Detection of interferon-γ response to tuberculosis in blood collected at commencement of exsanguination at slaughter from cattle sensitized with Mycobacterium bovis.

PubMed

Okafor, Chika C; Grooms, Daniel L; Bolin, Steven R; Kaneene, John B

2012-06-01

To determine whether an interferon (IFN)-γ response sufficient to categorize cattle as positive for tuberculosis can be detected in blood collected at commencement of exsanguination at slaughter. 15 Holstein cows. 12 cows were experimentally sensitized by SC injection with inactivated Mycobacterium bovis in mineral oil, which induced an immune response that mimicked natural infection with M bovis. Three nonsensitized control cows were injected SC with mineral oil alone. By 5 weeks after injection, only the 12 sensitized cows had positive results for tuberculosis with whole blood IFN-γ assay. At that time, all 15 cows were sent to slaughter and samples of blood were collected from each cow immediately before stunning and at commencement of exsanguination (within 90 seconds after stunning). A whole blood IFN-γ assay was performed on the samples. Conditional probability and paired t tests were used to analyze changes in the categorical test interpretation and qualitative IFN-γ production, respectively. All 12 sensitized cows had positive results for tuberculosis in samples obtained immediately before stunning, and 9 retained positive results for samples obtained at commencement of exsanguination. There was a significant decrease in the mean background-corrected IFN-γ ELISA optical density values for samples obtained at commencement of exsanguination. IFN-γ response sufficient to classify cattle as positive for tuberculosis could be detected in blood collected at commencement of exsanguination. These findings support further development and use of the IFN-γ assay on blood samples collected at exsanguination as part of a bovine tuberculosis surveillance program.

The Influence of Mark-Recapture Sampling Effort on Estimates of Rock Lobster Survival

PubMed Central

Kordjazi, Ziya; Frusher, Stewart; Buxton, Colin; Gardner, Caleb; Bird, Tomas

2016-01-01

Five annual capture-mark-recapture surveys on Jasus edwardsii were used to evaluate the effect of sample size and fishing effort on the precision of estimated survival probability. Datasets of different numbers of individual lobsters (ranging from 200 to 1,000 lobsters) were created by random subsampling from each annual survey. This process of random subsampling was also used to create 12 datasets of different levels of effort based on three levels of the number of traps (15, 30 and 50 traps per day) and four levels of the number of sampling-days (2, 4, 6 and 7 days). The most parsimonious Cormack-Jolly-Seber (CJS) model for estimating survival probability shifted from a constant model towards sex-dependent models with increasing sample size and effort. A sample of 500 lobsters or 50 traps used on four consecutive sampling-days was required for obtaining precise survival estimations for males and females, separately. Reduced sampling effort of 30 traps over four sampling days was sufficient if a survival estimate for both sexes combined was sufficient for management of the fishery. PMID:26990561

Consensus for second-order multi-agent systems with position sampled data

NASA Astrophysics Data System (ADS)

Wang, Rusheng; Gao, Lixin; Chen, Wenhai; Dai, Dameng

2016-10-01

In this paper, the consensus problem with position sampled data for second-order multi-agent systems is investigated. The interaction topology among the agents is depicted by a directed graph. The full-order and reduced-order observers with position sampled data are proposed, by which two kinds of sampled data-based consensus protocols are constructed. With the provided sampled protocols, the consensus convergence analysis of a continuous-time multi-agent system is equivalently transformed into that of a discrete-time system. Then, by using matrix theory and a sampled control analysis method, some sufficient and necessary consensus conditions based on the coupling parameters, spectrum of the Laplacian matrix and sampling period are obtained. While the sampling period tends to zero, our established necessary and sufficient conditions are degenerated to the continuous-time protocol case, which are consistent with the existing result for the continuous-time case. Finally, the effectiveness of our established results is illustrated by a simple simulation example. Project supported by the Natural Science Foundation of Zhejiang Province, China (Grant No. LY13F030005) and the National Natural Science Foundation of China (Grant No. 61501331).

Proteomic Challenges: Sample Preparation Techniques for Microgram-Quantity Protein Analysis from Biological Samples

PubMed Central

Feist, Peter; Hummon, Amanda B.

2015-01-01

Proteins regulate many cellular functions and analyzing the presence and abundance of proteins in biological samples are central focuses in proteomics. The discovery and validation of biomarkers, pathways, and drug targets for various diseases can be accomplished using mass spectrometry-based proteomics. However, with mass-limited samples like tumor biopsies, it can be challenging to obtain sufficient amounts of proteins to generate high-quality mass spectrometric data. Techniques developed for macroscale quantities recover sufficient amounts of protein from milligram quantities of starting material, but sample losses become crippling with these techniques when only microgram amounts of material are available. To combat this challenge, proteomicists have developed micro-scale techniques that are compatible with decreased sample size (100 μg or lower) and still enable excellent proteome coverage. Extraction, contaminant removal, protein quantitation, and sample handling techniques for the microgram protein range are reviewed here, with an emphasis on liquid chromatography and bottom-up mass spectrometry-compatible techniques. Also, a range of biological specimens, including mammalian tissues and model cell culture systems, are discussed. PMID:25664860

Zinc oxide hierarchical nanostructures for photocatalysis

NASA Astrophysics Data System (ADS)

Yukhnovets, O.; Semenova, A. A.; Levkevich, E. A.; Maximov, A. I.; Moshnikov, V. A.

2018-03-01

In this work, we perform the study of zinc oxide hierarchical structures synthesized by the low-temperature hydrothermal method. The paper considers morphological properties of obtained structures. Photocatalytic activity of samples was analysed by methyl orange degradation under UV irradiation. The sufficient decrease in methyl orange has been demonstrated.

[Carotid plaque assessment using inversion recovery T1 weighted-3 dimensions variable refocus flip angle turbo spin echo sampling perfection with application optimized contrast using different angle evolutions black blood imaging].

PubMed

Inoue, Yuji; Yoneyama, Masami; Nakamura, Masanobu; Ozaki, Satoshi; Ito, Kenjiro; Hiura, Mikio

2012-01-01

Vulnerable plaque can be attributed to induction of ischemic symptoms and magnetic resonance imaging of carotid artery is valuable to detect the plaque. Magnetization prepared rapid acquisition with gradient echo (MPRAGE) method could detect hemorrhagic vulnerable plaque as high intensity signal; however, blood flow is not sufficiently masked by this method. The contrast for plaque in T1 weighted image (T1WI) could not be obtained sufficiently with black blood image (BBI) by sampling perfection with application optimized contrast using different angle evolutions (SPACE) method as turbo spin echo (TSE). In addition, an appearance of artifact by slow flow is a problem. Considering these controversial situations in plaque imaging, we examined the modified BBI inversion recovery (IR)-SPACE in which IR was added for SPACE method so that the contrast for plaque in T1WI was optimized. We investigated the application of this method in plaque imaging. As a result of phantom imaging, the contrast for plaque in T1WI was definitely obtained by choosing an appropriate inversion time (TI) for the corresponding repetition time. In clinical cases, blood flow was sufficiently masked by IR-SPACE method and the plaque imaging was clearly obtained in clinical cases to the same extent as MPRAGE method. Since BBI with IR-SPACE method was derived from both IR pulse and flow void effect, this method could obtain the blood flow masking effect definitely. The present study suggested that SPACE method might be applicable to estimate properties of carotid artery plaque.

Laser capture microdissection of embryonic cells and preparation of RNA for microarray assays.

PubMed

Redmond, Latasha C; Pang, Christopher J; Dumur, Catherine; Haar, Jack L; Lloyd, Joyce A

2014-01-01

In order to compare the global gene expression profiles of different embryonic cell types, it is first necessary to isolate the specific cells of interest. The purpose of this chapter is to provide a step-by-step protocol to perform laser capture microdissection (LCM) on embryo samples and obtain sufficient amounts of high-quality RNA for microarray hybridizations. Using the LCM/microarray strategy on mouse embryo samples has some challenges, because the cells of interest are available in limited quantities. The first step in the protocol is to obtain embryonic tissue, and immediately cryoprotect and freeze it in a cryomold containing Optimal Cutting Temperature freezing media (Sakura Finetek), using a dry ice-isopentane bath. The tissue is then cryosectioned, and the microscope slides are processed to fix, stain, and dehydrate the cells. LCM is employed to isolate specific cell types from the slides, identified under the microscope by virtue of their morphology. Detailed protocols are provided for using the currently available ArcturusXT LCM instrument and CapSure(®) LCM Caps, to which the selected cells adhere upon laser capture. To maintain RNA integrity, upon removing a slide from the final processing step, or attaching the first cells on the LCM cap, LCM is completed within 20 min. The cells are then immediately recovered from the LCM cap using a denaturing solution that stabilizes RNA integrity. RNA is prepared using standard methods, modified for working with small samples. To ensure the validity of the microarray data, the quality of the RNA is assessed using the Agilent bioanalyzer. Only RNA that is of sufficient integrity and quantity is used to perform microarray assays. This chapter provides guidance regarding troubleshooting and optimization to obtain high-quality RNA from cells of limited availability, obtained from embryo samples by LCM.

Laser Capture Microdissection of Embryonic Cells and Preparation of RNA for Microarray Assays

PubMed Central

Redmond, Latasha C.; Pang, Christopher J.; Dumur, Catherine; Haar, Jack L.; Lloyd, Joyce A.

2014-01-01

In order to compare the global gene expression profiles of different embryonic cell types, it is first necessary to isolate the specific cells of interest. The purpose of this chapter is to provide a step-by-step protocol to perform laser capture microdissection (LCM) on embryo samples and obtain sufficient amounts of high-quality RNA for microarray hybridizations. Using the LCM/microarray strategy on mouse embryo samples has some challenges, because the cells of interest are available in limited quantities. The first step in the protocol is to obtain embryonic tissue, and immediately cryoprotect and freeze it in a cryomold containing Optimal Cutting Temperature freezing media (Sakura Finetek), using a dry ice–isopentane bath. The tissue is then cryosectioned, and the microscope slides are processed to fix, stain, and dehydrate the cells. LCM is employed to isolate specific cell types from the slides, identified under the microscope by virtue of their morphology. Detailed protocols are provided for using the currently available ArcturusXT LCM instrument and CapSure® LCM Caps, to which the selected cells adhere upon laser capture. To maintain RNA integrity, upon removing a slide from the final processing step, or attaching the first cells on the LCM cap, LCM is completed within 20 min. The cells are then immediately recovered from the LCM cap using a denaturing solution that stabilizes RNA integrity. RNA is prepared using standard methods, modified for working with small samples. To ensure the validity of the microarray data, the quality of the RNA is assessed using the Agilent bioanalyzer. Only RNA that is of sufficient integrity and quantity is used to perform microarray assays. This chapter provides guidance regarding troubleshooting and optimization to obtain high-quality RNA from cells of limited availability, obtained from embryo samples by LCM. PMID:24318813

Portable imaging system method and apparatus

DOEpatents

Freifeld, Barry M.; Kneafsley, Timothy J.; Pruess, Jacob; Tomutsa, Liviu; Reiter, Paul A.; deCastro, Ted M.

2006-07-25

An operator shielded X-ray imaging system has sufficiently low mass (less than 300 kg) and is compact enough to enable portability by reducing operator shielding requirements to a minimum shielded volume. The resultant shielded volume may require a relatively small mass of shielding in addition to the already integrally shielded X-ray source, intensifier, and detector. The system is suitable for portable imaging of well cores at remotely located well drilling sites. The system accommodates either small samples, or small cross-sectioned objects of unlimited length. By rotating samples relative to the imaging device, the information required for computer aided tomographic reconstruction may be obtained. By further translating the samples relative to the imaging system, fully three dimensional (3D) tomographic reconstructions may be obtained of samples having arbitrary length.

Ellipsometer

NASA Technical Reports Server (NTRS)

Ducharme, Stephen Paul (Inventor); El Hajj, Hassanayn Machlab (Inventor); Johs, Blaine D. (Inventor); Woollam, John A. (Inventor)

1997-01-01

In an ellipsometer, a phase-modulated, polarized light beam is applied to a sample, electrical signals are obtained representing the orthogonal planes of polarization of the light after it has interacted with the sample and the constants of the sample are calculated from the two resulting electrical signals. The phase modulation is sufficiently small so that the calibration errors are negligible. For this purpose, the phase modulator, phase modulates the light within a range of no more than ten degrees peak to peak. The two electrical signals are expanded by Fourier analysis and the coefficients thereof utilized to calculate psi and delta.

Entropy from State Probabilities: Hydration Entropy of Cations

PubMed Central

2013-01-01

Entropy is an important energetic quantity determining the progression of chemical processes. We propose a new approach to obtain hydration entropy directly from probability density functions in state space. We demonstrate the validity of our approach for a series of cations in aqueous solution. Extensive validation of simulation results was performed. Our approach does not make prior assumptions about the shape of the potential energy landscape and is capable of calculating accurate hydration entropy values. Sampling times in the low nanosecond range are sufficient for the investigated ionic systems. Although the presented strategy is at the moment limited to systems for which a scalar order parameter can be derived, this is not a principal limitation of the method. The strategy presented is applicable to any chemical system where sufficient sampling of conformational space is accessible, for example, by computer simulations. PMID:23651109

An assessment of re-randomization methods in bark beetle (Scolytidae) trapping bioassays

Treesearch

Christopher J. Fettig; Christopher P. Dabney; Stepehen R. McKelvey; Robert R. Borys

2006-01-01

Numerous studies have explored the role of semiochemicals in the behavior of bark beetles (Scolytidae). Multiple funnel traps are often used to elucidate these behavioral responses. Sufficient sample sizes are obtained by using large numbers of traps to which treatments are randomly assigned once, or by frequent collection of trap catches and subsequent re-...

Ion Beam Sputtered Coatings of Bioglass

NASA Technical Reports Server (NTRS)

Hench, Larry L.; Wilson, J.; Ruzakowski, Patricia Henrietta Anne

1982-01-01

The ion beam sputtering technique available at the NASA-Lewis was used to apply coatings of bioglass to ceramic, metallic, and polymeric substrates. Experiments in vivo and in vitro described investigate these coatings. Some degree of substrate masking was obtained in all samples although stability and reactivity equivalent to bulk bioglass was not observed in all coated samples. Some degree of stability was seen in all coated samples that were reacted in vitro. Both metallic and ceramic substrates coated in this manner failed to show significantly improved coatings over those obtained with existing techniques. Implantation of the coated ceramic substrate samples in bone gave no definite bonding as seen with bulk glass; however, partial and patchy bonding was seen. Polymeric substrates in these studies showed promise of success. The coatings applied were sufficient to mask the underlying reactive test surface and tissue adhesion of collagen to bioglass was seen. Hydrophilic, hydrophobic, charged, and uncharged polymeric surfaces were successfully coated.

A measurement system for the atmospheric trace gases CH4 and CO

NASA Technical Reports Server (NTRS)

Condon, E. P.

1977-01-01

A system for measuring ambient clean air levels of the atmospheric trace gases methane and carbon monoxide is described. The analytical method consists of a gas chromatographic technique that incorporates sample preconcentration with catalytic conversion of CO to CH4 and subsequent flame ionization detection of these gases. The system has sufficient sensitivity and repeatability to make the precise measurements required to establish concentration profiles for CO and CH4 in the planetary boundary layer. A discussion of the bottle sampling program being conducted to obtain the samples for the concentration profiles is also presented.

Tank 241-AZ-102 Privatization Push Mode Core Sampling and Analysis Plan

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

RASMUSSEN, J.H.

1999-08-02

This sampling and analysis plan (SAP) identifies characterization objectives pertaining to sample collection, laboratory analytical evaluation, and reporting requirements for samples obtained from tank 241-AZ-102. The purpose of this sampling event is to obtain information about the characteristics of the contents of 241-AZ-102 required to satisfy the Data Quality Objectives For TWRS Privatization Phase I: Confirm Tank TIS An Appropriate Feed Source For High-Level Waste Feed Batch X(HLW DQO) (Nguyen 1999a), Data Quality Objectives For TWRS Privatization Phase 1: Confirm Tank TIS An Appropriate Feed Source For Low-Activity Waste Feed Batch X (LAW DQO) (Nguyen 1999b), Low Activity Waste andmore » High Level Waste Feed Data Quality Objectives (L&H DQO) (Patello et al. 1999) and Characterization Data Needs for Development, Design, and Operation of Retrieval Equipment Developed through the Data Quality Objective Process (Equipment DQO) (Bloom 1996). The Tank Characterization Technical Sampling Basis document (Brown et al. 1998) indicates that these issues, except the Equipment DQO apply to tank 241-AZ-102 for this sampling event. The Equipment DQO is applied for shear strength measurements of the solids segments only. Poppiti (1999) requires additional americium-241 analyses of the sludge segments. Brown et al. (1998) also identify safety screening, regulatory issues and provision of samples to the Privatization Contractor(s) as applicable issues for this tank. However, these issues will not be addressed via this sampling event. Reynolds et al. (1999) concluded that information from previous sampling events was sufficient to satisfy the safety screening requirements for tank 241 -AZ-102. Push mode core samples will be obtained from risers 15C and 24A to provide sufficient material for the chemical analyses and tests required to satisfy these data quality objectives. The 222-S Laboratory will extrude core samples, composite the liquids and solids, perform chemical analyses, and provide subsamples to the Process Chemistry Laboratory. The Process Chemistry Laboratory will prepare test plans and perform process tests to evaluate the behavior of the 241-AZ-102 waste undergoing the retrieval and treatment scenarios defined in the applicable DQOs. Requirements for analyses of samples originating in the process tests will be documented in the corresponding test plan.« less

Application of mass spectrometry based electronic nose and chemometrics for fingerprinting radiation treatment

NASA Astrophysics Data System (ADS)

Gupta, Sumit; Variyar, Prasad S.; Sharma, Arun

2015-01-01

Volatile compounds were isolated from apples and grapes employing solid phase micro extraction (SPME) and subsequently analyzed by GC/MS equipped with a transfer line without stationary phase. Single peak obtained was integrated to obtain total mass spectrum of the volatile fraction of samples. A data matrix having relative abundance of all mass-to-charge ratios was subjected to principal component analysis (PCA) and linear discriminant analysis (LDA) to identify radiation treatment. PCA results suggested that there is sufficient variability between control and irradiated samples to build classification models based on supervised techniques. LDA successfully aided in segregating control from irradiated samples at all doses (0.1, 0.25, 0.5, 1.0, 1.5, 2.0 kGy). SPME-MS with chemometrics was successfully demonstrated as simple screening method for radiation treatment.

Individual Differences in ERPs during Mental Rotation of Characters: Lateralization, and Performance Level

ERIC Educational Resources Information Center

Beste, Christian; Heil, Martin; Konrad, Carsten

2010-01-01

The cognitive process of imaging an object turning around is called mental rotation. Many studies have been put forward analyzing mental rotation by means of event-related potentials (ERPs). Event-related potentials (ERPs) were measured during mental rotation of characters in a sample (N = 82) with a sufficient size to obtain even small effects. A…

DESCARTES' RULE OF SIGNS AND THE IDENTIFIABILITY OF POPULATION DEMOGRAPHIC MODELS FROM GENOMIC VARIATION DATA.

PubMed

Bhaskar, Anand; Song, Yun S

2014-01-01

The sample frequency spectrum (SFS) is a widely-used summary statistic of genomic variation in a sample of homologous DNA sequences. It provides a highly efficient dimensional reduction of large-scale population genomic data and its mathematical dependence on the underlying population demography is well understood, thus enabling the development of efficient inference algorithms. However, it has been recently shown that very different population demographies can actually generate the same SFS for arbitrarily large sample sizes. Although in principle this nonidentifiability issue poses a thorny challenge to statistical inference, the population size functions involved in the counterexamples are arguably not so biologically realistic. Here, we revisit this problem and examine the identifiability of demographic models under the restriction that the population sizes are piecewise-defined where each piece belongs to some family of biologically-motivated functions. Under this assumption, we prove that the expected SFS of a sample uniquely determines the underlying demographic model, provided that the sample is sufficiently large. We obtain a general bound on the sample size sufficient for identifiability; the bound depends on the number of pieces in the demographic model and also on the type of population size function in each piece. In the cases of piecewise-constant, piecewise-exponential and piecewise-generalized-exponential models, which are often assumed in population genomic inferences, we provide explicit formulas for the bounds as simple functions of the number of pieces. Lastly, we obtain analogous results for the "folded" SFS, which is often used when there is ambiguity as to which allelic type is ancestral. Our results are proved using a generalization of Descartes' rule of signs for polynomials to the Laplace transform of piecewise continuous functions.

DESCARTES’ RULE OF SIGNS AND THE IDENTIFIABILITY OF POPULATION DEMOGRAPHIC MODELS FROM GENOMIC VARIATION DATA1

PubMed Central

Bhaskar, Anand; Song, Yun S.

2016-01-01

The sample frequency spectrum (SFS) is a widely-used summary statistic of genomic variation in a sample of homologous DNA sequences. It provides a highly efficient dimensional reduction of large-scale population genomic data and its mathematical dependence on the underlying population demography is well understood, thus enabling the development of efficient inference algorithms. However, it has been recently shown that very different population demographies can actually generate the same SFS for arbitrarily large sample sizes. Although in principle this nonidentifiability issue poses a thorny challenge to statistical inference, the population size functions involved in the counterexamples are arguably not so biologically realistic. Here, we revisit this problem and examine the identifiability of demographic models under the restriction that the population sizes are piecewise-defined where each piece belongs to some family of biologically-motivated functions. Under this assumption, we prove that the expected SFS of a sample uniquely determines the underlying demographic model, provided that the sample is sufficiently large. We obtain a general bound on the sample size sufficient for identifiability; the bound depends on the number of pieces in the demographic model and also on the type of population size function in each piece. In the cases of piecewise-constant, piecewise-exponential and piecewise-generalized-exponential models, which are often assumed in population genomic inferences, we provide explicit formulas for the bounds as simple functions of the number of pieces. Lastly, we obtain analogous results for the “folded” SFS, which is often used when there is ambiguity as to which allelic type is ancestral. Our results are proved using a generalization of Descartes’ rule of signs for polynomials to the Laplace transform of piecewise continuous functions. PMID:28018011

A method for release and multiple strand amplification of small quantities of DNA from endospores of the fastidious bacterium Pasteuria penetrans.

PubMed

Mauchline, T H; Mohan, S; Davies, K G; Schaff, J E; Opperman, C H; Kerry, B R; Hirsch, P R

2010-05-01

To establish a reliable protocol to extract DNA from Pasteuria penetrans endospores for use as template in multiple strand amplification, thus providing sufficient material for genetic analyses. To develop a highly sensitive PCR-based diagnostic tool for P. penetrans. An optimized method to decontaminate endospores, release and purify DNA enabled multiple strand amplification. DNA purity was assessed by cloning and sequencing gyrB and 16S rRNA gene fragments obtained from PCR using generic primers. Samples indicated to be 100%P. penetrans by the gyrB assay were estimated at 46% using the 16S rRNA gene. No bias was detected on cloning and sequencing 12 housekeeping and sporulation gene fragments from amplified DNA. The detection limit by PCR with Pasteuria-specific 16S rRNA gene primers following multiple strand amplification of DNA extracted using the method was a single endospore. Generation of large quantities DNA will facilitate genomic sequencing of P. penetrans. Apparent differences in sample purity are explained by variations in 16S rRNA gene copy number in Eubacteria leading to exaggerated estimations of sample contamination. Detection of single endospores will facilitate investigations of P. penetrans molecular ecology. These methods will advance studies on P. penetrans and facilitate research on other obligate and fastidious micro-organisms where it is currently impractical to obtain DNA in sufficient quantity and quality.

One-day fluorescent-antibody procedure for detecting salmonellae in frozen and dried foods.

PubMed

Goepfert, J M; Mann, M E; Hicks, R

1970-12-01

The indirect fluorescent-antibody technique was used to examine 422 food samples for the presence of salmonellae. A cultural phase involving a 16-hr preenrichment in buffered nutrient broth-milk medium followed by a 4- to 5-hr subculture into fresh medium of the same composition was evaluated. This procedure yielded a sufficient population of salmonellae so that no false-negative results were obtained. Of the 31 false-positives obtained, 12 samples yielded positive cultural results upon extensive subculture of the original enrichment broths. Yeast cells and both vegetative and spore forms of bacilli were observed to fluoresce when stained with anti-Salmonella serum. Efforts to ascertain the cause of these cross-reactions and several alternate explanations are discussed.

242-16H 2H EVAPORATOR POT SAMPLING FINAL REPORT

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

Krementz, D; William Cheng, W

2008-06-11

Due to the materials that are processed through 2H Evaporator, scale is constantly being deposited on the surfaces of the evaporator pot. In order to meet the requirements of the Nuclear Criticality Safety Analysis/Evaluation (NCSA/NCSE) for 2H Evaporator, inspections of the pot are performed to determine the extent of scaling. Once the volume of scale reaches a certain threshold, the pot must be chemically cleaned to remove the scale. Prior to cleaning the pot, samples of the scale are obtained to determine the concentration of uranium and plutonium and also to provide information to assist with pot cleaning. Savannah Rivermore » National Laboratory (SRNL) was requested by Liquid Waste Organization (LWO) Engineering to obtain these samples from two locations within the evaporator. Past experience has proven the difficulty of successfully obtaining solids samples from the 2H Evaporator pot. To mitigate this risk, a total of four samplers were designed and fabricated to ensure that two samples could be obtained. Samples had previously been obtained from the cone surface directly below the vertical access riser using a custom scraping tool. This tool was fabricated and deployed successfully. A second scraper was designed to obtain sample from the nearby vertical thermowell and a third scraper was designed to obtain sample from the vertical pot wall. The newly developed scrapers both employed a pneumatically actuated elbow. The scrapers were designed to be easily attached/removed from the elbow assembly. These tools were fabricated and deployed successfully. A fourth tool was designed to obtain sample from the opposite side of the pot under the tube bundle. This tool was fabricated and tested, but the additional modifications required to make the tool field-ready could not be complete in time to meet the aggressive deployment schedule. Two samples were obtained near the pot entry location, one from the pot wall and the other from the evaporator feed pipe. Since a third sampler was available and all of the radiological controls were in place, the decision was made to obtain a third sample. The third sampler dropped directly below the riser to obtain a scrape sample from the evaporator cone. Samples were obtained from all of these locations in sufficient quantities to perform the required analysis.« less

How Many Samples and How Many Culture Media To Diagnose a Prosthetic Joint Infection: a Clinical and Microbiological Prospective Multicenter Study

PubMed Central

Léger, Julie; Tandé, Didier; Plouzeau, Chloé; Valentin, Anne Sophie; Jolivet-Gougeon, Anne; Lemarié, Carole; Kempf, Marie; Héry-Arnaud, Geneviève; Bret, Laurent; Juvin, Marie Emmanuelle; Giraudeau, Bruno; Burucoa, Christophe

2015-01-01

Although numerous perioperative samples and culture media are required to diagnose prosthetic joint infection (PJI), their exact number and types have not yet been definitely determined with a high level of proof. We conducted a prospective multicenter study to determine the minimal number of samples and culture media required for accurate diagnosis of PJI. Over a 2-year period, consecutive patients with clinical signs suggesting PJI were included, with five perioperative samples per patient. The bacteriological and PJI diagnosis criteria were assessed using a random selection of two, three, or four samples and compared with those obtained using the recommended five samples (references guidelines). The results obtained with two or three culture media were then compared with those obtained with five culture media for both criteria. The times-to-positivity of the different culture media were calculated. PJI was confirmed in 215/264 suspected cases, with a bacteriological criterion in 192 (89%). The PJI was monomicrobial (85%) or polymicrobial (15%). Percentages of agreement of 98.1% and 99.7%, respectively, for the bacteriological criterion and confirmed PJI diagnosis were obtained when four perioperative samples were considered. The highest percentages of agreement were obtained with the association of three culture media, a blood culture bottle, a chocolate agar plate, and Schaedler broth, incubated for 5, 7, and 14 days, respectively. This new procedure leads to significant cost saving. Our prospective multicenter study showed that four samples seeded on three culture media are sufficient for diagnosing PJI. PMID:26637380

How Many Samples and How Many Culture Media To Diagnose a Prosthetic Joint Infection: a Clinical and Microbiological Prospective Multicenter Study.

PubMed

Bémer, Pascale; Léger, Julie; Tandé, Didier; Plouzeau, Chloé; Valentin, Anne Sophie; Jolivet-Gougeon, Anne; Lemarié, Carole; Kempf, Marie; Héry-Arnaud, Geneviève; Bret, Laurent; Juvin, Marie Emmanuelle; Giraudeau, Bruno; Corvec, Stéphane; Burucoa, Christophe

2016-02-01

Although numerous perioperative samples and culture media are required to diagnose prosthetic joint infection (PJI), their exact number and types have not yet been definitely determined with a high level of proof. We conducted a prospective multicenter study to determine the minimal number of samples and culture media required for accurate diagnosis of PJI. Over a 2-year period, consecutive patients with clinical signs suggesting PJI were included, with five perioperative samples per patient. The bacteriological and PJI diagnosis criteria were assessed using a random selection of two, three, or four samples and compared with those obtained using the recommended five samples (references guidelines). The results obtained with two or three culture media were then compared with those obtained with five culture media for both criteria. The times-to-positivity of the different culture media were calculated. PJI was confirmed in 215/264 suspected cases, with a bacteriological criterion in 192 (89%). The PJI was monomicrobial (85%) or polymicrobial (15%). Percentages of agreement of 98.1% and 99.7%, respectively, for the bacteriological criterion and confirmed PJI diagnosis were obtained when four perioperative samples were considered. The highest percentages of agreement were obtained with the association of three culture media, a blood culture bottle, a chocolate agar plate, and Schaedler broth, incubated for 5, 7, and 14 days, respectively. This new procedure leads to significant cost saving. Our prospective multicenter study showed that four samples seeded on three culture media are sufficient for diagnosing PJI. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

One-chip biosensor for simultaneous disease marker/calibration substance measurement in human urine by electrochemical surface plasmon resonance method.

PubMed

Nakamoto, Kohei; Kurita, Ryoji; Niwa, Osamu

2010-12-15

We have developed a miniaturized electrochemical surface plasmon resonance biosensor for measuring two biomolecules that have very different molecular sizes, one is transferrin (MW=75 kDa) as a disease marker protein, the other is creatinine (MW=113) as a calibration marker for the accurate measurement of human urinary samples. The sensor has a PDMS based microchannel that is 2 mm wide and 20 μm deep. Two gold films were integrated in the microchannel; one was modified with anti-transferrin antibody for immuno-reaction, and the other was modified with osmium-poly-vinylpyridine wired horseradish peroxidase (Os-gel-HRP). We further immobilized a tri-enzyme layer of creatininase, creatinase and sarcosine oxidase in order to measure creatinine by converting it to hydrogen peroxide in the upstream channel. We measured the transferrin concentration from the refractive index change involved in an immuno-complex formation, and we were simultaneously able to measure creatinine by employing the refractive index change in the Os-gel-HRP caused by oxidation with the hydrogen peroxide produced from creatinine by the tri-enzyme. The effects of ascorbic acid and uric acid in urine samples were sufficiently eliminated by adding ascorbate oxidase and uricase to the urine samples during sampling. We were able to measure two analyte concentrations within 15 min by one simple injection of 50 μL of diluted human urine into our sensor. The detectable transferrin and creatinine ranges were 20 ng/mL to 10 μg/mL, and 10 μM to 10 mM, respectively, which are sufficient levels for clinical tests. Finally, we compared the results obtained using our sensor with those obtained with a conventional immunoassay and the Jaffe method. We obtained a similar trend that can reduce the fluctuation in the urinary transferrin concentration from three different samples by calibrating the creatinine concentration. Copyright © 2010 Elsevier B.V. All rights reserved.

Diagnosis and assessment of skeletal related disease using calcium 41

DOEpatents

Hillegonds, Darren J [Oakland, CA; Vogel, John S [San Jose, CA; Fitzgerald, Robert L [Encinitas, CA; Deftos, Leonard J [Del Mar, CA; Herold, David [Del Mar, CA; Burton, Douglas W [San Diego, CA

2012-05-15

A method of determining calcium metabolism in a patient comprises the steps of administering radioactive calcium isotope .sup.41Ca to the patient, allowing a period of time to elapse sufficient for dissemination and reaction of the radioactive calcium isotope .sup.41Ca by the patient, obtaining a sample of the radioactive calcium isotope .sup.41Ca from the patient, isolating the calcium content of the sample in a form suitable for precise measurement of isotopic calcium concentrations, and measuring the calcium content to determine parameters of calcium metabolism in the patient.

Diagnosis and assessment of skeletal related disease using calcium 41

DOEpatents

Hillegonds, Darren J.; Vogel, John S.; Fitzgerald, Robert L.; Deftos, Leonard J.; Herold, David; Burton, Douglas W.

2013-03-05

A method of determining calcium metabolism in a patient comprises the steps of administering radioactive calcium isotope .sup.41Ca to the patient, allowing a period of time to elapse sufficient for dissemination and reaction of the radioactive calcium isotope .sup.41Ca by the patient, obtaining a sample of the radioactive calcium isotope .sup.41Ca from the patient, isolating the calcium content of the sample in a form suitable for precise measurement of isotopic calcium concentrations, and measuring the calcium content to determine parameters of calcium metabolism in the patient.

RNA transcriptional biosignature analysis for identifying febrile infants with serious bacterial infections in the emergency department: a feasibility study.

PubMed

Mahajan, Prashant; Kuppermann, Nathan; Suarez, Nicolas; Mejias, Asuncion; Casper, Charlie; Dean, J Michael; Ramilo, Octavio

2015-01-01

To develop the infrastructure and demonstrate the feasibility of conducting microarray-based RNA transcriptional profile analyses for the diagnosis of serious bacterial infections in febrile infants 60 days and younger in a multicenter pediatric emergency research network. We designed a prospective multicenter cohort study with the aim of enrolling more than 4000 febrile infants 60 days and younger. To ensure success of conducting complex genomic studies in emergency department (ED) settings, we established an infrastructure within the Pediatric Emergency Care Applied Research Network, including 21 sites, to evaluate RNA transcriptional profiles in young febrile infants. We developed a comprehensive manual of operations and trained site investigators to obtain and process blood samples for RNA extraction and genomic analyses. We created standard operating procedures for blood sample collection, processing, storage, shipping, and analyses. We planned to prospectively identify, enroll, and collect 1 mL blood samples for genomic analyses from eligible patients to identify logistical issues with study procedures. Finally, we planned to batch blood samples and determined RNA quantity and quality at the central microarray laboratory and organized data analysis with the Pediatric Emergency Care Applied Research Network data coordinating center. Below we report on establishment of the infrastructure and the feasibility success in the first year based on the enrollment of a limited number of patients. We successfully established the infrastructure at 21 EDs. Over the first 5 months we enrolled 79% (74 of 94) of eligible febrile infants. We were able to obtain and ship 1 mL of blood from 74% (55 of 74) of enrolled participants, with at least 1 sample per participating ED. The 55 samples were shipped and evaluated at the microarray laboratory, and 95% (52 of 55) of blood samples were of adequate quality and contained sufficient RNA for expression analysis. It is possible to create a robust infrastructure to conduct genomic studies in young febrile infants in the context of a multicenter pediatric ED research setting. The sufficient quantity and high quality of RNA obtained suggests that whole blood transcriptional profile analysis for the diagnostic evaluation of young febrile infants can be successfully performed in this setting.

Techniques for immobilizing and bleeding marmots and woodrats.

PubMed

Frase, B A; Van Vuren, D

1989-07-01

Blood samples were obtained in the field by femoral vein puncture in bushy-tailed woodrats (Neotoma cinerea) and yellow-bellied marmots (Marmota flaviventris) that had been injected intramuscularly with ketamine hydrochloride. Dosages ranged from 50 mg/kg for marmots to 30 to 110 mg/kg for woodrats. Sedated animals were handled easily, and a volume of blood sufficient for hematological assays or electrophoresis could be collected.

Type-specific detection of high-risk human papillomavirus (HPV) in self-sampled cervicovaginal cells applied to FTA elute cartridge.

PubMed

Gustavsson, Inger; Sanner, Karin; Lindell, Monica; Strand, Anders; Olovsson, Matts; Wikström, Ingrid; Wilander, Erik; Gyllensten, Ulf

2011-08-01

Most procedures for self-sampling of cervical cells are based on liquid-based media for transportation and storage. An alternative is to use a solid support, such as dry filter paper media. To evaluate if self-sampling of cervicovaginal fluid using a cytobrush (Viba-brush; Rovers Medical Devices B.V., Oss, The Netherlands) and a solid support such as the Whatman Indicating FTA Elute cartridge (GE Healthcare, United Kingdom) can be used for reliable typing of human papillomavirus (HPV), as compared to cervical samples obtained by a physician using a cytobrush and the indicating FTA Elute Micro card and biopsy analysis. A total of 50 women with a previous high-risk (HR) HPV positive test were invited to perform self-sampling using the Viba-brush and the FTA cartridge and thereafter a physician obtained a cervical sample using the cytobrush and a FTA card, together with a cervical biopsy for histology and HPV typing. Detection of HR-HPV types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58 and 59 was performed using three multiplex real-time polymerase chain reaction (PCR) assays. All samples contained sufficient amounts of genomic DNA and the self-samples yielded on average 3.5 times more DNA than those obtained by the physician. All women that were positive for HR-HPV in the biopsy sample also typed positive both by self-sampling and physician-obtained sampling. For women with a histological diagnosis of cervical intraepithelial neoplasia grades 2-3 (CIN 2-3) all three HPV samples showed 100% concordance. A higher number of women were HPV positive by self-sampling than by physician-obtained sampling or by biopsy analysis. The Viba-brush and the FTA cartridge are suitable for self-sampling of vaginal cells and subsequent HR-HPV typing. Copyright © 2011 Elsevier B.V. All rights reserved.

Authentication of beef versus horse meat using 60 MHz 1H NMR spectroscopy

PubMed Central

Jakes, W.; Gerdova, A.; Defernez, M.; Watson, A.D.; McCallum, C.; Limer, E.; Colquhoun, I.J.; Williamson, D.C.; Kemsley, E.K.

2015-01-01

This work reports a candidate screening protocol to distinguish beef from horse meat based upon comparison of triglyceride signatures obtained by 60 MHz 1H NMR spectroscopy. Using a simple chloroform-based extraction, we obtained classic low-field triglyceride spectra from typically a 10 min acquisition time. Peak integration was sufficient to differentiate samples of fresh beef (76 extractions) and horse (62 extractions) using Naïve Bayes classification. Principal component analysis gave a two-dimensional “authentic” beef region (p = 0.001) against which further spectra could be compared. This model was challenged using a subset of 23 freeze–thawed training samples. The outcomes indicated that storing samples by freezing does not adversely affect the analysis. Of a further collection of extractions from previously unseen samples, 90/91 beef spectra were classified as authentic, and 16/16 horse spectra as non-authentic. We conclude that 60 MHz 1H NMR represents a feasible high-throughput approach for screening raw meat. PMID:25577043

Sample size planning for composite reliability coefficients: accuracy in parameter estimation via narrow confidence intervals.

PubMed

Terry, Leann; Kelley, Ken

2012-11-01

Composite measures play an important role in psychology and related disciplines. Composite measures almost always have error. Correspondingly, it is important to understand the reliability of the scores from any particular composite measure. However, the point estimates of the reliability of composite measures are fallible and thus all such point estimates should be accompanied by a confidence interval. When confidence intervals are wide, there is much uncertainty in the population value of the reliability coefficient. Given the importance of reporting confidence intervals for estimates of reliability, coupled with the undesirability of wide confidence intervals, we develop methods that allow researchers to plan sample size in order to obtain narrow confidence intervals for population reliability coefficients. We first discuss composite reliability coefficients and then provide a discussion on confidence interval formation for the corresponding population value. Using the accuracy in parameter estimation approach, we develop two methods to obtain accurate estimates of reliability by planning sample size. The first method provides a way to plan sample size so that the expected confidence interval width for the population reliability coefficient is sufficiently narrow. The second method ensures that the confidence interval width will be sufficiently narrow with some desired degree of assurance (e.g., 99% assurance that the 95% confidence interval for the population reliability coefficient will be less than W units wide). The effectiveness of our methods was verified with Monte Carlo simulation studies. We demonstrate how to easily implement the methods with easy-to-use and freely available software. ©2011 The British Psychological Society.

Tensile stress induced depolarization in [001]-poled transverse mode Pb(Zn{sub 1/3}Nb{sub 2/3})O{sub 3} -(6-7)%PbTiO{sub 3} single crystals

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

Shukla, Rahul; Department of Mechanical Engineering, National University of Singapore, Singapore 119260; Lim, Leong-Chew

2011-04-01

This paper investigates the effects of electrically induced and direct tensile stress on the deformation and dielectric properties of Pb(Zn{sub 1/3}Nb{sub 2/3})O{sub 3}-(6-7)%PbTiO{sub 3} single crystals of [110]{sup L}x[001]{sup T} cut by using a unimorph sample and a four-point-bend (FPB) sample, respectively. The results show a dip in tip displacement for the unimorph sample at sufficiently high electric field parallel to the poling field direction and a sudden rise in capacitance for the FPB sample at sufficiently high tensile stress in the [110] crystal direction, respectively. These phenomena are attributed to the tensile stress induced rhombohedral-to-orthorhombic phase transition and associatedmore » depolarization events in the crystal. For the said crystal cut, the obtained tensile depoling stress is in the range of 15-20 MPa. The present work furthermore shows that the occurrence of tensile stress-induced depolarization is possible even when the direction of the applied electric field is parallel to the poling field direction, as in the unimorph sample examined.« less

A pilot to examine the logistical and feasibility issues in testing deceased tissue donors for vCJD using tonsil as the analyte.

PubMed

Warwick, Ruth M; Armitage, W John; Chandrasekar, Akila; Mallinson, Gary; Poniatowski, Stefan; Clarkson, Anthony

2012-03-01

Transplanted tissues have transmitted transmissible spongiform encephalopathies and in the UK there have been more cases of variant Creutzfeldt-Jakob disease (vCJD) than elsewhere in the world. A pilot study was undertaken to look at the feasibility of testing for vCJD in deceased donors using tonsillar tissue. This pilot showed that obtaining consent for removal and testing tonsil tissue was feasible. Donor eligibility for inclusion in the pilot was limited to tissue donors from the National Health Service Blood and Transplant, Tissue Services and to donors shared with the Corneal Transplant Service Eye Banks. Obtaining tonsillar tissue in the immediate post-mortem period was limited by the presence of rigor mortis. Tonsillar tissue was suitable for routine analysis for the presence of prion associated with vCJD in deceased tissue donors. Production and processing of tissue was straightforward and a low assay background was obtained from most samples. Since palatine and lingual tonsil tissue can be obtained in pairs it was possible, in the majority of cases, to set aside an intact sample for confirmatory testing if required. In one instance a sample was reactive by Western blot. However, the pattern of reactivity was not typical for that obtained from vCJD patients. Unfortunately the sample was not of sufficient quality for the confirmatory test to provide a conclusive result.

Grain boundary diffusion behaviors in hot-deformed Nd2Fe14B magnets by PrNd-Cu low eutectic alloys

NASA Astrophysics Data System (ADS)

Tang, Xu; Chen, Renjie; Li, Ming; Jin, Chaoxiang; Yin, Wenzong; Lee, Don; Yan, Aru

2018-01-01

High coercivity of hot-deformed Nd2Fe14B magnets was obtained by grain boundary diffusion. Comparable squareness and similar magnetic properties for samples diffusing from side and pole surfaces show little discrepancies if quantities of the infiltrated PrNd-Cu low eutectic alloys is enough to obtain sufficient diffusion. However, the microstructures and higher characteristic peak ratios show preferable orientation of grains near surfaces of the sample diffused from side surfaces than that from pole surfaces. Amorphous Nd-rich phases and crystal Fe-rich phases were both observed in the diffused magnets. The enhancement of coercivity is considered to be resulted from grain boundary optimization and magnetic isolation which is caused by the thickened nonmagnetic intergranular phases.

A randomised trial of sheathed versus standard forceps for obtaining uncontaminated biopsy specimens of microbiota from the terminal ileum.

PubMed

Dave, Maneesh; Johnson, Laura A; Walk, Seth T; Young, Vincent B; Stidham, Ryan W; Chaudhary, Meghana N; Funnell, Jessica; Higgins, Peter D R

2011-08-01

The study of intestinal microbiota has been revolutionised by the use of molecular methods, including terminal restriction fragment length polymorphism (T-RFLP) analysis. Microbiota studies of Crohn's disease patients have examined samples from stool or from the neoterminal ileum with a standard biopsy forceps, which could be contaminated by colonic bacteria when the forceps passes through the colonoscope channel. To determine whether sheathed biopsy forceps are able to obtain terminal ileal microbiota samples with less colonic bacterial contamination compared with unsheathed (standard) biopsy forceps. Prospective randomised single-centre study. Four (paired) biopsy specimens were obtained from adjacent locations in the terminal ileum using the sheathed and standard forceps of 27 consecutive subjects undergoing colonoscopy and the microbiota were characterised using T-RFLP. The Bray-Curtis similarity index between samples (sheathed vs unsheathed forceps) was calculated within patients and significant differences were tested for across all patients. There was not a significant difference in the microbial diversity of samples obtained using sheathed versus unsheathed forceps. The difference in microbial diversity between patients was much greater than the variability within patients by proximal versus distal site or by forceps type. T-RFLP is based on PCR amplification, so it is not always sensitive to rare bacterial species. Standard unsheathed forceps appear to be sufficient for microbiota sample collection from the terminal ileum.

Advances in Assays and Analytical Approaches for Botulinum Toxin Detection

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

Grate, Jay W.; Ozanich, Richard M.; Warner, Marvin G.

2010-08-04

Methods to detect botulinum toxin, the most poisonous substance known, are reviewed. Current assays are being developed with two main objectives in mind: 1) to obtain sufficiently low detection limits to replace the mouse bioassay with an in vitro assay, and 2) to develop rapid assays for screening purposes that are as sensitive as possible while requiring an hour or less to process the sample an obtain the result. This review emphasizes the diverse analytical approaches and devices that have been developed over the last decade, while also briefly reviewing representative older immunoassays to provide background and context.

A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples

PubMed Central

Esteve-Codina, Anna; Arpi, Oriol; Martinez-García, Maria; Pineda, Estela; Mallo, Mar; Gut, Marta; Carrato, Cristina; Rovira, Anna; Lopez, Raquel; Tortosa, Avelina; Dabad, Marc; Del Barco, Sonia; Heath, Simon; Bagué, Silvia; Ribalta, Teresa; Alameda, Francesc; de la Iglesia, Nuria

2017-01-01

The molecular classification of glioblastoma (GBM) based on gene expression might better explain outcome and response to treatment than clinical factors. Whole transcriptome sequencing using next-generation sequencing platforms is rapidly becoming accepted as a tool for measuring gene expression for both research and clinical use. Fresh frozen (FF) tissue specimens of GBM are difficult to obtain since tumor tissue obtained at surgery is often scarce and necrotic and diagnosis is prioritized over freezing. After diagnosis, leftover tissue is usually stored as formalin-fixed paraffin-embedded (FFPE) tissue. However, RNA from FFPE tissues is usually degraded, which could hamper gene expression analysis. We compared RNA-Seq data obtained from matched pairs of FF and FFPE GBM specimens. Only three FFPE out of eleven FFPE-FF matched samples yielded informative results. Several quality-control measurements showed that RNA from FFPE samples was highly degraded but maintained transcriptomic similarities to RNA from FF samples. Certain issues regarding mutation analysis and subtype prediction were detected. Nevertheless, our results suggest that RNA-Seq of FFPE GBM specimens provides reliable gene expression data that can be used in molecular studies of GBM if the RNA is sufficiently preserved. PMID:28122052

Triple Gene Analysis Using Samples Obtained by Endobronchial Ultrasound-guided Transbronchial Needle Aspiration

PubMed Central

Lee, Kyungjong; Um, Sang-Won; Jeong, Byeong-Ho; Yang, Jung Wook; Choi, Yoon-La; Han, Joungho; Kim, Hojoong; Kwon, O Jung

2016-01-01

Objective A mutational analysis of tumor tissue samples is an important part of advanced lung cancer treatment strategies. This study evaluated the efficacy of a triple gene analysis using samples obtained via endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA). Methods Either metastatic lymph nodes or primary lung mass samples obtained by EBUS-TBNA were collected between May 2011 and May 2013. We consecutively analyzed epidermal growth factor receptor (EGFR), V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS), and anaplastic lymphoma kinase (ALK) fusion genes using remnant tissue samples. Results A total of 109 patients were diagnosed with non-small cell lung cancer (NSCLC). Of these, 70% were adenocarcinoma, 27% squamous cell carcinoma with NSCLC, and 3% were related to other types of lung cancer. EGFR mutations were detected in 23 cases (21.1%), KRAS mutations in 13 cases (11.9%), and ALK fusion genes in 5 cases (4.9%). The ALK fusion genes could not be analyzed in four cases because of insufficient tissue samples remaining after routine histochemistry and an EGFR/KRAS mutation analysis. We found that small biopsy samples from EBUS-TBNA were adequate for performing a triple gene analysis in 97 patients (96%). ALK fusion protein immunohistochemistry (IHC) was 100% consistent with fluorescence in situ hybridization (FISH). Conclusion Small samples obtained by EBUS-TBNA were found to be sufficient for performing a triple gene analysis following routine histology and IHC. ALK IHC showed a very good concordance with FISH for detecting ALK fusion genes. PMID:27803402

Bacteria detection instrument and method

NASA Technical Reports Server (NTRS)

Renner, W.; Fealey, R. D. (Inventor)

1972-01-01

A method and apparatus for screening a sample fluid for bacterial presence are disclosed wherein the fluid sample is mixed with culture media of sufficient quantity to permit bacterial growth in order to obtain a test solution. The concentration of oxygen dissolved in the test solution is then monitored using the potential difference between a reference electrode and a noble metal electrode which are in contact with the test solution. The change in oxygen concentration which occurs during a period of time as indicated by the electrode potential difference is compared with a detection criterion which exceeds the change which would occur absent bacteria.

Sampled-data H∞ filtering for Markovian jump singularly perturbed systems with time-varying delay and missing measurements

NASA Astrophysics Data System (ADS)

Yan, Yifang; Yang, Chunyu; Ma, Xiaoping; Zhou, Linna

2018-02-01

In this paper, sampled-data H∞ filtering problem is considered for Markovian jump singularly perturbed systems with time-varying delay and missing measurements. The sampled-data system is represented by a time-delay system, and the missing measurement phenomenon is described by an independent Bernoulli random process. By constructing an ɛ-dependent stochastic Lyapunov-Krasovskii functional, delay-dependent sufficient conditions are derived such that the filter error system satisfies the prescribed H∞ performance for all possible missing measurements. Then, an H∞ filter design method is proposed in terms of linear matrix inequalities. Finally, numerical examples are given to illustrate the feasibility and advantages of the obtained results.

Non-terminal blood sampling techniques in guinea pigs.

PubMed

Birck, Malene M; Tveden-Nyborg, Pernille; Lindblad, Maiken M; Lykkesfeldt, Jens

2014-10-11

Guinea pigs possess several biological similarities to humans and are validated experimental animal models(1-3). However, the use of guinea pigs currently represents a relatively narrow area of research and descriptive data on specific methodology is correspondingly scarce. The anatomical features of guinea pigs are slightly different from other rodent models, hence modulation of sampling techniques to accommodate for species-specific differences, e.g., compared to mice and rats, are necessary to obtain sufficient and high quality samples. As both long and short term in vivo studies often require repeated blood sampling the choice of technique should be well considered in order to reduce stress and discomfort in the animals but also to ensure survival as well as compliance with requirements of sample size and accessibility. Venous blood samples can be obtained at a number of sites in guinea pigs e.g., the saphenous and jugular veins, each technique containing both advantages and disadvantages(4,5). Here, we present four different blood sampling techniques for either conscious or anaesthetized guinea pigs. The procedures are all non-terminal procedures provided that sample volumes and number of samples do not exceed guidelines for blood collection in laboratory animals(6). All the described methods have been thoroughly tested and applied for repeated in vivo blood sampling in studies within our research facility.

Detecting higher-order wavefront errors with an astigmatic hybrid wavefront sensor.

PubMed

Barwick, Shane

2009-06-01

The reconstruction of wavefront errors from measurements over subapertures can be made more accurate if a fully characterized quadratic surface can be fitted to the local wavefront surface. An astigmatic hybrid wavefront sensor with added neural network postprocessing is shown to have this capability, provided that the focal image of each subaperture is sufficiently sampled. Furthermore, complete local curvature information is obtained with a single image without splitting beam power.

Development of Automated Moment Tensor Software at the Prototype International Data Center

DTIC Science & Technology

2000-09-01

Berkeley Digital Seismic Network stations in the 100 to 500 km distance range. With sufficient azimuthal coverage this method is found to perform...the solution reported by NIED (http://argent.geo.bosai.go.jp/ freesia /event/hypo/joho.html). The normal mechanism obtained by the three-component...Digital Seismic Network stations. These stations provide more than 100 degrees of azimuthal coverage, which is an adequate sampling of the focal

Forgery at the Snite Museum of Art? Improving AMS Radiocarbon Dating at the University of Notre Dame

NASA Astrophysics Data System (ADS)

Troyer, Laura; Bagwell, Connor; Anderson, Tyler; Clark, Adam; Nelson, Austin; Skulski, Michael; Collon, Philippe

2017-09-01

The Snite Museum of Art recently obtained several donations of artifacts. Five of the pieces lack sufficient background information to prove authenticity and require further analysis to positively determine the artwork's age. One method to determine the artwork's age is radiocarbon dating via Accelerator Mass Spectrometry (AMS) performed at the University of Notre Dame's Nuclear Science Laboratory. Samples are prepared by combustion of a small amount of material and subsequent reduction to carbon into an iron powder matrix (graphitization). The graphitization procedure affects the maximum measurement rate, and a poor graphitization can be detrimental to the AMS measurement of the sample. Previous graphitization procedures resulted in a particle current too low or inconsistent to optimize AMS measurements. Thus, there was a desire to design and refine the graphitization system. The finalized process yielded physically darker samples and increased sample currents by two orders of magnitude. Additionally, the first testing of the samples was successful, yet analysis of the dates proved inconclusive. AMS measurements will be performed again to obtain better sampling statistics in the hopes of narrowing the reported date ranges. NSF and JINA-CEE.

A Randomized Trial of Sheathed vs. Standard Forceps for Obtaining Uncontaminated Biopsy Specimens of Microbiota from the Terminal Ileum

PubMed Central

Dave, Maneesh; Johnson, Laura A.; Walk, Seth; Young, Vincent B.; Stidham, Ryan W.; Chaudhary, Meghana N.; FunNell, Jessica; Higgins, Peter D.R.

2014-01-01

Background The study of intestinal microbiota has been revolutionized by the use of molecular methods, including terminal restriction fragment length polymorphism (T-RFLP) analysis. A number of microbiota studies of Crohn’s disease patients have examined samples from stool or from the neoterminal ileum with a standard biopsy forceps, which could be contaminated by colonic bacteria when the forceps passes through the colonoscope channel. Objective To determine whether sheathed biopsy forceps are able to obtain terminal ileal microbiota samples with less colonic bacterial contamination compared to unsheathed (standard) biopsy forceps. Design Prospective randomized single center-study. Patients and Methods We obtained four (paired) biopsy specimens from adjacent locations in the terminal ileum using the sheathed and standard forceps of 27 consecutive subjects undergoing colonoscopy and characterized the microbiota using T-RFLP. We calculated the Bray Curtis similarity index (BCI) between samples (sheathed vs. unsheathed forceps) within patients and tested for significant differences across all patients. Results There was not a significant difference in the microbial diversity of samples obtained using sheathed vs. unsheathed forceps. The difference in microbial diversity between patients was much greater than the variability within patients by proximal vs. distal site or by forceps type. Limitations T-RFLP is based on PCR amplification, so it is not always sensitive to rare bacterial species. Conclusion Standard unsheathed forceps appear to be sufficient for microbiota sample collection from the terminal ileum. PMID:21317176

Sampling frequency of ciliated protozoan microfauna for seasonal distribution research in marine ecosystems.

PubMed

Xu, Henglong; Yong, Jiang; Xu, Guangjian

2015-12-30

Sampling frequency is important to obtain sufficient information for temporal research of microfauna. To determine an optimal strategy for exploring the seasonal variation in ciliated protozoa, a dataset from the Yellow Sea, northern China was studied. Samples were collected with 24 (biweekly), 12 (monthly), 8 (bimonthly per season) and 4 (seasonally) sampling events. Compared to the 24 samplings (100%), the 12-, 8- and 4-samplings recovered 94%, 94%, and 78% of the total species, respectively. To reveal the seasonal distribution, the 8-sampling regime may result in >75% information of the seasonal variance, while the traditional 4-sampling may only explain <65% of the total variance. With the increase of the sampling frequency, the biotic data showed stronger correlations with seasonal variables (e.g., temperature, salinity) in combination with nutrients. It is suggested that the 8-sampling events per year may be an optimal sampling strategy for ciliated protozoan seasonal research in marine ecosystems. Copyright © 2015 Elsevier Ltd. All rights reserved.

Analytical evaluation of BEA zeolite for the pre-concentration of polycyclic aromatic hydrocarbons and their subsequent chromatographic analysis in water samples.

PubMed

Wilson, Walter B; Costa, Andréia A; Wang, Huiyong; Dias, José A; Dias, Sílvia C L; Campiglia, Andres D

2012-07-06

The analytical performance of BEA - a commercial zeolite - is evaluated for the pre-concentration of fifteen Environmental Protection Agency - polycyclic aromatic hydrocarbons and their subsequent HPLC analysis in tap and lake water samples. The pre-concentration factors obtained with BEA have led to a method with excellent analytical figures of merit. One milliliter aliquots were sufficient to obtain excellent precision of measurements at the parts-per-trillion concentration level with relative standard deviations varying from 4.1% (dibenzo[a,h]anthracene) to 13.4% (pyrene). The limits of detection were excellent as well and varied between 1.1 (anthracene) and 49.9 ng L(-1) (indeno[1,2,3-cd]pyrene). The recovery values of all the studied compounds meet the criterion for regulated polycyclic aromatic hydrocarbons, which mandates relative standard deviations equal or lower than 25%. The small volume of organic solvents (100 μL per sample) and amount of BEA (2 mg per sample) makes sample pre-concentration environmentally friendly and cost effective. The extraction procedure is well suited for numerous samples as the small working volume (1 mL) facilitates the implementation of simultaneous sample extraction. These are attractive features when routine monitoring of numerous samples is contemplated. Copyright © 2012 Elsevier B.V. All rights reserved.

Production and optical constraints of ice tholin from charged particle irradiation of (1:6) C2H6/H2O at 77 K

NASA Astrophysics Data System (ADS)

Khare, B. N.; Thompson, W. R.; Cheng, L.; Chyba, C.; Sagan, C.; Arakawa, E. T.; Meisse, C.; Tuminello, P. S.

1993-06-01

Fifty separate irradiations of a 6:1 mixture of H2O/C2H6 ice conducted over a 5-month period have yielded sufficient tholin for the determination of its physical constants in the 0.06 to 40 micron range. While the imaginary part of the refractive index k was obtained by transmission measurements on thin-film samples and Kramers-Kronig analysis (KKA), the real part of the refractive index was obtained by KKA and ellipsometry; these data may prove useful in cometary and outer solar system spectrometric interpretation.

Authentication of beef versus horse meat using 60 MHz 1H NMR spectroscopy.

PubMed

Jakes, W; Gerdova, A; Defernez, M; Watson, A D; McCallum, C; Limer, E; Colquhoun, I J; Williamson, D C; Kemsley, E K

2015-05-15

This work reports a candidate screening protocol to distinguish beef from horse meat based upon comparison of triglyceride signatures obtained by 60 MHz (1)H NMR spectroscopy. Using a simple chloroform-based extraction, we obtained classic low-field triglyceride spectra from typically a 10 min acquisition time. Peak integration was sufficient to differentiate samples of fresh beef (76 extractions) and horse (62 extractions) using Naïve Bayes classification. Principal component analysis gave a two-dimensional "authentic" beef region (p=0.001) against which further spectra could be compared. This model was challenged using a subset of 23 freeze-thawed training samples. The outcomes indicated that storing samples by freezing does not adversely affect the analysis. Of a further collection of extractions from previously unseen samples, 90/91 beef spectra were classified as authentic, and 16/16 horse spectra as non-authentic. We conclude that 60 MHz (1)H NMR represents a feasible high-throughput approach for screening raw meat. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Beamforming using subspace estimation from a diagonally averaged sample covariance.

PubMed

Quijano, Jorge E; Zurk, Lisa M

2017-08-01

The potential benefit of a large-aperture sonar array for high resolution target localization is often challenged by the lack of sufficient data required for adaptive beamforming. This paper introduces a Toeplitz-constrained estimator of the clairvoyant signal covariance matrix corresponding to multiple far-field targets embedded in background isotropic noise. The estimator is obtained by averaging along subdiagonals of the sample covariance matrix, followed by covariance extrapolation using the method of maximum entropy. The sample covariance is computed from limited data snapshots, a situation commonly encountered with large-aperture arrays in environments characterized by short periods of local stationarity. Eigenvectors computed from the Toeplitz-constrained covariance are used to construct signal-subspace projector matrices, which are shown to reduce background noise and improve detection of closely spaced targets when applied to subspace beamforming. Monte Carlo simulations corresponding to increasing array aperture suggest convergence of the proposed projector to the clairvoyant signal projector, thereby outperforming the classic projector obtained from the sample eigenvectors. Beamforming performance of the proposed method is analyzed using simulated data, as well as experimental data from the Shallow Water Array Performance experiment.

Optimization of chemical and instrumental parameters in hydride generation laser-induced breakdown spectrometry for the determination of arsenic, antimony, lead and germanium in aqueous samples.

PubMed

Yeşiller, Semira Unal; Yalçın, Serife

2013-04-03

A laser induced breakdown spectrometry hyphenated with on-line continuous flow hydride generation sample introduction system, HG-LIBS, has been used for the determination of arsenic, antimony, lead and germanium in aqueous environments. Optimum chemical and instrumental parameters governing chemical hydride generation, laser plasma formation and detection were investigated for each element under argon and nitrogen atmosphere. Arsenic, antimony and germanium have presented strong enhancement in signal strength under argon atmosphere while lead has shown no sensitivity to ambient gas type. Detection limits of 1.1 mg L(-1), 1.0 mg L(-1), 1.3 mg L(-1) and 0.2 mg L(-1) were obtained for As, Sb, Pb and Ge, respectively. Up to 77 times enhancement in detection limit of Pb were obtained, compared to the result obtained from the direct analysis of liquids by LIBS. Applicability of the technique to real water samples was tested through spiking experiments and recoveries higher than 80% were obtained. Results demonstrate that, HG-LIBS approach is suitable for quantitative analysis of toxic elements and sufficiently fast for real time continuous monitoring in aqueous environments. Copyright © 2013 Elsevier B.V. All rights reserved.

Plasticizing Effects of Polyamines in Protein-Based Films

PubMed Central

Sabbah, Mohammed; Di Pierro, Prospero; Giosafatto, C. Valeria L.; Esposito, Marilena; Mariniello, Loredana; Regalado-Gonzales, Carlos; Porta, Raffaele

2017-01-01

Zeta potential and nanoparticle size were determined on film forming solutions of native and heat-denatured proteins of bitter vetch as a function of pH and of different concentrations of the polyamines spermidine and spermine, both in the absence and presence of the plasticizer glycerol. Our results showed that both polyamines decreased the negative zeta potential of all samples under pH 8.0 as a consequence of their ionic interaction with proteins. At the same time, they enhanced the dimension of nanoparticles under pH 8.0 as a result of macromolecular aggregations. By using native protein solutions, handleable films were obtained only from samples containing either a minimum of 33 mM glycerol or 4 mM spermidine, or both compounds together at lower glycerol concentrations. However, 2 mM spermidine was sufficient to obtain handleable film by using heat-treated samples without glycerol. Conversely, brittle materials were obtained by spermine alone, thus indicating that only spermidine was able to act as an ionic plasticizer. Lastly, both polyamines, mainly spermine, were found able to act as “glycerol-like” plasticizers at concentrations higher than 5 mM under experimental conditions at which their amino groups are undissociated. Our findings open new perspectives in obtaining protein-based films by using aliphatic polycations as components. PMID:28489025

Technique to quantitatively measure magnetic properties of thin structures at <10 NM spatial resolution

DOEpatents

Bajt, Sasa

2003-07-08

A highly sensitive and high resolution magnetic microscope images magnetic properties quantitatively. Imaging is done with a modified transmission electron microscope that allows imaging of the sample in a zero magnetic field. Two images from closely spaced planes, one in focus and one slightly out of focus, are sufficient to calculate the absolute values of the phase change imparted to the electrons, and hence obtain the magnetization vector field distribution.

Evoked Potential Studies of the Effects of Impact Acceleration on the Motor Nervous System,

DTIC Science & Technology

1983-01-01

experimental animals subjected to -Y ampere) were applied sufficient to obtain good (lateral impact) acceleration and animals sub- afferent evoked...NBDL -Y impact experiments were processed at the EP recorded from these animals before and after Texas Research Institute of Mental Sciences impact were...adjustments were made to playback discriminators and cord in a lateral (-Y) collision. Each and the sampling interval. The final digit. -e d, J animal was

Effective application of multiple locus variable number of tandem repeats analysis to tracing Staphylococcus aureus in food-processing environment.

PubMed

Rešková, Z; Koreňová, J; Kuchta, T

2014-04-01

A total of 256 isolates of Staphylococcus aureus were isolated from 98 samples (34 swabs and 64 food samples) obtained from small or medium meat- and cheese-processing plants in Slovakia. The strains were genotypically characterized by multiple locus variable number of tandem repeats analysis (MLVA), involving multiplex polymerase chain reaction (PCR) with subsequent separation of the amplified DNA fragments by an automated flow-through gel electrophoresis. With the panel of isolates, MLVA produced 31 profile types, which was a sufficient discrimination to facilitate the description of spatial and temporal aspects of contamination. Further data on MLVA discrimination were obtained by typing a subpanel of strains by multiple locus sequence typing (MLST). MLVA coupled to automated electrophoresis proved to be an effective, comparatively fast and inexpensive method for tracing S. aureus contamination of food-processing factories. Subspecies genotyping of microbial contaminants in food-processing factories may facilitate identification of spatial and temporal aspects of the contamination. This may help to properly manage the process hygiene. With S. aureus, multiple locus variable number of tandem repeats analysis (MLVA) proved to be an effective method for the purpose, being sufficiently discriminative, yet comparatively fast and inexpensive. The application of automated flow-through gel electrophoresis to separation of DNA fragments produced by multiplex PCR helped to improve the accuracy and speed of the method. © 2013 The Society for Applied Microbiology.

Electrical resistivity measurements on fragile organic single crystals in the diamond anvil cell

NASA Astrophysics Data System (ADS)

Adachi, T.; Tanaka, H.; Kobayashi, H.; Miyazaki, T.

2001-05-01

A method of sample assembly for four-probe resistivity measurements on fragile organic single crystals using a diamond anvil cell is presented. A procedure to keep insulation between the metal gasket and four leads of thin gold wires bonded to the sample crystal by gold paint is described in detail. The resistivity measurements performed on a single crystal of an organic semiconductor and that of neutral molecules up to 15 GPa and down to 4.2 K showed that this new procedure of four-probe diamond anvil resistivity measurements enables us to obtain sufficiently accurate resistivity data of organic crystals.

Method of quantitating dsDNA

DOEpatents

Stark, Peter C.; Kuske, Cheryl R.; Mullen, Kenneth I.

2002-01-01

A method for quantitating dsDNA in an aqueous sample solution containing an unknown amount of dsDNA. A first aqueous test solution containing a known amount of a fluorescent dye-dsDNA complex and at least one fluorescence-attenutating contaminant is prepared. The fluorescence intensity of the test solution is measured. The first test solution is diluted by a known amount to provide a second test solution having a known concentration of dsDNA. The fluorescence intensity of the second test solution is measured. Additional diluted test solutions are similarly prepared until a sufficiently dilute test solution having a known amount of dsDNA is prepared that has a fluorescence intensity that is not attenuated upon further dilution. The value of the maximum absorbance of this solution between 200-900 nanometers (nm), referred to herein as the threshold absorbance, is measured. A sample solution having an unknown amount of dsDNA and an absorbance identical to that of the sufficiently dilute test solution at the same chosen wavelength is prepared. Dye is then added to the sample solution to form the fluorescent dye-dsDNA-complex, after which the fluorescence intensity of the sample solution is measured and the quantity of dsDNA in the sample solution is determined. Once the threshold absorbance of a sample solution obtained from a particular environment has been determined, any similarly prepared sample solution taken from a similar environment and having the same value for the threshold absorbance can be quantified for dsDNA by adding a large excess of dye to the sample solution and measuring its fluorescence intensity.

A spinner magnetometer for large Apollo lunar samples.

PubMed

Uehara, M; Gattacceca, J; Quesnel, Y; Lepaulard, C; Lima, E A; Manfredi, M; Rochette, P

2017-10-01

We developed a spinner magnetometer to measure the natural remanent magnetization of large Apollo lunar rocks in the storage vault of the Lunar Sample Laboratory Facility (LSLF) of NASA. The magnetometer mainly consists of a commercially available three-axial fluxgate sensor and a hand-rotating sample table with an optical encoder recording the rotation angles. The distance between the sample and the sensor is adjustable according to the sample size and magnetization intensity. The sensor and the sample are placed in a two-layer mu-metal shield to measure the sample natural remanent magnetization. The magnetic signals are acquired together with the rotation angle to obtain stacking of the measured signals over multiple revolutions. The developed magnetometer has a sensitivity of 5 × 10 -7 Am 2 at the standard sensor-to-sample distance of 15 cm. This sensitivity is sufficient to measure the natural remanent magnetization of almost all the lunar basalt and breccia samples with mass above 10 g in the LSLF vault.

A spinner magnetometer for large Apollo lunar samples

NASA Astrophysics Data System (ADS)

Uehara, M.; Gattacceca, J.; Quesnel, Y.; Lepaulard, C.; Lima, E. A.; Manfredi, M.; Rochette, P.

2017-10-01

We developed a spinner magnetometer to measure the natural remanent magnetization of large Apollo lunar rocks in the storage vault of the Lunar Sample Laboratory Facility (LSLF) of NASA. The magnetometer mainly consists of a commercially available three-axial fluxgate sensor and a hand-rotating sample table with an optical encoder recording the rotation angles. The distance between the sample and the sensor is adjustable according to the sample size and magnetization intensity. The sensor and the sample are placed in a two-layer mu-metal shield to measure the sample natural remanent magnetization. The magnetic signals are acquired together with the rotation angle to obtain stacking of the measured signals over multiple revolutions. The developed magnetometer has a sensitivity of 5 × 10-7 Am2 at the standard sensor-to-sample distance of 15 cm. This sensitivity is sufficient to measure the natural remanent magnetization of almost all the lunar basalt and breccia samples with mass above 10 g in the LSLF vault.

Study on processing parameters of glass cutting by nanosecond 532 nm fiber laser

NASA Astrophysics Data System (ADS)

Wang, Jin; Gao, Fan; Xiong, Baoxing; Zhang, Xiang; Yuan, Xiao

2018-03-01

The processing parameters of soda-lime glass cutting with several nanosecond 532 nm pulsed fiber laser are studied in order to obtain sufficiently large ablation rate and better processing quality. The influences of laser processing parameters on effective cutting speed and cutting quality of 1 2 mm thick soda-lime glass are studied. The experimental results show that larger laser pulse energy will lead to higher effective cutting speed and larger maximum edge collapse of the front side of the glass samples. Compared with that of 1.1 mm thick glass samples, the 2.0 mm thick glass samples is more difficult to cut. With the pulse energy of 51.2 μJ, the maximum edge collapse is more than 200 μm for the 2.0 mm thick glass samples. In order to achieve the high effective cutting speed and good cutting quality at the same time, the dual energy overlapping method is used to obtain the better cutting performance for the 2.0 mm thick glass samples, and the cutting speed of 194 mm/s and the maximum edge collapse of less than 132 μm are realized.

Fermented probiotic beverages based on acid whey.

PubMed

Skryplonek, Katarzyna; Jasińska, Małgorzata

2015-01-01

Production of fermented probiotic beverages can be a good method for acid whey usage. The obtained products combine a high nutritional value of whey with health benefits claimed for probiotic bacteria. The aim of the study was to define quality properties of beverages based on fresh acid whey and milk with addition of buttermilk powder or sweet whey powder. Samples were inoculated with two strains of commercial probiotic cultures: Lactobacillus acidophilus La-5 or Bifidobacterium animalis Bb-12. After fermentation, samples were stored at refrigerated conditions. After 1, 4, 7, 14 and 21 days sensory characteristics, hardness, acetaldehyde content, titratable acidity, pH acidity and count of bacteria cells were evaluated. Throughout all storage period, the number of bacteria was higher than 8 log cfu/ml in the all samples. Beverages with La-5 strain had higher hardness and acidity, whilst samples with Bb-12 contained more acetaldehyde. Samples with buttermilk powder had better sensory properties than with sweet whey powder. Obtained products made of acid whey combined with milk and fortified with buttermilk powder or sweet whey powder, are good medium for growth and survival of examined probiotic bacteria strains. The level of bacteria was sufficient to provide health benefits to consumers.

Use of self-collected capillary blood samples for islet autoantibody screening in relatives: a feasibility and acceptability study.

