Dynamics of water molecules in the active-site cavity of human cytochromes P450

DEFF Research Database (Denmark)

Rydberg, Patrik; Rod, Thomas Holm; Olsen, Lars

2007-01-01

We have studied the dynamics of water molecules in six crystal structures of four human cytochromes P450, 2A6, 2C8, 2C9, and 3A4, with molecular dynamics simulations. In the crystal structures, only a few water molecules are seen and the reported sizes of the active-site cavity vary a lot....... In the simulations, the cavities are completely filled with water molecules, although with approximately 20% lower density than in bulk water. The 2A6 protein differs from the other three in that it has a very small cavity with only two water molecules and no exchange with the surroundings. The other three proteins...... channels, through which there is a quite frequent exchange of water molecules (one molecule is exchanged every 30-200 ps), except in 2A6. Most of the channels are observed also in the crystal structures, but two to three channels in each protein open only during the simulations. There are no water...

Characterization of Microbial Communities in Subsurface Nuclear Blast Cavities of the Nevada Test Site

Energy Technology Data Exchange (ETDEWEB)

Moser, Duane P.; Bruckner, Jim; Fisher, Jen; Czerwinski, Ken; Russell, Charles E.; Zavarin, Mavrik

2010-09-01

This U.S. Department of Energy (DOE) Environmental Remediation Sciences Project (ERSP) was designed to test fundamental hypotheses concerning the existence and nature of indigenous microbial populations of Nevada Test Site subsurface nuclear test/detonation cavities. Now called Subsurface Biogeochemical Research (SBR), this program’s Exploratory Research (ER) element, which funded this research, is designed to support high risk, high potential reward projects. Here, five cavities (GASCON, CHANCELLOR, NASH, ALEMAN, and ALMENDRO) and one tunnel (U12N) were sampled using bailers or pumps. Molecular and cultivation-based techniques revealed bacterial signatures at five sites (CHANCELLOR may be lifeless). SSU rRNA gene libraries contained diverse and divergent microbial sequences affiliated with known metal- and sulfur-cycling microorganisms, organic compound degraders, microorganisms from deep mines, and bacteria involved in selenate reduction and arsenite oxidation. Close relatives of Desulforudis audaxviator, a microorganism thought to subsist in the terrestrial deep subsurface on H2 and SO42- produced by radiochemical reactions, was detected in the tunnel waters. NTS-specific media formulations were used to culture and quantify nitrate-, sulfate-, iron-reducing, fermentative, and methanogenic microorganisms. Given that redox manipulations mediated by microorganisms can impact the mobility of DOE contaminants, our results should have implications for management strategies at this and other DOE sites.

Characterization of microbial communities in subsurface nuclear blast cavities of the Nevada Test Site

Energy Technology Data Exchange (ETDEWEB)

Moser, Duane P; Czerwinski, Ken; Russell, Charles E; Zavarin, Mavrik

2010-07-13

This US Department of Energy (DOE) Environmental Remediation Sciences Project (ERSP) was designed to test fundamental hypotheses concerning the existence and nature of indigenous microbial populations of Nevada Test Site subsurface nuclear test/detonation cavities. Now called Subsurface Biogeochemical Research (SBR), this program's Exploratory Research (ER) element, which funded this research, is designed to support high risk, high potential reward projects. Here, five cavities (GASCON, CHANCELLOR, NASH, ALEMAN, and ALMENDRO) and one tunnel (U12N) were sampled using bailers or pumps. Molecular and cultivation-based techniques revealed bacterial signatures at five sites (CHANCELLOR may be lifeless). SSU rRNA gene libraries contained diverse and divergent microbial sequences affiliated with known metal- and sulfur-cycling microorganisms, organic compound degraders, microorganisms from deep mines, and bacteria involved in selenate reduction and arsenite oxidation. Close relatives of Desulforudis audaxviator, a microorganism thought to subsist in the terrestrial deep subsurface on H2 and SO42- produced by radiochemical reactions, was detected in the tunnel waters. NTS-specific media formulations were used to culture and quantify nitrate-, sulfate-, iron-reducing, fermentative, and methanogenic microorganisms. Given that redox manipulations mediated by microorganisms can impact the mobility of DOE contaminants, our results should have implications for management strategies at this and other DOE sites.

Characterization of Microbial Communities in Subsurface Nuclear Blast Cavities of the Nevada Test Site

International Nuclear Information System (INIS)

Moser, Duane P.; Bruckner, Jim; Fisher, Jen; Czerwinski, Ken; Russell, Charles E.; Zavarin, Mavrik

2010-01-01

This U.S. Department of Energy (DOE) Environmental Remediation Sciences Project (ERSP) was designed to test fundamental hypotheses concerning the existence and nature of indigenous microbial populations of Nevada Test Site subsurface nuclear test/detonation cavities. Now called Subsurface Biogeochemical Research (SBR), this program's Exploratory Research (ER) element, which funded this research, is designed to support high risk, high potential reward projects. Here, five cavities (GASCON, CHANCELLOR, NASH, ALEMAN, and ALMENDRO) and one tunnel (U12N) were sampled using bailers or pumps. Molecular and cultivation-based techniques revealed bacterial signatures at five sites (CHANCELLOR may be lifeless). SSU rRNA gene libraries contained diverse and divergent microbial sequences affiliated with known metal- and sulfur-cycling microorganisms, organic compound degraders, microorganisms from deep mines, and bacteria involved in selenate reduction and arsenite oxidation. Close relatives of Desulforudis audaxviator, a microorganism thought to subsist in the terrestrial deep subsurface on H 2 and SO 4 2- produced by radiochemical reactions, was detected in the tunnel waters. NTS-specific media formulations were used to culture and quantify nitrate-, sulfate-, iron-reducing, fermentative, and methanogenic microorganisms. Given that redox manipulations mediated by microorganisms can impact the mobility of DOE contaminants, our results should have implications for management strategies at this and other DOE sites.

Prediction of the Lorentz Force Detuning and Pressure Sensitivity for a Pillbox Cavity

Energy Technology Data Exchange (ETDEWEB)

Parise, M. [Fermilab

2018-04-23

The Lorentz Force Detuning (LFD) and the pressure sensitivity are two critical concerns during the design of a Superconducting Radio Frequency (SRF) cavity resonator. The mechanical deformation of the bare Niobium cavity walls, due to the electromagnetic fields and fluctuation of the external pressure in the Helium bath, can dynamically and statically detune the frequency of the cavity and can cause beam phase errors. The frequency shift can be compensated by additional RF power, that is required to maintain the accelerating gradient, or by sophisticated tuning mechanisms and control-compensation algorithms. Passive stiffening is one of the simplest and most effective tools that can be used during the early design phase, capable of satisfying the Radio Frequency (RF) requisites. This approach requires several multiphysics simulations as well as a deep mechanical and RF knowledge of the phenomena involved. In this paper, is presented a new numerical model for a pillbox cavity that can predict the frequency shifts caused by the LFD and external pressure. This method allows to greatly reduce the computational effort, which is necessary to meet the RF requirements and to keep track of the frequency shifts without using the time consuming multiphysics simulations.

Text mining improves prediction of protein functional sites.

Directory of Open Access Journals (Sweden)

Karin M Verspoor

Full Text Available We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites. The structure analysis was carried out using Dynamics Perturbation Analysis (DPA, which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions.

Text Mining Improves Prediction of Protein Functional Sites

Science.gov (United States)

Cohn, Judith D.; Ravikumar, Komandur E.

2012-01-01

We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites). The structure analysis was carried out using Dynamics Perturbation Analysis (DPA), which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites) in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions. PMID:22393388

Prediction of glycosylation sites using random forests

Directory of Open Access Journals (Sweden)

Hirst Jonathan D

2008-11-01

Full Text Available Abstract Background Post translational modifications (PTMs occur in the vast majority of proteins and are essential for function. Prediction of the sequence location of PTMs enhances the functional characterisation of proteins. Glycosylation is one type of PTM, and is implicated in protein folding, transport and function. Results We use the random forest algorithm and pairwise patterns to predict glycosylation sites. We identify pairwise patterns surrounding glycosylation sites and use an odds ratio to weight their propensity of association with modified residues. Our prediction program, GPP (glycosylation prediction program, predicts glycosylation sites with an accuracy of 90.8% for Ser sites, 92.0% for Thr sites and 92.8% for Asn sites. This is significantly better than current glycosylation predictors. We use the trepan algorithm to extract a set of comprehensible rules from GPP, which provide biological insight into all three major glycosylation types. Conclusion We have created an accurate predictor of glycosylation sites and used this to extract comprehensible rules about the glycosylation process. GPP is available online at http://comp.chem.nottingham.ac.uk/glyco/.

Acoustic trapping in bubble-bounded micro-cavities

Science.gov (United States)

O'Mahoney, P.; McDougall, C.; Glynne-Jones, P.; MacDonald, M. P.

2016-12-01

We present a method for controllably producing longitudinal acoustic trapping sites inside microfluidic channels. Air bubbles are injected into a micro-capillary to create bubble-bounded `micro-cavities'. A cavity mode is formed that shows controlled longitudinal acoustic trapping between the two air/water interfaces along with the levitation to the centre of the channel that one would expect from a lower order lateral mode. 7 μm and 10 μm microspheres are trapped at the discrete acoustic trapping sites in these micro-cavities.We show this for several lengths of micro-cavity.

XenoSite: accurately predicting CYP-mediated sites of metabolism with neural networks.

Science.gov (United States)

Zaretzki, Jed; Matlock, Matthew; Swamidass, S Joshua

2013-12-23

Understanding how xenobiotic molecules are metabolized is important because it influences the safety, efficacy, and dose of medicines and how they can be modified to improve these properties. The cytochrome P450s (CYPs) are proteins responsible for metabolizing 90% of drugs on the market, and many computational methods can predict which atomic sites of a molecule--sites of metabolism (SOMs)--are modified during CYP-mediated metabolism. This study improves on prior methods of predicting CYP-mediated SOMs by using new descriptors and machine learning based on neural networks. The new method, XenoSite, is faster to train and more accurate by as much as 4% or 5% for some isozymes. Furthermore, some "incorrect" predictions made by XenoSite were subsequently validated as correct predictions by revaluation of the source literature. Moreover, XenoSite output is interpretable as a probability, which reflects both the confidence of the model that a particular atom is metabolized and the statistical likelihood that its prediction for that atom is correct.

Positive-Unlabeled Learning for Pupylation Sites Prediction

Directory of Open Access Journals (Sweden)

Ming Jiang

2016-01-01

Full Text Available Pupylation plays a key role in regulating various protein functions as a crucial posttranslational modification of prokaryotes. In order to understand the molecular mechanism of pupylation, it is important to identify pupylation substrates and sites accurately. Several computational methods have been developed to identify pupylation sites because the traditional experimental methods are time-consuming and labor-sensitive. With the existing computational methods, the experimentally annotated pupylation sites are used as the positive training set and the remaining nonannotated lysine residues as the negative training set to build classifiers to predict new pupylation sites from the unknown proteins. However, the remaining nonannotated lysine residues may contain pupylation sites which have not been experimentally validated yet. Unlike previous methods, in this study, the experimentally annotated pupylation sites were used as the positive training set whereas the remaining nonannotated lysine residues were used as the unlabeled training set. A novel method named PUL-PUP was proposed to predict pupylation sites by using positive-unlabeled learning technique. Our experimental results indicated that PUL-PUP outperforms the other methods significantly for the prediction of pupylation sites. As an application, PUL-PUP was also used to predict the most likely pupylation sites in nonannotated lysine sites.

Statistics of magnetoconductance in ballistic cavities

International Nuclear Information System (INIS)

Yang, X.; Ishio, H.; Burgdoerfer, J.

1995-01-01

The statistical properties of magnetoconductance in ballistic microcavities are investigated numerically. The distribution of conductance for chaotic cavities is found to follow the renormalized Porter-Thomas distribution suggested by random-matrix theory for the Gaussian ensemble while the conductance distribution of regular cavities in magnetic fields is nonuniversal and shifted towards the maximum value for a given number of open channels. The renormalized Porter-Thomas distribution implies a universal dependence of fluctuation amplitude on the mean conductance for chaotic cavities in the absence of time-reversal symmetry. The fluctuation amplitude for regular cavities is found to be larger than the saturation value of the fluctuation amplitude of chaotic cavities predicted by random-matrix theory. The change of the mean conductance as a function of the external magnetic field is consistent with semiclassical predictions

In-vivo autofluorescence diagnosis of the cancer of oral cavity

International Nuclear Information System (INIS)

Majumder, S.K.; Ghosh, N.; Mohanty, S.K.; Gupta, P.K.

2000-01-01

The results of an in-vivo study carried out on 25 patients with histologically confirmed squamous cell carcinoma (SCC) of the oral cavity are reported. Spectra from different sites of the oral cavity were recorded using a N 2 laser based portable fluorimeter developed in-house. The spectral data acquisition was computer controlled. On an average, 5 spectra from the SCC tissue sites and 4 spectra from the visually normal tissue sites were recorded.The autofluorescence spectra was recorded from different cancerous and normal sites of the oral cavity of a patient

Prediction of the flooding process at the Ronneburg site - results of an integrated approach

International Nuclear Information System (INIS)

Paul, M.; Saenger, H.-J.; Snagowski, S.; Maerten, H.; Eckart, M.

1998-01-01

The flooding process of the Ronneburg uranium mine (WISMUT) was initiated at the turn of the year 1997 to 1998. In order to prepare the flooding process and to derive and optimize technological measures an integrated modelling approach was chosen which includes several coupled modules. The most important issues to be answered are: (1) prediction of the flooding time (2) prediction of the groundwater level at the post-flooding stage, assessment of amount, location and quality of flooding waters entering the receiving streams at the final stage (3) water quality prediction within the mine during the flooding process (4) definition of technological measures and assessment of their efficiency A box model which includes the three-dimensional distribution of the cavity volume in the mine represents the model core. The model considers the various types of dewatered cavity volumes for each mine level / mining field and the degree of vertical and horizontal connection between the mining fields. Different types of open mine space as well as the dewatered geological pore and joint volume are considered taking into account the contour of the depression cone prior to flooding and the characteristics of the different rock types. Based on the mine water balance and the flooding technology the model predicts the rise of the water table over time during the flooding process for each mine field separately. In order to predict the mine water quality and the efficiency of in-situ water treatment the box model was linked to a geochemical model (PHREEQC). A three-dimensional flow model is used to evaluate the post-flooding situation at the Ronneburg site. This model is coupled to the box model. The modelling results of various flooding scenarios show that a prediction of the post-flooding geohydraulic situation is possible despite of uncertainties concerning the input parameters which still exist. The post-flooding water table in the central part of the Ronneburg mine will be 270 m

Pripper: prediction of caspase cleavage sites from whole proteomes

Directory of Open Access Journals (Sweden)

Salmi Jussi

2010-06-01

Full Text Available Abstract Background Caspases are a family of proteases that have central functions in programmed cell death (apoptosis and inflammation. Caspases mediate their effects through aspartate-specific cleavage of their target proteins, and at present almost 400 caspase substrates are known. There are several methods developed to predict caspase cleavage sites from individual proteins, but currently none of them can be used to predict caspase cleavage sites from multiple proteins or entire proteomes, or to use several classifiers in combination. The possibility to create a database from predicted caspase cleavage products for the whole genome could significantly aid in identifying novel caspase targets from tandem mass spectrometry based proteomic experiments. Results Three different pattern recognition classifiers were developed for predicting caspase cleavage sites from protein sequences. Evaluation of the classifiers with quality measures indicated that all of the three classifiers performed well in predicting caspase cleavage sites, and when combining different classifiers the accuracy increased further. A new tool, Pripper, was developed to utilize the classifiers and predict the caspase cut sites from an arbitrary number of input sequences. A database was constructed with the developed tool, and it was used to identify caspase target proteins from tandem mass spectrometry data from two different proteomic experiments. Both known caspase cleavage products as well as novel cleavage products were identified using the database demonstrating the usefulness of the tool. Pripper is not restricted to predicting only caspase cut sites, but it gives the possibility to scan protein sequences for any given motif(s and predict cut sites once a suitable cut site prediction model for any other protease has been developed. Pripper is freely available and can be downloaded from http://users.utu.fi/mijopi/Pripper. Conclusions We have developed Pripper, a tool for

Thermal conditions within tree cavities in ponderosa pine (Pinus ponderosa) forests: potential implications for cavity users

Science.gov (United States)

Vierling, Kerri T.; Lorenz, Teresa J.; Cunningham, Patrick; Potterf, Kelsi

2017-11-01

Tree cavities provide critical roosting and breeding sites for multiple species, and thermal environments in these cavities are important to understand. Our objectives were to (1) describe thermal characteristics in cavities between June 3 and August 9, 2014, and (2) investigate the environmental factors that influence cavity temperatures. We placed iButtons in 84 different cavities in ponderosa pine (Pinus ponderosa) forests in central Washington, and took hourly measurements for at least 8 days in each cavity. Temperatures above 40 °C are generally lethal to developing avian embryos, and 18% of the cavities had internal temperatures of ≥ 40 °C for at least 1 h of each day. We modeled daily maximum cavity temperature, the amplitude of daily cavity temperatures, and the difference between the mean internal cavity and mean ambient temperatures as a function of several environmental variables. These variables included canopy cover, tree diameter at cavity height, cavity volume, entrance area, the hardness of the cavity body, the hardness of the cavity sill (which is the wood below the cavity entrance which forms the barrier between the cavity and the external environment), and sill width. Ambient temperature had the largest effect size for maximum cavity temperature and amplitude. Larger trees with harder sills may provide more thermally stable cavity environments, and decayed sills were positively associated with maximum cavity temperatures. Summer temperatures are projected to increase in this region, and additional research is needed to determine how the thermal environments of cavities will influence species occupancy, breeding, and survival.

Prominence mass supply and the cavity

Energy Technology Data Exchange (ETDEWEB)

Schmit, Donald J.; Innes, D. [Max Planck Institute for Solar System Research, D-37191 Katlenburg-Lindau (Germany); Gibson, S. [High Altitude Observatory, National Center for Atmospheric Research, Boulder, CO 80307 (United States); Luna, M. [Instituto de Astrofísica de Canarias, E-38200 La Laguna, Tenerife (Spain); Karpen, J. [NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States)

2013-12-20

A prevalent but untested paradigm is often used to describe the prominence-cavity system: the cavity is under-dense because it is evacuated by supplying mass to the condensed prominence. The thermal non-equilibrium (TNE) model of prominence formation offers a theoretical framework to predict the thermodynamic evolution of the prominence and the surrounding corona. We examine the evidence for a prominence-cavity connection by comparing the TNE model with diagnostics of dynamic extreme ultraviolet (EUV) emission surrounding the prominence, specifically prominence horns. Horns are correlated extensions of prominence plasma and coronal plasma which appear to connect the prominence and cavity. The TNE model predicts that large-scale brightenings will occur in the Solar Dynamics Observatory Atmospheric Imaging Assembly 171 Å bandpass near the prominence that are associated with the cooling phase of condensation formation. In our simulations, variations in the magnitude of footpoint heating lead to variations in the duration, spatial scale, and temporal offset between emission enhancements in the other EUV bandpasses. While these predictions match well a subset of the horn observations, the range of variations in the observed structures is not captured by the model. We discuss the implications of our one-dimensional loop simulations for the three-dimensional time-averaged equilibrium in the prominence and the cavity. Evidence suggests that horns are likely caused by condensing prominence plasma, but the larger question of whether this process produces a density-depleted cavity requires a more tightly constrained model of heating and better knowledge of the associated magnetic structure.

Prominence Mass Supply and the Cavity

Science.gov (United States)

Schmit, Donald J.; Gibson, S.; Luna, M.; Karpen, J.; Innes, D.

2013-01-01

A prevalent but untested paradigm is often used to describe the prominence-cavity system; the cavity is under-dense because it it evacuated by supplying mass to the condensed prominence. The thermal non-equilibrium (TNE) model of prominence formation offers a theoretical framework to predict the thermodynamic evolutin of the prominence and the surrounding corona. We examine the evidence for a prominence-cavity connection by comparing the TNE model and diagnostics of dynamic extreme ultraviolet (EUV) emission surrounding the prominence, specifically prominence horns. Horns are correlated extensions of prminence plasma and coronal plasma which appear to connect the prominence and cavity. The TNE model predicts that large-scale brightenings will occur in the Solar Dynamics Observatory Atmospheric Imaging Assembly 171 A badpass near he prominence that are associated with the cooling phase of condensation formation. In our simulations, variations in the magnitude of footpoint heating lead to variations in the duration, spatial scale, and temporal offset between emission enhancements in the other EUV bandpasses. While these predictions match well a subset of the horn observations, the range of variations in the observed structures is not captured by the model. We discuss the implications of one-dimensional loop simulations for the three-dimensional time-averaged equilibrium in the prominence and the cavity. Evidence suggests that horns are likely caused by condensing prominence plasma, but the larger question of whether this process produces a density-depleted cavity requires a more tightly constrained model of heating and better knowledge of the associated magnetic structure.

Micro-Cavity Fluidic Dye Laser

DEFF Research Database (Denmark)

Helbo, Bjarne; Kristensen, Anders; Menon, Aric Kumaran

2003-01-01

We have successfully designed, fabricated and characterized a micro-cavity fluidic dye laser with metallic mirrors, which can be integrated with polymer based lab-on-a-chip microsystems without further processing steps. A simple rate-equation model is used to predict the average pumping power...... threshold for lasing as function of cavity-mirror reflectance, laser dye concentration and cavity length. The laser device is characterized using the laser dye Rhodamine 6G dissolved in ethanol. Lasing is observed, and the influence of dye concentration is investigated....

Sites of origin of oral cavity cancer in nonsmokers vs smokers: possible evidence of dental trauma carcinogenesis and its importance compared with human papillomavirus.

Science.gov (United States)

Perry, Brendan J; Zammit, Andrew P; Lewandowski, Andrew W; Bashford, Julia J; Dragovic, Adrian S; Perry, Emily J; Hayatbakhsh, Reza; Perry, Christopher F L

2015-01-01

The relatively high and possibly rising incidence of mouth squamous cell carcinoma in nonsmokers, especially women, without obvious cause has been noted by previous authors. Is chronic dental trauma and irritation a carcinogen, and what is its importance compared with human papillomavirus (HPV) oropharyngeal cancer in nonsmokers? To determine whether oral cavity cancers occurred more commonly at sites of dental trauma and how the position of these cancers varied between nonsmokers lacking major identified carcinogens and smokers. If these cancers occurred more frequently at sites of chronic trauma, especially in nonsmokers, it would suggest chronic dental trauma as a possible carcinogen. A retrospective analysis of 881 patients with oral cavity or oropharyngeal cancers seen through a tertiary referral hospital between 2001 and 2011 was performed. Patient medical records were analyzed to determine the location of the tumor within the oral cavity and oropharynx and how it relates to patient demographics, smoking and alcohol histories, and comorbidities. Dental histories were also sought, including use of dentures. Nonsmokers comprised 87 of 390 patients with mouth cancer (22%) and 48 of 334 patients with oropharyngeal cancer (14%). Female nonsmoking patients included 53 with oral cancer (61%) but only 12 with oropharyngeal squamous cell carcinoma (25%). Oral cancers occurred on the lateral tongue, a potential site of chronic dental trauma, in 57 nonsmokers (66%) compared with 107 smokers/ex-smokers (33%) (P Oral cavity cancers occur predominantly at sites of potential dental and denture trauma, especially in nonsmokers without other risk factors. Recognizing teeth irritation as a potential carcinogen would have an impact on prevention and treatment strategies.

An overview of the prediction of protein DNA-binding sites.

Science.gov (United States)

Si, Jingna; Zhao, Rui; Wu, Rongling

2015-03-06

Interactions between proteins and DNA play an important role in many essential biological processes such as DNA replication, transcription, splicing, and repair. The identification of amino acid residues involved in DNA-binding sites is critical for understanding the mechanism of these biological activities. In the last decade, numerous computational approaches have been developed to predict protein DNA-binding sites based on protein sequence and/or structural information, which play an important role in complementing experimental strategies. At this time, approaches can be divided into three categories: sequence-based DNA-binding site prediction, structure-based DNA-binding site prediction, and homology modeling and threading. In this article, we review existing research on computational methods to predict protein DNA-binding sites, which includes data sets, various residue sequence/structural features, machine learning methods for comparison and selection, evaluation methods, performance comparison of different tools, and future directions in protein DNA-binding site prediction. In particular, we detail the meta-analysis of protein DNA-binding sites. We also propose specific implications that are likely to result in novel prediction methods, increased performance, or practical applications.

An Overview of the Prediction of Protein DNA-Binding Sites

Directory of Open Access Journals (Sweden)

Jingna Si

2015-03-01

Full Text Available Interactions between proteins and DNA play an important role in many essential biological processes such as DNA replication, transcription, splicing, and repair. The identification of amino acid residues involved in DNA-binding sites is critical for understanding the mechanism of these biological activities. In the last decade, numerous computational approaches have been developed to predict protein DNA-binding sites based on protein sequence and/or structural information, which play an important role in complementing experimental strategies. At this time, approaches can be divided into three categories: sequence-based DNA-binding site prediction, structure-based DNA-binding site prediction, and homology modeling and threading. In this article, we review existing research on computational methods to predict protein DNA-binding sites, which includes data sets, various residue sequence/structural features, machine learning methods for comparison and selection, evaluation methods, performance comparison of different tools, and future directions in protein DNA-binding site prediction. In particular, we detail the meta-analysis of protein DNA-binding sites. We also propose specific implications that are likely to result in novel prediction methods, increased performance, or practical applications.

Human Splice-Site Prediction with Deep Neural Networks.

Science.gov (United States)

Naito, Tatsuhiko

2018-04-18

Accurate splice-site prediction is essential to delineate gene structures from sequence data. Several computational techniques have been applied to create a system to predict canonical splice sites. For classification tasks, deep neural networks (DNNs) have achieved record-breaking results and often outperformed other supervised learning techniques. In this study, a new method of splice-site prediction using DNNs was proposed. The proposed system receives an input sequence data and returns an answer as to whether it is splice site. The length of input is 140 nucleotides, with the consensus sequence (i.e., "GT" and "AG" for the donor and acceptor sites, respectively) in the middle. Each input sequence model is applied to the pretrained DNN model that determines the probability that an input is a splice site. The model consists of convolutional layers and bidirectional long short-term memory network layers. The pretraining and validation were conducted using the data set tested in previously reported methods. The performance evaluation results showed that the proposed method can outperform the previous methods. In addition, the pattern learned by the DNNs was visualized as position frequency matrices (PFMs). Some of PFMs were very similar to the consensus sequence. The trained DNN model and the brief source code for the prediction system are uploaded. Further improvement will be achieved following the further development of DNNs.

Wall compliance and violin cavity modes.

Science.gov (United States)

Bissinger, George

2003-03-01

Violin corpus wall compliance, which has a substantial effect on cavity mode frequencies, was added to Shaw's two-degree-of-freedom (2DOF) network model for A0 ("main air") and A1 (lowest length mode included in "main wood") cavity modes. The 2DOF model predicts a V(-0.25) volume dependence for A0 for rigid violin-shaped cavities, to which a semiempirical compliance correction term, V(-x(c)) (optimization parameter x(c)) consistent with cavity acoustical compliance and violin-based scaling was added. Optimizing x(c) over A0 and A1 frequencies measured for a Hutchins-Schelleng violin octet yielded x(c) approximately 0.08. This markedly improved A0 and A1 frequency predictions to within approximately +/- 10% of experiment over a range of about 4.5:1 in length, 10:1 in f-hole area, 3:1 in top plate thickness, and 128:1 in volume. Compliance is a plausible explanation for A1 falling close to the "main wood" resonance, not increasingly higher for the larger instruments, which were scaled successively shorter compared to the violin for ergonomic and practical reasons. Similarly incorporating compliance for A2 and A4 (lowest lower-/upper-bout modes, respectively) improves frequency predictions within +/-20% over the octet.

The use of microperforated plates to attenuate cavity resonances

DEFF Research Database (Denmark)

Fenech, Benjamin; Keith, Graeme; Jacobsen, Finn

2006-01-01

The use of microperforated plates to introduce damping in a closed cavity is examined. By placing a microperforated plate well inside the cavity instead of near a wall as traditionally done in room acoustics, high attenuation can be obtained for specific acoustic modes, compared with the lower...... attenuation that can be obtained in a broad frequency range with the conventional position of the plate. An analytical method for predicting the attenuation is presented. The method involves finding complex eigenvalues and eigenfunctions for the modified cavity and makes it possible to predict Green......'s functions. The results, which are validated experimentally, show that a microperforated plate can provide substantial attenuation of modes in a cavity. One possible application of these findings is the treatment of boiler tones in heat-exchanger cavities....

Cavity pressure history of contained nuclear explosions

Energy Technology Data Exchange (ETDEWEB)

Chapin, C E [Lawrence Radiation Laboratory, University of California, Livermore, CA (United States)

1970-05-01

Knowledge of pressure in cavities created by contained nuclear explosions is useful for estimating the possibility of venting radioactive debris to the atmosphere. Measurements of cavity pressure, or temperature, would be helpful in evaluating the correctness of present code predictions of underground explosions. In instrumenting and interpreting such measurements it is necessary to have good theoretical estimates of cavity pressures. In this paper cavity pressure is estimated at the time when cavity growth is complete. Its subsequent decrease due to heat loss from the cavity to the surrounding media is also predicted. The starting pressure (the pressure at the end of cavity growth) is obtained by adiabatic expansion to the final cavity size of the vaporized rock gas sphere created by the explosion. Estimates of cavity size can be obtained by stress propagation computer codes, such as SOC and TENSOR. However, such estimates require considerable time and effort. In this paper, cavity size is estimated using a scheme involving simple hand calculations. The prediction is complicated by uncertainties in the knowledge of silica water system chemistry and a lack of information concerning possible blowoff of wall material during cavity growth. If wall material blows off, it can significantly change the water content in the cavity, compared to the water content in the ambient media. After cavity growth is complete, the pressure will change because of heat loss to the surrounding media. Heat transfer by convection, radiation and conduction is considered, and its effect on the pressure is calculated. Analysis of cavity heat transfer is made difficult by the complex nature of processes which occur at the wall where melting, vaporization and condensation of the gaseous rock can all occur. Furthermore, the melted wall material could be removed by flowing or dripping to the cavity floor. It could also be removed by expansion of the steam contained in the melt (blowoff) and by

Photons in a spherical cavity

International Nuclear Information System (INIS)

Ionescu-Pallas, N.; Vlad, V.I.

1999-01-01

The spectrum of black body radiation at the absolute temperature T, in an ideal spherical cavity of radius R, is studied. The departures from the classical predictions of Planck's theory, due to the discrete energies of the radiation quanta confined inside the cavity, depend on the adiabatic invariant RT and are significant for RT≤ 1 cm K. Special attention was paid to evidence sudden changes in the spectrum intensities, forbidden bands of frequency, as well as major modifications of the total energy for RT≤ 1 cm K. Similar effects were present in case of a cubic cavity too. (authors)

A grammar inference approach for predicting kinase specific phosphorylation sites.

Science.gov (United States)

Datta, Sutapa; Mukhopadhyay, Subhasis

2015-01-01

Kinase mediated phosphorylation site detection is the key mechanism of post translational mechanism that plays an important role in regulating various cellular processes and phenotypes. Many diseases, like cancer are related with the signaling defects which are associated with protein phosphorylation. Characterizing the protein kinases and their substrates enhances our ability to understand the mechanism of protein phosphorylation and extends our knowledge of signaling network; thereby helping us to treat such diseases. Experimental methods for predicting phosphorylation sites are labour intensive and expensive. Also, manifold increase of protein sequences in the databanks over the years necessitates the improvement of high speed and accurate computational methods for predicting phosphorylation sites in protein sequences. Till date, a number of computational methods have been proposed by various researchers in predicting phosphorylation sites, but there remains much scope of improvement. In this communication, we present a simple and novel method based on Grammatical Inference (GI) approach to automate the prediction of kinase specific phosphorylation sites. In this regard, we have used a popular GI algorithm Alergia to infer Deterministic Stochastic Finite State Automata (DSFA) which equally represents the regular grammar corresponding to the phosphorylation sites. Extensive experiments on several datasets generated by us reveal that, our inferred grammar successfully predicts phosphorylation sites in a kinase specific manner. It performs significantly better when compared with the other existing phosphorylation site prediction methods. We have also compared our inferred DSFA with two other GI inference algorithms. The DSFA generated by our method performs superior which indicates that our method is robust and has a potential for predicting the phosphorylation sites in a kinase specific manner.

A Grammar Inference Approach for Predicting Kinase Specific Phosphorylation Sites

Science.gov (United States)

Datta, Sutapa; Mukhopadhyay, Subhasis

2015-01-01

Kinase mediated phosphorylation site detection is the key mechanism of post translational mechanism that plays an important role in regulating various cellular processes and phenotypes. Many diseases, like cancer are related with the signaling defects which are associated with protein phosphorylation. Characterizing the protein kinases and their substrates enhances our ability to understand the mechanism of protein phosphorylation and extends our knowledge of signaling network; thereby helping us to treat such diseases. Experimental methods for predicting phosphorylation sites are labour intensive and expensive. Also, manifold increase of protein sequences in the databanks over the years necessitates the improvement of high speed and accurate computational methods for predicting phosphorylation sites in protein sequences. Till date, a number of computational methods have been proposed by various researchers in predicting phosphorylation sites, but there remains much scope of improvement. In this communication, we present a simple and novel method based on Grammatical Inference (GI) approach to automate the prediction of kinase specific phosphorylation sites. In this regard, we have used a popular GI algorithm Alergia to infer Deterministic Stochastic Finite State Automata (DSFA) which equally represents the regular grammar corresponding to the phosphorylation sites. Extensive experiments on several datasets generated by us reveal that, our inferred grammar successfully predicts phosphorylation sites in a kinase specific manner. It performs significantly better when compared with the other existing phosphorylation site prediction methods. We have also compared our inferred DSFA with two other GI inference algorithms. The DSFA generated by our method performs superior which indicates that our method is robust and has a potential for predicting the phosphorylation sites in a kinase specific manner. PMID:25886273

Development and Validation of Spatially Explicit Habitat Models for Cavity-nesting Birds in Fishlake National Forest, Utah

Science.gov (United States)

Randall A., Jr. Schultz; Thomas C., Jr. Edwards; Gretchen G. Moisen; Tracey S. Frescino

2005-01-01

The ability of USDA Forest Service Forest Inventory and Analysis (FIA) generated spatial products to increase the predictive accuracy of spatially explicit, macroscale habitat models was examined for nest-site selection by cavity-nesting birds in Fishlake National Forest, Utah. One FIA-derived variable (percent basal area of aspen trees) was significant in the habitat...

Effects of prescribed burns on wintering cavity-nesting birds

Science.gov (United States)

Heather L. Bateman; Margaret A. O' Connell

2006-01-01

Primary cavity-nesting birds play a critical role in forest ecosystems by excavating cavities later used by other birds and mammals as nesting or roosting sites. Several species of cavity-nesting birds are non-migratory residents and consequently subject to winter conditions. We conducted winter bird counts from 1998 to 2000 to examine the abundance and habitat...

Climate Prediction Center - Site Index

Science.gov (United States)

Weather Service NWS logo - Click to go to the NWS home page Climate Prediction Center Home Site Map News Means Bulletins Annual Winter Stratospheric Ozone Climate Diagnostics Bulletin (Most Recent) Climate (Hazards Outlook) Climate Assessment: Dec. 1999-Feb. 2000 (Seasonal) Climate Assessment: Mar-May 2000

Cavity quantum electrodynamics studies with site-controlled InGaAs quantum dots integrated into high quality microcavities

DEFF Research Database (Denmark)

Reitzenstein, S.; Schneider, C.; Albert, F.

2011-01-01

Semiconductor quantum dots (QDs) are fascinating nanoscopic structures for photonics and future quantum information technology. However, the random position of self-organized QDs inhibits a deterministic coupling in devices relying on cavity quantum electrodynamics (cQED) effects which complicates......, e.g., the large scale fabrication of quantum light sources. As a result, large efforts focus on the growth and the device integration of site-controlled QDs. We present the growth of low density arrays of site-controlled In(Ga)As QDs where shallow etched nanoholes act as nucleation sites...... linewidth, the oscillator strength and the quantum efficiency. A stacked growth of strain coupled SCQDs forming on wet chemically etched nanoholes provide the smallest linewidth with an average value of 210 μeV. Using time resolved photoluminescence studies on samples with a varying thickness of the capping...

How does vegetation structure influence woodpeckers and secondary cavity nesting birds in African cork oak forest?

Science.gov (United States)

Segura, Amalia

2017-08-01

The Great Spotted Woodpecker provides important information about the status of a forest in terms of structure and age. As a primary cavity creator, it provides small-medium size cavities for passerines. However, despite its interest as an ecosystem engineer, studies of this species in Africa are scarce. Here, spatially explicit predictive models were used to investigate how forest structural variables are related to both the Great Spotted Woodpecker and secondary cavity nesting birds in Maamora cork oak forest (northwest Morocco). A positive association between Great Spotted Woodpecker and both dead-tree density and large mature trees (>60 cm dbh) was found. This study area, Maamora, has an old-growth forest structure incorporating a broad range of size and condition of live and dead trees, favouring Great Spotted Woodpecker by providing high availability of foraging and excavating sites. Secondary cavity nesting birds, represented by Great Tit, African Blue Tit, and Hoopoe, were predicted by Great Spotted Woodpecker detections. The findings suggest that the conservation of the Maamora cork oak forest could be key to maintaining these hole-nesting birds. However, this forest is threatened by forestry practises and livestock overgrazing and the challenge is therefore to find sustainable management strategies that ensure conservation while allowing its exploitation.

Site investigations, design, construction, operation, shutdown and surveillance of repositories for low- and intermediate-level radioactive wastes in rock cavities

International Nuclear Information System (INIS)

1984-01-01

The report provides an overview and technical guidelines for considerations and for activities to be undertaken for safety assessment, site investigations, design, construction, operation, shutdown and surveillance of repositories for the disposal of low- and intermediate-level radioactive wastes in rock cavities. A generalized sequence of investigations is introduced which proceeds through region and site selection to the stage where the site is confirmed by detailed geoscientific investigations as being suitable for a waste repository. The different procedures and somewhat specific investigative needs with respect to existing mines are dealt with separately. General design, as well as specific requirements with respect to the different stages of design and construction, are dealt with. A review of activities related to the operational and post-operational stages of repositories in rock cavities is presented. The report describes in general terms the procedures related to different stages of disposal operation; also the conditions for shutdown together with essential shutdown and sealing activities and the related safety assessment requirements. Guidance is also given on the surveillance programme which will allow for inspection, testing, maintenance and security of a disposal facility during the operational phase, as well as for the post-operational stage for periods determined as necessary by the national authorities

Seismic wave interaction with underground cavities

Science.gov (United States)

Schneider, Felix M.; Esterhazy, Sofi; Perugia, Ilaria; Bokelmann, Götz

2016-04-01

Realization of the future Comprehensive Nuclear Test Ban Treaty (CTBT) will require ensuring its compliance, making the CTBT a prime example of forensic seismology. Following indications of a nuclear explosion obtained on the basis of the (IMS) monitoring network further evidence needs to be sought at the location of the suspicious event. For such an On-Site Inspection (OSI) at a possible nuclear test site the treaty lists several techniques that can be carried out by the inspection team, including aftershock monitoring and the conduction of active seismic surveys. While those techniques are already well established, a third group of methods labeled as "resonance seismometry" is less well defined and needs further elaboration. A prime structural target that is expected to be present as a remnant of an underground nuclear explosion is a cavity at the location and depth the bomb was fired. Originally "resonance seismometry" referred to resonant seismic emission of the cavity within the medium that could be stimulated by an incident seismic wave of the right frequency and observed as peaks in the spectrum of seismic stations in the vicinity of the cavity. However, it is not yet clear which are the conditions for which resonant emissions of the cavity could be observed. In order to define distance-, frequency- and amplitude ranges at which resonant emissions could be observed we study the interaction of seismic waves with underground cavities. As a generic model for possible resonances we use a spherical acoustic cavity in an elastic full-space. To solve the forward problem for the full elastic wave field around acoustic spherical inclusions, we implemented an analytical solution (Korneev, 1993). This yields the possibility of generating scattering cross-sections, amplitude spectrums and synthetic seismograms for plane incident waves. Here, we focus on the questions whether or not we can expect resonant responses in the wave field scattered from the cavity. We show

X-ray imaging of superconducting radio frequency cavities

Science.gov (United States)

Musser, Susan Elizabeth

The goal of this research was to develop an improved diagnostic technique to identify the location of defects that limit superconducting radio frequency (SRF) cavity performance during cavity testing or in existing accelerators. SRF cavities are primarily constructed of niobium. Electrons within the metal of a cavity under high electric field gradient have a probability of tunneling through the potential barrier. i e. leave the surface or are field emitted in regions where defects are encountered. Field emitted electrons are accelerated in the electric fields within the cavity. The electrons can have complicated trajectories and strike the cavity walls thus producing x-rays via Coulomb interactions and/or bremsstrahlung radiation. The endpoint energy of an x-ray spectrum predicts the electron maximum final kinetic energy within the cavity. Field emission simulations can then predict the source of the field-emitted electrons and the defect(s). In a multicell cavity the cells are coupled together and act as a set of coupled oscillators. There are multiple passbands of excitation for a multicell structure operating in a particular mode. For different passbands of operation the direction and amplitude of the fields within a cavity change from that of the normal accelerating mode. Field emitted electrons have different trajectories depending on the mode and thus produce x-rays in different locations. Using a collimated sodium iodide detector and subjecting a cavity to multiple passband modes at high electric field gradient the source of a cavity's x-rays can be determined. Knowing the location of the x-rays and the maximum electron kinetic energy; field emission simulations for different passband modes can be used to determine and verify the source of the field emitted electrons from mode to mode. Once identified, the defect(s) can be repaired or modifications made to the manufacturing process.

The cavity approach to parallel dynamics of Ising spins on a graph

International Nuclear Information System (INIS)

Neri, I; Bollé, D

2009-01-01

We use the cavity method to study the parallel dynamics of disordered Ising models on a graph. In particular, we derive a set of recursive equations in single-site probabilities of paths propagating along the edges of the graph. These equations are analogous to the cavity equations for equilibrium models and are exact on a tree. On graphs with exclusively directed edges we find an exact expression for the stationary distribution. We present the phase diagrams for an Ising model on an asymmetric Bethe lattice and for a neural network with Hebbian interactions on an asymmetric scale-free graph. For graphs with a nonzero fraction of symmetric edges the equations can be solved for a finite number of time steps. Theoretical predictions are confirmed by simulations. Using a heuristic method the cavity equations are extended to a set of equations that determine the marginals of the stationary distribution of Ising models on graphs with a nonzero fraction of symmetric edges. The results from this method are discussed and compared with simulations

8-anilino-1-naphthaline sulfonate binds at the hemoglobin allosteric regulatory sites: inhibitory analyses

International Nuclear Information System (INIS)

Bokut', S.B.; Parul', D.A.; Yachnik, N.N.; Milyutin, A.A.

2001-01-01

The present study focused on the localization at least one of the ANS binding sites in the major form of human hemoglobin HbA. High-resolution docking predict ANS binding to the hemoglobin central cavity. Steady-state fluorescence titration data obtained in the absence/presence of natural effector inositol hexaphosphate (IHP) allowed to conclude that IHP competitively inhibited ANS binding to HbA. Thus, we must conclude that one of the ANS binding sites is central cavity, which makes it possible to monitor changes at this region upon ligation/deligation, effector binding and changes in hemoglobin structure

Cavity optomechanics in gallium phosphide microdisks

International Nuclear Information System (INIS)

Mitchell, Matthew; Barclay, Paul E.; Hryciw, Aaron C.

2014-01-01

We demonstrate gallium phosphide (GaP) microdisk optical cavities with intrinsic quality factors >2.8 × 10 5 and mode volumes 3 , and study their nonlinear and optomechanical properties. For optical intensities up to 8.0 × 10 4 intracavity photons, we observe optical loss in the microcavity to decrease with increasing intensity, indicating that saturable absorption sites are present in the GaP material, and that two-photon absorption is not significant. We observe optomechanical coupling between optical modes of the microdisk around 1.5 μm and several mechanical resonances, and measure an optical spring effect consistent with a theoretically predicted optomechanical coupling rate g 0 /2π∼30 kHz for the fundamental mechanical radial breathing mode at 488 MHz

Development of METAL-ACTIVE SITE and ZINCCLUSTER tool to predict active site pockets.

Science.gov (United States)

Ajitha, M; Sundar, K; Arul Mugilan, S; Arumugam, S

2018-03-01

The advent of whole genome sequencing leads to increasing number of proteins with known amino acid sequences. Despite many efforts, the number of proteins with resolved three dimensional structures is still low. One of the challenging tasks the structural biologists face is the prediction of the interaction of metal ion with any protein for which the structure is unknown. Based on the information available in Protein Data Bank, a site (METALACTIVE INTERACTION) has been generated which displays information for significant high preferential and low-preferential combination of endogenous ligands for 49 metal ions. User can also gain information about the residues present in the first and second coordination sphere as it plays a major role in maintaining the structure and function of metalloproteins in biological system. In this paper, a novel computational tool (ZINCCLUSTER) is developed, which can predict the zinc metal binding sites of proteins even if only the primary sequence is known. The purpose of this tool is to predict the active site cluster of an uncharacterized protein based on its primary sequence or a 3D structure. The tool can predict amino acids interacting with a metal or vice versa. This tool is based on the occurrence of significant triplets and it is tested to have higher prediction accuracy when compared to that of other available techniques. © 2017 Wiley Periodicals, Inc.

Coupling of an overdriven cavity

International Nuclear Information System (INIS)

Garbin, H.D.

1993-01-01

It is well known that when a nuclear test is conducted in a sufficiently large cavity, the resulting seismic signal is sharply reduced when compared to a normal tamped event. Cavity explosions are of interest in the seismic verification community because of this possibility of reducing the seismic energy generated which can lower signal amplitudes and make detection difficult. Reduced amplitudes would also lower seismic yield estimates which has implications in a Threshold Test Ban Treaty (TTBT). In the past several years, there have been a number of nuclear tests at NTS (Nevada Test Site) inside hemispherical cavities. Two such tests were MILL YARD and MISTY ECHO which had instrumentation at the surface and in the free-field. These two tests differ in one important aspect. MILL YARD was completely decoupled i.e., the cavity wall behaved in an elastic manner. It was estimated that MILL YARD's ground motion was reduced by a factor of at least 70. In contrast, MISTY ECHO was detonated in a hemispherical cavity with the same dimensions as MILL YARD, but with a much larger device yield. This caused an inelastic behavior on the wall and the explosion was not fully decoupled

Cavity-nesting bird abundance in thinned versus unthinned Massachusetts oak stands

Science.gov (United States)

Christopher J.E. Welsh; William M. Healy; Richard M. DeGraaf

1992-01-01

Cavity-nesting birds provide significant benefits to forest communities, but timber management techniques may negatively affect cavity-nesting species by reducing the availability of suitable nest and foraging sites. We surveyed cavity-nesting birds from transects in eight Massachusetts oak stands to examine the effect of thinning with retention of snag and wildlife...

Prediction of Underground Cavity Roof Collapse using the Hoek–Brown Failure Criterion

DEFF Research Database (Denmark)

Suchowerska, A. M.; Merifield, R. S.; Carter, J. P.

2012-01-01

Preventing roof collapse in underground cavities is a challenge to geotechnical engineering. In this study, three independent methods have been used to evaluate the roof collapse of underground rectangular cavities for a range of geometries and rock properties. The rock mass strength has been des...

Transcription factor binding sites prediction based on modified nucleosomes.

Directory of Open Access Journals (Sweden)

Mohammad Talebzadeh

Full Text Available In computational methods, position weight matrices (PWMs are commonly applied for transcription factor binding site (TFBS prediction. Although these matrices are more accurate than simple consensus sequences to predict actual binding sites, they usually produce a large number of false positive (FP predictions and so are impoverished sources of information. Several studies have employed additional sources of information such as sequence conservation or the vicinity to transcription start sites to distinguish true binding regions from random ones. Recently, the spatial distribution of modified nucleosomes has been shown to be associated with different promoter architectures. These aligned patterns can facilitate DNA accessibility for transcription factors. We hypothesize that using data from these aligned and periodic patterns can improve the performance of binding region prediction. In this study, we propose two effective features, "modified nucleosomes neighboring" and "modified nucleosomes occupancy", to decrease FP in binding site discovery. Based on these features, we designed a logistic regression classifier which estimates the probability of a region as a TFBS. Our model learned each feature based on Sp1 binding sites on Chromosome 1 and was tested on the other chromosomes in human CD4+T cells. In this work, we investigated 21 histone modifications and found that only 8 out of 21 marks are strongly correlated with transcription factor binding regions. To prove that these features are not specific to Sp1, we combined the logistic regression classifier with the PWM, and created a new model to search TFBSs on the genome. We tested the model using transcription factors MAZ, PU.1 and ELF1 and compared the results to those using only the PWM. The results show that our model can predict Transcription factor binding regions more successfully. The relative simplicity of the model and capability of integrating other features make it a superior method

Self-determined shapes and velocities of giant near-zero drag gas cavities

KAUST Repository

Vakarelski, Ivan Uriev

2017-09-09

Minimizing the retarding force on a solid moving in liquid is the canonical problem in the quest for energy saving by friction and drag reduction. For an ideal object that cannot sustain any shear stress on its surface, theory predicts that drag force will fall to zero as its speed becomes large. However, experimental verification of this prediction has been challenging. We report the construction of a class of self-determined streamlined structures with this free-slip surface, made up of a teardrop-shaped giant gas cavity that completely encloses a metal sphere. This stable gas cavity is formed around the sphere as it plunges at a sufficiently high speed into the liquid in a deep tank, provided that the sphere is either heated initially to above the Leidenfrost temperature of the liquid or rendered superhydrophobic in water at room temperature. These sphere-in-cavity structures have residual drag coefficients that are typically less than Embedded Image those of solid objects of the same dimensions, which indicates that they experienced very small drag forces. The self-determined shapes of the gas cavities are shown to be consistent with the Bernoulli equation of potential flow applied on the cavity surface. The cavity fall velocity is not arbitrary but is uniquely predicted by the sphere density and cavity volume, so larger cavities have higher characteristic velocities.

Coupled thermal-fluid analysis with flowpath-cavity interaction in a gas turbine engine

Science.gov (United States)

Fitzpatrick, John Nathan

This study seeks to improve the understanding of inlet conditions of a large rotor-stator cavity in a turbofan engine, often referred to as the drive cone cavity (DCC). The inlet flow is better understood through a higher fidelity computational fluid dynamics (CFD) modeling of the inlet to the cavity, and a coupled finite element (FE) thermal to CFD fluid analysis of the cavity in order to accurately predict engine component temperatures. Accurately predicting temperature distribution in the cavity is important because temperatures directly affect the material properties including Young's modulus, yield strength, fatigue strength, creep properties. All of these properties directly affect the life of critical engine components. In addition, temperatures cause thermal expansion which changes clearances and in turn affects engine efficiency. The DCC is fed from the last stage of the high pressure compressor. One of its primary functions is to purge the air over the rotor wall to prevent it from overheating. Aero-thermal conditions within the DCC cavity are particularly challenging to predict due to the complex air flow and high heat transfer in the rotating component. Thus, in order to accurately predict metal temperatures a two-way coupled CFD-FE analysis is needed. Historically, when the cavity airflow is modeled for engine design purposes, the inlet condition has been over-simplified for the CFD analysis which impacts the results, particularly in the region around the compressor disc rim. The inlet is typically simplified by circumferentially averaging the velocity field at the inlet to the cavity which removes the effect of pressure wakes from the upstream rotor blades. The way in which these non-axisymmetric flow characteristics affect metal temperatures is not well understood. In addition, a constant air temperature scaled from a previous analysis is used as the simplified cavity inlet air temperature. Therefore, the objectives of this study are: (a) model the

HPV and cancer of the oral cavity.

Science.gov (United States)

Hübbers, Christian U; Akgül, Baki

2015-01-01

Increased awareness of human papillomavirus (HPV) as an etiological cause of head and neck squamous cell carcinoma has increased the interest in analysis of distinct oral sub-sites. It is currently under debate, whether HPV plays a role in the development of squamous cell carcinoma of the oral cavity (OSCC). The weakness in most published studies is the lack of performing different HPV detection tests combined with analysis for biological activity of the virus. In addition, different sub-sites of the oral cavity had been combined to a single entity, which retrospectively leads to a highly heterogeneous basis of data. In this review we mainly discuss the unclear role of HPV in OSCC development.

Musite, a tool for global prediction of general and kinase-specific phosphorylation sites.

Science.gov (United States)

Gao, Jianjiong; Thelen, Jay J; Dunker, A Keith; Xu, Dong

2010-12-01

Reversible protein phosphorylation is one of the most pervasive post-translational modifications, regulating diverse cellular processes in various organisms. High throughput experimental studies using mass spectrometry have identified many phosphorylation sites, primarily from eukaryotes. However, the vast majority of phosphorylation sites remain undiscovered, even in well studied systems. Because mass spectrometry-based experimental approaches for identifying phosphorylation events are costly, time-consuming, and biased toward abundant proteins and proteotypic peptides, in silico prediction of phosphorylation sites is potentially a useful alternative strategy for whole proteome annotation. Because of various limitations, current phosphorylation site prediction tools were not well designed for comprehensive assessment of proteomes. Here, we present a novel software tool, Musite, specifically designed for large scale predictions of both general and kinase-specific phosphorylation sites. We collected phosphoproteomics data in multiple organisms from several reliable sources and used them to train prediction models by a comprehensive machine-learning approach that integrates local sequence similarities to known phosphorylation sites, protein disorder scores, and amino acid frequencies. Application of Musite on several proteomes yielded tens of thousands of phosphorylation site predictions at a high stringency level. Cross-validation tests show that Musite achieves some improvement over existing tools in predicting general phosphorylation sites, and it is at least comparable with those for predicting kinase-specific phosphorylation sites. In Musite V1.0, we have trained general prediction models for six organisms and kinase-specific prediction models for 13 kinases or kinase families. Although the current pretrained models were not correlated with any particular cellular conditions, Musite provides a unique functionality for training customized prediction models

Nest-site competition between invasive and native cavity nesting birds and its implication for conservation.

