

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

Sen, Satyabrata; Rao, Nageswara S; Wu, Qishi

There have been increasingly large deployments of radiation detection networks that require computationally fast algorithms to produce prompt results over ad-hoc sub-networks of mobile devices, such as smart-phones. These algorithms are in sharp contrast to complex network algorithms that necessitate all measurements to be sent to powerful central servers. In this work, at individual sensors, we employ Wald-statistic based detection algorithms which are computationally very fast, and are implemented as one of three Z-tests and four chi-square tests. At fusion center, we apply the K-out-of-N fusion to combine the sensors hard decisions. We characterize the performance of detection methods bymore » deriving analytical expressions for the distributions of underlying test statistics, and by analyzing the fusion performances in terms of K, N, and the false-alarm rates of individual detectors. We experimentally validate our methods using measurements from indoor and outdoor characterization tests of the Intelligence Radiation Sensors Systems (IRSS) program. In particular, utilizing the outdoor measurements, we construct two important real-life scenarios, boundary surveillance and portal monitoring, and present the results of our algorithms.« less

Investigating the degree of "stigma" associated with nuclear energy technologies: A cross-cultural examination of the case of fusion power.

PubMed

Horlick-Jones, Tom; Prades, Ana; Espluga, Josep

2012-07-01

The extent to which nuclear energy technologies are, in some sense, "stigmatised" by historical environmental and military associations is of particular interest in contemporary debates about sustainable energy policy. Recent claims in the literature suggest that despite such stigmatisation, lay views on such technologies may be shifting towards a "reluctant acceptance," in the light of concerns about issues like anthropogenic climate change. In this paper, we report on research into learning and reasoning processes concerned with a largely unknown nuclear energy technology; namely fusion power. We focus on the role of the nuclear label, or "brand," in informing how lay citizens make sense of the nature of this technology. Our findings derive from a comparative analysis of data generated in Spain and Britain, using the same methodology.

Visualizing interactions between Sindbis virus and cells by single particle tracking

NASA Astrophysics Data System (ADS)

Williard, Mary

2005-03-01

Sindbis virus infects both mammalian and insect cells. Though not pathogenic in humans, Sindbis is a model for many mosquito- borne viruses that cause human disease, such as West Nile virus. We have used real-time single particle fluorescence microscopy to observe individual Sindbis virus particles as they infect living cells. Fluorescent labels were incorporated into both the viral coat proteins and the lipid envelope of the virus. Kinetics characteristic of free diffusion in solution, slower diffusion inside cells, attachment to spots on the cell surface, and motor protein transport inside cells have been observed. Dequenching of the membrane label is used to report membrane fusion events during the infection process. Tracking individual viral particles allows multiple pathways to be determined without the requirement of synchronicity.

The Discover artificial disc replacement versus fusion in cervical radiculopathy--a randomized controlled outcome trial with 2-year follow-up.

PubMed

Skeppholm, Martin; Lindgren, Lars; Henriques, Thomas; Vavruch, Ludek; Löfgren, Håkan; Olerud, Claes

2015-06-01

Several previous studies comparing artificial disc replacement (ADR) and fusion have been conducted with cautiously positive results in favor of ADR. This study is not, in contrast to most previous studies, an investigational device exemption study required by the Food and Drug Administration for approval to market the product in the United States. This study was partially funded with unrestricted institutional research grants by the company marketing the artificial disc used in this study. To compare outcomes between the concepts of an artificial disc to treatment with anterior cervical decompression and fusion (ACDF) and to register complications associated to the two treatments during a follow-up time of 2 years. This is a randomized controlled multicenter trial, including three spine centers in Sweden. The study included patients seeking care for cervical radiculopathy who fulfilled inclusion criteria. In total, 153 patients were included. Self-assessment with Neck Disability Index (NDI) as a primary outcome variable and EQ-5D and visual analog scale as secondary outcome variables. Patients were randomly allocated to either treatment with the Depuy Discover artificial disc or fusion with iliac crest bone graft and plating. Randomization was blinded to both patient and caregivers until time for implantation. Adverse events, complications, and revision surgery were registered as well as loss of follow-up. Data were available in 137 (91%) of the included and initially treated patients. Both groups improved significantly after surgery. NDI changed from 63.1 to 39.8 in an intention-to-treat analysis. No statistically significant difference between the ADR and the ACDF groups could be demonstrated with NDI values of 39.1 and 40.1, respectively. Nor in secondary outcome measures (EQ-5D and visual analog scale) could any statistically significant differences be demonstrated between the groups. Nine patients in the ADR group and three in the fusion group underwent secondary surgery because of various reasons. Two patients in each group underwent secondary surgery because of adjacent segment pathology. Complication rates were not statistically significant between groups. Artificial disc replacement did not result in better outcome compared to fusion measured with NDI 2 years after surgery. Copyright © 2015 Elsevier Inc. All rights reserved.

Surgical outcomes of degenerative spondylolisthesis with L5-S1 disc degeneration: comparison between lumbar floating fusion and lumbosacral fusion at a minimum 5-year follow-up.

PubMed

Liao, Jen-Chung; Chen, Wen-Jer; Chen, Lih-Hui; Niu, Chi-Chien; Keorochana, Gun

2011-09-01

A retrospective clinical and radiographic study was performed. The purpose of this study was to compare outcomes of patients with degenerative spondylolisthesis and a preexisting degenerative L5-S1 disc treated with a lumbar floating fusion (LFF) versus lumbosacral fusion (LSF). Fusion for treatment of degenerative spondylolisthesis often ends at the L5 level. These patients usually had a preexisting L5-S1 disc degeneration; however, no literature mentions the role of prophylactic LSF in degenerative spondylolisthesis associated with L5-S1 disc degeneration. A total of 107 patients with a minimum 5-year follow-up who had lumbosacral or LFF with pedicle instrumentation for degenerative spondylolisthesis were included. UCLA (University of California, Los Angeles) classification was used to evaluate the radiographic results of the L5-S1 segment. The Oswestry Disability Index (ODI) and modified Brodsky's criteria were used to evaluate patients' clinical results. The incidence of adjacent segment disease (ASD) (includes radiographic and clinical ASD) of both ends was recorded. There were no statistically significant differences in sex, age distribution, or amount of follow-up between the LFF and LSF groups. The LSF group had a higher percentage of patients that underwent total L5 laminectomy with loss of L5-S1 posterior ligament integrity (LSF = 92% vs. LFF = 67%, P = 0.019). The higher incidence of cephalic ASD in the LSF group was statistically significant (LSF = 25% vs. LFF = 9.7%, P = 0.049). Although no patient in the LSF group developed L5-S1 ASD, need for L5-S1 segment revision surgery was not prevented with LSF. Clinical outcomes on the basis of the success rate (LFF = 85.5% vs.LSF = 70.8%, P = 0.103) and ODI difference (LFF = 28.97 ± 15.82 vs. LSF = 23.04 ± 10.97, P = 0.109), there were no statistically significant difference between these two groups. Posterior instrumentation with posterolateral LFF for the treatment of degenerative spondylolisthesis with concomitant L5-S1 disc degeneration results in a high percentage of satisfactory clinical results. Extended fusion to the sacrum did not provide a better clinical result. LSF could not reduce the incidence of revision surgery at the L5-S1 segment and involved greater incidence of cephalic ASD.

Complications, revision fusions, readmissions, and utilization over a 1-year period after bone morphogenetic protein use during primary cervical spine fusions.

PubMed

Goode, Adam P; Richardson, William J; Schectman, Robin M; Carey, Timothy S

2014-09-01

Nationwide estimates examining bone morphogenetic protein (BMP) use with cervical spine fusions have been limited to perioperative outcomes. To determine the 1-year risk of complications, cervical revision fusions, hospital readmissions, and health care services utilization. A retrospective cohort study from 2002 to 2009 using a nationwide claims database. There were 61,937 primary cervical spine fusions of which 1,677 received BMP. Complications, revision fusions, 30-day hospital readmission, and health care utilization. Data for these analyses come from the Thomson Reuters MarketScan Commercial Claims and Encounters Database 2010. Patients were aged 18 to 64 years, receiving and not receiving BMP with a primary (C2-C7) cervical spine fusion. All outcomes were defined by International Classification of Diseases, 9th edition Clinical Modification and Current Procedural and Terminology, 4th edition codes. Complications were analyzed as any complication and stratified by nervous system, wound, and dysphagia or hoarseness. Cervical revision fusions were determined in the 1-year follow-up. Hospital readmission discharge records defined 30-day hospital readmission and reason for the readmission. The utilization of at least one health care service of cervical spine imaging, epidural usage or rehabilitation service was examined. Poisson regression models were used to estimate the relative risk and 95% confidence interval (CI). Linear regression was used to determine the time to hospital readmission. Results were stratified by anterior or posterior and circumferential approaches. Patients receiving BMP were 29% more likely to have a complication (adjusted relative risk [aRR]=1.29 [95% CI, 1.14-1.46]) and a nervous system complication (aRR=1.42 [95% CI, 1.10-1.83]). Cervical revision fusions were more likely among patients receiving BMP (aRR=1.69 [95% CI, 1.35-2.13]). The risk of 30-day readmission was greater with BMP use (aRR=1.37 [95% CI, 1.07-1.73]) and readmission occurred 27.4% sooner on an average. Patients receiving BMP were more likely to receive computed tomography scans (aRR=1.34 [95% CI, 1.06-1.70]) and epidurals with anterior surgical approaches (aRR=1.29 [95% CI, 1.00-1.65]). These findings question both the safety and effectiveness of off-label BMP use in primary cervical spine fusions. Copyright © 2014 Elsevier Inc. All rights reserved.

Influence of incomplete fusion on complete fusion at energies above the Coulomb barrier

NASA Astrophysics Data System (ADS)

Shuaib, Mohd; Sharma, Vijay R.; Yadav, Abhishek; Sharma, Manoj Kumar; Singh, Pushpendra P.; Singh, Devendra P.; Kumar, R.; Singh, R. P.; Muralithar, S.; Singh, B. P.; Prasad, R.

2017-10-01

In the present work, excitation functions of several reaction residues in the system 19F+169Tm, populated via the complete and incomplete fusion processes, have been measured using off-line γ-ray spectroscopy. The analysis of excitation functions has been done within the framework of statistical model code pace4. The excitation functions of residues populated via xn and pxn channels are found to be in good agreement with those estimated by the theoretical model code, which confirms the production of these residues solely via complete fusion process. However, a significant enhancement has been observed in the cross-sections of residues involving α-emitting channels as compared to the theoretical predictions. The observed enhancement in the cross-sections has been attributed to the incomplete fusion processes. In order to have a better insight into the onset and strength of incomplete fusion, the incomplete fusion strength function has been deduced. At present, there is no theoretical model available which can satisfactorily explain the incomplete fusion reaction data at energies ≈4-6 MeV/nucleon. In the present work, the influence of incomplete fusion on complete fusion in the 19F+169Tm system has also been studied. The measured cross-section data may be important for the development of reactor technology as well. It has been found that the incomplete fusion strength function strongly depends on the α-Q value of the projectile, which is found to be in good agreement with the existing literature data. The analysis strongly supports the projectile-dependent mass-asymmetry systematics. In order to study the influence of Coulomb effect ({Z}{{P}}{Z}{{T}}) on incomplete fusion, the deduced strength function for the present work is compared with the nearby projectile-target combinations. The incomplete fusion strength function is found to increase linearly with {Z}{{P}}{Z}{{T}}, indicating a strong influence of Coulomb effect in the incomplete fusion reactions.

A Comprehensive Approach to Fusion for Microsensor Networks: Distributed and Hierarchical Inference, Communication, and Adaption

DTIC Science & Technology

2000-08-01

lecturer of LATIN 2006 , (Latin America Theoretical Informat- ics, 2006 ), Valdivia , Chile, March 2006 . 67. Sergio Verdu gave a Keynote Talk at the New...NUMBER OF PAGES 20. LIMITATION OF ABSTRACT UL - 31-Jan- 2006 Data Fusion in Large Arrays of Microsensors (SensorWeb): A Comprehensive Approach to...Transactions on Wireless Communications, February 2006 . 21. A.P. George, W.B. Powell, S.R. Kulkarni. The Statistics of Hierarchical Aggregation for

PAX3/7–FOXO1 fusion status in older rhabdomyosarcoma patient population by fluorescent in situ hybridization

PubMed Central

Lazar, Alexander J.; Bridge, Julia A.; Benjamin, Robert S.; Trent, Jonathan C.

2014-01-01

Purpose In pediatric alveolar rhabdomyosarcoma, the PAX3–FOXO1 and PAX7–FOXO1 gene fusions are prognostic indicators, while little is known concerning this disease in older patients. To determine whether PAX3/7–FOXO1 fusion gene status correlates with outcome in adolescent, young adult, and adult rhabdomyosarcoma patients, the histological, immunohistochemical, and clinical characteristics of 105 patients followed at The University of Texas MD Anderson Cancer Center from 1957 to 2001 were evaluated. Methods The samples were assembled into a tissue microarray, and fusion gene status was determined by fluorescence in situ hybridization using PAX3, PAX7, and FOXO1 loci-specific probes. The disease characteristics and specific gene fusion were correlated with patient outcomes using the log-rank test. Results Fifty-two percent of the samples exhibited a PAX3–FOXO1 fusion, 15% the PAX7–FOXO1 fusion, and 33% were negative for a rearrangement of these loci. The presence of PAX3/7–FOXO1 translocation was significantly associated with a higher frequency of metastatic disease. Although a statistically significant correlation between the PAX3/7–FOXO1 fusion gene status and overall survival was not identified, there was a trend toward better outcomes for patients with fusion-negative RMS. Conclusions Therefore, identification of a FOXO1 fusion appears to be an interesting tool for predicting outcomes in older rhabdomyosarcoma patients and is worth further investigations in this rare subgroup of RMS population. PMID:22089931

Funding for the 2ND IAEA technical meeting on fusion data processing, validation and analysis

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

Greenwald, Martin

The International Atomic Energy Agency (IAEA) will organize the second Technical Meeting on Fusion Da Processing, Validation and Analysis from 30 May to 02 June, 2017, in Cambridge, MA USA. The meeting w be hosted by the MIT Plasma Science and Fusion Center (PSFC). The objective of the meeting is to provide a platform where a set of topics relevant to fusion data processing, validation and analysis are discussed with the view of extrapolation needs to next step fusion devices such as ITER. The validation and analysis of experimental data obtained from diagnostics used to characterize fusion plasmas are crucialmore » for a knowledge based understanding of the physical processes governing the dynamics of these plasmas. The meeting will aim at fostering, in particular, discussions of research and development results that set out or underline trends observed in the current major fusion confinement devices. General information on the IAEA, including its mission and organization, can be found at the IAEA websit Uncertainty quantification (UQ) Model selection, validation, and verification (V&V) Probability theory and statistical analysis Inverse problems & equilibrium reconstru ction Integrated data analysis Real time data analysis Machine learning Signal/image proc essing & pattern recognition Experimental design and synthetic diagnostics Data management« less

Live-Cell Imaging of Early Steps of Single HIV-1 Infection.

PubMed

Francis, Ashwanth C; Melikyan, Gregory B

2018-05-19

Live-cell imaging of single HIV-1 entry offers a unique opportunity to delineate the spatio-temporal regulation of infection. Novel virus labeling and imaging approaches enable the visualization of key steps of HIV-1 entry leading to nuclear import, integration into the host genome, and viral protein expression. Here, we discuss single virus imaging strategies, focusing on live-cell imaging of single virus fusion and productive uncoating that culminates in HIV-1 infection.

Heterogeneous Multi-Metric Learning for Multi-Sensor Fusion

DTIC Science & Technology

2011-07-01

distance”. One of the most widely used methods is the k-nearest neighbor ( KNN ) method [4], which labels an input data sample to be the class with majority...despite of its simplicity, it can be an effective candidate and can be easily extended to handle multiple sensors. Distance based method such as KNN relies...Neighbor (LMNN) method [21] which will be briefly reviewed in the sequel. LMNN method tries to learn an optimal metric specifically for KNN classifier. The

Spatiotemporal Segmentation and Modeling of the Mitral Valve in Real-Time 3D Echocardiographic Images.

PubMed

Pouch, Alison M; Aly, Ahmed H; Lai, Eric K; Yushkevich, Natalie; Stoffers, Rutger H; Gorman, Joseph H; Cheung, Albert T; Gorman, Joseph H; Gorman, Robert C; Yushkevich, Paul A

2017-09-01

Transesophageal echocardiography is the primary imaging modality for preoperative assessment of mitral valves with ischemic mitral regurgitation (IMR). While there are well known echocardiographic insights into the 3D morphology of mitral valves with IMR, such as annular dilation and leaflet tethering, less is understood about how quantification of valve dynamics can inform surgical treatment of IMR or predict short-term recurrence of the disease. As a step towards filling this knowledge gap, we present a novel framework for 4D segmentation and geometric modeling of the mitral valve in real-time 3D echocardiography (rt-3DE). The framework integrates multi-atlas label fusion and template-based medial modeling to generate quantitatively descriptive models of valve dynamics. The novelty of this work is that temporal consistency in the rt-3DE segmentations is enforced during both the segmentation and modeling stages with the use of groupwise label fusion and Kalman filtering. The algorithm is evaluated on rt-3DE data series from 10 patients: five with normal mitral valve morphology and five with severe IMR. In these 10 data series that total 207 individual 3DE images, each 3DE segmentation is validated against manual tracing and temporal consistency between segmentations is demonstrated. The ultimate goal is to generate accurate and consistent representations of valve dynamics that can both visually and quantitatively provide insight into normal and pathological valve function.

DNA release from lipoplexes by anionic lipids: correlation with lipid mesomorphism, interfacial curvature, and membrane fusion

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

Tarahovsky, Yury S.; Koynova, Rumiana; MacDonald, Robert C.

2010-01-18

DNA release from lipoplexes is an essential step during lipofection and is probably a result of charge neutralization by cellular anionic lipids. As a model system to test this possibility, fluorescence resonance energy transfer between DNA and lipid covalently labeled with Cy3 and BODIPY, respectively, was used to monitor the release of DNA from lipid surfaces induced by anionic liposomes. The separation of DNA from lipid measured this way was considerably slower and less complete than that estimated with noncovalently labeled DNA, and depends on the lipid composition of both lipoplexes and anionic liposomes. This result was confirmed by centrifugalmore » separation of released DNA and lipid. X-ray diffraction revealed a clear correlation of the DNA release capacity of the anionic lipids with the interfacial curvature of the mesomorphic structures developed when the anionic and cationic liposomes were mixed. DNA release also correlated with the rate of fusion of anionic liposomes with lipoplexes. It is concluded that the tendency to fuse and the phase preference of the mixed lipid membranes are key factors for the rate and extent of DNA release. The approach presented emphasizes the importance of the lipid composition of both lipoplexes and target membranes and suggests optimal transfection may be obtained by tailoring lipoplex composition to the lipid composition of target cells.« less

Estimating A Reference Standard Segmentation With Spatially Varying Performance Parameters: Local MAP STAPLE

PubMed Central

Commowick, Olivier; Akhondi-Asl, Alireza; Warfield, Simon K.

2012-01-01

We present a new algorithm, called local MAP STAPLE, to estimate from a set of multi-label segmentations both a reference standard segmentation and spatially varying performance parameters. It is based on a sliding window technique to estimate the segmentation and the segmentation performance parameters for each input segmentation. In order to allow for optimal fusion from the small amount of data in each local region, and to account for the possibility of labels not being observed in a local region of some (or all) input segmentations, we introduce prior probabilities for the local performance parameters through a new Maximum A Posteriori formulation of STAPLE. Further, we propose an expression to compute confidence intervals in the estimated local performance parameters. We carried out several experiments with local MAP STAPLE to characterize its performance and value for local segmentation evaluation. First, with simulated segmentations with known reference standard segmentation and spatially varying performance, we show that local MAP STAPLE performs better than both STAPLE and majority voting. Then we present evaluations with data sets from clinical applications. These experiments demonstrate that spatial adaptivity in segmentation performance is an important property to capture. We compared the local MAP STAPLE segmentations to STAPLE, and to previously published fusion techniques and demonstrate the superiority of local MAP STAPLE over other state-of-the- art algorithms. PMID:22562727

Development of an efficient signal amplification strategy for label-free enzyme immunoassay using two site-specific biotinylated recombinant proteins.

PubMed

Tang, Jin-Bao; Tang, Ying; Yang, Hong-Ming

2015-02-15

Constructing a recombinant protein between a reporter enzyme and a detector protein to produce a homogeneous immunological reagent is advantageous over random chemical conjugation. However, the approach hardly recombines multiple enzymes in a difunctional fusion protein, which results in insufficient amplification of the enzymatic signal, thereby limiting its application in further enhancement of analytical signal. In this study, two site-specific biotinylated recombinant proteins, namely, divalent biotinylated alkaline phosphatase (AP) and monovalent biotinylated ZZ domain, were produced by employing the Avitag-BirA system. Through the high streptavidin (SA)-biotin interaction, the divalent biotinylated APs were clustered in the SA-biotin complex and then incorporated with the biotinylated ZZ. This incorporation results in the formation of a functional macromolecule that involves numerous APs, thereby enhancing the enzymatic signal, and in the production of several ZZ molecules for the interaction with immunoglobulin G (IgG) antibody. The advantage of this signal amplification strategy is demonstrated through ELISA, in which the analytical signal was substantially enhanced, with a 32-fold increase in the detection sensitivity compared with the ZZ-AP fusion protein approach. The proposed immunoassay without chemical modification can be an alternative strategy to enhance the analytical signals in various applications involving immunosensors and diagnostic chips, given that the label-free IgG antibody is suitable for the ZZ protein. Copyright © 2014 Elsevier B.V. All rights reserved.

Co-fuse: a new class discovery analysis tool to identify and prioritize recurrent fusion genes from RNA-sequencing data.

PubMed

Paisitkriangkrai, Sakrapee; Quek, Kelly; Nievergall, Eva; Jabbour, Anissa; Zannettino, Andrew; Kok, Chung Hoow

2018-06-07

Recurrent oncogenic fusion genes play a critical role in the development of various cancers and diseases and provide, in some cases, excellent therapeutic targets. To date, analysis tools that can identify and compare recurrent fusion genes across multiple samples have not been available to researchers. To address this deficiency, we developed Co-occurrence Fusion (Co-fuse), a new and easy to use software tool that enables biologists to merge RNA-seq information, allowing them to identify recurrent fusion genes, without the need for exhaustive data processing. Notably, Co-fuse is based on pattern mining and statistical analysis which enables the identification of hidden patterns of recurrent fusion genes. In this report, we show that Co-fuse can be used to identify 2 distinct groups within a set of 49 leukemic cell lines based on their recurrent fusion genes: a multiple myeloma (MM) samples-enriched cluster and an acute myeloid leukemia (AML) samples-enriched cluster. Our experimental results further demonstrate that Co-fuse can identify known driver fusion genes (e.g., IGH-MYC, IGH-WHSC1) in MM, when compared to AML samples, indicating the potential of Co-fuse to aid the discovery of yet unknown driver fusion genes through cohort comparisons. Additionally, using a 272 primary glioma sample RNA-seq dataset, Co-fuse was able to validate recurrent fusion genes, further demonstrating the power of this analysis tool to identify recurrent fusion genes. Taken together, Co-fuse is a powerful new analysis tool that can be readily applied to large RNA-seq datasets, and may lead to the discovery of new disease subgroups and potentially new driver genes, for which, targeted therapies could be developed. The Co-fuse R source code is publicly available at https://github.com/sakrapee/co-fuse .

Techniques of lumbar-sacral spine fusion in spondylosis: systematic literature review and meta-analysis of randomized clinical trials.

PubMed

Umeta, Ricardo S G; Avanzi, Osmar

2011-07-01

Spine fusions can be performed through different techniques and are used to treat a number of vertebral pathologies. However, there seems to be no consensus regarding which technique of fusion is best suited to treat each distinct spinal disease or group of diseases. To study the effectiveness and complications of the different techniques used for spinal fusion in patients with lumbar spondylosis. Systematic literature review and meta-analysis. Randomized clinical studies comparing the most commonly performed surgical techniques for spine fusion in lumbar-sacral spondylosis, as well as those reporting patient outcome were selected. Identify which technique, if any, presents the best clinical, functional, and radiographic outcome. Systematic literature review and meta-analysis based on scientific articles published and indexed to the following databases: PubMed (1966-2009), Cochrane Collaboration-CENTRAL, EMBASE (1980-2009), and LILACS (1982-2009). The general search strategy focused on the surgical treatment of patients with lumbar-sacral spondylosis. Eight studies met the inclusion criteria and were selected with a total of 1,136 patients. Meta-analysis showed that patients who underwent interbody fusion presented a significantly smaller blood loss (p=.001) and a greater rate of bone fusion (p=.02). Patients submitted to fusion using the posterolateral approach had a significantly shorter operative time (p=.007) and less perioperative complications (p=.03). No statistically significant difference was found for the other studied variables (pain, functional impairment, and return to work). The most commonly used techniques for lumbar spine fusion in patients with spondylosis were interbody fusion and posterolateral approach. Both techniques were comparable in final outcome, but the former presented better rates of fusion and the latter the less complications. Copyright © 2011 Elsevier Inc. All rights reserved.

Successful construction and stable expression of an anti-CD45RA scFv-EGFP fusion protein in Chinese hamster ovary cells.

PubMed

Wang, Zhujun; Chen, Yuanyuan; Li, Sisi; Cheng, Yuping; Zhao, Haizhao; Jia, Ming; Luo, Zebin; Tang, Yongmin

2014-02-01

CD45RA has been found highly expressed on leukemia cells and may be a potential target of the disease. In this study, an anti-CD45RA single-chain antibody fragment (scFv3A4) was genetically linked to the N terminus of the enhanced green fluorescent protein (EGFP) to generate a scFv3A4-EGFP fusion protein. The scFv3A4-EGFP with a molecular weight of 57kDa was stably expressed and secreted from the transfected CHO cells through the ER/Golgi-dependent pathway. The fusion protein was soluble in the culture supernatant and the yield was 1350μg/L. Flow cytometry analysis showed that the scFv3A4-EGFP had the same binding site and a very similar reactivity pattern with its parental murine monoclonal antibody (mAb) 3A4. Furthermore, comparing to conventional labeled 3A4-FITC antibody, the scFv3A4-EGFP was more resistant to illumination and more suitable for immunofluorescence histology (IFH) detection. Therefore, the scFv3A4-EGFP fusion protein can be a powerful tool to investigate the targeting of CD45RA on leukemia cells, biological activity of the target and possibly for the genetic manipulation of the antibody. Copyright © 2013 Elsevier Inc. All rights reserved.

Single-Virus Fusion Experiments Reveal Proton Influx into Vaccinia Virions and Hemifusion Lag Times

PubMed Central

Schmidt, Florian I.; Kuhn, Phillip; Robinson, Tom; Mercer, Jason; Dittrich, Petra S.

2013-01-01

Recent studies have revealed new insights into the endocytosis of vaccinia virus (VACV). However, the mechanism of fusion between viral and cellular membranes remains unknown. We developed a microfluidic device with a cell-trap array for immobilization of individual cells, with which we analyzed the acid-dependent fusion of single virions. VACV particles incorporating enhanced green fluorescent protein (EGFP) and labeled with self-quenching concentrations of R18 membrane dye were used in combination with total internal reflection fluorescence microscopy to measure the kinetics of R18 dequenching and thus single hemifusion events initiated by a fast low-pH trigger. These studies revealed unexpectedly long lag phases between pH change and hemifusion. In addition, we found that EGFP fluorescence in the virus was quenched upon acidification, indicating that protons could access the virus core, possibly through a proton channel. In a fraction of virus particles, EGFP fluorescence was recovered, presumably after fusion-pore formation and exposure of the core to the physiological pH of the host-cell cytosol. Given that virus-encoded cation channels play a crucial role in the life cycle of many viruses and can serve as antiviral drug targets, further investigations into a potential VACV viroporin are justified. Our findings indicate that the microfluidic device described may be highly beneficial to similar studies requiring fast kinetic measurements. PMID:23870263

Study on Hybrid Image Search Technology Based on Texts and Contents

NASA Astrophysics Data System (ADS)

Wang, H. T.; Ma, F. L.; Yan, C.; Pan, H.

2018-05-01

Image search was studied first here based on texts and contents, respectively. The text-based image feature extraction was put forward by integrating the statistical and topic features in view of the limitation of extraction of keywords only by means of statistical features of words. On the other hand, a search-by-image method was put forward based on multi-feature fusion in view of the imprecision of the content-based image search by means of a single feature. The layered-searching method depended on primarily the text-based image search method and additionally the content-based image search was then put forward in view of differences between the text-based and content-based methods and their difficult direct fusion. The feasibility and effectiveness of the hybrid search algorithm were experimentally verified.

Fusion-fission Study at JAEA for Heavy-element Synthesis

NASA Astrophysics Data System (ADS)

Nishio, K.

Fission fragment mass distributions were measured in the heavy-ion induced fission using 238U target nucleus. The mass distribu- tions changed drastically with incident energy. The results are explained by a change of the ratio between fusion and qasifission with nuclear orientation. A calculation based on a fluctuation dissipation model reproduced the mass distributions and their inci- dent energy dependence. Fusion probability was determined in the analysis. Evaporation residue cross sections were calculated with a statistical model in the reactions of 30Si+238U and 34S+238U using the obtained fusion probability in the entrance channel. The results agree with the measured cross sections of 263,264Sg and 267,268Hs, produced by 30Si+238U and 34S+238U, respectively. It is also suggested that the sub-barrier energies can be used for heavy element synthesis.

SCOPE in Cataloguing.

ERIC Educational Resources Information Center

Tom, Ellen; Reed, Sue

This report describes the Systematic Computerized Processing in Cataloguing system (SCOPE), an automated system for the catalog department of a university library. The system produces spine labels, pocket labels, book cards for the circulation system, catalog cards including shelf list, main entry, subject and added entry cards, statistics, an…

Synthesis and characterization of a Eu-DTPA-PEGO-MSH(4) derivative for evaluation of binding of multivalent molecules to melanocortin receptors.

PubMed

Xu, Liping; Vagner, Josef; Alleti, Ramesh; Rao, Venkataramanarao; Jagadish, Bhumasamudram; Morse, David L; Hruby, Victor J; Gillies, Robert J; Mash, Eugene A

2010-04-15

A labeled variant of MSH(4), a tetrapeptide that binds to the human melanocortin 4 receptor (hMC4R) with low microM affinity, was prepared by solid-phase synthesis methods, purified, and characterized. The labeled ligand, Eu-DTPA-PEGO-His-dPhe-Arg-Trp-NH(2), exhibited a K(d) for hMC4R of 9.1+/-1.4 microM, approximately 10-fold lower affinity than the parental ligand. The labeled MSH(4) derivative was employed in a competitive binding assay to characterize the interactions of hMC4R with monovalent and divalent MSH(4) constructs derived from squalene. The results were compared with results from a similar assay that employed a more potent labeled ligand, Eu-DTPA-NDP-alpha-MSH. While results from the latter assay reflected only statistical effects, results from the former assay reflected a mixture of statistical, proximity, and/or cooperative binding effects. Copyright 2010 Elsevier Ltd. All rights reserved.

Optimization of Statistical Methods Impact on Quantitative Proteomics Data.

PubMed

Pursiheimo, Anna; Vehmas, Anni P; Afzal, Saira; Suomi, Tomi; Chand, Thaman; Strauss, Leena; Poutanen, Matti; Rokka, Anne; Corthals, Garry L; Elo, Laura L

2015-10-02

As tools for quantitative label-free mass spectrometry (MS) rapidly develop, a consensus about the best practices is not apparent. In the work described here we compared popular statistical methods for detecting differential protein expression from quantitative MS data using both controlled experiments with known quantitative differences for specific proteins used as standards as well as "real" experiments where differences in protein abundance are not known a priori. Our results suggest that data-driven reproducibility-optimization can consistently produce reliable differential expression rankings for label-free proteome tools and are straightforward in their application.

Comparative effectiveness of open versus minimally invasive sacroiliac joint fusion.