PubMed

Liu, Y; Rafkin, L E; Matheson, D; Henderson, C; Boulware, D; Besser, R E J; Ferrara, C; Yu, L; Steck, A K; Bingley, P J

2017-07-01

To evaluate the feasibility of using self-collected capillary blood samples for islet autoantibody testing to identify risk in relatives of people with Type 1 diabetes. Participants were recruited via the observational TrialNet Pathway to Prevention study, which screens and monitors relatives of people with Type 1 diabetes for islet autoantibodies. Relatives were sent kits for capillary blood collection, with written instructions, an online instructional video link and a questionnaire. Sera from capillary blood samples were tested for autoantibodies to glutamic acid decarboxylase, islet antigen-2, insulin and zinc transporter 8. 'Successful' sample collection was defined as obtaining sufficient volume and quality to provide definitive autoantibody results, including confirmation of positive results by repeat assay. In 240 relatives who returned samples, the median (range) age was 15.5 (1-49) years and 51% were male. Of these samples, 98% were sufficient for glutamic acid decarboxylase, islet antigen-2 and zinc transporter 8 autoantibody testing and 84% for insulin autoantibody testing and complete autoantibody screen. The upper 90% confidence bound for unsuccessful collection was 4.4% for glutamic acid decarboxylase, islet antigen-2 and/or zinc transporter 8 autoantibody assays, and 19.3% for insulin autoantibodies. Despite 43% of 220 questionnaire respondents finding capillary blood collection uncomfortable or painful, 82% preferred home self-collection of capillary blood samples compared with outpatient venepuncture (90% of those aged <8 years, 83% of those aged 9-18 years and 73% of those aged >18 years). The perceived difficulty of collecting capillary blood samples did not affect success rate. Self-collected capillary blood sampling offers a feasible alternative to venous sampling, with the potential to facilitate autoantibody screening for Type 1 diabetes risk. © 2017 Diabetes UK.

Role of fish distribution on estimates of standing crop in a cooling reservoir

USGS Publications Warehouse

Barwick, D. Hugh

1984-01-01

Estimates of fish standing crop from coves in Keowee Reservoir, South Carolina, were obtained in May and August for 3 consecutive years. Estimates were significantly higher in May than in August for most of the major species of fish collected, suggesting that considerable numbers of fish had migrated from the coves by August. This change in fish distribution may have resulted from the operation of a 2,580-megawatt nuclear power plant which altered reservoir stratification. Because fish distribution is sensitive to conditions of reservoir stratification, and because power plants often alter reservoir stratification, annual cove sampling in August may not be sufficient to produce comparable estimates of fish standing crop on which to assess the impact of power plant operations on fish populations. Comparable estimates of fish standing crop can probably be obtained from cooling reservoirs by collecting annual samples at similar water temperatures and concentrations of dissolved oxygen.

Pharmacists' knowledge and the difficulty of obtaining emergency contraception.

PubMed

Bennett, Wendy; Petraitis, Carol; D'Anella, Alicia; Marcella, Stephen

2003-10-01

This cross-sectional study was performed to examine knowledge and attitudes among pharmacists about emergency contraception (EC) and determine the factors associated with their provision of EC. A random systematic sampling method was used to obtain a sample (N = 320) of pharmacies in Pennsylvania. A "mystery shopper" telephone survey method was utilized. Only 35% of pharmacists stated that they would be able to fill a prescription for EC that day. Also, many community pharmacists do not have sufficient or accurate information about EC. In a logistic regression model, pharmacists' lack of information relates to the low proportion of pharmacists able to dispense it. In conclusion, access to EC from community pharmacists in Pennsylvania is severely limited. Interventions to improve timely access to EC involve increased education for pharmacists, as well as increased community request for these products as an incentive for pharmacists to stock them.

Tank 241-AY-101 Privatization Push Mode Core Sampling and Analysis Plan

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

TEMPLETON, A.M.

2000-05-19

This sampling and analysis plan (SAP) identifies characterization objectives pertaining to sample collection, laboratory analytical evaluation, and reporting requirements for samples obtained from tank 241-AY-101. The purpose of this sampling event is to obtain information about the characteristics of the contents of 241-AY-101 required to satisfy ''Data Quality Objectives For RPP Privatization Phase I: Confirm Tank T Is An Appropriate Feed Source For High-Level Waste Feed Batch X(HLW DQO)' (Nguyen 1999a), ''Data Quality Objectives For TWRS Privatization Phase I: Confirm Tank T Is An Appropriate Feed Source For Low-Activity Waste Feed Butch X (LAW DQO) (Nguyen 1999b)'', ''Low Activity Wastemore » and High-Level Waste Feed Data Quality Objectives (L&H DQO)'' (Patello et al. 1999), and ''Characterization Data Needs for Development, Design, and Operation of Retrieval Equipment Developed through the Data Quality Objective Process (Equipment DQO)'' (Bloom 1996). Special instructions regarding support to the LAW and HLW DQOs are provided by Baldwin (1999). Push mode core samples will be obtained from risers 15G and 150 to provide sufficient material for the chemical analyses and tests required to satisfy these data quality objectives. The 222-S Laboratory will extrude core samples; composite the liquids and solids; perform chemical analyses on composite and segment samples; archive half-segment samples; and provide sub-samples to the Process Chemistry Laboratory. The Process Chemistry Laboratory will prepare test plans and perform process tests to evaluate the behavior of the 241-AY-101 waste undergoing the retrieval and treatment scenarios defined in the applicable DQOs. Requirements for analyses of samples originating in the process tests will be documented in the corresponding test plans and are not within the scope of this SAP.« less

Halo-free Phase Contrast Microscopy

NASA Astrophysics Data System (ADS)

Nguyen, Tan H.; Kandel, Mikhail; Shakir, Haadi M.; Best-Popescu, Catherine; Arikkath, Jyothi; Do, Minh N.; Popescu, Gabriel

2017-03-01

We present a new approach for retrieving halo-free phase contrast microscopy (hfPC) images by upgrading the conventional PC microscope with an external interferometric module, which generates sufficient data for reversing the halo artifact. Acquiring four independent intensity images, our approach first measures haloed phase maps of the sample. We solve for the halo-free sample transmission function by using a physical model of the image formation under partial spatial coherence. Using this halo-free sample transmission, we can numerically generate artifact-free PC images. Furthermore, this transmission can be further used to obtain quantitative information about the sample, e.g., the thickness with known refractive indices, dry mass of live cells during their cycles. We tested our hfPC method on various control samples, e.g., beads, pillars and validated its potential for biological investigation by imaging live HeLa cells, red blood cells, and neurons.

Constructing first-principles phase diagrams of amorphous LixSi using machine-learning-assisted sampling with an evolutionary algorithm

NASA Astrophysics Data System (ADS)

Artrith, Nongnuch; Urban, Alexander; Ceder, Gerbrand

2018-06-01

The atomistic modeling of amorphous materials requires structure sizes and sampling statistics that are challenging to achieve with first-principles methods. Here, we propose a methodology to speed up the sampling of amorphous and disordered materials using a combination of a genetic algorithm and a specialized machine-learning potential based on artificial neural networks (ANNs). We show for the example of the amorphous LiSi alloy that around 1000 first-principles calculations are sufficient for the ANN-potential assisted sampling of low-energy atomic configurations in the entire amorphous LixSi phase space. The obtained phase diagram is validated by comparison with the results from an extensive sampling of LixSi configurations using molecular dynamics simulations and a general ANN potential trained to ˜45 000 first-principles calculations. This demonstrates the utility of the approach for the first-principles modeling of amorphous materials.

Isolating cells from female/male blood mixtures using florescence in situ hybridization combined with low volume PCR and its application in forensic science.

PubMed

Feng, Lei; Li, Cai-Xia; Han, Jun-Ping; Xu, Cheng; Hu, Lan

2015-11-01

To obtain single-source short tandem repeat (STR) profiles in trace female/male blood mixture samples, we combined florescence in situ hybridization (FISH), laser microdissection, and low volume PCR (LV-PCR) to isolate male/female cells and improve sensitivity. The results showed that isolation of as few as 10 leukocytes was sufficient to yield full STR profiles in fresh female or male blood samples for 32 independent tests with a low additional alleles rate (3.91%) and drop-out alleles rate (5.01%). Moreover, this procedure was tested in two fresh blood mixture series at three ratios (1:5, 1:10, and 1:20), two mock female/male blood mixture casework samples, and one practical casework sample. Male and female STR profiles were successfully detected in all of these samples, showing that this procedure could be used in forensic casework in the future.

VizieR Online Data Catalog: Properties of late M-dwarfs (Janson+, 2014)

NASA Astrophysics Data System (ADS)

Janson, M.; Bergfors, C.; Brandner, W.; Kudryavtseva, N.; Hormuth, F.; Hippler, S.; Henning, T.

2017-03-01

The targets in this study were selected from the Lepine & Gaidos (2011, J/AJ/142/138) sample, where stars with a spectral type (SpT) estimate of M5 or later were selected if they were sufficiently bright (J <= 10.0 mag) and sufficiently far north (>-15°) to be meaningfully observed with AstraLux Norte. In total, this gave an input sample of 408 potential targets, of which 286 were actually observed. All observations in this program were acquired with the AstraLux Norte camera on the 2.2 m telescope at Calar Alto in Spain. The 2.2 m telescope is on an equatorial mount. AstraLux uses an Andor DV887-UVB camera head equipped with a thinned, back-illuminated, electron-multiplying 512 x 512 pixel monolithic CCD. The CCD is equipped with two readout registers, one for conventional readout, and one 536 stage electron multiplication register. Each of the two registers comes with its own output amplifier. All Lucky Imaging data were obtained using the electron multiplication mode, and the associated output amplifier. (3 data files).

In-gas-cell laser ionization studies of plutonium isotopes at IGISOL

NASA Astrophysics Data System (ADS)

Pohjalainen, I.; Moore, I. D.; Kron, T.; Raeder, S.; Sonnenschein, V.; Tomita, H.; Trautmann, N.; Voss, A.; Wendt, K.

2016-06-01

In-gas-cell resonance laser ionization has been performed on long-lived isotopes of Pu at the IGISOL facility, Jyväskylä. This initiates a new programme of research towards high-resolution optical spectroscopy of heavy actinide elements which can be produced in sufficient quantities at research reactors and transported to facilities elsewhere. In this work a new gas cell has been constructed for fast extraction of laser-ionized elements. Samples of 238-240,242Pu and 244Pu have been evaporated from Ta filaments, laser ionized, mass separated and delivered to the collinear laser spectroscopy station. Here we report on the performance of the gas cell through studies of the mass spectra obtained in helium and argon, before and after the radiofrequency quadrupole cooler-buncher. This provides valuable insight into the gas phase chemistry exhibited by Pu, which has been additionally supported by measurements of ion time profiles. The resulting monoatomic yields are sufficient for collinear laser spectroscopy. A gamma-ray spectroscopic analysis of the Pu samples shows a good agreement with the assay provided by the Mainz Nuclear Chemistry department.

An Easy Method to Eliminate the Effect of Lupus Anticoagulants in the Coagulation Factor Assay.

PubMed

Tang, Ning; Yin, Shiyu

2016-07-01

To build and evaluate intrinsic coagulation factor assays which can eliminate the effect of lupus anticoagulants (LAC). Commercial silica clotting time confirmatory (SCT-C) reagent containing sufficient synthetic phospholipid and routine activated partial thromboplastin time (APTT) reagent were each used for one-stage detection of FVIII, FIX, and FXI activities, in samples with or without LAC, and the results were compared. For samples without LAC, consistent results of FVIII, FIX, and FXI using both SCT-C reagent and APTT reagent were obtained. For samples with LAC, the assays with SCT-C reagent not only could eliminate the effect of strong lupus anticoagulants but also needed fewer dilutions than that with routine APTT reagent. The intrinsic factor detections by SCT-C reagent are credible and convenient to be used for samples with LAC.

Characterizations of linear sufficient statistics

NASA Technical Reports Server (NTRS)

Peters, B. C., Jr.; Reoner, R.; Decell, H. P., Jr.

1977-01-01

A surjective bounded linear operator T from a Banach space X to a Banach space Y must be a sufficient statistic for a dominated family of probability measures defined on the Borel sets of X. These results were applied, so that they characterize linear sufficient statistics for families of the exponential type, including as special cases the Wishart and multivariate normal distributions. The latter result was used to establish precisely which procedures for sampling from a normal population had the property that the sample mean was a sufficient statistic.

Tank 241-AY-101 Privatization Push Mode Core Sampling and Analysis Plan

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

TEMPLETON, A.M.

2000-01-12

This sampling and analysis plan (SAP) identifies characterization objectives pertaining to sample collection, laboratory analytical evaluation, and reporting requirements for samples obtained from tank 241-AY-101. The purpose of this sampling event is to obtain information about the characteristics of the contents of 241-AY-101 required to satisfy Data Quality Objectives For RPP Privatization Phase I: Confirm Tank T Is An Appropriate Feed Source For High-Level Waste Feed Batch X(HLW DQO) (Nguyen 1999a), Data Quality Objectives For TWRS Privatization Phase I : Confirm Tank T Is An Appropriate Feed Source For Low-Activity Waste Feed Batch X (LAW DQO) (Nguyen 1999b), Low Activitymore » Waste and High-Level Waste Feed Data Quality Objectives (L and H DQO) (Patello et al. 1999), and Characterization Data Needs for Development, Design, and Operation of Retrieval Equipment Developed through the Data Quality Objective Process (Equipment DQO) (Bloom 1996). Special instructions regarding support to the LAW and HLW DQOs are provided by Baldwin (1999). Push mode core samples will be obtained from risers 15G and 150 to provide sufficient material for the chemical analyses and tests required to satisfy these data quality objectives. The 222-S Laboratory will extrude core samples; composite the liquids and solids; perform chemical analyses on composite and segment samples; archive half-segment samples; and provide subsamples to the Process Chemistry Laboratory. The Process Chemistry Laboratory will prepare test plans and perform process tests to evaluate the behavior of the 241-AY-101 waste undergoing the retrieval and treatment scenarios defined in the applicable DQOs. Requirements for analyses of samples originating in the process tests will be documented in the corresponding test plans and are not within the scope of this SAP.« less

Comparison of the Cytobrush®, dermatological curette and oral CDx® brush test as methods for obtaining samples of RNA for molecular analysis of oral cytology.

PubMed

Reboiras-López, M D; Pérez-Sayáns, M; Somoza-Martín, J M; Gayoso-Diz, P; Barros-Angueira, F; Gándara-Rey, J M; García-García, A

2012-06-01

Interest in oral exfoliative cytology has increased with the availability of molecular markers that may lead to the earlier diagnosis of oral squamous cell carcinoma. This research aims to compare the efficacy of three different instruments (Cytobrush, curette and Oral CDx brush) in providing adequate material for molecular analysis. One hundred and four cytological samples obtained from volunteer healthy subjects were analysed using all three instruments. The clinical and demographical variables under study were age, sex and smoking habits. The three instruments were compared for their ability to obtain adequate samples and for the amount of RNA obtained using quantitative real-time polymerase chain reaction (PCR-qRT) analysis of the Abelson (ABL) housekeeping gene. RNA of the ABL gene has been quantified by number of copies. Adequate samples were more likely to be obtained with a curette (90.6%) or Oral CDx (80.0%) than a Cytobrush (48.6%); P < 0.001. Similarly, the RNA quantification was 17.64 ± 21.10 with a curette, 16.04 ± 15.81 with Oral CDx and 6.82 ± 6.71 with a Cytobrush. There were statistically significant differences between the Cytobrush and curette (P = 0.008) and between the Cytobrush and OralCDx (P = 0.034). There was no difference according to the demographical variables. Oral exfoliative cytology is a simple, non-invasive technique that provides sufficient RNA to perform studies on gene expression. Although material was obtained with all three instruments, adequate samples were more likely to be obtained with the curette or Oral CDx than with a Cytobrush. The Oral CDx is a less aggressive instrument than the curette, so could be a useful tool in a clinical setting. © 2011 Blackwell Publishing Ltd.

[Effect of sampling effort on taxa richness of aquatic macroinvertebrates and the BMWP/Atitlán index].

PubMed

Reyes-Morales, Fátima; Springer, Monika

2014-04-01

Aquatic macroinvertebrates are the group of organisms most commonly used to determine ecosystem health in water quality studies and freshwater biomonitoring. Nevertheless, the methods and collecting time of biomonitoring have not yet been sufficiently adapted and tested in tropical aquatic environments. Twelve rivers in the Lago de Atitlán watershed in Guatemala were assessed with different collecting times, during the dry season. The method involved the collection of organic and inorganic material including benthic organisms, from different microhabitats, for a pre-established time period (5, 10, 15 min) with a D-frame net. Samples were preserved with 95% ethanol in the field, and sorted in the laboratory. As expected, the analysis showed that the abundance and taxonomic richness was higher with increasing sampling effort. The water quality categories obtained from the newly proposed BMWP/Atitlán index varied among sampling times. However, the Kruskal-Wallis test showed no significant differences between the categories obtained with the index and the number of taxa collected at 10 and 15 min. Therefore, we recommend a reduction of sample time, but maintaining the tree subsamples in order to include most variety of microhabitats and assure a representative sample of the aquatic macroinvertebrates.

Experimental and Computational Studies of Carbonyl Diazide (CON6) as a Precursor to Diazirinone (CON2)

NASA Astrophysics Data System (ADS)

Esselman, Brian J.; Amberger, Brent K.; Nolan, Alex M.; Woods, R. Claude; McMahon, R. J.

2011-10-01

Intrigued by the reported 2005 synthesis of diazirinone (1), we carried out further experimental and theoretical studies aimed at the detailed matrix-isolation and millimeter-wave spectroscopic characterizations of 1. Diazirinone (1) is a peculiar isoconjugate of two very stable molecules and may be of astrochemical interest. Unfortunately, the original reported methods of diazirinone (1) generation did not yield this species, rather its decomposition products. Inspired by a more recent gas phase pyrolysis of CON6 (2) to yield CON2 (1), we proposed a new method of generating CON6 (2) in solution as a precursor of diazirinone (1). This new synthesis may allow us to generate larger quantities of both CON6 and CON2 for investigation by millimeter-wave spectroscopy. We are able to safely generate carbonyl diazide (2) in sufficient yield from the reaction of triphosgene (3) and tetrabutylammonium azide in diethyl ether. This has allowed us to obtain both matrix-isolation and gas phase IR spectra of carbonyl diazide (2). After purification, it has a gas-phase lifetime that allows samples to be useable for up to several weeks. However, it is a shock-sensitive material that must be handled with care to prevent violent decomposition. In order to provide better mechanistic insight into the decomposition of carbonyl diazide (2) to diazirinone (1), we have engaged in a DFT and ab initio computational study. We have found a pathway between the two species via the triplet acylnitrene, CON4, and an oxaziridine CON2 species, but not at sufficiently low energies to allow for the trapping and detection of diazirinone (1). Preliminary millimeter-wave spectra have been obtained from several synthesized and purified samples of CON6 (2). However, the assignment of the spectra lines has been unexpectedly problematic. We have placed several CON6 (2) samples, confirmed by IR spectroscopy at the time of sample loading, into our instrument and obtained two different sets of rotational lines. This rotational puzzle will be investigated further with a significantly upgraded millimeter-wave spectrometer.

Effect of Geometry on Electrokinetic Characterization of Solid Surfaces.

PubMed

Kumar, Abhijeet; Kleinen, Jochen; Venzmer, Joachim; Gambaryan-Roisman, Tatiana

2017-08-01

An analytical approach is presented to describe pressure-driven streaming current (I str ) and streaming potential (U str ) generation in geometrically complex samples, for which the classical Helmholtz-Smoluchowski (H-S) equation is known to be inaccurate. The new approach is valid under the same prerequisite conditions that are used for the development of the H-S equation, that is, the electrical double layers (EDLs) are sufficiently thin and surface conductivity and electroviscous effects are negligible. The analytical methodology is developed using linear velocity profiles to describe liquid flow inside of EDLs and using simplifying approximations to describe macroscopic flow. At first, a general expression is obtained to describe the I str generated in different cross sections of an arbitrarily shaped sample. Thereafter, assuming that the generated U str varies only along the pressure-gradient direction, an expression describing the variation of generated U str along the sample length is obtained. These expressions describing I str and U str generation constitute the theoretical foundation of this work, which is first applied to a set of three nonuniform cross-sectional capillaries and thereafter to a square array of cylindrical fibers (model porous media) for both parallel and transverse fiber orientation cases. Although analytical solutions cannot be obtained for real porous substrates because of their random structure, the new theory provides useful insights into the effect of important factors such as fiber orientation, sample porosity, and sample dimensions. The solutions obtained for the model porous media are used to device strategies for more accurate zeta potential determination of porous fiber plugs. The new approach could be thus useful in resolving the long-standing problem of sample geometry dependence of zeta potential measurements.

Impression cytology: a novel sampling technique for conjunctival cytology of the feline eye.

PubMed

Eördögh, Réka; Schwendenwein, Ilse; Tichy, Alexander; Nell, Barbara

2015-07-01

Impression cytology is a noninvasive investigation of the ocular surface. It uses the adhesive features of different filter papers to collect a monolayer of epithelial cells from the cornea and/or conjunctiva. Samples obtained by impression cytology exhibit all characteristics of an ideal cytology specimen. The aim of this study was to test the feasibility of impression cytology and determine the most appropriate filter paper to achieve maximum diagnostic value of the feline eye. Ten healthy cats. The study was conducted in two phases. In the first phase, eight different filter papers (FPs) with various pore sizes were tested: 3.0-, 1.2-, 0.8-, 0.45-, 0.22-, 0.05- and 0.025-μm cellulose acetate papers and a 0.4-μm Biopore membrane (BM). Samples were obtained from the superior bulbar and from the inferior palpebral conjunctiva. In the second phase, three different sampling methods - with and without topical anesthesia, and with topical anesthesia and drying of the conjunctiva - were compared employing the BM encased in the intended BM device (BMD). Samples were evaluated for cellularity and quality of cells. In the first phase, samples obtained from the superior bulbar conjunctiva with the BM had the most sufficient cellularity and quality. In the second phase, BMD with topical anesthesia and additional drying of the conjunctiva was the most ideal method. The BMD may prove to be a suitable diagnostic tool for clinicians. Sampling is quick, processing is simple, and a large area of intact cells can be harvested. © 2014 American College of Veterinary Ophthalmologists.

Clinical evaluation of a miniaturized desktop breath hydrogen analyzer.

PubMed

Duan, L P; Braden, B; Clement, T; Caspary, W F; Lembcke, B

1994-10-01

A small desktop electrochemical H2 analyzer (EC-60-Hydrogen monitor) was compared with a stationary electrochemical H2 monitor (GMI-exhaled Hydrogen monitor). The EC-60-H2 monitor shows a high degree of precision for repetitive (n = 10) measurements of standard hydrogen mixtures (CV 1-8%). The response time for completion of measurement is shorter than that of the GMI-exhaled H2 monitor (37 sec. vs 53 sec.; p < 0.0001), while reset times are almost identical (54 sec. vs 51 sec. n.s). In a clinical setting, breath H2-concentrations measured with the EC-60-H2 monitor and the GMI-exhaled H2 monitor were in excellent agreement with a linear correlation (Y = 1.12X + 1.022, r2 = 0.9617, n = 115). With increasing H2-concentrations the EC-60-H2 monitor required larger sample volumes for maintaining sufficient precision, and sample volumes greater than 200 ml were required with H2-concentrations > 30 ppm. For routine gastrointestinal function testing, the EC-60-H2 monitor is an satisfactory and reliable, easy to use and inexpensive desktop breath hydrogen analyzer, whereas in patients with difficulty in cooperating (children, people with severe pulmonary insufficiency), special care has to be applied to obtain sufficiently large breath samples.

Surveying multiple health professional team members within institutional settings: an example from the nursing home industry.

PubMed

Clark, Melissa A; Roman, Anthony; Rogers, Michelle L; Tyler, Denise A; Mor, Vincent

2014-09-01

Quality improvement and cost containment initiatives in health care increasingly involve interdisciplinary teams of providers. To understand organizational functioning, information is often needed from multiple members of a leadership team since no one person may have sufficient knowledge of all aspects of the organization. To minimize survey burden, it is ideal to ask unique questions of each member of the leadership team in areas of their expertise. However, this risks substantial missing data if all eligible members of the organization do not respond to the survey. Nursing home administrators (NHA) and directors of nursing (DoN) play important roles in the leadership of long-term care facilities. Surveys were administered to NHAs and DoNs from a random, nationally representative sample of U.S. nursing homes about the impact of state policies, market forces, and organizational factors that impact provider performance and residents' outcomes. Responses were obtained from a total of 2,686 facilities (response rate [RR] = 66.6%) in which at least one individual completed the questionnaire and 1,693 facilities (RR = 42.0%) in which both providers participated. No evidence of nonresponse bias was detected. A high-quality representative sample of two providers in a long-term care facility can be obtained. It is possible to optimize data collection by obtaining unique information about the organization from each provider while minimizing the number of items asked of each individual. However, sufficient resources must be available for follow-up to nonresponders with particular attention paid to lower resourced, lower quality facilities caring for higher acuity residents in highly competitive nursing home markets. © The Author(s) 2014.

Surveying Multiple Health Professional Team Members within Institutional Settings: An Example from the Nursing Home Industry

PubMed Central

Clark, Melissa A.; Roman, Anthony; Rogers, Michelle L.; Tyler, Denise A.; Mor, Vincent

2015-01-01

Quality improvement and cost containment initiatives in health care increasingly involve interdisciplinary teams of providers. To understand organizational functioning, information is often needed from multiple members of a leadership team since no one person may have sufficient knowledge of all aspects of the organization. To minimize survey burden, it is ideal to ask unique questions of each member of the leadership team in areas of their expertise. However, this risks substantial missing data if all eligible members of the organization do not respond to the survey. Nursing Home Administrators (NHA) and Directors of Nursing (DoN) play important roles in the leadership of long-term care facilities. Surveys were administered to NHAs and DoNs from a random, nationally-representative sample of U.S. nursing homes about the impact of state policies, market forces, and organizational factors that impact provider performance and residents’ outcomes. Responses were obtained from a total of 2686 facilities [Response Rate=66.6%] in which at least one individual completed the questionnaire and 1693 facilities [Response Rate=42.0%] in which both providers participated. No evidence of non-response bias was detected. A high-quality representative sample of two providers in a long-term care facility can be obtained. It is possible to optimize data collection by obtaining unique information about the organization from each provider while minimizing the number of items asked of each individual. However, sufficient resources must be available for follow-up to non-responders with particular attention paid to lower resourced, lower quality facilities caring for higher acuity residents in highly competitive nursing home markets. PMID:24500999

Measuring the subjective: revisiting the psychometric properties of three rating scales that assess the acute effects of hallucinogens.

PubMed

Bouso, José Carlos; Pedrero-Pérez, Eduardo José; Gandy, Sam; Alcázar-Córcoles, Miguel Ángel

2016-09-01

In the present study we explored the psychometric properties of three widely used questionnaires to assess the subjective effects of hallucinogens: the Hallucinogen Rating Scale (HRS), the Mystical Experience Questionnaire (MEQ), and the Addiction Research Center Inventory (ARCI). These three questionnaires were administered to a sample of 158 subjects (100 men) after taking ayahuasca, a hallucinogen whose main active component is N,N-dimethyltryptamine (DMT). A confirmatory factorial study was conducted to check the adjustment of previous data obtained via theoretical proposals. When this was not possible, we used an exploratory factor analysis without restrictions, based on tetrachoric and polychoric matrices and correlations. Our results sparsely match the theoretical proposals of the authors, perhaps because previous studies have not always employed psychometric methods appropriate to the data obtained. However, these data should be considered preliminary, pending larger samples to confirm or reject the proposed structures obtained. It is crucial that instruments of sufficiently precise measurement are utilized to make sense of the information obtained in the study of the subjective effects of psychedelic drugs. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Influence of Multidimensionality on Convergence of Sampling in Protein Simulation

NASA Astrophysics Data System (ADS)

Metsugi, Shoichi

2005-06-01

We study the problem of convergence of sampling in protein simulation originating in the multidimensionality of protein’s conformational space. Since several important physical quantities are given by second moments of dynamical variables, we attempt to obtain the time of simulation necessary for their sufficient convergence. We perform a molecular dynamics simulation of a protein and the subsequent principal component (PC) analysis as a function of simulation time T. As T increases, PC vectors with smaller amplitude of variations are identified and their amplitudes are equilibrated before identifying and equilibrating vectors with larger amplitude of variations. This sequential identification and equilibration mechanism makes protein simulation a useful method although it has an intrinsic multidimensional nature.

Bi-PROF

PubMed Central

Gries, Jasmin; Schumacher, Dirk; Arand, Julia; Lutsik, Pavlo; Markelova, Maria Rivera; Fichtner, Iduna; Walter, Jörn; Sers, Christine; Tierling, Sascha

2013-01-01

The use of next generation sequencing has expanded our view on whole mammalian methylome patterns. In particular, it provides a genome-wide insight of local DNA methylation diversity at single nucleotide level and enables the examination of single chromosome sequence sections at a sufficient statistical power. We describe a bisulfite-based sequence profiling pipeline, Bi-PROF, which is based on the 454 GS-FLX Titanium technology that allows to obtain up to one million sequence stretches at single base pair resolution without laborious subcloning. To illustrate the performance of the experimental workflow connected to a bioinformatics program pipeline (BiQ Analyzer HT) we present a test analysis set of 68 different epigenetic marker regions (amplicons) in five individual patient-derived xenograft tissue samples of colorectal cancer and one healthy colon epithelium sample as a control. After the 454 GS-FLX Titanium run, sequence read processing and sample decoding, the obtained alignments are quality controlled and statistically evaluated. Comprehensive methylation pattern interpretation (profiling) assessed by analyzing 102-104 sequence reads per amplicon allows an unprecedented deep view on pattern formation and methylation marker heterogeneity in tissues concerned by complex diseases like cancer. PMID:23803588

Sequim Marine Research Laboratory routine environmental measurements during CY-1977

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

Fix, J.J.; Blumer, P.J.

1978-06-01

Beginning in 1976, a routine environmental program was established at the Marine Research Laboratory (MRL) at Sequim, Washington. The program is intended to demonstrate the negligible impact of current MRL operations on the surrounding environs and to provide baseline data through which any cumulative impact could be detected. The sampling frequency is greater during the first 2 years of the program to provide sufficient initial information to allow reliable estimates of observed radionuclide concentrations and to construct a long-term sampling program. The program is designed, primarily, to determine levels of radioactivity present in selected biota in Sequim Bay. The biotamore » were selected because of their presence near the laboratory and their capacity to concentrate trace elements. Other samples were obtained to determine the radionuclides in Sequim Bay and laboratory drinking water, as well as the ambient radiation exposure levels and surface deposition of fallout radionuclides for the laboratory area. Appendix A provides a summary of the analytical methods used. The present document includes data obtained during CY 1977 in addition to CY-1976 data published previously.« less

Spirolit-2 instrument used to test pulmonary ventilation

NASA Astrophysics Data System (ADS)

Zhuravlev, V. V.

1985-02-01

At the present time, the Spirolit-2 automatic analyzer of main respiratory gases, of the Junkalor Dessau firm, is used to examine parameters of gas exchange, levels of energy expended by man and animals with different degrees of activity. However, the capabilities of this model of the instrument are limited. A method of determining pulmonary ventilation with use of the Spirolit-2 is described. An additional exhalation valve is built into a valve box to which an anesthesia machine rubber bag is attached. Samples are collected into another bag concurrently with the usual tests on the Spirolit-2 instrument. Four to five minutes are sufficient to obtain stable parameters at relative rest of oxygen uptake, determine carbon dioxide output per minute and collect samples in for analysis of exhaled air. The proposed method can furnish information about the dynamics of development of respiratory function of the lungs at virtually any moment with a constant physical load. For this, there must be spare bags to collect samples. Stage-by-stage data can be obtained analogously as to ventilation volume during a step test while determining maximum oxygen uptake.

A 'feather-trap' for collecting DNA samples from birds.

PubMed

Maurer, Golo; Beck, Nadeena; Double, Michael C

2010-01-01

Genetic analyses of birds are usually based on DNA extracted from a blood sample. For some species, however, obtaining blood samples is difficult because they are sensitive to handling, pose a conservation or animal welfare concern, or evade capture. In such cases, feathers obtained from live birds in the wild can provide an alternative source of DNA. Here, we provide the first description and evaluation of a 'feather-trap', consisting of small strips of double-sided adhesive tape placed close to a nest with chicks, as a simple, inexpensive and minimally invasive method to collect feathers. The feather-trap was tested in tropical conditions on the Australian pheasant coucal (Centropus phasianinus). None of the 12 pairs of coucals on which the feather-trap was used abandoned the nest, and feeding rates did not differ from those of birds not exposed to a feather-trap. On average, 4.2 feathers were collected per trap over 2-5 days and, despite exposure to monsoonal rain, DNA was extracted from 71.4% of samples, albeit at low concentrations. The amount of genomic DNA extracted from each feather was sufficient to reliably genotype individuals at up to five microsatellite loci for parentage analysis. We show that a feather-trap can provide a reliable alternative for obtaining DNA in species where taking blood is difficult. It may also prove useful for collecting feather samples for other purposes, e.g. stable-isotope analysis. © 2009 Blackwell Publishing Ltd.

Preparing Monodisperse Macromolecular Samples for Successful Biological Small-Angle X-ray and Neutron Scattering Experiments

PubMed Central

Jeffries, Cy M.; Graewert, Melissa A.; Blanchet, Clément E.; Langley, David B.; Whitten, Andrew E.; Svergun, Dmitri I

2017-01-01

Small-angle X-ray and neutron scattering (SAXS and SANS) are techniques used to extract structural parameters and determine the overall structures and shapes of biological macromolecules, complexes and assemblies in solution. The scattering intensities measured from a sample contain contributions from all atoms within the illuminated sample volume including the solvent and buffer components as well as the macromolecules of interest. In order to obtain structural information, it is essential to prepare an exactly matched solvent blank so that background scattering contributions can be accurately subtracted from the sample scattering to obtain the net scattering from the macromolecules in the sample. In addition, sample heterogeneity caused by contaminants, aggregates, mismatched solvents, radiation damage or other factors can severely influence and complicate data analysis so it is essential that the samples are pure and monodisperse for the duration of the experiment. This Protocol outlines the basic physics of SAXS and SANS and reveals how the underlying conceptual principles of the techniques ultimately ‘translate’ into practical laboratory guidance for the production of samples of sufficiently high quality for scattering experiments. The procedure describes how to prepare and characterize protein and nucleic acid samples for both SAXS and SANS using gel electrophoresis, size exclusion chromatography and light scattering. Also included are procedures specific to X-rays (in-line size exclusion chromatography SAXS) and neutrons, specifically preparing samples for contrast matching/variation experiments and deuterium labeling of proteins. PMID:27711050

Photo-induced ultrasound microscopy for photo-acoustic imaging of non-absorbing specimens

NASA Astrophysics Data System (ADS)

Tcarenkova, Elena; Koho, Sami V.; Hänninen, Pekka E.

2017-08-01

Photo-Acoustic Microscopy (PAM) has raised high interest in in-vivo imaging due to its ability to preserve the near-diffraction limited spatial resolution of optical microscopes, whilst extending the penetration depth to the mm-range. Another advantage of PAM is that it is a label-free technique - any substance that absorbs PAM excitation laser light can be viewed. However, not all sample structures desired to be observed absorb sufficiently to provide contrast for imaging. This work describes a novel imaging method that makes it possible to visualize optically transparent samples that lack intrinsic photo-acoustic contrast, without the addition of contrast agents. A thin, strongly light absorbing layer next to sample is used to generate a strong ultrasonic signal. This signal, when recorded from opposite side, contains ultrasonic transmission information of the sample and thus the method can be used to obtain an ultrasound transmission image on any PAM.

Multi-edge X-ray absorption spectroscopy study of road dust samples from a traffic area of Venice using stoichiometric and environmental references

NASA Astrophysics Data System (ADS)

Valotto, Gabrio; Cattaruzza, Elti; Bardelli, Fabrizio

2017-02-01

The appropriate selection of representative pure compounds to be used as reference is a crucial step for successful analysis of X-ray absorption near edge spectroscopy (XANES) data, and it is often not a trivial task. This is particularly true when complex environmental matrices are investigated, being their elemental speciation a priori unknown. In this paper, an investigation on the speciation of Cu, Zn, and Sb based on the use of conventional (stoichiometric compounds) and non-conventional (environmental samples or relevant certified materials) references is explored. This method can be useful in when the effectiveness of XANES analysis is limited because of the difficulty in obtaining a set of references sufficiently representative of the investigated samples. Road dust samples collected along the bridge connecting Venice to the mainland were used to show the potentialities and the limits of this approach.

Broad Surveys of DNA Viral Diversity Obtained through Viral Metagenomics of Mosquitoes

PubMed Central

Ng, Terry Fei Fan; Willner, Dana L.; Lim, Yan Wei; Schmieder, Robert; Chau, Betty; Nilsson, Christina; Anthony, Simon; Ruan, Yijun; Rohwer, Forest; Breitbart, Mya

2011-01-01

Viruses are the most abundant and diverse genetic entities on Earth; however, broad surveys of viral diversity are hindered by the lack of a universal assay for viruses and the inability to sample a sufficient number of individual hosts. This study utilized vector-enabled metagenomics (VEM) to provide a snapshot of the diversity of DNA viruses present in three mosquito samples from San Diego, California. The majority of the sequences were novel, suggesting that the viral community in mosquitoes, as well as the animal and plant hosts they feed on, is highly diverse and largely uncharacterized. Each mosquito sample contained a distinct viral community. The mosquito viromes contained sequences related to a broad range of animal, plant, insect and bacterial viruses. Animal viruses identified included anelloviruses, circoviruses, herpesviruses, poxviruses, and papillomaviruses, which mosquitoes may have obtained from vertebrate hosts during blood feeding. Notably, sequences related to human papillomaviruses were identified in one of the mosquito samples. Sequences similar to plant viruses were identified in all mosquito viromes, which were potentially acquired through feeding on plant nectar. Numerous bacteriophages and insect viruses were also detected, including a novel densovirus likely infecting Culex erythrothorax. Through sampling insect vectors, VEM enables broad survey of viral diversity and has significantly increased our knowledge of the DNA viruses present in mosquitoes. PMID:21674005

A LOW-E MAGIC ANGLE SPINNING PROBE FOR BIOLOGICAL SOLID STATE NMR AT 750 MHz

PubMed Central

McNeill, Seth A.; Gor’kov, Peter L.; Shetty, Kiran; Brey, William W.; Long, Joanna R.

2009-01-01

Crossed-coil NMR probes are a useful tool for reducing sample heating for biological solid state NMR. In a crossed-coil probe, the higher frequency 1H field, which is the primary source of sample heating in conventional probes, is produced by a separate low-inductance resonator. Because a smaller driving voltage is required, the electric field across the sample and the resultant heating is reduced. In this work we describe the development of a magic angle spinning (MAS) solid state NMR probe utilizing a dual resonator. This dual resonator approach, referred to as “Low-E,” was originally developed to reduce heating in samples of mechanically aligned membranes. The study of inherently dilute systems, such as proteins in lipid bilayers, via MAS techniques requires large sample volumes at high field to obtain spectra with adequate signal-to-noise ratio under physiologically relevant conditions. With the Low-E approach, we are able to obtain homogeneous and sufficiently strong radiofrequency fields for both 1H and 13C frequencies in a 4 mm probe with a 1H frequency of 750 MHz. The performance of the probe using windowless dipolar recoupling sequences is demonstrated on model compounds as well as membrane embedded peptides. PMID:19138870

Analytical Parameters of an Amperometric Glucose Biosensor for Fast Analysis in Food Samples.

PubMed

Artigues, Margalida; Abellà, Jordi; Colominas, Sergi

2017-11-14

Amperometric biosensors based on the use of glucose oxidase (GOx) are able to combine the robustness of electrochemical techniques with the specificity of biological recognition processes. However, very little information can be found in literature about the fundamental analytical parameters of these sensors. In this work, the analytical behavior of an amperometric biosensor based on the immobilization of GOx using a hydrogel (Chitosan) onto highly ordered titanium dioxide nanotube arrays (TiO₂NTAs) has been evaluated. The GOx-Chitosan/TiO₂NTAs biosensor showed a sensitivity of 5.46 μA·mM -1 with a linear range from 0.3 to 1.5 mM; its fundamental analytical parameters were studied using a commercial soft drink. The obtained results proved sufficient repeatability (RSD = 1.9%), reproducibility (RSD = 2.5%), accuracy (95-105% recovery), and robustness (RSD = 3.3%). Furthermore, no significant interferences from fructose, ascorbic acid and citric acid were obtained. In addition, the storage stability was further examined, after 30 days, the GOx-Chitosan/TiO₂NTAs biosensor retained 85% of its initial current response. Finally, the glucose content of different food samples was measured using the biosensor and compared with the respective HPLC value. In the worst scenario, a deviation smaller than 10% was obtained among the 20 samples evaluated.

Use of buccal swabs for sampling DNA from nestling and adult birds

USGS Publications Warehouse

Handel, Colleen M.; Pajot, Lisa; Talbot, Sandra L.; Sage, George K.

2006-01-01

We evaluated the feasibility and efficiency of using swabs to collect buccal epithelial cells fromsmall (2‐ to 13‐g) birds as a source of DNA for genetic studies. We used commercially available buccal swab kits to collect samples from 42 adult and 39 nestling (4‐ to 8‐day‐old) black‐capped chickadees (Poecile atricapillus) and from6 4‐day‐old nestling boreal chickadees (P. hudsonica). We compared DNA from buccal epithelial samples to that fromblood samples from the same individuals. We extracted sufficient quantities of DNA for analysis from all buccalsamples, and samples remained viable even after being stored in original plastic sampling tubes at room temperature for up to 18 months. Yields were equivalent whether extracted using the proprietary quick‐extraction solution provided with buccal swab kits or using a salt‐extraction process with inexpensive reagents. Yields of DNA from buccal samples were consistently lower than those from blood samples, but quantities were sufficient for all analyses. Assignment of sex, based on DNA extracted from paired buccal and blood samples, was identical for all 87 birds. We found no difference in the genotypes obtained from buccal and blood samples for 12 individuals tested using 5 microsatellite loci and found perfect concordance in sequencing of an 823‐base‐pair segment within the control region of mitochondrial DNA for 7 individuals tested. Use of buccal swabs is highly recommended as a rapid, noninvasive technique for sampling avian genomic DNA, especially for extremely young altricial nestlings or small‐bodied adults, or for any birds for which blood sampling may be impossible or stressful.

Reference samples for the earth sciences

USGS Publications Warehouse

Flanagan, F.J.

1974-01-01

A revised list of reference samples of interest to geoscientists has been extended to include samples for the agronomist, the archaeologist and the environmentalist. In addition to the source from which standard samples may be obtained, references or pertinent notes for some samples are included. The number of rock reference samples is now almost adequate, and the variety of ore samples will soon be sufficient. There are very few samples for microprobe work. Oil shales will become more important because of the outlook for world petroleum resources. The dryland equivalent of a submarine basalt might be useful in studies of sea-floor spreading and of the geochemistry of basalts. The Na- and K-feldspars of BCS (British Chemical Standards-Bureau of Analysed Samples), NBS (National Bureau of Standards), and ANRT (Association Kationale de la Recherche Technique) could serve as trace-element standards if such data were available. Similarly, the present NBS flint and plastic clays, as well as their predecessors, might be useful for archaeological pottery studies. The International Decade for Ocean Exploration may stimulate the preparation of ocean-water standards for trace elements or pollutants and a standard for manganese nodules. ?? 1974.

The High Prevalence of Vitamin D Insufficiency in Cord Blood in Calgary, Alberta (APrON-D Study).

PubMed

Aghajafari, Fariba; Field, Catherine J; Kaplan, Bonnie J; Maggiore, Jack A; O'Beirne, Maeve; Hanley, David A; Eliasziw, Misha; Dewey, Deborah; Ross, Sue; Rabi, Doreen

2017-05-01

Vitamin D is important in promoting healthy pregnancy and fetal development. We undertook this study to measure 25-hydroxyvitamin D in maternal and cord blood and to identify maternal factors related to vitamin D status in Calgary. Blood samples collected at the time of delivery from the Alberta Pregnancy Outcomes and Nutrition study cohort (ApronStudy.ca) participants were processed for plasma and assayed using liquid chromatography mass spectrometry methodology for 25(OH)D 3 . Ninety-two pairs of maternal and cord blood samples were obtained. The prevalence of 25(OH)D 3 insufficiency-25(OH)D 3 <75 nmol/L-was 38% and 80% in women and neonates, respectively. Vitamin D supplementation was the only clinical factor associated with 25(OH)D 3 sufficiency, and the odds of sufficiency were 3.75 (95% CI 1.00 to 14.07) higher for women and 5.27 (95% CI 1.37 to 20.27) when over 2000 IU/day were used. Using liquid chromatography mass spectrometry, we demonstrated a very high prevalence of vitamin D insufficiency in cord blood and that the use of high dose vitamin D was associated with greater odds of sufficiency in pregnant women and cord blood in Alberta. Copyright © 2017 The Society of Obstetricians and Gynaecologists of Canada/La Société des obstétriciens et gynécologues du Canada. Published by Elsevier Inc. All rights reserved.

Facial expression reconstruction on the basis of selected vertices of triangle mesh

NASA Astrophysics Data System (ADS)

Peszor, Damian; Wojciechowska, Marzena

2016-06-01

Facial expression reconstruction is an important issue in the field of computer graphics. While it is relatively easy to create an animation based on meshes constructed through video recordings, this kind of high-quality data is often not transferred to another model because of lack of intermediary, anthropometry-based way to do so. However, if a high-quality mesh is sampled with sufficient density, it is possible to use obtained feature points to encode the shape of surrounding vertices in a way that can be easily transferred to another mesh with corresponding feature points. In this paper we present a method used for obtaining information for the purpose of reconstructing changes in facial surface on the basis of selected feature points.

Injection current minimization of InAs/InGaAs quantum dot laser by optimization of its active region and reflectivity of laser cavity edges

NASA Astrophysics Data System (ADS)

Korenev, V. V.; Savelyev, A. V.; Zhukov, A. E.; Maximov, M. V.

2015-11-01

The ways to optimize key parameters of active region and edge reflectivity of edge- emitting semiconductor quantum dot laser are provided. It is shown that in the case of optimal cavity length and sufficiently large dispersion lasing spectrum of a given width can be obtained at injection current up to an order of magnitude lower in comparison to non-optimized sample. The influence of internal loss and edge reflection is also studied in details.

Structural difference rule for amorphous alloy formation by ion mixing

NASA Technical Reports Server (NTRS)

Liu, B.-X.; Johnson, W. L.; Nicolet, M.A.; Lau, S. S.

1983-01-01

A rule is formulated which establishes a sufficient condition that an amorphous binary alloy will be formed by ion mixing of multilayered samples when the two constituent metals are of different crystalline structure, regardless of their atomic sizes and electronegativities. The rule is supported by the experimental results obtained on six selected binary metal systems, as well as by the previous data reported in the literature. The amorphization mechanism is discussed in terms of the competition between two different structures resulting in frustration of the crystallization process.

Hydrogen as an Auxiliary Fuel in Compression-Ignition Engines

NASA Technical Reports Server (NTRS)

Gerrish, Harold C; Foster, H

1936-01-01

An investigation was made to determine whether a sufficient amount of hydrogen could be efficiently burned in a compression-ignition engine to compensate for the increase of lift of an airship due to the consumption of the fuel oil. The performance of a single-cylinder four-stroke-cycle compression-ignition engine operating on fuel oil alone was compared with its performance when various quantities of hydrogen were inducted with the inlet air. Engine-performance data, indicator cards, and exhaust-gas samples were obtained for each change in engine-operating conditions.

Blood platelet counts, morphology and morphometry in lions, Panthera leo.

PubMed

Du Plessis, L

2009-09-01

Due to logistical problems in obtaining sufficient blood samples from apparently healthy animals in the wild in order to establish normal haematological reference values, only limited information regarding the blood platelet count and morphology of free-living lions (Panthera leo) is available. This study provides information on platelet counts and describes their morphology with particular reference to size in two normal, healthy and free-ranging lion populations. Blood samples were collected from a total of 16 lions. Platelet counts, determined manually, ranged between 218 and 358 x 10(9)/l. Light microscopy showed mostly activated platelets of various sizes with prominent granules. At the ultrastructural level the platelets revealed typical mammalian platelet morphology. However, morphometric analysis revealed a significant difference (P < 0.001) in platelet size between the two groups of animals. Basic haematological information obtained in this study may be helpful in future comparative studies between animals of the same species as well as in other felids.

Silicon drift detectors as a tool for time-resolved fluorescence XAFS on low-concentrated samples in catalysis.

PubMed

Kappen, Peter; Tröger, Larc; Materlik, Gerhard; Reckleben, Christian; Hansen, Karsten; Grunwaldt, Jan-Dierk; Clausen, Bjerne S

2002-07-01

A silicon drift detector (SDD) was used for ex situ and time-resolved in situ fluorescence X-ray absorption fine structure (XAFS) on low-concentrated catalyst samples. For a single-element and a seven-element SDD the energy resolution and the peak-to-background ratio were verified at high count rates, sufficient for fluorescence XAFS. An experimental set-up including the seven-element SDD without any cooling and an in situ cell with gas supply and on-line gas analysis was developed. With this set-up the reduction and oxidation of a zeolite supported catalyst containing 0.3 wt% platinum was followed by fluorescence near-edge scans with a time resolution of 10 min each. From ex situ experiments on low-concentrated platinum- and gold-based catalysts fluorescence XAFS scans could be obtained with sufficient statistical quality for a quantitative analysis. Structural information on the gold and platinum particles could be extracted by both the Fourier transforms and the near-edge region of the XAFS spectra. Moreover, it was found that with the seven-element SDD concentrations of the element of interest as low as 100 ppm can be examined by fluorescence XAFS.

Characterization and Distribution of Lunar Mare Basalt Types Using Remote Sensing Techniques. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Pieters, C.

1977-01-01

The types of basal to be found on the moon were identified using reflectance spectra from a variety of lunar mare surfaces and craters as well as geochemical interpretations of laboratory measurements of reflectance from lunar, terrestrial, and meteoritic samples. Findings indicate that major basaltic units are not represented in lunar sample collections. The existence of late stage high titanium basalts is confirmed. All maria contain lateral variations of compositionally heterogenous basalts; some are vertically inhomogenous with distinctly different subsurface composition. Some basalt types are spectrally gradational, suggesting minor variations in composition. Mineral components of unsampled units can be defined if spectra are obtained with sufficient spectral coverage (.3 to 2.5 micron m) and spatial resolution (approximating .5 km).

A High-Precision Counter Using the DSP Technique

DTIC Science & Technology

2004-09-01

DSP is not good enough to process all the 1-second samples. The cache memory is also not sufficient to store all the sampling data. So we cut the...sampling number in a cycle is not good enough to achieve an accuracy less than 2×10-11. For this reason, a correlation operation is performed for... not good enough to process all the 1-second samples. The cache memory is also not sufficient to store all the sampling data. We will solve this

Preparation and Respirometric Assessment of Mitochondria Isolated from Skeletal Muscle Tissue Obtained by Percutaneous Needle Biopsy

PubMed Central

Bharadwaj, Manish S.; Tyrrell, Daniel J.; Lyles, Mary F.; Demons, Jamehl L.; Rogers, George W.; Molina, Anthony J. A.

2015-01-01

Respirometric profiling of isolated mitochondria is commonly used to investigate electron transport chain function. We describe a method for obtaining samples of human Vastus lateralis, isolating mitochondria from minimal amounts of skeletal muscle tissue, and plate based respirometric profiling using an extracellular flux (XF) analyzer. Comparison of respirometric profiles obtained using 1.0, 2.5 and 5.0 μg of mitochondria indicate that 1.0 μg is sufficient to measure respiration and that 5.0 μg provides most consistent results based on comparison of standard errors. Western blot analysis of isolated mitochondria for mitochondrial marker COX IV and non-mitochondrial tissue marker GAPDH indicate that there is limited non-mitochondrial contamination using this protocol. The ability to study mitochondrial respirometry in as little as 20 mg of muscle tissue allows users to utilize individual biopsies for multiple study endpoints in clinical research projects. PMID:25741892

Evaluation of residual uranium contamination in the dirt floor of an abandoned metal rolling mill.

PubMed

Glassford, Eric; Spitz, Henry; Lobaugh, Megan; Spitler, Grant; Succop, Paul; Rice, Carol

2013-02-01

A single, large, bulk sample of uranium-contaminated material from the dirt floor of an abandoned metal rolling mill was separated into different types and sizes of aliquots to simulate samples that would be collected during site remediation. The facility rolled approximately 11,000 tons of hot-forged ingots of uranium metal approximately 60 y ago, and it has not been used since that time. Thirty small mass (≈ 0.7 g) and 15 large mass (≈ 70 g) samples were prepared from the heterogeneously contaminated bulk material to determine how measurements of the uranium contamination vary with sample size. Aliquots of bulk material were also resuspended in an exposure chamber to produce six samples of respirable particles that were obtained using a cascade impactor. Samples of removable surface contamination were collected by wiping 100 cm of the interior surfaces of the exposure chamber with 47-mm-diameter fiber filters. Uranium contamination in each of the samples was measured directly using high-resolution gamma ray spectrometry. As expected, results for isotopic uranium (i.e., U and U) measured with the large-mass and small-mass samples are significantly different (p < 0.001), and the coefficient of variation (COV) for the small-mass samples was greater than for the large-mass samples. The uranium isotopic concentrations measured in the air and on the wipe samples were not significantly different and were also not significantly different (p > 0.05) from results for the large- or small-mass samples. Large-mass samples are more reliable for characterizing heterogeneously distributed radiological contamination than small-mass samples since they exhibit the least variation compared to the mean. Thus, samples should be sufficiently large in mass to insure that the results are truly representative of the heterogeneously distributed uranium contamination present at the facility. Monitoring exposure of workers and the public as a result of uranium contamination resuspended during site remediation should be evaluated using samples of sufficient size and type to accommodate the heterogeneous distribution of uranium in the bulk material.

Recycle of Zirconium from Used Nuclear Fuel Cladding: A Major Element of Waste Reduction

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

Collins, Emory D; DelCul, Guillermo D; Terekhov, Dmitri

2011-01-01

Feasibility tests were initiated to determine if the zirconium in commercial used nuclear fuel (UNF) cladding can be recovered in sufficient purity to permit re-use, and if the recovery process can be operated economically. Initial tests are being performed with unirradiated, non-radioactive samples of various types of Zircaloy materials that are used in UNF cladding to develop the recovery process and determine the degree of purification that can be obtained. Early results indicate that quantitative recovery can be accomplished and product contamination with alloy constituents can be controlled sufficiently to meet purification requirements. Future tests with actual radioactive UNF claddingmore » are planned. The objective of current research is to determine the feasibility of recovery and recycle of zirconium from used fuel cladding wastes. Zircaloy cladding, which contains 98+% of hafnium-free zirconium, is the second largest mass, on average {approx}25 wt %, of the components in used U.S. light-water-reactor fuel assemblies. Therefore, recovery and recycle of the zirconium would enable a large reduction in geologic waste disposal for advanced fuel cycles. Current practice is to compact or grout the cladding waste and store it for subsequent disposal in a geologic repository. This paper describes results of initial tests being performed with unirradiated, non-radioactive samples of various types of Zircaloy materials that are used in UNF cladding to develop the recovery process and determine the degree of purification that can be obtained. Future tests with actual radioactive UNF cladding are planned.« less

Motions and entropies in proteins as seen in NMR relaxation experiments and molecular dynamics simulations.

PubMed

Allnér, Olof; Foloppe, Nicolas; Nilsson, Lennart

2015-01-22

Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory data. NMR relaxation is the most widely used experimental method to obtain data on dynamics of proteins, but it is limited to relatively short timescales and to motions of backbone amides or in some cases (13)C-H vectors. By relating the experimental data to the all-atom picture obtained in molecular dynamics simulations, valuable insights on the interpretation of the experiment can be gained. We have estimated the internal dynamics and their timescales by calculating the generalized order parameters (O) for different time windows. We then calculate the quasiharmonic entropy (S) and compare it to the entropy calculated from the NMR-derived generalized order parameter of the amide vectors. Special emphasis is put on characterizing dynamics that are not expressed through the motions of the amide group. The NMR and MD methods suffer from complementary limitations, with NMR being restricted to local vectors and dynamics on a timescale determined by the rotational diffusion of the solute, while in simulations, it may be difficult to obtain sufficient sampling to ensure convergence of the results. We also evaluate the amount of sampling obtained with molecular dynamics simulations and how it is affected by the length of individual simulations, by clustering of the sampled conformations. We find that two structural turns act as hinges, allowing the α helix between them to undergo large, long timescale motions that cannot be detected in the time window of the NMR dipolar relaxation experiments. We also show that the entropy obtained from the amide vector does not account for correlated motions of adjacent residues. Finally, we show that the sampling in a total of 100 ns molecular dynamics simulation can be increased by around 50%, by dividing the trajectory into 10 replicas with different starting velocities.

Pilot Metabolome-Wide Association Study of Benzo(a)pyrene in Serum from Military Personnel

PubMed Central

Walker, Douglas I.; Pennell, Kurt D.; Uppal, Karan; Xia, Xiaoyan; Hopke, Philip K.; Utell, Mark J.; Phipps, Richard P.; Sime, Patricia J.; Rohrbeck, Patricia; Mallon, COL Timothy M.; Jones, Dean P.

2016-01-01

Objective A pilot study was conducted to test the feasibility of using Department of Defense Serum Repository (DoDSR) samples to study health and exposure-related effects. Methods Thirty unidentified human serum samples were obtained from the DoDSR and analyzed for normal serum metabolites with high-resolution mass spectrometry and serum levels of free benzo(a)pyrene (BaP) by gas chromatography-mass spectrometry. Metabolic associations with BaP were determined using a metabolome wide association study (MWAS) and metabolic pathway enrichment. Results The serum analysis detected normal ranges of glucose, selected amino acids, fatty acids, and creatinine. Free BaP was detected in a broad concentration range. MWAS of BaP showed associations with lipids, fatty acids, and sulfur amino acid metabolic pathways. Conclusion The results show the DoDSR samples are of sufficient quality for chemical profiling of DoD personnel. PMID:27501104

Pilot Metabolome-Wide Association Study of Benzo(a)pyrene in Serum From Military Personnel.

PubMed

Walker, Douglas I; Pennell, Kurt D; Uppal, Karan; Xia, Xiaoyan; Hopke, Philip K; Utell, Mark J; Phipps, Richard P; Sime, Patricia J; Rohrbeck, Patricia; Mallon, Col Timothy M; Jones, Dean P

2016-08-01

A pilot study was conducted to test the feasibility of using Department of Defense Serum Repository (DoDSR) samples to study health and exposure-related effects. Thirty unidentified human serum samples were obtained from the DoDSR and analyzed for normal serum metabolites with high-resolution mass spectrometry and serum levels of free benzo(a)pyrene (BaP) by gas chromatography-mass spectrometry. Metabolic associations with BaP were determined using a metabolome-wide association study (MWAS) and metabolic pathway enrichment. The serum analysis detected normal ranges of glucose, selected amino acids, fatty acids, and creatinine. Free BaP was detected in a broad concentration range. MWAS of BaP showed associations with lipids, fatty acids, and sulfur amino acid metabolic pathways. The results show that the DoDSR samples are of sufficient quality for chemical profiling of DoD personnel.

Endoductal tissue sampling of biliary strictures through endoscopic retrograde cholangiopan creatography (ERCP).

PubMed

Pugliese, V; Antonelli, G; Vincenti, M; Gatteschi, B

1997-01-01

Pathological proof of malignant in biliary strictures is useful in the preoperative setting as it helps define therapeutic planning and prognosis, and reduces the length of the subsequent surgical intervention. However, it is difficult to obtain. The aim of this study was to evaluate the yield of histological and cytological examination of endobiliary samples obtained during endoscopic retrograde cholangiopancreatography (ERCP). Endobiliary forceps biopsy and brush cytology were performed during ERCP examination in 52 consecutive patients, 36 with malignant and 16 with benign strictures. Histology and cytology turned out to have the same sensitivity (53%). The gain in sensitivity achieved by combining the two techniques was limited, reaching a value of 61%. The specificity, however, was 100% for both methods. Most of the few complications observed were due to sphincterotomy and subsided spontaneously or with medical treatment. However, one patient experienced a serous complication and chose to be treated by surgical intervention. The complication was caused by forceps biopsy. This study shows that 1) sampling of biliary strictures during ERCP is the primary approach to tissue diagnosis; 2) brush cytology alone is sufficient in clinical practice; 3) forceps biopsy must always be used to sample intra-ampullary strictures but should be considered as a secondary step to sample strictures located more proximally, in the bile ducta, if previous cytology was negative.

Using paleomagnetism to uncover long-runout pyroclastic flows

NASA Astrophysics Data System (ADS)

Lerner, G. A.; Cronin, S. J.; Turner, G. M.

2017-12-01

Understanding the conditions under which volcanic deposits were emplaced is vital to better preparing for hazards at an active stratovolcano. The coherence of paleomagnetic directions in different parts of the blocking temperature spectrum between the clasts of mass flow deposits has proven to be a useful tool for ascertaining emplacement temperatures. These temperature estimates can help in distinguishing between hot pyroclastic density currents (PDCs) and cold lahars. In the case of more clast-poor distal deposits, however, it can be difficult to obtain sufficient clast material for effective paleomagnetic study. In this study, the problem was remedied by using oriented and strengthened samples of matrix material from mass flow deposits in the 11,500 BP Warea Formation from Mt. Taranaki, New Zealand. Paleomagnetic data from matrix samples was used to supplement the limited data obtained from the traditional clast analysis in order to determine the emplacement temperature of the deposits. Comparison of paleomagnetic directions obtained from matrix samples at several sites within the Warea Formation revealed it as a PDC with matrix temperatures over 200°C and clasts reaching temperatures of up to 410°C at the time of deposition. This discovery of hot PDC deposits at distances >20 km from the summit of the volcano extends their known range at this volcano by 5 km. These findings will significantly change the hazard mapping and emergency planning for this region.

Three-dimensional locations of gold-labeled proteins in a whole mount eukaryotic cell obtained with 3nm precision using aberration-corrected scanning transmission electron microscopy.

PubMed

Dukes, Madeline J; Ramachandra, Ranjan; Baudoin, Jean-Pierre; Gray Jerome, W; de Jonge, Niels

2011-06-01

Three-dimensional (3D) maps of proteins within the context of whole cells are important for investigating cellular function. However, 3D reconstructions of whole cells are challenging to obtain using conventional transmission electron microscopy (TEM). We describe a methodology to determine the 3D locations of proteins labeled with gold nanoparticles on whole eukaryotic cells. The epidermal growth factor receptors on COS7 cells were labeled with gold nanoparticles, and critical-point dried whole-mount cell samples were prepared. 3D focal series were obtained with aberration-corrected scanning transmission electron microscopy (STEM), without tilting the specimen. The axial resolution was improved with deconvolution. The vertical locations of the nanoparticles in a whole-mount cell were determined with a precision of 3nm. From the analysis of the variation of the axial positions of the labels we concluded that the cellular surface was ruffled. To achieve sufficient stability of the sample under electron beam irradiation during the recording of the focal series, the sample was carbon coated. A quantitative method was developed to analyze the stability of the ultrastructure after electron beam irradiation using TEM. The results of this study demonstrate the feasibility of using aberration-corrected STEM to study the 3D nanoparticle distribution in whole cells. Copyright © 2011 Elsevier Inc. All rights reserved.

Analytical Parameters of an Amperometric Glucose Biosensor for Fast Analysis in Food Samples

PubMed Central

2017-01-01

Amperometric biosensors based on the use of glucose oxidase (GOx) are able to combine the robustness of electrochemical techniques with the specificity of biological recognition processes. However, very little information can be found in literature about the fundamental analytical parameters of these sensors. In this work, the analytical behavior of an amperometric biosensor based on the immobilization of GOx using a hydrogel (Chitosan) onto highly ordered titanium dioxide nanotube arrays (TiO2NTAs) has been evaluated. The GOx–Chitosan/TiO2NTAs biosensor showed a sensitivity of 5.46 μA·mM−1 with a linear range from 0.3 to 1.5 mM; its fundamental analytical parameters were studied using a commercial soft drink. The obtained results proved sufficient repeatability (RSD = 1.9%), reproducibility (RSD = 2.5%), accuracy (95–105% recovery), and robustness (RSD = 3.3%). Furthermore, no significant interferences from fructose, ascorbic acid and citric acid were obtained. In addition, the storage stability was further examined, after 30 days, the GOx–Chitosan/TiO2NTAs biosensor retained 85% of its initial current response. Finally, the glucose content of different food samples was measured using the biosensor and compared with the respective HPLC value. In the worst scenario, a deviation smaller than 10% was obtained among the 20 samples evaluated. PMID:29135931

Three-dimensional locations of gold-labeled proteins in a whole mount eukaryotic cell obtained with 3 nm precision using aberration-corrected scanning transmission electron microscopy

PubMed Central

Dukes, Madeline J.; Ramachandra, Ranjan; Baudoin, Jean-Pierre; Jerome, W. Gray; de Jonge, Niels

2011-01-01

Three-dimensional (3D) maps of proteins within the context of whole cells are important for investigating cellular function. However, 3D reconstructions of whole cells are challenging to obtain using conventional transmission electron microscopy (TEM). We describe a methodology to determine the 3D locations of proteins labeled with gold nanoparticles on whole eukaryotic cells. The epidermal growth factor receptors on COS7 cells were labeled with gold nanoparticles, and critical-point dried whole-mount cell samples were prepared. 3D focal series were obtained with aberration-corrected scanning transmission electron microscopy (STEM), without tilting the specimen. The axial resolution was improved with deconvolution. The vertical locations of the nanoparticles in a whole-mount cell were determined with a precision of 3 nm. From the analysis of the variation of the axial positions of the labels we concluded that the cellular surface was ruffled. To achieve sufficient stability of the sample under the electron beam irradiation during the recording of the focal series, the sample was carbon coated. A quantitative method was developed to analyze the stability of the ultrastructure after electron beam irradiation using TEM. The results of this study demonstrate the feasibility of using aberration-corrected STEM to study the 3D nanoparticle distribution in whole cells. PMID:21440635

Level 1 environmental assessment performance evaluation. Final report jun 77-oct 78

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

Estes, E.D.; Smith, F.; Wagoner, D.E.

1979-02-01

The report gives results of a two-phased evaluation of Level 1 environmental assessment procedures. Results from Phase I, a field evaluation of the Source Assessment Sampling System (SASS), showed that the SASS train performed well within the desired factor of 3 Level 1 accuracy limit. Three sample runs were made with two SASS trains sampling simultaneously and from approximately the same sampling point in a horizontal duct. A Method-5 train was used to estimate the 'true' particulate loading. The sampling systems were upstream of the control devices to ensure collection of sufficient material for comparison of total particulate, particle sizemore » distribution, organic classes, and trace elements. Phase II consisted of providing each of three organizations with three types of control samples to challenge the spectrum of Level 1 analytical procedures: an artificial sample in methylene chloride, an artificial sample on a flyash matrix, and a real sample composed of the combined XAD-2 resin extracts from all Phase I runs. Phase II results showed that when the Level 1 analytical procedures are carefully applied, data of acceptable accuracy is obtained. Estimates of intralaboratory and interlaboratory precision are made.« less

Multi-edge X-ray absorption spectroscopy study of road dust samples from a traffic area of Venice using stoichiometric and environmental references.

PubMed

Valotto, Gabrio; Cattaruzza, Elti; Bardelli, Fabrizio

2017-02-15

The appropriate selection of representative pure compounds to be used as reference is a crucial step for successful analysis of X-ray absorption near edge spectroscopy (XANES) data, and it is often not a trivial task. This is particularly true when complex environmental matrices are investigated, being their elemental speciation a priori unknown. In this paper, an investigation on the speciation of Cu, Zn, and Sb based on the use of conventional (stoichiometric compounds) and non-conventional (environmental samples or relevant certified materials) references is explored. This method can be useful in when the effectiveness of XANES analysis is limited because of the difficulty in obtaining a set of references sufficiently representative of the investigated samples. Road dust samples collected along the bridge connecting Venice to the mainland were used to show the potentialities and the limits of this approach. Copyright © 2016 Elsevier B.V. All rights reserved.

Optimized measurement of radium-226 concentration in liquid samples with radon-222 emanation.

PubMed

Perrier, Frédéric; Aupiais, Jean; Girault, Frédéric; Przylibski, Tadeusz A; Bouquerel, Hélène

2016-06-01

Measuring radium-226 concentration in liquid samples using radon-222 emanation remains competitive with techniques such as liquid scintillation, alpha or mass spectrometry. Indeed, we show that high-precision can be obtained without air circulation, using an optimal air to liquid volume ratio and moderate heating. Cost-effective and efficient measurement of radon concentration is achieved by scintillation flasks and sufficiently long counting times for signal and background. More than 400 such measurements were performed, including 39 dilution experiments, a successful blind measurement of six reference test solutions, and more than 110 repeated measurements. Under optimal conditions, uncertainties reach 5% for an activity concentration of 100 mBq L(-1) and 10% for 10 mBq L(-1). While the theoretical detection limit predicted by Monte Carlo simulation is around 3 mBq L(-1), a conservative experimental estimate is rather 5 mBq L(-1), corresponding to 0.14 fg g(-1). The method was applied to 47 natural waters, 51 commercial waters, and 17 wine samples, illustrating that it could be an option for liquids that cannot be easily measured by other methods. Counting of scintillation flasks can be done in remote locations in absence of electricity supply, using a solar panel. Thus, this portable method, which has demonstrated sufficient accuracy for numerous natural liquids, could be useful in geological and environmental problems, with the additional benefit that it can be applied in isolated locations and in circumstances when samples cannot be transported. Copyright © 2016 Elsevier Ltd. All rights reserved.

Assessment of DNA extracted from FTA® cards for use on the Illumina iSelect BeadChip

PubMed Central

McClure, Matthew C; McKay, Stephanie D; Schnabel, Robert D; Taylor, Jeremy F

2009-01-01

Background As FTA® cards provide an ideal medium for the field collection of DNA we sought to assess the quality of genomic DNA extracted from this source for use on the Illumina BovineSNP50 iSelect BeadChip which requires unbound, relatively intact (fragment sizes ≥ 2 kb), and high-quality DNA. Bovine blood and nasal swab samples collected on FTA cards were extracted using the commercially available GenSolve kit with a minor modification. The call rate and concordance of genotypes from each sample were compared to those obtained from whole blood samples extracted by standard PCI extraction. Findings An ANOVA analysis indicated no significant difference (P > 0.72) in BovineSNP50 genotype call rate between DNA extracted from FTA cards by the GenSolve kit or extracted from whole blood by PCI. Two sample t-tests demonstrated that the DNA extracted from the FTA cards produced genotype call and concordance rates that were not different to those produced by assaying DNA samples extracted by PCI from whole blood. Conclusion We conclude that DNA extracted from FTA cards by the GenSolve kit is of sufficiently high quality to produce results comparable to those obtained from DNA extracted from whole blood when assayed by the Illumina iSelect technology. Additionally, we validate the use of nasal swabs as an alternative to venous blood or buccal samples from animal subjects for reliably producing high quality genotypes on this platform. PMID:19531223

Assessment of DNA extracted from FTA cards for use on the Illumina iSelect BeadChip.

PubMed

McClure, Matthew C; McKay, Stephanie D; Schnabel, Robert D; Taylor, Jeremy F

2009-06-16

As FTA cards provide an ideal medium for the field collection of DNA we sought to assess the quality of genomic DNA extracted from this source for use on the Illumina BovineSNP50 iSelect BeadChip which requires unbound, relatively intact (fragment sizes >or= 2 kb), and high-quality DNA. Bovine blood and nasal swab samples collected on FTA cards were extracted using the commercially available GenSolve kit with a minor modification. The call rate and concordance of genotypes from each sample were compared to those obtained from whole blood samples extracted by standard PCI extraction. An ANOVA analysis indicated no significant difference (P > 0.72) in BovineSNP50 genotype call rate between DNA extracted from FTA cards by the GenSolve kit or extracted from whole blood by PCI. Two sample t-tests demonstrated that the DNA extracted from the FTA cards produced genotype call and concordance rates that were not different to those produced by assaying DNA samples extracted by PCI from whole blood. We conclude that DNA extracted from FTA cards by the GenSolve kit is of sufficiently high quality to produce results comparable to those obtained from DNA extracted from whole blood when assayed by the Illumina iSelect technology. Additionally, we validate the use of nasal swabs as an alternative to venous blood or buccal samples from animal subjects for reliably producing high quality genotypes on this platform.

Can We Monitor Ecosystem Function Using Keeling Plot Analyses of Nocturnal Cold-Air Drainage?

NASA Astrophysics Data System (ADS)

Bond, B. J.; Ocheltree, T.; Pypker, T.; Unsworth, M. H.; Mix, A. C.; William, R.

2003-12-01

The carbon isotope signature of ecosystem respiration, δ 13CR, as measured by the Keeling Plot approach, has been related to short-term variations in weather and ecosystem function in several recent studies. In order to obtain an adequate range of [CO2] and to sample a consistent vegetation type, investigators typically select sampling locations in relatively flat terrain and uniform canopy cover, but these are unusual conditions for many forested ecosystems. In a pilot study, we are collecting samples for Keeling Plot analyses in cold-air drainage systems in small (60-100 ha), deeply-incised watersheds, one covered with old-growth (ca 450-years-old) Douglas-fir/hemlock forest and one covered with young (ca 45-years-old) Douglas-fir forest. We found that the nightly range of [CO2] was typically 380-460 ppm, sufficient to develop good estimates of δ 13CR. At any point in time there was little variation in [CO2] with height through the canopy (0.5-30m), so the required range was obtained by sampling over several hours. There was no indication that samples taken from different heights or at different times of night represented sources with different isotopic signatures. The isotopic signature of respired CO2 in the older watershed averaged about 1 per mil greater than that of the young watershed, and δ 13CR of both locations correlated with modeled stomatal conductance 6 days prior to flask sampling.