Science.gov (United States)

Charter, Motti; Izhaki, Ido; Ben Mocha, Yitzchak; Kark, Salit

2016-10-01

Nesting cavities are often a limited resource that multiple species use. There is an ongoing discussion on whether invasive cavity nesting birds restrict the availability of this key limited resource. While the answer to this question has important conservation implications, little experimental work has been done to examine it. Here, we aimed to experimentally test whether alien cavity nesting birds affect the occupancy of cavities and the resulting breeding success of native cavity breeders in a large urban park located in Tel Aviv, Israel. Over three breeding seasons, we manipulated the entry size of nest boxes and compared the occupancy and breeding success of birds in nest boxes of two treatments. These included nest boxes with large-entrance and small-entrance holes. The large-entrance holes allowed access for both the native and invasive birds (the two main aliens in the park are the common mynas and rose-ringed parakeets). The smaller-entrance boxes, on the other hand, allowed only the smaller sized native cavity breeders (great tits and house sparrows) to enter the boxes but prevented the alien species from entering. We found that the large-entrance nest boxes were occupied by five different bird species, comprising three natives (great tit, house sparrow, Scops owl) and two invasive species (common myna, rose-ringed parakeet) while the small-entrance boxes were only occupied by the two native species. The alien common mynas and rose-ringed parakeets occupied 77.5% of the large-entrance nest boxes whereas native species, mainly great tits, occupied less than 9% of the large-entrance boxes and 36.5% of the small-entrance boxes. When examining the occupancy of those cavities that were not occupied by the aliens, natives occupied both the small and large-entrance nest boxes equally. Three quarters (78%) of the great tits breeding in the large-entrance boxes were usurped by common mynas during the breeding season and as a result breeding success was

Foraging habitat quality constrains effectiveness of artificial nest-site provisioning in reversing population declines in a colonial cavity nester.

Directory of Open Access Journals (Sweden)

Inês Catry

Full Text Available Among birds, breeding numbers are mainly limited by two resources of major importance: food supply and nest-site availability. Here, we investigated how differences in land-use and nest-site availability affected the foraging behaviour, breeding success and population trends of the colonial cavity-dependent lesser kestrel Falco naumanni inhabiting two protected areas. Both areas were provided with artificial nests to increase nest-site availability. The first area is a pseudo-steppe characterized by traditional extensive cereal cultivation, whereas the second area is a previous agricultural zone now abandoned or replaced by forested areas. In both areas, lesser kestrels selected extensive agricultural habitats, such as fallows and cereal fields, and avoided scrubland and forests. In the second area, tracked birds from one colony travelled significantly farther distances (6.2 km ± 1.7 vs. 1.8 km ± 0.4 and 1.9 km ± 0.6 and had significant larger foraging-ranges (144 km(2 vs. 18.8 and 14.8 km(2 when compared to the birds of two colonies in the extensive agricultural area. Longer foraging trips were reflected in lower chick feeding rates, lower fledging success and reduced chick fitness. Availability and occupation of artificial nests was high in both areas but population followed opposite trends, with a positive increment recorded exclusively in the first area with a large proportion of agricultural areas. Progressive habitat loss around the studied colony in the second area (suitable habitat decreased from 32% in 1990 to only 7% in 2002 is likely the main driver of the recorded population decline and suggests that the effectiveness of bird species conservation based on nest-site provisioning is highly constrained by habitat quality in the surrounding areas. Therefore, the conservation of cavity-dependent species may be enhanced firstly by finding the best areas of remaining habitat and secondly by increasing the carrying capacity of high

Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins

Directory of Open Access Journals (Sweden)

Selbig Joachim

2009-04-01

Full Text Available Abstract Background Phosphorylation of proteins plays a crucial role in the regulation and activation of metabolic and signaling pathways and constitutes an important target for pharmaceutical intervention. Central to the phosphorylation process is the recognition of specific target sites by protein kinases followed by the covalent attachment of phosphate groups to the amino acids serine, threonine, or tyrosine. The experimental identification as well as computational prediction of phosphorylation sites (P-sites has proved to be a challenging problem. Computational methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding phosphorylation sites. Results We characterized the spatial context of phosphorylation sites and assessed its usability for improved phosphorylation site predictions. We identified 750 non-redundant, experimentally verified sites with three-dimensional (3D structural information available in the protein data bank (PDB and grouped them according to their respective kinase family. We studied the spatial distribution of amino acids around phosphorserines, phosphothreonines, and phosphotyrosines to extract signature 3D-profiles. Characteristic spatial distributions of amino acid residue types around phosphorylation sites were indeed discernable, especially when kinase-family-specific target sites were analyzed. To test the added value of using spatial information for the computational prediction of phosphorylation sites, Support Vector Machines were applied using both sequence as well as structural information. When compared to sequence-only based prediction methods, a small but consistent performance improvement was obtained when the prediction was informed by 3D-context information. Conclusion While local one-dimensional amino acid sequence information was observed to harbor most of the discriminatory power, spatial context information was identified as

Inter-assemblage facilitation: the functional diversity of cavity-producing beetles drives the size diversity of cavity-nesting bees.

Science.gov (United States)

Sydenham, Markus A K; Häusler, Lise D; Moe, Stein R; Eldegard, Katrine

2016-01-01

Inter-specific interactions are important drivers and maintainers of biodiversity. Compared to trophic and competitive interactions, the role of non-trophic facilitation among species has received less attention. Cavity-nesting bees nest in old beetle borings in dead wood, with restricted diameters corresponding to the body size of the bee species. The aim of this study was to test the hypothesis that the functional diversity of cavity-producing wood boring beetles - in terms of cavity diameters - drives the size diversity of cavity-nesting bees. The invertebrate communities were sampled in 30 sites, located in forested landscapes along an elevational gradient. We regressed the species richness and abundance of cavity nesting bees against the species richness and abundance of wood boring beetles, non-wood boring beetles and elevation. The proportion of cavity nesting bees in bee species assemblage was regressed against the species richness and abundance of wood boring beetles. We also tested the relationships between the size diversity of cavity nesting bees and wood boring beetles. The species richness and abundance of cavity nesting bees increased with the species richness and abundance of wood boring beetles. No such relationship was found for non-wood boring beetles. The abundance of wood boring beetles was also related to an increased proportion of cavity nesting bee individuals. Moreover, the size diversity of cavity-nesting bees increased with the functional diversity of wood boring beetles. Specifically, the mean and dispersion of bee body sizes increased with the functional dispersion of large wood boring beetles. The positive relationships between cavity producing bees and cavity nesting bees suggest that non-trophic facilitative interactions between species assemblages play important roles in organizing bee species assemblages. Considering a community-wide approach may therefore be required if we are to successfully understand and conserve wild bee

Sterility of the uterine cavity

DEFF Research Database (Denmark)

Møller, Birger R.; Kristiansen, Frank V.; Thorsen, Poul

1995-01-01

from the same sites. Nearly a quarter of all the patients harbored one or more microorganisms in the uterus, mostly Gardnerella vaginalis, Enterobacter and Streptococcus agalactiae. We found that in a significant number of cases, the uterine cavity is colonized with potentially pathogenic organisms...

Microscopic investigation of RF surfaces of 3 GHz niobium accelerator cavities following RF processing

International Nuclear Information System (INIS)

Graber, J.; Barnes, P.; Flynn, T.; Kirchgessner, J.; Knobloch, J.; Moffat, D.; Muller, H.; Padamsee, H.; Sears, J.

1993-01-01

RF processing of Superconducting accelerating cavities is achieved through a change in the electron field emission (FE) characteristics of the RF surface. The authors have examined the RF surfaces of several single-cell 3 GHz cavities, following RF processing, in a Scanning Electron Microscope (SEM). The RF processing sessions included both High Peak Power (P ≤ 50 kW) pulsed processing, and low power (≤ 20 W) continuous wave processing. The experimental apparatus also included a thermometer array on the cavity outer wall, allowing temperature maps to characterize the emission before and after RF processing gains. Multiple sites have been located in cavities which showed improvements in cavity behavior due to RF processing. Several SEM-located sites can be correlated with changes in thermometer signals, indicating a direct relationship between the surface site and emission reduction due to RF processing. Information gained from the SEM investigations and thermometry are used to enhance the theoretical model of RF processing

A resonance shift prediction based on the Boltzmann-Ehrenfest principle for cylindrical cavities with a rigid sphere.

Science.gov (United States)

Santillan, Arturo O; Cutanda-Henríquez, Vicente

2008-11-01

An investigation on the resonance frequency shift for a plane-wave mode in a cylindrical cavity produced by a rigid sphere is reported in this paper. This change of the resonance frequency has been previously considered as a cause of oscillational instabilities in single-mode acoustic levitation devices. It is shown that the use of the Boltzmann-Ehrenfest principle of adiabatic invariance allows the derivation of an expression for the resonance frequency shift in a simpler and more direct way than a method based on a Green's function reported in literature. The position of the sphere can be any point along the axis of the cavity. Obtained predictions of the resonance frequency shift with the deduced equation agree quite well with numerical simulations based on the boundary element method. The results are also confirmed by experiments. The equation derived from the Boltzmann-Ehrenfest principle appears to be more general, and for large spheres, it gives a better approximation than the equation previously reported.

Vacuum field energy and spontaneous emission in anomalously dispersive cavities

International Nuclear Information System (INIS)

Bradshaw, Douglas H.; Di Rosa, Michael D.

2011-01-01

Anomalously dispersive cavities, particularly white-light cavities, may have larger bandwidth to finesse ratios than their normally dispersive counterparts. Partly for this reason, they have been proposed for use in laser interferometer gravitational-wave observatory (LIGO)-like gravity-wave detectors and in ring-laser gyroscopes. In this paper we analyze the quantum noise associated with anomalously dispersive cavity modes. The vacuum field energy associated with a particular cavity mode is proportional to the cavity-averaged group velocity of that mode. For anomalously dispersive cavities with group index values between 1 and 0, this means that the total vacuum field energy associated with a particular cavity mode must exceed (ℎ/2π)ω/2. For white-light cavities in particular, the group index approaches zero and the vacuum field energy of a particular spatial mode may be significantly enhanced. We predict enhanced spontaneous emission rates into anomalously dispersive cavity modes and broadened laser linewidths when the linewidth of intracavity emitters is broader than the cavity linewidth.

A systems biology approach to transcription factor binding site prediction.

Directory of Open Access Journals (Sweden)

Xiang Zhou

2010-03-01

Full Text Available The elucidation of mammalian transcriptional regulatory networks holds great promise for both basic and translational research and remains one the greatest challenges to systems biology. Recent reverse engineering methods deduce regulatory interactions from large-scale mRNA expression profiles and cross-species conserved regulatory regions in DNA. Technical challenges faced by these methods include distinguishing between direct and indirect interactions, associating transcription regulators with predicted transcription factor binding sites (TFBSs, identifying non-linearly conserved binding sites across species, and providing realistic accuracy estimates.We address these challenges by closely integrating proven methods for regulatory network reverse engineering from mRNA expression data, linearly and non-linearly conserved regulatory region discovery, and TFBS evaluation and discovery. Using an extensive test set of high-likelihood interactions, which we collected in order to provide realistic prediction-accuracy estimates, we show that a careful integration of these methods leads to significant improvements in prediction accuracy. To verify our methods, we biochemically validated TFBS predictions made for both transcription factors (TFs and co-factors; we validated binding site predictions made using a known E2F1 DNA-binding motif on E2F1 predicted promoter targets, known E2F1 and JUND motifs on JUND predicted promoter targets, and a de novo discovered motif for BCL6 on BCL6 predicted promoter targets. Finally, to demonstrate accuracy of prediction using an external dataset, we showed that sites matching predicted motifs for ZNF263 are significantly enriched in recent ZNF263 ChIP-seq data.Using an integrative framework, we were able to address technical challenges faced by state of the art network reverse engineering methods, leading to significant improvement in direct-interaction detection and TFBS-discovery accuracy. We estimated the accuracy

Impact of Lorentz forces on a Spoke cavity with β 0.15 and on a Spiral-2 cavity with β 0.12

International Nuclear Information System (INIS)

Gassot, H.

2007-01-01

Mono-spoke superconducting cavities have been proposed for the acceleration of radioactive ion beams. The interaction of the electromagnetic field with the surface electrical current generates Lorentz forces that operate on the intern wall of the cavity, the distribution of these forces is highly non-linear and varying. The stability of a superconducting cavity is directly linked to the frequency variation due to Lorentz forces and as a consequence the optimized design of a cavity must take into account these forces. In order to optimize the design of a cavity, 3 complementary software have been developed: Catia, a computer-aided-design software, Soprano for electromagnetic modeling and Cast3m for mechanical modeling. Preliminary results show a good agreement between predicted values and experimental data. (A.C.)

Fast dynamics perturbation analysis for prediction of protein functional sites

Directory of Open Access Journals (Sweden)

Cohn Judith D

2008-01-01

Full Text Available Abstract Background We present a fast version of the dynamics perturbation analysis (DPA algorithm to predict functional sites in protein structures. The original DPA algorithm finds regions in proteins where interactions cause a large change in the protein conformational distribution, as measured using the relative entropy Dx. Such regions are associated with functional sites. Results The Fast DPA algorithm, which accelerates DPA calculations, is motivated by an empirical observation that Dx in a normal-modes model is highly correlated with an entropic term that only depends on the eigenvalues of the normal modes. The eigenvalues are accurately estimated using first-order perturbation theory, resulting in a N-fold reduction in the overall computational requirements of the algorithm, where N is the number of residues in the protein. The performance of the original and Fast DPA algorithms was compared using protein structures from a standard small-molecule docking test set. For nominal implementations of each algorithm, top-ranked Fast DPA predictions overlapped the true binding site 94% of the time, compared to 87% of the time for original DPA. In addition, per-protein recall statistics (fraction of binding-site residues that are among predicted residues were slightly better for Fast DPA. On the other hand, per-protein precision statistics (fraction of predicted residues that are among binding-site residues were slightly better using original DPA. Overall, the performance of Fast DPA in predicting ligand-binding-site residues was comparable to that of the original DPA algorithm. Conclusion Compared to the original DPA algorithm, the decreased run time with comparable performance makes Fast DPA well-suited for implementation on a web server and for high-throughput analysis.

Variable context Markov chains for HIV protease cleavage site prediction.

Science.gov (United States)

Oğul, Hasan

2009-06-01

Deciphering the knowledge of HIV protease specificity and developing computational tools for detecting its cleavage sites in protein polypeptide chain are very desirable for designing efficient and specific chemical inhibitors to prevent acquired immunodeficiency syndrome. In this study, we developed a generative model based on a generalization of variable order Markov chains (VOMC) for peptide sequences and adapted the model for prediction of their cleavability by certain proteases. The new method, called variable context Markov chains (VCMC), attempts to identify the context equivalence based on the evolutionary similarities between individual amino acids. It was applied for HIV-1 protease cleavage site prediction problem and shown to outperform existing methods in terms of prediction accuracy on a common dataset. In general, the method is a promising tool for prediction of cleavage sites of all proteases and encouraged to be used for any kind of peptide classification problem as well.

Short-cavity squeezing in barium

Science.gov (United States)

Hope, D. M.; Bachor, H-A.; Manson, P. J.; Mcclelland, D. E.

1992-01-01

Broadband phase sensitive noise and squeezing were experimentally observed in a system of barium atoms interacting with a single mode of a short optical cavity. Squeezing of 13 +/- 3 percent was observed. A maximum possible squeezing of 45 +/- 8 percent could be inferred for out experimental conditions, after correction for measured loss factors. Noise reductions below the quantum limit were found over a range of detection frequencies 60-170 MHz and were best for high cavity transmission and large optical depths. The amount of squeezing observed is consistent with theoretical predictions from a full quantum statistical model of the system.

PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites.

Directory of Open Access Journals (Sweden)

Jiangning Song

Full Text Available The ability to catalytically cleave protein substrates after synthesis is fundamental for all forms of life. Accordingly, site-specific proteolysis is one of the most important post-translational modifications. The key to understanding the physiological role of a protease is to identify its natural substrate(s. Knowledge of the substrate specificity of a protease can dramatically improve our ability to predict its target protein substrates, but this information must be utilized in an effective manner in order to efficiently identify protein substrates by in silico approaches. To address this problem, we present PROSPER, an integrated feature-based server for in silico identification of protease substrates and their cleavage sites for twenty-four different proteases. PROSPER utilizes established specificity information for these proteases (derived from the MEROPS database with a machine learning approach to predict protease cleavage sites by using different, but complementary sequence and structure characteristics. Features used by PROSPER include local amino acid sequence profile, predicted secondary structure, solvent accessibility and predicted native disorder. Thus, for proteases with known amino acid specificity, PROSPER provides a convenient, pre-prepared tool for use in identifying protein substrates for the enzymes. Systematic prediction analysis for the twenty-four proteases thus far included in the database revealed that the features we have included in the tool strongly improve performance in terms of cleavage site prediction, as evidenced by their contribution to performance improvement in terms of identifying known cleavage sites in substrates for these enzymes. In comparison with two state-of-the-art prediction tools, PoPS and SitePrediction, PROSPER achieves greater accuracy and coverage. To our knowledge, PROSPER is the first comprehensive server capable of predicting cleavage sites of multiple proteases within a single substrate

Output field-quadrature measurements and squeezing in ultrastrong cavity-QED

Science.gov (United States)

Stassi, Roberto; Savasta, Salvatore; Garziano, Luigi; Spagnolo, Bernardo; Nori, Franco

2016-12-01

We study the squeezing of output quadratures of an electro-magnetic field escaping from a resonator coupled to a general quantum system with arbitrary interaction strengths. The generalized theoretical analysis of output squeezing proposed here is valid for all the interaction regimes of cavity-quantum electrodynamics: from the weak to the strong, ultrastrong, and deep coupling regimes. For coupling rates comparable or larger then the cavity resonance frequency, the standard input-output theory for optical cavities fails to calculate the variance of output field-quadratures and predicts a non-negligible amount of output squeezing, even if the system is in its ground state. Here we show that, for arbitrary interaction strength and for general cavity-embedded quantum systems, no squeezing can be found in the output-field quadratures if the system is in its ground state. We also apply the proposed theoretical approach to study the output squeezing produced by: (i) an artificial two-level atom embedded in a coherently-excited cavity; and (ii) a cascade-type three-level system interacting with a cavity field mode. In the latter case the output squeezing arises from the virtual photons of the atom-cavity dressed states. This work extends the possibility of predicting and analyzing the results of continuous-variable optical quantum-state tomography when optical resonators interact very strongly with other quantum systems.

Control of Acoustics and Store Separation in a Cavity in Supersonic Flow

National Research Council Canada - National Science Library

Sahoo, Debashis

2005-01-01

.... For the first problem, an innovative cavity acoustics model is developed that rigorously explains the role of leading edge microjets in cavity noise suppression and predicts the magnitude of noise...

Distribution of cavity trees in midwestern old-growth and second-growth forests

Science.gov (United States)

Zhaofei Fan; Stephen R. Shifley; Martin A. Spetich; Frank R. Thompson; David R. Larsen

2003-01-01

We used classification and regression tree analysis to determine the primary variables associated with the occurrence of cavity trees and the hierarchical structure among those variables. We applied that information to develop logistic models predicting cavity tree probability as a function of diameter, species group, and decay class. Inventories of cavity abundance in...

Thermal Protection System Cavity Heating for Simplified and Actual Geometries Using Computational Fluid Dynamics Simulations with Unstructured Grids

Science.gov (United States)

McCloud, Peter L.

2010-01-01

Thermal Protection System (TPS) Cavity Heating is predicted using Computational Fluid Dynamics (CFD) on unstructured grids for both simplified cavities and actual cavity geometries. Validation was performed using comparisons to wind tunnel experimental results and CFD predictions using structured grids. Full-scale predictions were made for simplified and actual geometry configurations on the Space Shuttle Orbiter in a mission support timeframe.

MetWAMer: eukaryotic translation initiation site prediction

Directory of Open Access Journals (Sweden)

Brendel Volker

2008-09-01

Full Text Available Abstract Background Translation initiation site (TIS identification is an important aspect of the gene annotation process, requisite for the accurate delineation of protein sequences from transcript data. We have developed the MetWAMer package for TIS prediction in eukaryotic open reading frames of non-viral origin. MetWAMer can be used as a stand-alone, third-party tool for post-processing gene structure annotations generated by external computational programs and/or pipelines, or directly integrated into gene structure prediction software implementations. Results MetWAMer currently implements five distinct methods for TIS prediction, the most accurate of which is a routine that combines weighted, signal-based translation initiation site scores and the contrast in coding potential of sequences flanking TISs using a perceptron. Also, our program implements clustering capabilities through use of the k-medoids algorithm, thereby enabling cluster-specific TIS parameter utilization. In practice, our static weight array matrix-based indexing method for parameter set lookup can be used with good results in data sets exhibiting moderate levels of 5'-complete coverage. Conclusion We demonstrate that improvements in statistically-based models for TIS prediction can be achieved by taking the class of each potential start-methionine into account pending certain testing conditions, and that our perceptron-based model is suitable for the TIS identification task. MetWAMer represents a well-documented, extensible, and freely available software system that can be readily re-trained for differing target applications and/or extended with existing and novel TIS prediction methods, to support further research efforts in this area.

Predictive Temperature Equations for Three Sites at the Grand Canyon

Science.gov (United States)

McLaughlin, Katrina Marie Neitzel

Climate data collected at a number of automated weather stations were used to create a series of predictive equations spanning from December 2009 to May 2010 in order to better predict the temperatures along hiking trails within the Grand Canyon. The central focus of this project is how atmospheric variables interact and can be combined to predict the weather in the Grand Canyon at the Indian Gardens, Phantom Ranch, and Bright Angel sites. Through the use of statistical analysis software and data regression, predictive equations were determined. The predictive equations are simple or multivariable best fits that reflect the curvilinear nature of the data. With data analysis software curves resulting from the predictive equations were plotted along with the observed data. Each equation's reduced chi2 was determined to aid the visual examination of the predictive equations' ability to reproduce the observed data. From this information an equation or pair of equations was determined to be the best of the predictive equations. Although a best predictive equation for each month and season was determined for each site, future work may refine equations to result in a more accurate predictive equation.

Roosting records in tree cavities by a forest-dwelling bat species (Histiotus magellanicus) in Andean temperate ecosystems of southern Chile

OpenAIRE

Altamirano, Tomás A; Ibarra, José Tomás; Novoa, Fernando; Vermehren, Alejandra; Martin, Kathy; Bonacic, Cristián

2017-01-01

Tree cavities can provide critical roosting sites for cavity-using vertebrates. These sites can directly affect productivity and survival of bats. Histiotus magellanicus, one of the bat species with the southernmost distribution in the world, is suspected to use tree cavities, under bark, caves and human buildings for roosting. We document the first records of this bat roosting in tree cavities created by both cavity-facilitators (i.e., excavators) and tree-decay processes on standing dead an...

Cavity parameters identification for TESLA control system development

Energy Technology Data Exchange (ETDEWEB)

Czarski, T.; Pozniak, K.T.; Romaniuk, R.S. [Warsaw Univ. of Technology (Poland). ELHEP Lab., ISE; Simrock, S. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

2005-07-01

The control system modeling for the TESLA - TeV-Energy Superconducting Linear Accelerator project has been developed for the efficient stabilization of the pulsed, accelerating EM field of the resonator. The cavity parameters identification is an essential task for the comprehensive control algorithm. The TESLA cavity simulator has been successfully implemented by applying very high speed FPGA - Field Programmable Gate Array technology. The electromechanical model of the cavity resonator includes the basic features - Lorentz force detuning and beam loading. The parameters identification bases on the electrical model of the cavity. The model is represented by the state space equation for the envelope of the cavity voltage driven by the current generator and the beam loading. For a given model structure, the over-determined matrix equation is created covering the long enough measurement range with the solution according to the least squares method. A low degree polynomial approximation is applied to estimate the time-varying cavity detuning during the pulse. The measurement channel distortion is considered, leading to the external cavity model seen by the controller. The comprehensive algorithm of the cavity parameters identification has been implemented in the Matlab system with different modes of the operation. Some experimental results have been presented for different cavity operational conditions. The following considerations have lead to the synthesis of the efficient algorithm for the cavity control system predicted for the potential FPGA technology implementation. (orig.)

Cavity parameters identification for TESLA control system development

International Nuclear Information System (INIS)

Czarski, T.; Pozniak, K.T.; Romaniuk, R.S.

2005-01-01

The control system modeling for the TESLA - TeV-Energy Superconducting Linear Accelerator project has been developed for the efficient stabilization of the pulsed, accelerating EM field of the resonator. The cavity parameters identification is an essential task for the comprehensive control algorithm. The TESLA cavity simulator has been successfully implemented by applying very high speed FPGA - Field Programmable Gate Array technology. The electromechanical model of the cavity resonator includes the basic features - Lorentz force detuning and beam loading. The parameters identification bases on the electrical model of the cavity. The model is represented by the state space equation for the envelope of the cavity voltage driven by the current generator and the beam loading. For a given model structure, the over-determined matrix equation is created covering the long enough measurement range with the solution according to the least squares method. A low degree polynomial approximation is applied to estimate the time-varying cavity detuning during the pulse. The measurement channel distortion is considered, leading to the external cavity model seen by the controller. The comprehensive algorithm of the cavity parameters identification has been implemented in the Matlab system with different modes of the operation. Some experimental results have been presented for different cavity operational conditions. The following considerations have lead to the synthesis of the efficient algorithm for the cavity control system predicted for the potential FPGA technology implementation. (orig.)

The prevalence of squamous cell carcinoma in different sites of oral cavity at our Rural Health Care Centre in Loni, Maharashtra – a retrospective 10-year study

Science.gov (United States)

Dadhich, Anuj; Saluja, Harish; Bawane, Shilpa; Sachdeva, Shivani

2017-01-01

Aim of the study Oral cancer ranks in the top three of all cancers in India and is quickly becoming a global health priority. More than 90% of oral and oropharyngeal cancers are squamous cell carcinoma. The purpose of this study was to document its incidence depending upon the involvement of different sites of oral cavity, and its variation with age and gender. Material and methods Histopathologically proven oral squamous cell carcinoma cases were collected from the department of oral and maxillofacial surgery RDC, PIMS. The cases were systematically grouped under three headings: anatomical sub-site of oral cavity, age group, and gender, which were analysed to calculate the prevalence of oral cancer. The study was undertaken after obtaining approval from the institutional Ethical Committee board. Results Among the different sites of oral cavity, the highest incidence (31.47%) of oral squamous cell carcinoma was seen for buccal mucosa in our study. The most affected age group (39.50%) were patients above 50 years old, predominantly involving males. Conclusions The population in this study were mostly from remote areas, among which a high rate of occurrence of oral cancer was encountered because the people were of low socio-economic class, had a casual attitude towards their health, high rate of tobacco consumption, and limited health care facilities. This study provides valuable data of the prevalence of oral cancer among the rural population. PMID:28947890

The prevalence of squamous cell carcinoma in different sites of oral cavity at our Rural Health Care Centre in Loni, Maharashtra – a retrospective 10-year study

Directory of Open Access Journals (Sweden)

Parul Tandon

2017-06-01

Full Text Available Aim of the study : Oral cancer ranks in the top three of all cancers in India and is quickly becoming a global health priority. More than 90% of oral and oropharyngeal cancers are squamous cell carcinoma. The purpose of this study was to document its incidence depending upon the involvement of different sites of oral cavity, and its variation with age and gender. Material and methods : Histopathologically proven oral squamous cell carcinoma cases were collected from the department of oral and maxillofacial surgery RDC, PIMS. The cases were systematically grouped under three headings: anatomical sub-site of oral cavity, age group, and gender, which were analysed to calculate the prevalence of oral cancer. The study was undertaken after obtaining approval from the institutional Ethical Committee board. Results : Among the different sites of oral cavity, the highest incidence (31.47% of oral squamous cell carcinoma was seen for buccal mucosa in our study. The most affected age group (39.50% were patients above 50 years old, predominantly involving males. Conclusions : The population in this study were mostly from remote areas, among which a high rate of occurrence of oral cancer was encountered because the people were of low socio-economic class, had a casual attitude towards their health, high rate of tobacco consumption, and limited health care facilities. This study provides valuable data of the prevalence of oral cancer among the rural population.

Detection of hazardous cavities with combined geophysical methods

Science.gov (United States)

Hegymegi, Cs.; Nyari, Zs.; Pattantyus-Abraham, M.

2003-04-01

Unknown near-surface cavities often cause problems for municipal communities all over the world. This is the situation in Hungary in many towns and villages, too. Inhabitants and owners of real estates (houses, cottages, lands) are responsible for the safety and stability of their properties. The safety of public sites belongs to the local municipal community. Both (the owner and the community) are interested in preventing accidents. Near-surface cavities (unknown caves or earlier built and forgotten cellars) usually can be easily detected by surface geophysical methods. Traditional and recently developed measuring techniques in seismics, geoelectrics and georadar are suitable for economical investigation of hazardous, potentially collapsing cavities, prior to excavation and reinforcement. This poster will show some example for detection of cellars and caves being dangerous for civil population because of possible collapse under public sites (road, yard, playground, agricultural territory, etc.). The applied and presented methods are ground penetrating radar, seismic surface tomography and analysis of single traces, geoelectric 2D and 3D resistivity profiling. Technology and processing procedure will be presented.

The discrete Planck spectrum of a spherical cavity

International Nuclear Information System (INIS)

Vlad, V.I.; Ionescu-Pallas, N.

1999-03-01

The energy spectrum of black body radiation at the absolute temperature, T, in an ideal spherical cavity of radius, R, is studied. The departures from the classical predictions of Planck's theory, due to the discrete energies of the radiation quanta confined inside the cavity, depend on the adiabatic invariant RT and are significant for RT ≤ 40 cm · K. Special attention was paid to evidence strong changes in the spectrum intensities, forbidden bands of frequency, as well as major modifications of the total energy for RT ≤ 2 cm · K. Similar effects were present in the case of a cubic cavity. (author)

Better estimation of protein-DNA interaction parameters improve prediction of functional sites

Directory of Open Access Journals (Sweden)

O'Flanagan Ruadhan A

2008-12-01

Full Text Available Abstract Background Characterizing transcription factor binding motifs is a common bioinformatics task. For transcription factors with variable binding sites, we need to get many suboptimal binding sites in our training dataset to get accurate estimates of free energy penalties for deviating from the consensus DNA sequence. One procedure to do that involves a modified SELEX (Systematic Evolution of Ligands by Exponential Enrichment method designed to produce many such sequences. Results We analyzed low stringency SELEX data for E. coli Catabolic Activator Protein (CAP, and we show here that appropriate quantitative analysis improves our ability to predict in vitro affinity. To obtain large number of sequences required for this analysis we used a SELEX SAGE protocol developed by Roulet et al. The sequences obtained from here were subjected to bioinformatic analysis. The resulting bioinformatic model characterizes the sequence specificity of the protein more accurately than those sequence specificities predicted from previous analysis just by using a few known binding sites available in the literature. The consequences of this increase in accuracy for prediction of in vivo binding sites (and especially functional ones in the E. coli genome are also discussed. We measured the dissociation constants of several putative CAP binding sites by EMSA (Electrophoretic Mobility Shift Assay and compared the affinities to the bioinformatics scores provided by methods like the weight matrix method and QPMEME (Quadratic Programming Method of Energy Matrix Estimation trained on known binding sites as well as on the new sites from SELEX SAGE data. We also checked predicted genome sites for conservation in the related species S. typhimurium. We found that bioinformatics scores based on SELEX SAGE data does better in terms of prediction of physical binding energies as well as in detecting functional sites. Conclusion We think that training binding site detection

Principles for designing proteins with cavities formed by curved β sheets

Energy Technology Data Exchange (ETDEWEB)

Marcos, Enrique; Basanta, Benjamin; Chidyausiku, Tamuka M.; Tang, Yuefeng; Oberdorfer, Gustav; Liu, Gaohua; Swapna, G. V. T.; Guan, Rongjin; Silva, Daniel-Adriano; Dou, Jiayi; Pereira, Jose Henrique; Xiao, Rong; Sankaran, Banumathi; Zwart, Peter H.; Montelione, Gaetano T.; Baker, David

2017-01-12

Active sites and ligand-binding cavities in native proteins are often formed by curved β sheets, and the ability to control β-sheet curvature would allow design of binding proteins with cavities customized to specific ligands. Toward this end, we investigated the mechanisms controlling β-sheet curvature by studying the geometry of β sheets in naturally occurring protein structures and folding simulations. The principles emerging from this analysis were used to design, de novo, a series of proteins with curved β sheets topped with α helices. Nuclear magnetic resonance and crystal structures of the designs closely match the computational models, showing that β-sheet curvature can be controlled with atomic-level accuracy. Our approach enables the design of proteins with cavities and provides a route to custom design ligand-binding and catalytic sites.

A GIS approach for predicting prehistoric site locations.

Energy Technology Data Exchange (ETDEWEB)

Kuiper, J. A.; Wescott, K. L.

1999-08-04

Use of geographic information system (GIS)-based predictive mapping to locate areas of high potential for prehistoric archaeological sites is becoming increasingly popular among archaeologists. Knowledge of the environmental variables influencing activities of original inhabitants is used to produce GIS layers representing the spatial distribution of those variables. The GIS layers are then analyzed to identify locations where combinations of environmental variables match patterns observed at known prehistoric sites. Presented are the results of a study to locate high-potential areas for prehistoric sites in a largely unsurveyed area of 39,000 acres in the Upper Chesapeake Bay region, including details of the analysis process. The project used environmental data from over 500 known sites in other parts of the region and the results corresponded well with known sites in the study area.

Primary Tumor Site as a Predictor of Treatment Outcome for Definitive Radiotherapy of Advanced-Stage Oral Cavity Cancers

International Nuclear Information System (INIS)

Lin, Chien-Yu; Wang, Hung-Ming; Kang, Chung-Jan; Lee, Li-Yu; Huang, Shiang-Fu; Fan, Kang-Hsing; Chen, Eric Yen-Chao

2010-01-01

Purpose: To evaluate the outcome of definitive radiotherapy (RT) for oral cavity cancers and to assess prognostic factors. Methods and Materials: Definitive RT was performed on 115 patients with oral cavity cancers at Stages III, IVA, and IVB, with a distribution of 6%, 47%, and 47%, respectively. The median dose of RT was 72Gy (range, 62-76Gy). Cisplatin-based chemotherapy was administered to 95% of the patients. Eleven patients underwent salvage surgery after RT failure. Results: Eight-eight (76.5%) patients responded partially and 23 (20%) completely; of the patients who responded, 18% and 57%, respectively, experienced a durable effect of treatment. The 3-year overall survival, disease-specific survival, and progression-free survival were 22%, 27%, and 25%, respectively. The 3-year PFS rates based on the primary tumor sites were as follows: Group I (buccal, mouth floor, and gum) 51%, Group II (retromolar and hard palate) 18%, and Group III (tongue and lip) 6% (p < 0.0001). The 3-year progression-free survival was 41% for N0 patients and 19% for patients with N+ disease (p = 0.012). The T stage and RT technique did not affect survival. The patients who underwent salvage surgery demonstrated better 3-year overall survival and disease-specific survival (53% vs. 19%, p = 0.015 and 53% vs. 24%, p = 0.029, respectively). Subsite group, N+, and salvage surgery were the only significant prognostic factors for survival after multivariate analysis. Conclusion: The primary tumor site and neck stage are prognostic predictors in advanced-stage oral cancer patients who received radical RT. The primary tumor extension and RT technique did not influence survival.

Possible salt mine and brined cavity sites for radioactive waste disposal in the northeastern southern peninsula of Michigan

International Nuclear Information System (INIS)

Landes, K.K.; Bourne, H.L.

1976-01-01

A reconnaissance report on the possibilities for disposal of radioactive waste covers Michigan only, and is more detailed than an earlier one involving the northeastern states. Revised ''ground rules'' for pinpointing both mine and dissolved salt cavern sites for waste disposal include environmental, geologic, and economic factors. The Michigan basin is a structural bowl of Paleozoic sediments resting on downwarped Precambrian rocks. The center of the bowl is in Clare and Gladwin Counties, a short distance north of the middle of the Southern Peninsula. The strata dip toward this central area, and some stratigraphic sequences, including especially the salt-containing Silurian section, increase considerably in thickness in that direction. Lesser amounts of salt are also present in the north central part of the Lower Peninsula. Michigan has been an oil and gas producing state since 1925 and widespread exploration has had two effects on the selection of waste disposal sites: (1) large areas are leased for oil and gas; and (2) the borehole concentrations, whether producing wells, dry holes, or industrial brine wells that penetrated the salt section, should be avoided. Two types of nuclear waste, low level and high level, can be stored in man-made openings in salt beds. The storage facilities are created by (1) the development of salt mines where the depths are less than 3000 ft, and (2) cavities produced by pumping water into a salt bed, and bringing brine back out. The high level waste disposal must be confined to mines of limited depth, but the low level wastes can be accommodated in brine cavities at any depth. Seven potential prospects have been investigated and are described in detail

Aero-Heating of Shallow Cavities in Hypersonic Freestream Flow

Science.gov (United States)

Everhart, Joel L.; Berger, Karen T.; Merski, N. R., Jr.; Woods, William A.; Hollingsworth, Kevin E.; Hyatt, Andrew; Prabhu, Ramadas K.

2010-01-01

The purpose of these experiments and analysis was to augment the heating database and tools used for assessment of impact-induced shallow-cavity damage to the thermal protection system of the Space Shuttle Orbiter. The effect of length and depth on the local heating disturbance of rectangular cavities tested at hypersonic freestream conditions has been globally assessed using the two-color phosphor thermography method. These rapid-response experiments were conducted in the Langley 31-Inch Mach 10 Tunnel and were initiated immediately prior to the launch of STS-114, the initial flight in the Space Shuttle Return-To-Flight Program, and continued during the first week of the mission. Previously-designed and numerically-characterized blunted-nose baseline flat plates were used as the test surfaces. Three-dimensional computational predictions of the entire model geometry were used as a check on the design process and the two-dimensional flow assumptions used for the data analysis. The experimental boundary layer state conditions were inferred using the measured heating distributions on a no-cavity test article. Two test plates were developed, each containing 4 equally-spaced spanwise-distributed cavities. The first test plate contained cavities with a constant length-to-depth ratio of 8 with design point depth-to-boundary-layer-thickness ratios of 0.1, 0.2, 0.35, and 0.5. The second test plate contained cavities with a constant design point depth-to-boundary-layer-thickness ratio of 0.35 with length-to-depth ratios of 8, 12, 16, and 20. Cavity design parameters and the test condition matrix were established using the computational predictions. Preliminary results indicate that the floor-averaged Bump Factor (local heating rate nondimensionalized by upstream reference) at the tested conditions is approximately 0.3 with a standard deviation of 0.04 for laminar-in/laminar-out conditions when the cavity length-to-boundary-layer thickness is between 2.5 and 10 and for

POLYAR, a new computer program for prediction of poly(A sites in human sequences

Directory of Open Access Journals (Sweden)

Qamar Raheel

2010-11-01

Full Text Available Abstract Background mRNA polyadenylation is an essential step of pre-mRNA processing in eukaryotes. Accurate prediction of the pre-mRNA 3'-end cleavage/polyadenylation sites is important for defining the gene boundaries and understanding gene expression mechanisms. Results 28761 human mapped poly(A sites have been classified into three classes containing different known forms of polyadenylation signal (PAS or none of them (PAS-strong, PAS-weak and PAS-less, respectively and a new computer program POLYAR for the prediction of poly(A sites of each class was developed. In comparison with polya_svm (till date the most accurate computer program for prediction of poly(A sites while searching for PAS-strong poly(A sites in human sequences, POLYAR had a significantly higher prediction sensitivity (80.8% versus 65.7% and specificity (66.4% versus 51.7% However, when a similar sort of search was conducted for PAS-weak and PAS-less poly(A sites, both programs had a very low prediction accuracy, which indicates that our knowledge about factors involved in the determination of the poly(A sites is not sufficient to identify such polyadenylation regions. Conclusions We present a new classification of polyadenylation sites into three classes and a novel computer program POLYAR for prediction of poly(A sites/regions of each of the class. In tests, POLYAR shows high accuracy of prediction of the PAS-strong poly(A sites, though this program's efficiency in searching for PAS-weak and PAS-less poly(A sites is not very high but is comparable to other available programs. These findings suggest that additional characteristics of such poly(A sites remain to be elucidated. POLYAR program with a stand-alone version for downloading is available at http://cub.comsats.edu.pk/polyapredict.htm.

Nonlinear Analysis of Cavities in Rock Salt

DEFF Research Database (Denmark)

Ottosen, N. S.; Krenk, Steen

1979-01-01

The paper covers some material and computational aspects of the rock mechanics of leached cavities in salt. A material model is presented in which the instantaneous stiffness of the salt is obtained by interpolation between the unloaded state and a relevant failure state. The model enables predic...... prediction of short term triaxial behaviour from uniaxial stress-strain curves. Key results from a nonlinear finite element calculation of a gas-filled cavity are given, and the general features are related to a simple nonlinear method of stress evaluation....

Predicting protein amidation sites by orchestrating amino acid sequence features

Science.gov (United States)

Zhao, Shuqiu; Yu, Hua; Gong, Xiujun

2017-08-01

Amidation is the fourth major category of post-translational modifications, which plays an important role in physiological and pathological processes. Identifying amidation sites can help us understanding the amidation and recognizing the original reason of many kinds of diseases. But the traditional experimental methods for predicting amidation sites are often time-consuming and expensive. In this study, we propose a computational method for predicting amidation sites by orchestrating amino acid sequence features. Three kinds of feature extraction methods are used to build a feature vector enabling to capture not only the physicochemical properties but also position related information of the amino acids. An extremely randomized trees algorithm is applied to choose the optimal features to remove redundancy and dependence among components of the feature vector by a supervised fashion. Finally the support vector machine classifier is used to label the amidation sites. When tested on an independent data set, it shows that the proposed method performs better than all the previous ones with the prediction accuracy of 0.962 at the Matthew's correlation coefficient of 0.89 and area under curve of 0.964.

CaMELS: In silico prediction of calmodulin binding proteins and their binding sites.

Science.gov (United States)

Abbasi, Wajid Arshad; Asif, Amina; Andleeb, Saiqa; Minhas, Fayyaz Ul Amir Afsar

2017-09-01

Due to Ca 2+ -dependent binding and the sequence diversity of Calmodulin (CaM) binding proteins, identifying CaM interactions and binding sites in the wet-lab is tedious and costly. Therefore, computational methods for this purpose are crucial to the design of such wet-lab experiments. We present an algorithm suite called CaMELS (CalModulin intEraction Learning System) for predicting proteins that interact with CaM as well as their binding sites using sequence information alone. CaMELS offers state of the art accuracy for both CaM interaction and binding site prediction and can aid biologists in studying CaM binding proteins. For CaM interaction prediction, CaMELS uses protein sequence features coupled with a large-margin classifier. CaMELS models the binding site prediction problem using multiple instance machine learning with a custom optimization algorithm which allows more effective learning over imprecisely annotated CaM-binding sites during training. CaMELS has been extensively benchmarked using a variety of data sets, mutagenic studies, proteome-wide Gene Ontology enrichment analyses and protein structures. Our experiments indicate that CaMELS outperforms simple motif-based search and other existing methods for interaction and binding site prediction. We have also found that the whole sequence of a protein, rather than just its binding site, is important for predicting its interaction with CaM. Using the machine learning model in CaMELS, we have identified important features of protein sequences for CaM interaction prediction as well as characteristic amino acid sub-sequences and their relative position for identifying CaM binding sites. Python code for training and evaluating CaMELS together with a webserver implementation is available at the URL: http://faculty.pieas.edu.pk/fayyaz/software.html#camels. © 2017 Wiley Periodicals, Inc.

Establishing a predictive maintenance (PdM) program at the Hanford Site

International Nuclear Information System (INIS)

Murray, W.A.; Winslow, R.G.

1994-02-01

The production reactors have been shut down for some time. But for the rest of the site, there is currently about 16,000 people engaged in a multi-billion dollar effort to safely process wastes which have been stored at the site since the 1940's. This effort also includes demolition of some older facilities and environmental restoration of much of the site. This is expected to take approximately 30 to 40 years. The concept of a site-wide predictive maintenance (PdM) program began to form in early 1993. Several informal studies showed that the stand alone predictive maintenance groups which had prevailed on site to date were less than 15% effective at trending equipment conditions and predicting failures. To improve the effectiveness of PdM within the company, an engineering analysis by Rick Winslow confirmed that utilization of software networking technology which was now available would significantly overcome many of these built in handicaps. A site-wide predictive maintenance network would make PdM technology accessible to all of the areas and facilities at the site regardless of geographical distances and company division lines. Site resident vibration experts can easily be located and provide consultations on the network. However, it was recognized that strong leadership and management skills would be required within each of the two organizations for effective implementation. To start this process, a letter of understanding and agreement between the facilities and Tank Farm divisions was drafted and endorsed by company management. The agreement assigned the primary responsibility of acquiring the network software and licensee to the Tank Farms division. The acquisition and installation of the network server would be the responsibility of the facilities division. This paper describes the rest of the network development and implementation process

Cavity Heating Experiments Supporting Shuttle Columbia Accident Investigation

Science.gov (United States)

Everhart, Joel L.; Berger, Karen T.; Bey, Kim S.; Merski, N. Ronald; Wood, William A.

2011-01-01

The two-color thermographic phosphor method has been used to map the local heating augmentation of scaled idealized cavities at conditions simulating the windward surface of the Shuttle Orbiter Columbia during flight STS-107. Two experiments initiated in support of the Columbia Accident Investigation were conducted in the Langley 20-Inch Mach 6 Tunnel. Generally, the first test series evaluated open (length-to-depth less than 10) rectangular cavity geometries proposed as possible damage scenarios resulting from foam and ice impact during launch at several discrete locations on the vehicle windward surface, though some closed (length-to-depth greater than 13) geometries were briefly examined. The second test series was designed to parametrically evaluate heating augmentation in closed rectangular cavities. The tests were conducted under laminar cavity entry conditions over a range of local boundary layer edge-flow parameters typical of re-entry. Cavity design parameters were developed using laminar computational predictions, while the experimental boundary layer state conditions were inferred from the heating measurements. An analysis of the aeroheating caused by cavities allowed exclusion of non-breeching damage from the possible loss scenarios being considered during the investigation.

A survey of cavity-nesting bees and wasps in loblolly pine stands of the Savannah River Site, Aiken County, South Carolina.

Energy Technology Data Exchange (ETDEWEB)

Horn, S.; Hanula, J., L.

2004-03-10

Horn, Scott, and James L. Hanula. 2004. A survey of cavity-nesting bees and wasps in loblolly pine stands of the Savannah River Site, Aiken County, South Carolina. 39(3): 464-469. Abstract: In recent years concern over widespread losses in biodiversity has grown to include a possible decline of many native pollinators, primarily bees. Factors such as habitat fragmentation, agricultural practices, use of pesticides, the introduction of invasive species, or changes in land use may negatively impact these vital organisims. Most reported studies show that human impacts on pollinators are overwhelmingly negative. Reductions in pollinator populations may profoundly impact plant population dynamics and ecosystem function. Little baseline data exists on the diversity and relative abundance of bees and wasps in southern forests. The objective of this study was to develop a simple, effective method of surveying cavity-nesting bees and wasps and to determine species diversity in mature forests of loblolly pine, the most widely planted tree species in the southern United States.

Estimates of potential radionuclide migration at the Bullion site

International Nuclear Information System (INIS)

Brikowski, T.H.

1992-04-01

The Bullion site in Area 20 of the Nevada Test Site has been selected for an intensive study of the hydrologic consequences of underground testing, including subsequent radionuclide migration. The bulk of the chimney and cavity lie in zeolitized tuffs of low hydraulic conductivity, while the base of the cavity may extend downward into more conductive rhyolite flows. A mathematical analog to the Bullion setting is used here to estimate expected radionuclide migration rates and concentrations. Because of a lack of hydrologic data at the site, two contrasting scenarios are considered. The first is downward-transport, in which downward hydraulic gradients flush chimney contents into the conductive underlying units, enhancing migration. The other is upward-transport, in which upward gradients tend to drive chimney contents into the low-conductivity zeolitized tuffs, discouraging migration. In the downward-transport scenario, radionuclide travel times and concentrations are predicted to be similar to those encountered at Cheshire, requiring approximately 10 years to reach a proposed well 300 m downgradient. The upward transport scenario yields predicted travel times on the order of 2,000 years to the downgradient well. The most likely scenario is a combination of these results, with vertical movement playing a limited role. Radionuclides injected directly into the rhyolites should migrate laterally very quickly, with travel times as in the downward-transport scenario. Those in the zeolitized tuff-walled portion of the chimney should migrate extremely slowly, as in the upward-transport scenario

High density of tree-cavities and snags in tropical dry forest of western Mexico raises questions for a latitudinal gradient.

Directory of Open Access Journals (Sweden)

Leopoldo Vázquez

Full Text Available It has been suggested that a latitudinal gradient exists of a low density of snags and high density of naturally-formed tree-cavities in tropical vs. temperate forests, though few cavities may have characteristics suitable for nesting by birds. We determined snag and cavity density, characteristics, and suitability for birds in a tropical dry forest biome of western Mexico, and evaluated whether our data fits the trend of snag and cavity density typically found in tropical moist and wet forests. We established five 0.25-ha transects to survey and measure tree-cavities and snags in each of three vegetation types of deciduous, semi-deciduous, and mono-dominant Piranhea mexicana forest, comprising a total of 3.75 ha. We found a high density of 77 cavities/ha, with 37 cavities suitable for birds/ha, where density, and characteristics of cavities varied significantly among vegetation types. Lowest abundance of cavities occurred in deciduous forest, and these were in smaller trees, at a lower height, and with a narrower entrance diameter. Only 8.6% of cavities were excavated by woodpeckers, and only 11% of cavities were occupied, mainly by arthropods, though 52% of all cavities were unsuitable for birds. We also found a high density of 56 snags/ha, with greatest density in deciduous forest (70 snags/ha, though these were of significantly smaller diameter, and snags of larger diameter were more likely to contain cavities. The Chamela-Cuixmala tropical dry forest had the highest density of snags recorded for any tropical or temperate forest, and while snag density was significantly correlated with mean snag dbh, neither latitude nor mean dbh predicted snag density in ten forest sites. The high spatial aggregation of snag and cavity resources in tropical dry forest may limit their availability, particularly for large-bodied cavity adopters, and highlights the importance of habitat heterogeneity in providing resources for primary and secondary cavity-nesters.

High density of tree-cavities and snags in tropical dry forest of western Mexico raises questions for a latitudinal gradient.

Science.gov (United States)

Vázquez, Leopoldo; Renton, Katherine

2015-01-01

It has been suggested that a latitudinal gradient exists of a low density of snags and high density of naturally-formed tree-cavities in tropical vs. temperate forests, though few cavities may have characteristics suitable for nesting by birds. We determined snag and cavity density, characteristics, and suitability for birds in a tropical dry forest biome of western Mexico, and evaluated whether our data fits the trend of snag and cavity density typically found in tropical moist and wet forests. We established five 0.25-ha transects to survey and measure tree-cavities and snags in each of three vegetation types of deciduous, semi-deciduous, and mono-dominant Piranhea mexicana forest, comprising a total of 3.75 ha. We found a high density of 77 cavities/ha, with 37 cavities suitable for birds/ha, where density, and characteristics of cavities varied significantly among vegetation types. Lowest abundance of cavities occurred in deciduous forest, and these were in smaller trees, at a lower height, and with a narrower entrance diameter. Only 8.6% of cavities were excavated by woodpeckers, and only 11% of cavities were occupied, mainly by arthropods, though 52% of all cavities were unsuitable for birds. We also found a high density of 56 snags/ha, with greatest density in deciduous forest (70 snags/ha), though these were of significantly smaller diameter, and snags of larger diameter were more likely to contain cavities. The Chamela-Cuixmala tropical dry forest had the highest density of snags recorded for any tropical or temperate forest, and while snag density was significantly correlated with mean snag dbh, neither latitude nor mean dbh predicted snag density in ten forest sites. The high spatial aggregation of snag and cavity resources in tropical dry forest may limit their availability, particularly for large-bodied cavity adopters, and highlights the importance of habitat heterogeneity in providing resources for primary and secondary cavity-nesters.

Novel immunohistochemistry-based signatures to predict metastatic site of triple-negative breast cancers.

Science.gov (United States)

Klimov, Sergey; Rida, Padmashree Cg; Aleskandarany, Mohammed A; Green, Andrew R; Ellis, Ian O; Janssen, Emiel Am; Rakha, Emad A; Aneja, Ritu

2017-09-05

Although distant metastasis (DM) in breast cancer (BC) is the most lethal form of recurrence and the most common underlying cause of cancer related deaths, the outcome following the development of DM is related to the site of metastasis. Triple negative BC (TNBC) is an aggressive form of BC characterised by early recurrences and high mortality. Athough multiple variables can be used to predict the risk of metastasis, few markers can predict the specific site of metastasis. This study aimed at identifying a biomarker signature to predict particular sites of DM in TNBC. A clinically annotated series of 322 TNBC were immunohistochemically stained with 133 biomarkers relevant to BC, to develop multibiomarker models for predicting metastasis to the bone, liver, lung and brain. Patients who experienced metastasis to each site were compared with those who did not, by gradually filtering the biomarker set via a two-tailed t-test and Cox univariate analyses. Biomarker combinations were finally ranked based on statistical significance, and evaluated in multivariable analyses. Our final models were able to stratify TNBC patients into high risk groups that showed over 5, 6, 7 and 8 times higher risk of developing metastasis to the bone, liver, lung and brain, respectively, than low-risk subgroups. These models for predicting site-specific metastasis retained significance following adjustment for tumour size, patient age and chemotherapy status. Our novel IHC-based biomarkers signatures, when assessed in primary TNBC tumours, enable prediction of specific sites of metastasis, and potentially unravel biomarkers previously unknown in site tropism.

