A Radio-Map Automatic Construction Algorithm Based on Crowdsourcing

PubMed Central

Yu, Ning; Xiao, Chenxian; Wu, Yinfeng; Feng, Renjian

2016-01-01

Traditional radio-map-based localization methods need to sample a large number of location fingerprints offline, which requires huge amount of human and material resources. To solve the high sampling cost problem, an automatic radio-map construction algorithm based on crowdsourcing is proposed. The algorithm employs the crowd-sourced information provided by a large number of users when they are walking in the buildings as the source of location fingerprint data. Through the variation characteristics of users’ smartphone sensors, the indoor anchors (doors) are identified and their locations are regarded as reference positions of the whole radio-map. The AP-Cluster method is used to cluster the crowdsourced fingerprints to acquire the representative fingerprints. According to the reference positions and the similarity between fingerprints, the representative fingerprints are linked to their corresponding physical locations and the radio-map is generated. Experimental results demonstrate that the proposed algorithm reduces the cost of fingerprint sampling and radio-map construction and guarantees the localization accuracy. The proposed method does not require users’ explicit participation, which effectively solves the resource-consumption problem when a location fingerprint database is established. PMID:27070623

Reference Intervals of Common Clinical Chemistry Analytes for Adults in Hong Kong.

PubMed

Lo, Y C; Armbruster, David A

2012-04-01

Defining reference intervals is a major challenge because of the difficulty in recruiting volunteers to participate and testing samples from a significant number of healthy reference individuals. Historical literature citation intervals are often suboptimal because they're be based on obsolete methods and/or only a small number of poorly defined reference samples. Blood donors in Hong Kong gave permission for additional blood to be collected for reference interval testing. The samples were tested for twenty-five routine analytes on the Abbott ARCHITECT clinical chemistry system. Results were analyzed using the Rhoads EP evaluator software program, which is based on the CLSI/IFCC C28-A guideline, and defines the reference interval as the 95% central range. Method specific reference intervals were established for twenty-five common clinical chemistry analytes for a Chinese ethnic population. The intervals were defined for each gender separately and for genders combined. Gender specific or combined gender intervals were adapted as appropriate for each analyte. A large number of healthy, apparently normal blood donors from a local ethnic population were tested to provide current reference intervals for a new clinical chemistry system. Intervals were determined following an accepted international guideline. Laboratories using the same or similar methodologies may adapt these intervals if deemed validated and deemed suitable for their patient population. Laboratories using different methodologies may be able to successfully adapt the intervals for their facilities using the reference interval transference technique based on a method comparison study.

40 CFR Appendix O to Part 50 - Reference Method for the Determination of Coarse Particulate Matter as PM10-2.5 in the Atmosphere

Code of Federal Regulations, 2010 CFR

2010-07-01

....5 sample collection filter is weighed (after moisture and temperature conditioning) before and after... ambient temperature and pressure and the sampling time. The mass concentrations of both PM10c and PM2.5 in... in micrograms per cubic meter (µg/m3)at local temperature and pressure conditions. The mass...

Molecular Identification of Commercialized Medicinal Plants in Southern Morocco

PubMed Central

Krüger, Åsa; Rydberg, Anders; Abbad, Abdelaziz; Björk, Lars; Martin, Gary

2012-01-01

Background Medicinal plant trade is important for local livelihoods. However, many medicinal plants are difficult to identify when they are sold as roots, powders or bark. DNA barcoding involves using a short, agreed-upon region of a genome as a unique identifier for species– ideally, as a global standard. Research Question What is the functionality, efficacy and accuracy of the use of barcoding for identifying root material, using medicinal plant roots sold by herbalists in Marrakech, Morocco, as a test dataset. Methodology In total, 111 root samples were sequenced for four proposed barcode regions rpoC1, psbA-trnH, matK and ITS. Sequences were searched against a tailored reference database of Moroccan medicinal plants and their closest relatives using BLAST and Blastclust, and through inference of RAxML phylograms of the aligned market and reference samples. Principal Findings Sequencing success was high for rpoC1, psbA-trnH, and ITS, but low for matK. Searches using rpoC1 alone resulted in a number of ambiguous identifications, indicating insufficient DNA variation for accurate species-level identification. Combining rpoC1, psbA-trnH and ITS allowed the majority of the market samples to be identified to genus level. For a minority of the market samples, the barcoding identification differed significantly from previous hypotheses based on the vernacular names. Conclusions/Significance Endemic plant species are commercialized in Marrakech. Adulteration is common and this may indicate that the products are becoming locally endangered. Nevertheless the majority of the traded roots belong to species that are common and not known to be endangered. A significant conclusion from our results is that unknown samples are more difficult to identify than earlier suggested, especially if the reference sequences were obtained from different populations. A global barcoding database should therefore contain sequences from different populations of the same species to assure the reference sequences characterize the species throughout its distributional range. PMID:22761800

Collaboration of general practitioners and exercise providers in promotion of physical activity a written survey among general practitioners.

PubMed

Leemrijse, C J; de Bakker, D H; Ooms, L; Veenhof, C

2015-08-06

General practitioners have an ideal position to motivate inactive patients to increase their physical activity. Most patients are able to exercise in regular local facilities outside the health care setting. The purpose of this study was to get insight into general practitioners perceptions and current practices regarding referral of patients to local exercise facilities. Furthermore, collaboration with exercise providers in the community was investigated, and motivators and barriers for referral. A written questionnaire sent to a representative random sample of 800 Dutch general practitioners. Descriptive statistics and Chi(2) tests were used. All responding general practitioners (340) recommend their patients to take more exercise when necessary and 87 % say to refer patients sometimes. Limited motivation of the patient (44 %) and reduced health status (34 %) are the most mentioned barriers for advising patients to increase physical activity. When referred, most patients are send to a physical therapist (69 %) but also local exercise facilities were mentioned (54 %). The most important barrier for referring patients to local exercise activities are patients limited financial possibilities (46 %). Restricted knowledge of local exercise- or sport facilities was an additional barrier (19 %). There is little structural collaboration between general practitioners and exercise providers, but when collaboration exists general practitioners refer more often. Positive experiences of patients (67 %), affordable offers (59 %) and information of local exercise facilities (46 %) are seen as important promoting factors for referral. Although 32 % of the general practitioners think that good collaboration would be stimulating, regular meetings with sports and exercise providers were considered the least important for increasing referral (3 %). Dutch physicians have a positive attitude towards stimulating physical activity but referral to local exercise facilities is low. Referral is partly hindered by restricted knowledge of local exercise facilities. Although general practitioners think that collaboration is important for physical activity promotion, it should not cost them much extra time. A coordinator with knowledge of the local situation can facilitate contacts between GP practices and sports providers.

Method and apparatus for detecting a desired behavior in digital image data

DOEpatents

Kegelmeyer, Jr., W. Philip

1997-01-01

A method for detecting stellate lesions in digitized mammographic image data includes the steps of prestoring a plurality of reference images, calculating a plurality of features for each of the pixels of the reference images, and creating a binary decision tree from features of randomly sampled pixels from each of the reference images. Once the binary decision tree has been created, a plurality of features, preferably including an ALOE feature (analysis of local oriented edges), are calculated for each of the pixels of the digitized mammographic data. Each of these plurality of features of each pixel are input into the binary decision tree and a probability is determined, for each of the pixels, corresponding to the likelihood of the presence of a stellate lesion, to create a probability image. Finally, the probability image is spatially filtered to enforce local consensus among neighboring pixels and the spatially filtered image is output.

Method and apparatus for detecting a desired behavior in digital image data

DOEpatents

Kegelmeyer, Jr., W. Philip

1997-01-01

A method for detecting stellate lesions in digitized mammographic image data includes the steps of prestoring a plurality of reference images, calculating a plurality of features for each of the pixels of the reference images, and creating a binary decision tree from features of randomly sampled pixels from each of the reference images. Once the binary decision tree has been created, a plurality of features, preferably including an ALOE feature (analysis of local oriented edges), are calculated for each of the pixels of the digitized mammographic data. Each of these plurality of features of each pixel are input into the binary decision tree and a probability is determined, for each of the pixels, corresponding to the likelihood of the presence of a stellate lesion, to create a probability image. Finally, the probability image is spacially filtered to enforce local consensus among neighboring pixels and the spacially filtered image is output.