Incomplete reactions in nanothermite composites

NASA Astrophysics Data System (ADS)

Jacob, Rohit J.; Ortiz-Montalvo, Diana L.; Overdeep, Kyle R.; Weihs, Timothy P.; Zachariah, Michael R.

2017-02-01

Exothermic reactions between oxophilic metals and transition/post transition metal-oxides have been well documented owing to their fast reaction time scales (≈10 μs). This article examines the extent of the reaction in nano-aluminum based thermite systems through a forensic inspection of the products formed during reaction. Three nanothermite systems (Al/CuO, Al/Bi2O3, and Al/WO3) were selected owing to their diverse combustion characteristics, thereby providing sufficient generality and breadth to the analysis. Microgram quantities of the sample were coated onto a fine platinum wire, which was resistively heated at high heating rates (≈105 K/s) to ignite the sample. The subsequent products were captured/quenched very rapidly (≈500 μs) in order to preserve the chemistry/morphology during initiation and subsequent reaction and were quantitatively analyzed using electron microscopy and focused ion beam cross-sectioning followed by energy dispersive X-ray spectroscopy. Elemental examination of the cross-section of the quenched particles shows that oxygen is predominantly localized in the regions containing aluminum, implying the occurrence of the redox reaction. The Al/CuO system, which has simultaneous gaseous oxygen release and ignition (TIgnition ≈ TOxygen Release), shows a substantially lower oxygen content within the product particles as opposed to Al/Bi2O3 and Al/WO3 thermites, which are postulated to undergo a condensed phase reaction (TIgnition ≪ TOxygen Release). An effective Al:O composition for the interior section was obtained for all the mixtures, with the smaller particles generally showing a higher oxygen content than the larger ones. The observed results were further corroborated with the reaction temperature, obtained using a high-speed spectro-pyrometer, and bomb calorimetry conducted on larger samples (≈15 mg). The results suggest that thermites that produce sufficient amounts of gaseous products generate smaller product particles and achieve higher extents of completion.

Advances in Charge-Compensation in Secondary Ion Mass Spectrometry (SIMS)

NASA Astrophysics Data System (ADS)

Hervig, R. L.; Chen, J.; Schauer, S.; Stanley, B. D.; Moore, G. M.; Roggensack, K.

2012-12-01

In secondary ion mass spectrometry (SIMS), a sample is bombarded by a charged particle beam (the primary ion) and sputtered positive or negative secondary ions are analyzed in a mass spectrometer. When the target is not conducting (like many geological materials), sample charging can result in variable deflection of secondary ions away from the mass spectrometer and a low, unstable, or absent signal. Applying a thin conducting coat (e.g., C, Au) to polished samples is required, and if the primary ion beam is negatively-charged, the build-up of negative charge can be alleviated by secondary electrons draining to the conducting coat at the edge of the crater (if a positive potential is applied to the sample for the collection of positive secondary ions) or accelerated away from the crater (if a negative potential is applied for negative ion study). Unless the sputtered crater in the conducting coat becomes too large, sample charging can be kept at a controllable level, and high-quality trace element analyses and isotope ratios have been obtained using this technique over the past 3+ decades. When a positive primary beam is used, the resulting build-up of positive charge in the sample requires an electron gun to deliver sufficient negative charge to the sputtered crater. While there are many examples of successful analyses using this approach, the purpose of this presentation is to describe a very simple technique for aligning the electron gun on Cameca nf and 1270/80 SIMS instruments. This method allows reproducible analyses of insulating phases with a Cs+ primary beam and detection of negative secondary ions. Normally, the filament voltage on the E-gun is the same as the sample voltage; thus electrons do not strike the sample except when a positive charge has built up (e.g., in the analysis crater!). In this method, we decrease the sample voltage by 3 or more kV, so that the impact energy of the electrons is sufficient to induce a cathodoluminescent (CL) image on an appropriate sample (e.g., GaN). The CL image is made circular and homogeneous by adjusting the deflectors and a lens in the electron steering assembly, and the sample voltage is subsequently returned to the same value as the filament. Very minor corrections of the electron tuning (mostly by an external magnet known as Bx or B1) will then produce a uniform secondary ion image on a test insulator (a gold-coated glass slide) under Cs bombardment. The uniform electron density is correlated with reproducible calibration for hydrogen and carbon concentrations over a multi-day session and from session to session over a period of months. Outside visitors to the lab can use this set-up and obtain high-quality analyses with little to no previous training. Obtaining a homogeneous distribution of electrons over a maximum diameter (100+ microns) also reduces problems associated with changes in the position of the electron beam induced by stray magnetic fields. As a result, analyses of hydrogen isotopes and/or multi-element analysis routines using elemental H species are simplified.

Evaluation of four automated protocols for extraction of DNA from FTA cards.

PubMed

Stangegaard, Michael; Børsting, Claus; Ferrero-Miliani, Laura; Frank-Hansen, Rune; Poulsen, Lena; Hansen, Anders J; Morling, Niels

2013-10-01

Extraction of DNA using magnetic bead-based techniques on automated DNA extraction instruments provides a fast, reliable, and reproducible method for DNA extraction from various matrices. Here, we have compared the yield and quality of DNA extracted from FTA cards using four automated extraction protocols on three different instruments. The extraction processes were repeated up to six times with the same pieces of FTA cards. The sample material on the FTA cards was either blood or buccal cells. With the QIAamp DNA Investigator and QIAsymphony DNA Investigator kits, it was possible to extract DNA from the FTA cards in all six rounds of extractions in sufficient amount and quality to obtain complete short tandem repeat (STR) profiles on a QIAcube and a QIAsymphony SP. With the PrepFiler Express kit, almost all the extractable DNA was extracted in the first two rounds of extractions. Furthermore, we demonstrated that it was possible to successfully extract sufficient DNA for STR profiling from previously processed FTA card pieces that had been stored at 4 °C for up to 1 year. This showed that rare or precious FTA card samples may be saved for future analyses even though some DNA was already extracted from the FTA cards.

Powerful Statistical Inference for Nested Data Using Sufficient Summary Statistics

PubMed Central

Dowding, Irene; Haufe, Stefan

2018-01-01

Hierarchically-organized data arise naturally in many psychology and neuroscience studies. As the standard assumption of independent and identically distributed samples does not hold for such data, two important problems are to accurately estimate group-level effect sizes, and to obtain powerful statistical tests against group-level null hypotheses. A common approach is to summarize subject-level data by a single quantity per subject, which is often the mean or the difference between class means, and treat these as samples in a group-level t-test. This “naive” approach is, however, suboptimal in terms of statistical power, as it ignores information about the intra-subject variance. To address this issue, we review several approaches to deal with nested data, with a focus on methods that are easy to implement. With what we call the sufficient-summary-statistic approach, we highlight a computationally efficient technique that can improve statistical power by taking into account within-subject variances, and we provide step-by-step instructions on how to apply this approach to a number of frequently-used measures of effect size. The properties of the reviewed approaches and the potential benefits over a group-level t-test are quantitatively assessed on simulated data and demonstrated on EEG data from a simulated-driving experiment. PMID:29615885

Error estimates of Lagrange interpolation and orthonormal expansions for Freud weights

NASA Astrophysics Data System (ADS)

Kwon, K. H.; Lee, D. W.

2001-08-01

Let Sn[f] be the nth partial sum of the orthonormal polynomials expansion with respect to a Freud weight. Then we obtain sufficient conditions for the boundedness of Sn[f] and discuss the speed of the convergence of Sn[f] in weighted Lp space. We also find sufficient conditions for the boundedness of the Lagrange interpolation polynomial Ln[f], whose nodal points are the zeros of orthonormal polynomials with respect to a Freud weight. In particular, if W(x)=e-(1/2)x2 is the Hermite weight function, then we obtain sufficient conditions for the inequalities to hold:andwhere and k=0,1,2...,r.

A theory of photometric stereo for a class of diffuse non-Lambertian surfaces

NASA Technical Reports Server (NTRS)

Tagare, Hemant D.; Defigueiredo, Rui J. P.

1991-01-01

A theory of photometric stereo is proposed for a large class of non-Lambertian reflectance maps. The authors review the different reflectance maps proposed in the literature for modeling reflection from real-world surfaces. From this, they obtain a mathematical class of reflectance maps to which the maps belong. They show that three lights can be sufficient for a unique inversion of the photometric stereo equation for the entire class of reflectance maps. They also obtain a constraint on the positions of light sources for obtaining this solution. They investigate the sufficiency of three light sources to estimate the surface normal and the illuminant strength. The issue of completeness of reconstruction is addressed. They shown that if k lights are sufficient for a unique inversion, 2k lights are necessary for a complete inversion.

A novel condition for stable nonlinear sampled-data models using higher-order discretized approximations with zero dynamics.

PubMed

Zeng, Cheng; Liang, Shan; Xiang, Shuwen

2017-05-01

Continuous-time systems are usually modelled by the form of ordinary differential equations arising from physical laws. However, the use of these models in practice and utilizing, analyzing or transmitting these data from such systems must first invariably be discretized. More importantly, for digital control of a continuous-time nonlinear system, a good sampled-data model is required. This paper investigates the new consistency condition which is weaker than the previous similar results presented. Moreover, given the stability of the high-order approximate model with stable zero dynamics, the novel condition presented stabilizes the exact sampled-data model of the nonlinear system for sufficiently small sampling periods. An insightful interpretation of the obtained results can be made in terms of the stable sampling zero dynamics, and the new consistency condition is surprisingly associated with the relative degree of the nonlinear continuous-time system. Our controller design, based on the higher-order approximate discretized model, extends the existing methods which mainly deal with the Euler approximation. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

The 90-day report for SL4 experiment S019: UV stellar astronomy

NASA Technical Reports Server (NTRS)

1974-01-01

The use of Experiment S019 to obtain moderate dispersion stellar spectra extending down to 1300A with sufficient spectral resolution to permit the study of ultraviolet (UV) line spectra and of spectral energy distributions of early-type stars is studied. Data obtained from this experiment should be of sufficient accuracy to permit detailed physical analysis of individual stars and nebulae, but an even more basic consideration is the expectation of obtaining spectra of a sufficient number of stars so that a statistically meaningful survey may be made of the UV spectra of a wide variety of star types. These should include all luminosity classes of spectral types O, B and A, as well as peculiar stars such as Wolf-Rayet stars and Ap or Am stars. An attempt was also made to obtain, in the no-prism mode, low dispersion UV spectra in a number of Milky Way star fields and in nearby galaxies.

Synchronous motor with soft start element formed between the motor rotor and motor output shaft to successfully synchronize loads that have high inertia and/or high torque

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

Umans, Stephen D; Nisley, Donald L; Melfi, Michael J

A line-start synchronous motor has a housing, a rotor shaft, and an output shaft. A soft-start coupling portion is operatively coupled to the output shaft and the rotor shaft. The soft-start coupling portion is configurable to enable the synchronous motor to obtain synchronous operation and to drive, at least near synchronous speed during normal steady state operation of the motor, a load having characteristics sufficient to prevent obtaining normal synchronous operation of the motor when the motor is operatively connected to the load in the absence of the soft-start coupling. The synchronous motor is sufficiently rated to obtain synchronous operationmore » and to drive, at least near synchronous speed during normal steady state operation of the motor, a load having characteristics sufficient to prevent obtaining normal synchronous operation of the motor when the motor is operatively connected to the load in the absence of the soft-start coupling.« less

Standardization of a fluconazole bioassay and correlation of results with those obtained by high-pressure liquid chromatography.

PubMed Central

Rex, J H; Hanson, L H; Amantea, M A; Stevens, D A; Bennett, J E

1991-01-01

An improved bioassay for fluconazole was developed. This assay is sensitive in the clinically relevant range (2 to 40 micrograms/ml) and analyzes plasma, serum, and cerebrospinal fluid specimens; bioassay results correlate with results obtained by high-pressure liquid chromatography (HPLC). Bioassay and HPLC analyses of spiked plasma, serum, and cerebrospinal fluid samples (run as unknowns) gave good agreement with expected values. Analysis of specimens from patients gave equivalent results by both HPLC and bioassay. HPLC had a lower within-run coefficient of variation (less than 2.5% for HPLC versus less than 11% for bioassay) and a lower between-run coefficient of variation (less than 5% versus less than 12% for bioassay) and was more sensitive (lower limit of detection, 0.1 micrograms/ml [versus 2 micrograms/ml for bioassay]). The bioassay is, however, sufficiently accurate and sensitive for clinical specimens, and its relative simplicity, low sample volume requirement, and low equipment cost should make it the technique of choice for analysis of routine clinical specimens. PMID:1854166

Measurement and Modeling of Water-Vapor Diffusion in Elastomers with Impact in Humidity and Vacuum Measurements

NASA Astrophysics Data System (ADS)

Šetina, Janez; Sefa, Makfir; Erjavec, Bojan; Hudoklin, Domen

2013-03-01

The dynamics of water-vapor dissolution in Viton O-rings is measured with a gravimetric method using a precise mass comparator. A sample gasket was degassed in high vacuum for a sufficiently long period to remove more than 99 % of the dissolved water vapor. After that, it was exposed to the ambient atmosphere with a controlled temperature, and relative humidity and water-vapor uptake curves were measured gravimetrically with a precise balance. The dynamics of a water-vapor release into vacuum from another sample that was previously saturated with water vapor at room temperature was determined. The sample was placed in a vacuum outgassing rate measurement apparatus. The time dependence of the evolved water vapor was calculated by integrating the measured outgassing rate. The physical process of water absorption can be described by the diffusion equation. The geometry of the samples required solving the diffusion equation in cylindrical coordinates. This was done numerically using a finite-difference method. As a result of the modeling, room temperature values of the diffusion constant D, the solubility s, and the permeability K = D× s of water vapor in the sample material (Viton A-401C) were obtained. For sample 1, we obtained D = 8.0 × 10 ^{-8} cm2 {\\cdot } s^{-1} and s = 6.5 × 10^{-7} g {\\cdot } cm^-3 Pa^{-1}, while for sample 2, D = 3.0 × 10^{-7} cm2 s^{-1} and s = 3.5 × 10^{-7} g {\\cdot } cm^{-3} {\\cdot } Pa^{-1}.

A diurnal component to the variation in sieve tube amino acid content in wheat.

PubMed

Gattolin, Stefano; Newbury, H John; Bale, Jeffrey S; Tseng, Hua-Ming; Barrett, David A; Pritchard, Jeremy

2008-06-01

We have used high-sensitivity capillary electrophoresis coupled to a laser-induced fluorescence detection method to quantify 16 amino acids in wheat (Triticum aestivum) sieve tube (ST) samples as small as 2 nL collected by severing the stylets of feeding aphids. The sensitivity of the method was sufficient to determine a quantitative amino acid profile of individual STs without the need to bulk samples to produce larger volumes for analysis. This allowed the observation of the full range of variation that exists in individual STs. Some of the total concentrations of amino acids recorded are higher than those reported previously. The results obtained show variation in the concentrations of phenylalanine (Phe), histidine/valine (His/Val), leucine/isoleucine (Leu/Ile), arginine, asparagine, glutamine, tyrosine (Tyr), and lysine (Lys) across the ST samples. These could not be explained by plant-to-plant variation. Statistical analyses revealed five analytes (Tyr, Lys, Phe, His/Val, and Leu/Ile) that showed striking covariation in their concentrations across ST samples. A regression analysis revealed a significant relationship between the concentrations of Tyr, Lys, Phe, Leu/Ile, His/Val, asparagine, arginine, and proline and the time of collection of ST samples, with these amino acids increasing in concentration during the afternoon. This increase was confirmed to occur in individual STs by analyzing samples obtained from stylet bundles exuding for many hours. Finally, an apparent relationship between the exudation rate of ST sap and its total amino acid concentration was observed: samples containing higher total amino acid concentrations were observed to exude from the severed stylet bundles more slowly.

Evaluation of the effects of insufficient blood volume samples on the performance of blood glucose self-test meters.

PubMed

Pfützner, Andreas; Schipper, Christina; Ramljak, Sanja; Flacke, Frank; Sieber, Jochen; Forst, Thomas; Musholt, Petra B

2013-11-01

Accuracy of blood glucose readings is (among other things) dependent on the test strip being completely filled with sufficient sample volume. The devices are supposed to display an error message in case of incomplete filling. This laboratory study was performed to test the performance of 31 commercially available devices in case of incomplete strip filling. Samples with two different glucose levels (60-90 and 300-350 mg/dl) were used to generate three different sample volumes: 0.20 µl (too low volume for any device), 0.32 µl (borderline volume), and 1.20 µl (low but supposedly sufficient volume for all devices). After a point-of-care capillary reference measurement (StatStrip, NovaBiomedical), the meter strip was filled (6x) with the respective volume, and the response of the meters (two devices) was documented (72 determinations/meter type). Correct response was defined as either an error message indicating incomplete filling or a correct reading (±20% compared with reference reading). Only five meters showed 100% correct responses [BGStar and iBGStar (both Sanofi), ACCU-CHEK Compact+ and ACCU-CHEK Mobile (both Roche Diagnostics), OneTouch Verio (LifeScan)]. The majority of the meters (17) had up to 10% incorrect reactions [predominantly incorrect readings with sufficient volume; Precision Xceed and Xtra, FreeStyle Lite, and Freedom Lite (all Abbott); GlucoCard+ and GlucoMen GM (both Menarini); Contour, Contour USB, and Breeze2 (all Bayer); OneTouch Ultra Easy, Ultra 2, and Ultra Smart (all LifeScan); Wellion Dialog and Premium (both MedTrust); FineTouch (Terumo); ACCU-CHEK Aviva (Roche); and GlucoTalk (Axis-Shield)]. Ten percent to 20% incorrect reactions were seen with OneTouch Vita (LifeScan), ACCU-CHEK Aviva Nano (Roche), OmniTest+ (BBraun), and AlphaChek+ (Berger Med). More than 20% incorrect reactions were obtained with Pura (Ypsomed), GlucoCard Meter and GlucoMen LX (both Menarini), Elite (Bayer), and MediTouch (Medisana). In summary, partial and incomplete blood filling of glucose meter strips is often associated with inaccurate reading. These findings underline the importance of appropriate patient education on this aspect of blood glucose self-monitoring. © 2013 Diabetes Technology Society.

Reliability of the European Society of Human Reproduction and Embryology/European Society for Gynaecological Endoscopy and American Society for Reproductive Medicine classification systems for congenital uterine anomalies detected using three-dimensional ultrasonography.

PubMed

Ludwin, Artur; Ludwin, Inga; Kudla, Marek; Kottner, Jan

2015-09-01

To estimate the inter-rater/intrarater reliability of the European Society of Human Reproduction and Embryology/European Society for Gynaecological Endoscopy (ESHRE-ESGE) classification of congenital uterine malformations and to compare the results obtained with the reliability of the American Society for Reproductive Medicine (ASRM) classification supplemented with additional morphometric criteria. Reliability/agreement study. Private clinic. Uterine malformations (n = 50 patients, consecutively included) and normal uterus (n = 62 women, randomly selected) constituted the study. These were classified based on real-time three-dimensional ultrasound single volume transvaginal (or transrectal in the case of virgins, 4 cases) ultrasonography findings, which were assessed by an expert rater based on the ESHRE-ESGE criteria. The samples were obtained from women of reproductive age. Unprocessed three-dimensional datasets were independently evaluated offline by two experienced, blinded raters using both classification systems. The κ-values and proportions of agreement. Standardized interpretation indicated that the ESHRE-ESGE system has substantial/good or almost perfect/very good reliability (κ >0.60 and >0.80), but the interpretation of the clinically relevant cutoffs of κ-values showed insufficient reliability for clinical use (κ < 0.90), especially in the diagnosis of septate uterus. The ASRM system had sufficient reliability (κ > 0.95). The low reliability of the ESHRE-ESGE system may lead to a lack of consensus about the management of common uterine malformations and biased research interpretations. The use of the ASRM classification, supplemented with simple morphometric criteria, may be preferred if their sufficient reliability can be confirmed real-time in a large sample size. Copyright © 2015 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Do bacterial cell numbers follow a theoretical Poisson distribution? Comparison of experimentally obtained numbers of single cells with random number generation via computer simulation.

PubMed

Koyama, Kento; Hokunan, Hidekazu; Hasegawa, Mayumi; Kawamura, Shuso; Koseki, Shigenobu

2016-12-01

We investigated a bacterial sample preparation procedure for single-cell studies. In the present study, we examined whether single bacterial cells obtained via 10-fold dilution followed a theoretical Poisson distribution. Four serotypes of Salmonella enterica, three serotypes of enterohaemorrhagic Escherichia coli and one serotype of Listeria monocytogenes were used as sample bacteria. An inoculum of each serotype was prepared via a 10-fold dilution series to obtain bacterial cell counts with mean values of one or two. To determine whether the experimentally obtained bacterial cell counts follow a theoretical Poisson distribution, a likelihood ratio test between the experimentally obtained cell counts and Poisson distribution which parameter estimated by maximum likelihood estimation (MLE) was conducted. The bacterial cell counts of each serotype sufficiently followed a Poisson distribution. Furthermore, to examine the validity of the parameters of Poisson distribution from experimentally obtained bacterial cell counts, we compared these with the parameters of a Poisson distribution that were estimated using random number generation via computer simulation. The Poisson distribution parameters experimentally obtained from bacterial cell counts were within the range of the parameters estimated using a computer simulation. These results demonstrate that the bacterial cell counts of each serotype obtained via 10-fold dilution followed a Poisson distribution. The fact that the frequency of bacterial cell counts follows a Poisson distribution at low number would be applied to some single-cell studies with a few bacterial cells. In particular, the procedure presented in this study enables us to develop an inactivation model at the single-cell level that can estimate the variability of survival bacterial numbers during the bacterial death process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microorganism Identification Based On MALDI-TOF-MS Fingerprints

NASA Astrophysics Data System (ADS)

Elssner, Thomas; Kostrzewa, Markus; Maier, Thomas; Kruppa, Gary

Advances in MALDI-TOF mass spectrometry have enabled the ­development of a rapid, accurate and specific method for the identification of bacteria directly from colonies picked from culture plates, which we have named the MALDI Biotyper. The picked colonies are placed on a target plate, a drop of matrix solution is added, and a pattern of protein molecular weights and intensities, "the protein fingerprint" of the bacteria, is produced by the MALDI-TOF mass spectrometer. The obtained protein mass fingerprint representing a molecular signature of the microorganism is then matched against a database containing a library of previously measured protein mass fingerprints, and scores for the match to every library entry are produced. An ID is obtained if a score is returned over a pre-set threshold. The sensitivity of the techniques is such that only approximately 104 bacterial cells are needed, meaning that an overnight culture is sufficient, and the results are obtained in minutes after culture. The improvement in time to result over biochemical methods, and the capability to perform a non-targeted identification of bacteria and spores, potentially makes this method suitable for use in the detect-to-treat timeframe in a bioterrorism event. In the case of white-powder samples, the infectious spore is present in sufficient quantity in the powder so that the MALDI Biotyper result can be obtained directly from the white powder, without the need for culture. While spores produce very different patterns from the vegetative colonies of the corresponding bacteria, this problem is overcome by simply including protein fingerprints of the spores in the library. Results on spores can be returned within minutes, making the method suitable for use in the "detect-to-protect" timeframe.

Optical Riblet Sensor: Beam Parameter Requirements for the Probing Laser Source.

PubMed

Tschentscher, Juliane; Hochheim, Sven; Brüning, Hauke; Brune, Kai; Voit, Kay-Michael; Imlau, Mirco

2016-03-30

Beam parameters of a probing laser source in an optical riblet sensor are studied by considering the high demands on a sensors' precision and reliability for the determination of deviations of the geometrical shape of a riblet. Mandatory requirements, such as minimum intensity and light polarization, are obtained by means of detailed inspection of the optical response of the riblet using ray and wave optics; the impact of wavelength is studied. Novel measures for analyzing the riblet shape without the necessity of a measurement with a reference sample are derived; reference values for an ideal riblet structure obtained with the optical riblet sensor are given. The application of a low-cost, frequency-doubled Nd:YVO₄ laser pointer sufficient to serve as a reliable laser source in an appropriate optical riblet sensor is discussed.

Optical Riblet Sensor: Beam Parameter Requirements for the Probing Laser Source

PubMed Central

Tschentscher, Juliane; Hochheim, Sven; Brüning, Hauke; Brune, Kai; Voit, Kay-Michael; Imlau, Mirco

2016-01-01

Beam parameters of a probing laser source in an optical riblet sensor are studied by considering the high demands on a sensors’ precision and reliability for the determination of deviations of the geometrical shape of a riblet. Mandatory requirements, such as minimum intensity and light polarization, are obtained by means of detailed inspection of the optical response of the riblet using ray and wave optics; the impact of wavelength is studied. Novel measures for analyzing the riblet shape without the necessity of a measurement with a reference sample are derived; reference values for an ideal riblet structure obtained with the optical riblet sensor are given. The application of a low-cost, frequency-doubled Nd:YVO4 laser pointer sufficient to serve as a reliable laser source in an appropriate optical riblet sensor is discussed. PMID:27043567

Forensic DNA typing from teeth using demineralized root tips.

PubMed

Corrêa, Heitor Simões Dutra; Pedro, Fabio Luis Miranda; Volpato, Luiz Evaristo Ricci; Pereira, Thiago Machado; Siebert Filho, Gilberto; Borges, Álvaro Henrique

2017-11-01

Teeth are widely used samples in forensic human genetic identification due to their persistence and practical sampling and processing. Their processing, however, has changed very little in the last 20 years, usually including powdering or pulverization of the tooth. The objective of this study was to present demineralized root tips as DNA sources while, at the same time, not involving powdering the samples or expensive equipment for teeth processing. One to five teeth from each of 20 unidentified human bodies recovered from midwest Brazil were analyzed. Whole teeth were demineralized in EDTA solution with daily solution change. After a maximum of approximately seven days, the final millimeters of the root tip was excised. This portion of the sample was used for DNA extraction through a conventional organic protocol. DNA quantification and STR amplification were performed using commercial kits followed by capillary electrophoresis on 3130 or 3500 genetic analyzers. For 60% of the unidentified bodies (12 of 20), a full genetic profile was obtained from the extraction of the first root tip. By the end of the analyses, full genetic profiles were obtained for 85% of the individuals studied, of which 80% were positively identified. This alternative low-tech approach for postmortem teeth processing is capable of extracting DNA in sufficient quantity and quality for forensic casework, showing that root tips are viable nuclear DNA sources even after demineralization. Copyright © 2017 Elsevier B.V. All rights reserved.

Statistical description of non-Gaussian samples in the F2 layer of the ionosphere during heliogeophysical disturbances

NASA Astrophysics Data System (ADS)

Sergeenko, N. P.

2017-11-01

An adequate statistical method should be developed in order to predict probabilistically the range of ionospheric parameters. This problem is solved in this paper. The time series of the critical frequency of the layer F2- foF2( t) were subjected to statistical processing. For the obtained samples {δ foF2}, statistical distributions and invariants up to the fourth order are calculated. The analysis shows that the distributions differ from the Gaussian law during the disturbances. At levels of sufficiently small probability distributions, there are arbitrarily large deviations from the model of the normal process. Therefore, it is attempted to describe statistical samples {δ foF2} based on the Poisson model. For the studied samples, the exponential characteristic function is selected under the assumption that time series are a superposition of some deterministic and random processes. Using the Fourier transform, the characteristic function is transformed into a nonholomorphic excessive-asymmetric probability-density function. The statistical distributions of the samples {δ foF2} calculated for the disturbed periods are compared with the obtained model distribution function. According to the Kolmogorov's criterion, the probabilities of the coincidence of a posteriori distributions with the theoretical ones are P 0.7-0.9. The conducted analysis makes it possible to draw a conclusion about the applicability of a model based on the Poisson random process for the statistical description and probabilistic variation estimates during heliogeophysical disturbances of the variations {δ foF2}.

Do deep convolutional neural networks really need to be deep when applied for remote scene classification?

NASA Astrophysics Data System (ADS)

Luo, Chang; Wang, Jie; Feng, Gang; Xu, Suhui; Wang, Shiqiang

2017-10-01

Deep convolutional neural networks (CNNs) have been widely used to obtain high-level representation in various computer vision tasks. However, for remote scene classification, there are not sufficient images to train a very deep CNN from scratch. From two viewpoints of generalization power, we propose two promising kinds of deep CNNs for remote scenes and try to find whether deep CNNs need to be deep for remote scene classification. First, we transfer successful pretrained deep CNNs to remote scenes based on the theory that depth of CNNs brings the generalization power by learning available hypothesis for finite data samples. Second, according to the opposite viewpoint that generalization power of deep CNNs comes from massive memorization and shallow CNNs with enough neural nodes have perfect finite sample expressivity, we design a lightweight deep CNN (LDCNN) for remote scene classification. With five well-known pretrained deep CNNs, experimental results on two independent remote-sensing datasets demonstrate that transferred deep CNNs can achieve state-of-the-art results in an unsupervised setting. However, because of its shallow architecture, LDCNN cannot obtain satisfactory performance, regardless of whether in an unsupervised, semisupervised, or supervised setting. CNNs really need depth to obtain general features for remote scenes. This paper also provides baseline for applying deep CNNs to other remote sensing tasks.

[Transciptome among Mexicans: a large scale methodology to analyze the genetics expression profile of simultaneous samples in muscle, adipose tissue and lymphocytes obtained from the same individual].

PubMed

Bastarrachea, Raúl A; López-Alvarenga, Juan Carlos; Kent, Jack W; Laviada-Molina, Hugo A; Cerda-Flores, Ricardo M; Calderón-Garcidueñas, Ana Laura; Torres-Salazar, Amada; Torres-Salazar, Amanda; Nava-González, Edna J; Solis-Pérez, Elizabeth; Gallegos-Cabrales, Esther C; Cole, Shelley A; Comuzzie, Anthony G

2008-01-01

We describe the methodology used to analyze multiple transcripts using microarray techniques in simultaneous biopsies of muscle, adipose tissue and lymphocytes obtained from the same individual as part of the standard protocol of the Genetics of Metabolic Diseases in Mexico: GEMM Family Study. We recruited 4 healthy male subjects with BM1 20-41, who signed an informed consent letter. Subjects participated in a clinical examination that included anthropometric and body composition measurements, muscle biopsies (vastus lateralis) subcutaneous fat biopsies anda blood draw. All samples provided sufficient amplified RNA for microarray analysis. Total RNA was extracted from the biopsy samples and amplified for analysis. Of the 48,687 transcript targets queried, 39.4% were detectable in a least one of the studied tissues. Leptin was not detectable in lymphocytes, weakly expressed in muscle, but overexpressed and highly correlated with BMI in subcutaneous fat. Another example was GLUT4, which was detectable only in muscle and not correlated with BMI. Expression level concordance was 0.7 (p< 0.001) for the three tissues studied. We demonstrated the feasibility of carrying out simultaneous analysis of gene expression in multiple tissues, concordance of genetic expression in different tissues, and obtained confidence that this method corroborates the expected biological relationships among LEPand GLUT4. TheGEMM study will provide a broad and valuable overview on metabolic diseases, including obesity and type 2 diabetes.

Finite Element Modeling of the Bulk Magnitization of Railroad Wheels to Improve Test Conditions for Magnetoacoustic Residual Stress Measurements

NASA Technical Reports Server (NTRS)

Fulton, J. P.; Wincheski, B.; Namkung, M.; Utrata, D.

1992-01-01

The magnetoacoustic measurement technique has been used successfully for residual stress measurements in laboratory samples. However, when used to field test samples with complex geometries, such as railroad wheels, the sensitivity of the method declines dramatically. It has been suggested that the decrease in performance may be due, in part, to an insufficient or nonuniform magnetic induction in the test sample. The purpose of this paper is to optimize the test conditions by using finite element modeling to predict the distribution of the induced bulk magnetization of railroad wheels. The results suggest that it is possible to obtain a sufficiently large and uniform bulk magnetization by altering the shape of the electromagnet used in the tests. Consequently, problems associated with bulk magnetization can be overcome, and should not prohibit the magnetoacoustic technique from being used to make residual stress measurements in railroad wheels. We begin by giving a brief overview of the magnetoacoustic technique as it applies to residual stress measurements of railroad wheels. We then define the finite element model used to predict the behavior of the current test configuration along with the nonlinear constitutive relations which we obtained experimentally through measurements on materials typically used to construct both railroad wheels and electromagnets. Finally, we show that by modifying the pole of the electromagnet it is possible to obtain a significantly more uniform bulk magnetization in the region of interest.

Sol-gel derived sorbents

DOEpatents

Sigman, Michael E.; Dindal, Amy B.

2003-11-11

Described is a method for producing copolymerized sol-gel derived sorbent particles for the production of copolymerized sol-gel derived sorbent material. The method for producing copolymerized sol-gel derived sorbent particles comprises adding a basic solution to an aqueous metal alkoxide mixture for a pH.ltoreq.8 to hydrolyze the metal alkoxides. Then, allowing the mixture to react at room temperature for a precalculated period of time for the mixture to undergo an increased in viscosity to obtain a desired pore size and surface area. The copolymerized mixture is then added to an immiscible, nonpolar solvent that has been heated to a sufficient temperature wherein the copolymerized mixture forms a solid upon the addition. The solid is recovered from the mixture, and is ready for use in an active sampling trap or activated for use in a passive sampling trap.

A non-invasive technique to bleed incubating birds without trapping: A blood-sucking bug in a hollow egg

USGS Publications Warehouse

Becker, P.H.; Voigt, C.C.; Arnold, J.M.; Nagel, R.

2006-01-01

We describe a non-invasive technique to obtain blood samples from incubating birds without trapping and handling. A larval instar of the blood-sucking bug Dipetalogaster maximus (Heteroptera) was put in a hollowed artificial egg which was placed in a common tern Sterna hirundo) nest. A gauze-covered hole in the egg allowed the bug to draw blood from the brood patch of breeding adults. We successfully collected 68 blood samples of sufficient amount (median=187 ??l). The daily success rate was highest during the early breeding season and averaged 34% for all trials. We could not detect any visible response by the incubating bird to the sting of the bug. This technique allows for non-invasive blood collection from bird species of various sizes without disturbance. ?? Dt. Ornithologen-Gesellschaft e.V. 2005.

Materials identification using a small-scale pixellated x-ray diffraction system

NASA Astrophysics Data System (ADS)

O'Flynn, D.; Crews, C.; Drakos, I.; Christodoulou, C.; Wilson, M. D.; Veale, M. C.; Seller, P.; Speller, R. D.

2016-05-01

A transmission x-ray diffraction system has been developed using a pixellated, energy-resolving detector (HEXITEC) and a small-scale, mains operated x-ray source (Amptek Mini-X). HEXITEC enables diffraction to be measured without the requirement of incident spectrum filtration, or collimation of the scatter from the sample, preserving a large proportion of the useful signal compared with other diffraction techniques. Due to this efficiency, sufficient molecular information for material identification can be obtained within 5 s despite the relatively low x-ray source power. Diffraction data are presented from caffeine, hexamine, paracetamol, plastic explosives and narcotics. The capability to determine molecular information from aspirin tablets inside their packaging is demonstrated. Material selectivity and the potential for a sample classification model is shown with principal component analysis, through which each different material can be clearly resolved.

Radiocarbon dating of silica sinter deposits in shallow drill cores from the Upper Geyser Basin, Yellowstone National Park

USGS Publications Warehouse

Lowenstern, Jacob B.; Hurwitz, Shaul; McGeehin, John

2016-01-01

To explore the timing of hydrothermal activity at the Upper Geyser Basin (UGB) in Yellowstone National Park, we obtained seven new accelerator mass spectrometry (AMS) radiocarbon 14C ages of carbonaceous material trapped within siliceous sinter. Five samples came from depths of 15–152 cm within the Y-1 well, and two samples were from well Y-7 (depths of 24 cm and 122 cm). These two wells, at Black Sand and Biscuit Basins, respectively, were drilled in 1967 as part of a scientific drilling program by the U.S. Geological Survey (White et al., 1975). Even with samples as small as 15 g, we obtained sufficient carbonaceous material (a mixture of thermophilic mats, pollen, and charcoal) for the 14C analyses. Apparent time of deposition ranged from 3775 ± 25 and 2910 ± 30 14C years BP at the top of the cores to about 8000 years BP at the bottom. The dates are consistent with variable rates of sinter formation at individual sites within the UGB over the Holocene. On a basin-wide scale, though, these and other existing 14C dates hint that hydrothermal activity at the UGB may have been continuous throughout the Holocene.

Evaluation of a molecularly imprinted polymer for determination of steroids in goat milk by matrix solid phase dispersion.

PubMed

Gañán, Judith; Morante-Zarcero, Sonia; Gallego-Picó, Alejandrina; Garcinuño, Rosa María; Fernández-Hernando, Pilar; Sierra, Isabel

2014-08-01

A molecularly imprinted polymer-matrix solid-phase dispersion methodology for simultaneous determination of five steroids in goat milk samples was proposed. Factors affecting the extraction recovery such as sample/dispersant ratio and washing and elution solvents were investigated. The molecularly imprinted polymer used as dispersant in the matrix solid-phase dispersion procedure showed high affinity to steroids, and the obtained extracts were sufficiently cleaned to be directly analyzed. Analytical separation was performed by micellar electrokinetic chromatography using a capillary electrophoresis system equipped with a diode array detector. A background electrolyte composed of borate buffer (25mM, pH 9.3), sodium dodecyl sulfate (10mM) and acetonitrile (20%) was used. The developed MIP-MSPD methodology was applied for direct determination of testosterone (T), estrone (E1), 17β-estradiol (17β-E2), 17α-ethinylestradiol (EE2) and progesterone (P) in different goat milk samples. Mean recoveries obtained ranged from 81% to 110%, with relative standard deviations (RSD)≤12%. The molecularly imprinted polymer-matrix solid-phase dispersion method is fast, selective, cost-effective and environment-friendly compared with other pretreatment methods used for extraction of steroids in milk. Copyright © 2014 Elsevier B.V. All rights reserved.

Computed Potential Energy Surfaces and Minimum Energy Pathways for Chemical Reactions

NASA Technical Reports Server (NTRS)

Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

1994-01-01

Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. For some dynamics methods, global potential energy surfaces are required. In this case, it is necessary to obtain the energy at a complete sampling of all the possible arrangements of the nuclei, which are energetically accessible, and then a fitting function must be obtained to interpolate between the computed points. In other cases, characterization of the stationary points and the reaction pathway connecting them is sufficient. These properties may be readily obtained using analytical derivative methods. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives usefull results for a number of chemically important systems. The talk will focus on a number of applications including global potential energy surfaces, H + O2, H + N2, O(3p) + H2, and reaction pathways for complex reactions, including reactions leading to NO and soot formation in hydrocarbon combustion.

Human blood RNA stabilization in samples collected and transported for a large biobank

PubMed Central

2012-01-01

Background The Norwegian Mother and Child Cohort Study (MoBa) is a nation-wide population-based pregnancy cohort initiated in 1999, comprising more than 108.000 pregnancies recruited between 1999 and 2008. In this study we evaluated the feasibility of integrating RNA analyses into existing MoBa protocols. We compared two different blood RNA collection tube systems – the PAXgene™ Blood RNA system and the Tempus™ Blood RNA system - and assessed the effects of suboptimal blood volumes in collection tubes and of transportation of blood samples by standard mail. Endpoints to characterize the samples were RNA quality and yield, and the RNA transcript stability of selected genes. Findings High-quality RNA could be extracted from blood samples stabilized with both PAXgene and Tempus tubes. The RNA yields obtained from the blood samples collected in Tempus tubes were consistently higher than from PAXgene tubes. Higher RNA yields were obtained from cord blood (3 – 4 times) compared to adult blood with both types of tubes. Transportation of samples by standard mail had moderate effects on RNA quality and RNA transcript stability; the overall RNA quality of the transported samples was high. Some unexplained changes in gene expression were noted, which seemed to correlate with suboptimal blood volumes collected in the tubes. Temperature variations during transportation may also be of some importance. Conclusions Our results strongly suggest that special collection tubes are necessary for RNA stabilization and they should be used for establishing new biobanks. We also show that the 50,000 samples collected in the MoBa biobank provide RNA of high quality and in sufficient amounts to allow gene expression analyses for studying the association of disease with altered patterns of gene expression. PMID:22988904

Distinct Gene Expression Patterns between Nasal Mucosal Cells and Blood Collected from Allergic Rhinitis Sufferers.

PubMed

Watts, Annabelle M; West, Nicholas P; Cripps, Allan W; Smith, Pete K; Cox, Amanda J

2018-06-19

Investigations of gene expression in allergic rhinitis (AR) typically rely on invasive nasal biopsies (site of inflammation) or blood samples (systemic immunity) to obtain sufficient genetic material for analysis. New methodologies to circumvent the need for invasive sample collection offer promise to further the understanding of local immune mechanisms relevant in AR. A within-subject design was employed to compare immune gene expression profiles obtained from nasal washing/brushing and whole blood samples collected during peak pollen season. Twelve adults (age: 46.3 ± 12.3 years) with more than a 2-year history of AR and a confirmed grass pollen allergy participated in the study. Gene expression analysis was performed using a panel of 760 immune genes with the NanoString nCounter platform on nasal lavage/brushing cell lysates and compared to RNA extracted from blood. A total of 355 genes were significantly differentially expressed between sample types (9.87 to -9.71 log2 fold change). The top 3 genes significantly upregulated in nasal lysate samples were Mucin 1 (MUC1), Tight Junction Protein 1 (TJP1), and Lipocalin-2 (LCN2). The top 3 genes significantly upregulated in blood samples were cluster of differentiation 3e (CD3E), FYN Proto-Oncogene Src Family Tyrosine Kinase (FYN) and cluster of differentiation 3d (CD3D). Overall, the blood and nasal lavage samples showed vastly distinct gene expression profiles and functional gene pathways which reflect their anatomical and functional origins. Evaluating immune gene expression of the nasal mucosa in addition to blood samples may be beneficial in understanding AR pathophysiology and response to allergen challenge. © 2018 S. Karger AG, Basel.

Placental Transfer of Maternally-Derived IgA Precludes the Use of Guthrie Card Eluates as a Screening Tool for Primary Immunodeficiency Diseases

PubMed Central

Borte, Stephan; Janzi, Magdalena; Pan-Hammarström, Qiang; von Döbeln, Ulrika; Nordvall, Lennart; Winiarski, Jacek; Fasth, Anders; Hammarström, Lennart

2012-01-01

There is a need for neonatal screening tools to improve the long-term clinical outcome of patients with primary immunodeficiency diseases (PID). Recently, a PCR-based screening method for both TRECs and KRECs using Guthrie card samples has been developed. However, the applicability of these excision circle assays is limited to patients with severe T or B cell lymphopenia (SCID, XLA and A-T), whereas the most common forms of PID are not detected. Absence of serum IgA is seen in a major fraction of patients with immunological defects. As serum IgA in newborns is considered to be of fetal origin, eluates from routinely collected dried blood spot samples might thus be suitable for identification of children with PID. To assess the applicability of such screening assays, stored Guthrie card samples were obtained from 47 patients with various forms of primary immunodeficiency diseases (SCID, XLA, A-T, HIGM and IgAD), 20 individuals with normal serum IgA levels born to IgA-deficient mothers and 51 matched healthy newborns. Surprisingly, normal serum IgA levels were found in all SCID, XLA, A-T and HIGM patients and, additionally, in all those IgAD patients born to IgA-sufficient mothers. Conversely, no serum IgA was found in any of the 16 IgAD patients born by IgA-deficient mothers. Moreover, half of the IgA-sufficient individuals born by IgA-deficient mothers also lacked IgA at birth whereas no IgA-deficient individuals were found among the controls. IgA in neonatal dried blood samples thus appears to be of both maternal and fetal origin and precludes its use as a reliable marker for neonatal screening of primary immunodeficiency diseases. PMID:22916257

Placental transfer of maternally-derived IgA precludes the use of guthrie card eluates as a screening tool for primary immunodeficiency diseases.

PubMed

Borte, Stephan; Janzi, Magdalena; Pan-Hammarström, Qiang; von Döbeln, Ulrika; Nordvall, Lennart; Winiarski, Jacek; Fasth, Anders; Hammarström, Lennart

2012-01-01

There is a need for neonatal screening tools to improve the long-term clinical outcome of patients with primary immunodeficiency diseases (PID). Recently, a PCR-based screening method for both TRECs and KRECs using Guthrie card samples has been developed. However, the applicability of these excision circle assays is limited to patients with severe T or B cell lymphopenia (SCID, XLA and A-T), whereas the most common forms of PID are not detected. Absence of serum IgA is seen in a major fraction of patients with immunological defects. As serum IgA in newborns is considered to be of fetal origin, eluates from routinely collected dried blood spot samples might thus be suitable for identification of children with PID. To assess the applicability of such screening assays, stored Guthrie card samples were obtained from 47 patients with various forms of primary immunodeficiency diseases (SCID, XLA, A-T, HIGM and IgAD), 20 individuals with normal serum IgA levels born to IgA-deficient mothers and 51 matched healthy newborns. Surprisingly, normal serum IgA levels were found in all SCID, XLA, A-T and HIGM patients and, additionally, in all those IgAD patients born to IgA-sufficient mothers. Conversely, no serum IgA was found in any of the 16 IgAD patients born by IgA-deficient mothers. Moreover, half of the IgA-sufficient individuals born by IgA-deficient mothers also lacked IgA at birth whereas no IgA-deficient individuals were found among the controls. IgA in neonatal dried blood samples thus appears to be of both maternal and fetal origin and precludes its use as a reliable marker for neonatal screening of primary immunodeficiency diseases.

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

Belinsky, Steven A; Palmisano, William A

A molecular marker-based method for monitoring and detecting cancer in humans. Aberrant methylation of gene promoters is a marker for cancer risk in humans. A two-stage, or "nested" polymerase chain reaction method is disclosed for detecting methylated DNA sequences at sufficiently high levels of sensitivity to permit cancer screening in biological fluid samples, such as sputum, obtained non-invasively. The method is for detecting the aberrant methylation of the p16 gene, O 6-methylguanine-DNA methyltransferase gene, Death-associated protein kinase gene, RAS-associated family 1 gene, or other gene promoters. The method offers a potentially powerful approach to population-based screening for the detection ofmore » lung and other cancers.« less

The production of multiprotein complexes in insect cells using the baculovirus expression system.

PubMed

Abdulrahman, Wassim; Radu, Laura; Garzoni, Frederic; Kolesnikova, Olga; Gupta, Kapil; Osz-Papai, Judit; Berger, Imre; Poterszman, Arnaud

2015-01-01

The production of a homogeneous protein sample in sufficient quantities is an essential prerequisite not only for structural investigations but represents also a rate-limiting step for many functional studies. In the cell, a large fraction of eukaryotic proteins exists as large multicomponent assemblies with many subunits, which act in concert to catalyze specific activities. Many of these complexes cannot be obtained from endogenous source material, so recombinant expression and reconstitution are then required to overcome this bottleneck. This chapter describes current strategies and protocols for the efficient production of multiprotein complexes in large quantities and of high quality, using the baculovirus/insect cell expression system.

Use of focused ultrasonication in activity-based profiling of deubiquitinating enzymes in tissue.

PubMed

Nanduri, Bindu; Shack, Leslie A; Rai, Aswathy N; Epperson, William B; Baumgartner, Wes; Schmidt, Ty B; Edelmann, Mariola J

2016-12-15

To develop a reproducible tissue lysis method that retains enzyme function for activity-based protein profiling, we compared four different methods to obtain protein extracts from bovine lung tissue: focused ultrasonication, standard sonication, mortar & pestle method, and homogenization combined with standard sonication. Focused ultrasonication and mortar & pestle methods were sufficiently effective for activity-based profiling of deubiquitinases in tissue, and focused ultrasonication also had the fastest processing time. We used focused-ultrasonicator for subsequent activity-based proteomic analysis of deubiquitinases to test the compatibility of this method in sample preparation for activity-based chemical proteomics. Copyright © 2016 Elsevier Inc. All rights reserved.

Getting water from the water of hydration on Mars

NASA Technical Reports Server (NTRS)

Gwynne, O.; Cozzatti, J. P.; Zent, A. P.; Mckay, C. P.

1991-01-01

Both Viking landers found evidence of water in small concentration in the soils of Mars. Using the gas chromatograph mass spectrometer the soil samples on Mars were heated to 500 C to release the water. This result lead researchers to believe that the water in the soil of Mars was tightly bound in a hydration state. In the laboratory several Mars analog soils and a few bench mark soils were run through a microwave to determine the amount of water released using this method. The results suggest that sufficient water can be obtained using this method to augment the activities of a human base on Mars.

Population dynamical behavior of Lotka-Volterra system under regime switching

NASA Astrophysics Data System (ADS)

Li, Xiaoyue; Jiang, Daqing; Mao, Xuerong

2009-10-01

In this paper, we investigate a Lotka-Volterra system under regime switching where B(t) is a standard Brownian motion. The aim here is to find out what happens under regime switching. We first obtain the sufficient conditions for the existence of global positive solutions, stochastic permanence and extinction. We find out that both stochastic permanence and extinction have close relationships with the stationary probability distribution of the Markov chain. The limit of the average in time of the sample path of the solution is then estimated by two constants related to the stationary distribution and the coefficients. Finally, the main results are illustrated by several examples.

Preserving correlations between trajectories for efficient path sampling

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

Gingrich, Todd R.; Geissler, Phillip L.; Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720

2015-06-21

Importance sampling of trajectories has proved a uniquely successful strategy for exploring rare dynamical behaviors of complex systems in an unbiased way. Carrying out this sampling, however, requires an ability to propose changes to dynamical pathways that are substantial, yet sufficiently modest to obtain reasonable acceptance rates. Satisfying this requirement becomes very challenging in the case of long trajectories, due to the characteristic divergences of chaotic dynamics. Here, we examine schemes for addressing this problem, which engineer correlation between a trial trajectory and its reference path, for instance using artificial forces. Our analysis is facilitated by a modern perspective onmore » Markov chain Monte Carlo sampling, inspired by non-equilibrium statistical mechanics, which clarifies the types of sampling strategies that can scale to long trajectories. Viewed in this light, the most promising such strategy guides a trial trajectory by manipulating the sequence of random numbers that advance its stochastic time evolution, as done in a handful of existing methods. In cases where this “noise guidance” synchronizes trajectories effectively, as the Glauber dynamics of a two-dimensional Ising model, we show that efficient path sampling can be achieved for even very long trajectories.« less

Frequency of thermophilic Campylobacter in broiler chickens during industrial processing in a Southern Brazil slaughterhouse.

PubMed

Franchin, P R; Ogliari, P J; Batista, C R V

2007-04-01

1. The frequency of thermophilic Campylobacter spp. on broiler carcases was determined during processing in a Southern Brazil slaughterhouse. Samples were collected after defeathering, evisceration, water chilling and freezing. In addition, samples were obtained from the water of the chiller tank and from the surface of equipment in direct contact with the chicken. 2. Samples (335) were analysed and 71.3% were positive for Campylobacter. The frequency of Campylobacter spp. on carcases rinsed in BPW and skin samples from carcases was 49 of 72 (68.0%) after defeathering, 50 of 72 (69.4%) after evisceration, 61 of 72 (84.7%) after chilling, and 46 of 72 (63.9%) after freezing. Campylobacter was positive for 21 of 23 (91.3%) samples in the chilling water and for 12 of 24 (50.0%) samples on the table surface. 3. The frequency of qualitative analysis for Campylobacter spp. was reduced in frozen chickens, but not during the slaughtering process. The use of drinking water alone as a decontaminant to reduce the incidence of Campylobacter spp. during slaughter is therefore not sufficient. Furthermore, to ensure food safety, chickens must be cooked properly before consuming.

Indirect competitive immunoassay for the detection of fungicide Thiabendazole in whole orange samples by Surface Plasmon Resonance.

PubMed

Estevez, M-Carmen; Belenguer, Jose; Gomez-Montes, Silvia; Miralles, Javier; Escuela, Alfonso M; Montoya, Angel; Lechuga, Laura M

2012-12-07

A highly sensitive and specific SPR-based competitive immunoassay for the detection of Thiabendazole (TBZ) has been developed. An indirect format where a TBZ-protein conjugate is immobilized onto gold surfaces has been selected. Under the optimal conditions, a LOD of 0.67 nM (0.13 μg L(-1)) and an IC(50) of 3.2 nM (0.64 μg L(-1)) have been achieved which are comparable to the values obtained by conventional ELISA. Analysis of real samples has been attempted by first evaluating the influence of complex matrix samples coming from whole oranges and secondly measuring samples containing TBZ previously evaluated by chromatographic methods. A methanolic extraction procedure followed by a simple dilution in assay buffer has proven to be sufficient to measure orange samples using the developed immunoassay with an excellent recovery percentage. The sensitivity and the feasibility of measuring whole orange samples demonstrate the effectiveness and robustness of the SPR biosensor, which can be useful for the determination of TBZ in food at concentrations below the Maximum Residue Levels (MRLs) established by the European legislation.

Indicator organisms in meat and poultry slaughter operations: their potential use in process control and the role of emerging technologies.

PubMed

Saini, Parmesh K; Marks, Harry M; Dreyfuss, Moshe S; Evans, Peter; Cook, L Victor; Dessai, Uday

2011-08-01

Measuring commonly occurring, nonpathogenic organisms on poultry products may be used for designing statistical process control systems that could result in reductions of pathogen levels. The extent of pathogen level reduction that could be obtained from actions resulting from monitoring these measurements over time depends upon the degree of understanding cause-effect relationships between processing variables, selected output variables, and pathogens. For such measurements to be effective for controlling or improving processing to some capability level within the statistical process control context, sufficiently frequent measurements would be needed to help identify processing deficiencies. Ultimately the correct balance of sampling and resources is determined by those characteristics of deficient processing that are important to identify. We recommend strategies that emphasize flexibility, depending upon sampling objectives. Coupling the measurement of levels of indicator organisms with practical emerging technologies and suitable on-site platforms that decrease the time between sample collections and interpreting results would enhance monitoring process control.

Study on nondestructive discrimination of genuine and counterfeit wild ginsengs using NIRS

NASA Astrophysics Data System (ADS)

Lu, Q.; Fan, Y.; Peng, Z.; Ding, H.; Gao, H.

2012-07-01

A new approach for the nondestructive discrimination between genuine wild ginsengs and the counterfeit ones by near infrared spectroscopy (NIRS) was developed. Both discriminant analysis and back propagation artificial neural network (BP-ANN) were applied to the model establishment for discrimination. Optimal modeling wavelengths were determined based on the anomalous spectral information of counterfeit samples. Through principal component analysis (PCA) of various wild ginseng samples, genuine and counterfeit, the cumulative percentages of variance of the principal components were obtained, serving as a reference for principal component (PC) factor determination. Discriminant analysis achieved an identification ratio of 88.46%. With sample' truth values as its outputs, a three-layer BP-ANN model was built, which yielded a higher discrimination accuracy of 100%. The overall results sufficiently demonstrate that NIRS combined with BP-ANN classification algorithm performs better on ginseng discrimination than discriminant analysis, and can be used as a rapid and nondestructive method for the detection of counterfeit wild ginsengs in food and pharmaceutical industry.

Baseline well inventory and groundwater-quality data from a potential shale gas resource area in parts of Lee and Chatham Counties, North Carolina, October 2011-August 2012

USGS Publications Warehouse

Chapman, Melinda J.; Gurley, Laura N.; Fitzgerald, Sharon A.

2014-01-01

Records were obtained for 305 wells and 1 spring in northwestern Lee and southeastern Chatham counties, North Carolina. Well depths ranged from 26 to 720 feet and yields ranged from 0.25 to 100 gallons per minute. A subset of 56 wells and 1 spring were sampled for baseline groundwaterquality constituents including the following: major ions; dissolved metals; nutrients; dissolved gases (including methane); volatile and semivolatile organic compounds; glycols; isotopes of strontium, radium, methane (if sufficient concentration), and water; and dissolved organic and inorganic carbon. Dissolved methane gas concentrations were low, ranging from less than 0.00007 (lowest reporting level) to 0.48 milligrams per liter. Concentrations of nitrate, boron, iron, manganese, sulfate, chloride, total dissolved solids, and measurements of pH exceeded federal and state drinking water standards in a few samples. Iron and manganese concentrations exceeded the secondary (aesthetic) drinking water standard in approximately 35 to 37 percent of the samples.

DNA extraction and amplification from contemporary Polynesian bark-cloth.

PubMed

Moncada, Ximena; Payacán, Claudia; Arriaza, Francisco; Lobos, Sergio; Seelenfreund, Daniela; Seelenfreund, Andrea

2013-01-01

Paper mulberry has been used for thousands of years in Asia and Oceania for making paper and bark-cloth, respectively. Museums around the world hold valuable collections of Polynesian bark-cloth. Genetic analysis of the plant fibers from which the textiles were made may answer a number of questions of interest related to provenance, authenticity or species used in the manufacture of these textiles. Recovery of nucleic acids from paper mulberry bark-cloth has not been reported before. We describe a simple method for the extraction of PCR-amplifiable DNA from small samples of contemporary Polynesian bark-cloth (tapa) using two types of nuclear markers. We report the amplification of about 300 bp sequences of the ITS1 region and of a microsatellite marker. Sufficient DNA was retrieved from all bark-cloth samples to permit successful PCR amplification. This method shows a means of obtaining useful genetic information from modern bark-cloth samples and opens perspectives for the analyses of small fragments derived from ethnographic materials.

DNA Extraction and Amplification from Contemporary Polynesian Bark-Cloth

PubMed Central

Moncada, Ximena; Payacán, Claudia; Arriaza, Francisco; Lobos, Sergio; Seelenfreund, Daniela; Seelenfreund, Andrea

2013-01-01

Background Paper mulberry has been used for thousands of years in Asia and Oceania for making paper and bark-cloth, respectively. Museums around the world hold valuable collections of Polynesian bark-cloth. Genetic analysis of the plant fibers from which the textiles were made may answer a number of questions of interest related to provenance, authenticity or species used in the manufacture of these textiles. Recovery of nucleic acids from paper mulberry bark-cloth has not been reported before. Methodology We describe a simple method for the extraction of PCR-amplifiable DNA from small samples of contemporary Polynesian bark-cloth (tapa) using two types of nuclear markers. We report the amplification of about 300 bp sequences of the ITS1 region and of a microsatellite marker. Conclusions Sufficient DNA was retrieved from all bark-cloth samples to permit successful PCR amplification. This method shows a means of obtaining useful genetic information from modern bark-cloth samples and opens perspectives for the analyses of small fragments derived from ethnographic materials. PMID:23437166

Automated Microflow NMR: Routine Analysis of Five-Microliter Samples

PubMed Central

Jansma, Ariane; Chuan, Tiffany; Geierstanger, Bernhard H.; Albrecht, Robert W.; Olson, Dean L.; Peck, Timothy L.

2006-01-01

A microflow CapNMR probe double-tuned for 1H and 13C was installed on a 400-MHz NMR spectrometer and interfaced to an automated liquid handler. Individual samples dissolved in DMSO-d6 are submitted for NMR analysis in vials containing as little as 10 μL of sample. Sets of samples are submitted in a low-volume 384-well plate. Of the 10 μL of sample per well, as with vials, 5 μL is injected into the microflow NMR probe for analysis. For quality control of chemical libraries, 1D NMR spectra are acquired under full automation from 384-well plates on as many as 130 compounds within 24 h using 128 scans per spectrum and a sample-to-sample cycle time of ∼11 min. Because of the low volume requirements and high mass sensitivity of the microflow NMR system, 30 nmol of a typical small molecule is sufficient to obtain high-quality, well-resolved, 1D proton or 2D COSY NMR spectra in ∼6 or 20 min of data acquisition time per experiment, respectively. Implementation of pulse programs with automated solvent peak identification and suppression allow for reliable data collection, even for samples submitted in fully protonated DMSO. The automated microflow NMR system is controlled and monitored using web-based software. PMID:16194121

Validation of Genotyping-By-Sequencing Analysis in Populations of Tetraploid Alfalfa by 454 Sequencing

PubMed Central

Rocher, Solen; Jean, Martine; Castonguay, Yves; Belzile, François

2015-01-01

Genotyping-by-sequencing (GBS) is a relatively low-cost high throughput genotyping technology based on next generation sequencing and is applicable to orphan species with no reference genome. A combination of genome complexity reduction and multiplexing with DNA barcoding provides a simple and affordable way to resolve allelic variation between plant samples or populations. GBS was performed on ApeKI libraries using DNA from 48 genotypes each of two heterogeneous populations of tetraploid alfalfa (Medicago sativa spp. sativa): the synthetic cultivar Apica (ATF0) and a derived population (ATF5) obtained after five cycles of recurrent selection for superior tolerance to freezing (TF). Nearly 400 million reads were obtained from two lanes of an Illumina HiSeq 2000 sequencer and analyzed with the Universal Network-Enabled Analysis Kit (UNEAK) pipeline designed for species with no reference genome. Following the application of whole dataset-level filters, 11,694 single nucleotide polymorphism (SNP) loci were obtained. About 60% had a significant match on the Medicago truncatula syntenic genome. The accuracy of allelic ratios and genotype calls based on GBS data was directly assessed using 454 sequencing on a subset of SNP loci scored in eight plant samples. Sequencing depth in this study was not sufficient for accurate tetraploid allelic dosage, but reliable genotype calls based on diploid allelic dosage were obtained when using additional quality filtering. Principal Component Analysis of SNP loci in plant samples revealed that a small proportion (<5%) of the genetic variability assessed by GBS is able to differentiate ATF0 and ATF5. Our results confirm that analysis of GBS data using UNEAK is a reliable approach for genome-wide discovery of SNP loci in outcrossed polyploids. PMID:26115486

Analytical Scheme Leading to Integrated High-Sensitivity Profiling of Glycosphingolipids Together with N- and O-Glycans from One Sample

NASA Astrophysics Data System (ADS)

Benktander, John D.; Gizaw, Solomon T.; Gaunitz, Stefan; Novotny, Milos V.

2018-05-01

Glycoconjugates are directly or indirectly involved in many biological processes. Due to their complex structures, the structural elucidation of glycans and the exploration of their role in biological systems have been challenging. Glycan pools generated through release from glycoprotein or glycolipid mixtures can often be very complex. For the sake of procedural simplicity, many glycan profiling studies choose to concentrate on a single class of glycoconjugates. In this paper, we demonstrate it feasible to cover glycosphingolipids, N-glycans, and O-glycans isolated from the same sample. Small volumes of human blood serum and ascites fluid as well as small mouse brain tissue samples are sufficient to profile sequentially glycans from all three classes of glycoconjugates and even positively identify some mixture components through MALDI-MS and LC-ESI-MS. The results show that comprehensive glycan profiles can be obtained from the equivalent of 500-μg protein starting material or possibly less. These methodological improvements can help accelerating future glycomic comprehensive studies, especially for precious clinical samples.

Ultrasound-guided three-dimensional needle steering in biological tissue with curved surfaces

PubMed Central

Abayazid, Momen; Moreira, Pedro; Shahriari, Navid; Patil, Sachin; Alterovitz, Ron; Misra, Sarthak

2015-01-01

In this paper, we present a system capable of automatically steering a bevel-tipped flexible needle under ultrasound guidance toward a physical target while avoiding a physical obstacle embedded in gelatin phantoms and biological tissue with curved surfaces. An ultrasound pre-operative scan is performed for three-dimensional (3D) target localization and shape reconstruction. A controller based on implicit force control is developed to align the transducer with curved surfaces to assure the maximum contact area, and thus obtain an image of sufficient quality. We experimentally investigate the effect of needle insertion system parameters such as insertion speed, needle diameter and bevel angle on target motion to adjust the parameters that minimize the target motion during insertion. A fast sampling-based path planner is used to compute and periodically update a feasible path to the target that avoids obstacles. We present experimental results for target reconstruction and needle insertion procedures in gelatin-based phantoms and biological tissue. Mean targeting errors of 1.46 ± 0.37 mm, 1.29 ± 0.29 mm and 1.82 ± 0.58 mm are obtained for phantoms with inclined, curved and combined (inclined and curved) surfaces, respectively, for insertion distance of 86–103 mm. The achieved targeting errors suggest that our approach is sufficient for targeting lesions of 3 mm radius that can be detected using clinical ultrasound imaging systems. PMID:25455165

Effect of Drought on Streamflow and Stream-Water Quality in Colorado, July through September 2002

USGS Publications Warehouse

Chafin, Daniel T.; Druliner, A. Douglas

2007-01-01

During 2002, Colorado experienced the State's worst drought since 1977. In 2003, the U.S. Geological Survey entered into cooperative agreement with the Colorado Department of Public Health and Environment to evaluate the general effects of drought on the water quality of streams in Colorado during summer 2002 by analyzing a water-quality data set obtained during summer 2002 in cooperation with a variety of State and local governments. Water samples were collected at 148 stream sites in Colorado and were measured or analyzed for field properties, major ions, nutrients, organic carbon, bacteria, and dissolved and total recoverable metals. Mean annual streamflow was analyzed at 134 sites in Colorado, and mean summer (July-September) streamflow for 2002 was determined for 146 sites for water years 1978-2002. Mean annual streamflow for 2002 had an average percentile of 29.4 and mean summer streamflow for 2002 had an average percentile of 7.6 relative to 1978-2002. These results indicate that streamflow in Colorado was substantially less than median streamflow for the period and that the effect of drought on streamflow was greater during summer 2002 than during water year 2002 (October 1, 2001, through September 30, 2002). Few measured constituent concentrations or values were elevated or depressed on a widespread basis during summer 2002. Specific conductance was elevated (in the upper quartile relative to historical data) in five of the seven basins that had sufficient data for characterization, indicating that specific conductance likely was affected by drought in those basins. Chloride concentrations were elevated in three of five basins with sufficient data and indicate that chloride concentration generally was affected by drought in those basins. Sulfate concentration was elevated in four of six basins with sufficient data. The widespread elevation of specific conductance and concentrations of chloride and sulfate indicates that salinity generally was affected by drought in Colorado streams during July-September 2002, likely because streamflow at most sites was dominated by base flow of ground water, which usually has substantially greater salinity compared to runoff from precipitation. Total-recoverable iron and manganese concentrations were depressed (in the lower quartile of historical data) in the Arkansas River Basin, which likely was due to reduced land-surface washoff of sediment containing oxyhydroxides of these metals. Of the 246 water samples collected at 148 sites during the summer of 2002, constituents in 115 exceeded Colorado water-quality standards. Constituents that exceeded water-quality standards were pH (all 9.0 standard unit exceedances; 9 samples), chloride (1 sample), sulfate (9 samples), dissolved ammonia (10 samples), dissolved nitrite nitrogen (3 samples), E. coli (Escherichia coli) bacteria (34 samples, 20 in Arkansas River Basin), fecal-coliform bacteria (18 samples, all in Arkansas River Basin), dissolved copper (1 sample), dissolved iron (3 samples), total-recoverable iron (3 samples), dissolved manganese (13 samples), dissolved selenium (10 samples), and dissolved zinc (1 sample). Of these 115 exceedances, historical data were sufficient to conclude that 21 probably were affected by drought, that 39 probably were not affected by drought, and that 55 were of indeterminate nature. Specific conductance indicates that the San Juan River Basin (average percentile 95.2) experienced the greatest effects of drought on water quality during summer 2002 compared to other basins in Colorado, followed by the Upper Colorado (90.0) and Dolores River (85.7) Basins. The South Platte River Basin (70.9) experienced the least effect of drought, and the Yampa and White River Basin group (73.7) had the second smallest effect. The Gunnison River (82.1) and Arkansas River (81.2) Basins had intermediate drought effects. The Rio Grande had insufficient data to rank the relative effect of drought on salinity.

Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis

PubMed Central

Zhao, Hongjuan; Hastie, Trevor; Whitfield, Michael L; Børresen-Dale, Anne-Lise; Jeffrey, Stefanie S

2002-01-01

Background T7 based linear amplification of RNA is used to obtain sufficient antisense RNA for microarray expression profiling. We optimized and systematically evaluated the fidelity and reproducibility of different amplification protocols using total RNA obtained from primary human breast carcinomas and high-density cDNA microarrays. Results Using an optimized protocol, the average correlation coefficient of gene expression of 11,123 cDNA clones between amplified and unamplified samples is 0.82 (0.85 when a virtual array was created using repeatedly amplified samples to minimize experimental variation). Less than 4% of genes show changes in expression level by 2-fold or greater after amplification compared to unamplified samples. Most changes due to amplification are not systematic both within one tumor sample and between different tumors. Amplification appears to dampen the variation of gene expression for some genes when compared to unamplified poly(A)+ RNA. The reproducibility between repeatedly amplified samples is 0.97 when performed on the same day, but drops to 0.90 when performed weeks apart. The fidelity and reproducibility of amplification is not affected by decreasing the amount of input total RNA in the 0.3–3 micrograms range. Adding template-switching primer, DNA ligase, or column purification of double-stranded cDNA does not improve the fidelity of amplification. The correlation coefficient between amplified and unamplified samples is higher when total RNA is used as template for both experimental and reference RNA amplification. Conclusion T7 based linear amplification reproducibly generates amplified RNA that closely approximates original sample for gene expression profiling using cDNA microarrays. PMID:12445333

Antiretroviral drug susceptibility among drug-naive adults with recent HIV infection in Rakai, Uganda

PubMed Central

Eshleman, Susan H.; Laeyendecker, Oliver; Parkin, Neil; Huang, Wei; Chappey, Colombe; Paquet, Agnes C.; Serwadda, David; Reynolds, Steven J.; Kiwanuka, Noah; Quinn, Thomas C.; Gray, Ronald; Wawer, Maria

2009-01-01

Objective To analyze antiretroviral drug susceptibility in HIV from recently infected adults in Rakai, Uganda, prior to the availability of antiretroviral drug treatment. Methods Samples obtained at the time of HIV seroconversion (1998–2003) were analyzed using the GeneSeq HIV and PhenoSense HIV assays (Monogram Biosciences, Inc., South San Francisco, California, USA). Results Test results were obtained for 104 samples (subtypes: 26A, 1C, 66D, 9A/D, 1C/D, 1 intersubtype recombinant). Mutations used for genotypic surveillance of transmitted antiretroviral drug resistance were identified in six samples: three had nucleoside reverse transcriptase inhibitor (NRTI) surveillance mutations (two had M41L, one had K219R), and three had protease inhibitor surveillance mutations (I47V, F53L, N88D); none had nonnucleoside reverse transcriptase inhibitor (NNRTI) surveillance mutations. Other resistance-associated mutations were identified in some samples. However, none of the samples had a sufficient number of mutations to predict reduced antiretroviral drug susceptibility. Ten (9.6%) of the samples had reduced phenotypic susceptibility to at least one drug (one had partial susceptibility to didanosine, one had nevirapine resistance, and eight had resistance or partial susceptibility to at least one protease inhibitor). Fifty-three (51%) of the samples had hypersusceptibility to at least one drug (seven had zidovudine hypersusceptibility, 28 had NNRTI hypersusceptibility, 34 had protease inhibitor hypersusceptibility). Delavirdine hyper-susceptibility was more frequent in subtype A than D. In subtype D, efavirenz hypersusceptibility was associated with substitutions at codon 11 in HIV-reverse transcriptase. Conclusion Phenotyping detected reduced antiretroviral drug susceptibility and hypersusceptibility in HIV from some antiretroviral-naive Ugandan adults that was not predicted by genotyping. Phenotyping may complement genotyping for analysis of antiretroviral drug susceptibility in populations with nonsubtype B HIV infection. PMID:19276794

Antiretroviral drug susceptibility among drug-naive adults with recent HIV infection in Rakai, Uganda.

PubMed

Eshleman, Susan H; Laeyendecker, Oliver; Parkin, Neil; Huang, Wei; Chappey, Colombe; Paquet, Agnes C; Serwadda, David; Reynolds, Steven J; Kiwanuka, Noah; Quinn, Thomas C; Gray, Ronald; Wawer, Maria

2009-04-27

To analyze antiretroviral drug susceptibility in HIV from recently infected adults in Rakai, Uganda, prior to the availability of antiretroviral drug treatment. Samples obtained at the time of HIV seroconversion (1998-2003) were analyzed using the GeneSeq HIV and PhenoSense HIV assays (Monogram Biosciences, Inc., South San Francisco, California, USA). Test results were obtained for 104 samples (subtypes: 26A, 1C, 66D, 9A/D, 1C/D, 1 intersubtype recombinant). Mutations used for genotypic surveillance of transmitted antiretroviral drug resistance were identified in six samples: three had nucleoside reverse transcriptase inhibitor (NRTI) surveillance mutations (two had M41L, one had K219R), and three had protease inhibitor surveillance mutations (I47V, F53L, N88D); none had nonnucleoside reverse transcriptase inhibitor (NNRTI) surveillance mutations. Other resistance-associated mutations were identified in some samples. However, none of the samples had a sufficient number of mutations to predict reduced antiretroviral drug susceptibility. Ten (9.6%) of the samples had reduced phenotypic susceptibility to at least one drug (one had partial susceptibility to didanosine, one had nevirapine resistance, and eight had resistance or partial susceptibility to at least one protease inhibitor). Fifty-three (51%) of the samples had hypersusceptibility to at least one drug (seven had zidovudine hypersusceptibility, 28 had NNRTI hypersusceptibility, 34 had protease inhibitor hypersusceptibility). Delavirdine hypersusceptibility was more frequent in subtype A than D. In subtype D, efavirenz hypersusceptibility was associated with substitutions at codon 11 in HIV-reverse transcriptase. Phenotyping detected reduced antiretroviral drug susceptibility and hypersusceptibility in HIV from some antiretroviral-naive Ugandan adults that was not predicted by genotyping. Phenotyping may complement genotyping for analysis of antiretroviral drug susceptibility in populations with nonsubtype B HIV infection.