PubMed

Ledonio, Charles Gt; Polly, David W; Swiontkowski, Marc F; Cummings, John T

2014-01-01

The mainstay of sacroiliac joint disruption/degenerative sacroiliitis therapy has been nonoperative management. This nonoperative management often includes a regimen of physical therapy, chiropractic treatment, therapeutic injections, and possibly radiofrequency ablation at the discretion of the treating physician. When these clinical treatments fail, sacroiliac joint fusion has been recommended as the standard treatment. Open and minimally invasive (MIS) surgical techniques are typical procedures. This study aims to compare the perioperative measures and Oswestry Disability Index (ODI) outcomes associated with each of these techniques. A comparative retrospective chart review of patients with sacroiliac joint fusion and a minimum of 1 year of follow-up was performed. Perioperative measures and ODI scores were compared using the Fisher's exact test and two nonparametric tests, ie, the Mann-Whitney U test and the Wilcoxon signed-rank test. The results are presented as percent or median with range, as appropriate. Forty-nine patients from two institutions underwent sacroiliac joint fusion between 2006 and 2012. Ten patients were excluded because of incomplete data, leaving 39 evaluable patients, of whom 22 underwent open and 17 underwent MIS sacroiliac joint fusion. The MIS group was significantly older (median age 66 [39-82] years) than the open group (median age 51 [34-74] years). Surgical time and hospital stay were significantly shorter in the MIS group than in the open group. Preoperative ODI was significantly greater in the open group (median 64 [44-78]) than in the MIS group (median 53 [14-84]). Postoperative improvement in ODI was statistically significant within and between groups, with MIS resulting in greater improvement. The open and MIS sacroiliac joint fusion techniques resulted in statistically and clinically significant improvement for patients with degenerative sacroiliitis refractory to nonoperative management. However, the number of patients reaching the minimal clinically important difference and those showing overall improvement were greater in the MIS group.

Comparative effectiveness of open versus minimally invasive sacroiliac joint fusion

PubMed Central

Ledonio, Charles GT; Polly, David W; Swiontkowski, Marc F; Cummings, John T

2014-01-01

Background The mainstay of sacroiliac joint disruption/degenerative sacroiliitis therapy has been nonoperative management. This nonoperative management often includes a regimen of physical therapy, chiropractic treatment, therapeutic injections, and possibly radiofrequency ablation at the discretion of the treating physician. When these clinical treatments fail, sacroiliac joint fusion has been recommended as the standard treatment. Open and minimally invasive (MIS) surgical techniques are typical procedures. This study aims to compare the perioperative measures and Oswestry Disability Index (ODI) outcomes associated with each of these techniques. Methods A comparative retrospective chart review of patients with sacroiliac joint fusion and a minimum of 1 year of follow-up was performed. Perioperative measures and ODI scores were compared using the Fisher’s exact test and two nonparametric tests, ie, the Mann–Whitney U test and the Wilcoxon signed-rank test. The results are presented as percent or median with range, as appropriate. Results Forty-nine patients from two institutions underwent sacroiliac joint fusion between 2006 and 2012. Ten patients were excluded because of incomplete data, leaving 39 evaluable patients, of whom 22 underwent open and 17 underwent MIS sacroiliac joint fusion. The MIS group was significantly older (median age 66 [39–82] years) than the open group (median age 51 [34–74] years). Surgical time and hospital stay were significantly shorter in the MIS group than in the open group. Preoperative ODI was significantly greater in the open group (median 64 [44–78]) than in the MIS group (median 53 [14–84]). Postoperative improvement in ODI was statistically significant within and between groups, with MIS resulting in greater improvement. Conclusion The open and MIS sacroiliac joint fusion techniques resulted in statistically and clinically significant improvement for patients with degenerative sacroiliitis refractory to nonoperative management. However, the number of patients reaching the minimal clinically important difference and those showing overall improvement were greater in the MIS group. PMID:24940087

Spinal Implant Density and Postoperative Lumbar Lordosis as Predictors for the Development of Proximal Junctional Kyphosis in Adult Spinal Deformity.

PubMed

McClendon, Jamal; Smith, Timothy R; Sugrue, Patrick A; Thompson, Sara E; O'Shaughnessy, Brian A; Koski, Tyler R

2016-11-01

To evaluate spinal implant density and proximal junctional kyphosis (PJK) in adult spinal deformity (ASD). Consecutive patients with ASD receiving ≥5 level fusions were retrospectively analyzed between 2007 and 2010. ASD, elective fusions, minimum 2-year follow-up. age <18 years, neuromuscular or congenital scoliosis, cervical or cervicothoracic fusions, nonelective conditions (infection, tumor, trauma). Instrumented fusions were classified by the Scoliosis Research Society-Schwab ASD classification. Statistical analysis consisted of descriptives (measures of central tendency, dispersion, frequencies), independent Student t tests, χ 2 , analysis of variance, and logistic regression to determine association of implant density [(number of screws + number of hooks)/surgical levels of fusion] and PJK. Mean and median follow-up was 2.8 and 2.7 years, respectively. Eighty-three patients (17 male, 66 female) with a mean age of 59.7 years (standard deviation, 10.3) were analyzed. Mean body mass index (BMI) was 29.5 kg/m 2 (range, 18-56 kg/m 2 ) with mean preoperative Oswestry Disability Index of 48.67 (range, 6-86) and mean preoperative sagittal vertical axis of 8.42. The mean levels fused were 9.95 where 54 surgeries had interbody fusion. PJK prevalence was 21.7%, and pseudoarthrosis was 19.3%. Mean postoperative Oswestry Disability Index was 27.4 (range, 0-74). Independent Student t tests showed that PJK was not significant for age, gender, BMI, rod type, mean postoperative sagittal vertical axis, or Scoliosis Research Society-Schwab ASD classification; but iliac fixation approached significance (P = 0.077). Implant density and postoperative lumbar lordosis (LL) were predictors for PJK (P = 0.018 and 0.045, respectively). Controlling for age, BMI, and gender, postoperative LL (not implant density) continued to show significance in multivariate logistic regression model. PJK, although influenced by a multitude of factors, may be statistically related to implant density and LL. Copyright © 2016. Published by Elsevier Inc.

Information theoretic partitioning and confidence based weight assignment for multi-classifier decision level fusion in hyperspectral target recognition applications

NASA Astrophysics Data System (ADS)

Prasad, S.; Bruce, L. M.

2007-04-01

There is a growing interest in using multiple sources for automatic target recognition (ATR) applications. One approach is to take multiple, independent observations of a phenomenon and perform a feature level or a decision level fusion for ATR. This paper proposes a method to utilize these types of multi-source fusion techniques to exploit hyperspectral data when only a small number of training pixels are available. Conventional hyperspectral image based ATR techniques project the high dimensional reflectance signature onto a lower dimensional subspace using techniques such as Principal Components Analysis (PCA), Fisher's linear discriminant analysis (LDA), subspace LDA and stepwise LDA. While some of these techniques attempt to solve the curse of dimensionality, or small sample size problem, these are not necessarily optimal projections. In this paper, we present a divide and conquer approach to address the small sample size problem. The hyperspectral space is partitioned into contiguous subspaces such that the discriminative information within each subspace is maximized, and the statistical dependence between subspaces is minimized. We then treat each subspace as a separate source in a multi-source multi-classifier setup and test various decision fusion schemes to determine their efficacy. Unlike previous approaches which use correlation between variables for band grouping, we study the efficacy of higher order statistical information (using average mutual information) for a bottom up band grouping. We also propose a confidence measure based decision fusion technique, where the weights associated with various classifiers are based on their confidence in recognizing the training data. To this end, training accuracies of all classifiers are used for weight assignment in the fusion process of test pixels. The proposed methods are tested using hyperspectral data with known ground truth, such that the efficacy can be quantitatively measured in terms of target recognition accuracies.

Selection of Fusion Levels Using the Fulcrum Bending Radiograph for the Management of Adolescent Idiopathic Scoliosis Patients with Alternate Level Pedicle Screw Strategy: Clinical Decision-making and Outcomes.

PubMed

Samartzis, Dino; Leung, Yee; Shigematsu, Hideki; Natarajan, Deepa; Stokes, Oliver; Mak, Kin-Cheung; Yao, Guanfeng; Luk, Keith D K; Cheung, Kenneth M C

2015-01-01

Selecting fusion levels based on the Luk et al criteria for operative management of thoracic adolescent idiopathic scoliosis (AIS) with hook and hybrid systems yields acceptable curve correction and balance parameters; however, it is unknown whether utilizing a purely pedicle screw strategy is effective. Utilizing the fulcrum bending radiographic (FBR) to assess curve flexibility to select fusion levels, the following study assessed the efficacy of pedicle screw fixation with alternate level screw strategy (ALSS) for thoracic AIS. A retrospective study with prospective radiographic data collection/analyses (preoperative, postoperative 1-week and minimum 2-year follow-up) of 28 operative thoracic AIS patients undergoing ALSS was performed. Standing coronal/sagittal and FBR Cobb angles, FBR flexibility, fulcrum bending correction index (FBCI), trunkal shift, radiographic shoulder height (RSH), and list were assessed on x-rays. Fusion level selection was based on the Luk et al criteria and compared to conventional techniques. In the primary curve, the mean preoperative and postoperative 1 week and last follow-up standing coronal Cobb angles were 59.9, 17.2 and 20.0 degrees, respectively. Eighteen patients (64.3%) had distal levels saved (mean: 1.6 levels) in comparison to conventional techniques. Mean immediate and last follow-up FBCIs were 122.6% and 115.0%, respectively. Sagittal alignment did not statistically differ between any assessment intervals (p>0.05). A decrease in trunkal shift was noted from preoperative to last follow-up (p = 0.003). No statistically significant difference from preoperative to last follow-up was noted in RSH and list (p>0.05). No "add-on" of other vertebra or decompensation was noted and all patients achieved fusion. This is the first report to note that using the FBR for decision-making in selecting fusion levels in thoracic AIS patients undergoing management with pedicle screw constructs (e.g. ALSS) is a cost-effective strategy that can achieve clinically-relevant deformity correction that is maintained and without compromising fusion levels.

Mass spectra and fusion cross sections for /sup 20/Ne+/sup 24/Mg interaction at 55 and 85 MeV

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

Grotowski, K.; Belery, P.; Delbar, T.

1981-06-01

Inclusive ..gamma.. spectra from the /sup 20/Ne+/sup 24/Mg interaction have been measured using 55- and 85-MeV /sup 20/Ne ions. The identification of ..gamma.. lines allows the determination of mass spectra in the region 12< or =A< or =43. Experimental results are compared with statistical model calculations. The total reaction and fusion cross sections are extracted. Cross sections for inelastic scattering, few nucleon transfers, and deep inelastic scattering are estimated.

Fusion of multiscale wavelet-based fractal analysis on retina image for stroke prediction.

PubMed

Che Azemin, M Z; Kumar, Dinesh K; Wong, T Y; Wang, J J; Kawasaki, R; Mitchell, P; Arjunan, Sridhar P

2010-01-01

In this paper, we present a novel method of analyzing retinal vasculature using Fourier Fractal Dimension to extract the complexity of the retinal vasculature enhanced at different wavelet scales. Logistic regression was used as a fusion method to model the classifier for 5-year stroke prediction. The efficacy of this technique has been tested using standard pattern recognition performance evaluation, Receivers Operating Characteristics (ROC) analysis and medical prediction statistics, odds ratio. Stroke prediction model was developed using the proposed system.

Distributed video data fusion and mining

NASA Astrophysics Data System (ADS)

Chang, Edward Y.; Wang, Yuan-Fang; Rodoplu, Volkan

2004-09-01

This paper presents an event sensing paradigm for intelligent event-analysis in a wireless, ad hoc, multi-camera, video surveillance system. In particilar, we present statistical methods that we have developed to support three aspects of event sensing: 1) energy-efficient, resource-conserving, and robust sensor data fusion and analysis, 2) intelligent event modeling and recognition, and 3) rapid deployment, dynamic configuration, and continuous operation of the camera networks. We outline our preliminary results, and discuss future directions that research might take.

Enhanced disease characterization through multi network functional normalization in fMRI.

PubMed

Çetin, Mustafa S; Khullar, Siddharth; Damaraju, Eswar; Michael, Andrew M; Baum, Stefi A; Calhoun, Vince D

2015-01-01

Conventionally, structural topology is used for spatial normalization during the pre-processing of fMRI. The co-existence of multiple intrinsic networks which can be detected in the resting brain are well-studied. Also, these networks exhibit temporal and spatial modulation during cognitive task vs. rest which shows the existence of common spatial excitation patterns between these identified networks. Previous work (Khullar et al., 2011) has shown that structural and functional data may not have direct one-to-one correspondence and functional activation patterns in a well-defined structural region can vary across subjects even for a well-defined functional task. The results of this study and the existence of the neural activity patterns in multiple networks motivates us to investigate multiple resting-state networks as a single fusion template for functional normalization for multi groups of subjects. We extend the previous approach (Khullar et al., 2011) by co-registering multi group of subjects (healthy control and schizophrenia patients) and by utilizing multiple resting-state networks (instead of just one) as a single fusion template for functional normalization. In this paper we describe the initial steps toward using multiple resting-state networks as a single fusion template for functional normalization. A simple wavelet-based image fusion approach is presented in order to evaluate the feasibility of combining multiple functional networks. Our results showed improvements in both the significance of group statistics (healthy control and schizophrenia patients) and the spatial extent of activation when a multiple resting-state network applied as a single fusion template for functional normalization after the conventional structural normalization. Also, our results provided evidence that the improvement in significance of group statistics lead to better accuracy results for classification of healthy controls and schizophrenia patients.

Benchmarking quantitative label-free LC-MS data processing workflows using a complex spiked proteomic standard dataset.

PubMed

Ramus, Claire; Hovasse, Agnès; Marcellin, Marlène; Hesse, Anne-Marie; Mouton-Barbosa, Emmanuelle; Bouyssié, David; Vaca, Sebastian; Carapito, Christine; Chaoui, Karima; Bruley, Christophe; Garin, Jérôme; Cianférani, Sarah; Ferro, Myriam; Van Dorssaeler, Alain; Burlet-Schiltz, Odile; Schaeffer, Christine; Couté, Yohann; Gonzalez de Peredo, Anne

2016-01-30

Proteomic workflows based on nanoLC-MS/MS data-dependent-acquisition analysis have progressed tremendously in recent years. High-resolution and fast sequencing instruments have enabled the use of label-free quantitative methods, based either on spectral counting or on MS signal analysis, which appear as an attractive way to analyze differential protein expression in complex biological samples. However, the computational processing of the data for label-free quantification still remains a challenge. Here, we used a proteomic standard composed of an equimolar mixture of 48 human proteins (Sigma UPS1) spiked at different concentrations into a background of yeast cell lysate to benchmark several label-free quantitative workflows, involving different software packages developed in recent years. This experimental design allowed to finely assess their performances in terms of sensitivity and false discovery rate, by measuring the number of true and false-positive (respectively UPS1 or yeast background proteins found as differential). The spiked standard dataset has been deposited to the ProteomeXchange repository with the identifier PXD001819 and can be used to benchmark other label-free workflows, adjust software parameter settings, improve algorithms for extraction of the quantitative metrics from raw MS data, or evaluate downstream statistical methods. Bioinformatic pipelines for label-free quantitative analysis must be objectively evaluated in their ability to detect variant proteins with good sensitivity and low false discovery rate in large-scale proteomic studies. This can be done through the use of complex spiked samples, for which the "ground truth" of variant proteins is known, allowing a statistical evaluation of the performances of the data processing workflow. We provide here such a controlled standard dataset and used it to evaluate the performances of several label-free bioinformatics tools (including MaxQuant, Skyline, MFPaQ, IRMa-hEIDI and Scaffold) in different workflows, for detection of variant proteins with different absolute expression levels and fold change values. The dataset presented here can be useful for tuning software tool parameters, and also testing new algorithms for label-free quantitative analysis, or for evaluation of downstream statistical methods. Copyright © 2015 Elsevier B.V. All rights reserved.

Posterolateral lumbar fusion using Escherichia coli-derived rhBMP-2/hydroxyapatite in the mini pig.

PubMed

Kong, Chang-Bae; Lee, Jae Hyup; Baek, Hae-Ri; Lee, Choon-Ki; Chang, Bong-Soon

2014-12-01

Hydroxyapatite (HA) is used as a bone graft extender for posterolateral spinal fusion in human. It is also useful as a recombinant human bone morphogenetic protein (rhBMP)-2 carrier because of its high affinity for rhBMP-2. To assess the osteoinductivity of Escherichia coli-derived rhBMP-2 (E-BMP-2) using HA granules as a carrier and to evaluate the bone-forming ability depending on the different dosages of E-BMP-2. A mini-pig lumbar posterolateral fusion model using microcomputed tomography (μCT) scanning. Thirty-one adult male mini pigs were randomized into a single control group (n=8) without E-BMP-2 and two experimental groups with two different doses of E-BMP-2 (1 mg per side, n=8 and 3 mg per side, n=15). Outcome was measured by plain radiography, manual palpation, CT, three-dimensional μCT, and histologic examinations. Bilateral intertransverse process arthrodesis was performed, and E-BMP-2 (0, 1.0, 3.0 mg per side) was implanted into the intertransverse space using HA granules as a carrier. Three mini pigs were removed because of death. Among 28 experimental subjects, 19 animals achieved solid bony union. The fusion rates were 37.5% for control group, 71.4% for 1 mg group, and 84.6% for 3 mg group. Fusion rates were significantly different among groups (p=.031). However, there was no statistically significant difference in fusion rates between 1 and 3 mg groups (p=.587). Thirty-eight intertransverse fusion masses of 19 subjects underwent μCT scanning. The bone volumes determined by μCT were 12,603±3,240 mm(3) for control group, 18,718±3,000 mm(3) for 1 mg group, and 26,768±7,256 mm(3) for 3 mg group, and the difference between groups was statistically significant (p<.001). This study shows that E-BMP-2 has osteoinductive activity in dose-dependent fashion, and porous HA granule is suitable for E-BMP-2 carrier in a porcine posterolateral fusion model. These preliminary findings suggest that E-BMP-2-adsorbed porous HA granules could be a novel effective bone graft substitute. Copyright © 2014 Elsevier Inc. All rights reserved.

Multiple-labelling immunoEM using different sizes of colloidal gold: alternative approaches to test for differential distribution and colocalization in subcellular structures.

PubMed

Mayhew, Terry M; Lucocq, John M

2011-03-01

Various methods for quantifying cellular immunogold labelling on transmission electron microscope thin sections are currently available. All rely on sound random sampling principles and are applicable to single immunolabelling across compartments within a given cell type or between different experimental groups of cells. Although methods are also available to test for colocalization in double/triple immunogold labelling studies, so far, these have relied on making multiple measurements of gold particle densities in defined areas or of inter-particle nearest neighbour distances. Here, we present alternative two-step approaches to codistribution and colocalization assessment that merely require raw counts of gold particles in distinct cellular compartments. For assessing codistribution over aggregate compartments, initial statistical evaluation involves combining contingency table and chi-squared analyses to provide predicted gold particle distributions. The observed and predicted distributions allow testing of the appropriate null hypothesis, namely, that there is no difference in the distribution patterns of proteins labelled by different sizes of gold particle. In short, the null hypothesis is that of colocalization. The approach for assessing colabelling recognises that, on thin sections, a compartment is made up of a set of sectional images (profiles) of cognate structures. The approach involves identifying two groups of compartmental profiles that are unlabelled and labelled for one gold marker size. The proportions in each group that are also labelled for the second gold marker size are then compared. Statistical analysis now uses a 2 × 2 contingency table combined with the Fisher exact probability test. Having identified double labelling, the profiles can be analysed further in order to identify characteristic features that might account for the double labelling. In each case, the approach is illustrated using synthetic and/or experimental datasets and can be refined to correct observed labelling patterns to specific labelling patterns. These simple and efficient approaches should be of more immediate utility to those interested in codistribution and colocalization in multiple immunogold labelling investigations.

Antigen Binding and Site-Directed Labeling of Biosilica-Immobilized Fusion Proteins Expressed in Diatoms.

PubMed

Ford, Nicole R; Hecht, Karen A; Hu, DeHong; Orr, Galya; Xiong, Yijia; Squier, Thomas C; Rorrer, Gregory L; Roesijadi, Guritno

2016-03-18

The diatom Thalassiosira pseudonana was genetically modified to express biosilica-targeted fusion proteins comprising either enhanced green fluorescent protein (EGFP) or single chain antibodies engineered with a tetracysteine tagging sequence. Of interest were the site-specific binding of (1) the fluorescent biarsenical probe AsCy3 and AsCy3e to the tetracysteine tagged fusion proteins and (2) high and low molecular mass antigens, the Bacillus anthracis surface layer protein EA1 or small molecule explosive trinitrotoluene (TNT), to biosilica-immobilized single chain antibodies. Analysis of biarsenical probe binding using fluorescence and structured illumination microscopy indicated differential colocalization with EGFP in nascent and mature biosilica, supporting the use of either EGFP or bound AsCy3 and AsCy3e in studying biosilica maturation. Large increases in the lifetime of a fluorescent analogue of TNT upon binding single chain antibodies provided a robust signal capable of discriminating binding to immobilized antibodies in the transformed frustule from nonspecific binding to the biosilica matrix. In conclusion, our results demonstrate an ability to engineer diatoms to create antibody-functionalized mesoporous silica able to selectively bind chemical and biological agents for the development of sensing platforms.

Psychometric properties of revised Thought-Action Fusion questionnaire (TAF-R) in an Iranian population.

PubMed

Pourfaraj, Majid; Mohammadi, Nourallah; Taghavi, Mohammadreza

2008-12-01

The purpose of this study is to examine the psychometric properties of Thought-Action Fusion revised scale (TAF-R; Amir, N., freshman, M., Ramsey, B., Neary, E., & Brigidi, B. (2001). Thought-action fusion in individuals with OCD symptoms. Behaviour Research and Therapy, 39, 765-776) in a sample of 565 (321 female) students of Shiraz university. The results of factor analysis with using varimax rotation yielded eight factors that explained 80% variances of total scale. These factors are labeled: moral TAF, responsibility for positive thoughts, likelihood negative events, likelihood positive events, responsibility for negative thoughts, responsibility for harm avoidance, likelihood harm avoidance and likelihood self, respectively. The reliability coefficients of total scale are calculated by two methods: internal consistency and test-retest, which were 0.81 and 0.61, respectively. Concurrent validity showed that TAF-R scores positively and significantly correlate with responsibility, guilt and obsessive-compulsive symptoms. Confirming the expectations, there were people with high obsessive-compulsive symptoms having higher TAF-R scores than those with low symptoms. Moreover, subscales-total correlations showed that the correlations between subscales were low, but subscales correlating with total score of TAF-R were moderated.

Average Throughput Performance of Myopic Policy in Energy Harvesting Wireless Sensor Networks.

PubMed

Gul, Omer Melih; Demirekler, Mubeccel

2017-09-26

This paper considers a single-hop wireless sensor network where a fusion center collects data from M energy harvesting wireless sensors. The harvested energy is stored losslessly in an infinite-capacity battery at each sensor. In each time slot, the fusion center schedules K sensors for data transmission over K orthogonal channels. The fusion center does not have direct knowledge on the battery states of sensors, or the statistics of their energy harvesting processes. The fusion center only has information of the outcomes of previous transmission attempts. It is assumed that the sensors are data backlogged, there is no battery leakage and the communication is error-free. An energy harvesting sensor can transmit data to the fusion center whenever being scheduled only if it has enough energy for data transmission. We investigate average throughput of Round-Robin type myopic policy both analytically and numerically under an average reward (throughput) criterion. We show that Round-Robin type myopic policy achieves optimality for some class of energy harvesting processes although it is suboptimal for a broad class of energy harvesting processes.

Calculation of Excitation Function of Some Structural Fusion Material for (n, p) Reactions up to 25 MeV

NASA Astrophysics Data System (ADS)

Reshid, Tarik S.

2013-04-01

Fusion serves an inexhaustible energy for humankind. Although there have been significant research and development studies on the inertial and magnetic fusion reactor technology, Furthermore, there are not radioactive nuclear waste problems in the fusion reactors. In this study, (n, p) reactions for some structural fusion materials such as 27Al, 51V, 52Cr, 55Mn and 56Fe have been investigated. The new calculations on the excitation functions of 27 Al(n, p) 27 Mg, 51 V(n, p) 51 Ti, 52 Cr(n, p) 52 V, 55 Mn(n, p) 55 Cr and 56 Fe(n, p) 56 Mn reactions have been carried out up to 30 MeV incident neutron energy. Statistical model calculations, based on the Hauser-Feshbach formalism, have been carried out using the TALYS-1.0 and were compared with available experimental data in the literature and with ENDF/B-VII, T = 300 K; JENDL-3.3, T = 300 K and JEFF-3.1, T = 300 K evaluated libraries.

Average Throughput Performance of Myopic Policy in Energy Harvesting Wireless Sensor Networks

PubMed Central

Demirekler, Mubeccel

2017-01-01

This paper considers a single-hop wireless sensor network where a fusion center collects data from M energy harvesting wireless sensors. The harvested energy is stored losslessly in an infinite-capacity battery at each sensor. In each time slot, the fusion center schedules K sensors for data transmission over K orthogonal channels. The fusion center does not have direct knowledge on the battery states of sensors, or the statistics of their energy harvesting processes. The fusion center only has information of the outcomes of previous transmission attempts. It is assumed that the sensors are data backlogged, there is no battery leakage and the communication is error-free. An energy harvesting sensor can transmit data to the fusion center whenever being scheduled only if it has enough energy for data transmission. We investigate average throughput of Round-Robin type myopic policy both analytically and numerically under an average reward (throughput) criterion. We show that Round-Robin type myopic policy achieves optimality for some class of energy harvesting processes although it is suboptimal for a broad class of energy harvesting processes. PMID:28954420

M2-brane surface operators and gauge theory dualities in Toda

NASA Astrophysics Data System (ADS)

Gomis, Jaume; Le Floch, Bruno

2016-04-01

We give a microscopic two dimensional {N} = (2, 2) gauge theory description of arbitrary M2-branes ending on N f M5-branes wrapping a punctured Riemann surface. These realize surface operators in four dimensional {N} = 2 field theories. We show that the expectation value of these surface operators on the sphere is captured by a Toda CFT correlation function in the presence of an additional degenerate vertex operator labelled by a representation {R} of SU( N f ), which also labels M2-branes ending on M5-branes. We prove that symmetries of Toda CFT correlators provide a geometric realization of dualities between two dimensional gauge theories, including {N} = (2, 2) analogues of Seiberg and Kutasov-Schwimmer dualities. As a bonus, we find new explicit conformal blocks, braiding matrices, and fusion rules in Toda CFT.

Novel chromosomal rearrangements and break points at the t(6;9) in salivary adenoid cystic carcinoma: association with MYB-NFIB chimeric fusion, MYB expression, and clinical outcome.

PubMed

Mitani, Yoshitsugu; Rao, Pulivarthi H; Futreal, P Andrew; Roberts, Dianna B; Stephens, Philip J; Zhao, Yi-Jue; Zhang, Li; Mitani, Mutsumi; Weber, Randal S; Lippman, Scott M; Caulin, Carlos; El-Naggar, Adel K

2011-11-15

To investigate the molecular genetic heterogeneity associated with the t(6:9) in adenoid cystic carcinoma (ACC) and correlate the findings with patient clinical outcome. Multimolecular and genetic techniques complemented with massive pair-ended sequencing and single-nucleotide polymorphism array analyses were used on tumor specimens from 30 new and 52 previously analyzed fusion transcript-negative ACCs by reverse transcriptase PCR (RT-PCR). MYB mRNA expression level was determined by quantitative RT-PCR. The results of 102 tumors (30 new and 72 previously reported cases) were correlated with the clinicopathologic factors and patients' survival. The FISH analysis showed 34 of 82 (41.5%) fusion-positive tumors and molecular techniques identified fusion transcripts in 21 of the 82 (25.6%) tumors. Detailed FISH analysis of 11 out the 15 tumors with gene fusion without transcript formation showed translocation of NFIB sequences to proximal or distal sites of the MYB gene. Massive pair-end sequencing of a subset of tumors confirmed the proximal translocation to an NFIB sequence and led to the identification of a new fusion gene (NFIB-AIG1) in one of the tumors. Overall, MYB-NFIB gene fusion rate by FISH was in 52.9% whereas fusion transcript forming incidence was 38.2%. Significant statistical association between the 5' MYB transcript expression and patient survival was found. We conclude that: (i) t(6;9) results in complex genetic and molecular alterations in ACC, (ii) MYB-NFIB gene fusion may not always be associated with chimeric transcript formation, (iii) noncanonical MYB-NFIB gene fusions occur in a subset of tumors, (iv) high MYB expression correlates with worse patient survival.

Novel Chromosomal Rearrangements and breakpoints at the t(6;9) in Salivary Adenoid Cystic Carcinoma: association with MYB-NFIB chimeric fusion, MYB expression, and clinical outcome

PubMed Central

Mitani, Yoshitsugu; Rao, Pulivarthi H.; Futreal, P. Andrew; Roberts, Dianna B.; Stephens, Philip J.; Zhao, Yi-Jue; Zhang, Li; Mitani, Mutsumi; Weber, Randal S.; Lippman, Scott M.; Caulin, Carlos; El-Naggar, Adel K.

2011-01-01

Objective To investigate the molecular-genetic heterogeneity associated with the t(6:9) in adenoid cystic carcinoma (ACC) and correlate the findings with patient clinical outcome. Experimental Design Multi-molecular and genetic techniques complemented with massive pair-ended sequencing and SNP array analyses were used on tumor specimens from 30 new and 52 previously RT-PCR analyzed fusion transcript negative ACCs. MYB mRNA expression level was determined by quantitative RT-PCR. The results of 102 tumors (30 new and 72 previously reported cases) were correlated with the clinicopathologic factors and patients’ survival. Results The FISH analysis showed 34/82 (41.5%) fusion positive tumors and molecular techniques identified fusion transcripts in 21 of the 82 (25.6%) tumors. Detailed FISH analysis of 11 out the 15 tumors with gene fusion without transcript formation showed translocation of NFIB sequences to proximal or distal sites of the MYB gene. Massive pair-end sequencing of a subset of tumors confirmed the proximal translocation to an NFIB sequence and led to the identification of a new fusion gene (NFIB-AIG1) in one of the tumors. Overall, MYB-NFIB gene fusion rate by FISH was in 52.9% while fusion transcript forming incidence was 38.2%. Significant statistical association between the 5′ MYB transcript expression and patient survival was found. Conclusions We conclude that: 1) t(6;9) results in a complex genetic and molecular alterations in ACC, 2) MYB-NFIB gene fusion may not always be associated with chimeric transcript formation, 3) non-canonical MYB, NFIB gene fusions occur in a subset of tumors, 4) high MYB expression correlates with worse patient survival. PMID:21976542

Data Fusion for a Vision-Radiological System: a Statistical Calibration Algorithm

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

Enqvist, Andreas; Koppal, Sanjeev; Riley, Phillip

2015-07-01

Presented here is a fusion system based on simple, low-cost computer vision and radiological sensors for tracking of multiple objects and identifying potential radiological materials being transported or shipped. The main focus of this work is the development of calibration algorithms for characterizing the fused sensor system as a single entity. There is an apparent need for correcting for a scene deviation from the basic inverse distance-squared law governing the detection rates even when evaluating system calibration algorithms. In particular, the computer vision system enables a map of distance-dependence of the sources being tracked, to which the time-dependent radiological datamore » can be incorporated by means of data fusion of the two sensors' output data. (authors)« less

[Targeted detecting HER2 expression with recombinant anti HER2 ScFv-GFP fusion antibody].