Development of a new integrated local trajectory planning and tracking control framework for autonomous ground vehicles

NASA Astrophysics Data System (ADS)

Li, Xiaohui; Sun, Zhenping; Cao, Dongpu; Liu, Daxue; He, Hangen

2017-03-01

This study proposes a novel integrated local trajectory planning and tracking control (ILTPTC) framework for autonomous vehicles driving along a reference path with obstacles avoidance. For this ILTPTC framework, an efficient state-space sampling-based trajectory planning scheme is employed to smoothly follow the reference path. A model-based predictive path generation algorithm is applied to produce a set of smooth and kinematically-feasible paths connecting the initial state with the sampling terminal states. A velocity control law is then designed to assign a speed value at each of the points along the generated paths. An objective function considering both safety and comfort performance is carefully formulated for assessing the generated trajectories and selecting the optimal one. For accurately tracking the optimal trajectory while overcoming external disturbances and model uncertainties, a combined feedforward and feedback controller is developed. Both simulation analyses and vehicle testing are performed to verify the effectiveness of the proposed ILTPTC framework, and future research is also briefly discussed.

DNA Identification of Commingled Human Remains from the Cemetery Relocated by Flooding in Central Bosnia and Herzegovina.

PubMed

Čakar, Jasmina; Pilav, Amela; Džehverović, Mirela; Ahatović, Anesa; Haverić, Sanin; Ramić, Jasmin; Marjanović, Damir

2018-01-01

The floods in Bosnia and Herzegovina in May 2014 caused landslides all over the country. In the small village of Šerići, near the town of Zenica, a landslide destroyed the local cemetery, relocated graves, and commingled skeletal remains. As the use of other physical methods of identification (facial recognition, fingerprint analysis, dental analysis, etc.) was not possible, DNA analysis was applied. DNA was isolated from 20 skeletal remains (bone and tooth samples) and six reference samples (blood from living relatives) and amplified using PowerPlex ® Fusion and PowerPlex ® Y23 kits. DNA profiles were generated for all reference samples and 17 skeletal remains. A statistical analysis (calculation of paternity, maternity, and sibling indexes and matching probabilities) resulted in 10 positive identifications. In this study, 5 individuals were identified based on one reference sample. This has once again demonstrated the significance of DNA analysis in resolving the most complicated cases, such as the identification of commingled human skeletal remains. © 2017 American Academy of Forensic Sciences.

Deep-Reaching Hydrodynamic Flow Confinement: Micrometer-Scale Liquid Localization for Open Substrates With Topographical Variations.

PubMed

Oskooei, Ali; Kaigala, Govind V

2017-06-01

We present a method for nonintrusive localization and reagent delivery on immersed biological samples with topographical variation on the order of hundreds of micrometers. Our technique, which we refer to as the deep-reaching hydrodynamic flow confinement (DR-HFC), is simple and passive: it relies on a deep-reaching hydrodynamic confinement delivered through a simple microfluidic probe design to perform localized microscale alterations on substrates as deep as 600 μm. Designed to scan centimeter-scale areas of biological substrates, our method passively prevents sample intrusion by maintaining a large gap between the probe and the substrate. The gap prevents collision of the probe and the substrate and reduces the shear stress experienced by the sample. We present two probe designs: linear and annular DR-HFC. Both designs comprise a reagent-injection aperture and aspiration apertures that serve to confine the reagent. We identify the design parameters affecting reagent localization and depth by DR-HFC and study their individual influence on the operation of DR-HFC numerically. Using DR-HFC, we demonstrate localized binding of antihuman immunoglobulin G (IgG) onto an activated substrate at various depths from 50 to 600 μm. DR-HFC provides a readily implementable approach for noninvasive processing of biological samples applicable to the next generation of diagnostic and bioanalytical devices.

Teaching the Rules of Debit and Credit

ERIC Educational Resources Information Center

Potts, Andrew J.

1974-01-01

A fundamental method of explaining the basic accounting principles and concepts (debit, credit, basic accounting equation) which includes visual aids, reference to local businesses, and drill, does much toward increasing the student's skill and enhancing his understanding of the subject matter. (Sample transparencies are included.) (Author/AJ)

VizieR Online Data Catalog: Local Swift-BAT AGN observed with Herschel (Lutz+, 2018)

NASA Astrophysics Data System (ADS)

Lutz, D.; Shimizu, T.; Davies, R. I.; Herrera Camus, R.; Sturm, E.; Tacconi, L. J.; Veilleux, S.

2017-09-01

Table A.1 lists the basic properties of the BAT AGN and reference samples, and the derived far-infrared sizes. For guidance, part of the table and related notes are also included in an appendix to the paper. (1 data file).

A Modified Content Analysis of Existing School Psychology Reports

ERIC Educational Resources Information Center

Mallin, Barry; Schellenberg, Miriam E.; Smith, Christiane

2012-01-01

Discrepancies between our university's training program's report-writing guidelines and common practice in Manitoba could not be resolved by reference to the literature. To inform the discussion, we collected a sample of local real world school psychology reports and undertook a modified content analysis to operationally define and measure…

Preference and Utilities for Prostate Cancer Screening and Treatment: Assessment of the Underlying Decision Making Process

DTIC Science & Technology

2005-01-01

Watkins-Bruner, Deborah radio advertisements was overwhelming! In between radio ads we continued to recruit through outreach activities and advertising ...in local newspapers. E. Conclusions: Radio advertisement has proved to be a very effective media for recruitment of our control sample. F. References

A Planning Guide for Instructional Networks, Part I.

ERIC Educational Resources Information Center

Daly, Kevin F.

1994-01-01

Discusses three phases in implementing a master plan for a school-based local area network (LAN): (1) network software selection; (2) hardware selection, network topology, and site preparation; and (3) implementation time table. Sample planning and specification worksheets and a list of planning guides are included. (Contains six references.) (KRN)

Do You Have a Crisis Management Plan?

ERIC Educational Resources Information Center

Pleviak, Walter; Milkevitch, Frank

2001-01-01

Although certain crises cannot be prevented, reactions to many can be planned. A crisis-management team should be organized for each building. Critical crisis-plan elements include telephone trees, forms, reference articles, sample letters, and processes for dealing with local media. Spokespersons should have facts straight before speaking. (MLH)

“Direct” Gas-phase Metallicity in Local Analogs of High-redshift Galaxies: Empirical Metallicity Calibrations for High-redshift Star-forming Galaxies

NASA Astrophysics Data System (ADS)

Bian, Fuyan; Kewley, Lisa J.; Dopita, Michael A.

2018-06-01

We study the direct gas-phase oxygen abundance using the well-detected auroral line [O III]λ4363 in the stacked spectra of a sample of local analogs of high-redshift galaxies. These local analogs share the same location as z ∼ 2 star-forming galaxies on the [O III]λ5007/Hβ versus [N II]λ6584/Hα Baldwin–Phillips–Terlevich diagram. This type of analog has the same ionized interstellar medium (ISM) properties as high-redshift galaxies. We establish empirical metallicity calibrations between the direct gas-phase oxygen abundances (7.8< 12+{log}({{O}}/{{H}})< 8.4) and the N2 (log([N II]λ6584/Hα))/O3N2 (log(([O III]λ5007/Hβ)/([N II]λ6584/Hα))) indices in our local analogs. We find significant systematic offsets between the metallicity calibrations for our local analogs of high-redshift galaxies and those derived from the local H II regions and a sample of local reference galaxies selected from the Sloan Digital Sky Survey (SDSS). The N2 and O3N2 metallicities will be underestimated by 0.05–0.1 dex relative to our calibration, if one simply applies the local metallicity calibration in previous studies to high-redshift galaxies. Local metallicity calibrations also cause discrepancies of metallicity measurements in high-redshift galaxies using the N2 and O3N2 indicators. In contrast, our new calibrations produce consistent metallicities between these two indicators. We also derive metallicity calibrations for R23 (log(([O III]λλ4959,5007+[O II]λλ3726,3729)/Hβ)), O32(log([O III]λλ4959,5007/[O II]λλ3726,3729)), {log}([O III]λ5007/Hβ), and log([Ne III]λ3869/[O II]λ3727) indices in our local analogs, which show significant offset compared to those in the SDSS reference galaxies. By comparing with MAPPINGS photoionization models, the different empirical metallicity calibration relations in the local analogs and the SDSS reference galaxies can be shown to be primarily due to the change of ionized ISM conditions. Assuming that temperature structure variations are minimal and ISM conditions do not change dramatically from z ∼ 2 to z ∼ 5, these empirical calibrations can be used to measure relative metallicities in galaxies with redshifts up to z ∼ 5.0 in ground-based observations.

Standard wool fabric as a reference material. [for fire toxicity tests

NASA Technical Reports Server (NTRS)

Hilado, C. J.; Cumming, H. J.