The electronically excited states of LH2 complexes from Rhodopseudomonas acidophila strain 10050 studied by time-resolved spectroscopy and dynamic Monte Carlo simulations. I. Isolated, non-interacting LH2 complexes.

PubMed

Pflock, Tobias J; Oellerich, Silke; Southall, June; Cogdell, Richard J; Ullmann, G Matthias; Köhler, Jürgen

2011-07-21

We have employed time-resolved spectroscopy on the picosecond time scale in combination with dynamic Monte Carlo simulations to investigate the photophysical properties of light-harvesting 2 (LH2) complexes from the purple photosynthetic bacterium Rhodopseudomonas acidophila. The variations of the fluorescence transients were studied as a function of the excitation fluence, the repetition rate of the excitation and the sample preparation conditions. Here we present the results obtained on detergent solubilized LH2 complexes, i.e., avoiding intercomplex interactions, and show that a simple four-state model is sufficient to grasp the experimental observations quantitatively without the need for any free parameters. This approach allows us to obtain a quantitative measure for the singlet-triplet annihilation rate in isolated, noninteracting LH2 complexes.

Detection and differentiation of biological species using microcalorimetric spectroscopy.

PubMed

Arakawa, E T; Lavrik, N V; Rajic, S; Datskos, P G

2003-01-01

We report on the application of infrared (IR) microcalorimetric spectroscopy ( micro -CalSpec) to the identification and detection of trace amounts of biological species. Our approach combines principles of photothermal IR spectroscopy with ultrasensitive microcantilever (MC) thermal detectors. We have obtained photothermal IR spectra for DNA and RNA bases and for Bacillus Cereus (an anthrax simulant) in the wavelength range of 2.5-14.5 micro m (4000-690 cm(-1)). The measurements are accomplished by absorbing biological materials directly on a MC thermal detector. The main advantage of the developed micro -CalSpec is its unprecedented sensitivity as compared to any of the previously explored IR techniques, including FTIR and photothermal FTIR methods. Our results demonstrate that <10(-9)g of a biological sample is sufficient to obtain its characteristic micro -CalSpec spectrum that contains information-rich chemical (vibrational) signatures. This opens up a new opportunity to create inexpensive high-throughput analytical systems for biochemical detection.

Characterization of Nanoporous Materials with Atom Probe Tomography.

PubMed

Pfeiffer, Björn; Erichsen, Torben; Epler, Eike; Volkert, Cynthia A; Trompenaars, Piet; Nowak, Carsten

2015-06-01

A method to characterize open-cell nanoporous materials with atom probe tomography (APT) has been developed. For this, open-cell nanoporous gold with pore diameters of around 50 nm was used as a model system, and filled by electron beam-induced deposition (EBID) to obtain a compact material. Two different EBID precursors were successfully tested-dicobalt octacarbonyl [Co2(CO)8] and diiron nonacarbonyl [Fe2(CO)9]. Penetration and filling depth are sufficient for focused ion beam-based APT sample preparation. With this approach, stable APT analysis of the nanoporous material can be performed. Reconstruction reveals the composition of the deposited precursor and the nanoporous material, as well as chemical information of the interfaces between them. Thus, it is shown that, using an appropriate EBID process, local chemical information in three dimensions with sub-nanometer resolution can be obtained from nanoporous materials using APT.

The effect of guessing on the speech reception thresholds of children.

PubMed

Moodley, A

1990-01-01

Speech audiometry is an essential part of the assessment of hearing impaired children and it is now widely used throughout the United Kingdom. Although instructions are universally agreed upon as an important aspect in the administration of any form of audiometric testing, there has been little, if any, research towards evaluating the influence which instructions that are given to a listener have on the Speech Reception Threshold obtained. This study attempts to evaluate what effect guessing has on the Speech Reception Threshold of children. A sample of 30 secondary school pupils between 16 and 18 years of age with normal hearing was used in the study. It is argued that the type of instruction normally used for Speech Reception Threshold in audiometric testing may not provide a sufficient amount of control for guessing and the implications of this, using data obtained in the study, are examined.

Comparison of Spectrophotometry, Chromate Inhibition, and Cytofluorometry Versus Gene Sequencing for Detection of Heterozygously Glucose-6-Phosphate Dehydrogenase-Deficient Females.

PubMed

Peters, Anna L; Veldthuis, Martijn; van Leeuwen, Karin; Bossuyt, Patrick M M; Vlaar, Alexander P J; van Bruggen, Robin; de Korte, Dirk; Van Noorden, Cornelis J F; van Zwieten, Rob

2017-11-01

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common enzyme deficiency worldwide. Detection of heterozygously deficient females can be difficult as residual activity in G6PD-sufficient red blood cells (RBCs) can mask deficiency. In this study, we compared accuracy of 4 methods for detection of G6PD deficiency in females. Blood samples from females more than 3 months of age were used for spectrophotometric measurement of G6PD activity and for determination of the percentage G6PD-negative RBCs by cytofluorometry. An additional sample from females suspected to have G6PD deficiency based on the spectrophotometric G6PD activity was used for measuring chromate inhibition and sequencing of the G6PD gene. Of 165 included females, 114 were suspected to have heterozygous deficiency. From 75 females, an extra sample was obtained. In this group, mutation analysis detected 27 heterozygously deficient females. The sensitivity of spectrophotometry, cytofluorometry, and chromate inhibition was calculated to be 0.52 (confidence interval [CI]: 0.32-0.71), 0.85 (CI: 0.66-0.96), and 0.96 (CI: 0.71-1.00, respectively, and the specificity was 1.00 (CI: 0.93-1.00), 0.88 (CI: 0.75-0.95), and 0.98 (CI: 0.89-1.00), respectively. Heterozygously G6PD-deficient females with a larger percentage of G6PD-sufficient RBCs are missed by routine methods measuring total G6PD activity. However, the majority of these females can be detected with both chromate inhibition and cytofluorometry.

Headspace needle-trap analysis of priority volatile organic compounds from aqueous samples: application to the analysis of natural and waste waters.

PubMed

Alonso, Monica; Cerdan, Laura; Godayol, Anna; Anticó, Enriqueta; Sanchez, Juan M

2011-11-11

Combining headspace (HS) sampling with a needle-trap device (NTD) to determine priority volatile organic compounds (VOCs) in water samples results in improved sensitivity and efficiency when compared to conventional static HS sampling. A 22 gauge stainless steel, 51-mm needle packed with Tenax TA and Carboxen 1000 particles is used as the NTD. Three different HS-NTD sampling methodologies are evaluated and all give limits of detection for the target VOCs in the ng L⁻¹ range. Active (purge-and-trap) HS-NTD sampling is found to give the best sensitivity but requires exhaustive control of the sampling conditions. The use of the NTD to collect the headspace gas sample results in a combined adsorption/desorption mechanism. The testing of different temperatures for the HS thermostating reveals a greater desorption effect when the sample is allowed to diffuse, whether passively or actively, through the sorbent particles. The limits of detection obtained in the simplest sampling methodology, static HS-NTD (5 mL aqueous sample in 20 mL HS vials, thermostating at 50 °C for 30 min with agitation), are sufficiently low as to permit its application to the analysis of 18 priority VOCs in natural and waste waters. In all cases compounds were detected below regulated levels. Copyright © 2011 Elsevier B.V. All rights reserved.

Challenges in collecting clinical samples for research from pregnant women of South Asian origin: evidence from a UK study.

PubMed

Neelotpol, Sharmind; Hay, Alastair W M; Jolly, A Jim; Woolridge, Mike W

2016-08-31

To recruit South Asian pregnant women, living in the UK, into a clinicoepidemiological study for the collection of lifestyle survey data and antenatal blood and to retain the women for the later collection of cord blood and meconium samples from their babies for biochemical analysis. A longitudinal study recruiting pregnant women of South Asian and Caucasian origin living in the UK. Recruitment of the participants, collection of clinical samples and survey data took place at the 2 sites within a single UK Northern Hospital Trust. Pregnant women of South Asian origin (study group, n=98) and of Caucasian origin (comparison group, n=38) living in Leeds, UK. Among the participants approached, 81% agreed to take part in the study while a 'direct approach' method was followed. The retention rate of the participants was a remarkable 93.4%. The main challenges in recruiting the ethnic minority participants were their cultural and religious conservativeness, language barrier, lack of interest and feeling of extra 'stress' in taking part in research. The chief investigator developed an innovative participant retention method, associated with the women's cultural and religious practices. The method proved useful in retaining the participants for about 5 months and in enabling successful collection of clinical samples from the same mother-baby pairs. The collection of clinical samples and lifestyle data exceeded the calculated sample size required to give the study sufficient power. The numbers of samples obtained were: maternal blood (n=171), cord blood (n=38), meconium (n=176), lifestyle questionnaire data (n=136) and postnatal records (n=136). Recruitment and retention of participants, according to the calculated sample size, ensured sufficient power and success for a clinicoepidemiological study. Results suggest that development of trust and confidence between the participant and the researcher is the key to the success of a clinical and epidemiological study involving ethnic minorities. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Dilute acid/metal salt hydrolysis of lignocellulosics

DOEpatents

Nguyen, Quang A.; Tucker, Melvin P.

2002-01-01

A modified dilute acid method of hydrolyzing the cellulose and hemicellulose in lignocellulosic material under conditions to obtain higher overall fermentable sugar yields than is obtainable using dilute acid alone, comprising: impregnating a lignocellulosic feedstock with a mixture of an amount of aqueous solution of a dilute acid catalyst and a metal salt catalyst sufficient to provide higher overall fermentable sugar yields than is obtainable when hydrolyzing with dilute acid alone; loading the impregnated lignocellulosic feedstock into a reactor and heating for a sufficient period of time to hydrolyze substantially all of the hemicellulose and greater than 45% of the cellulose to water soluble sugars; and recovering the water soluble sugars.

Method and apparatus for nitrogen oxide determination

DOEpatents

Hohorst, Frederick A.

1990-01-01

Method and apparatus for determining nitrogen oxide content in a high temperature process gas, which involves withdrawing a sample portion of a high temperature gas containing nitrogen oxide from a source to be analyzed. The sample portion is passed through a restrictive flow conduit, which may be a capillary or a restriction orifice. The restrictive flow conduit is heated to a temperature sufficient to maintain the flowing sample portion at an elevated temperature at least as great as the temperature of the high temperature gas source, to thereby provide that deposition of ammonium nitrate within the restrictive flow conduit cannot occur. The sample portion is then drawn into an aspirator device. A heated motive gas is passed to the aspirator device at a temperature at least as great as the temperature of the high temperature gas source. The motive gas is passed through the nozzle of the aspirator device under conditions sufficient to aspirate the heated sample portion through the restrictive flow conduit and produce a mixture of the sample portion in the motive gas at a dilution of the sample portion sufficient to provide that deposition of ammonium nitrate from the mixture cannot occur at reduced temperature. A portion of the cooled dilute mixture is then passed to analytical means capable of detecting nitric oxide.

Design, development, and field demonstration of a remotely deployable water quality monitoring system

NASA Technical Reports Server (NTRS)

Wallace, J. W.; Lovelady, R. W.; Ferguson, R. L.

1981-01-01

A prototype water quality monitoring system is described which offers almost continuous in situ monitoring. The two-man portable system features: (1) a microprocessor controlled central processing unit which allows preprogrammed sampling schedules and reprogramming in situ; (2) a subsurface unit for multiple depth capability and security from vandalism; (3) an acoustic data link for communications between the subsurface unit and the surface control unit; (4) eight water quality parameter sensors; (5) a nonvolatile magnetic bubble memory which prevents data loss in the event of power interruption; (6) a rechargeable power supply sufficient for 2 weeks of unattended operation; (7) a water sampler which can collect samples for laboratory analysis; (8) data output in direct engineering units on printed tape or through a computer compatible link; (9) internal electronic calibration eliminating external sensor adjustment; and (10) acoustic location and recovery systems. Data obtained in Saginaw Bay, Lake Huron are tabulated.

State prison mental heath services recipients perception of care survey.

PubMed

Way, Bruce B; Sawyer, Don A; Kahkejian, Deborah; Moffitt, Catherine; Lilly, Stephanie N

2007-12-01

Studies have demonstrated the importance of patient perceptions' of mental health service quality. No studies, however, could be found that surveyed recipients in prison, despite the rapid growth of patients, and litigation in these settings. Patients were asked to complete an anonymous survey in private, and sealed it in an envelope. Of 613 respondents, most were satisfied (79%), agreed they had sufficient access to therapists (78%), were involved with treatment decisions (84%), and thought the MH services they had received would help them better deal with a crisis and emotional stress (75%). There were differences among mental health programs/housing units. Several of perception questions were significantly correlated with medication compliance, admission to crisis observation cells, and receiving disciplinary infractions. Random samples were requested, but likely only a convenience sample was obtained. However, the positive results suggest the need to strive to enhance patient quality of care ratings.

Development of an X-ray surface analyzer for planetary exploration

NASA Technical Reports Server (NTRS)

Clark, B. C.

1972-01-01

An ultraminiature X-ray fluorescence spectrometer was developed which can obtain data on element composition not provided by present spacecraft instrumentation. The apparatus employs two radioisotope sources (Fe-55 and Cd-109) which irradiate adjacent areas on a soil sample. Fluorescent X-rays emitted by the sample are detected by four thin-window proportional counters. Using pulse-height discrimination, the energy spectra are determined. Virtually all elements above sodium in the periodic table are detected if present at sufficient levels. Minimum detection limits range from 30 ppm to several percent, depending upon the element and the matrix. For most elements, they are below 0.5 percent. Accuracies likewise depend upon the matrix, but are generally better than plus or minus 0.5 percent for all elements of atomic number greater than 14. Elements below sodium are also detected, but as a single group.

Characterizing Conformational Dynamics of Proteins Using Evolutionary Couplings.

PubMed

Feng, Jiangyan; Shukla, Diwakar

2018-01-25

Understanding of protein conformational dynamics is essential for elucidating molecular origins of protein structure-function relationship. Traditionally, reaction coordinates, i.e., some functions of protein atom positions and velocities have been used to interpret the complex dynamics of proteins obtained from experimental and computational approaches such as molecular dynamics simulations. However, it is nontrivial to identify the reaction coordinates a priori even for small proteins. Here, we evaluate the power of evolutionary couplings (ECs) to capture protein dynamics by exploring their use as reaction coordinates, which can efficiently guide the sampling of a conformational free energy landscape. We have analyzed 10 diverse proteins and shown that a few ECs are sufficient to characterize complex conformational dynamics of proteins involved in folding and conformational change processes. With the rapid strides in sequencing technology, we expect that ECs could help identify reaction coordinates a priori and enhance the sampling of the slow dynamical process associated with protein folding and conformational change.

A comparison of maximum likelihood and other estimators of eigenvalues from several correlated Monte Carlo samples

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

Beer, M.

1980-12-01

The maximum likelihood method for the multivariate normal distribution is applied to the case of several individual eigenvalues. Correlated Monte Carlo estimates of the eigenvalue are assumed to follow this prescription and aspects of the assumption are examined. Monte Carlo cell calculations using the SAM-CE and VIM codes for the TRX-1 and TRX-2 benchmark reactors, and SAM-CE full core results are analyzed with this method. Variance reductions of a few percent to a factor of 2 are obtained from maximum likelihood estimation as compared with the simple average and the minimum variance individual eigenvalue. The numerical results verify that themore » use of sample variances and correlation coefficients in place of the corresponding population statistics still leads to nearly minimum variance estimation for a sufficient number of histories and aggregates.« less

a Novel Deep Convolutional Neural Network for Spectral-Spatial Classification of Hyperspectral Data

NASA Astrophysics Data System (ADS)

Li, N.; Wang, C.; Zhao, H.; Gong, X.; Wang, D.

2018-04-01

Spatial and spectral information are obtained simultaneously by hyperspectral remote sensing. Joint extraction of these information of hyperspectral image is one of most import methods for hyperspectral image classification. In this paper, a novel deep convolutional neural network (CNN) is proposed, which extracts spectral-spatial information of hyperspectral images correctly. The proposed model not only learns sufficient knowledge from the limited number of samples, but also has powerful generalization ability. The proposed framework based on three-dimensional convolution can extract spectral-spatial features of labeled samples effectively. Though CNN has shown its robustness to distortion, it cannot extract features of different scales through the traditional pooling layer that only have one size of pooling window. Hence, spatial pyramid pooling (SPP) is introduced into three-dimensional local convolutional filters for hyperspectral classification. Experimental results with a widely used hyperspectral remote sensing dataset show that the proposed model provides competitive performance.

Reflectance of polytetrafluoroethylene for xenon scintillation light

NASA Astrophysics Data System (ADS)

Silva, C.; Pinto da Cunha, J.; Pereira, A.; Chepel, V.; Lopes, M. I.; Solovov, V.; Neves, F.

2010-03-01

Gaseous and liquid xenon particle detectors are being used in a number of applications including dark matter search and neutrino-less double beta decay experiments. Polytetrafluoroethylene (PTFE) is often used in these detectors both as electrical insulator and as a light reflector to improve the efficiency of detection of scintillation photons. However, xenon emits in the vacuum ultraviolet (VUV) wavelength region (λ ≃175 nm) where the reflecting properties of PTFE are not sufficiently known. In this work, we report on measurements of PTFE reflectance, including its angular distribution, for the xenon scintillation light. Various samples of PTFE, manufactured by different processes (extruded, expanded, skived, and pressed) have been studied. The data were interpreted with a physical model comprising both specular and diffuse reflections. The reflectance obtained for these samples ranges from about 47% to 66% for VUV light. Other fluoropolymers, namely, ethylene tetrafluoroethylene (ETFE), fluorinated ethylene propylene (FEP), and perfluoro-alkoxyalkane (PFA) were also measured.

Detection of Methamphetamine and Morphine in Urine and Saliva Using Excitation-Emission Matrix Fluorescence and a Second-Order Calibration Algorithm

NASA Astrophysics Data System (ADS)

Xu, B. Y.; Ye, Y.; Liao, L. C.

2016-07-01

A new method was developed to determine the methamphetamine and morphine concentrations in urine and saliva based on excitation-emission matrix fluorescence coupled to a second-order calibration algorithm. In the case of single-drug abuse, the results showed that the average recoveries of methamphetamine and morphine were 95.3 and 96.7% in urine samples, respectively, and 98.1 and 106.2% in saliva samples, respectively. The relative errors were all below 5%. The simultaneous determination of methamphetamine and morphine in urine using two second-order algorithms was also investigated. Satisfactory results were obtained with a self-weighted alternating trilinear decomposition algorithm. The root-mean-square errors of the predictions were 0.540 and 0.0382 μg/mL for methamphetamine and morphine, respectively. The limits of detection of the proposed methods were very low and sufficient for studying methamphetamine and morphine in urine.

A New Electromagnetic Acoustic Transducer Design for Generating and Receiving S0 Lamb Waves in Ferromagnetic Steel Plate

PubMed Central

He, Jianpeng; Dixon, Steve; Hill, Samuel; Xu, Ke

2017-01-01

Electromagnetic acoustic transducers (EMATs) are non-contact, ultrasonic transducers that are usually kept within 5 mm from the sample surface to obtain a sufficient signal-to-noise ratio (SNR). One important issue associated with operation on a ferromagnetic plate is that the strong attraction force from the magnet can affect measurements and make scanning difficult. This paper investigates a method to generate fundamental, symmetric Lamb waves on a ferromagnetic plate. A coil-only, low-weight, generation EMAT is designed and investigated, operating at lift-offs of over 5 mm. Another design of an EMAT is investigated using a rectangular magnet with a much higher lift-off than the coil, of up to 19 mm. This results in a much lower force between the EMAT and sample, making scanning the EMAT much easier. PMID:28471377

Quality assurance in RT-PCR-based BCR/ABL diagnostics--results of an interlaboratory test and a standardization approach.

PubMed

Burmeister, T; Maurer, J; Aivado, M; Elmaagacli, A H; Grünebach, F; Held, K R; Hess, G; Hochhaus, A; Höppner, W; Lentes, K U; Lübbert, M; Schäfer, K L; Schafhausen, P; Schmidt, C A; Schüler, F; Seeger, K; Seelig, R; Thiede, C; Viehmann, S; Weber, C; Wilhelm, S; Christmann, A; Clement, J H; Ebener, U; Enczmann, J; Leo, R; Schleuning, M; Schoch, R; Thiel, E

2000-10-01

Here we describe the results of an interlaboratory test for RT-PCR-based BCR/ABL analysis. The test was organized in two parts. The number of participating laboratories in the first and second part was 27 and 20, respectively. In the first part samples containing various concentrations of plasmids with the ela2, b2a2 or b3a2 BCR/ABL transcripts were analyzed by PCR. In the second part of the test, cell samples containing various concentrations of BCR/ABL-positive cells were analyzed by RT-PCR. Overall PCR sensitivity was sufficient in approximately 90% of the tests, but a significant number of false positive results were obtained. There were significant differences in sensitivity in the cell-based analysis between the various participants. The results are discussed, and proposals are made regarding the choice of primers, controls, conditions for RNA extraction and reverse transcription.

Internal friction and velocity measurements. [vacuum effects on lunar basalt resonance

NASA Technical Reports Server (NTRS)

Tittmann, B. R.; Ahlberg, L.; Curnow, J.

1976-01-01

The Q of a lunar basalt sample was measured under varying vacuum conditions, and it was found that even at pressures as low as 10 to the -7th to 10 to the -10th torr, substantial increases in Q with decreasing pressure are observed, while the resonant frequency increases only slightly. This suggests that only small amounts of volatiles are sufficient to increase the internal friction (lower the Q) dramatically. The technique of vibrating encapsulated samples in the torsional mode was used to measure Q of terrestrial rocks as a function of hydrostatic pressure under lunar vacuum conditions. Young's modulus measurements in the temperature range 25-600 C under a variety of conditions including high vacuum show no evidence of any irreversibility upon temperature cycling and no indication that the high Q-values obtained are associated with any permanent structure changes such as the formation of lossless 'welded' contacts.

EEG source localization: Sensor density and head surface coverage.

PubMed

Song, Jasmine; Davey, Colin; Poulsen, Catherine; Luu, Phan; Turovets, Sergei; Anderson, Erik; Li, Kai; Tucker, Don

2015-12-30

The accuracy of EEG source localization depends on a sufficient sampling of the surface potential field, an accurate conducting volume estimation (head model), and a suitable and well-understood inverse technique. The goal of the present study is to examine the effect of sampling density and coverage on the ability to accurately localize sources, using common linear inverse weight techniques, at different depths. Several inverse methods are examined, using the popular head conductivity. Simulation studies were employed to examine the effect of spatial sampling of the potential field at the head surface, in terms of sensor density and coverage of the inferior and superior head regions. In addition, the effects of sensor density and coverage are investigated in the source localization of epileptiform EEG. Greater sensor density improves source localization accuracy. Moreover, across all sampling density and inverse methods, adding samples on the inferior surface improves the accuracy of source estimates at all depths. More accurate source localization of EEG data can be achieved with high spatial sampling of the head surface electrodes. The most accurate source localization is obtained when the voltage surface is densely sampled over both the superior and inferior surfaces. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Sample size adjustments for varying cluster sizes in cluster randomized trials with binary outcomes analyzed with second-order PQL mixed logistic regression.

PubMed

Candel, Math J J M; Van Breukelen, Gerard J P

2010-06-30

Adjustments of sample size formulas are given for varying cluster sizes in cluster randomized trials with a binary outcome when testing the treatment effect with mixed effects logistic regression using second-order penalized quasi-likelihood estimation (PQL). Starting from first-order marginal quasi-likelihood (MQL) estimation of the treatment effect, the asymptotic relative efficiency of unequal versus equal cluster sizes is derived. A Monte Carlo simulation study shows this asymptotic relative efficiency to be rather accurate for realistic sample sizes, when employing second-order PQL. An approximate, simpler formula is presented to estimate the efficiency loss due to varying cluster sizes when planning a trial. In many cases sampling 14 per cent more clusters is sufficient to repair the efficiency loss due to varying cluster sizes. Since current closed-form formulas for sample size calculation are based on first-order MQL, planning a trial also requires a conversion factor to obtain the variance of the second-order PQL estimator. In a second Monte Carlo study, this conversion factor turned out to be 1.25 at most. (c) 2010 John Wiley & Sons, Ltd.

Method for Measuring Thermal Conductivity of Small Samples Having Very Low Thermal Conductivity

NASA Technical Reports Server (NTRS)

Miller, Robert A.; Kuczmarski, Maria a.

2009-01-01

This paper describes the development of a hot plate method capable of using air as a standard reference material for the steady-state measurement of the thermal conductivity of very small test samples having thermal conductivity on the order of air. As with other approaches, care is taken to ensure that the heat flow through the test sample is essentially one-dimensional. However, unlike other approaches, no attempt is made to use heated guards to block the flow of heat from the hot plate to the surroundings. It is argued that since large correction factors must be applied to account for guard imperfections when sample dimensions are small, it may be preferable to simply measure and correct for the heat that flows from the heater disc to directions other than into the sample. Experimental measurements taken in a prototype apparatus, combined with extensive computational modeling of the heat transfer in the apparatus, show that sufficiently accurate measurements can be obtained to allow determination of the thermal conductivity of low thermal conductivity materials. Suggestions are made for further improvements in the method based on results from regression analyses of the generated data.

High-capacity ice-recrystallization endpoint assay employing superhydrophobic coatings that is equivalent to the 'splat' assay.

PubMed

Graham, Laurie A; Agrawal, Prashant; Oleschuk, Richard D; Davies, Peter L

2018-04-01

We have developed an ice recrystallization inhibition (IRI) assay system that allows the side-by-side comparison of up to a dozen samples treated in an identical manner. This system is ideal for determining, by serial dilution, the IRI 'endpoint' where the concentration of a sample is reached that can no longer inhibit recrystallization. Samples can be an order of magnitude smaller in volume (<1 μL) than those used for the conventional 'splat' assay. The samples are pipetted into wells cut out of a superhydrophobic coating on sapphire slides that are covered with a second slide and then snap-frozen in liquid nitrogen. Sapphire is greatly superior to glass in its ability to cool quickly without cracking. As a consequence, the samples freeze evenly as a multi-crystalline mass. The ice grain size is slightly larger than that obtained by the 'splat' assay but can be followed sufficiently well to assess IRI activity by changes in mean grain boundary size. The slides can be washed in detergent and reused with no carryover of IRI activity even from the highest protein concentrations. Copyright © 2018 Elsevier Inc. All rights reserved.

Halo-free phase contrast microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Nguyen, Tan H.; Kandel, Mikhail E.; Shakir, Haadi M.; Best, Catherine; Do, Minh N.; Popescu, Gabriel

2017-02-01

The phase contrast (PC) method is one of the most impactful developments in the four-century long history of microscopy. It allows for intrinsic, nondestructive contrast of transparent specimens, such as live cells. However, PC is plagued by the halo artifact, a result of insufficient spatial coherence in the illumination field, which limits its applicability. We present a new approach for retrieving halo-free phase contrast microscopy (hfPC) images by upgrading the conventional PC microscope with an external interferometric module, which generates sufficient data for reversing the halo artifact. Measuring four independent intensity images, our approach first measures haloed phase maps of the sample. We solve for the halo-free sample transmission function by using a physical model of the image formation under partial spatial coherence. Using this halo-free sample transmission, we can numerically generate artifact-free PC images. Furthermore, this transmission can be further used to obtain quantitative information about the sample, e.g., the thickness with known refractive indices, dry mass of live cells during their cycles. We tested our hfPC method on various control samples, e.g., beads, pillars and validated its potential for biological investigation by imaging live HeLa cells, red blood cells, and neurons.

Evaluating noninvasive genetic sampling techniques to estimate large carnivore abundance.

PubMed

Mumma, Matthew A; Zieminski, Chris; Fuller, Todd K; Mahoney, Shane P; Waits, Lisette P

2015-09-01

Monitoring large carnivores is difficult because of intrinsically low densities and can be dangerous if physical capture is required. Noninvasive genetic sampling (NGS) is a safe and cost-effective alternative to physical capture. We evaluated the utility of two NGS methods (scat detection dogs and hair sampling) to obtain genetic samples for abundance estimation of coyotes, black bears and Canada lynx in three areas of Newfoundland, Canada. We calculated abundance estimates using program capwire, compared sampling costs, and the cost/sample for each method relative to species and study site, and performed simulations to determine the sampling intensity necessary to achieve abundance estimates with coefficients of variation (CV) of <10%. Scat sampling was effective for both coyotes and bears and hair snags effectively sampled bears in two of three study sites. Rub pads were ineffective in sampling coyotes and lynx. The precision of abundance estimates was dependent upon the number of captures/individual. Our simulations suggested that ~3.4 captures/individual will result in a < 10% CV for abundance estimates when populations are small (23-39), but fewer captures/individual may be sufficient for larger populations. We found scat sampling was more cost-effective for sampling multiple species, but suggest that hair sampling may be less expensive at study sites with limited road access for bears. Given the dependence of sampling scheme on species and study site, the optimal sampling scheme is likely to be study-specific warranting pilot studies in most circumstances. © 2015 John Wiley & Sons Ltd.

Simple and accurate quantification of BTEX in ambient air by SPME and GC-MS.

PubMed

Baimatova, Nassiba; Kenessov, Bulat; Koziel, Jacek A; Carlsen, Lars; Bektassov, Marat; Demyanenko, Olga P

2016-07-01

Benzene, toluene, ethylbenzene and xylenes (BTEX) comprise one of the most ubiquitous and hazardous groups of ambient air pollutants of concern. Application of standard analytical methods for quantification of BTEX is limited by the complexity of sampling and sample preparation equipment, and budget requirements. Methods based on SPME represent simpler alternative, but still require complex calibration procedures. The objective of this research was to develop a simpler, low-budget, and accurate method for quantification of BTEX in ambient air based on SPME and GC-MS. Standard 20-mL headspace vials were used for field air sampling and calibration. To avoid challenges with obtaining and working with 'zero' air, slope factors of external standard calibration were determined using standard addition and inherently polluted lab air. For polydimethylsiloxane (PDMS) fiber, differences between the slope factors of calibration plots obtained using lab and outdoor air were below 14%. PDMS fiber provided higher precision during calibration while the use of Carboxen/PDMS fiber resulted in lower detection limits for benzene and toluene. To provide sufficient accuracy, the use of 20mL vials requires triplicate sampling and analysis. The method was successfully applied for analysis of 108 ambient air samples from Almaty, Kazakhstan. Average concentrations of benzene, toluene, ethylbenzene and o-xylene were 53, 57, 11 and 14µgm(-3), respectively. The developed method can be modified for further quantification of a wider range of volatile organic compounds in air. In addition, the new method is amenable to automation. Copyright © 2016 Elsevier B.V. All rights reserved.

How the reference values for serum parathyroid hormone concentration are (or should be) established?

PubMed

Souberbielle, J-C; Brazier, F; Piketty, M-L; Cormier, C; Minisola, S; Cavalier, E

2017-03-01

Well-validated reference values are necessary for a correct interpretation of a serum PTH concentration. Establishing PTH reference values needs recruiting a large reference population. Exclusion criteria for this population can be defined as any situation possibly inducing an increase or a decrease in PTH concentration. As recommended in the recent guidelines on the diagnosis and management of asymptomatic primary hyperparathyroidism, PTH reference values should be established in vitamin D-replete subjects with a normal renal function with possible stratification according to various factors such as age, gender, menopausal status, body mass index, and race. A consensus about analytical/pre-analytical aspects of PTH measurement is also needed with special emphasis on the nature of the sample (plasma or serum), the time and the fasting/non-fasting status of the blood sample. Our opinion is that blood sample for PTH measurement should be obtained in the morning after an overnight fast. Furthermore, despite longer stability of the PTH molecule in EDTA plasma, we prefer serum as it allows to measure calcium, a prerequisite for a correct interpretation of a PTH concentration, on the same sample. Once a consensus is reached, we believe an important international multicentre work should be performed to recruit a very extensive reference population of apparently healthy vitamin D-replete subjects with a normal renal function in order to establish the PTH normative data. Due to the huge inter-method variability in PTH measurement, a sufficient quantity of blood sample should be obtained to allow measurement with as many PTH kits as possible.

A Contribution to the Kinetic Study of the Metatectic Reaction U+U$sub 3$Si$sub 2$$Yields$U$sub 3$Si; CONTRIBUTION AL ESTUDIO CINETICO DE LA REACCION METATECTICA U+U$sub 3$Si$sub 2$$Yields$U$sub 3$Si

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

Ruiperez, J.A.; Hernandez, J.A.E.

1962-01-01

An experimental study was made to decide upon the advantages and drawbacks of the different methods and reagents employed in the metallography of U-Si alloys. It has been observed that all samples thermally treated to the epsilon-phase undergo a coalescence of the U/sub 3/Si/sub 2/ particles. The coalescence decreases the surface available for reaction and consequently the reaction rate. The growth of the U/sub 3/Si/sub 2/ phase particles was determined as a function of time and temperature. To obtain samples with nuclei sufficiently isolated so that the U/sub 3/Si rings will not interfere their respective growth, the conditions that regulatemore » coalescence, Si content and thermal treatment, were determined. Data rel1tive to the growth of the U/sub 3/ Si phase-rings were obtained. Curves relating growth, time, and temperature are presented. The parameters that define the diffusion regulated reaction can be deduced from these curves. (auth)« less

Study samples are too small to produce sufficiently precise reliability coefficients.

PubMed

Charter, Richard A

2003-04-01

In a survey of journal articles, test manuals, and test critique books, the author found that a mean sample size (N) of 260 participants had been used for reliability studies on 742 tests. The distribution was skewed because the median sample size for the total sample was only 90. The median sample sizes for the internal consistency, retest, and interjudge reliabilities were 182, 64, and 36, respectively. The author presented sample size statistics for the various internal consistency methods and types of tests. In general, the author found that the sample sizes that were used in the internal consistency studies were too small to produce sufficiently precise reliability coefficients, which in turn could cause imprecise estimates of examinee true-score confidence intervals. The results also suggest that larger sample sizes have been used in the last decade compared with those that were used in earlier decades.

Isolation and molecular characterization of Leptospira borgpetersenii serovar Hardjo strain Hardjobovis in the urine of naturally infected cattle in Brazil.

PubMed

Chideroli, R T; Pereira, U P; Gonçalves, D D; Nakamura, A Y; Alfieri, A A; Alfieri, A F; Freitas, J C

2016-02-19

Most epidemiologic studies on bovine leptospirosis are based on serological tests that use antibodies against several serotypes, including the serovar Hardjo, which is widespread and considered to be the most adapted to bovine hosts. However, using only serological studies is not sufficient to identify and distinguish species of leptospires. The aim of this study was report the first isolation in Brazil of two strains serovar Hardjo obtained in urine samples from naturally infected cows in a small Brazilian dairy herd and find the genetic species and consequently the type strain Hardjobovis by molecular characterization. Fifteen dairy cows with a history of reproductive failure, such as abortion and infertility, were selected. Urine samples obtained from each animal were immediately seeded in tubes containing Ellinghausen-McCullough-Johnson-Harris culture medium. The identification of the isolates was performed by Multilocus variable-number tandem-repeat analysis (MLVA) technique and phylogenetic analysis of partial sequence of gene sec Y. From the 15 urine samples evaluated, two Leptospira were found and identified as the Londrina 49 and Londrina 54 strains. The MLVA profiles and sequencing of gene sec Y characterized the isolates as L. borgpetersenii serovar Hardjo strain Hadjobovis because it has different genetic pattern of Leptospira interrogans serovar Hardjo strain Hardjoprajitno. Therefore, more studies are needed including isolation and molecular characterization from regional strains to obtain a better knowledge about epidemiology of serovar Hardjo in bovine which may assist in future strategies of prevention and control of bovine leptospirosis.

Strategies for the structural analysis of multi-protein complexes: lessons from the 3D-Repertoire project.

PubMed

Collinet, B; Friberg, A; Brooks, M A; van den Elzen, T; Henriot, V; Dziembowski, A; Graille, M; Durand, D; Leulliot, N; Saint André, C; Lazar, N; Sattler, M; Séraphin, B; van Tilbeurgh, H

2011-08-01

Structural studies of multi-protein complexes, whether by X-ray diffraction, scattering, NMR spectroscopy or electron microscopy, require stringent quality control of the component samples. The inability to produce 'keystone' subunits in a soluble and correctly folded form is a serious impediment to the reconstitution of the complexes. Co-expression of the components offers a valuable alternative to the expression of single proteins as a route to obtain sufficient amounts of the sample of interest. Even in cases where milligram-scale quantities of purified complex of interest become available, there is still no guarantee that good quality crystals can be obtained. At this step, protein engineering of one or more components of the complex is frequently required to improve solubility, yield or the ability to crystallize the sample. Subsequent characterization of these constructs may be performed by solution techniques such as Small Angle X-ray Scattering and Nuclear Magnetic Resonance to identify 'well behaved' complexes. Herein, we recount our experiences gained at protein production and complex assembly during the European 3D Repertoire project (3DR). The goal of this consortium was to obtain structural information on multi-protein complexes from yeast by combining crystallography, electron microscopy, NMR and in silico modeling methods. We present here representative set case studies of complexes that were produced and analyzed within the 3DR project. Our experience provides useful insight into strategies that are more generally applicable for structural analysis of protein complexes. Copyright © 2011 Elsevier Inc. All rights reserved.

Linear stable unity-feedback system - Necessary and sufficient conditions for stability under nonlinear plant perturbations

NASA Technical Reports Server (NTRS)

Desoer, C. A.; Kabuli, M. G.

1989-01-01

The authors consider a linear (not necessarily time-invariant) stable unity-feedback system, where the plant and the compensator have normalized right-coprime factorizations. They study two cases of nonlinear plant perturbations (additive and feedback), with four subcases resulting from: (1) allowing exogenous input to Delta P or not; 2) allowing the observation of the output of Delta P or not. The plant perturbation Delta P is not required to be stable. Using the factorization approach, the authors obtain necessary and sufficient conditions for all cases in terms of two pairs of nonlinear pseudostate maps. Simple physical considerations explain the form of these necessary and sufficient conditions. Finally, the authors obtain the characterization of all perturbations Delta P for which the perturbed system remains stable.

Analysis of the fractures of metallic materials using optical coherence tomography

NASA Astrophysics Data System (ADS)

Hutiu, Gh.; Duma, V.-F.; Demian, D.; Bradu, A.; Podoleanu, A. Gh.

2017-06-01

Forensic in situ investigations, for example for aviation, maritime, road, or rail accidents would benefit from a method that may allow to distinguish ductile from brittle fractures of metals - as material defects are one of the potential causes of such accidents. Currently, the gold standard in material studies is represented by scanning electron microscopy (SEM). However, SEM are large, lab-based systems, therefore in situ measurements are excluded. In addition, they are expensive and time-consuming. We have approached this problem and propose the use of Optical Coherence Tomography (OCT) in such investigations in order to overcome these disadvantages of SEM. In this respect, we demonstrate the capability to perform such fracture analysis by obtaining the topography of metallic surfaces using OCT. Different materials have been analyzed; in this presentation a sample of low soft carbon steel with the chemical composition of C 0.2%, Mn 1.15%, S 0.04%, P 0.05 % and Fe for the rest has been considered. An in-house developed Swept Source (SS) OCT system has been used, and height profiles have been generated for the sample surface. This profile allowed for concluding that the carbon steel sample was subjected to a ductile fracture. A validation of the OCT images obtained with a 10 microns resolution has been made with SEM images obtained with a 4 nm resolution. Although the OCT resolution is much lower than the one of SEM, we thus demonstrate that it is sufficient in order to obtain clear images of the grains of the metallic materials and thus to distinguish between ductile and brittle fractures. This study analysis opens avenues for a range of applications, including: (i) to determine the causes that have generated pipe ruptures, or structural failures of metallic bridges and buildings, as well as damages of machinery parts; (ii) to optimize the design of various machinery; (iii) to obtain data regarding the structure of metallic alloys); (iv) to improve the manufacturing technologies of metallic parts.

The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data.

PubMed

Duchêne, Sebastián; Duchêne, David; Holmes, Edward C; Ho, Simon Y W

2015-07-01

Rates and timescales of viral evolution can be estimated using phylogenetic analyses of time-structured molecular sequences. This involves the use of molecular-clock methods, calibrated by the sampling times of the viral sequences. However, the spread of these sampling times is not always sufficient to allow the substitution rate to be estimated accurately. We conducted Bayesian phylogenetic analyses of simulated virus data to evaluate the performance of the date-randomization test, which is sometimes used to investigate whether time-structured data sets have temporal signal. An estimate of the substitution rate passes this test if its mean does not fall within the 95% credible intervals of rate estimates obtained using replicate data sets in which the sampling times have been randomized. We find that the test sometimes fails to detect rate estimates from data with no temporal signal. This error can be minimized by using a more conservative criterion, whereby the 95% credible interval of the estimate with correct sampling times should not overlap with those obtained with randomized sampling times. We also investigated the behavior of the test when the sampling times are not uniformly distributed throughout the tree, which sometimes occurs in empirical data sets. The test performs poorly in these circumstances, such that a modification to the randomization scheme is needed. Finally, we illustrate the behavior of the test in analyses of nucleotide sequences of cereal yellow dwarf virus. Our results validate the use of the date-randomization test and allow us to propose guidelines for interpretation of its results. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems.

PubMed

Pan, Albert C; Weinreich, Thomas M; Piana, Stefano; Shaw, David E

2016-03-08

Molecular dynamics (MD) simulations can describe protein motions in atomic detail, but transitions between protein conformational states sometimes take place on time scales that are infeasible or very expensive to reach by direct simulation. Enhanced sampling methods, the aim of which is to increase the sampling efficiency of MD simulations, have thus been extensively employed. The effectiveness of such methods when applied to complex biological systems like proteins, however, has been difficult to establish because even enhanced sampling simulations of such systems do not typically reach time scales at which convergence is extensive enough to reliably quantify sampling efficiency. Here, we obtain sufficiently converged simulations of three proteins to evaluate the performance of simulated tempering, a member of a widely used class of enhanced sampling methods that use elevated temperature to accelerate sampling. Simulated tempering simulations with individual lengths of up to 100 μs were compared to (previously published) conventional MD simulations with individual lengths of up to 1 ms. With two proteins, BPTI and ubiquitin, we evaluated the efficiency of sampling of conformational states near the native state, and for the third, the villin headpiece, we examined the rate of folding and unfolding. Our comparisons demonstrate that simulated tempering can consistently achieve a substantial sampling speedup of an order of magnitude or more relative to conventional MD.

Absolute mass scale calibration in the inverse problem of the physical theory of fireballs.

NASA Astrophysics Data System (ADS)

Kalenichenko, V. V.

A method of the absolute mass scale calibration is suggested for solving the inverse problem of the physical theory of fireballs. The method is based on the data on the masses of the fallen meteorites whose fireballs have been photographed in their flight. The method may be applied to those fireballs whose bodies have not experienced considerable fragmentation during their destruction in the atmosphere and have kept their form well enough. Statistical analysis of the inverse problem solution for a sufficiently representative sample makes it possible to separate a subsample of such fireballs. The data on the Lost City and Innisfree meteorites are used to obtain calibration coefficients.

Permanence and asymptotic behaviors of stochastic predator-prey system with Markovian switching and Lévy noise

NASA Astrophysics Data System (ADS)

Wang, Sheng; Wang, Linshan; Wei, Tengda

2018-04-01

This paper concerns the dynamics of a stochastic predator-prey system with Markovian switching and Lévy noise. First, the existence and uniqueness of global positive solution to the system is proved. Then, by combining stochastic analytical techniques with M-matrix analysis, sufficient conditions of stochastic permanence and extinction are obtained. Furthermore, for the stochastic permanence case, by means of four constants related to the stationary probability distribution of the Markov chain and the parameters of the subsystems, both the superior limit and the inferior limit of the average in time of the sample path of the solution are estimated. Finally, our conclusions are illustrated through an example.

Nested methylation-specific polymerase chain reaction cancer detection method

DOEpatents

Belinsky, Steven A [Albuquerque, NM; Palmisano, William A [Edgewood, NM

2007-05-08

A molecular marker-based method for monitoring and detecting cancer in humans. Aberrant methylation of gene promoters is a marker for cancer risk in humans. A two-stage, or "nested" polymerase chain reaction method is disclosed for detecting methylated DNA sequences at sufficiently high levels of sensitivity to permit cancer screening in biological fluid samples, such as sputum, obtained non-invasively. The method is for detecting the aberrant methylation of the p16 gene, O 6-methylguanine-DNA methyltransferase gene, Death-associated protein kinase gene, RAS-associated family 1 gene, or other gene promoters. The method offers a potentially powerful approach to population-based screening for the detection of lung and other cancers.

Observations of emission in bright, low redshift quasars

NASA Technical Reports Server (NTRS)

1983-01-01

Ultraviolet, infrared, and optical spectra were combined to obtain a data set sample as broad as possible in the range of hydrogen lines in individual quasars. From the measured Lyman fluxes, coupled with Balmer and Paschen line fluxes measured in these same objects, an effort was made to establish observational constraints that would guide models of the broad emission line regions of quasars. It was found that IUE spectra were generally of sufficiently high quality to derive line profiles of the ultraviolet lines Lyman alpha and CIV 1550 A, which were compared to the Balmer line profiles. The objects observed and the line fluxes are tabulated. Plots of line profiles are included.

Mapping the human atria with optical coherence tomography

NASA Astrophysics Data System (ADS)

Lye, Theresa H.; Gan, Yu; Hendon, Christine P.

2017-02-01

Atrial structure plays an important role in the mechanisms of atrial disease. However, detailed imaging of human atria remains limited due to many imaging modalities lacking sufficient resolution. We propose the use of optical coherence tomography (OCT), which has micrometer resolution and millimeter-scale imaging depth well-suited for the atria, combined with image stitching algorithms, to develop large, detailed atria image maps. Human atria samples (n = 7) were obtained under approved protocols from the National Disease Research Interchange (NDRI). One right atria sample was imaged using an ultrahigh-resolution spectral domain OCT system, with 5.52 and 2.72 μm lateral and axial resolution in air, respectively, and 1.78 mm imaging depth. Six left atria and five pulmonary vein samples were imaged using the spectral domain OCT system, Telesto I (Thorlabs GmbH, Germany) with 15 and 6.5 μm lateral and axial resolution in air, respectively, and 2.51 mm imaging depth. Overlapping image volumes were obtained from areas of the human left and right atria and the pulmonary veins. Regions of collagen, adipose, and myocardium could be identified within the OCT images. Image stitching was applied to generate fields of view with side dimensions up to about 3 cm. This study established steps towards mapping large regions of the human atria and pulmonary veins in high resolution using OCT.

Optimization of crystallization conditions for biological macromolecules.

PubMed

McPherson, Alexander; Cudney, Bob

2014-11-01

For the successful X-ray structure determination of macromolecules, it is first necessary to identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals are frequently microcrystals or clusters, and often have unfavorable morphologies or yield poor diffraction intensities. It is therefore generally necessary to improve upon these initial conditions in order to obtain better crystals of sufficient quality for X-ray data collection. Even when the initial samples are suitable, often marginally, refinement of conditions is recommended in order to obtain the highest quality crystals that can be grown. The quality of an X-ray structure determination is directly correlated with the size and the perfection of the crystalline samples; thus, refinement of conditions should always be a primary component of crystal growth. The improvement process is referred to as optimization, and it entails sequential, incremental changes in the chemical parameters that influence crystallization, such as pH, ionic strength and precipitant concentration, as well as physical parameters such as temperature, sample volume and overall methodology. It also includes the application of some unique procedures and approaches, and the addition of novel components such as detergents, ligands or other small molecules that may enhance nucleation or crystal development. Here, an attempt is made to provide guidance on how optimization might best be applied to crystal-growth problems, and what parameters and factors might most profitably be explored to accelerate and achieve success.

Optimization of crystallization conditions for biological macromolecules

PubMed Central

McPherson, Alexander; Cudney, Bob

2014-01-01

For the successful X-ray structure determination of macromolecules, it is first necessary to identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals are frequently microcrystals or clusters, and often have unfavorable morphologies or yield poor diffraction intensities. It is therefore generally necessary to improve upon these initial conditions in order to obtain better crystals of sufficient quality for X-ray data collection. Even when the initial samples are suitable, often marginally, refinement of conditions is recommended in order to obtain the highest quality crystals that can be grown. The quality of an X-ray structure determination is directly correlated with the size and the perfection of the crystalline samples; thus, refinement of conditions should always be a primary component of crystal growth. The improvement process is referred to as optimization, and it entails sequential, incremental changes in the chemical parameters that influence crystallization, such as pH, ionic strength and precipitant concentration, as well as physical parameters such as temperature, sample volume and overall methodology. It also includes the application of some unique procedures and approaches, and the addition of novel components such as detergents, ligands or other small molecules that may enhance nucleation or crystal development. Here, an attempt is made to provide guidance on how optimization might best be applied to crystal-growth problems, and what parameters and factors might most profitably be explored to accelerate and achieve success. PMID:25372810

PCR for the identification and differentiation of Histomonas meleagridis, Tetratrichomonas gallinarum and Blastocystis spp.

PubMed

Grabensteiner, E; Hess, M

2006-12-20

In the present investigation PCR assays were developed for the rapid detection and differentiation of two poultry flagellates: Histomonas meleagridis and Tetratrichomonas gallinarum as well as the protozoan microorganism: Blastocystis spp. The nucleotide sequences of the small subunit ribosomal RNAs were used for primer construction obtaining fragments which vary in size for each microorganism. The established PCRs were able to detect DNA obtained from one microorganism of T. gallinarum and Blastocystis spp. propagated in vitro, proving the high analytical sensitivity of the method. DNA isolated from 10 protozoa was sufficient to detect H. meleagridis. To assess specificity, each PCR assay was performed with DNA from either H. meleagridis and/or T. gallinarum and/or Blastocystis spp. as well as with DNA from several other protozoan parasites (Eimeria tenella, Toxoplasma gondii, Cryptosporidia spp., Trichomonas gallinae, Entamoeba invadens, Entamoeba ranarum), fungi (Aspergillus fumigatus, Candida albicans), bacteria (Staphylococcae, Streptococcae, E. coli, Clostridium perfringens, Camplyobacter jejuni, Proteus) and viruses (fowl adenovirus serotype 4, avian reovirus) as well as livers and caecal samples from turkeys and specified pathogen free (spf) chickens. No cross-reactions with any of these samples were observed with the primer sets for the detection of H. meleagridis and Blastocystis spp. The primers designed for the identification of T. gallinarum yielded a PCR product with DNA of Trichomonas gallinae that had the identical size as the amplicon obtained with DNA from T. gallinarum. However, no PCR products resulted from any of the other samples tested with these primers. Liver and caecal samples from turkeys and chickens from flocks with outbreaks of histomonosis also named as "histomoniasis" originating from geographically distinct regions were investigated with the established PCRs. This is also the first report about the detection of the nucleic acid of H. meleagridis, T. gallinarum and Blastocystis spp. nucleic acid in the livers and/or caeca of laying hens and turkeys obtained from field outbreaks. Hence, the established PCR assays proved to be a rapid and sensitive diagnostic tool for the direct detection and differentiation of H. meleagridis, T. gallinarum and Blastocystis spp. nucleic acid in organ samples of infected turkeys and chickens regardless of the geographic origin.

Automated cell counts on CSF samples: A multicenter performance evaluation of the GloCyte system.

PubMed

Hod, E A; Brugnara, C; Pilichowska, M; Sandhaus, L M; Luu, H S; Forest, S K; Netterwald, J C; Reynafarje, G M; Kratz, A

2018-02-01

Automated cell counters have replaced manual enumeration of cells in blood and most body fluids. However, due to the unreliability of automated methods at very low cell counts, most laboratories continue to perform labor-intensive manual counts on many or all cerebrospinal fluid (CSF) samples. This multicenter clinical trial investigated if the GloCyte System (Advanced Instruments, Norwood, MA), a recently FDA-approved automated cell counter, which concentrates and enumerates red blood cells (RBCs) and total nucleated cells (TNCs), is sufficiently accurate and precise at very low cell counts to replace all manual CSF counts. The GloCyte System concentrates CSF and stains RBCs with fluorochrome-labeled antibodies and TNCs with nucleic acid dyes. RBCs and TNCs are then counted by digital image analysis. Residual adult and pediatric CSF samples obtained for clinical analysis at five different medical centers were used for the study. Cell counts were performed by the manual hemocytometer method and with the GloCyte System following the same protocol at all sites. The limits of the blank, detection, and quantitation, as well as precision and accuracy of the GloCyte, were determined. The GloCyte detected as few as 1 TNC/μL and 1 RBC/μL, and reliably counted as low as 3 TNCs/μL and 2 RBCs/μL. The total coefficient of variation was less than 20%. Comparison with cell counts obtained with a hemocytometer showed good correlation (>97%) between the GloCyte and the hemocytometer, including at very low cell counts. The GloCyte instrument is a precise, accurate, and stable system to obtain red cell and nucleated cell counts in CSF samples. It allows for the automated enumeration of even very low cell numbers, which is crucial for CSF analysis. These results suggest that GloCyte is an acceptable alternative to the manual method for all CSF samples, including those with normal cell counts. © 2017 John Wiley & Sons Ltd.

Voids and constraints on nonlinear clustering of galaxies

NASA Technical Reports Server (NTRS)

Vogeley, Michael S.; Geller, Margaret J.; Park, Changbom; Huchra, John P.

1994-01-01

Void statistics of the galaxy distribution in the Center for Astrophysics Redshift Survey provide strong constraints on galaxy clustering in the nonlinear regime, i.e., on scales R equal to or less than 10/h Mpc. Computation of high-order moments of the galaxy distribution requires a sample that (1) densely traces the large-scale structure and (2) covers sufficient volume to obtain good statistics. The CfA redshift survey densely samples structure on scales equal to or less than 10/h Mpc and has sufficient depth and angular coverage to approach a fair sample on these scales. In the nonlinear regime, the void probability function (VPF) for CfA samples exhibits apparent agreement with hierarchical scaling (such scaling implies that the N-point correlation functions for N greater than 2 depend only on pairwise products of the two-point function xi(r)) However, simulations of cosmological models show that this scaling in redshift space does not necessarily imply such scaling in real space, even in the nonlinear regime; peculiar velocities cause distortions which can yield erroneous agreement with hierarchical scaling. The underdensity probability measures the frequency of 'voids' with density rho less than 0.2 -/rho. This statistic reveals a paucity of very bright galaxies (L greater than L asterisk) in the 'voids.' Underdensities are equal to or greater than 2 sigma more frequent in bright galaxy samples than in samples that include fainter galaxies. Comparison of void statistics of CfA samples with simulations of a range of cosmological models favors models with Gaussian primordial fluctuations and Cold Dark Matter (CDM)-like initial power spectra. Biased models tend to produce voids that are too empty. We also compare these data with three specific models of the Cold Dark Matter cosmogony: an unbiased, open universe CDM model (omega = 0.4, h = 0.5) provides a good match to the VPF of the CfA samples. Biasing of the galaxy distribution in the 'standard' CDM model (omega = 1, b = 1.5; see below for definitions) and nonzero cosmological constant CDM model (omega = 0.4, h = 0.6 lambda(sub 0) = 0.6, b = 1.3) produce voids that are too empty. All three simulations match the observed VPF and underdensity probability for samples of very bright (M less than M asterisk = -19.2) galaxies, but produce voids that are too empty when compared with samples that include fainter galaxies.

Whale sharks target dense prey patches of sergestid shrimp off Tanzania

PubMed Central

Rohner, Christoph A.; Armstrong, Amelia J.; Pierce, Simon J.; Prebble, Clare E. M.; Cagua, E. Fernando; Cochran, Jesse E. M.; Berumen, Michael L.; Richardson, Anthony J.

2015-01-01

Large planktivores require high-density prey patches to make feeding energetically viable. This is a major challenge for species living in tropical and subtropical seas, such as whale sharks Rhincodon typus. Here, we characterize zooplankton biomass, size structure and taxonomic composition from whale shark feeding events and background samples at Mafia Island, Tanzania. The majority of whale sharks were feeding (73%, 380 of 524 observations), with the most common behaviour being active surface feeding (87%). We used 20 samples collected from immediately adjacent to feeding sharks and an additional 202 background samples for comparison to show that plankton biomass was ∼10 times higher in patches where whale sharks were feeding (25 vs. 2.6 mg m−3). Taxonomic analyses of samples showed that the large sergestid Lucifer hanseni (∼10 mm) dominated while sharks were feeding, accounting for ∼50% of identified items, while copepods (<2 mm) dominated background samples. The size structure was skewed towards larger animals representative of L.hanseni in feeding samples. Thus, whale sharks at Mafia Island target patches of dense, large, zooplankton dominated by sergestids. Large planktivores, such as whale sharks, which generally inhabit warm oligotrophic waters, aggregate in areas where they can feed on dense prey to obtain sufficient energy. PMID:25814777

Compact ultrahigh vacuum sample environments for x-ray nanobeam diffraction and imaging.

PubMed

Evans, P G; Chahine, G; Grifone, R; Jacques, V L R; Spalenka, J W; Schülli, T U

2013-11-01

X-ray nanobeams present the opportunity to obtain structural insight in materials with small volumes or nanoscale heterogeneity. The effective spatial resolution of the information derived from nanobeam techniques depends on the stability and precision with which the relative position of the x-ray optics and sample can be controlled. Nanobeam techniques include diffraction, imaging, and coherent scattering, with applications throughout materials science and condensed matter physics. Sample positioning is a significant mechanical challenge for x-ray instrumentation providing vacuum or controlled gas environments at elevated temperatures. Such environments often have masses that are too large for nanopositioners capable of the required positional accuracy of the order of a small fraction of the x-ray spot size. Similarly, the need to place x-ray optics as close as 1 cm to the sample places a constraint on the overall size of the sample environment. We illustrate a solution to the mechanical challenge in which compact ion-pumped ultrahigh vacuum chambers with masses of 1-2 kg are integrated with nanopositioners. The overall size of the environment is sufficiently small to allow their use with zone-plate focusing optics. We describe the design of sample environments for elevated-temperature nanobeam diffraction experiments demonstrate in situ diffraction, reflectivity, and scanning nanobeam imaging of the ripening of Au crystallites on Si substrates.

Compact ultrahigh vacuum sample environments for x-ray nanobeam diffraction and imaging

NASA Astrophysics Data System (ADS)

Evans, P. G.; Chahine, G.; Grifone, R.; Jacques, V. L. R.; Spalenka, J. W.; Schülli, T. U.

2013-11-01

X-ray nanobeams present the opportunity to obtain structural insight in materials with small volumes or nanoscale heterogeneity. The effective spatial resolution of the information derived from nanobeam techniques depends on the stability and precision with which the relative position of the x-ray optics and sample can be controlled. Nanobeam techniques include diffraction, imaging, and coherent scattering, with applications throughout materials science and condensed matter physics. Sample positioning is a significant mechanical challenge for x-ray instrumentation providing vacuum or controlled gas environments at elevated temperatures. Such environments often have masses that are too large for nanopositioners capable of the required positional accuracy of the order of a small fraction of the x-ray spot size. Similarly, the need to place x-ray optics as close as 1 cm to the sample places a constraint on the overall size of the sample environment. We illustrate a solution to the mechanical challenge in which compact ion-pumped ultrahigh vacuum chambers with masses of 1-2 kg are integrated with nanopositioners. The overall size of the environment is sufficiently small to allow their use with zone-plate focusing optics. We describe the design of sample environments for elevated-temperature nanobeam diffraction experiments demonstrate in situ diffraction, reflectivity, and scanning nanobeam imaging of the ripening of Au crystallites on Si substrates.

48 CFR 9.105-1 - Obtaining information.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 48 Federal Acquisition Regulations System 1 2013-10-01 2013-10-01 false Obtaining information. 9... information. (a) Before making a determination of responsibility, the contracting officer shall possess or obtain information sufficient to be satisfied that a prospective contractor currently meets the...

Highest Resolution Topography of 433 Eros and Implications for MUSES-C

NASA Technical Reports Server (NTRS)

Cheng, A. F.; Barnouin-Jha, O.

2003-01-01

The highest resolution observations of surface morphology and topography at asteroid 433 Eros were obtained by the Near Earth Asteroid Rendezvous (NEAR) Shoemaker spacecraft on 12 February 2001, as it landed within a ponded deposit on Eros. Coordinated observations were obtained by the imager and the laser rangefinder, at best image resolution of 1 cm/pixel and best topographic resolution of 0.4 m. The NEAR landing datasets provide unique information on rock size and height distributions and regolith processes. Rocks and soil can be distinguished photometrically, suggesting that bare rock is indeed exposed. The NEAR landing data are the only data at sufficient resolution to be relevant to hazard assessment on future landed missions to asteroids, such as the MUSES-C mission which will land on asteroid 25143 (1998 SF36) in order to obtain samples. In a typical region just outside the pond where NEAR landed, the areal coverage by resolved positive topographic features is 18%. At least one topographic feature in the vicinity of the NEAR landing site would have been hazardous for a spacecraft.

Nonuniform sampling and non-Fourier signal processing methods in multidimensional NMR

PubMed Central

Mobli, Mehdi; Hoch, Jeffrey C.

2017-01-01

Beginning with the introduction of Fourier Transform NMR by Ernst and Anderson in 1966, time domain measurement of the impulse response (the free induction decay, FID) consisted of sampling the signal at a series of discrete intervals. For compatibility with the discrete Fourier transform (DFT), the intervals are kept uniform, and the Nyquist theorem dictates the largest value of the interval sufficient to avoid aliasing. With the proposal by Jeener of parametric sampling along an indirect time dimension, extension to multidimensional experiments employed the same sampling techniques used in one dimension, similarly subject to the Nyquist condition and suitable for processing via the discrete Fourier transform. The challenges of obtaining high-resolution spectral estimates from short data records using the DFT were already well understood, however. Despite techniques such as linear prediction extrapolation, the achievable resolution in the indirect dimensions is limited by practical constraints on measuring time. The advent of non-Fourier methods of spectrum analysis capable of processing nonuniformly sampled data has led to an explosion in the development of novel sampling strategies that avoid the limits on resolution and measurement time imposed by uniform sampling. The first part of this review discusses the many approaches to data sampling in multidimensional NMR, the second part highlights commonly used methods for signal processing of such data, and the review concludes with a discussion of other approaches to speeding up data acquisition in NMR. PMID:25456315

When Sufficiently Processed, Semantically Related Distractor Pictures Hamper Picture Naming.

PubMed

Matushanskaya, Asya; Mädebach, Andreas; Müller, Matthias M; Jescheniak, Jörg D

2016-11-01

Prominent speech production models view lexical access as a competitive process. According to these models, a semantically related distractor picture should interfere with target picture naming more strongly than an unrelated one. However, several studies failed to obtain such an effect. Here, we demonstrate that semantic interference is obtained, when the distractor picture is sufficiently processed. Participants named one of two pictures presented in close temporal succession, with color cueing the target. Experiment 1 induced the prediction that the target appears first. When this prediction was violated (distractor first), semantic interference was observed. Experiment 2 ruled out that the time available for distractor processing was the driving force. These results show that semantically related distractor pictures interfere with the naming response when they are sufficiently processed. The data thus provide further support for models viewing lexical access as a competitive process.

Quantification of drugs in plasma without primary reference standards by liquid chromatography-chemiluminescence nitrogen detection: application to tramadol metabolite ratios.

PubMed

Ojanperä, Suvi; Rasanen, Ilpo; Sistonen, Johanna; Pelander, Anna; Vuori, Erkki; Ojanperä, Ilkka

2007-08-01

Lack of availability of reference standards for drug metabolites, newly released drugs, and illicit drugs hinders the analysis of these substances in biologic samples. To counter this problem, an approach is presented here for quantitative drug analysis in plasma without primary reference standards by liquid chromatography-chemiluminescence nitrogen detection (LC-CLND). To demonstrate the feasibility of the method, metabolic ratios of the opioid drug tramadol were determined in the setting of a pharmacogenetic study. Four volunteers were given a single 100-mg oral dose of tramadol, and a blood sample was collected from each subject 1 hour later. Tramadol, O-desmethyltramadol, and nortramadol were determined in plasma by LC-CLND without reference standards and by a gas chromatography-mass spectrometry reference method. In contrast to previous CLND studies lacking an extraction step, a liquid-liquid extraction system was created for 5-mL plasma samples using n-butyl chloride-isopropyl alcohol (98 + 2) at pH 10. Extraction recovery estimation was based on model compounds chosen according to their similar physicochemical characteristics (retention time, pKa, logD). Instrument calibration was performed with a single secondary standard (caffeine) using the equimolar response of the detector to nitrogen. The mean differences between the results of the LC-CLND and gas chromatography-mass spectrometry methods for tramadol, O-desmethyltramadol, and nortramadol were 8%, 32%, and 19%, respectively. The sensitivity of LC-CLND was sufficient for therapeutic concentrations of tramadol and metabolites. A good correlation was obtained between genotype, expressed by the number of functional genes, and the plasma metabolite ratios. This experiment suggests that a recovery-corrected LC-CLND analysis produces sufficiently accurate results to be useful in a clinical context, particularly in instances in which reference standards are not readily accessible.

RECOMMENDATIONS FOR SAMPLING OF TANK 18 IN F TANK FARM

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

Shine, G.

2009-12-14

Representative sampling is required for characterization of the residual floor material in Tank 18 prior to operational closure. Tank 18 is an 85-foot diameter, 34-foot high carbon steel tank with nominal operating volume of 1,300,000 gallons. It is a Type IV tank, and has been in service storing radioactive materials since 1959. Recent mechanical cleaning of the tank removed all mounds of material. Anticipating a low level of solids in the residual material, Huff and Thaxton [2009] developed a plan to sample the material during the final clean-up process while it would still be resident in sufficient quantities to supportmore » analytical determinations in four quadrants of the tank. Execution of the plan produced fewer solids than expected to support analytical determinations in all four quadrants. Huff and Thaxton [2009] then restructured the plan to characterize the residual floor material separately in the North and the South regions: two 'hemispheres.' This document provides sampling recommendations to complete the characterization of the residual material on the tank bottom following the guidance in Huff and Thaxton [2009] to split the tank floor into a North and a South hemisphere. The number of samples is determined from a modification of the formula previously published in Edwards [2001] and the sample characterization data for previous sampling of Tank 18 described by Oji [2009]. The uncertainty is quantified by an upper 95% confidence limit (UCL95%) on each analyte's mean concentration in Tank 18. The procedure computes the uncertainty in analyte concentration as a function of the number of samples, and the final number of samples is determined when the reduction in the uncertainty from an additional sample no longer has a practical impact on results. The characterization of the full suite of analytes in the North hemisphere is currently supported by a single Mantis rover sample obtained from a compact region near the center riser. A floor scrape sample was obtained from a compact region near the northeast riser and has been analyzed for a shortened list of key analytes. Since the unused portion of the floor scrape sample material is archived and available in sufficient quantity, additional analyses need to be performed to complete results for the full suite of constituents. The characterization of the full suite of analytes in the South hemisphere is currently supported by a single Mantis rover sample; there have been no floor scrape samples previously taken from the South hemisphere. The criterion to determine the number of additional samples was based on the practical reduction in the uncertainty when a new sample is added. This was achieved when five additional samples are obtained. In addition, two archived samples will be used if a contingency such as failing to demonstrate the comparability of the Mantis samples to the floor scrape samples occurs. To complete sampling of the Tank 18 residual floor material, three additional samples should be taken from the North hemisphere and four additional samples should be taken from the South hemisphere. One of the samples from each hemisphere will be archived in case of need. Two of the three additional samples from the North hemisphere and three of the four additional samples from the South hemisphere will be analyzed. Once the results are available, differences between the Mantis and three floor scrape samples (the sample previously obtained near NE riser plus the two additional samples that will be analyzed) results will be evaluated. If there are no statistically significant analyte concentration differences between the Mantis and floor scrape samples, those results will be combined and then UCL95%s will be calculated. If the analyte concentration differences between the Mantis and floor scrape samples are statistically significant, the UCL95%s will be calculated without the Mantis sample results. If further reduction in the upper confidence limits is needed and can be achieved by the addition of the archived samples, they will be analyzed and included in the statistical computations. Initially, the analyte concentrations in the residual material on the floor of Tank 18 will be determined separately in the North and the South hemispheres. However, if final sampling results show that differences between the North and South samples are consistent within sampling variation, then the final computations can be based on consolidating all sample results from the tank floor. Recommended locations may be subject to physical tank access and sampling constraints for the additional samples. The recommendations have been discussed in Section 4 and are based on partitioning the Tank 18 floor into an inner and an outer ring and six 60{sup o} sectors depicted in Figure 1. The location of the border between the inner and outer rings is based on dividing the residual material into two approximately equal volumes.« less

A comparative study on the information ethics of junior high school students cognition and behavior between Taiwan and China: Kaohsiung and Nanjing regions used as examples.

PubMed

Chiang, Wen-Jiuh; Chen, Chihchia; Teng, Chiachien; Gu, Jiangjun

2008-03-01

A great deal of progress has been made on information ethics. Which portion is not sufficient? That might be the comparison from countries to countries. The purpose of this study was closely examined using the cross-cultural method for comparison. To determine the ethics cognitions and behaviors of the students, a comprehensive survey was distributed. The questionnaire for the study used Mason's four essential factors in information ethics that included Privacy, Accuracy, Property and Accessibility (PAPA). The samples were comprised of Kaohsiung Taiwan and Nanjing China, junior high school students in 2006. The sample and the survey were obtained from two stages of random sampling that was conducted using an Internet website. Students could read the online questionnaire in the computer laboratory and then send immediate feedback to the website server. The result of the experiment showed the divergence of information ethics in cognition and behavior between Kaohsiung and Nanjing school children. The effects of background and correlation are from cognition and behavior between two regions.

Effect of high hydrostatic pressure processing and squeezing pressure on some quality properties of pomegranate juice against thermal treatment

NASA Astrophysics Data System (ADS)

Subasi, B. G.; Alpas, H.

2017-01-01

The aim of this study was to investigate the effect of high hydrostatic pressure (HHP) treatment (200, 300, 400 MPa; 5°C, 15°C and 25°C; 5 and 10 min) on some quality properties of pomegranate juice. Juice samples are obtained under industrial conditions at two different squeezing pressure levels (100 and 150 psi - 0.689 and 1.033 MPa, respectively). Results are compared against conventional thermal treatment (85°C/10 min) and raw sample. For all three processing temperature, HHP combinations at 400 MPa for 10 min were sufficient to decrease the microbial load around 4.0 log cycles for both squeeze levels. All HHP treatments showed no significant decrease at antioxidant activity, total phenolic content and monomeric anthocyanin pigment concentrations, while there was a significant decrease (p ≤ .05) in thermal-treated samples. Being the highest sugar alcohol in pomegranate juice, mannitol content must be considered for determining the authenticity, and mannitol content increased with squeezing pressure and thermal treatment.

Factor validity and norms for the aberrant behavior checklist in a community sample of children with mental retardation.

PubMed

Marshburn, E C; Aman, M G

1992-09-01

The Aberrant Behavior Checklist (ABC) is a 58-item rating scale that was developed primarily to measure the effects of pharmacological intervention in individuals living in residential facilities. This study investigated the use of the ABC in a sample of community children with mental retardation. Teacher ratings on the ABC were collected on 666 students attending special classes. The data were factor analyzed and compared with other studies using the ABC. In addition, subscales were analyzed as a function of age, sex, and classroom placement, and preliminary norms were derived. A four-factor solution of the ABC was obtained. Congruence between the four derived factors and corresponding factors from the original ABC was high (congruence coefficients ranged between .87 and .96). Classroom placement and age had significant effects on subscale scores, whereas sex failed to affect ratings. The current results are sufficiently close to the original factor solution that the original scoring method can be used with community samples, although further studies are needed to look at this in more detail.

Active antioxidants in ex-vivo examination of burn wound healing by means of IR and Raman spectroscopies-Preliminary comparative research

NASA Astrophysics Data System (ADS)

Pielesz, Anna; Biniaś, Dorota; Sarna, Ewa; Bobiński, Rafał; Kawecki, Marek; Glik, Justyna; Klama-Baryła, Agnieszka; Kitala, Diana; Łabuś, Wojciech; Paluch, Jadwiga; Kraut, Małgorzata

2017-02-01

Being a complex traumatic event, burn injury also affects other organ systems apart from the skin. Wounds undergo various pathological changes which are accompanied by alterations in the molecular environment. Information about molecules may be obtained with the use of Raman spectroscopy and Fourier-transform infrared spectroscopy, and when combined, both methods are a powerful tool for providing material characterization. Alterations in the molecular environment may lead to identifying objective markers of acute wound healing. In general, incubation of samples in solutions of L-ascorbic acid and 5% and 7% orthosilicic acid organizes the collagen structure, whereas the increased intensity of the Raman bands in the region of 1500-800 cm- 1 reveals regeneration of the burn tissue. Since oxidative damage is one of the mechanisms responsible for local and distant pathophysiological events after burn, antioxidant therapy can prove to be beneficial in minimizing burn wounds, which was examined on the basis of human skin samples and chicken skin samples, the latter being subject to modification when heated to a temperature sufficient for the simulation of a burn incident.