PubMed

Gao, Guohui; Chen, Chong; Yang, Yanmei; Yang, Han; Wang, Jindan; Zheng, Yi; Huang, Qidi; Hu, Xiaoqu

2012-08-01

To verify the reliability of targeted detecting HER2 positive cancer cells and clinical pathological tissue specimens with a recombinant anti HER2 single chain antibody in single chain Fv fragment (scFv) format, we have constructed the fusion variable regions of the ScFv specific for HER2/neu. labeled a green-fluorescent protein(GFP). The humanized recombinant Anti HER2 ScFv-GFP gene was inserted into pFast Bac HT A, and expressed in insect cells sf9. Then the recombinant fusion protein Anti HER2 ScFv-GFP was properly purified with Ni2+-NTA affinity chromatography from the infected sf9 cells used to test the specificity of the fusion antibody for HER2 positive cancer cells. Firstly, the purified antibody incubated with HER2 positive breast cancer cells SKBR3, BT474 and HER2 negative breast cancer cells MCF7 for 12 h/24 h/48 h at 37 degrees C, in order to confirm targeted detecting HER2 positive breast cancer cells by Laser Confocal Microscopy. Furthermore, the same clinical pathological tissue samples were assessed by immunohistochemistry (IHC) and the fusion antibody Anti HER2 ScFv-GFP in the meanwhile. The data obtained indicated that the recombinant eukaryotic expression plasmid pFast Bac HT A/Anti HER2 ScFv-GFP was constructed successfully In addition, obvious green fluorescent was observed in insect cells sf9. When the purified fusion antibody was incubated with different cancer cells, much more green fluorescent was observed on the surface of the HER2 positive cancer cells SKBR3 and BT474. In contrast, no green fluorescent on the surface of the HER2 negative cancer cells MCF7 was detected. The concentration of the purified fusion antibody was 115.5 microg/mL, of which protein relative molecular weight was 60 kDa. The analysis showed the purity was about 97% and the titer was about 1:64. The detection results of IHC and fusion antibody testing indicated the conformity. In summary, the study showed that the new fusion antibody Anti HER2 ScFv-GFP can test HER2 positive cancer cells, indicating a potential candidate method for clinical HER2 positive specimens detection.

Use of the Nanofitin Alternative Scaffold as a GFP-Ready Fusion Tag

PubMed Central

Huet, Simon; Gorre, Harmony; Perrocheau, Anaëlle; Picot, Justine; Cinier, Mathieu

2015-01-01

With the continuous diversification of recombinant DNA technologies, the possibilities for new tailor-made protein engineering have extended on an on-going basis. Among these strategies, the use of the green fluorescent protein (GFP) as a fusion domain has been widely adopted for cellular imaging and protein localization. Following the lead of the direct head-to-tail fusion of GFP, we proposed to provide additional features to recombinant proteins by genetic fusion of artificially derived binders. Thus, we reported a GFP-ready fusion tag consisting of a small and robust fusion-friendly anti-GFP Nanofitin binding domain as a proof-of-concept. While limiting steric effects on the carrier, the GFP-ready tag allows the capture of GFP or its blue (BFP), cyan (CFP) and yellow (YFP) alternatives. Here, we described the generation of the GFP-ready tag from the selection of a Nanofitin variant binding to the GFP and its spectral variants with a nanomolar affinity, while displaying a remarkable folding stability, as demonstrated by its full resistance upon thermal sterilization process or the full chemical synthesis of Nanofitins. To illustrate the potential of the Nanofitin-based tag as a fusion partner, we compared the expression level in Escherichia coli and activity profile of recombinant human tumor necrosis factor alpha (TNFα) constructs, fused to a SUMO or GFP-ready tag. Very similar expression levels were found with the two fusion technologies. Both domains of the GFP-ready tagged TNFα were proved fully active in ELISA and interferometry binding assays, allowing the simultaneous capture by an anti-TNFα antibody and binding to the GFP, and its spectral mutants. The GFP-ready tag was also shown inert in a L929 cell based assay, demonstrating the potent TNFα mediated apoptosis induction by the GFP-ready tagged TNFα. Eventually, we proposed the GFP-ready tag as a versatile capture and labeling system in addition to expected applications of anti-GFP Nanofitins (as illustrated with previously described state-of-the-art anti-GFP binders applied to living cells and in vitro applications). Through a single fusion domain, the GFP-ready tagged proteins benefit from subsequent customization within a wide range of fluorescence spectra upon indirect binding of a chosen GFP variant. PMID:26539718

Use of the Nanofitin Alternative Scaffold as a GFP-Ready Fusion Tag.

PubMed

Huet, Simon; Gorre, Harmony; Perrocheau, Anaëlle; Picot, Justine; Cinier, Mathieu

2015-01-01

With the continuous diversification of recombinant DNA technologies, the possibilities for new tailor-made protein engineering have extended on an on-going basis. Among these strategies, the use of the green fluorescent protein (GFP) as a fusion domain has been widely adopted for cellular imaging and protein localization. Following the lead of the direct head-to-tail fusion of GFP, we proposed to provide additional features to recombinant proteins by genetic fusion of artificially derived binders. Thus, we reported a GFP-ready fusion tag consisting of a small and robust fusion-friendly anti-GFP Nanofitin binding domain as a proof-of-concept. While limiting steric effects on the carrier, the GFP-ready tag allows the capture of GFP or its blue (BFP), cyan (CFP) and yellow (YFP) alternatives. Here, we described the generation of the GFP-ready tag from the selection of a Nanofitin variant binding to the GFP and its spectral variants with a nanomolar affinity, while displaying a remarkable folding stability, as demonstrated by its full resistance upon thermal sterilization process or the full chemical synthesis of Nanofitins. To illustrate the potential of the Nanofitin-based tag as a fusion partner, we compared the expression level in Escherichia coli and activity profile of recombinant human tumor necrosis factor alpha (TNFα) constructs, fused to a SUMO or GFP-ready tag. Very similar expression levels were found with the two fusion technologies. Both domains of the GFP-ready tagged TNFα were proved fully active in ELISA and interferometry binding assays, allowing the simultaneous capture by an anti-TNFα antibody and binding to the GFP, and its spectral mutants. The GFP-ready tag was also shown inert in a L929 cell based assay, demonstrating the potent TNFα mediated apoptosis induction by the GFP-ready tagged TNFα. Eventually, we proposed the GFP-ready tag as a versatile capture and labeling system in addition to expected applications of anti-GFP Nanofitins (as illustrated with previously described state-of-the-art anti-GFP binders applied to living cells and in vitro applications). Through a single fusion domain, the GFP-ready tagged proteins benefit from subsequent customization within a wide range of fluorescence spectra upon indirect binding of a chosen GFP variant.

The Influence of Level of Discrepancy on the Identification of Students with Learning Disabilities.

ERIC Educational Resources Information Center

McLeskey, James

1989-01-01

Investigation of the relationship between a statistically determined severe discrepancy between expected and actual achievement levels and subsequent labeling of 733 students as learning disabled found only a slight majority of labeled students manifesting a severe discrepancy suggesting this criterion is inconsistently applied in making…

Time-Resolved Visualisation of Nearly-Native Influenza A Virus Progeny Ribonucleoproteins and Their Individual Components in Live Infected Cells

PubMed Central

Avilov, Sergiy; Magnus, Julie; Cusack, Stephen; Naffakh, Nadia

2016-01-01

Influenza viruses are a global health concern because of the permanent threat of novel emerging strains potentially capable of causing pandemics. Viral ribonucleoproteins (vRNPs) containing genomic RNA segments, nucleoprotein oligomers, and the viral polymerase, play a central role in the viral replication cycle. Our knowledge about critical events such as vRNP assembly and interactions with other viral and cellular proteins is poor and could be substantially improved by time lapse imaging of the infected cells. However, such studies are limited by the difficulty to achieve live-cell compatible labeling of active vRNPs. Previously we designed the first unimpaired recombinant influenza WSN-PB2-GFP11 virus allowing fluorescent labeling of the PB2 subunit of the viral polymerase (Avilov et al., J.Virol. 2012). Here, we simultaneously labeled the viral PB2 protein using the above-mentioned strategy, and virus-encoded progeny RNPs through spontaneous incorporation of transiently expressed NP-mCherry fusion proteins during RNP assembly in live infected cells. This dual labeling enabled us to visualize progeny vRNPs throughout the infection cycle and to characterize independently the mobility, oligomerization status and interactions of vRNP components in the nuclei of live infected cells. PMID:26978069

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

Zhao, T; Ruan, D

Purpose: The growing size and heterogeneity in training atlas necessitates sophisticated schemes to identify only the most relevant atlases for the specific multi-atlas-based image segmentation problem. This study aims to develop a model to infer the inaccessible oracle geometric relevance metric from surrogate image similarity metrics, and based on such model, provide guidance to atlas selection in multi-atlas-based image segmentation. Methods: We relate the oracle geometric relevance metric in label space to the surrogate metric in image space, by a monotonically non-decreasing function with additive random perturbations. Subsequently, a surrogate’s ability to prognosticate the oracle order for atlas subset selectionmore » is quantified probabilistically. Finally, important insights and guidance are provided for the design of fusion set size, balancing the competing demands to include the most relevant atlases and to exclude the most irrelevant ones. A systematic solution is derived based on an optimization framework. Model verification and performance assessment is performed based on clinical prostate MR images. Results: The proposed surrogate model was exemplified by a linear map with normally distributed perturbation, and verified with several commonly-used surrogates, including MSD, NCC and (N)MI. The derived behaviors of different surrogates in atlas selection and their corresponding performance in ultimate label estimate were validated. The performance of NCC and (N)MI was similarly superior to MSD, with a 10% higher atlas selection probability and a segmentation performance increase in DSC by 0.10 with the first and third quartiles of (0.83, 0.89), compared to (0.81, 0.89). The derived optimal fusion set size, valued at 7/8/8/7 for MSD/NCC/MI/NMI, agreed well with the appropriate range [4, 9] from empirical observation. Conclusion: This work has developed an efficacious probabilistic model to characterize the image-based surrogate metric on atlas selection. Analytical insights lead to valid guiding principles on fusion set size design.« less

Gata4-Dependent Differentiation of c-Kit+ Derived Endothelial Cells Underlies Artefactual Cardiomyocyte Regeneration in the Heart.

PubMed

Maliken, Bryan D; Kanisicak, Onur; Karch, Jason; Khalil, Hadi; Fu, Xing; Boyer, Justin G; Prasad, Vikram; Zheng, Yi; Molkentin, Jeffery D

2018-04-17

Background -While c-Kit + adult progenitor cells were initially reported to produce new cardiomyocytes in the heart, recent genetic evidence suggests that such events are exceedingly rare. However, to determine if these rare events represent true de novo cardiomyocyte formation we deleted the necessary cardiogenic transcription factors Gata4 and Gata6 from c-Kit-expressing cardiac progenitor cells (CPCs). Methods - Kit allele-dependent lineage tracing and fusion analysis was performed in mice following simultaneous Gata4 and Gata6 cell-type specific deletion to examine rates of putative de novo cardiomyocyte formation from c-Kit + cells. Bone marrow transplantation experiments were used to define the contribution of Kit allele-derived hematopoietic cells versus Kit lineage-dependent cells endogenous to the heart in contributing to apparent de novo lineage-traced cardiomyocytes. A Tie2 CreERT2 transgene was also used to examine the global impact of Gata4 deletion on the mature cardiac endothelial cell network, which was further evaluated with select angiogenesis assays. Results -Deletion of Gata4 in Kit lineage-derived endothelial cells or in total endothelial cells using the Tie2 CreERT2 transgene, but not from bone morrow cells, resulted in profound endothelial cell expansion, defective endothelial cell differentiation, leukocyte infiltration into the heart and a dramatic increase in Kit allele-dependent lineage-traced cardiomyocytes. However, this increase in labeled cardiomyocytes was an artefact of greater leukocyte-cardiomyocyte cellular fusion due to defective endothelial cell differentiation in the absence of Gata4 Conclusions -Past identification of presumed de novo cardiomyocyte formation in the heart from c-Kit + cells using Kit allele lineage tracing appears to be an artefact of labeled leukocyte fusion with cardiomyocytes. Deletion of Gata4 from c-Kit + endothelial progenitor cells or adult endothelial cells negatively impacted angiogenesis and capillary network integrity.

Radiolabelling of glycosylated MFE-23::CPG2 fusion protein (MFECP1) with 99mTc for quantitation of tumour antibody-enzyme localisation in antibody-directed enzyme pro-drug therapy (ADEPT).

PubMed

Francis, R J; Mather, S J; Chester, K; Sharma, S K; Bhatia, J; Pedley, R B; Waibel, R; Green, A J; Begent, R H J

2004-08-01

MFECP1 is a glycosylated recombinant fusion protein composed of MFE-23, a high-affinity anti-carcinoembryonic antigen (CEA) single chain Fv (scFv), fused to the enzyme carboxypeptidase G2 (CPG2), and has been constructed for use in antibody-directed enzyme pro-drug therapy (ADEPT). Radiolabelling of glycosylated MFECP1 with technetium-99m was developed for the purpose of determining tumour localisation of MFECP1 in a phase I ADEPT clinical study. The method used was 99mTc-carbonyl [99mTc(H2O)3(CO)3]+ (abbreviated to TcCO) mediated labelling of 99mTc to the hexahistidine (His) tag of MFECP1. MFECP1 fusion protein was labelled with TcCO under a variety of conditions, and this was shown to be a relatively simple and robust method. Tissue biodistribution was assessed in a CEA-expressing LS174T (human colon carcinoma) nude mouse xenograft model. Tissues were taken at 1, 4 and 6 h for assessment of distribution of radioactivity and for measurement of CPG2 enzyme levels. The amount of radioactivity retained by the tumour proved to be an accurate estimation of actual measured enzyme activity, indicating that this radiolabelling method does not appear to damage the antibody-antigen binding or the enzyme activity of MFECP1. However, correlation between CPG2 enzyme activity and measured radioactivity in liver, spleen and kidney was poor, indicating retention of radioactivity in non-tumour sites but loss of enzyme activity. The high retention of technetium radioisotope in normal tissues may limit the clinical applicability of this radiolabelling method for MFECP1; however, these results suggest that this technique does have applicability for measuring the biodistribution of His-tagged recombinant proteins.

A dual-channel fusion system of visual and infrared images based on color transfer

NASA Astrophysics Data System (ADS)

Pei, Chuang; Jiang, Xiao-yu; Zhang, Peng-wei; Liang, Hao-cong

2013-09-01

A dual-channel fusion system of visual and infrared images based on color transfer The increasing availability and deployment of imaging sensors operating in multiple spectrums has led to a large research effort in image fusion, resulting in a plethora of pixel-level image fusion algorithms. However, most of these algorithms have gray or false color fusion results which are not adapt to human vision. Transfer color from a day-time reference image to get natural color fusion result is an effective way to solve this problem, but the computation cost of color transfer is expensive and can't meet the request of real-time image processing. We developed a dual-channel infrared and visual images fusion system based on TMS320DM642 digital signal processing chip. The system is divided into image acquisition and registration unit, image fusion processing unit, system control unit and image fusion result out-put unit. The image registration of dual-channel images is realized by combining hardware and software methods in the system. False color image fusion algorithm in RGB color space is used to get R-G fused image, then the system chooses a reference image to transfer color to the fusion result. A color lookup table based on statistical properties of images is proposed to solve the complexity computation problem in color transfer. The mapping calculation between the standard lookup table and the improved color lookup table is simple and only once for a fixed scene. The real-time fusion and natural colorization of infrared and visual images are realized by this system. The experimental result shows that the color-transferred images have a natural color perception to human eyes, and can highlight the targets effectively with clear background details. Human observers with this system will be able to interpret the image better and faster, thereby improving situational awareness and reducing target detection time.

Geographic identification of Boletus mushrooms by data fusion of FT-IR and UV spectroscopies combined with multivariate statistical analysis

NASA Astrophysics Data System (ADS)

Yao, Sen; Li, Tao; Li, JieQing; Liu, HongGao; Wang, YuanZhong

2018-06-01

Boletus griseus and Boletus edulis are two well-known wild-grown edible mushrooms which have high nutrition, delicious flavor and high economic value distributing in Yunnan Province. In this study, a rapid method using Fourier transform infrared (FT-IR) and ultraviolet (UV) spectroscopies coupled with data fusion was established for the discrimination of Boletus mushrooms from seven different geographical origins with pattern recognition method. Initially, the spectra of 332 mushroom samples obtained from the two spectroscopic techniques were analyzed individually and then the classification performance based on data fusion strategy was investigated. Meanwhile, the latent variables (LVs) of FT-IR and UV spectra were extracted by partial least square discriminant analysis (PLS-DA) and two datasets were concatenated into a new matrix for data fusion. Then, the fusion matrix was further analyzed by support vector machine (SVM). Compared with single spectroscopic technique, data fusion strategy can improve the classification performance effectively. In particular, the accuracy of correct classification of SVM model in training and test sets were 99.10% and 100.00%, respectively. The results demonstrated that data fusion of FT-IR and UV spectra can provide higher synergic effect for the discrimination of different geographical origins of Boletus mushrooms, which may be benefit for further authentication and quality assessment of edible mushrooms.

Geographic identification of Boletus mushrooms by data fusion of FT-IR and UV spectroscopies combined with multivariate statistical analysis.

PubMed

Yao, Sen; Li, Tao; Li, JieQing; Liu, HongGao; Wang, YuanZhong

2018-06-05

Boletus griseus and Boletus edulis are two well-known wild-grown edible mushrooms which have high nutrition, delicious flavor and high economic value distributing in Yunnan Province. In this study, a rapid method using Fourier transform infrared (FT-IR) and ultraviolet (UV) spectroscopies coupled with data fusion was established for the discrimination of Boletus mushrooms from seven different geographical origins with pattern recognition method. Initially, the spectra of 332 mushroom samples obtained from the two spectroscopic techniques were analyzed individually and then the classification performance based on data fusion strategy was investigated. Meanwhile, the latent variables (LVs) of FT-IR and UV spectra were extracted by partial least square discriminant analysis (PLS-DA) and two datasets were concatenated into a new matrix for data fusion. Then, the fusion matrix was further analyzed by support vector machine (SVM). Compared with single spectroscopic technique, data fusion strategy can improve the classification performance effectively. In particular, the accuracy of correct classification of SVM model in training and test sets were 99.10% and 100.00%, respectively. The results demonstrated that data fusion of FT-IR and UV spectra can provide higher synergic effect for the discrimination of different geographical origins of Boletus mushrooms, which may be benefit for further authentication and quality assessment of edible mushrooms. Copyright © 2018 Elsevier B.V. All rights reserved.

Statistical Model to Analyze Quantitative Proteomics Data Obtained by 18O/16O Labeling and Linear Ion Trap Mass Spectrometry

PubMed Central

Jorge, Inmaculada; Navarro, Pedro; Martínez-Acedo, Pablo; Núñez, Estefanía; Serrano, Horacio; Alfranca, Arántzazu; Redondo, Juan Miguel; Vázquez, Jesús

2009-01-01

Statistical models for the analysis of protein expression changes by stable isotope labeling are still poorly developed, particularly for data obtained by 16O/18O labeling. Besides large scale test experiments to validate the null hypothesis are lacking. Although the study of mechanisms underlying biological actions promoted by vascular endothelial growth factor (VEGF) on endothelial cells is of considerable interest, quantitative proteomics studies on this subject are scarce and have been performed after exposing cells to the factor for long periods of time. In this work we present the largest quantitative proteomics study to date on the short term effects of VEGF on human umbilical vein endothelial cells by 18O/16O labeling. Current statistical models based on normality and variance homogeneity were found unsuitable to describe the null hypothesis in a large scale test experiment performed on these cells, producing false expression changes. A random effects model was developed including four different sources of variance at the spectrum-fitting, scan, peptide, and protein levels. With the new model the number of outliers at scan and peptide levels was negligible in three large scale experiments, and only one false protein expression change was observed in the test experiment among more than 1000 proteins. The new model allowed the detection of significant protein expression changes upon VEGF stimulation for 4 and 8 h. The consistency of the changes observed at 4 h was confirmed by a replica at a smaller scale and further validated by Western blot analysis of some proteins. Most of the observed changes have not been described previously and are consistent with a pattern of protein expression that dynamically changes over time following the evolution of the angiogenic response. With this statistical model the 18O labeling approach emerges as a very promising and robust alternative to perform quantitative proteomics studies at a depth of several thousand proteins. PMID:19181660

Cross-modality PET/CT and contrast-enhanced CT imaging for pancreatic cancer

PubMed Central

Zhang, Jian; Zuo, Chang-Jing; Jia, Ning-Yang; Wang, Jian-Hua; Hu, Sheng-Ping; Yu, Zhong-Fei; Zheng, Yuan; Zhang, An-Yu; Feng, Xiao-Yuan

2015-01-01

AIM: To explore the diagnostic value of the cross-modality fusion images provided by positron emission tomography/computed tomography (PET/CT) and contrast-enhanced CT (CECT) for pancreatic cancer (PC). METHODS: Data from 70 patients with pancreatic lesions who underwent CECT and PET/CT examinations at our hospital from August 2010 to October 2012 were analyzed. PET/CECT for the cross-modality image fusion was obtained using TureD software. The diagnostic efficiencies of PET/CT, CECT and PET/CECT were calculated and compared with each other using a χ2 test. P < 0.05 was considered to indicate statistical significance. RESULTS: Of the total 70 patients, 50 had PC and 20 had benign lesions. The differences in the sensitivity, negative predictive value (NPV), and accuracy between CECT and PET/CECT in detecting PC were statistically significant (P < 0.05 for each). In 15 of the 31 patients with PC who underwent a surgical operation, peripancreatic vessel invasion was verified. The differences in the sensitivity, positive predictive value, NPV, and accuracy of CECT vs PET/CT and PET/CECT vs PET/CT in diagnosing peripancreatic vessel invasion were statistically significant (P < 0.05 for each). In 19 of the 31 patients with PC who underwent a surgical operation, regional lymph node metastasis was verified by postsurgical histology. There was no statistically significant difference among the three methods in detecting regional lymph node metastasis (P > 0.05 for each). In 17 of the 50 patients with PC confirmed by histology or clinical follow-up, distant metastasis was confirmed. The differences in the sensitivity and NPV between CECT and PET/CECT in detecting distant metastasis were statistically significant (P < 0.05 for each). CONCLUSION: Cross-modality image fusion of PET/CT and CECT is a convenient and effective method that can be used to diagnose and stage PC, compensating for the defects of PET/CT and CECT when they are conducted individually. PMID:25780297

State Estimation Using Dependent Evidence Fusion: Application to Acoustic Resonance-Based Liquid Level Measurement.

PubMed

Xu, Xiaobin; Li, Zhenghui; Li, Guo; Zhou, Zhe

2017-04-21

Estimating the state of a dynamic system via noisy sensor measurement is a common problem in sensor methods and applications. Most state estimation methods assume that measurement noise and state perturbations can be modeled as random variables with known statistical properties. However in some practical applications, engineers can only get the range of noises, instead of the precise statistical distributions. Hence, in the framework of Dempster-Shafer (DS) evidence theory, a novel state estimatation method by fusing dependent evidence generated from state equation, observation equation and the actual observations of the system states considering bounded noises is presented. It can be iteratively implemented to provide state estimation values calculated from fusion results at every time step. Finally, the proposed method is applied to a low-frequency acoustic resonance level gauge to obtain high-accuracy measurement results.

Prevalence of Abelson murine leukemia viral oncogene homolog-breakpoint cluster region fusions and correlation with peripheral blood parameters in chronic myelogenous leukemia patients in Lorestan Province, Iran.

PubMed

Kiani, Ali Asghar; Shahsavar, Farhad; Gorji, Mojtaba; Ahmadi, Kolsoum; Nazarabad, Vahideh Heydari; Bahmani, Banafsheh

2016-01-01

Chronic myelogenous leukemia (CML) is a chronic malignancy of myeloid linage associated with a significant increase in granulocytes in bone marrow and peripheral blood. CML diagnosis is based on detection of Philadelphia chromosome and "Abelson murine leukemia viral oncogene homolog" (ABL)-"breakpoint cluster region protein" fusions (ABL-BCR fusions). In this study, patients with CML morphology were studied according to ABL-BCR fusions and the relationship between the fusions and peripheral blood cell changes was examined. All patients suspected to chronic myeloproliferative disorders in Lorestan Province visiting subspecialist hematology clinics who were confirmed by oncologist were studied over a period of 5 years. After completing basic data questionnaire, blood samples were obtained with informed consent from the patients. Blood cell count and morphology were investigated and RNA was extracted from blood samples. cDNA was synthesized from RNA and ABL-BCR fusions including b3a2 and b2a2 (protein 210 kd or p210), e1a2 (protein 190 kdor p190), and e19a2 (protein 230 kdor p230) were studied by multiplex reverse transcription polymerase chain reaction method. Coexistence of e1a2 and b2a2 (p210/p190) fusions was also studied. The prevalence of mutations and their correlation with the blood parameters were statistically analyzed. Of 58 patients positive for ABL-BCR fusion, 18 (30.5%) had b2a2 fusion, 37 (62.71%) had b3a2 fusion and three (3.08%) had e1a2 fusion. Coexistence of e1a2 and b2a2 (p210/p190) was not observed. There was no significant correlation between ABL-BCR fusions and white blood cell count, platelet count, and hemoglobin concentration. The ABL-BCR fusions in Lorestan Province were similar to other studies in Iran, and b3a2 fusion had the highest prevalence in the studied patients studied.

Kernel-Based Sensor Fusion With Application to Audio-Visual Voice Activity Detection

NASA Astrophysics Data System (ADS)

Dov, David; Talmon, Ronen; Cohen, Israel

2016-12-01

In this paper, we address the problem of multiple view data fusion in the presence of noise and interferences. Recent studies have approached this problem using kernel methods, by relying particularly on a product of kernels constructed separately for each view. From a graph theory point of view, we analyze this fusion approach in a discrete setting. More specifically, based on a statistical model for the connectivity between data points, we propose an algorithm for the selection of the kernel bandwidth, a parameter, which, as we show, has important implications on the robustness of this fusion approach to interferences. Then, we consider the fusion of audio-visual speech signals measured by a single microphone and by a video camera pointed to the face of the speaker. Specifically, we address the task of voice activity detection, i.e., the detection of speech and non-speech segments, in the presence of structured interferences such as keyboard taps and office noise. We propose an algorithm for voice activity detection based on the audio-visual signal. Simulation results show that the proposed algorithm outperforms competing fusion and voice activity detection approaches. In addition, we demonstrate that a proper selection of the kernel bandwidth indeed leads to improved performance.

Solid-state nuclear magnetic resonance (NMR) spectroscopy of human immunodeficiency virus gp41 protein that includes the fusion peptide: NMR detection of recombinant Fgp41 in inclusion bodies in whole bacterial cells and structural characterization of purified and membrane-associated Fgp41.

PubMed

Vogel, Erica P; Curtis-Fisk, Jaime; Young, Kaitlin M; Weliky, David P

2011-11-22

Human immunodeficiency virus (HIV) infection of a host cell begins with fusion of the HIV and host cell membranes and is mediated by the gp41 protein, a single-pass integral membrane protein of HIV. The 175 N-terminal residues make up the ectodomain that lies outside the virus. This work describes the production and characterization of an ectodomain construct containing the 154 N-terminal gp41 residues, including the fusion peptide (FP) that binds to target cell membranes. The Fgp41 sequence was derived from one of the African clade A strains of HIV-1 that have been less studied than European/North American clade B strains. Fgp41 expression at a level of ~100 mg/L of culture was evidenced by an approach that included amino acid type (13)CO and (15)N labeling of recombinant protein and solid-state NMR (SSNMR) spectroscopy of lyophilized whole cells. The approach did not require any protein solubilization or purification and may be a general approach for detection of recombinant protein. The purified Fgp41 yield was ~5 mg/L of culture. SSNMR spectra of membrane-associated Fgp41 showed high helicity for the residues C-terminal of the FP. This was consistent with a "six-helix bundle" (SHB) structure that is the final gp41 state during membrane fusion. This observation and negligible Fgp41-induced vesicle fusion supported a function for SHB gp41 of membrane stabilization and fusion arrest. SSNMR spectra of residues in the membrane-associated FP provided evidence of a mixture of molecular populations with either helical or β-sheet FP conformation. These and earlier SSNMR data strongly support the existence of these populations in the SHB state of membrane-associated gp41. © 2011 American Chemical Society

Single-virus fusion experiments reveal proton influx into vaccinia virions and hemifusion lag times.

PubMed

Schmidt, Florian I; Kuhn, Phillip; Robinson, Tom; Mercer, Jason; Dittrich, Petra S

2013-07-16

Recent studies have revealed new insights into the endocytosis of vaccinia virus (VACV). However, the mechanism of fusion between viral and cellular membranes remains unknown. We developed a microfluidic device with a cell-trap array for immobilization of individual cells, with which we analyzed the acid-dependent fusion of single virions. VACV particles incorporating enhanced green fluorescent protein (EGFP) and labeled with self-quenching concentrations of R18 membrane dye were used in combination with total internal reflection fluorescence microscopy to measure the kinetics of R18 dequenching and thus single hemifusion events initiated by a fast low-pH trigger. These studies revealed unexpectedly long lag phases between pH change and hemifusion. In addition, we found that EGFP fluorescence in the virus was quenched upon acidification, indicating that protons could access the virus core, possibly through a proton channel. In a fraction of virus particles, EGFP fluorescence was recovered, presumably after fusion-pore formation and exposure of the core to the physiological pH of the host-cell cytosol. Given that virus-encoded cation channels play a crucial role in the life cycle of many viruses and can serve as antiviral drug targets, further investigations into a potential VACV viroporin are justified. Our findings indicate that the microfluidic device described may be highly beneficial to similar studies requiring fast kinetic measurements. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Turbulent Transport at High Reynolds Numbers in an Inertial Confinement Fusion Context

DTIC Science & Technology

2014-09-01

Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794 P . Rao1 Department of Applied Mathematics and Statistics...scales, 1Corresponding author. Contributed by the Fluids Engineering Division of ASME for publication in the JOURNAL OF FLUIDS ENGINEERING...Engineering SEPTEMBER 2014, Vol. 136 / 091206-1Copyright VC 2014 by ASME Downloaded From: http://fluidsengineering.asmedigitalcollection.asme.org/ on

The Acquisition of Gender Labels in Infancy: Implications for Gender-Typed Play

ERIC Educational Resources Information Center

Zosuls, Kristina M.; Ruble, Diane N.; Tamis-LeMonda, Catherine S.; Shrout, Patrick E.; Bornstein, Marc H.; Greulich, Faith K.

2009-01-01

Two aspects of children's early gender development--the spontaneous production of gender labels and gender-typed play--were examined longitudinally in a sample of 82 children. Survival analysis, a statistical technique well suited to questions involving developmental transitions, was used to investigate the timing of the onset of children's gender…

Diagnostic Labeling: Individual Differences in the Behavior of Clinicians Conducting Presentence Evaluations.

ERIC Educational Resources Information Center

Holland, Terrill R.

1979-01-01

Clinicians with highly deviant recommendation rates also exhibited extreme differences in their use of the normal and sociopathic categories. It was concluded that biases in the definition and assignment of labels might be reduced by means of a combined clinical-statistical approach to gathering and utilizing diagnostic information. (Author)

Listeriosis downregulates hepatic cytochrome P450 enzymes in sublethal murine infection.