1977-01-01

Standard wool fabric is investigated as a potential reference material. A screening test method for relative toxicity exposes four albino male rats enclosed in a 4.2 liter hemispherical chamber to pyrolysis effluents produced by pyrolyzing a 1.00 g sample under a variety of test conditions (200-800 C with a 40 C/min heating rate). It is found that for fabrics containing 86-100% wool, animal response remains virtually unchanged, although a 100% wool fabric is preferred as it eliminates local composition differences as a source of variation.

Method for outlier detection: a tool to assess the consistency between laboratory data and ultraviolet-visible absorbance spectra in wastewater samples.

PubMed

Zamora, D; Torres, A

2014-01-01

Reliable estimations of the evolution of water quality parameters by using in situ technologies make it possible to follow the operation of a wastewater treatment plant (WWTP), as well as improving the understanding and control of the operation, especially in the detection of disturbances. However, ultraviolet (UV)-Vis sensors have to be calibrated by means of a local fingerprint laboratory reference concentration-value data-set. The detection of outliers in these data-sets is therefore important. This paper presents a method for detecting outliers in UV-Vis absorbances coupled to water quality reference laboratory concentrations for samples used for calibration purposes. Application to samples from the influent of the San Fernando WWTP (Medellín, Colombia) is shown. After the removal of outliers, improvements in the predictability of the influent concentrations using absorbance spectra were found.

Radiometric dates from Alaska: A 1975 compilation

USGS Publications Warehouse

Turner, D.L.; Grybeck, Donald; Wilson, Frederic H.

1975-01-01

The following table of radiometric dates from Alaska includes published material through 1972 as well as some selected later data. The table includes 726 mineral and whole-rock dates determined by the K-Ar, Rb-Sr, fission-track U-Pb, and Pb-alpha techniques.The data are organized in alphabetical order of the 1:250,000 scale quadrangles in which the dated rocks are located. The latitude and longitude of each sample are given. In addition, each sample is located on a 1:250,000 quadrangle map by a grid system. The initial point of the grid is taken as the southwest corner of the quadrangle and the location of the sample is measured in inches east and inches north from that corner, e.g., "156E 126N" indicated 15.6 inches east and 12.6 inches north of the southwest corner of the quadrangle. Zeroes in the location columns for some dates indicate that accurate locations are not available.Rock type, dating method, mineral dated, radiometric age, sample identification number, and reference are also listed where possible. Short comments, mostly geographic locality names, are given for some dates. These comments have been taken from the original references.Sample identification numbers beginning with "AA" or "BB" have been assigned arbitrarily in cases where sample numbers were not assigned in the original references. Abbreviations are explained in the appendix at the end of table 1.

CLSI-based transference of CALIPER pediatric reference intervals to Beckman Coulter AU biochemical assays.

PubMed

Abou El Hassan, Mohamed; Stoianov, Alexandra; Araújo, Petra A T; Sadeghieh, Tara; Chan, Man Khun; Chen, Yunqi; Randell, Edward; Nieuwesteeg, Michelle; Adeli, Khosrow

2015-11-01

The CALIPER program has established a comprehensive database of pediatric reference intervals using largely the Abbott ARCHITECT biochemical assays. To expand clinical application of CALIPER reference standards, the present study is aimed at transferring CALIPER reference intervals from the Abbott ARCHITECT to Beckman Coulter AU assays. Transference of CALIPER reference intervals was performed based on the CLSI guidelines C28-A3 and EP9-A2. The new reference intervals were directly verified using up to 100 reference samples from the healthy CALIPER cohort. We found a strong correlation between Abbott ARCHITECT and Beckman Coulter AU biochemical assays, allowing the transference of the vast majority (94%; 30 out of 32 assays) of CALIPER reference intervals previously established using Abbott assays. Transferred reference intervals were, in general, similar to previously published CALIPER reference intervals, with some exceptions. Most of the transferred reference intervals were sex-specific and were verified using healthy reference samples from the CALIPER biobank based on CLSI criteria. It is important to note that the comparisons performed between the Abbott and Beckman Coulter assays make no assumptions as to assay accuracy or which system is more correct/accurate. The majority of CALIPER reference intervals were transferrable to Beckman Coulter AU assays, allowing the establishment of a new database of pediatric reference intervals. This further expands the utility of the CALIPER database to clinical laboratories using the AU assays; however, each laboratory should validate these intervals for their analytical platform and local population as recommended by the CLSI. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Comparing Local TV News with National TV News in Cancer Coverage: An Exploratory Content Analysis

PubMed Central

Lee, Chul-joo; Long, Marilee; Slater, Michael D.; Song, Wen

2014-01-01

We compared local TV news with national TV news in terms of cancer coverage using a nationally representative sample of local nightly TV and national network TV (i.e., ABC, CBS, NBC, and CNN) cancer news stories that aired during 2002 and 2003. Compared to national TV news, local TV cancer stories were (a) much shorter in length, (b) less likely to report on cancer prevention (i.e., preventive behaviors and screening tests), and (c) less likely to reference national organizations (i.e., NCI, ACS, NIH, CDC, FDA) that have made clear recommendations about ways to prevent cancer. The implications of these findings for health communication research and cancer education were discussed. PMID:24750022

Industrial Work Experience I. Curriculum Guide. General Related Study Units.

ERIC Educational Resources Information Center

Virginia Polytechnic Inst. and State Univ., Blacksburg. Div. of Vocational-Technical Education.

The primary purpose of this guide is to present basic sample instructional materials for the Industrial Work Experience (IWE) Program. It is designed to aid those charged with local administration and coordination of programs in secondary level trade and industrial education, referred to as the IWE training program. The guide contains 10 units of…

Pediatric reference intervals for general clinical chemistry components - merging of studies from Denmark and Sweden.

PubMed

Ridefelt, Peter; Hilsted, Linda; Juul, Anders; Hellberg, Dan; Rustad, Pål

2018-05-28

Reference intervals are crucial tools aiding clinicians when making medical decisions. However, for children such values often are lacking or incomplete. The present study combines data from separate pediatric reference interval studies of Denmark and Sweden in order to increase sample size and to include also pre-school children who were lacking in the Danish study. Results from two separate studies including 1988 healthy children and adolescents aged 6 months to 18 years of age were merged and recalculated. Eighteen general clinical chemistry components were measured on Abbott and Roche platforms. To facilitate commutability, the NFKK Reference Serum X was used. Age- and gender-specific pediatric reference intervals were defined by calculating 2.5 and 97.5 percentiles. The data generated are primarily applicable to a Nordic population, but could be used by any laboratory if validated for the local patient population.

Application toward Confocal Full-Field Microscopic X-ray Absorption Near Edge Structure Spectroscopy.

PubMed

Tack, Pieter; Vekemans, Bart; Laforce, Brecht; Rudloff-Grund, Jennifer; Hernández, Willinton Y; Garrevoet, Jan; Falkenberg, Gerald; Brenker, Frank; Van Der Voort, Pascal; Vincze, Laszlo

2017-02-07

Using X-ray absorption near edge structure (XANES) spectroscopy, information on the local chemical structure and oxidation state of an element of interest can be acquired. Conventionally, this information can be obtained in a spatially resolved manner by scanning a sample through a focused X-ray beam. Recently, full-field methods have been developed to obtain direct 2D chemical state information by imaging a large sample area. These methods are usually in transmission mode, thus restricting the use to thin and transmitting samples. Here, a fluorescence method is displayed using an energy-dispersive pnCCD detector, the SLcam, characterized by measurement times far superior to what is generally applicable. Additionally, this method operates in confocal mode, thus providing direct 3D spatially resolved chemical state information from a selected subvolume of a sample, without the need of rotating a sample. The method is applied to two samples: a gold-supported magnesia catalyst (Au/MgO) and a natural diamond containing Fe-rich inclusions. Both samples provide XANES spectra that can be overlapped with reference XANES spectra, allowing this method to be used for fingerprinting and linear combination analysis of known XANES reference compounds.

The height-, weight-, and BMI-for-age of Polish school-aged children and adolescents relative to international and local growth references.