Acoustic Enrichment of Extracellular Vesicles from Biological Fluids.

PubMed

Ku, Anson; Lim, Hooi Ching; Evander, Mikael; Lilja, Hans; Laurell, Thomas; Scheding, Stefan; Ceder, Yvonne

2018-06-11

Extracellular vesicles (EVs) have emerged as a rich source of biomarkers providing diagnostic and prognostic information in diseases such as cancer. Large-scale investigations into the contents of EVs in clinical cohorts are warranted, but a major obstacle is the lack of a rapid, reproducible, efficient, and low-cost methodology to enrich EVs. Here, we demonstrate the applicability of an automated acoustic-based technique to enrich EVs, termed acoustic trapping. Using this technology, we have successfully enriched EVs from cell culture conditioned media and urine and blood plasma from healthy volunteers. The acoustically trapped samples contained EVs ranging from exosomes to microvesicles in size and contained detectable levels of intravesicular microRNAs. Importantly, this method showed high reproducibility and yielded sufficient quantities of vesicles for downstream analysis. The enrichment could be obtained from a sample volume of 300 μL or less, an equivalent to 30 min of enrichment time, depending on the sensitivity of downstream analysis. Taken together, acoustic trapping provides a rapid, automated, low-volume compatible, and robust method to enrich EVs from biofluids. Thus, it may serve as a novel tool for EV enrichment from large number of samples in a clinical setting with minimum sample preparation.

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

Holladay, S.K.; Anderson, H.M.; Benson, S.B.

Quality assurance (QA) objectives for Phase 2 were that (1) scientific data generated would withstand scientific and legal scrutiny; (2) data would be gathered using appropriate procedures for sample collection, sample handling and security, chain of custody, laboratory analyses, and data reporting; (3) data would be of known precision and accuracy; and (4) data would meet data quality objectives defined in the Phase 2 Sampling and Analysis Plan. A review of the QA systems and quality control (QC) data associated with the Phase 2 investigation is presented to evaluate whether the data were of sufficient quality to satisfy Phase 2more » objectives. The data quality indicators of precision, accuracy, representativeness, comparability, completeness, and sensitivity were evaluated to determine any limitations associated with the data. Data were flagged with qualifiers that were associated with appropriate reason codes and documentation relating the qualifiers to the reviewer of the data. These qualifiers were then consolidated into an overall final qualifier to represent the quality of the data to the end user. In summary, reproducible, precise, and accurate measurements consistent with CRRI objectives and the limitations of the sampling and analytical procedures used were obtained for the data collected in support of the Phase 2 Remedial Investigation.« less

Turbidimetric Analysis of Water and Wastewater Samples Using a Spectrofluorimeter

NASA Astrophysics Data System (ADS)

Evans, Jason J.

2000-12-01

As student interest in environmental science grows, many colleges and universities are developing new courses in environmental chemistry. Environmental analysis in the "real world" has become increasingly instrumental, and it is important to introduce students to the instruments and procedures that are commonly used in environmental laboratories. Turbidimetric analysis of water and wastewater is ordinarily performed in environmental laboratories using a nephelometer. This experiment illustrates that a spectrofluorimeter can be successfully employed for these types of analysis. Samples from various stages of the water and wastewater treatment processes were collected from the Carlisle Water and Wastewater Treatment Plants. The students in our Environmental Chemistry laboratory used the spectrofluorimeter to measure the scattering intensity from the samples and from a series of formazine standards. The standard curve produced from their data gave a correlation coefficient of .999, and the detection limit was 0.03 Standard Turbidity Units, which is sufficient to obtain meaningful data on most water samples. This experiment was an excellent supplement to lecture material covering water and wastewater treatment because the students were able to monitor the level of suspended particulates in the water as it makes its way through the treatment plants.

A simplified approach for monitoring hydrophobic organic contaminants associated with suspended sediment: Methodology and applications

USGS Publications Warehouse

Mahler, B.J.; Van Metre, P.C.

2003-01-01

Hydrophobic organic contaminants, although frequently detected in bed sediment and in aquatic biota, are rarely detected in whole-water samples, complicating determination of their occurrence, load, and source. A better approach for the investigation of hydrophobic organic contaminants is the direct analysis of sediment in suspension, but procedures for doing so are expensive and cumbersome. We describe a simple, inexpensive methodology for the dewatering of sediment and present the results of two case studies. Isolation of a sufficient mass of sediment for analyses of organochlorine compounds and PAHs is obtained by in-line filtration of large volumes of water. The sediment is removed from the filters and analyzed directly by standard laboratory methods. In the first case study, suspended-sediment sampling was used to determine occurrence, loads, and yields of contaminants in urban runoff affecting biota in Town Lake, Austin, TX. The second case study used suspended-sediment sampling to locate a point source of PCBs in the Donna Canal in south Texas, where fish are contaminated with PCBs. The case studies demonstrate that suspended-sediment sampling can be an effective tool for determining the occurrence, load, and source of hydrophobic organic contaminants in transport.

Focused conformational sampling in proteins

NASA Astrophysics Data System (ADS)

Bacci, Marco; Langini, Cassiano; Vymětal, Jiří; Caflisch, Amedeo; Vitalis, Andreas

2017-11-01

A detailed understanding of the conformational dynamics of biological molecules is difficult to obtain by experimental techniques due to resolution limitations in both time and space. Computer simulations avoid these in theory but are often too short to sample rare events reliably. Here we show that the progress index-guided sampling (PIGS) protocol can be used to enhance the sampling of rare events in selected parts of biomolecules without perturbing the remainder of the system. The method is very easy to use as it only requires as essential input a set of several features representing the parts of interest sufficiently. In this feature space, new states are discovered by spontaneous fluctuations alone and in unsupervised fashion. Because there are no energetic biases acting on phase space variables or projections thereof, the trajectories PIGS generates can be analyzed directly in the framework of transition networks. We demonstrate the possibility and usefulness of such focused explorations of biomolecules with two loops that are part of the binding sites of bromodomains, a family of epigenetic "reader" modules. This real-life application uncovers states that are structurally and kinetically far away from the initial crystallographic structures and are also metastable. Representative conformations are intended to be used in future high-throughput virtual screening campaigns.

General administrative rulings and decisions; amendment to the examination and investigation sample requirements; companion document to direct final rule--FDA. Proposed rule.

PubMed

1998-09-25

The Food and Drug Administration (FDA) is proposing to amend its regulations regarding the collection of twice the quantity of food, drug, or cosmetic estimated to be sufficient for analysis. This action increases the dollar amount that FDA will consider to determine whether to routinely collect a reserve sample of a food, drug, or cosmetic product in addition to the quantity sufficient for analysis. Experience has demonstrated that the current dollar amount does not adequately cover the cost of most quantities sufficient for analysis plus reserve samples. This proposed rule is a companion to the direct final rule published elsewhere in this issue of the Federal Register. This action is part of FDA's continuing effort to achieve the objectives of the President's "Reinventing Government" initiative, and it is intended to reduce the burden of unnecessary regulations on food, drugs, and cosmetics without diminishing the protection of the public health.

Two conditions for equivalence of 0-norm solution and 1-norm solution in sparse representation.

PubMed

Li, Yuanqing; Amari, Shun-Ichi

2010-07-01

In sparse representation, two important sparse solutions, the 0-norm and 1-norm solutions, have been receiving much of attention. The 0-norm solution is the sparsest, however it is not easy to obtain. Although the 1-norm solution may not be the sparsest, it can be easily obtained by the linear programming method. In many cases, the 0-norm solution can be obtained through finding the 1-norm solution. Many discussions exist on the equivalence of the two sparse solutions. This paper analyzes two conditions for the equivalence of the two sparse solutions. The first condition is necessary and sufficient, however, difficult to verify. Although the second is necessary but is not sufficient, it is easy to verify. In this paper, we analyze the second condition within the stochastic framework and propose a variant. We then prove that the equivalence of the two sparse solutions holds with high probability under the variant of the second condition. Furthermore, in the limit case where the 0-norm solution is extremely sparse, the second condition is also a sufficient condition with probability 1.

Sex determination in skeletal remains from the medieval Eastern Adriatic coast – discriminant function analysis of humeri

PubMed Central

Bašić, Željana; Anterić, Ivana; Vilović, Katarina; Petaros, Anja; Bosnar, Alan; Madžar, Tomislav; Polašek, Ozren; Anđelinović, Šimun

2013-01-01

Aim To investigate the usefulness of humerus measurement for sex determination in a sample of medieval skeletons from the Eastern Adriatic Coast. Additional aim was to compare the results with contemporary female population. Methods Five humerus measurements (maximum length, epicondylar width, maximum vertical diameter of the head, maximum and minimum diameter of the humerus at midshaft) for 80 male and 35 female medieval and 19 female contemporary humeri were recorded. Only sufficiently preserved skeletons and those with no obvious pathological or traumatic changes that could affect the measurements were included. For ten samples, analysis of DNA was performed in order to determine sex using amelogenin. Results The initial comparison of men and women indicated significant differences in all five measures (P < 0.001). Discriminant function for sex determination indicated that as much as 85% of cases could be properly categorized, with better results in men (86%) than women (80%). Furthermore, the comparison of the medieval and contemporary women did not show significant difference in any of the measured features. Sex results obtained by anthropological and DNA analysis matched in all 10 cases. Conclusion The results indicate that humerus measurement in Croatian medieval population may be sufficient to determine the sex of the skeleton. Furthermore, it seems that secular changes have not substantially affected contemporary population, suggesting that the results of this study are transferable to contemporary population as well. PMID:23771758

Sample size calculation in cost-effectiveness cluster randomized trials: optimal and maximin approaches.

PubMed

Manju, Md Abu; Candel, Math J J M; Berger, Martijn P F

2014-07-10

In this paper, the optimal sample sizes at the cluster and person levels for each of two treatment arms are obtained for cluster randomized trials where the cost-effectiveness of treatments on a continuous scale is studied. The optimal sample sizes maximize the efficiency or power for a given budget or minimize the budget for a given efficiency or power. Optimal sample sizes require information on the intra-cluster correlations (ICCs) for effects and costs, the correlations between costs and effects at individual and cluster levels, the ratio of the variance of effects translated into costs to the variance of the costs (the variance ratio), sampling and measuring costs, and the budget. When planning, a study information on the model parameters usually is not available. To overcome this local optimality problem, the current paper also presents maximin sample sizes. The maximin sample sizes turn out to be rather robust against misspecifying the correlation between costs and effects at the cluster and individual levels but may lose much efficiency when misspecifying the variance ratio. The robustness of the maximin sample sizes against misspecifying the ICCs depends on the variance ratio. The maximin sample sizes are robust under misspecification of the ICC for costs for realistic values of the variance ratio greater than one but not robust under misspecification of the ICC for effects. Finally, we show how to calculate optimal or maximin sample sizes that yield sufficient power for a test on the cost-effectiveness of an intervention.

Static versus dynamic sampling for data mining

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

John, G.H.; Langley, P.

1996-12-31

As data warehouses grow to the point where one hundred gigabytes is considered small, the computational efficiency of data-mining algorithms on large databases becomes increasingly important. Using a sample from the database can speed up the datamining process, but this is only acceptable if it does not reduce the quality of the mined knowledge. To this end, we introduce the {open_quotes}Probably Close Enough{close_quotes} criterion to describe the desired properties of a sample. Sampling usually refers to the use of static statistical tests to decide whether a sample is sufficiently similar to the large database, in the absence of any knowledgemore » of the tools the data miner intends to use. We discuss dynamic sampling methods, which take into account the mining tool being used and can thus give better samples. We describe dynamic schemes that observe a mining tool`s performance on training samples of increasing size and use these results to determine when a sample is sufficiently large. We evaluate these sampling methods on data from the UCI repository and conclude that dynamic sampling is preferable.« less

Determination of cadmium in coal using solid sampling graphite furnace high-resolution continuum source atomic absorption spectrometry.

PubMed

da Silva, Alessandra Furtado; Borges, Daniel L G; Lepri, Fábio Grandis; Welz, Bernhard; Curtius, Adilson J; Heitmann, Uwe

2005-08-01

This work describes the development of a method to determine cadmium in coal, in which iridium is used as a permanent chemical modifier and calibration is performed against aqueous standards by high-resolution continuum source atomic absorption spectrometry (HR-CS AAS). This new instrumental concept makes the whole spectral environment in the vicinity of the analytical line accessible, providing a lot more data than just the change in absorbance over time available from conventional instruments. The application of Ir (400 microg) as a permanent chemical modifier, thermally deposited on the pyrolytic graphite platform surface, allowed pyrolysis temperatures of 700 degrees C to be used, which was sufficiently high to significantly reduce the continuous background that occurred before the analyte signal at pyrolysis temperatures <700 degrees C. Structured background absorption also occurred after the analyte signal when atomization temperatures of >1600 degrees C were used, which arose from the electron-excitation spectrum (with rotational fine structure) of a diatomic molecule. Under optimized conditions (pyrolysis at 700 degrees C and atomization at 1500 degrees C), interference-free determination of cadmium in seven certified coal reference materials and two real samples was achieved by direct solid sampling and calibrating against aqueous standards, resulting in good agreement with the certified values (where available) at the 95% confidence level. A characteristic mass of 0.4 pg and a detection limit of 2 ng g(-1), calculated for a sample mass of 1.0 mg coal, was obtained. A precision (expressed as the relative standard deviation, RSD) of <10% was typically obtained when coal samples in the mass range 0.6-1.2 mg were analyzed.

Continual in situ monitoring of pore water stable isotopes in the subsurface

NASA Astrophysics Data System (ADS)

Volkmann, T. H. M.; Weiler, M.

2014-05-01

Stable isotope signatures provide an integral fingerprint of origin, flow paths, transport processes, and residence times of water in the environment. However, the full potential of stable isotopes to quantitatively characterize subsurface water dynamics is yet unfolded due to the difficulty in obtaining extensive, detailed, and repeated measurements of pore water in the unsaturated and saturated zone. This paper presents a functional and cost-efficient system for non-destructive continual in situ monitoring of pore water stable isotope signatures with high resolution. Automatic controllable valve arrays are used to continuously extract diluted water vapor in soil air via a branching network of small microporous probes into a commercial laser-based isotope analyzer. Normalized liquid-phase isotope signatures are then obtained based on a specific on-site calibration approach along with basic corrections for instrument bias and temperature dependent isotopic fractionation. The system was applied to sample depth profiles on three experimental plots with varied vegetation cover in southwest Germany. Two methods (i.e., based on advective versus diffusive vapor extraction) and two modes of sampling (i.e., using multiple permanently installed probes versus a single repeatedly inserted probe) were tested and compared. The results show that the isotope distribution along natural profiles could be resolved with sufficiently high accuracy and precision at sampling intervals of less than four minutes. The presented in situ approaches may thereby be used interchangeably with each other and with concurrent laboratory-based direct equilibration measurements of destructively collected samples. It is thus found that the introduced sampling techniques provide powerful tools towards a detailed quantitative understanding of dynamic and heterogeneous shallow subsurface and vadose zone processes.

Methodological Approaches toward Chemico-Biological Diagnostics of the State of Soils in Technogenically Transformed Territories

NASA Astrophysics Data System (ADS)

Fokina, A. I.; Dabakh, E. V.; Domracheva, L. I.; Skugoreva, S. G.; Lyalina, E. I.; Ashikhmina, T. Ya.; Zykova, Yu. N.; Leonova, K. A.

2018-05-01

The comprehensive diagnostics of the state of soils in the impact zone of thermal power station (TPS-5) in the city of Kirov was performed on the basis of the soil chemical analyses and the study of biota response to the loads at different organization levels. The chemical analyses attested to a satisfactory state of the soils. However, the use of soil cyanobacteria and bird's-foot trefoil ( Lótus corniculátus) as test objects showed the toxicity of studied soil samples. The toxicity of the samples was judged from the bioindication effects of cyanophytization and melanization of soil microbial complexes. The obtained results demonstrated that at relatively low concentrations of total and mobile heavy metal compounds in the soil samples, their amount released into the tested soil water (1: 4) extract exceeded the limit allowable for normal functioning of living organisms. For the first time, the express cyanobacterial tetrazole-topographic method of biotesting was applied in the geoecological study to estimate the toxicity of the soil samples. The results obtained with the help of traditional and express methods proved to be comparable. The express-method was sufficiently sensitive and efficient. It allowed the determination of the samples' toxicity in five hours, i.e., four to five times faster than the traditional technique. An inverse relationship between the number of viable cells of cyanobacteria (as judged from the inclusion of formazan crystals) and the concentration of lead ions in the tested soil extracts was found. This finding can be considered a prerequisite for further study and application of the express method in the practice of geoecological monitoring. Our study demonstrated the necessity of a comprehensive approach for the assessment of the real ecological state of soils in the investigated impact zone of the thermal power station.

Automation of DNA and miRNA co-extraction for miRNA-based identification of human body fluids and tissues.

PubMed

Kulstein, Galina; Marienfeld, Ralf; Miltner, Erich; Wiegand, Peter

2016-10-01

In the last years, microRNA (miRNA) analysis came into focus in the field of forensic genetics. Yet, no standardized and recommendable protocols for co-isolation of miRNA and DNA from forensic relevant samples have been developed so far. Hence, this study evaluated the performance of an automated Maxwell® 16 System-based strategy (Promega) for co-extraction of DNA and miRNA from forensically relevant (blood and saliva) samples compared to (semi-)manual extraction methods. Three procedures were compared on the basis of recovered quantity of DNA and miRNA (as determined by real-time PCR and Bioanalyzer), miRNA profiling (shown by Cq values and extraction efficiency), STR profiles, duration, contamination risk and handling. All in all, the results highlight that the automated co-extraction procedure yielded the highest miRNA and DNA amounts from saliva and blood samples compared to both (semi-)manual protocols. Also, for aged and genuine samples of forensically relevant traces the miRNA and DNA yields were sufficient for subsequent downstream analysis. Furthermore, the strategy allows miRNA extraction only in cases where it is relevant to obtain additional information about the sample type. Besides, this system enables flexible sample throughput and labor-saving sample processing with reduced risk of cross-contamination. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development and application of non-invasive biomarkers for carcinogen-DNA adduct analysis in occupationally exposed populations.

PubMed

Talaska, G; Cudnik, J; Jaeger, M; Rothman, N; Hayes, R; Bhatnagar, V J; Kayshup, S J

1996-07-17

Biological monitoring of exposures to carcinogenic compounds in the workplace can be a valuable adjunct to environmental sampling and occupational medicine. Carcinogen-DNA adduct analysis has promise as a biomarker of effective dose if target organ samples can be obtained non-invasively. We have developed non-invasive techniques using exfoliated urothelial and bronchial cells collected in urine and sputum, respectively. First morning urine samples were collected from 33 workers exposed to benzidine or benzidine-based dyes and controls matched for age, education, and smoking status. Sufficient DNA for 32P-postlabelling analysis was obtained from every sample. Mean levels of a specific DNA adduct (which co-chromatographed with standard characterized by MS) were elevated significantly in the benzidine-exposed workers relative to controls. In addition, workers exposed to benzidine had higher adduct levels than those exposed to benzidine-based dyes. This study demonstrates the usefulness of these non-invasive techniques for exposure/effect assessment. To be useful in occupational studies, biomarkers must also be sensitive to exposure interventions. We have conducted topical application studies of used gasoline engine oils in mice and found that the levels of carcinogen-DNA adducts in skin and lung can be significantly lowered if skin cleaning is conducted in a timely manner. The combination of useful, non-invasive techniques to monitor exposure and effect and industrial hygiene interventions can be used to detect and prevent exposures to a wide range of carcinogens including those found in used gasoline engine oils and jet exhausts.

The Performance of a PN Spread Spectrum Receiver Preceded by an Adaptive Interference Suppression Filter.

DTIC Science & Technology

1982-12-01

Sequence dj Estimate of the Desired Signal DEL Sampling Time Interval DS Direct Sequence c Sufficient Statistic E/T Signal Power Erfc Complimentary Error...Namely, a white Gaussian noise (WGN) generator was added. Also, a statistical subroutine was added in order to assess performance improvement at the...reference code and then passed through a correlation detector whose output is the sufficient 1 statistic , e . Using a threshold device and the sufficient

Validation of 31 of the most commonly used immunohistochemical antibodies in cytology prepared using the Cellient(®) automated cell block system.

PubMed

Montgomery, Eric; Gao, Chen; de Luca, Julie; Bower, Jessie; Attwood, Kristropher; Ylagan, Lourdes

2014-12-01

The Cellient(®) cell block system has become available as an alternative, partially automated method to create cell blocks in cytology. We sought to show a validation method for immunohistochemical (IHC) staining on the Cellient cell block system (CCB) in comparison with the formalin fixed paraffin embedded traditional cell block (TCB). Immunohistochemical staining was performed using 31 antibodies on 38 patient samples for a total of 326 slides. Split samples were processed using both methods by following the Cellient(®) manufacturer's recommendations for the Cellient cell block (CCB) and the Histogel method for preparing the traditional cell block (TCB). Interpretation was performed by three pathologists and two cytotechnologists. Immunohistochemical stains were scored as: 0/1+ (negative) and 2/3+ (positive). Inter-rater agreement for each antibody was evaluated for CCB and TCB, as well as the intra-rater agreement between TCB and CCB between observers. Interobserver staining concordance for the TCB was obtained with statistical significance (P < 0.05) in 24 of 31 antibodies. Interobserver staining concordance for the CCB was obtained with statistical significance in 27 of 31 antibodies. Intra-observer staining concordance between TCB and CCB was obtained with statistical significance in 24 of 31 antibodies tested. In conclusions, immunohistochemical stains on cytologic specimens processed by the Cellient system are reliable and concordant with stains performed on the same split samples processed via a formalin fixed-paraffin embedded (FFPE) block. The Cellient system is a welcome adjunct to cytology work-flow by producing cell block material of sufficient quality to allow the use of routine IHC. © 2014 Wiley Periodicals, Inc.

Evaluation and reporting of enzyme immunoassay determinations of antibody to herpes simplex virus in sera and cerebrospinal fluid.

PubMed Central

Cremer, N E; Cossen, C K; Hanson, C V; Shell, G R

1982-01-01

Several methods for evaluating and reporting enzyme immunoassay (EIA) determinations of antibody to herpes simplex virus derived from one dilution of single serum samples were studied. An EIA ratio method for serological evidence of current infection from paired serum samples was also evaluated. Optical density (OD) of the reaction at a 1:100 serum dilution and estimated titers obtained by reference of the OD of the serum dilution to a standard curve were compared to the corresponding plotted EIA titer obtained by titration to endpoint. Neither the OD per se nor the estimated titer was completely predictive of the plotted titer (correlation coefficient [r] of 0.824 and 0.817, respectively), and they provided only a semiquantitative measurement of antibody concentration. For an antibody status report, however, OD would be sufficient if related to the cutoff value as an EIA index (OD of sample divided by cutoff OD for positive specimens). The OD of the EIA reaction at a single dilution (1:5) of cerebrospinal fluid, on the other hand, correlated quite well with the titer obtained by titration (r = 0.950). For serological diagnosis of current infection, the OD ratio of convalescence-phase/acute-phase sera was determined at several dilutions. A ratio of greater than or equal to 1.54 was calculated as a reliable index for a significant rise in antibody concentration and compatible with current infection. By determining the convalescent-phase/acute-phase serum ratio at two dilutions, 1:100 and 1:1,000, the EIA ratio method appeared to be a sensitive as or more sensitive than, complement fixation in diagnosing current infection. PMID:6284791

Innovations in Sampling Pore Fluids From Deep-Sea Hydrate Sites

NASA Astrophysics Data System (ADS)

Lapham, L. L.; Chanton, J. P.; Martens, C. S.; Schaefer, H.; Chapman, N. R.; Pohlman, J. W.

2003-12-01

We have developed a sea-floor probe capable of collecting and returning undecompressed pore water samples at in situ pressures for determination of dissolved gas concentrations and isotopic values in deep-sea sediments. In the summer of 2003, we tested this instrument in sediments containing gas hydrates off Vancouver Island, Cascadia Margin from ROPOS (a remotely operated vehicle) and in the Gulf of Mexico from Johnson-Sea-Link I (a manned submersible). Sediment push cores were collected alongside the probe to compare methane concentrations and stable carbon isotope compositions in decompressed samples vs. in situ samples obtained by probe. When sufficient gas was available, ethane and propane concentrations and isotopes were also compared. Preliminary data show maximum concentrations of dissolved methane to be 5mM at the Cascadia Margin Fish Boat site (850m water depth) and 12mM in the Gulf of Mexico Bush Hill hydrate site (550m water depth). Methane concentrations were, on average, five times as high in probe samples as in the cores. Carbon isotopic values show a thermogenic input and oxidative effects approaching the sediment-water interface at both sites. This novel data set will provide information that is critical to the understanding of the in situ processes and environmental conditions controlling gas hydrate occurrences in sediments.

Traceability of sulfonamide antibiotic treatment by immunochemical analysis of farm animal hair samples.

PubMed

Adrian, Javier; Gratacós-Cubarsí, Marta; Sánchez-Baeza, Francisco; Garcia Regueiro, Jose-Antonio; Castellari, Massimo; Marco, M-Pilar

2009-10-01

The use of hair to trace use of unauthorized substances, therapeutic agents, or their misuse is becoming very attractive since residues can be detected for a long time after treatment. For this purpose, an indirect enzyme-linked immunosorbent assay (ELISA) has been evaluated for its capability to trace sulfonamide antibiotic treatment by analyzing cattle and pig hair samples. Pigmented and nonpigmented hair samples from control and sulfamethazine (SMZ)-treated pigs and calves were collected, extracted under different alkaline conditions, and analyzed by ELISA after just diluting the extracts with the assay buffer. Data analysis following the European recommendations for screening methods demonstrates that the ELISA can detect SMZ in hair samples with a limit of detection (90% of the zero dose (IC(90))) between 30 and 75 ng g(-1). The same samples have been analyzed by HPLC after a dual solid-phase extraction. The ELISA results matched very well those obtained by the chromatographic method, demonstrating that the immunochemical method can be used as a screening tool to trace animal treatments. Between the benefits of this method are the possibility to directly analyze hair extracts with sufficient detectability and its high-throughput capability. Preliminary validation data are reported using an experimental approach inspired on the Commission Decision 2002/657/EC criteria for screening methods.

Determination of plutonium and its isotopic ratio in marine sediment samples using quadrupole ICP-MS with the shield torch system under normal plasma conditions.

PubMed

Zheng, Jian; Yamada, Masatoshi; Wang, Zhongliang; Aono, Tatsuo; Kusakabe, Masashi

2004-06-01

An analytical method for determining (239)Pu and (240)Pu in marine sediment samples, which uses quadrupole ICP-MS, was developed in this work. A simple anion-exchange chromatography system was employed for the separation and purification of Pu from the sample matrix. A sufficient decontamination factor of 1.4 x 10(4) for U, which interferes with the determination of (239)Pu, was achieved. High sensitivity Pu determination was obtained, which led to an extremely low concentration detection limit of approximately 8 fg/ml (0.019 mBq/ml for (239)Pu; 0.071 mBq/ml for (240)Pu) in a sample solution, or an absolute detection limit of 42 fg in a 5 ml sample solution, by using the shield torch technique. Analytical results for the determination of the (239+240)Pu and the (240)Pu/(239)Pu ratio in IAEA 368 (ocean sediment) reference material indicated that the accuracy of the method was satisfactory. The method developed was successfully applied to a study of Pu behavior in the sediments from Sagami Bay, Japan. The observed high (240)Pu/(239)Pu ratio in the sediment core indicated that there was additional Pu input derived from close-in fallout in addition to the global fallout.

Toward MRI microimaging of single biological cells

NASA Astrophysics Data System (ADS)

Seeber, Derek Allan

There is a great advantage in signal to noise ratio (SNR) that can be obtained in nuclear magnetic resonance (NMR) on very small samples (having spatial dimensions ˜100 mum or less) if one employs NMR "microcoils" that are of similarly small dimensions. These gains in SNR could enable magnetic resonance imaging (MRI) microscopy with spatial resolutions of ˜1--2 mum, much better than currently available. We report the design and testing of a NMR microcoil receiver apparatus, employing solenoidal microcoils of dimensions of tens to hundreds of microns, using an applied field of 9 Tesla (proton frequency 383 MHz). For the smallest receiver coils we attain sensitivity sufficient to observe proton NMR with SNR one in a single scan applied to ˜10 mum3 (10 fl) water sample, containing 7 x 1011 total proton spins. In addition to the NMR applications, microcoils have been applied to MRI producing images with spatial resolutions as low as 2 mum x 3.5 mum x 14.8 mum on phantom images of rods and beads. This resolution can be further improved. MRI imaging of small sample volumes requires significant hardware modifications and improvements, all of which are discussed. Specifically, MRI microscopy requires very strong (>10 T/m), rapidly switchable triaxial magnetic field gradients. We report the design and construction of such a triaxial gradient system, producing gradient substantially greater than 15 T/m in all three directions, x, y, and z (as high as 50 T/m for the x direction). The gradients are power by a custom designed power supply capable of providing currents in excess of 200 amps and switching times of less than 5 mus corresponding to slew rates of greater that 107 T/m/s. The gradients are adequately uniform (within 5% over a volume of 600 mum3) and sufficient for microcoil MRI of small samples.

Working toward Self-Sufficiency.

ERIC Educational Resources Information Center

Caplan, Nathan

1985-01-01

Upon arrival in the United States, the Southeast Asian "Boat People" faced a multitude of problems that would seem to have hindered their achieving economic self-sufficiency. Nonetheless, by the time of a 1982 research study which interviewed nearly 1,400 refugee households, 25 percent of all the households in the sample had achieved…

Interpretation; Apollo 9 photography of parts of southern Arizona and southern New Mexico

USGS Publications Warehouse

Owen, J. Robert; Shown, Lynn M.

1973-01-01

Examination of small-scale (approximately 1:650,000) multispectral photographs obtained on the Apollo 9 mission in March 1969 revealed that in semiarid, regions features due to differences in soils or quantity of vegetation could most easily be discriminated on the color infrared photographs. Where there is sufficient ground truth, it is possible to delineate regional wildland plant communities on the basis of tone, however, the precision of the method may be improved by using photographs obtained two or more times during the year. Sites where vegetation-improvement practices have been completed are not always discernible. For example, where waterspreaders have been constructed, there was sufficient change in the density of vegetation to be readily detected on the photographs; however, pinyon-juniper to grass, conversions or contour furrowing did not always produce a sufficient change in the vegetation to be detected on the photographs.

7 CFR 58.244 - Number of samples.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 3 2013-01-01 2013-01-01 false Number of samples. 58.244 Section 58.244 Agriculture... Procedures § 58.244 Number of samples. As many samples shall be taken from each dryer production lot as is necessary to assure proper composition and quality control. A sufficient number of representative samples...

7 CFR 58.244 - Number of samples.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Number of samples. 58.244 Section 58.244 Agriculture... Procedures § 58.244 Number of samples. As many samples shall be taken from each dryer production lot as is necessary to assure proper composition and quality control. A sufficient number of representative samples...

Symmetry-breaking phase transitions in highly concentrated semen

PubMed Central

Creppy, Adama; Plouraboué, Franck; Praud, Olivier; Druart, Xavier; Cazin, Sébastien; Yu, Hui

2016-01-01

New experimental evidence of self-motion of a confined active suspension is presented. Depositing fresh semen sample in an annular shaped microfluidic chip leads to a spontaneous vortex state of the fluid at sufficiently large sperm concentration. The rotation occurs unpredictably clockwise or counterclockwise and is robust and stable. Furthermore, for highly active and concentrated semen, richer dynamics can occur such as self-sustained or damped rotation oscillations. Experimental results obtained with systematic dilution provide a clear evidence of a phase transition towards collective motion associated with local alignment of spermatozoa akin to the Vicsek model. A macroscopic theory based on previously derived self-organized hydrodynamics models is adapted to this context and provides predictions consistent with the observed stationary motion. PMID:27733694

The effectiveness of AMT investment in UK metal component manufacture

NASA Astrophysics Data System (ADS)

Hamblin, David; Nugent, Edward

1991-11-01

The aim of the research was to investigate the effectiveness of capital investment, particularly investment in Advanced Manufacturing Technology (AMT). AMT encompasses not only production, but also design and administration areas. The intention was to make recommendations for the future direction of investment in the industry. The structure of the industry which comprises 54 companies is outlined. In order to obtain sufficiently detailed and accurate data, each company was visited. Discussions were held with managers covering the areas of production, engineering, finance, design, sales and marketing, quality and other strategic issues affecting investment decision making. The study conclusions and recommendations are presented. An overview of the industry and the survey sample are given. Company performance, practice relationships which link practice, and performance are discussed.

Hydrodynamic injection with pneumatic valving for microchip electrophoresis with total analyte utilization

PubMed Central

Sun, Xuefei; Kelly, Ryan T.; Danielson, William F.; Agrawal, Nitin; Tang, Keqi; Smith, Richard D.

2011-01-01

A novel hydrodynamic injector that is directly controlled by a pneumatic valve has been developed for reproducible microchip capillary electrophoresis (CE) separations. The poly(dimethylsiloxane) (PDMS) devices used for evaluation comprise a separation channel, a side channel for sample introduction, and a pneumatic valve aligned at the intersection of the channels. A low pressure (≤ 3 psi) applied to the sample reservoir is sufficient to drive sample into the separation channel. The rapidly actuated pneumatic valve enables injection of discrete sample plugs as small as ~100 pL for CE separation. The injection volume can be easily controlled by adjusting the intersection geometry, the solution back pressure and the valve actuation time. Sample injection could be reliably operated at different frequencies (< 0.1 Hz to >2 Hz) with good reproducibility (peak height relative standard deviation ≤ 3.6%) and no sampling biases associated with the conventional electrokinetic injections. The separation channel was dynamically coated with a cationic polymer, and FITC-labeled amino acids were employed to evaluate the CE separation. Highly efficient (≥ 7.0 × 103 theoretical plates for the ~2.4 cm long channel) and reproducible CE separations were obtained. The demonstrated method has numerous advantages compared with the conventional techniques, including repeatable and unbiased injections, little sample waste, high duty cycle, controllable injected sample volume, and fewer electrodes with no need for voltage switching. The prospects of implementing this injection method for coupling multidimensional separations, for multiplexing CE separations and for sample-limited bioanalyses are discussed. PMID:21520147

Electrolytes for Hydrocarbon Air Fuel Cells.

DTIC Science & Technology

1981-01-01

finding an electrolyte with sufficient electrochemical activity and stability to replace phosphoric acid in direct oxidation fuel cells. Commercially...and stability to replace phosphoric acid in direct oxidation fuel cells. Commercially available materials received prime consideration. However, ECO’s...was to obtain an electrolyte with sufficient electrochemical activity and stability to replace phosphoric acid in direct oxidation fuel cells. This

Evaluation of the Ticket to Work Program: Assessment of Post-Rollout Implementation and Early Impacts, Volume 1

ERIC Educational Resources Information Center

Thornton, Craig; Livermore, Gina; Fraker, Thomas; Stapleton, David; O'Day, Bonnie; Wittenburg, David; Weathers, Robert; Goodman, Nanette; Silva, Tim; Martin, Emily Sama; Gregory, Jesse; Wright, Debra; Mamun, Arif

2007-01-01

Ticket to Work and Self-Sufficiency program (TTW) was designed to enhance the market for services that help disability beneficiaries become economically self-sufficient by providing beneficiaries with a wide range of choices for obtaining services and to give employment-support service providers new financial incentives to serve beneficiaries…

Simultaneous determination of rifabutin and human serum albumin in pharmaceutical formulations by capillary electrophoresis.

PubMed

Ermolenko, Yu; Anshakova, A; Osipova, N; Kamentsev, M; Maksimenko, O; Balabanyan, V; Gelperina, S

Capillary zone electrophoresis (CZE) was used for determination of rifabutin (RFB), an anti-tuberculosis antibiotic drug, in various pharmaceutical formulations. Apart from that, simultaneous determination of RFB and human serum albumin (HSA) was performed. Electrophoretic behaviour of RFB was examined at various pH levels. CE conditions: a quartz capillary tube (internal diameter 75mm, effective length 50cm, total length 60cm), the capillary temperature was 25°С, the voltage applied to the capillary tube was +20kV, the UV detection wavelength was 214nm, hydrodynamic injection of the sample was performed at 30mbar for 5s, tetraborate buffer solution (0.01М, рН9.2). The obtained results are characterized by high efficiency (number of theoretical plates up to 260,000) and sufficient sensitivity (LOQ starting from 0.02μg/ml for RFB). The obtained data are in good accord with both HPLC results (for RFB) and spectrophotometry (for HSA). Copyright © 2017 Elsevier Inc. All rights reserved.

Laminar, Transitional, and Turbulent Heating on Mid Lift-to-Drag Ratio Entry Vehicles

NASA Technical Reports Server (NTRS)

Hollis, Brian R.; Hollingsworth, Kevin E.

2013-01-01

The boundary-layer transition characteristics and convective aeroheating levels on mid lift-to-drag ratio entry vehicle configurations have been studied through wind-tunnel testing. Several configurations were investigated, including elliptically blunted cylinders with both circular and elliptically flattened cross sections, biconic geometries based on launch vehicle dual-use shrouds, and parametrically optimized analytic geometries. Vehicles of this class have been proposed for high-mass Mars missions, such as sample return and crewed exploration, for which the conventional sphere-cone entry-vehicle geometries of previous Mars missions are insufficient. Testing was conducted at Mach 6 over a range of Reynolds numbers sufficient to generate laminar, transitional, and turbulent flow. Transition onset locations, both straight-line and cross-flow, and heating rates were obtained through global phosphor thermography. Supporting computations were performed to obtain heating rates for comparison with the data. Laminar data and predictions agreed to well within the experimental uncertainty. Fully turbulent data and predictions also agreed well. However, in transitional flow regions, greater differences were observed.

Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR

DOE PAGES

Zinke, Maximilian; Fricke, Pascal; Samson, Camille; ...

2017-07-07

Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH,more » (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail-tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.« less

Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR

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

Zinke, Maximilian; Fricke, Pascal; Samson, Camille

Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH,more » (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail-tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.« less

Tracking strategies for laser ranging to multiple satellite targets

NASA Technical Reports Server (NTRS)

Robbins, J. W.; Smith, D. E.; Kolenkiewicz, R.

1994-01-01

By the middle of the decade, several new Laser Geodynamic Satellites will be launched to join the current constellation comprised of the laser geodynamic satellite (LAGEOS) (US), Starlette (France), Ajisai (Japan), and Etalon I and II (USSR). The satellites to be launched, LAGEOS II and III (US & Italy), and Stella (France), will be injected into orbits that differ from the existing constellation so that geodetic and gravimetric quantities are sampled to enhance their resolution and accuracy. An examination of various possible tracking strategies adopted by the network of laser tracking stations has revealed that the recovery of precise geodetic parameters can be obtained over shorter intervals than is currently obtainable with the present constellation of satellites. This is particularly important in the planning of mobile laser tracking operations, given a network of permanently operating tracking sites. Through simulations, it is shown that laser tracking of certain satellite passes, pre-selected to provide optimal sky-coverage, provides the means to acquire a sufficient amount of data to allow the recovery of 1 cm station positions.

Report on objective ride quality evaluation

NASA Technical Reports Server (NTRS)

Wambold, J. C.; Park, W. H.

1974-01-01

The correlation of absorbed power as an objective ride measure to the subjective evaluation for the bus data was investigated. For some individual bus rides the correlations were poor, but when a sufficient number of rides was used to give reasonable sample base, an excellent correlation was obtained. The following logarithmical function was derived: S = 1.7245 1n (39.6849 AP), where S = one subjective rating of the ride; and AP = the absorbed power in watts. A six-degree-of-freedom method developed for aircraft data was completed. Preliminary correlation of absorbed power with ISO standards further enhances the bus ride and absorbed power correlation numbers since the AP's obtained are of the same order of magnitude for both correlations. While it would then appear that one could just use ISO standards, there is no way to add the effect of three degrees of freedom. The absorbed power provides a method of adding the effects due to the three major directions plus the pitch and roll.

Applications and limitations of electron correlation microscopy to study relaxation dynamics in supercooled liquids

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

Zhang, Pei; He, Li; Besser, Matthew F.

Here, electron correlation microscopy (ECM) is a way to measure structural relaxation times, τ, of liquids with nanometer-scale spatial resolution using coherent electron scattering equivalent of photon correlation spectroscopy. We have applied ECM with a 3.5 nm diameter probe to Pt 57.5Cu 14.7Ni 5.3P 22.5 amorphous nanorods and Pd 40Ni 40P 20 bulk metallic glass (BMG) heated inside the STEM into the supercooled liquid region. These data demonstrate that the ECM technique is limited by the characteristics of the time series, which must be at least 40τ to obtain a well-converged correlation function g 2(t), and the time per frame,more » which must be less than 0.1τ to obtain sufficient sampling. A high-speed direct electron camera enables fast acquisition and affords reliable g 2(t) data even with low signal per frame.« less

Applications and limitations of electron correlation microscopy to study relaxation dynamics in supercooled liquids

DOE PAGES

Zhang, Pei; He, Li; Besser, Matthew F.; ...

2016-09-08

Here, electron correlation microscopy (ECM) is a way to measure structural relaxation times, τ, of liquids with nanometer-scale spatial resolution using coherent electron scattering equivalent of photon correlation spectroscopy. We have applied ECM with a 3.5 nm diameter probe to Pt 57.5Cu 14.7Ni 5.3P 22.5 amorphous nanorods and Pd 40Ni 40P 20 bulk metallic glass (BMG) heated inside the STEM into the supercooled liquid region. These data demonstrate that the ECM technique is limited by the characteristics of the time series, which must be at least 40τ to obtain a well-converged correlation function g 2(t), and the time per frame,more » which must be less than 0.1τ to obtain sufficient sampling. A high-speed direct electron camera enables fast acquisition and affords reliable g 2(t) data even with low signal per frame.« less

Motif finding in DNA sequences based on skipping nonconserved positions in background Markov chains.

PubMed

Zhao, Xiaoyan; Sze, Sing-Hoi

2011-05-01

One strategy to identify transcription factor binding sites is through motif finding in upstream DNA sequences of potentially co-regulated genes. Despite extensive efforts, none of the existing algorithms perform very well. We consider a string representation that allows arbitrary ignored positions within the nonconserved portion of single motifs, and use O(2(l)) Markov chains to model the background distributions of motifs of length l while skipping these positions within each Markov chain. By focusing initially on positions that have fixed nucleotides to define core occurrences, we develop an algorithm to identify motifs of moderate lengths. We compare the performance of our algorithm to other motif finding algorithms on a few benchmark data sets, and show that significant improvement in accuracy can be obtained when the sites are sufficiently conserved within a given sample, while comparable performance is obtained when the site conservation rate is low. A software program (PosMotif ) and detailed results are available online at http://faculty.cse.tamu.edu/shsze/posmotif.

Data on xylem sap proteins from Mn- and Fe-deficient tomato plants obtained using shotgun proteomics.

PubMed

Ceballos-Laita, Laura; Gutierrez-Carbonell, Elain; Takahashi, Daisuke; Abadía, Anunciación; Uemura, Matsuo; Abadía, Javier; López-Millán, Ana Flor

2018-04-01

This article contains consolidated proteomic data obtained from xylem sap collected from tomato plants grown in Fe- and Mn-sufficient control, as well as Fe-deficient and Mn-deficient conditions. Data presented here cover proteins identified and quantified by shotgun proteomics and Progenesis LC-MS analyses: proteins identified with at least two peptides and showing changes statistically significant (ANOVA; p ≤ 0.05) and above a biologically relevant selected threshold (fold ≥ 2) between treatments are listed. The comparison between Fe-deficient, Mn-deficient and control xylem sap samples using a multivariate statistical data analysis (Principal Component Analysis, PCA) is also included. Data included in this article are discussed in depth in the research article entitled "Effects of Fe and Mn deficiencies on the protein profiles of tomato ( Solanum lycopersicum) xylem sap as revealed by shotgun analyses" [1]. This dataset is made available to support the cited study as well to extend analyses at a later stage.

Enhancement of low pressure cold sprayed copper coating adhesion by laser texturing on aluminum substrates

NASA Astrophysics Data System (ADS)

Knapp, Wolfgang; Gillet, Vincent; Courant, Bruno; Aubignat, Emilie; Costil, Sophie; Langlade, Cécile

2017-02-01

Surface pre-treatment is fundamental in thermal spraying processes to obtain a sufficient bonding strength between substrate and coating. Different pre-treatments can be used, mostly grit-blasting for current industrial applications. This study is focused on Cu-Al2O3 coatings obtained by Low Pressure Cold Spray on AW5083 aluminum alloy substrate. Bonding strength is measured by tensile adhesion test, while deposition efficiency is measured. Substrates are textured by laser, using a pattern of equally spaced grooves with almost constant diameter and variations of depth. Results show that bonding strength is improved up to +81% compared to non-treated substrate, while deposition efficiency remains constant. The study of the samples after rupture reveals a modification of the failure mode, from mixed failure to cohesive failure. A modification of crack propagation is also noticed, the shape of laser textured grooves induces a deviation of cracks inside the coating instead of following the interface between the layers.

Vulnerabilities of fingerprint reader to fake fingerprints attacks.

PubMed

Espinoza, Marcela; Champod, Christophe; Margot, Pierre

2011-01-30

The purpose of this research is to assess the vulnerabilities of a high resolution fingerprint sensor when confronted with fake fingerprints. The study has not been focused on the decision outcome of the biometric device, but essentially on the scores obtained following the comparison between a query (genuine or fake) and a template using an AFIS system. To do this, fake fingerprints of 12 subjects have been produced with and without their cooperation. These fake fingerprints have been used alongside with real fingers. The study led to three major observations: First, genuine fingerprints produced scores higher than fake fingers (translating a closer proximity) and this tendency is observed considering each subject separately. Second, scores are however not sufficient as a single measure to differentiate these samples (fake from genuine) given the variation due to the donors themselves. That explains why fingerprint readers without vitality detection can be fooled. Third, production methods and subjects greatly influence the scores obtained for fake fingerprints. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Estimation of local stresses and elastic properties of a mortar sample by FFT computation of fields on a 3D image

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

Escoda, J.; Departement Materiaux et Mecanique des Composants, Electricite de France, Moret-sur-Loing; Willot, F., E-mail: francois.willot@ensmp.f

2011-05-15

This study concerns the prediction of the elastic properties of a 3D mortar image, obtained by micro-tomography, using a combined image segmentation and numerical homogenization approach. The microstructure is obtained by segmentation of the 3D image into aggregates, voids and cement paste. Full-fields computations of the elastic response of mortar are undertaken using the Fast Fourier Transform method. Emphasis is made on highly-contrasted properties between aggregates and matrix, to anticipate needs for creep or damage computation. The representative volume element, i.e. the volume size necessary to compute the effective properties with a prescribed accuracy, is given. Overall, the volumes usedmore » in this work were sufficient to estimate the effective response of mortar with a precision of 5%, 6% and 10% for contrast ratios of 100, 1000 and 10,000, resp. Finally, a statistical and local characterization of the component of the stress field parallel to the applied loading is carried out.« less

System and method for liquid extraction electrospray-assisted sample transfer to solution for chemical analysis

DOEpatents

Kertesz, Vilmos; Van Berkel, Gary J.

2016-07-12

A system for sampling a surface includes a surface sampling probe comprising a solvent liquid supply conduit and a distal end, and a sample collector for suspending a sample collection liquid adjacent to the distal end of the probe. A first electrode provides a first voltage to solvent liquid at the distal end of the probe. The first voltage produces a field sufficient to generate electrospray plume at the distal end of the probe. A second electrode provides a second voltage and is positioned to produce a plume-directing field sufficient to direct the electrospray droplets and ions to the suspended sample collection liquid. The second voltage is less than the first voltage in absolute value. A voltage supply system supplies the voltages to the first electrode and the second electrode. The first electrode can apply the first voltage directly to the solvent liquid. A method for sampling for a surface is also disclosed.

Reflectance of metallic indium for solar energy applications

NASA Technical Reports Server (NTRS)

Bouquet, F. L.; Hasegawa, T.

1984-01-01

An investigation has been conducted in order to compile quantitative data on the reflective properties of metallic indium. The fabricated samples were of sufficiently high quality that differences from similar second-surface silvered mirrors were not apparent to the human eye. Three second-surface mirror samples were prepared by means of vacuum deposition techniques, yielding indium thicknesses of approximately 1000 A. Both hemispherical and specular measurements were made. It is concluded that metallic indium possesses a sufficiently high specular reflectance to be potentially useful in many solar energy applications.

Stochastic stability properties of jump linear systems

NASA Technical Reports Server (NTRS)

Feng, Xiangbo; Loparo, Kenneth A.; Ji, Yuandong; Chizeck, Howard J.

1992-01-01

Jump linear systems are defined as a family of linear systems with randomly jumping parameters (usually governed by a Markov jump process) and are used to model systems subject to failures or changes in structure. The authors study stochastic stability properties in jump linear systems and the relationship among various moment and sample path stability properties. It is shown that all second moment stability properties are equivalent and are sufficient for almost sure sample path stability, and a testable necessary and sufficient condition for second moment stability is derived. The Lyapunov exponent method for the study of almost sure sample stability is discussed, and a theorem which characterizes the Lyapunov exponents of jump linear systems is presented.

Synchrotron X-ray measurement techniques for thermal barrier coated cylindrical samples under thermal gradients.

PubMed

Siddiqui, Sanna F; Knipe, Kevin; Manero, Albert; Meid, Carla; Wischek, Janine; Okasinski, John; Almer, Jonathan; Karlsson, Anette M; Bartsch, Marion; Raghavan, Seetha

2013-08-01

Measurement techniques to obtain accurate in situ synchrotron strain measurements of thermal barrier coating systems (TBCs) applied to hollow cylindrical specimens are presented in this work. The Electron Beam Physical Vapor Deposition coated specimens with internal cooling were designed to achieve realistic temperature gradients over the TBC coated material such as that occurring in the turbine blades of aeroengines. Effects of the circular cross section on the x-ray diffraction (XRD) measurements in the various layers, including the thermally grown oxide, are investigated using high-energy synchrotron x-rays. Multiple approaches for beam penetration including collection, tangential, and normal to the layers, along with variations in collection parameters are compared for their ability to attain high-resolution XRD data from the internal layers. This study displays the ability to monitor in situ, the response of the internal layers within the TBC, while implementing a thermal gradient across the thickness of the coated sample. The thermal setup maintained coating surface temperatures in the range of operating conditions, while monitoring the substrate cooling, for a controlled thermal gradient. Through variation in measurement location and beam parameters, sufficient intensities are obtained from the internal layers which can be used for depth resolved strain measurements. Results are used to establish the various techniques for obtaining XRD measurements through multi-layered coating systems and their outcomes will pave the way towards goals in achieving realistic in situ testing of these coatings.

Synchrotron X-ray measurement techniques for thermal barrier coated cylindrical samples under thermal gradients

NASA Astrophysics Data System (ADS)

Siddiqui, Sanna F.; Knipe, Kevin; Manero, Albert; Meid, Carla; Wischek, Janine; Okasinski, John; Almer, Jonathan; Karlsson, Anette M.; Bartsch, Marion; Raghavan, Seetha

2013-08-01

Measurement techniques to obtain accurate in situ synchrotron strain measurements of thermal barrier coating systems (TBCs) applied to hollow cylindrical specimens are presented in this work. The Electron Beam Physical Vapor Deposition coated specimens with internal cooling were designed to achieve realistic temperature gradients over the TBC coated material such as that occurring in the turbine blades of aeroengines. Effects of the circular cross section on the x-ray diffraction (XRD) measurements in the various layers, including the thermally grown oxide, are investigated using high-energy synchrotron x-rays. Multiple approaches for beam penetration including collection, tangential, and normal to the layers, along with variations in collection parameters are compared for their ability to attain high-resolution XRD data from the internal layers. This study displays the ability to monitor in situ, the response of the internal layers within the TBC, while implementing a thermal gradient across the thickness of the coated sample. The thermal setup maintained coating surface temperatures in the range of operating conditions, while monitoring the substrate cooling, for a controlled thermal gradient. Through variation in measurement location and beam parameters, sufficient intensities are obtained from the internal layers which can be used for depth resolved strain measurements. Results are used to establish the various techniques for obtaining XRD measurements through multi-layered coating systems and their outcomes will pave the way towards goals in achieving realistic in situ testing of these coatings.

[Evaluation of the usefulness of various PCR method variations and nucleic acid hybridization for CMV infection in immunosuppressed patients].

PubMed

Siennicka, J; Trzcińska, A; Litwińska, B; Durlik, M; Seferyńska, I; Pałynyczko, G; Kańtoch, M

2000-01-01

In diagnosis of CMV infection various laboratory methods are used. The methods based on detection of viral nucleic acids have been introduced routinely in many laboratories. The aim of this study was to compare nucleic acid hybridisation method and various variants of PCR methods with respect to their ability to detect CMV DNA. The studied material comprised 60 blood samples from 19 patients including 13 renal transplant recipients and 6 with acute leukaemia. The samples were subjected to hybridisation (Murex Hybrid Capture System CMV DNA) and PCR carried out in 3 variants: with one pair of primers (single PCR), nested PCR and Digene SHARP System with detection of PCR product using a genetic probe in ELISA system. The sensitivity of the variants ranged from 10(0) particles of viral DNA in nested PCR to 10(2) in single PCR. The producer claimed the sensitivity of the hybridisation test to be 3 x 10(5) and it seems to be sufficient for detection of CMV infection. The obtained results show that sensitivity of hybridisation was comparable to that of single PCR and the possibility of obtaining quantitative results makes it superior, on efficacy of antiviral therapy, especially in monitoring CMV infection in immunossuppressed patients and in following the efficacy of antiviral treatment.

Advances in 193 nm excimer lasers for mass spectrometry applications

NASA Astrophysics Data System (ADS)

Delmdahl, Ralph; Esser, Hans-Gerd; Bonati, Guido

2016-03-01

Ongoing progress in mass analysis applications such as laser ablation inductively coupled mass spectrometry of solid samples and ultraviolet photoionization mediated sequencing of peptides and proteins is to a large extent driven by ultrashort wavelength excimer lasers at 193 nm. This paper will introduce the latest improvements achieved in the development of compact high repetition rate excimer lasers and elaborate on the impact on mass spectrometry instrumentation. Various performance and lifetime measurements obtained in a long-term endurance test over the course of 18 months will be shown and discussed in view of the laser source requirements of different mass spectrometry tasks. These sampling type applications are served by excimer lasers delivering pulsed 193 nm output of several mJ as well as fast repetition rates which are already approaching one Kilohertz. In order to open up the pathway from the laboratory to broader market industrial use, sufficient component lifetimes and long-term stable performance behavior have to be ensured. The obtained long-term results which will be presented are based on diverse 193 nm excimer laser tube improvements aiming at e.g. optimizing the gas flow dynamics and have extended the operational life the laser tube for the first time over several billion pulses even under high duty-cycle conditions.

Dried Blood Spot RNA Transcriptomes Correlate with Transcriptomes Derived from Whole Blood RNA.

PubMed

Reust, Mary J; Lee, Myung Hee; Xiang, Jenny; Zhang, Wei; Xu, Dong; Batson, Tatiana; Zhang, Tuo; Downs, Jennifer A; Dupnik, Kathryn M

2018-05-01

Obtaining RNA from clinical samples collected in resource-limited settings can be costly and challenging. The goals of this study were to 1) optimize messenger RNA extraction from dried blood spots (DBS) and 2) determine how transcriptomes generated from DBS RNA compared with RNA isolated from blood collected in Tempus tubes. We studied paired samples collected from eight adults in rural Tanzania. Venous blood was collected on Whatman 903 Protein Saver cards and in tubes with RNA preservation solution. Our optimal DBS RNA extraction used 8 × 3-mm DBS punches as the starting material, bead beater disruption at maximum speed for 60 seconds, extraction with Illustra RNAspin Mini RNA Isolation kit, and purification with Zymo RNA Concentrator kit. Spearman correlations of normalized gene counts in DBS versus whole blood ranged from 0.887 to 0.941. Bland-Altman plots did not show a trend toward over- or under-counting at any gene size. We report a method to obtain sufficient RNA from DBS to generate a transcriptome. The DBS transcriptome gene counts correlated well with whole blood transcriptome gene counts. Dried blood spots for transcriptome studies could be an option when field conditions preclude appropriate collection, storage, or transport of whole blood for RNA studies.

Automated tru-cut imaging-guided core needle biopsy of canine orbital neoplasia. A prospective feasibility study

PubMed Central

Cirla, A.; Rondena, M.; Bertolini, G.

2016-01-01

The purpose of this study was to evaluate the diagnostic value of imaging-guided core needle biopsy for canine orbital mass diagnosis. A second excisional biopsy obtained during surgery or necropsy was used as the reference standard. A prospective feasibility study was conducted in 23 canine orbital masses at a single centre. A complete ophthalmic examination was always followed by orbital ultrasound and computed tomography (CT) examination of the head. All masses were sampled with the patient still on the CT table using ultrasound (US) guided automatic tru-cut device. The most suitable sampling approach to the orbit was chosen each time based on the CT image analysis. One of the following different approaches was used: trans-orbital, trans-conjunctival or trans-masseteric. In all cases, the imaging-guided biopsy provided a sufficient amount of tissue for the histopathological diagnosis, which concurred with the biopsies obtained using the excisional technique. CT examination was essential for morphological diagnosis and provided detailed topographic information that allowed us to choose the safest orbital approach for the biopsy. US guided automatic tru-cut biopsy based on CT images, performed with patient still on the CT table, resulted in a minimally invasive, relatively easy, and accurate diagnostic procedure in dogs with orbital masses. PMID:27540512

Automated tru-cut imaging-guided core needle biopsy of canine orbital neoplasia. A prospective feasibility study.

PubMed

Cirla, A; Rondena, M; Bertolini, G

2016-01-01

The purpose of this study was to evaluate the diagnostic value of imaging-guided core needle biopsy for canine orbital mass diagnosis. A second excisional biopsy obtained during surgery or necropsy was used as the reference standard. A prospective feasibility study was conducted in 23 canine orbital masses at a single centre. A complete ophthalmic examination was always followed by orbital ultrasound and computed tomography (CT) examination of the head. All masses were sampled with the patient still on the CT table using ultrasound (US) guided automatic tru-cut device. The most suitable sampling approach to the orbit was chosen each time based on the CT image analysis. One of the following different approaches was used: trans-orbital, trans-conjunctival or trans-masseteric. In all cases, the imaging-guided biopsy provided a sufficient amount of tissue for the histopathological diagnosis, which concurred with the biopsies obtained using the excisional technique. CT examination was essential for morphological diagnosis and provided detailed topographic information that allowed us to choose the safest orbital approach for the biopsy. US guided automatic tru-cut biopsy based on CT images, performed with patient still on the CT table, resulted in a minimally invasive, relatively easy, and accurate diagnostic procedure in dogs with orbital masses.

The X-Ray Light Curve of the Very Luminous Supernova SN 1978K in NGC 1313

NASA Astrophysics Data System (ADS)

Schlegel, Eric M.; Petre, R.; Colbert, E. J. M.

1996-01-01

We present the 0.5-2.0 keV light curve of the X-ray luminous supernova SN 1978K in NGC 1313, based on six ROSAT observations spanning 1990 July to t994 July. SN 1978K is one of a few supernovae or supernova remnants that are very luminous (˜1039-1040 ergs s-1) in the X-ray, optical, and radio bands, and the first, at a supernova age of 10-20 yr, for which sufficient data exist to create an X-ray light curve. The X-ray flux is approximately constant over the 4 yr sampled by our observations, which were obtained 12-16 yr after the initial explosion. Three models exist to explain the large X-ray luminosity: pulsar input, a reverse shock running back into the expanding debris of the supernova, and the outgoing shock crushing of cloudlets in the debris field. Based upon calculations of Chevalier & Fransson, a pulsar cannot provide sufficient energy to produce the soft X-ray luminosity. Based upon the models and the light curve to date, it is not possible to discern the evolutionary phase of the supernova.

Preanalytical Errors in Hematology Laboratory- an Avoidable Incompetence.

PubMed

HarsimranKaur, Vikram Narang; Selhi, Pavneet Kaur; Sood, Neena; Singh, Aminder

2016-01-01

Quality assurance in the hematology laboratory is a must to ensure laboratory users of reliable test results with high degree of precision and accuracy. Even after so many advances in hematology laboratory practice, pre-analytical errors remain a challenge for practicing pathologists. This study was undertaken with an objective to evaluate the types and frequency of preanalytical errors in hematology laboratory of our center. All the samples received in the Hematology Laboratory of Dayanand Medical College and Hospital, Ludhiana, India over a period of one year (July 2013-July 2014) were included in the study and preanalytical variables like clotted samples, quantity not sufficient, wrong sample, without label, wrong label were studied. Of 471,006 samples received in the laboratory, preanalytical errors, as per the above mentioned categories was found in 1802 samples. The most common error was clotted samples (1332 samples, 0.28% of the total samples) followed by quantity not sufficient (328 sample, 0.06%), wrong sample (96 samples, 0.02%), without label (24 samples, 0.005%) and wrong label (22 samples, 0.005%). Preanalytical errors are frequent in laboratories and can be corrected by regular analysis of the variables involved. Rectification can be done by regular education of the staff.

Equilibrating high-molecular-weight symmetric and miscible polymer blends with hierarchical back-mapping.

PubMed

Ohkuma, Takahiro; Kremer, Kurt; Daoulas, Kostas

2018-05-02

Understanding properties of polymer alloys with computer simulations frequently requires equilibration of samples comprised of microscopically described long molecules. We present the extension of an efficient hierarchical backmapping strategy, initially developed for homopolymer melts, to equilibrate high-molecular-weight binary blends. These mixtures present significant interest for practical applications and fundamental polymer physics. In our approach, the blend is coarse-grained into models representing polymers as chains of soft blobs. Each blob stands for a subchain with N b microscopic monomers. A hierarchy of blob-based models with different resolution is obtained by varying N b . First the model with the largest N b is used to obtain an equilibrated blend. This configuration is sequentially fine-grained, reinserting at each step the degrees of freedom of the next in the hierarchy blob-based model. Once the blob-based description is sufficiently detailed, the microscopic monomers are reinserted. The hard excluded volume is recovered through a push-off procedure and the sample is re-equilibrated with molecular dynamics (MD), requiring relaxation on the order of the entanglement time. For the initial method development we focus on miscible blends described on microscopic level through a generic bead-spring model, which reproduces hard excluded volume, strong covalent bonds, and realistic liquid density. The blended homopolymers are symmetric with respect to molecular architecture and liquid structure. To parameterize the blob-based models and validate equilibration of backmapped samples, we obtain reference data from independent hybrid simulations combining MD and identity exchange Monte Carlo moves, taking advantage of the symmetry of the blends. The potential of the backmapping strategy is demonstrated by equilibrating blend samples with different degree of miscibility, containing 500 chains with 1000 monomers each. Equilibration is verified by comparing chain conformations and liquid structure in backmapped blends with the reference data. Possible directions for further methodological developments are discussed.

Equilibrating high-molecular-weight symmetric and miscible polymer blends with hierarchical back-mapping

NASA Astrophysics Data System (ADS)

Ohkuma, Takahiro; Kremer, Kurt; Daoulas, Kostas

2018-05-01

Understanding properties of polymer alloys with computer simulations frequently requires equilibration of samples comprised of microscopically described long molecules. We present the extension of an efficient hierarchical backmapping strategy, initially developed for homopolymer melts, to equilibrate high-molecular-weight binary blends. These mixtures present significant interest for practical applications and fundamental polymer physics. In our approach, the blend is coarse-grained into models representing polymers as chains of soft blobs. Each blob stands for a subchain with N b microscopic monomers. A hierarchy of blob-based models with different resolution is obtained by varying N b. First the model with the largest N b is used to obtain an equilibrated blend. This configuration is sequentially fine-grained, reinserting at each step the degrees of freedom of the next in the hierarchy blob-based model. Once the blob-based description is sufficiently detailed, the microscopic monomers are reinserted. The hard excluded volume is recovered through a push-off procedure and the sample is re-equilibrated with molecular dynamics (MD), requiring relaxation on the order of the entanglement time. For the initial method development we focus on miscible blends described on microscopic level through a generic bead-spring model, which reproduces hard excluded volume, strong covalent bonds, and realistic liquid density. The blended homopolymers are symmetric with respect to molecular architecture and liquid structure. To parameterize the blob-based models and validate equilibration of backmapped samples, we obtain reference data from independent hybrid simulations combining MD and identity exchange Monte Carlo moves, taking advantage of the symmetry of the blends. The potential of the backmapping strategy is demonstrated by equilibrating blend samples with different degree of miscibility, containing 500 chains with 1000 monomers each. Equilibration is verified by comparing chain conformations and liquid structure in backmapped blends with the reference data. Possible directions for further methodological developments are discussed.

Biobriefcase aerosol collector

DOEpatents

Bell, Perry M [Tracy, CA; Christian, Allen T [Madison, WI; Bailey, Christopher G [Pleasanton, CA; Willis, Ladona [Manteca, CA; Masquelier, Donald A [Tracy, CA; Nasarabadi, Shanavaz L [Livermore, CA

2009-09-22

A system for sampling air and collecting particles entrained in the air that potentially include bioagents. The system comprises providing a receiving surface, directing a liquid to the receiving surface and producing a liquid surface. Collecting samples of the air and directing the samples of air so that the samples of air with particles entrained in the air impact the liquid surface. The particles potentially including bioagents become captured in the liquid. The air with particles entrained in the air impacts the liquid surface with sufficient velocity to entrain the particles into the liquid but cause minor turbulence. The liquid surface has a surface tension and the collector samples the air and directs the air to the liquid surface so that the air with particles entrained in the air impacts the liquid surface with sufficient velocity to entrain the particles into the liquid, but cause minor turbulence on the surface resulting in insignificant evaporation of the liquid.

Microfluidic Serial Dilution Circuit

PubMed Central

Paegel, Brian M.; Grover, William H.; Skelley, Alison M.; Mathies, Richard A.; Joyce, Gerald F.

2008-01-01

In vitro evolution of RNA molecules requires a method for executing many consecutive serial dilutions. To solve this problem, a microfluidic circuit has been fabricated in a three-layer glass-PDMS-glass device. The 400-nL serial dilution circuit contains five integrated membrane valves: three two-way valves arranged in a loop to drive cyclic mixing of the diluent and carryover, and two bus valves to control fluidic access to the circuit through input and output channels. By varying the valve placement in the circuit, carryover fractions from 0.04 to 0.2 were obtained. Each dilution process, which is comprised of a diluent flush cycle followed by a mixing cycle, is carried out with no pipeting, and a sample volume of 400 nL is sufficient for conducting an arbitrary number of serial dilutions. Mixing is precisely controlled by changing the cyclic pumping rate, with a minimum mixing time of 22 s. This microfluidic circuit is generally applicable for integrating automated serial dilution and sample preparation in almost any microfluidic architecture. PMID:17073422

Prehospital delay in individuals with acute coronary disease: concordance of medical records and follow-up phone interviews.

PubMed

Goldberg, Robert J; Osganian, Stavroula; Zapka, Jane; Mitchell, Paul; Bittner, Vera; Daya, Mo; Luepker, Russell

2002-01-01

Patient-associated delay in seeking medical care in persons with acute coronary disease is receiving increasing importance given the time-dependent benefits associated with myocardial reperfusion therapies. We examined the extent of concordance between self-reported information about prehospital delay provided by patients to hospital staff at the time of hospitalization for coronary disease compared with information obtained from a telephone interview approximately 2 months following hospital discharge. The sample included 316 patients with acute myocardial infarction or unstable angina at 43 hospitals who had delay time information available from both data sources. The extent of agreement between the medical record and telephone accounts of delay was 47% in the total study sample, 53% in patients with acute myocardial infarction, and 40% in patients with unstable angina. These results suggest that a telephone interview carried out several months following hospitalization for acute coronary disease may not provide sufficiently reliable information about prehospital delay. Copyright 2002 S. Karger AG, Basel

A simple autocorrelation algorithm for determining grain size from digital images of sediment

USGS Publications Warehouse

Rubin, D.M.

2004-01-01

Autocorrelation between pixels in digital images of sediment can be used to measure average grain size of sediment on the bed, grain-size distribution of bed sediment, and vertical profiles in grain size in a cross-sectional image through a bed. The technique is less sensitive than traditional laboratory analyses to tails of a grain-size distribution, but it offers substantial other advantages: it is 100 times as fast; it is ideal for sampling surficial sediment (the part that interacts with a flow); it can determine vertical profiles in grain size on a scale finer than can be sampled physically; and it can be used in the field to provide almost real-time grain-size analysis. The technique can be applied to digital images obtained using any source with sufficient resolution, including digital cameras, digital video, or underwater digital microscopes (for real-time grain-size mapping of the bed). ?? 2004, SEPM (Society for Sedimentary Geology).

Effect of cooking procedures of kiymali pide, a traditional Turkish fast-food, on destruction of Escherichia coli O157:H7.

PubMed

Ilhak, Osman İrfan; Dikici, Abdullah; Can, Ozlem Pelin; Seker, Pınar; Oksüztepe, Gülsüm; Calıcıoğlu, Mehmet

2013-06-01

The objective of the present study was to obtain data about cooking time and temperature of kiymali pide in the restaurants and to investigate thermal inactivation of E. coli O157:H7 during experimental kiymali pide making. A field study was conducted in randomly selected 23 of 87 pide restaurants. Processing parameters including oven temperature, cooking period and post-cooking temperature were determined. Kiymali pide samples were prepared using ground beef filling experimentally inoculated with E. coli O157:H7 (7.6 log10 CFU/g). Pide samples were cooked at a conventional oven at 180 °C for 180, 240, 270, 300 and 330 s. Results of the current study suggest that cooking kiymali pide at 180 °C for at least 330 s (5.5 min) may provide sufficient food safety assurance (≥6 log10 CFU/g) for E. coli O157:H7. Copyright © 2013 Elsevier Ltd. All rights reserved.

Wang-Landau Reaction Ensemble Method: Simulation of Weak Polyelectrolytes and General Acid-Base Reactions.

PubMed

Landsgesell, Jonas; Holm, Christian; Smiatek, Jens

2017-02-14

We present a novel method for the study of weak polyelectrolytes and general acid-base reactions in molecular dynamics and Monte Carlo simulations. The approach combines the advantages of the reaction ensemble and the Wang-Landau sampling method. Deprotonation and protonation reactions are simulated explicitly with the help of the reaction ensemble method, while the accurate sampling of the corresponding phase space is achieved by the Wang-Landau approach. The combination of both techniques provides a sufficient statistical accuracy such that meaningful estimates for the density of states and the partition sum can be obtained. With regard to these estimates, several thermodynamic observables like the heat capacity or reaction free energies can be calculated. We demonstrate that the computation times for the calculation of titration curves with a high statistical accuracy can be significantly decreased when compared to the original reaction ensemble method. The applicability of our approach is validated by the study of weak polyelectrolytes and their thermodynamic properties.

3D Printing in Zero-G Experiment, In Space Manufacturing (LPS, 4)

NASA Technical Reports Server (NTRS)

Bean, Quincy; Cooper, Ken; Werkheiser, Niki

2015-01-01

The 3D Printing in Zero-G Experiment has been an ongoing effort for several years. In June 2014 the technology demonstration 3D printer was launched to the International Space Station. In November 2014 the first 21 parts were manufactured in orbit marking the beginning of a paradigm shift that will allow astronauts to be more self-sufficient and pave the way to larger scale orbital manufacturing. Prior to launch the 21 parts were built on the ground with the flight unit with the same feedstock. These ground control samples are to be tested alongside the flight samples in order to determine if there is a measurable difference between parts built on the ground vs. parts built in space. As of this writing, testing has not yet commenced. Tests to be performed are structured light scanning for volume and geometric discrepancies, CT scanning for density measurement, destructive testing of mechanical samples, and SEM analysis for inter-laminar adhesion discrepancies. Additionally, an ABS material characterization was performed on mechanical samples built from the same CAD files as the flight and ground samples on different machine / feedstock combinations. The purpose of this testing was twofold: first to obtain mechanical data in order to have a baseline comparison for the flight and ground samples and second to ascertain if there is a measurable difference between machines and feedstock.

A simplified field protocol for genetic sampling of birds using buccal swabs

USGS Publications Warehouse

Vilstrup, Julia T.; Mullins, Thomas D.; Miller, Mark P.; McDearman, Will; Walters, Jeffrey R.; Haig, Susan M.

2018-01-01

DNA sampling is an essential prerequisite for conducting population genetic studies. For many years, blood sampling has been the preferred method for obtaining DNA in birds because of their nucleated red blood cells. Nonetheless, use of buccal swabs has been gaining favor because they are less invasive yet still yield adequate amounts of DNA for amplifying mitochondrial and nuclear markers; however, buccal swab protocols often include steps (e.g., extended air-drying and storage under frozen conditions) not easily adapted to field settings. Furthermore, commercial extraction kits and swabs for buccal sampling can be expensive for large population studies. We therefore developed an efficient, cost-effective, and field-friendly protocol for sampling wild birds after comparing DNA yield among 3 inexpensive buccal swab types (2 with foam tips and 1 with a cotton tip). Extraction and amplification success was high (100% and 97.2% respectively) using inexpensive generic swabs. We found foam-tipped swabs provided higher DNA yields than cotton-tipped swabs. We further determined that omitting a drying step and storing swabs in Longmire buffer increased efficiency in the field while still yielding sufficient amounts of DNA for detailed population genetic studies using mitochondrial and nuclear markers. This new field protocol allows time- and cost-effective DNA sampling of juveniles or small-bodied birds for which drawing blood may cause excessive stress to birds and technicians alike.