PubMed

Kummer, Anne; Nishanth, Gopala; Koschel, Josephin; Klawonn, Frank; Schlüter, Dirk; Jänsch, Lothar

2016-10-01

Listeria monocytogenes (Lm) can cross the intestinal barrier in humans and then disseminates into different organs. Invasion of the liver occurs even in sublethal infections, however, knowledge of affected physiological processes is scarce. This study employed a sublethal murine infection model to investigate liver responses systematically by proteomics. Liver samples from three stages of the sublethal infection covering the initial invasion, the peak of infection, and the clearance phase (1, 3, 9 days postinoculation) were analyzed in comparison to samples from noninfected mice. Apart from flow cytometry and RT-PCRs for immune status control, liver responses were analyzed by quantitative peptide sequencing (HPLC-Orbitrap Fusion) using 4-plex iTRAQ-labeling. Accurate MS characterized about 3600 proteins and statistics revealed 15% of the hepatic proteome as regulated. Immunological data as well as protein regulation dynamics strongly indicate stage-specific hepatic responses in sublethal infections. Most notably, this study detected a comprehensive deregulation of drug metabolizing enzymes at all stages, including 25 components of the cytochrome P450 system. Sublethal Lm infection deregulates hepatic drug metabolizing pathways. This finding indicates the need to monitor drug administration along Lm infections, especially in all patients needing constant medication. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Protein Mobility within Secretory Granules

PubMed Central

Weiss, Annita Ngatchou; Bittner, Mary A.; Holz, Ronald W.; Axelrod, Daniel

2014-01-01

We investigated the basis for previous observations that fluorescent-labeled neuropeptide Y (NPY) is usually released within 200 ms after fusion, whereas labeled tissue plasminogen activator (tPA) is often discharged over many seconds. We found that tPA and NPY are endogenously expressed in small and different subpopulations of bovine chromaffin cells in culture. We measured the mobility of these proteins (tagged with fluorophore) within the lumen of individual secretory granules in living chromaffin cells, and related their mobilities to postfusion release kinetics. A method was developed that is not limited by standard optical resolution, in which a bright flash of strongly decaying evanescent field (∼64 nm exponential decay constant) produced by total internal reflection (TIR) selectively bleaches cerulean-labeled protein proximal to the glass coverslip within individual granules. Fluorescence recovery occurred as unbleached protein from distal regions within the 300 nm granule diffused into the bleached proximal regions. The fractional bleaching of tPA-cerulean (tPA-cer) was greater when subsequently probed with TIR excitation than with epifluorescence, indicating that tPA-cer mobility was low. The almost equal NPY-cer bleaching when probed with TIR and epifluorescence indicated that NPY-cer equilibrated within the 300 ms bleach pulse, and therefore had a greater mobility than tPA-cer. TIR-fluorescence recovery after photobleaching revealed a significant recovery of tPA-cer (but not NPY-cer) fluorescence within several hundred milliseconds after bleaching. Numerical simulations, which take into account bleach duration, granule diameter, and the limited number of fluorophores in a granule, are consistent with tPA-cer being 100% mobile, with a diffusion coefficient of 2 × 10−10 cm2/s (∼1/3000 of that for a protein of similar size in aqueous solution). However, the low diffusive mobility of tPA cannot alone explain its slow postfusion release. In the accompanying study, we suggest that, additionally, tPA itself stabilizes the fusion pore with dimensions that restrict its own exit. PMID:24988337

Outcomes of Posterolateral Fusion with and without Instrumentation and of Interbody Fusion for Isthmic Spondylolisthesis: A Prospective Study.

PubMed

Endler, Peter; Ekman, Per; Möller, Hans; Gerdhem, Paul

2017-05-03

Various methods for the treatment of isthmic spondylolisthesis are available. The aim of this study was to compare outcomes after posterolateral fusion without instrumentation, posterolateral fusion with instrumentation, and interbody fusion. The Swedish Spine Register was used to identify 765 patients who had been operated on for isthmic spondylolisthesis and had at least preoperative and 2-year outcome data; 586 of them had longer follow-up (a mean of 6.9 years). The outcome measures were a global assessment of leg and back pain, the Oswestry Disability Index (ODI), the EuroQol-5 Dimensions (EQ-5D) Questionnaire, the Short Form-36 (SF-36), a visual analog scale (VAS) for back and leg pain, and satisfaction with treatment. Data on additional lumbar spine surgery was searched for in the register, with the mean duration of follow-up for this variable being 10.6 years after the index procedure. Statistical analyses were performed with analysis of covariance or competing-risks proportional hazards regression, adjusted for baseline differences in the studied variables, smoking, employment status, and level of fusion. Posterolateral fusion without instrumentation was performed in 102 patients; posterolateral fusion with instrumentation, in 452; and interbody fusion, in 211. At 1 year, improvement was reported in the global assessment for back pain by 54% of the patients who had posterolateral fusion without instrumentation, 68% of those treated with posterolateral fusion with instrumentation, and 70% of those treated with interbody fusion (p = 0.009). The VAS for back pain and reported satisfaction with treatment showed similar patterns (p = 0.003 and p = 0.017, respectively), whereas other outcomes did not differ among the treatment groups at 1 year. At 2 years, the global assessment for back pain indicated improvement in 57% of the patients who had undergone posterolateral fusion without instrumentation, 70% of those who had posterolateral fusion with instrumentation, and 71% of those treated with interbody fusion (p = 0.022). There were no significant outcome differences at the mean 6.9-year follow-up interval. There was an increased hazard ratio for additional lumbar spine surgery after interbody fusion (4.34; 95% confidence interval [CI] = 1.71 to 11.03) and posterolateral fusion with instrumentation (2.56; 95% CI = 1.02 to 6.42) compared with after posterolateral fusion without instrumentation (1.00; reference). Fusion with instrumentation, with or without interbody fusion, was associated with more improvement in back pain scores and higher satisfaction with treatment compared with fusion without instrumentation at 1 year, but the difference was attenuated with longer follow-up. Fusion with instrumentation was associated with a significantly higher risk of additional spine surgery. Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.

Hybrid testing of lumbar CHARITE discs versus fusions.

PubMed

Panjabi, Manohar; Malcolmson, George; Teng, Edward; Tominaga, Yasuhiro; Henderson, Gweneth; Serhan, Hassan

2007-04-20

An in vitro human cadaveric biomechanical study. To quantify effects on operated and other levels, including adjacent levels, due to CHARITE disc implantations versus simulated fusions, using follower load and the new hybrid test method in flexion-extension and bilateral torsion. Spinal fusion has been associated with long-term accelerated degeneration at adjacent levels. As opposed to the fusion, artificial discs are designed to preserve motion and diminish the adjacent-level effects. Five fresh human cadaveric lumbar specimens (T12-S1) underwent multidirectional testing in flexion-extension and bilateral torsion with 400 N follower load. Intact specimen total ranges of motion were determined with +/-10 Nm unconstrained pure moments. The intact range of motion was used as input for the hybrid tests of 5 constructs: 1) CHARITE disc at L5-S1; 2) fusion at L5-S1; 3) CHARITE discs at L4-L5 and L5-S1; 4) CHARITE disc at L4-L5 and fusion at L5-S1; and 5) 2-level fusion at L4-L5-S1. Using repeated-measures single factor analysis of variance and Bonferroni statistical tests (P < 0.05), intervertebral motion redistribution of each construct was compared with the intact. In flexion-extension, 1-level CHARITE disc preserved motion at the operated and other levels, while 2-level CHARITE showed some amount of other-level effects. In contrast, 1- and 2-level fusions increased other-level motions (average, 21.0% and 61.9%, respectively). In torsion, both 1- and 2-level discs preserved motions at all levels. The 2-level simulated fusion increased motions at proximal levels (22.9%), while the 1-level fusion produced no significant changes. In general, CHARITE discs preserved operated- and other-level motions. Fusion simulations affected motion redistribution at other levels, including adjacent levels.

Investigations of image fusion

NASA Astrophysics Data System (ADS)

Zhang, Zhong

1999-12-01

The objective of image fusion is to combine information from multiple images of the same scene. The result of image fusion is a single image which is more suitable for the purpose of human visual perception or further image processing tasks. In this thesis, a region-based fusion algorithm using the wavelet transform is proposed. The identification of important features in each image, such as edges and regions of interest, are used to guide the fusion process. The idea of multiscale grouping is also introduced and a generic image fusion framework based on multiscale decomposition is studied. The framework includes all of the existing multiscale-decomposition- based fusion approaches we found in the literature which did not assume a statistical model for the source images. Comparisons indicate that our framework includes some new approaches which outperform the existing approaches for the cases we consider. Registration must precede our fusion algorithms. So we proposed a hybrid scheme which uses both feature-based and intensity-based methods. The idea of robust estimation of optical flow from time- varying images is employed with a coarse-to-fine multi- resolution approach and feature-based registration to overcome some of the limitations of the intensity-based schemes. Experiments show that this approach is robust and efficient. Assessing image fusion performance in a real application is a complicated issue. In this dissertation, a mixture probability density function model is used in conjunction with the Expectation- Maximization algorithm to model histograms of edge intensity. Some new techniques are proposed for estimating the quality of a noisy image of a natural scene. Such quality measures can be used to guide the fusion. Finally, we study fusion of images obtained from several copies of a new type of camera developed for video surveillance. Our techniques increase the capability and reliability of the surveillance system and provide an easy way to obtain 3-D information of objects in the space monitored by the system.

Connexin 43 expression of foreign body giant cells after implantation of nanoparticulate hydroxyapatite.

PubMed

Herde, Katja; Hartmann, Sonja; Brehm, Ralph; Kilian, Olaf; Heiss, Christian; Hild, Anne; Alt, Volker; Bergmann, Martin; Schnettler, Reinhard; Wenisch, Sabine

2007-11-01

In bone a role of connexin 43 has been implicated with the fusion of mononuclear precursors of the monocyte/macrophage lineage into multinucleated cells. In order to investigate the putative role of connexin 43 in formation of bone osteoclast-like foreign body giant cells which are formed in response to implantation of biomaterials, nanoparticulate hydroxyapatite had been implanted into defects of minipig femura. After 20 days the defect areas were harvested and connexin 43 expression and synthesis were investigated by using immunohistochemistry, Western Blot, and in situ hybridization within macrophages and osteoclast-like foreign body giant cells. Morphological analysis of gap junctions is performed ultrastructurally. As shown on protein and mRNA level numerous connexin 43 positive macrophages and foreign body giant cells (FBGC) were localized within the granulation tissue and along the surfaces of the implanted hydroxyapatite (HA). Besides, the formation of FBGC by fusion of macrophages could be shown ultrastructurally. Connexin 43 labeling observed on the protein and mRNA level could be attributed to gap junctions identified ultrastructurally between macrophages, between FBGC, and between FBGC and macrophages. Annular gap junctions in the cytoplasm of FBGC pointed to degradation of the channels, and the ubiquination that had occurred in the course of degradation was confirmed by Western blot analysis. All in all, the presently observed pattern of connexin 43 labeling refers to an functional role of gap junctional communication in the formation of osteoclast-like foreign body giant cells formed in response to implantation of the nanoparticulate HA.

Proteomic Analysis of Rat Hippocampus under Simulated Microgravity

NASA Astrophysics Data System (ADS)

Wang, Yun; Li, Yujuan; Zhang, Yongqian; Liu, Yahui; Deng, Yulin

It has been found that microgravity may lead to impairments in cognitive functions performed by CNS. However, the exact mechanism of effects of microgravity on the learning and memory function in animal nervous system is not elucidated yet. Brain function is mainly mediated by membrane proteins and their dysfunction causes degeneration of the learning and memory. To induce simulated microgravity, the rat tail suspension model was established. Comparative O (18) labeling quantitative proteomic strategy was applied to detect the differentially expressed proteins in rat brain hippocampus. The proteins in membrane fraction from rat hippocampus were digested by trypsin and then the peptides were separated by off-gel for the first dimension with 24 wells device encompassing the pH range of 3 - 10. An off-gel fraction was subjected into LC-ESI-QTOF in triplicate. Preliminary results showed that nearly 77% of the peptides identified were specific to one fraction. 676 proteins were identified among which 108 proteins were found differentially expressed under simulated microgravity. Using the KOBAS server, many enriched pathways, such as metabolic pathway, synaptic vesicle cycle, endocytosis, calcium signaling pathway, and SNAREs pathway were identified. Furthermore, it has been found that neurotransmitter released by Ca (2+) -triggered synaptic vesicles fusion may play key role in neural function. Rab 3A might inhibit the membrane fusion and neurotransmitter release. The protein alteration of the synaptic vesicle cycle may further explain the effects of microgravity on learning and memory function in rats. Key words: Microgravity; proteomics; synaptic vesicle; O (18) ({}) -labeling

Relationship between binocular vision, visual acuity, and fine motor skills.

PubMed

O'Connor, Anna R; Birch, Eileen E; Anderson, Susan; Draper, Hayley

2010-12-01

The aims of this study were to analyze the relationship between the performance on fine motor skills tasks and peripheral and bifoveal sensory fusion, phasic and tonic motor fusion, the level of visual acuity (VA) in the poorer seeing eye, and the interocular VA difference. Subjects aged 12 to 28 years with a range of levels of binocular vision and VA performed three tasks: Purdue pegboard (number of pegs placed in 30 s), bead threading task (with two sizes of bead to increase the difficulty, time taken to thread a fixed number of beads), and a water pouring task (accuracy and time to pour a fixed quantity into five glass cylinders). Ophthalmic measures included peripheral (Worth 4 dot) and bifoveal (4 prism diopter) sensory fusion, phasic (prism bar) and tonic (Risley rotary prism) motor fusion ranges, and monocular VA. One hundred twenty-one subjects with a mean age of 18.8 years were tested; 18.2% had a manifest strabismus. Performance on fine motor skills tasks was significantly better in subjects with sensory and motor fusion compared with those without for most tasks, with significant differences between those with and without all measures of fusion on the pegboard and bead task. Both the acuity in the poorer seeing eye (highest r value of all motor tasks = 0.43) and the interocular acuity difference were statistically significantly related to performance on the motor skill tasks. Both sensory and motor fusion and good VA in both eyes are of benefit in the performance of fine motor skills tasks, with the presence of some binocular vision being beneficial compared with no fusion on certain sensorimotor tasks. This evidence supports the need to maximize fusion and VA outcomes.

A Comparative Study of Thought Fusion Beliefs and Thought Control Strategies in Patient With Obsessive-Compulsive Disorder, Major Depressive Disorder and Normal People

PubMed Central

Amiri Pichakolaei, Ahmad; Fahimi, Samad; Bakhshipour Roudsari, Abbas; Fakhari, Ali; Akbari, Ebrahim; Rahimkhanli, Masoumeh

2014-01-01

Objective: The present study aimed to investigate the metacognitive model of obsessive-compulsive disorder (OCD), through a comparative study of thought fusion beliefs and thought control strategies between patients with OCD, depression, and normal people. Methods: This is a causal-comparative study. About 20 patients were selected with OCD, and 20 patients with major depression disorder (MDD), and 20 normal individuals. Participants completed a thought fusion instrument and thought control questionnaire. Data were analyzed using multivariate analysis of variance. Results: Results indicated that patients with OCD obtained higher scores than two other groups. Also, there was a statistical significant difference between the three groups in thought control strategies and punishment, worry, and distraction subscales. Conclusion: Therefore, the results of the present study supported the metacognitive model of obsessive and showed thought fusion beliefs and thought control strategies can be effective in onset and continuity of OCD. PMID:25780373

Continuous Indoor Positioning Fusing WiFi, Smartphone Sensors and Landmarks

PubMed Central

Deng, Zhi-An; Wang, Guofeng; Qin, Danyang; Na, Zhenyu; Cui, Yang; Chen, Juan

2016-01-01

To exploit the complementary strengths of WiFi positioning, pedestrian dead reckoning (PDR), and landmarks, we propose a novel fusion approach based on an extended Kalman filter (EKF). For WiFi positioning, unlike previous fusion approaches setting measurement noise parameters empirically, we deploy a kernel density estimation-based model to adaptively measure the related measurement noise statistics. Furthermore, a trusted area of WiFi positioning defined by fusion results of previous step and WiFi signal outlier detection are exploited to reduce computational cost and improve WiFi positioning accuracy. For PDR, we integrate a gyroscope, an accelerometer, and a magnetometer to determine the user heading based on another EKF model. To reduce accumulation error of PDR and enable continuous indoor positioning, not only the positioning results but also the heading estimations are recalibrated by indoor landmarks. Experimental results in a realistic indoor environment show that the proposed fusion approach achieves substantial positioning accuracy improvement than individual positioning approaches including PDR and WiFi positioning. PMID:27608019

Continuous Indoor Positioning Fusing WiFi, Smartphone Sensors and Landmarks.

PubMed

Deng, Zhi-An; Wang, Guofeng; Qin, Danyang; Na, Zhenyu; Cui, Yang; Chen, Juan

2016-09-05

To exploit the complementary strengths of WiFi positioning, pedestrian dead reckoning (PDR), and landmarks, we propose a novel fusion approach based on an extended Kalman filter (EKF). For WiFi positioning, unlike previous fusion approaches setting measurement noise parameters empirically, we deploy a kernel density estimation-based model to adaptively measure the related measurement noise statistics. Furthermore, a trusted area of WiFi positioning defined by fusion results of previous step and WiFi signal outlier detection are exploited to reduce computational cost and improve WiFi positioning accuracy. For PDR, we integrate a gyroscope, an accelerometer, and a magnetometer to determine the user heading based on another EKF model. To reduce accumulation error of PDR and enable continuous indoor positioning, not only the positioning results but also the heading estimations are recalibrated by indoor landmarks. Experimental results in a realistic indoor environment show that the proposed fusion approach achieves substantial positioning accuracy improvement than individual positioning approaches including PDR and WiFi positioning.

Fusion of LBP and SWLD using spatio-spectral information for hyperspectral face recognition

NASA Astrophysics Data System (ADS)

Xie, Zhihua; Jiang, Peng; Zhang, Shuai; Xiong, Jinquan

2018-01-01

Hyperspectral imaging, recording intrinsic spectral information of the skin cross different spectral bands, become an important issue for robust face recognition. However, the main challenges for hyperspectral face recognition are high data dimensionality, low signal to noise ratio and inter band misalignment. In this paper, hyperspectral face recognition based on LBP (Local binary pattern) and SWLD (Simplified Weber local descriptor) is proposed to extract discriminative local features from spatio-spectral fusion information. Firstly, the spatio-spectral fusion strategy based on statistical information is used to attain discriminative features of hyperspectral face images. Secondly, LBP is applied to extract the orientation of the fusion face edges. Thirdly, SWLD is proposed to encode the intensity information in hyperspectral images. Finally, we adopt a symmetric Kullback-Leibler distance to compute the encoded face images. The hyperspectral face recognition is tested on Hong Kong Polytechnic University Hyperspectral Face database (PolyUHSFD). Experimental results show that the proposed method has higher recognition rate (92.8%) than the state of the art hyperspectral face recognition algorithms.

Adaptive multiple super fast simulated annealing for stochastic microstructure reconstruction

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

Ryu, Seun; Lin, Guang; Sun, Xin

2013-01-01

Fast image reconstruction from statistical information is critical in image fusion from multimodality chemical imaging instrumentation to create high resolution image with large domain. Stochastic methods have been used widely in image reconstruction from two point correlation function. The main challenge is to increase the efficiency of reconstruction. A novel simulated annealing method is proposed for fast solution of image reconstruction. Combining the advantage of very fast cooling schedules, dynamic adaption and parallelization, the new simulation annealing algorithm increases the efficiencies by several orders of magnitude, making the large domain image fusion feasible.

Trends, Costs, and Complications of Anterior Cervical Discectomy and Fusion With and Without Bone Morphogenetic Protein in the United States Medicare Population.

PubMed

Lord, Elizabeth L; Cohen, Jeremiah R; Buser, Zorica; Meisel, Hans-Joerg; Brodke, Darrel S; Yoon, S Tim; Youssef, Jim A; Wang, Jeffrey C; Park, Jong-Beom

2017-10-01

Retrospective database review. After the Food and Drug Administration approved bone morphogenetic protein-2 (BMP) in 2002, BMP was used off-label in the cervical spine to increase bone growth and bony fusion. Since then, concerns have been raised regarding complication rates and safety. This study was conducted to examine the use of BMP in anterior cervical discectomy and fusion (ACDF) in the Medicare population and to determine risk of complications and associated costs within 90 days of surgery. Patients who underwent ACDF were identified using Current Procedural Terminology (CPT) and International Classification of Diseases, Ninth Revision Procedure codes (ICD9-P). Complications were identified using ICD9 diagnostic codes. Charges were calculated as amount billed, and reimbursements were calculated as amounts paid by Medicare. Data for these analyses came from a nationwide claims database. A total of 215 047 patients were identified who had ACDF from 2005 to 2011. For the majority of the procedures (89.0%), BMP was not used. BMP use rose from 11.84% in 2005 to a peak of 16.73% in 2007 before decreasing to 12.01% in 2011. BMP was used 16% more in women than men. BMP use was the highest in the West (13.6%) followed by Midwest (11.8%), South (10.6%), and Northeast (7.5%). There was a higher overall complication rate in the BMP group (2.1%) compared with the non-BMP group (1.9%) (odds ratio [OR] = 1.11, 95% CI = 1.01-1.22). The BMP group also had a higher rate of wound complications (0.98% vs 0.76%, OR = 1.29, 95% CI = 1.12-1.48). In this study population, there was no difference in dysphagia/hoarseness, neurologic, medical, or other complications. During the 90-day perioperative period, BMP surgeries were charged at 17.6% higher than non-BMP surgeries. The use of BMP in ACDF in the Medicare population has decreased since a peak in 2007. The rate of wound and overall complications for BMP use with ACDF was higher than without. Our results regarding dysphagia/hoarseness did not show a statistically meaningful difference, which is in contrast with many other studies. Charges associated with BMP use were higher during the 90-day perioperative period.

Trends, Costs, and Complications of Anterior Cervical Discectomy and Fusion With and Without Bone Morphogenetic Protein in the United States Medicare Population

PubMed Central

Cohen, Jeremiah R.; Buser, Zorica; Meisel, Hans-Joerg; Brodke, Darrel S.; Yoon, S. Tim; Youssef, Jim A.; Wang, Jeffrey C.; Park, Jong-Beom

2017-01-01

Study Design: Retrospective database review. Objectives: After the Food and Drug Administration approved bone morphogenetic protein–2 (BMP) in 2002, BMP was used off-label in the cervical spine to increase bone growth and bony fusion. Since then, concerns have been raised regarding complication rates and safety. This study was conducted to examine the use of BMP in anterior cervical discectomy and fusion (ACDF) in the Medicare population and to determine risk of complications and associated costs within 90 days of surgery. Methods: Patients who underwent ACDF were identified using Current Procedural Terminology (CPT) and International Classification of Diseases, Ninth Revision Procedure codes (ICD9-P). Complications were identified using ICD9 diagnostic codes. Charges were calculated as amount billed, and reimbursements were calculated as amounts paid by Medicare. Data for these analyses came from a nationwide claims database. Results: A total of 215 047 patients were identified who had ACDF from 2005 to 2011. For the majority of the procedures (89.0%), BMP was not used. BMP use rose from 11.84% in 2005 to a peak of 16.73% in 2007 before decreasing to 12.01% in 2011. BMP was used 16% more in women than men. BMP use was the highest in the West (13.6%) followed by Midwest (11.8%), South (10.6%), and Northeast (7.5%). There was a higher overall complication rate in the BMP group (2.1%) compared with the non-BMP group (1.9%) (odds ratio [OR] = 1.11, 95% CI = 1.01-1.22). The BMP group also had a higher rate of wound complications (0.98% vs 0.76%, OR = 1.29, 95% CI = 1.12-1.48). In this study population, there was no difference in dysphagia/hoarseness, neurologic, medical, or other complications. During the 90-day perioperative period, BMP surgeries were charged at 17.6% higher than non-BMP surgeries. Conclusions: The use of BMP in ACDF in the Medicare population has decreased since a peak in 2007. The rate of wound and overall complications for BMP use with ACDF was higher than without. Our results regarding dysphagia/hoarseness did not show a statistically meaningful difference, which is in contrast with many other studies. Charges associated with BMP use were higher during the 90-day perioperative period. PMID:28989837

Commercial portion-controlled foods in research studies: how accurate are label weights?

PubMed

Conway, Joan M; Rhodes, Donna G; Rumpler, William V

2004-09-01

The purpose of this study was to evaluate the reliability of label weights as surrogates for actual weights in commercial portion-controlled foods used in a research setting. Actual weights of replicate samples of 82 portion-controlled food items and 17 discrete units of food from larger packaging were determined over time. Comparison was made to the package label weights for the portion-controlled food items and the per-serving weights for the discrete units. The study was conducted at the US Department of Agriculture's Beltsville Human Nutrition Research Center's Human Study Facility, which houses a metabolic kitchen and human nutrition research facility. The primary outcome measures were the actual and label weights of 99 food items consumed by human volunteers during controlled feeding studies. Statistical analyses performed The difference between label and actual weights was tested by the paired t test for those data that complied with the assumptions of normality. The Wilcoxon signed rank test was used for the remainder of the data. Compliance with federal guidelines for packaged weights was also assessed. There was no statistical difference between actual and label weights for only 37 food items. The actual weights of 15 portion-controlled food items were 1% or more less than label weights, making them potentially out of compliance with federal guidelines. With advance planning and continuous monitoring, well-controlled feeding studies could incorporate portion-controlled food items and discrete units, especially beverages and confectionery products. Dietetics professionals should encourage individuals with diabetes and others on strict dietary regimens to check actual weights of portion-controlled products carefully against package weights.

Integrating image quality in 2nu-SVM biometric match score fusion.

PubMed

Vatsa, Mayank; Singh, Richa; Noore, Afzel

2007-10-01

This paper proposes an intelligent 2nu-support vector machine based match score fusion algorithm to improve the performance of face and iris recognition by integrating the quality of images. The proposed algorithm applies redundant discrete wavelet transform to evaluate the underlying linear and non-linear features present in the image. A composite quality score is computed to determine the extent of smoothness, sharpness, noise, and other pertinent features present in each subband of the image. The match score and the corresponding quality score of an image are fused using 2nu-support vector machine to improve the verification performance. The proposed algorithm is experimentally validated using the FERET face database and the CASIA iris database. The verification performance and statistical evaluation show that the proposed algorithm outperforms existing fusion algorithms.

Posterior fusion only for thoracic adolescent idiopathic scoliosis of more than 80 degrees: pedicle screws versus hybrid instrumentation.

PubMed

Di Silvestre, Mario; Bakaloudis, Georgios; Lolli, Francesco; Vommaro, Francesco; Martikos, Konstantinos; Parisini, Patrizio

2008-10-01

The treatment of thoracic adolescent idiopathic scoliosis (AIS) of more than 80 degrees traditionally consisted of a combined procedure, an anterior release performed through an open thoracotomy followed by a posterior fusion. Recently, some studies have reassessed the role of posterior fusion only as treatment for severe thoracic AIS; the correction rate of the thoracic curves was comparable to most series of combined anterior and posterior surgery, with shorter surgery time and without the negative effect on pulmonary function of anterior transthoracic exposure. Compared with other studies published so far on the use of posterior fusion alone for severe thoracic AIS, the present study examines a larger group of patients (52 cases) reviewed at a longer follow-up (average 6.7 years, range 4.5-8.5 years). The aim of the study was to evaluate the clinical and radiographic outcome of surgical treatment for severe thoracic (>80 degrees) AIS treated with posterior spinal fusion alone, and compare comprehensively the results of posterior fusion with a hybrid construct (proximal hooks and distal pedicle screws) versus a pedicle screw instrumentation. All patients (n = 52) with main thoracic AIS curves greater than 80 degrees (Lenke type 1, 2, 3, and 4), surgically treated between 1996 and 2000 at one institution, by posterior spinal fusion either with hybrid instrumentation (PSF-H group; n = 27 patients), or with pedicle screw-only construct (PSF-S group; n = 25 patients) were reviewed. There were no differences between the two groups in terms of age, Risser's sign, Cobb preoperative main thoracic (MT) curve magnitude (PSF-H: 92 degrees vs. PSF-S: 88 degrees), or flexibility on bending films (PSF-H: 27% vs. PSF-S: 25%). Statistical analysis was performed using the t test (paired and unpaired), Wilcoxon test for non-parametric paired analysis, and the Mann-Whitney test for non-parametric unpaired analysis. At the last follow-up, the PSF-S group, when compared to the PSF-H group had a final MT correction rate of 52.4 versus 44.52% (P = 0.001), with a loss of -1.9 degrees versus -11.3 degrees (P = 0.0005), a TL/L correction of 50 versus 43% (ns), a greater correction of the lowest instrumented vertebra translation (-1.00 vs. -0.54 cm; P = 0.04), and tilt (-19 degrees vs. -10 degrees; P = 0.005) on the coronal plane. There were no statistically significant differences in sagittal and global coronal alignment between the two groups (C7-S1 offset: PSF-H = 0.5 cm vs. PSF-S = 0 cm). In the hybrid series (27 patients) surgery-related complications necessitated three revision surgeries, whereas in the screw group (25 patients) one revision surgery was performed. No neurological complications or deep wound infection occurred in this series. In conclusion, posterior spinal fusion for severe thoracic AIS with pedicle screws only, when compared to hybrid construct, allowed a greater coronal correction of both main thoracic and secondary lumbar curves, less loss of the postoperative correction achieved, and fewer revision surgeries. Posterior-only fusion with pedicle screws enabled a good and stable correction of severe scoliosis. However, severe curves may be amenable to hybrid instrumentation that produced analogous results to the screws-only constructs concerning patient satisfaction; at the latest follow-up, SRS-30 and SF-36 scores did not show any statistical differences between the two groups.

Matched Comparison of Fusion Rates between Hydroxyapatite Demineralized Bone Matrix and Autograft in Lumbar Interbody Fusion.

PubMed

Kim, Dae Hwan; Lee, Nam; Shin, Dong Ah; Yi, Seong; Kim, Keung Nyun; Ha, Yoon

2016-07-01

To compare the fusion rate of a hydroxyapatite demineralized bone matrix (DBM) with post-laminectomy acquired autograft in lumbar interbody fusion surgery and to evaluate the correlation between fusion rate and clinical outcome. From January 2013 to April 2014, 98 patients underwent lumbar interbody fusion surgery with hydroxyapatite DBM (HA-DBM group) in our institute. Of those patients, 65 received complete CT scans for 12 months postoperatively in order to evaluate fusion status. For comparison with autograft, we selected another 65 patients who underwent lumbar interbody fusion surgery with post-laminectomy acquired autograft (Autograft group) during the same period. Both fusion material groups were matched in terms of age, sex, body mass index (BMI), and bone mineral density (BMD). To evaluate the clinical outcomes, we analyzed the results of visual analogue scale (VAS), Oswestry Disability Index (ODI), and Short Form Health Survey (SF-36). We reviewed the CT scans of 149 fusion levels in 130 patients (HA-DBM group, 75 levels/65 patients; Autograft group, 74 levels/65 patients). Age, sex, BMI, and BMD were not significantly different between the groups (p=0.528, p=0.848, p=0.527, and p=0.610, respectively). The HA-DBM group showed 39 of 75 fused levels (52%), and the Autograft group showed 46 of 74 fused levels (62.2%). This difference was not statistically significant (p=0.21). In the HA-DBM group, older age and low BMD were significantly associated with non-fusion (61.24 vs. 66.68, p=0.027; -1.63 vs. -2.29, p=0.015, respectively). VAS and ODI showed significant improvement after surgery when fusion was successfully achieved in both groups (p=0.004, p=0.002, HA-DBM group; p=0.012, p=0.03, Autograft group). The fusion rates of the hydroxyapatite DBM and Autograft groups were not significantly different. In addition, clinical outcomes were similar between the groups. However, older age and low BMD are risk factors that might induce non-union after surgery with hydroxyapatite DBM.

Matched Comparison of Fusion Rates between Hydroxyapatite Demineralized Bone Matrix and Autograft in Lumbar Interbody Fusion

PubMed Central

Kim, Dae Hwan; Lee, Nam; Shin, Dong Ah; Yi, Seong; Kim, Keung Nyun

2016-01-01

Objective To compare the fusion rate of a hydroxyapatite demineralized bone matrix (DBM) with post-laminectomy acquired autograft in lumbar interbody fusion surgery and to evaluate the correlation between fusion rate and clinical outcome. Methods From January 2013 to April 2014, 98 patients underwent lumbar interbody fusion surgery with hydroxyapatite DBM (HA-DBM group) in our institute. Of those patients, 65 received complete CT scans for 12 months postoperatively in order to evaluate fusion status. For comparison with autograft, we selected another 65 patients who underwent lumbar interbody fusion surgery with post-laminectomy acquired autograft (Autograft group) during the same period. Both fusion material groups were matched in terms of age, sex, body mass index (BMI), and bone mineral density (BMD). To evaluate the clinical outcomes, we analyzed the results of visual analogue scale (VAS), Oswestry Disability Index (ODI), and Short Form Health Survey (SF-36). Results We reviewed the CT scans of 149 fusion levels in 130 patients (HA-DBM group, 75 levels/65 patients; Autograft group, 74 levels/65 patients). Age, sex, BMI, and BMD were not significantly different between the groups (p=0.528, p=0.848, p=0.527, and p=0.610, respectively). The HA-DBM group showed 39 of 75 fused levels (52%), and the Autograft group showed 46 of 74 fused levels (62.2%). This difference was not statistically significant (p=0.21). In the HA-DBM group, older age and low BMD were significantly associated with non-fusion (61.24 vs. 66.68, p=0.027; -1.63 vs. -2.29, p=0.015, respectively). VAS and ODI showed significant improvement after surgery when fusion was successfully achieved in both groups (p=0.004, p=0.002, HA-DBM group; p=0.012, p=0.03, Autograft group). Conclusion The fusion rates of the hydroxyapatite DBM and Autograft groups were not significantly different. In addition, clinical outcomes were similar between the groups. However, older age and low BMD are risk factors that might induce non-union after surgery with hydroxyapatite DBM. PMID:27446517

Study of incomplete fusion reaction dynamics in 13C +165 Ho system and its dependence on various entrance channel parameters

NASA Astrophysics Data System (ADS)

Tali, Suhail A.; Kumar, Harish; Ansari, M. Afzal; Ali, Asif; Singh, D.; Ali, Rahbar; Giri, Pankaj K.; Linda, Sneha B.; Parashari, Siddharth; Kumar, R.; Singh, R. P.; Muralithar, S.