Radionuclide Partitioning in an Underground Nuclear Test Cavity

Energy Technology Data Exchange (ETDEWEB)

Rose, T P; Hu, Q; Zhao, P; Conrado, C L; Dickerson, R; Eaton, G F; Kersting, A B; Moran, J E; Nimz, G; Powell, B A; Ramon, E C; Ryerson, F J; Williams, R W; Wooddy, P T; Zavarin, M

2009-01-09

In 2004, a borehole was drilled into the 1983 Chancellor underground nuclear test cavity to investigate the distribution of radionuclides within the cavity. Sidewall core samples were collected from a range of depths within the re-entry hole and two sidetrack holes. Upon completion of drilling, casing was installed and a submersible pump was used to collect groundwater samples. Test debris and groundwater samples were analyzed for a variety of radionuclides including the fission products {sup 99}Tc, {sup 125}Sb, {sup 129}I, {sup 137}Cs, and {sup 155}Eu, the activation products {sup 60}Co, {sup 152}Eu, and {sup 154}Eu, and the actinides U, Pu, and Am. In addition, the physical and bulk chemical properties of the test debris were characterized using Scanning Electron Microscopy (SEM) and Electron Microprobe measurements. Analytical results were used to evaluate the partitioning of radionuclides between the melt glass, rubble, and groundwater phases in the Chancellor test cavity. Three comparative approaches were used to calculate partitioning values, though each method could not be applied to every nuclide. These approaches are based on: (1) the average Area 19 inventory from Bowen et al. (2001); (2) melt glass, rubble, and groundwater mass estimates from Zhao et al. (2008); and (3) fission product mass yield data from England and Rider (1994). The U and Pu analyses of the test debris are classified and partitioning estimates for these elements were calculated directly from the classified Miller et al. (2002) inventory for the Chancellor test. The partitioning results from this study were compared to partitioning data that were previously published by the IAEA (1998). Predictions of radionuclide distributions from the two studies are in agreement for a majority of the nuclides under consideration. Substantial differences were noted in the partitioning values for {sup 99}Tc, {sup 125}Sb, {sup 129}I, and uranium. These differences are attributable to two factors

Building of radio frequency cavity for Superconducting Cyclotron

International Nuclear Information System (INIS)

Ahammed, M.; DuttaGupta, A.; Mandal, B.Ch.; Saha, S.; Bhattacharya, P.; Manna, B.; Hembrom, B.; Murmu, S.; Sur, S.; Murali, S.; Chaudhuri, J.; Bhandari, R.K.

2009-01-01

Full text: RF cavity for Superconducting Cyclotron is a room temperature cavity having 10 m tall coaxial structure placed symmetrically above and below the median plane. The structure is made of copper and operates within the frequency range of 9 to 27 MHz. The frequency is varied with the help of sliding shorts, which moves up and down. Part of the cavity is in air and rest is in vacuum. After fabrication of individual components, assembly of sub-system has been started by carrying out numeral critical (around 500 joints approx.) soldering and brazing joints of which some of them are located within centimeter of distance. All these joints were tested for vacuum and water sealing including many temporary joints sealed by O rings and C seals. Main criticalities involve in fabricating these sub-assemblies are maintaining dimensional accuracies, concentricity and parallelism. Moreover challenges faced during transportation and handling of this subassembly while carrying out soldering and actual site assembly, were overcome by employing several specially designed fixtures. Fixtures were used to control distortion that would take place during soldering and brazing and to avoid any damage which is likely to occur because of less mechanical strength of soldering and brazing joint. This paper highlights the above difficulties and challenges faced during the actual site assembly of the whole RF system because of its limited accessibility, compactness, requirements of upper and lower resonator cavity to be symmetric and ultra cleanliness. (author)

Using TESS to predict transcription factor binding sites in DNA sequence.

Science.gov (United States)

Schug, Jonathan

2008-03-01

This unit describes how to use the Transcription Element Search System (TESS). This Web site predicts transcription factor binding sites (TFBS) in DNA sequence using two different kinds of models of sites, strings and positional weight matrices. The binding of transcription factors to DNA is a major part of the control of gene expression. Transcription factors exhibit sequence-specific binding; they form stronger bonds to some DNA sequences than to others. Identification of a good binding site in the promoter for a gene suggests the possibility that the corresponding factor may play a role in the regulation of that gene. However, the sequences transcription factors recognize are typically short and allow for some amount of mismatch. Because of this, binding sites for a factor can typically be found at random every few hundred to a thousand base pairs. TESS has features to help sort through and evaluate the significance of predicted sites.

Interacting Factors Driving a Major Loss of Large Trees with Cavities in a Forest Ecosystem

Science.gov (United States)

Lindenmayer, David B.; Blanchard, Wade; McBurney, Lachlan; Blair, David; Banks, Sam; Likens, Gene E.; Franklin, Jerry F.; Laurance, William F.; Stein, John A. R.; Gibbons, Philip

2012-01-01

Large trees with cavities provide critical ecological functions in forests worldwide, including vital nesting and denning resources for many species. However, many ecosystems are experiencing increasingly rapid loss of large trees or a failure to recruit new large trees or both. We quantify this problem in a globally iconic ecosystem in southeastern Australia – forests dominated by the world's tallest angiosperms, Mountain Ash (Eucalyptus regnans). Tree, stand and landscape-level factors influencing the death and collapse of large living cavity trees and the decay and collapse of dead trees with cavities are documented using a suite of long-term datasets gathered between 1983 and 2011. The historical rate of tree mortality on unburned sites between 1997 and 2011 was >14% with a mortality spike in the driest period (2006–2009). Following a major wildfire in 2009, 79% of large living trees with cavities died and 57–100% of large dead trees were destroyed on burned sites. Repeated measurements between 1997 and 2011 revealed no recruitment of any new large trees with cavities on any of our unburned or burned sites. Transition probability matrices of large trees with cavities through increasingly decayed condition states projects a severe shortage of large trees with cavities by 2039 that will continue until at least 2067. This large cavity tree crisis in Mountain Ash forests is a product of: (1) the prolonged time required (>120 years) for initiation of cavities; and (2) repeated past wildfires and widespread logging operations. These latter factors have resulted in all landscapes being dominated by stands ≤72 years and just 1.16% of forest being unburned and unlogged. We discuss how the features that make Mountain Ash forests vulnerable to a decline in large tree abundance are shared with many forest types worldwide. PMID:23071486

Interacting factors driving a major loss of large trees with cavities in a forest ecosystem.

Directory of Open Access Journals (Sweden)

David B Lindenmayer

Full Text Available Large trees with cavities provide critical ecological functions in forests worldwide, including vital nesting and denning resources for many species. However, many ecosystems are experiencing increasingly rapid loss of large trees or a failure to recruit new large trees or both. We quantify this problem in a globally iconic ecosystem in southeastern Australia--forests dominated by the world's tallest angiosperms, Mountain Ash (Eucalyptus regnans. Tree, stand and landscape-level factors influencing the death and collapse of large living cavity trees and the decay and collapse of dead trees with cavities are documented using a suite of long-term datasets gathered between 1983 and 2011. The historical rate of tree mortality on unburned sites between 1997 and 2011 was >14% with a mortality spike in the driest period (2006-2009. Following a major wildfire in 2009, 79% of large living trees with cavities died and 57-100% of large dead trees were destroyed on burned sites. Repeated measurements between 1997 and 2011 revealed no recruitment of any new large trees with cavities on any of our unburned or burned sites. Transition probability matrices of large trees with cavities through increasingly decayed condition states projects a severe shortage of large trees with cavities by 2039 that will continue until at least 2067. This large cavity tree crisis in Mountain Ash forests is a product of: (1 the prolonged time required (>120 years for initiation of cavities; and (2 repeated past wildfires and widespread logging operations. These latter factors have resulted in all landscapes being dominated by stands ≤72 years and just 1.16% of forest being unburned and unlogged. We discuss how the features that make Mountain Ash forests vulnerable to a decline in large tree abundance are shared with many forest types worldwide.

Interacting factors driving a major loss of large trees with cavities in a forest ecosystem.

Science.gov (United States)

Lindenmayer, David B; Blanchard, Wade; McBurney, Lachlan; Blair, David; Banks, Sam; Likens, Gene E; Franklin, Jerry F; Laurance, William F; Stein, John A R; Gibbons, Philip

2012-01-01

Large trees with cavities provide critical ecological functions in forests worldwide, including vital nesting and denning resources for many species. However, many ecosystems are experiencing increasingly rapid loss of large trees or a failure to recruit new large trees or both. We quantify this problem in a globally iconic ecosystem in southeastern Australia--forests dominated by the world's tallest angiosperms, Mountain Ash (Eucalyptus regnans). Tree, stand and landscape-level factors influencing the death and collapse of large living cavity trees and the decay and collapse of dead trees with cavities are documented using a suite of long-term datasets gathered between 1983 and 2011. The historical rate of tree mortality on unburned sites between 1997 and 2011 was >14% with a mortality spike in the driest period (2006-2009). Following a major wildfire in 2009, 79% of large living trees with cavities died and 57-100% of large dead trees were destroyed on burned sites. Repeated measurements between 1997 and 2011 revealed no recruitment of any new large trees with cavities on any of our unburned or burned sites. Transition probability matrices of large trees with cavities through increasingly decayed condition states projects a severe shortage of large trees with cavities by 2039 that will continue until at least 2067. This large cavity tree crisis in Mountain Ash forests is a product of: (1) the prolonged time required (>120 years) for initiation of cavities; and (2) repeated past wildfires and widespread logging operations. These latter factors have resulted in all landscapes being dominated by stands ≤72 years and just 1.16% of forest being unburned and unlogged. We discuss how the features that make Mountain Ash forests vulnerable to a decline in large tree abundance are shared with many forest types worldwide.

Effects of Freestream Turbulence on Cavity Tone and Sound Source

Directory of Open Access Journals (Sweden)

Hiroshi Yokoyama

2016-01-01

Full Text Available To clarify the effects of freestream turbulence on cavity tones, flow and acoustic fields were directly predicted for cavity flows with various intensities of freestream turbulence. The freestream Mach number was 0.09 and the Reynolds number based on the cavity length was 4.0 × 104. The depth-to-length ratio of the cavity, D/L, was 0.5 and 2.5, where the acoustic resonance of a depth-mode occurs for D/L = 2.5. The incoming boundary layer was laminar. The results for the intensity of freestream turbulence of Tu = 2.3% revealed that the reduced level of cavity tones in a cavity flow with acoustic resonance (D/L=2.5 was greater than that without acoustic resonance (D/L=0.5. To clarify the reason for this, the sound source based on Lighthill’s acoustic analogy was computed, and the contributions of the intensity and spanwise coherence of the sound source to the reduction of the cavity tone were estimated. As a result, the effects of the reduction of spanwise coherence on the cavity tone were greater in the cavity flow with acoustic resonance than in that without resonance, while the effects of the intensity were comparable for both flows.

AutoSite: an automated approach for pseudo-ligands prediction—from ligand-binding sites identification to predicting key ligand atoms

Science.gov (United States)

Ravindranath, Pradeep Anand; Sanner, Michel F.

2016-01-01

Motivation: The identification of ligand-binding sites from a protein structure facilitates computational drug design and optimization, and protein function assignment. We introduce AutoSite: an efficient software tool for identifying ligand-binding sites and predicting pseudo ligand corresponding to each binding site identified. Binding sites are reported as clusters of 3D points called fills in which every point is labelled as hydrophobic or as hydrogen bond donor or acceptor. From these fills AutoSite derives feature points: a set of putative positions of hydrophobic-, and hydrogen-bond forming ligand atoms. Results: We show that AutoSite identifies ligand-binding sites with higher accuracy than other leading methods, and produces fills that better matches the ligand shape and properties, than the fills obtained with a software program with similar capabilities, AutoLigand. In addition, we demonstrate that for the Astex Diverse Set, the feature points identify 79% of hydrophobic ligand atoms, and 81% and 62% of the hydrogen acceptor and donor hydrogen ligand atoms interacting with the receptor, and predict 81.2% of water molecules mediating interactions between ligand and receptor. Finally, we illustrate potential uses of the predicted feature points in the context of lead optimization in drug discovery projects. Availability and Implementation: http://adfr.scripps.edu/AutoDockFR/autosite.html Contact: sanner@scripps.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27354702

Predicted effectiveness of in-situ activated carbon amendment for field sediment sites with variable site- and compound-specific characteristics

Energy Technology Data Exchange (ETDEWEB)

Choi, Yongju, E-mail: ychoi81@snu.ac.kr [Department of Civil and Environmental Engineering, Seoul National University, Seoul 151-744 (Korea, Republic of); Cho, Yeo-Myoung; Luthy, Richard G. [Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305-4020 (United States); Werner, David [School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU (United Kingdom)

2016-01-15

Highlights: • The model accounts for the heterogeneity of AC distribution in field applications. • AC amendment effectiveness is predicted for ten sediment sites. • An HOC mass transfer model and calibrated parameters provide reliable predictions. • AC amendment is predicted to be effective for most sites. • K{sub ow}, K{sub d}, and equilibrium-based calculations are useful indicators. - Abstract: A growing body of evidence shows that the effectiveness of in-situ activated carbon (AC) amendment to treat hydrophobic organic contaminants (HOCs) in sediments can be reliably predicted using a mass transfer modeling approach. This study analyzes available field data for characterizing AC-sediment distribution after mechanical mixing of AC into sediment. Those distributions are used to develop an HOC mass transfer model that accounts for plausible heterogeneities resulting from mixing of AC into sediment. The model is applied to ten field sites in the U.S. and Europe with 2–3 representative HOCs from each site using site- and HOC-specific model parameters collected from the literature. The model predicts that the AC amendment reduces the pore-water HOC concentrations by more than 95% fifteen years after AC deployment for 18 of the 25 total simulated cases when the AC is applied at doses of 1.5 times sediment total organic carbon content with an upper limit of 5 dry wt%. The predicted effectiveness shows negative correlation with the HOC octanol–water partitioning coefficients and the sediment-water distribution coefficients, and positive correlation with the effectiveness calculated based on equilibrium coefficients of sediment and AC, suggesting the possibility for use of the values for screening-level assessments.

Predicted effectiveness of in-situ activated carbon amendment for field sediment sites with variable site- and compound-specific characteristics

International Nuclear Information System (INIS)

Choi, Yongju; Cho, Yeo-Myoung; Luthy, Richard G.; Werner, David

2016-01-01

Highlights: • The model accounts for the heterogeneity of AC distribution in field applications. • AC amendment effectiveness is predicted for ten sediment sites. • An HOC mass transfer model and calibrated parameters provide reliable predictions. • AC amendment is predicted to be effective for most sites. • K ow , K d , and equilibrium-based calculations are useful indicators. - Abstract: A growing body of evidence shows that the effectiveness of in-situ activated carbon (AC) amendment to treat hydrophobic organic contaminants (HOCs) in sediments can be reliably predicted using a mass transfer modeling approach. This study analyzes available field data for characterizing AC-sediment distribution after mechanical mixing of AC into sediment. Those distributions are used to develop an HOC mass transfer model that accounts for plausible heterogeneities resulting from mixing of AC into sediment. The model is applied to ten field sites in the U.S. and Europe with 2–3 representative HOCs from each site using site- and HOC-specific model parameters collected from the literature. The model predicts that the AC amendment reduces the pore-water HOC concentrations by more than 95% fifteen years after AC deployment for 18 of the 25 total simulated cases when the AC is applied at doses of 1.5 times sediment total organic carbon content with an upper limit of 5 dry wt%. The predicted effectiveness shows negative correlation with the HOC octanol–water partitioning coefficients and the sediment-water distribution coefficients, and positive correlation with the effectiveness calculated based on equilibrium coefficients of sediment and AC, suggesting the possibility for use of the values for screening-level assessments.

Atmospheric signals produced by cavity rebound

International Nuclear Information System (INIS)

Jones, E.M.; App, F.N.; Whitaker, R.W.

1993-01-01

An analysis of the atmospheric acoustic signals produced by a class of low-yield tests conducted just below the base of the alluvial cover in Yucca Flat of the Nevada Test Site (NTS), has revealed a clear manifestation of an elastic, cavity rebound signal. We use modeling as the basis for understanding the observed phenomena

Observing mode propagation inside a laser cavity

CSIR Research Space (South Africa)

Naidoo, Darryl

2012-05-01

Full Text Available components, to study the forward and backward propagating waves everywhere inside a laser cavity. We verify the previous theoretical-only prediction that the two fields may differ substantially in their amplitude profile, even for stable resonator systems, a...

The fundamental science of nitrogen-doping of niobium superconducting cavities

Science.gov (United States)

Gonnella, Daniel Alfred

Doping of niobium superconducting RF cavities with impurities has been demonstrated to have the ability to significantly improve the cryogenic efficiency of the accelerating structures. Doping SRF cavities with nitrogen is a relatively simple additional step to cavity preparation that can make drastic improvements in a cavity's intrinsic quality factor, Q0. Nitrogen-doping consists of treating SRF cavities at high temperatures in a low nitrogen-atmosphere. This leads to two important effects: an improvement in Q0 at low fields, and the presence of an "anti-Q slope" in which the cryogenic efficiency of doped cavities actually improves at higher fields. After its initial discovery, nitrogen-doping showed real promise but many fundamental scientific questions remained about the process. Nitrogen-doped cavities consistently quenched at lower fields than un-doped cavities, cooling the cavities through their critical temperature slowly led to poor performance, and the mechanism behind the Q0 improvement was not well understood. This dissertation focuses on addressing these issues. Single-cell 1.3 GHz cavities were prepared with different nitrogen-dopings and their effects studied systematically. It was found that nitrogen-doping drastically lowers the mean free path of the RF penetration layer of the niobium, leading to a lowering of the temperature-dependent BCS resistance, RBCS, at low fields. Theoretical work to predict the anti-Q slope was compared with experimental results to more fundamentally understand the nature of the field dependence of RBCS. Nitrogen-doped cavities were found to have a much larger sensitivity of residual resistance from trapped magnetic flux than un-doped cavities. Fast cool downs with large spatial temperature gradients through Tc were found to more efficiently expel magnetic flux. The full dependence of this sensitivity to trapped magnetic flux was studied as a function of changing mean free path and found to be in good agreement with

The nasopharynx, the paranasal sinuses, and nasal cavity

International Nuclear Information System (INIS)

Mancuso, A.A.

1985-01-01

In considering malignancies of the head and neck region, a number of sites mutually lend themselves to the presentation of diagnostic imaging and treatment. Some of these sites are the nasopharynx, the paranasal sinuses, and the nasal cavity, which are primarily concerned with the intake of air and are, in essence, the beginning of the respiratory tract. Because of its function, the tract is exposed to many environmental antigens and pollutants. For example, carcinoma of the nasopharynx is especially common among southern Chinese and seems to be related to environmental rather than genetic factors. However, the Epstein-Barr virus is associated with nasopharyngeal carcinomas in all races. The incidence of carcinomas of the nasal cavity and the paranasal sinuses has been found to be increased in furniture workers and appears to be related to wood dust inhalation

Dynamics of interacting Dicke model in a coupled-cavity array

Science.gov (United States)

Badshah, Fazal; Qamar, Shahid; Paternostro, Mauro

2014-09-01

We consider the dynamics of an array of mutually interacting cavities, each containing an ensemble of N two-level atoms. By exploring the possibilities offered by ensembles of various dimensions and a range of atom-light and photon-hopping values, we investigate the generation of multisite entanglement, as well as the performance of excitation transfer across the array, resulting from the competition between on-site nonlinearities of the matter-light interaction and intersite photon hopping. In particular, for a three-cavity interacting system it is observed that the initial excitation in the first cavity completely transfers to the ensemble in the third cavity through the hopping of photons between the adjacent cavities. Probabilities of the transfer of excitation of the cavity modes and ensembles exhibit characteristics of fast and slow oscillations governed by coupling and hopping parameters, respectively. In the large-hopping case, by seeding an initial excitation in the cavity at the center of the array, a tripartite W state, as well as a bipartite maximally entangled state, is obtained, depending on the interaction time. Population of the ensemble in a cavity has a positive impact on the rate of excitation transfer between the ensembles and their local cavity modes. In particular, for ensembles of five to seven atoms, tripartite W states can be produced even when the hopping rate is comparable to the cavity-atom coupling rate. A similar behavior of the transfer of excitation is observed for a four-coupled-cavity system with two initial excitations.

Improvement of cavity performance in the Saclay/Cornell/DESY's SC cavities

International Nuclear Information System (INIS)

Kako, E.; Noguchi, S.; Ono, M.

2000-01-01

Development of 1.3 GHz Nb superconducting cavities for TESLA (TeV Energy Superconducting Linear Collider) has been carried out with international collaboration. Three Saclay single-cell cavities, one Cornell two-cell cavity and one DESY nine-cell cavity were sent to KEK in order to compare the cavity performance. These cavities were tested at KEK after the following surface treatment: 1) high pressure rinsing, HPR, 2) chemical polishing and HPR, 3) electropolishing and HPR. The test results, especially, improvement of the cavity performance due to electropolishing are reported in this paper. (author)

Site and stand analysis for growth prediction of Eucalyptus grandis ...

African Journals Online (AJOL)

The integration of site information with that of tree growth is of special importance in Zululand, where sustainable supply of timber is essential for local processing and export commitments. Site prediction growth models need to be based on easily attainable input variables that are suitable for operational implementation by ...

All-Optical Switching in Photonic Crystal Cavities

DEFF Research Database (Denmark)

Heuck, Mikkel

All-Optical switching in photonic crystal waveguide-cavity structures is studied predominantly theoretically and numerically, but also from an experimental point of view. We have calculated the first order perturbations to the resonance frequency and decay rate of cavity modes, using a mathematical...... exhibiting Fano resonances. These devices were predicted to be superior to structures with the more well-known Lorentzian line shape in terms of energy consumption and switching contrast. Finally, the mathematical framework of optimal control theory was employed as a general setting, in which the optical...... faster than the photon lifetime by utilizing interference effects....

Site-specific data confirm arsenic exposure predicted by the U.S. Environmental Protection Agency.

Science.gov (United States)

Walker, S; Griffin, S

1998-03-01

The EPA uses an exposure assessment model to estimate daily intake to chemicals of potential concern. At the Anaconda Superfund site in Montana, the EPA exposure assessment model was used to predict total and speciated urinary arsenic concentrations. Predicted concentrations were then compared to concentrations measured in children living near the site. When site-specific information on concentrations of arsenic in soil, interior dust, and diet, site-specific ingestion rates, and arsenic absorption rates were used, measured and predicted urinary arsenic concentrations were in reasonable agreement. The central tendency exposure assessment model successfully described the measured urinary arsenic concentration for the majority of children at the site. The reasonable maximum exposure assessment model successfully identified the uppermost exposed population. While the agreement between measured and predicted urinary arsenic is good, it is not exact. The variables that were identified which influenced agreement included soil and dust sample collection methodology, daily urinary volume, soil ingestion rate, and the ability to define the exposure unit. The concentration of arsenic in food affected agreement between measured and predicted total urinary arsenic, but was not considered when comparing measured and predicted speciated urinary arsenic. Speciated urinary arsenic is the recommended biomarker for recent inorganic arsenic exposure. By using site-specific data in the exposure assessment model, predicted risks from exposure to arsenic were less than predicted risks would have been if the EPA's default values had been used in the exposure assessment model. This difference resulted in reduced magnitude and cost of remediation while still protecting human health.

Protein-protein interaction site predictions with minimum covariance determinant and Mahalanobis distance.

Science.gov (United States)

Qiu, Zhijun; Zhou, Bo; Yuan, Jiangfeng

2017-11-21

Protein-protein interaction site (PPIS) prediction must deal with the diversity of interaction sites that limits their prediction accuracy. Use of proteins with unknown or unidentified interactions can also lead to missing interfaces. Such data errors are often brought into the training dataset. In response to these two problems, we used the minimum covariance determinant (MCD) method to refine the training data to build a predictor with better performance, utilizing its ability of removing outliers. In order to predict test data in practice, a method based on Mahalanobis distance was devised to select proper test data as input for the predictor. With leave-one-validation and independent test, after the Mahalanobis distance screening, our method achieved higher performance according to Matthews correlation coefficient (MCC), although only a part of test data could be predicted. These results indicate that data refinement is an efficient approach to improve protein-protein interaction site prediction. By further optimizing our method, it is hopeful to develop predictors of better performance and wide range of application. Copyright © 2017 Elsevier Ltd. All rights reserved.

Size versus polarizability in protein-ligand interactions: binding of noble gases within engineered cavities in phage T4 lysozyme.

Science.gov (United States)

Quillin, M L; Breyer, W A; Griswold, I J; Matthews, B W

2000-09-29

To investigate the relative importance of size and polarizability in ligand binding within proteins, we have determined the crystal structures of pseudo wild-type and cavity-containing mutant phage T4 lysozymes in the presence of argon, krypton, and xenon. These proteins provide a representative sample of predominantly apolar cavities of varying size and shape. Even though the volumes of these cavities range up to the equivalent of five xenon atoms, the noble gases bind preferentially at highly localized sites that appear to be defined by constrictions in the walls of the cavities, coupled with the relatively large radii of the noble gases. The cavities within pseudo wild-type and L121A lysozymes each bind only a single atom of noble gas, while the cavities within mutants L133A and F153A have two independent binding sites, and the L99A cavity has three interacting sites. The binding of noble gases within two double mutants was studied to characterize the additivity of binding at such sites. In general, when a cavity in a protein is created by a "large-to-small" substitution, the surrounding residues relax somewhat to reduce the volume of the cavity. The binding of xenon and, to a lesser degree, krypton and argon, tend to expand the volume of the cavity and to return it closer to what it would have been had no relaxation occurred. In nearly all cases, the extent of binding of the noble gases follows the trend xenon>krypton>argon. Pressure titrations of the L99A mutant have confirmed that the crystallographic occupancies accurately reflect fractional saturation of the binding sites. The trend in noble gas affinity can be understood in terms of the effects of size and polarizability on the intermolecular potential. The plasticity of the protein matrix permits repulsion due to increased ligand size to be more than compensated for by attraction due to increased ligand polarizability. These results have implications for the mechanism of general anesthesia, the migration

DeepSite: protein-binding site predictor using 3D-convolutional neural networks.

Science.gov (United States)

Jiménez, J; Doerr, S; Martínez-Rosell, G; Rose, A S; De Fabritiis, G

2017-10-01

An important step in structure-based drug design consists in the prediction of druggable binding sites. Several algorithms for detecting binding cavities, those likely to bind to a small drug compound, have been developed over the years by clever exploitation of geometric, chemical and evolutionary features of the protein. Here we present a novel knowledge-based approach that uses state-of-the-art convolutional neural networks, where the algorithm is learned by examples. In total, 7622 proteins from the scPDB database of binding sites have been evaluated using both a distance and a volumetric overlap approach. Our machine-learning based method demonstrates superior performance to two other competitive algorithmic strategies. DeepSite is freely available at www.playmolecule.org. Users can submit either a PDB ID or PDB file for pocket detection to our NVIDIA GPU-equipped servers through a WebGL graphical interface. gianni.defabritiis@upf.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Cavity mode control in side-coupled periodic waveguides: theory and experiment

DEFF Research Database (Denmark)

Ha, Sangwoo; Sukhorukov, A.; Lavrinenko, Andrei

2010-01-01

We demonstrate that the modes of coupled cavities created in periodic waveguides can depend critically on the longitudinal shift between the cavities. In the absence of such shift, the modes feature symmetric or antisymmetric profiles, and their frequency splitting generally increases...... as the cavities are brought closer. We show that the longitudinal shift enables flexible control over the fundamental modes, whose frequency detuning can be reduced down to zero. Our coupled-mode theory analysis reveals an intrinsic link between the mode tuning and the transformation of slow-light dispersion...... at the photonic band-edge.We illustrate our approach through numerical modeling of cavities created in arrays of dielectric rods, and confirm our predictions with experimental observations....

Clinical and mycological analysis of dog's oral cavity

Directory of Open Access Journals (Sweden)

Rosema Santin

2013-01-01

Full Text Available The oral microbiota of humans and animals is made up of a wide variety of yeasts and bacteria, but microbiota of dogs is not totally described. Although such identification is an important step to establish the etiopathogenesis and adequate therapy for the periodontal disease The aim of this study was to evaluate and correlate oral alterations with the presence of yeasts in oral cavity of female dogs. After clinical evaluation samples from healthy and from dogs with oral diseases were obtained from three different oral sites by swabs, curettes, millimeter periodontal probes and HA membrane tip in cellulose ester. Yeast identification was performed through macroscopic and microscopic colony features and biochemical tests. Dental calculus was the most prevalent occurrence in the oral cavity of 59 females. However, the isolation of yeasts was significantly higher (p < 0.05 in animals suffering from halitosis. Eleven yeast species were identified, namely: Malassezia pachydermatis, Rhodotorula spp., Candida albicans, C. catenulata, C. famata, C. guilliermondii, C. parapsilosis, C. intermedia, Trichosporon asahii, T. mucoides and Cryptococcus albidus. It could be concluded that the yeasts are part of the microbiota from the different sites of the oral cavity of the female canines studied without causing any significant alterations except halitosis.

Diagnostics and treatment of 1.3 GHz Nb cavities

Energy Technology Data Exchange (ETDEWEB)

Tamashevich, Yegor

2017-01-15

increase the accuracy of the measurements. A new program code for quench localisation calculating the path of the second-sound wave was developed. This allows the signals from all sensors to be used, regardless of their position relative to the quench site. The new approach was validated using additional techniques such as a temperature mapping and an optical inspection of the inner cavity surface. Furthermore, a new multi-sensor for second-sound wave detection in the helium vessel of a cavity was developed and successfully tested on a serial-production XFEL cavity. The determined quench site location was confirmed by subsequent optical inspection. The algorithm localises the quench without mode measurements i.e. there is no need to dismount HOM-antennas which requires special procedures and must be performed in a clean-room. The mathematical approach described in this paper can be applied for second-sound tests of superconductive cavities of various shapes and dimensions.

Diagnostics and treatment of 1.3 GHz Nb cavities

International Nuclear Information System (INIS)

Tamashevich, Yegor

2017-01-01

for quench localisation calculating the path of the second-sound wave was developed. This allows the signals from all sensors to be used, regardless of their position relative to the quench site. The new approach was validated using additional techniques such as a temperature mapping and an optical inspection of the inner cavity surface. Furthermore, a new multi-sensor for second-sound wave detection in the helium vessel of a cavity was developed and successfully tested on a serial-production XFEL cavity. The determined quench site location was confirmed by subsequent optical inspection. The algorithm localises the quench without mode measurements i.e. there is no need to dismount HOM-antennas which requires special procedures and must be performed in a clean-room. The mathematical approach described in this paper can be applied for second-sound tests of superconductive cavities of various shapes and dimensions.

Predictability of bone density at posterior mandibular implant sites using cone-beam computed tomography intensity values.

Science.gov (United States)

Alkhader, Mustafa; Hudieb, Malik; Khader, Yousef

2017-01-01

The aim of this study was to investigate the predictability of bone density at posterior mandibular implant sites using cone-beam computed tomography (CBCT) intensity values. CBCT cross-sectional images for 436 posterior mandibular implant sites were selected for the study. Using Invivo software (Anatomage, San Jose, California, USA), two observers classified the bone density into three categories: low, intermediate, and high, and CBCT intensity values were generated. Based on the consensus of the two observers, 15.6% of sites were of low bone density, 47.9% were of intermediate density, and 36.5% were of high density. Receiver-operating characteristic analysis showed that CBCT intensity values had a high predictive power for predicting high density sites (area under the curve [AUC] =0.94, P < 0.005) and intermediate density sites (AUC = 0.81, P < 0.005). The best cut-off value for intensity to predict intermediate density sites was 218 (sensitivity = 0.77 and specificity = 0.76) and the best cut-off value for intensity to predict high density sites was 403 (sensitivity = 0.93 and specificity = 0.77). CBCT intensity values are considered useful for predicting bone density at posterior mandibular implant sites.

Heralded entangling quantum gate via cavity-assisted photon scattering

Science.gov (United States)

Borges, Halyne S.; Rossatto, Daniel Z.; Luiz, Fabrício S.; Villas-Boas, Celso J.

2018-01-01

We theoretically investigate the generation of heralded entanglement between two identical atoms via cavity-assisted photon scattering in two different configurations, namely, either both atoms confined in the same cavity or trapped into locally separated ones. Our protocols are given by a very simple and elegant single-step process, the key mechanism of which is a controlled-phase-flip gate implemented by impinging a single photon on single-sided cavities. In particular, when the atoms are localized in remote cavities, we introduce a single-step parallel quantum circuit instead of the serial process extensively adopted in the literature. We also show that such parallel circuit can be straightforwardly applied to entangle two macroscopic clouds of atoms. Both protocols proposed here predict a high entanglement degree with a success probability close to unity for state-of-the-art parameters. Among other applications, our proposal and its extension to multiple atom-cavity systems step toward a suitable route for quantum networking, in particular for quantum state transfer, quantum teleportation, and nonlocal quantum memory.

A review of influenza detection and prediction through social networking sites.

Science.gov (United States)

Alessa, Ali; Faezipour, Miad

2018-02-01

Early prediction of seasonal epidemics such as influenza may reduce their impact in daily lives. Nowadays, the web can be used for surveillance of diseases. Search engines and social networking sites can be used to track trends of different diseases seven to ten days faster than government agencies such as Center of Disease Control and Prevention (CDC). CDC uses the Illness-Like Influenza Surveillance Network (ILINet), which is a program used to monitor Influenza-Like Illness (ILI) sent by thousands of health care providers in order to detect influenza outbreaks. It is a reliable tool, however, it is slow and expensive. For that reason, many studies aim to develop methods that do real time analysis to track ILI using social networking sites. Social media data such as Twitter can be used to predict the spread of flu in the population and can help in getting early warnings. Today, social networking sites (SNS) are used widely by many people to share thoughts and even health status. Therefore, SNS provides an efficient resource for disease surveillance and a good way to communicate to prevent disease outbreaks. The goal of this study is to review existing alternative solutions that track flu outbreak in real time using social networking sites and web blogs. Many studies have shown that social networking sites can be used to conduct real time analysis for better predictions.

Site-specific data confirm arsenic exposure predicted by the U.S. Environmental Protection Agency.

OpenAIRE

Walker, S; Griffin, S

1998-01-01

The EPA uses an exposure assessment model to estimate daily intake to chemicals of potential concern. At the Anaconda Superfund site in Montana, the EPA exposure assessment model was used to predict total and speciated urinary arsenic concentrations. Predicted concentrations were then compared to concentrations measured in children living near the site. When site-specific information on concentrations of arsenic in soil, interior dust, and diet, site-specific ingestion rates, and arsenic abso...

Physics and chemistry of niobium materials in the context of superconducting RF cavity applications

International Nuclear Information System (INIS)

Roy, S.B.

2016-01-01

Superconducting radio frequency (SCRF) cavities excel over the normal conducting RF cavities in the long pulse or continuous wave high energy particle accelerations, and niobium (Nb) is currently the material of choice for fabrication of such SCRF cavities. However the accelerating gradients attained in the Nb SCRF cavities deployed in various high energy particle accelerators are significantly below the theoretical limit predicted by the superconducting properties of Nb. Thus it is very important to understand the physics and chemistry of Nb materials in some details so as to maximize the SCRF cavity performance. This abstract will discuss some issues which help in the development of high gradient and energy efficient Nb SCRF cavities in a cost effective manner. (author)

Prediction of protein-protein interaction sites in sequences and 3D structures by random forests.

Directory of Open Access Journals (Sweden)

Mile Sikić

2009-01-01

Full Text Available Identifying interaction sites in proteins provides important clues to the function of a protein and is becoming increasingly relevant in topics such as systems biology and drug discovery. Although there are numerous papers on the prediction of interaction sites using information derived from structure, there are only a few case reports on the prediction of interaction residues based solely on protein sequence. Here, a sliding window approach is combined with the Random Forests method to predict protein interaction sites using (i a combination of sequence- and structure-derived parameters and (ii sequence information alone. For sequence-based prediction we achieved a precision of 84% with a 26% recall and an F-measure of 40%. When combined with structural information, the prediction performance increases to a precision of 76% and a recall of 38% with an F-measure of 51%. We also present an attempt to rationalize the sliding window size and demonstrate that a nine-residue window is the most suitable for predictor construction. Finally, we demonstrate the applicability of our prediction methods by modeling the Ras-Raf complex using predicted interaction sites as target binding interfaces. Our results suggest that it is possible to predict protein interaction sites with quite a high accuracy using only sequence information.

Plasma Evolution within an Erupting Coronal Cavity

Science.gov (United States)

Long, David M.; Harra, Louise K.; Matthews, Sarah A.; Warren, Harry P.; Lee, Kyoung-Sun; Doschek, George A.; Hara, Hirohisa; Jenkins, Jack M.

2018-03-01

Coronal cavities have previously been observed to be associated with long-lived quiescent filaments and are thought to correspond to the associated magnetic flux rope. Although the standard flare model predicts a coronal cavity corresponding to the erupting flux rope, these have only been observed using broadband imaging data, restricting an analysis to the plane-of-sky. We present a unique set of spectroscopic observations of an active region filament seen erupting at the solar limb in the extreme ultraviolet. The cavity erupted and expanded rapidly, with the change in rise phase contemporaneous with an increase in nonthermal electron energy flux of the associated flare. Hot and cool filamentary material was observed to rise with the erupting flux rope, disappearing suddenly as the cavity appeared. Although strongly blueshifted plasma continued to be observed flowing from the apex of the erupting flux rope, this outflow soon ceased. These results indicate that the sudden injection of energy from the flare beneath forced the rapid eruption and expansion of the flux rope, driving strong plasma flows, which resulted in the eruption of an under-dense filamentary flux rope.

A web server for analysis, comparison and prediction of protein ligand binding sites.

Science.gov (United States)

Singh, Harinder; Srivastava, Hemant Kumar; Raghava, Gajendra P S

2016-03-25

One of the major challenges in the field of system biology is to understand the interaction between a wide range of proteins and ligands. In the past, methods have been developed for predicting binding sites in a protein for a limited number of ligands. In order to address this problem, we developed a web server named 'LPIcom' to facilitate users in understanding protein-ligand interaction. Analysis, comparison and prediction modules are available in the "LPIcom' server to predict protein-ligand interacting residues for 824 ligands. Each ligand must have at least 30 protein binding sites in PDB. Analysis module of the server can identify residues preferred in interaction and binding motif for a given ligand; for example residues glycine, lysine and arginine are preferred in ATP binding sites. Comparison module of the server allows comparing protein-binding sites of multiple ligands to understand the similarity between ligands based on their binding site. This module indicates that ATP, ADP and GTP ligands are in the same cluster and thus their binding sites or interacting residues exhibit a high level of similarity. Propensity-based prediction module has been developed for predicting ligand-interacting residues in a protein for more than 800 ligands. In addition, a number of web-based tools have been integrated to facilitate users in creating web logo and two-sample between ligand interacting and non-interacting residues. In summary, this manuscript presents a web-server for analysis of ligand interacting residue. This server is available for public use from URL http://crdd.osdd.net/raghava/lpicom .

Resource quantity and quality determine the inter-specific associations between ecosystem engineers and resource users in a cavity-nest web.

Science.gov (United States)

Robles, Hugo; Martin, Kathy

2013-01-01

While ecosystem engineering is a widespread structural force of ecological communities, the mechanisms underlying the inter-specific associations between ecosystem engineers and resource users are poorly understood. A proper knowledge of these mechanisms is, however, essential to understand how communities are structured. Previous studies suggest that increasing the quantity of resources provided by ecosystem engineers enhances populations of resource users. In a long-term study (1995-2011), we show that the quality of the resources (i.e. tree cavities) provided by ecosystem engineers is also a key feature that explains the inter-specific associations in a tree cavity-nest web. Red-naped sapsuckers (Sphyrapicusnuchalis) provided the most abundant cavities (52% of cavities, 0.49 cavities/ha). These cavities were less likely to be used than other cavity types by mountain bluebirds (Sialiacurrucoides), but provided numerous nest-sites (41% of nesting cavities) to tree swallows (Tachycinetabicolour). Swallows experienced low reproductive outputs in northern flicker (Colaptesauratus) cavities compared to those in sapsucker cavities (1.1 vs. 2.1 fledglings/nest), but the highly abundant flickers (33% of cavities, 0.25 cavities/ha) provided numerous suitable nest-sites for bluebirds (58%). The relative shortage of cavities supplied by hairy woodpeckers (Picoidesvillosus) and fungal/insect decay (high quality nest-sites for both bluebirds and swallows. Because both the quantity and quality of resources supplied by different ecosystem engineers may explain the amount of resources used by each resource user, conservation strategies may require different management actions to be implemented for the key ecosystem engineer of each resource user. We, therefore, urge the incorporation of both resource quantity and quality into models that assess community dynamics to improve conservation actions and our understanding of ecological communities based on ecosystem engineering.

A statistical model for field emission in superconducting cavities

International Nuclear Information System (INIS)

Padamsee, H.; Green, K.; Jost, W.; Wright, B.

1993-01-01

A statistical model is used to account for several features of performance of an ensemble of superconducting cavities. The input parameters are: the number of emitters/area, a distribution function for emitter β values, a distribution function for emissive areas, and a processing threshold. The power deposited by emitters is calculated from the field emission current and electron impact energy. The model can successfully account for the fraction of tests that reach the maximum field Epk in an ensemble of cavities, for eg, 1-cells at sign 3 GHz or 5-cells at sign 1.5 GHz. The model is used to predict the level of power needed to successfully process cavities of various surface areas with high pulsed power processing (HPP)

First-principles calculations of niobium hydride formation in superconducting radio-frequency cavities

Science.gov (United States)

Ford, Denise C.; Cooley, Lance D.; Seidman, David N.

2013-09-01

Niobium hydride is suspected to be a major contributor to degradation of the quality factor of niobium superconducting radio-frequency (SRF) cavities. In this study, we connect the fundamental properties of hydrogen in niobium to SRF cavity performance and processing. We modeled several of the niobium hydride phases relevant to SRF cavities and present their thermodynamic, electronic, and geometric properties determined from calculations based on density functional theory. We find that the absorption of hydrogen from the gas phase into niobium is exothermic and hydrogen becomes somewhat anionic. The absorption of hydrogen by niobium lattice vacancies is strongly preferred over absorption into interstitial sites. A single vacancy can accommodate six hydrogen atoms in the symmetrically equivalent lowest energy sites and additional hydrogen in the nearby interstitial sites affected by the strain field: this indicates that a vacancy can serve as a nucleation center for hydride phase formation. Small hydride precipitates may then occur near lattice vacancies upon cooling. Vacancy clusters and extended defects should also be enriched in hydrogen, potentially resulting in extended hydride phase regions upon cooling. We also assess the phase changes in the niobium-hydrogen system based on charge transfer between niobium and hydrogen, the strain field associated with interstitial hydrogen, and the geometry of the hydride phases. The results of this study stress the importance of not only the hydrogen content in niobium, but also the recovery state of niobium for the performance of SRF cavities.

First-principles calculations of niobium hydride formation in superconducting radio-frequency cavities

International Nuclear Information System (INIS)

Ford, Denise C; Cooley, Lance D; Seidman, David N

2013-01-01

Niobium hydride is suspected to be a major contributor to degradation of the quality factor of niobium superconducting radio-frequency (SRF) cavities. In this study, we connect the fundamental properties of hydrogen in niobium to SRF cavity performance and processing. We modeled several of the niobium hydride phases relevant to SRF cavities and present their thermodynamic, electronic, and geometric properties determined from calculations based on density functional theory. We find that the absorption of hydrogen from the gas phase into niobium is exothermic and hydrogen becomes somewhat anionic. The absorption of hydrogen by niobium lattice vacancies is strongly preferred over absorption into interstitial sites. A single vacancy can accommodate six hydrogen atoms in the symmetrically equivalent lowest energy sites and additional hydrogen in the nearby interstitial sites affected by the strain field: this indicates that a vacancy can serve as a nucleation center for hydride phase formation. Small hydride precipitates may then occur near lattice vacancies upon cooling. Vacancy clusters and extended defects should also be enriched in hydrogen, potentially resulting in extended hydride phase regions upon cooling. We also assess the phase changes in the niobium–hydrogen system based on charge transfer between niobium and hydrogen, the strain field associated with interstitial hydrogen, and the geometry of the hydride phases. The results of this study stress the importance of not only the hydrogen content in niobium, but also the recovery state of niobium for the performance of SRF cavities. (paper)

Assessment of Mars Exploration Rover Landing Site Predictions

Science.gov (United States)

Golombek, M. P.

2005-05-01

Comprehensive analyses of remote sensing data during the 3-year effort to select the Mars Exploration Rover landing sites at Gusev crater and Meridiani Planum correctly predicted the safe and trafficable surfaces explored by the two rovers. Gusev crater was predicted to be a relatively low relief surface that was comparably dusty, but less rocky than the Viking landing sites. Available data for Meridiani Planum indicated a very flat plain composed of basaltic sand to granules and hematite that would look completely unlike any of the existing landing sites with a dark, low albedo surface, little dust and very few rocks. Orbital thermal inertia measurements of 315 J m-2 s-0.5 K-1 at Gusev suggested surfaces dominated by duricrust to cemented soil-like materials or cohesionless sand or granules, which is consistent with observed soil characteristics and measured thermal inertias from the surface. THEMIS thermal inertias along the traverse at Gusev vary from 285 at the landing site to 330 around Bonneville rim and show systematic variations that can be related to the observed increase in rock abundance (5-30%). Meridiani has an orbital bulk inertia of ~200, similar to measured surface inertias that correspond to observed surfaces dominated by 0.2 mm sand size particles. Rock abundance derived from orbital thermal differencing techniques suggested that Meridiani Planum would have very low rock abundance, consistent with the rock free plain traversed by Opportunity. Spirit landed in an 8% orbital rock abundance pixel, consistent with the measured 7% of the surface covered by rocks >0.04 m diameter at the landing site, which is representative of the plains away from craters. The orbital albedo of the Spirit traverse varies from 0.19 to 0.30, consistent with surface measurements in and out of dust devil tracks. Opportunity is the first landing in a low albedo portion of Mars as seen from orbit, which is consistent with the dark, dust-free surface and measured albedos. The

Orion EFT-1 Cavity Heating Tile Experiments and Environment Reconstruction

Science.gov (United States)

Salazar, Giovanni; Amar, Adam; Oliver, Brandon; Hyatt, Andrew; Rezin, Marc

2016-01-01

Developing aerothermodynamic environments for deep cavities, such as those produced by micrometeoroids and orbital debris impacts, poses a great challenge for engineers. In order to assess existing cavity heating models, two one-inch diameter cavities were flown on the Orion Multi-Purpose Crew Vehicle during Exploration Flight Test 1 (EFT1). These cavities were manufactured with depths of 1.0 in and 1.4 in, and they were both instrumented. Instrumentation included surface thermocouples upstream, downstream and within the cavities, and additional thermocouples at the TPS-structure interface. This paper will present the data obtained, and comparisons with computational predictions will be shown. Additionally, the development of a 3D material thermal model will be described, which will be used to account for the three-dimensionality of the problem when interpreting the data. Furthermore, using a multi-dimensional inverse heat conduction approach, a reconstruction of a time- and space-dependent flight heating distribution during EFT1 will be presented. Additional discussions will focus on instrumentation challenges and calibration techniques specific to these experiments. The analysis shown will highlight the accuracies and/or deficiencies of current computational techniques to model cavity flows during hypersonic re-entry.

A Many-Atom Cavity QED System with Homogeneous Atom-Cavity Coupling

OpenAIRE

Lee, Jongmin; Vrijsen, Geert; Teper, Igor; Hosten, Onur; Kasevich, Mark A.

2013-01-01

We demonstrate a many-atom-cavity system with a high-finesse dual-wavelength standing wave cavity in which all participating rubidium atoms are nearly identically coupled to a 780-nm cavity mode. This homogeneous coupling is enforced by a one-dimensional optical lattice formed by the field of a 1560-nm cavity mode.

The effects of cavity length on nest size, sex ratio and mortality of Centris (Heterocentris) analis (Hymenoptera, Apidae, Centridini)

OpenAIRE

Alonso , Juliana; Silva , Janaina; Garófalo , Carlos

2012-01-01

International audience; This study investigated the effects of different cavity lengths in trap-nests on the number of cells constructed per nest, sex ratio and mortality of offspring of Centris analis at three sites in Ribeirão Preto, São Paulo, Brazil. Cavity length did not affect the occupation rates of the trap-nests, with the exception of a preference for the shortest trap-nests found at one site. The number of cells per nest increased with trap-nest length. Cavity length affected neithe...

Segmented trapped vortex cavity

Science.gov (United States)

Grammel, Jr., Leonard Paul (Inventor); Pennekamp, David Lance (Inventor); Winslow, Jr., Ralph Henry (Inventor)

2010-01-01

An annular trapped vortex cavity assembly segment comprising includes a cavity forward wall, a cavity aft wall, and a cavity radially outer wall there between defining a cavity segment therein. A cavity opening extends between the forward and aft walls at a radially inner end of the assembly segment. Radially spaced apart pluralities of air injection first and second holes extend through the forward and aft walls respectively. The segment may include first and second expansion joint features at distal first and second ends respectively of the segment. The segment may include a forward subcomponent including the cavity forward wall attached to an aft subcomponent including the cavity aft wall. The forward and aft subcomponents include forward and aft portions of the cavity radially outer wall respectively. A ring of the segments may be circumferentially disposed about an axis to form an annular segmented vortex cavity assembly.

Comparative population structure of cavity-nesting sea ducks

Science.gov (United States)

Pearce, John M.; Eadie, John M.; Savard, Jean-Pierre L.; Christensen, Thomas K.; Berdeen, James; Taylor, Eric J.; Boyd, Sean; Einarsson, Árni

2014-01-01

A growing collection of mtDNA genetic information from waterfowl species across North America suggests that larger-bodied cavity-nesting species exhibit greater levels of population differentiation than smaller-bodied congeners. Although little is known about nest-cavity availability for these species, one hypothesis to explain differences in population structure is reduced dispersal tendency of larger-bodied cavity-nesting species due to limited abundance of large cavities. To investigate this hypothesis, we examined population structure of three cavity-nesting waterfowl species distributed across much of North America: Barrow's Goldeneye (Bucephala islandica), Common Goldeneye (B. clangula), and Bufflehead (B. albeola). We compared patterns of population structure using both variation in mtDNA control-region sequences and band-recovery data for the same species and geographic regions. Results were highly congruent between data types, showing structured population patterns for Barrow's and Common Goldeneye but not for Bufflehead. Consistent with our prediction, the smallest cavity-nesting species, the Bufflehead, exhibited the lowest level of population differentiation due to increased dispersal and gene flow. Results provide evidence for discrete Old and New World populations of Common Goldeneye and for differentiation of regional groups of both goldeneye species in Alaska, the Pacific Northwest, and the eastern coast of North America. Results presented here will aid management objectives that require an understanding of population delineation and migratory connectivity between breeding and wintering areas. Comparative studies such as this one highlight factors that may drive patterns of genetic diversity and population trends.

Intra-oral cone radiation therapy for selected carcinomas of the oral cavity

International Nuclear Information System (INIS)

Wang, C.C.; Doppke, K.P.; Biggs, P.J.

1983-01-01

A study of 101 patients with early carcinomas of the oral cavity, T1 and T2, treated by external cobalt 60 beam and/or intra-oral cone (IOC) radiation therapy between 1964 through 1980 was made. The two year disease-free survival rate, including surgical salvage, was 88% and the local control rate was 85%. The incidence of radiation complications, i.e., soft tissue ulceration and/or osteoradionecrosis, was 14% and varied with various tumor sites and radiation doses delivered. The present review shows that local control and radiation complications are closely related to radiation doses and varies with different tumor sites of the oral cavity. Radiation therapy dosages expressed in terms of TDF values for these lesions are herein recommended. With proper selections of lesions arising from the oral cavity, combined external beam and IOC radiation therapy has been found extremely efficacious in achieving good local tumor control and high survival rates with excellent cosmetic and functional results and minimum radiation sequalae

Combining specificity determining and conserved residues improves functional site prediction

Directory of Open Access Journals (Sweden)

Gelfand Mikhail S

2009-06-01

Full Text Available Abstract Background Predicting the location of functionally important sites from protein sequence and/or structure is a long-standing problem in computational biology. Most current approaches make use of sequence conservation, assuming that amino acid residues conserved within a protein family are most likely to be functionally important. Most often these approaches do not consider many residues that act to define specific sub-functions within a family, or they make no distinction between residues important for function and those more relevant for maintaining structure (e.g. in the hydrophobic core. Many protein families bind and/or act on a variety of ligands, meaning that conserved residues often only bind a common ligand sub-structure or perform general catalytic activities. Results Here we present a novel method for functional site prediction based on identification of conserved positions, as well as those responsible for determining ligand specificity. We define Specificity-Determining Positions (SDPs, as those occupied by conserved residues within sub-groups of proteins in a family having a common specificity, but differ between groups, and are thus likely to account for specific recognition events. We benchmark the approach on enzyme families of known 3D structure with bound substrates, and find that in nearly all families residues predicted by SDPsite are in contact with the bound substrate, and that the addition of SDPs significantly improves functional site prediction accuracy. We apply SDPsite to various families of proteins containing known three-dimensional structures, but lacking clear functional annotations, and discusse several illustrative examples. Conclusion The results suggest a better means to predict functional details for the thousands of protein structures determined prior to a clear understanding of molecular function.

Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity.

Science.gov (United States)

Paramo, Teresa; East, Alexandra; Garzón, Diana; Ulmschneider, Martin B; Bond, Peter J

2014-05-13

Protein cavities and tunnels are critical in determining phenomena such as ligand binding, molecular transport, and enzyme catalysis. Molecular dynamics (MD) simulations enable the exploration of the flexibility and conformational plasticity of protein cavities, extending the information available from static experimental structures relevant to, for example, drug design. Here, we present a new tool (trj_cavity) implemented within the GROMACS ( www.gromacs.org ) framework for the rapid identification and characterization of cavities detected within MD trajectories. trj_cavity is optimized for usability and computational efficiency and is applicable to the time-dependent analysis of any cavity topology, and optional specialized descriptors can be used to characterize, for example, protein channels. Its novel grid-based algorithm performs an efficient neighbor search whose calculation time is linear with system size, and a comparison of performance with other widely used cavity analysis programs reveals an orders-of-magnitude improvement in the computational cost. To demonstrate its potential for revealing novel mechanistic insights, trj_cavity has been used to analyze long-time scale simulation trajectories for three diverse protein cavity systems. This has helped to reveal, respectively, the lipid binding mechanism in the deep hydrophobic cavity of a soluble mite-allergen protein, Der p 2; a means for shuttling carbohydrates between the surface-exposed substrate-binding and catalytic pockets of a multidomain, membrane-proximal pullulanase, PulA; and the structural basis for selectivity in the transmembrane pore of a voltage-gated sodium channel (NavMs), embedded within a lipid bilayer environment. trj_cavity is available for download under an open-source license ( http://sourceforge.net/projects/trjcavity ). A simplified, GROMACS-independent version may also be compiled.