Model-Based Design of Long-Distance Tracer Transport Experiments in Plants.

PubMed

Bühler, Jonas; von Lieres, Eric; Huber, Gregor J

2018-01-01

Studies of long-distance transport of tracer isotopes in plants offer a high potential for functional phenotyping, but so far measurement time is a bottleneck because continuous time series of at least 1 h are required to obtain reliable estimates of transport properties. Hence, usual throughput values are between 0.5 and 1 samples h -1 . Here, we propose to increase sample throughput by introducing temporal gaps in the data acquisition of each plant sample and measuring multiple plants one after each other in a rotating scheme. In contrast to common time series analysis methods, mechanistic tracer transport models allow the analysis of interrupted time series. The uncertainties of the model parameter estimates are used as a measure of how much information was lost compared to complete time series. A case study was set up to systematically investigate different experimental schedules for different throughput scenarios ranging from 1 to 12 samples h -1 . Selected designs with only a small amount of data points were found to be sufficient for an adequate parameter estimation, implying that the presented approach enables a substantial increase of sample throughput. The presented general framework for automated generation and evaluation of experimental schedules allows the determination of a maximal sample throughput and the respective optimal measurement schedule depending on the required statistical reliability of data acquired by future experiments.

Laser capture microdissection: should an ultraviolet or infrared laser be used?

PubMed

Vandewoestyne, Mado; Goossens, Karen; Burvenich, Christian; Van Soom, Ann; Peelman, Luc; Deforce, Dieter

2013-08-15

Laser capture microdissection (LCM) is a well-established cell separation technique. It combines microscopy with laser beam technology and allows targeting of specific cells or tissue regions that need to be separated from others. Consequently, this biological material can be used for genome or transcriptome analyses. Appropriate methods of sample preparation, however, are crucial for the success of downstream molecular analysis. The aim of this study was to objectively compare the two main LCM systems, one based on an ultraviolet (UV) laser and the other based on an infrared (IR) laser, on different criteria ranging from user-friendliness to sample quality. The comparison was performed on two types of samples: peripheral blood mononuclear cells and blastocysts. The UV laser LCM system had several advantages over the IR laser LCM system. Not only does the UV system allow faster and more precise sample collection, but also the obtained samples-even single cell samples-can be used for DNA extraction and downstream polymerase chain reaction (PCR) applications. RNA-based applications are more challenging for both LCM systems. Although sufficient RNA can be extracted from as few as 10 cells for reverse transcription quantitative PCR (RT-qPCR) analysis, the low RNA quality should be taken into account when designing the RT-qPCR assays. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

A comparison of impact force reduction by polymer materials used for mouthguard fabrication.

PubMed

Gawlak, Dominika; Mańka-Malara, Katarzyna; Mierzwińska-Nastalska, Elżbieta; Gieleta, Roman; Kamiński, Tomasz; Łuniewska, Magdalena

2017-01-01

The essential function of mouthguards is protection against the effects of injuries sustained during sports activities. This purpose will be successfully achieved if appropriate materials ensuring sufficient reduction of the injury force are used for mouthguard fabrication. The objective of the study was to investigate the force reduction capability of selected materials as well as to identify which material reduces the impact force to the highest degree. The material for the study were samples of polymers (6 samples in total), obtained during the process of deep pressing (2 samples), flasking (3 samples) and thermal injection (1 sample), which were tested for impact force damping using an impact device - Charpy impact hammer. The control group comprised of the ceramic material samples subjected to the hammer impact. The statistical analysis applied in this study were one-way Welch ANOVA with post-hoc Games-Howell pairwise comparisons. The test materials reduced the impact force of the impact hammer to varying degrees. The greatest damping capability was demonstrated for the following materials: Impak with 1:1 powder-to-liquid weight ratio polymerized with the conventional flasking technique, and Corflex Orthodontic used in the thermal injection technique of mouthguard fabrication. Impak with 1:1 weight ratio and Corflex Orthodontic should be recommended for the fabrication of mouthguards since they demonstrated the most advantageous damping properties.

Decontamination of poultry feed from ochratoxin A by UV and sunlight radiations.

PubMed

Ameer Sumbal, Gul; Hussain Shar, Zahid; Hussain Sherazi, Syed Tufail; Sirajuddin; Nizamani, Shafi Muhammad; Mahesar, Safaraz Ahmed

2016-06-01

Mycotoxin-contaminated feed is very dangerous for the growth and even life of poultry. The objective of the current study was to investigate the efficacy of ultra-violet irradiation for decontamination of ochratoxin A (OTA) in spiked and naturally contaminated poultry feed samples. Spiked and naturally contaminated feed samples were irradiated with ultra-violet light (UV) at distance of 25 cm over the feed samples. In vitro, the effect of UV intensity (0.1 mW cm(-2) at 254 nm UV-C) on different types of poultry feeds contaminated with OTA was evaluated. The same samples were also irradiated with sunlight and analysed for OTA by an indirect enzyme linked immunosorbent assay method. Poultry feed samples containing 500 µg kg(-1) were 100% decontaminated in 180 min with UV radiation while OTA was decreased to 70-95 µg kg(-1) using the same poultry feed samples after 8 h sunlight irradiation. Therefore, UV light was found to be more effective. Only 1 h of UV irradiation was found to be sufficient to bring the OTA level to the maximum regulatory limit suggested for poultry feeds (100 µg kg(-1) ), while 8 h were needed to obtain this level using sunlight radiations. The proposed approach is a viable option to reduce the level of OTA in contaminated poultry feeds. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

Rapid analysis of ecstasy and related phenethylamines in seized tablets by Raman spectroscopy.

PubMed

Bell, S E; Burns, D T; Dennis, A C; Speers, J S

2000-03-01

Raman spectroscopy with far-red excitation has been used to study seized, tableted samples of MDMA (N-methyl-3,4-methylenedioxyamphetamine) and related compounds (MDA, MDEA, MBDB, 2C-B and amphetamine sulfate), as well as pure standards of these drugs. We have found that by using far-red (785 nm) excitation the level of fluorescence background even in untreated seized samples is sufficiently low that there is little difficulty in obtaining good quality data with moderate 2 min data accumulation times. The spectra can be used to distinguish between even chemically-similar substances, such as the geometrical isomers MDEA and MBDB, and between different polymorphic/hydrated forms of the same drug. Moreover, these differences can be found even in directly recorded spectra of seized samples which have been bulked with other materials, giving a rapid and non-destructive method for drug identification. The spectra can be processed to give unambiguous identification of both drug and excipients (even when more than one compound has been used as the bulking agent) and the relative intensities of drug and excipient bands can be used for quantitative or at least semi-quantitative analysis. Finally, the simple nature of the measurements lends itself to automatic sample handling so that sample throughputs of 20 samples per hour can be achieved with no real difficulty.

Latex samples for RAMSES electrophoresis experiment on IML 2

NASA Technical Reports Server (NTRS)

Seaman, Geoffrey V. F.; Knox, Robert J.

1994-01-01

The objectives of these reported studies were to provide ground based support services for the flight experiment team for the RAMSES experiment to be flown aboard IML-2. The specific areas of support included consultation on the performance of particle based electrophoresis studies, development of methods for the preparation of suitable samples for the flight hardware, the screening of particles to obtain suitable candidates for the flight experiment, and the electrophoretic characterization of sample particle preparations. The first phases of these studies were performed under this contract, while the follow on work was performed under grant number NAG8 1081, 'Preparation and Characterization of Latex Samples for RAMSES Experiment on IML 2.' During this first phase of the experiment the following benchmarks were achieved: Methods were tested for the concentration and resuspension of latex samples in the greater than 0.4 micron diameter range to provide moderately high solids content samples free of particle aggregation which interferred with the normal functioning of the RAMSES hardware. Various candidate latex preparations were screened and two candidate types of latex were identified for use in the flight experiments, carboxylate modified latex (CML) and acrylic acid-acrylamide modified latex (AAM). These latexes have relatively hydrophilic surfaces, are not prone to aggregate, and display sufficiently low electrophoretic mobilities in the flight buffer so that they can be used to make mixtures to test the resolving power of the flight hardware.

12 CFR 715.8 - Requirements for verification of accounts and passbooks.

Code of Federal Regulations, 2010 CFR

2010-01-01

... selection: (ii) A sample which is representative of the population from which it was selected; (iii) An equal chance of selecting each dollar in the population; (iv) Sufficient accounts in both number and... consistent with GAAS if such methods provide for: (i) Sufficient accounts in both number and scope on which...

Empirical evaluation of sufficient similarity in dose-response for environmental risk assessment of a mixture of 11 pyrethroids.

EPA Science Inventory

Chemical mixtures in the environment are often the result of a dynamic process. When dose-response data are available on random samples throughout the process, equivalence testing can be used to determine whether the mixtures are sufficiently similar based on a pre-specified biol...

Nonuniform sampling and non-Fourier signal processing methods in multidimensional NMR.

PubMed

Mobli, Mehdi; Hoch, Jeffrey C

2014-11-01

Beginning with the introduction of Fourier Transform NMR by Ernst and Anderson in 1966, time domain measurement of the impulse response (the free induction decay, FID) consisted of sampling the signal at a series of discrete intervals. For compatibility with the discrete Fourier transform (DFT), the intervals are kept uniform, and the Nyquist theorem dictates the largest value of the interval sufficient to avoid aliasing. With the proposal by Jeener of parametric sampling along an indirect time dimension, extension to multidimensional experiments employed the same sampling techniques used in one dimension, similarly subject to the Nyquist condition and suitable for processing via the discrete Fourier transform. The challenges of obtaining high-resolution spectral estimates from short data records using the DFT were already well understood, however. Despite techniques such as linear prediction extrapolation, the achievable resolution in the indirect dimensions is limited by practical constraints on measuring time. The advent of non-Fourier methods of spectrum analysis capable of processing nonuniformly sampled data has led to an explosion in the development of novel sampling strategies that avoid the limits on resolution and measurement time imposed by uniform sampling. The first part of this review discusses the many approaches to data sampling in multidimensional NMR, the second part highlights commonly used methods for signal processing of such data, and the review concludes with a discussion of other approaches to speeding up data acquisition in NMR. Copyright © 2014 Elsevier B.V. All rights reserved.

Remote sensing data with the conditional latin hypercube sampling and geostatistical approach to delineate landscape changes induced by large chronological physical disturbances.

PubMed

Lin, Yu-Pin; Chu, Hone-Jay; Wang, Cheng-Long; Yu, Hsiao-Hsuan; Wang, Yung-Chieh

2009-01-01

This study applies variogram analyses of normalized difference vegetation index (NDVI) images derived from SPOT HRV images obtained before and after the ChiChi earthquake in the Chenyulan watershed, Taiwan, as well as images after four large typhoons, to delineate the spatial patterns, spatial structures and spatial variability of landscapes caused by these large disturbances. The conditional Latin hypercube sampling approach was applied to select samples from multiple NDVI images. Kriging and sequential Gaussian simulation with sufficient samples were then used to generate maps of NDVI images. The variography of NDVI image results demonstrate that spatial patterns of disturbed landscapes were successfully delineated by variogram analysis in study areas. The high-magnitude Chi-Chi earthquake created spatial landscape variations in the study area. After the earthquake, the cumulative impacts of typhoons on landscape patterns depended on the magnitudes and paths of typhoons, but were not always evident in the spatiotemporal variability of landscapes in the study area. The statistics and spatial structures of multiple NDVI images were captured by 3,000 samples from 62,500 grids in the NDVI images. Kriging and sequential Gaussian simulation with the 3,000 samples effectively reproduced spatial patterns of NDVI images. However, the proposed approach, which integrates the conditional Latin hypercube sampling approach, variogram, kriging and sequential Gaussian simulation in remotely sensed images, efficiently monitors, samples and maps the effects of large chronological disturbances on spatial characteristics of landscape changes including spatial variability and heterogeneity.

Global Hopf bifurcation analysis on a BAM neural network with delays

NASA Astrophysics Data System (ADS)

Sun, Chengjun; Han, Maoan; Pang, Xiaoming

2007-01-01

A delayed differential equation that models a bidirectional associative memory (BAM) neural network with four neurons is considered. By using a global Hopf bifurcation theorem for FDE and a Bendixon's criterion for high-dimensional ODE, a group of sufficient conditions for the system to have multiple periodic solutions are obtained when the sum of delays is sufficiently large.

Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive

PubMed Central

Nakazato, Takeru; Bono, Hidemasa

2017-01-01

Abstract It is important for public data repositories to promote the reuse of archived data. In the growing field of omics science, however, the increasing number of submissions of high-throughput sequencing (HTSeq) data to public repositories prevents users from choosing a suitable data set from among the large number of search results. Repository users need to be able to set a threshold to reduce the number of results to obtain a suitable subset of high-quality data for reanalysis. We calculated the quality of sequencing data archived in a public data repository, the Sequence Read Archive (SRA), by using the quality control software FastQC. We obtained quality values for 1 171 313 experiments, which can be used to evaluate the suitability of data for reuse. We also visualized the data distribution in SRA by integrating the quality information and metadata of experiments and samples. We provide quality information of all of the archived sequencing data, which enable users to obtain sufficient quality sequencing data for reanalyses. The calculated quality data are available to the public in various formats. Our data also provide an example of enhancing the reuse of public data by adding metadata to published research data by a third party. PMID:28449062

On the stability of motion of several types of heavy symmetric gyroscopes with damping torques

NASA Astrophysics Data System (ADS)

Ge, Z.-M.; Wu, M.-H.

Sufficient conditions for the stability of motion of several gyroscopes are obtained using Liapunov's direct method. The stability of a 'temporarily' sleeping top with damping torque is considered for the cases of the support being fixed, being in vertical harmonic motion, and being in vertical periodic motion. Sufficient conditions are also obtained for the stability of a heavy symmetric gyroscope with damping torque and motor torque for the cases of regular precession, vertical axis permanent rotation with and without the axis of the outer gimbal being inclined, and the gyroscope being in a Newtonian central gravitational field.

On a program manifold's stability of one contour automatic control systems

NASA Astrophysics Data System (ADS)

Zumatov, S. S.

2017-12-01

Methodology of analysis of stability is expounded to the one contour systems automatic control feedback in the presence of non-linearities. The methodology is based on the use of the simplest mathematical models of the nonlinear controllable systems. Stability of program manifolds of one contour automatic control systems is investigated. The sufficient conditions of program manifold's absolute stability of one contour automatic control systems are obtained. The Hurwitz's angle of absolute stability was determined. The sufficient conditions of program manifold's absolute stability of control systems by the course of plane in the mode of autopilot are obtained by means Lyapunov's second method.

Amendment to examination and investigation sample requirements--FDA. Direct final rule.

PubMed

1998-09-25

The Food and Drug Administration (FDA) is amending its regulations regarding the collection of twice the quantity of food, drug, or cosmetic estimated to be sufficient for analysis. This action increases the dollar amount that FDA will consider to determine whether to routinely collect a reserve sample of a food, drug, or cosmetic product in addition to the quantity sufficient for analysis. Experience has demonstrated that the current dollar amount does not adequately cover the cost of most quantities sufficient for analysis plus reserve samples. This direct final rule is part of FDA's continuing effort to achieve the objectives of the President's "Reinventing Government" initiative, and is intended to reduce the burden of unnecessary regulations on food, drugs, and cosmetics without diminishing the protection of the public health. Elsewhere in this issue of the Federal Register, FDA is publishing a companion proposed rule under FDA's usual procedures for notice and comment to provide a procedural framework to finalize the rule in the event the agency receives any significant adverse comment and withdraws this direct final rule.

ADEQUACY OF VISUALLY CLASSIFIED PARTICLE COUNT STATISTICS FROM REGIONAL STREAM HABITAT SURVEYS

EPA Science Inventory

Streamlined sampling procedures must be used to achieve a sufficient sample size with limited resources in studies undertaken to evaluate habitat status and potential management-related habitat degradation at a regional scale. At the same time, these sampling procedures must achi...

40 CFR 265.91 - Ground-water monitoring system.

Code of Federal Regulations, 2010 CFR

2010-07-01

... sufficient to yield ground-water samples that are: (i) Representative of background ground-water quality in... not required provided that provisions for sampling upgradient and downgradient water quality will... perforated, and packed with gravel or sand where necessary, to enable sample collection at depths where...

Stochastic approach for an unbiased estimation of the probability of a successful separation in conventional chromatography and sequential elution liquid chromatography.

PubMed

Ennis, Erin J; Foley, Joe P

2016-07-15

A stochastic approach was utilized to estimate the probability of a successful isocratic or gradient separation in conventional chromatography for numbers of sample components, peak capacities, and saturation factors ranging from 2 to 30, 20-300, and 0.017-1, respectively. The stochastic probabilities were obtained under conditions of (i) constant peak width ("gradient" conditions) and (ii) peak width increasing linearly with time ("isocratic/constant N" conditions). The isocratic and gradient probabilities obtained stochastically were compared with the probabilities predicted by Martin et al. [Anal. Chem., 58 (1986) 2200-2207] and Davis and Stoll [J. Chromatogr. A, (2014) 128-142]; for a given number of components and peak capacity the same trend is always observed: probability obtained with the isocratic stochastic approach

A comparison of Thellier-type and multispecimen paleointensity determinations on Pleistocene and historical lava flows from Lanzarote (Canary Islands, Spain)

NASA Astrophysics Data System (ADS)

Calvo-Rathert, Manuel; Morales-Contreras, Juan; Carrancho, Ángel; Goguitchaichvili, Avto

2016-09-01

Sixteen Miocene, Pleistocene, and historic lava flows have been sampled in Lanzarote (Canary Islands) for paleointensity analysis with both the Coe and multispecimen methods. Besides obtaining new data, the main goal of the study was the comparison of paleointensity results determined with two different techniques. Characteristic Remanent Magnetization (ChRM) directions were obtained in 15 flows, and 12 were chosen for paleointensity determination. In Thellier-type experiments, a selection of reliable paleointensity determinations (43 of 78 studied samples) was performed using sets of criteria of different stringency, trying to relate the quality of results to the strictness of the chosen criteria. Uncorrected and fraction and domain-state corrected multispecimen paleointensity results were obtained in all flows. Results with the Coe method on historical flows either agree with the expected values or show moderately lower ones, but multispecimen determinations display a large deviation from the expected result in one case. No relation can be detected between correct or anomalous results and paleointensity determination quality or rock-magnetic properties. However, results on historical flows suggest that agreement between both methods could be a good indicator of correct determinations. Comparison of results obtained with both methods on seven Pleistocene flows yields an excellent agreement in four and disagreements in three cases. Pleistocene determinations were only accepted if either results from both methods agreed or a result was based on a sufficiently large number (n > 4) of individual Thellier-type determinations. In most Pleistocene flows, a VADM around 5 × 1022 Am2 was observed, although two flows displayed higher values around 9 × 1022 Am2.

7A projection map of the S-layer protein sbpA obtained with trehalose-embedded monolayer crystals.

PubMed

Norville, Julie E; Kelly, Deborah F; Knight, Thomas F; Belcher, Angela M; Walz, Thomas

2007-12-01

Two-dimensional crystallization on lipid monolayers is a versatile tool to obtain structural information of proteins by electron microscopy. An inherent problem with this approach is to prepare samples in a way that preserves the crystalline order of the protein array and produces specimens that are sufficiently flat for high-resolution data collection at high tilt angles. As a test specimen to optimize the preparation of lipid monolayer crystals for electron microscopy imaging, we used the S-layer protein sbpA, a protein with potential for designing arrays of both biological and inorganic materials with engineered properties for a variety of nanotechnology applications. Sugar embedding is currently considered the best method to prepare two-dimensional crystals of membrane proteins reconstituted into lipid bilayers. We found that using a loop to transfer lipid monolayer crystals to an electron microscopy grid followed by embedding in trehalose and quick-freezing in liquid ethane also yielded the highest resolution images for sbpA lipid monolayer crystals. Using images of specimens prepared in this way we could calculate a projection map of sbpA at 7A resolution, one of the highest resolution projection structures obtained with lipid monolayer crystals to date.

Determination of quaternary ammonium compounds by potentiometric titration with an ionic surfactant electrode: single-laboratory validation.

PubMed

Price, Randi; Wan, Ping

2010-01-01

A potentiometric titration for determining the quaternary ammonium compounds (QAC) commonly found in antimicrobial products was validated by a single laboratory. Traditionally, QACs were determined by using a biphasic (chloroform and water) manual titration procedure. Because of safety considerations regarding chloroform, as well as the subjectivity of color indicator-based manual titration determinations, an automatic potentiometric titration procedure was tested with quaternary nitrogen product formulations. By using the Metrohm Titrando system coupled with an ionic surfactant electrode and an Ag/AgCl reference electrode, titrations were performed with various QAC-containing formulation products/matrixes; a standard sodium lauryl sulfate solution was used as the titrant. Results for the products tested are sufficiently reproducible and accurate for the purpose of regulatory product enforcement. The robustness of the method was measured by varying pH levels, as well as by comparing buffered versus unbuffered titration systems. A quantitation range of 1-1000 ppm quaternary nitrogen was established. Eight commercially available antimicrobial products covering a variety of matrixes were assayed; the results obtained were comparable to those obtained by the manual titration method. Recoveries of 94 to 104% were obtained for spiked samples.

Experimental Aeroheating Study of Mid-L/D Entry Vehicle Geometries: NASA LaRC 20-Inch Mach 6 Air Tunnel Test 6966

NASA Technical Reports Server (NTRS)

Hollis, Brian R.; Hollingsworth, Kevin E.

2014-01-01

Aeroheating data on mid lift-to-drag ratio entry vehicle configurations has been obtained through hypersonic wind tunnel testing. Vehicles of this class have been proposed for high-mass Mars missions, such as sample return and crewed exploration, for which the conventional sphere-cone entry vehicle geometries of previous Mars missions are insufficient. Several configurations were investigated, including elliptically-blunted cylinders with both circular and elliptical cross sections, biconic geometries based on launch vehicle dual-use shrouds, and parametrically-optimized analytic geometries. Testing was conducted at Mach 6 over a range of Reynolds numbers sufficient to generate laminar, transitional, and turbulent flow. Global aeroheating data were obtained using phosphor thermography. Both stream-wise and cross-flow transition occured on different configurations. Comparisons were made with laminar and turbulent computational predictions generated with an algebraic turbulence model. Predictions were generally in good agreement in regions of laminar or fully-turbulent flow; however for transitional cases, the lack of a transition onset prediction capability produced less accurate comparisons. The data obtained in this study are intended to be used for prelimary mission design studies and the development and validation of computational methods.

Sample size and power calculations for detecting changes in malaria transmission using antibody seroconversion rate.

PubMed

Sepúlveda, Nuno; Paulino, Carlos Daniel; Drakeley, Chris

2015-12-30

Several studies have highlighted the use of serological data in detecting a reduction in malaria transmission intensity. These studies have typically used serology as an adjunct measure and no formal examination of sample size calculations for this approach has been conducted. A sample size calculator is proposed for cross-sectional surveys using data simulation from a reverse catalytic model assuming a reduction in seroconversion rate (SCR) at a given change point before sampling. This calculator is based on logistic approximations for the underlying power curves to detect a reduction in SCR in relation to the hypothesis of a stable SCR for the same data. Sample sizes are illustrated for a hypothetical cross-sectional survey from an African population assuming a known or unknown change point. Overall, data simulation demonstrates that power is strongly affected by assuming a known or unknown change point. Small sample sizes are sufficient to detect strong reductions in SCR, but invariantly lead to poor precision of estimates for current SCR. In this situation, sample size is better determined by controlling the precision of SCR estimates. Conversely larger sample sizes are required for detecting more subtle reductions in malaria transmission but those invariantly increase precision whilst reducing putative estimation bias. The proposed sample size calculator, although based on data simulation, shows promise of being easily applicable to a range of populations and survey types. Since the change point is a major source of uncertainty, obtaining or assuming prior information about this parameter might reduce both the sample size and the chance of generating biased SCR estimates.

DNA barcoding using skin exuviates can improve identification and biodiversity studies of snakes.

PubMed

Khedkar, Trupti; Sharma, Rashmi; Tiknaik, Anita; Khedkar, Gulab; Naikwade, Bhagwat S; Ron, Tetsuzan Benny; Haymer, David

2016-01-01

Snakes represent a taxonomically underdeveloped group of animals in India with a lack of experts and incomplete taxonomic descriptions being the main deterrents to advances in this area. Molecular taxonomic approaches using DNA barcoding could aid in snake identification as well as studies of biodiversity. Here a non-invasive sampling method using DNA barcoding is tested using skin exuviates. Taxonomically authenticated samples were collected and tested for validation and comparisons to unknown snake exuviate samples. This approach was also used to construct the first comprehensive study targeting the snake species from Maharashtra state in India. A total of 92 skin exuviate samples were collected and tested for this study. Of these, 81 samples were successfully DNA barcoded and compared with unknown samples for assignment of taxonomic identity. Good quality DNA was obtained irrespective of age and quality of the exuviate material, and all unknown samples were successfully identified. A total of 23 species of snakes were identified, six of which were in the list of Endangered species (Red Data Book). Intra- and inter-specific distance values were also calculated, and these were sufficient to allow discrimination among species and between species without ambiguity in most cases. Two samples were suspected to represent cryptic species based on deep K2P divergence values (>3%), and one sample could be identified to the genus level only. Eleven samples failed to amplify COI sequences, suggesting the need for alternative PCR primer pairs. This study clearly documents how snake skin exuviates can be used for DNA barcoding, estimates of diversity and population genetic structuring in a noninvasive manner.

Electrophoretic sample insertion. [device for uniformly distributing samples in flow path

NASA Technical Reports Server (NTRS)

Mccreight, L. R. (Inventor)

1974-01-01

Two conductive screens located in the flow path of an electrophoresis sample separation apparatus are charged electrically. The sample is introduced between the screens, and the charge is sufficient to disperse and hold the samples across the screens. When the charge is terminated, the samples are uniformly distributed in the flow path. Additionally, a first separation by charged properties has been accomplished.

Multiplex picodroplet digital PCR to detect KRAS mutations in circulating DNA from the plasma of colorectal cancer patients.

PubMed

Taly, Valerie; Pekin, Deniz; Benhaim, Leonor; Kotsopoulos, Steve K; Le Corre, Delphine; Li, Xinyu; Atochin, Ivan; Link, Darren R; Griffiths, Andrew D; Pallier, Karine; Blons, Hélène; Bouché, Olivier; Landi, Bruno; Hutchison, J Brian; Laurent-Puig, Pierre

2013-12-01

Multiplex digital PCR (dPCR) enables noninvasive and sensitive detection of circulating tumor DNA with performance unachievable by current molecular-detection approaches. Furthermore, picodroplet dPCR facilitates simultaneous screening for multiple mutations from the same sample. We investigated the utility of multiplex dPCR to screen for the 7 most common mutations in codons 12 and 13 of the KRAS (Kirsten rat sarcoma viral oncogene homolog) oncogene from plasma samples of patients with metastatic colorectal cancer. Fifty plasma samples were tested from patients for whom the primary tumor biopsy tissue DNA had been characterized by quantitative PCR. Tumor characterization revealed that 19 patient tumors had KRAS mutations. Multiplex dPCR analysis of the plasma DNA prepared from these samples identified 14 samples that matched the mutation identified in the tumor, 1 sample contained a different KRAS mutation, and 4 samples had no detectable mutation. Among the tumor samples that were wild type for KRAS, 2 KRAS mutations were identified in the corresponding plasma samples. Duplex dPCR (i.e., wild-type and single-mutation assay) was also used to analyze plasma samples from patients with KRAS-mutated tumors and 5 samples expected to contain the BRAF (v-raf murine sarcoma viral oncogene homolog B) V600E mutation. The results for the duplex analysis matched those for the multiplex analysis for KRAS-mutated samples and, owing to its higher sensitivity, enabled detection of 2 additional samples with low levels of KRAS-mutated DNA. All 5 samples with BRAF mutations were detected. This work demonstrates the clinical utility of multiplex dPCR to screen for multiple mutations simultaneously with a sensitivity sufficient to detect mutations in circulating DNA obtained by noninvasive blood collection.

Accuracy assessment with complex sampling designs

Treesearch

Raymond L. Czaplewski

2010-01-01

A reliable accuracy assessment of remotely sensed geospatial data requires a sufficiently large probability sample of expensive reference data. Complex sampling designs reduce cost or increase precision, especially with regional, continental and global projects. The General Restriction (GR) Estimator and the Recursive Restriction (RR) Estimator separate a complex...

3D-Printing for Analytical Ultracentrifugation

PubMed Central

Desai, Abhiksha; Krynitsky, Jonathan; Pohida, Thomas J.; Zhao, Huaying

2016-01-01

Analytical ultracentrifugation (AUC) is a classical technique of physical biochemistry providing information on size, shape, and interactions of macromolecules from the analysis of their migration in centrifugal fields while free in solution. A key mechanical element in AUC is the centerpiece, a component of the sample cell assembly that is mounted between the optical windows to allow imaging and to seal the sample solution column against high vacuum while exposed to gravitational forces in excess of 300,000 g. For sedimentation velocity it needs to be precisely sector-shaped to allow unimpeded radial macromolecular migration. During the history of AUC a great variety of centerpiece designs have been developed for different types of experiments. Here, we report that centerpieces can now be readily fabricated by 3D printing at low cost, from a variety of materials, and with customized designs. The new centerpieces can exhibit sufficient mechanical stability to withstand the gravitational forces at the highest rotor speeds and be sufficiently precise for sedimentation equilibrium and sedimentation velocity experiments. Sedimentation velocity experiments with bovine serum albumin as a reference molecule in 3D printed centerpieces with standard double-sector design result in sedimentation boundaries virtually indistinguishable from those in commercial double-sector epoxy centerpieces, with sedimentation coefficients well within the range of published values. The statistical error of the measurement is slightly above that obtained with commercial epoxy, but still below 1%. Facilitated by modern open-source design and fabrication paradigms, we believe 3D printed centerpieces and AUC accessories can spawn a variety of improvements in AUC experimental design, efficiency and resource allocation. PMID:27525659

29 CFR 1403.3 - Obtaining data on labor-management disputes.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 29 Labor 4 2010-07-01 2010-07-01 false Obtaining data on labor-management disputes. 1403.3 Section... FUNCTIONS AND DUTIES § 1403.3 Obtaining data on labor-management disputes. When the existence of a labor... information to determine if the Service should proffer its services under its policies. If sufficient data on...

20 CFR 404.1617 - Reasonable efforts to obtain review by a qualified psychiatrist or psychologist.

Code of Federal Regulations, 2011 CFR

2011-04-01

...)). Where it does not have sufficient resources to make the necessary reviews, the State agency must attempt to obtain the resources needed. If the State agency is unable to obtain additional psychiatrists and psychologists because of low salary rates or fee schedules it should attempt to raise the State agency's levels...

20 CFR 416.1017 - Reasonable efforts to obtain review by a qualified psychiatrist or psychologist.

Code of Federal Regulations, 2011 CFR

2011-04-01

...)). Where it does not have sufficient resources to make the necessary reviews, the State agency must attempt to obtain the resources needed. If the State agency is unable to obtain additional psychiatrists and psychologists because of low salary rates or fee schedules it should attempt to raise the State agency's levels...

20 CFR 404.1617 - Reasonable efforts to obtain review by a qualified psychiatrist or psychologist.

Code of Federal Regulations, 2013 CFR

2013-04-01

...)). Where it does not have sufficient resources to make the necessary reviews, the State agency must attempt to obtain the resources needed. If the State agency is unable to obtain additional psychiatrists and psychologists because of low salary rates or fee schedules it should attempt to raise the State agency's levels...

20 CFR 416.1017 - Reasonable efforts to obtain review by a qualified psychiatrist or psychologist.

Code of Federal Regulations, 2012 CFR

2012-04-01

...)). Where it does not have sufficient resources to make the necessary reviews, the State agency must attempt to obtain the resources needed. If the State agency is unable to obtain additional psychiatrists and psychologists because of low salary rates or fee schedules it should attempt to raise the State agency's levels...

20 CFR 416.1017 - Reasonable efforts to obtain review by a qualified psychiatrist or psychologist.

Code of Federal Regulations, 2014 CFR

2014-04-01

...)). Where it does not have sufficient resources to make the necessary reviews, the State agency must attempt to obtain the resources needed. If the State agency is unable to obtain additional psychiatrists and psychologists because of low salary rates or fee schedules it should attempt to raise the State agency's levels...

20 CFR 404.1617 - Reasonable efforts to obtain review by a qualified psychiatrist or psychologist.

Code of Federal Regulations, 2012 CFR

2012-04-01

...)). Where it does not have sufficient resources to make the necessary reviews, the State agency must attempt to obtain the resources needed. If the State agency is unable to obtain additional psychiatrists and psychologists because of low salary rates or fee schedules it should attempt to raise the State agency's levels...

20 CFR 416.1017 - Reasonable efforts to obtain review by a qualified psychiatrist or psychologist.

Code of Federal Regulations, 2013 CFR

2013-04-01

...)). Where it does not have sufficient resources to make the necessary reviews, the State agency must attempt to obtain the resources needed. If the State agency is unable to obtain additional psychiatrists and psychologists because of low salary rates or fee schedules it should attempt to raise the State agency's levels...

20 CFR 404.1617 - Reasonable efforts to obtain review by a qualified psychiatrist or psychologist.

Code of Federal Regulations, 2014 CFR

2014-04-01

...)). Where it does not have sufficient resources to make the necessary reviews, the State agency must attempt to obtain the resources needed. If the State agency is unable to obtain additional psychiatrists and psychologists because of low salary rates or fee schedules it should attempt to raise the State agency's levels...

Cloud Tracking from Satellite Pictures.

DTIC Science & Technology

1981-07-01

sufficiently smooth contours, this information can be obtained from very few low-order coefficients. The inverse transform of the two lowest-order...obtained from very few low- order coefficients. The inverse transform of the two lowest-order coefficients is an ellipse approximating the original...coefficients obtained from the contour of Fig. 9. .. . ........ .. .. ... ..... 67 11. Inverse transform of truncated FD series .. .. . .. .... 67 12

48 CFR 245.7302-5 - Mailing lists.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Mailing lists. (a) The plant clearance officer will ensure the contractor solicits a sufficient number of bidders to obtain adequate competition. (b) When large quantities of property, special commodities, or unusual geographic locations are involved, the plant clearance officer is encouraged to obtain additional...

Genotyping of Campylobacter jejuni from broiler carcasses and slaughterhouse environment by amplified fragment length polymorphism.

PubMed

Johnsen, G; Kruse, H; Hofshagen, M

2006-12-01

We examined the occurrence and diversity of Campylobacter jejuni on broiler carcasses during slaughter of an infected flock and in the slaughterhouse environment during slaughter and postdisinfection before a new production run. During the slaughter of a known C. jejuni infected broiler flock, samples were taken from broiler carcasses at 7 different stages during the process. Thirty-seven sites in the slaughterhouse environment were sampled both during process and postdisinfection. The samples were analyzed for C. jejuni, and genetic fingerprinting was performed using amplified fragment length polymorphism. All carcass samples were positive. Of the environmental samples collected during slaughter, 89% were positive; 100% of those from the arrival, stunning, scalding, defeathering, and evisceration facilities and 67% of those from the cooling and sorting facilities. Postdisinfection, 41% of the samples were positive; 71% of those from the arrival and stunning area, 60% of those from the scalding and defeathering area, and 20% of those from the evisceration, cooling, and sorting area. The C. jejuni isolates (n = 60) recovered were grouped into 4 different amplified fragment length polymorphism clones with a similarity index of 95% or greater. All isolates obtained from the flock and 94% of the isolates obtained from the environment during slaughtering belonged to clone A, whereas 1 environmental isolate belonged to each of the clones B and C. Isolates from clones A, B, and D were present postdisinfection. Only clone B was detected on flocks slaughtered during the previous week. The high level and continuous presence of Campylobacter in the environment constitutes a risk for transmission to negative carcasses. In Norway, where above 96% of the broiler flocks are Campylobacter-negative, this aspect is of special importance. The ability of Campylobacter to remain in the slaughterhouse environment through washing and disinfection is associated with constructional conditions of equipment and buildings, complicating cleaning and providing sufficient moisture. To reduce the probability of the workers acquiring campylobacteriosis, precautions should be taken when slaughtering Campylobacter-positive flocks.

Limitation in the detection of Listeria monocytogenes in food in the presence of competing Listeria innocua.

PubMed

Oravcová, K; Trncíková, T; Kuchta, T; Kaclíková, E

2008-02-01

Detectability of Listeria monocytogenes at 10(0) CFU per food sample in the presence of Listeria innocua using standard microbiological detection was evaluated and compared with the real-time PCR-based method. Enrichment in half-Fraser broth followed by subculture in Fraser broth according to EN ISO 11290-1 was used. False-negative detection of 10(0) CFU L. monocytogenes was obtained in the presence of 10(1) CFU L. innocua per sample using the standard detection method in contrast to more than 10(5) CFU L. innocua per sample using real-time PCR. Identification of L. monocytogenes on the chromogenic medium by the standard procedure was impossible if L. innocua was able to overgrow L. monocytogenes by more than three orders of magnitude after the enrichment in model samples. These results were confirmed using naturally contaminated food samples. Standard microbiological method was insufficient for the reliable detection of 10(0) CFU L. monocytogenes in the presence of more than 10(0) CFU of L. innocua per sample. On the other hand, if the growth of L. monocytogenes was sufficient to reach the concentration equal to the detection limit of PCR, the amount of the other microflora present in the food sample including L. innocua was not relevant for success of the PCR detection of L. monocytogenes. After the enrichment, the PCR detection is more convenient than the standard one as PCR detection is not compromised by other present microflora.

Testicular biopsy in psittacine birds (Psittaciformes): comparative evaluation of testicular reproductive status by endoscopic, histologic, and cytologic examination.

PubMed

Hänse, Maria; Krautwald-Junghanns, Maria-Elisabeth; Reitemeier, Susanne; Einspanier, Almuth; Schmidt, Volker

2013-12-01

Knowledge of the reproductive cycle of male parrots is important for examining the male genital tract and for successful breeding, especially of endangered species. To evaluate different diagnostic methods and criteria concerning the classification of reproductive stages, we examined 20 testicular samples obtained at necropsy in psittacine birds of different species and testicular biopsy samples collected from 9 cockatiels (Nymphicus hollandicus) and 7 rose-ringed parakeets (Psittacula krameri) by endoscopy 4 times over a 12-month period. The testicular reproductive status was assessed histologically and then compared with the macroscopic appearance of the testicles and cytologic results. The histologic examination was nondiagnostic in 19 of 59 testicular biopsy samples. By contrast, the cytologic preparations were diagnostic in 57 of 59 biopsy samples. The results of the cytologic examination coincided with the histologic results in 34 of 38 biopsy samples and 18 of 20 necropsy samples. Macroscopic parameters displayed some differences between reproductive stages but provided an unreliable indication of the reproductive status. These results suggest that microscopic examination of a testicular biopsy sample is a reliable method for evaluating the reproductive status of male parrots and is preferable to the macroscopic evaluation of the testicle. Cytologic examination provides fast preliminary results, even when the histologic preparation is not sufficient for evaluation, but results may be erroneous. Thus, a combination of histologic and cytologic examination is recommended for evaluating testicular reproductive status.

Post-acquisition data processing for the screening of transformation products of different organic contaminants. Two-year monitoring of river water using LC-ESI-QTOF-MS and GCxGC-EI-TOF-MS.

PubMed

López, S Herrera; Ulaszewska, M M; Hernando, M D; Martínez Bueno, M J; Gómez, M J; Fernández-Alba, A R

2014-11-01

This study describes a comprehensive strategy for detecting and elucidating the chemical structures of expected and unexpected transformation products (TPs) from chemicals found in river water and effluent wastewater samples, using liquid chromatography coupled to electrospray ionization quadrupole-time-of-flight mass spectrometer (LC-ESI-QTOF-MS), with post-acquisition data processing and an automated search using an in-house database. The efficacy of the mass defect filtering (MDF) approach to screen metabolites from common biotransformation pathways was tested, and it was shown to be sufficiently sensitive and applicable for detecting metabolites in environmental samples. Four omeprazole metabolites and two venlafaxine metabolites were identified in river water samples. This paper reports the analytical results obtained during 2 years of monitoring, carried out at eight sampling points along the Henares River (Spain). Multiresidue monitoring, for targeted analysis, includes a group of 122 chemicals, amongst which are pharmaceuticals, personal care products, pesticides and PAHs. For this purpose, two analytical methods were used based on direct injection with a LC-ESI-QTOF-MS system and stir bar sorptive extraction (SBSE) with bi-dimensional gas chromatography coupled with a time-of-flight spectrometer (GCxGC-EI-TOF-MS).

Laboratory-based x-ray phase-contrast tomography enables 3D virtual histology

NASA Astrophysics Data System (ADS)

Töpperwien, Mareike; Krenkel, Martin; Quade, Felix; Salditt, Tim

2016-09-01

Due to the large penetration depth and small wavelength hard x-rays offer a unique potential for 3D biomedical and biological imaging, combining capabilities of high resolution and large sample volume. However, in classical absorption-based computed tomography, soft tissue only shows a weak contrast, limiting the actual resolution. With the advent of phase-contrast methods, the much stronger phase shift induced by the sample can now be exploited. For high resolution, free space propagation behind the sample is particularly well suited to make the phase shift visible. Contrast formation is based on the self-interference of the transmitted beam, resulting in object-induced intensity modulations in the detector plane. As this method requires a sufficiently high degree of spatial coherence, it was since long perceived as a synchrotron-based imaging technique. In this contribution we show that by combination of high brightness liquid-metal jet microfocus sources and suitable sample preparation techniques, as well as optimized geometry, detection and phase retrieval, excellent three-dimensional image quality can be obtained, revealing the anatomy of a cobweb spider in high detail. This opens up new opportunities for 3D virtual histology of small organisms. Importantly, the image quality is finally augmented to a level accessible to automatic 3D segmentation.

Using Language Sampling in Clinical Assessments with Bilingual Children: Challenges and Future Directions

PubMed Central

Gutiérrez-Clellen, Vera F.; Simon-Cereijido, Gabriela

2012-01-01

Current language tests designed to assess Spanish-English-speaking children have limited clinical accuracy and do not provide sufficient information to plan language intervention. In contrast, spontaneous language samples obtained in the two languages can help identify language impairment with higher accuracy. In this article, we describe several diagnostic indicators that can be used in language assessments based on spontaneous language samples. First, based on previous research with monolingual and bilingual English speakers, we show that a verb morphology composite measure in combination with a measure of mean length of utterance (MLU) can provide valuable diagnostic information for English development in bilingual children. Dialectal considerations are discussed. Second, we discuss the available research with bilingual Spanish speakers and show a series of procedures to be used for the analysis of Spanish samples: (a) limited MLU and proportional use of ungrammatical utterances; (b) limited grammatical accuracy on articles, verbs, and clitic pronouns; and (c) limited MLU, omission of theme arguments, and limited use of ditransitive verbs. Third, we illustrate the analysis of verb argument structure using a rubric as an assessment tool. Estimated scores on morphological and syntactic measures are expected to increase the sensitivity of clinical assessments with young bilingual children. Further research using other measures of language will be needed for older school-age children. PMID:19851951

Overcoming the matched-sample bottleneck: an orthogonal approach to integrate omic data.

PubMed

Nguyen, Tin; Diaz, Diana; Tagett, Rebecca; Draghici, Sorin

2016-07-12

MicroRNAs (miRNAs) are small non-coding RNA molecules whose primary function is to regulate the expression of gene products via hybridization to mRNA transcripts, resulting in suppression of translation or mRNA degradation. Although miRNAs have been implicated in complex diseases, including cancer, their impact on distinct biological pathways and phenotypes is largely unknown. Current integration approaches require sample-matched miRNA/mRNA datasets, resulting in limited applicability in practice. Since these approaches cannot integrate heterogeneous information available across independent experiments, they neither account for bias inherent in individual studies, nor do they benefit from increased sample size. Here we present a novel framework able to integrate miRNA and mRNA data (vertical data integration) available in independent studies (horizontal meta-analysis) allowing for a comprehensive analysis of the given phenotypes. To demonstrate the utility of our method, we conducted a meta-analysis of pancreatic and colorectal cancer, using 1,471 samples from 15 mRNA and 14 miRNA expression datasets. Our two-dimensional data integration approach greatly increases the power of statistical analysis and correctly identifies pathways known to be implicated in the phenotypes. The proposed framework is sufficiently general to integrate other types of data obtained from high-throughput assays.

DMSO Assisted Electrospray Ionization for the Detection of Small Peptide Hormones in Urine by Dilute-and-Shoot-Liquid-Chromatography-High Resolution Mass Spectrometry

NASA Astrophysics Data System (ADS)

Judák, Péter; Grainger, Janelle; Goebel, Catrin; Van Eenoo, Peter; Deventer, Koen

2017-08-01

The mobile phase additive (DMSO) has been described as a useful tool to enhance electrospray ionization (ESI) of peptides and proteins. So far, this technique has mainly been used in proteomic/peptide research, and its applicability in a routine clinical laboratory setting (i.e., doping control analysis) has not been described yet. This work provides a simple, easy to implement screening method for the detection of doping relevant small peptides (GHRPs, GnRHs, GHS, and vasopressin-analogues) with molecular weight less than 2 kDa applying DMSO in the mobile phase. The gain in sensitivity was sufficient to inject the urine samples after a 2-fold dilution step omitting a time consuming sample preparation. The employed analytical procedure was validated for the qualitative determination of 36 compounds, including 13 metabolites. The detection limits (LODs) ranged between 50 and 1000 pg/mL and were compliant with the 2 ng/mL minimum detection level required by the World Anti-Doping Agency (WADA) for all the target peptides. To demonstrate the feasibility of the work, urine samples obtained from patients who have been treated with desmopressin or leuprolide and urine samples that have been declared as adverse analytical findings were analyzed.

Dynamics of a stochastic HIV-1 infection model with logistic growth

NASA Astrophysics Data System (ADS)

Jiang, Daqing; Liu, Qun; Shi, Ningzhong; Hayat, Tasawar; Alsaedi, Ahmed; Xia, Peiyan

2017-03-01

This paper is concerned with a stochastic HIV-1 infection model with logistic growth. Firstly, by constructing suitable stochastic Lyapunov functions, we establish sufficient conditions for the existence of ergodic stationary distribution of the solution to the HIV-1 infection model. Then we obtain sufficient conditions for extinction of the infection. The stationary distribution shows that the infection can become persistent in vivo.

Evaluation of Xpert® MTB/RIF Assay in Induced Sputum and Gastric Lavage Samples from Young Children with Suspected Tuberculosis from the MVA85A TB Vaccine Trial.

PubMed

Bunyasi, Erick Wekesa; Tameris, Michele; Geldenhuys, Hennie; Schmidt, Bey-Marrie; Luabeya, Angelique Kany Kany; Mulenga, Humphrey; Scriba, Thomas J; Hanekom, Willem A; Mahomed, Hassan; McShane, Helen; Hatherill, Mark

2015-01-01

Diagnosis of childhood tuberculosis is limited by the paucibacillary respiratory samples obtained from young children with pulmonary disease. We aimed to compare accuracy of the Xpert® MTB/RIF assay, an automated nucleic acid amplification test, between induced sputum and gastric lavage samples from young children in a tuberculosis endemic setting. We analyzed standardized diagnostic data from HIV negative children younger than four years of age who were investigated for tuberculosis disease near Cape Town, South Africa [2009-2012]. Two paired, consecutive induced sputa and early morning gastric lavage samples were obtained from children with suspected tuberculosis. Samples underwent Mycobacterial Growth Indicator Tube [MGIT] culture and Xpert MTB/RIF assay. We compared diagnostic yield across samples using the two-sample test of proportions and McNemar's χ2 test; and Wilson's score method to calculate sensitivity and specificity. 1,020 children were evaluated for tuberculosis during 1,214 admission episodes. Not all children had 4 samples collected. 57 of 4,463[1.3%] and 26 of 4,606[0.6%] samples tested positive for Mycobacterium tuberculosis on MGIT culture and Xpert MTB/RIF assay respectively. 27 of 2,198[1.2%] and 40 of 2,183[1.8%] samples tested positive [on either Xpert MTB/RIF assay or MGIT culture] on induced sputum and gastric lavage samples, respectively. 19/1,028[1.8%] and 33/1,017[3.2%] admission episodes yielded a positive MGIT culture or Xpert MTB/RIF assay from induced sputum and gastric lavage, respectively. Sensitivity of Xpert MTB/RIF assay was 8/30[26.7%; 95% CI: 14.2-44.4] for two induced sputum samples and 7/31[22.6%; 11.4-39.8] [p = 0.711] for two gastric lavage samples. Corresponding specificity was 893/893[100%;99.6-100] and 885/890[99.4%;98.7-99.8] respectively [p = 0.025]. Sensitivity of Xpert MTB/RIF assay was low, compared to MGIT culture, but diagnostic performance of Xpert MTB/RIF did not differ sufficiently between induced sputum and gastric lavage to justify selection of one sampling method over the other, in young children with suspected pulmonary TB. ClinicalTrials.gov NCT00953927.

An audit of the statistics and the comparison with the parameter in the population

NASA Astrophysics Data System (ADS)

Bujang, Mohamad Adam; Sa'at, Nadiah; Joys, A. Reena; Ali, Mariana Mohamad

2015-10-01

The sufficient sample size that is needed to closely estimate the statistics for particular parameters are use to be an issue. Although sample size might had been calculated referring to objective of the study, however, it is difficult to confirm whether the statistics are closed with the parameter for a particular population. All these while, guideline that uses a p-value less than 0.05 is widely used as inferential evidence. Therefore, this study had audited results that were analyzed from various sub sample and statistical analyses and had compared the results with the parameters in three different populations. Eight types of statistical analysis and eight sub samples for each statistical analysis were analyzed. Results found that the statistics were consistent and were closed to the parameters when the sample study covered at least 15% to 35% of population. Larger sample size is needed to estimate parameter that involve with categorical variables compared with numerical variables. Sample sizes with 300 to 500 are sufficient to estimate the parameters for medium size of population.

Sampling methods for amphibians in streams in the Pacific Northwest.

Treesearch

R. Bruce Bury; Paul Stephen Corn

1991-01-01

Methods describing how to sample aquatic and semiaquatic amphibians in small streams and headwater habitats in the Pacific Northwest are presented. We developed a technique that samples 10-meter stretches of selected streams, which was adequate to detect presence or absence of amphibian species and provided sample sizes statistically sufficient to compare abundance of...

Physical activity trends in Queensland (2002 to 2008): are women becoming more active than men?

PubMed

Vandelanotte, Corneel; Duncan, Mitch J; Caperchione, Cristina; Hanley, Christine; Mummery, W Kerry

2010-06-01

Regular monitoring of population levels of physical activity is an effective way to assess change over time towards meeting public health recommendations. The objective of this study was to determine physical activity trends in Central Queensland over the period 2002 to 2008. Data was obtained from the Central Queensland Social Survey (CQSS) conducted annually from 2002 to 2008. A total sample of 8,936 adults aged 18 and over participated in seven cross-sectional surveys. Physical activity was measured using the Active Australia Questionnaire. Binary logistic regression was used to examine trends in sufficient physical activity. Averaged over all survey years 46.5% of study participants met national physical activity guidelines. A small significant upward trend was found for meeting physical activity recommendations across all years (OR=1.03; 95%CI=1.01-1.05), indicating that the odds of meeting the guidelines increased by an average of 3% per year from 2002 to 2008. Slightly more men than women met the activity guidelines (ns); however a significant positive trend in achieving sufficient activity levels was present in women only (4%). Although an increasing trend for sufficient physical activity was observed, overall physical activity levels in Central Queensland remain suboptimal and more efforts to increase physical activity are needed. The gender differences in physical activity trends indicate that men and women might need to be targeted differently in health promotion messages. The continuous monitoring of population levels of physical activity in Australia, which allow both state specific and international comparisons, is needed.

Dual function microscope for quantitative DIC and birefringence imaging

NASA Astrophysics Data System (ADS)

Li, Chengshuai; Zhu, Yizheng

2016-03-01

A spectral multiplexing interferometry (SXI) method is presented for integrated birefringence and phase gradient measurement on label-free biological specimens. With SXI, the retardation and orientation of sample birefringence are simultaneously encoded onto two separate spectral carrier waves, generated by a crystal retarder oriented at a specific angle. Thus sufficient information for birefringence determination can be obtained from a single interference spectrum, eliminating the need for multiple acquisitions with mechanical rotation or electrical modulation. In addition, with the insertion of a Nomarski prism, the setup can then acquire quantitative differential interference contrast images. Red blood cells infected by malaria parasites are imaged for birefringence retardation as well as phase gradient. The results demonstrate that the SXI approach can achieve both quantitative phase imaging and birefringence imaging with a single, high-sensitivity system.

A Flight Investigation of Exhaust-heat De-icing

NASA Technical Reports Server (NTRS)

Jones, Alun R; Rodert, Lewis A

1940-01-01

The National Advisory Committee for Aeronautics conducted exhaust-heat de-icing tests in flight to provide data needed in the application of this method. The capacity to extract heat from the exhaust gas for de-icing purposes, the quantity of heat required, and other factors were examined. The results indicate that a wing-heating system employing a spanwise exhaust tube within the leading edge of the wing removed 30 to 35 percent of the heat from exhaust gas entering the wing. Data are given from which the heat required for ice prevention can be calculated. Sample calculations have been made on the basis of existing engine power/wing area ratios to show that sufficient heating can be obtained for ice protection on modern transportation airplanes, provided that uniform distribution of the heat can be secured.

VizieR Online Data Catalog: Broadband photometry of Neptune from K2 (Rowe+, 2017)

NASA Astrophysics Data System (ADS)

Rowe, J. F.; Gaulme, P.; Lissauer, J. J.; Marley, M. S.; Simon, A. A.; Hammel, H. B.; Silva Aguirre, V.; Barclay, T.; Benomar, O.; Boumier, P.; Caldwell, D. A.; Casewell, S. L.; Chaplin, W. J.; Colon, K. D.; Corsaro, E.; Davies, G. R.; Fortney, J. J.; Garcia, R. A.; Gizis, J. E.; Haas, M. R.; Mosser, B.; Schmider, F.-X.

2017-08-01

The K2 C3 field provided the first opportunity to observe the planet Neptune for up to 80 days with short-cadence (1 minute) sampling (the C3 campaign had an actual duration of 69.2 days, limited by on-board data storage). We were awarded sufficient pixel allocation from Guest Observer Programs GO3060 (PI: Rowe) and GO3057 (PI: Gaulme) to continuously monitor Neptune for 49 days. Short-cadence target pixel files were obtained from Mikulski Archive for Space Telescopes (MAST). The Neptune short-cadence subraster was spread across 161 FITS files. Each file contained 1 column of time-series pixel data. Each target pixel file contains observations starting on 2014 November 15 and finishing on 2015 January 18. (1 data file).

Calculation of the Local Free Energy Landscape in the Restricted Region by the Modified Tomographic Method.

PubMed

Chen, Changjun

2016-03-31

The free energy landscape is the most important information in the study of the reaction mechanisms of the molecules. However, it is difficult to calculate. In a large collective variable space, a molecule must take a long time to obtain the sufficient sampling during the simulation. To save the calculation quantity, decreasing the sampling region and constructing the local free energy landscape is required in practice. However, the restricted region in the collective variable space may have an irregular shape. Simply restricting one or more collective variables of the molecule cannot satisfy the requirement. In this paper, we propose a modified tomographic method to perform the simulation. First, it divides the restricted region by some hyperplanes and connects the centers of hyperplanes together by a curve. Second, it forces the molecule to sample on the curve and the hyperplanes in the simulation and calculates the free energy data on them. Finally, all the free energy data are combined together to form the local free energy landscape. Without consideration of the area outside the restricted region, this free energy calculation can be more efficient. By this method, one can further optimize the path quickly in the collective variable space.

Robust reliable sampled-data control for switched systems with application to flight control

NASA Astrophysics Data System (ADS)

Sakthivel, R.; Joby, Maya; Shi, P.; Mathiyalagan, K.

2016-11-01

This paper addresses the robust reliable stabilisation problem for a class of uncertain switched systems with random delays and norm bounded uncertainties. The main aim of this paper is to obtain the reliable robust sampled-data control design which involves random time delay with an appropriate gain control matrix for achieving the robust exponential stabilisation for uncertain switched system against actuator failures. In particular, the involved delays are assumed to be randomly time-varying which obeys certain mutually uncorrelated Bernoulli distributed white noise sequences. By constructing an appropriate Lyapunov-Krasovskii functional (LKF) and employing an average-dwell time approach, a new set of criteria is derived for ensuring the robust exponential stability of the closed-loop switched system. More precisely, the Schur complement and Jensen's integral inequality are used in derivation of stabilisation criteria. By considering the relationship among the random time-varying delay and its lower and upper bounds, a new set of sufficient condition is established for the existence of reliable robust sampled-data control in terms of solution to linear matrix inequalities (LMIs). Finally, an illustrative example based on the F-18 aircraft model is provided to show the effectiveness of the proposed design procedures.

Radiation effects on interface reactions of U/Fe, U/(Fe+Cr), and U/(Fe+Cr+Ni)

DOE PAGES

Shao, Lin; Chen, Di; Wei, Chaochen; ...

2014-10-01

We study the effects of radiation damage on interdiffusion and intermetallic phase formation at the interfaces of U/Fe, U/(Fe + Cr), and U/(Fe + Cr + Ni) diffusion couples. Magnetron sputtering is used to deposit thin films of Fe, Fe + Cr, or Fe + Cr + Ni on U substrates to form the diffusion couples. One set of samples are thermally annealed under high vacuum at 450 C or 550 C for one hour. A second set of samples are annealed identically but with concurrent 3.5 MeV Fe++ ion irradiation. The Fe++ ion penetration depth is sufficient to reachmore » the original interfaces. Rutherford backscattering spectrometry analysis with high fidelity spectral simulations is used to obtain interdiffusion profiles, which are used to examine differences in U diffusion and intermetallic phase formation at the buried interfaces. For all three diffusion systems, Fe++ ion irradiations enhance U diffusion. Furthermore, the irradiations accelerate the formation of intermetallic phases. In U/Fe couples, for example, the unirradiated samples show typical interdiffusion governed by Fick’s laws, while the irradiated ones show step-like profiles influenced by Gibbs phase rules.« less

In Situ X-ray Diffraction Studies of Li(sub x)Mn(sub 2)O(sub 4) Cathode Materials by Synchrotron X-ray Radiation

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

Yang, X. Q.; Sun, X.; Lee, S. J.

In Situ x-ray diffraction studies on Li{sub x}Mn{sub 2}O{sub 4} spinel cathode materials during charge-discharge cycles were carried out by using a synchrotron as x-ray source. Lithium rich (x = 1.03-1.06) spinel materials obtained from two different sources were studied. Three cubic phases with different lattice constants were observed during charge-discharge cycles in all the samples when a Sufficiently low charge-discharge rate (C/10) was used. There are two regions of two-phase coexistence between these three phases, indicating that both phase transitions are first order. The separation of the Bragg peaks representing these three phases varies from sample to sample andmore » also depends on the charge-discharge rate. These results show that the de-intercalation of lithium in lithium-rich spinel cathode materials proceeds through a series of phase transitions from a lithium-rich phase to a lithium-poor phase and finally to a {lambda}-MnO{sub 2} like cubic phase, rather than through a continuous lattice constant contraction in a single phase.« less

The effects of environmental variability and spatial sampling on the three-dimensional inversion problem.

PubMed

Bender, Christopher M; Ballard, Megan S; Wilson, Preston S

2014-06-01

The overall goal of this work is to quantify the effects of environmental variability and spatial sampling on the accuracy and uncertainty of estimates of the three-dimensional ocean sound-speed field. In this work, ocean sound speed estimates are obtained with acoustic data measured by a sparse autonomous observing system using a perturbative inversion scheme [Rajan, Lynch, and Frisk, J. Acoust. Soc. Am. 82, 998-1017 (1987)]. The vertical and horizontal resolution of the solution depends on the bandwidth of acoustic data and on the quantity of sources and receivers, respectively. Thus, for a simple, range-independent ocean sound speed profile, a single source-receiver pair is sufficient to estimate the water-column sound-speed field. On the other hand, an environment with significant variability may not be fully characterized by a large number of sources and receivers, resulting in uncertainty in the solution. This work explores the interrelated effects of environmental variability and spatial sampling on the accuracy and uncertainty of the inversion solution though a set of case studies. Synthetic data representative of the ocean variability on the New Jersey shelf are used.

(abstract) Undercooling Studies of the Bulk Metallic Glass Forming Zr(sub 41.2)Ti(sub 13.8)Cu(sub 12.5)Ni(sub 10.0)Be(sub 22.5) Alloy During Containerless Electrostatic Levitation Processing

NASA Technical Reports Server (NTRS)

Kim, Y. J.; Busch, R.; Johnson, W. L.; Rulison, A. J.; Rhim, W. K.

1995-01-01

Bulk glass forming metallic alloys have long been desired for technological applications and for investigation into liquid undercooling, solidification processes, and thermophysical properties. A glass forming alloy Zr(sub 41.2)Ti(sub 13.8)Cu(sub 12.5)Ni(sub 10.0)Be(sub 22.5) was used to investigate the thermal treatments affecting undercooling and vitrification. The experiments were performed using the high temperature high vacuum electrostatic levitator at JPL. A sample approximately 3 mm in diameter was melted, superheated, undercooled, and solidified while levitated in high vacuum. The results show that when the sample was held above its melting temperature for a sufficient period of time to dissolve oxides and then cooled faster than a critical cooling rate, it undercooled to the glass transition temperature, T(sub g), and formed a glassy alloy. The required critical cooling rate for metallic glass formation was obtained to be between 0.9 K per second and 1.2 K per second for the 42.4 mg sample.

Detection of the HTLV-I gene on cytologic smear slides.

PubMed

Kashima, Kenji; Nagahama, Junji; Sato, Keiji; Tanamachi, Hiroyuki; Gamachi, Ayako; Daa, Tsutomu; Nakayama, Iwao; Yokoyama, Shigeo

2002-01-01

To apply the polymerase chain reaction (PCR) for detection of the HTLV-I gene from cytologic smear slides. Samples were from seven cases of serum anti-ATL antibody (ATLA)-positive T-cell lymphoma and three from ATLA-negative T-cell lymphoma. Six of the seven ATLA-positive cases were confirmed to be ATLL by Southern blotting. From the seventh case a fresh sample for blotting could not obtained. DNA was extracted from the cytologic smear slides of all 10 cases; they had been stained with Papanicolaou or May-Giemsa stain, digested with proteinase K and precipitated with phenol and ethanol. The target sequence in the pX region of the HTLV-I gene was amplified by PCR. All seven ATLA-positive cases, including one that had not yet been confirmed by Southern blotting, showed a single band, as predicted, while the three ATLA-negative cases showed no band. If cytologic smear slides are available but a fresh sample is not, the PCR method should provide evidence that the virus is present since in our study sufficient DNA templates were successfully extracted from the stained cytologic smear slides for detection of the virus.

Hydrodynamic injection with pneumatic valving for microchip electrophoresis with total analyte utilization

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

Sun, Xuefei; Kelly, Ryan T.; Danielson, William F.

2011-04-26

A novel hydrodynamic injector that is directly controlled by a pneumatic valve has been developed for reproducible microchip capillary electrophoresis (CE) separations. The poly(dimethylsiloxane) (PDMS) devices used for evaluation comprise a separation channel, a side channel for sample introduction, and a pneumatic valve aligned at the intersection of the channels. A low pressure (≤ 3 psi) applied to the sample reservoir is sufficient to drive sample into the separation channel. The rapidly actuated pneumatic valve enables injection of discrete sample plugs as small as ~100 pL for CE separation. The injection volume can be easily controlled by adjusting the intersectionmore » geometry, the solution back pressure and the valve actuation time. Sample injection could be reliably operated at different frequencies (< 0.1 Hz to >2 Hz) with good reproducibility (peak height relative standard deviation ≤ 3.6%) and no sampling biases associated with the conventional electrokinetic injections. The separation channel was dynamically coated with a cationic polymer, and FITC-labeled amino acids were employed to evaluate the CE separation. Highly efficient (≥ 7.0 × 103 theoretical plates for the ~2.4 cm long channel) and reproducible CE separations were obtained. The demonstrated method has numerous advantages compared with the conventional techniques, including repeatable and unbiased injections, no sample waste, high duty cycle, controllable injected sample volume, and fewer electrodes with no need for voltage switching. The prospects of implementing this injection method for coupling multidimensional separations, for multiplexing CE separations and for sample-limited bioanalyses are discussed.« less

Evaluating single-pass catch as a tool for identifying spatial pattern in fish distribution

USGS Publications Warehouse

Bateman, Douglas S.; Gresswell, Robert E.; Torgersen, Christian E.

2005-01-01

We evaluate the efficacy of single-pass electrofishing without blocknets as a tool for collecting spatially continuous fish distribution data in headwater streams. We compare spatial patterns in abundance, sampling effort, and length-frequency distributions from single-pass sampling of coastal cutthroat trout (Oncorhynchus clarki clarki) to data obtained from a more precise multiple-pass removal electrofishing method in two mid-sized (500–1000 ha) forested watersheds in western Oregon. Abundance estimates from single- and multiple-pass removal electrofishing were positively correlated in both watersheds, r = 0.99 and 0.86. There were no significant trends in capture probabilities at the watershed scale (P > 0.05). Moreover, among-sample variation in fish abundance was higher than within-sample error in both streams indicating that increased precision of unit-scale abundance estimates would provide less information on patterns of abundance than increasing the fraction of habitat units sampled. In the two watersheds, respectively, single-pass electrofishing captured 78 and 74% of the estimated population of cutthroat trout with 7 and 10% of the effort. At the scale of intermediate-sized watersheds, single-pass electrofishing exhibited a sufficient level of precision to be effective in detecting spatial patterns of cutthroat trout abundance and may be a useful tool for providing the context for investigating fish-habitat relationships at multiple scales.

Possibilities for serial femtosecond crystallography sample delivery at future light sourcesa)

PubMed Central

Chavas, L. M. G.; Gumprecht, L.; Chapman, H. N.

2015-01-01

Serial femtosecond crystallography (SFX) uses X-ray pulses from free-electron laser (FEL) sources that can outrun radiation damage and thereby overcome long-standing limits in the structure determination of macromolecular crystals. Intense X-ray FEL pulses of sufficiently short duration allow the collection of damage-free data at room temperature and give the opportunity to study irreversible time-resolved events. SFX may open the way to determine the structure of biological molecules that fail to crystallize readily into large well-diffracting crystals. Taking advantage of FELs with high pulse repetition rates could lead to short measurement times of just minutes. Automated delivery of sample suspensions for SFX experiments could potentially give rise to a much higher rate of obtaining complete measurements than at today's third generation synchrotron radiation facilities, as no crystal alignment or complex robotic motions are required. This capability will also open up extensive time-resolved structural studies. New challenges arise from the resulting high rate of data collection, and in providing reliable sample delivery. Various developments for fully automated high-throughput SFX experiments are being considered for evaluation, including new implementations for a reliable yet flexible sample environment setup. Here, we review the different methods developed so far that best achieve sample delivery for X-ray FEL experiments and present some considerations towards the goal of high-throughput structure determination with X-ray FELs. PMID:26798808

How Good Are Statistical Models at Approximating Complex Fitness Landscapes?

PubMed Central

du Plessis, Louis; Leventhal, Gabriel E.; Bonhoeffer, Sebastian

2016-01-01

Fitness landscapes determine the course of adaptation by constraining and shaping evolutionary trajectories. Knowledge of the structure of a fitness landscape can thus predict evolutionary outcomes. Empirical fitness landscapes, however, have so far only offered limited insight into real-world questions, as the high dimensionality of sequence spaces makes it impossible to exhaustively measure the fitness of all variants of biologically meaningful sequences. We must therefore revert to statistical descriptions of fitness landscapes that are based on a sparse sample of fitness measurements. It remains unclear, however, how much data are required for such statistical descriptions to be useful. Here, we assess the ability of regression models accounting for single and pairwise mutations to correctly approximate a complex quasi-empirical fitness landscape. We compare approximations based on various sampling regimes of an RNA landscape and find that the sampling regime strongly influences the quality of the regression. On the one hand it is generally impossible to generate sufficient samples to achieve a good approximation of the complete fitness landscape, and on the other hand systematic sampling schemes can only provide a good description of the immediate neighborhood of a sequence of interest. Nevertheless, we obtain a remarkably good and unbiased fit to the local landscape when using sequences from a population that has evolved under strong selection. Thus, current statistical methods can provide a good approximation to the landscape of naturally evolving populations. PMID:27189564

Monitoring Species of Concern Using Noninvasive Genetic Sampling and Capture-Recapture Methods

DTIC Science & Technology

2016-11-01

ABBREVIATIONS AICc Akaike’s Information Criterion with small sample size correction AZGFD Arizona Game and Fish Department BMGR Barry M. Goldwater...MNKA Minimum Number Known Alive N Abundance Ne Effective Population Size NGS Noninvasive Genetic Sampling NGS-CR Noninvasive Genetic...parameter estimates from capture-recapture models require sufficient sample sizes , capture probabilities and low capture biases. For NGS-CR, sample

Gestation-specific changes in maternal thyroglobulin during pregnancy and lactation in an iodine-sufficient region in China: a longitudinal study.

PubMed

Zhang, Xiaowen; Li, Chenyan; Mao, Jinyuan; Wang, Weiwei; Xie, Xiaochen; Peng, Shiqiao; Wang, Zhaojun; Han, Cheng; Zhang, Xiaomei; Wang, Danyang; Fan, Chenling; Shan, Zhongyan; Teng, Weiping

2017-02-01

To describe the changes in thyroglobulin (Tg) based upon gestational and postpartum concentrations in healthy pregnant women from an iodine-sufficient region in China, and to evaluate the use of Tg as a biomarker for iodine-sufficient pregnant women. A longitudinal study of Tg change in normal pregnant women from an iodine-sufficient region. Blood and urine samples were obtained from 133 pregnant women. Urinary iodine concentration (UIC) was measured using an ammonium persulfate method. Serum iodine concentration was required by inductively coupled plasma mass spectrometry (ICP-MS). Serum thyroid-stimulating hormone (TSH), free thyroxine (FT4), free triiodothyronine (FT3), total thyroxine (TT4), total triiodothyronine (TT3), antithyroid peroxidase antibody (TPOAb), antithyroglobulin antibody (TgAb) and Tg were measured using an electrochemiluminescence immunoassay. Thyroglobulin concentrations were higher in early pregnancy (pregnancy at 8 weeks vs nonpregnancy: 11·42 ng/ml vs 8·8 ng/ml, P < 0·01) and maintained a stable level, and then increased greatly at the 36th week. After delivery, Tg decreased to nonpregnant levels. During pregnancy, maternal Tg was not correlated with thyroid function, UIC or urine iodine-creatinine ratio (UI/Cr). Cord blood Tg was much higher compared to maternal Tg levels at the 36w (57·34 vs 14·86 ng/ml, P < 0·001) and correlated positively with cord FT4 (r = 0·256, P < 0·05), cord TT4 (r = 0·263, P < 0·05) and maternal UI/Cr at 36w (r = -0·214, P < 0·05). Our work demonstrates that Tg is elevated during pregnancy, and the effect of pregnancy should be taken into consideration when Tg is used as a biomarker for the iodine status. Cord blood Tg is much higher than maternal Tg levels at the 36w and is correlated with maternal iodine status. © 2016 John Wiley & Sons Ltd.

Stability analysis of fractional-order Hopfield neural networks with time delays.

PubMed

Wang, Hu; Yu, Yongguang; Wen, Guoguang

2014-07-01

This paper investigates the stability for fractional-order Hopfield neural networks with time delays. Firstly, the fractional-order Hopfield neural networks with hub structure and time delays are studied. Some sufficient conditions for stability of the systems are obtained. Next, two fractional-order Hopfield neural networks with different ring structures and time delays are developed. By studying the developed neural networks, the corresponding sufficient conditions for stability of the systems are also derived. It is shown that the stability conditions are independent of time delays. Finally, numerical simulations are given to illustrate the effectiveness of the theoretical results obtained in this paper. Copyright © 2014 Elsevier Ltd. All rights reserved.

Charge collection and field profile studies of heavily irradiated strip sensors for the ATLAS inner tracker upgrade

NASA Astrophysics Data System (ADS)

Hara, K.; Allport, P. P.; Baca, M.; Broughton, J.; Chisholm, A.; Nikolopoulos, K.; Pyatt, S.; Thomas, J. P.; Wilson, J. A.; Kierstead, J.; Kuczewski, P.; Lynn, D.; Arratia, M.; Hommels, L. B. A.; Ullan, M.; Bloch, I.; Gregor, I. M.; Tackmann, K.; Trofimov, A.; Yildirim, E.; Hauser, M.; Jakobs, K.; Kuehn, S.; Mahboubi, K.; Mori, R.; Parzefall, U.; Clark, A.; Ferrere, D.; Gonzalez Sevilla, S.; Ashby, J.; Blue, A.; Bates, R.; Buttar, C.; Doherty, F.; McMullen, T.; McEwan, F.; O'Shea, V.; Kamada, S.; Yamamura, K.; Ikegami, Y.; Nakamura, K.; Takubo, Y.; Unno, Y.; Takashima, R.; Chilingarov, A.; Fox, H.; Affolder, A. A.; Casse, G.; Dervan, P.; Forshaw, D.; Greenall, A.; Wonsak, S.; Wormald, M.; Cindro, V.; Kramberger, G.; Mandić, I.; Mikuž, M.; Gorelov, I.; Hoeferkamp, M.; Palni, P.; Seidel, S.; Taylor, A.; Toms, K.; Wang, R.; Hessey, N. P.; Valencic, N.; Hanagaki, K.; Dolezal, Z.; Kodys, P.; Bohm, J.; Mikestikova, M.; Bevan, A.; Beck, G.; Milke, C.; Domingo, M.; Fadeyev, V.; Galloway, Z.; Hibbard-Lubow, D.; Liang, Z.; Sadrozinski, H. F.-W.; Seiden, A.; To, K.; French, R.; Hodgson, P.; Marin-Reyes, H.; Parker, K.; Jinnouchi, O.; Hara, K.; Sato, K.; Sato, K.; Hagihara, M.; Iwabuchi, S.; Bernabeu, J.; Civera, J. V.; Garcia, C.; Lacasta, C.; Marti i. Garcia, S.; Rodriguez, D.; Santoyo, D.; Solaz, C.; Soldevila, U.