2018-02-01

The excitation functions for the evaporation residues populated in the interaction of 13C +165 Ho system have been measured at projectile energies ≈ 4-7 MeV/nucleon. Stacked foil activation technique followed by off-line γ-ray spectroscopy have been employed in the present work. The experimentally measured cross-sections are analyzed in the frame work of statistical model code PACE4, which takes into account only the complete fusion reaction cross-sections. The evaporation residues populated via xn and pxn channels were found to be in good agreement with the PACE4 predictions, while a significant enhancement in the measured cross-sections over PACE4 predictions is observed in case of α-emitting channels, which may be attributed to the incomplete fusion process. For the better understanding of incomplete fusion dynamics, the incomplete fusion fraction has also been deduced and its sensitivity with various entrance channel parameters like: projectile energy, mass-asymmetry, projectile structure in terms of Qα-value and Coulomb effect has been studied in the present work. The incomplete fusion fraction is found to increase with increasing the projectile energy and a strong projectile structure dependent mass-asymmetry systematic is also observed. The incomplete fusion fraction is also found to be small for more negative Qα-value projectile (13C) induced reactions as compared to less negative Qα-value projectiles (12C, 16O and 20Ne) induced reactions with the same target nucleus 165Ho. An interesting trend is obtained on further investigation of incomplete fusion dependence on Coulomb effect (ZPZT).

Isoform-specific PKA dynamics revealed by dye-triggered aggregation and DAKAP1alpha-mediated localization in living cells.

PubMed

Martin, Brent R; Deerinck, Thomas J; Ellisman, Mark H; Taylor, Susan S; Tsien, Roger Y

2007-09-01

The tetracysteine sequence YRECCPGCCMWR fused to the N terminus of green fluorescent protein (GFP) self-aggregates upon biarsenical labeling in living cells or in vitro. Such dye-triggered aggregates form temperature-dependent morphologies and are dispersed by photobleaching. Fusion of the biarsenical aggregating GFP to the regulatory (R) or catalytic (C) subunit of PKA traps intact holoenzyme in compact fluorescent puncta upon biarsenical labeling. Contrary to the classical model of PKA activation, elevated cAMP does not allow RIalpha and Calpha to diffuse far apart unless the pseudosubstrate inhibitor PKI or locally concentrated substrate is coexpressed. However, RIIalpha releases Calpha upon elevated cAMP alone, dependent on autophosphorylation of the RIIalpha inhibitory domain. DAKAP1alpha overexpression induced R and C outer mitochondrial colocalization and showed similar regulation. Overall, effective separation of type I PKA is substrate dependent, whereas type II PKA dissociation relies on autophosphorylation.

OBSERVATIONS ON THE UPTAKE OF TRITIATED THYMIDINE IN THE PRONUCLEI OF FERTILIZED SAND DOLLAR EMBRYOS.

PubMed

Simmel, E B; Karnofsky, D A

1961-05-01

Following fertilization of the egg of the sand dollar Echinarachnius parma, tritiated thymidine (H(3)TDR) was taken up independently by the male and female pronuclei beginning within about 15 to 20 minutes, and the labeled pronuclei fused at about 30 to 40 minutes. At cleavage 90 minutes later the labeled nuclear material was distributed to both daughter cells. Unfertilized eggs and sperm exposed to H(3)TDR did not show nuclear localization of thymidine. DNA replication, thus, is initiated in the haploid pronuclei shortly after fertilization and prior to fusion. The major portion of DNA synthesis, as evidenced by thymidine uptake, appears to be during a 20 to 30 minute period after fertilization. Fertilization is associated with the activation of a mechanism which initiates early and independent replication of DNA in both the male and female pronuclei.

OBSERVATIONS ON THE UPTAKE OF TRITIATED THYMIDINE IN THE PRONUCLEI OF FERTILIZED SAND DOLLAR EMBRYOS

PubMed Central

Simmel, Eva B.; Karnofsky, David A.

1961-01-01

Following fertilization of the egg of the sand dollar Echinarachnius parma, tritiated thymidine (H3TDR) was taken up independently by the male and female pronuclei beginning within about 15 to 20 minutes, and the labeled pronuclei fused at about 30 to 40 minutes. At cleavage 90 minutes later the labeled nuclear material was distributed to both daughter cells. Unfertilized eggs and sperm exposed to H3TDR did not show nuclear localization of thymidine. DNA replication, thus, is initiated in the haploid pronuclei shortly after fertilization and prior to fusion. The major portion of DNA synthesis, as evidenced by thymidine uptake, appears to be during a 20 to 30 minute period after fertilization. Fertilization is associated with the activation of a mechanism which initiates early and independent replication of DNA in both the male and female pronuclei. PMID:19866590

Assessing Climate Change Impacts for DoD installations in the Southwest United States During the Warm Season

DTIC Science & Technology

2017-03-10

20 4. Statistical analysis methods to characterize distributions and trends...duration precipitation diagram from convective- permitting simulations for Barry Goldwater Range, Arizona. ix Figure 60: Statistically ...Same as Fig. 60 for other DoD facilities in the Southwest as labeled. Figure 62: Statistically significant model ensemble changes in rainfall

Adult Perceptions of In-Class Collaborative Problem Solving as Mitigation for Statistics Anxiety

ERIC Educational Resources Information Center

Kinkead, Karl J.; Miller, Heather; Hammett, Richard

2016-01-01

Two purposes existed for initiating this qualitative case study involving adults who had completed a college-level business statistics course. The first purpose was to explore adult challenges with stress and anxiety during the course: a phenomenon labeled statistics anxiety in the literature. The second purpose was to gain insight into adult…

Results of the prospective, randomized, controlled multicenter Food and Drug Administration investigational device exemption study of the ProDisc-C total disc replacement versus anterior discectomy and fusion for the treatment of 1-level symptomatic cervical disc disease.

PubMed

Murrey, Daniel; Janssen, Michael; Delamarter, Rick; Goldstein, Jeffrey; Zigler, Jack; Tay, Bobby; Darden, Bruce

2009-04-01

Cervical total disc replacement (TDR) is intended to address radicular pain and preserve functional motion between two vertebral bodies in patients with symptomatic cervical disc disease (SCDD). The purpose of this trial is to compare the safety and efficacy of cervical TDR, ProDisc-C (Synthes Spine Company, L.P., West Chester, PA), to anterior cervical discectomy and fusion (ACDF) surgery for the treatment of one-level SCDD between C3 and C7. The study was conducted at 13 sites. A noninferiority design with a 1:1 randomization was used. Two hundred nine patients were randomized and treated (106 ACDF; 103 ProDisc-C). Visual analog scale (VAS) pain and intensity (neck and arm), VAS satisfaction, neck disability index (NDI), neurological exam, device success, adverse event occurrence, and short form-36 (SF-36) standardized questionnaires. A prospective, randomized, controlled clinical trial was performed. Patients were enrolled and treated in accordance with the US Food and Drug Administration (FDA)-approved protocol. Patients were assessed pre- and postoperatively at six weeks, 3, 6, 12, 18, and 24 months. Demographics were similar between the two patient groups (ProDisc-C: 42.1+/-8.4 years, 44.7% males; Fusion: 43.5 +/- 7.1 years, 46.2% males). The most commonly treated level was C5-C6 (ProDisc-C: 56.3%; Fusion=57.5%). NDI and SF-36 scores were significantly less compared with presurgery scores at all follow-up visits for both the treatment groups (p<.0001). VAS neck pain intensity and frequency as well as VAS arm pain intensity and frequency were statistically lower at all follow-up timepoints compared with preoperative levels (p<.0001) but were not different between treatments. Neurologic success (improvement or maintenance) was achieved at 24 months in 90.9% of ProDisc-C and 88.0% of Fusion patients (p=.638). Results show that at 24 months postoperatively, 84.4% of ProDisc-C patients achieved a more than or equal to 4 degrees of motion or maintained motion relative to preoperative baseline at the operated level. There was a statistically significant difference in the number of secondary surgeries with 8.5% of Fusion patients needing a re-operation, revision, or supplemental fixation within the 24 month postoperative period compared with 1.8% of ProDisc-C patients (p=.033). At 24 months, there was a statistically significant difference in medication usage with 89.9% of ProDisc-C patients not on strong narcotics or muscle relaxants, compared with 81.5% of Fusion patients. The results of this clinical trial demonstrate that ProDisc-C is a safe and effective surgical treatment for patients with disabling cervical radiculopathy because of single-level disease. By all primary and secondary measures evaluated, clinical outcomes after ProDisc-C implantation were either equivalent or superior to those same clinical outcomes after Fusion.

Sensor data validation and reconstruction. Phase 1: System architecture study

NASA Technical Reports Server (NTRS)

1991-01-01

The sensor validation and data reconstruction task reviewed relevant literature and selected applicable validation and reconstruction techniques for further study; analyzed the selected techniques and emphasized those which could be used for both validation and reconstruction; analyzed Space Shuttle Main Engine (SSME) hot fire test data to determine statistical and physical relationships between various parameters; developed statistical and empirical correlations between parameters to perform validation and reconstruction tasks, using a computer aided engineering (CAE) package; and conceptually designed an expert system based knowledge fusion tool, which allows the user to relate diverse types of information when validating sensor data. The host hardware for the system is intended to be a Sun SPARCstation, but could be any RISC workstation with a UNIX operating system and a windowing/graphics system such as Motif or Dataviews. The information fusion tool is intended to be developed using the NEXPERT Object expert system shell, and the C programming language.

Long-term Clinical and Radiographic Outcomes of Pedicle Subtraction Osteotomy for Fixed Sagittal Imbalance: Does Level of Proximal Fusion Affect the Outcome? Minimum 5-Year Follow-up.

PubMed

Yagi, Mitsuru; King, Akilah B; Cunningham, Matthew E; Boachie-Adjei, Oheneba

2013-03-01

Retrospective case series of surgically treated adult patients with fixed sagittal imbalance. To assess clinical and radiographic changes after pedicle subtraction osteotomy (PSO) to treat adult fixed sagittal imbalance. Although recent reports have shown favorable clinical outcomes for PSO, few reports have published long-term follow-up outcomes. It is also unknown whether long-term outcomes are correlated with the level of proximal fusion and the radiographic changes that are observed after PSO. We reviewed the charts, X-rays, and postoperative SRS-22 and Oswestry Disability Index (ODI) scores of 32 adult patients who presented with fixed sagittal imbalance and were treated with lumbar PSO. Long fusions were defined as those proximal to T6, and short fusions were defined as those below T8. Measured radiographic parameters included thoracic kyphosis, lumbar lordosis (LL), sacral slope, pelvic incidence, and sagittal balance (SVA). Statistical analysis included Student t test and chi-square test. A p value of < .05 and a confidence interval of 95% were considered statistically significant. Among the reviewed cases were 23 women and 9 men, with a mean age of 50.9 years (range, 33-76 years) and a mean follow-up 8.6 years (range, 5-16 years). The LL increased from -16.0° preoperatively to -52.1° postoperatively. This metric decreased to -51.0° at final follow-up. The SVA decreased from 10.4 cm preoperatively to 3.6 cm postoperatively. The SVA increased to 5.4 cm at the final follow-up visit. There were 17 long fusions and 15 short fusions. The SRS scores at the final follow-up time point were: total, 3.63; function, 3.59; pain, 3.68; self-image, 3.46; mental health, 3.56; satisfaction, 4.26. A total of 16 patients exhibited minimal disability, 11 exhibited moderate disability, and 2 exhibited severe disability in ODI scores at the final follow-up visit (average, 28.2%). The SRS and ODI scores were not significantly different between groups (p = .64 for SRS; p = .59 for ODI). We observed no significant differences between groups with respect to the LL, sacral slope, or pelvic incidence. The observed increase in SVA at the final follow-up visit was significantly larger in the short fusion group compared with the increase we observed in the long fusion group (p = .03). The thoracic kyphosis (T5-T12) and proximal junctional angle at the final follow-up visit also significantly increased in patients who underwent a short fusion (p < .001). A total of 14 major complications occurred in 12 patients (8 in the short fusion group and 6 in the long fusion group) (p = .43). Eight patients required additional surgery to treat these complications. In a group of adults presenting with fixed sagittal imbalance, PSO provided good sagittal balance and maintained favorable clinical outcomes in both the short and long fusion groups despite a slight decrease in the SVA and a high complication rate. The data suggest that the loss of sagittal balance may be attributed to increase global and junctional kyphosis in short fusion groups, and should be monitored for long-term outcomes. Particular attention should be paid to the long-term deterioration of the SVA in adults who present with fixed sagittal imbalance after PSO. Copyright © 2013 Scoliosis Research Society. Published by Elsevier Inc. All rights reserved.

Productivity benefits of minimally invasive surgery in patients with chronic sacroiliac joint dysfunction.

PubMed

Saavoss, Josh D; Koenig, Lane; Cher, Daniel J

2016-01-01

Sacroiliac joint (SIJ) dysfunction is associated with a marked decrease in quality of life. Increasing evidence supports minimally invasive SIJ fusion as a safe and effective procedure for the treatment of chronic SIJ dysfunction. The impact of SIJ fusion on worker productivity is not known. Regression modeling using data from the National Health Interview Survey was applied to determine the relationship between responses to selected interview questions related to function and economic outcomes. Regression coefficients were then applied to prospectively collected, individual patient data in a randomized trial of SIJ fusion (INSITE, NCT01681004) to estimate expected differences in economic outcomes across treatments. Patients who receive SIJ fusion using iFuse Implant System(®) have an expected increase in the probability of working of 16% (95% confidence interval [CI] 11%-21%) relative to nonsurgical patients. The expected change in earnings across groups was US $3,128 (not statistically significant). Combining the two metrics, the annual increase in worker productivity given surgical vs nonsurgical care was $6,924 (95% CI $1,890-$11,945). For employees with chronic, severe SIJ dysfunction, minimally invasive SIJ fusion may improve worker productivity compared to nonsurgical treatment.

Outcomes of bilateral sacroiliac joint fusions and the importance of understanding potential coexisting lumbosacral pathology that might also require surgical treatment.

PubMed

Dall, Bruce E; Eden, Sonia V

2015-06-01

Only one study in the literature describes performing a bilateral sacroiliac joint fusion, and the results were poor. Many patients needing a bilateral sacroiliac joint fusion frequently have had previous lumbosacral surgeries and present with lumbosacral pain as well. This study reviews our results in consecutive patients having had a bilateral sacroiliac joint fusion over a five-year period. Fifteen patients had bilateral sacroiliac joint fusions with 13 having concurrent lumbosacral fusions. The modified posterior midline fascial splitting approach, first described by Belanger was utilized. Patients were followed for an average of 30.3 months. There were no infections, neurovascular injuries, lasting morbidity or deaths. One non-union of a sacroiliac joint (7%) occurred, which after revision was satisfactory. There was a statistically significant drop in pain (p=0.01488) using the VAS, and patient satisfaction rates were 86%. With all those patients saying they would have the surgery again for the same result. There was no significant increase in functionality. Patients needing bilateral sacroiliac joint fusions frequently fall into the "failed back" category, and it is important to evaluate both the sacroiliac joints and the lumbosacral spine for potential pain generators. This study shows that by treating all the pain generators in both areas there were significant decreases in pain, low complications, low re-operation rates, and high patient satisfaction scores. Overall functionality, however, was not positively affected.

Grafton and local bone have comparable outcomes to iliac crest bone in instrumented single-level lumbar fusions.

PubMed

Kang, James; An, Howard; Hilibrand, Alan; Yoon, S Tim; Kavanagh, Eoin; Boden, Scott

2012-05-20

Prospective multicenter randomized clinical trail. The goal of our 2-year prospective study was to perform a randomized clinical trial comparing the outcomes of Grafton demineralized bone matrix (DBM) Matrix with local bone with that of iliac crest bone graft (ICBG) in a single-level instrumented posterior lumbar fusion. There has been extensive research and development in identifying a suitable substitute to replace autologous ICBG that is associated with known morbidities. DBMs are a class of commercially available grafting agents that are prepared from allograft bone. Many such products have been commercially available for clinical use; however, their efficacy for spine fusion has been mostly based on anecdotal evidence rather than randomized controlled clinical trials. Forty-six patients were randomly assigned (2:1) to receive Grafton DBM Matrix with local bone (30 patients) or autologous ICBG (16 patients). The mean age was 64 (females [F] = 21, males [M] = 9) in the DBM group and 65 (F = 9, M = 5) in the ICBG group. An independent radiologist evaluated plain radiographs and computed tomographic scans at 6-month, 1-year, and 2-year time points. Clinical outcomes were measured using Oswestry Disability Index (ODI) and Medical Outcomes Study 36-Item Short Form Health Survey. Forty-one patients (DBM = 28 and ICBG = 13) completed the 2-year follow-up. Final fusion rates were 86% (Grafton Matrix) versus 92% (ICBG) (P = 1.0 not significant). The Grafton group showed slightly better improvement in ODI score than the ICBG group at the final 2-year follow-up (Grafton [16.2] and ICBG [22.7]); however, the difference was not statistically significant (P = 0.2346 at 24 mo). Grafton showed consistently higher physical function scores at 24 months; however, differences were not statistically significant (P = 0.0823). Similar improvements in the physical component summary scores were seen in both the Grafton and ICBG groups. There was a statistically significant greater mean intraoperative blood loss in the ICBG group than in the Grafton group (P < 0.0031). At 2-year follow-up, subjects who were randomized to Grafton Matrix and local bone achieved an 86% overall fusion rate and improvements in clinical outcomes that were comparable with those in the ICBG group.

Automated Volumetry and Regional Thickness Analysis of Hippocampal Subfields and Medial Temporal Cortical Structures in Mild Cognitive Impairment

PubMed Central

Yushkevich, Paul A.; Pluta, John B.; Wang, Hongzhi; Xie, Long; Ding, Song-Lin; Gertje, E. C.; Mancuso, Lauren; Kliot, Daria; Das, Sandhitsu R.; Wolk, David A.

2014-01-01

We evaluate a fully automatic technique for labeling hippocampal subfields and cortical subregions in the medial temporal lobe (MTL) in in vivo 3 Tesla MRI. The method performs segmentation on a T2-weighted MRI scan with 0.4 × 0.4 × 2.0 mm3 resolution, partial brain coverage, and oblique orientation. Hippocampal subfields, entorhinal cortex, and perirhinal cortex are labeled using a pipeline that combines multi-atlas label fusion and learning-based error correction. In contrast to earlier work on automatic subfield segmentation in T2-weighted MRI (Yushkevich et al., 2010), our approach requires no manual initialization, labels hippocampal subfields over a greater anterior-posterior extent, and labels the perirhinal cortex, which is further subdivided into Brodmann areas 35 and 36. The accuracy of the automatic segmentation relative to manual segmentation is measured using cross-validation in 29 subjects from a study of amnestic Mild Cognitive Impairment (aMCI), and is highest for the dentate gyrus (Dice coefficient is 0.823), CA1 (0.803), perirhinal cortex (0.797) and entorhinal cortex (0.786) labels. A larger cohort of 83 subjects is used to examine the effects of aMCI in the hippocampal region using both subfield volume and regional subfield thickness maps. Most significant differences between aMCI and healthy aging are observed bilaterally in the CA1 subfield and in the left Brodmann area 35. Thickness analysis results are consistent with volumetry, but provide additional regional specificity and suggest non-uniformity in the effects of aMCI on hippocampal subfields and MTL cortical subregions. PMID:25181316

Technical Topic 3.2.2.d Bayesian and Non-Parametric Statistics: Integration of Neural Networks with Bayesian Networks for Data Fusion and Predictive Modeling

DTIC Science & Technology

2016-05-31

and included explosives such as TATP, HMTD, RDX, RDX, ammonium nitrate , potassium perchlorate, potassium nitrate , sugar, and TNT. The approach...Distribution Unlimited UU UU UU UU 31-05-2016 15-Apr-2014 14-Jan-2015 Final Report: Technical Topic 3.2.2. d Bayesian and Non- parametric Statistics...of Papers published in non peer-reviewed journals: Final Report: Technical Topic 3.2.2. d Bayesian and Non-parametric Statistics: Integration of Neural

Phosphorylation and nuclear localization of the varicella-zoster virus gene 63 protein.

PubMed Central

Stevenson, D; Xue, M; Hay, J; Ruyechan, W T

1996-01-01

The protein encoded by varicella-zoster virus open reading frame 63 and carboxy-terminal deletions of the same were expressed either as fusion proteins at the carboxy terminus of the maltose-binding protein in Escherichia coli or independently in transfected mammalian cells. The truncations contained amino acids 1 to 142 (63 delta N) or 1 to 210 (63 delta K) of the complete 278-amino-acid primary sequence. Recombinant casein kinase II phosphorylated the 63F and 63 delta KF fusion proteins in vitro but did not phosphorylate the 63 delta NF fusion protein, implying that phosphorylation occurred between amino acids 142 and 210. Immunoprecipitation of 35S- or 32P-labelled extracts of cells transfected with plasmids expressing 63, 63 delta N, or 63 delta K also indicated that in situ phosphorylation most likely occurred between amino acids 142 and 210. These combined results suggest that casein kinase II plays a significant role in the phosphorylation of the varicella-zoster virus 63 protein. Indirect immunofluorescence of transfected cells indicated nuclear localization of the 63 protein and cytoplasmic localization of 63 delta K and 63 delta N, implying a requirement for sequences between amino acids 210 and 278 for efficient nuclear localization. PMID:8523589

Effects of Conflicts of Interest on Practice Patterns and Complication Rates in Spine Surgery.

PubMed

Cook, Ralph W; Weiner, Joseph A; Schallmo, Michael S; Chun, Danielle S; Barth, Kathryn A; Singh, Sameer K; Hsu, Wellington K

2017-09-01

Retrospective cohort study. We sought to determine whether financial relationships with industry had any impact on operative and/or complication rates of spine surgeons performing fusion surgeries. Recent actions from Congress and the Institute of Medicine have highlighted the importance of conflicts of interest among physicians. Orthopedic surgeons and neurosurgeons have been identified as receiving the highest amount of industry payments among all specialties. No study has yet investigated the potential effects of disclosed industry payments with quality and choices of patient care. A comprehensive database of spine surgeons in the United States with compiled data of industry payments, operative fusion rates, and complication rates was created. Practice pattern data were derived from a publicly available Medicare-based database generated from selected CPT codes from 2011 to 2012. Complication rate data from 2009 to 2013 were extracted from the ProPublica-Surgeon-Scorecard database, which utilizes postoperative inhospital mortality and 30-day-readmission for designated conditions as complications of surgery. Data regarding industry payments from 2013 to 2014 were derived from the Open Payments website. Surgeons performing <10 fusions, those without complication data, and those whose identity could not be verified through public records were excluded. Pearson correlation coefficients and multivariate regression analyses were used to determine the relationship between industry payments, operative fusion rate, and/or complication rate. A total of 2110 surgeons met the inclusion criteria for our database. The average operative fusion rate was 8.8% (SD 4.8%), whereas the average complication rate for lumbar and cervical fusion was 4.1% and 1.9%, respectively. Pearson correlation analysis revealed a statistically significant but negligible relationship between disclosed payments/transactions and both operative fusion and complication rates. Our findings do not support a strong correlation between the payments a surgeon receives from industry and their decisions to perform spine fusion or associated complication rates. Large variability in the rate of fusions performed suggests a poor consensus for indications for spine fusion surgery. 3.

Multidirectional testing of one- and two-level ProDisc-L versus simulated fusions.

PubMed

Panjabi, Manohar; Henderson, Gweneth; Abjornson, Celeste; Yue, James

2007-05-20

An in vitro human cadaveric biomechanical study. To evaluate intervertebral rotation changes due to lumbar ProDisc-L compared with simulated fusion, using follower load and multidirectional testing. Artificial discs, as opposed to the fusions, are thought to decrease the long-term accelerated degeneration at adjacent levels. A biomechanical assessment can be helpful, as the long-term clinical evaluation is impractical. Six fresh human cadaveric lumbar specimens (T12-S1) underwent multidirectional testing in flexion-extension, bilateral lateral bending, and bilateral torsion using the Hybrid test method. First, intact specimen total range of rotation (T12-S1) was determined. Second, using pure moments again, this range of rotation was achieved in each of the 5 constructs: A) ProDisc-L at L5-S1; B) fusion at L5-S1; C) ProDisc-L at L4-L5 and fusion at L5-S1; D) ProDisc-L at L4-L5 and L5-S1; and E) 2-level fusion at L4-L5 to L5-S1. Significant changes in the intervertebral rotations due to each construct were determined at the operated and nonoperated levels using repeated measures single factor ANOVA and Bonferroni statistical tests (P < 0.05). Adjacent-level effects (ALEs) were defined as the percentage changes in intervertebral rotations at the nonoperated levels due to the constructs. One- and 2-level ProDisc-L constructs showed only small ALE in any of the 3 rotations. In contrast, 1- and 2-level fusions showed increased ALE in all 3 directions (average, 7.8% and 35.3%, respectively, for 1 and 2 levels). In the disc plus fusion combination (construct C), the ALEs were similar to the 1-level fusion alone. In general, ProDisc-L preserved physiologic motions at all spinal levels, while the fusion simulations resulted in significant ALE.

Graph-based segmentation for RGB-D data using 3-D geometry enhanced superpixels.

PubMed

Yang, Jingyu; Gan, Ziqiao; Li, Kun; Hou, Chunping

2015-05-01

With the advances of depth sensing technologies, color image plus depth information (referred to as RGB-D data hereafter) is more and more popular for comprehensive description of 3-D scenes. This paper proposes a two-stage segmentation method for RGB-D data: 1) oversegmentation by 3-D geometry enhanced superpixels and 2) graph-based merging with label cost from superpixels. In the oversegmentation stage, 3-D geometrical information is reconstructed from the depth map. Then, a K-means-like clustering method is applied to the RGB-D data for oversegmentation using an 8-D distance metric constructed from both color and 3-D geometrical information. In the merging stage, treating each superpixel as a node, a graph-based model is set up to relabel the superpixels into semantically-coherent segments. In the graph-based model, RGB-D proximity, texture similarity, and boundary continuity are incorporated into the smoothness term to exploit the correlations of neighboring superpixels. To obtain a compact labeling, the label term is designed to penalize labels linking to similar superpixels that likely belong to the same object. Both the proposed 3-D geometry enhanced superpixel clustering method and the graph-based merging method from superpixels are evaluated by qualitative and quantitative results. By the fusion of color and depth information, the proposed method achieves superior segmentation performance over several state-of-the-art algorithms.

C-Terminal Fluorescent Labeling Impairs Functionality of DNA Mismatch Repair Proteins

PubMed Central

Brieger, Angela; Plotz, Guido; Hinrichsen, Inga; Passmann, Sandra; Adam, Ronja; Zeuzem, Stefan

2012-01-01

The human DNA mismatch repair (MMR) process is crucial to maintain the integrity of the genome and requires many different proteins which interact perfectly and coordinated. Germline mutations in MMR genes are responsible for the development of the hereditary form of colorectal cancer called Lynch syndrome. Various mutations mainly in two MMR proteins, MLH1 and MSH2, have been identified so far, whereas 55% are detected within MLH1, the essential component of the heterodimer MutLα (MLH1 and PMS2). Most of those MLH1 variants are pathogenic but the relevance of missense mutations often remains unclear. Many different recombinant systems are applied to filter out disease-associated proteins whereby fluorescent tagged proteins are frequently used. However, dye labeling might have deleterious effects on MutLα's functionality. Therefore, we analyzed the consequences of N- and C-terminal fluorescent labeling on expression level, cellular localization and MMR activity of MutLα. Besides significant influence of GFP- or Red-fusion on protein expression we detected incorrect shuttling of single expressed C-terminal GFP-tagged PMS2 into the nucleus and found that C-terminal dye labeling impaired MMR function of MutLα. In contrast, N-terminal tagged MutLαs retained correct functionality and can be recommended both for the analysis of cellular localization and MMR efficiency. PMID:22348133

Sequential Monte Carlo tracking of the marginal artery by multiple cue fusion and random forest regression.

PubMed

Cherry, Kevin M; Peplinski, Brandon; Kim, Lauren; Wang, Shijun; Lu, Le; Zhang, Weidong; Liu, Jianfei; Wei, Zhuoshi; Summers, Ronald M

2015-01-01

Given the potential importance of marginal artery localization in automated registration in computed tomography colonography (CTC), we have devised a semi-automated method of marginal vessel detection employing sequential Monte Carlo tracking (also known as particle filtering tracking) by multiple cue fusion based on intensity, vesselness, organ detection, and minimum spanning tree information for poorly enhanced vessel segments. We then employed a random forest algorithm for intelligent cue fusion and decision making which achieved high sensitivity and robustness. After applying a vessel pruning procedure to the tracking results, we achieved statistically significantly improved precision compared to a baseline Hessian detection method (2.7% versus 75.2%, p<0.001). This method also showed statistically significantly improved recall rate compared to a 2-cue baseline method using fewer vessel cues (30.7% versus 67.7%, p<0.001). These results demonstrate that marginal artery localization on CTC is feasible by combining a discriminative classifier (i.e., random forest) with a sequential Monte Carlo tracking mechanism. In so doing, we present the effective application of an anatomical probability map to vessel pruning as well as a supplementary spatial coordinate system for colonic segmentation and registration when this task has been confounded by colon lumen collapse. Published by Elsevier B.V.

FUSION ENERGY SCIENCES WORKSHOP ON PLASMA MATERIALS INTERACTIONS: Report on Science Challenges and Research Opportunities in Plasma Materials Interactions

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

Maingi, Rajesh; Zinkle, Steven J.; Foster, Mark S.

2015-05-01

The realization of controlled thermonuclear fusion as an energy source would transform society, providing a nearly limitless energy source with renewable fuel. Under the auspices of the U.S. Department of Energy, the Fusion Energy Sciences (FES) program management recently launched a series of technical workshops to “seek community engagement and input for future program planning activities” in the targeted areas of (1) Integrated Simulation for Magnetic Fusion Energy Sciences, (2) Control of Transients, (3) Plasma Science Frontiers, and (4) Plasma-Materials Interactions aka Plasma-Materials Interface (PMI). Over the past decade, a number of strategic planning activities1-6 have highlighted PMI and plasmamore » facing components as a major knowledge gap, which should be a priority for fusion research towards ITER and future demonstration fusion energy systems. There is a strong international consensus that new PMI solutions are required in order for fusion to advance beyond ITER. The goal of the 2015 PMI community workshop was to review recent innovations and improvements in understanding the challenging PMI issues, identify high-priority scientific challenges in PMI, and to discuss potential options to address those challenges. The community response to the PMI research assessment was enthusiastic, with over 80 participants involved in the open workshop held at Princeton Plasma Physics Laboratory on May 4-7, 2015. The workshop provided a useful forum for the scientific community to review progress in scientific understanding achieved during the past decade, and to openly discuss high-priority unresolved research questions. One of the key outcomes of the workshop was a focused set of community-initiated Priority Research Directions (PRDs) for PMI. Five PRDs were identified, labeled A-E, which represent community consensus on the most urgent near-term PMI scientific issues. For each PRD, an assessment was made of the scientific challenges, as well as a set of actions to address those challenges. No prioritization was attempted amongst these five PRDs. We note that ITER, an international collaborative project to substantially extend fusion science and technology, is implicitly a driver and beneficiary of the research described in these PRDs; specific ITER issues are discussed in the background and PRD chapters. For succinctness, we describe these PRDs directly below; a brief introduction to magnetic fusion and the workshop process/timeline is given in Chapter I, and panelists are listed in the Appendix.« less

[Effect of image fusion technology of radioactive particles implantation before and after the planning target and dosimetry].