PubMed

Kulaga, Zbigniew; Litwin, Mieczysław; Tkaczyk, Marcin; Rózdzyńska, Agnieszka; Barwicka, Katarzyna; Grajda, Aneta; Swiader, Anna; Gurzkowska, Beata; Napieralska, Ewelina; Pan, Huiqi

2010-03-04

The growth of children is an indicator of health and society's wellbeing. Growth references are useful in monitoring a child's growth, which is a very important part of child care. Poland's growth references are not updated regularly. Although several growth reference ranges have been developed in Poland over recent years, sampling was restricted to urban populations of major cities. The aim of this study was to assess how well Polish children match with, or diverge from, regional charts and to compare them with international growth references. Four Polish and two international (WHO 2007 and USCDC2000) growth references were used to calculate the height, weight and BMI z-scores in a recent, large, population-representative sample of school-aged children and adolescents in Poland. The distributions of z-scores were analysed with descriptive and inferential statistical methods. Mean height z-scores calculated with the use of the WHO 2007 and USCDC2000 references were positive and significantly different from zero over the entire age range. The mean height z-score was closest to zero in the Poznan reference for boys (0.05) and Warszawa reference for girls (0.01). Median weight z-scores were positive under all weight references over the entire age range with only the exception of 18-year-old girls' weight z-score calculated relative to USCDC2000. Median BMI z-scores were positive in males in early childhood, decreasing with age. In the case of girls, the median BMI z-score calculated using WHO 2007 and USCDC2000 was close to zero in early childhood, decreased in adolescents and reached minimum values at age 18 years. Median BMI z-scores calculated with the use of the Lodz reference fluctuated between 0.05 and 0.2 over the studied age range. In this contemporary sample of Polish school-aged children, distributions of height, weight and BMI differed from those of children from the international growth references. These differences should be considered when using the references. There exist certain limitations to the analysis of height, weight, and BMI z-scores when Polish regional references are used.

The height-, weight-, and BMI-for-age of Polish school-aged children and adolescents relative to international and local growth references

PubMed Central

2010-01-01

Background The growth of children is an indicator of health and society's wellbeing. Growth references are useful in monitoring a child's growth, which is a very important part of child care. Poland's growth references are not updated regularly. Although several growth reference ranges have been developed in Poland over recent years, sampling was restricted to urban populations of major cities. The aim of this study was to assess how well Polish children match with, or diverge from, regional charts and to compare them with international growth references. Methods Four Polish and two international (WHO 2007 and USCDC2000) growth references were used to calculate the height, weight and BMI z-scores in a recent, large, population-representative sample of school-aged children and adolescents in Poland. The distributions of z-scores were analysed with descriptive and inferential statistical methods. Results Mean height z-scores calculated with the use of the WHO 2007 and USCDC2000 references were positive and significantly different from zero over the entire age range. The mean height z-score was closest to zero in the Poznan reference for boys (0.05) and Warszawa reference for girls (0.01). Median weight z-scores were positive under all weight references over the entire age range with only the exception of 18-year-old girls' weight z-score calculated relative to USCDC2000. Median BMI z-scores were positive in males in early childhood, decreasing with age. In the case of girls, the median BMI z-score calculated using WHO 2007 and USCDC2000 was close to zero in early childhood, decreased in adolescents and reached minimum values at age 18 years. Median BMI z-scores calculated with the use of the Lodz reference fluctuated between 0.05 and 0.2 over the studied age range. Conclusions In this contemporary sample of Polish school-aged children, distributions of height, weight and BMI differed from those of children from the international growth references. These differences should be considered when using the references. There exist certain limitations to the analysis of height, weight, and BMI z-scores when Polish regional references are used. PMID:20199693

The influence of a local, media covered hospital incident on public trust in health care.

PubMed

van der Schee, Evelien; de Jong, Judith D; Groenewegen, Peter P

2012-08-01

Incidents in health care happen every now and then. Incidents are often extensively covered by the news media. In this study, we investigated the impact of an incident in a Dutch hospital on public trust in health care in the population living in the vicinity of where the incident took place and in the national population. News media coverage of the incident started in Fall 2008. We collected data in three samples, using a postal questionnaire on public trust in health care. Two samples were a cross-section of the Dutch population; one was questioned in October 2006 and the other in October 2008. The third sample, also questioned in October 2008, consisted of 1000 people living in the surrounding area of the hospital where the incident occurred. The cross-sectional sample of October 2006 was a reference group, and at that time no incidents in health care were covered in the media. In the local population, the incident had a strong impact on public trust in the hospital and among the specialists working there. Also, in the local population, the impact of the incident was generalized to trust in hospitals and specialists in general. In the national population, no impact of the incident on the public's trust was found, despite national news media coverage. Local incidents have an impact on public trust in health care in the local population. However, these incidents do not influence public trust in health care in the national population.

CLSI-based transference and verification of CALIPER pediatric reference intervals for 29 Ortho VITROS 5600 chemistry assays.

PubMed

Higgins, Victoria; Truong, Dorothy; Woroch, Amy; Chan, Man Khun; Tahmasebi, Houman; Adeli, Khosrow

2018-03-01

Evidence-based reference intervals (RIs) are essential to accurately interpret pediatric laboratory test results. To fill gaps in pediatric RIs, the Canadian Laboratory Initiative on Pediatric Reference Intervals (CALIPER) project developed an age- and sex-specific pediatric RI database based on healthy pediatric subjects. Originally established for Abbott ARCHITECT assays, CALIPER RIs were transferred to assays on Beckman, Roche, Siemens, and Ortho analytical platforms. This study provides transferred reference intervals for 29 biochemical assays for the Ortho VITROS 5600 Chemistry System (Ortho). Based on Clinical Laboratory Standards Institute (CLSI) guidelines, a method comparison analysis was performed by measuring approximately 200 patient serum samples using Abbott and Ortho assays. The equation of the line of best fit was calculated and the appropriateness of the linear model was assessed. This equation was used to transfer RIs from Abbott to Ortho assays. Transferred RIs were verified using 84 healthy pediatric serum samples from the CALIPER cohort. RIs for most chemistry analytes successfully transferred from Abbott to Ortho assays. Calcium and CO 2 did not meet statistical criteria for transference (r 2 <0.70). Of the 32 transferred reference intervals, 29 successfully verified with approximately 90% of results from reference samples falling within transferred confidence limits. Transferred RIs for total bilirubin, magnesium, and LDH did not meet verification criteria and are not reported. This study broadens the utility of the CALIPER pediatric RI database to laboratories using Ortho VITROS 5600 biochemical assays. Clinical laboratories should verify CALIPER reference intervals for their specific analytical platform and local population as recommended by CLSI. Copyright © 2018 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Precision enhancement of pavement roughness localization with connected vehicles

NASA Astrophysics Data System (ADS)

Bridgelall, R.; Huang, Y.; Zhang, Z.; Deng, F.

2016-02-01

Transportation agencies rely on the accurate localization and reporting of roadway anomalies that could pose serious hazards to the traveling public. However, the cost and technical limitations of present methods prevent their scaling to all roadways. Connected vehicles with on-board accelerometers and conventional geospatial position receivers offer an attractive alternative because of their potential to monitor all roadways in real-time. The conventional global positioning system is ubiquitous and essentially free to use but it produces impractically large position errors. This study evaluated the improvement in precision achievable by augmenting the conventional geo-fence system with a standard speed bump or an existing anomaly at a pre-determined position to establish a reference inertial marker. The speed sensor subsequently generates position tags for the remaining inertial samples by computing their path distances relative to the reference position. The error model and a case study using smartphones to emulate connected vehicles revealed that the precision in localization improves from tens of metres to sub-centimetre levels, and the accuracy of measuring localized roughness more than doubles. The research results demonstrate that transportation agencies will benefit from using the connected vehicle method to achieve precision and accuracy levels that are comparable to existing laser-based inertial profilers.

Computing the Free Energy Barriers for Less by Sampling with a Coarse Reference Potential while Retaining Accuracy of the Target Fine Model.

PubMed

Plotnikov, Nikolay V

2014-08-12

Proposed in this contribution is a protocol for calculating fine-physics (e.g., ab initio QM/MM) free-energy surfaces at a high level of accuracy locally (e.g., only at reactants and at the transition state for computing the activation barrier) from targeted fine-physics sampling and extensive exploratory coarse-physics sampling. The full free-energy surface is still computed but at a lower level of accuracy from coarse-physics sampling. The method is analytically derived in terms of the umbrella sampling and the free-energy perturbation methods which are combined with the thermodynamic cycle and the targeted sampling strategy of the paradynamics approach. The algorithm starts by computing low-accuracy fine-physics free-energy surfaces from the coarse-physics sampling in order to identify the reaction path and to select regions for targeted sampling. Thus, the algorithm does not rely on the coarse-physics minimum free-energy reaction path. Next, segments of high-accuracy free-energy surface are computed locally at selected regions from the targeted fine-physics sampling and are positioned relative to the coarse-physics free-energy shifts. The positioning is done by averaging the free-energy perturbations computed with multistep linear response approximation method. This method is analytically shown to provide results of the thermodynamic integration and the free-energy interpolation methods, while being extremely simple in implementation. Incorporating the metadynamics sampling to the algorithm is also briefly outlined. The application is demonstrated by calculating the B3LYP//6-31G*/MM free-energy barrier for an enzymatic reaction using a semiempirical PM6/MM reference potential. These modifications allow computing the activation free energies at a significantly reduced computational cost but at the same level of accuracy compared to computing full potential of mean force.