Predicting sumoylation sites using support vector machines based on various sequence features, conformational flexibility and disorder.

Science.gov (United States)

Yavuz, Ahmet Sinan; Sezerman, Osman Ugur

2014-01-01

Sumoylation, which is a reversible and dynamic post-translational modification, is one of the vital processes in a cell. Before a protein matures to perform its function, sumoylation may alter its localization, interactions, and possibly structural conformation. Abberations in protein sumoylation has been linked with a variety of disorders and developmental anomalies. Experimental approaches to identification of sumoylation sites may not be effective due to the dynamic nature of sumoylation, laborsome experiments and their cost. Therefore, computational approaches may guide experimental identification of sumoylation sites and provide insights for further understanding sumoylation mechanism. In this paper, the effectiveness of using various sequence properties in predicting sumoylation sites was investigated with statistical analyses and machine learning approach employing support vector machines. These sequence properties were derived from windows of size 7 including position-specific amino acid composition, hydrophobicity, estimated sub-window volumes, predicted disorder, and conformational flexibility. 5-fold cross-validation results on experimentally identified sumoylation sites revealed that our method successfully predicts sumoylation sites with a Matthew's correlation coefficient, sensitivity, specificity, and accuracy equal to 0.66, 73%, 98%, and 97%, respectively. Additionally, we have showed that our method compares favorably to the existing prediction methods and basic regular expressions scanner. By using support vector machines, a new, robust method for sumoylation site prediction was introduced. Besides, the possible effects of predicted conformational flexibility and disorder on sumoylation site recognition were explored computationally for the first time to our knowledge as an additional parameter that could aid in sumoylation site prediction.

Preoperative CT evaluation on nasal cavity for transsphenoidal approach

International Nuclear Information System (INIS)

Saeki, Naokatsu; Yamaura, Akira; Hoshi, Seiichiro; Sunada, Souichi; Sunami, Kenro

1997-01-01

Preoperative bone CT scans sliced parallel to the surgical plane were evaluated in 32 cases of transsphenoidal surgery. This method predicted patients with narrow nasal cavity, and helped to determine the rhinological maneuvers for providing a wider operative field. In addition, it helps to plan the need and extent of sella floor removal in re-operated cases. There was relatively little difference in the width and length of the nasal cavity between acromegalic and non-acromegalic patients. Hence, bone CT scans are useful in the preoperative evaluation of patients undergoing transsphenoidal surgery. (author)

Analysis and prediction of gene splice sites in four Aspergillus genomes

DEFF Research Database (Denmark)

Wang, Kai; Ussery, David; Brunak, Søren

2009-01-01

Several Aspergillus fungal genomic sequences have been published, with many more in progress. Obviously, it is essential to have high-quality, consistently annotated sets of proteins from each of the genomes, in order to make meaningful comparisons. We have developed a dedicated, publicly available......, splice site prediction program called NetAspGene, for the genus Aspergillus. Gene sequences from Aspergillus fumigatus, the most common mould pathogen, were used to build and test our model. Compared to many animals and plants, Aspergillus contains smaller introns; thus we have applied a larger window...... better splice site prediction than other available tools. NetAspGene will be very helpful for the study in Aspergillus splice sites and especially in alternative splicing. A webpage for NetAspGene is publicly available at http://www.cbs.dtu.dk/services/NetAspGene....

Cavity Cooling of Nanoparticles: Towards Matter-Wave experiments

Science.gov (United States)

Millen, James; Kuhn, Stefan; Arndt, Markus

2016-05-01

Levitated systems are a fascinating addition to the world of optically-controlled mechanical resonators. It is predicted that nanoparticles can be cooled to their c.o.m. ground state via the interaction with an optical cavity. By freeing the oscillator from clamping forces dissipation and decoherence is greatly reduced, leading to the potential to produce long-lived, macroscopically spread, mechanical quantum states, allowing tests of collapse models and any mass limit of quantum physics. Reaching the low pressures required to cavity-cool to the ground state has proved challenging. Our approach is to cavity cool a beam of nanoparticles in high vacuum. We can cool the c.o.m. motion of nanospheres a few hundred nanometers in size. Looking forward, we will utilize novel microcavities to enhance optomechanical cooling, preparing particles in a coherent beam ideally suited to ultra-high mass interferometry at 107 a.m.u.

Polyadenylation site prediction using PolyA-iEP method.

Science.gov (United States)

Kavakiotis, Ioannis; Tzanis, George; Vlahavas, Ioannis

2014-01-01

This chapter presents a method called PolyA-iEP that has been developed for the prediction of polyadenylation sites. More precisely, PolyA-iEP is a method that recognizes mRNA 3'ends which contain polyadenylation sites. It is a modular system which consists of two main components. The first exploits the advantages of emerging patterns and the second is a distance-based scoring method. The outputs of the two components are finally combined by a classifier. The final results reach very high scores of sensitivity and specificity.

Regular monitoring, analysis and forecast of radioecological environment of Azgir test site

International Nuclear Information System (INIS)

Akhmetov, E.; Agymov, I.; Gilmanov, Zh.; Ermanov, A.; Zhetbaev, A.

1996-01-01

The objective of investigations: basing on the results of regular annual measurements of radiation conditions on the sites of underground nuclear cavities of the Azgir test site, specific concentrations of radionuclides and heavy metals in soil and underground aquifers on the test site and adjacent territories to obtain data on migration and transfer of radionuclides and heavy metals. This will give a real possibility to make probability predictions of ways and qualitative characteristics of spreading of radionuclides and heavy metals in the region of the northern Pricaspian lowland. The Essence of the Problem The Azgir test site is located in the arid zone of the Great Azgir salt cupola near the Azgir village of Kurmangazinskiy rayon, Atyrau region. This cupola is located in the western periphery of Pricaspian salt-bearing province situated to the north of the Caspian sea between the Volga and Emba rivers. Major Tasks: - Development of technical requirements for carrying out regular examination of radionuclide and heavy metal contamination of the Azgir test site. - Preparation of material and technical base for field works on the Azgir test site. - Radiometric measurements on the sites and around them. - Taking of soil, soil and ground waters samples both on the test site and on the adjacent territories. - Spectrometric and radiochemical investigations of soil, soil and ground water samples. - Analysis and generalization of the results creating premises for forecasting of the radioecological conditions. - Investigation of the possibility of radioactive waste disposal in underground cavities. Expected Results: - Detection and outlining of local areas of radioactive contamination on the site and adjacent territories. - Data on real structure of spreading and concentration of artificial and natural radionuclides and heavy metals in soil layer of the test site region. - Results of analytic investigations of water samples of underground sources of the site and adjacent

Acoustic cavity transducers for the manipulation of cells and biomolecules

Science.gov (United States)

Tovar, Armando; Patel, Maulik; Lee, Abraham P.

2010-02-01

A novel fluidic actuator that is simple to fabricate, integrate, and operate is demonstrated for use within microfluidic systems. The actuator is designed around the use of trapped air bubbles in lateral cavities and the resultant acoustic streaming generated from an outside acoustic energy source. The orientation of the lateral cavities to the main microchannel is used to control the bulk fluid motion within the device. The first order flow generated by the oscillating bubble is used to develop a pumping platform that is capable of driving fluid within a chip. This pump is integrated into a recirculation immunoassay device for enhanced biomolecule binding through fluid flow for convection limited transport. The recirculation system showed an increase in binding site concentration when compared with traditional passive and flow-through methods. The acoustic cavity transducer has also been demonstrated for application in particle switching. Bursts of acoustic energy are used to generate a second order streaming pattern near the cavity interface to drive particles away or towards the cavity. The use of this switching mechanism is being extended to the application of sorting cells and other particles within a microfluidic system.

Characterization of nasal cavity-associated lymphoid tissue in ducks.

Science.gov (United States)

Kang, Haihong; Yan, Mengfei; Yu, Qinghua; Yang, Qian

2014-05-01

The nasal mucosa is involved in immune defense, as it is the first barrier for pathogens entering the body through the respiratory tract. The nasal cavity-associated lymphoid tissue (NALT), which is found in the mucosa of the nasal cavity, is considered to be the main mucosal immune inductive site in the upper respiratory tract. NALT has been found in humans and many mammals, which contributes to local and systemic immune responses after intranasal vaccination. However, there are very few data on NALT in avian species, especially waterfowl. For this study, histological sections of the nasal cavities of Cherry Valley ducks were used to examine the anatomical location and histological characteristics of NALT. The results showed that several lymphoid aggregates are present in the ventral wall of the nasal cavity near the choanal cleft, whereas several more lymphoid aggregates were located on both sides of the nasal septum. In addition, randomly distributed intraepithelial lymphocytes and isolated lymphoid follicles were observed in the regio respiratoria of the nasal cavity. There were also a few lymphoid aggregates located in the lamina propria of the regio vestibularis, which was covered with a stratified squamous epithelium. This study focused on the anatomic and histological characteristics of the nasal cavity of the duck and performed a systemic overview of NALT. This will be beneficial for further understanding of immune mechanisms after nasal vaccination and the development of effective nasal vaccines for waterfowls. Copyright © 2014 Wiley Periodicals, Inc.

Spontaneous dressed-state polarization in the strong driving regime of cavity QED.

Science.gov (United States)

Armen, Michael A; Miller, Anthony E; Mabuchi, Hideo

2009-10-23

We utilize high-bandwidth phase-quadrature homodyne measurement of the light transmitted through a Fabry-Perot cavity, driven strongly and on resonance, to detect excess phase noise induced by a single intracavity atom. We analyze the correlation properties and driving-strength dependence of the atom-induced phase noise to establish that it corresponds to the long-predicted phenomenon of spontaneous dressed-state polarization. Our experiment thus provides a demonstration of cavity quantum electrodynamics in the strong-driving regime in which one atom interacts strongly with a many-photon cavity field to produce novel quantum stochastic behavior.

Deactivation of nuclear explosions cavities in the salt domes by freezing method

International Nuclear Information System (INIS)

Belyashov, D.N.; Mokhov, V.A.; Murzadilov, T.D.

1998-01-01

I. There is a lot of negative consequences of underground nuclear explosions, conducted for creating some cavities of the gas condensate saving at the Azgir site and Karachaganak deposit. Some of them are radioactivity escape, ground pollution, underground water pollution, as result of depressurization and irrigation of cavities. Besides that there are dissolution of infected salt, displacement of brine from the cavities. Existing prolonged exchanges of rock-salt, brines and water can be accompanied by accumulation and throw outing of free chlorine and hydrogen with hydrochloric acid formation, ('white fog' of Azgir site). These questions demand supplementary researches. 2. It is known that more dangerous fission fragments are 9 0S r and 1 31C s, with half life periods equaled 27.7 and 30.3. Duration of their existence determines a period of an object danger. Radionuclide migration come with rock dispersion or with their concentration on the different physical, chemical, including sorptive, barriers on the way of radioactive water displacement. 3. The task of prevention of negative consequences is to save the forms and sizes of cavities, to immobilize the radioactive fluid's in the cavities and closed zone for the half-life time of the main nuclide mass. 4. Solving the task by laying of empty space with hard materials (concrete, rock) demand of big expenses because of cavities size, occurrence depth (850-900 m), high value of materials, their processing and transportation. The problem to render harmless and to utilize of displacing radioactive brines is not solved yet. 5, Freezing of flooding cavities appears to be an alternative, which allows to fill the space by hard ice and to less the moving of radioactive brines into the rocks around the cavities, and, what is more important, along the bore-holes above the cavities, blocking the radionuclides moving into the fractured rocks. This process divides onto 2 stages: (1) freezing with organizing of intensive heat

Dental cavities

Science.gov (United States)

... this page: //medlineplus.gov/ency/article/001055.htm Dental cavities To use the sharing features on this page, please enable JavaScript. Dental cavities are holes (or structural damage) in the ...

Underground siting of nuclear power plants

International Nuclear Information System (INIS)

Pinto, S.; Telleschi, P.

1978-10-01

Two of the main underground siting alternatives, the rock cavity plant and the pit siting, have been investigated in detail and two layouts, developed for specific sites, have been proposed. The influence of this type of siting on normal operating conditions and during abnormal occurences have been investigated. (Auth.)

Beating quantum limits in an optomechanical sensor by cavity detuning

International Nuclear Information System (INIS)

Arcizet, O.; Briant, T.; Heidmann, A.; Pinard, M.

2006-01-01

We study the quantum limits in an optomechanical sensor based on a detuned high-finesse cavity with a movable mirror. We show that the radiation pressure exerted on the mirror by the light in the detuned cavity induces a modification of the mirror dynamics and makes the mirror motion sensitive to the signal. This leads to an amplification of the signal by the mirror dynamics, and to an improvement of the sensor sensitivity beyond the standard quantum limit, up to an ultimate quantum limit only related to the mechanical dissipation of the mirror. This improvement is somewhat similar to the one predicted in detuned signal-recycled gravitational-wave interferometers, and makes a high-finesse cavity a model system to test these quantum effects

Superconducting TESLA cavities

Directory of Open Access Journals (Sweden)

B. Aune

2000-09-01

Full Text Available The conceptional design of the proposed linear electron-positron collider TESLA is based on 9-cell 1.3 GHz superconducting niobium cavities with an accelerating gradient of E_{acc}≥25 MV/m at a quality factor Q_{0}≥5×10^{9}. The design goal for the cavities of the TESLA Test Facility (TTF linac was set to the more moderate value of E_{acc}≥15 MV/m. In a first series of 27 industrially produced TTF cavities the average gradient at Q_{0}=5×10^{9} was measured to be 20.1±6.2 MV/m, excluding a few cavities suffering from serious fabrication or material defects. In the second production of 24 TTF cavities, additional quality control measures were introduced, in particular, an eddy-current scan to eliminate niobium sheets with foreign material inclusions and stringent prescriptions for carrying out the electron-beam welds. The average gradient of these cavities at Q_{0}=5×10^{9} amounts to 25.0±3.2 MV/m with the exception of one cavity suffering from a weld defect. Hence only a moderate improvement in production and preparation techniques will be needed to meet the ambitious TESLA goal with an adequate safety margin. In this paper we present a detailed description of the design, fabrication, and preparation of the TESLA Test Facility cavities and their associated components and report on cavity performance in test cryostats and with electron beam in the TTF linac. The ongoing research and development towards higher gradients is briefly addressed.

Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information

DEFF Research Database (Denmark)

Hebsgaard, Stefan M.; Korning, Peter G.; Tolstrup, Niels

1996-01-01

Artificial neural networks have been combined with a rule based system to predict intron splice sites in the dicot plant Arabidopsis thaliana. A two step prediction scheme, where a global prediction of the coding potential regulates a cutoff level for a local predicition of splice sites, is refin...

Characteristics of roost cavities used by Lilian's Lovebird Agapornis ...

African Journals Online (AJOL)

Lilian's Lovebird Agapornis lilianae is a non-excavating cavity user of mopane Colophospermum mopane woodlands. We investigated roost characteristics of Lilian's Lovebirds in Liwonde National Park, Malawi. We quantified tree and roost site variables for roost and non-roost trees. Sixty-six roosts were found. Roosts ...

Ensemble approach combining multiple methods improves human transcription start site prediction.

LENUS (Irish Health Repository)

Dineen, David G

2010-01-01

The computational prediction of transcription start sites is an important unsolved problem. Some recent progress has been made, but many promoters, particularly those not associated with CpG islands, are still difficult to locate using current methods. These methods use different features and training sets, along with a variety of machine learning techniques and result in different prediction sets.

Prediction of protein hydration sites from sequence by modular neural networks

DEFF Research Database (Denmark)

Ehrlich, L.; Reczko, M.; Bohr, Henrik

1998-01-01

The hydration properties of a protein are important determinants of its structure and function. Here, modular neural networks are employed to predict ordered hydration sites using protein sequence information. First, secondary structure and solvent accessibility are predicted from sequence with two...... separate neural networks. These predictions are used as input together with protein sequences for networks predicting hydration of residues, backbone atoms and sidechains. These networks are teined with protein crystal structures. The prediction of hydration is improved by adding information on secondary...... structure and solvent accessibility and, using actual values of these properties, redidue hydration can be predicted to 77% accuracy with a Metthews coefficient of 0.43. However, predicted property data with an accuracy of 60-70% result in less than half the improvement in predictive performance observed...

Benign Tumors and Tumor-like Lesions of the Oral Cavity and Jaws ...

African Journals Online (AJOL)

2016-06-15

Jun 15, 2016 ... Purpose: The purpose was to examine the prevalence, gender, age and site(s) of odontogenic and nonodontogenic benign tumors, and tumor‑like lesions occurring in the oral cavity and jaws in a Turkish population, particularly, in the Eastern Turkey, and to compare findings of this study with other reports.

Investigating the probability of detection of typical cavity shapes through modelling and comparison of geophysical techniques

Science.gov (United States)

James, P.

2011-12-01

With a growing need for housing in the U.K., the government has proposed increased development of brownfield sites. However, old mine workings and natural cavities represent a potential hazard before, during and after construction on such sites, and add further complication to subsurface parameters. Cavities are hence a limitation to certain redevelopment and their detection is an ever important consideration. The current standard technique for cavity detection is a borehole grid, which is intrusive, non-continuous, slow and expensive. A new robust investigation standard in the detection of cavities is sought and geophysical techniques offer an attractive alternative. Geophysical techniques have previously been utilised successfully in the detection of cavities in various geologies, but still has an uncertain reputation in the engineering industry. Engineers are unsure of the techniques and are inclined to rely on well known techniques than utilise new technologies. Bad experiences with geophysics are commonly due to the indiscriminate choice of particular techniques. It is imperative that a geophysical survey is designed with the specific site and target in mind at all times, and the ability and judgement to rule out some, or all, techniques. To this author's knowledge no comparative software exists to aid technique choice. Also, previous modelling software limit the shapes of bodies and hence typical cavity shapes are not represented. Here, we introduce 3D modelling software (Matlab) which computes and compares the response to various cavity targets from a range of techniques (gravity, gravity gradient, magnetic, magnetic gradient and GPR). Typical near surface cavity shapes are modelled including shafts, bellpits, various lining and capping materials, and migrating voids. The probability of cavity detection is assessed in typical subsurface and noise conditions across a range of survey parameters. Techniques can be compared and the limits of detection distance

Prediction of P53 mutants (multiple sites transcriptional activity based on structural (2D&3D properties.

Directory of Open Access Journals (Sweden)

R Geetha Ramani

Full Text Available Prediction of secondary site mutations that reinstate mutated p53 to normalcy has been the focus of intense research in the recent past owing to the fact that p53 mutants have been implicated in more than half of all human cancers and restoration of p53 causes tumor regression. However laboratory investigations are more often laborious and resource intensive but computational techniques could well surmount these drawbacks. In view of this, we formulated a novel approach utilizing computational techniques to predict the transcriptional activity of multiple site (one-site to five-site p53 mutants. The optimal MCC obtained by the proposed approach on prediction of one-site, two-site, three-site, four-site and five-site mutants were 0.775,0.341,0.784,0.916 and 0.655 respectively, the highest reported thus far in literature. We have also demonstrated that 2D and 3D features generate higher prediction accuracy of p53 activity and our findings revealed the optimal results for prediction of p53 status, reported till date. We believe detection of the secondary site mutations that suppress tumor growth may facilitate better understanding of the relationship between p53 structure and function and further knowledge on the molecular mechanisms and biological activity of p53, a targeted source for cancer therapy. We expect that our prediction methods and reported results may provide useful insights on p53 functional mechanisms and generate more avenues for utilizing computational techniques in biological data analysis.

Computational prediction of muon stopping sites using ab initio random structure searching (AIRSS)

Science.gov (United States)

Liborio, Leandro; Sturniolo, Simone; Jochym, Dominik

2018-04-01

The stopping site of the muon in a muon-spin relaxation experiment is in general unknown. There are some techniques that can be used to guess the muon stopping site, but they often rely on approximations and are not generally applicable to all cases. In this work, we propose a purely theoretical method to predict muon stopping sites in crystalline materials from first principles. The method is based on a combination of ab initio calculations, random structure searching, and machine learning, and it has successfully predicted the MuT and MuBC stopping sites of muonium in Si, diamond, and Ge, as well as the muonium stopping site in LiF, without any recourse to experimental results. The method makes use of Soprano, a Python library developed to aid ab initio computational crystallography, that was publicly released and contains all the software tools necessary to reproduce our analysis.

Local temperatures predict breeding phenology but do not result in breeding synchrony among a community of resident cavity-nesting birds.

Science.gov (United States)

Drake, Anna; Martin, Kathy

2018-02-09

Weather and ecological factors are known to influence breeding phenology and thus individual fitness. We predicted concordance between weather conditions and annual variation in phenology within a community of eight resident, cavity-nesting bird species over a 17-year period. We show that, although clutch initiation dates for six of our eight species are correlated with local daily maximum temperatures, this common driver does not produce a high degree of breeding synchrony due to species-specific responses to conditions during different periods of the preceding winter or spring. These "critical temperature periods" were positively associated with average lay date for each species, although the interval between critical periods and clutch initiation varied from 4-78 days. The ecological factors we examined (cavity availability and a food pulse) had an additional influence on timing in only one of our eight focal species. Our results have strong implications for understanding heterogeneous wildlife responses to climate change: divergent responses would be expected within communities where species respond to local conditions within different temporal windows, due to differing warming trends between winter and spring. Our system therefore indicates that climate change could alter relative breeding phenology among sympatric species in temperate ecosystems.

Cavity quantum electrodynamics

International Nuclear Information System (INIS)

Walther, Herbert; Varcoe, Benjamin T H; Englert, Berthold-Georg; Becker, Thomas

2006-01-01

This paper reviews the work on cavity quantum electrodynamics of free atoms. In recent years, cavity experiments have also been conducted on a variety of solid-state systems resulting in many interesting applications, of which microlasers, photon bandgap structures and quantum dot structures in cavities are outstanding examples. Although these phenomena and systems are very interesting, discussion is limited here to free atoms and mostly single atoms because these systems exhibit clean quantum phenomena and are not disturbed by a variety of other effects. At the centre of our review is the work on the one-atom maser, but we also give a survey of the entire field, using free atoms in order to show the large variety of problems dealt with. The cavity interaction can be separated into two main regimes: the weak coupling in cavity or cavity-like structures with low quality factors Q and the strong coupling when high-Q cavities are involved. The weak coupling leads to modification of spontaneous transitions and level shifts, whereas the strong coupling enables one to observe a periodic exchange of photons between atoms and the radiation field. In this case, atoms and photons are entangled, this being the basis for a variety of phenomena observed, some of them leading to interesting applications in quantum information processing. The cavity experiments with free atoms reached a new domain with the advent of experiments in the visible spectral region. A review on recent achievements in this area is also given

Wake-field studies on photonic band gap accelerator cavities

International Nuclear Information System (INIS)

Li, D.; Kroll, N.; Stanford Linear Accelerator Center, M/S 26, P.O. Box 4349, Stanford, California; Smith, D.R.; Schultz, S.

1997-01-01

We have studied the wake-field of several metal Photonic Band Gap (PBG) cavities which consist of either a square or a hexagonal array of metal cylinders, bounded on top and bottom by conducting or superconducting sheets, surrounded by placing microwave absorber at the periphery or by replacing outer rows of metal cylinders with lossy dielectric ones, or by metallic walls. A removed cylinder from the center of the array constitutes a site defect where a localized electromagnetic mode can occur. While both monopole and dipole wake-fields have been studied, we confine our attention here mainly to the dipole case. The dipole wake-field is produced by modes in the propagation bands which tend to fill the entire cavity more or less uniformly and are thus easy to damp selectively. MAFIA time domain simulation of the transverse wake-field has been compared with that of a cylindrical pill-box comparison cavity. Even without damping the wake-field of the metal PBG cavity is substantially smaller than that of the pill-box cavity and may be further reduced by increasing the size of the lattice. By introducing lossy material at the periphery we have been able to produce Q factors for the dipole modes in the 40 to 120 range without significantly degrading the accelerating mode. copyright 1997 American Institute of Physics

Applications of the theory of cavity growth to dual-ion swelling experiments

International Nuclear Information System (INIS)

Hayns, M.R.; Mansur, L.K.

1980-01-01

The rate theory of cavity growth is applied to study the effects of helium gas on cavity swelling. The variation of swelling with temperature is emphasized: (1) expressions are derived showing that the primary effect of the helium is in pressurizing cavities and that a secondary effect is in altering the microstructural sink strengths. The expressions simplify in the parameter range of engineering interest such that the temperature regime of swelling is predicted to shift upward in approximately direct proportion to the cavity gas pressure; (2) recent experimental data on swelling of a pure stainless steel type alloy under dual-nickel and helium-ion bombardment is interpreted. Helium-free, helium-coimplanted, and helium-preimplanted swelling results can be explained by the theory. It is necessary to account for the partitioning of the helium to dislocations as well as to cavities in order to explain the experimental results for helium coimplantation; (3) model studies for physically reasonable parameters reveal the importance of the He/dpa ratio

Prediction of occult lymph node metastasis in squamous cell carcinoma of the oral cavity and the oropharynx using peritumoral Prospero homeobox protein 1 lymphatic nuclear quantification.

Science.gov (United States)

Mermod, Maxime; Bongiovanni, Massimo; Petrova, Tatiana V; Dubikovskaya, Elena A; Simon, Christian; Tolstonog, Genrich; Monnier, Yan

2016-09-01

The use of lymphatic vessel density as a predictor of occult lymph node metastasis (OLNM) in head and neck squamous cell carcinoma (HNSCC) has never been reported. Staining of the specific lymphatic endothelial cells nuclear marker, PROX1, as an indicator of lymphatic vessel density was determined by counting the number of positive cells in squamous cell carcinomas (SCCs) of the oral cavity and the oropharynx with clinically negative necks. Correlation with histopathological data was established. Peritumoral PROX1 lymphatic nuclear count significantly correlated with the detection of OLNM in multivariate analysis (p oral cavity and the oropharynx allows accurate prediction of occult lymph node metastasis. © 2016 Wiley Periodicals, Inc. Head Neck 38: 1407-1415, 2016. © 2016 Wiley Periodicals, Inc.

Automated optical inspection and image analysis of superconducting radio-frequency cavities

Science.gov (United States)

Wenskat, M.

2017-05-01

The inner surface of superconducting cavities plays a crucial role to achieve highest accelerating fields and low losses. For an investigation of this inner surface of more than 100 cavities within the cavity fabrication for the European XFEL and the ILC HiGrade Research Project, an optical inspection robot OBACHT was constructed. To analyze up to 2325 images per cavity, an image processing and analysis code was developed and new variables to describe the cavity surface were obtained. The accuracy of this code is up to 97 % and the positive predictive value (PPV) 99 % within the resolution of 15.63 μm. The optical obtained surface roughness is in agreement with standard profilometric methods. The image analysis algorithm identified and quantified vendor specific fabrication properties as the electron beam welding speed and the different surface roughness due to the different chemical treatments. In addition, a correlation of ρ = -0.93 with a significance of 6 σ between an obtained surface variable and the maximal accelerating field was found.

Temperature and EUV Intensity in a Coronal Prominence Cavity and Streamer

Science.gov (United States)

Kucera, T. A.; Gibson, S.E.; Schmit, D. J.; Landi, E.; Tripathi, D.

2012-01-01

We analyze the temperature and EUV line emission of a coronal cavity and surrounding streamer in terms of a morphological forward model. We use a series of iron line ratios observed with the Hinode Extreme-ultraviolet Imaging Spectrograph (EIS) on 2007 Aug. 9 to constrain temperature as a function of altitude in a morphological forward model of the streamer and cavity. We also compare model prediction of the EIS EUV line intensities and polarized brightness (pB) data from the Mauna Loa Solar Observatory (MLSO) MK4. This work builds on earlier analysis using the same model to determine geometry of and density in the same cavity and streamer. The fit to the data with altitude dependent temperature profiles indicates that both the streamer and cavity have temperatures in the range 1.4-1.7 MK. However, the cavity exhibits substantial substructure such that the altitude dependent temperature profile is not sufficient to completely model conditions in the cavity. Coronal prominence cavities are structured by magnetism so clues to this structure are to be found in their plasma properties. These temperature substructures are likely related to structures in the cavity magnetic field. Furthermore, we find that the model overestimates the line intensities by a factor of 4-10, while overestimating pB data by no more than a factor of 1.4. One possible explanation for this is that there may be a significant amount of material at temperatures outside of the range log T(K) approximately equals 5.8 - 6.7 in both the cavity and the streamer.

Probabilistic Assessment of Above Zone Pressure Predictions at a Geologic Carbon Storage Site

Energy Technology Data Exchange (ETDEWEB)

Namhata, Argha; Oladyshkin, Sergey; Dilmore, Robert M.; Zhang, Liwei; Nakles, David V.

2016-12-01

Carbon dioxide (CO2) storage into geological formations is regarded as an important mitigation strategy for anthropogenic CO2 emissions to the atmosphere. This study first simulates the leakage of CO2 and brine from a storage reservoir through the caprock. Then, we estimate the resulting pressure changes at the zone overlying the caprock also known as Above Zone Monitoring Interval (AZMI). A data-driven approach of arbitrary Polynomial Chaos (aPC) Expansion is then used to quantify the uncertainty in the above zone pressure prediction based on the uncertainties in different geologic parameters. Finally, a global sensitivity analysis is performed with Sobol indices based on the aPC technique to determine the relative importance of different parameters on pressure prediction. The results indicate that there can be uncertainty in pressure prediction locally around the leakage zones. The degree of such uncertainty in prediction depends on the quality of site specific information available for analysis. The scientific results from this study provide substantial insight that there is a need for site-specific data for efficient predictions of risks associated with storage activities. The presented approach can provide a basis of optimized pressure based monitoring network design at carbon storage sites.

Heat loss investigation from spherical cavity receiver of solar concentrator

Energy Technology Data Exchange (ETDEWEB)

Shewale, V. C. [Dept. of Mechanical Engineering, NDMVPS KBT College of Engineering, Nashik (India); Dongarwar, P. R. [Dept. of Mechanical Engineering, College of Military Engineering, Pune (India); Gawande, R. P. [Dept. of Mechanical Engineering, B.D.C.O.E. Wardha, Nagpur University, NagpurI (India)

2016-11-15

The heat losses are mainly affects on the performance of cavity receiver of solar concentrator. In this paper, the experimental and numerical study is carried out for different heat losses from spherical cavity receiver of 0.385 m cavity diameter and 0.154 m opening diameter. The total and convection losses are studied experimentally to no wind and wind conditions for the temperature range of 150 °C to 300 °C at 0°, 30°, 45°, 60° and 90° inclination angle of cavity receiver. The experimental set up mainly consists of copper tube material cavity receiver wrapped with nichrome heating coil to heat the cavity and insulated with glasswool insulation. The numerical analysis was carried out with Fluent Computational fluid dynamics (CFD) software, to study connective heat losses for no wind condition only. The numerical results are compared with experimental results and found good agreement with maximum deviation of 12 %. The effect of inclination angle of cavity receiver on total losses and convection losses shows that as the inclination angle increases from 0o to 90o, both losses decreased due to decreased in convective zone into the cavity receiver. The effect of operating temperature of cavity shows that as the temperature of cavity receiver increases, the total and convective losses goes on increasing. The effect of external wind at 2 m/s and 4 m/s in two directions (side-on wind and head-on wind) is also studied experimentally for total and convective heat losses. The result shows that the heat losses are higher for head-on wind condition compared to side-on wind and no wind condition at all inclination angle of cavity receiver. The present results are also compared to the convective losses obtained from the correlations of Stine and Mcdonald and M. Prakash. The convective loss from these correlations shows nearest prediction to both experimental and numerical results.

Heat loss investigation from spherical cavity receiver of solar concentrator

International Nuclear Information System (INIS)

Shewale, V. C.; Dongarwar, P. R.; Gawande, R. P.

2016-01-01

The heat losses are mainly affects on the performance of cavity receiver of solar concentrator. In this paper, the experimental and numerical study is carried out for different heat losses from spherical cavity receiver of 0.385 m cavity diameter and 0.154 m opening diameter. The total and convection losses are studied experimentally to no wind and wind conditions for the temperature range of 150 °C to 300 °C at 0°, 30°, 45°, 60° and 90° inclination angle of cavity receiver. The experimental set up mainly consists of copper tube material cavity receiver wrapped with nichrome heating coil to heat the cavity and insulated with glasswool insulation. The numerical analysis was carried out with Fluent Computational fluid dynamics (CFD) software, to study connective heat losses for no wind condition only. The numerical results are compared with experimental results and found good agreement with maximum deviation of 12 %. The effect of inclination angle of cavity receiver on total losses and convection losses shows that as the inclination angle increases from 0o to 90o, both losses decreased due to decreased in convective zone into the cavity receiver. The effect of operating temperature of cavity shows that as the temperature of cavity receiver increases, the total and convective losses goes on increasing. The effect of external wind at 2 m/s and 4 m/s in two directions (side-on wind and head-on wind) is also studied experimentally for total and convective heat losses. The result shows that the heat losses are higher for head-on wind condition compared to side-on wind and no wind condition at all inclination angle of cavity receiver. The present results are also compared to the convective losses obtained from the correlations of Stine and Mcdonald and M. Prakash. The convective loss from these correlations shows nearest prediction to both experimental and numerical results

Cross-prediction of the groundwater chemistry at the SKB sites in Sweden. Pilot study

International Nuclear Information System (INIS)

Skaarman, C.; Laaksoharju, M.

1997-08-01

The possibility to perform a large scale prediction throughout Sweden was tested. The aim of the work was: to collect data and create a groundwater database for current and future use; to see if there is any correlation between data at different sites; to perform a modelling where the groundwater composition at different regions in Sweden is predicted. The outcome of the predictions were compared with the measured data at different sites. The results show that it is possible but more work needs to be done to improve the prediction models. More measurements at depth are needed to enable the use of 3D models. It is also important to include hydrogeological parameters in the groundwater chemical prediction models that are used

Seismic Hazard Assessment in Site Evaluation for Nuclear Installations: Ground Motion Prediction Equations and Site Response

International Nuclear Information System (INIS)

2016-07-01

The objective of this publication is to provide the state-of-the-art practice and detailed technical elements related to ground motion evaluation by ground motion prediction equations (GMPEs) and site response in the context of seismic hazard assessments as recommended in IAEA Safety Standards Series No. SSG-9, Seismic Hazards in Site Evaluation for Nuclear Installations. The publication includes the basics of GMPEs, ground motion simulation, selection and adjustment of GMPEs, site characterization, and modelling of site response in order to improve seismic hazard assessment. The text aims at delineating the most important aspects of these topics (including current practices, criticalities and open problems) within a coherent framework. In particular, attention has been devoted to filling conceptual gaps. It is written as a reference text for trained users who are responsible for planning preparatory seismic hazard analyses for siting of all nuclear installations and/or providing constraints for anti-seismic design and retrofitting of existing structures

Advantages and disadvantages of hysterosonosalpingography in the assessment of the reproductive status of uterine cavity and fallopian tubes

International Nuclear Information System (INIS)

Radic, Vanja; Canic, Tomislav; Valetic, Josip; Duic, Zeljko

2005-01-01

Background: Hysterosonosalpingography as a contrast ultrasound method is safer, cheaper and easier to perform than hysterosalpingography in the assessment of the uterine cavity and fallopian tubes. Is it feasible for all patients? Which is the main problem in the evaluation of target structures by ultrasound? Methods: In a prospective study, 68 patients in the initial stage of the infertility treatment were examined by hysterosonosalpingography using saline NaCl infundibile[reg] and Echovist[reg] as contrast media. Subsequently, further status of the tubes and uterine cavity was assessed by the 'gold standards', laparoscopy and hysteroscopy. Results: Sensitivity and specificity of hysterosonosalpingography using NaCl infundibile[reg] for evaluation of the uterine cavity was 100 and 88.8%, respectively. Negative predictive value was 100% and positive predictive value 97%. Sensitivity and specificity of the method for the assessment of the tubal status was 100 and 66%, respectively, negative predictive value was 100% and positive predictive value was 61%. For the assessment of tubal patency using positive contrast Echovist[reg] the method has shown 100% sensibility and negative predictive value again but it reached a specificity of 77% and a positive predictive value of 70%. There were no evident complications during or after the procedure. Conclusion: Hysterosonosalpingography is useful in making decisions regarding further procedures for the diagnosis and treatment of infertility. Uterine cavity evaluation using saline is the method of choice. Tubal patency can be assessed only under ideal sonographic conditions. The method is feasible for early assessment of the reproductive status of uterine cavity and fallopian tubes as a simple, safe and cheap outpatient method prior to any following invasive procedure or even histerosalpingography

Advantages and disadvantages of hysterosonosalpingography in the assessment of the reproductive status of uterine cavity and fallopian tubes

Energy Technology Data Exchange (ETDEWEB)

Radic, Vanja; Canic, Tomislav; Valetic, Josip; Duic, Zeljko

2005-02-01

Background: Hysterosonosalpingography as a contrast ultrasound method is safer, cheaper and easier to perform than hysterosalpingography in the assessment of the uterine cavity and fallopian tubes. Is it feasible for all patients? Which is the main problem in the evaluation of target structures by ultrasound? Methods: In a prospective study, 68 patients in the initial stage of the infertility treatment were examined by hysterosonosalpingography using saline NaCl infundibile[reg] and Echovist[reg] as contrast media. Subsequently, further status of the tubes and uterine cavity was assessed by the 'gold standards', laparoscopy and hysteroscopy. Results: Sensitivity and specificity of hysterosonosalpingography using NaCl infundibile[reg] for evaluation of the uterine cavity was 100 and 88.8%, respectively. Negative predictive value was 100% and positive predictive value 97%. Sensitivity and specificity of the method for the assessment of the tubal status was 100 and 66%, respectively, negative predictive value was 100% and positive predictive value was 61%. For the assessment of tubal patency using positive contrast Echovist[reg] the method has shown 100% sensibility and negative predictive value again but it reached a specificity of 77% and a positive predictive value of 70%. There were no evident complications during or after the procedure. Conclusion: Hysterosonosalpingography is useful in making decisions regarding further procedures for the diagnosis and treatment of infertility. Uterine cavity evaluation using saline is the method of choice. Tubal patency can be assessed only under ideal sonographic conditions. The method is feasible for early assessment of the reproductive status of uterine cavity and fallopian tubes as a simple, safe and cheap outpatient method prior to any following invasive procedure or even histerosalpingography.

Dependence of pKa on solute cavity for diprotic and triprotic acids.

Science.gov (United States)

Lee, Tae Bum; McKee, Michael L

2011-06-07

A systematic study of ΔG(aq)/pK(a) for monoprotic, diprotic, and triprotic acids has been carried out based on DFT/aug-cc-pVTZ combined with CPCM and SMD solvation modeling. All DFT/cavity set combinations considered showed similar accuracy for ΔG(aq)(1)/pK(a1) (70% within ±2.5 kcal mol(-1) of experiment) while only the M05-2X/Pauling cavity combination gave reasonable results for ΔG(aq)(2)/pK(a2) when both pK(a) values are separated by more than three units (70% within ±5.0 kcal mol(-1) of experiment). The choice of experimental data is critical to the interpretation of the calculated accuracy especially for several inorganic acids. For the calculation of ΔG(aq)(3)/pK(a3), the larger experimental uncertainty and an unrealistic orbital population of diffuse function for trianions in the gas phase hinders an evaluation of the predictive performance. We find the M05-2X functional with the Pauling cavity set is the best choice for ΔG(aq)(2)/pK(a2) prediction in aqueous media while all DFT/cavity sets considered were competitive for ΔG(aq)(1)/pK(a1).

Theoretical investigation of anomalously high efficiency in a three cavity gyroklystron amplifier

International Nuclear Information System (INIS)

Latham, P.E.; Koc, U.V.; Main, W.; Tantawi, S.G.

1992-01-01

The University of Maryland's three cavity gyroklystron amplifier operating at a frequency of 10 GHz, voltage of 425 kV, current of 160 A, and pitch angle (v perpendicular/v z ) near .82, has demonstrated an efficiency of 35%. The author's simulations using fixed field profiles predict a significantly lower efficiency, primarily because of the small pitch angle in the experiment. They will be investigating two methods of improving the efficiency in their simulations: Beam-wave interaction after the output cavity, and modification of the first two cavity Qs due to beam loading. Results of their nonlinear code will be given for both cases

Generation of 3D templates of active sites of proteins with rigid prosthetic groups

OpenAIRE

Nebel, Jean-Christophe

2006-01-01

MOTIVATION: With the increasing availability of protein structures, the generation of biologically meaningful 3D patterns from the simultaneous alignment of several protein structures is an exciting prospect: active sites could be better understood, protein functions and protein 3D structures could be predicted more accurately. Although patterns can already be generated at the fold and topological levels, no system produces high-resolution 3D patterns including atom and cavity positions. To a...

Quantum-Noise-Limited Sensitivity Enhancement of a Passive Optical Cavity by a Fast-Light Medium

Science.gov (United States)

Smith, David D.; Luckay, H. A.; Chang, Hongrok; Myneni, Krishna

2016-01-01

We demonstrate for a passive optical cavity containing a dispersive atomic medium, the increase in scale factor near the critical anomalous dispersion is not cancelled by mode broadening or attenuation, resulting in an overall increase in the predicted quantum-noise-limited sensitivity. Enhancements of over two orders of magnitude are measured in the scale factor, which translates to greater than an order-of-magnitude enhancement in the predicted quantum-noise-limited measurement precision, by temperature tuning a low-pressure vapor of non-interacting atoms in a low-finesse cavity close to the critical anomalous dispersion condition. The predicted enhancement in sensitivity is confirmed through Monte-Carlo numerical simulations.

Quantum-Noise-Limited Sensitivity-Enhancement of a Passive Optical Cavity by a Fast-Light Medium

Science.gov (United States)

Smith, David D.; Luckay, H. A.; Chang, Hongrok; Myneni, Krishna

2016-01-01

We demonstrate for a passive optical cavity containing an intracavity dispersive atomic medium, the increase in scale factor near the critical anomalous dispersion is not cancelled by mode broadening or attenuation, resulting in an overall increase in the predicted quantum-noiselimited sensitivity. Enhancements of over two orders of magnitude are measured in the scale factor, which translates to greater than an order-of-magnitude enhancement in the predicted quantumnoise- limited measurement precision, by temperature tuning a low-pressure vapor of noninteracting atoms in a low-finesse cavity close to the critical anomalous dispersion condition. The predicted enhancement in sensitivity is confirmed through Monte-Carlo numerical simulations.

Disposal of low- and intermediate-level solid radioactive wastes in rock cavities

International Nuclear Information System (INIS)

1983-01-01

This Guidebook summarizes the factors to be considered and the activities to be undertaken in the overall planning and development of a disposal system for solid or solidified low- and intermediate-level wastes in rock cavities. Aspects related to repository site selection, design, construction, operation, shutdown, surveillance, regulation and safety assessment are discussed here in general terms. They will be covered in greater technical detail in a separate document. This report considers the emplacement of wastes in categories II, III, IV and V, as defined in Table 3.1, in different kinds of cavities located at various depths from just below the surface to deep continental rock. The choice of the type of cavity and its depth and of the disposal site itself is related to the radiological protection requirements for the wastes concerned. The repositories considered include natural caves and abandoned mines as well as specially excavated cavities in various geological formations. Consideration is also given to hydrogeological, environmental and societal factors. The guidelines given in the report are made sufficiently general to cover a broad variety of different circumstances. Consequently, the practical application of these guidelines needs a case-by-case consideration which takes into account the local conditions, e.g. natural circumstances, the characteristics of the wastes and national and international regulations and practices

Nest-site selection in the acorn woodpecker

Science.gov (United States)

Hooge, P.N.; Stanback, M.T.; Koenig, Walter D.

1999-01-01

Acorn Woodpeckers (Melanerpes formicivorus) at Hastings Reservation in central California prefer to nest in dead limbs in large, dead valley oaks (Quercus lobata) and California sycamores (Platanus racemosa) that are also frequently used as acorn storage trees. Based on 232 nest cavities used over an 18-year period, we tested whether preferred or modal nest-site characters were associated with increased reproductive success (the "nest-site quality" hypothesis). We also examined whether more successful nests were likely to experience more favorable microclimatic conditions or to be less accessible to terrestrial predators. We found only equivocal support for the nest-site quality hypothesis: only 1 of 5 preferred characters and 2 of 10 characters exhibiting a clear modality were correlated with higher reproductive success. All three characteristics of nests known or likely to be associated with a more favorable microclimate, and two of five characteristics likely to render nests less accessible to predators, were correlated with higher reproductive success. These results suggest that nest cavities in this population are built in part to take advantage of favorable microclimatic conditions and, to a lesser extent, to reduce access to predators. However, despite benefits of particular nest characteristics, birds frequently nested in apparently suboptimal cavities. We also found a significant relationship between mean group size and the history of occupancy of particular territories and the probability of nest cavities being built in microclimatically favorable live limbs, suggesting that larger groups residing on more stable territories were better able to construct nests with optimal characteristics. This indicates that there may be demographic, as well as ecological, constraints on nest-site selection in this primary cavity nester.

Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites.

Directory of Open Access Journals (Sweden)

Amy L Bauer

2010-11-01

Full Text Available An important step in understanding gene regulation is to identify the DNA binding sites recognized by each transcription factor (TF. Conventional approaches to prediction of TF binding sites involve the definition of consensus sequences or position-specific weight matrices and rely on statistical analysis of DNA sequences of known binding sites. Here, we present a method called SiteSleuth in which DNA structure prediction, computational chemistry, and machine learning are applied to develop models for TF binding sites. In this approach, binary classifiers are trained to discriminate between true and false binding sites based on the sequence-specific chemical and structural features of DNA. These features are determined via molecular dynamics calculations in which we consider each base in different local neighborhoods. For each of 54 TFs in Escherichia coli, for which at least five DNA binding sites are documented in RegulonDB, the TF binding sites and portions of the non-coding genome sequence are mapped to feature vectors and used in training. According to cross-validation analysis and a comparison of computational predictions against ChIP-chip data available for the TF Fis, SiteSleuth outperforms three conventional approaches: Match, MATRIX SEARCH, and the method of Berg and von Hippel. SiteSleuth also outperforms QPMEME, a method similar to SiteSleuth in that it involves a learning algorithm. The main advantage of SiteSleuth is a lower false positive rate.

Natural convection and wall radiation in tall cavities

Energy Technology Data Exchange (ETDEWEB)

Balaji, C [Regional Engineering College, Tiruchirapalli (India). Dept. of Mechanical Engineering; Venkateshan, S P [Indian Inst. of Tech., Madras (India). Dept. of Mechanical Engineering

1996-12-01

The problem of combined natural convection and wall radiation in tall cavities has been taken up for a detailed numerical investigation. The governing equations for fluid flow have been solved by a finite volume method and the radiation has been treated by the radiosity-irradiation method. The analysis has been specifically made for the case where the emissivity of the hot left wall is different from that of the cold right wall. For this case it was found that decoupling radiation from free convection can lead to considerable error. Correlations have been suggested for predicting both the convective as well as the radiative heat transfer rates across the cavity. (author). 7 refs., 3 figs., 3 tabs.

Natural convection and wall radiation in tall cavities

International Nuclear Information System (INIS)

Balaji, C.; Venkateshan, S.P.

1996-01-01

The problem of combined natural convection and wall radiation in tall cavities has been taken up for a detailed numerical investigation. The governing equations for fluid flow have been solved by a finite volume method and the radiation has been treated by the radiosity-irradiation method. The analysis has been specifically made for the case where the emissivity of the hot left wall is different from that of the cold right wall. For this case it was found that decoupling radiation from free convection can lead to considerable error. Correlations have been suggested for predicting both the convective as well as the radiative heat transfer rates across the cavity. (author). 7 refs., 3 figs., 3 tabs

Improved reactor cavity

International Nuclear Information System (INIS)

Katz, L.R.; Demarchais, W.E.

1984-01-01

A reactor pressure vessel disposed in a cavity has coolant inlet or outlet pipes extending through passages in the cavity walls and welded to pressure nozzles. The cavity wall has means for directing fluid away from a break at a weld away from the pressure vessel, and means for inhibiting flow of fluid toward the vessel. (author)

Experimental studies of 7-cell dual axis asymmetric cavity for energy recovery linac

Directory of Open Access Journals (Sweden)

I. V. Konoplev

2017-10-01

Full Text Available High average current, transportable energy recovery linacs (ERLs can be very attractive tools for a number of applications including next generation high-luminosity, compact light sources. Conventional ERLs are based on an electron beam circulating through the same set of rf cavity cells. This leads to an accumulation of high-order modes inside the cavity cells, resulting in the development of a beam breakup (BBU instability, unless the beam current is kept below the BBU start current. This limits the maximum current which can be transported through the ERL and hence the intensity of the photon beam generated. It has recently been proposed that splitting the accelerating and decelerating stages, tuning them separately and coupling them via a resonance coupler can increase the BBU start current. The paper presents the first experimental rf studies of a dual axis 7-cell asymmetric cavity and confirms the properties predicted by the theoretical model. The field structures of the symmetric and asymmetric modes are measured and good agreement with the numerical predictions is demonstrated. The operating mode field flatness was also measured and discussed. A novel approach based on the coupled mode (Fano-like model has been developed for the description of the cavity eigenmode spectrum and good agreement between analytical theory, numerical predictions and experimental data is shown. Numerical and experimental results observed are analyzed, discussed and a good agreement between theory and experiment is demonstrated.

Comparison of the immune microenvironment of the oral cavity and cervix in healthy women

Science.gov (United States)

Fakhry, Carole; Marks, Morgan A.; Gilman, Robert H.; Cabrerra, Lilia; Yori, Pablo; Kosek, Margaret; Gravitt, Patti E.

2013-01-01

Background Despite similar frequencies of exposure, the low prevalence of certain sexually transmitted infections such as Chlamydia, HPV and HIV-1 in the oral cavity relative to the cervix is poorly understood. This could be explained in part by differences in host immune microenvironments between these two anatomic sites. Objective We compared the concentration and correlation of 27 different immune markers in paired secretion specimens collected from the oral and cervical mucosa of healthy women. Methods Paired oral and cervical secretion specimens were collected from thirty-nine women. The concentration of twenty-seven different immune markers was estimated using a Luminex multiplex assay. Marker concentration was normalized to total protein present in the specimen. Median immune marker concentrations were compared across anatomic sites. Unsupervised hierarchical clustering analysis was utilized to identify groups of markers that shared similar patterns of relative concentrations across anatomic sites. Results The oral cavity had significantly higher concentrations of eotaxin, IFN-γ, IL-2, IL-4, IL-5, IL-7, IL-9, IL-13, IL-15, PDGF-BB, TNF-α, (p < 0.01 for each) while the cervix had higher concentrations of proinflammatory markers such as FGF-basic, IL-1ra, IL-1β, IL-6, IL-8, IP-10, G-CSF, GM-CSF, MCP-1, MIP-1β, VEGF (p < 0.01 for each). Hierarchical cluster analysis identified two groups of immune markers comprised of T-cell related immune markers with significantly higher concentrations in the oral cavity relative to the cervix, and a third cluster consisting of mostly inflammatory immune markers which were higher concentrations in the cervix. The oral cavity had a larger number of significant inter-marker correlations as compared to the cervix. Conclusions The oral cavity and cervix have significantly different immune marker profiles, which may in part explain the significantly lower burden of sexually transmitted infections such as Chlamydia, HPV, and

Space shuttle solid rocket booster water entry cavity collapse loads

Science.gov (United States)

Keefe, R. T.; Rawls, E. A.; Kross, D. A.

1982-01-01

Solid rocket booster cavity collapse flight measurements included external pressures on the motor case and aft skirt, internal motor case pressures, accelerometers located in the forward skirt, mid-body area, and aft skirt, as well as strain gages located on the skin of the motor case. This flight data yielded applied pressure longitudinal and circumferential distributions which compare well with model test predictions. The internal motor case ullage pressure, which is below atmospheric due to the rapid cooling of the hot internal gas, was more severe (lower) than anticipated due to the ullage gas being hotter than predicted. The structural dynamic response characteristics were as expected. Structural ring and wall damage are detailed and are considered to be attributable to the direct application of cavity collapse pressure combined with the structurally destabilizing, low internal motor case pressure.