PubMed

Jiang, Y L; Yu, J P; Sun, H T; Guo, F X; Ji, Z; Fan, J H; Zhang, L J; Li, X; Wang, J J

2017-08-01

Objective: To compare the post-implant target volumes and dosimetric evaluation with pre-plan, the gross tumor volume(GTV) by CT image fusion-based and the manual delineation of target volume in CT guided radioactive seeds implantation. Methods: A total of 10 patients treated under CT-guidance (125)I seed implantation during March 2016 to April 2016 were analyzed in Peking University Third Hospital.All patients underwent pre-operative CT simulation, pre-operative planning, implantation seeds, CT scanning after seed implantation and dosimetric evaluation of GTV.In every patient, post-implant target volumes were delineated by both two methods, and were divided into two groups. Group 1: image fusion pre-implantation simulation and post-operative CT image, then the contours of GTV were automatically performed by brachytherapy treatment planning system; Group 2: the contouring of the GTV on post-operative CT image were performed manually by three senior radiation oncologists independently. The average of three data was sets. Statistical analyses were performed using SPSS software, version 3.2.0. The paired t -test was used to compare the target volumes and D(90) parameters in two modality. Results: In Group 1, average volume of GTV in post-operation group was 12-167(73±56) cm(3). D(90) was 101-153 (142±19)Gy. In Group 2, they were 14-186(80±58)cm(3) and 96-146(122±16) Gy respectively. In both target volumes and D(90), there was no statistical difference between pre-operation and post-operation in Group 1.The D(90) was slightly lower than that of pre-plan group, but there was no statistical difference ( P =0.142); in Group 2, between pre-operation and post-operation group, there was a significant statistical difference in the GTV ( P =0.002). The difference of D(90) was similarly ( P <0.01). Conclusion: The method of delineation of post-implant GTV through fusion pre-implantation simulation and post-operative CT scan images, the contours of GTV are automatically performed by brachytherapy treatment planning system appears to have improved more accuracy, reproducibility and convenience than manual delineation of target volume by maximum reduce the interference from artificial factor and metal artifacts. Further work and more cases are required in the future.

A Preliminary Report on the CO2 Laser for Lumbar Fusion: Safety, Efficacy and Technical Considerations.

PubMed

Villavicencio, Alan T; Burneikiene, Sigita; Babuska, Jason M; Nelson, Ewell L; Mason, Alexander; Rajpal, Sharad

2015-04-01

The purpose of this study was to evaluate potential technical advantages of the CO2 laser technology in mini-open transforaminal lumbar interbody fusion (TLIF) surgeries and report our preliminary clinical data on the safety and clinical outcomes. There is currently no literature discussing the recently redeveloped CO2 laser technology application for lumbar fusion. Safety and clinical outcomes were compared between two groups: 24 patients that underwent CO2 laser-assisted one-level TLIF surgeries and 30 patients that underwent standard one-level TLIF surgeries without the laser. There were no neural thermal injuries or other intraoperative laser-related complications encountered in this cohort of patients. At a mean follow-up of 17.4 months, significantly reduced lower back pain scores (P=0.013) were reported in the laser-assisted patient group compared to a standard fusion patient group. Lower extremity radicular pain intensity scores were similar in both groups. Laser-assisted TLIF surgeries showed a tendency (P = 0.07) of shorter operative times that was not statistically significant. Based on this preliminary clinical report, the safety of the CO2 laser device for lumbar fusion surgeries was assessed. There were no neural thermal injuries or other intraoperative laser-related complications encountered in this cohort of patients. Further investigation of CO2 laser-assisted lumbar fusion procedures is warranted in order to evaluate its effect on clinical outcomes.

Facility Monitoring: A Qualitative Theory for Sensor Fusion

NASA Technical Reports Server (NTRS)

Figueroa, Fernando

2001-01-01

Data fusion and sensor management approaches have largely been implemented with centralized and hierarchical architectures. Numerical and statistical methods are the most common data fusion methods found in these systems. Given the proliferation and low cost of processing power, there is now an emphasis on designing distributed and decentralized systems. These systems use analytical/quantitative techniques or qualitative reasoning methods for date fusion.Based on other work by the author, a sensor may be treated as a highly autonomous (decentralized) unit. Each highly autonomous sensor (HAS) is capable of extracting qualitative behaviours from its data. For example, it detects spikes, disturbances, noise levels, off-limit excursions, step changes, drift, and other typical measured trends. In this context, this paper describes a distributed sensor fusion paradigm and theory where each sensor in the system is a HAS. Hence, given the reach qualitative information from each HAS, a paradigm and formal definitions are given so that sensors and processes can reason and make decisions at the qualitative level. This approach to sensor fusion makes it possible the implementation of intuitive (effective) methods to monitor, diagnose, and compensate processes/systems and their sensors. This paradigm facilitates a balanced distribution of intelligence (code and/or hardware) to the sensor level, the process/system level, and a higher controller level. The primary application of interest is in intelligent health management of rocket engine test stands.

Click chemistry for the conservation of cellular structures and fluorescent proteins: ClickOx.

PubMed

Löschberger, Anna; Niehörster, Thomas; Sauer, Markus

2014-05-01

Reactive oxygen species (ROS), including hydrogen peroxide, are known to cause structural damage not only in living, but also in fixed, cells. Copper-catalyzed azide-alkyne cycloaddition (click chemistry) is known to produce ROS. Therefore, fluorescence imaging of cellular structures, such as the actin cytoskeleton, remains challenging when combined with click chemistry protocols. In addition, the production of ROS substantially weakens the fluorescence signal of fluorescent proteins. This led us to develop ClickOx, which is a new click chemistry protocol for improved conservation of the actin structure and better conservation of the fluorescence signal of green fluorescent protein (GFP)-fusion proteins. Herein we demonstrate that efficient oxygen removal by addition of an enzymatic oxygen scavenger system (ClickOx) considerably reduces ROS-associated damage during labeling of nascent DNA with ATTO 488 azide by Cu(I)-catalyzed click chemistry. Standard confocal and super-resolution fluorescence images of phalloidin-labeled actin filaments and GFP/yellow fluorescent protein-labeled cells verify the conservation of the cytoskeleton microstructure and fluorescence intensity, respectively. Thus, ClickOx can be used advantageously for structure preservation in conventional and most notably in super-resolution microscopy methods. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Do labeled versus unlabeled treatments of alternatives' names influence stated choice outputs? Results from a mode choice study.

PubMed

Jin, Wen; Jiang, Hai; Liu, Yimin; Klampfl, Erica

2017-01-01

Discrete choice experiments have been widely applied to elicit behavioral preferences in the literature. In many of these experiments, the alternatives are named alternatives, meaning that they are naturally associated with specific names. For example, in a mode choice study, the alternatives can be associated with names such as car, taxi, bus, and subway. A fundamental issue that arises in stated choice experiments is whether to treat the alternatives' names as labels (that is, labeled treatment), or as attributes (that is, unlabeled treatment) in the design as well as the presentation phases of the choice sets. In this research, we investigate the impact of labeled versus unlabeled treatments of alternatives' names on the outcome of stated choice experiments, a question that has not been thoroughly investigated in the literature. Using results from a mode choice study, we find that the labeled or the unlabeled treatment of alternatives' names in either the design or the presentation phase of the choice experiment does not statistically affect the estimates of the coefficient parameters. We then proceed to measure the influence toward the willingness-to-pay (WTP) estimates. By using a random-effects model to relate the conditional WTP estimates to the socioeconomic characteristics of the individuals and the labeled versus unlabeled treatments of alternatives' names, we find that: a) Given the treatment of alternatives' names in the presentation phase, the treatment of alternatives' names in the design phase does not statistically affect the estimates of the WTP measures; and b) Given the treatment of alternatives' names in the design phase, the labeled treatment of alternatives' names in the presentation phase causes the corresponding WTP estimates to be slightly higher.

Do labeled versus unlabeled treatments of alternatives’ names influence stated choice outputs? Results from a mode choice study

PubMed Central

Jin, Wen; Jiang, Hai; Liu, Yimin; Klampfl, Erica

2017-01-01

Discrete choice experiments have been widely applied to elicit behavioral preferences in the literature. In many of these experiments, the alternatives are named alternatives, meaning that they are naturally associated with specific names. For example, in a mode choice study, the alternatives can be associated with names such as car, taxi, bus, and subway. A fundamental issue that arises in stated choice experiments is whether to treat the alternatives’ names as labels (that is, labeled treatment), or as attributes (that is, unlabeled treatment) in the design as well as the presentation phases of the choice sets. In this research, we investigate the impact of labeled versus unlabeled treatments of alternatives’ names on the outcome of stated choice experiments, a question that has not been thoroughly investigated in the literature. Using results from a mode choice study, we find that the labeled or the unlabeled treatment of alternatives’ names in either the design or the presentation phase of the choice experiment does not statistically affect the estimates of the coefficient parameters. We then proceed to measure the influence toward the willingness-to-pay (WTP) estimates. By using a random-effects model to relate the conditional WTP estimates to the socioeconomic characteristics of the individuals and the labeled versus unlabeled treatments of alternatives’ names, we find that: a) Given the treatment of alternatives’ names in the presentation phase, the treatment of alternatives’ names in the design phase does not statistically affect the estimates of the WTP measures; and b) Given the treatment of alternatives’ names in the design phase, the labeled treatment of alternatives’ names in the presentation phase causes the corresponding WTP estimates to be slightly higher. PMID:28806764

Semantic Indexing of Multimedia Content Using Visual, Audio, and Text Cues

NASA Astrophysics Data System (ADS)

Adams, W. H.; Iyengar, Giridharan; Lin, Ching-Yung; Naphade, Milind Ramesh; Neti, Chalapathy; Nock, Harriet J.; Smith, John R.

2003-12-01

We present a learning-based approach to the semantic indexing of multimedia content using cues derived from audio, visual, and text features. We approach the problem by developing a set of statistical models for a predefined lexicon. Novel concepts are then mapped in terms of the concepts in the lexicon. To achieve robust detection of concepts, we exploit features from multiple modalities, namely, audio, video, and text. Concept representations are modeled using Gaussian mixture models (GMM), hidden Markov models (HMM), and support vector machines (SVM). Models such as Bayesian networks and SVMs are used in a late-fusion approach to model concepts that are not explicitly modeled in terms of features. Our experiments indicate promise in the proposed classification and fusion methodologies: our proposed fusion scheme achieves more than 10% relative improvement over the best unimodal concept detector.

Multi-focus image fusion algorithm using NSCT and MPCNN

NASA Astrophysics Data System (ADS)

Liu, Kang; Wang, Lianli

2018-04-01

Based on nonsubsampled contourlet transform (NSCT) and modified pulse coupled neural network (MPCNN), the paper proposes an effective method of image fusion. Firstly, the paper decomposes the source image into the low-frequency components and high-frequency components using NSCT, and then processes the low-frequency components by regional statistical fusion rules. For high-frequency components, the paper calculates the spatial frequency (SF), which is input into MPCNN model to get relevant coefficients according to the fire-mapping image of MPCNN. At last, the paper restructures the final image by inverse transformation of low-frequency and high-frequency components. Compared with the wavelet transformation (WT) and the traditional NSCT algorithm, experimental results indicate that the method proposed in this paper achieves an improvement both in human visual perception and objective evaluation. It indicates that the method is effective, practical and good performance.

Study of Heavy-ion Induced Fission for Heavy Element Synthesis

NASA Astrophysics Data System (ADS)

Nishio, K.; Ikezoe, H.; Hofmann, S.; Ackermann, D.; Aritomo, Y.; Comas, V. F.; Düllmann, Ch. E.; Heinz, S.; Heredia, J. A.; Heßberger, F. P.; Hirose, K.; Khuyagbaatar, J.; Kindler, B.; Kojouharov, I.; Lommel, B.; Makii, M.; Mann, R.; Mitsuoka, S.; Nishinaka, I.; Ohtsuki, T.; Saro, S.; Schädel, M.; Popeko, A. G.; Türler, A.; Wakabayashi, Y.; Watanabe, Y.; Yakushev, A.; Yeremin, A.

2014-05-01

Fission fragment mass distributions were measured in heavy-ion induced fission of 238U. The mass distributions changed drastically with incident energy. The results are explained by a change of the ratio between fusion and quasifission with nuclear orientation. A calculation based on a fluctuation dissipation model reproduced the mass distributions and their incident energy dependence. Fusion probability was determined in the analysis. Evaporation residue cross sections were calculated with a statistical model for the reactions of 30Si+238U and 34S+238U using the obtained fusion probability in the entrance channel. The results agree with the measured cross sections of 263,264Sg and 267,268Hs, produced by 30Si+238U and 34S+238U, respectively. It is also suggested that sub-barrier energies can be used for heavy element synthesis.

Statistical Mechanics of Viral Entry

NASA Astrophysics Data System (ADS)

Zhang, Yaojun; Dudko, Olga K.

2015-01-01

Viruses that have lipid-membrane envelopes infect cells by fusing with the cell membrane to release viral genes. Membrane fusion is known to be hindered by high kinetic barriers associated with drastic structural rearrangements—yet viral infection, which occurs by fusion, proceeds on remarkably short time scales. Here, we present a quantitative framework that captures the principles behind the invasion strategy shared by all enveloped viruses. The key to this strategy—ligand-triggered conformational changes in the viral proteins that pull the membranes together—is treated as a set of concurrent, bias field-induced activated rate processes. The framework results in analytical solutions for experimentally measurable characteristics of virus-cell fusion and enables us to express the efficiency of the viral strategy in quantitative terms. The predictive value of the theory is validated through simulations and illustrated through recent experimental data on influenza virus infection.

Hybrid Surgery Combined with Dynamic Stabilization System and Fusion for the Multilevel Degenerative Disease of the Lumbosacral Spine.

PubMed

Lee, Soo Eon; Jahng, Tae-Ahn; Kim, Hyun Jib

2015-01-01

As motion-preserving technique has been developed, the concept of hybrid surgery involves simultaneous application of two different kinds of devices, dynamic stabilization system and fusion technique. In the present study, the application of hybrid surgery for lumbosacral degenerative disease involving two-segments and its long-term outcome were investigated. Fifteen patients with hybrid surgery (Hybrid group) and 10 patients with two-segment fusion (Fusion group) were retrospectively compared. Preoperative grade for disc degeneration was not different between the two groups, and the most common operated segment had the most degenerated disc grade in both groups; L4-5 and L5-S1 in the Hybrid group, and L3-4 and L4-5 in Fusion group. Over 48 months of follow-up, lumbar lordosis and range of motion (ROM) at the T12-S1 global segment were preserved in the Hybrid group, and the segmental ROM at the dynamic stabilized segment maintained at final follow-up. The Fusion group had a significantly decreased global ROM and a decreased segmental ROM with larger angles compared to the Hybrid group. Defining a 2-mm decrease in posterior disc height (PDH) as radiologic adjacent segment pathology (ASP), these changes were observed in 6 and 7 patients in the Hybrid and Fusion group, respectively. However, the last PDH at the above adjacent segment had statistically higher value in Hybrid group. Pain score for back and legs was much reduced in both groups. Functional outcome measured by Oswestry disability index (ODI), however, had better improvement in Hybrid group. Hybrid surgery, combined dynamic stabilization system and fusion, can be effective surgical treatment for multilevel degenerative lumbosacral spinal disease, maintaining lumbar motion and delaying disc degeneration.

Hybrid Surgery Combined with Dynamic Stabilization System and Fusion for the Multilevel Degenerative Disease of the Lumbosacral Spine

PubMed Central

Lee, Soo Eon; Kim, Hyun Jib

2015-01-01

Background As motion-preserving technique has been developed, the concept of hybrid surgery involves simultaneous application of two different kinds of devices, dynamic stabilization system and fusion technique. In the present study, the application of hybrid surgery for lumbosacral degenerative disease involving two-segments and its long-term outcome were investigated. Methods Fifteen patients with hybrid surgery (Hybrid group) and 10 patients with two-segment fusion (Fusion group) were retrospectively compared. Results Preoperative grade for disc degeneration was not different between the two groups, and the most common operated segment had the most degenerated disc grade in both groups; L4-5 and L5-S1 in the Hybrid group, and L3-4 and L4-5 in Fusion group. Over 48 months of follow-up, lumbar lordosis and range of motion (ROM) at the T12-S1 global segment were preserved in the Hybrid group, and the segmental ROM at the dynamic stabilized segment maintained at final follow-up. The Fusion group had a significantly decreased global ROM and a decreased segmental ROM with larger angles compared to the Hybrid group. Defining a 2-mm decrease in posterior disc height (PDH) as radiologic adjacent segment pathology (ASP), these changes were observed in 6 and 7 patients in the Hybrid and Fusion group, respectively. However, the last PDH at the above adjacent segment had statistically higher value in Hybrid group. Pain score for back and legs was much reduced in both groups. Functional outcome measured by Oswestry disability index (ODI), however, had better improvement in Hybrid group. Conclusion Hybrid surgery, combined dynamic stabilization system and fusion, can be effective surgical treatment for multilevel degenerative lumbosacral spinal disease, maintaining lumbar motion and delaying disc degeneration. PMID:26484008

Direct labeling of serum proteins by fluorescent dye for antibody microarray.

PubMed

Klimushina, M V; Gumanova, N G; Metelskaya, V A

2017-05-06

Analysis of serum proteome by antibody microarray is used to identify novel biomarkers and to study signaling pathways including protein phosphorylation and protein-protein interactions. Labeling of serum proteins is important for optimal performance of the antibody microarray. Proper choice of fluorescent label and optimal concentration of protein loaded on the microarray ensure good quality of imaging that can be reliably scanned and processed by the software. We have optimized direct serum protein labeling using fluorescent dye Arrayit Green 540 (Arrayit Corporation, USA) for antibody microarray. Optimized procedure produces high quality images that can be readily scanned and used for statistical analysis of protein composition of the serum. Copyright © 2017 Elsevier Inc. All rights reserved.

Comparison of transforaminal lumbar interbody fusion outcomes in patients receiving rhBMP-2 versus autograft.

PubMed

Khan, Taleef R; Pearce, Kalin R; McAnany, Steven J; Peters, Colleen M; Gupta, Munish C; Zebala, Lukas P

2018-03-01

Recombinant human bone morphogenetic protein 2 (rhBMP-2) plays a pivotal role in complex spine surgery. Despite its limited approval, the off-label use of rhBMP-2 is prevalent, particularly in transforaminal lumbar interbody fusions (TLIFs). To determine the effectiveness and safety of rhBMP-2 use in TLIF procedures versus autograft. Retrospective cohort study. Patients older than 18 years undergoing spine surgery for lumbar degenerative spine disease at a single academic institution. Clinical outcome was determined according to patient records. Radiographic outcome was determined according to plain X-rays and computed tomography (CT). A retrospective study from 1997 to 2014 was conducted on 191 adults undergoing anterior-posterior instrumented spinal fusion with TLIF at a single academic institution. Patient data were gathered from operative notes, follow-up clinic notes, and imaging studies to determine complications and fusion rates. One hundred eighty-seven patients fit the criteria, which included patients with a minimum of one TLIF, and had a minimum 2-year radiographic and clinical follow-up. Patients were further classified into a BMP group (n=83) or non-BMP group (n=104). Three logistic regression models were run using rhBMP-2 exposure as the independent variable. The respective outcome variables were TLIF-related complications (radiculitis, seroma, osteolysis, and ectopic bone), surgical complications, and all complications. Bone morphogenetic protein (n=83) and non-BMP (n=104) groups had similar baseline demographics (sex, diabetes, pre-existing cancer). On average, the BMP and non-BMP groups were similarly aged (51.9 vs. 47.9 years, p>.05), but the BMP group had a shorter follow-up time (3.03 vs. 4.06 years; p<.001) and fewer smokers (8 vs. 21 patients; p<.048). The fusion rate for the BMP and non-BMP groups was 92.7% and 92.3%, respectively. The pseudoarthrosis rate was 7.5% (14 of 187 patients). Radiculitis was observed in seven patients in the BMP group (8.4%) and two patients in the non-BMP group (1.9%). Seroma was observed in two patients in the BMP group (2.4%) and none in the non-BMP group. No deep infections were observed in the BMP group, and in one patient in the non-BMP group (0.96%). Although patients exposed to BMP were at a significantlygreater risk of developing radiculitis and seroma (odds ratio [OR]=4.53, confidence interval [CI]=1.42-14.5), BMP exposure was not a significant predictor of surgical complications (OR=0.32, CI=0.10-1.00) or overall complications (OR=1.11, CI=0.53-2.34). The outcome of TLIF-related complications was too rare and the confidence interval too wide for practical significance of the first model. Evidence supports the hypothesis that off-label use of rhBMP-2 in TLIF procedures is relatively effective for achieving bone fusion at rates similar to patients receiving autograft. Patients exhibited similar complication rates between the two groups, with the BMP group exhibiting slightly higher rates of radiculitis and seroma. Copyright © 2017 Elsevier Inc. All rights reserved.

Expression of a synthetic gene encoding human insulin-like growth factor I in cultured mouse fibroblasts

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

Bayne, M.L.; Cascieri, M.A.; Kelder, B.

1987-05-01

A synthetic gene encoding human insulin-like growth factor I (hIGF-I) was assembled and inserted into an expression vector containing the cytomegalovirus immediate early (CMV-IE) transcriptional regulatory region and portions of the bovine growth hormone gene. The recombinant plasmid encodes a 97 amino acid fusion protein containing the first 27 amino acids of the bovine growth hormone precursor and the 70 amino acids of hIGF-I. This plasmid, when transiently introduced into cultured mouse fibroblasts, directs synthesis of the fusion protein, subsequent proteolytic removal of the bovine growth hormone signal peptide, and secretion of hIGF-I into the culture medium. Conditioned medium frommore » transfected cells inhibits binding of /sup 125/I-labeled IGF-I to type I IGF receptors on human placental membranes and to acid-stable human serum carrier proteins. The recombinant hIGF-I produced is biologically active, as monitored by the stimulation of DNA synthesis in vascular smooth muscle cells.« less

Long Term Non-Invasive Imaging of Embryonic Stem Cells Using Reporter Genes

PubMed Central

Sun, Ning; Lee, Andrew; Wu, Joseph C.

2013-01-01

Development of non-invasive and accurate methods to track cell fate following delivery will greatly expedite transition of embryonic stem (ES) cell therapy to the clinic. Here we describe a protocol for the in vivo monitoring of stem cell survival, proliferation, and migration using reporter genes. We established stable ES cell lines constitutively expressing double fusion (DF; enhanced green fluorescent protein and firefly luciferase) or triple fusion (TF; monomeric red fluorescent protein, firefly luciferase, and herpes simplex virus thymidine kinase) reporter genes using lentiviral transduction. We used fluorescence activated cell sorting to purify these populations in vitro, bioluminescence imaging and positron emission tomography imaging to track them in vivo, and fluorescence immunostaining to confirm the results ex vivo. Unlike other methods of cell tracking such as iron particle and radionuclide labeling, reporter genes are inherited genetically and can be used to monitor cell proliferation and survival for the lifetime of transplanted cells and their progeny. PMID:19617890

Bone Morphogenetic Protein Usage in Anterior Lumbar Interbody Fusion: What Else Can Go Wrong?

PubMed

Elias, Elias; Nasser, Zeina; Winegan, Lona; Verla, Terence; Omeis, Ibrahim

2018-03-01

Bone morphogenetic protein (BMP) graft showed promising outcome during early phases of its use. However, unreported adverse events and off-label use shattered its safe profile and raised concerns regarding its indication. In 2008 the U.S. Food and Drug Administration prohibited its use in anterior cervical spine procedures due to the possibility of edema, hematoma, and need to intubate. At the molecular level, BMPs act as multifactorial growth factors playing a role in cartilage, heart, and bone formation. However, its unfavorable effect on bone overgrowth or heterotopic ossification post spine surgeries has been described. Reported cases in the literature were limited to epidural bone formation. We present a rare and interesting case of a 59-year-old female, in whom BMP caused intradural bone growth several years after an anterior lumbar interbody fusion surgery. Caution must be exercised while using BMPs because of inadvertent complications. Copyright © 2017 Elsevier Inc. All rights reserved.

Effectiveness of FDA's new over-the-counter acetaminophen warning label in improving consumer risk perception of liver damage.

PubMed

Goyal, R K; Rajan, S S; Essien, E J; Sansgiry, S S

2012-12-01

The Food and Drug Administration (FDA) issued new organ-specific warning label requirements for over-the-counter (OTC) analgesic products in order to make consumers aware of the risk of liver damage when using acetaminophen. However, awareness of a health risk alone cannot ensure consumers' engagement in safe and preventive behaviour. In this study, we attempted to: (i) measure consumer risk perception of liver damage due to the OTC acetaminophen products and (ii) analyse the effectiveness of the new organ-specific warning label in improving consumer risk perception of liver damage and intention to perform protective behaviours while using OTC acetaminophen products. This within-subject experimental study used a convenience sample of English-speaking adults visiting OTC segments of selected pharmacy stores in Houston. Participants were randomly exposed to the old and new warning labels and their respective risk perception (measured on a visual analogue scale, 0%, no risk, to 100%, extreme risk) and behavioural intention (measured on a 7-point Likert scale) were recorded using a validated, self-administered questionnaire. Descriptive statistics and non-parametric Wilcoxon signed-rank tests were performed using sas statistical software (v 9.2) at a priori significance level of 0.05. Majority of participants (74.4%) were not aware of the new warnings; however, majority (67.8%) had prior knowledge of the risk. The mean risk perception score for the new warning label was found to be significantly higher (72.2% vs. 65.9%, P < 0.0001) than the old warning label. Similarly, the average intention score for the new warning label was significantly higher (5.06 vs. 4.86, P < 0.0001) than the old warning label. The new warning label mandated by FDA is effective in improving consumer risk perception of potential liver damage and may encourage protective behaviour. However, future studies are essential to assess the impact of the new label on actual changes in consumer behaviour and subsequent reduction in acetaminophen-related morbidity and mortality. © 2012 Blackwell Publishing Ltd.

Large-scale online semantic indexing of biomedical articles via an ensemble of multi-label classification models.

PubMed

Papanikolaou, Yannis; Tsoumakas, Grigorios; Laliotis, Manos; Markantonatos, Nikos; Vlahavas, Ioannis

2017-09-22

In this paper we present the approach that we employed to deal with large scale multi-label semantic indexing of biomedical papers. This work was mainly implemented within the context of the BioASQ challenge (2013-2017), a challenge concerned with biomedical semantic indexing and question answering. Our main contribution is a MUlti-Label Ensemble method (MULE) that incorporates a McNemar statistical significance test in order to validate the combination of the constituent machine learning algorithms. Some secondary contributions include a study on the temporal aspects of the BioASQ corpus (observations apply also to the BioASQ's super-set, the PubMed articles collection) and the proper parametrization of the algorithms used to deal with this challenging classification task. The ensemble method that we developed is compared to other approaches in experimental scenarios with subsets of the BioASQ corpus giving positive results. In our participation in the BioASQ challenge we obtained the first place in 2013 and the second place in the four following years, steadily outperforming MTI, the indexing system of the National Library of Medicine (NLM). The results of our experimental comparisons, suggest that employing a statistical significance test to validate the ensemble method's choices, is the optimal approach for ensembling multi-label classifiers, especially in contexts with many rare labels.

Spin distributions and cross sections of evaporation residues in the 28Si+176Yb reaction

NASA Astrophysics Data System (ADS)

Sudarshan, K.; Tripathi, R.; Sodaye, S.; Sharma, S. K.; Pujari, P. K.; Gehlot, J.; Madhavan, N.; Nath, S.; Mohanto, G.; Mukul, I.; Jhingan, A.; Mazumdar, I.

2017-02-01

Background: Non-compound-nucleus fission in the preactinide region has been an active area of investigation in the recent past. Based on the measurements of fission-fragment mass distributions in the fission of 202Po, populated by reactions with varying entrance channel mass asymmetry, the onset of non-compound-nucleus fission was proposed to be around ZpZt˜1000 [Phys. Rev. C 77, 024606 (2008), 10.1103/PhysRevC.77.024606], where Zp and Zt are the projectile and target proton numbers, respectively. Purpose: The present paper is aimed at the measurement of cross sections and spin distributions of evaporation residues in the 28Si+176Yb reaction (ZpZt=980 ) to investigate the fusion hindrance which, in turn, would give information about the contribution from non-compound-nucleus fission in this reaction. Method: Evaporation-residue cross sections were measured in the beam energy range of 129-166 MeV using the hybrid recoil mass analyzer (HYRA) operated in the gas-filled mode. Evaporation-residue cross sections were also measured by the recoil catcher technique followed by off-line γ -ray spectrometry at few intermediate energies. γ -ray multiplicities of evaporation residues were measured to infer about their spin distribution. The measurements were carried out using NaI(Tl) detector-based 4π-spin spectrometer from the Tata Institute of Fundamental Research, Mumbai, coupled to the HYRA. Results: Evaporation-residue cross sections were significantly lower compared to those calculated using the statistical model code pace2 [Phys. Rev. C 21, 230 (1980), 10.1103/PhysRevC.21.230] with the coupled-channel fusion model code ccfus [Comput. Phys. Commun. 46, 187 (1987), 10.1016/0010-4655(87)90045-2] at beam energies close to the entrance channel Coulomb barrier. At higher beam energies, experimental cross sections were close to those predicted by the model. Average γ -ray multiplicities or angular momentum values of evaporation residues were in agreement with the calculations of the code ccfus + pace2 within the experimental uncertainties at all the beam energies. Conclusions: Deviation of evaporation-residue cross sections from the "fusion + statistical model" predictions at beam energies close to the entrance channel Coulomb barrier indicates fusion hindrance at these beam energies which would lead to non-compound-nucleus fission. However, reasonable agreement of average angular momentum values of evaporation residues at these beam energies with those calculated using the coupled-channel fusion model with the statistical model codes ccfus + pace2 suggests that fusion suppression at beam energies close to the entrance channel Coulomb barrier where populated l waves are low is not l dependent.

User's Manual for Downscaler Fusion Software

EPA Science Inventory

Recently, a series of 3 papers has been published in the statistical literature that details the use of downscaling to obtain more accurate and precise predictions of air pollution across the conterminous U.S. This downscaling approach combines CMAQ gridded numerical model output...

Membrane fusion between baculovirus budded virus-enveloped particles and giant liposomes generated using a droplet-transfer method for the incorporation of recombinant membrane proteins.

PubMed

Nishigami, Misako; Mori, Takaaki; Tomita, Masahiro; Takiguchi, Kingo; Tsumoto, Kanta

2017-07-01

Giant proteoliposomes are generally useful as artificial cell membranes in biochemical and biophysical studies, and various procedures for their preparation have been reported. We present here a novel preparation technique that involves the combination of i) cell-sized lipid vesicles (giant unilamellar vesicles, GUVs) that are generated using the droplet-transfer method, where lipid monolayer-coated water-in-oil microemulsion droplets interact with oil/water interfaces to form enclosed bilayer vesicles, and ii) budded viruses (BVs) of baculovirus (Autographa californica nucleopolyhedrovirus) that express recombinant transmembrane proteins on their envelopes. GP64, a fusogenic glycoprotein on viral envelopes, is activated by weak acids and is thought to cause membrane fusion with liposomes. Using confocal laser scanning microscopy (CLSM), we observed that the single giant liposomes fused with octadecyl rhodamine B chloride (R18)-labeled wild-type BV envelopes with moderate leakage of entrapped soluble compounds (calcein), and the fusion profile depended on the pH of the exterior solution: membrane fusion occurred at pH ∼4-5. We further demonstrated that recombinant transmembrane proteins, a red fluorescent protein (RFP)-tagged GPCR (corticotropin-releasing hormone receptor 1, CRHR1) and envelope protein GP64 could be partly incorporated into membranes of the individual giant liposomes with a reduction of the pH value, though there were also some immobile fluorescent spots observed on their circumferences. This combination may be useful for preparing giant proteoliposomes containing the desired membranes and inner phases. Copyright © 2017 Elsevier B.V. All rights reserved.