Computing the Free Energy Barriers for Less by Sampling with a Coarse Reference Potential while Retaining Accuracy of the Target Fine Model

PubMed Central

2015-01-01

Proposed in this contribution is a protocol for calculating fine-physics (e.g., ab initio QM/MM) free-energy surfaces at a high level of accuracy locally (e.g., only at reactants and at the transition state for computing the activation barrier) from targeted fine-physics sampling and extensive exploratory coarse-physics sampling. The full free-energy surface is still computed but at a lower level of accuracy from coarse-physics sampling. The method is analytically derived in terms of the umbrella sampling and the free-energy perturbation methods which are combined with the thermodynamic cycle and the targeted sampling strategy of the paradynamics approach. The algorithm starts by computing low-accuracy fine-physics free-energy surfaces from the coarse-physics sampling in order to identify the reaction path and to select regions for targeted sampling. Thus, the algorithm does not rely on the coarse-physics minimum free-energy reaction path. Next, segments of high-accuracy free-energy surface are computed locally at selected regions from the targeted fine-physics sampling and are positioned relative to the coarse-physics free-energy shifts. The positioning is done by averaging the free-energy perturbations computed with multistep linear response approximation method. This method is analytically shown to provide results of the thermodynamic integration and the free-energy interpolation methods, while being extremely simple in implementation. Incorporating the metadynamics sampling to the algorithm is also briefly outlined. The application is demonstrated by calculating the B3LYP//6-31G*/MM free-energy barrier for an enzymatic reaction using a semiempirical PM6/MM reference potential. These modifications allow computing the activation free energies at a significantly reduced computational cost but at the same level of accuracy compared to computing full potential of mean force. PMID:25136268

Determination of As, Cd, Hg and Pb in herbs using slurry sampling electrothermal vaporisation inductively coupled plasma mass spectrometry.

PubMed

Lin, Mei-Ling; Jiang, Shiuh-Jen

2013-12-01

Inductively coupled plasma mass spectrometry coupled with ultrasonic slurry sampling electrothermal vaporisation (USS-ETV-ICP-MS) has been applied to determine As, Cd, Hg and Pb in 0.5% m/v slurries of several herb samples. 1% m/v 8-Hydroxyquinoline was used as the modifier to enhance the ion signals. The influences of instrument operating conditions, slurry preparation and interferences on the ion signals were reported. This method has been applied to the determination of As, Cd, Hg and Pb in NIST SRM 1547 peach leaves and SRM 1573a tomato leaves reference materials and three herb samples purchased from the local market and ground to 150 μm. The analysis results of the standard reference materials agreed with the certified values which are at sub μg g(-1) levels. Precision between sample replicates was better than 4% for all the determinations. The method detection limits estimated from standard addition curves were about 0.3, 0.1, 0.1 and 0.2 ng g(-1) for As, Cd, Hg and Pb, respectively, in original herb samples. Copyright © 2013 Elsevier Ltd. All rights reserved.

Advances in locally constrained k-space-based parallel MRI.

PubMed

Samsonov, Alexey A; Block, Walter F; Arunachalam, Arjun; Field, Aaron S

2006-02-01

In this article, several theoretical and methodological developments regarding k-space-based, locally constrained parallel MRI (pMRI) reconstruction are presented. A connection between Parallel MRI with Adaptive Radius in k-Space (PARS) and GRAPPA methods is demonstrated. The analysis provides a basis for unified treatment of both methods. Additionally, a weighted PARS reconstruction is proposed, which may absorb different weighting strategies for improved image reconstruction. Next, a fast and efficient method for pMRI reconstruction of data sampled on non-Cartesian trajectories is described. In the new technique, the computational burden associated with the numerous matrix inversions in the original PARS method is drastically reduced by limiting direct calculation of reconstruction coefficients to only a few reference points. The rest of the coefficients are found by interpolating between the reference sets, which is possible due to the similar configuration of points participating in reconstruction for highly symmetric trajectories, such as radial and spirals. As a result, the time requirements are drastically reduced, which makes it practical to use pMRI with non-Cartesian trajectories in many applications. The new technique was demonstrated with simulated and actual data sampled on radial trajectories. Copyright 2006 Wiley-Liss, Inc.

Local-order metric for condensed-phase environments

NASA Astrophysics Data System (ADS)

Martelli, Fausto; Ko, Hsin-Yu; Oǧuz, Erdal C.; Car, Roberto

2018-02-01

We introduce a local order metric (LOM) that measures the degree of order in the neighborhood of an atomic or molecular site in a condensed medium. The LOM maximizes the overlap between the spatial distribution of sites belonging to that neighborhood and the corresponding distribution in a suitable reference system. The LOM takes a value tending to zero for completely disordered environments and tending to one for environments that perfectly match the reference. The site-averaged LOM and its standard deviation define two scalar order parameters, S and δ S , that characterize with excellent resolution crystals, liquids, and amorphous materials. We show with molecular dynamics simulations that S , δ S , and the LOM provide very insightful information in the study of structural transformations, such as those occurring when ice spontaneously nucleates from supercooled water or when a supercooled water sample becomes amorphous upon progressive cooling.

Local diversity hot spots in the Middle Miocene of the Central Paratethys: influence of environment and sampling

NASA Astrophysics Data System (ADS)

Nawrot, Rafal; Zuschin, Martin; Harzhauser, Mathias; Kroh, Andreas; Mandic, Oleg

2015-04-01

Species richness captured by historical fossil inventories is a complex function of true local diversity, degree of outcrop-scale heterogeneity in species composition and sampling intensity. Disentangling these factors is hindered by the fact that the 'systematists follow the fossils' (Raup, 1977) and thus non-uniform research effort may both drive apparent diversity patterns and follow the actual presence of highly fossiliferous strata. The molluscan fauna of Lapugiu de Sus (Hunedoara District, Romania) constitutes one of the most diverse Early Badenian (Langhian) assemblages of the Paratethys Sea, with almost one thousand species reported during 170 years of extensive studies. We evaluate whether this exceptional richness reflects the actual diversity hot spot or just a long history of fossil-collecting by comparing the fauna of Lapugiu with other Paratethyan molluscan lagerstätten of similar age. The literature-derived species lists for each section were contrasted with independent abundance data based on a standardized sampling protocol (42 samples, 24,000 specimens, and 530 species from six localities). Although individual samples from other localities can exhibit comparable diversity levels, richness estimates for samples from Lapugiu are all consistently high, reflecting increasing evenness in more offshore depositional settings. This translates to the highest diversity at the outcrop scale when all samples are pooled. In contrast to other localities, however, for which data from historical inventories corresponds well to our quantitative estimates of total richness, the number of species described from Lapugiu is much higher than expected. This excessive richness likely reflects the 'Bonanza Effect' (sensu Dunhill et al., 2012), where uniformly species-rich deposits were attracting intensive taxonomic studies. The strong positive feedback between palaeontological sampling effort and fossil diversity may thus greatly overestimate the true differences in species richness between the most diverse faunas and more typical, background, fossil assemblages. References Raup, D.M., 1977. Paleobiology, 3: 328-329. Dunhill, A.M. et al., 2012. Palaeontology, 55: 1155-1175.

The local clinical validation of a new lithium heparin tube with a barrier: BD Vacutainer® Barricor LH Plasma tube.