Cavity contour segmentation in chest radiographs using supervised learning and dynamic programming

International Nuclear Information System (INIS)

Maduskar, Pragnya; Hogeweg, Laurens; Sánchez, Clara I.; Ginneken, Bram van; Jong, Pim A. de; Peters-Bax, Liesbeth; Dawson, Rodney; Ayles, Helen

2014-01-01

Purpose: Efficacy of tuberculosis (TB) treatment is often monitored using chest radiography. Monitoring size of cavities in pulmonary tuberculosis is important as the size predicts severity of the disease and its persistence under therapy predicts relapse. The authors present a method for automatic cavity segmentation in chest radiographs. Methods: A two stage method is proposed to segment the cavity borders, given a user defined seed point close to the center of the cavity. First, a supervised learning approach is employed to train a pixel classifier using texture and radial features to identify the border pixels of the cavity. A likelihood value of belonging to the cavity border is assigned to each pixel by the classifier. The authors experimented with four different classifiers:k-nearest neighbor (kNN), linear discriminant analysis (LDA), GentleBoost (GB), and random forest (RF). Next, the constructed likelihood map was used as an input cost image in the polar transformed image space for dynamic programming to trace the optimal maximum cost path. This constructed path corresponds to the segmented cavity contour in image space. Results: The method was evaluated on 100 chest radiographs (CXRs) containing 126 cavities. The reference segmentation was manually delineated by an experienced chest radiologist. An independent observer (a chest radiologist) also delineated all cavities to estimate interobserver variability. Jaccard overlap measure Ω was computed between the reference segmentation and the automatic segmentation; and between the reference segmentation and the independent observer's segmentation for all cavities. A median overlap Ω of 0.81 (0.76 ± 0.16), and 0.85 (0.82 ± 0.11) was achieved between the reference segmentation and the automatic segmentation, and between the segmentations by the two radiologists, respectively. The best reported mean contour distance and Hausdorff distance between the reference and the automatic segmentation were

Cavity contour segmentation in chest radiographs using supervised learning and dynamic programming

Energy Technology Data Exchange (ETDEWEB)

Maduskar, Pragnya, E-mail: pragnya.maduskar@radboudumc.nl; Hogeweg, Laurens; Sánchez, Clara I.; Ginneken, Bram van [Diagnostic Image Analysis Group, Radboud University Medical Center, Nijmegen, 6525 GA (Netherlands); Jong, Pim A. de [Department of Radiology, University Medical Center Utrecht, 3584 CX (Netherlands); Peters-Bax, Liesbeth [Department of Radiology, Radboud University Medical Center, Nijmegen, 6525 GA (Netherlands); Dawson, Rodney [University of Cape Town Lung Institute, Cape Town 7700 (South Africa); Ayles, Helen [Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT (United Kingdom)

2014-07-15

Purpose: Efficacy of tuberculosis (TB) treatment is often monitored using chest radiography. Monitoring size of cavities in pulmonary tuberculosis is important as the size predicts severity of the disease and its persistence under therapy predicts relapse. The authors present a method for automatic cavity segmentation in chest radiographs. Methods: A two stage method is proposed to segment the cavity borders, given a user defined seed point close to the center of the cavity. First, a supervised learning approach is employed to train a pixel classifier using texture and radial features to identify the border pixels of the cavity. A likelihood value of belonging to the cavity border is assigned to each pixel by the classifier. The authors experimented with four different classifiers:k-nearest neighbor (kNN), linear discriminant analysis (LDA), GentleBoost (GB), and random forest (RF). Next, the constructed likelihood map was used as an input cost image in the polar transformed image space for dynamic programming to trace the optimal maximum cost path. This constructed path corresponds to the segmented cavity contour in image space. Results: The method was evaluated on 100 chest radiographs (CXRs) containing 126 cavities. The reference segmentation was manually delineated by an experienced chest radiologist. An independent observer (a chest radiologist) also delineated all cavities to estimate interobserver variability. Jaccard overlap measure Ω was computed between the reference segmentation and the automatic segmentation; and between the reference segmentation and the independent observer's segmentation for all cavities. A median overlap Ω of 0.81 (0.76 ± 0.16), and 0.85 (0.82 ± 0.11) was achieved between the reference segmentation and the automatic segmentation, and between the segmentations by the two radiologists, respectively. The best reported mean contour distance and Hausdorff distance between the reference and the automatic segmentation were

Nest-site habitat of cavity-nesting birds at the San Joaquin Experimental Range

Science.gov (United States)

Kathryn L. Purcell; Jared. Verner

2008-01-01

Detailed information about the nesting habitats of birds, including those needed for successful nesting, can provide a better understanding of the ecological factors that permit coexistence of different species and may aid in conservation efforts. From 1989 through 1994, we studied the nesting habitat of secondary cavity-nesting birds in oak woodlands at the San...

accelerating cavity

CERN Multimedia

On the inside of the cavity there is a layer of niobium. Operating at 4.2 degrees above absolute zero, the niobium is superconducting and carries an accelerating field of 6 million volts per metre with negligible losses. Each cavity has a surface of 6 m2. The niobium layer is only 1.2 microns thick, ten times thinner than a hair. Such a large area had never been coated to such a high accuracy. A speck of dust could ruin the performance of the whole cavity so the work had to be done in an extremely clean environment.

Multipacting studies in elliptic SRF cavities

Science.gov (United States)

Prakash, Ram; Jana, Arup Ratan; Kumar, Vinit

2017-09-01

Multipacting is a resonant process, where the number of unwanted electrons resulting from a parasitic discharge rapidly grows to a larger value at some specific locations in a radio-frequency cavity. This results in a degradation of the cavity performance indicators (e.g. the quality factor Q and the maximum achievable accelerating gradient Eacc), and in the case of a superconducting radiofrequency (SRF) cavity, it leads to a quenching of superconductivity. Numerical simulations are essential to pre-empt the possibility of multipacting in SRF cavities, such that its design can be suitably refined to avoid this performance limiting phenomenon. Readily available computer codes (e.g.FishPact, MultiPac,CST-PICetc.) are widely used to simulate the phenomenon of multipacting in such cases. Most of the contemporary two dimensional (2D) codes such as FishPact, MultiPacetc. are unable to detect the multipacting in elliptic cavities because they use a simplistic secondary emission model, where it is assumed that all the secondary electrons are emitted with same energy. Some three-dimensional (3D) codes such as CST-PIC, which use a more realistic secondary emission model (Furman model) by following a probability distribution for the emission energy of secondary electrons, are able to correctly predict the occurrence of multipacting. These 3D codes however require large data handling and are slower than the 2D codes. In this paper, we report a detailed analysis of the multipacting phenomenon in elliptic SRF cavities and development of a 2D code to numerically simulate this phenomenon by employing the Furman model to simulate the secondary emission process. Since our code is 2D, it is faster than the 3D codes. It is however as accurate as the contemporary 3D codes since it uses the Furman model for secondary emission. We have also explored the possibility to further simplify the Furman model, which enables us to quickly estimate the growth rate of multipacting without

Work characteristics predict the development of multi-site musculoskeletal pain

NARCIS (Netherlands)

Oakman, J.; Wind, A. de; Heuvel, S.G. van den; Beek, A.J. van der

2017-01-01

Purpose. Musculoskeletal pain in more than one body region is common and a barrier to sustaining employment. We aimed to examine whether work characteristics predict the development of multi-site pain (MSP), and to determine differences in work-related predictors between age groups. Methods. This

Frequency-feedback cavity enhanced spectrometer

Science.gov (United States)

Hovde, David Christian; Gomez, Anthony

2015-08-18

A spectrometer comprising an optical cavity, a light source capable of producing light at one or more wavelengths transmitted by the cavity and with the light directed at the cavity, a detector and optics positioned to collect light transmitted by the cavity, feedback electronics causing oscillation of amplitude of the optical signal on the detector at a frequency that depends on cavity losses, and a sensor measuring the oscillation frequency to determine the cavity losses.

An investigation of the RCS (radar cross section) computation of grid cavities

International Nuclear Information System (INIS)

Sabihi, Ahmad

2014-01-01

In this paper, the aperture of a cavity is covered by a metallic grid net. This metallic grid is to reduce RCS deduced by impinging radar ray on the aperture. A radar ray incident on a grid net installed on a cavity may create six types of propagation. 1-Incident rays entering inside the cavity and backscattered from it.2-Incidebnt rays on the grid net and created reection rays as an array of scatterers. These rays may create a wave with phase difference of 180 degree with respect to the exiting rays from the cavity.3-Incident rays on the grid net create surface currents owing on the net and make travelling waves, which regenerate the magnetic and electric fields. These fields make again propagated waves against incident ones.4-Creeping waves.5-Diffracted rays due to leading edges of net’s elements.6-Mutual impedance among elements of the net could be effective on the resultant RCS. Therefore, the author compares the effects of three out of six properties to a cavity without grid net. This comparison shows that RCS prediction of cavity having a grid net is much more reduced than that of without one

An investigation of the RCS (radar cross section) computation of grid cavities

Energy Technology Data Exchange (ETDEWEB)

Sabihi, Ahmad [Department of Mathematical Sciences, Sharif University of Technology, Tehran (Iran, Islamic Republic of)

2014-12-10

In this paper, the aperture of a cavity is covered by a metallic grid net. This metallic grid is to reduce RCS deduced by impinging radar ray on the aperture. A radar ray incident on a grid net installed on a cavity may create six types of propagation. 1-Incident rays entering inside the cavity and backscattered from it.2-Incidebnt rays on the grid net and created reection rays as an array of scatterers. These rays may create a wave with phase difference of 180 degree with respect to the exiting rays from the cavity.3-Incident rays on the grid net create surface currents owing on the net and make travelling waves, which regenerate the magnetic and electric fields. These fields make again propagated waves against incident ones.4-Creeping waves.5-Diffracted rays due to leading edges of net’s elements.6-Mutual impedance among elements of the net could be effective on the resultant RCS. Therefore, the author compares the effects of three out of six properties to a cavity without grid net. This comparison shows that RCS prediction of cavity having a grid net is much more reduced than that of without one.

Characterization technique for long optical fiber cavities based on beating spectrum of multi-longitudinal mode fiber laser and beating spectrum in the RF domain

Science.gov (United States)

Adib, George A.; Sabry, Yasser M.; Khalil, Diaa

2016-03-01

The characterization of long fiber cavities is essential for many systems to predict the system practical performance. The conventional techniques for optical cavity characterization are not suitable for long fiber cavities due to the cavities' small free spectral ranges and due to the length variations caused by the environmental effects. In this work, we present a novel technique to characterize long fiber cavities using multi-longitudinal mode fiber laser source and RF spectrum analyzer. The fiber laser source is formed in a ring configuration, where the fiber laser cavity length is chosen to be 15 km to ensure that the free spectral range is much smaller than the free spectral range of the characterized passive fiber cavities. The method has been applied experimentally to characterize ring cavities with lengths of 6.2 m and 2.4 km. The results are compared to theoretical predictions with very good agreement.

Consequences of habitat change and resource selection specialization for population limitation in cavity-nesting birds

Science.gov (United States)

Martin, Thomas E.

2015-01-01

Resource selection specialization may increase vulnerability of populations to environmental change. One environmental change that may negatively impact some populations is the broad decline of quaking aspen Populus tremuloides, a preferred nest tree of cavity-nesting organisms who are commonly limited by nest-site availability. However, the long-term consequences of this habitat change for cavity-nesting bird populations are poorly studied.

Benign tumors and tumor-like lesions of the oral cavity and jaws: An ...

African Journals Online (AJOL)

Purpose: The purpose was to examine the prevalence, gender, age and site(s) of odontogenic and nonodontogenic benign tumors, and tumor‑like lesions occurring in the oral cavity and jaws in a Turkish population, particularly, in the Eastern Turkey, and to compare findings of this study with other reports. Materials and ...

SITE-94. Discrete-feature modelling of the Aespoe Site: 3. Predictions of hydrogeological parameters for performance assessment

International Nuclear Information System (INIS)

Geier, J.E.

1996-12-01

A 3-dimensional, discrete-feature hydrological model is developed. The model integrates structural and hydrologic data for the Aespoe site, on scales ranging from semi regional fracture zones to individual fractures in the vicinity of the nuclear waste canisters. Predicted parameters for the near field include fracture spacing, fracture aperture, and Darcy velocity at each of forty canister deposition holes. Parameters for the far field include discharge location, Darcy velocity, effective longitudinal dispersion coefficient and head gradient, flow porosity, and flow wetted surface, for each canister source that discharges to the biosphere. Results are presented in the form of statistical summaries for a total of 42 calculation cases, which treat a set of 25 model variants in various combinations. The variants for the SITE-94 Reference Case model address conceptual and parametric uncertainty related to the site-scale hydrogeologic model and its properties, the fracture network within the repository, effective semi regional boundary conditions for the model, and the disturbed-rock zone around the repository tunnels and shafts. Two calculation cases simulate hydrologic conditions that are predicted to occur during future glacial episodes. 30 refs

Lymphangiogenesis and angiogenesis in oral cavity and lower lip squamous cell carcinoma.

Science.gov (United States)

Alaeddini, Mojgan; Etemad-Moghadam, Shahroo

2016-01-01

Tumors of the lip and oral cavity differ in various aspects; therefore a clarification of the distinctions among these sites may help to better understand the biologic behavior of neoplasms occurring in these locations. Considering that angiogenesis and lymphangiogenesis are two major elements that can influence various aspects of tumor biology, we aimed to compare these factors between squamous cell carcinoma of the lower lip and oral cavity. A total of 84 primary squamous cell carcinomas including 45 oral and 39 lower lip tumors were selected and immunohistochemically stained with monoclonal antibody against D2-40 and CD105. Mean microvessel density was assessed in tumoral tissue, while lymphatic vessel density was calculated in both neoplastic tissue and invasion front. Data were statistically analyzed using t-test and p-values of oral cavity and 27.54±20.8 in lower lip squamous cell carcinomas, with no significant difference (p=0.32). Mean lymphatic vessel density±standard deviation was 13.05±8.2 and 16.57±10.79 in of oral cavity and lower lip neoplastic tissue, respectively. The corresponding values were 9.94±5.59 and 12.50±7.8 in the invasive front. Significant differences were not observed in either of the lymphatic vessel density variables between the two sites. According to our results, it seems that the search for additional factors other than those related to the vasculature should continue, to help clarify the differences in biologic behavior between lower lip and oral cavity squamous cell carcinomas. Copyright © 2015 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.

Prediction of break-out sound from a rectangular cavity via an elastically mounted panel.

Science.gov (United States)

Wang, Gang; Li, Wen L; Du, Jingtao; Li, Wanyou

2016-02-01

The break-out sound from a cavity via an elastically mounted panel is predicted in this paper. The vibroacoustic system model is derived based on the so-called spectro-geometric method in which the solution over each sub-domain is invariably expressed as a modified Fourier series expansion. Unlike the traditional modal superposition methods, the continuity of the normal velocities is faithfully enforced on the interfaces between the flexible panel and the (interior and exterior) acoustic media. A fully coupled vibro-acoustic system is obtained by taking into account the strong coupling between the vibration of the elastic panel and the sound fields on the both sides. The typical time-consuming calculations of quadruple integrals encountered in determining the sound power radiation from a panel has been effectively avoided by reducing them, via discrete cosine transform, into a number of single integrals which are subsequently calculated analytically in a closed form. Several numerical examples are presented to validate the system model, understand the effects on the sound transmissions of panel mounting conditions, and demonstrate the dependence on the size of source room of the "measured" transmission loss.

Suppression of hydride precipitates in niobium superconducting radio-frequency cavities

Science.gov (United States)

Ford, Denise C.; Cooley, Lance D.; Seidman, David N.

2013-10-01

Niobium hydride is a suspected contributor to degraded niobium superconducting radio-frequency (SRF) cavity performance by Q slope and Q disease. The concentration and distribution of hydrogen atoms in niobium can be strongly affected by the cavity processing treatments. This study provides guidance for cavity processing based on density functional theory calculations of the properties of common processing impurity species—hydrogen, oxygen, nitrogen, and carbon—in the body-centered cubic (bcc) niobium lattice. We demonstrate that some fundamental properties are shared between the impurity atoms, such as anionic character in niobium. The strain field produced, however, by hydrogen atoms is both geometrically different and substantially weaker than the strain field produced by the other impurities. We focus on the interaction between oxygen and hydrogen atoms in the lattice, and demonstrate that the elastic interactions between these species and the bcc niobium lattice cause trapping of hydrogen and oxygen atoms by bcc niobium lattice vacancies. We also show that the attraction of oxygen to a lattice vacancy is substantially stronger than the attraction of hydrogen to the vacancy. Additionally, hydrogen dissolved in niobium tetrahedral interstitial sites can be trapped by oxygen, nitrogen and possibly carbon atoms dissolved in octahedral interstitial sites. These results indicate that the concentration of oxygen in the bcc lattice can have a strong impact on the ability of hydrogen to form detrimental phases. Based on our results and a literature survey, we propose a mechanism for the success of the low-temperature annealing step applied to niobium SRF cavities. We also recommend further examination of nitrogen and carbon in bcc niobium, and particularly the role that nitrogen can play in preventing detrimental hydride phase formation.

G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures.

Science.gov (United States)

Lee, Hui Sun; Im, Wonpil

2017-01-01

Recent advances in high-throughput structure determination and computational protein structure prediction have significantly enriched the universe of protein structure. However, there is still a large gap between the number of available protein structures and that of proteins with annotated function in high accuracy. Computational structure-based protein function prediction has emerged to reduce this knowledge gap. The identification of a ligand binding site and its structure is critical to the determination of a protein's molecular function. We present a computational methodology for predicting small molecule ligand binding site and ligand structure using G-LoSA, our protein local structure alignment and similarity measurement tool. All the computational procedures described here can be easily implemented using G-LoSA Toolkit, a package of standalone software programs and preprocessed PDB structure libraries. G-LoSA and G-LoSA Toolkit are freely available to academic users at http://compbio.lehigh.edu/GLoSA . We also illustrate a case study to show the potential of our template-based approach harnessing G-LoSA for protein function prediction.

Experimental investigation of cavity flows

Energy Technology Data Exchange (ETDEWEB)

Loeland, Tore

1998-12-31

This thesis uses LDV (Laser Doppler Velocimetry), PIV (Particle Image Velocimetry) and Laser Sheet flow Visualisation to study flow inside three different cavity configurations. For sloping cavities, the vortex structure inside the cavities is found to depend upon the flow direction past the cavity. The shape of the downstream corner is a key factor in destroying the boundary layer flow entering the cavity. The experimental results agree well with numerical simulations of the same geometrical configurations. The results of the investigations are used to find the influence of the cavity flow on the accuracy of the ultrasonic flowmeter. A method to compensate for the cavity velocities is suggested. It is found that the relative deviation caused by the cavity velocities depend linearly on the pipe flow. It appears that the flow inside the cavities should not be neglected as done in the draft for the ISO technical report on ultrasonic flowmeters. 58 refs., 147 figs., 2 tabs.

Experimental investigation of cavity flows

Energy Technology Data Exchange (ETDEWEB)

Loeland, Tore

1999-12-31

This thesis uses LDV (Laser Doppler Velocimetry), PIV (Particle Image Velocimetry) and Laser Sheet flow Visualisation to study flow inside three different cavity configurations. For sloping cavities, the vortex structure inside the cavities is found to depend upon the flow direction past the cavity. The shape of the downstream corner is a key factor in destroying the boundary layer flow entering the cavity. The experimental results agree well with numerical simulations of the same geometrical configurations. The results of the investigations are used to find the influence of the cavity flow on the accuracy of the ultrasonic flowmeter. A method to compensate for the cavity velocities is suggested. It is found that the relative deviation caused by the cavity velocities depend linearly on the pipe flow. It appears that the flow inside the cavities should not be neglected as done in the draft for the ISO technical report on ultrasonic flowmeters. 58 refs., 147 figs., 2 tabs.

Early 500 MHz prototype LEP RF Cavity with superposed storage cavity

CERN Multimedia

CERN PhotoLab

1981-01-01

The principle of transferring the RF power back and forth between the accelerating cavity and a side-coupled storage cavity was demonstrated with this 500 MHz prototype. In LEP, the accelerating frequency was 352.2 MHz, and accelerating and storage cavities were consequently larger. See also 8002294, 8006061, 8407619X, and Annual Reports 1980, p.115; 1981, p.95; 1985, vol.I, p.13.

The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

Science.gov (United States)

Roche, Daniel B; Buenavista, Maria T; Tetchner, Stuart J; McGuffin, Liam J

2011-07-01

The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind the server development were as follows: (i) to provide a simple unified resource that makes our prediction software accessible to all and (ii) to produce integrated output for predictions that can be easily interpreted. The output for predictions is presented as a simple table that summarizes all results graphically via plots and annotated 3D models. The raw machine readable data files for each set of predictions are also provided for developers, which comply with the Critical Assessment of Methods for Protein Structure Prediction (CASP) data standards. The server comprises an integrated suite of five novel methods: nFOLD4, for tertiary structure prediction; ModFOLD 3.0, for model quality assessment; DISOclust 2.0, for disorder prediction; DomFOLD 2.0 for domain prediction; and FunFOLD 1.0, for ligand binding site prediction. Predictions from the IntFOLD server were found to be competitive in several categories in the recent CASP9 experiment. The IntFOLD server is available at the following web site: http://www.reading.ac.uk/bioinf/IntFOLD/.

Cavity Control and Cooling of Nanoparticles in High Vacuum

Science.gov (United States)

Millen, James

2016-05-01

Levitated systems are a fascinating addition to the world of optically-controlled mechanical resonators. It is predicted that nanoparticles can be cooled to their c.o.m. ground state via the interaction with an optical cavity. By freeing the oscillator from clamping forces dissipation and decoherence is greatly reduced, leading to the potential to produce long-lived, macroscopically spread, mechanical quantum states, allowing tests of collapse models and any mass limit of quantum physics. Reaching the low pressures required to cavity-cool to the ground state has proved challenging. Our approach is to cavity cool a beam of nanoparticles in high vacuum. We can cool the c.o.m. motion of nanospheres, and control the rotation of nanorods, with the potential to produce cold, aligned nanostructures. Looking forward, we will utilize novel microcavities to enhance optomechanical cooling, preparing particles in a coherent beam ideally suited to ultra-high mass interferometry at 107 a.m.u.

Evolution of pH during in-situ leaching in small concrete cavities

Energy Technology Data Exchange (ETDEWEB)

Saguees, A.A. [Univ. of South Florida, Tampa, FL (United States). Dept. of Civil and Environmental Engineering; Moreno, E.I. [Univ. of South Florida, Tampa, FL (United States). Dept. of Civil and Environmental Engineering]|[CINVESTAV Merida-Unit (Mexico); Andrade, C. [CSIC, Madrid (Spain). Inst. Eduardo Torroja de Ciencias de la Construccion

1997-11-01

Small amounts (0.4 cc) of neutral water placed in small cylindrical cavities (5 mm diameter) in concrete exposed to 100% relative humidity first developed a pH comparable to that of a saturated Ca(OH){sub 2} solution. The pH then increased over a period of days-weeks toward a higher terminal value. A micro pH electrode arrangement was used. This behavior was observed in samples of 12 different concrete mix designs, including some with pozzolanic additions. The average terminal cavity pH closely approached that of expressed pore water from the same concretes. A simplified mathematical model reproduced the experimentally observed behavior. The model assumed inward diffusional transport of the pH-determining species in the surrounding concrete pore solution. The experimental results were consistent with the model predictions when using diffusion parameters on the order of those previously reported for alkali cations in concrete. The cavity size, cavity water content, and exposure to atmospheric CO{sub 2} should be minimized when attempting to obtain cavity pH values approaching those of the surrounding pore water.

A model of gas cavity breakup behind a blockage in fast breeder reactor subassembly geometry

International Nuclear Information System (INIS)

Fukuzawa, Y.

1980-05-01

A semi-empirical model has been developed to describe the transient behaviour of a gas cavity due to breakup behind a blockage in Liquid Metal Fast Breeder Reactor subassembly geometry. The main mechanisms assumed for gas cavity breakup in the present model are as follows: The gas cavity is broken up by the pressure fluctuation at the interface due to turbulence in the liquid. The centrifugal force on the liquid opposes breakup. The model is able to describe experimental results on the transient behaviour of a gas cavity due to breakup after the termination of gas injection. On the basis of the present model the residence time of a gas cavity behind a blockage in sodium is predicted and the dependence of the residence time on blockage size is discussed. (orig.) [de

SPS RF Accelerating Cavity

CERN Multimedia

1979-01-01

This picture shows one of the 2 new cavities installed in 1978-1979. The main RF-system of the SPS comprises four cavities: two of 20 m length and two of 16.5 m length. They are all installed in one long straight section (LSS 3). These cavities are of the travelling-wave type operating at a centre frequency of 200.2 MHz. They are wideband, filling time about 700 ns and untuned. The power amplifiers, using tetrodes are installed in a surface building 200 m from the cavities. Initially only two cavities were installed, a third cavity was installed in 1978 and a forth one in 1979. The number of power amplifiers was also increased: to the first 2 MW plant a second 2 MW plant was added and by end 1979 there were 8 500 kW units combined in pairs to feed each of the 4 cavities with up to about 1 MW RF power, resulting in a total accelerating voltage of about 8 MV. See also 7412016X, 7412017X, 7411048X

A Study on the Flow Characterization in the Reactor Cavity

Energy Technology Data Exchange (ETDEWEB)

Lee, Ho Jung; Ko, Kwang Jeok; Kim, Sung Hwan; Kim, Min Gyu; Cho, Yeon Ho; Kim, Hyun Min [KEPCO Engineering and Construction Co. Ltd., Deajeon (Korea, Republic of)

2016-10-15

In this study, the flow characterization of the cooling air in reactor cavity nearby RCPSA has been analyzed by using a 3 dimensional model and the ANSYS CFX software in order to predict the Convective Heat Transfer Coefficient (CHTC) of the RCPSA. The Reactor Cavity is the annular space by the concrete structure, the Reactor Cavity Pool Seal Assembly (RCPSA), which consists of the welded steel and is designed to be installed between the RV and the refueling pool floor, and the Reactor Vessel (RV). For such reason, the RCPSA should be designed to provide the cooling air passage for ventilation to circulate high temperature air passing by the RV during the reactor operation. It means that the RCPSA is influenced by the convection of cooling air and the thermal expansion of the RV. Therefore, the flow characterization at the reactor cavity is one of the factors of the RCPSA design during the reactor operation. The flow distribution of the cooling air in reactor cavity nearby RCPSA has been analyzed using ANSYS CFX software to obtain the CHTC at surface of the RCPSA. 1) The temperature from the RV and the insulation is one of the critical factors for the thermal gradient of the cooling air and the CHTC in the reactor cavity. 2) The rapid change of the CHTC in inner region nearby inner and outer flexure is related to the geometry shape of the RCPSA and velocity of cooling air.

Features generated for computational splice-site prediction correspond to functional elements

Directory of Open Access Journals (Sweden)

Wilbur W John

2007-10-01

Full Text Available Abstract Background Accurate selection of splice sites during the splicing of precursors to messenger RNA requires both relatively well-characterized signals at the splice sites and auxiliary signals in the adjacent exons and introns. We previously described a feature generation algorithm (FGA that is capable of achieving high classification accuracy on human 3' splice sites. In this paper, we extend the splice-site prediction to 5' splice sites and explore the generated features for biologically meaningful splicing signals. Results We present examples from the observed features that correspond to known signals, both core signals (including the branch site and pyrimidine tract and auxiliary signals (including GGG triplets and exon splicing enhancers. We present evidence that features identified by FGA include splicing signals not found by other methods. Conclusion Our generated features capture known biological signals in the expected sequence interval flanking splice sites. The method can be easily applied to other species and to similar classification problems, such as tissue-specific regulatory elements, polyadenylation sites, promoters, etc.

Upper-limit on the Advanced Virgo output mode cleaner cavity length noise

Science.gov (United States)

Bonnand, R.; Ducrot, M.; Gouaty, R.; Marion, F.; Masserot, A.; Mours, B.; Pacaud, E.; Rolland, L.; Was, M.

2017-09-01

The Advanced Virgo detector uses two monolithic optical cavities at its output port to suppress higher order modes and radio frequency sidebands from the carrier light used for gravitational wave detection. These two cavities in series form the output mode cleaner. We present a measured upper limit on the length noise of these cavities that is consistent with the thermo-refractive noise prediction of 8×10-16~m~Hz-1/2 at 15 Hz. The cavity length is controlled using Peltier cells and piezo-electric actuators to maintain resonance on the incoming light. A length lock precision of 3.5×10-13 m is achieved. These two results are combined to demonstrate that the broadband length noise of the output mode cleaner in the 10-60 Hz band is at least a factor 10 below other expected noise sources in the Advanced Virgo detector design configuration.

CFD Simulation of Flow Tones from Grazing Flow past a Deep Cavity

International Nuclear Information System (INIS)

T Bagwell

2006-01-01

Locked-in flow tones due to shear flow over a deep cavity are investigated using Large Eddy Simulation (LES). An isentropic form of the compressible Navier-Stokes equations (pseudo-compressibility) is used to couple the vertical flow over the cavity mouth with the deep cavity resonances (1). Comparisons to published experimental data (2) show that the pseudo-compressible LES formulation is capable of predicting the feedforward excitation of the deep cavity resonator, as well as the feedback process from the resonator to the flow source. By systematically increasing the resonator damping level, it is shown that strong lock-in results in a more organized shear layer than is observed for the locked-out flow state. By comparison, weak interactions (non-locked-in) produce no change in the shear layer characteristics. This supports the 40 dB definition of lock-in defined in the experiment

Middle ear cavity morphology is consistent with an aquatic origin for testudines.

Directory of Open Access Journals (Sweden)

Katie L Willis

Full Text Available The position of testudines in vertebrate phylogeny is being re-evaluated. At present, testudine morphological and molecular data conflict when reconstructing phylogenetic relationships. Complicating matters, the ecological niche of stem testudines is ambiguous. To understand how turtles have evolved to hear in different environments, we examined middle ear morphology and scaling in most extant families, as well as some extinct species, using 3-dimensional reconstructions from micro magnetic resonance (MR and submillimeter computed tomography (CT scans. All families of testudines exhibited a similar shape of the bony structure of the middle ear cavity, with the tympanic disk located on the rostrolateral edge of the cavity. Sea Turtles have additional soft tissue that fills the middle ear cavity to varying degrees. When the middle ear cavity is modeled as an air-filled sphere of the same volume resonating in an underwater sound field, the calculated resonances for the volumes of the middle ear cavities largely fell within testudine hearing ranges. Although there were some differences in morphology, there were no statistically significant differences in the scaling of the volume of the bony middle ear cavity with head size among groups when categorized by phylogeny and ecology. Because the cavity is predicted to resonate underwater within the testudine hearing range, the data support the hypothesis of an aquatic origin for testudines, and function of the middle ear cavity in underwater sound detection.

TEMPERATURE AND EXTREME-ULTRAVIOLET INTENSITY IN A CORONAL PROMINENCE CAVITY AND STREAMER

Energy Technology Data Exchange (ETDEWEB)

Kucera, T. A. [NASA/GSFC, Code 671, Greenbelt, MD 20771 (United States); Gibson, S. E.; Schmit, D. J. [HAO/NCAR, P.O. Box 3000, Boulder, CO 80307-3000 (United States); Landi, E. [Department of Atmospheric, Oceanic and Space Science, Space Research Building, University of Michigan, 2455 Hayward St., Ann Arbor, MI 48109-2143 (United States); Tripathi, D. [Inter-University Centre for Astronomy and Astrophysics, Post Bag-4, Ganeshkhind, Pune University Campus, Pune 411 007 (India)

2012-09-20

We analyze the temperature and EUV line emission of a coronal cavity and surrounding streamer in terms of a morphological forward model. We use a series of iron line ratios observed with the Hinode Extreme-ultraviolet Imaging Spectrograph (EIS) on 2007 August 9 to constrain temperature as a function of altitude in a morphological forward model of the streamer and cavity. We also compare model predictions to the EIS EUV line intensities and polarized brightness (pB) data from the Mauna Loa Solar Observatory (MLSO) Mark 4 K-coronameter. This work builds on earlier analysis using the same model to determine geometry of and density in the same cavity and streamer. The fit to the data with altitude-dependent temperature profiles indicates that both the streamer and cavity have temperatures in the range 1.4-1.7 MK. However, the cavity exhibits substantial substructure such that the altitude-dependent temperature profile is not sufficient to completely model conditions in the cavity. Coronal prominence cavities are structured by magnetism so clues to this structure are to be found in their plasma properties. These temperature substructures are likely related to structures in the cavity magnetic field. Furthermore, we find that the model overestimates the EUV line intensities by a factor of 4-10, without overestimating pB. We discuss this difference in terms of filling factors and uncertainties in density diagnostics and elemental abundances.

Prediction of protein modification sites of pyrrolidone carboxylic acid using mRMR feature selection and analysis.

Directory of Open Access Journals (Sweden)

Lu-Lu Zheng

Full Text Available Pyrrolidone carboxylic acid (PCA is formed during a common post-translational modification (PTM of extracellular and multi-pass membrane proteins. In this study, we developed a new predictor to predict the modification sites of PCA based on maximum relevance minimum redundancy (mRMR and incremental feature selection (IFS. We incorporated 727 features that belonged to 7 kinds of protein properties to predict the modification sites, including sequence conservation, residual disorder, amino acid factor, secondary structure and solvent accessibility, gain/loss of amino acid during evolution, propensity of amino acid to be conserved at protein-protein interface and protein surface, and deviation of side chain carbon atom number. Among these 727 features, 244 features were selected by mRMR and IFS as the optimized features for the prediction, with which the prediction model achieved a maximum of MCC of 0.7812. Feature analysis showed that all feature types contributed to the modification process. Further site-specific feature analysis showed that the features derived from PCA's surrounding sites contributed more to the determination of PCA sites than other sites. The detailed feature analysis in this paper might provide important clues for understanding the mechanism of the PCA formation and guide relevant experimental validations.

Analysis and prediction of Multiple-Site Damage (MSD) fatigue crack growth

Science.gov (United States)

Dawicke, D. S.; Newman, J. C., Jr.

1992-08-01

A technique was developed to calculate the stress intensity factor for multiple interacting cracks. The analysis was verified through comparison with accepted methods of calculating stress intensity factors. The technique was incorporated into a fatigue crack growth prediction model and used to predict the fatigue crack growth life for multiple-site damage (MSD). The analysis was verified through comparison with experiments conducted on uniaxially loaded flat panels with multiple cracks. Configuration with nearly equal and unequal crack distribution were examined. The fatigue crack growth predictions agreed within 20 percent of the experimental lives for all crack configurations considered.

Analysis and prediction of Multiple-Site Damage (MSD) fatigue crack growth

Science.gov (United States)

Dawicke, D. S.; Newman, J. C., Jr.

1992-01-01

A technique was developed to calculate the stress intensity factor for multiple interacting cracks. The analysis was verified through comparison with accepted methods of calculating stress intensity factors. The technique was incorporated into a fatigue crack growth prediction model and used to predict the fatigue crack growth life for multiple-site damage (MSD). The analysis was verified through comparison with experiments conducted on uniaxially loaded flat panels with multiple cracks. Configuration with nearly equal and unequal crack distribution were examined. The fatigue crack growth predictions agreed within 20 percent of the experimental lives for all crack configurations considered.

Analysis of reactor cavity radiation streaming: some practical considerations

International Nuclear Information System (INIS)

Simmons, G.L.

1979-01-01

A description is presented of a cost effective analysis procedure for use in the prediction of radiation environments in the cavity and containment building of a nuclear power reactor. Comments are offered on potential problems in certification of analysis procedures and the availability of benchmarkable data sets, both measurements and calculations

Photon correlations in a two-site nonlinear cavity system under coherent drive and dissipation

International Nuclear Information System (INIS)

Ferretti, Sara; Andreani, Lucio Claudio; Tuereci, Hakan E.; Gerace, Dario

2010-01-01

We calculate the normalized second-order correlation function for a system of two tunnel-coupled photonic resonators, each one exhibiting a single-photon nonlinearity of the Kerr type. We employ a full quantum formulation: The master equation for the model, which takes into account both a coherent continuous drive and radiative as well as nonradiative dissipation channels, is solved analytically in steady state through a perturbative approach, and the results are compared to exact numerical simulations. The degree of second-order coherence displays values between 0 and 1, and divides the diagram identified by the two energy scales of the system - the tunneling and the nonlinear Kerr interaction - into two distinct regions separated by a crossover. When the tunneling term dominates over the nonlinear one, the system state is delocalized over both cavities, and the emitted light is coherent. In the opposite limit, photon blockade sets in, and the system shows an insulatorlike state with photons locked on each cavity, identified by antibunching of emitted light.

Ultimate Cavity Dynamics of Hydrophobic Spheres Impacting on Free Water Surfaces

KAUST Repository

Mansoor, Mohammad M.

2012-12-01

Cavity formation resulting from the water-entry of solid objects has been the subject of extensive research owing to its practical relevance in naval, military, industrial, sports and biological applications. The cavity formed by an impacting hydrophobic sphere normally seals at two places, one below (deep seal) and the other above the water surface (surface seal). For Froude numbers , the air flow into the resulting cavity is strong enough to suck the splash crown above the surface and disrupt the cavity dynamics before it deep seals. In this research work we eliminate surface seals by means of a novel practice of using cone splash-guards and examine the undisturbed transient cavity dynamics by impact of hydrophobic spheres for Froude numbers ranging . This enabled the measurement of extremely accurate pinch-off heights, pinch-off times, radial cavity collapse rates, and jet speeds in an extended range of Froude numbers compared to the previous work of Duclaux et al. (2007). Results in the extended regime were in remarkable agreement with the theoretical prediction of scaled pinch-off depth, and experimentally derived pinch-off time for . Furthermore, we investigated the influence of confinement on cavity formation by varying the cross-sectional area of the tank of liquid. In conjunction with surface seal elimination we observed the formation of multiple pinch-off points where a maximum of four deep seals were obtained in a sequential order for the Froude number range investigated. The presence of an elongated cavity beneath the first pinch-off point 5 resulted in evident "kinks" primarily related to the greatly diminished air pressure at the necking region caused by supersonic air flows (Gekle et al. 2010). Such flows passing through second pinch-offs were also found to choke the cavities beneath the first pinch- off depths causing radial expansion and hence disappearance of downward jets.

Crab cavities for linear colliders

CERN Document Server

Burt, G; Carter, R; Dexter, A; Tahir, I; Beard, C; Dykes, M; Goudket, P; Kalinin, A; Ma, L; McIntosh, P; Shulte, D; Jones, Roger M; Bellantoni, L; Chase, B; Church, M; Khabouline, T; Latina, A; Adolphsen, C; Li, Z; Seryi, Andrei; Xiao, L

2008-01-01

Crab cavities have been proposed for a wide number of accelerators and interest in crab cavities has recently increased after the successful operation of a pair of crab cavities in KEK-B. In particular crab cavities are required for both the ILC and CLIC linear colliders for bunch alignment. Consideration of bunch structure and size constraints favour a 3.9 GHz superconducting, multi-cell cavity as the solution for ILC, whilst bunch structure and beam-loading considerations suggest an X-band copper travelling wave structure for CLIC. These two cavity solutions are very different in design but share complex design issues. Phase stabilisation, beam loading, wakefields and mode damping are fundamental issues for these crab cavities. Requirements and potential design solutions will be discussed for both colliders.

SPS accelerating cavity

CERN Multimedia

CERN PhotoLab

1976-01-01

The SPS started up with 2 accelerating cavities (each consisting of 5 tank sections) in LSS3. They have a 200 MHz travelling wave structure (see 7411032 and 7802190) and 750 kW of power is fed to each of the cavities from a 1 MW tetrode power amplifier, located in a surface building above, via a coaxial transmission line. Clemens Zettler, builder of the SPS RF system, is standing at the side of one of the cavities. In 1978 and 1979 another 2 cavities were added and entered service in 1980. These were part of the intensity improvement programme and served well for the new role of the SPS as proton-antiproton collider. See also 7411032, 8011289, 8104138, 8302397.

Generation of 3D templates of active sites of proteins with rigid prosthetic groups.

Science.gov (United States)

Nebel, Jean-Christophe

2006-05-15

With the increasing availability of protein structures, the generation of biologically meaningful 3D patterns from the simultaneous alignment of several protein structures is an exciting prospect: active sites could be better understood, protein functions and protein 3D structures could be predicted more accurately. Although patterns can already be generated at the fold and topological levels, no system produces high-resolution 3D patterns including atom and cavity positions. To address this challenge, our research focuses on generating patterns from proteins with rigid prosthetic groups. Since these groups are key elements of protein active sites, the generated 3D patterns are expected to be biologically meaningful. In this paper, we present a new approach which allows the generation of 3D patterns from proteins with rigid prosthetic groups. Using 237 protein chains representing proteins containing porphyrin rings, our method was validated by comparing 3D templates generated from homologues with the 3D structure of the proteins they model. Atom positions were predicted reliably: 93% of them had an accuracy of 1.00 A or less. Moreover, similar results were obtained regarding chemical group and cavity positions. Results also suggested our system could contribute to the validation of 3D protein models. Finally, a 3D template was generated for the active site of human cytochrome P450 CYP17, the 3D structure of which is unknown. Its analysis showed that it is biologically meaningful: our method detected the main patterns of the cytochrome P450 superfamily and the motifs linked to catalytic reactions. The 3D template also suggested the position of a residue, which could be involved in a hydrogen bond with CYP17 substrates and the shape and location of a cavity. Comparisons with independently generated 3D models comforted these hypotheses. Alignment software (Nestor3D) is available at http://www.kingston.ac.uk/~ku33185/Nestor3D.html

Increasing the mode-locking efficiency of a cw solid-state laser with an auxiliary cavity

International Nuclear Information System (INIS)

Kalashnikov, V.L.; Kalosha, V.P.; Mikhailov, V.P.; Demchuk, M.I.

1992-01-01

It is predicted theoretically that the efficiency of self-mode locking can be raised by means of a bleachable shutter in the main cavity or an auxiliary cavity. The laser emits a stable train of ultrashort pulses under these conditions. The theory is based on a fluctuation model of the operation of a cw solid-state laser with a linear auxiliary cavity. The increase in efficiency involves a broadening of the region of parameter values of the system in which self-mode locking occurs, a significant decrease in the threshold pump intensity, and a reduced sensitivity of the operation to the phase mismatch of the lengths of the cavities. It is shown, for the first time, that a stable train of double ultrashort pulses can be generated by a system with a shutter in the auxiliary cavity. It is also shown that a self-mode locking is possible in the case in which there is a phase mismatch of the cavity lengths and there is no phase self-modulation in the main cavity. 15 refs., 8 figs

Effect of finite cavity width on flow oscillation in a low-Mach-number cavity flow

Energy Technology Data Exchange (ETDEWEB)

Zhang, Ke; Naguib, Ahmed M. [Michigan State University, East Lansing, MI (United States)

2011-11-15

The current study is focused on examining the effect of the cavity width and side walls on the self-sustained oscillation in a low Mach number cavity flow with a turbulent boundary layer at separation. An axisymmetric cavity geometry is employed in order to provide a reference condition that is free from any side-wall influence, which is not possible to obtain with a rectangular cavity. The cavity could then be partially filled to form finite-width geometry. The unsteady surface pressure is measured using microphone arrays that are deployed on the cavity floor along the streamwise direction and on the downstream wall along the azimuthal direction. In addition, velocity measurements using two-component Laser Doppler Anemometer are performed simultaneously with the array measurements in different azimuthal planes. The compiled data sets are used to investigate the evolution of the coherent structures generating the pressure oscillation in the cavity using linear stochastic estimation of the velocity field based on the wall-pressure signature on the cavity end wall. The results lead to the discovery of pronounced harmonic pressure oscillations near the cavity's side walls. These oscillations, which are absent in the axisymmetric cavity, are linked to the establishment of a secondary mean streamwise circulating flow pattern near the side walls and the interaction of this secondary flow with the shear layer above the cavity. (orig.)

SPEER-SERVER: a web server for prediction of protein specificity determining sites.

Science.gov (United States)

Chakraborty, Abhijit; Mandloi, Sapan; Lanczycki, Christopher J; Panchenko, Anna R; Chakrabarti, Saikat

2012-07-01

Sites that show specific conservation patterns within subsets of proteins in a protein family are likely to be involved in the development of functional specificity. These sites, generally termed specificity determining sites (SDS), might play a crucial role in binding to a specific substrate or proteins. Identification of SDS through experimental techniques is a slow, difficult and tedious job. Hence, it is very important to develop efficient computational methods that can more expediently identify SDS. Herein, we present Specificity prediction using amino acids' Properties, Entropy and Evolution Rate (SPEER)-SERVER, a web server that predicts SDS by analyzing quantitative measures of the conservation patterns of protein sites based on their physico-chemical properties and the heterogeneity of evolutionary changes between and within the protein subfamilies. This web server provides an improved representation of results, adds useful input and output options and integrates a wide range of analysis and data visualization tools when compared with the original standalone version of the SPEER algorithm. Extensive benchmarking finds that SPEER-SERVER exhibits sensitivity and precision performance that, on average, meets or exceeds that of other currently available methods. SPEER-SERVER is available at http://www.hpppi.iicb.res.in/ss/.

The LHC superconducting cavities

CERN Document Server

Boussard, Daniel; Häbel, E; Kindermann, H P; Losito, R; Marque, S; Rödel, V; Stirbet, M

1999-01-01

The LHC RF system, which must handle high intensity (0.5 A d.c.) beams, makes use of superconducting single-cell cavities, best suited to minimizing the effects of periodic transient beam loading. There will be eight cavities per beam, each capable of delivering 2 MV (5 MV/m accelerating field) at 400 MHz. The cavities themselves are now being manufactured by industry, using niobium-on-copper technology which gives full satisfaction at LEP. A cavity unit includes a helium tank (4.5 K operating temperature) built around a cavity cell, RF and HOM couplers and a mechanical tuner, all housed in a modular cryostat. Four-unit modules are ultimately foreseen for the LHC (two per beam), while at present a prototype version with two complete units is being extensively tested. In addition to a detailed description of the cavity and its ancillary equipment, the first test results of the prototype will be reported.

Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12.

Science.gov (United States)

Thieffry, D; Salgado, H; Huerta, A M; Collado-Vides, J

1998-06-01

As one of the best-characterized free-living organisms, Escherichia coli and its recently completed genomic sequence offer a special opportunity to exploit systematically the variety of regulatory data available in the literature in order to make a comprehensive set of regulatory predictions in the whole genome. The complete genome sequence of E.coli was analyzed for the binding of transcriptional regulators upstream of coding sequences. The biological information contained in RegulonDB (Huerta, A.M. et al., Nucleic Acids Res.,26,55-60, 1998) for 56 different transcriptional proteins was the support to implement a stringent strategy combining string search and weight matrices. We estimate that our search included representatives of 15-25% of the total number of regulatory binding proteins in E.coli. This search was performed on the set of 4288 putative regulatory regions, each 450 bp long. Within the regions with predicted sites, 89% are regulated by one protein and 81% involve only one site. These numbers are reasonably consistent with the distribution of experimental regulatory sites. Regulatory sites are found in 603 regions corresponding to 16% of operon regions and 10% of intra-operonic regions. Additional evidence gives stronger support to some of these predictions, including the position of the site, biological consistency with the function of the downstream gene, as well as genetic evidence for the regulatory interaction. The predictions described here were incorporated into the map presented in the paper describing the complete E.coli genome (Blattner,F.R. et al., Science, 277, 1453-1461, 1997). The complete set of predictions in GenBank format is available at the url: http://www. cifn.unam.mx/Computational_Biology/E.coli-predictions ecoli-reg@cifn.unam.mx, collado@cifn.unam.mx

Method of predicting Splice Sites based on signal interactions

Directory of Open Access Journals (Sweden)

Deogun Jitender S

2006-04-01

Full Text Available Abstract Background Predicting and proper ranking of canonical splice sites (SSs is a challenging problem in bioinformatics and machine learning communities. Any progress in SSs recognition will lead to better understanding of splicing mechanism. We introduce several new approaches of combining a priori knowledge for improved SS detection. First, we design our new Bayesian SS sensor based on oligonucleotide counting. To further enhance prediction quality, we applied our new de novo motif detection tool MHMMotif to intronic ends and exons. We combine elements found with sensor information using Naive Bayesian Network, as implemented in our new tool SpliceScan. Results According to our tests, the Bayesian sensor outperforms the contemporary Maximum Entropy sensor for 5' SS detection. We report a number of putative Exonic (ESE and Intronic (ISE Splicing Enhancers found by MHMMotif tool. T-test statistics on mouse/rat intronic alignments indicates, that detected elements are on average more conserved as compared to other oligos, which supports our assumption of their functional importance. The tool has been shown to outperform the SpliceView, GeneSplicer, NNSplice, Genio and NetUTR tools for the test set of human genes. SpliceScan outperforms all contemporary ab initio gene structural prediction tools on the set of 5' UTR gene fragments. Conclusion Designed methods have many attractive properties, compared to existing approaches. Bayesian sensor, MHMMotif program and SpliceScan tools are freely available on our web site. Reviewers This article was reviewed by Manyuan Long, Arcady Mushegian and Mikhail Gelfand.

Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites

DEFF Research Database (Denmark)

Julenius, Karin; Mølgaard, Anne; Gupta, Ramneek

2005-01-01

could be predicted from averaged properties together with the fact that glycosylation sites are not precisely conserved indicates that mucin-type glycosylation in most cases is a bulk property and not a very site-specific one. NetOGlyc 3.1 is made available at www.cbs.dtu.dk/services/netoglyc....

Velocity Measurements in Nasal Cavities by Means of Stereoscopic Piv - Preliminary Tests

Science.gov (United States)

Cozzi, Fabio; Felisati, Giovanni; Quadrio, Maurizio

2017-08-01

The prediction of detailed flow patterns in human nasal cavities using computational fluid dynamics (CFD) can provide essential information on the potential relationship between patient-specific geometrical characteristics of the nasal anatomy and health problems, and ultimately led to improved surgery. The complex flow structure and the intricate geometry of the nasal cavities make achieving such goals a challenge for CFD specialists. The need for experimental data to validate and improve the numerical simulations is particularly crucial. To this aim an experimental set-up based on Stereo PIV and a silicon phantom of nasal cavities have been designed and realized at Politecnico di Milano. This work describes the main features and challenges of the set-up along with some preliminary results.

Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms

Science.gov (United States)

Jian, Jhih-Wei; Elumalai, Pavadai; Pitti, Thejkiran; Wu, Chih Yuan; Tsai, Keng-Chang; Chang, Jeng-Yih; Peng, Hung-Pin; Yang, An-Suei

2016-01-01

Predicting ligand binding sites (LBSs) on protein structures, which are obtained either from experimental or computational methods, is a useful first step in functional annotation or structure-based drug design for the protein structures. In this work, the structure-based machine learning algorithm ISMBLab-LIG was developed to predict LBSs on protein surfaces with input attributes derived from the three-dimensional probability density maps of interacting atoms, which were reconstructed on the query protein surfaces and were relatively insensitive to local conformational variations of the tentative ligand binding sites. The prediction accuracy of the ISMBLab-LIG predictors is comparable to that of the best LBS predictors benchmarked on several well-established testing datasets. More importantly, the ISMBLab-LIG algorithm has substantial tolerance to the prediction uncertainties of computationally derived protein structure models. As such, the method is particularly useful for predicting LBSs not only on experimental protein structures without known LBS templates in the database but also on computationally predicted model protein structures with structural uncertainties in the tentative ligand binding sites. PMID:27513851

Cavity-enhanced spectroscopies

CERN Document Server

van Zee, Roger

2003-01-01

""Cavity-Enhanced Spectroscopy"" discusses the use of optical resonators and lasers to make sensitive spectroscopic measurements. This volume is written by the researcchers who pioneered these methods. The book reviews both the theory and practice behind these spectroscopic tools and discusses the scientific discoveries uncovered by these techniques. It begins with a chapter on the use of optical resonators for frequency stabilization of lasers, which is followed by in-depth chapters discussing cavity ring-down spectroscopy, frequency-modulated, cavity-enhanced spectroscopy, intracavity spectr

Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility.

Science.gov (United States)

Liu, Sheng; Zibetti, Cristina; Wan, Jun; Wang, Guohua; Blackshaw, Seth; Qian, Jiang

2017-07-27

Computational prediction of transcription factor (TF) binding sites in different cell types is challenging. Recent technology development allows us to determine the genome-wide chromatin accessibility in various cellular and developmental contexts. The chromatin accessibility profiles provide useful information in prediction of TF binding events in various physiological conditions. Furthermore, ChIP-Seq analysis was used to determine genome-wide binding sites for a range of different TFs in multiple cell types. Integration of these two types of genomic information can improve the prediction of TF binding events. We assessed to what extent a model built upon on other TFs and/or other cell types could be used to predict the binding sites of TFs of interest. A random forest model was built using a set of cell type-independent features such as specific sequences recognized by the TFs and evolutionary conservation, as well as cell type-specific features derived from chromatin accessibility data. Our analysis suggested that the models learned from other TFs and/or cell lines performed almost as well as the model learned from the target TF in the cell type of interest. Interestingly, models based on multiple TFs performed better than single-TF models. Finally, we proposed a universal model, BPAC, which was generated using ChIP-Seq data from multiple TFs in various cell types. Integrating chromatin accessibility information with sequence information improves prediction of TF binding.The prediction of TF binding is transferable across TFs and/or cell lines suggesting there are a set of universal "rules". A computational tool was developed to predict TF binding sites based on the universal "rules".

Hydroforming of elliptical cavities

Science.gov (United States)

Singer, W.; Singer, X.; Jelezov, I.; Kneisel, P.

2015-02-01

Activities of the past several years in developing the technique of forming seamless (weldless) cavity cells by hydroforming are summarized. An overview of the technique developed at DESY for the fabrication of single cells and multicells of the TESLA cavity shape is given and the major rf results are presented. The forming is performed by expanding a seamless tube with internal water pressure while simultaneously swaging it axially. Prior to the expansion the tube is necked at the iris area and at the ends. Tube radii and axial displacements are computer controlled during the forming process in accordance with results of finite element method simulations for necking and expansion using the experimentally obtained strain-stress relationship of tube material. In cooperation with industry different methods of niobium seamless tube production have been explored. The most appropriate and successful method is a combination of spinning or deep drawing with flow forming. Several single-cell niobium cavities of the 1.3 GHz TESLA shape were produced by hydroforming. They reached accelerating gradients Eacc up to 35 MV /m after buffered chemical polishing (BCP) and up to 42 MV /m after electropolishing (EP). More recent work concentrated on fabrication and testing of multicell and nine-cell cavities. Several seamless two- and three-cell units were explored. Accelerating gradients Eacc of 30 - 35 MV /m were measured after BCP and Eacc up to 40 MV /m were reached after EP. Nine-cell niobium cavities combining three three-cell units were completed at the company E. Zanon. These cavities reached accelerating gradients of Eacc=30 - 35 MV /m . One cavity is successfully integrated in an XFEL cryomodule and is used in the operation of the FLASH linear accelerator at DESY. Additionally the fabrication of bimetallic single-cell and multicell NbCu cavities by hydroforming was successfully developed. Several NbCu clad single-cell and double-cell cavities of the TESLA shape have been

Cavity Processing and Preparation of 650 MHz Elliptical Cell Cavities for PIP-II

Energy Technology Data Exchange (ETDEWEB)

Rowe, Allan [Fermilab; Chandrasekaran, Saravan Kumar [Fermilab; Grassellino, Anna [Fermilab; Melnychuk, Oleksandr [Fermilab; Merio, Margherita [Fermilab; Reid, Thomas [Argonne (main); Sergatskov, Dmitri [Fermilab

2017-05-01

The PIP-II project at Fermilab requires fifteen 650 MHz SRF cryomodules as part of the 800 MeV LINAC that will provide a high intensity proton beam to the Fermilab neutrino program. A total of fifty-seven high-performance SRF cavities will populate the cryomodules and will operate in both pulsed and continuous wave modes. These cavities will be processed and prepared for performance testing utilizing adapted cavity processing infrastructure already in place at Fermilab and Argonne. The processing recipes implemented for these structures will incorporate state-of-the art processing and cleaning techniques developed for 1.3 GHz SRF cavities for the ILC, XFEL, and LCLS-II projects. This paper describes the details of the processing recipes and associated chemistry, heat treatment, and cleanroom processes at the Fermilab and Argonne cavity processing facilities. This paper also presents single and multi-cell cavity test results with quality factors above 5·10¹⁰ and accelerating gradients above 30 MV/m.