Summary Statistics, Educational Achievement Gaps and the Ecological Fallacy

ERIC Educational Resources Information Center

Connolly, Paul

2006-01-01

Summary statistics continue to play an important role in identifying and monitoring patterns and trends in educational inequalities between differing groups of pupils over time. However, this article argues that their uncritical use can also encourage the labelling of whole groups of pupils as "underachievers" or…

Is less always more? The effects of low-fat labeling and caloric information on food intake, calorie estimates, taste preference, and health attributions.

PubMed

Ebneter, Daria S; Latner, Janet D; Nigg, Claudio R

2013-09-01

The present study examined whether low-fat labeling and caloric information affect food intake, calorie estimates, taste preference, and health perceptions. Participants included 175 female undergraduate students who were randomly assigned to one of four experimental conditions. A 2×2 between subjects factorial design was used in which the fat content label and caloric information of chocolate candy was manipulated. The differences in food intake across conditions did not reach statistical significance. However, participants significantly underestimated the calorie content of low-fat-labeled candy. Participants also rated low-fat-labeled candy as significantly better tasting when they had caloric information available. Participants endorsed more positive health attributions for low-fat-labeled candy than for regular-labeled candy, independent of caloric information. The inclusion of eating attitudes and behaviors as covariates did not alter the results. The study findings may be related to the "health halo" associated with low-fat foods and add to the research base by examining the interaction between low-fat and calorie labeling. Copyright © 2013 Elsevier Ltd. All rights reserved.

The acquisition of gender labels in infancy: implications for gender-typed play.

PubMed

Zosuls, Kristina M; Ruble, Diane N; Tamis-Lemonda, Catherine S; Shrout, Patrick E; Bornstein, Marc H; Greulich, Faith K

2009-05-01

Two aspects of children's early gender development-the spontaneous production of gender labels and gender-typed play-were examined longitudinally in a sample of 82 children. Survival analysis, a statistical technique well suited to questions involving developmental transitions, was used to investigate the timing of the onset of children's gender labeling as based on mothers' biweekly telephone interviews regarding their children's language from 9 through 21 months. Videotapes of children's play both alone and with mother during home visits at 17 and 21 months were independently analyzed for play with gender-stereotyped and gender-neutral toys. Finally, the relation between gender labeling and gender-typed play was examined. Children transitioned to using gender labels at approximately 19 months, on average. Although girls and boys showed similar patterns in the development of gender labeling, girls began labeling significantly earlier than boys. Modest sex differences in play were present at 17 months and increased at 21 months. Gender labeling predicted increases in gender-typed play, suggesting that knowledge of gender categories might influence gender typing before the age of 2. Copyright 2009 APA, all rights reserved

The acquisition of gender labels in infancy: Implications for sex-typed play

PubMed Central

Zosuls, Kristina M.; Ruble, Diane N.; Tamis-LeMonda, Catherine S.; Shrout, Patrick E.; Bornstein, Marc H.; Greulich, Faith K.

2009-01-01

Two aspects of children’s early gender development - the spontaneous production of gender labels and sex-typed play - were examined longitudinally in a sample of 82 children. Survival analysis, a statistical technique well suited to questions involving developmental transitions, was used to investigate the timing of the onset of children’s gender labeling as based on mothers’ biweekly reports on their children’s language from 9 through 21 months. Videotapes of children’s play both alone and with mother at 17 and 21 months were independently analyzed for play with gender stereotyped and neutral toys. Finally, the relation between gender labeling and sex-typed play was examined. Children transitioned to using gender labels at approximately 19 months on average. Although girls and boys showed similar patterns in the development of gender labeling, girls began labeling significantly earlier than boys. Modest sex differences in play were present at 17 months and increased at 21 months. Gender labeling predicted increases in sex-typed play, suggesting that knowledge of gender categories might influence sex-typing before the age of 2. PMID:19413425

Impact of food labelling systems on food choices and eating behaviours: a systematic review and meta-analysis of randomized studies.

PubMed

Cecchini, M; Warin, L

2016-03-01

Food labels are considered a crucial component of strategies tackling unhealthy diets and obesity. This study aims at assessing the effectiveness of food labelling in increasing the selection of healthier products and in reducing calorie intake. In addition, this study compares the relative effectiveness of traffic light schemes, Guideline Daily Amount and other food labelling schemes. A comprehensive set of databases were searched to identify randomized studies. Studies reporting homogeneous outcomes were pooled together and analysed through meta-analyses. Publication bias was evaluated with a funnel plot. Food labelling would increase the amount of people selecting a healthier food product by about 17.95% (confidence interval: +11.24% to +24.66%). Food labelling would also decrease calorie intake/choice by about 3.59% (confidence interval: -8.90% to +1.72%), but results are not statistically significant. Traffic light schemes are marginally more effective in increasing the selection of healthier options. Other food labels and Guideline Daily Amount follow. The available evidence did not allow studying the effects of single labelling schemes on calorie intake/choice. Findings of this study suggest that nutrition labelling may be an effective approach to empowering consumers in choosing healthier products. Interpretive labels, as traffic light labels, may be more effective. © 2015 World Obesity.

A comparison of commercially available demineralized bone matrix for spinal fusion.

PubMed

Wang, Jeffrey C; Alanay, A; Mark, Davies; Kanim, Linda E A; Campbell, Pat A; Dawson, Edgar G; Lieberman, Jay R

2007-08-01

In an effort to augment the available grafting material as well as to increase spinal fusion rates, the utilization of a demineralized bone matrix (DBM) as a graft extender or replacement is common. There are several commercially available DBM substances available for use in spinal surgery, each with different amounts of DBM containing osteoinductive proteins. Each product may have different osteoinductivity potential due to different methods of preparation, storage, and donor specifications. The purpose of this study is to prospectively compare the osteoinductive potential of three different commercially available DBM substances in an athymic rodent spinal fusion model and to discuss the reasons of the variability in osteoinductivity. A posterolateral fusion was performed in 72 mature athymic nude female rats. Three groups of 18 rats were implanted with 1 of 3 DBMs (Osteofil, Grafton, and Dynagraft). A fourth group was implanted with rodent autogenous iliac crest bone graft. The rats were sacrificed at 2, 4, 6, and 8 weeks. A dose of 0.3 cm(3) per side (0.6 cm(3)per animal) was used for each substance. Radiographs were taken at 2 weeks intervals until sacrifice. Fusion was determined by radiographs, manual palpation, and histological analysis. The Osteofil substance had the highest overall fusion rate (14/18), and the highest early 4 weeks fusion rate of (4/5). Grafton produced slightly lower fusion rates of (11/17) overall, and lower early 4 weeks fusion rate of (2/5). There was no statistically significant difference between the rate of fusion after implantation of Osteofil and Grafton. None of the sites implanted with Dynagraft fused at any time point (0/17), and there was a significantly lower fusion rate between the Dynagraft and the other two substances at the six-week-time point and for final fusion rate (P = 0.0001, Fischer's exact test). None of the autogenous iliac crest animals fused at any time point. Non-decalcified histology confirmed the presence of a pseudarthrosis or the presence of a solid fusion, and the results were highly correlated with the manual testing. Although all products claim to have significant osteoinductive capabilities, this study demonstrates that there are significant differences between some of the tested products.

Evaluation of Anterior Vertebral Interbody Fusion Using Osteogenic Mesenchymal Stem Cells Transplanted in Collagen Sponge.

PubMed

Yang, Wencheng; Dong, Youhai; Hong, Yang; Guang, Qian; Chen, Xujun

2016-05-01

The study used a rabbit model to achieve anterior vertebral interbody fusion using osteogenic mesenchymal stem cells (OMSCs) transplanted in collagen sponge. We investigated the effectiveness of graft material for anterior vertebral interbody fusion using a rabbit model by examining the OMSCs transplanted in collagen sponge. Anterior vertebral interbody fusion is commonly performed. Although autogenous bone graft remains the gold-standard fusion material, it requires a separate surgical procedure and is associated with significant short-term and long-term morbidity. Recently, mesenchymal stem cells from bone marrow have been studied in various fields, including posterolateral spinal fusion. Thus, we hypothesized that cultured OMSCs transplanted in porous collagen sponge could be used successfully even in anterior vertebral interbody fusion. Forty mature male White Zealand rabbits (weight, 3.5-4.5 kg) were randomly allocated to receive one of the following graft materials: porous collagen sponge plus cultured OMSCs (group I); porous collagen sponge alone (group II); autogenous bone graft (group III); and nothing (group IV). All animals underwent anterior vertebral interbody fusion at the L4/L5 level. The lumbar spine was harvested en bloc, and the new bone formation and spinal fusion was evaluated using radiographic analysis, microcomputed tomography, manual palpation test, and histologic examination at 8 and 12 weeks after surgery. New bone formation and bony fusion was evident as early as 8 weeks in groups I and III. And there was no statistically significant difference between 8 and 12 weeks. At both time points, by microcomputed tomography and histologic analysis, new bone formation was observed in both groups I and III, fibrous tissue was observed and there was no new bone in both groups II and IV; by manual palpation test, bony fusion was observed in 40% (4/10) of rabbits in group I, 70% (7/10) of rabbits in group III, and 0% (0/10) of rabbits in both groups II and IV. These findings suggest that mesenchymal stem cells that have been cultured with osteogenic differentiation medium and loaded with collagen sponge could induce bone formation and anterior vertebral interbody fusion. And the rabbit model we developed will be useful in evaluating the effects of graft materials for anterior vertebral interbody fusion. Further study is needed to determine the most appropriate carrier for OMSCs and the feasibility in the clinical setting.

Brief communication: timing of spheno-occipital closure in modern Western Australians.

PubMed

Franklin, Daniel; Flavel, Ambika

2014-01-01

The spheno-occipital synchondrosis is a craniofacial growth centre between the occipital and sphenoid bones-its ossification persists into adolescence, which for the skeletal biologist, means it has potential application for estimating subadult age. Based on previous research the timing of spheno-occipital fusion is widely variable between and within populations, with reports of complete fusion in individuals as young as 11 years of age and nonfusion in adults. The aim of this study is, therefore, to examine this structure in a mixed sex sample of Western Australian individuals that developmentally span late childhood to adulthood. The objective is to develop statistically quantified age estimation standards based on scoring the degree of spheno-occipital fusion. The sample comprises multidetector computed tomography (MDCT) scans of 312 individuals (169 male; 143 female) between 5 and 25 years of age. Each MDCT scan is visualized in a standardized sagittal plane using three-dimensional oblique multiplanar reformatting. Fusion status is scored according to a four-stage system. Transition analysis is used to calculate age ranges for each defined stage and determine the mean age for transition between an unfused, fusing and fused status. The maximum likelihood estimates for the transition from open to fusing in the endocranial half is 14.44 years (male) and 11.42 years (female); transition from fusion in the ectocranial half to complete fusion is 16.16 years (male) and 13.62 years (female). This study affirms the potential value of assessing the degree of fusion in the spheno-occipital synchondrosis as an indicator of skeletal age. Copyright © 2013 Wiley Periodicals, Inc.

Anterior lumbar instrumentation improves correction of severe lumbar Lenke C curves in double major idiopathic scoliosis

PubMed Central

Yeon, Howard B.; Weinberg, Jacob; Arlet, Vincent; Ouelett, Jean A.

2007-01-01

Fifteen skeletally immature patients with double major adolescent idiopathic scoliosis with large lumbar curves and notable L4 and L5 coronal plane obliquity were retrospectively studied. Seven patients who underwent anterior release and fusion of the lumbar curve with segmental anterior instrumentation and subsequent posterior instrumentation ending at L3 were compared with eight patients treated with anterior release and fusion without anterior instrumentation followed by posterior instrumentation to L3 or L4. At 4.5 years follow-up (range 2.5–7 years), curve correction, coronal balance and fusion rate were not statistically different between the two groups; however, the group with anterior instrumentation had improved coronal plane, near normalangulation in the distal unfused segment compared with the group without anterior instrumentation. In cases involving severe lumbar curvatures in the context of double major scoliosis, when as a first stage anterior release is chosen, the addition of instrumentation appears to restore normal coronal alignment of the distal unfused lumbar segment, and may in certain cases save a level compared with traditional fusions to L4. PMID:17464517

Intensity-hue-saturation-based image fusion using iterative linear regression

NASA Astrophysics Data System (ADS)

Cetin, Mufit; Tepecik, Abdulkadir

2016-10-01

The image fusion process basically produces a high-resolution image by combining the superior features of a low-resolution spatial image and a high-resolution panchromatic image. Despite its common usage due to its fast computing capability and high sharpening ability, the intensity-hue-saturation (IHS) fusion method may cause some color distortions, especially when a large number of gray value differences exist among the images to be combined. This paper proposes a spatially adaptive IHS (SA-IHS) technique to avoid these distortions by automatically adjusting the exact spatial information to be injected into the multispectral image during the fusion process. The SA-IHS method essentially suppresses the effects of those pixels that cause the spectral distortions by assigning weaker weights to them and avoiding a large number of redundancies on the fused image. The experimental database consists of IKONOS images, and the experimental results both visually and statistically prove the enhancement of the proposed algorithm when compared with the several other IHS-like methods such as IHS, generalized IHS, fast IHS, and generalized adaptive IHS.

Knee Joint Vibration Signal Analysis with Matching Pursuit Decomposition and Dynamic Weighted Classifier Fusion

PubMed Central

Cai, Suxian; Yang, Shanshan; Zheng, Fang; Lu, Meng; Wu, Yunfeng; Krishnan, Sridhar

2013-01-01

Analysis of knee joint vibration (VAG) signals can provide quantitative indices for detection of knee joint pathology at an early stage. In addition to the statistical features developed in the related previous studies, we extracted two separable features, that is, the number of atoms derived from the wavelet matching pursuit decomposition and the number of significant signal turns detected with the fixed threshold in the time domain. To perform a better classification over the data set of 89 VAG signals, we applied a novel classifier fusion system based on the dynamic weighted fusion (DWF) method to ameliorate the classification performance. For comparison, a single leastsquares support vector machine (LS-SVM) and the Bagging ensemble were used for the classification task as well. The results in terms of overall accuracy in percentage and area under the receiver operating characteristic curve obtained with the DWF-based classifier fusion method reached 88.76% and 0.9515, respectively, which demonstrated the effectiveness and superiority of the DWF method with two distinct features for the VAG signal analysis. PMID:23573175

A Study for Texture Feature Extraction of High-Resolution Satellite Images Based on a Direction Measure and Gray Level Co-Occurrence Matrix Fusion Algorithm

PubMed Central

Zhang, Xin; Cui, Jintian; Wang, Weisheng; Lin, Chao

2017-01-01

To address the problem of image texture feature extraction, a direction measure statistic that is based on the directionality of image texture is constructed, and a new method of texture feature extraction, which is based on the direction measure and a gray level co-occurrence matrix (GLCM) fusion algorithm, is proposed in this paper. This method applies the GLCM to extract the texture feature value of an image and integrates the weight factor that is introduced by the direction measure to obtain the final texture feature of an image. A set of classification experiments for the high-resolution remote sensing images were performed by using support vector machine (SVM) classifier with the direction measure and gray level co-occurrence matrix fusion algorithm. Both qualitative and quantitative approaches were applied to assess the classification results. The experimental results demonstrated that texture feature extraction based on the fusion algorithm achieved a better image recognition, and the accuracy of classification based on this method has been significantly improved. PMID:28640181

Technique for writing of fiber Bragg gratings over or near preliminary formed macro-structure defects in silica optical fibers

NASA Astrophysics Data System (ADS)

Evtushenko, Alexander S.; Faskhutdinov, Lenar M.; Kafarova, Anastasia M.; Kazakov, Vadim S.; Kuznetzov, Artem A.; Minaeva, Alina Yu.; Sevruk, Nikita L.; Nureev, Ilnur I.; Vasilets, Alexander A.; Andreev, Vladimir A.; Morozov, Oleg G.; Burdin, Vladimir A.; Bourdine, Anton V.

2017-04-01

This work presents method for performing precision macro-structure defects "tapers" and "up-tapers" written in conventional silica telecommunication multimode optical fibers by commercially available field fusion splicer with modified software settings and following writing fiber Bragg gratings over or near them. We developed technique for macrodefect geometry parameters estimation via analysis of photo-image performed after defect writing and displayed on fusion splicer screen. Some research results of defect geometry dependence on fusion current and fusion time values re-set in splicer program are represented that provided ability to choose their "the best" combination. Also experimental statistical researches concerned with "taper" and "up-taper" diameter stability as well as their insertion loss values during their writing under fixed corrected splicer program parameters were performed. We developed technique for FBG writing over or near macro-structure defect. Some results of spectral response measurements produced for short-length samples of multimode optical fiber with fiber Bragg gratings written over and near macro-defects prepared by using proposed technique are presented.

Identification of an intracellular protein that specifically interacts with photoaffinity-labeled oncogenic p21 protein.

PubMed

Lee, G; Ronai, Z A; Pincus, M R; Brandt-Rauf, P W; Murphy, R B; Delohery, T M; Nishimura, S; Yamaizumi, Z; Weinstein, I B

1989-11-01

An oncogenic 21-kDa (p21) protein (Harvey RAS protein with Val-12) has been covalently modified with a functional reagent that contains a photoactivatable aromatic azide group. This modified p21 protein has been introduced quantitatively into NIH 3T3 cells using an erythrocyte-mediated fusion technique. The introduced p21 protein was capable of inducing enhanced pinocytosis and DNA synthesis in the recipient cells. To identify the putative intracellular protein(s) that specifically interact with the modified p21 protein, the cells were pulsed with [35S]methionine at selected times after fusion and then UV-irradiated to activate the azide group. The resulting nitrene covalently binds to amino acid residues in adjacent proteins, thus linking the p21 protein to these proteins. The cells were then lysed, and the lysate was immunoprecipitated with the anti-p21 monoclonal antibody Y13-259. The immunoprecipitate was analyzed by SDS/PAGE to identify p21-protein complexes. By using this technique, we found that three protein complexes of 51, 64, and 82 kDa were labeled specifically and reproducibly. The most prominent band is the 64-kDa protein complex that shows a time-dependent rise and fall, peaking within a 5-hr period after introduction of the p21 protein into the cells. These studies provide evidence that in vitro the p21 protein becomes associated with a protein whose mass is about 43 kDa. We suggest that the formation of this complex may play a role in mediating early events involved with cell transformation induced by RAS oncogenes.

Bi-directional exchange of membrane components occurs during co-culture of mesenchymal stem cells and nucleus pulposus cells.

PubMed

Strassburg, Sandra; Hodson, Nigel W; Hill, Patrick I; Richardson, Stephen M; Hoyland, Judith A

2012-01-01

Mesenchymal stem cell (MSC)-based therapies have been proposed as novel treatments for intervertebral disc (IVD) degeneration. We have previously demonstrated that when MSCs are co-cultured with nucleus pulposus (NP) cells with direct cell-cell contact, they differentiate along the NP lineage and simultaneously stimulate the degenerate NP cell population to regain a normal (non-degenerate) phenotype, an effect which requires cell-cell communication. However, the mechanisms by which NP cells and MSCs interact in this system are currently unclear. Thus, in this study we investigated a range of potential mechanisms for exchange of cellular components or information that may direct these changes, including cell fusion, gap-junctional communication and exchange of membrane components by direct transfer or via microvesicle formation. Flow cytometry of fluorescently labeled MSCs and NP cells revealed evidence of some cell fusion and formation of gapjunctions, although at the three timepoints studied these phenomena were detectable only in a small proportion of cells. While these mechanisms may play a role in cell-cell communication, the data suggests they are not the predominant mechanism of interaction. However, flow cytometry of fluorescently dual-labeled cells showed that extensive bi-directional transfer of membrane components is operational during direct co-culture of MSCs and NP cells. Furthermore, there was also evidence for secretion and internalization of membrane-bound microvesicles by both cell types. Thus, this study highlights bi-directional intercellular transfer of membrane components as a possible mechanism of cellular communication between MSC and NP cells.

The movement protein of cucumber mosaic virus traffics into sieve elements in minor veins of nicotiana clevelandii

PubMed Central

Blackman, LM; Boevink, P; Cruz, SS; Palukaitis, P; Oparka, KJ

1998-01-01

The location of the 3a movement protein (MP) of cucumber mosaic virus (CMV) was studied by quantitative immunogold labeling of the wild-type 3a MP in leaves of Nicotiana clevelandii infected by CMV as well as by using a 3a-green fluorescent protein (GFP) fusion expressed from a potato virus X (PVX) vector. Whether expressed from CMV or PVX, the 3a MP targeted plasmodesmata and accumulated in the central cavity of the pore. Within minor veins, the most extensively labeled plasmodesmata were those connecting sieve elements and companion cells. In addition to targeting plasmodesmata, the 3a MP accumulated in the parietal layer of mature sieve elements. Confocal imaging of cells expressing the 3a-GFP fusion protein showed that the 3a MP assembled into elaborate fibrillar formations in the sieve element parietal layer. The ability of 3a-GFP, expressed from PVX rather than CMV, to enter sieve elements demonstrates that neither the CMV RNA nor the CMV coat protein is required for trafficking of the 3a MP into sieve elements. CMV virions were not detected in plasmodesmata from CMV-infected tissue, although large CMV aggregates were often found in the parietal layer of sieve elements and were usually surrounded by 3a MP. These data suggest that CMV traffics into minor vein sieve elements as a ribonucleoprotein complex that contains the viral RNA, coat protein, and 3a MP, with subsequent viral assembly occurring in the sieve element parietal layer. PMID:9548980

Weakly supervised image semantic segmentation based on clustering superpixels

NASA Astrophysics Data System (ADS)

Yan, Xiong; Liu, Xiaohua

2018-04-01

In this paper, we propose an image semantic segmentation model which is trained from image-level labeled images. The proposed model starts with superpixel segmenting, and features of the superpixels are extracted by trained CNN. We introduce a superpixel-based graph followed by applying the graph partition method to group correlated superpixels into clusters. For the acquisition of inter-label correlations between the image-level labels in dataset, we not only utilize label co-occurrence statistics but also exploit visual contextual cues simultaneously. At last, we formulate the task of mapping appropriate image-level labels to the detected clusters as a problem of convex minimization. Experimental results on MSRC-21 dataset and LableMe dataset show that the proposed method has a better performance than most of the weakly supervised methods and is even comparable to fully supervised methods.

Stacked sparse autoencoder in hyperspectral data classification using spectral-spatial, higher order statistics and multifractal spectrum features

NASA Astrophysics Data System (ADS)

Wan, Xiaoqing; Zhao, Chunhui; Wang, Yanchun; Liu, Wu

2017-11-01

This paper proposes a novel classification paradigm for hyperspectral image (HSI) using feature-level fusion and deep learning-based methodologies. Operation is carried out in three main steps. First, during a pre-processing stage, wave atoms are introduced into bilateral filter to smooth HSI, and this strategy can effectively attenuate noise and restore texture information. Meanwhile, high quality spectral-spatial features can be extracted from HSI by taking geometric closeness and photometric similarity among pixels into consideration simultaneously. Second, higher order statistics techniques are firstly introduced into hyperspectral data classification to characterize the phase correlations of spectral curves. Third, multifractal spectrum features are extracted to characterize the singularities and self-similarities of spectra shapes. To this end, a feature-level fusion is applied to the extracted spectral-spatial features along with higher order statistics and multifractal spectrum features. Finally, stacked sparse autoencoder is utilized to learn more abstract and invariant high-level features from the multiple feature sets, and then random forest classifier is employed to perform supervised fine-tuning and classification. Experimental results on two real hyperspectral data sets demonstrate that the proposed method outperforms some traditional alternatives.

Labeling of Medication and Placebo Alters the Outcome of Episodic Migraine Attacks

PubMed Central

Kam-Hansen, Slavenka; Jakubowski, Moshe; Kelley, John M.; Kirsch, Irving; Hoaglin, David C.; Kaptchuk, Ted J.; Burstein, Rami

2014-01-01

Information provided to patients is thought to influence placebo and drug effects. We investigated the potential relationship between treatment labeling and its outcome in a prospective, within-subjects, repeated measures study of episodic migraine. A cohort of 66 participants documented 7 separate migraine attack: one untreated attack, followed by six attacks that were randomly assigned for either rizatriptan (10 mg Maxalt) or placebo treatments, each of which labeled once as ‘Maxalt’, once as ‘Placebo’, and once as ‘Maxalt or Placebo’ (459 documented attacks). Data were analyzed using generalized linear mixed model statistics. While Maxalt was generally superior to placebo, the placebo effect, and to a lesser extent Maxalt efficacy, increased monotonically with treatment labeling as follows: ‘Placebo’ label < ‘Maxalt or placebo’ label ≤ ‘Maxalt’ label. Efficacy of Maxalt mislabeled as placebo was not significantly different from the efficacy of placebo mislabeled as Maxalt. The placebo effect was significant under each labeling condition relative to no treatment, amounting in magnitude to >50% of Maxalt effect under the corresponding labeling condition. Thus, incremental “positive” information yielded incremental efficacy of placebo and medication during migraine attacks. PMID:24401940

Learning Object Names at Different Hierarchical Levels Using Cross-Situational Statistics

ERIC Educational Resources Information Center

Chen, Chi-hsin; Zhang, Yayun; Yu, Chen

2018-01-01

Objects in the world usually have names at different hierarchical levels (e.g., "beagle," "dog," "animal"). This research investigates adults' ability to use cross-situational statistics to simultaneously learn object labels at individual and category levels. The results revealed that adults were able to use…

Effect of pulsed current GTA welding parameters on the fusion zone microstructure of AA 6061 aluminium alloy

NASA Astrophysics Data System (ADS)

Kumar, T. Senthil; Balasubramanian, V.; Babu, S.; Sanavullah, M. Y.

2007-08-01

AA6061 aluminium alloy (Al-Mg-Si alloy) has gathered wide acceptance in the fabrication of food processing equipment, chemical containers, passenger cars, road tankers, and railway transport systems. The preferred process for welding these aluminium alloys is frequently Gas Tungsten Arc (GTA) welding due to its comparatively easy applicability and lower cost. In the case of single pass GTA welding of thinner sections of this alloy, the pulsed current has been found beneficial due to its advantages over the conventional continuous current processes. The use of pulsed current parameters has been found to improve the mechanical properties of the welds compared to those of continuous current welds of this alloy due to grain refinement occurring in the fusion zone. In this investigation, an attempt has been made to develop a mathematical model to predict the fusion zone grain diameter incorporating pulsed current welding parameters. Statistical tools such as design of experiments, analysis of variance, and regression analysis are used to develop the mathematical model. The developed model can be effectively used to predict the fusion grain diameter at a 95% confidence level for the given pulsed current parameters. The effect of pulsed current GTA welding parameters on the fusion zone grain diameter of AA 6061 aluminium alloy welds is reported in this paper.

QUARTERLY PROGRESS REPORT NO. 83,

DTIC Science & Technology

Topics included are: microwave spectroscopy; radio astronomy; solid-state microwave electronics; optical and infrared spectroscopy; physical electronics and surface physics; physical acoustics; plasma physics; gaseous electronics; plasmas and controlled nuclear fusion ; energy conversion research; statistical communication theory; linguistics; cognitive information processing; communications biophysics; neurophysiology; computation research.

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

Visweswara Sathanur, Arun; Choudhury, Sutanay; Joslyn, Cliff A.

Property graphs can be used to represent heterogeneous networks with attributed vertices and edges. Given one property graph, simulating another graph with same or greater size with identical statistical properties with respect to the attributes and connectivity is critical for privacy preservation and benchmarking purposes. In this work we tackle the problem of capturing the statistical dependence of the edge connectivity on the vertex labels and using the same distribution to regenerate property graphs of the same or expanded size in a scalable manner. However, accurate simulation becomes a challenge when the attributes do not completely explain the network structure.more » We propose the Property Graph Model (PGM) approach that uses an attribute (or label) augmentation strategy to mitigate the problem and preserve the graph connectivity as measured via degree distribution, vertex label distributions and edge connectivity. Our proposed algorithm is scalable with a linear complexity in the number of edges in the target graph. We illustrate the efficacy of the PGM approach in regenerating and expanding the datasets by leveraging two distinct illustrations.« less

Estimation of Cell Proliferation Dynamics Using CFSE Data

PubMed Central

Banks, H.T.; Sutton, Karyn L.; Thompson, W. Clayton; Bocharov, Gennady; Roose, Dirk; Schenkel, Tim; Meyerhans, Andreas

2010-01-01

Advances in fluorescent labeling of cells as measured by flow cytometry have allowed for quantitative studies of proliferating populations of cells. The investigations (Luzyanina et al. in J. Math. Biol. 54:57–89, 2007; J. Math. Biol., 2009; Theor. Biol. Med. Model. 4:1–26, 2007) contain a mathematical model with fluorescence intensity as a structure variable to describe the evolution in time of proliferating cells labeled by carboxyfluorescein succinimidyl ester (CFSE). Here, this model and several extensions/modifications are discussed. Suggestions for improvements are presented and analyzed with respect to statistical significance for better agreement between model solutions and experimental data. These investigations suggest that the new decay/label loss and time dependent effective proliferation and death rates do indeed provide improved fits of the model to data. Statistical models for the observed variability/noise in the data are discussed with implications for uncertainty quantification. The resulting new cell dynamics model should prove useful in proliferation assay tracking and modeling, with numerous applications in the biomedical sciences. PMID:20195910

The cyclic nucleotide gated cation channel AtCNGC10 traffics from the ER via Golgi vesicles to the plasma membrane of Arabidopsis root and leaf cells.

PubMed

Christopher, David A; Borsics, Tamas; Yuen, Christen Y L; Ullmer, Wendy; Andème-Ondzighi, Christine; Andres, Marilou A; Kang, Byung-Ho; Staehelin, L Andrew

2007-09-19

The cyclic nucleotide-gated ion channels (CNGCs) maintain cation homeostasis essential for a wide range of physiological processes in plant cells. However, the precise subcellular locations and trafficking of these membrane proteins are poorly understood. This is further complicated by a general deficiency of information about targeting pathways of membrane proteins in plants. To investigate CNGC trafficking and localization, we have measured Atcngc5 and Atcngc10 expression in roots and leaves, analyzed AtCNGC10-GFP fusions transiently expressed in protoplasts, and conducted immunofluorescence labeling of protoplasts and immunoelectron microscopic analysis of high pressure frozen leaves and roots. AtCNGC10 mRNA and protein levels were 2.5-fold higher in roots than leaves, while AtCNGC5 mRNA and protein levels were nearly equal in these tissues. The AtCNGC10-EGFP fusion was targeted to the plasma membrane in leaf protoplasts, and lightly labeled several intracellular structures. Immunofluorescence microscopy with affinity purified CNGC-specific antisera indicated that AtCNGC5 and AtCNGC10 are present in the plasma membrane of protoplasts. Immunoelectron microscopy demonstrated that AtCNGC10 was associated with the plasma membrane of mesophyll, palisade parenchyma and epidermal cells of leaves, and the meristem, columella and cap cells of roots. AtCNCG10 was also observed in the endoplasmic reticulum and Golgi cisternae and vesicles of 50-150 nm in size. Patch clamp assays of an AtCNGC10-GFP fusion expressed in HEK293 cells measured significant cation currents. AtCNGC5 and AtCNGC10 are plasma membrane proteins. We postulate that AtCNGC10 traffics from the endoplasmic reticulum via the Golgi apparatus and associated vesicles to the plasma membrane. The presence of the cation channel, AtCNGC10, in root cap meristem cells, cell plate, and gravity-sensing columella cells, combined with the previously reported antisense phenotypes of decreased gravitropic and cell enlargement responses, suggest roles of AtCNGC10 in modulating cation balance required for root gravitropism, cell division and growth.

Bone morphogenetic protein use in spine surgery-complications and outcomes: a systematic review.