2016-09-01

The ATLAS group has evaluated the charge collection in silicon microstrip sensors irradiated up to a fluence of 1 ×1016 neq/cm2, exceeding the maximum of 1.6 ×1015 neq/cm2 expected for the strip tracker during the high luminosity LHC (HL-LHC) period including a safety factor of 2. The ATLAS12, n+-on-p type sensor, which is fabricated by Hamamatsu Photonics (HPK) on float zone (FZ) substrates, is the latest barrel sensor prototype. The charge collection from the irradiated 1×1 cm2 barrel test sensors has been evaluated systematically using penetrating β-rays and an Alibava readout system. The data obtained at different measurement sites are compared with each other and with the results obtained from the previous ATLAS07 design. The results are very consistent, in particular, when the deposit charge is normalized by the sensor's active thickness derived from the edge transient current technique (edge-TCT) measurements. The measurements obtained using β-rays are verified to be consistent with the measurements using an electron beam. The edge-TCT is also effective for evaluating the field profiles across the depth. The differences between the irradiated ATLAS07 and ATLAS12 samples have been examined along with the differences among the samples irradiated with different radiation sources: neutrons, protons, and pions. The studies of the bulk properties of the devices show that the devices can yield a sufficiently large signal for the expected fluence range in the HL-LHC, thereby acting as precision tracking sensors.

The Effect of Selected Intervention Tactics on Self-Sufficient Behaviors of the Homeless: An Application of the Theory of Planned Behavior.

ERIC Educational Resources Information Center

Moroz, Pauline

A sample of 24 voluntary participants in a federally funded vocational training and placement program for homeless people in El Paso, Texas, was studied to identify specific interventions that increase self-sufficient behaviors of homeless individuals. Case study data were collected from orientation discussions, career counseling sessions, and…

MSEBAG: a dynamic classifier ensemble generation based on `minimum-sufficient ensemble' and bagging

NASA Astrophysics Data System (ADS)

Chen, Lei; Kamel, Mohamed S.

2016-01-01

In this paper, we propose a dynamic classifier system, MSEBAG, which is characterised by searching for the 'minimum-sufficient ensemble' and bagging at the ensemble level. It adopts an 'over-generation and selection' strategy and aims to achieve a good bias-variance trade-off. In the training phase, MSEBAG first searches for the 'minimum-sufficient ensemble', which maximises the in-sample fitness with the minimal number of base classifiers. Then, starting from the 'minimum-sufficient ensemble', a backward stepwise algorithm is employed to generate a collection of ensembles. The objective is to create a collection of ensembles with a descending fitness on the data, as well as a descending complexity in the structure. MSEBAG dynamically selects the ensembles from the collection for the decision aggregation. The extended adaptive aggregation (EAA) approach, a bagging-style algorithm performed at the ensemble level, is employed for this task. EAA searches for the competent ensembles using a score function, which takes into consideration both the in-sample fitness and the confidence of the statistical inference, and averages the decisions of the selected ensembles to label the test pattern. The experimental results show that the proposed MSEBAG outperforms the benchmarks on average.

Work-life balance and subjective well-being: the mediating role of need fulfilment.

PubMed

Gröpel, Peter; Kuhl, Julius

2009-05-01

The relationship between work-life balance (WLB) (i.e. the perceived sufficiency of the time available for work and social life) and well-being is well-documented. However, previous research failed to sufficiently explain why this relationship exists. In this research, the hypothesis was tested that a sufficient amount of the time available increases well-being because it facilitates satisfaction of personal needs. Using two separate samples (students and employees), the mediating role of need fulfilment in the relationship between WLB and well-being was supported. The results suggest that perceived sufficiency of the time available for work and social life predicts the level of well-being only if the individual's needs are fulfilled within that time.

Optimization of a New Mass Spectrometry Method for Measurement of Breast Milk Iodine Concentrations and an Assessment of the Effect of Analytic Method and Timing of Within-Feed Sample Collection on Breast Milk Iodine Concentrations.

PubMed

Dold, Susanne; Baumgartner, Jeannine; Zeder, Christophe; Krzystek, Adam; Osei, Jennifer; Haldimann, Max; Zimmermann, Michael B; Andersson, Maria

2016-02-01

Breast milk iodine concentration (BMIC) may be an indicator of iodine status during lactation, but there are few data comparing different analytical methods or timing of sampling. The aims of this study were: (i) to optimize a new inductively coupled plasma mass spectrometry (ICP-MS) method; and (ii) to evaluate the effect of analytical method and timing of within-feed sample collection on BMIC. The colorimetric Sandell-Kolthoff method was evaluated with (a) or without (b) alkaline ashing, and ICP-MS was evaluated using a new (129)I isotope ratio approach including Tellurium (Te) for mass bias correction (c) or external standard curve (d). From iodine-sufficient lactating women (n = 97), three samples were collected within one breast-feeding session (fore-, mid-, and hind-feed samples) and BMIC was analyzed using (c) and (d). Iodine recovery from NIST SRM1549a whole milk powder for methods (a)-(d) was 67%, 24%, 105%, and 102%, respectively. Intra- and inter-assay coefficients of variation for ICP-MS comparing (c) and (d) were 1.3% versus 5.6% (p = 0.04) and 1.1% versus 2.4% (p = 0.33). The limit of detection (LOD) was lower for (c) (0.26 μg/kg) than it was for (d) (2.54 μg/kg; p = 0.02). Using (c), the median [95% confidence interval (CI) obtained by bootstrap] BMIC (μg/kg) in foremilk (179 [CI 161-206]) and in mid-feed milk (184 [CI 160-220]) were not significantly different (p = 0.017), but were higher than in hindmilk (175 [CI 153-216]; p < 0.001). In foremilk using (d), BMIC was 199 ([CI 182-257]; p < 0.001 vs. (c)). The variation in BMIC comparing (c) and (d) (13%) was greater than variation within feeding (5%; p < 0.001). Because of poor recoveries, (a) and (b) should not be used to measure BMIC. Compared with (d), (c) has the advantages of higher precision and a lower LOD. In iodine-sufficient women, BMIC shows low variation within a breast-feeding session, so timing of sampling is not a major determinant of BMIC.

Optimization of a New Mass Spectrometry Method for Measurement of Breast Milk Iodine Concentrations and an Assessment of the Effect of Analytic Method and Timing of Within-Feed Sample Collection on Breast Milk Iodine Concentrations

PubMed Central

Baumgartner, Jeannine; Zeder, Christophe; Krzystek, Adam; Osei, Jennifer; Haldimann, Max; Zimmermann, Michael B.; Andersson, Maria

2016-01-01

Background: Breast milk iodine concentration (BMIC) may be an indicator of iodine status during lactation, but there are few data comparing different analytical methods or timing of sampling. The aims of this study were: (i) to optimize a new inductively coupled plasma mass spectrometry (ICP-MS) method; and (ii) to evaluate the effect of analytical method and timing of within-feed sample collection on BMIC. Methods: The colorimetric Sandell–Kolthoff method was evaluated with (a) or without (b) alkaline ashing, and ICP-MS was evaluated using a new 129I isotope ratio approach including Tellurium (Te) for mass bias correction (c) or external standard curve (d). From iodine-sufficient lactating women (n = 97), three samples were collected within one breast-feeding session (fore-, mid-, and hind-feed samples) and BMIC was analyzed using (c) and (d). Results: Iodine recovery from NIST SRM1549a whole milk powder for methods (a)–(d) was 67%, 24%, 105%, and 102%, respectively. Intra- and inter-assay coefficients of variation for ICP-MS comparing (c) and (d) were 1.3% versus 5.6% (p = 0.04) and 1.1% versus 2.4% (p = 0.33). The limit of detection (LOD) was lower for (c) (0.26 μg/kg) than it was for (d) (2.54 μg/kg; p = 0.02). Using (c), the median [95% confidence interval (CI) obtained by bootstrap] BMIC (μg/kg) in foremilk (179 [CI 161–206]) and in mid-feed milk (184 [CI 160–220]) were not significantly different (p = 0.017), but were higher than in hindmilk (175 [CI 153–216]; p < 0.001). In foremilk using (d), BMIC was 199 ([CI 182–257]; p < 0.001 vs. (c)). The variation in BMIC comparing (c) and (d) (13%) was greater than variation within feeding (5%; p < 0.001). Conclusions: Because of poor recoveries, (a) and (b) should not be used to measure BMIC. Compared with (d), (c) has the advantages of higher precision and a lower LOD. In iodine-sufficient women, BMIC shows low variation within a breast-feeding session, so timing of sampling is not a major determinant of BMIC. PMID:26563466

A Multifaceted Sampling Approach to Better Understanding Biogeochemical and Hydrogeological Controls on Uranium Mobility at a Former Uranium Mill Tailings Site in Riverton, Wyoming

NASA Astrophysics Data System (ADS)

Dam, W. L.; Johnson, R. H.; Campbell, S.; Bone, S. E.; Noel, V.; Bargar, J.

2015-12-01

Understanding uranium mobility in subsurface environments is not trivial. Obtaining sufficient data to accurately represent soil and aquifer characteristics can require unique approaches that evolve with added site knowledge. At Riverton, the primary source of uranium mill tailings remaining from ore processing was removed but contaminant plumes have persisted longer than predicted by groundwater modeling. What are the primary mechanisms controlling plume persistence? DOE is conducting new characterization studies to assist our understanding of underlying biogeochemical and hydrogeological mechanisms affecting secondary sources. A variety of field sampling techniques are being sequentially employed including augering, trenching, pore water sampling, and installing multi-level wells. In August 2012, vadose zone soil samples from 34 locations and groundwater from 103 boreholes were collected with Geoprobe ® direct push rods. Lower than expected uranium concentrations in composited shallow soils indicated the need for more focused and deeper samples. In May 2014, soil samples containing evaporites were collected along the bank of the Little Wind River; elevated uranium concentrations in evaporite minerals correlated with plume configurations and reflect contaminated groundwater discharge at the river. In September 2014, hand anger samples collected by the river and oxbow lake also indicated the presence of organic rich zones containing elevated uranium (>50 mg/kg). Subsequent samples collected from five backhoe trenches in May 2015 revealed a highly heterogeneous vadose zone composed of clay, silt, sand and cobbles containing evaporites and organic rich zones which may interact with groundwater plumes.Plans for August 2015 include sonic drilling to obtain continuous cores from the surface down to the base of the surficial aquifer with multi-level monitoring wells constructed in each borehole to assess vertical variation in groundwater chemistry. Temporary well-points will be installed adjacent to the river to assess geochemical and flow controls in the area of plume stagnation. Analyses include critical element speciation (C, S, Fe, and U), microbes, isotopes, diffusivity and flow characteristics. These activities support a dramatically improved understanding of plume persistence.

U-Pb SHRIMP dating of uraniferous opals

USGS Publications Warehouse

Nemchin, A.A.; Neymark, L.A.; Simons, S.L.

2006-01-01

U-Pb and U-series analyses of four U-rich opal samples using sensitive high-resolution ion microprobe (SHRIMP) demonstrate the potential of this technique for the dating of opals with ages ranging from several tens of thousand years to millions of years. The major advantages of the technique, compared to the conventional thermal ionisation mass spectrometry (TIMS), are the high spatial resolution (???20 ??m), the ability to analyse in situ all isotopes required to determine both U-Pb and U-series ages, and a relatively short analysis time which allows obtaining a growth rate of opal as a result of a single SHRIMP session. There are two major limitations to this method, determined by both current level of development of ion probes and understanding of ion sputtering processes. First, sufficient secondary ion beam intensities can only be obtained for opal samples with U concentrations in excess of ???20 ??g/g. However, this restriction still permits dating of a large variety of opals. Second, U-Pb ratios in all analyses drifted with time and were only weakly correlated with changes in other ratios (such as U/UO). This drift, which is difficult to correct for, remains the main factor currently limiting the precision and accuracy of the U-Pb SHRIMP opal ages. Nevertheless, an assumption of similar behaviour of standard and unknown opals under similar analytical conditions allowed successful determination of ages with precisions of ???10% for the samples investigated in this study. SHRIMP-based U-series and U-Pb ages are consistent with TIMS dating results of the same materials and known geological timeframes. ?? 2005 Elsevier B.V. All rights reserved.

Development and evaluation of a multi-locus sequence typing scheme for Mycoplasma synoviae.

PubMed

Dijkman, R; Feberwee, A; Landman, W J M

2016-08-01

Reproducible molecular Mycoplasma synoviae typing techniques with sufficient discriminatory power may help to expand knowledge on its epidemiology and contribute to the improvement of control and eradication programmes of this mycoplasma species. The present study describes the development and validation of a novel multi-locus sequence typing (MLST) scheme for M. synoviae. Thirteen M. synoviae isolates originating from different poultry categories, farms and lesions, were subjected to whole genome sequencing. Their sequences were compared to that of M. synoviae reference strain MS53. A high number of single nucleotide polymorphisms (SNPs) indicating considerable genetic diversity were identified. SNPs were present in over 40 putative target genes for MLST of which five target genes were selected (nanA, uvrA, lepA, ruvB and ugpA) for the MLST scheme. This scheme was evaluated analysing 209 M. synoviae samples from different countries, categories of poultry, farms and lesions. Eleven clonal clusters and 76 different sequence types (STs) were obtained. Clustering occurred following geographical origin, supporting the hypothesis of regional population evolution. M. synoviae samples obtained from epidemiologically linked outbreaks often harboured the same ST. In contrast, multiple M. synoviae lineages were found in samples originating from swollen joints or oviducts from hens that produce eggs with eggshell apex abnormalities indicating that further research is needed to identify the genetic factors of M. synoviae that may explain its variations in tissue tropism and disease inducing potential. Furthermore, MLST proved to have a higher discriminatory power compared to variable lipoprotein and haemagglutinin A typing, which generated 50 different genotypes on the same database.

Analysis of the breast milk of giant pandas (Ailuropoda melanoleuca) and the preparation of substitutes

PubMed Central

ZHANG, Zhihe; HOU, Rong; LAN, Jingchao; WANG, Hairui; KUROKAWA, Hiroyuki; TAKATSU, Zenta; KOBAYASHI, Toyokazu; KOIE, Hiroshi; KAMATA, Hiroshi; KANAYAMA, Kiichi; WATANABE, Toshi

2016-01-01

The first milk substitute for giant panda cubs was developed in 1988 based on limited data about giant panda breast milk and that of certain types of bear. Mixtures of other formulas have also been fed to cubs at some facilities. However, they are not of sufficient nutritional quality for promoting growth in panda cubs. Here, we report analysis of giant panda breast milk and propose new milk substitutes for cubs, which were developed based on the results of our analysis. The Chengdu Research Base of Giant Panda Breeding obtained breast milk samples from three giant pandas. Up to 30 ml of breast milk were collected from each mother by hand. Then, the milk samples were frozen and sent to Nihon University. The levels of protein, fat, carbohydrates, ash, moisture, vitamins, minerals, total amino acids, fatty acids, lactose and other carbohydrates in the milk were analyzed. The breast milk samples exhibited the following nutritional values: protein: 6.6–8.5%, fat: 6.9–16.4%, carbohydrates: 2.5–9.1%, ash: 0.9–1.0% and moisture: 67–83%. We designed two kinds of milk substitutes based on the data obtained and the nutritional requirements of dogs, cats and rodents. The nutritional composition of the milk substitutes for the first and second stages was as follows: protein: 38 and 26%, fat: 40 and 40%, carbohydrates: 13 and 25%, ash: 6 and 6% and moisture: 3 and 3%, respectively. In addition, the substitutes contained vitamins, minerals, taurine, docosahexaenoic acid, lactoferrin, nucleotides and other nutrients. PMID:26781707

ANALYSIS OF DIOXINS IN CONTAMINATED SOILS WITH THE CALUX AND CAFLUX BIOASSAYS, AN IMMUNOASSAY, AND GAS CHROMATOGRAPHY/HIGH-RESOLUTION MASS SPECTROMETRY

PubMed Central

Nording, Malin; Denison, Michael S.; Baston, David; Persson, Ylva; Spinnel, Erik; Haglund, Peter

2010-01-01

The chemically activated luciferase expression assay, the chemically activated fluorescence expression assay, and the enzyme-linked immunosorbent assay (ELISA) are all bioanalytical methods that have been used for the detection and quantification of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs). However, no comparisons of the results obtained by these three methods have been published analyzing identical replicates of purified sample extracts. Therefore, we have evaluated the performance of each of these methods for analyzing PCDD/Fs in aliquots of extracts from aged-contaminated soil samples and compared the results with those obtained by gas chromatography/high-resolution mass spectrometry (GC/HRMS). The quantitative performance was assessed and the effects of sample purification and data interpretation on the quality of the bioassay results were investigated. Results from the bioanalytical techniques were, in principle, not significantly different from each other or from the GC/HRMS data (p = 0.05). Furthermore, properly used, all of the bioanalytical techniques examined were found to be sufficiently sensitive, selective, and accurate to be used in connection with soil remediation activities when aiming at the remediation goal recommended by the U.S. Environmental Protection Agency (i.e., < 1,000 pg toxic equivalency/g). However, a site-specific correction factor should be applied with the use of the ELISA to account for differences between the toxic equivalency factors and the ELISA cross-reactivities of the various PCDD/F congeners, which otherwise might significantly underestimate the PCDD/F content. PMID:17571676

Reexamining Sample Size Requirements for Multivariate, Abundance-Based Community Research: When Resources are Limited, the Research Does Not Have to Be.

PubMed

Forcino, Frank L; Leighton, Lindsey R; Twerdy, Pamela; Cahill, James F

2015-01-01

Community ecologists commonly perform multivariate techniques (e.g., ordination, cluster analysis) to assess patterns and gradients of taxonomic variation. A critical requirement for a meaningful statistical analysis is accurate information on the taxa found within an ecological sample. However, oversampling (too many individuals counted per sample) also comes at a cost, particularly for ecological systems in which identification and quantification is substantially more resource consuming than the field expedition itself. In such systems, an increasingly larger sample size will eventually result in diminishing returns in improving any pattern or gradient revealed by the data, but will also lead to continually increasing costs. Here, we examine 396 datasets: 44 previously published and 352 created datasets. Using meta-analytic and simulation-based approaches, the research within the present paper seeks (1) to determine minimal sample sizes required to produce robust multivariate statistical results when conducting abundance-based, community ecology research. Furthermore, we seek (2) to determine the dataset parameters (i.e., evenness, number of taxa, number of samples) that require larger sample sizes, regardless of resource availability. We found that in the 44 previously published and the 220 created datasets with randomly chosen abundances, a conservative estimate of a sample size of 58 produced the same multivariate results as all larger sample sizes. However, this minimal number varies as a function of evenness, where increased evenness resulted in increased minimal sample sizes. Sample sizes as small as 58 individuals are sufficient for a broad range of multivariate abundance-based research. In cases when resource availability is the limiting factor for conducting a project (e.g., small university, time to conduct the research project), statistically viable results can still be obtained with less of an investment.

Chemical Evidence for Smectites and Zeolites on Mars: Criteria and Limitations

NASA Technical Reports Server (NTRS)

Clark, B. C.; Ming, D.; Vaniman, D.; Wiens, R.; Gellert, R.; Bridges, J. C.; Morris, D.

2014-01-01

Aqueous alteration on Mars can produce a range of tell-tale secondary minerals [1]. Surface missions typically obtain detailed and highly localized element compositional information, but not always mineralogical information, whereas orbital missions deduce mineralogy from relatively high spatial resolution IR spectral mapping (decameters scale, for CRISM), but obtain element data only over much larger areas of martian terrain (200 km). Surface missions have also discovered several occurrences of major geochemical alteration of igneous precursors, for many of which elemental compositional is the only diagnostic information available. Many types of clays and zeolites have quasi-unique element profiles which may be used to implicate their presence. In some cases, one or more candidate minerals are sufficiently close in their component elements and their stoichiometry that ambiguity must remain, unless other constraints can be brought to bear. Geochemical characteristics of alteration products most likely on Mars can be compared to results from MER and MSL rover missions (e.g. Independence [4] and Esperance samples). These considerations are needed for MER Opportunity rover now that Mini-TES is no longer operational. It also has importance for exploration by the MSL Curiosity rover because inferences and deductions available from ChemCam (CCAM) remote LIBS and/or in situ x-ray fluorescence (APXS) can be used as indicators for triage to select materials to sample for limited-resource instruments, SAM and Chemin.

Influence of riders' skill on plasma cortisol levels of horses walking on forest and field trekking courses.

PubMed

Ono, Ayaka; Matsuura, Akihiro; Yamazaki, Yumi; Sakai, Wakako; Watanabe, Kentaro; Nakanowatari, Toshihiko; Kobayashi, Hiroshi; Irimajiri, Mami; Hodate, Koichi

2017-10-01

The aim of this study was to evaluate the influence of rider's skill on the plasma cortisol levels of trekking horses on two courses, walking on field and forest courses (about 4.5 to 5.1 km each). Three riders of different skills did horse trekking (HT) in a tandem line under a fixed order: advanced-leading, beginner-second and intermediate-last. A total of six horses were used and they experienced all positions in both courses; a total of 12 experiments were done. Blood samples were obtained before HT, immediately after and 2 h after HT. As a control, additional blood samples were obtained from the same horses on non-riding days. Irrespective of the course and the rider's skill, the cortisol level before HT was higher than that of control (P < 0.05). In both courses, the cortisol levels immediately after HT ridden by the advanced rider were higher than that of control (P < 0.05). However, in every case, the cortisol level 2 h after HT was closely similar to the level of the control. Thus, we concluded the stress of trekking horse was not sufficient to disturb the circadian rhythm of the cortisol level, irrespective of the course and the rider's skill. © 2017 Japanese Society of Animal Science.

Automated multimodal spectral histopathology for quantitative diagnosis of residual tumour during basal cell carcinoma surgery.

PubMed

Boitor, Radu; Kong, Kenny; Shipp, Dustin; Varma, Sandeep; Koloydenko, Alexey; Kulkarni, Kusum; Elsheikh, Somaia; Schut, Tom Bakker; Caspers, Peter; Puppels, Gerwin; van der Wolf, Martin; Sokolova, Elena; Nijsten, T E C; Salence, Brogan; Williams, Hywel; Notingher, Ioan

2017-12-01

Multimodal spectral histopathology (MSH), an optical technique combining tissue auto-fluorescence (AF) imaging and Raman micro-spectroscopy (RMS), was previously proposed for detection of residual basal cell carcinoma (BCC) at the surface of surgically-resected skin tissue. Here we report the development of a fully-automated prototype instrument based on MSH designed to be used in the clinic and operated by a non-specialist spectroscopy user. The algorithms for the AF image processing and Raman spectroscopy classification had been first optimised on a manually-operated laboratory instrument and then validated on the automated prototype using skin samples from independent patients. We present results on a range of skin samples excised during Mohs micrographic surgery, and demonstrate consistent diagnosis obtained in repeat test measurement, in agreement with the reference histopathology diagnosis. We also show that the prototype instrument can be operated by clinical users (a skin surgeon and a core medical trainee, after only 1-8 hours of training) to obtain consistent results in agreement with histopathology. The development of the new automated prototype and demonstration of inter-instrument transferability of the diagnosis models are important steps on the clinical translation path: it allows the testing of the MSH technology in a relevant clinical environment in order to evaluate its performance on a sufficiently large number of patients.

THE CHALLENGE OF DETECTING CLASSICAL SWINE FEVER VIRUS CIRCULATION IN WILD BOAR (SUS SCROFA): SIMULATION OF SAMPLING OPTIONS.

PubMed

Sonnenburg, Jana; Schulz, Katja; Blome, Sandra; Staubach, Christoph

2016-10-01

Classical swine fever (CSF) is one of the most important viral diseases of domestic pigs ( Sus scrofa domesticus) and wild boar ( Sus scrofa ). For at least 4 decades, several European Union member states were confronted with outbreaks among wild boar and, as it had been shown that infected wild boar populations can be a major cause of primary outbreaks in domestic pigs, strict control measures for both species were implemented. To guarantee early detection and to demonstrate freedom from disease, intensive surveillance is carried out based on a hunting bag sample. In this context, virologic investigations play a major role in the early detection of new introductions and in regions immunized with a conventional vaccine. The required financial resources and personnel for reliable testing are often large, and sufficient sample sizes to detect low virus prevalences are difficult to obtain. We conducted a simulation to model the possible impact of changes in sample size and sampling intervals on the probability of CSF virus detection based on a study area of 65 German hunting grounds. A 5-yr period with 4,652 virologic investigations was considered. Results suggest that low prevalences could not be detected with a justifiable effort. The simulation of increased sample sizes per sampling interval showed only a slightly better performance but would be unrealistic in practice, especially outside the main hunting season. Further studies on other approaches such as targeted or risk-based sampling for virus detection in connection with (marker) antibody surveillance are needed.

Lunar placement of Mars quarantine facility

NASA Technical Reports Server (NTRS)

Davidson, James E.; Mitchell, W. F.

1988-01-01

Advanced mission scenarios are currently being contemplated that would call for the retrieval of surface samples from Mars, from a comet, and from other places in the solar system. An important consideration for all of these sample return missions is quarantine. Quarantine facilities on the Moon offer unique advantages over other locations. The Moon offers gravity, distance, and vacuum. It is sufficiently near the Earth to allow rapid resupply and easy communication. It is sufficiently distant to lessen the psychological impact of a quarantine facility on Earth's human inhabitants. Finally, the Moon is airless, and seems to be devoid of life. It is, therefore, more suited to contamination control efforts.

50 CFR 679.93 - Amendment 80 Program recordkeeping, permits, monitoring, and catch accounting.

Code of Federal Regulations, 2011 CFR

2011-10-01

... CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED... moved to the fish bin. (6) Sample storage. There is sufficient space to accommodate a minimum of 10 observer sampling baskets. This space must be within or adjacent to the observer sample station. (7) Pre...

Evaluation of errors in quantitative determination of asbestos in rock

NASA Astrophysics Data System (ADS)

Baietto, Oliviero; Marini, Paola; Vitaliti, Martina

2016-04-01

The quantitative determination of the content of asbestos in rock matrices is a complex operation which is susceptible to important errors. The principal methodologies for the analysis are Scanning Electron Microscopy (SEM) and Phase Contrast Optical Microscopy (PCOM). Despite the PCOM resolution is inferior to that of SEM, PCOM analysis has several advantages, including more representativity of the analyzed sample, more effective recognition of chrysotile and a lower cost. The DIATI LAA internal methodology for the analysis in PCOM is based on a mild grinding of a rock sample, its subdivision in 5-6 grain size classes smaller than 2 mm and a subsequent microscopic analysis of a portion of each class. The PCOM is based on the optical properties of asbestos and of the liquids with note refractive index in which the particles in analysis are immersed. The error evaluation in the analysis of rock samples, contrary to the analysis of airborne filters, cannot be based on a statistical distribution. In fact for airborne filters a binomial distribution (Poisson), which theoretically defines the variation in the count of fibers resulting from the observation of analysis fields, chosen randomly on the filter, can be applied. The analysis in rock matrices instead cannot lean on any statistical distribution because the most important object of the analysis is the size of the of asbestiform fibers and bundles of fibers observed and the resulting relationship between the weights of the fibrous component compared to the one granular. The error evaluation generally provided by public and private institutions varies between 50 and 150 percent, but there are not, however, specific studies that discuss the origin of the error or that link it to the asbestos content. Our work aims to provide a reliable estimation of the error in relation to the applied methodologies and to the total content of asbestos, especially for the values close to the legal limits. The error assessments must be made through the repetition of the same analysis on the same sample to try to estimate the error on the representativeness of the sample and the error related to the sensitivity of the operator, in order to provide a sufficiently reliable uncertainty of the method. We used about 30 natural rock samples with different asbestos content, performing 3 analysis on each sample to obtain a trend sufficiently representative of the percentage. Furthermore we made on one chosen sample 10 repetition of the analysis to try to define more specifically the error of the methodology.

An innovative piston corer for large‐volume sediment samples

PubMed Central

Haselmair, Alexandra; Stachowitsch, Michael; Zuschin, Martin

2016-01-01

Abstract Coring is one of several standard procedures to extract sediments and their faunas from open marine, estuarine, and limnic environments. Achieving sufficiently deep penetration, obtaining large sediment volumes in single deployments, and avoiding sediment loss upon retrieval remain problematic. We developed a piston corer with a diameter of 16 cm that enables penetration down to 1.5 m in a broad range of soft bottom types, yields sufficient material for multiple analyses, and prevents sediment loss due to a specially designed hydraulic core catcher. A novel extrusion system enables very precise slicing and preserves the original sediment stratification by keeping the liners upright. The corer has moderate purchase costs and a robust and simple design that allows for a deployment from relatively small vessels as available at most marine science institutions. It can easily be operated by two to three researchers rather than by specially trained technicians. In the northern Adriatic Sea, the corer successfully extracted more than 50 cores from a range of fine mud to coarse sand, at water depths from three to 45 m. The initial evaluation of the cores demonstrated their usefulness for fauna sequences along with heavy metal, nutrient and pollutant analyses. Their length is particularly suited for historical ecological work requiring sedimentary and faunal sequences to reconstruct benthic communities over the last millennia. PMID:28111529

Disclosure of congenital cleft lip and palate to Japanese patients: reported patient experiences and relationship to self-esteem.

PubMed

Omiya, Tomoko; Ito, Mikiko; Yamazaki, Yoshihiko

2014-12-16

The present study investigated when and how Japanese people with cleft lip and palate (CL/P) learn that their condition is congenital; the perceived effects of withholding the CL/P diagnosis on patients; and whether the resulting social experience and self-esteem are related. A questionnaire survey was conducted in 71 adults with CL/P recruited through a hospital, a patients' association, and by snowball sampling. The participants became aware of their physical difference in childhood, but many reported difficulty in understanding their condition. Participants reported that their families avoided the topic of diagnosis. Participants who understood their condition during childhood rather than in adulthood were significantly more likely to consider this scenario as positive (p < 0.001). Although stigmatising experiences were extremely painful, most patients hid their suffering, making it more difficult to obtain social support. Participants with high self-esteem were more likely to feel that they received adequate support. It is important to explain the congenital nature of CL/P sufficiently and early. In addition, openness by the family about the diagnosis, rather than avoidance, may improve patients' self-esteem. Sufficient support from family, health care providers, and significant others is needed for patients to develop adequate self-esteem.

Epidemiological Paradox or Immigrant Vulnerability? Obesity Among Young Children of Immigrants

PubMed Central

Baker, Elizabeth H.; Rendall, Michael S.; Weden, Margaret M.

2015-01-01

According to the “immigrant epidemiological paradox,” immigrants and their children enjoy health advantages over their U.S.-born peers—advantages that diminish with greater acculturation. We investigated child obesity as a potentially significant deviation from this paradox for second-generation immigrant children. We evaluated two alternate measures of mother's acculturation: age at arrival in the United States and English language proficiency. To obtain sufficient numbers of second-generation immigrant children, we pooled samples across two related, nationally representative surveys. Each included measured (not parent-reported) height and weight of kindergartners. We also estimated models that alternately included and excluded mother's pre-pregnancy weight status as a predictor. Our findings are opposite to those predicted by the immigrant epidemiological paradox: children of U.S.-born mothers were less likely to be obese than otherwise similar children of foreign-born mothers; and the children of the least-acculturated immigrant mothers, as measured by low English language proficiency, were the most likely to be obese. Foreign-born mothers had lower (healthier) pre-pregnancy weight than U.S.-born mothers, and this was protective against their second-generation children's obesity. This protection, however, was not sufficiently strong to outweigh factors associated or correlated with the mothers' linguistic isolation and marginal status as immigrants. PMID:26111970

Epidemiological Paradox or Immigrant Vulnerability? Obesity Among Young Children of Immigrants.

PubMed

Baker, Elizabeth H; Rendall, Michael S; Weden, Margaret M

2015-08-01

According to the "immigrant epidemiological paradox," immigrants and their children enjoy health advantages over their U.S.-born peers--advantages that diminish with greater acculturation. We investigated child obesity as a potentially significant deviation from this paradox for second-generation immigrant children. We evaluated two alternate measures of mother's acculturation: age at arrival in the United States and English language proficiency. To obtain sufficient numbers of second-generation immigrant children, we pooled samples across two related, nationally representative surveys. Each included measured (not parent-reported) height and weight of kindergartners. We also estimated models that alternately included and excluded mother's pre-pregnancy weight status as a predictor. Our findings are opposite to those predicted by the immigrant epidemiological paradox: children of U.S.-born mothers were less likely to be obese than otherwise similar children of foreign-born mothers; and the children of the least-acculturated immigrant mothers, as measured by low English language proficiency, were the most likely to be obese. Foreign-born mothers had lower (healthier) pre-pregnancy weight than U.S.-born mothers, and this was protective against their second-generation children's obesity. This protection, however, was not sufficiently strong to outweigh factors associated or correlated with the mothers' linguistic isolation and marginal status as immigrants.

Abortion and subsequent excretion of chlamydiae from the reproductive tract of sheep during estrus.

PubMed Central

Papp, J R; Shewen, P E; Gartley, C J

1994-01-01

Chlamydia psittaci serovar 1 infection in pregnant sheep typically causes abortion or the birth of weak lambs. Eight sheep that experienced chlamydia-induced abortion during their first pregnancy were successfully rebred yearly for the past 2 years. Chlamydia-specific lipopolysaccharide was detectable for approximately 3 weeks in vaginal swabs taken from the experimentally infected sheep following abortion. There was no evidence of chlamydiae in vaginal, placental, or neonatal samples obtained immediately after each subsequent successful pregnancy. Sera collected from the experimentally infected sheep had persistent, high antibody levels to C. psittaci, suggesting continued exposure of the immune system to the organism. Examination of vaginal specimens obtained during various stages of the estrus cycle revealed detectable levels of chlamydiae only when the animal was near ovulation. Chlamydiae were not detected in swabs from sheep that did not experience abortion. Enhanced chlamydial excretion during the periovulation period of sheep may provide sufficient stimulation of the immune system to account for the persistent antibody response. Furthermore, the association between estrus and chlamydial shedding has important implications for transmission of infection to other ewes during breeding. PMID:8063395

Laminar, Transitional, and Turbulent Heating on Mid Lift-to-Drag Ratio Entry Vehicles

NASA Technical Reports Server (NTRS)

Hollis, Brian R.; Hollingsworth, Kevin E.

2012-01-01

The boundary-layer transition characteristics and convective aeroheating levels on mid lift-to-drag ratio entry vehicle configurations have been studied through wind tunnel testing. Several configurations were investigated, including elliptically-blunted cylinders with both circular and elliptically-flattened cross sections, biconic geometries based on launch vehicle dual-use shrouds, and parametrically-optimized analytic geometries. Vehicles of this class have been proposed for high-mass Mars missions, such as sample return and crewed exploration, for which the conventional sphere-cone entry-vehicle geometries of previous Mars missions are insufficient. Testing was conducted at Mach 6 over a range of Reynolds numbers sufficient to generate laminar, transitional, and turbulent flow. Transition onset locations - both straight-line and cross-flow - and heating rates were obtained through global phosphor thermography. Supporting computations were performed to obtain heating rates for comparison with the data. Laminar data and predictions agreed to well within the experimental uncertainty. Fully-turbulent data and predictions also agreed well. However, in transitional flow regions, greater differences were observed. Additional aerodynamic performance data were also generated through Modified-Newtonian analyses of the geometries.

Genetic variation in the midcontinental population of sandhill cranes, Grus canadensis.

PubMed

Petersen, Jessica L; Bischof, Richard; Krapu, Gary L; Szalanski, Allen L

2003-02-01

Three subspecies of sandhill crane (Grus canadensis) are recognized in the Midcontinental population, the lesser (Grus c. canadensis), Canadian (G. c. rowani), and greater (G. c. tabida). Blood samples collected on the population's primary spring staging area in Nebraska, U.S.A., were used to resolve the genetic relationship among these subspecies. Phylogenetic analysis of 27 G. canadensis, by DNA sequencing of a 675 bp region of the mtDNA, supports the subspecies designations of G. c. canadensis and G. c. tabida. G. c. rowani individuals were intermediate with each of the other two subspecies. Genetic divergence ranged from 6.5 to 14.5% between G. c. canadensis and G. c. tabida, 0.5 to 6.6% within G. c. canadensis, and 0.1 to 6.0% within G. c. tabida. Sufficient DNA for analysis was obtained from shed feathers indicating a source of genetic material that does not require the capture or sacrifice of the birds. Other genetic markers and methods, including satellite telemetry, are required for obtaining detailed information on crane distributions as needed to establish effective management units for the MCP.

Lagrangian statistics of turbulent dispersion from 81923 direct numerical simulation of isotropic turbulence

NASA Astrophysics Data System (ADS)

Buaria, Dhawal; Yeung, P. K.; Sawford, B. L.

2016-11-01

An efficient massively parallel algorithm has allowed us to obtain the trajectories of 300 million fluid particles in an 81923 simulation of isotropic turbulence at Taylor-scale Reynolds number 1300. Conditional single-particle statistics are used to investigate the effect of extreme events in dissipation and enstrophy on turbulent dispersion. The statistics of pairs and tetrads, both forward and backward in time, are obtained via post-processing of single-particle trajectories. For tetrads, since memory of shape is known to be short, we focus, for convenience, on samples which are initially regular, with all sides of comparable length. The statistics of tetrad size show similar behavior as the two-particle relative dispersion, i.e., stronger backward dispersion at intermediate times with larger backward Richardson constant. In contrast, the statistics of tetrad shape show more robust inertial range scaling, in both forward and backward frames. However, the distortion of shape is stronger for backward dispersion. Our results suggest that the Reynolds number reached in this work is sufficient to settle some long-standing questions concerning Lagrangian scale similarity. Supported by NSF Grants CBET-1235906 and ACI-1036170.

An integrated approach for identifying wrongly labelled samples when performing classification in microarray data.

PubMed

Leung, Yuk Yee; Chang, Chun Qi; Hung, Yeung Sam

2012-01-01

Using hybrid approach for gene selection and classification is common as results obtained are generally better than performing the two tasks independently. Yet, for some microarray datasets, both classification accuracy and stability of gene sets obtained still have rooms for improvement. This may be due to the presence of samples with wrong class labels (i.e. outliers). Outlier detection algorithms proposed so far are either not suitable for microarray data, or only solve the outlier detection problem on their own. We tackle the outlier detection problem based on a previously proposed Multiple-Filter-Multiple-Wrapper (MFMW) model, which was demonstrated to yield promising results when compared to other hybrid approaches (Leung and Hung, 2010). To incorporate outlier detection and overcome limitations of the existing MFMW model, three new features are introduced in our proposed MFMW-outlier approach: 1) an unbiased external Leave-One-Out Cross-Validation framework is developed to replace internal cross-validation in the previous MFMW model; 2) wrongly labeled samples are identified within the MFMW-outlier model; and 3) a stable set of genes is selected using an L1-norm SVM that removes any redundant genes present. Six binary-class microarray datasets were tested. Comparing with outlier detection studies on the same datasets, MFMW-outlier could detect all the outliers found in the original paper (for which the data was provided for analysis), and the genes selected after outlier removal were proven to have biological relevance. We also compared MFMW-outlier with PRAPIV (Zhang et al., 2006) based on same synthetic datasets. MFMW-outlier gave better average precision and recall values on three different settings. Lastly, artificially flipped microarray datasets were created by removing our detected outliers and flipping some of the remaining samples' labels. Almost all the 'wrong' (artificially flipped) samples were detected, suggesting that MFMW-outlier was sufficiently powerful to detect outliers in high-dimensional microarray datasets.

EBUS-Guided Cautery-Assisted Transbronchial Forceps Biopsies: Safety and Sensitivity Relative to Transbronchial Needle Aspiration

PubMed Central

Bramley, Kyle; Pisani, Margaret A.; Murphy, Terrence E.; Araujo, Katy; Homer, Robert; Puchalski, Jonathan

2016-01-01

Background EBUS-guided transbronchial needle aspiration (TBNA) is important in the evaluation of thoracic lymphadenopathy. Reliably providing excellent diagnostic yield for malignancy, its diagnosis of sarcoidosis is inconsistent. Furthermore, when larger “core” biopsy samples of malignant tissue are required, TBNA may not suffice. The primary objective of this study was to determine if the sequential use of TBNA and a novel technique called cautery-assisted transbronchial forceps biopsies (ca-TBFB) was safe. Secondary outcomes included sensitivity and successful acquisition of tissue. Methods Fifty unselected patients undergoing convex probe EBUS were prospectively enrolled. Under EBUS guidance, all lymph nodes ≥ 1 cm were sequentially biopsied using TBNA and ca-TBFB. Safety and sensitivity were assessed at the nodal level for 111 nodes. Results of each technique were also reported on a per-patient basis. Results There were no significant adverse events. In nodes determined to be malignant, TBNA provided higher sensitivity (100%) than ca-TBFB (78%). However, among nodes with granulomatous inflammation, ca-TBFB exhibited higher sensitivity (90%) than TBNA (33%). For analysis based on patients rather than nodes, 6 of the 31 patients with malignancy would have been missed or understaged if the diagnosis was based on samples obtained by ca-TBFB. On the other hand, 3 of 8 patients with sarcoidosis would have been missed if analysis was based only on TBNA samples. In some cases only ca-TBFB acquired sufficient tissue for the core samples needed in clinical trials of malignancy. Conclusions The sequential use of TBNA and ca-TBFB appears to be safe. The larger samples obtained from ca-TBFB increased its sensitivity to detect granulomatous disease and provided specimens for clinical trials of malignancy when needle biopsies were insufficient. For thoracic surgeons and advanced bronchoscopists, we advocate ca-TBFB as an alternative to TBNA in select clinical scenarios. PMID:26912301

Endobronchial Ultrasound-Guided Cautery-Assisted Transbronchial Forceps Biopsies: Safety and Sensitivity Relative to Transbronchial Needle Aspiration.

PubMed

Bramley, Kyle; Pisani, Margaret A; Murphy, Terrence E; Araujo, Katy L; Homer, Robert J; Puchalski, Jonathan T

2016-05-01

Endobronchial ultrasound (EBUS)-guided transbronchial needle aspiration (TBNA) is important in the evaluation of thoracic lymphadenopathy. Reliably providing excellent diagnostic yield for malignancy, its diagnosis of sarcoidosis is inconsistent. Furthermore, TBNA may not suffice when larger "core biopsy" samples of malignant tissue are required. The primary objective of this study was to determine if the sequential use of TBNA and a novel technique called cautery-assisted transbronchial forceps biopsy (ca-TBFB) was safe. Secondary outcomes included sensitivity and successful acquisition of tissue. The study prospectively enrolled 50 unselected patients undergoing convex-probe EBUS. All lymph nodes exceeding 1 cm were sequentially biopsied under EBUS guidance using TBNA and ca-TBFB. Safety and sensitivity were assessed at the nodal level for 111 nodes. Results of each technique were also reported for each patient. There were no significant adverse events. In nodes determined to be malignant, TBNA provided higher sensitivity (100%) than ca-TBFB (78%). However, among nodes with granulomatous inflammation, ca-TBFB exhibited higher sensitivity (90%) than TBNA (33%). On the one hand, for analysis based on patients rather than nodes, 6 of the 31 patients with malignancy would have been missed or understaged if the diagnosis were based on samples obtained by ca-TBFB. On the other hand, 3 of 8 patients with sarcoidosis would have been missed if analysis were based only on TBNA samples. In some patients, only ca-TBFB acquired sufficient tissue for the core samples needed in clinical trials of malignancy. The sequential use of TBNA and ca-TBFB appears to be safe. The larger samples obtained from ca-TBFB increased its sensitivity to detect granulomatous disease and provided adequate specimens for clinical trials of malignancy when specimens from needle biopsies were insufficient. For thoracic surgeons and advanced bronchoscopists, we advocate ca-TBFB as an alternative to TBNA in select clinical scenarios. Copyright © 2016 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive.

PubMed

Ohta, Tazro; Nakazato, Takeru; Bono, Hidemasa

2017-06-01

It is important for public data repositories to promote the reuse of archived data. In the growing field of omics science, however, the increasing number of submissions of high-throughput sequencing (HTSeq) data to public repositories prevents users from choosing a suitable data set from among the large number of search results. Repository users need to be able to set a threshold to reduce the number of results to obtain a suitable subset of high-quality data for reanalysis. We calculated the quality of sequencing data archived in a public data repository, the Sequence Read Archive (SRA), by using the quality control software FastQC. We obtained quality values for 1 171 313 experiments, which can be used to evaluate the suitability of data for reuse. We also visualized the data distribution in SRA by integrating the quality information and metadata of experiments and samples. We provide quality information of all of the archived sequencing data, which enable users to obtain sufficient quality sequencing data for reanalyses. The calculated quality data are available to the public in various formats. Our data also provide an example of enhancing the reuse of public data by adding metadata to published research data by a third party. © The Authors 2017. Published by Oxford University Press.

A review of population-based prevalence studies of physical activity in adults in the Asia-Pacific region

PubMed Central

2012-01-01

Background Physical activity (PA) surveillance is an important component of non-communicable disease risk factor monitoring, and occurs through national and international surveillance systems. This review identifies population PA estimates for adults in the Asia-Pacific region, and examines variation in trends and prevalence rates obtained using different PA measures. Methods Data were obtained from a MEDLINE search; World Health Organization's Global Health Infobase; Government websites and reference lists of relevant papers. Inclusion criteria included: national studies or those reporting large scale population-level data; data published from 2000 to 2010 and trend data prior; sample sizes over n = 1000, or fewer subjects in small nations. Results In total, 56 population surveys from 29 Asia-Pacific countries were identified. Data on 'sufficient physical activity' amongst adults were available from 45 studies (80%), with estimates ranging from 7% to 93% (median 62%, inter-quartile range 40%-85%). For 14 countries, estimates of 'sufficient activity' were documented in multiple surveys using different methods, with the largest variation from 18% to 92% in Nepal. Median or mean MET-minutes/day, reported in 20 studies, ranged from 6 to 1356. Serial trend data were available for 11 countries (22%), for periods spanning 2-10 years. Of these, five countries demonstrated increases in physical activity over time, four demonstrated decreases and three showed no changes. Conclusions Many countries in the Asia-Pacific region collect population-level PA data. This review highlights differences in estimates within and between countries. Some differences may be real, others due to variation in the PA questions asked and survey methods used. Use of standardized protocols and measures, and combined reporting of data are essential goals of improved international PA surveillance. PMID:22251660

Analysis of sesterterpenoids from Aspergillus terreus using ESI-QTOF and ESI-IT.

PubMed

Wu, Zhi-Jun; Fang, Dong-Mei; Han, Dan; Li, Guo-You; Chen, Xiao-Zhen; Qi, Hua-Yi; Zhang, Guo-Lin

2010-01-01

Biosynthesis of terretonin was studied due to the interesting skeleton of this series of sesterterpenoids. Very recently, López-Gresa reported two new sesterterpenoids (terretonins E and F) which are inhibitors of the mammalian mitochondrial respiratory chain. Mass spectrometry (MS), especially tandem mass spectrometry, has been one of the most important physicochemical methods for the identification of trace natural products due to it rapidity, sensitivity and low levels of sample consumption. The potential application prospect and unique skeleton prompted us to study structural characterisation using MS. To obtain sufficient information for rapid structural elucidation of this class of compounds using MS. The elemental composition of the product ions was confirmed by low-energy ESI-CID-QTOF-MS/MS analyses. The fragmentation pathways were postulated on the basis of ESI-QTOF-MS/MS/MS and ESI-IT-MS(n) spectra. Common features and major differences between ESI-QTOF-MS/MS and IT-MS(n) spectra were compared. For ESI-QTOF-MS/MS/MS experiments, capillary exit voltage was raised to induce in-source dissociation. Ammonium acetate or acetic acid were added into solutions to improve the intensity of [M + H]+. The collision energy was optimised to achieve sufficient fragmentation. Some fragmentation pathways were unambiguously proposed by the variety of abundance of fragment ions at different collision energies even without MS(n) spectra. Fragmentation pathways of five representative sesterterpenoids were elucidated using ESI-QTOF-MS/MS/MS and ESI-IT-MS(n) in both positive- and negative-ion mode. The key group of characterising fragmentation profiles was ring B, and these fragmentation patterns are helpful to identify different types of sestertepenoids. Complementary information obtained from fragmentation experiments of [M + H]+ (or [M + NH4]+ and [M-H](-) precursor ions is especially valuable for rapid identification of this kind of sesterterpenoid.

AXAF-I ghost ray study: On orbit case

NASA Technical Reports Server (NTRS)

Gaetz, T. J.

1993-01-01

The problem of baffles for control of singly reflected (and nonreflected) ghost rays is considered. The theory of baffle design for Wolter Type I grazing incidence optics is reviewed, and a set of sample baffle parameters is obtained subject to the assumptions of nominal mirror figures and perfect manufacture and alignment of baffles. It is found that baffles forward of the optics (in the thermal precollimator) and between the mirror elements (at the CAP) are sufficient to allow the simultaneous ghost image and vignetting requirements to be satisfied for HRMA shells P1H1, P3H3, and P4H4. However, these baffles are not sufficient for the innermost shell P6H6; at best the requirements are slightly violated and there is no margin for tolerances. The addition of a baffle interior to the P6 space at an axial station about one third of the way forward from the aft end of the paraboloid will allow the ghost ray and vignetting requirements to be met. The minimum ghost ray angles and the vignetting angles are sensitive functions of the baffle positions and radii; tolerances of considerably better than 1 mm will be required. The sensitivities are coupled and correlated; further investigations should be undertaken in order to obtain baffle parameters which, combined with likely achievable tolerances, will minimize the risk of the vignetting/ghost ray requirements not being met. The lightweight carbon-epoxy composite used for thermal baffles has insufficient X-ray opacity to be a suitable material for construction of the controlling X-ray baffles; further study is needed to determine an appropriate material and to investigate its thermal and mechanical implications.

Abiding by the sufficiency economy philosophy to develop the quality of life of teachers and educational personnel in the central region

NASA Astrophysics Data System (ADS)

Khumkhong, Tippawan

2018-01-01

This research aimed to 1) study the ideas and procedures of the Sufficiency Economy Philosophy (SEP) to make it fully implemented to develop the quality of life of teachers and educational personnel in the central region, 2) study the results of implementing the SEP and 3) offer some guidelines in implementing the SEP to develop the quality of life. The samples were the teachers and educational personnel, the cremation service welfare members of 2015 in 9 provinces of the central region namely Bangkok, Sing Buri, Saraburi, Chai Nat, Nonthaburi, Pathum Thani, Pha Nakhon Si Ayuttaya, Lop Buri and Ang Thong. The qualitative research's samples were the 6 key informants selected purposely, collected by depth-interview, analyzed using inductive method, checked by the methodological triangulation and the key informants. The quantitative research's samples were the 398 offered obtained by stratified random sampling having regard to the ratio, collected by questionnaire with the reliability value of 0.982, analyzed by percentage, mean and standard deviation. The findings were as follows: 1) As for the ideas towards the SEP and the ethical principles of Buddhism are one and the same thing. All levels of people can follow this philosophy. The procedures towards the SEP to develop the quality of life by performing in harmony with their daily lives regarding to the moderation, the reasonableness, building self-immunity with knowledge and ethical qualification. 2) The SEP helps develop the better quality of life, happiness, sound life, sound economy with great satisfaction of the living. 3) On offering some guidelines in implementing the SEP to develop the quality of life: 3.1) the performers must have good understanding in the philosophy and accept to bring it into use 3.2) lead a life according to the ethical principles of Buddhism or to the ones of the religion you believe. 3.3) members of the family had to cooperate in leading lives according to the SEP and 3.4) save money when having more than enough. 4) The teachers and educational personnel are able to implement the ideas offered at a high level.

Gender-Specific Barriers to Self-Sufficiency among Former Supplemental Security Income Drug Addiction and Alcoholism Beneficiaries: Implications for Welfare-To-Work Programs and Services

PubMed Central

Hogan, Sean R; Unick, George J.; Speiglman, Richard; Norris, Jean C.

2011-01-01

This study examines barriers to economic self-sufficiency among a panel of 219 former Supplemental Security Income (SSI) drug addiction and alcoholism (DA&A) recipients following elimination of DA&A as an eligibility category for SSI disability benefits. Study participants were comprehensively surveyed at six measurement points following the policy change. Generalized estimating equations were used to examine full-sample and gender-specific barriers to economic self-sufficiency. Results indicate that access to transportation, age, and time are the strongest predictors of achieving self-sufficiency for both men and women leaving the welfare system. Gender-specific barriers are also identified. Future research needs to assess the generalizability of these results to other public assistance recipients. PMID:21625301

Method for detection of long-lived radioisotopes in small biochemical samples

DOEpatents

Turteltaub, K.W.; Vogel, J.S.; Felton, J.S.; Gledhill, B.L.; Davis, J.C.

1994-11-22

Disclosed is a method for detection of long-lived radioisotopes in small biochemical samples, comprising: a. selecting a biological host in which radioisotopes are present in concentrations equal to or less than those in the ambient biosphere, b. preparing a long-lived radioisotope labeled reactive chemical specie, c. administering the chemical specie to the biologist host in doses sufficiently low to avoid significant overt damage to the biological system, d. allowing a period of time to elapse sufficient for dissemination and interaction of the chemical specie with the host throughout the biological system of the host, e. isolating a reacted fraction of the biological substance from the host in a manner sufficient to avoid contamination of the substance from extraneous sources, f. converting the fraction of biological substance by suitable means to a material which efficiently produces charged ions in at least one of several possible ion sources without introduction of significant isotopic fractionation, and, g. measuring the radioisotope concentration in the material by means of direct isotopic counting. 5 figs.

Exploration of the factor structure of the Kirton Adaption-Innovation Inventory using bootstrapping estimation.

PubMed

Im, Subin; Min, Soonhong

2013-04-01

Exploratory factor analyses of the Kirton Adaption-Innovation Inventory (KAI), which serves to measure individual cognitive styles, generally indicate three factors: sufficiency of originality, efficiency, and rule/group conformity. In contrast, a 2005 study by Im and Hu using confirmatory factor analysis supported a four-factor structure, dividing the sufficiency of originality dimension into two subdimensions, idea generation and preference for change. This study extends Im and Hu's (2005) study of a derived version of the KAI by providing additional evidence of the four-factor structure. Specifically, the authors test the robustness of the parameter estimates to the violation of normality assumptions in the sample using bootstrap methods. A bias-corrected confidence interval bootstrapping procedure conducted among a sample of 356 participants--members of the Arkansas Household Research Panel, with middle SES and average age of 55.6 yr. (SD = 13.9)--showed that the four-factor model with two subdimensions of sufficiency of originality fits the data significantly better than the three-factor model in non-normality conditions.

Method for detection of long-lived radioisotopes in small biochemical samples

DOEpatents

Turteltaub, Kenneth W.; Vogel, John S.; Felton, James S.; Gledhill, Barton L.; Davis, Jay C.

1994-01-01

Disclosed is a method for detection of long-lived radioisotopes in small bio-chemical samples, comprising: a. selecting a biological host in which radioisotopes are present in concentrations equal to or less than those in the ambient biosphere, b. preparing a long-lived radioisotope labeled reactive chemical specie, c. administering said chemical specie to said biologist host in doses sufficiently low to avoid significant overt damage to the biological system thereof, d. allowing a period of time to elapse sufficient for dissemination and interaction of said chemical specie with said host throughout said biological system of said host, e. isolating a reacted fraction of the biological substance from said host in a manner sufficient to avoid contamination of said substance from extraneous sources, f. converting said fraction of biological substance by suitable means to a material which efficiently produces charged ions in at least one of several possible ion sources without introduction of significant isotopic fractionation, and, g. measuring the radioisotope concentration in said material by means of direct isotopic counting.

Quality of sunglasses available in the Iranian market; a study with emphasis on sellers’ license

PubMed Central

Bazzazi, Nooshin; Heydarian, Samira; Vahabi, Reihaneh; Akbarzadeh, Siamak; Fouladi, Daniel F

2015-01-01

Context: Sunglasses should follow minimum requirements to sufficiently protect eyes. It is not known whether all items obtainable from the market are appropriately designed. Aims: To compare ultraviolet (UV)-protective properties of commercially available sunglasses obtained from authorized and unauthorized Iranian sellers. Settings and Study Design: An analytic-descriptive study performed in a metropolitan area (Tehran). Materials and Methods: Using a UV-visible standard spectrophotometer, the percentage transmittance was scanned between 280 and 400 nm in 348 pairs of nonprescription sunglasses (price range: 20–80 US$) obtained anonymously and randomly from authorized (permitted by the Ministry of Health, 189 pairs) and unauthorized (159 pairs) sellers in the Iranian capital city, Tehran. The Australian/New Zealand Standard (AS/NZS) and the American National Standards Institute [ANSI] standards were followed. Statistical Analysis: Chi-square test, independent samples t-test or Mann–Whitney U-test. Results: UV-protective properties of the sunglasses obtained from authorized sellers complied with AS/NZS and ANSI guidelines in 92.6% and 95.2% of items, respectively. The corresponding rates for sunglasses obtained from unauthorized sellers were 0% and 8.2%, respectively (P < 0.001 for both). The rate of defective polarizing capability of lenses was 27.4% in sunglasses obtained from authorized sellers versus 90.4% in sunglasses obtained from unauthorized sellers (P < 0.001). Neither brand nor price played significant contributions to UV protection/lens polarizing capability of sunglasses obtained from authorized sellers. Conclusions: Sunglasses provided by unauthorized sellers are alarmingly unreliable and could be potentially hazardous for the eye. Brand and price do not guarantee optimal protection against UV radiation or polarizing performance of the lens. PMID:25827547

Hawking-like radiation does not require a trapped region.

PubMed

Barceló, Carlos; Liberati, Stefano; Sonego, Sebastiano; Visser, Matt

2006-10-27

We discuss the issue of quasiparticle production by "analogue black holes" with particular attention paid to the possibility of reproducing Hawking radiation in a laboratory. By constructing simple geometric acoustic models, we obtain a somewhat unexpected result: We show that, in order to obtain a stationary and Planckian emission of quasiparticles, it is not necessary to create a trapped region in the acoustic spacetime (corresponding to a supersonic regime in the fluid flow). It is sufficient to set up a dynamically changing flow asymptotically approaching a sonic regime with sufficient rapidity in laboratory time. This result is generic to curved-space quantum field theory, the "analogue spacetimes" we consider providing a guide to physical intuition, and a possible route to laboratory experiments.

Global exponential stability and lag synchronization for delayed memristive fuzzy Cohen-Grossberg BAM neural networks with impulses.

PubMed

Yang, Wengui; Yu, Wenwu; Cao, Jinde; Alsaadi, Fuad E; Hayat, Tasawar

2018-02-01

This paper investigates the stability and lag synchronization for memristor-based fuzzy Cohen-Grossberg bidirectional associative memory (BAM) neural networks with mixed delays (asynchronous time delays and continuously distributed delays) and impulses. By applying the inequality analysis technique, homeomorphism theory and some suitable Lyapunov-Krasovskii functionals, some new sufficient conditions for the uniqueness and global exponential stability of equilibrium point are established. Furthermore, we obtain several sufficient criteria concerning globally exponential lag synchronization for the proposed system based on the framework of Filippov solution, differential inclusion theory and control theory. In addition, some examples with numerical simulations are given to illustrate the feasibility and validity of obtained results. Copyright © 2017 Elsevier Ltd. All rights reserved.

Improved technique that allows the performance of large-scale SNP genotyping on DNA immobilized by FTA technology.

PubMed

He, Hongbin; Argiro, Laurent; Dessein, Helia; Chevillard, Christophe

2007-01-01

FTA technology is a novel method designed to simplify the collection, shipment, archiving and purification of nucleic acids from a wide variety of biological sources. The number of punches that can normally be obtained from a single specimen card are often however, insufficient for the testing of the large numbers of loci required to identify genetic factors that control human susceptibility or resistance to multifactorial diseases. In this study, we propose an improved technique to perform large-scale SNP genotyping. We applied a whole genome amplification method to amplify DNA from buccal cell samples stabilized using FTA technology. The results show that using the improved technique it is possible to perform up to 15,000 genotypes from one buccal cell sample. Furthermore, the procedure is simple. We consider this improved technique to be a promising methods for performing large-scale SNP genotyping because the FTA technology simplifies the collection, shipment, archiving and purification of DNA, while whole genome amplification of FTA card bound DNA produces sufficient material for the determination of thousands of SNP genotypes.

Solid-Phase Extraction Coupled to a Paper-Based Technique for Trace Copper Detection in Drinking Water.

PubMed

Quinn, Casey W; Cate, David M; Miller-Lionberg, Daniel D; Reilly, Thomas; Volckens, John; Henry, Charles S

2018-03-20

Metal contamination of natural and drinking water systems poses hazards to public and environmental health. Quantifying metal concentrations in water typically requires sample collection in the field followed by expensive laboratory analysis that can take days to weeks to obtain results. The objective of this work was to develop a low-cost, field-deployable method to quantify trace levels of copper in drinking water by coupling solid-phase extraction/preconcentration with a microfluidic paper-based analytical device. This method has the advantages of being hand-powered (instrument-free) and using a simple "read by eye" quantification motif (based on color distance). Tap water samples collected across Fort Collins, CO, were tested with this method and validated against ICP-MS. We demonstrate the ability to quantify the copper content of tap water within 30% of a reference technique at levels ranging from 20 to 500 000 ppb. The application of this technology, which should be sufficient as a rapid screening tool, can lead to faster, more cost-effective detection of soluble metals in water systems.

Rapid quantification of multi-components in alcohol precipitation liquid of Codonopsis Radix using near infrared spectroscopy (NIRS).

PubMed

Luo, Yu; Li, Wen-Long; Huang, Wen-Hua; Liu, Xue-Hua; Song, Yan-Gang; Qu, Hai-Bin

2017-05-01

A near infrared spectroscopy (NIRS) approach was established for quality control of the alcohol precipitation liquid in the manufacture of Codonopsis Radix. By applying NIRS with multivariate analysis, it was possible to build variation into the calibration sample set, and the Plackett-Burman design, Box-Behnken design, and a concentrating-diluting method were used to obtain the sample set covered with sufficient fluctuation of process parameters and extended concentration information. NIR data were calibrated to predict the four quality indicators using partial least squares regression (PLSR). In the four calibration models, the root mean squares errors of prediction (RMSEPs) were 1.22 μg/ml, 10.5 μg/ml, 1.43 μg/ml, and 0.433% for lobetyolin, total flavonoids, pigments, and total solid contents, respectively. The results indicated that multi-components quantification of the alcohol precipitation liquid of Codonopsis Radix could be achieved with an NIRS-based method, which offers a useful tool for real-time release testing (RTRT) of intermediates in the manufacture of Codonopsis Radix.

Ultrasound data for laboratory calibration of an analytical model to calculate crack depth on asphalt pavements.

PubMed

Franesqui, Miguel A; Yepes, Jorge; García-González, Cándida

2017-08-01

This article outlines the ultrasound data employed to calibrate in the laboratory an analytical model that permits the calculation of the depth of partial-depth surface-initiated cracks on bituminous pavements using this non-destructive technique. This initial calibration is required so that the model provides sufficient precision during practical application. The ultrasonic pulse transit times were measured on beam samples of different asphalt mixtures (semi-dense asphalt concrete AC-S; asphalt concrete for very thin layers BBTM; and porous asphalt PA). The cracks on the laboratory samples were simulated by means of notches of variable depths. With the data of ultrasound transmission time ratios, curve-fittings were carried out on the analytical model, thus determining the regression parameters and their statistical dispersion. The calibrated models obtained from laboratory datasets were subsequently applied to auscultate the evolution of the crack depth after microwaves exposure in the research article entitled "Top-down cracking self-healing of asphalt pavements with steel filler from industrial waste applying microwaves" (Franesqui et al., 2017) [1].

Population density estimated from locations of individuals on a passive detector array

USGS Publications Warehouse

Efford, Murray G.; Dawson, Deanna K.; Borchers, David L.

2009-01-01

The density of a closed population of animals occupying stable home ranges may be estimated from detections of individuals on an array of detectors, using newly developed methods for spatially explicit capture–recapture. Likelihood-based methods provide estimates for data from multi-catch traps or from devices that record presence without restricting animal movement ("proximity" detectors such as camera traps and hair snags). As originally proposed, these methods require multiple sampling intervals. We show that equally precise and unbiased estimates may be obtained from a single sampling interval, using only the spatial pattern of detections. This considerably extends the range of possible applications, and we illustrate the potential by estimating density from simulated detections of bird vocalizations on a microphone array. Acoustic detection can be defined as occurring when received signal strength exceeds a threshold. We suggest detection models for binary acoustic data, and for continuous data comprising measurements of all signals above the threshold. While binary data are often sufficient for density estimation, modeling signal strength improves precision when the microphone array is small.

The latent structure of post-traumatic stress disorder among Arabic-speaking refugees receiving psychiatric treatment in Denmark.

PubMed

Vindbjerg, Erik; Carlsson, Jessica; Mortensen, Erik Lykke; Elklit, Ask; Makransky, Guido

2016-09-05

Refugees are known to have high rates of post-traumatic stress disorder (PTSD). Although recent years have seen an increase in the number of refugees from Arabic speaking countries in the Middle East, no study so far has validated the construct of PTSD in an Arabic speaking sample of refugees. Responses to the Harvard Trauma Questionnaire (HTQ) were obtained from 409 Arabic-speaking refugees diagnosed with PTSD and undergoing treatment in Denmark. Confirmatory factor analysis was used to test and compare five alternative models. All four- and five-factor models provided sufficient fit indices. However, a combination of excessively small clusters, and a case of mistranslation in the official Arabic translation of the HTQ, rendered results two of the models inadmissible. A post hoc analysis revealed that a simpler factor structure is supported, once local dependence is addressed. Overall, the construct of PTSD is supported in this sample of Arabic-speaking refugees. Apart from pursuing maximum fit, future studies may wish to test simpler, potentially more stable models, which allow a more informative analysis of individual items.

Two-dimensional sparse wavenumber recovery for guided wavefields

NASA Astrophysics Data System (ADS)

Sabeti, Soroosh; Harley, Joel B.

2018-04-01

The multi-modal and dispersive behavior of guided waves is often characterized by their dispersion curves, which describe their frequency-wavenumber behavior. In prior work, compressive sensing based techniques, such as sparse wavenumber analysis (SWA), have been capable of recovering dispersion curves from limited data samples. A major limitation of SWA, however, is the assumption that the structure is isotropic. As a result, SWA fails when applied to composites and other anisotropic structures. There have been efforts to address this issue in the literature, but they either are not easily generalizable or do not sufficiently express the data. In this paper, we enhance the existing approaches by employing a two-dimensional wavenumber model to account for direction-dependent velocities in anisotropic media. We integrate this model with tools from compressive sensing to reconstruct a wavefield from incomplete data. Specifically, we create a modified two-dimensional orthogonal matching pursuit algorithm that takes an undersampled wavefield image, with specified unknown elements, and determines its sparse wavenumber characteristics. We then recover the entire wavefield from the sparse representations obtained with our small number of data samples.

Multivariate Welch t-test on distances

PubMed Central

2016-01-01

Motivation: Permutational non-Euclidean analysis of variance, PERMANOVA, is routinely used in exploratory analysis of multivariate datasets to draw conclusions about the significance of patterns visualized through dimension reduction. This method recognizes that pairwise distance matrix between observations is sufficient to compute within and between group sums of squares necessary to form the (pseudo) F statistic. Moreover, not only Euclidean, but arbitrary distances can be used. This method, however, suffers from loss of power and type I error inflation in the presence of heteroscedasticity and sample size imbalances. Results: We develop a solution in the form of a distance-based Welch t-test, TW2, for two sample potentially unbalanced and heteroscedastic data. We demonstrate empirically the desirable type I error and power characteristics of the new test. We compare the performance of PERMANOVA and TW2 in reanalysis of two existing microbiome datasets, where the methodology has originated. Availability and Implementation: The source code for methods and analysis of this article is available at https://github.com/alekseyenko/Tw2. Further guidance on application of these methods can be obtained from the author. Contact: alekseye@musc.edu PMID:27515741

Multivariate Welch t-test on distances.

PubMed

Alekseyenko, Alexander V

2016-12-01

Permutational non-Euclidean analysis of variance, PERMANOVA, is routinely used in exploratory analysis of multivariate datasets to draw conclusions about the significance of patterns visualized through dimension reduction. This method recognizes that pairwise distance matrix between observations is sufficient to compute within and between group sums of squares necessary to form the (pseudo) F statistic. Moreover, not only Euclidean, but arbitrary distances can be used. This method, however, suffers from loss of power and type I error inflation in the presence of heteroscedasticity and sample size imbalances. We develop a solution in the form of a distance-based Welch t-test, [Formula: see text], for two sample potentially unbalanced and heteroscedastic data. We demonstrate empirically the desirable type I error and power characteristics of the new test. We compare the performance of PERMANOVA and [Formula: see text] in reanalysis of two existing microbiome datasets, where the methodology has originated. The source code for methods and analysis of this article is available at https://github.com/alekseyenko/Tw2 Further guidance on application of these methods can be obtained from the author. alekseye@musc.edu. © The Author 2016. Published by Oxford University Press.

Dark field imaging system for size characterization of magnetic micromarkers

NASA Astrophysics Data System (ADS)

Malec, A.; Haiden, C.; Kokkinis, G.; Keplinger, F.; Giouroudi, I.

2017-05-01

In this paper we demonstrate a dark field video imaging system for the detection and size characterization of individual magnetic micromarkers suspended in liquid and the detection of pathogens utilizing magnetically labelled E.coli. The system follows dynamic processes and interactions of moving micro/nano objects close to or below the optical resolution limit, and is especially suitable for small sample volumes ( 10 μl). The developed detection method can be used to obtain clinical information about liquid contents when an additional biological protocol is provided, i.e., binding of microorganisms (e.g. E.coli) to specific magnetic markers. Some of the major advantages of our method are the increased sizing precision in the micro- and nano-range as well as the setup's simplicity making it a perfect candidate for miniaturized devices. Measurements can thus be carried out in a quick, inexpensive, and compact manner. A minor limitation is that the concentration range of micromarkers in a liquid sample needs to be adjusted in such a manner that the number of individual particles in the microscope's field of view is sufficient.

Density matters: Review of approaches to setting organism-based ballast water discharge standards

USGS Publications Warehouse

Lee II,; Frazier,; Ruiz,

2010-01-01

As part of their effort to develop national ballast water discharge standards under NPDES permitting, the Office of Water requested that WED scientists identify and review existing approaches to generating organism-based discharge standards for ballast water. Six potential approaches were identified and the utility and uncertainties of each approach was evaluated. During the process of reviewing the existing approaches, the WED scientists, in conjunction with scientists at the USGS and Smithsonian Institution, developed a new approach (per capita invasion probability or "PCIP") that addresses many of the limitations of the previous methodologies. THE PCIP approach allows risk managers to generate quantitative discharge standards using historical invasion rates, ballast water discharge volumes, and ballast water organism concentrations. The statistical power of sampling ballast water for both the validation of ballast water treatment systems and ship-board compliance monitoring with the existing methods, though it should be possible to obtain sufficient samples during treatment validation. The report will go to a National Academy of Sciences expert panel that will use it in their evaluation of approaches to developing ballast water discharge standards for the Office of Water.

Analytic nuclear forces and molecular properties from full configuration interaction quantum Monte Carlo

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

Thomas, Robert E.; Overy, Catherine; Opalka, Daniel

Unbiased stochastic sampling of the one- and two-body reduced density matrices is achieved in full configuration interaction quantum Monte Carlo with the introduction of a second, “replica” ensemble of walkers, whose population evolves in imaginary time independently from the first and which entails only modest additional computational overheads. The matrices obtained from this approach are shown to be representative of full configuration-interaction quality and hence provide a realistic opportunity to achieve high-quality results for a range of properties whose operators do not necessarily commute with the Hamiltonian. A density-matrix formulated quasi-variational energy estimator having been already proposed and investigated, themore » present work extends the scope of the theory to take in studies of analytic nuclear forces, molecular dipole moments, and polarisabilities, with extensive comparison to exact results where possible. These new results confirm the suitability of the sampling technique and, where sufficiently large basis sets are available, achieve close agreement with experimental values, expanding the scope of the method to new areas of investigation.« less

Comparison of rapid methods for chemical analysis of milligram samples of ultrafine clays

USGS Publications Warehouse

Rettig, S.L.; Marinenko, J.W.; Khoury, Hani N.; Jones, B.F.