Hierarchical creep cavity formation in an ultramylonite and implications for phase mixing

Science.gov (United States)

Gilgannon, James; Fusseis, Florian; Menegon, Luca; Regenauer-Lieb, Klaus; Buckman, Jim

2017-12-01

Establishing models for the formation of well-mixed polyphase domains in ultramylonites is difficult because the effects of large strains and thermo-hydro-chemo-mechanical feedbacks can obscure the transient phenomena that may be responsible for domain production. We use scanning electron microscopy and nanotomography to offer critical insights into how the microstructure of a highly deformed quartzo-feldspathic ultramylonite evolved. The dispersal of monomineralic quartz domains in the ultramylonite is interpreted to be the result of the emergence of synkinematic pores, called creep cavities. The cavities can be considered the product of two distinct mechanisms that formed hierarchically: Zener-Stroh cracking and viscous grain-boundary sliding. In initially thick and coherent quartz ribbons deforming by grain-size-insensitive creep, cavities were generated by the Zener-Stroh mechanism on grain boundaries aligned with the YZ plane of finite strain. The opening of creep cavities promoted the ingress of fluids to sites of low stress. The local addition of a fluid lowered the adhesion and cohesion of grain boundaries and promoted viscous grain-boundary sliding. With the increased contribution of viscous grain-boundary sliding, a second population of cavities formed to accommodate strain incompatibilities. Ultimately, the emergence of creep cavities is interpreted to be responsible for the transition of quartz domains from a grain-size-insensitive to a grain-size-sensitive rheology.

Subharmonic generation, chaos, and subharmonic resurrection in an acoustically driven fluid-filled cavity.

Science.gov (United States)

Cantrell, John H; Adler, Laszlo; Yost, William T

2015-02-01

Traveling wave solutions of the nonlinear acoustic wave equation are obtained for the fundamental and second harmonic resonances of a fluid-filled cavity. The solutions lead to the development of a non-autonomous toy model for cavity oscillations. Application of the Melnikov method to the model equation predicts homoclinic bifurcation of the Smale horseshoe type leading to a cascade of period doublings with increasing drive displacement amplitude culminating in chaos. The threshold value of the drive displacement amplitude at tangency is obtained in terms of the acoustic drive frequency and fluid attenuation coefficient. The model prediction of subharmonic generation leading to chaos is validated from acousto-optic diffraction measurements in a water-filled cavity using a 5 MHz acoustic drive frequency and from the measured frequency spectrum in the bifurcation cascade regime. The calculated resonant threshold amplitude of 0.2 nm for tangency is consistent with values estimated for the experimental set-up. Experimental evidence for the appearance of a stable subharmonic beyond chaos is reported.

A novel, highly efficient cavity backshort design for far-infrared TES detectors

Science.gov (United States)

Bracken, C.; de Lange, G.; Audley, M. D.; Trappe, N.; Murphy, J. A.; Gradziel, M.; Vreeling, W.-J.; Watson, D.

2018-03-01

In this paper we present a new cavity backshort design for TES (transition edge sensor) detectors which will provide increased coupling of the incoming astronomical signal to the detectors. The increased coupling results from the improved geometry of the cavities, where the geometry is a consequence of the proposed chemical etching manufacturing technique. Using a number of modelling techniques, predicted results of the performance of the cavities for frequencies of 4.3-10 THz are presented and compared to more standard cavity designs. Excellent optical efficiency is demonstrated, with improved response flatness across the band. In order to verify the simulated results, a scaled model cavity was built for testing at the lower W-band frequencies (75-100 GHz) with a VNA system. Further testing of the scale model at THz frequencies was carried out using a globar and bolometer via an FTS measurement set-up. The experimental results are presented, and compared to the simulations. Although there is relatively poor comparison between simulation and measurement at some frequencies, the discrepancies are explained by means of higher-mode excitation in the measured cavity which are not accounted for in the single-mode simulations. To verify this assumption, a better behaved cylindrical cavity is simulated and measured, where excellent agreement is demonstrated in those results. It can be concluded that both the simulations and the supporting measurements give confidence that this novel cavity design will indeed provide much-improved optical coupling for TES detectors in the far-infrared/THz band.

Estimating cavity tree and snag abundance using negative binomial regression models and nearest neighbor imputation methods

Science.gov (United States)

Bianca N.I. Eskelson; Hailemariam Temesgen; Tara M. Barrett

2009-01-01

Cavity tree and snag abundance data are highly variable and contain many zero observations. We predict cavity tree and snag abundance from variables that are readily available from forest cover maps or remotely sensed data using negative binomial (NB), zero-inflated NB, and zero-altered NB (ZANB) regression models as well as nearest neighbor (NN) imputation methods....

Formation of coronal cavities

International Nuclear Information System (INIS)

An, C.H.; Suess, S.T.; Tandberg-Hanssen, E.; Steinolfson, R.S.

1986-01-01

A theoretical study of the formation of a coronal cavity and its relation to a quiescent prominence is presented. It is argued that the formation of a cavity is initiated by the condensation of plasma which is trapped by the coronal magnetic field in a closed streamer and which then flows down to the chromosphere along the field lines due to lack of stable magnetic support against gravity. The existence of a coronal cavity depends on the coronal magnetic field strength; with low strength, the plasma density is not high enough for condensation to occur. Furthermore, we suggest that prominence and cavity material is supplied from the chromospheric level. Whether a coronal cavity and a prominence coexist depends on the magnetic field configuration; a prominence requires stable magnetic support

Temperature Sensitivity of an Atomic Vapor Cell-Based Dispersion-Enhanced Optical Cavity

Science.gov (United States)

Myneni, K.; Smith, D. D.; Chang, H.; Luckay, H. A.

2015-01-01

Enhancement of the response of an optical cavity to a change in optical path length, through the use of an intracavity fast-light medium, has previously been demonstrated experimentally and described theoretically for an atomic vapor cell as the intracavity resonant absorber. This phenomenon may be used to enhance both the scale factor and sensitivity of an optical cavity mode to the change in path length, e.g. in gyroscopic applications. We study the temperature sensitivity of the on-resonant scale factor enhancement, S(sub o), due to the thermal sensitivity of the lower-level atom density in an atomic vapor cell, specifically for the case of the Rb-87 D(sub 2) transition. A semi-empirical model of the temperature-dependence of the absorption profile, characterized by two parameters, a(sub o)(T) and gamma(sub a)(T) allows the temperature-dependence of the cavity response, S(sub o)(T) and dS(sub o)/dT to be predicted over a range of temperature. We compare the predictions to experiment. Our model will be useful in determining the useful range for S(sub o), given the practical constraints on temperature stability for an atomic vapor cell.

Cofactor-binding sites in proteins of deviating sequence: comparative analysis and clustering in torsion angle, cavity, and fold space.

Science.gov (United States)

Stegemann, Björn; Klebe, Gerhard

2012-02-01

Small molecules are recognized in protein-binding pockets through surface-exposed physicochemical properties. To optimize binding, they have to adopt a conformation corresponding to a local energy minimum within the formed protein-ligand complex. However, their conformational flexibility makes them competent to bind not only to homologous proteins of the same family but also to proteins of remote similarity with respect to the shape of the binding pockets and folding pattern. Considering drug action, such observations can give rise to unexpected and undesired cross reactivity. In this study, datasets of six different cofactors (ADP, ATP, NAD(P)(H), FAD, and acetyl CoA, sharing an adenosine diphosphate moiety as common substructure), observed in multiple crystal structures of protein-cofactor complexes exhibiting sequence identity below 25%, have been analyzed for the conformational properties of the bound ligands, the distribution of physicochemical properties in the accommodating protein-binding pockets, and the local folding patterns next to the cofactor-binding site. State-of-the-art clustering techniques have been applied to group the different protein-cofactor complexes in the different spaces. Interestingly, clustering in cavity (Cavbase) and fold space (DALI) reveals virtually the same data structuring. Remarkable relationships can be found among the different spaces. They provide information on how conformations are conserved across the host proteins and which distinct local cavity and fold motifs recognize the different portions of the cofactors. In those cases, where different cofactors are found to be accommodated in a similar fashion to the same fold motifs, only a commonly shared substructure of the cofactors is used for the recognition process. Copyright © 2011 Wiley Periodicals, Inc.

The Superconducting TESLA Cavities

CERN Document Server

Aune, B.; Bloess, D.; Bonin, B.; Bosotti, A.; Champion, M.; Crawford, C.; Deppe, G.; Dwersteg, B.; Edwards, D.A.; Edwards, H.T.; Ferrario, M.; Fouaidy, M.; Gall, P-D.; Gamp, A.; Gössel, A.; Graber, J.; Hubert, D.; Hüning, M.; Juillard, M.; Junquera, T.; Kaiser, H.; Kreps, G.; Kuchnir, M.; Lange, R.; Leenen, M.; Liepe, M.; Lilje, L.; Matheisen, A.; Möller, W-D.; Mosnier, A.; Padamsee, H.; Pagani, C.; Pekeler, M.; Peters, H-B.; Peters, O.; Proch, D.; Rehlich, K.; Reschke, D.; Safa, H.; Schilcher, T.; Schmüser, P.; Sekutowicz, J.; Simrock, S.; Singer, W.; Tigner, M.; Trines, D.; Twarowski, K.; Weichert, G.; Weisend, J.; Wojtkiewicz, J.; Wolff, S.; Zapfe, K.

2000-01-01

The conceptional design of the proposed linear electron-positron colliderTESLA is based on 9-cell 1.3 GHz superconducting niobium cavities with anaccelerating gradient of Eacc >= 25 MV/m at a quality factor Q0 > 5E+9. Thedesign goal for the cavities of the TESLA Test Facility (TTF) linac was set tothe more moderate value of Eacc >= 15 MV/m. In a first series of 27industrially produced TTF cavities the average gradient at Q0 = 5E+9 wasmeasured to be 20.1 +- 6.2 MV/m, excluding a few cavities suffering fromserious fabrication or material defects. In the second production of 24 TTFcavities additional quality control measures were introduced, in particular aneddy-current scan to eliminate niobium sheets with foreign material inclusionsand stringent prescriptions for carrying out the electron-beam welds. Theaverage gradient of these cavities at Q0 = 5E+9 amounts to 25.0 +- 3.2 MV/mwith the exception of one cavity suffering from a weld defect. Hence only amoderate improvement in production and preparation technique...

Acoustic energy harvesting by piezoelectric curved beams in the cavity of a sonic crystal

International Nuclear Information System (INIS)

Wang, Wei-Chung; Wu, Liang-Yu; Chen, Lien-Wen; Liu, Chia-Ming

2010-01-01

Acoustic energy harvesting by piezoelectric curved beams in the cavity of a sonic crystal is investigated. A resonant cavity of the sonic crystal is used to localize the acoustic wave as the acoustic waves are incident into the sonic crystal at the resonant frequency. The piezoelectric curved beam is placed in the resonant cavity and vibrated by the acoustic wave. The energy harvesting can be achieved as the acoustic waves are incident at the resonant frequency. A model for energy harvesting of the piezoelectric curved beam is also developed to predict the output voltage and power of the energy harvesting. The experimental results are compared with the theoretical

Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces.

Directory of Open Access Journals (Sweden)

Ching-Tai Chen

Full Text Available Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins and were tested on an independent dataset (consisting of 142 proteins. The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted

Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces

Science.gov (United States)

Chen, Ching-Tai; Peng, Hung-Pin; Jian, Jhih-Wei; Tsai, Keng-Chang; Chang, Jeng-Yih; Yang, Ei-Wen; Chen, Jun-Bo; Ho, Shinn-Ying; Hsu, Wen-Lian; Yang, An-Suei

2012-01-01

Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with

Dosimetric response of variable-size cavities in photon-irradiated media and the behaviour of the Spencer-Attix cavity integral with increasing Δ.

Science.gov (United States)

Kumar, Sudhir; Deshpande, Deepak D; Nahum, Alan E

2016-04-07

Cavity theory is fundamental to understanding and predicting dosimeter response. Conventional cavity theories have been shown to be consistent with one another by deriving the electron (+positron) and photon fluence spectra with the FLURZnrc user-code (EGSnrc Monte-Carlo system) in large volumes under quasi-CPE for photon beams of 1 MeV and 10 MeV in three materials (water, aluminium and copper) and then using these fluence spectra to evaluate and then inter-compare the Bragg-Gray, Spencer-Attix and 'large photon' 'cavity integrals'. The behaviour of the 'Spencer-Attix dose' (aka restricted cema), D S-A(▵), in a 1-MeV photon field in water has been investigated for a wide range of values of the cavity-size parameter ▵: D S-A(▵) decreases far below the Monte-Carlo dose (D MC) for ▵ greater than  ≈  30 keV due to secondary electrons with starting energies below ▵ not being 'counted'. We show that for a quasi-scatter-free geometry (D S-A(▵)/D MC) is closely equal to the proportion of energy transferred to Compton electrons with initial (kinetic) energies above ▵, derived from the Klein-Nishina (K-N) differential cross section. (D S-A(▵)/D MC) can be used to estimate the maximum size of a detector behaving as a Bragg-Gray cavity in a photon-irradiated medium as a function of photon-beam quality (under quasi CPE) e.g. a typical air-filled ion chamber is 'Bragg-Gray' at (monoenergetic) beam energies  ⩾260 keV. Finally, by varying the density of a silicon cavity (of 2.26 mm diameter and 2.0 mm thickness) in water, the response of different cavity 'sizes' was simulated; the Monte-Carlo-derived ratio D w/D Si for 6 MV and 15 MV photons varied from very close to the Spencer-Attix value at 'gas' densities, agreed well with Burlin cavity theory as ρ increased, and approached large photon behaviour for ρ  ≈  10 g cm(-3). The estimate of ▵ for the Si cavity was improved by incorporating a Monte-Carlo-derived correction for

Radial dependence of foreshock cavities: a case study

Directory of Open Access Journals (Sweden)

D. G. Sibeck

2004-12-01

Full Text Available We present a case study of Geotail, Interball-1, IMP-8, and Wind observations of density and magnetic field strength cavities excavated by the enhanced pressures associated with bursts of energetic ions in the foreshock. Consistent with theoretical predictions, the pressure of the energetic ions diminishes rapidly with upstream distance due to a decrease in the flux of energetic ions and a transition from near-isotropic to streaming pitch angle distributions. Consequently, the cavities can only be observed immediately upstream from the bow shock. A comparison of conditions upstream from the pre- and post-noon bow shock demonstrates that foreshock cavities introduce perturbations into the oncoming solar wind flow with dimensions smaller than those of the magnetosphere. Dayside geosynchronous magnetic field strength variations observed by GOES-8 do not track the density variations seen by any of the spacecraft upstream from the bow shock in a one-to-one manner, indicating that none of these spacecraft observed the precise sequence of density variations that actually struck the subsolar magnetopause. Key words. Interplanetary physics (energetic particles; planetary bow shocks – Magnetospheric physics (solar wind-magnetosphere interactions

Radial dependence of foreshock cavities: a case study

Directory of Open Access Journals (Sweden)

D. G. Sibeck

2004-12-01

Full Text Available We present a case study of Geotail, Interball-1, IMP-8, and Wind observations of density and magnetic field strength cavities excavated by the enhanced pressures associated with bursts of energetic ions in the foreshock. Consistent with theoretical predictions, the pressure of the energetic ions diminishes rapidly with upstream distance due to a decrease in the flux of energetic ions and a transition from near-isotropic to streaming pitch angle distributions. Consequently, the cavities can only be observed immediately upstream from the bow shock. A comparison of conditions upstream from the pre- and post-noon bow shock demonstrates that foreshock cavities introduce perturbations into the oncoming solar wind flow with dimensions smaller than those of the magnetosphere. Dayside geosynchronous magnetic field strength variations observed by GOES-8 do not track the density variations seen by any of the spacecraft upstream from the bow shock in a one-to-one manner, indicating that none of these spacecraft observed the precise sequence of density variations that actually struck the subsolar magnetopause.

Key words. Interplanetary physics (energetic particles; planetary bow shocks – Magnetospheric physics (solar wind-magnetosphere interactions

Study of liquid metal mixed convection in cavities

International Nuclear Information System (INIS)

Abadie, Philippe.

1979-10-01

This study has enabled some results to be obtained on the flow of liquid metals in cavities. The effects of different adimensional parameters characteristic of mixed convection flows were experimentally demonstrated. In the case of a roof heated cavity, three zones were distinguished: the mixing zone at the channel exit, a quasi constant temperature recirculation zone and a stratified zone at the top of the cavity. The thickness of this last region depends on natural convection effects: it disappears completely in a pure forced convection regime. A simple model using a critical Richardson number concept was developed in order to be able to predict the thickness of this region. Heat transfer correlation formulas were established both for the heated roof and forward direction heated wall cases. Some data was also obtained on temperature fluctuations for both cases. The different topics investigated are useful for defining heat transfers in certain regions of fast neutron sodium cooled reactors. A more extensive program is currently being developed in order to be able to investigate a wider range of variations in the above mentioned parameters and to more closely approximate reactor vessels [fr

Ensemble approach combining multiple methods improves human transcription start site prediction

LENUS (Irish Health Repository)

Dineen, David G

2010-11-30

Abstract Background The computational prediction of transcription start sites is an important unsolved problem. Some recent progress has been made, but many promoters, particularly those not associated with CpG islands, are still difficult to locate using current methods. These methods use different features and training sets, along with a variety of machine learning techniques and result in different prediction sets. Results We demonstrate the heterogeneity of current prediction sets, and take advantage of this heterogeneity to construct a two-level classifier (\\'Profisi Ensemble\\') using predictions from 7 programs, along with 2 other data sources. Support vector machines using \\'full\\' and \\'reduced\\' data sets are combined in an either\\/or approach. We achieve a 14% increase in performance over the current state-of-the-art, as benchmarked by a third-party tool. Conclusions Supervised learning methods are a useful way to combine predictions from diverse sources.

Conversion of localized lower hybrid oscillations and fast magnetosonic waves at a plasma density cavity

International Nuclear Information System (INIS)

Hall, J.O.

2004-01-01

Analytic expressions are presented for conversion of localized lower hybrid oscillations and magnetosonic waves by scattering off a small scale density cavity. The governing equations are solved in slab geometry with wave vectors perpendicular to both the ambient magnetic field and the density gradient associated with density cavity using a scale length separation method. The theory predicts strong excitation of localized lower hybrid oscillations for a set of frequencies between the lower hybrid frequency of the ambient plasma and the minimum lower hybrid frequency inside the cavity. The theory is relevant for the lower hybrid solitary structures observed in space plasmas

Disposal of low- and intermediate-level solid radioactive wastes in rock cavities. A guidebook

Energy Technology Data Exchange (ETDEWEB)

1983-01-01

This Guidebook summarizes the factors to be considered and the activities to be undertaken in the overall planning and development of a disposal system for solid or solidified low- and intermediate-level wastes in rock cavities. Aspects related to repository site selection, design, construction, operation, shutdown, surveillance, regulation and safety assessment are discussed here in general terms. They will be covered in greater technical detail in a separate document. This report considers the emplacement of wastes in categories II, III, IV and V, as defined in Table 3.1, in different kinds of cavities located at various depths from just below the surface to deep continental rock. The choice of the type of cavity and its depth and of the disposal site itself is related to the radiological protection requirements for the wastes concerned. The repositories considered include natural caves and abandoned mines as well as specially excavated cavities in various geological formations. Consideration is also given to hydrogeological, environmental and societal factors. The guidelines given in the report are made sufficiently general to cover a broad variety of different circumstances. Consequently, the practical application of these guidelines needs a case-by-case consideration which takes into account the local conditions, e.g. natural circumstances, the characteristics of the wastes and national and international regulations and practices.

A study of intergranular cavity growth controlled by the coupling of diffusion and power law creep

International Nuclear Information System (INIS)

Wang, J.S.; Martinez, L.; Nix, W.D.

1983-01-01

A technique based on pre-creeping and sintering is used to create large, widely spaced cavities at grain boundaries in copper. The size and spacing of the cavities is such that cavity growth is expected to be controlled by the coupling of diffusion and power law creep. The rupture properties of these pre-cavitated samples are studied over a range of stresses and temperatures and the results are compared with the predictions of various theoretical treatments of cavity growth. The stress and temperature dependence of rupture can be described using an analysis of the type suggested by Chen and Argon, provided that the diffusional length is based on the ligament stress rather than the applied stress

Prediction of pollution into ore bearing aquifer from ISL-site

International Nuclear Information System (INIS)

Dolgopolov, V.; Kayukov, P.; Vyatchennikova, L.; Shishkov, I.

2002-01-01

Outcomes of present mineralogical investigations explain some phenomena observed in previous sorption experiences. First of all they elucidate cutback of filtration coefficients of sediments exposed under pollution process as granulometric fractions of these permeable sediments decreased in its weight ratio in according to impermeable ones. Then sorption graphics are explained by chemical and mineralogical changes in experienced substance. Explores made diagnoses and estimation about 45 authigenous and technogenous minerals playing the essential role in the process of mass transfer of uranium and polluted components in ISL-sites. They are considered in all basic fractions of studied sediments. Bright peculiarities are noticed for gravel and coarse sands, which went to pieces as a result of dilution or decomposition of its cement. Mineral composition of clayey fraction also significantly changed after pollution process. Steep lost of weight of fraction 0.005-0.001mm consisted with partial decomposition of clayey minerals basically of montmorillonite. These investigations show also that ones of the main minerals playing such the essential role are sorptive such as silica, silica gel, common opal, opal-CT, noble opal, allophane, montmorillonite and zeolite minerals. In conclusion the given work shows some filtration properties of aquifer in an ISL-site and predicts the spread of a possible pollution for ISL-site to environment. The extension of pollution could be more one-two dimension of affected by ISL-process. The prediction would be exact if the previous investigation included the desorptive characteristics and sorptive data depending on temperature and pressure. Current investigations continued pervious ones after which some inexplicable matters of migration of contaminated halo from an ISL-polygon are as follows: Identification and specification of all minerals outside ISL-polygon; Calculation of mineral balance for contaminated sites; Specification of flow

Hydroforming of elliptical cavities

Directory of Open Access Journals (Sweden)

W. Singer

2015-02-01

Full Text Available Activities of the past several years in developing the technique of forming seamless (weldless cavity cells by hydroforming are summarized. An overview of the technique developed at DESY for the fabrication of single cells and multicells of the TESLA cavity shape is given and the major rf results are presented. The forming is performed by expanding a seamless tube with internal water pressure while simultaneously swaging it axially. Prior to the expansion the tube is necked at the iris area and at the ends. Tube radii and axial displacements are computer controlled during the forming process in accordance with results of finite element method simulations for necking and expansion using the experimentally obtained strain-stress relationship of tube material. In cooperation with industry different methods of niobium seamless tube production have been explored. The most appropriate and successful method is a combination of spinning or deep drawing with flow forming. Several single-cell niobium cavities of the 1.3 GHz TESLA shape were produced by hydroforming. They reached accelerating gradients E_{acc} up to 35  MV/m after buffered chemical polishing (BCP and up to 42  MV/m after electropolishing (EP. More recent work concentrated on fabrication and testing of multicell and nine-cell cavities. Several seamless two- and three-cell units were explored. Accelerating gradients E_{acc} of 30–35  MV/m were measured after BCP and E_{acc} up to 40  MV/m were reached after EP. Nine-cell niobium cavities combining three three-cell units were completed at the company E. Zanon. These cavities reached accelerating gradients of E_{acc}=30–35  MV/m. One cavity is successfully integrated in an XFEL cryomodule and is used in the operation of the FLASH linear accelerator at DESY. Additionally the fabrication of bimetallic single-cell and multicell NbCu cavities by hydroforming was successfully developed. Several NbCu clad single-cell and

Binding of copper and nickel to cavities in silicon formed by helium ion implantation

International Nuclear Information System (INIS)

Myers, S.M.; Follstaedt, D.M.; Bishop, D.M.

1993-01-01

Cavities formed in Si by He ion implantation and annealing are shown to be strong traps for Cu and Ni impurities. Experiments utilizing ion-beam analysis and transmission electron microscopy indicate that Cu is trapped at the internal surfaces of cavities up to ∼1 monolayer coverage with a binding energy of 2.2±0.2 eV relative to solution. This is greater than the heat of solution from the precipitated Cu 3 Si phase, determined to be 1.7 eV in agreement with earlier work. Copper at cavity-wall sites is reversibly replaced by H during heating in H 2 gas, indicating the relative stability of the two surface terminations. Initial results for Ni impurities indicate that trapping at cavities is again energetically preferred to silicide formation. The saturation coverage of Ni on the internal surfaces, however, is an order of magnitude smaller for Ni than Cu, consistent with published studies of external-surface adsorption. These results suggest that cavity trapping may getter metallic impurities in Si more effectively than methods based on silicide precipitation

X-ray and gamma ray waveguide, cavity and method

International Nuclear Information System (INIS)

Vali, V.; Krogstad, R.S.; Willard, H.R.

1978-01-01

An x-ray and gamma ray waveguide, cavity, and method for directing electromagnetic radiation of the x-ray, gamma ray, and extreme ultraviolet wavelengths are described. A hollow fiber is used as the waveguide and is manufactured from a material having an index of refraction less than unity for these wavelengths. The internal diameter of the hollow fiber waveguide and the radius of curvature for the waveguide are selectively predetermined in light of the wavelength of the transmitted radiation to minimize losses. The electromagnetic radiation is obtained from any suitable source ad upon introduction into the waveguide is transmitted along a curvilinear path. The waveguide may be formed as a closed loop to create a cavity or may be used to direct the electromagnetic radiation to a utilization site

Soil attributes drive nest-site selection by the campo miner Geositta poeciloptera

Science.gov (United States)

Teixeira, João Paulo Gusmão; Solar, Ricardo; Vasconcelos, Bruno Nery F.; Fernandes, Raphael B. A.; Lopes, Leonardo Esteves

2018-01-01

Substrate type is a key-factor in nest-site selection and nest architecture of burrowing birds. However, little is known about which factors drive nest-site selection for these species, especially in the tropics. We studied the influence of soil attributes on nest-site selection by the campo miner Geositta poeciloptera, an open grassland bird that builds its nests within soil cavities. For all nests found, we measured the depth of the nest cavity and the resistance of the soil to penetration, and identified the soil horizon in which the nest was located. In soil banks with nests, we collected soil samples for granulometric analysis around each nest cavity, while in soil banks without nests we collected these samples at random points. From 43 nests found, 86% were located in the deeper soil horizons (C-horizon), and only 14% in the shallower horizons (B-horizon). Granulometric analysis showed that the C-horizons possessed a high similar granulometric composition, with high silt and low clay contents. These characteristics are associated with a low degree of structural development of the soil, which makes it easier to excavate. Contrarily, soil resistance to penetration does not seem to be an important criterion for nest site selection, although nests in more resistant the soils tend to have shallower nest cavities. Among the soil banks analyzed, 40% of those without cavities possessed a larger proportion of B-horizon relative to the C-horizon, and their texture was more clayey. On the other hand, almost all soil banks containing nest cavities had a larger C-horizon and a silty texture, indicating that soil attributes drive nest-site selection by G. poeciloptera. Thus, we conclude that the patchy distribution of G. poeciloptera can attributed to the infrequent natural exposure of the C-horizon in the tropical region, where well developed, deep and permeable soils are more common. PMID:29381768

Soil attributes drive nest-site selection by the campo miner Geositta poeciloptera.

Science.gov (United States)

Meireles, Ricardo Camargos de; Teixeira, João Paulo Gusmão; Solar, Ricardo; Vasconcelos, Bruno Nery F; Fernandes, Raphael B A; Lopes, Leonardo Esteves

2018-01-01

Substrate type is a key-factor in nest-site selection and nest architecture of burrowing birds. However, little is known about which factors drive nest-site selection for these species, especially in the tropics. We studied the influence of soil attributes on nest-site selection by the campo miner Geositta poeciloptera, an open grassland bird that builds its nests within soil cavities. For all nests found, we measured the depth of the nest cavity and the resistance of the soil to penetration, and identified the soil horizon in which the nest was located. In soil banks with nests, we collected soil samples for granulometric analysis around each nest cavity, while in soil banks without nests we collected these samples at random points. From 43 nests found, 86% were located in the deeper soil horizons (C-horizon), and only 14% in the shallower horizons (B-horizon). Granulometric analysis showed that the C-horizons possessed a high similar granulometric composition, with high silt and low clay contents. These characteristics are associated with a low degree of structural development of the soil, which makes it easier to excavate. Contrarily, soil resistance to penetration does not seem to be an important criterion for nest site selection, although nests in more resistant the soils tend to have shallower nest cavities. Among the soil banks analyzed, 40% of those without cavities possessed a larger proportion of B-horizon relative to the C-horizon, and their texture was more clayey. On the other hand, almost all soil banks containing nest cavities had a larger C-horizon and a silty texture, indicating that soil attributes drive nest-site selection by G. poeciloptera. Thus, we conclude that the patchy distribution of G. poeciloptera can attributed to the infrequent natural exposure of the C-horizon in the tropical region, where well developed, deep and permeable soils are more common.

Tuner Design for PEFP Superconducting RF Cavities

International Nuclear Information System (INIS)

Tang, Yazhe; An, Sun; Zhang, Liping; Cho, Yong Sub

2009-01-01

A superconducting radio frequency (SRF) cavity will be used to accelerate a proton beam after 100 MeV at 700 MHz in a linac of the Proton Engineering Frontier Project (PEFP) and its extended project. In order to control the SRF cavity's operating frequency at a low temperature, a new tuner has been developed for the PEFP SRF cavities. Each PEFP superconducting RF cavity has one tuner to match the cavity resonance frequency with the desired accelerator operating frequency; or to detune a cavity frequency a few bandwidths away from a resonance, so that the beam will not excite the fundamental mode, when the cavity is not being used for an acceleration. The PEFP cavity tuning is achieved by varying the total length of the cavity. The length of the cavity is controlled differentially by tuner acting with respect to the cavity body. The PEFP tuner is attached to the helium vessel and drives the cavity Field Probe (FP) side to change the frequency of the cavity

Comparative Simulation Studies of Multipacting in Higher-Order-Mode Couplers of Superconducting RF Cavities

International Nuclear Information System (INIS)

Li, Y. M.; Liu, Kexin; Geng, Rongli

2014-01-01

Multipacting (MP) in higher-order-mode (HOM) couplers of the International Linear Collider (ILC) baseline cavity and the Continuous Electron Beam Accelerator Facility (CEBAF) 12 GeV upgrade cavity is studied by using the ACE3P suites, developed by the Advanced Computations Department at SLAC. For the ILC cavity HOM coupler, the simulation results show that resonant trajectories exist in three zones, corresponding to an accelerating gradient range of 0.6A-1.6 MV/m, 21A-34 MV/m, 32A-35 MV/m, and > 40MV/m, respectively. For the CEBAF 12 GeV upgrade cavity HOM coupler, resonant trajectories exist in one zone, corresponding to an accelerating gradient range of 6A-13 MV/m. Potential implications of these MP barriers are discussed in the context of future high energy pulsed as well as medium energy continuous wave (CW) accelerators based on superconducting radio frequency cavities. Frequency scaling of MPA's predicted in HOM couplers of the ILC, CBEAF upgrade, SNS and FLASH third harmonic cavity is given and found to be in good agreement with the analytical result based on the parallel plate model

Comparative Simulation Studies of Multipacting in Higher-Order-Mode Couplers of Superconducting RF Cavities

Energy Technology Data Exchange (ETDEWEB)

Li, Y. M. [Peking University, Beijing (China); Thomas Jefferson National Accelerator Facility, Newport News, VA (United States); Liu, Kexin [Peking University, Beijing (China); Geng, Rongli [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States)

2014-02-01

Multipacting (MP) in higher-order-mode (HOM) couplers of the International Linear Collider (ILC) baseline cavity and the Continuous Electron Beam Accelerator Facility (CEBAF) 12 GeV upgrade cavity is studied by using the ACE3P suites, developed by the Advanced Computations Department at SLAC. For the ILC cavity HOM coupler, the simulation results show that resonant trajectories exist in three zones, corresponding to an accelerating gradient range of 0.6-1.6 MV/m, 21-34 MV/m, 32-35 MV/m, and > 40MV/m, respectively. For the CEBAF 12 GeV upgrade cavity HOM coupler, resonant trajectories exist in one zone, corresponding to an accelerating gradient range of 6-13 MV/m. Potential implications of these MP barriers are discussed in the context of future high energy pulsed as well as medium energy continuous wave (CW) accelerators based on superconducting radio frequency cavities. Frequency scaling of MP's predicted in HOM couplers of the ILC, CBEAF upgrade, SNS and FLASH third harmonic cavity is given and found to be in good agreement with the analytical result based on the parallel plate model.

Cavities in bromeliad stolons used as nest sites by Euglossa cordata (Hymenoptera, Euglossini

Directory of Open Access Journals (Sweden)

Samuel Boff

2018-02-01

Full Text Available Herein, we describe nests of the orchid bee Euglossa cordata that were constructed in cavities of Aechmea distichantha (Bromeliaceae stolons. We present data about nest and cell size, number of adults and brood, and analyses of larval provisions. The presence of E. cordata carcasses embedded in the resin of nest partitions indicates that these nests were used by multiple generations. Based on larval provisioning, E. cordata is polylectic and relies heavily on a few plant species.

LEP copper accelerating cavities

CERN Multimedia

Laurent Guiraud

1999-01-01

These copper cavities were used to generate the radio frequency electric field that was used to accelerate electrons and positrons around the 27-km Large Electron-Positron (LEP) collider at CERN, which ran from 1989 to 2000. The copper cavities were gradually replaced from 1996 with new superconducting cavities allowing the collision energy to rise from 90 GeV to 200 GeV by mid-1999.

Mucoceles of the oral cavity in pediatric patients

Directory of Open Access Journals (Sweden)

Chung Wei Wu

2011-07-01

Full Text Available Mucoceles are quite common in the oral cavity, but reports on pediatric patients are very rare. The aims of this study were to present our data and experience in the treatment of mucoceles of the oral cavity in pediatric patients, to compare them with those of other countries, and to remind the pediatric physician to devote much attention to lesions of the oral cavity in children. This retrospective study is based on the record of the patients who received surgical treatment for mucoceles of the oral cavity with pathologic confirmation at the Department of Dentistry, Kaohsiung Medical University Hospital, Taiwan, between 2000 and 2004. Patients younger than 18 years were included in this study. The analyzed data included age, gender, site, size, histopathologic findings, surgical methods, and complications. There were a total of 289 patients with mucoceles confirmed by histopathologic examination. As many as 64 patients were younger than 18 years. Of the 64, 34 were girls and 30 were boys; 89.1% of the lesions were in the lower lip; and 48.4% of the lesions were less than 5 mm in diameter. Histopathologic findings showed that all mucoceles were of the extravasation type. As many as 30 patients were treated by carbon dioxide laser vaporization, and two cases recurred (6.67%; 34 patients were treated by surgical excision, and the recurrence rate (5.88% was not statistically different for the treatment methods. The laser vaporization has the advantage of less bleeding, no sutures, and saving time, especially suitable for children with oral mucocele.

Predicting ecological flow regime at ungaged sites: A comparison of methods

Science.gov (United States)

Murphy, Jennifer C.; Knight, Rodney R.; Wolfe, William J.; Gain, W. Scott

2012-01-01

Nineteen ecologically relevant streamflow characteristics were estimated using published rainfall–runoff and regional regression models for six sites with observed daily streamflow records in Kentucky. The regional regression model produced median estimates closer to the observed median for all but two characteristics. The variability of predictions from both models was generally less than the observed variability. The variability of the predictions from the rainfall–runoff model was greater than that from the regional regression model for all but three characteristics. Eight characteristics predicted by the rainfall–runoff model display positive or negative bias across all six sites; biases are not as pronounced for the regional regression model. Results suggest that a rainfall–runoff model calibrated on a single characteristic is less likely to perform well as a predictor of a range of other characteristics (flow regime) when compared with a regional regression model calibrated individually on multiple characteristics used to represent the flow regime. Poor model performance may misrepresent hydrologic conditions, potentially distorting the perceived risk of ecological degradation. Without prior selection of streamflow characteristics, targeted calibration, and error quantification, the widespread application of general hydrologic models to ecological flow studies is problematic. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

Effects of cavity-cavity interaction on the entanglement dynamics of a generalized double Jaynes-Cummings model

Science.gov (United States)

Pandit, Mahasweta; Das, Sreetama; Singha Roy, Sudipto; Shekhar Dhar, Himadri; Sen, Ujjwal

2018-02-01

We consider a generalized double Jaynes-Cummings model consisting of two isolated two-level atoms, each contained in a lossless cavity that interact with each other through a controlled photon-hopping mechanism. We analytically show that at low values of such a mediated cavity-cavity interaction, the temporal evolution of entanglement between the atoms, under the effects of cavity perturbation, exhibits the well-known phenomenon of entanglement sudden death (ESD). Interestingly, for moderately large interaction values, a complete preclusion of ESD is achieved, irrespective of its value in the initial atomic state. Our results provide a model to sustain entanglement between two atomic qubits, under the adverse effect of cavity induced perturbation, by introducing a non-intrusive inter-cavity photon exchange that can be physically realized through cavity-QED setups in contemporary experiments.

Transient dynamics in cavity electromagnetically induced transparency with ion Coulomb crystals

Science.gov (United States)

Albert, Magnus; Dantan, Aurélien; Drewsen, Michael

2018-03-01

We experimentally investigate the transient dynamics of an optical cavity field interacting with large ion Coulomb crystals in a situation of electromagnetically induced transparency (EIT). EIT is achieved by injecting a probe field at the single photon level and a more intense control field with opposite circular polarization into the same mode of an optical cavity to couple Zeeman substates of a metastable level in ? ions. The EIT interaction dynamics are investigated both in the frequency-domain - by measuring the probe field steady state reflectivity spectrum - and in the time-domain - by measuring the progressive buildup of transparency. The experimental results are observed to be in excellent agreement with theoretical predictions taking into account the inhomogeneity of the control field in the interaction volume, and confirm the high degree of control on light-matter interaction that can be achieved with ion Coulomb crystals in optical cavities.

Predicting on-site environmental impacts of municipal engineering works

International Nuclear Information System (INIS)

Gangolells, Marta; Casals, Miquel; Forcada, Núria; Macarulla, Marcel

2014-01-01

The research findings fill a gap in the body of knowledge by presenting an effective way to evaluate the significance of on-site environmental impacts of municipal engineering works prior to the construction stage. First, 42 on-site environmental impacts of municipal engineering works were identified by means of a process-oriented approach. Then, 46 indicators and their corresponding significance limits were determined on the basis of a statistical analysis of 25 new-build and remodelling municipal engineering projects. In order to ensure the objectivity of the assessment process, direct and indirect indicators were always based on quantitative data from the municipal engineering project documents. Finally, two case studies were analysed and found to illustrate the practical use of the proposed model. The model highlights the significant environmental impacts of a particular municipal engineering project prior to the construction stage. Consequently, preventive actions can be planned and implemented during on-site activities. The results of the model also allow a comparison of proposed municipal engineering projects and alternatives with respect to the overall on-site environmental impact and the absolute importance of a particular environmental aspect. These findings are useful within the framework of the environmental impact assessment process, as they help to improve the identification and evaluation of on-site environmental aspects of municipal engineering works. The findings may also be of use to construction companies that are willing to implement an environmental management system or simply wish to improve on-site environmental performance in municipal engineering projects. -- Highlights: • We present a model to predict the environmental impacts of municipal engineering works. • It highlights significant on-site environmental impacts prior to the construction stage. • Findings are useful within the environmental impact assessment process. • They also

Predicting on-site environmental impacts of municipal engineering works

Energy Technology Data Exchange (ETDEWEB)

Gangolells, Marta, E-mail: marta.gangolells@upc.edu; Casals, Miquel, E-mail: miquel.casals@upc.edu; Forcada, Núria, E-mail: nuria.forcada@upc.edu; Macarulla, Marcel, E-mail: marcel.macarulla@upc.edu

2014-01-15

The research findings fill a gap in the body of knowledge by presenting an effective way to evaluate the significance of on-site environmental impacts of municipal engineering works prior to the construction stage. First, 42 on-site environmental impacts of municipal engineering works were identified by means of a process-oriented approach. Then, 46 indicators and their corresponding significance limits were determined on the basis of a statistical analysis of 25 new-build and remodelling municipal engineering projects. In order to ensure the objectivity of the assessment process, direct and indirect indicators were always based on quantitative data from the municipal engineering project documents. Finally, two case studies were analysed and found to illustrate the practical use of the proposed model. The model highlights the significant environmental impacts of a particular municipal engineering project prior to the construction stage. Consequently, preventive actions can be planned and implemented during on-site activities. The results of the model also allow a comparison of proposed municipal engineering projects and alternatives with respect to the overall on-site environmental impact and the absolute importance of a particular environmental aspect. These findings are useful within the framework of the environmental impact assessment process, as they help to improve the identification and evaluation of on-site environmental aspects of municipal engineering works. The findings may also be of use to construction companies that are willing to implement an environmental management system or simply wish to improve on-site environmental performance in municipal engineering projects. -- Highlights: • We present a model to predict the environmental impacts of municipal engineering works. • It highlights significant on-site environmental impacts prior to the construction stage. • Findings are useful within the environmental impact assessment process. • They also

Temperature Structure of a Coronal Cavity

Science.gov (United States)

Kucera, T. A.; Gibson, S. E.; Schmit, D. J.

2011-01-01

we analyze the temperature structure of a coronal cavity observed in Aug. 2007. coronal cavities are long, low-density structures located over filament neutral lines and are often seen as dark elliptical features at the solar limb in white light, EUV and x-rays. when these structures erupt they form the cavity portions of CMEs. It is important to establish the temperature structure of cavities in order to understand the thermodynamics of cavities in relation to their three-dimensional magnetic structure. To analyze the temperature we compare temperature ratios of a series of iron lines observed by the Hinode/EUv Imaging spectrometer (EIS). We also use those lines to constrain a forward model of the emission from the cavity and streamer. The model assumes a coronal streamer with a tunnel-like cavity with elliptical cross-section and a Gaussian variation of height along the tunnel lenth. Temperature and density can be varied as a function of altitude both in the cavity and streamer. The general cavity morphology and the cavity and streamer density have already been modeled using data from STEREO's SECCHI/EUVI and Hinode/EIS (Gibson et al 2010 and Schmit & Gibson 2011).

Cavity-Type DNA Origami-Based Plasmonic Nanostructures for Raman Enhancement.

Science.gov (United States)

Zhao, Mengzhen; Wang, Xu; Ren, Shaokang; Xing, Yikang; Wang, Jun; Teng, Nan; Zhao, Dongxia; Liu, Wei; Zhu, Dan; Su, Shao; Shi, Jiye; Song, Shiping; Wang, Lihua; Chao, Jie; Wang, Lianhui

2017-07-05

DNA origami has been established as addressable templates for site-specific anchoring of gold nanoparticles (AuNPs). Given that AuNPs are assembled by charged DNA oligonucleotides, it is important to reduce the charge repulsion between AuNPs-DNA and the template to realize high yields. Herein, we developed a cavity-type DNA origami as templates to organize 30 nm AuNPs, which formed dimer and tetramer plasmonic nanostructures. Transmission electron microscopy images showed that high yields of dimer and tetramer plasmonic nanostructures were obtained by using the cavity-type DNA origami as the template. More importantly, we observed significant Raman signal enhancement from molecules covalently attached to the plasmonic nanostructures, which provides a new way to high-sensitivity Raman sensing.

Normal Conducting RF Cavity for MICE

International Nuclear Information System (INIS)

Li, D.; DeMello, A.; Virostek, S.; Zisman, M.; Summers, D.

2010-01-01

Normal conducting RF cavities must be used for the cooling section of the international Muon Ionization Cooling Experiment (MICE), currently under construction at Rutherford Appleton Laboratory (RAL) in the UK. Eight 201-MHz cavities are needed for the MICE cooling section; fabrication of the first five cavities is complete. We report the cavity fabrication status including cavity design, fabrication techniques and preliminary low power RF measurements.

Overburden characterization and post-burn study of the Hanna IV, underground coal gasification site, Wyoming, and comparison to other Wyoming UCG sites

Energy Technology Data Exchange (ETDEWEB)

Marcouiller, B.A.; Burns, L.K.; Ethridge, F.G.

1984-11-01

Analysis of 21 post-burn cores taken from the Hanna IV UCG site allows 96 m (315 ft) of overburden to be subdivided into four local stratigraphic units. The 7.6 m (25 ft) thick Hanna No. 1 coal seam is overlain by a laterally discontinuous, 3.3 m (11 ft) thick shaley mudstone (Unit A') in part of the Hanna IV site. A more widespread, 30 m (90 ft) thick well-indurated sandstone (Unit A) overlies the A' unit. Unit A is the roof rock for both of the Hanna IV cavities. Overlying Unit A is a 33 m (108 ft) thick sequence of mudstone and claystone (Unit B), and the uppermost unit at the Hanna IV site (Unit C) is a coarse-grained sandstone that ranges in thickness from 40 to 67 m (131 to 220 ft). Two elliptical cavities were formed during the two phases of the Hanna IV experiment. The larger cavity, Hanna IVa, is 45 x 15 m in plan and has a maximum height of 18 m (59 ft) from the base of the coal seam to the top of the cavity; the Hanna IVb cavity is 40 x 15 m in plan and has a maximum height of 11 m (36 ft) from the base of the coal seam to the top of the cavity. Geotechnical tests indicated that the Hanna IV overburden rocks were moderately strong to strong, based on the empirical classification of Broch and Franklin (1972), and a positive, linear correlation exists between rock strength and volume percent calcite cement. There is an inverse linear correlation between rock strength and porosity for the Hanna IV overburden rocks. 28 refs., 34 figs., 13 tabs..

Successful intraosseous infusion in the critically ill patient does not require a medullary cavity.

LENUS (Irish Health Repository)

McCarthy, Gerard

2012-02-03

OBJECTIVES: To demonstrate that successful intraosseous infusion in critically ill patients does not require bone that contains a medullary cavity. DESIGN: Infusion of methyl green dye via standard intraosseous needles into bones without medullary cavity-in this case calcaneus and radial styloid-in cadaveric specimens. SETTING: University department of anatomy. PARTICIPANTS: Two adult cadaveric specimens. MAIN OUTCOME MEASURES: Observation of methyl green dye in peripheral veins of the limb in which the intraosseous infusion was performed. RESULTS: Methyl green dye was observed in peripheral veins of the chosen limb in five out of eight intraosseous infusions into bones without medullary cavity-calcaneus and radial styloid. CONCLUSIONS: Successful intraosseous infusion does not always require injection into a bone with a medullary cavity. Practitioners attempting intraosseous access on critically ill patients in the emergency department or prehospital setting need not restrict themselves to such bones. Calcaneus and radial styloid are both an acceptable alternative to traditional recommended sites.

LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation

Directory of Open Access Journals (Sweden)

Schroeder Michael

2006-09-01

Full Text Available Abstract Background Identifying pockets on protein surfaces is of great importance for many structure-based drug design applications and protein-ligand docking algorithms. Over the last ten years, many geometric methods for the prediction of ligand-binding sites have been developed. Results We present LIGSITEcsc, an extension and implementation of the LIGSITE algorithm. LIGSITEcsc is based on the notion of surface-solvent-surface events and the degree of conservation of the involved surface residues. We compare our algorithm to four other approaches, LIGSITE, CAST, PASS, and SURFNET, and evaluate all on a dataset of 48 unbound/bound structures and 210 bound-structures. LIGSITEcsc performs slightly better than the other tools and achieves a success rate of 71% and 75%, respectively. Conclusion The use of the Connolly surface leads to slight improvements, the prediction re-ranking by conservation to significant improvements of the binding site predictions. A web server for LIGSITEcsc and its source code is available at scoppi.biotec.tu-dresden.de/pocket.

Using dynamic N-mixture models to test cavity limitation on northern flying squirrel demographic parameters using experimental nest box supplementation.

Science.gov (United States)

Priol, Pauline; Mazerolle, Marc J; Imbeau, Louis; Drapeau, Pierre; Trudeau, Caroline; Ramière, Jessica

2014-06-01

Dynamic N-mixture models have been recently developed to estimate demographic parameters of unmarked individuals while accounting for imperfect detection. We propose an application of the Dail and Madsen (2011: Biometrics, 67, 577-587) dynamic N-mixture model in a manipulative experiment using a before-after control-impact design (BACI). Specifically, we tested the hypothesis of cavity limitation of a cavity specialist species, the northern flying squirrel, using nest box supplementation on half of 56 trapping sites. Our main purpose was to evaluate the impact of an increase in cavity availability on flying squirrel population dynamics in deciduous stands in northwestern Québec with the dynamic N-mixture model. We compared abundance estimates from this recent approach with those from classic capture-mark-recapture models and generalized linear models. We compared apparent survival estimates with those from Cormack-Jolly-Seber (CJS) models. Average recruitment rate was 6 individuals per site after 4 years. Nevertheless, we found no effect of cavity supplementation on apparent survival and recruitment rates of flying squirrels. Contrary to our expectations, initial abundance was not affected by conifer basal area (food availability) and was negatively affected by snag basal area (cavity availability). Northern flying squirrel population dynamics are not influenced by cavity availability at our deciduous sites. Consequently, we suggest that this species should not be considered an indicator of old forest attributes in our study area, especially in view of apparent wide population fluctuations across years. Abundance estimates from N-mixture models were similar to those from capture-mark-recapture models, although the latter had greater precision. Generalized linear mixed models produced lower abundance estimates, but revealed the same relationship between abundance and snag basal area. Apparent survival estimates from N-mixture models were higher and less precise

Social Networking Site Use Predicts Changes in Young Adults’ Psychological Adjustment

Science.gov (United States)

Szwedo, David E.; Mikami, Amori Yee; Allen, Joseph P.

2012-01-01

This study examined youths’ friendships and posted pictures on social networking sites as predictors of changes in their adjustment over time. Observational, self-report, and peer report data were obtained from a community sample of 89 young adults interviewed at age 21 and again at age 22. Findings were consistent with a leveling effect for online friendships, predicting decreases in internalizing symptoms for youth with lower initial levels of social acceptance, but increases in symptoms for youth with higher initial levels over the following year. Across the entire sample, deviant behavior in posted photos predicted increases in young adults’ problematic alcohol use over time. The importance of considering the interplay between online and offline social factors for predicting adjustment is discussed. PMID:23109797

Hollow waveguide cavity ringdown spectroscopy

Science.gov (United States)

Dreyer, Chris (Inventor); Mungas, Greg S. (Inventor)

2012-01-01

Laser light is confined in a hollow waveguide between two highly reflective mirrors. This waveguide cavity is used to conduct Cavity Ringdown Absorption Spectroscopy of loss mechanisms in the cavity including absorption or scattering by gases, liquid, solids, and/or optical elements.

Model for initiation of quality factor degradation at high accelerating fields in superconducting radio-frequency cavities

International Nuclear Information System (INIS)

Dzyuba, A; Romanenko, A; Cooley, L D

2010-01-01

A model for the onset of the reduction in superconducting radio-frequency (SRF) cavity quality factor, the so-called Q-drop, at high accelerating electric fields is presented. Since magnetic fields at the cavity equator are tied to accelerating electric fields by a simple geometric factor, the onset of magnetic flux penetration determines the onset of Q-drop. We consider breakdown of the surface barrier at triangular grooves to predict the magnetic field of first flux penetration H pen . Such defects were argued to be the worst case by Buzdin and Daumens (1998 Physica C 294 257), whose approach, moreover, incorporates both the geometry of the groove and local contamination via the Ginzburg-Landau parameter κ. Since previous Q-drop models focused on either topography or contamination alone, the proposed model allows new comparisons of one effect in relation to the other. The model predicts equivalent reduction of H pen when either roughness or contamination were varied alone, so smooth but dirty surfaces limit cavity performance about as much as rough but clean surfaces do. Still lower H pen was predicted when both effects were combined, i.e. contamination should exacerbate the negative effects of roughness and vice versa. To test the model with actual data, coupons were prepared by buffered chemical polishing and electropolishing, and stylus profilometry was used to obtain distributions of angles. From these data, curves for surface resistance generated by simple flux flow as a function of magnetic field were generated by integrating over the distribution of angles for reasonable values of κ. This showed that combined effects of roughness and contamination indeed reduce the Q-drop onset field by ∼ 20%, and that contamination contributes to Q-drop as much as roughness. The latter point may be overlooked by SRF cavity research, since access to the cavity interior by spectroscopy tools is very difficult, whereas optical images have become commonplace. The model

Model for initiation of quality factor degradation at high accelerating fields in superconducting radio-frequency cavities

Science.gov (United States)

Dzyuba, A.; Romanenko, A.; Cooley, L. D.