PubMed

Faundez, Antonio; Tournier, Clément; Garcia, Matthieu; Aunoble, Stéphane; Le Huec, Jean-Charles

2016-06-01

Because of significant complications related to the use of autologous bone grafts in spinal fusion surgery, bone substitutes and growth factors such as bone morphogenetic protein (BMP) have been developed. One of them, recombinant human (rh) BMP-2, has been approved by the Food and Drug Administration (FDA) for use under precise conditions. However, rhBMP-2-related side effects have been reported, used in FDA-approved procedures, but also in off-label use.A systematic review of clinical data was conducted to analyse the rhBMP-2-related adverse events (AEs), in order to assess their prevalence and the associated surgery practices. Medline search with keywords "bone morphogenetic protein 2", "lumbar spine", "anterolateral interbody fusion" (ALIF) and the filter "clinical trial". FDA published reports were also included. Study assessment was made by authors (experienced spine surgeons), based on quality of study designs and level of evidence. Extensive review of randomised controlled trials (RCTs) and controlled series published up to the present point, reveal no evidence of a significant increase of AEs related to rhBMP-2 use during ALIF surgeries, provided that it is used following FDA guidelines. Two additional RCTs performed with rhBMP-2 in combination with allogenic bone dowels reported increased bone remodelling in BMP-treated patients. This AE was transient and had no consequence on the clinical outcome of the patients. No other BMP-related AEs were reported in these studies. This literature review confirms that the use of rhBMP-2 following FDA-approved recommendations (i.e. one-level ALIF surgery with an LT-cage) is safe. The rate of complications is low and the AEs had been identified by the FDA during the pre-marketing clinical trials. The clinical efficiency of rhBMP-2 is equal or superior to that of allogenic or autologous bone graft in respect to fusion rate, low back pain disability, patient satisfaction and rate of re-operations. For all other off-label use, the safety and effectiveness of rhBMP-2 have not been established, and further RCTs with high level of evidence are required.

SU-E-I-71: Quality Assessment of Surrogate Metrics in Multi-Atlas-Based Image Segmentation

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

Zhao, T; Ruan, D

Purpose: With the ever-growing data of heterogeneous quality, relevance assessment of atlases becomes increasingly critical for multi-atlas-based image segmentation. However, there is no universally recognized best relevance metric and even a standard to compare amongst candidates remains elusive. This study, for the first time, designs a quantification to assess relevance metrics’ quality, based on a novel perspective of the metric as surrogate for inferring the inaccessible oracle geometric agreement. Methods: We first develop an inference model to relate surrogate metrics in image space to the underlying oracle relevance metric in segmentation label space, with a monotonically non-decreasing function subject tomore » random perturbations. Subsequently, we investigate model parameters to reveal key contributing factors to surrogates’ ability in prognosticating the oracle relevance value, for the specific task of atlas selection. Finally, we design an effective contract-to-noise ratio (eCNR) to quantify surrogates’ quality based on insights from these analyses and empirical observations. Results: The inference model was specialized to a linear function with normally distributed perturbations, with surrogate metric exemplified by several widely-used image similarity metrics, i.e., MSD/NCC/(N)MI. Surrogates’ behaviors in selecting the most relevant atlases were assessed under varying eCNR, showing that surrogates with high eCNR dominated those with low eCNR in retaining the most relevant atlases. In an end-to-end validation, NCC/(N)MI with eCNR of 0.12 compared to MSD with eCNR of 0.10 resulted in statistically better segmentation with mean DSC of about 0.85 and the first and third quartiles of (0.83, 0.89), compared to MSD with mean DSC of 0.84 and the first and third quartiles of (0.81, 0.89). Conclusion: The designed eCNR is capable of characterizing surrogate metrics’ quality in prognosticating the oracle relevance value. It has been demonstrated to be correlated with the performance of relevant atlas selection and ultimate label fusion.« less

Tibiotalocalcaneal Arthrodesis Nails: A Comparison of Nails With and Without Internal Compression.

PubMed

Taylor, James; Lucas, Douglas E; Riley, Aimee; Simpson, G Alex; Philbin, Terrence M

2016-03-01

Hindfoot arthrodesis with tibiotalocalcaneal (TTC) intramedullary nails is used commonly when treating ankle and subtalar arthritis and other hindfoot pathology. Adequate compression is paramount to avoid nonunion and fatigue fracture of the hardware. Arthrodesis systems with internal compression have demonstrated superior compression to systems relying on external methods. This study examined the speed of union with TTC fusion nails with internal compression over nails without internal compression. A retrospective review was performed identifying nail type and time to union of the subtalar joint (STJ) and tibiotalar joint (TTJ). A total of 198 patients were included from 2003 to 2011. The median time to STJ fusion without internal compression was 104 days compared to 92 days with internal compression (P = .044). The median time to TTJ fusion without internal compression was 111 days compared to 93 days with internal compression (P = .010). Adjusting for diabetes, there was no significant difference in fusion speed with or without internal compression for the STJ (P = .561) or TTJ (P = .358). Nonunion rates were 24.5% for the STJ and 17.0% for the TTJ with internal compression, and 43.4% for the STJ and 42.1% for the TTJ without internal compression. This difference remained statistically significant after adjusting for diabetes for the TTJ (P = .001) but not for the STJ (P = .194). The intramedullary hindfoot arthrodesis nail was a viable treatment option in degenerative joint disease of the TTC joint. There appeared to be an advantage using systems with internal compression; however, there was no statistically significant difference after controlling for diabetes. Level III, retrospective comparative series. © The Author(s) 2015.

Multi-modal data fusion using source separation: Two effective models based on ICA and IVA and their properties

PubMed Central

Adali, Tülay; Levin-Schwartz, Yuri; Calhoun, Vince D.

2015-01-01

Fusion of information from multiple sets of data in order to extract a set of features that are most useful and relevant for the given task is inherent to many problems we deal with today. Since, usually, very little is known about the actual interaction among the datasets, it is highly desirable to minimize the underlying assumptions. This has been the main reason for the growing importance of data-driven methods, and in particular of independent component analysis (ICA) as it provides useful decompositions with a simple generative model and using only the assumption of statistical independence. A recent extension of ICA, independent vector analysis (IVA) generalizes ICA to multiple datasets by exploiting the statistical dependence across the datasets, and hence, as we discuss in this paper, provides an attractive solution to fusion of data from multiple datasets along with ICA. In this paper, we focus on two multivariate solutions for multi-modal data fusion that let multiple modalities fully interact for the estimation of underlying features that jointly report on all modalities. One solution is the Joint ICA model that has found wide application in medical imaging, and the second one is the the Transposed IVA model introduced here as a generalization of an approach based on multi-set canonical correlation analysis. In the discussion, we emphasize the role of diversity in the decompositions achieved by these two models, present their properties and implementation details to enable the user make informed decisions on the selection of a model along with its associated parameters. Discussions are supported by simulation results to help highlight the main issues in the implementation of these methods. PMID:26525830

Biomechanical demands on posterior fusion instrumentation during lordosis restoration procedures.

PubMed

Kuo, Calvin C; Martin, Audrey; Telles, Connor; Leasure, Jeremi; Iezza, Alex; Ames, Christopher; Kondrashov, Dimitriy

2016-09-01

OBJECTIVE The goal of this study was to investigate the forces placed on posterior fusion instrumentation by 3 commonly used intraoperative techniques to restore lumbar lordosis: 1) cantilever bending; 2) in situ bending; and 3) compression and/or distraction of screws along posterior fusion rods. METHODS Five cadaveric torsos were instrumented with pedicle screws at the L1-5 levels. Specimens underwent each of the 3 lordosis restoration procedures. The pedicle screw pullout force was monitored in real time via strain gauges that were mounted unilaterally at each level. The degree of correction was noted through fluoroscopic imaging. The peak loads experienced on the screws during surgery, total demand on instrumentation, and resting loads after corrective maneuvers were measured. RESULTS A mean overall lordotic correction of 10.9 ± 4.7° was achieved. No statistically significant difference in lordotic correction was observed between restoration procedures. In situ bending imparted the largest loads intraoperatively with an average of 1060 ± 599.9 N, followed by compression/distraction (971 ± 534.1 N) and cantilever bending (705 ± 413.0 N). In situ bending produced the largest total demand and postoperative loads at L-1 (1879 ± 1064.1 and 487 ± 118.8 N, respectively), which were statistically higher than cantilever bending and compression/distraction (786 ± 272.1 and 138 ± 99.2 N, respectively). CONCLUSIONS In situ bending resulted in the highest mechanical demand on posterior lumbar instrumentation, as well as the largest postoperative loads at L-1. These results suggest that the forces generated with in situ bending indicate a greater chance of intraoperative instrumentation failure and postoperative proximal pedicle screw pullout when compared with cantilever bending and/or compression/distraction options. The results are aimed at optimizing correction and fusion strategies in lordosis restoration cases.

Change Detection of High-Resolution Remote Sensing Images Based on Adaptive Fusion of Multiple Features

NASA Astrophysics Data System (ADS)

Wang, G. H.; Wang, H. B.; Fan, W. F.; Liu, Y.; Chen, C.

2018-04-01

In view of the traditional change detection algorithm mainly depends on the spectral information image spot, failed to effectively mining and fusion of multi-image feature detection advantage, the article borrows the ideas of object oriented analysis proposed a multi feature fusion of remote sensing image change detection algorithm. First by the multi-scale segmentation of image objects based; then calculate the various objects of color histogram and linear gradient histogram; utilizes the color distance and edge line feature distance between EMD statistical operator in different periods of the object, using the adaptive weighted method, the color feature distance and edge in a straight line distance of combination is constructed object heterogeneity. Finally, the curvature histogram analysis image spot change detection results. The experimental results show that the method can fully fuse the color and edge line features, thus improving the accuracy of the change detection.

In-beam fissio study at JAEA for heavy element synthesis

NASA Astrophysics Data System (ADS)

Nishio, K.; Ikezoe, H.; Hofmann, S.; Ackermann, D.; Aritomo, Y.; Comas, V. F.; Düllmann, Ch. E.; Heinz, S.; Heredia, J. A.; Heßberger, F. P.; Hirose, K.; Khuyagbaatar, J.; Kindler, B.; Kojouharov, I.; Lommel, B.; Makii, M.; Mann, R.; Mitsuoka, S.; Nishinaka, I.; Ohtsuki, T.; Saro, S.; Schädel, M.; Popeko, A. G.; Türler, A.; Wakabayashi, Y.; Watanabe, Y.; Yakushev, A.; Yeremin, A.

2013-04-01

Fission fragment mass distributions were measured in the heavy-ion induced fission using 238U target nucleus. The mass distributions changed drastically with incident energy. The results are explained by a change of the ratio between fusion and qasifission with nuclear orientation. A calculation based on a fluctuation dissipation model reproduced the mass distributions and their incident energy dependence. Fusion probability was determined in the analysis. Evaporation residue cross sections were calculated with a statistical model in the reactions of 30Si+238U and 34S+238U using the obtained fusion probability in the entrance channel. The results agree with the measured cross sections of 263,264Sg and 267,268Hs, produced by 30Si+238U and 34S+238U, respectively. It is also suggested that the sub-barrier energies can be used for heavy element synthesis.

Causal Models and Exploratory Analysis in Heterogeneous Information Fusion for Detecting Potential Terrorists

DTIC Science & Technology

2015-11-01

issues and made some of the same distinctions (Walker, Lempert, and Kwakkel ; Bankes, Lempert, and Popper, 2005), but it did appear that we had more than...Statistics,” British Journal of Mathematical Statistics and Pscyhology, 66, pp. 8-38. Jaynes, Edwin T., and G . Larry Bretthorst (ed.) (2003) , Probability...Giroux. Lempert, Robert J., David G . Groves, Steven W. Popper, and Steven C. Bankes (2006), “A General Analytic Method for Generating Robust

A new hearing protector rating: The Noise Reduction Statistic for use with A weighting (NRSA).

NASA Astrophysics Data System (ADS)

Berger, Elliott H.; Gauger, Dan

2004-05-01

An important question to ask in regard to hearing protection devices (HPDs) is how much hearing protection they can provide. With respect to the law, at least, this question was answered in 1979 when the U. S. Environmental Protection Agency (EPA) promulgated a labeling regulation specifying a Noise Reduction Rating (NRR) measured in decibels (dB). In the intervening 25 years many concerns have arisen over this regulation. Currently the EPA is considering proposing a revised rule. This report examines the relevant issues in order to provide recommendations for new ratings and a new method of obtaining the test data. The conclusion is that a Noise Reduction Statistic for use with A weighting (NRSA), an A-A' rating computed in a manner that considers both intersubject and interspectrum variation in protection, yields sufficient precision. Two such statistics ought to be specified on the primary package label-the smaller one to indicate the protection that is possible for most users to exceed, and a larger one such that the range between the two numbers conveys to the user the uncertainty in protection provided. Guidance on how to employ these numbers, and a suggestion for an additional, more precise, graphically oriented rating to be provided on a secondary label, are also included.

Four-point bending as a method for quantitatively evaluating spinal arthrodesis in a rat model.

PubMed

Robinson, Samuel T; Svet, Mark T; Kanim, Linda A; Metzger, Melodie F

2015-02-01

The most common method of evaluating the success (or failure) of rat spinal fusion procedures is manual palpation testing. Whereas manual palpation provides only a subjective binary answer (fused or not fused) regarding the success of a fusion surgery, mechanical testing can provide more quantitative data by assessing variations in strength among treatment groups. We here describe a mechanical testing method to quantitatively assess single-level spinal fusion in a rat model, to improve on the binary and subjective nature of manual palpation as an end point for fusion-related studies. We tested explanted lumbar segments from Sprague-Dawley rat spines after single-level posterolateral fusion procedures at L4-L5. Segments were classified as 'not fused,' 'restricted motion,' or 'fused' by using manual palpation testing. After thorough dissection and potting of the spine, 4-point bending in flexion then was applied to the L4-L5 motion segment, and stiffness was measured as the slope of the moment-displacement curve. Results demonstrated statistically significant differences in stiffness among all groups, which were consistent with preliminary grading according to manual palpation. In addition, the 4-point bending results provided quantitative information regarding the quality of the bony union formed and therefore enabled the comparison of fused specimens. Our results demonstrate that 4-point bending is a simple, reliable, and effective way to describe and compare results among rat spines after fusion surgery.

[Detection of EML4-ALK fusion gene in non-small cell lung cancer and its clinicopathologic correlation].

PubMed

Zhong, Shan; Zhang, Hai-ping; Zheng, Jie; Bai, Dong-yu; Fu, Li; Chen, Pei-qiong

2013-04-01

To investigate the frequency of EML4-ALK fusion gene in non-small-cell lung cancer (NSCLC) patients, and its correlation with clinicopathologic features. Real-time PCR was used to detect the presence of EML4-ALK fusion gene in 268 cases of NSCLCs using paraffin-embedded tissue samples(among which 164 samples were re-validated by Sanger sequencing). Related clinicopathological correlation was analyzed. EML4-ALK fusion gene was found in 4.1% (11/268) of the cases. One hundred and sixty four samples were verified by Sanger sequencing, and the overall coincidence of the results of two methods (Sanger sequencing and Real-time PCR) was 100%. Female patients (5.9%, 5/85), ≤ 60 years of age (4.3%, 6/140), non-smokers (6.8%, 8/118) and adenocarcinomas (7.6%, 10/132) had a higher mutation rate than that in male patients (3.3%, 6/183), > 60 years of age (4.0%, 5/124), smokers (1.6%, 2/132) and squamous cell carcinomas (1.3%, 1/79), although no statistical significance in age (P = 0.918), gender (P = 0.503), smoking history (P = 0.092) and histological type (P = 0.094). Chinese NSCLC patients have a 4.1% detection rate of EML4-ALK fusion gene in the tumor tissues. Female, non-smoker and adenocarcinoma histological subtype tend to be associated with a higher rate of EML4-ALK gene fusion.

Proliferative changes in the bronchial epithelium of former smokers treated with retinoids.

PubMed

Hittelman, Walter N; Liu, Diane D; Kurie, Jonathan M; Lotan, Reuben; Lee, Jin Soo; Khuri, Fadlo; Ibarguen, Heladio; Morice, Rodolfo C; Walsh, Garrett; Roth, Jack A; Minna, John; Ro, Jae Y; Broxson, Anita; Hong, Waun Ki; Lee, J Jack

2007-11-07

Retinoids have shown antiproliferative and chemopreventive activity. We analyzed data from a randomized, placebo-controlled chemoprevention trial to determine whether a 3-month treatment with either 9-cis-retinoic acid (RA) or 13-cis-RA and alpha-tocopherol reduced Ki-67, a proliferation biomarker, in the bronchial epithelium. Former smokers (n = 225) were randomly assigned to receive 3 months of daily oral 9-cis-RA (100 mg), 13-cis-RA (1 mg/kg) and alpha-tocopherol (1200 IU), or placebo. Bronchoscopic biopsy specimens obtained before and after treatment were immunohistochemically assessed for changes in the Ki-67 proliferative index (i.e., percentage of cells with Ki-67-positive nuclear staining) in the basal and parabasal layers of the bronchial epithelium. Per-subject and per-biopsy site analyses were conducted. Multicovariable analyses, including a mixed-effects model and a generalized estimating equations model, were used to investigate the treatment effect (Ki-67 labeling index and percentage of bronchial epithelial biopsy sites with a Ki-67 index > or = 5%) with adjustment for multiple covariates, such as smoking history and metaplasia. Coefficient estimates and 95% confidence intervals (CIs) were obtained from the models. All statistical tests were two-sided. In per-subject analyses, Ki-67 labeling in the basal layer was not changed by any treatment; the percentage of subjects with a high Ki-67 labeling in the parabasal layer dropped statistically significantly after treatment with 13-cis-RA and alpha-tocopherol treatment (P = .04) compared with placebo, but the drop was not statistically significant after 9-cis-RA treatment (P = .17). A similar effect was observed in the parabasal layer in a per-site analysis; the percentage of sites with high Ki-67 labeling dropped statistically significantly after 9-cis-RA treatment (coefficient estimate = -0.72, 95% CI = -1.24 to -0.20; P = .007) compared with placebo, and after 13-cis-RA and alpha-tocopherol treatment (coefficient estimate = -0.66, 95% CI = -1.15 to -0.17; P = .008). In per-subject analyses, treatment with 13-cis-RA and alpha-tocopherol, compared with placebo, was statistically significantly associated with reduced bronchial epithelial cell proliferation; treatment with 9-cis-RA was not. In per-site analyses, statistically significant associations were obtained with both treatments.

Proliferative Changes in the Bronchial Epithelium of Former Smokers Treated With Retinoids

PubMed Central

Hittelman, Walter N.; Liu, Diane D.; Kurie, Jonathan M.; Lotan, Reuben; Lee, Jin Soo; Khuri, Fadlo; Ibarguen, Heladio; Morice, Rodolfo C.; Walsh, Garrett; Roth, Jack A.; Minna, John; Ro, Jae Y.; Broxson, Anita; Hong, Waun Ki; Lee, J. Jack

2012-01-01

Background Retinoids have shown antiproliferative and chemopreventive activity. We analyzed data from a randomized, placebo-controlled chemoprevention trial to determine whether a 3-month treatment with either 9-cis-retinoic acid (RA) or 13-cis-RA and α-tocopherol reduced Ki-67, a proliferation biomarker, in the bronchial epithelium. Methods Former smokers (n = 225) were randomly assigned to receive 3 months of daily oral 9-cis-RA (100 mg), 13-cis-RA (1 mg/kg) and α-tocopherol (1200 IU), or placebo. Bronchoscopic biopsy specimens obtained before and after treatment were immunohistochemically assessed for changes in the Ki-67 proliferative index (i.e., percentage of cells with Ki-67–positive nuclear staining) in the basal and parabasal layers of the bronchial epithelium. Per-subject and per–biopsy site analyses were conducted. Multicovariable analyses, including a mixed-effects model and a generalized estimating equations model, were used to investigate the treatment effect (Ki-67 labeling index and percentage of bronchial epithelial biopsy sites with a Ki-67 index ≥ 5%) with adjustment for multiple covariates, such as smoking history and metaplasia. Coefficient estimates and 95% confidence intervals (CIs) were obtained from the models. All statistical tests were two-sided. Results In per-subject analyses, Ki-67 labeling in the basal layer was not changed by any treatment; the percentage of subjects with a high Ki-67 labeling in the parabasal layer dropped statistically significantly after treatment with 13-cis-RA and α-tocopherol treatment (P = .04) compared with placebo, but the drop was not statistically significant after 9-cis-RA treatment (P = .17). A similar effect was observed in the parabasal layer in a per-site analysis; the percentage of sites with high Ki-67 labeling dropped statistically significantly after 9-cis-RA treatment (coefficient estimate = −0.72, 95% CI = −1.24 to −0.20; P = .007) compared with placebo, and after 13-cis-RA and α-tocopherol treatment (coefficient estimate = −0.66, 95% CI = −1.15 to −0.17; P = .008). Conclusions In per-subject analyses, treatment with 13-cis-RA and α-tocopherol, compared with placebo, was statistically significantly associated with reduced bronchial epithelial cell proliferation; treatment with 9-cis-RA was not. In per-site analyses, statistically significant associations were obtained with both treatments. PMID:17971525

Recombinant human bone morphogenetic protein-2 versus autogenous iliac crest bone graft for lumbar fusion: a meta-analysis of ten randomized controlled trials.

PubMed

Chen, Zhiguang; Ba, Gen; Shen, Tao; Fu, Qin

2012-12-01

Recombinant human bone morphogenetic protein-2 (rhBMP-2) as a substitute for iliac crest bone graft (ICBG) has been increasingly widely used in lumbar fusion. It has been proven non-inferior in fusion success and clinical outcomes when compared with ICBG. However, increasingly, some potentially uncommon and serious complications associated with the use of rhBMP-2 have been of great concern to surgeons. The purpose of this study was to determine whether rhBMP-2 could be considered an effective and, more importantly, a relatively safe substitute for ICBG in lumbar fusion. Randomized controlled trials that compared rhBMP-2 with ICBG for lumbar fusion were identified by computer and manual searching. The risk of bias and clinical relevance of the included studies were assessed. Publication bias was explored using funnel plot and statistical tests (Egger's test and Begg's test). Meta-analyses were performed using the Cochrane systematic review methods. Ten randomized controlled trials (1,342 patients) met the inclusion criteria. Compared with ICBG, the use of rhBMP-2 significantly decreased the risk of fusion failure at all time intervals (6 months: p < 0.0001, RR = 0.55, 95 % CI = 0.42-0.72; 12 months: p = 0.0003, RR = 0.53, 95 % CI = 0.37-0.75; 24 months: p < 0.00001, RR = 0.31, 95 % CI = 0.21-0.46) and the rate of reoperation (p = 0.0001, RR = 0.52, 95 % CI = 0.37-0.72). There was no statistical difference in clinical improvement on the Oswestry Disability Index, although a favorable trend in the rhBMP-2 group was found (p = 0.12, RR = 0.73, 95 % CI = 0.49-1.08). Subgroup analyses stratified by the type of surgical procedure yielded similar results. Owing to the different data formats, meta-analysis on adverse events was not performed. RhBMP-2 was superior to the ICBG for achieving fusion success and avoiding reoperation. However, evidence from the Food and Drug Administration document and subsequent independent studies has demonstrated that original, industry-sponsored trials underestimated rhBMP-2-related adverse events. There are still security risks in the use of rhBMP-2.

Phenotypic conversion of distinct muscle fiber populations to electrocytes in a weakly electric fish.

PubMed

Unguez, G A; Zakon, H H

1998-09-14

In most groups of electric fish, the electric organ (EO) derives from striated muscle cells that suppress many muscle phenotypic properties. This phenotypic conversion is recapitulated during regeneration of the tail in the weakly electric fish Sternopygus macrurus. Mature electrocytes, the cells of the electric organ, are considerably larger than the muscle fibers from which they derive, and it is not known whether this is a result of muscle fiber hypertrophy and/or fiber fusion. In this study, electron micrographs revealed fusion of differentiated muscle fibers during the formation of electrocytes. There was no evidence of hypertrophy of muscle fibers during their phenotypic conversion. Furthermore, although fish possess distinct muscle phenotypes, the extent to which each fiber population contributes to the formation of the EO has not been determined. By using myosin ATPase histochemistry and anti-myosin heavy chain (MHC) monoclonal antibodies (mAbs), different fiber types were identified in fascicles of muscle in the adult tail. Mature electrocytes were not stained by the ATPase reaction, nor were they labeled by any of the anti-MHC mAbs. In contrast, mature muscle fibers exhibited four staining patterns. The four fiber types were spatially arranged in distinct compartments with little intermixing; peripherally were two populations of type I fibers with small cross-sectional areas, whereas more centrally were two populations of type II fibers with larger cross-sectional areas. In 2- and 3-week regenerating blastema, three fiber types were clearly discerned. Most (> 95%) early-forming electrocytes had an MHC phenotype similar to that of type II fibers. In contrast, fusion among type I fibers was rare. Together, ultrastructural and immunohistochemical analyses revealed that the fusion of muscle fibers gives rise to electrocytes and that this fusion occurs primarily among the population of type II fibers in regenerating blastema.

Degenerative lumbar scoliosis in elderly patients: dynamic stabilization without fusion versus posterior instrumented fusion.

PubMed

Di Silvestre, Mario; Lolli, Francesco; Bakaloudis, Georgios

2014-01-01

Posterolateral fusion with pedicle screw instrumentation is currently the most widely accepted technique for degenerative lumbar scoliosis in elderly patients. However, a high incidence of complications has been reported in most series. Dynamic stabilization without fusion in patients older than 60 years has not previously been compared with the use of posterior fusion in degenerative lumbar scoliosis. To compare dynamic stabilization without fusion and posterior instrumented fusion in the treatment of degenerative lumbar scoliosis in elderly patients, in terms of perioperative findings, clinical outcomes, and adverse events. A retrospective study. Fifty-seven elderly patients were included. There were 45 women (78%) and 12 men (22%) with a mean age of 68.1 years (range, 61-78 years). All patients had degenerative de novo lumbar scoliosis, associated with vertebral canal stenosis in 51 cases (89.4%) and degenerative spondylolisthesis in 24 patients (42.1%). Clinical (Oswestry Disability Index, visual analog scale, Roland-Morris Disability Questionnaire) and radiological (scoliosis and lordosis corrections) outcomes as well as incidence of complications. Patients were divided into two groups: 32 patients (dynamic group) had dynamic stabilization without fusion and 25 patients (fusion group) underwent posterior instrumented fusion. All the patients' medical records and X-rays were reviewed. Preoperative, postoperative, and follow-up questionnaires were obtained to evaluate clinical outcomes. At an average follow-up of 64 months (range, 42-90 months), clinical results improved similarly in both groups of patients. Statistically superior scoliosis and final lordosis corrections were achieved with posterior fusion (56.9% vs. 37.3% and -46.8° vs. -35.8°, respectively). However, in the dynamic group, incidence of overall complications was lower (25% vs. 44%), and fewer patients required revision surgery (6.2% vs. 16%). Furthermore, lower average values of operative duration (190 vs. 240 minutes) and blood loss (950 vs. 1,400 cc) were observed in the dynamic group than in the fusion group. In elderly patients with degenerative lumbar scoliosis, pedicle screw-based dynamic stabilization was less invasive with shorter operative duration, less blood loss, and lower adverse event rates than instrumented posterior fusion. Scoliosis curve reduction and lumbar lordosis were superior after fusion; however, dynamic stabilization achieved satisfying values of both these parameters, and these results were stable after an average follow-up of more than 5 years. Furthermore, there was no difference between the two techniques in terms of functional clinical outcomes at the last follow-up. Copyright © 2014 Elsevier Inc. All rights reserved.

Analysis of sugars and pH in commercially available soft drinks in Saudi Arabia with a brief review on their dental implications.

PubMed

Idris, Ali Mohamed; Vani, Nandimandalam Venkata; Almutari, Dhafi A; Jafar, Mohammed A; Boreak, Nezar

2016-12-01

To determine the amount of sugar and pH in commercially available soft drinks in Jazan, Saudi Arabia. This was further compared with their labeled values in order to inform the regulations. The effects of these drinks on teeth is reviewed. Ten brands of popular soft drinks including 6 regular carbonated drinks and 4 energy drinks were obtained from the local markets. Their pH was determined using a pH meter. The amount of total sugar, glucose, fructose, and sucrose was estimated using high performance liquid chromatography (using Dionex ICS 5000 ion chromatography) at the Saudi Food and Drug Authority. Descriptive statistics was done to obtain the mean and standard deviation. Intergroup comparison was performed using independent t -test, and the labeled and estimated values within the group were compared with paired t -test. The labeled and estimated sugar in energy drinks (14.3 ± 0.48 and 15.6 ± 2.3, respectively) were higher than the carbonated drinks (11.2 ± 0.46 and 12.8 ± 0.99), which was statistically significant. In addition, there was a significant difference in the concentration of glucose in energy drinks (5.7 ± 1.7) compared to carbonated drinks (4.1 ± 1.4). The pH of these drinks ranged from 2.4 to 3.2. The differences between the estimated and labeled sugar in carbonated drinks showed statistical significance. Mild variation was observed in total sugar, glucose, fructose, and sucrose levels among different bottles of the same brand of these drinks. The low pH and high sugar content in these drinks are detrimental to dental health. Comparison of the estimated sugar with their labeled values showed variation in most of the brands. Preventive strategies should be implemented to reduce the health risks posed by these soft drinks.

Analysis of sugars and pH in commercially available soft drinks in Saudi Arabia with a brief review on their dental implications

PubMed Central

Idris, Ali Mohamed; Vani, Nandimandalam Venkata; Almutari, Dhafi A.; Jafar, Mohammed A.; Boreak, Nezar

2016-01-01

Objective: To determine the amount of sugar and pH in commercially available soft drinks in Jazan, Saudi Arabia. This was further compared with their labeled values in order to inform the regulations. The effects of these drinks on teeth is reviewed. Materials and Methods: Ten brands of popular soft drinks including 6 regular carbonated drinks and 4 energy drinks were obtained from the local markets. Their pH was determined using a pH meter. The amount of total sugar, glucose, fructose, and sucrose was estimated using high performance liquid chromatography (using Dionex ICS 5000 ion chromatography) at the Saudi Food and Drug Authority. Descriptive statistics was done to obtain the mean and standard deviation. Intergroup comparison was performed using independent t-test, and the labeled and estimated values within the group were compared with paired t-test. Results: The labeled and estimated sugar in energy drinks (14.3 ± 0.48 and 15.6 ± 2.3, respectively) were higher than the carbonated drinks (11.2 ± 0.46 and 12.8 ± 0.99), which was statistically significant. In addition, there was a significant difference in the concentration of glucose in energy drinks (5.7 ± 1.7) compared to carbonated drinks (4.1 ± 1.4). The pH of these drinks ranged from 2.4 to 3.2. The differences between the estimated and labeled sugar in carbonated drinks showed statistical significance. Mild variation was observed in total sugar, glucose, fructose, and sucrose levels among different bottles of the same brand of these drinks. Conclusion: The low pH and high sugar content in these drinks are detrimental to dental health. Comparison of the estimated sugar with their labeled values showed variation in most of the brands. Preventive strategies should be implemented to reduce the health risks posed by these soft drinks. PMID:28217536

Automatic detection of adverse events to predict drug label changes using text and data mining techniques.

PubMed

Gurulingappa, Harsha; Toldo, Luca; Rajput, Abdul Mateen; Kors, Jan A; Taweel, Adel; Tayrouz, Yorki

2013-11-01

The aim of this study was to assess the impact of automatically detected adverse event signals from text and open-source data on the prediction of drug label changes. Open-source adverse effect data were collected from FAERS, Yellow Cards and SIDER databases. A shallow linguistic relation extraction system (JSRE) was applied for extraction of adverse effects from MEDLINE case reports. Statistical approach was applied on the extracted datasets for signal detection and subsequent prediction of label changes issued for 29 drugs by the UK Regulatory Authority in 2009. 76% of drug label changes were automatically predicted. Out of these, 6% of drug label changes were detected only by text mining. JSRE enabled precise identification of four adverse drug events from MEDLINE that were undetectable otherwise. Changes in drug labels can be predicted automatically using data and text mining techniques. Text mining technology is mature and well-placed to support the pharmacovigilance tasks. Copyright © 2013 John Wiley & Sons, Ltd.