1983-01-01

Two rapid methods for the decomposition and chemical analysis of clays were adapted for use with 20–40-mg size samples, typical amounts of ultrafine products (≤0.5-µm diameter) obtained by modern separation methods for clay minerals. The results of these methods were compared with those of “classical” rock analyses. The two methods consisted of mixed lithium metaborate fusion and heated decomposition with HF in a closed vessel. The latter technique was modified to include subsequent evaporation with concentrated H2SO4 and re-solution in HCl, which reduced the interference of the fluoride ion in the determination of Al, Fe, Ca, Mg, Na, and K. Results from the two methods agree sufficiently well with those of the “classical” techniques to minimize error in the calculation of clay mineral structural formulae. Representative maximum variations, in atoms per unit formula of the smectite type based on 22 negative charges, are 0.09 for Si, 0.03 for Al, 0.015 for Fe, 0.07 for Mg, 0.03 for Na, and 0.01 for K.

Equilibrium Droplets on Deformable Substrates: Equilibrium Conditions.

PubMed

Koursari, Nektaria; Ahmed, Gulraiz; Starov, Victor M

2018-05-15

Equilibrium conditions of droplets on deformable substrates are investigated, and it is proven using Jacobi's sufficient condition that the obtained solutions really provide equilibrium profiles of both the droplet and the deformed support. At the equilibrium, the excess free energy of the system should have a minimum value, which means that both necessary and sufficient conditions of the minimum should be fulfilled. Only in this case, the obtained profiles provide the minimum of the excess free energy. The necessary condition of the equilibrium means that the first variation of the excess free energy should vanish, and the second variation should be positive. Unfortunately, the mentioned two conditions are not the proof that the obtained profiles correspond to the minimum of the excess free energy and they could not be. It is necessary to check whether the sufficient condition of the equilibrium (Jacobi's condition) is satisfied. To the best of our knowledge Jacobi's condition has never been verified for any already published equilibrium profiles of both the droplet and the deformable substrate. A simple model of the equilibrium droplet on the deformable substrate is considered, and it is shown that the deduced profiles of the equilibrium droplet and deformable substrate satisfy the Jacobi's condition, that is, really provide the minimum to the excess free energy of the system. To simplify calculations, a simplified linear disjoining/conjoining pressure isotherm is adopted for the calculations. It is shown that both necessary and sufficient conditions for equilibrium are satisfied. For the first time, validity of the Jacobi's condition is verified. The latter proves that the developed model really provides (i) the minimum of the excess free energy of the system droplet/deformable substrate and (ii) equilibrium profiles of both the droplet and the deformable substrate.

Assessing Disfluencies in School-Age Children Who Stutter: How Much Speech Is Enough?

ERIC Educational Resources Information Center

Gregg, Brent A.; Sawyer, Jean

2015-01-01

The question of what size speech sample is sufficient to accurately identify stuttering and its myriad characteristics is a valid one. Short samples have a risk of over- or underrepresenting disfluency types or characteristics. In recent years, there has been a trend toward using shorter samples because they are less time-consuming for…

Sequence-based screening for self-sufficient P450 monooxygenase from a metagenome library.

PubMed

Kim, B S; Kim, S Y; Park, J; Park, W; Hwang, K Y; Yoon, Y J; Oh, W K; Kim, B Y; Ahn, J S

2007-05-01

Cytochrome P450 monooxygenases (CYPs) are useful catalysts for oxidation reactions. Self-sufficient CYPs harbour a reductive domain covalently connected to a P450 domain and are known for their robust catalytic activity with great potential as biocatalysts. In an effort to expand genetic sources of self-sufficient CYPs, we devised a sequence-based screening system to identify them in a soil metagenome. We constructed a soil metagenome library and performed sequence-based screening for self-sufficient CYP genes. A new CYP gene, syk181, was identified from the metagenome library. Phylogenetic analysis revealed that SYK181 formed a distinct phylogenic line with 46% amino-acid-sequence identity to CYP102A1 which has been extensively studied as a fatty acid hydroxylase. The heterologously expressed SYK181 showed significant hydroxylase activity towards naphthalene and phenanthrene as well as towards fatty acids. Sequence-based screening of metagenome libraries is expected to be a useful approach for searching self-sufficient CYP genes. The translated product of syk181 shows self-sufficient hydroxylase activity towards fatty acids and aromatic compounds. SYK181 is the first self-sufficient CYP obtained directly from a metagenome library. The genetic and biochemical information on SYK181 are expected to be helpful for engineering self-sufficient CYPs with broader catalytic activities towards various substrates, which would be useful for bioconversion of natural products and biodegradation of organic chemicals.

Robust gene selection methods using weighting schemes for microarray data analysis.

PubMed

Kang, Suyeon; Song, Jongwoo

2017-09-02

A common task in microarray data analysis is to identify informative genes that are differentially expressed between two different states. Owing to the high-dimensional nature of microarray data, identification of significant genes has been essential in analyzing the data. However, the performances of many gene selection techniques are highly dependent on the experimental conditions, such as the presence of measurement error or a limited number of sample replicates. We have proposed new filter-based gene selection techniques, by applying a simple modification to significance analysis of microarrays (SAM). To prove the effectiveness of the proposed method, we considered a series of synthetic datasets with different noise levels and sample sizes along with two real datasets. The following findings were made. First, our proposed methods outperform conventional methods for all simulation set-ups. In particular, our methods are much better when the given data are noisy and sample size is small. They showed relatively robust performance regardless of noise level and sample size, whereas the performance of SAM became significantly worse as the noise level became high or sample size decreased. When sufficient sample replicates were available, SAM and our methods showed similar performance. Finally, our proposed methods are competitive with traditional methods in classification tasks for microarrays. The results of simulation study and real data analysis have demonstrated that our proposed methods are effective for detecting significant genes and classification tasks, especially when the given data are noisy or have few sample replicates. By employing weighting schemes, we can obtain robust and reliable results for microarray data analysis.

Neuro-genetic system for optimization of GMI samples sensitivity.

PubMed

Pitta Botelho, A C O; Vellasco, M M B R; Hall Barbosa, C R; Costa Silva, E

2016-03-01

Magnetic sensors are largely used in several engineering areas. Among them, magnetic sensors based on the Giant Magnetoimpedance (GMI) effect are a new family of magnetic sensing devices that have a huge potential for applications involving measurements of ultra-weak magnetic fields. The sensitivity of magnetometers is directly associated with the sensitivity of their sensing elements. The GMI effect is characterized by a large variation of the impedance (magnitude and phase) of a ferromagnetic sample, when subjected to a magnetic field. Recent studies have shown that phase-based GMI magnetometers have the potential to increase the sensitivity by about 100 times. The sensitivity of GMI samples depends on several parameters, such as sample length, external magnetic field, DC level and frequency of the excitation current. However, this dependency is yet to be sufficiently well-modeled in quantitative terms. So, the search for the set of parameters that optimizes the samples sensitivity is usually empirical and very time consuming. This paper deals with this problem by proposing a new neuro-genetic system aimed at maximizing the impedance phase sensitivity of GMI samples. A Multi-Layer Perceptron (MLP) Neural Network is used to model the impedance phase and a Genetic Algorithm uses the information provided by the neural network to determine which set of parameters maximizes the impedance phase sensitivity. The results obtained with a data set composed of four different GMI sample lengths demonstrate that the neuro-genetic system is able to correctly and automatically determine the set of conditioning parameters responsible for maximizing their phase sensitivities. Copyright © 2015 Elsevier Ltd. All rights reserved.

High-Grading Lunar Samples for Return to Earth

NASA Technical Reports Server (NTRS)

Allen, Carlton; Sellar, Glenn; Nunez, Jorge; Winterhalter, Daniel; Farmer, Jack

2009-01-01

Astronauts on long-duration lunar missions will need the capability to "high-grade" their samples to select the highest value samples for transport to Earth and to leave others on the Moon. We are supporting studies to defile the "necessary and sufficient" measurements and techniques for highgrading samples at a lunar outpost. A glovebox, dedicated to testing instruments and techniques for high-grading samples, is in operation at the JSC Lunar Experiment Laboratory.

Synthesis and Characterization of BaFe12O19 Thin Films Using Suspension of Nano Powders

NASA Astrophysics Data System (ADS)

Salemizadeh, Saman; Seyyed Ebrahimi, S. A.

BaM thin films have been synthesized by dispersing the dried gel nano powders prepared by Sol-Gel method. The solution was made by dissolving iron nitrate Fe(NO3).9H2O, barium nitrate Ba(NO3)2 and citric acid in deyonized water and methanol. This sol was slowly evaporated until a dried gel was formed. This dried gel was then added to ethylene glycol. The final solution was vigorously shaken and mixed in ultrasonic cleaner for 30 min to disperse particles sufficiently. Then the prepared solution spin coated on Si(110) substrate. The obtained thin films were dried at 120 °C and then calcined at 900 °C for 1 h. The films were characterized using X-ray diffraction (XRD) and vibrating sample magnetometer (VSM).

Registered nurses' perceptions of cultural and linguistic hospital resources.

PubMed

Whitman, Marilyn V; Davis, Jullet A

2009-01-01

As the patient population continues to diversify, the need to provide care that is culturally and linguistically appropriate is intensifying. This study describes the perceptions of registered nurses (RNs) in Alabama hospitals regarding the training and resources available for providing culturally and linguistically appropriate care. The population consists of all RNs working in Alabama hospitals. A sample of 1976 RNs was obtained using an online survey. The findings indicate that although some resources and training are currently provided to nurses, the majority of respondents still lack sufficient resources and training to provide culturally and linguistically appropriate care. The lack of uniformity in resources and training makes it difficult to ensure that all healthcare providers are receiving the same information. However, hospitals do have the flexibility to tailor training to areas that are specific to their population needs.

[Questionnaire for the mobbing risk: CDL2.0].

PubMed

Gilioli, R; Cassitto, M G; Campanini, P; Punzi, S; Consonni, D; Rengo, C; Fattorini, E; Foá, V

2005-01-01

The aim of the study is to develop and validate a questionnaire able to evaluate the risk of mobbing at the workplace. A multiple-choice questionnaire has been developed which contains, among the different items, only one revealing a mobbing situation. The questionnaire has been administered to two groups (group A--243 subjects in a mobbing situation and group B--63 subjects without exposure to mobbing) and the differences in the scores obtained have been analysed. The questionnaire has proved to be valid and reliable. The results show that the presence of five mobbing actions is sufficient to define the workplace situation as potentially at risk for mobbing. The study reveals some limits in the selection of the two samples thus needing some adjustment. However, the questionnaire, also in the present form, can be considered a tool able to detect the mobbing situations.

Building test data from real outbreaks for evaluating detection algorithms.

PubMed

Texier, Gaetan; Jackson, Michael L; Siwe, Leonel; Meynard, Jean-Baptiste; Deparis, Xavier; Chaudet, Herve

2017-01-01

Benchmarking surveillance systems requires realistic simulations of disease outbreaks. However, obtaining these data in sufficient quantity, with a realistic shape and covering a sufficient range of agents, size and duration, is known to be very difficult. The dataset of outbreak signals generated should reflect the likely distribution of authentic situations faced by the surveillance system, including very unlikely outbreak signals. We propose and evaluate a new approach based on the use of historical outbreak data to simulate tailored outbreak signals. The method relies on a homothetic transformation of the historical distribution followed by resampling processes (Binomial, Inverse Transform Sampling Method-ITSM, Metropolis-Hasting Random Walk, Metropolis-Hasting Independent, Gibbs Sampler, Hybrid Gibbs Sampler). We carried out an analysis to identify the most important input parameters for simulation quality and to evaluate performance for each of the resampling algorithms. Our analysis confirms the influence of the type of algorithm used and simulation parameters (i.e. days, number of cases, outbreak shape, overall scale factor) on the results. We show that, regardless of the outbreaks, algorithms and metrics chosen for the evaluation, simulation quality decreased with the increase in the number of days simulated and increased with the number of cases simulated. Simulating outbreaks with fewer cases than days of duration (i.e. overall scale factor less than 1) resulted in an important loss of information during the simulation. We found that Gibbs sampling with a shrinkage procedure provides a good balance between accuracy and data dependency. If dependency is of little importance, binomial and ITSM methods are accurate. Given the constraint of keeping the simulation within a range of plausible epidemiological curves faced by the surveillance system, our study confirms that our approach can be used to generate a large spectrum of outbreak signals.

Digital simulation of an arbitrary stationary stochastic process by spectral representation.

PubMed

Yura, Harold T; Hanson, Steen G

2011-04-01

In this paper we present a straightforward, efficient, and computationally fast method for creating a large number of discrete samples with an arbitrary given probability density function and a specified spectral content. The method relies on initially transforming a white noise sample set of random Gaussian distributed numbers into a corresponding set with the desired spectral distribution, after which this colored Gaussian probability distribution is transformed via an inverse transform into the desired probability distribution. In contrast to previous work, where the analyses were limited to auto regressive and or iterative techniques to obtain satisfactory results, we find that a single application of the inverse transform method yields satisfactory results for a wide class of arbitrary probability distributions. Although a single application of the inverse transform technique does not conserve the power spectra exactly, it yields highly accurate numerical results for a wide range of probability distributions and target power spectra that are sufficient for system simulation purposes and can thus be regarded as an accurate engineering approximation, which can be used for wide range of practical applications. A sufficiency condition is presented regarding the range of parameter values where a single application of the inverse transform method yields satisfactory agreement between the simulated and target power spectra, and a series of examples relevant for the optics community are presented and discussed. Outside this parameter range the agreement gracefully degrades but does not distort in shape. Although we demonstrate the method here focusing on stationary random processes, we see no reason why the method could not be extended to simulate non-stationary random processes. © 2011 Optical Society of America

Building test data from real outbreaks for evaluating detection algorithms

PubMed Central

Texier, Gaetan; Jackson, Michael L.; Siwe, Leonel; Meynard, Jean-Baptiste; Deparis, Xavier; Chaudet, Herve

2017-01-01

Benchmarking surveillance systems requires realistic simulations of disease outbreaks. However, obtaining these data in sufficient quantity, with a realistic shape and covering a sufficient range of agents, size and duration, is known to be very difficult. The dataset of outbreak signals generated should reflect the likely distribution of authentic situations faced by the surveillance system, including very unlikely outbreak signals. We propose and evaluate a new approach based on the use of historical outbreak data to simulate tailored outbreak signals. The method relies on a homothetic transformation of the historical distribution followed by resampling processes (Binomial, Inverse Transform Sampling Method—ITSM, Metropolis-Hasting Random Walk, Metropolis-Hasting Independent, Gibbs Sampler, Hybrid Gibbs Sampler). We carried out an analysis to identify the most important input parameters for simulation quality and to evaluate performance for each of the resampling algorithms. Our analysis confirms the influence of the type of algorithm used and simulation parameters (i.e. days, number of cases, outbreak shape, overall scale factor) on the results. We show that, regardless of the outbreaks, algorithms and metrics chosen for the evaluation, simulation quality decreased with the increase in the number of days simulated and increased with the number of cases simulated. Simulating outbreaks with fewer cases than days of duration (i.e. overall scale factor less than 1) resulted in an important loss of information during the simulation. We found that Gibbs sampling with a shrinkage procedure provides a good balance between accuracy and data dependency. If dependency is of little importance, binomial and ITSM methods are accurate. Given the constraint of keeping the simulation within a range of plausible epidemiological curves faced by the surveillance system, our study confirms that our approach can be used to generate a large spectrum of outbreak signals. PMID:28863159

A passive guard for low thermal conductivity measurement of small samples by the hot plate method

NASA Astrophysics Data System (ADS)

Jannot, Yves; Degiovanni, Alain; Grigorova-Moutiers, Veneta; Godefroy, Justine

2017-01-01

Hot plate methods under steady state conditions are based on a 1D model to estimate the thermal conductivity, using measurements of the temperatures T 0 and T 1 of the two sides of the sample and of the heat flux crossing it. To be consistent with the hypothesis of the 1D heat flux, either a hot plate guarded apparatus is used, or the temperature is measured at the centre of the sample. On one hand the latter method can be used only if the ratio thickness/width of the sample is sufficiently low and on the other hand the guarded hot plate method requires large width samples (typical cross section of 0.6  ×  0.6 m2). That is why both methods cannot be used for low width samples. The method presented in this paper is based on an optimal choice of the temperatures T 0 and T 1 compared to the ambient temperature T a, enabling the estimation of the thermal conductivity with a centered hot plate method, by applying the 1D heat flux model. It will be shown that these optimal values do not depend on the size or on the thermal conductivity of samples (in the range 0.015-0.2 W m-1 K-1), but only on T a. The experimental results obtained validate the method for several reference samples for values of the ratio thickness/width up to 0.3, thus enabling the measurement of the thermal conductivity of samples having a small cross-section, down to 0.045  ×  0.045 m2.

Precipitation estimation in mountainous terrain using multivariate geostatistics. Part I: structural analysis

USGS Publications Warehouse

Hevesi, Joseph A.; Istok, Jonathan D.; Flint, Alan L.

1992-01-01

Values of average annual precipitation (AAP) are desired for hydrologic studies within a watershed containing Yucca Mountain, Nevada, a potential site for a high-level nuclear-waste repository. Reliable values of AAP are not yet available for most areas within this watershed because of a sparsity of precipitation measurements and the need to obtain measurements over a sufficient length of time. To estimate AAP over the entire watershed, historical precipitation data and station elevations were obtained from a network of 62 stations in southern Nevada and southeastern California. Multivariate geostatistics (cokriging) was selected as an estimation method because of a significant (p = 0.05) correlation of r = .75 between the natural log of AAP and station elevation. A sample direct variogram for the transformed variable, TAAP = ln [(AAP) 1000], was fitted with an isotropic, spherical model defined by a small nugget value of 5000, a range of 190 000 ft, and a sill value equal to the sample variance of 163 151. Elevations for 1531 additional locations were obtained from topographic maps to improve the accuracy of cokriged estimates. A sample direct variogram for elevation was fitted with an isotropic model consisting of a nugget value of 5500 and three nested transition structures: a Gaussian structure with a range of 61 000 ft, a spherical structure with a range of 70 000 ft, and a quasi-stationary, linear structure. The use of an isotropic, stationary model for elevation was considered valid within a sliding-neighborhood radius of 120 000 ft. The problem of fitting a positive-definite, nonlinear model of coregionalization to an inconsistent sample cross variogram for TAAP and elevation was solved by a modified use of the Cauchy-Schwarz inequality. A selected cross-variogram model consisted of two nested structures: a Gaussian structure with a range of 61 000 ft and a spherical structure with a range of 190 000 ft. Cross validation was used for model selection and for comparing the geostatistical model with six alternate estimation methods. Multivariate geostatistics provided the best cross-validation results.

Evaluation of four fast-response flow measurement devices

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

Gero, A.J.; Suppers, K.L.; Tomb, T.F.

1988-01-01

The Federal Mine Safety and Health Act of 1977 requires that sampling of dust in coal mine environments be conducted with an approved sampler operating at a flow rate of 2.0 liters of air per minute or at such other flow rate as prescribed by the Secretaries of Labor and of Health and Human Services. Standard procedures for calibration of these samplers within the Mine Safety and Health Administration utilize either a 3.0 liter capacity wet test meter or a 1.0 liter soap film calibrator. Several new flow calibrating devices have become commercially available. This paper describes an evaluation conductedmore » on four such devices: the Mast Model 823-2 bubble flowmeter, the Buck Calibrator, the Kurz Model 541S mass flowmeter and the Kurz Pocket Calibrator. The precision of a series of measurements made with each instrument was compared to the precision of a series of measurements made with the wet test meter. The comparison showed that the variability of calibration measurements obtained with the fast response flow calibrators was between 1.5 and 4.5 times larger than that obtained with the WTM; however, with all of the calibration devices evaluated, three repetitive measurements were sufficient to obtain a precision of {plus minus}0.1 liters per minute. 4 refs., 2 figs., 1 tab.« less

Assessing the precision of a time-sampling-based study among GPs: balancing sample size and measurement frequency.

PubMed

van Hassel, Daniël; van der Velden, Lud; de Bakker, Dinny; van der Hoek, Lucas; Batenburg, Ronald

2017-12-04

Our research is based on a technique for time sampling, an innovative method for measuring the working hours of Dutch general practitioners (GPs), which was deployed in an earlier study. In this study, 1051 GPs were questioned about their activities in real time by sending them one SMS text message every 3 h during 1 week. The required sample size for this study is important for health workforce planners to know if they want to apply this method to target groups who are hard to reach or if fewer resources are available. In this time-sampling method, however, standard power analyses is not sufficient for calculating the required sample size as this accounts only for sample fluctuation and not for the fluctuation of measurements taken from every participant. We investigated the impact of the number of participants and frequency of measurements per participant upon the confidence intervals (CIs) for the hours worked per week. Statistical analyses of the time-use data we obtained from GPs were performed. Ninety-five percent CIs were calculated, using equations and simulation techniques, for various different numbers of GPs included in the dataset and for various frequencies of measurements per participant. Our results showed that the one-tailed CI, including sample and measurement fluctuation, decreased from 21 until 3 h between one and 50 GPs. As a result of the formulas to calculate CIs, the increase of the precision continued and was lower with the same additional number of GPs. Likewise, the analyses showed how the number of participants required decreased if more measurements per participant were taken. For example, one measurement per 3-h time slot during the week requires 300 GPs to achieve a CI of 1 h, while one measurement per hour requires 100 GPs to obtain the same result. The sample size needed for time-use research based on a time-sampling technique depends on the design and aim of the study. In this paper, we showed how the precision of the measurement of hours worked each week by GPs strongly varied according to the number of GPs included and the frequency of measurements per GP during the week measured. The best balance between both dimensions will depend upon different circumstances, such as the target group and the budget available.

Biocompatible, smooth, plasma-treated nickel-titanium surface--an adequate platform for cell growth.

PubMed

Chrzanowski, W; Szade, J; Hart, A D; Knowles, J C; Dalby, M J

2012-02-01

High nickel content is believed to reduce the number of biomedical applications of nickel-titanium alloy due to the reported toxicity of nickel. The reduction in nickel release and minimized exposure of the cell to nickel can optimize the biocompatibility of the alloy and increase its use in the application where its shape memory effects and pseudoelasticity are particularly useful, e.g., spinal implants. Many treatments have been tried to improve the biocompatibility of Ni-Ti, and results suggest that a native, smooth surface could provide sufficient tolerance, biologically. We hypothesized that the native surface of nickel-titanium supports cell differentiation and insures good biocompatibility. Three types of surface modifications were investigated: thermal oxidation, alkali treatment, and plasma sputtering, and compared with smooth, ground surface. Thermal oxidation caused a drop in surface nickel content, while negligible chemistry changes were observed for plasma-modified samples when compared with control ground samples. In contrast, alkali treatment caused significant increase in surface nickel concentration and accelerated nickel release. Nickel release was also accelerated in thermally oxidized samples at 600 °C, while in other samples it remained at low level. Both thermal oxidation and alkali treatment increased the roughness of the surface, but mean roughness R(a) was significantly greater for the alkali-treated ones. Ground and plasma-modified samples had 'smooth' surfaces with R(a)=4 nm. Deformability tests showed that the adhesion of the surface layers on samples oxidized at 600 °C and alkali treatment samples was not sufficient; the layer delaminated upon deformation. It was observed that the cell cytoskeletons on the samples with a high nickel content or release were less developed, suggesting some negative effects of nickel on cell growth. These effects were observed primarily during initial cell contact with the surface. The most favorable cell responses were observed for ground and plasma-sputtered surfaces. These studies indicated that smooth, plasma-modified surfaces provide sufficient properties for cells to grow. © The Author(s), 2011.

Management Plans Technical Appendix - Phase 1 (Central Puget Sound). Volume 4

DTIC Science & Technology

1988-06-01

measure without substantially more samples and analysis or significantly reducing the desired confidence level . Consequently, the study participants...disposal occurs in ac- (9) An application and a lease fee will be charged at a cordance with permit conditions. Compliance measures rate sufficient to...site are sufficient to characterize the material. The bloassays are a cost effective measure of the biological effects of concern within the disposal

How Important Are 'Entry Effects' in Financial Incentive Programs for Welfare Recipients? Experimental Evidence from the Self-Sufficiency Project. SRDC Working Papers.

ERIC Educational Resources Information Center

Card, David; Robins, Philip K.; Lin, Winston

The Self-Sufficiency Project (SSP) entry effect experiment was designed to measure the effect of the future availability of an earnings supplement on the behavior of newly enrolled income assistance (IA) recipients. It used a classical randomized design. From a sample of 3,315 single parents who recently started a new period of IA, one-half were…

Mass spectrometry-based proteomic analysis of human liver cytochrome(s) P450

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

Shrivas, Kamlesh; Mindaye, Samuel T.; Getie-Kebtie, Melkamu

2013-02-15

The major objective of personalized medicine is to select optimized drug therapies and to a large degree such mission is determined by the expression profiles of cytochrome(s) P450 (CYP). Accordingly, a proteomic case study in personalized medicine is provided by the superfamily of cytochromes P450. Our knowledge about CYP isozyme expression on a protein level is very limited and based exclusively on DNA/mRNA derived data. Such information is not sufficient because transcription and translation events do not lead to correlated levels of expressed proteins. Here we report expression profiles of CYPs in human liver obtained by mass spectrometry (MS)-based proteomicmore » approach. We analyzed 32 samples of human liver microsomes (HLM) of different sexes, ages and ethnicity along with samples of recombinant human CYPs. We have experimentally confirmed that each CYP isozyme can be effectively differentiated by their unique isozyme-specific tryptic peptide(s). Trypsin digestion patterns for almost 30 human CYP isozymes were established. Those findings should assist in selecting tryptic peptides suitable for MS-based quantitation. The data obtained demonstrate remarkable differences in CYP expression profiles. CYP2E1, CYP2C8 and CYP4A11 were the only isozymes found in all HLM samples. Female and pediatric HLM samples revealed much more diverse spectrum of expressed CYPs isozymes compared to male HLM. We have confirmed expression of a number of “rare” CYP (CYP2J2, CYP4B1, CYP4V2, CYP4F3, CYP4F11, CYP8B1, CYP19A1, CYP24A1 and CYP27A1) and obtained first direct experimental data showing expression of such CYPs as CYP2F1, CYP2S1, CYP2W1, CYP4A22, CYP4X1, and CYP26A1 on a protein level. - Highlights: ► First detailed proteomic analysis of CYP isozymes expression in human liver ► Trypsin digestion patterns for almost 30 human CYP isozymes established ► The data obtained demonstrate remarkable differences in CYP expression profiles. ► Female HLM samples revealed more diverse spectrum of CYP isozymes than male. ► First data showing expression of 2F1, 2S1, 2W1, 4A22, 4X1, 26A1 on a protein level.« less

Defense Infrastructure: Improved Guidance Needed for Estimating Alternatively Financed Project Liabilities

DTIC Science & Technology

2013-04-01

auditing standards. Those standards require that we plan and perform the audit to obtain sufficient, appropriate evidence to provide a reasonable basis for...our findings and conclusions based on our audit objectives. We believe that the evidence obtained provides a reasonable basis for our findings and...majority of the project financing is obtained from financial institutions in the form of construction loans or military housing bonds. The servicemembers

An optimal sampling approach to modelling whole-body vibration exposure in all-terrain vehicle driving.

PubMed

Lü, Xiaoshu; Takala, Esa-Pekka; Toppila, Esko; Marjanen, Ykä; Kaila-Kangas, Leena; Lu, Tao

2017-08-01

Exposure to whole-body vibration (WBV) presents an occupational health risk and several safety standards obligate to measure WBV. The high cost of direct measurements in large epidemiological studies raises the question of the optimal sampling for estimating WBV exposures given by a large variation in exposure levels in real worksites. This paper presents a new approach to addressing this problem. A daily exposure to WBV was recorded for 9-24 days among 48 all-terrain vehicle drivers. Four data-sets based on root mean squared recordings were obtained from the measurement. The data were modelled using semi-variogram with spectrum analysis and the optimal sampling scheme was derived. The optimum sampling period was 140 min apart. The result was verified and validated in terms of its accuracy and statistical power. Recordings of two to three hours are probably needed to get a sufficiently unbiased daily WBV exposure estimate in real worksites. The developed model is general enough that is applicable to other cumulative exposures or biosignals. Practitioner Summary: Exposure to whole-body vibration (WBV) presents an occupational health risk and safety standards obligate to measure WBV. However, direct measurements can be expensive. This paper presents a new approach to addressing this problem. The developed model is general enough that is applicable to other cumulative exposures or biosignals.

Orphan radon daughters at Denver Radium site

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

Holub, R.F.; Droullard, R.F.; Davis, T.H.

During 18 mo of sampling airborne radioactively at a National Priority List ({open_quotes}Superfund{close_quotes}) site in metroPOlitan Denver, Bureau of mines personnel discovered radon daughters that are not supported by the parent radon gas. We refer to them as {open_quotes}orphan{close_quotes} daughters because the parent, radon, is not present in sufficient concentration to support the measured daughter products. Measurements of the {open_quotes}orphan{close_quotes} daughters were made continuously, using the Bureau-developed radon and working-level (radon-daughter) monitors. The data showed high equilibrium ratios, ranging from 0.7 to 3.5, for long periods of time. Repeated, high-volume, 15-min grab samples were made, using the modified Tsivoglou method,more » to measure radon daughters, to which thoron daughters contributed 26 {+-} 12%. On average 28 {+-} 6% of the particulate activity was contributed by thoron daughters. Most samples were mixtures in which the {sup 218}Po concentration was lower than that of {sup 214}Pb and {sup 214}Bi, in agreement with the high-equilibrium factors obtained from the continuous sampling data. In view of the short half-life of radon progeny, we conclude that the source of the orphan daughters is not far from the Superfund sites. The mechanism of this phenomenon is not understood at this time, but we will discuss its possible significance in evaluating population doses.« less

Flex-rigid pleuroscopic biopsy with the SB knife Jr is a novel technique for diagnosis of malignant or benign fibrothorax.

PubMed

Wang, Xiao-Bo; Yin, Yan; Miao, Yuan; Eberhardt, Ralf; Hou, Gang; Herth, Felix J; Kang, Jian

2016-11-01

Diagnosing pleural effusion is challenging, especially in patients with malignant or benign fibrothorax, which is difficult to sample using standard flexible forceps (SFF) via flex-rigid pleuroscopy. An adequate sample is crucial for the differential diagnosis of malignant fibrothorax (malignant pleural mesothelioma, metastatic lung carcinoma, etc.) from benign fibrothorax (benign asbestos pleural disease, tuberculous pleuritis, etc.). Novel biopsy techniques are required in flex-rigid pleuroscopy to improve the sample size and quality. The SB knife Jr, which is a scissor forceps that uses a mono-pole high frequency, was developed to allow convenient and accurate resection of larger lesions during endoscopic dissection (ESD). Herein, we report two patients with fibrothorax who underwent a pleural biopsy using an SB knife Jr to investigate the potential use of this tool in flex-rigid pleuroscopy when pleural lesions are difficult to biopsy via SFF. The biopsies were successful, with sufficient size and quality for definitive diagnosis. We also successfully performed adhesiolysis with the SB knife Jr in one case, and adequate biopsies were conducted. No complications were observed. Electrosurgical biopsy with the SB knife Jr during flex-rigid pleuroscopy allowed us to obtain adequate samples for the diagnosis of malignant versus benign fibrothorax, which is usually not possible with SFF. The SB knife Jr also demonstrated a potential use for pleuropulmonary adhesions.

DNA Yield From Tissue Samples in Surgical Pathology and Minimum Tissue Requirements for Molecular Testing.

PubMed

Austin, Melissa C; Smith, Christina; Pritchard, Colin C; Tait, Jonathan F

2016-02-01

Complex molecular assays are increasingly used to direct therapy and provide diagnostic and prognostic information but can require relatively large amounts of DNA. To provide data to pathologists to help them assess tissue adequacy and provide prospective guidance on the amount of tissue that should be procured. We used slide-based measurements to establish a relationship between processed tissue volume and DNA yield by A260 from 366 formalin-fixed, paraffin-embedded tissue samples submitted for the 3 most common molecular assays performed in our laboratory (EGFR, KRAS, and BRAF). We determined the average DNA yield per unit of tissue volume, and we used the distribution of DNA yields to calculate the minimum volume of tissue that should yield sufficient DNA 99% of the time. All samples with a volume greater than 8 mm(3) yielded at least 1 μg of DNA, and more than 80% of samples producing less than 1 μg were extracted from less than 4 mm(3) of tissue. Nine square millimeters of tissue should produce more than 1 μg of DNA 99% of the time. We conclude that 2 tissue cores, each 1 cm long and obtained with an 18-gauge needle, will almost always provide enough DNA for complex multigene assays, and our methodology may be readily extrapolated to individual institutional practice.

Sufficient condition for a finite-time singularity in a high-symmetry Euler flow: Analysis and statistics

NASA Astrophysics Data System (ADS)

Ng, C. S.; Bhattacharjee, A.

1996-08-01

A sufficient condition is obtained for the development of a finite-time singularity in a highly symmetric Euler flow, first proposed by Kida [J. Phys. Soc. Jpn. 54, 2132 (1995)] and recently simulated by Boratav and Pelz [Phys. Fluids 6, 2757 (1994)]. It is shown that if the second-order spatial derivative of the pressure (pxx) is positive following a Lagrangian element (on the x axis), then a finite-time singularity must occur. Under some assumptions, this Lagrangian sufficient condition can be reduced to an Eulerian sufficient condition which requires that the fourth-order spatial derivative of the pressure (pxxxx) at the origin be positive for all times leading up to the singularity. Analytical as well as direct numerical evaluation over a large ensemble of initial conditions demonstrate that for fixed total energy, pxxxx is predominantly positive with the average value growing with the numbers of modes.

Supervision of Ethylene Propylene Diene M-Class (EPDM) Rubber Vulcanization and Recovery Processes Using Attenuated Total Reflection Fourier Transform Infrared (ATR FT-IR) Spectroscopy and Multivariate Analysis.

PubMed

Riba Ruiz, Jordi-Roger; Canals, Trini; Cantero, Rosa

2017-01-01

Ethylene propylene diene monomer (EPDM) rubber is widely used in a diverse type of applications, such as the automotive, industrial and construction sectors among others. Due to its appealing features, the consumption of vulcanized EPDM rubber is growing significantly. However, environmental issues are forcing the application of devulcanization processes to facilitate recovery, which has led rubber manufacturers to implement strict quality controls. Consequently, it is important to develop methods for supervising the vulcanizing and recovery processes of such products. This paper deals with the supervision process of EPDM compounds by means of Fourier transform mid-infrared (FT-IR) spectroscopy and suitable multivariate statistical methods. An expedited and nondestructive classification approach was applied to a sufficient number of EPDM samples with different applied processes, that is, with and without application of vulcanizing agents, vulcanized samples, and microwave treated samples. First the FT-IR spectra of the samples is acquired and next it is processed by applying suitable feature extraction methods, i.e., principal component analysis and canonical variate analysis to obtain the latent variables to be used for classifying test EPDM samples. Finally, the k nearest neighbor algorithm was used in the classification stage. Experimental results prove the accuracy of the proposed method and the potential of FT-IR spectroscopy in this area, since the classification accuracy can be as high as 100%.

Effect of static pressure on absolute paleointensity recording with implications for meteorites

NASA Astrophysics Data System (ADS)

Volk, Michael W. R.; Gilder, Stuart A.

2016-08-01

We investigated the influence of hydrostatic and nonhydrostatic stress on the recording process of magnetic field intensity with particular relevance for meteorites that experienced pressures lower than 5 GPa corresponding to the lowest shock stage classification (S1) in meteorites. Thermal remanent magnetizations were imparted on natural obsidian samples containing pseudo-single domain titanomagnetite, analogous to some achondritic meteorites. Thellier-type paleointensity experiments were carried out at ambient conditions after pressure cycling to 0.6, 1.2, and 1.8 GPa. Each experiment used 10 samples to assess reproducibility, which is better than ±5%. The recorded paleointensity decreased 10%/GPa under hydrostatic stress and 20%/GPa under nonhydrostatic stress, leading to the fundamental conclusion that paleointensity results from meteorites may be appreciably underestimated. Pressure cycling shifts the blocking and unblocking spectra, thereby producing more linear slopes on an Arai diagram with increasing strain. We explain why, for samples with a single magnetization component that does not alter, a two-step paleointensity protocol sufficiently resolves the true paleointensity. Moreover, we propose that pressure cycling of pseudo-single domain bearing samples will remove the inherent curvature of the Arai slope, thereby allowing one to obtain a more accurate estimate of the true paleointensity. This likely also holds true for samples possessing multidomain grains. Conversely, linear trends on Arai plots in meteorites might have their origin in a pressure effect that does not necessarily reflect the ubiquitous presence of single domain particles.

Challenges of DNA-based mark-recapture studies of American black bears

USGS Publications Warehouse

Settlage, K.E.; Van Manen, F.T.; Clark, J.D.; King, T.L.

2008-01-01

We explored whether genetic sampling would be feasible to provide a region-wide population estimate for American black bears (Ursus americanus) in the southern Appalachians, USA. Specifically, we determined whether adequate capture probabilities (p >0.20) and population estimates with a low coefficient of variation (CV <20%) could be achieved given typical agency budget and personnel constraints. We extracted DNA from hair collected from baited barbed-wire enclosures sampled over a 10-week period on 2 study areas: a high-density black bear population in a portion of Great Smoky Mountains National Park and a lower density population on National Forest lands in North Carolina, South Carolina, and Georgia. We identified individual bears by their unique genotypes obtained from 9 microsatellite loci. We sampled 129 and 60 different bears in the National Park and National Forest study areas, respectively, and applied closed mark–recapture models to estimate population abundance. Capture probabilities and precision of the population estimates were acceptable only for sampling scenarios for which we pooled weekly sampling periods. We detected capture heterogeneity biases, probably because of inadequate spatial coverage by the hair-trapping grid. The logistical challenges of establishing and checking a sufficiently high density of hair traps make DNA-based estimates of black bears impractical for the southern Appalachian region. Alternatives are to estimate population size for smaller areas, estimate population growth rates or survival using mark–recapture methods, or use independent marking and recapturing techniques to reduce capture heterogeneity.

Thermo-mechanical characterization of silicone foams

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

Rangaswamy, Partha; Smith, Nickolaus A.; Cady, Carl M.

Cellular solids such as elastomeric foams are used in many structural applications to absorb and dissipate energy, due to their light weight (low density) and high energy absorption capability. In this paper we will discuss foams derived from S5370, a silicone foam formulation developed by Dow Corning. In the application presented, the foam is consolidated into a cushion component of constant thickness but variable density. A mechanical material model developed by Lewis (2013), predicts material response, in part, as a function of relative density. To determine the required parameters for this model we have obtained the mechanical response in compressionmore » for ambient, cold and hot temperatures. The variable density cushion provided samples sufficient samples so that the effect of sample initial density on the mechanical response could be studied. The mechanical response data showed extreme sensitivity to relative density. We also observed at strains corresponding to 1 MPa a linear relationship between strain and initial density for all temperatures. Samples taken from parts with a history of thermal cycling demonstrated a stiffening response that was a function of temperature, with the trend of more stiffness as temperature increased above ambient. This observation is in agreement with the entropic effects on the thermo-mechanical behavior of silicone polymers. In this study, we present the experimental methods necessary for the development of a material model, the testing protocol, analysis of test data, and a discussion of load (stress) and gap (strain) as a function of sample initial densities and temperatures« less

Comparison of Submental Blood Collection with the Retroorbital and Submandibular Methods in Mice (Mus musculus)

PubMed Central

Regan, Rainy D; Fenyk-Melody, Judy E; Tran, Sam M; Chen, Guang; Stocking, Kim L

2016-01-01

Nonterminal blood sample collection of sufficient volume and quality for research is complicated in mice due to their small size and anatomy. Large (>100 μL) nonterminal volumes of unhemolyzed or unclotted blood currently are typically collected from the retroorbital sinus or submandibular plexus. We developed a third method—submental blood collection—which is similar in execution to the submandibular method but with minor changes in animal restraint and collection location. Compared with other techniques, submental collection is easier to perform due to the direct visibility of the target vessels, which are located in a sparsely furred region. Compared with the submandibular method, the submental method did not differ regarding weight change and clotting score but significantly decreased hemolysis and increased the overall number of high-quality samples. The submental method was performed with smaller lancets for the majority of the bleeds, yet resulted in fewer repeat collection attempts, fewer insufficient samples, and less extraneous blood loss and was qualitatively less traumatic. Compared with the retroorbital technique, the submental method was similar regarding weight change but decreased hemolysis, clotting, and the number of overall high-quality samples; however the retroorbital method resulted in significantly fewer incidents of insufficient sample collection. Extraneous blood loss was roughly equivalent between the submental and retroorbital methods. We conclude that the submental method is an acceptable venipuncture technique for obtaining large, nonterminal volumes of blood from mice. PMID:27657712

Local residue coupling strategies by neural network for InSAR phase unwrapping

NASA Astrophysics Data System (ADS)

Refice, Alberto; Satalino, Giuseppe; Chiaradia, Maria T.

1997-12-01

Phase unwrapping is one of the toughest problems in interferometric SAR processing. The main difficulties arise from the presence of point-like error sources, called residues, which occur mainly in close couples due to phase noise. We present an assessment of a local approach to the resolution of these problems by means of a neural network. Using a multi-layer perceptron, trained with the back- propagation scheme on a series of simulated phase images, fashion the best pairing strategies for close residue couples. Results show that god efficiencies and accuracies can have been obtained, provided a sufficient number of training examples are supplied. Results show that good efficiencies and accuracies can be obtained, provided a sufficient number of training examples are supplied. The technique is tested also on real SAR ERS-1/2 tandem interferometric images of the Matera test site, showing a good reduction of the residue density. The better results obtained by use of the neural network as far as local criteria are adopted appear justified given the probabilistic nature of the noise process on SAR interferometric phase fields and allows to outline a specifically tailored implementation of the neural network approach as a very fast pre-processing step intended to decrease the residue density and give sufficiently clean images to be processed further by more conventional techniques.

Adaptive control of turbulence intensity is accelerated by frugal flow sampling.

PubMed

Quinn, Daniel B; van Halder, Yous; Lentink, David

2017-11-01

The aerodynamic performance of vehicles and animals, as well as the productivity of turbines and energy harvesters, depends on the turbulence intensity of the incoming flow. Previous studies have pointed at the potential benefits of active closed-loop turbulence control. However, it is unclear what the minimal sensory and algorithmic requirements are for realizing this control. Here we show that very low-bandwidth anemometers record sufficient information for an adaptive control algorithm to converge quickly. Our online Newton-Raphson algorithm tunes the turbulence in a recirculating wind tunnel by taking readings from an anemometer in the test section. After starting at 9% turbulence intensity, the algorithm converges on values ranging from 10% to 45% in less than 12 iterations within 1% accuracy. By down-sampling our measurements, we show that very-low-bandwidth anemometers record sufficient information for convergence. Furthermore, down-sampling accelerates convergence by smoothing gradients in turbulence intensity. Our results explain why low-bandwidth anemometers in engineering and mechanoreceptors in biology may be sufficient for adaptive control of turbulence intensity. Finally, our analysis suggests that, if certain turbulent eddy sizes are more important to control than others, frugal adaptive control schemes can be particularly computationally effective for improving performance. © 2017 The Author(s).

Composite elastomeric polyurethane scaffolds incorporating small intestinal submucosa for soft tissue engineering.

PubMed

Da, Lincui; Gong, Mei; Chen, Anjing; Zhang, Yi; Huang, Yizhou; Guo, Zhijun; Li, Shengfu; Li-Ling, Jesse; Zhang, Li; Xie, Huiqi

2017-09-01

Although soft tissue replacement has been clinically successful in many cases, the corresponding procedure has many limitations including the lack of resilience and mechanical integrity, significant donor-site morbidity, volume loss with time, and fibrous capsular contracture. These disadvantages can be alleviated by utilizing bio-absorbable scaffolds with high resilience and large strain, which are capable of stimulating natural tissue regeneration. Hence, the chemically crosslinked tridimensional scaffolds obtained by incorporating water-based polyurethane (PU) (which was synthesized from polytetramethylene ether glycol, isophorone diisocyanate, and 2,2-bis(hydroxymethyl) butyric acid) into a bioactive extracellular matrix consisting of small intestinal submucosa (SIS) have been tested in this study to develop a new approach for soft tissue engineering. After characterizing the structure and properties of the produced PU/SIS composites, the strength, Young's modulus, and resilience of wet PU/SIS samples were compared with those of crosslinked PU. In addition, the fabricated specimens were investigated using human umbilical vein endothelial cells to evaluate their ability to enhance cell attachment and proliferation. As a result, the synthesized PU/SIS samples exhibited high resilience and were capable of enhancing cell viability with no evidence of cytotoxicity. Subcutaneous implantation in animals and the subsequent testing conducted after 2, 4, and 8weeks indicated that sound implant integration and vascularization occurred inside the PU/SIS composites, while the presence of SIS promoted cell infiltration, angiogenesis, and ultimately tissue regeneration. The obtained results revealed that the produced PU/SIS composites were characterized by high bioactivity and resilience, and, therefore, could be used for soft tissue engineering applications. Hybrid composites containing synthetic polymers with high mechanical strength and naturally derived components, which create a bio-mimetic environment, are one of the most promising biomaterials. Although synthetic polymer/ECM composites have been previously used for soft tissue repair, their resilience properties were not investigated in sufficient detail, while the development of elastic composites composed of synthetic polymers and ECMs in nontoxic aqueous solutions remains a rather challenging task. In this study, porous PU/SIS composites were fabricated in a non-toxic manner; the obtained materials exhibited sufficient mechanical support, which promote cell growth, angiogenesis, and tissue regeneration. The described method can be adapted for the development of scaffolds with various acellular matrices and subsequently used during the restoration of particular types of tissue. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

ELECTROFISHING DISTANCE AND NUMBER OF SPECIES COLLECTED FROM THREE RAFTABLE WESTERN RIVERS

EPA Science Inventory

A key issue in assessing a fish assemblage at a site is determining a sufficient sampling effort to adequately represent the species in an assemblage. Inadequate effort produces considerable noise in multiple samples at the site or under-represents the species present. Excessiv...

Carotenoid-rich dietary patterns during midlife and subsequent cognitive function.

PubMed

Kesse-Guyot, Emmanuelle; Andreeva, Valentina A; Ducros, Véronique; Jeandel, Claude; Julia, Chantal; Hercberg, Serge; Galan, Pilar

2014-03-14

Carotenoids may help to prevent the ageing of the brain. Previous findings regarding β-carotene alone are not consistent. In the present study, we evaluated the cross-time association between a carotenoid-rich dietary pattern (CDP) and subsequent cognitive performance using a sample of 2983 middle-aged adults participating in the SU.VI.MAX (Supplémentation en Vitamines et Minéraux Antioxydants) study. Cognitive performance was assessed in 2007-9 using six neuropsychological tests, and a composite cognitive score was computed. The cognitive data were related to dietary data obtained by repeated 24 h dietary records (1994-6) and to measurements of baseline plasma concentrations of carotenoids (lutein, zeaxanthin, β-cryptoxanthin, lycopene, α-carotene, trans-β-carotene and cis-β-carotene). DP were extracted using the reduced rank regression method for 381 participants and then extrapolated to the whole sample using plasma carotenoid concentrations as response variables. Associations between a CDP and cognitive function measured 13 years later were estimated with ANCOVA providing mean difference values and 95 % CI across the tertiles of CDP. A correlation between CDP and consumption of orange- and green-coloured fruits and vegetables, vegetable oils and soup was observed. CDP was found to be associated with a higher composite cognitive score (mean difference 1·04, 95 % CI 0·20, 1·87, P for trend 0·02), after adjustment for sociodemographic, lifestyle and health factors. Similar findings were obtained for scores obtained in the cued recall task, backward digit span task, trail making test and semantic fluency task (all P for trend < 0·05). Further studies ought to confirm whether a diet providing sufficient quantity and variety of coloured fruits and vegetables may contribute to the preservation of cognitive function during ageing.

Healing of polymer interfaces: Interfacial dynamics, entanglements, and strength

NASA Astrophysics Data System (ADS)

Ge, Ting; Robbins, Mark O.; Perahia, Dvora; Grest, Gary S.

2014-07-01

Self-healing of polymer films often takes place as the molecules diffuse across a damaged region, above their melting temperature. Using molecular dynamics simulations we probe the healing of polymer films and compare the results with those obtained for thermal welding of homopolymer slabs. These two processes differ from each other in their interfacial structure since damage leads to increased polydispersity and more short chains. A polymer sample was cut into two separate films that were then held together in the melt state. The recovery of the damaged film was followed as time elapsed and polymer molecules diffused across the interface. The mass uptake and formation of entanglements, as obtained from primitive path analysis, are extracted and correlated with the interfacial strength obtained from shear simulations. We find that the diffusion across the interface is significantly faster in the damaged film compared to welding because of the presence of short chains. Though interfacial entanglements increase more rapidly for the damaged films, a large fraction of these entanglements are near chain ends. As a result, the interfacial strength of the healing film increases more slowly than for welding. For both healing and welding, the interfacial strength saturates as the bulk entanglement density is recovered across the interface. However, the saturation strength of the damaged film is below the bulk strength for the polymer sample. At saturation, cut chains remain near the healing interface. They are less entangled and as a result they mechanically weaken the interface. Chain stiffness increases the density of entanglements, which increases the strength of the interface. Our results show that a few entanglements across the interface are sufficient to resist interfacial chain pullout and enhance the mechanical strength.

Testing the use of juvenile Salmo trutta L. as biomonitors of heavy metal pollution in freshwater.

PubMed

Lamas, S; Fernández, J A; Aboal, J R; Carballeira, A

2007-02-01

Individual specimens of Salmo trutta were captured, from four sampling sites in Galician rivers (NW Spain) affected by different types of contamination: diffuse urban waste, run-off from an unrestored dump at a copper mine and waste from a fish farm. The ages of the captured trouts were established and only those belonging to the 1+ age class were selected for study. The liver and kidney were removed from each fish and analysed to determine the tissue concentrations of Cu, Fe and Zn. The results obtained showed that: (i) the use of 1+ individuals allowed differentiation of contamination scenarios on the basis of the tissue concentrations of metal; (ii) the use of 1+ individuals allowed standardization of the time of exposure, which was sufficiently long for differential uptake to have taken place; (iii) liver tissue provided the best results as, less effort was required than for processing kidney tissue, and significant differences between sampling sites were detected because the intrapopulational variability in metal levels was lower than for kidney, and (iv) the levels of elements detected were not affected by basal tissue concentrations or residual concentrations due to past contamination, which older trouts may have been exposed to. In addition, the use of 1+ trout may provide better results in annual environmental sampling surveys.

Combination of LC/TOF-MS and LC/Ion Trap MS/MS for the Identification of Diphenhydramine in Sediment Samples

USGS Publications Warehouse

Ferrer, I.; Heine, C.E.; Thurman, E.M.

2004-01-01

Diphenhydramine (Benadryl) is a popular over-the-counter antihistaminic medication used for the treatment of allergies. After consumption, excretion, and subsequent discharge from wastewater treatment plants, it is possible that diphenhydramine will be found in environmental sediments due to its hydrophobicity (log P = 3.27). This work describes a methodology for the first unequivocal determination of diphenhydramine bound to environmental sediments. The drug is removed from the sediments by accelerated solvent extraction and then analyzed by liquid chromatography with a time-of-flight mass spectrometer and an ion trap mass spectrometer. This combination of techniques provided unequivocal identification and confirmation of diphenhydramine in two sediment samples. The accurate mass measurements of the protonated molecules were m/z 256.1703 and 256.1696 compared to the calculated mass of m/z 256.1701, resulting in errors of 0.8 and 2.3 ppm. This mass accuracy was sufficient to verify the elemental composition of diphenhydramine in each sample. Furthermore, accurate mass measurements of the primary fragment ion were obtained. This work is the first application of time-of-flight mass spectrometry for the identification of diphenhydramine and shows the accumulation of an over-the-counter medication in aquatic sediments at five different locations.

Factors affecting cadmium absorbed by pistachio kernel in calcareous soils, southeast of Iran.

PubMed

Shirani, H; Hosseinifard, S J; Hashemipour, H

2018-03-01

Cadmium (Cd) which does not have a biological role is one of the most toxic heavy metals for organisms. This metal enters environment through industrial processes and fertilizers. The main objective of this study was to determine the relationships between absorbed Cd by pistachio kernel and some of soil physical and chemical characteristics using modeling by stepwise regression and Artificial Neural Network (ANN), in calcareous soils in Rafsanjan region, southeast of Iran. For these purposes, 220 pistachio orchards were selected, and soil samples were taken from two depths of 0-40 and 40-80cm. Besides, fruit and leaf samples from branches with and without fruit were taken in each sampling point. The results showed that affecting factors on absorbed Cd by pistachio kernel which were obtained by regression method (pH and clay percent) were not interpretable, and considering unsuitable vales of determinant coefficient (R 2 ) and Root Mean Squares Error (RMSE), the model did not have sufficient validity. However, ANN modeling was highly accurate and reliable. Based on its results, soil available P and Zn and soil salinity were the most important factors affecting the concentration of Cd in pistachio kernel in pistachio growing areas of Rafsanjan. Copyright © 2017 Elsevier B.V. All rights reserved.

Genome-wide single-nucleotide polymorphism arrays demonstrate high fidelity of multiple displacement-based whole-genome amplification.

PubMed

Tzvetkov, Mladen V; Becker, Christian; Kulle, Bettina; Nürnberg, Peter; Brockmöller, Jürgen; Wojnowski, Leszek

2005-02-01

Whole-genome DNA amplification by multiple displacement (MD-WGA) is a promising tool to obtain sufficient DNA amounts from samples of limited quantity. Using Affymetrix' GeneChip Human Mapping 10K Arrays, we investigated the accuracy and allele amplification bias in DNA samples subjected to MD-WGA. We observed an excellent concordance (99.95%) between single-nucleotide polymorphisms (SNPs) called both in the nonamplified and the corresponding amplified DNA. This concordance was only 0.01% lower than the intra-assay reproducibility of the genotyping technique used. However, MD-WGA failed to amplify an estimated 7% of polymorphic loci. Due to the algorithm used to call genotypes, this was detected only for heterozygous loci. We achieved a 4.3-fold reduction of noncalled SNPs by combining the results from two independent MD-WGA reactions. This indicated that inter-reaction variations rather than specific chromosomal loci reduced the efficiency of MD-WGA. Consistently, we detected no regions of reduced amplification, with the exception of several SNPs located near chromosomal ends. Altogether, despite a substantial loss of polymorphic sites, MD-WGA appears to be the current method of choice to amplify genomic DNA for array-based SNP analyses. The number of nonamplified loci can be substantially reduced by amplifying each DNA sample in duplicate.

Seasonal dynamics of freshwater pathogens as measured by microarray at Lake Sapanca, a drinking water source in the north-eastern part of Turkey.

PubMed

Akçaalan, Reyhan; Albay, Meric; Koker, Latife; Baudart, Julia; Guillebault, Delphine; Fischer, Sabine; Weigel, Wilfried; Medlin, Linda K

2017-12-22

Monitoring drinking water quality is an important public health issue. Two objectives from the 4 years, six nations, EU Project μAqua were to develop hierarchically specific probes to detect and quantify pathogens in drinking water using a PCR-free microarray platform and to design a standardised water sampling program from different sources in Europe to obtain sufficient material for downstream analysis. Our phylochip contains barcodes (probes) that specifically identify freshwater pathogens that are human health risks in a taxonomic hierarchical fashion such that if species is present, the entire taxonomic hierarchy (genus, family, order, phylum, kingdom) leading to it must also be present, which avoids false positives. Molecular tools are more rapid, accurate and reliable than traditional methods, which means faster mitigation strategies with less harm to humans and the community. We present microarray results for the presence of freshwater pathogens from a Turkish lake used drinking water and inferred cyanobacterial cell equivalents from samples concentrated from 40 into 1 L in 45 min using hollow fibre filters. In two companion studies from the same samples, cyanobacterial toxins were analysed using chemical methods and those dates with highest toxin values also had highest cell equivalents as inferred from this microarray study.

Selective solid-phase extraction based on molecularly imprinted technology for the simultaneous determination of 20 triazole pesticides in cucumber samples using high-performance liquid chromatography-tandem mass spectrometry.

PubMed

Zhao, Fengnian; She, Yongxin; Zhang, Chao; Cao, Xiaolin; Wang, Shanshan; Zheng, Lufei; Jin, Maojun; Shao, Hua; Jin, Fen; Wang, Jing

2017-10-01

A selective analytical method for the simultaneous determination of 20 triazole fungicides and plant growth regulators in cucumber samples was developed using solid-phase extraction with specific molecularly imprinted polymers (MIPs) as adsorbents. The MIPs were successfully prepared by precipitation polymerization using triadimefon as the template molecule, methacrylic acid as the functional monomer, trimethylolpropane trimethacrylate as the crosslinker, and acetonitrile as the porogen. The performance and recognition mechanism for both the MIPs and non-molecularly imprinted polymers were evaluated using adsorption isotherms and adsorption kinetics. Liquid chromatography-tandem quadrupole mass spectrometry was used to identify and quantify the target analytes. The solid-phase extraction using the MIPs was rapid, convenient, and efficient for extraction and enrichment of the 20 triazole pesticides from cucumber samples. The recoveries obtained at three concentration levels (1, 2, and 10μgL -1 ) ranged from 82.3% to 117.6% with relative standard deviations of less than 11.8% (n=5) for all analytes. The limits of detection for the 20 triazole pesticides were all less than 0.4μgL -1 , and were sufficient to meet international standards. Copyright © 2017 Elsevier B.V. All rights reserved.

MSX ₁ gene variant and non-syndromic clefting: association or rejection?

PubMed

Reddy, Naveen Admala; Gopinath, Adusumilli; Reddy, Jayaprakash Thirumala; Devanna, Raghu; Saravanan, Pichai; Rohra, Mayur G

2014-01-01

Non-syndromic cleft lip/palate (NSCL/P) is a congenital anomaly with significant medical, psychological and social ramifications. There is sufficient evidence to hypothesize that locus for this condition can be identified by candidate genes. The aim of this study is to amplify the chosen region (799 G >T) of MSX 1 gene, investigate the degree of association and perform a mutation research from Raichur cleft lip and palate patient sample. Case history and clinical examination of the patient were recorded to rule. Written consent was obtained from patients and controls for in vivo study. STUDY WAS DESIGNED IN FOUR STEPS AS FOLLOWS: a. Collection of a blood sample; b. Genomic deoxyribonucleic acid (DNA) extraction; c. Polymerase chain reaction (PCR); d. Restriction fragment length polymorphism (RFLP). Blood samples were collected from 50 subjects having NSCL/P and 50 controls. Genomic DNA was extracted, PCR and RFLP was performed for digestion products that were evaluated. Chi-square test with P value at 95% confidence intervals. The results showed a positive correlation between MSX 1 799 G >T gene variant and NSCL/P patients in Raichur patients. From a genetically diverse etiology MSX 1 799 G >T gene variant may be a good screening marker for NSCL/P in Raichur patients.

Performance of a Heating Block System Designed for Studying the Heat Resistance of Bacteria in Foods

NASA Astrophysics Data System (ADS)

Kou, Xiao-Xi; Li, Rui; Hou, Li-Xia; Huang, Zhi; Ling, Bo; Wang, Shao-Jin

2016-07-01

Knowledge of bacteria’s heat resistance is essential for developing effective thermal treatments. Choosing an appropriate test method is important to accurately determine bacteria’s heat resistances. Although being a major factor to influence the thermo-tolerance of bacteria, the heating rate in samples cannot be controlled in water or oil bath methods due to main dependence on sample’s thermal properties. A heating block system (HBS) was designed to regulate the heating rates in liquid, semi-solid and solid foods using a temperature controller. Distilled water, apple juice, mashed potato, almond powder and beef were selected to evaluate the HBS’s performance by experiment and computer simulation. The results showed that the heating rates of 1, 5 and 10 °C/min with final set-point temperatures and holding times could be easily and precisely achieved in five selected food materials. A good agreement in sample central temperature profiles was obtained under various heating rates between experiment and simulation. The experimental and simulated results showed that the HBS could provide a sufficiently uniform heating environment in food samples. The effect of heating rate on bacterial thermal resistance was evaluated with the HBS. The system may hold potential applications for rapid and accurate assessments of bacteria’s thermo-tolerances.

Venus, Mars, and the ices on Mercury and the moon: astrobiological implications and proposed mission designs.

PubMed

Schulze-Makuch, Dirk; Dohm, James M; Fairén, Alberto G; Baker, Victor R; Fink, Wolfgang; Strom, Robert G

2005-12-01

Venus and Mars likely had liquid water bodies on their surface early in the Solar System history. The surfaces of Venus and Mars are presently not a suitable habitat for life, but reservoirs of liquid water remain in the atmosphere of Venus and the subsurface of Mars, and with it also the possibility of microbial life. Microbial organisms may have adapted to live in these ecological niches by the evolutionary force of directional selection. Missions to our neighboring planets should therefore be planned to explore these potentially life-containing refuges and return samples for analysis. Sample return missions should also include ice samples from Mercury and the Moon, which may contain information about the biogenic material that catalyzed the early evolution of life on Earth (or elsewhere). To obtain such information, science-driven exploration is necessary through varying degrees of mission operation autonomy. A hierarchical mission design is envisioned that includes spaceborne (orbital), atmosphere (airborne), surface (mobile such as rover and stationary such as lander or sensor), and subsurface (e.g., ground-penetrating radar, drilling, etc.) agents working in concert to allow for sufficient mission safety and redundancy, to perform extensive and challenging reconnaissance, and to lead to a thorough search for evidence of life and habitability.

Characterisation of the aerobic bacterial flora of boid snakes: application of MALDI-TOF mass spectrometry.

PubMed

Plenz, Bastian; Schmidt, Volker; Grosse-Herrenthey, Anke; Krüger, Monika; Pees, Michael

2015-03-14

The aim of this study was to identify aerobic bacterial isolates from the respiratory tract of boids with matrix-assisted laser desorption ionisation-time-of-flight mass spectrometry (MALDI-TOF MS). From 47 boid snakes, swabs from the oral cavity, tracheal wash samples and, in cases in which postmortem examination was performed, pulmonary tissue samples were taken. Each snake was classified as having inflammation of the respiratory tract and/or oral cavity, or without evidence of inflammation based on combination of clinical, cytological and histopathological findings. Samples collected from the respiratory tract and oral cavity were inoculated onto routine media and bacteria were cultured aerobically. All morphologically distinct individual colonies obtained were analysed using MALDI-TOF MS. Unidentified isolates detected in more than three snakes were selected for further 16S rDNA PCR and sequencing. Among all examined isolates (n=243), 49 per cent (n=119) could be sufficiently speciated using MALDI-TOF MS. Molecular biology revealed several bacterial species that have not been previously described in reptiles. With an average of 6.3 different isolates from the respiratory tract and/or oral cavity, boids with inflammatory disease harboured significantly more bacterial species than boids without inflammatory disease (average 2.8 isolates). British Veterinary Association.

Circulation of Coxiella burnetii in a Naturally Infected Flock of Dairy Sheep: Shedding Dynamics, Environmental Contamination, and Genotype Diversity

PubMed Central

Joulié, A.; Laroucau, K.; Bailly, X.; Prigent, M.; Gasqui, P.; Lepetitcolin, E.; Blanchard, B.; Rousset, E.; Sidi-Boumedine, K.

2015-01-01

Q fever is a worldwide zoonosis caused by Coxiella burnetii. Domestic ruminants are considered to be the main reservoir. Sheep, in particular, may frequently cause outbreaks in humans. Because within-flock circulation data are essential to implementing optimal management strategies, we performed a follow-up study of a naturally infected flock of dairy sheep. We aimed to (i) describe C. burnetii shedding dynamics by sampling vaginal mucus, feces, and milk, (ii) assess circulating strain diversity, and (iii) quantify barn environmental contamination. For 8 months, we sampled vaginal mucus and feces every 3 weeks from aborting and nonaborting ewes (n = 11 and n = 26, respectively); for lactating females, milk was obtained as well. We also sampled vaginal mucus from nine ewe lambs. Dust and air samples were collected every 3 and 6 weeks, respectively. All samples were screened using real-time PCR, and strongly positive samples were further analyzed using quantitative PCR. Vaginal and fecal samples with sufficient bacterial burdens were then genotyped by multiple-locus variable-number tandem-repeat analysis (MLVA) using 17 markers. C. burnetii burdens were higher in vaginal mucus and feces than in milk, and they peaked in the first 3 weeks postabortion or postpartum. Primiparous females and aborting females tended to shed C. burnetii longer and have higher bacterial burdens than nonaborting and multiparous females. Six genotype clusters were identified; they were independent of abortion status, and within-individual genotype diversity was observed. C. burnetii was also detected in air and dust samples. Further studies should determine whether the within-flock circulation dynamics observed here are generalizable. PMID:26253679

Impact of sample collection participation on the validity of estimated measures of association in the National Birth Defects Prevention Study when assessing gene-environment interactions.

PubMed

Jenkins, Mary M; Reefhuis, Jennita; Herring, Amy H; Honein, Margaret A

2017-12-01

To better understand the impact that nonresponse for specimen collection has on the validity of estimates of association, we examined associations between self-reported maternal periconceptional smoking, folic acid use, or pregestational diabetes mellitus and six birth defects among families who did and did not submit buccal cell samples for DNA following a telephone interview as part of the National Birth Defects Prevention Study (NBDPS). Analyses included control families with live born infants who had no birth defects (N = 9,465), families of infants with anorectal atresia or stenosis (N = 873), limb reduction defects (N = 1,037), gastroschisis (N = 1,090), neural tube defects (N = 1,764), orofacial clefts (N = 3,836), or septal heart defects (N = 4,157). Estimated dates of delivery were between 1997 and 2009. For each exposure and birth defect, odds ratios and 95% confidence intervals were calculated using logistic regression stratified by race-ethnicity and sample collection status. Tests for interaction were applied to identify potential differences between estimated measures of association based on sample collection status. Significant differences in estimated measures of association were observed in only four of 48 analyses with sufficient sample sizes. Despite lower than desired participation rates in buccal cell sample collection, this validation provides some reassurance that the estimates obtained for sample collectors and noncollectors are comparable. These findings support the validity of observed associations in gene-environment interaction studies for the selected exposures and birth defects among NBDPS participants who submitted DNA samples. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

Structural Properties and Estimation of Delay Systems. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Kwong, R. H. S.

1975-01-01

Two areas in the theory of delay systems were studied: structural properties and their applications to feedback control, and optimal linear and nonlinear estimation. The concepts of controllability, stabilizability, observability, and detectability were investigated. The property of pointwise degeneracy of linear time-invariant delay systems is considered. Necessary and sufficient conditions for three dimensional linear systems to be made pointwise degenerate by delay feedback were obtained, while sufficient conditions for this to be possible are given for higher dimensional linear systems. These results were applied to obtain solvability conditions for the minimum time output zeroing control problem by delay feedback. A representation theorem is given for conditional moment functionals of general nonlinear stochastic delay systems, and stochastic differential equations are derived for conditional moment functionals satisfying certain smoothness properties.

Thermographic analysis of waveguide-irradiated insect pupae

NASA Astrophysics Data System (ADS)

Olsen, Richard G.; Hammer, Wayne C.

1982-01-01

Pupae of the insect Tenebrio molitor L. were thermographically imaged during waveguide irradiation through longitudinal slots. T. molitor pupae have been subjects of microwave-induced teratology for a number of years, but until now the smallness of the insect has prevented detailed dosimetry. High-resolution thermographic imaging equipment was used to obtain the magnitude and spatial distribution of absorbed microwave energy at three frequencies, 1.3, 5.95, and 10 GHz. The detail of the thermal images obtained is sufficient to show the differential heating of structures as small as a single insect leg. Results show that the electrical properties of the head, thorax, and abdomen are sufficiently different to seriously impair the usefulness of any theoretical dosimetric model of homogeneous composition. Some general features of correlation with a slab model in waveguide are given.

Second-order data obtained by beta-cyclodextrin complexes: a novel approach for multicomponent analysis with three-way multivariate calibration methods.

PubMed

Khani, Rouhollah; Ghasemi, Jahan B; Shemirani, Farzaneh

2014-10-01

This research reports the first application of β-cyclodextrin (β-CD) complexes as a new method for generation of three way data, combined with second-order calibration methods for quantification of a binary mixture of caffeic (CA) and vanillic (VA) acids, as model compounds in fruit juices samples. At first, the basic experimental parameters affecting the formation of inclusion complexes between target analytes and β-CD were investigated and optimized. Then under the optimum conditions, parallel factor analysis (PARAFAC) and bilinear least squares/residual bilinearization (BLLS/RBL) were applied for deconvolution of trilinear data to get spectral and concentration profiles of CA and VA as a function of β-CD concentrations. Due to severe concentration profile overlapping between CA and VA in β-CD concentration dimension, PARAFAC could not be successfully applied to the studied samples. So, BLLS/RBL performed better than PARAFAC. The resolution of the model compounds was possible due to differences in the spectral absorbance changes of the β-CD complexes signals of the investigated analytes, opening a new approach for second-order data generation. The proposed method was validated by comparison with a reference method based on high-performance liquid chromatography photodiode array detection (HPLC-PDA), and no significant differences were found between the reference values and the ones obtained with the proposed method. Such a chemometrics-based protocol may be a very promising tool for more analytical applications in real samples monitoring, due to its advantages of simplicity, rapidity, accuracy, sufficient spectral resolution and concentration prediction even in the presence of unknown interferents. Copyright © 2014 Elsevier B.V. All rights reserved.

Generalized bipartite quantum state discrimination problems with sequential measurements

NASA Astrophysics Data System (ADS)

Nakahira, Kenji; Kato, Kentaro; Usuda, Tsuyoshi Sasaki

2018-02-01

We investigate an optimization problem of finding quantum sequential measurements, which forms a wide class of state discrimination problems with the restriction that only local operations and one-way classical communication are allowed. Sequential measurements from Alice to Bob on a bipartite system are considered. Using the fact that the optimization problem can be formulated as a problem with only Alice's measurement and is convex programming, we derive its dual problem and necessary and sufficient conditions for an optimal solution. Our results are applicable to various practical optimization criteria, including the Bayes criterion, the Neyman-Pearson criterion, and the minimax criterion. In the setting of the problem of finding an optimal global measurement, its dual problem and necessary and sufficient conditions for an optimal solution have been widely used to obtain analytical and numerical expressions for optimal solutions. Similarly, our results are useful to obtain analytical and numerical expressions for optimal sequential measurements. Examples in which our results can be used to obtain an analytical expression for an optimal sequential measurement are provided.

Assessment of Fine Needle Aspiration Feasibility and Specimen Adequacy for Molecular Diagnostics of Benign Vocal Fold Lesions

PubMed Central

Li, Nicole Y. K.; Dailey, Seth; Thibeault, Susan L.

2014-01-01

Objectives/Hypothesis The use of molecular testing is becoming more significant for the diagnosis and classification of disease. The application of fine-needle aspiration (FNA) biopsy as the means of sampling lesions in union with molecular testing could be a powerful combination in laryngology. The objectives of this study were to investigate 1) if FNA was feasible to sample benign vocal fold lesions; 2) if FNA samples provided sufficient RNA quality for molecular analysis; and 3) if gene expression of FNA samples matched paired surgical excised specimens. Study Design Prospective cross-sectional. Methods Fifteen vocal fold specimens were obtained from adult patients undergoing routine surgical removal for benign vocal fold lesions using FNA and surgical excision. Comparisons were made between FNA and excision biopsies for RNA quality. Correlative analysis was completed for RNA expression of nine genes, including decorin (DCN), connective tissue growth factor (CTGF), vascular endothelial growth factor (VEGF), collagen type VI alpha 3 (COL6A3), superoxide dismutase 1 (SOD1), glutathione S-transferase (GST2), collagen type I alpha 2 (COL1A2), ATP binding cassette (ABC), and procollagen I alpha 1 (COL1A1). Results FNA and excision samples demonstrated similar RNA quality (P > 0.05). Per gene expression, four out of nine genes were moderately correlated between the paired samples (P < 0.05). Conclusions FNA of the vocal fold lamina propria is technically feasible to perform. Further improvement in the FNA technology is desirable to optimize RNA quality for reliable gene expression analysis. PMID:23404571

Conservation genetics of maned wolves in a highly impacted area of the Brazilian Cerrado biome.

PubMed

Lion, Marília Bruzzi; Eizirik, Eduardo; Garda, Adrian Antonio; Fontoura-Rodrigues, Manoel Ludwig da; Rodrigues, Flávio Henrique Guimarães; Marinho-Filho, Jader Soares

2011-03-01

Maned wolves are large canids currently considered vulnerable to extinction due to habitat loss. They are still commonly found within the urban mesh inside the Brazilian Federal District (Distrito Federal--DF), in nearby Protected Areas (PAs), and in surrounding farms. We evaluated the genetic diversity of maned wolves in three PAs of the DF, using both invasive and noninvasive techniques to obtain DNA that was later amplified for five microsatellite markers. We sampled 23 wolves: 10 with the noninvasive method, three captured in traps, six road-killed, and four rescued in urban areas. In Águas Emendadas Ecological Station (ESECAE) we also used samples from six specimens captured between 1997 and 1998 for a temporal comparison. For maned wolves, non-invasive techniques are affordable and easier to conduct in the field, while laboratory costs are much lower for invasive samples. Hence, a sampling strategy combining both techniques may provide an interesting approach for molecular ecology studies requiring comprehensive coverage of local individuals. On the basis of such integrated sampling scheme, our analyses indicated that none of the investigated populations currently present deviations from Hardy-Weinberg expectations or indication of inbreeding. Furthermore, in ESECAE there was no reduction in genetic diversity during the last 9 years. Overall, maned wolves did not present evidence of genetic structuring among the three sampled PAs. These results thus indicate that individual exchange among PAs is still occurring at sufficient rates to avoid differentiation, and/or that the recent fragmentation in the region has not yet produced measurable effects in the genetic diversity of maned wolves.