2010-12-01

A model for the onset of the reduction in superconducting radio-frequency (SRF) cavity quality factor, the so-called Q-drop, at high accelerating electric fields is presented. Since magnetic fields at the cavity equator are tied to accelerating electric fields by a simple geometric factor, the onset of magnetic flux penetration determines the onset of Q-drop. We consider breakdown of the surface barrier at triangular grooves to predict the magnetic field of first flux penetration Hpen. Such defects were argued to be the worst case by Buzdin and Daumens (1998 Physica C 294 257), whose approach, moreover, incorporates both the geometry of the groove and local contamination via the Ginzburg-Landau parameter κ. Since previous Q-drop models focused on either topography or contamination alone, the proposed model allows new comparisons of one effect in relation to the other. The model predicts equivalent reduction of Hpen when either roughness or contamination were varied alone, so smooth but dirty surfaces limit cavity performance about as much as rough but clean surfaces do. Still lower Hpen was predicted when both effects were combined, i.e. contamination should exacerbate the negative effects of roughness and vice versa. To test the model with actual data, coupons were prepared by buffered chemical polishing and electropolishing, and stylus profilometry was used to obtain distributions of angles. From these data, curves for surface resistance generated by simple flux flow as a function of magnetic field were generated by integrating over the distribution of angles for reasonable values of κ. This showed that combined effects of roughness and contamination indeed reduce the Q-drop onset field by ~ 20%, and that contamination contributes to Q-drop as much as roughness. The latter point may be overlooked by SRF cavity research, since access to the cavity interior by spectroscopy tools is very difficult, whereas optical images have become commonplace. The model was

New method to improve the accuracy of quench position measurement on a superconducting cavity by a second sound method

Directory of Open Access Journals (Sweden)

ZhenChao Liu

2012-09-01

Full Text Available Quench is a common phenomenon in a superconducting cavity and often limits the accelerating gradient of the cavity. Accurate location of the quench site, typically located at a material or geometrical defect, is the key to improve the cavity accelerating gradient. Here, the second sound propagation in liquid helium II is used to detect the quench location on the cavity. The technique is relatively convenient and complements the traditional temperature mapping which measures the “prequench” temperature rise on the cavity using an array of sensors. The speed of the second sound in liquid helium II is roughly 1.7  cm/ms at 2 K which is sufficiently fast to provide a millimeter-size position resolution. However, the dynamics of the quench at the cavity surface are also found to significantly affect the achievable resolution with real cavities. Here we use a dynamic quench model, based on ANSYS, to calculate the quench area and the temperature distribution on the cavity. The detection error caused by the thermal conduction in the niobium was calculated.

Predicting ambient aerosol thermal-optical reflectance (TOR) measurements from infrared spectra: extending the predictions to different years and different sites

Science.gov (United States)

Reggente, Matteo; Dillner, Ann M.; Takahama, Satoshi

2016-02-01

Organic carbon (OC) and elemental carbon (EC) are major components of atmospheric particulate matter (PM), which has been associated with increased morbidity and mortality, climate change, and reduced visibility. Typically OC and EC concentrations are measured using thermal-optical methods such as thermal-optical reflectance (TOR) from samples collected on quartz filters. In this work, we estimate TOR OC and EC using Fourier transform infrared (FT-IR) absorbance spectra from polytetrafluoroethylene (PTFE Teflon) filters using partial least square regression (PLSR) calibrated to TOR OC and EC measurements for a wide range of samples. The proposed method can be integrated with analysis of routinely collected PTFE filter samples that, in addition to OC and EC concentrations, can concurrently provide information regarding the functional group composition of the organic aerosol. We have used the FT-IR absorbance spectra and TOR OC and EC concentrations collected in the Interagency Monitoring of PROtected Visual Environments (IMPROVE) network (USA). We used 526 samples collected in 2011 at seven sites to calibrate the models, and more than 2000 samples collected in 2013 at 17 sites to test the models. Samples from six sites are present both in the calibration and test sets. The calibrations produce accurate predictions both for samples collected at the same six sites present in the calibration set (R2 = 0.97 and R2 = 0.95 for OC and EC respectively), and for samples from 9 of the 11 sites not included in the calibration set (R2 = 0.96 and R2 = 0.91 for OC and EC respectively). Samples collected at the other two sites require a different calibration model to achieve accurate predictions. We also propose a method to anticipate the prediction error; we calculate the squared Mahalanobis distance in the feature space (scores determined by PLSR) between new spectra and spectra in the calibration set. The squared Mahalanobis distance provides a crude method for assessing the

Long bunch trains measured using a prototype cavity beam position monitor for the Compact Linear Collider

Directory of Open Access Journals (Sweden)

F. J. Cullinan

2015-11-01

Full Text Available The Compact Linear Collider (CLIC requires beam position monitors (BPMs with 50 nm spatial resolution for alignment of the beam line elements in the main linac and beam delivery system. Furthermore, the BPMs must be able to make multiple independent measurements within a single 156 ns long bunch train. A prototype cavity BPM for CLIC has been manufactured and tested on the probe beam line at the 3rd CLIC Test Facility (CTF3 at CERN. The transverse beam position is determined from the electromagnetic resonant modes excited by the beam in the two cavities of the pickup, the position cavity and the reference cavity. The mode that is measured in each cavity resonates at 15 GHz and has a loaded quality factor that is below 200. Analytical expressions for the amplitude, phase and total energy of signals from long trains of bunches have been derived and the main conclusions are discussed. The results of the beam tests are presented. The variable gain of the receiver electronics has been characterized using beam excited signals and the form of the signals for different beam pulse lengths with the 2/3  ns bunch spacing has been observed. The sensitivity of the reference cavity signal to charge and the horizontal position signal to beam offset have been measured and are compared with theoretical predictions based on laboratory measurements of the BPM pickup and the form of the resonant cavity modes as determined by numerical simulation. Finally, the BPM was calibrated so that the beam position jitter at the BPM location could be measured. It is expected that the beam jitter scales linearly with the beam size and so the results are compared to predicted values for the latter.

Long bunch trains measured using a prototype cavity beam position monitor for the Compact Linear Collider

Science.gov (United States)

Cullinan, F. J.; Boogert, S. T.; Farabolini, W.; Lefevre, T.; Lunin, A.; Lyapin, A.; Søby, L.; Towler, J.; Wendt, M.

2015-11-01

The Compact Linear Collider (CLIC) requires beam position monitors (BPMs) with 50 nm spatial resolution for alignment of the beam line elements in the main linac and beam delivery system. Furthermore, the BPMs must be able to make multiple independent measurements within a single 156 ns long bunch train. A prototype cavity BPM for CLIC has been manufactured and tested on the probe beam line at the 3rd CLIC Test Facility (CTF3) at CERN. The transverse beam position is determined from the electromagnetic resonant modes excited by the beam in the two cavities of the pickup, the position cavity and the reference cavity. The mode that is measured in each cavity resonates at 15 GHz and has a loaded quality factor that is below 200. Analytical expressions for the amplitude, phase and total energy of signals from long trains of bunches have been derived and the main conclusions are discussed. The results of the beam tests are presented. The variable gain of the receiver electronics has been characterized using beam excited signals and the form of the signals for different beam pulse lengths with the 2 /3 ns bunch spacing has been observed. The sensitivity of the reference cavity signal to charge and the horizontal position signal to beam offset have been measured and are compared with theoretical predictions based on laboratory measurements of the BPM pickup and the form of the resonant cavity modes as determined by numerical simulation. Finally, the BPM was calibrated so that the beam position jitter at the BPM location could be measured. It is expected that the beam jitter scales linearly with the beam size and so the results are compared to predicted values for the latter.

Superconducting Radio-Frequency Cavities

Science.gov (United States)

Padamsee, Hasan S.

2014-10-01

Superconducting cavities have been operating routinely in a variety of accelerators with a range of demanding applications. With the success of completed projects, niobium cavities have become an enabling technology, offering upgrade paths for existing facilities and pushing frontier accelerators for nuclear physics, high-energy physics, materials science, and the life sciences. With continued progress in basic understanding of radio-frequency superconductivity, the performance of cavities has steadily improved to approach theoretical capabilities.

Monitoring of subsurface extended cavities prone to instabilities

Science.gov (United States)

Bigarre, Pascal; Nadim, Charles-Édouard; Lahaie, Frantz

2010-05-01

Natural or abandoned anthropogenic cavities are to be found in various contexts all around the world. In France, shallow cavities count rises up to several hundreds of thousands. It concerns complex cavities as old abandoned multilevel quarries, extended mines or naturally interlaced karsts. Risk assessment related to these cavities, such as sinkholes or pillar failure, conducts usually to short term strategy based on regular visual inspections until a more definitive risk reduction strategy is adopted. However, if no definitive remediation appears as feasible, for technical or socio-economic reasons, monitoring by regular visual inspection of specialists rises several crucial issues in the long term: safety conditions for the inspection team, limited reactivity of the monitoring due to the period between two inspections and finally difficulties to detect reliably and exhaustively early signs of evolution when local disorders are spread over a large underground area. Several well-proofed techniques are available to detect subsurface cavities, but it is less common when considering field instrumentation applied to permanent monitoring in such context. Indeed, classical geotechnical measurement based on strain and displacement sensors give very local information and cannot be deployed at a large scale with a correct coverage within a reasonable cost/benefit ratio. Moreover this type of instrumentation requires significant efforts and equipment for installation underground, must be placed right inside the most hazardous zones whenever it is feasible and is often not retrievable. Yet a continuous remote monitoring can save a regular control on site and may provide unique information about the kinetic of potential sinkholes and local ground failures. To proceed with this matter, INERIS develops and tests new tools and methods to facilitate the setting up of operational devices for remote monitoring and alert applied to subsurface extended cavities. Such systems aim to

Prediction of allosteric sites on protein surfaces with an elastic-network-model-based thermodynamic method.

Science.gov (United States)

Su, Ji Guo; Qi, Li Sheng; Li, Chun Hua; Zhu, Yan Ying; Du, Hui Jing; Hou, Yan Xue; Hao, Rui; Wang, Ji Hua

2014-08-01

Allostery is a rapid and efficient way in many biological processes to regulate protein functions, where binding of an effector at the allosteric site alters the activity and function at a distant active site. Allosteric regulation of protein biological functions provides a promising strategy for novel drug design. However, how to effectively identify the allosteric sites remains one of the major challenges for allosteric drug design. In the present work, a thermodynamic method based on the elastic network model was proposed to predict the allosteric sites on the protein surface. In our method, the thermodynamic coupling between the allosteric and active sites was considered, and then the allosteric sites were identified as those where the binding of an effector molecule induces a large change in the binding free energy of the protein with its ligand. Using the proposed method, two proteins, i.e., the 70 kD heat shock protein (Hsp70) and GluA2 alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor, were studied and the allosteric sites on the protein surface were successfully identified. The predicted results are consistent with the available experimental data, which indicates that our method is a simple yet effective approach for the identification of allosteric sites on proteins.

X-ray quantum optics with Moessbauer nuclei in thin-film cavities

Energy Technology Data Exchange (ETDEWEB)

Heeg, Kilian Peter

2014-12-09

In this thesis thin-film cavities with embedded Moessbauer nuclei probed by near-resonant X-ray light are studied from a quantum optical perspective. A theoretical framework is developed and compact expressions for the observables are derived for the linear excitation regime, which is encountered in current experiments. Even advanced cavity layouts can be modeled in excellent agreement with the results of previous experiments and semi-classical approaches. In the absence of magnetic hyperfine splitting, the spectral response of the system is found to be formed by tunable Fano profiles. An experimental implementation of this line shape control allows to extract spectroscopic signatures with high precision and to reconstruct the phase of the nuclear transition in good agreement with the theoretical predictions. The alignment of medium magnetization and polarization control of the X-rays enable to engineer advanced quantum optical level schemes, in which vacuum induced coherence effects are predicted and successfully demonstrated in an experiment. Furthermore, it is shown that group velocity control for x-ray pulses can be achieved in the cavity. A scheme for its observation is proposed and then employed to experimentally confirm sub-luminal X-ray propagation. Finally, non-linear effects, which could become accessible with future light sources, are explored and a non-linear line shape control mechanism is discussed.

Submandibular Gland Involvement in Early Stage Oral Cavity Carcinomas: Can the Gland be left behind

International Nuclear Information System (INIS)

Ashfaq, K.; Ashfaq, M.; Ahmed, A.; Khan, M.; Azhar, M.

2014-01-01

Objective: To determine the frequency of submandibular gland involvement in early oral cavity tumors. Study Design: Observational study. Place and Duration of Study: ENT Department, CMH, Rawalpindi, from January 2008 to December 2011. Methodology: Data of 110 oral cavity tumors operated over 2008 - 2011 was retrieved from ENT OPD, tumor registry in AFIP and from Head and Neck Oncology Forum Registry. Cases of oral cavity tumors that had undergone elective neck dissections were retrospectively studied for invasion of the submandibular gland, TNM Staging, perineural, perivascular, lymphovascular invasion, site specific frequency of oral cavity tumors and frequency of lymph node metastasis. Results: Tumors of tongue were the most common constituting 42%, squamous cell carcinoma was the histological diagnosis in 90% cases. Sixty eight (61.8%) cases were node negative. Selective neck dissection was done in 55.5% of the cases. Submandibular gland was involved in 2 cases (1.8%). Conclusion: Submandibular gland metastasis from early oral cavity tumors is rare; any neoplastic involvement of the gland usually occurs via direct spread. (author)

High DNA melting temperature predicts transcription start site location in human and mouse.

LENUS (Irish Health Repository)

Dineen, David G

2009-12-01

The accurate computational prediction of transcription start sites (TSS) in vertebrate genomes is a difficult problem. The physicochemical properties of DNA can be computed in various ways and a many combinations of DNA features have been tested in the past for use as predictors of transcription. We looked in detail at melting temperature, which measures the temperature, at which two strands of DNA separate, considering the cooperative nature of this process. We find that peaks in melting temperature correspond closely to experimentally determined transcription start sites in human and mouse chromosomes. Using melting temperature alone, and with simple thresholding, we can predict TSS with accuracy that is competitive with the most accurate state-of-the-art TSS prediction methods. Accuracy is measured using both experimentally and manually determined TSS. The method works especially well with CpG island containing promoters, but also works when CpG islands are absent. This result is clear evidence of the important role of the physical properties of DNA in the process of transcription. It also points to the importance for TSS prediction methods to include melting temperature as prior information.

HPV and high-risk gene expression profiles predict response to chemoradiotherapy in head and neck cancer, independent of clinical factors

International Nuclear Information System (INIS)

Jong, Monique C. de; Pramana, Jimmy; Knegjens, Joost L.; Balm, Alfons J.M.; Brekel, Michiel W.M. van den; Hauptmann, Michael; Begg, Adrian C.; Rasch, Coen R.N.

2010-01-01

Purpose: The purpose of this study was to combine gene expression profiles and clinical factors to provide a better prediction model of local control after chemoradiotherapy for advanced head and neck cancer. Material and methods: Gene expression data were available for a series of 92 advanced stage head and neck cancer patients treated with primary chemoradiotherapy. The effect of the Chung high-risk and Slebos HPV expression profiles on local control was analyzed in a model with age at diagnosis, gender, tumor site, tumor volume, T-stage and N-stage and HPV profile status. Results: Among 75 patients included in the study, the only factors significantly predicting local control were tumor site (oral cavity vs. Pharynx, hazard ratio 4.2 [95% CI 1.4-12.5]), Chung gene expression status (high vs. Low risk profile, hazard ratio 4.4 [95% CI 1.5-13.3]) and HPV profile (negative vs. Positive profile, hazard ratio 6.2 [95% CI 1.7-22.5]). Conclusions: Chung high-risk expression profile and a negative HPV expression profile were significantly associated with increased risk of local recurrence after chemoradiotherapy in advanced pharynx and oral cavity tumors, independent of clinical factors.

A SURVEY OF CORONAL CAVITY DENSITY PROFILES

International Nuclear Information System (INIS)

Fuller, J.; Gibson, S. E.

2009-01-01

Coronal cavities are common features of the solar corona that appear as darkened regions at the base of coronal helmet streamers in coronagraph images. Their darkened appearance indicates that they are regions of lowered density embedded within the comparatively higher density helmet streamer. Despite interfering projection effects of the surrounding helmet streamer (which we refer to as the cavity rim), Fuller et al. have shown that under certain conditions it is possible to use a Van de Hulst inversion of white-light polarized brightness (pB) data to calculate the electron density of both the cavity and cavity rim plasma. In this article, we apply minor modifications to the methods of Fuller et al. in order to improve the accuracy and versatility of the inversion process, and use the new methods to calculate density profiles for both the cavity and cavity rim in 24 cavity systems. We also examine trends in cavity morphology and how departures from the model geometry affect our density calculations. The density calculations reveal that in all 24 cases the cavity plasma has a flatter density profile than the plasma of the cavity rim, meaning that the cavity has a larger density depletion at low altitudes than it does at high altitudes. We find that the mean cavity density is over four times greater than that of a coronal hole at an altitude of 1.2 R sun and that every cavity in the sample is over twice as dense as a coronal hole at this altitude. Furthermore, we find that different cavity systems near solar maximum span a greater range in density at 1.2 R sun than do cavity systems near solar minimum, with a slight trend toward higher densities for systems nearer to solar maximum. Finally, we found no significant correlation of cavity density properties with cavity height-indeed, cavities show remarkably similar density depletions-except for the two smallest cavities that show significantly greater depletion.

radiofrequency cavity

CERN Multimedia

1988-01-01

The pulse of a particle accelerator. 128 of these radio frequency cavities were positioned around CERN's 27-kilometre LEP ring to accelerate electrons and positrons. The acceleration was produced by microwave electric oscillations at 352 MHz. The electrons and positrons were grouped into bunches, like beads on a string, and the copper sphere at the top stored the microwave energy between the passage of individual bunches. This made for valuable energy savings as it reduced the heat generated in the cavity.

Considering multiple occupancy of cavities in clathrate hydrate phase equilibrium calculations

Energy Technology Data Exchange (ETDEWEB)

Asiaee, Alireza; Raeissi, Sona [Natural Gas Engineering Department, School of Chemical and Petroleum Engineering, Shiraz University, Shiraz 71345 (Iran, Islamic Republic of); Shariati, Alireza, E-mail: shariati@shirazu.ac.i [Natural Gas Engineering Department, School of Chemical and Petroleum Engineering, Shiraz University, Shiraz 71345 (Iran, Islamic Republic of)

2011-05-15

Research highlights: A model is presented to predict dissociation pressures of gas hydrates at various temperatures. The present model is applicable on a wide range of equilibrium conditions. The simple calculation procedure presented here saves considerably the calculation time. - Abstract: One of the major assumptions of the original van der Waals-Platteeuw (vdWP) model is the single occupancy of hydrate cavities. In this work, the vdWP model is modified to also account for multiple occupancies of hydrate cavities by small molecules. The developed model is evaluated by calculating the hydrate equilibrium conditions with either oxygen or nitrogen as guest molecules in pure form, as well as mixtures of nitrogen and propane (molecules of these pure gases and those in (nitrogen + propane) have double occupancy in large cavities of structure II up to a certain concentration of propane). The results of this modified model show good agreement with the experimental data reported in the literature.

Considering multiple occupancy of cavities in clathrate hydrate phase equilibrium calculations

International Nuclear Information System (INIS)

Asiaee, Alireza; Raeissi, Sona; Shariati, Alireza

2011-01-01

Research highlights: → A model is presented to predict dissociation pressures of gas hydrates at various temperatures. → The present model is applicable on a wide range of equilibrium conditions. → The simple calculation procedure presented here saves considerably the calculation time. - Abstract: One of the major assumptions of the original van der Waals-Platteeuw (vdWP) model is the single occupancy of hydrate cavities. In this work, the vdWP model is modified to also account for multiple occupancies of hydrate cavities by small molecules. The developed model is evaluated by calculating the hydrate equilibrium conditions with either oxygen or nitrogen as guest molecules in pure form, as well as mixtures of nitrogen and propane (molecules of these pure gases and those in (nitrogen + propane) have double occupancy in large cavities of structure II up to a certain concentration of propane). The results of this modified model show good agreement with the experimental data reported in the literature.

Earth-ionosphere cavity

International Nuclear Information System (INIS)

Tran, A.; Polk, C.

1976-01-01

To analyze ELF wave propagation in the earth-ionosphere cavity, a flat earth approximation may be derived from the exact equations, which are applicable to the spherical cavity, by introducing a second-order or Debye approximation for the spherical Hankel functions. In the frequency range 3 to 30 Hz, however, the assumed conditions for the Debye approximation are not satisfied. For this reason an exact evaluation of the spherical Hankel functions is used to study the effects of the flat earth approximation on various propagation and resonance parameters. By comparing the resonance equation for a spherical cavity with its flat earth counterpart and by assuming that the surface impedance Z/sub i/ at the upper cavity boundary is known, the relation between the eigenvalue ν and S/sub v/, the sine of the complex angle of incidence at the lower ionosphere boundary, is established as ν(ν + 1) = (kaS/sub v/) 2 . It is also shown that the approximation ν(ν + 1) approximately equals (ν + 1/2) 2 which was used by some authors is not adequate below 30 Hz. Numerical results for both spherical and planar stratification show that (1) planar stratification is adequate for the computation of the lowest three ELF resonance frequencies to within 0.1 Hz; (2) planar stratification will lead to errors in cavity Q and wave attenuation which increase with frequency; (3) computation of resonance frequencies to within 0.1 Hz requires the extension of the lower boundary of the ionosphere to a height where the ratio of conduction current to displacement current, (sigma/ωepsilon 0 ), is less than 0.3; (4) atmospheric conductivity should be considered down to ground level in computing cavity Q and wave attenuation

Cavity design programs

International Nuclear Information System (INIS)

Nelson, E.M.

1996-01-01

Numerous computer programs are available to help accelerator physicists and engineers model and design accelerator cavities and other microwave components. This article discusses the problems these programs solve and the principles upon which these programs are based. Some examples of how these programs are used in the design of accelerator cavities are also given

Partial Cavity Flows at High Reynolds Numbers

Science.gov (United States)

Makiharju, Simo; Elbing, Brian; Wiggins, Andrew; Dowling, David; Perlin, Marc; Ceccio, Steven

2009-11-01

Partial cavity flows created for friction drag reduction were examined on a large-scale. Partial cavities were investigated at Reynolds numbers up to 120 million, and stable cavities with frictional drag reduction of more than 95% were attained at optimal conditions. The model used was a 3 m wide and 12 m long flat plate with a plenum on the bottom. To create the partial cavity, air was injected at the base of an 18 cm backwards-facing step 2.1 m from the leading edge. The geometry at the cavity closure was varied for different flow speeds to optimize the closure of the cavity. Cavity gas flux, thickness, frictional loads, and cavity pressures were measured over a range of flow speeds and air injection fluxes. High-speed video was used extensively to investigate the unsteady three dimensional cavity closure, the overall cavity shape and oscillations.

Radiotherapy and verrucous carcinoma of the oral cavity

International Nuclear Information System (INIS)

Vidyasagar, M.S.; Fernandes, D.J.; Pai Kasturi, D.; Akhileshwaran, R.; Rao, K.; Rao, S.; Rao, R.V.; Solomon, J.G.R.

1992-01-01

One hundred and seven cases of oral verrucous carcinoma treated with radiotherapy at Kasturba Hospital, Manipal, India between 1977 and 1987 were analysed concerning location within the oral cavity, clinical extent, and effectiveness of radiotherapy. The most common site was the buccal mucosa followed by the buccogingival sulcus. Only 13.2% of the patients presented with T1 or T2 tumours and 32.7% had clinically negative nodes. Biopsy had to be repeated more than once in 22 patients to get confirmation in invasive carcinoma. The 5-year survival rate was 35% for stage III and 26% for stage IV. The treatment results with radiotherapy were comparable with those for ordinary squamous cell carcinoma of the oral cavity. It is felt that the treatment policy for verrucous carcinoma can be the same as for ordinary squamous cell carcinoma. In order to prevent delay in diagnosis and treatment, proper cooperation between the treating oncologist and the pathologist is essential. (orig.)

TEM observations of crack tip: cavity interactions

International Nuclear Information System (INIS)

Horton, J.A.; Ohr, S.M.; Jesser, W.A.

1981-01-01

Crack tip-cavity interactions have been studied by performing room temperature deformation experiments in a transmission electron microscope on ion-irradiated type 316 stainless steel with small helium containing cavities. Slip dislocations emitted from a crack tip cut, sheared, and thereby elongated cavities without a volume enlargement. As the crack tip approached, a cavity volume enlargement occurred. Instead of the cavities continuing to enlarge until they touch, the walls between the cavities fractured. Fracture surface dimples do not correlate in size or density with these enlarged cavities

Evolution of iris colour in relation to cavity nesting and parental care in passerine birds.

Science.gov (United States)

Davidson, Gabrielle L; Thornton, Alex; Clayton, Nicola S

2017-01-01

Strong selection pressures are known to act on animal coloration. Although many animals vary in eye colour, virtually no research has investigated the functional significance of these colour traits. Passeriformes have a range of iris colours, making them an ideal system to investigate how and why iris colour has evolved. Using phylogenetic comparative methods, we tested the hypothesis that conspicuous iris colour in passerine birds evolved in response to (a) coordination of offspring care and (b) cavity nesting, two traits thought to be involved in intra-specific gaze sensitivity. We found that iris colour and cooperative offspring care by two or more individuals evolved independently, suggesting that bright eyes are not important for coordinating parental care through eye gaze. Furthermore, we found that evolution between iris colour and nesting behaviour did occur in a dependent manner, but contrary to predictions, transitions to coloured eyes were not more frequent in cavity nesters than non-cavity nesters. Instead, our results indicate that selection away from having bright eyes was much stronger in non-cavity nesters than cavity nesters, perhaps because conspicuous eye coloration in species not concealed within a cavity would be more visible to predators. © 2017 The Authors.

STRUCTURAL ANALYSIS OF SUPERCONDUCTING ACCELERATOR CAVITIES

International Nuclear Information System (INIS)

Schrage, D.

2000-01-01

The static and dynamic structural behavior of superconducting cavities for various projects was determined by finite element structural analysis. The β = 0.61 cavity shape for the Neutron Science Project was studied in detail and found to meet all design requirements if fabricated from five millimeter thick material with a single annular stiffener. This 600 MHz cavity will have a Lorentz coefficient of minus1.8 Hz/(Mv/meter) 2 and a lowest structural resonance of more than 100 Hz. Cavities at β = 0.48, 0.61, and 0.77 were analyzed for a Neutron Science Project concept which would incorporate 7-cell cavities. The medium and high beta cavities were found to meet all criteria but it was not possible to generate a β = 0.48 cavity with a Lorentz coefficient of less than minus3 Hz/(Mv/meter) 2

Superconducting cavities developments efforts at RRCAT

International Nuclear Information System (INIS)

Puntambekar, A.; Bagre, M.; Dwivedi, J.; Shrivastava, P.; Mundra, G.; Joshi, S.C.; Potukuchi, P.N.

2011-01-01

Superconducting RE cavities are the work-horse for many existing and proposed linear accelerators. Raja Ramanna Centre for Advanced Technology (RRCAT) has initiated a comprehensive R and D program for development of Superconducting RF cavities suitable for high energy accelerator application like SNS and ADS. For the initial phase of technology demonstration several prototype 1.3 GHz single cell-cavities have been developed. The work began with development of prototype single cell cavities in aluminum and copper. This helped in development of cavity manufacturing process, proving various tooling and learning on various mechanical and RF qualification processes. The parts manufacturing was done at RRCAT and Electron beam welding was carried out at Indian industry. These cavities further served during commissioning trials for various cavity processing infrastructure being developed at RRCAT and are also a potential candidate for Niobium thin film deposition R and D. Based on the above experience, few single cell cavities were developed in fine grain niobium. The critical technology of forming and machining of niobium and the intermediate RF qualification were developed at RRCAT. The EB welding of bulk niobium cavities was carried out in collaboration with IUAC, New Delhi at their facility. As a next logical step efforts are now on for development of multicell cavities. The prototype dumbbells and end group made of aluminium, comprising of RF and HOM couplers ports have also been developed, with their LB welding done at Indian industry. In this paper we shall present the development efforts towards manufacturing of 1.3 GHz single cell cavities and their initial processing and qualification. (author)

Comparative simulation studies of multipacting in higher-order-mode couplers of superconducting rf cavities

Directory of Open Access Journals (Sweden)

Y. M. Li

2014-02-01

Full Text Available Multipacting (MP in higher-order-mode (HOM couplers of the International Linear Collider (ILC baseline cavity and the Continuous Electron Beam Accelerator Facility (CEBAF 12 GeV upgrade cavity is studied by using the ACE3P suites, developed by the Advanced Computations Department at SLAC. For the ILC cavity HOM coupler, the simulation results show that resonant trajectories exist in three zones, corresponding to an accelerating gradient range of 0.6–1.6  MV/m, 21–34   MV/m, 32–35  MV/m and >40  MV/m, respectively. For the CEBAF 12 GeV upgrade cavity HOM coupler, resonant trajectories exist in one zone, corresponding to an accelerating gradient range of 6–13  MV/m. Potential implications of these MP barriers are discussed in the context of future high-energy pulsed as well as medium-energy continuous wave accelerators based on superconducting radio frequency cavities. Frequency scaling of MP’s predicted in HOM couplers of the ILC, CEBAF upgrade, Spallation Neutron Source (SNS, and Free-Electron Laser in Hamburg (FLASH third harmonic cavity is given and found to be in good agreement with the analytical result based on the parallel plate model.

Effect of cavity disinfectants on antibacterial activity and microtensile bond strength in class I cavity.

Science.gov (United States)

Kim, Bo-Ram; Oh, Man-Hwan; Shin, Dong-Hoon

2017-05-31

This study was performed to compare the antibacterial activities of three cavity disinfectants [chlorhexidine (CHX), NaOCl, urushiol] and to evaluate their effect on the microtensile bond strength of Scotchbond Universal Adhesive (3M-ESPE, St. Paul, MN, USA) in class I cavities. In both experiments, class I cavities were prepared in dentin. After inoculation with Streptococcus mutans, the cavities of control group were rinsed and those of CHX, NaOCl and urushiol groups were treated with each disinfectant. Standardized amounts of dentin chips were collected and number of S. mutans was determined. Following the same cavity treatment, same adhesive was applied in etch-and-rinse mode. Then, microtensile bond strength was evaluated. The number of S. mutans was significantly reduced in the cavities treated with CHX, NaOCl, and urushiol compared with control group (p<0.05). However, there was a significant bond strength reduction in NaOCl group, which showed statistical difference compared to the other groups (p<0.05).

Modeling the Rapid Boil-Off of a Cryogenic Liquid When Injected into a Low Pressure Cavity

Science.gov (United States)

Lira, Eric

2016-01-01

Many launch vehicle cryogenic applications require the modeling of injecting a cryogenic liquid into a low pressure cavity. The difficulty of such analyses lies in accurately predicting the heat transfer coefficient between the cold liquid and a warm wall in a low pressure environment. The heat transfer coefficient and the behavior of the liquid is highly dependent on the mass flow rate into the cavity, the cavity wall temperature and the cavity volume. Testing was performed to correlate the modeling performed using Thermal Desktop and Sinda Fluint Thermal and Fluids Analysis Software. This presentation shall describe a methodology to model the cryogenic process using Sinda Fluint, a description of the cryogenic test set up, a description of the test procedure and how the model was correlated to match the test results.

Mucoceles of the oral cavity in pediatric patients.

Science.gov (United States)

Wu, Chung Wei; Kao, Yu-Hsun; Chen, Chao-Ming; Hsu, Han Jen; Chen, Chun-Ming; Huang, I-Yueh

2011-07-01

Mucoceles are quite common in the oral cavity, but reports on pediatric patients are very rare. The aims of this study were to present our data and experience in the treatment of mucoceles of the oral cavity in pediatric patients, to compare them with those of other countries, and to remind the pediatric physician to devote much attention to lesions of the oral cavity in children. This retrospective study is based on the record of the patients who received surgical treatment for mucoceles of the oral cavity with pathologic confirmation at the Department of Dentistry, Kaohsiung Medical University Hospital, Taiwan, between 2000 and 2004. Patients younger than 18 years were included in this study. The analyzed data included age, gender, site, size, histopathologic findings, surgical methods, and complications. There were a total of 289 patients with mucoceles confirmed by histopathologic examination. As many as 64 patients were younger than 18 years. Of the 64, 34 were girls and 30 were boys; 89.1% of the lesions were in the lower lip; and 48.4% of the lesions were less than 5mm in diameter. Histopathologic findings showed that all mucoceles were of the extravasation type. As many as 30 patients were treated by carbon dioxide laser vaporization, and two cases recurred (6.67%); 34 patients were treated by surgical excision, and the recurrence rate (5.88%) was not statistically different for the treatment methods. The laser vaporization has the advantage of less bleeding, no sutures, and saving time, especially suitable for children with oral mucocele. Copyright © 2011 Elsevier Taiwan LLC. All rights reserved.

21 CFR 872.3260 - Cavity varnish.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Cavity varnish. 872.3260 Section 872.3260 Food and... DENTAL DEVICES Prosthetic Devices § 872.3260 Cavity varnish. (a) Identification. Cavity varnish is a device that consists of a compound intended to coat a prepared cavity of a tooth before insertion of...

Geometric Model of a Coronal Cavity

Science.gov (United States)

Kucera, Therese A.; Gibson, S. E.; Ratawicki, D.; Dove, J.; deToma, G.; Hao, J.; Hudson, H. S.; Marque, C.; McIntosh, P. S.; Reeves, K. K.;

Nest defense behaviors of native cavity-nesting birds to European Starlings

Science.gov (United States)

Rodney G. Olsen; Kathryn L. Purcell; David. Grubbs

2008-01-01

We used behavioral experiments to evaluate competition for nest sites and the extent to which European Starlings (Sturnus vulgaris) are seen as a threat by native bird species at the San Joaquin Experimental Range, Madera County, CA. We quantified the level of aggressive behavior of four species of native cavity-nesting birds to starlings at active...

Development of superconducting cavities at JAERI

International Nuclear Information System (INIS)

Ouchi, N.

2001-01-01

Development of superconducting (SC) cavities is continued for the high intensity proton accelerator in JAERI. In FY-1999, we carried out R and D work; (1) 2nd vertical test of β=0.886 single-cell cavity, (2) vertical test for observation of Q-disease without heat treatment after electropolishing, (3) vertical test of β=0.5 5-cell cavity, (4) pretuning, surface treatment and vertical test of β=0.886 5-cell cavity, (5) pulsed operation of β=0.886 single-cell cavity in the vertical test to confirm the validity of a new model calculation. This paper describes the present status of the R and D work for the SC cavities in JAERI. (author)

accelerating cavity from LEP

CERN Multimedia

This is an accelerating cavity from LEP, with a layer of niobium on the inside. Operating at 4.2 degrees above absolute zero, the niobium is superconducting and carries an accelerating field of 6 million volts per metre with negligible losses. Each cavity has a surface of 6 m2. The niobium layer is only 1.2 microns thick, ten times thinner than a hair. Such a large area had never been coated to such a high accuracy. A speck of dust could ruin the performance of the whole cavity so the work had to be done in an extremely clean environment. These challenging requirements pushed European industry to new achievements. 256 of these cavities are now used in LEP to double the energy of the particle beams.

Fundamental limitations of cavity-assisted atom interferometry

Science.gov (United States)

Dovale-Álvarez, M.; Brown, D. D.; Jones, A. W.; Mow-Lowry, C. M.; Miao, H.; Freise, A.

2017-11-01

Atom interferometers employing optical cavities to enhance the beam splitter pulses promise significant advances in science and technology, notably for future gravitational wave detectors. Long cavities, on the scale of hundreds of meters, have been proposed in experiments aiming to observe gravitational waves with frequencies below 1 Hz, where laser interferometers, such as LIGO, have poor sensitivity. Alternatively, short cavities have also been proposed for enhancing the sensitivity of more portable atom interferometers. We explore the fundamental limitations of two-mirror cavities for atomic beam splitting, and establish upper bounds on the temperature of the atomic ensemble as a function of cavity length and three design parameters: the cavity g factor, the bandwidth, and the optical suppression factor of the first and second order spatial modes. A lower bound to the cavity bandwidth is found which avoids elongation of the interaction time and maximizes power enhancement. An upper limit to cavity length is found for symmetric two-mirror cavities, restricting the practicality of long baseline detectors. For shorter cavities, an upper limit on the beam size was derived from the geometrical stability of the cavity. These findings aim to aid the design of current and future cavity-assisted atom interferometers.

Position-specific prediction of methylation sites from sequence conservation based on information theory.

Science.gov (United States)

Shi, Yinan; Guo, Yanzhi; Hu, Yayun; Li, Menglong

2015-07-23

Protein methylation plays vital roles in many biological processes and has been implicated in various human diseases. To fully understand the mechanisms underlying methylation for use in drug design and work in methylation-related diseases, an initial but crucial step is to identify methylation sites. The use of high-throughput bioinformatics methods has become imperative to predict methylation sites. In this study, we developed a novel method that is based only on sequence conservation to predict protein methylation sites. Conservation difference profiles between methylated and non-methylated peptides were constructed by the information entropy (IE) in a wider neighbor interval around the methylation sites that fully incorporated all of the environmental information. Then, the distinctive neighbor residues were identified by the importance scores of information gain (IG). The most representative model was constructed by support vector machine (SVM) for Arginine and Lysine methylation, respectively. This model yielded a promising result on both the benchmark dataset and independent test set. The model was used to screen the entire human proteome, and many unknown substrates were identified. These results indicate that our method can serve as a useful supplement to elucidate the mechanism of protein methylation and facilitate hypothesis-driven experimental design and validation.

A preliminary study on sentinel lymph node biopsy. Feasibility and predictive ability in oral cavity cancer

International Nuclear Information System (INIS)

Chikamatsu, Kazuaki; Kamada, Hideo; Ninomiya, Hiroshi; Takahashi, Katsumasa; Sakurai, Tsutomu; Oriuchi, Noboru; Furuya, Nobuhiko

2004-01-01

The main factor that affects the prognosis of patients with head and neck cancer (HNC) is regional lymph node metastases. For this reason, the accurate evaluation of neck metastases is required for neck management. This study investigates the sentinel lymph node identification and the accuracy of the histopathology of the sentinel lymph node in patients with HNC. Eleven patients with histologically proven oral squamous cell carcinoma accessible to radiocolloid injection were enrolled in this study. Using both lymphoscintigraphy and a handheld gamma probe, the sentinel lymph node could be identified in all 11 patients. Subsequently, the sentinel lymph nodes and the neck dissection specimen were examined for lymph node involvement due to tumor. The histopathology of sentinel lymph nodes was consistent with the pathological N classification in all 11 patients. Furthermore, the histopathology of sentinel lymph nodes was superior to physical examination, computed tomography (CT), magnetic resonance imaging (MRI) and positron emission tomography (PET) scan. The results of this study indicate that sentinel lymph node identification is technically feasible and predicts cervical metastases in patients with oral cavity cancer. This may be a useful diagnostic technique for identifying lymph node disease in staging lymph node dissection. (author)

Optimization of photonic crystal cavities

DEFF Research Database (Denmark)

Wang, Fengwen; Sigmund, Ole

2017-01-01

We present optimization of photonic crystal cavities. The optimization problem is formulated to maximize the Purcell factor of a photonic crystal cavity. Both topology optimization and air-hole-based shape optimization are utilized for the design process. Numerical results demonstrate...... that the Purcell factor of the photonic crystal cavity can be significantly improved through optimization....

Site characterization and validation. Stage 2 - Preliminary predictions

International Nuclear Information System (INIS)

Olsson, O.; Black, J.H.; Gale, J.E.; Holmes, D.C.

1989-05-01

The Site Characterization and Validation (SCV) project is designed to assess how well we can characterize a volume of rock prior to using it as a repository. The programme of work focuses on the validation of the techniques used in site characterization. The SCV project contains 5 stages of work arranged in two 'cycles' of data-gathering, prediction, and validation. The first stage of work has included drilling of 6 boreholes (N2, N3, N4, W1, W2 and V3) and measurements of geology, fracture characteristics, stess, single borehole geophysical logging, radar, seismics and hydrogeology. The rock at the SCV site is granite with small lithological variations. Based essentially on radar and seismic results 5 'fracture zones' have been identified, named GA, GB, GC, GH and GI. They all extend acroos the entire SCV site. They aer basically in in two groups (GA, GB, GC and GH, GI). The first group are aligned N40 degree E with a dip of 35 degree to the south. The second group are aligned approximately N10 degree W dipping 60 degree E. From the stochastic analysis of the joint data it was possible to identify three main fracture orientation clusters. The orientation of two of these clusters agree roughly with orientation of the main features. Cluster B has roughly the same orientation as GH and GI, while features GA, GB and GC have an orientation similar to the more loosely defined cluster C. The orientation of the third cluster (A) is northwest with a dip to northeast. It is found that 94% of all measured hydraulic transmissivity is accounted for by 4% of the tested rock, not all of this 'concentrated' transmissivity is with the major features defined by geophysics. When the hydraulic connections across the site are examied they show that there are several welldefined zones which permit rapid transmission of hydraulic signals. These are essentially from the northeast to the southwest. (66 figs., 21 tabs., 33 refs.)

White lesions in the oral cavity: A clinicopathological study from a tertiary care dermatology centre in Kerala, India

Directory of Open Access Journals (Sweden)

S M Simi

2013-01-01

Full Text Available Context: White lesions in the oral cavity may be benign, pre-malignant or malignant. There are no signs and symptoms which can reliably predict whether a leukoplakia will undergo malignant change or not. Many systemic conditions appear initially in the oral cavity and prompt diagnosis and management can help in minimizing disease progression and organ destruction. Aim : The aim of the paper was to study the clinical and histopathological patterns of white lesions in the oral cavity presented at the study setting and to study the factors associated with the histopathological patterns of the lesions. Settings and Design: A hospital based cross-sectional study of patients with white lesions in the oral cavity attending the Department of Dermatology and Venereology, Medical College, Thiruvananthapuram was done. Materials and Methods: After taking a detailed history, microscopic examination of Potassium hydroxide smear and an oral biopsy with histopathologial examination was done. Results : Out of the 50 patients in the study, clinically the diagnoses made were Lichen planus (32 patients; 64%, Frictional Keratosis (4;8%, Dysplasia (2;4%, Oral Hairy Leukoplakia (1;2%, Pemphigus Vulgaris (2;4%, Cutaneous Lupus Erythematosus (1;2%, Oral Submucous fibrosis (3;6% and Oral Candidiasis alone (5;10%. Out of the 45 patients who had undergone biopsy, 25 (55.6% had Lichen planus, 9 (20% had Frictional Keratosis and mild Dysplasia was found in 4 (8.9% patients. Conclusion : The measure of agreement between the clinical and pathological diagnosis was only 32%. Older age, difficulty in opening the mouth, consumption of non-smoked tobacco, site of the lesion (gingival, floor of mouth or lingual vestibule and presence of tenderness on the lesion were significantly associated with Dysplasia.

TESLA superconducting RF cavity development

International Nuclear Information System (INIS)

Koepke, K.

1995-01-01

The TESLA collaboration has made steady progress since its first official meeting at Cornell in 1990. The infrastructure necessary to assemble and test superconducting rf cavities has been installed at the TESLA Test Facility (TTF) at DESY. 5-cell, 1.3 GHz cavities have been fabricated and have reached accelerating fields of 25 MV/m. Full sized 9-cell copper cavities of TESLA geometry have been measured to verify the higher order modes present and to evaluate HOM coupling designs. The design of the TESLA 9-cell cavity has been finalized and industry has started delivery. Two prototype 9-cell niobium cavities in their first tests have reached accelerating fields of 10 MV/m and 15 MV/m in a vertical dewar after high peak power (HPP) conditioning. The first 12 m TESLA cryomodule that will house 8 9-cell cavities is scheduled to be delivered in Spring 1995. A design report for the TTF is in progress. The TTF test linac is scheduled to be commissioned in 1996/1997. (orig.)

CAVITY LIKE COMPLETIONS IN WEAK SANDS PREFERRED UPSTREAM MANAGEMENT PRACTICES

Energy Technology Data Exchange (ETDEWEB)

Ian Palmer; John McLennan

2004-04-30

The technology referred to as Cavity Like Completions (CLC) offers a new technique to complete wells in friable and unconsolidated sands. A successfully designed CLC provides significant increases in well PI (performance index) at lower costs than alternative completion techniques. CLC technology is being developed and documented by a partnership of major oil and gas companies through a GPRI (Global Petroleum Research Institute) joint venture. Through the DOE-funded PUMP program, the experiences of the members of the joint venture will be described for other oil and gas producing companies. To date six examples of CLC completions have been investigated by the JV. The project was performed to introduce a new type of completion (or recompletion) technique to the industry that, in many cases, offers a more cost effective method to produce oil and gas from friable reservoirs. The project's scope of work included: (1) Further develop theory, laboratory and field data into a unified model to predict performance of cavity completion; (2) Perform at least one well test for cavity completion (well provided by one of the sponsor companies); (3) Provide summary of geo-mechanical models for PI increase; and (4) Develop guidelines to evaluate success of potential cavity completion. The project tracks the experiences of a joint industry consortium (GPRI No. 17) over a three year period and compiles results of the activities of this group.

An economical wireless cavity-nest viewer

Science.gov (United States)

Daniel P. Huebner; Sarah R. Hurteau

2007-01-01

Inspection of cavity nests and nest boxes is often required during studies of cavity-nesting birds, and fiberscopes and pole-mounted video cameras are sometimes used for such inspection. However, the cost of these systems may be prohibitive for some potential users. We describe a user-built, wireless cavity viewer that can be used to access cavities as high as 15 m and...

Effect of the Tuner on the Field Flatness of SNS Superconducting RF Cavities

CERN Document Server

Sun, A

2004-01-01

Field flatness in a multi-cell superconducting cavity affects not only the net accelerating voltage, but also the peak surface field and the Lorenz Force detuning coefficient. Our measurement indicates that the field flatness changes both external Q of the Fundamental Power Coupler (FPC) and external Q of the Field Probe (FP). The field amplitude tilts linearly to the distance between the cell center and the cavity’s geometry center (pivot point). The tilt rate has been measured in a cryomodule cold (2 K) test, being about 2%/100 kHz, relative the field flatness at the cavity’s center frequency of 805 MHz. Bead-pull measurements confirmed that the field flatness change is 2.0%/100 kHz for a medium β cavity with helium vessel, and 1.72%/100 kHz without helium vessel. These results matched the predictions of simulations using ANSYS and SUPERFISH. A detailed analysis reveals that longitudinal capacitive gap deformation is the main cause of the frequency change. Field flatness change ...

Prediction of Poly(A Sites by Poly(A Read Mapping.

Directory of Open Access Journals (Sweden)

Thomas Bonfert

Full Text Available RNA-seq reads containing part of the poly(A tail of transcripts (denoted as poly(A reads provide the most direct evidence for the position of poly(A sites in the genome. However, due to reduced coverage of poly(A tails by reads, poly(A reads are not routinely identified during RNA-seq mapping. Nevertheless, recent studies for several herpesviruses successfully employed mapping of poly(A reads to identify herpesvirus poly(A sites using different strategies and customized programs. To more easily allow such analyses without requiring additional programs, we integrated poly(A read mapping and prediction of poly(A sites into our RNA-seq mapping program ContextMap 2. The implemented approach essentially generalizes previously used poly(A read mapping approaches and combines them with the context-based approach of ContextMap 2 to take into account information provided by other reads aligned to the same location. Poly(A read mapping using ContextMap 2 was evaluated on real-life data from the ENCODE project and compared against a competing approach based on transcriptome assembly (KLEAT. This showed high positive predictive value for our approach, evidenced also by the presence of poly(A signals, and considerably lower runtime than KLEAT. Although sensitivity is low for both methods, we show that this is in part due to a high extent of spurious results in the gold standard set derived from RNA-PET data. Sensitivity improves for poly(A sites of known transcripts or determined with a more specific poly(A sequencing protocol and increases with read coverage on transcript ends. Finally, we illustrate the usefulness of the approach in a high read coverage scenario by a re-analysis of published data for herpes simplex virus 1. Thus, with current trends towards increasing sequencing depth and read length, poly(A read mapping will prove to be increasingly useful and can now be performed automatically during RNA-seq mapping with ContextMap 2.

Forward Modeling of a Coronal Cavity

Science.gov (United States)

Kucera, T. A.; Gibson, S. E.; Schmit, D. J.

2011-01-01

We apply a forward model of emission from a coronal cavity in an effort to determine the temperature and density distribution in the cavity. Coronal cavities are long, low-density structures located over filament neutral lines and are often seen as dark elliptical features at the solar limb in white light, EUV and X-rays. When these structures erupt they form the cavity portions of CMEs The model consists of a coronal streamer model with a tunnel-like cavity with elliptical cross-section and a Gaussian variation of height along the tunnel length. Temperature and density can be varied as a function of altitude both in the cavity and streamer. We apply this model to a cavity observed in Aug. 2007 by a wide array of instruments including Hinode/EIS, STEREO/EUVI and SOHO/EIT. Studies such as these will ultimately help us understand the the original structures which erupt to become CMEs and ICMES, one of the prime Solar Orbiter objectives.

Highly efficient generation of ultraintense high-energy ion beams using laser-induced cavity pressure acceleration

Energy Technology Data Exchange (ETDEWEB)

Badziak, J.; Jablonski, S.; Raczka, P. [Institute of Plasma Physics and Laser Microfusion, Euratom Association, 01-497 Warsaw (Poland)

2012-08-20

Results of particle-in-cell (PIC) simulations of fast ion generation in the recently proposed laser-induced cavity pressure acceleration (LICPA) scheme in which a picosecond circularly polarized laser pulse of intensity {approx}10{sup 21} W/cm{sup 2} irradiates a carbon target placed in a cavity are presented. It is shown that due to circulation of the laser pulse in the cavity, the laser-ions energy conversion efficiency in the LICPA scheme is more than twice as high as that for the conventional (without a cavity) radiation pressure acceleration scheme and a quasi-monoenergetic carbon ion beam of the mean ion energy {approx}0.5 GeV and the energy fluence {approx}0.5 GJ/cm{sup 2} is produced with the efficiency {approx}40%. The results of PIC simulations are found to be in fairly good agreement with the predictions of the generalized light-sail model.

Technical tasks in superconducting cavities

Energy Technology Data Exchange (ETDEWEB)

Saito, Kenji [High Energy Accelerator Research Organization, Tsukuba, Ibaraki (Japan)

1997-11-01

The feature of superconducting rf cavities is an extremely small surface resistance on the wall. It brings a large energy saving in the operation, even those are cooled with liquid helium. That also makes possible to operate themselves in a higher field gradient comparing to normal conducting cavities, and brings to make accelerators compact. These merits are very important for the future accelerator engineering which is planed at JAERI for the neutron material science and nuclear waste transmutation. This machine is a high intensity proton linac and uses sc cavities in the medium and high {beta} sections. In this paper, starting R and D of proton superconducting cavities, several important technical points which come from the small surface resistance of sc cavities, are present to succeed it and also differences between the medium and high - {beta} structures are discussed. (author)

Self-consistent Maxwell-Bloch model of quantum-dot photonic-crystal-cavity lasers

Science.gov (United States)

Cartar, William; Mørk, Jesper; Hughes, Stephen

2017-08-01

We present a powerful computational approach to simulate the threshold behavior of photonic-crystal quantum-dot (QD) lasers. Using a finite-difference time-domain (FDTD) technique, Maxwell-Bloch equations representing a system of thousands of statistically independent and randomly positioned two-level emitters are solved numerically. Phenomenological pure dephasing and incoherent pumping is added to the optical Bloch equations to allow for a dynamical lasing regime, but the cavity-mediated radiative dynamics and gain coupling of each QD dipole (artificial atom) is contained self-consistently within the model. These Maxwell-Bloch equations are implemented by using Lumerical's flexible material plug-in tool, which allows a user to define additional equations of motion for the nonlinear polarization. We implement the gain ensemble within triangular-lattice photonic-crystal cavities of various length N (where N refers to the number of missing holes), and investigate the cavity mode characteristics and the threshold regime as a function of cavity length. We develop effective two-dimensional model simulations which are derived after studying the full three-dimensional passive material structures by matching the cavity quality factors and resonance properties. We also demonstrate how to obtain the correct point-dipole radiative decay rate from Fermi's golden rule, which is captured naturally by the FDTD method. Our numerical simulations predict that the pump threshold plateaus around cavity lengths greater than N =9 , which we identify as a consequence of the complex spatial dynamics and gain coupling from the inhomogeneous QD ensemble. This behavior is not expected from simple rate-equation analysis commonly adopted in the literature, but is in qualitative agreement with recent experiments. Single-mode to multimode lasing is also observed, depending on the spectral peak frequency of the QD ensemble. Using a statistical modal analysis of the average decay rates, we also

Pharmacological considerations for predicting PK/PD at the site of action for therapeutic proteins.

Science.gov (United States)

Wang, Weirong; Zhou, Honghui

For therapeutic proteins whose sites of action are distal to the systemic circulation, both drug and target concentrations at the tissue sites are not necessarily proportional to those in systemic circulation, highlighting the importance of understanding pharmacokinetic/pharmacodynamic (PK/PD) relationship at the sites of action. This review summarizes the pharmacological considerations for predicting local PK/PD and the importance of measuring PK and PD at site of action. Three case examples are presented to show how mechanistic and physiologically based PK/PD (PBPK/PD) models which incorporated the PK and PD at the tissue site can be used to facilitate understanding the exposure-response relationship for therapeutic proteins. Copyright © 2016. Published by Elsevier Ltd.

Optically coupled cavities for wavelength switching

Energy Technology Data Exchange (ETDEWEB)

Costazo-Caso, Pablo A; Granieri, Sergio; Siahmakoun, Azad, E-mail: pcostanzo@ing.unlp.edu.ar, E-mail: granieri@rose-hulman.edu, E-mail: siahmako@rose-hulman.edu [Department of Physics and Optical Engineering, Rose-Hulman Institute of Technology, 5500 Wabash Avenue, Terre Haute, IN 47803 (United States)

2011-01-01

An optical bistable device which presents hysteresis behavior is proposed and experimentally demonstrated. The system finds applications in wavelength switching, pulse reshaping and optical bistability. It is based on two optically coupled cavities named master and slave. Each cavity includes a semiconductor optical amplifier (SOA), acting as the gain medium of the laser, and two pair of fiber Bragg gratings (FBG) which define the lasing wavelength (being different in each cavity). Finally, a variable optical coupler (VOC) is employed to couple both cavities. Experimental characterization of the system performance is made analyzing the effects of the coupling coefficient between the two cavities and the driving current in each SOA. The properties of the hysteretic bistable curve and switching can be controlled by adjusting these parameters and the loss in the cavities. By selecting the output wavelength ({lambda}{sub 1} or {lambda}{sub 2}) with an external filter it is possible to choose either the invert or non-invert switched signal. Experiments were developed employing both optical discrete components and a photonic integrated circuit. They show that for 8 m-long cavities the maximum switching frequency is about 500 KHz, and for 4 m-long cavities a minimum rise-time about 21 ns was measured. The switching time can be reduced by shortening the cavity lengths and using photonic integrated circuits.