PubMed

Arslan, Fatma Demet; Karakoyun, Inanc; Basok, Banu Isbilen; Aksit, Merve Zeytinli; Baysoy, Anil; Ozturk, Yasemin Kilic; Guclu, Yusuf Adnan; Duman, Can

2017-10-15

Although serum-providing blood tubes with a barrier are still widely used due to their significant advantages, the use of blood tubes with a barrier to provide plasma is becoming widespread. We compared 22 analytes in a BD Vacutainer® Barricor LH Plasma tube for local clinical validation of this new lithium heparin tube with a barrier. Samples from 44 volunteers were collected in different tubes (Becton Dickinson and Company): Z tube without additive (reference), clot-activator tube with gel (SST), lithium heparin tube without gel (LiH), and lithium heparin tube with barrier (Barricor). Analyte concentrations in different tubes were compared with the reference tube. All tubes were also evaluated according to additional testing (different centrifugation durations, blood-sampling techniques and individual differences). Aspartate aminotransferase (AST), glucose (Glc), potassium (K), lactate dehydrogenase (LD), sodium (Na), and total protein (TP) had a significant bias in Barricor (9.19%, - 3.24%, - 4.88%, 21.60%, - 0.40%, 5.03%, respectively) relative to the reference tube. There was no statistical difference between different centrifugation durations and individual differences for AST, K and LD in LiH and/or Barricor (P > 0.05). There was a significant bias for LD between LiH and Barricor in terms of blood-sampling techniques (21.2% and 12.4%, respectively). Recently, the use of plasma has become prominent due to some of its advantages. In this study, plasma AST, K, LD, Glc and TP levels in Barricor were clinically different in comparison to serum. The results of additional tests showed that higher levels of LD in Barricor did not result from haemolysis, and they might be related to other factors including number of platelets, cellular fragility, or functional environment.

Integrative missing value estimation for microarray data.

PubMed

Hu, Jianjun; Li, Haifeng; Waterman, Michael S; Zhou, Xianghong Jasmine

2006-10-12

Missing value estimation is an important preprocessing step in microarray analysis. Although several methods have been developed to solve this problem, their performance is unsatisfactory for datasets with high rates of missing data, high measurement noise, or limited numbers of samples. In fact, more than 80% of the time-series datasets in Stanford Microarray Database contain less than eight samples. We present the integrative Missing Value Estimation method (iMISS) by incorporating information from multiple reference microarray datasets to improve missing value estimation. For each gene with missing data, we derive a consistent neighbor-gene list by taking reference data sets into consideration. To determine whether the given reference data sets are sufficiently informative for integration, we use a submatrix imputation approach. Our experiments showed that iMISS can significantly and consistently improve the accuracy of the state-of-the-art Local Least Square (LLS) imputation algorithm by up to 15% improvement in our benchmark tests. We demonstrated that the order-statistics-based integrative imputation algorithms can achieve significant improvements over the state-of-the-art missing value estimation approaches such as LLS and is especially good for imputing microarray datasets with a limited number of samples, high rates of missing data, or very noisy measurements. With the rapid accumulation of microarray datasets, the performance of our approach can be further improved by incorporating larger and more appropriate reference datasets.

Statistical Analyses of Brain Surfaces Using Gaussian Random Fields on 2-D Manifolds

PubMed Central

Staib, Lawrence H.; Xu, Dongrong; Zhu, Hongtu; Peterson, Bradley S.

2008-01-01

Interest in the morphometric analysis of the brain and its subregions has recently intensified because growth or degeneration of the brain in health or illness affects not only the volume but also the shape of cortical and subcortical brain regions, and new image processing techniques permit detection of small and highly localized perturbations in shape or localized volume, with remarkable precision. An appropriate statistical representation of the shape of a brain region is essential, however, for detecting, localizing, and interpreting variability in its surface contour and for identifying differences in volume of the underlying tissue that produce that variability across individuals and groups of individuals. Our statistical representation of the shape of a brain region is defined by a reference region for that region and by a Gaussian random field (GRF) that is defined across the entire surface of the region. We first select a reference region from a set of segmented brain images of healthy individuals. The GRF is then estimated as the signed Euclidean distances between points on the surface of the reference region and the corresponding points on the corresponding region in images of brains that have been coregistered to the reference. Correspondences between points on these surfaces are defined through deformations of each region of a brain into the coordinate space of the reference region using the principles of fluid dynamics. The warped, coregistered region of each subject is then unwarped into its native space, simultaneously bringing into that space the map of corresponding points that was established when the surfaces of the subject and reference regions were tightly coregistered. The proposed statistical description of the shape of surface contours makes no assumptions, other than smoothness, about the shape of the region or its GRF. The description also allows for the detection and localization of statistically significant differences in the shapes of the surfaces across groups of subjects at both a fine and coarse scale. We demonstrate the effectiveness of these statistical methods by applying them to study differences in shape of the amygdala and hippocampus in a large sample of normal subjects and in subjects with attention deficit/hyperactivity disorder (ADHD). PMID:17243583

Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques.

PubMed

Xu, Chao; Dong, Wenpan; Shi, Shuo; Cheng, Tao; Li, Changhao; Liu, Yanlei; Wu, Ping; Wu, Hongkun; Gao, Peng; Zhou, Shiliang

2015-11-01

A well-covered reference library is crucial for successful identification of species by DNA barcoding. The biggest difficulty in building such a reference library is the lack of materials of organisms. Herbarium collections are potentially an enormous resource of materials. In this study, we demonstrate that it is likely to build such reference libraries using the reconstructed (self-primed PCR amplified) DNA from the herbarium specimens. We used 179 rosaceous specimens to test the effects of DNA reconstruction, 420 randomly sampled specimens to estimate the usable percentage and another 223 specimens of true cherries (Cerasus, Rosaceae) to test the coverage of usable specimens to the species. The barcode rbcLb (the central four-sevenths of rbcL gene) and matK was each amplified in two halves and sequenced on Roche GS 454 FLX+. DNA from the herbarium specimens was typically shorter than 300 bp. DNA reconstruction enabled amplification fragments of 400-500 bp without bringing or inducing any sequence errors. About one-third of specimens in the national herbarium of China (PE) were proven usable after DNA reconstruction. The specimens in PE cover all Chinese true cherry species and 91.5% of vascular species listed in Flora of China. It is very possible to build well-covered reference libraries for DNA barcoding of vascular species in China. As exemplified in this study, DNA reconstruction and DNA-labelled next-generation sequencing can accelerate the construction of local reference libraries. By putting the local reference libraries together, a global library for DNA barcoding becomes closer to reality. © 2015 John Wiley & Sons Ltd.

Local Sampling of the Wigner Function at Telecom Wavelength with Loss-Tolerant Detection of Photon Statistics.

PubMed

Harder, G; Silberhorn, Ch; Rehacek, J; Hradil, Z; Motka, L; Stoklasa, B; Sánchez-Soto, L L

2016-04-01

We report the experimental point-by-point sampling of the Wigner function for nonclassical states created in an ultrafast pulsed type-II parametric down-conversion source. We use a loss-tolerant time-multiplexed detector based on a fiber-optical setup and a pair of photon-number-resolving avalanche photodiodes. By capitalizing on an expedient data-pattern tomography, we assess the properties of the light states with outstanding accuracy. The method allows us to reliably infer the squeezing of genuine two-mode states without any phase reference.

On the selection of gantry and collimator angles for isocenter localization using Winston-Lutz tests.

PubMed

Du, Weiliang; Johnson, Jennifer L; Jiang, Wei; Kudchadker, Rajat J

2016-01-08

In Winston-Lutz (WL) tests, the isocenter of a linear accelerator (linac) is determined as the intersection of radiation central axes (CAX) from multiple gantry, collimator, and couch angles. It is well known that the CAX can wobble due to mechanical imperfections of the linac. Previous studies suggested that the wobble varies with gantry and collimator angles. Therefore, the isocenter determined in the WL tests has a profound dependence on the gantry and collimator angles at which CAX are sampled. In this study, we evaluated the systematic and random errors in the iso-centers determined with different CAX sampling schemes. Digital WL tests were performed on six linacs. For each WL test, 63 CAX were sampled at nine gantry angles and seven collimator angles. Subsets of these data were used to simulate the effects of various CAX sampling schemes. An isocenter was calculated from each subset of CAX and compared against the reference isocenter, which was calculated from 48 opposing CAX. The differences between the calculated isocenters and the reference isocenters ranged from 0 to 0.8 mm. The differences diminished to less than 0.2 mm when 24 or more CAX were sampled. Isocenters determined with collimator 0° were vertically lower than those determined with collimator 90° and 270°. Isocenter localization errors in the longitudinal direction (along the axis of gantry rotation) showed a strong dependence on the collimator angle selected. The errors in all directions were significantly reduced when opposing collimator angles and opposing gantry angles were employed. The isocenter localization errors were less than 0.2 mm with the common CAX sampling scheme, which used four cardinal gantry angles and two opposing collimator angles. Reproducibility stud-ies on one linac showed that the mean and maximum variations of CAX during the WL tests were 0.053 mm and 0.30 mm, respectively. The maximal variation in the resulting isocenters was 0.068 mm if 48 CAX were used, or 0.13 mm if four CAX were used. Quantitative results from this study are useful for understanding and minimizing the isocenter uncertainty in WL tests.