Underwater sound transmission through arrays of disk cavities in a soft elastic medium.

Science.gov (United States)

Calvo, David C; Thangawng, Abel L; Layman, Christopher N; Casalini, Riccardo; Othman, Shadi F

2015-10-01

Scattering from a cavity in a soft elastic medium, such as silicone rubber, resembles scattering from an underwater bubble in that low-frequency monopole resonance is obtainable in both cases. Arrays of cavities can therefore be used to reduce underwater sound transmission using thin layers and low void fractions. This article examines the role of cavity shape by microfabricating arrays of disk-shaped air cavities into single and multiple layers of polydimethylsiloxane. Comparison is made with the case of equivalent volume cylinders which approximate spheres. Measurements of ultrasonic underwater sound transmission are compared with finite element modeling predictions. The disks provide a deeper transmission minimum at a lower frequency owing to the drum-type breathing resonance. The resonance of a single disk cavity in an unbounded medium is also calculated and compared with a derived estimate of the natural frequency of the drum mode. Variation of transmission is determined as a function of disk tilt angle, lattice constant, and layer thickness. A modeled transmission loss of 18 dB can be obtained at a wavelength about 20 times the three-layer thickness, and thinner results (wavelength/thickness ∼ 240) are possible for the same loss with a single layer depending on allowable hydrostatic pressure.

A homology-based pipeline for global prediction of post-translational modification sites

Science.gov (United States)

Chen, Xiang; Shi, Shao-Ping; Xu, Hao-Dong; Suo, Sheng-Bao; Qiu, Jian-Ding

2016-05-01

The pathways of protein post-translational modifications (PTMs) have been shown to play particularly important roles for almost any biological process. Identification of PTM substrates along with information on the exact sites is fundamental for fully understanding or controlling biological processes. Alternative computational strategies would help to annotate PTMs in a high-throughput manner. Traditional algorithms are suited for identifying the common organisms and tissues that have a complete PTM atlas or extensive experimental data. While annotation of rare PTMs in most organisms is a clear challenge. In this work, to this end we have developed a novel homology-based pipeline named PTMProber that allows identification of potential modification sites for most of the proteomes lacking PTMs data. Cross-promotion E-value (CPE) as stringent benchmark has been used in our pipeline to evaluate homology to known modification sites. Independent-validation tests show that PTMProber achieves over 58.8% recall with high precision by CPE benchmark. Comparisons with other machine-learning tools show that PTMProber pipeline performs better on general predictions. In addition, we developed a web-based tool to integrate this pipeline at http://bioinfo.ncu.edu.cn/PTMProber/index.aspx. In addition to pre-constructed prediction models of PTM, the website provides an extensional functionality to allow users to customize models.

Prediction of citrullination sites by incorporating k-spaced amino acid pairs into Chou's general pseudo amino acid composition.

Science.gov (United States)

Ju, Zhe; Wang, Shi-Yun

2018-04-22

As one of the most important and common protein post-translational modifications, citrullination plays a key role in regulating various biological processes and is associated with several human diseases. The accurate identification of citrullination sites is crucial for elucidating the underlying molecular mechanisms of citrullination and designing drugs for related human diseases. In this study, a novel bioinformatics tool named CKSAAP_CitrSite is developed for the prediction of citrullination sites. With the assistance of support vector machine algorithm, the highlight of CKSAAP_CitrSite is to adopt the composition of k-spaced amino acid pairs surrounding a query site as input. As illustrated by 10-fold cross-validation, CKSAAP_CitrSite achieves a satisfactory performance with a Sensitivity of 77.59%, a Specificity of 95.26%, an Accuracy of 89.37% and a Matthew's correlation coefficient of 0.7566, which is much better than those of the existing prediction method. Feature analysis shows that the N-terminal space containing pairs may play an important role in the prediction of citrullination sites, and the arginines close to N-terminus tend to be citrullinated. The conclusions derived from this study could offer useful information for elucidating the molecular mechanisms of citrullination and related experimental validations. A user-friendly web-server for CKSAAP_CitrSite is available at 123.206.31.171/CKSAAP_CitrSite/. Copyright © 2017. Published by Elsevier B.V.

Effect of cavity inclination on a temperature and concentration controlled double diffusive convection at ice plate melting

Energy Technology Data Exchange (ETDEWEB)

Sugawara, M.; Ishikura, T. [Akita University, Department of Mechanical Engineering, Akita (Japan); Beer, H. [Technische Unversitat Darmstadt, Institut fur Technische Thermodynamik, Darmstadt (Germany)

2005-03-01

This paper is concerned with the double diffusive convection due to the melting of an ice plate into a calcium chloride aqueous solution inside a rectangular cavity. It is mainly considered the effect of the cavity inclination {theta} on the melting rate and the mean melting Nusselt- and Sherwood-numbers, experimentally as well as numerically. The ice plate melts spontaneously with decreasing temperature at the melting front even if initially there does not exist a temperature difference between the ice and the liquid. The concentration- and temperature-gradients near the melting front induce double diffusive convection in the liquid, which will affect the melting rate. Experiments reveal that the mean melting mass increases monotonically with increasing cavity inclination. The numerical analysis based on the laminar assumption predicts well the melting mass in the range of {theta}=0-90 , however, under-predicts the melting mass in the range of {theta}=90-180 as compared with the experimental results. (orig.)

Remnants of semiclassical bistability in the few-photon regime of cavity QED.

Science.gov (United States)

Kerckhoff, Joseph; Armen, Michael A; Mabuchi, Hideo

2011-11-21

Broadband homodyne detection of the light transmitted by a Fabry-Perot cavity containing a strongly-coupled (133)Cs atom is used to probe the dynamic optical response in a regime where semiclassical theory predicts bistability but strong quantum corrections should apply. While quantum fluctuations destabilize true equilibrium bistability, our observations confirm the existence of metastable states with finite lifetimes and a hysteretic response is apparent when the optical drive is modulated on comparable timescales. Our experiment elucidates remnant semiclassical behavior in the attojoule (~10 photon) regime of single-atom cavity QED, of potential significance for ultra-low power photonic signal processing. © 2011 Optical Society of America

Scheme for the implementation of a universal quantum cloning machine via cavity-assisted atomic collisions in cavity QED

International Nuclear Information System (INIS)

Zou Xubo; Pahlke, K.; Mathis, W.

2003-01-01

We propose a scheme to implement the 1→2 universal quantum cloning machine of Buzek and Hillery [Phys. Rev. A 54, 1844 (1996)] in the context of cavity QED. The scheme requires cavity-assisted collision processes between atoms, which cross through nonresonant cavity fields in the vacuum states. The cavity fields are only virtually excited to face the decoherence problem. That's why the requirements on the cavity quality factor can be loosened

LHC crab-cavity aspects and strategy

International Nuclear Information System (INIS)

Calaga, R.; Tomas, R.; Zimmermann, F.

2010-01-01

The 3rd LHC Crab Cavity workshop (LHC-CC09) took place at CERN in October 2009. It reviewed the current status and identified a clear strategy towards a future crab-cavity implementation. Following the success of crab cavities in KEK-B and the strong potential for luminosity gain and leveling, CERN will pursue crab crossing for the LHC upgrade. We present a summary and outcome of the variousworkshop sessions which have led to the LHC crab-cavity strategy, covering topics like layout, cavity design, integration, machine protection, and a potential validation test in the SPS.

Modelling of diamond deposition microwave cavity generated plasmas

International Nuclear Information System (INIS)

Hassouni, K; Silva, F; Gicquel, A

2010-01-01

Some aspects of the numerical modelling of diamond deposition plasmas generated using microwave cavity systems are discussed. The paper mainly focuses on those models that allow (i) designing microwave cavities in order to optimize the power deposition in the discharge and (ii) estimating the detailed plasma composition in the vicinity of the substrate surface. The development of hydrogen plasma models that may be used for the self-consistent simulation of microwave cavity discharge is first discussed. The use of these models for determining the plasma configuration, composition and temperature is illustrated. Examples showing how to use these models in order to optimize the cavity structure and to obtain stable process operations are also given. A transport model for the highly reactive H 2 /CH 4 moderate pressure discharges is then presented. This model makes possible the determination of the time variation of plasma composition and temperature on a one-dimensional domain located on the plasma axis. The use of this model to analyse the transport phenomena and the chemical process in diamond deposition plasmas is illustrated. The model is also utilized to analyse pulsed mode discharges and the benefit they can bring as far as diamond growth rate and quality enhancement are concerned. We, in particular, show how the model can be employed to optimize the pulse waveform in order to improve the deposition process. Illustrations on how the model can give estimates of the species density at the growing substrate surface over a wide domain of deposition conditions are also given. This brings us to discuss the implication of the model prediction in terms of diamond growth rate and quality. (topical review)

Nuclear reactor cavity streaming shield

International Nuclear Information System (INIS)

Klotz, R.J.; Stephen, D.W.

1978-01-01

The upper portion of a nuclear reactor vessel supported in a concrete reactor cavity has a structure mounted below the top of the vessel between the outer vessel wall and the reactor cavity wall which contains hydrogenous material which will attenuate radiation streaming upward between vessel and the reactor cavity wall while preventing pressure buildup during a loss of coolant accident

Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs

Directory of Open Access Journals (Sweden)

Sheng Zhi-Ya

2008-02-01

Full Text Available Abstract Background As one of the most common protein post-translational modifications, glycosylation is involved in a variety of important biological processes. Computational identification of glycosylation sites in protein sequences becomes increasingly important in the post-genomic era. A new encoding scheme was employed to improve the prediction of mucin-type O-glycosylation sites in mammalian proteins. Results A new protein bioinformatics tool, CKSAAP_OGlySite, was developed to predict mucin-type O-glycosylation serine/threonine (S/T sites in mammalian proteins. Using the composition of k-spaced amino acid pairs (CKSAAP based encoding scheme, the proposed method was trained and tested in a new and stringent O-glycosylation dataset with the assistance of Support Vector Machine (SVM. When the ratio of O-glycosylation to non-glycosylation sites in training datasets was set as 1:1, 10-fold cross-validation tests showed that the proposed method yielded a high accuracy of 83.1% and 81.4% in predicting O-glycosylated S and T sites, respectively. Based on the same datasets, CKSAAP_OGlySite resulted in a higher accuracy than the conventional binary encoding based method (about +5.0%. When trained and tested in 1:5 datasets, the CKSAAP encoding showed a more significant improvement than the binary encoding. We also merged the training datasets of S and T sites and integrated the prediction of S and T sites into one single predictor (i.e. S+T predictor. Either in 1:1 or 1:5 datasets, the performance of this S+T predictor was always slightly better than those predictors where S and T sites were independently predicted, suggesting that the molecular recognition of O-glycosylated S/T sites seems to be similar and the increase of the S+T predictor's accuracy may be a result of expanded training datasets. Moreover, CKSAAP_OGlySite was also shown to have better performance when benchmarked against two existing predictors. Conclusion Because of CKSAAP

Nesting sites characteristics of stingless bees (Hymenoptera: Apidae in Central Sulawesi, Indonesia

Directory of Open Access Journals (Sweden)

Nelky Suriawanto

2017-06-01

Full Text Available Stingless bees (Hymenoptera: Apidae is eusocial insects that live together in a colony. This research was aimed to study the nesting site characteristics of stingless bees in the settlement areas at Central Sulawesi, Indonesia. The nesting sites were observed by purposive sampling method from July 2015 to January 2016. Four species belong to genus Tetragonula were found, namely T. fuscobalteata, T. biroi, T. sapiens, and T. laeviceps. Two spesies, T. biroi and T. sapiens are the new record in Sulawesi island. The highest abundance of stingless bees colony was T. fuscobalteata (92.26%, followed by T. biroi (4.17%, T. sapiens (2.98%, and T. laeviceps (0.59%. Nesting sites of T. fuscobalteata were found in the stone, brick wall, wooden wall, bamboo, and iron cavities, T. biroi in the wooden wall, stone, and brick wall cavities, T. sapiens in stone cavities, while T. laeviceps in wooden walls.

Offline estimation of decay time for an optical cavity with a low pass filter cavity model.

Science.gov (United States)

Kallapur, Abhijit G; Boyson, Toby K; Petersen, Ian R; Harb, Charles C

2012-08-01

This Letter presents offline estimation results for the decay-time constant for an experimental Fabry-Perot optical cavity for cavity ring-down spectroscopy (CRDS). The cavity dynamics are modeled in terms of a low pass filter (LPF) with unity DC gain. This model is used by an extended Kalman filter (EKF) along with the recorded light intensity at the output of the cavity in order to estimate the decay-time constant. The estimation results using the LPF cavity model are compared to those obtained using the quadrature model for the cavity presented in previous work by Kallapur et al. The estimation process derived using the LPF model comprises two states as opposed to three states in the quadrature model. When considering the EKF, this means propagating two states and a (2×2) covariance matrix using the LPF model, as opposed to propagating three states and a (3×3) covariance matrix using the quadrature model. This gives the former model a computational advantage over the latter and leads to faster execution times for the corresponding EKF. It is shown in this Letter that the LPF model for the cavity with two filter states is computationally more efficient, converges faster, and is hence a more suitable method than the three-state quadrature model presented in previous work for real-time estimation of the decay-time constant for the cavity.

AthMethPre: a web server for the prediction and query of mRNA m6A sites in Arabidopsis thaliana.

Science.gov (United States)

Xiang, Shunian; Yan, Zhangming; Liu, Ke; Zhang, Yaou; Sun, Zhirong

2016-10-18

N 6 -Methyladenosine (m 6 A) is the most prevalent and abundant modification in mRNA that has been linked to many key biological processes. High-throughput experiments have generated m 6 A-peaks across the transcriptome of A. thaliana, but the specific methylated sites were not assigned, which impedes the understanding of m 6 A functions in plants. Therefore, computational prediction of mRNA m 6 A sites becomes emergently important. Here, we present a method to predict the m 6 A sites for A. thaliana mRNA sequence(s). To predict the m 6 A sites of an mRNA sequence, we employed the support vector machine to build a classifier using the features of the positional flanking nucleotide sequence and position-independent k-mer nucleotide spectrum. Our method achieved good performance and was applied to a web server to provide service for the prediction of A. thaliana m 6 A sites. The server also provides a comprehensive database of predicted transcriptome-wide m 6 A sites and curated m 6 A-seq peaks from the literature for query and visualization. The AthMethPre web server is the first web server that provides a user-friendly tool for the prediction and query of A. thaliana mRNA m 6 A sites, which is freely accessible for public use at .

Modelling for the Stripa site characterization and validation drift inflow: prediction of flow through fractured rock

International Nuclear Information System (INIS)

Herbert, A.; Gale, J.; MacLeod, R.; Lanyon, G.

1991-12-01

We present our approach to predicting flow through a fractured rock site; the site characterization and validation region in the Stripa mine. Our approach is based on discrete fracture network modelling using the NAPSAC computer code. We describe the conceptual models and assumptions that we have used to interpret the geometry and flow properties of the fracture networks, from measurements at the site. These are used to investigate large scale properties of the network and we show that for flows on scales larger than about 10 m, porous medium approximation should be used. The porous medium groundwater flow code CFEST is used to predict the large scale flows through the mine and the SCV region. This, in turn, is used to provide boundary conditions for more detailed models, which predict the details of flow, using a discrete fracture network model, on scales of less than 10 m. We conclude that a fracture network approach is feasible and that it provides a better understanding of details of flow than conventional porous medium approaches and a quantification of the uncertainty associated with predictive flow modelling characterised from field measurement in fractured rock. (au)

Influence of natural convection and diluent inerting on H2 and CO oxidation in the reactor cavity

International Nuclear Information System (INIS)

Wong, C.C.

1988-01-01

The question of complete in-cavity oxidation of combustible gases produced by core-concrete interactions following vessel breach has been investigated. It is overly optimistic to assume a complete oxidation because a variety of phenomena, such as steam inerting and oxygen transport by natural convection, may influence the degree of in-cavity oxidation that takes place. HECTR analyses of an ice-condenser containment during an S2HF drain-closed accident show that the in-cavity oxidation process is limited by the rate at which oxygen is transported into the reactor cavity region. Accumulation and subsequent combustion of hydrogen and carbon monoxide in the upper and lower compartments generate a peak pressure of 384 kPa (56 psig) at 7.4 h, that an earlier IDCOR analysis did not predict. (orig.)

ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites.

Science.gov (United States)

Konc, Janez; Janežič, Dušanka

2014-07-01

The ProBiS-ligands web server predicts binding of ligands to a protein structure. Starting with a protein structure or binding site, ProBiS-ligands first identifies template proteins in the Protein Data Bank that share similar binding sites. Based on the superimpositions of the query protein and the similar binding sites found, the server then transposes the ligand structures from those sites to the query protein. Such ligand prediction supports many activities, e.g. drug repurposing. The ProBiS-ligands web server, an extension of the ProBiS web server, is open and free to all users at http://probis.cmm.ki.si/ligands. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Design of half-reentrant SRF cavities

International Nuclear Information System (INIS)

Meidlinger, M.; Grimm, T.L.; Hartung, W.

2006-01-01

The shape of a TeSLA inner cell can be improved to lower the peak surface magnetic field at the expense of a higher peak surface electric field by making the cell reentrant. Such a single-cell cavity was designed and tested at Cornell, setting a world record accelerating gradient [V. Shemelin et al., An optimized shape cavity for TESLA: concept and fabrication, 11th Workshop on RF Superconductivity, Travemuende, Germany, September 8-12, 2003; R. Geng, H. Padamsee, Reentrant cavity and first test result, Pushing the Limits of RF Superconductivity Workshop, Argonne National Laboratory, September 22-24, 2004]. However, the disadvantage to a cavity is that liquids become trapped in the reentrant portion when it is vertically hung during high pressure rinsing. While this was overcome for Cornell's single-cell cavity by flipping it several times between high pressure rinse cycles, this may not be feasible for a multi-cell cavity. One solution to this problem is to make the cavity reentrant on only one side, leaving the opposite wall angle at six degrees for fluid drainage. This idea was first presented in 2004 [T.L. Grimm et al., IEEE Transactions on Applied Superconductivity 15(6) (2005) 2393]. Preliminary designs of two new half-reentrant (HR) inner cells have since been completed, one at a high cell-to-cell coupling of 2.1% (high-k cc HR) and the other at 1.5% (low-k cc HR). The parameters of a HR cavity are comparable to a fully reentrant cavity, with the added benefit that a HR cavity can be easily cleaned with current technology

VAC Therapy Direct to the Medullary Cavity for Chronic Tibial Osteomyelitis.

Science.gov (United States)

Miyamura, Satoshi; Tsuji, Shigeyoshi; Iwai, Takao; Hamada, Masayuki

2016-06-01

Vacuum-assisted wound closure (VAC) is useful for difficult wound beds, although sites where bleeding or infection is expected are usually regarded as problematic for this therapy. This report outlines the treatment of chronic tibial osteomyelitis (Cierny- Mader type III) due to mixed infection with Nocardia spp and Bacteroi- des fragilis by postoperative VAC therapy direct to the medullary cavity, followed by wound coverage with a gastrocnemius myocutaneous skin flap. A 64-year-old man developed chronic left tibial os- teomyelitis after a work injury. The nonviable tissues were debrided, including a sequestrum. Nocardia spp and B. fragilis were isolated from surgical bone specimens, and chronic tibial osteomyelitis due to mixed infection was diagnosed. Postoperatively, VAC therapy was performed directly to the open medullary cavity of the tibia and sub- sequently covered the residual soft tissue defect with a gastrocnemius myocutaneous flap. The authors could not find any English literature on VAC therapy direct to the medullary cavity combined with transplantation of a myocutaneous flap for osteomyelitis. Nocardia spp can cause a variety of infections, among which osteomyelitis occupies a relatively small percentage. This case raises the possibil- ity of treating chronic tibial osteomyelitis caused by mixed infection with Nocardia spp and B. fragilis by applying postoperative VAC ther- apy directly to the medullary cavity and covering the residual wound with a gastrocnemius myocutaneous flap.

Present status of superconducting cavity developments

Energy Technology Data Exchange (ETDEWEB)

Ouchi, Nobuo; Kusano, Joichi; Hasegawa, Kazuo [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment] [and others

1997-11-01

An R and D work of a superconducting (SC) cavity for the high intensity proton linac has begun at JAERI in collaboration with KEK. The RF field calculation and the structural analysis have been made to determine the cavity shape in the proton energy range between 100 and 1500 MeV. The results indicate the feasibility of a SC proton linac. A vertical test stand with clean room, water rinsing system, cavity evacuation pumping system, cryostat and data acquisition system has been installed to demonstrate the cavity performance. A single cell cavity of {beta}=0.5 has been fabricated and tested at the test stand to obtain the Q-value and the maximum surface electric field strength. The measured Q-values have been found to be high enough for our requirement while the field strength was limited to about 75% of the specification by the multipacting. We describe the preliminary design of the SC cavity, the overview of the vertical test stand and experimental results of the single cell cavity. (author)

Photoprocesses of photosensitizing drugs within cyclodextrin cavities.

Science.gov (United States)

Monti, Sandra; Sortino, Salvatore

2002-09-01

Recently some interest has been focused on the photobehavior of CD-drug inclusion complexes in relation to the problem of the biological photosensitization by drugs. This review is dedicated to the illustration of the mechanistic aspects of the photoprocesses occurring in some non-steroidal anti-inflammatory drugs (NSAIDs), with photosensitising side effects, within CD cavities. It is shown how the photobehavior of the CD-drug associates can help to model the photoreactivity of the drugs in biological sites. The limitations for the use of CDs as protective systems for the clinical administration of photosensitising drugs is also evidenced.

Optical cavity furnace for semiconductor wafer processing

Science.gov (United States)

Sopori, Bhushan L.

2014-08-05

An optical cavity furnace 10 having multiple optical energy sources 12 associated with an optical cavity 18 of the furnace. The multiple optical energy sources 12 may be lamps or other devices suitable for producing an appropriate level of optical energy. The optical cavity furnace 10 may also include one or more reflectors 14 and one or more walls 16 associated with the optical energy sources 12 such that the reflectors 14 and walls 16 define the optical cavity 18. The walls 16 may have any desired configuration or shape to enhance operation of the furnace as an optical cavity 18. The optical energy sources 12 may be positioned at any location with respect to the reflectors 14 and walls defining the optical cavity. The optical cavity furnace 10 may further include a semiconductor wafer transport system 22 for transporting one or more semiconductor wafers 20 through the optical cavity.

Tuned optical cavity magnetometer

Science.gov (United States)

Okandan, Murat; Schwindt, Peter

2010-11-02

An atomic magnetometer is disclosed which utilizes an optical cavity formed from a grating and a mirror, with a vapor cell containing an alkali metal vapor located inside the optical cavity. Lasers are used to magnetically polarize the alkali metal vapor and to probe the vapor and generate a diffracted laser beam which can be used to sense a magnetic field. Electrostatic actuators can be used in the magnetometer for positioning of the mirror, or for modulation thereof. Another optical cavity can also be formed from the mirror and a second grating for sensing, adjusting, or stabilizing the position of the mirror.

Gasbuggy Site Assessment and Risk Evaluation

Energy Technology Data Exchange (ETDEWEB)

None

2011-03-01

The Gasbuggy site is in northern New Mexico in the San Juan Basin, Rio Arriba County (Figure 1-1). The Gasbuggy experiment was designed to evaluate the use of a nuclear detonation to enhance natural gas production from the Pictured Cliffs Formation, a tight, gas-bearing sandstone formation. The 29-kiloton-yield nuclear device was placed in a 17.5-inch wellbore at 4,240 feet (ft) below ground surface (bgs), approximately 40 ft below the Pictured Cliffs/Lewis shale contact, in an attempt to force the cavity/chimney formed by the detonation up into the Pictured Cliffs Sandstone. The test was conducted below the southwest quarter of Section 36, Township 29 North, Range 4 West, New Mexico Principal Meridian. The device was detonated on December 10, 1967, creating a 335-ft-high chimney above the detonation point and a cavity 160 ft in diameter. The gas produced from GB-ER (the emplacement and reentry well) during the post-detonation production tests was radioactive and diluted, primarily by carbon dioxide. After 2 years, the energy content of the gas had recovered to 80 percent of the value of gas in conventionally developed wells in the area. There is currently no technology capable of remediating deep underground nuclear detonation cavities and chimneys. Consequently, the U.S. Department of Energy (DOE) must continue to manage the Gasbuggy site to ensure that no inadvertent intrusion into the residual contamination occurs. DOE has complete control over the 1/4 section (160 acres) containing the shot cavity, and no drilling is permitted on that property. However, oil and gas leases are on the surrounding land. Therefore, the most likely route of intrusion and potential exposure would be through contaminated natural gas or contaminated water migrating into a producing natural gas well outside the immediate vicinity of ground zero. The purpose of this report is to describe the current site conditions and evaluate the potential health risks posed by the most plausible

Magnesium Diboride thin Films, multilayers, and coatings for SRF cavities

Energy Technology Data Exchange (ETDEWEB)

Xi, Xiaoxing [Temple Univ., Philadelphia, PA (United States)

2017-08-17

Superconducting radio frequency (SRF) cavities currently use low-temperature superconductor niobium, and the Nb SRF cavities have approached the performance levels predicted theoretically. Compared to Nb, MgB₂ becomes superconducting at a much higher temperature and promises a better RF performance in terms of higher quality factor Q and higher acceleration capability. An MgB₂ SRF technology can significantly reduce the operating costs of particle accelerators when these potentials are realized. This project aimed to advance the development of an MgB₂ SRF technology. It had two main objectives: (1) materials issues of MgB₂ thin films and multilayers related to their applications in SRF cavities; and (2) coating single-cell cavities for testing at RF frequencies. The key technical thrust of the project is the deposition of high quality clean MgB₂ films and coatings by the hybrid physical-chemical vapor deposition (HPCVD) technique, which was developed in my group. We have achieved technical progress in each of the two areas. For the first objective, we have confirmed that MgB₂ thin film coatings can be used to effectively enhance the vortex penetration field of an SRF cavity. A vortex is a normal region in the shape of spaghetti that threads through a superconductor. Its existence is due to an applied magnetic field that is greater than a so-called lower critical field, H_c1. Once a vortex enters the superconductor, its movement leads to loss. This has been shown to be the reason for an SRF cavity to break down. Thus, enhancing the magnetic field for a vortex to enter the superconductor that forms the SRF cavity has be a goal of intense research. To this end, Gurevich proposed that a coating of thin superconductor layer can impede the vortex entrance. In this project, we have done two important experiment to test this concept. One, we showed that the enhancement of H_c1 can be

Geospatial Analytics in Retail Site Selection and Sales Prediction.

Science.gov (United States)

Ting, Choo-Yee; Ho, Chiung Ching; Yee, Hui Jia; Matsah, Wan Razali

2018-03-01

Studies have shown that certain features from geography, demography, trade area, and environment can play a vital role in retail site selection, largely due to the impact they asserted on retail performance. Although the relevant features could be elicited by domain experts, determining the optimal feature set can be intractable and labor-intensive exercise. The challenges center around (1) how to determine features that are important to a particular retail business and (2) how to estimate retail sales performance given a new location? The challenges become apparent when the features vary across time. In this light, this study proposed a nonintervening approach by employing feature selection algorithms and subsequently sales prediction through similarity-based methods. The results of prediction were validated by domain experts. In this study, data sets from different sources were transformed and aggregated before an analytics data set that is ready for analysis purpose could be obtained. The data sets included data about feature location, population count, property type, education status, and monthly sales from 96 branches of a telecommunication company in Malaysia. The finding suggested that (1) optimal retail performance can only be achieved through fulfillment of specific location features together with the surrounding trade area characteristics and (2) similarity-based method can provide solution to retail sales prediction.

Discrete vapour cavity model with improved timing of opening and collapse of cavities

NARCIS (Netherlands)

Bergant, A.; Tijsseling, A.S.; Vítkovský, J.P.; Simpson, A.R.; Lambert, M.F.

2007-01-01

Transient vaporous cavitation occurs in hydraulic piping systems when the liquid pressure falls to the vapour pressure. Cavitation may occur as a localized vapour cavity (large void fraction) or as distributed vaporous cavitation (small void fraction). The discrete vapour cavity model (DVCM) with

Conduction cooling systems for linear accelerator cavities

Science.gov (United States)

Kephart, Robert

2017-05-02

A conduction cooling system for linear accelerator cavities. The system conducts heat from the cavities to a refrigeration unit using at least one cavity cooler interconnected with a cooling connector. The cavity cooler and cooling connector are both made from solid material having a very high thermal conductivity of approximately 1.times.10.sup.4 W m.sup.-1 K.sup.-1 at temperatures of approximately 4 degrees K. This allows for very simple and effective conduction of waste heat from the linear accelerator cavities to the cavity cooler, along the cooling connector, and thence to the refrigeration unit.

Prediction of glutathionylation sites in proteins using minimal sequence information and their experimental validation.

Science.gov (United States)

Pal, Debojyoti; Sharma, Deepak; Kumar, Mukesh; Sandur, Santosh K

2016-09-01

S-glutathionylation of proteins plays an important role in various biological processes and is known to be protective modification during oxidative stress. Since, experimental detection of S-glutathionylation is labor intensive and time consuming, bioinformatics based approach is a viable alternative. Available methods require relatively longer sequence information, which may prevent prediction if sequence information is incomplete. Here, we present a model to predict glutathionylation sites from pentapeptide sequences. It is based upon differential association of amino acids with glutathionylated and non-glutathionylated cysteines from a database of experimentally verified sequences. This data was used to calculate position dependent F-scores, which measure how a particular amino acid at a particular position may affect the likelihood of glutathionylation event. Glutathionylation-score (G-score), indicating propensity of a sequence to undergo glutathionylation, was calculated using position-dependent F-scores for each amino-acid. Cut-off values were used for prediction. Our model returned an accuracy of 58% with Matthew's correlation-coefficient (MCC) value of 0.165. On an independent dataset, our model outperformed the currently available model, in spite of needing much less sequence information. Pentapeptide motifs having high abundance among glutathionylated proteins were identified. A list of potential glutathionylation hotspot sequences were obtained by assigning G-scores and subsequent Protein-BLAST analysis revealed a total of 254 putative glutathionable proteins, a number of which were already known to be glutathionylated. Our model predicted glutathionylation sites in 93.93% of experimentally verified glutathionylated proteins. Outcome of this study may assist in discovering novel glutathionylation sites and finding candidate proteins for glutathionylation.

Pacer processing: cavity inventory relationships

International Nuclear Information System (INIS)

Dietz, R.J.; Gritzo, L.A.

1975-09-01

The pacer cavity and its associated primary power loop comprise a recirculating system in which materials are introduced by a series of thermonuclear explosions while debris is continuously removed by radioactive decay, sorption phenomena, and deliberate processing. Safe, reliable, and economical realization of the Pacer concept depends on the removal and control of both noxious and valuable by-products of the fusion reaction. Mathematical relationships are developed that describe the quantities of materials that are introduced into the Pacer cavity by a series of discrete events and are removed continuously by processing and decay. An iterative computer program based on these relationships is developed that allows both the total cavity inventory and the amounts of important individual species to be determined at any time during the lifetime of the cavity in order to establish the effects of the thermonuclear event, the cavity, the flow, and various processing parameters on Pacer design requirements

Beam position diagnostics with higher order modes in third harmonic superconducting accelerating cavities

International Nuclear Information System (INIS)

Zhang, Pei

2013-02-01

various dipole modes on the oset of the excitation beam were subsequently studied using a spectrum analyzer. Various data analysis methods were used: modal identication, direct linear regression, singular value decomposition and k-means clustering. These studies lead to three modal options promising for beam position diagnostics, upon which a set of test electronics has been built. The experiments with these electronics suggest a resolution of 50 micron accuracy in predicting local beam position in the cavity and a global resolution of 20 micron over the complete module. This constitutes the first demonstration of HOM-based beam diagnostics in a third harmonic 3.9 GHz superconducting cavity module. These studies have finalized the design of the online HOM-BPM for 3.9 GHz cavities at FLASH.

Beam position diagnostics with higher order modes in third harmonic superconducting accelerating cavities

Energy Technology Data Exchange (ETDEWEB)

Zhang, Pei

2013-02-15

various dipole modes on the oset of the excitation beam were subsequently studied using a spectrum analyzer. Various data analysis methods were used: modal identication, direct linear regression, singular value decomposition and k-means clustering. These studies lead to three modal options promising for beam position diagnostics, upon which a set of test electronics has been built. The experiments with these electronics suggest a resolution of 50 micron accuracy in predicting local beam position in the cavity and a global resolution of 20 micron over the complete module. This constitutes the first demonstration of HOM-based beam diagnostics in a third harmonic 3.9 GHz superconducting cavity module. These studies have finalized the design of the online HOM-BPM for 3.9 GHz cavities at FLASH.

Continuous-wave cavity ringdown spectroscopy based on the control of cavity reflection.

Science.gov (United States)

Li, Zhixin; Ma, Weiguang; Fu, Xiaofang; Tan, Wei; Zhao, Gang; Dong, Lei; Zhang, Lei; Yin, Wangbao; Jia, Suotang

2013-07-29

A new type of continuous-wave cavity ringdown spectrometer based on the control of cavity reflection for trace gas detection was designed and evaluated. The technique separated the acquisitions of the ringdown event and the trigger signal to optical switch by detecting the cavity reflection and transmission, respectively. A detailed description of the time sequence of the measurement process was presented. In order to avoid the wrong extraction of ringdown time encountered accidentally in fitting procedure, the laser frequency and cavity length were scanned synchronously. Based on the statistical analysis of measured ringdown times, the frequency normalized minimum detectable absorption in the reflection control mode was 1.7 × 10(-9)cm(-1)Hz(-1/2), which was 5.4 times smaller than that in the transmission control mode. However the signal-to-noise ratio of the absorption spectrum was only 3 times improved since the etalon effect existed. Finally, the peak absorption coefficients of the C(2)H(2) transition near 1530.9nm under different pressures showed a good agreement with the theoretical values.

Responses of cavity-nesting birds to stand-replacement fire and salvage logging in ponderosa pine/Douglas-fir forests of southwestern Idaho

Science.gov (United States)

Victoria A. Saab; Jonathan G. Dudley

1998-01-01

From 1994 to 1996, researchers monitored 695 nests of nine cavity-nesting bird species and measured vegetation at nest sites and at 90 randomly located sites in burned ponderosa pine forests of southwestern Idaho. Site treatments included two types of salvage logging, and unlogged controls. All bird species selected nest sites with higher tree densities, larger...

Numerical and Experimental Analysis on the Cavity Formation and Shrinkage for Investment Cast Alloy 738 4 mm-Thick Rectangular Tube

International Nuclear Information System (INIS)

Park, Myeong-Il; Choi, Yoon Suk; Yoo, Jae-Hyun; Park, Sang-Hu; Kim, Kyeong-Min; Lee, Yeong-Chul; Lee, Jung-Seok; Lee, Jae-Hyun

2017-01-01

Investment casting for the thin (4 mm thick) rectangular tube (40 mm wide, 80 mm high and 200 mm long) was carried out numerically and experimentally for Alloy 738, which is a precipitation-hardened Ni-base superalloy. Two types of rectangular tubes, one with a regular array (10 mm by 10 mm square array) of protruded rods (3 mm in diameter and 3mm in height) embedded on the outer surface and the other with just smooth surface, were investment-cast at the same time through the side feeding mold design. The investment casting simulation predicted the presence of cavities, particularly in the area away from the gate for both types of rectangular tubes. In particular, for the rectangular tube with embedded protruded rods cavities were found mainly in the areas between the protruded rods. This simulation result was qualitatively consistent with the experimental observation from the X-ray analysis. Also, both prediction and experiment showed that the dimensional shrinkage (particularly in the longitudinal direction) of the investment-cast rectangular tube is reduced by having protruded rods embedded on the outer surface. Additional numerical attempts were made to check how the amount of cavities and dimensional shrinkage change by varying the preheating temperature and the thickness of the mold. The results predicted that the amount of cavities and the dimensional shrinkage are significantly reduced by increasing the preheating temperature of the mold by 200 ℃. However, an increase in mold thickness from 10 mm to 12 mm showed almost no difference in cavity population and a slight decrease in dimensional shrinkage.

Numerical and Experimental Analysis on the Cavity Formation and Shrinkage for Investment Cast Alloy 738 4 mm-Thick Rectangular Tube

Energy Technology Data Exchange (ETDEWEB)

Park, Myeong-Il; Choi, Yoon Suk; Yoo, Jae-Hyun; Park, Sang-Hu [Pusan National University, Busan (Korea, Republic of); Kim, Kyeong-Min; Lee, Yeong-Chul [Sung Il Turbine Co., Ltd., Busan (Korea, Republic of); Lee, Jung-Seok; Lee, Jae-Hyun [Changwon National University, Changwon (Korea, Republic of)

2017-02-15

Investment casting for the thin (4 mm thick) rectangular tube (40 mm wide, 80 mm high and 200 mm long) was carried out numerically and experimentally for Alloy 738, which is a precipitation-hardened Ni-base superalloy. Two types of rectangular tubes, one with a regular array (10 mm by 10 mm square array) of protruded rods (3 mm in diameter and 3mm in height) embedded on the outer surface and the other with just smooth surface, were investment-cast at the same time through the side feeding mold design. The investment casting simulation predicted the presence of cavities, particularly in the area away from the gate for both types of rectangular tubes. In particular, for the rectangular tube with embedded protruded rods cavities were found mainly in the areas between the protruded rods. This simulation result was qualitatively consistent with the experimental observation from the X-ray analysis. Also, both prediction and experiment showed that the dimensional shrinkage (particularly in the longitudinal direction) of the investment-cast rectangular tube is reduced by having protruded rods embedded on the outer surface. Additional numerical attempts were made to check how the amount of cavities and dimensional shrinkage change by varying the preheating temperature and the thickness of the mold. The results predicted that the amount of cavities and the dimensional shrinkage are significantly reduced by increasing the preheating temperature of the mold by 200 ℃. However, an increase in mold thickness from 10 mm to 12 mm showed almost no difference in cavity population and a slight decrease in dimensional shrinkage.

Design of rf conditioner cavities

International Nuclear Information System (INIS)

Govil, R.; Rimmer, R.A.; Sessler, A.; Kirk, H.G.

1992-06-01

Theoretical studies are made of radio frequency structures which can be used to condition electron beams so as to greatly reduce the stringent emittance requirements for successful lasing in a free-electron laser. The basic strategy of conditioning calls for modulating an electron beam in the transverse dimension, by a periodic focusing channel, while it traverses a series of rf cavities, each operating in a TM 210 mode. In this paper, we analyze the cavities both analytically and numerically (using MAFIA simulations). We find that when cylindrical symmetry is broken the coupling impedance can be greatly enhanced. We present results showing various performance characteristics as a function of cavity parameters, as well as possible designs for conditioning cavities

Cavity QED with single trapped Ca+-ions

International Nuclear Information System (INIS)

Mundt, A.B.

2003-02-01

This thesis reports on the design and setup of a vacuum apparatus allowing the investigation of cavity QED effects with single trapped 40 Ca + ions. The weak coupling of ion and cavity in the 'bad cavity limit' may serve to inter--convert stationary and flying qubits. The ion is confined in a miniaturized Paul trap and cooled via the Doppler effect to the Lamb--Dicke regime. The extent of the atomic wave function is less than 30 nm. The ion is enclosed by a high finesse optical cavity. The technically--involved apparatus allows movement of the trap relative to the cavity and the trapped ion can be placed at any position in the standing wave. By means of a transfer lock the cavity can be resonantly stabilized with the S 1/2 ↔ D 5/2 quadrupole transition at 729 nm (suitable as a qubit) without light at that wavelength being present in the cavity. The coupling of the cavity field to the S 1/2 ↔ D 5/2 quadrupole transition is investigated with various techniques in order to determine the spatial dependence as well as the temporal dynamics. The orthogonal coupling of carrier and first--order sideband transitions at field nodes and antinodes is explored. The coherent interaction of the ion and the cavity field is confirmed by exciting Rabi oscillations with short resonant pulses injected into the cavity. Finally, first experimental steps towards the observation of cavity enhanced spontaneous emission have been taken. (author)

NBA-Palm: prediction of palmitoylation site implemented in Naïve Bayes algorithm.

Science.gov (United States)

Xue, Yu; Chen, Hu; Jin, Changjiang; Sun, Zhirong; Yao, Xuebiao

2006-10-17

Protein palmitoylation, an essential and reversible post-translational modification (PTM), has been implicated in cellular dynamics and plasticity. Although numerous experimental studies have been performed to explore the molecular mechanisms underlying palmitoylation processes, the intrinsic feature of substrate specificity has remained elusive. Thus, computational approaches for palmitoylation prediction are much desirable for further experimental design. In this work, we present NBA-Palm, a novel computational method based on Naïve Bayes algorithm for prediction of palmitoylation site. The training data is curated from scientific literature (PubMed) and includes 245 palmitoylated sites from 105 distinct proteins after redundancy elimination. The proper window length for a potential palmitoylated peptide is optimized as six. To evaluate the prediction performance of NBA-Palm, 3-fold cross-validation, 8-fold cross-validation and Jack-Knife validation have been carried out. Prediction accuracies reach 85.79% for 3-fold cross-validation, 86.72% for 8-fold cross-validation and 86.74% for Jack-Knife validation. Two more algorithms, RBF network and support vector machine (SVM), also have been employed and compared with NBA-Palm. Taken together, our analyses demonstrate that NBA-Palm is a useful computational program that provides insights for further experimentation. The accuracy of NBA-Palm is comparable with our previously described tool CSS-Palm. The NBA-Palm is freely accessible from: http://www.bioinfo.tsinghua.edu.cn/NBA-Palm.

Voltage control of cavity magnon polariton

Energy Technology Data Exchange (ETDEWEB)

Kaur, S., E-mail: kaurs3@myumanitoba.ca; Rao, J. W.; Gui, Y. S.; Hu, C.-M., E-mail: hu@physics.umanitoba.ca [Department of Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba R3T 2N2 (Canada); Yao, B. M. [Department of Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba R3T 2N2 (Canada); National Laboratory for Infrared Physics, Chinese Academy of Sciences, Shanghai 200083 (China)

2016-07-18

We have experimentally investigated the microwave transmission of the cavity-magnon-polariton (CMP) generated by integrating a low damping magnetic insulator onto a 2D microwave cavity. The high tunability of our planar cavity allows the cavity resonance frequency to be precisely controlled using a DC voltage. By appropriately tuning the voltage and magnetic bias, we can observe the cavity photon magnon coupling and the magnetic coupling between a magnetostatic mode and the generated CMP. The dispersion of the generated CMP was measured by either tuning the magnetic field or the applied voltage. This electrical control of CMP may open up avenues for designing advanced on-chip microwave devices that utilize light-matter interaction.

Superconducting cavity driving with FPGA controller

Energy Technology Data Exchange (ETDEWEB)

Czarski, T.; Koprek, W.; Pozniak, K.T.; Romaniuk, R.S. [Warsaw Univ. of Technology (Poland); Simrock, S.; Brand, A. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Chase, B.; Carcagno, R.; Cancelo, G. [Fermi National Accelerator Lab., Batavia, IL (United States); Koeth, T.W. [Rutgers - the State Univ. of New Jersey, NJ (United States)

2006-07-01

The digital control of several superconducting cavities for a linear accelerator is presented. The laboratory setup of the CHECHIA cavity and ACC1 module of the VU-FEL TTF in DESY-Hamburg have both been driven by a Field Programmable Gate Array (FPGA) based system. Additionally, a single 9-cell TESLA Superconducting cavity of the FNPL Photo Injector at FERMILAB has been remotely controlled from WUT-ISE laboratory with the support of the DESY team using the same FPGA control system. These experiments focused attention on the general recognition of the cavity features and projected control methods. An electrical model of the resonator was taken as a starting point. Calibration of the signal path is considered key in preparation for the efficient driving of a cavity. Identification of the resonator parameters has been proven to be a successful approach in achieving required performance; i.e. driving on resonance during filling and field stabilization during flattop time while requiring reasonable levels of power consumption. Feed-forward and feedback modes were successfully applied in operating the cavities. Representative results of the experiments are presented for different levels of the cavity field gradient. (orig.)

Superconducting cavity driving with FPGA controller

International Nuclear Information System (INIS)

Czarski, T.; Koprek, W.; Pozniak, K.T.; Romaniuk, R.S.; Simrock, S.; Brand, A.; Chase, B.; Carcagno, R.; Cancelo, G.; Koeth, T.W.

2006-01-01

The digital control of several superconducting cavities for a linear accelerator is presented. The laboratory setup of the CHECHIA cavity and ACC1 module of the VU-FEL TTF in DESY-Hamburg have both been driven by a Field Programmable Gate Array (FPGA) based system. Additionally, a single 9-cell TESLA Superconducting cavity of the FNPL Photo Injector at FERMILAB has been remotely controlled from WUT-ISE laboratory with the support of the DESY team using the same FPGA control system. These experiments focused attention on the general recognition of the cavity features and projected control methods. An electrical model of the resonator was taken as a starting point. Calibration of the signal path is considered key in preparation for the efficient driving of a cavity. Identification of the resonator parameters has been proven to be a successful approach in achieving required performance; i.e. driving on resonance during filling and field stabilization during flattop time while requiring reasonable levels of power consumption. Feed-forward and feedback modes were successfully applied in operating the cavities. Representative results of the experiments are presented for different levels of the cavity field gradient. (orig.)

Computational prediction of cAMP receptor protein (CRP binding sites in cyanobacterial genomes

Directory of Open Access Journals (Sweden)

Su Zhengchang

2009-01-01

Full Text Available Abstract Background Cyclic AMP receptor protein (CRP, also known as catabolite gene activator protein (CAP, is an important transcriptional regulator widely distributed in many bacteria. The biological processes under the regulation of CRP are highly diverse among different groups of bacterial species. Elucidation of CRP regulons in cyanobacteria will further our understanding of the physiology and ecology of this important group of microorganisms. Previously, CRP has been experimentally studied in only two cyanobacterial strains: Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120; therefore, a systematic genome-scale study of the potential CRP target genes and binding sites in cyanobacterial genomes is urgently needed. Results We have predicted and analyzed the CRP binding sites and regulons in 12 sequenced cyanobacterial genomes using a highly effective cis-regulatory binding site scanning algorithm. Our results show that cyanobacterial CRP binding sites are very similar to those in E. coli; however, the regulons are very different from that of E. coli. Furthermore, CRP regulons in different cyanobacterial species/ecotypes are also highly diversified, ranging from photosynthesis, carbon fixation and nitrogen assimilation, to chemotaxis and signal transduction. In addition, our prediction indicates that crp genes in modern cyanobacteria are likely inherited from a common ancestral gene in their last common ancestor, and have adapted various cellular functions in different environments, while some cyanobacteria lost their crp genes as well as CRP binding sites during the course of evolution. Conclusion The CRP regulons in cyanobacteria are highly diversified, probably as a result of divergent evolution to adapt to various ecological niches. Cyanobacterial CRPs may function as lineage-specific regulators participating in various cellular processes, and are important in some lineages. However, they are dispensable in some other lineages. The

Predicting the Parturition Date in Bitches of Different Body Weight by Ultrasonographic Measurements of Inner Chorionic Cavity Diameter and Biparietal Diameter.

Science.gov (United States)

Socha, P; Janowski, T

2014-04-01

Predicting the parturition date in dogs by taking ultrasonographic foetometry has opened interesting research areas of veterinary obstetrics. Recently developed calculation formulas of inner chorionic cavity diameter (ICC) and biparietal diameter (BP) are formulas by Luvoni and Grioni (2000). This study is one of the first reports referring to ICC and BP with the use of Luvoni and Grioni formulas for predicting the parturition time in dogs of different body weight in clinical practice conditions. The research material consists of 70 clinically healthy pregnant bitches of 27 breeds and cross-breeds. Bitches were divided into 4 groups according to their body weight. In each of the bitches, ultrasonographic examination of pregnancy was performed at least twice (ICC and BP measurements). Parturition dates for dogs with a body weight over 25 kg were calculated based on formulas intended for the group of medium dogs. It was caused by the lack of appropriate formulas for these groups of dogs. The predicting parturition dates were compared with the actual dates of delivery provided by the bitch owners. Generally, the results obtained in this study are very encouraging and similar or even better than those published by other authors using foetometric measurements. In our research, when comparing the effectiveness of predicting the delivery date based on foetometric formulas by Luvoni and Grioni (2000), it was proved that in all groups of dogs, even those over 25 kg, ICC and BP measurements at both accuracy levels were characterized similar reliability. © 2014 Blackwell Verlag GmbH.

Prediction of suspended-sediment concentrations at selected sites in the Fountain Creek watershed, Colorado, 2008-09

Science.gov (United States)

Stogner, Sr., Robert W.; Nelson, Jonathan M.; McDonald, Richard R.; Kinzel, Paul J.; Mau, David P.

2013-01-01

In 2008, the U.S. Geological Survey (USGS), in cooperation with Pikes Peak Area Council of Governments, Colorado Water Conservation Board, Colorado Springs City Engineering, and the Lower Arkansas Valley Water Conservancy District, began a small-scale pilot study to evaluate the effectiveness of the use of a computational model of streamflow and suspended-sediment transport for predicting suspended-sediment concentrations and loads in the Fountain Creek watershed in Colorado. Increased erosion and sedimentation damage have been identified by the Fountain Creek Watershed Plan as key problems within the watershed. A recommendation in the Fountain Creek Watershed plan for management of the basin is to establish measurable criteria to determine if progress in reducing erosion and sedimentation damage is being made. The major objective of this study was to test a computational method to predict local suspended-sediment loads at two sites with different geomorphic characteristics in order to evaluate the feasibility of using such an approach to predict local suspended-sediment loads throughout the entire watershed. Detailed topographic surveys, particle-size data, and suspended-sediment samples were collected at two gaged sites: Monument Creek above Woodmen Road at Colorado Springs, Colorado (USGS gage 07103970), and Sand Creek above mouth at Colorado Springs, Colorado (USGS gage 07105600). These data were used to construct three-dimensional computational models of relatively short channel reaches at each site. The streamflow component of these models predicted a spatially distributed field of water-surface elevation, water velocity, and bed shear stress for a range of stream discharges. Using the model predictions, along with measured particle sizes, the sediment-transport component of the model predicted the suspended-sediment concentration throughout the reach of interest. These computed concentrations were used with predicted flow patterns and channel morphology to

Image transmission through a stable paraxial cavity

International Nuclear Information System (INIS)

Gigan, Sylvain; Lopez, Laurent; Treps, Nicolas; Maitre, Agnes; Fabre, Claude

2005-01-01

We study the transmission of a monochromatic 'image' through a paraxial cavity. Using the formalism of self-transform functions, we show that a transverse degenerate cavity transmits the self-transform part of the image, with respect to the field transformation over one round-trip of the cavity. This formalism gives insight into the understanding of the behavior of a transverse degenerate cavity, complementary to the transverse mode picture. An experiment of image transmission through a hemiconfocal cavity shows the interest of this approach

Mapping the heparin-binding site of the BMP antagonist gremlin by site-directed mutagenesis based on predictive modelling.

Science.gov (United States)

Tatsinkam, Arnold Junior; Mulloy, Barbara; Rider, Christopher C

2015-08-15

Gremlin is a member of the CAN (cerberus and DAN) family of secreted BMP (bone morphogenetic protein) antagonists and also an agonist of VEGF (vascular endothelial growth factor) receptor-2. It is critical in limb skeleton and kidney development and is re-expressed during tissue fibrosis. Gremlin binds strongly to heparin and heparan sulfate and, in the present study, we sought to investigate its heparin-binding site. In order to explore a putative non-contiguous binding site predicted by computational molecular modelling, we substituted a total of 11 key arginines and lysines located in three basic residue sequence clusters with homologous sequences from cerberus and DAN (differential screening selected gene abberative in neuroblastoma), CAN proteins which lack basic residues in these positions. A panel of six Myc-tagged gremlin mutants, MGR-1-MGR-6 (MGR, mutant gremlin), each containing different combinations of targeted substitutions, all showed markedly reduced affinity for heparin as demonstrated by their NaCl elution on heparin affinity chromatography, thus verifying our predictions. Both MGR-5 and MGR-6 retained BMP-4-binding activity comparable to that of wild-type gremlin. Low-molecular-mass heparin neither promoted nor inhibited BMP-4 binding. Finally, glutaraldehyde cross-linking demonstrated that gremlin forms non-covalent dimers, similar behaviour to that of DAN and also PRDC (protein related to cerberus and DAN), another CAN protein. The resulting dimer would possess two heparin-binding sites, each running along an exposed surface on the second β-strand finger loop of one of the monomers. © 2015 Authors; published by Portland Press Limited.

New achievements in RF cavity manufacturing

International Nuclear Information System (INIS)

Lippmann, G.; Pimiskern, K.; Kaiser, H.

1993-01-01

Dornier has been engaged in development, manufacturing and testing of Cu-, Cu/Nb- and Nb-cavities for many years. Recently, several different types of RF cavities were manufactured. A prototype superconducting (s.c.) B-Factory accelerating cavity (1-cell, 500 MHz) was delivered to Cornell University, Laboratory of Nuclear Studies. A second lot of 6 s.c. cavities (20-cell, 3000 MHz) was fabricated on contract from Technical University of Darmstadt for the S-DALINAC facility. Finally, the first copper RF structures (9-cell, 1300 MHz) for TESLA were finished and delivered to DESY, two s.c. niobium structures of the same design are in production. Highlights from the manufacturing processes of these cavities are described and first performance results will be reported

Cryostat for TRISTAN superconducting cavity

International Nuclear Information System (INIS)

Mitsunobu, S.; Furuya, T.; Hara, K.

1990-01-01

Superconducting cavities generate rather high heat load of hundreds watts in one cryostat and have high sensitivity for pressure. We adopted usual pool-boiling type cooling for its stable pressure operation. Two 5-cell Nb cavities were installed in one flange type cryostat. Tuning mechanics actuated by a pulse-motor and a Piezo-electric element are set at outside of vacuum end flange. The design and performance of the cryostat for TRISTAN superconducting cavities are described. (author)

Designs of two and three cavity gyroklystron amplifiers operating at fundamental, second, and fourth harmonics