Moderate MAS enhances local (1)H spin exchange and spin diffusion.

PubMed

Roos, Matthias; Micke, Peter; Saalwächter, Kay; Hempel, Günter

2015-11-01

Proton NMR spin-diffusion experiments are often combined with magic-angle spinning (MAS) to achieve higher spectral resolution of solid samples. Here we show that local proton spin diffusion can indeed become faster at low (<10 kHz) spinning rates as compared to static conditions. Spin diffusion under static conditions can thus be slower than the often referred value of 0.8 nm(2)/ms, which was determined using slow MAS (Clauss et al., 1993). The enhancement of spin diffusion by slow MAS relies on the modulation of the orientation-dependent dipolar couplings during sample rotation and goes along with transient level crossings in combination with dipolar truncation. The experimental finding and its explanation is supported by density matrix simulations, and also emphasizes the sensitivity of spin diffusion to the local coupling topology. The amplification of spin diffusion by slow MAS cannot be explained by any model based on independent spin pairs; at least three spins have to be considered. Copyright © 2015 Elsevier Inc. All rights reserved.

Macroecology of biodiversity: disentangling local and regional effects.

PubMed

Pärtel, Meelis; Bennett, Jonathan A; Zobel, Martin

2016-07-01

Contents 404 I. 404 II. 404 III. 405 IV. 406 V. 407 VI. 408 409 References 409 SUMMARY: Macroecology of biodiversity disentangles local and regional drivers of biodiversity by exploring large-scale biodiversity relationships with environmental or biotic gradients, generalizing local biodiversity relationships across regions, or comparing biodiversity patterns among species groups. A macroecological perspective is also important at local scales: a full understanding of local biodiversity drivers, including human impact, demands that regional processes be taken into account. This requires knowledge of which species could inhabit a site (the species pool), including those that are currently absent (dark diversity). Macroecology of biodiversity is currently advancing quickly owing to an unprecedented accumulation of biodiversity data, new sampling techniques and analytical methods, all of which better equip us to face current and future challenges in ecology and biodiversity conservation. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Assessment of swine-specific bacteriophages of Bacteroides fragilis in swine farms with different antibiotic practices.

PubMed

Leknoi, Yuranan; Mongkolsuk, Skorn; Sirikanchana, Kwanrawee

2017-04-01

We assessed the occurrence and specificity of bacteriophages of Bacteroides fragilis in swine farms for their potential application in microbial source tracking. A local B. fragilis host strain, SP25 (DSM29413), was isolated from a pooled swine feces sample taken from a non-antibiotic farm. This strain was highly specific to swine fecal materials because it did not detect bacteriophages in any samples from human sewage, sheep, goats, cattle, dogs, and cats. The reference B. fragilis strain, RYC2056, could detect phages in swine samples but also detected phages in most human sewage and polluted urban canal samples. Phages of SP25 exist in the proximity of certain swine farms, regardless of their antibiotic use (p > 0.05). B. fragilis strain SP25 exhibited relatively high resistance to most of the veterinary antimicrobial agents tested. Interestingly, most farms that were positive for SP25 phages were also positive for RYC2056 phages. In conclusion, the swine-specific SP25 strain has the potential to indicate swine fecal contamination in certain bodies of water. Bacterial isolates with larger distributions are being studied and validated. This study highlights the importance of assessing the abundance of phages in local swine populations before determining their potential applicability for source tracking in local surface waters.

Use of sediment-trace element geochemical models for the identification of local fluvial baseline concentrations

USGS Publications Warehouse

Horowitz, A.J.; Elrick, K.A.; Demas, C.R.; Demcheck, D.K.

1991-01-01

Studies have demonstrated the utility of fluvial bed sediment chemical data in assesing local water-quality conditions. However, establishing local background trace element levels can be difficult. Reference to published average concentrations or the use of dated cores are often of little use in small areas of diverse local petrology, geology, land use, or hydrology. An alternative approach entails the construction of a series of sediment-trace element predictive models based on data from environmentally diverse but unaffected areas. Predicted values could provide a measure of local background concentrations and comparison with actual measured concentrations could identify elevated trace elements and affected sites. Such a model set was developed from surface bed sediments collected nationwide in the United States. Tests of the models in a small Louisiana basin indicated that they could be used to establish local trace element background levels, but required recalibration to account for local geochemical conditions outside the range of samples used to generate the nationwide models.

Analytical Bias Exceeding Desirable Quality Goal in 4 out of 5 Common Immunoassays: Results of a Native Single Serum Sample External Quality Assessment Program for Cobalamin, Folate, Ferritin, Thyroid-Stimulating Hormone, and Free T4 Analyses.

PubMed

Kristensen, Gunn B B; Rustad, Pål; Berg, Jens P; Aakre, Kristin M

2016-09-01

We undertook this study to evaluate method differences for 5 components analyzed by immunoassays, to explore whether the use of method-dependent reference intervals may compensate for method differences, and to investigate commutability of external quality assessment (EQA) materials. Twenty fresh native single serum samples, a fresh native serum pool, Nordic Federation of Clinical Chemistry Reference Serum X (serum X) (serum pool), and 2 EQA materials were sent to 38 laboratories for measurement of cobalamin, folate, ferritin, free T4, and thyroid-stimulating hormone (TSH) by 5 different measurement procedures [Roche Cobas (n = 15), Roche Modular (n = 4), Abbott Architect (n = 8), Beckman Coulter Unicel (n = 2), and Siemens ADVIA Centaur (n = 9)]. The target value for each component was calculated based on the mean of method means or measured by a reference measurement procedure (free T4). Quality specifications were based on biological variation. Local reference intervals were reported from all laboratories. Method differences that exceeded acceptable bias were found for all components except folate. Free T4 differences from the uncommonly used reference measurement procedure were large. Reference intervals differed between measurement procedures but also within 1 measurement procedure. The serum X material was commutable for all components and measurement procedures, whereas the EQA materials were noncommutable in 13 of 50 occasions (5 components, 5 methods, 2 EQA materials). The bias between the measurement procedures was unacceptably large in 4/5 tested components. Traceability to reference materials as claimed by the manufacturers did not lead to acceptable harmonization. Adjustment of reference intervals in accordance with method differences and use of commutable EQA samples are not implemented commonly. © 2016 American Association for Clinical Chemistry.

Criminal investigation of child sexual abuse: a comparison of cases referred to the prosecutor to those not referred.

PubMed

Stroud, D D; Martens, S L; Barker, J

2000-05-01

The present study sought to identify characteristics of child sexual abuse cases which differentiate cases referred for criminal prosecution ("criminal-action") from those not referred ("dropped") by investigators. The study sample consisted of 1043 children who completed a forensic interview for sexual abuse that allegedly occurred at the hands of an adult between January 1, 1993 and December 31, 1996 in Bernalillo County of New Mexico. Data was systematically obtained from forensic interview files and offender records at the local prosecutor's office. Differences between criminal-action and dropped cases were found in relation to the children (age, sex and ethnicity), the alleged offenders (age, sex and relationship to child), and the case characteristics (disclosure and injury to the child). The present study provided insight into the characteristics of a previously ignored population (reported child sexual abuse cases that are not referred for prosecution). Recommendations are made to address the needs of these children and their families.

Identification of human remains from the Second World War mass graves uncovered in Bosnia and Herzegovina

PubMed Central

Marjanović, Damir; Hadžić Metjahić, Negra; Čakar, Jasmina; Džehverović, Mirela; Dogan, Serkan; Ferić, Elma; Džijan, Snježana; Škaro, Vedrana; Projić, Petar; Madžar, Tomislav; Rod, Eduard; Primorac, Dragan

2015-01-01

Aim To present the results obtained in the identification of human remains from World War II found in two mass graves in Ljubuški, Bosnia and Herzegovina. Methods Samples from 10 skeletal remains were collected. Teeth and femoral fragments were collected from 9 skeletons and only a femoral fragment from 1 skeleton. DNA was isolated from bone and teeth samples using an optimized phenol/chloroform DNA extraction procedure. All samples required a pre-extraction decalcification with EDTA and additional post-extraction DNA purification using filter columns. Additionally, DNA from 12 reference samples (buccal swabs from potential living relatives) was extracted using the Qiagen DNA extraction method. QuantifilerTM Human DNA Quantification Kit was used for DNA quantification. PowerPlex ESI kit was used to simultaneously amplify 15 autosomal short tandem repeat (STR) loci, and PowerPlex Y23 was used to amplify 23 Y chromosomal STR loci. Matching probabilities were estimated using a standard statistical approach. Results A total of 10 samples were processed, 9 teeth and 1 femoral fragment. Nine of 10 samples were profiled using autosomal STR loci, which resulted in useful DNA profiles for 9 skeletal remains. A comparison of established victims' profiles against a reference sample database yielded 6 positive identifications. Conclusion DNA analysis may efficiently contribute to the identification of remains even seven decades after the end of the World War II. The significant percentage of positively identified remains (60%), even when the number of the examined possible living relatives was relatively small (only 12), proved the importance of cooperation with the members of the local community, who helped to identify the closest missing persons’ relatives and collect referent samples from them. PMID:26088850

Identification of human remains from the Second World War mass graves uncovered in Bosnia and Herzegovina.

PubMed

Marjanović, Damir; Hadžić Metjahić, Negra; Čakar, Jasmina; Džehverović, Mirela; Dogan, Serkan; Ferić, Elma; Džijan, Snježana; Škaro, Vedrana; Projić, Petar; Madžar, Tomislav; Rod, Eduard; Primorac, Dragan

2015-06-01

To present the results obtained in the identification of human remains from World War II found in two mass graves in Ljubuški, Bosnia and Herzegovina. Samples from 10 skeletal remains were collected. Teeth and femoral fragments were collected from 9 skeletons and only a femoral fragment from 1 skeleton. DNA was isolated from bone and teeth samples using an optimized phenol/chloroform DNA extraction procedure. All samples required a pre-extraction decalcification with EDTA and additional post-extraction DNA purification using filter columns. Additionally, DNA from 12 reference samples (buccal swabs from potential living relatives) was extracted using the Qiagen DNA extraction method. QuantifilerTM Human DNA Quantification Kit was used for DNA quantification. PowerPlex ESI kit was used to simultaneously amplify 15 autosomal short tandem repeat (STR) loci, and PowerPlex Y23 was used to amplify 23 Y chromosomal STR loci. Matching probabilities were estimated using a standard statistical approach. A total of 10 samples were processed, 9 teeth and 1 femoral fragment. Nine of 10 samples were profiled using autosomal STR loci, which resulted in useful DNA profiles for 9 skeletal remains. A comparison of established victims' profiles against a reference sample database yielded 6 positive identifications. DNA analysis may efficiently contribute to the identification of remains even seven decades after the end of the World War II. The significant percentage of positively identified remains (60%), even when the number of the examined possible living relatives was relatively small (only 12), proved the importance of cooperation with the members of the local community, who helped to identify the closest missing persons' relatives and collect referent samples from them.

Mercury Slovenian soils: High, medium and low sample density geochemical maps

NASA Astrophysics Data System (ADS)

Gosar, Mateja; Šajn, Robert; Teršič, Tamara

2017-04-01

Regional geochemical survey was conducted in whole territory of Slovenia (20273 km2). High, medium and low sample density surveys were compared. High sample density represented the regional geochemical data set supplemented by local high-density sampling data (irregular grid, n=2835). Medium-density soil sampling was performed in a 5 x 5 km grid (n=817) and low-density geochemical survey was conducted in a sampling grid 25 x 25 km (n=54). Mercury distribution in Slovenian soils was determined with models of mercury distribution in soil using all three data sets. A distinct Hg anomaly in western part of Slovenia is evident on all three models. It is a consequence of 500-years of mining and ore processing in the second largest mercury mine in the world, the Idrija mine. The determined mercury concentrations revealed an important difference between the western and the eastern parts of the country. For the medium scale geochemical mapping is the median value (0.151 mg /kg) for western Slovenia almost 2-fold higher than the median value (0.083 mg/kg) in eastern Slovenia. Besides the Hg median for the western part of Slovenia exceeds the Hg median for European soil by a factor of 4 (Gosar et al., 2016). Comparing these sample density surveys, it was shown that high sampling density allows the identification and characterization of anthropogenic influences on a local scale, while medium- and low-density sampling reveal general trends in the mercury spatial distribution, but are not appropriate for identifying local contamination in industrial regions and urban areas. The resolution of the pattern generated is the best when the high-density survey on a regional scale is supplemented with the geochemical data of the high-density surveys on a local scale. References: Gosar, M, Šajn, R, Teršič, T. Distribution pattern of mercury in the Slovenian soil: geochemical mapping based on multiple geochemical datasets. Journal of geochemical exploration, 2016, 167/38-48.

Chemistry of water collected from an unventilated drift, Yucca Mountain, Nevada

USGS Publications Warehouse

Marshall, B.D.; Oliver, T.A.; Peterman, Z.E.

2007-01-01

Water samples (referred to as puddle water samples) were collected from the surfaces of a conveyor belt and plastic sheeting in the unventilated portion of the Enhanced Characterization of the Repository Block (ECRB) Cross Drift in 2003 and 2005 at Yucca Mountain, Nevada. The chemistry of these puddle water samples is very different than that of pore water samples from borehole cores in the same region of the Cross Drift or than seepage water samples collected from the Exploratory Studies Facility tunnel in 2005. The origin of the puddle water is condensation on surfaces of introduced materials and its chemistry is dominated by components of the introduced materials. Large CO2 concentrations may be indicative of localized chemical conditions induced by biologic activity. ?? 2007 Materials Research Society.

Single grating x-ray imaging for dynamic biological systems

NASA Astrophysics Data System (ADS)

Morgan, Kaye S.; Paganin, David M.; Parsons, David W.; Donnelley, Martin; Yagi, Naoto; Uesugi, Kentaro; Suzuki, Yoshio; Takeuchi, Akihisa; Siu, Karen K. W.

2012-07-01

Biomedical studies are already benefiting from the excellent contrast offered by phase contrast x-ray imaging, but live imaging work presents several challenges. Living samples make it particularly difficult to achieve high resolution, sensitive phase contrast images, as exposures must be short and cannot be repeated. We therefore present a single-exposure, high-flux method of differential phase contrast imaging [1, 2, 3] in the context of imaging live airways for Cystic Fibrosis (CF) treatment assessment [4]. The CF study seeks to non-invasively observe the liquid lining the airways, which should increase in depth in response to effective treatments. Both high spatial resolution and sensitivity are required in order to track micron size changes in a liquid that is not easily differentiated from the tissue on which it lies. Our imaging method achieves these goals by using a single attenuation grating or grid as a reference pattern, and analyzing how the sample deforms the pattern to quantitatively retrieve the phase depth of the sample. The deformations are mapped at each pixel in the image using local cross-correlations comparing each 'sample and pattern' image with a reference 'pattern only' image taken before the sample is introduced. This produces a differential phase image, which may be integrated to give the sample phase depth.

Usage of Leptospira spp. local strains as antigens increases the sensitivity of the serodiagnosis of bovine leptospirosis.

PubMed

Pinto, Priscila S; Loureiro, Ana P; Penna, Bruno; Lilenbaum, Walter

2015-09-01

Leptospirosis is a zoonotic disease that occurs worldwide, particularly in tropical countries. In livestock the agent is responsible for reproductive problems such as infertility and abortion. Serogroup Sejroe, particularly serovar Hardjo, prevails in cattle in several regions. The microscopic agglutination test (MAT) is the current method for diagnosing leptospirosis. It has been proposed that the inclusion of local strains could detect a larger set of seroreactive animals. In that context, the aim of the present study was to evaluate if the usage of local strains as antigens increases the sensitivity of the serodiagnosis of bovine leptospirosis. Blood and urine samples were collected from 314 bovines from several herds randomly selected in a slaughterhouse in Rio de Janeiro, Brazil. Serological diagnosis was made with MAT using a 21 reference-strains panel (MAT21). Additionally, 12 local strains (MAT33) were included as antigens. PCR was performed with the urine samples and it was positive on 71 out of 222 samples (31.9%). MAT21 identified as seroreactive 173 (55.1%) out of the 314 animals studied, with Sejroe the most common (38.1%). In MAT33, 204 (65.0%) animals were seroreactive with a significant increase on seroreactivity (9.9%). In conclusion, MAT presented with a significant increase of sensitivity when local strains were used as antigens. Among the local strains, 2013_U152 (KP263062) (serogroup Shermani) and 2013_U280 (KP263069) (serogroup Grippotyphosa) showed to be more antigenic. Copyright © 2015. Published by Elsevier B.V.

Age- and Gender-Specific Reference Intervals for Fasting Blood Glucose and Lipid Levels in School Children Measured With Abbott Architect c8000 Chemistry Analyzer.

PubMed

Tamimi, Waleed; Albanyan, Esam; Altwaijri, Yasmin; Tamim, Hani; Alhussein, Fahad

2012-04-01

Reference intervals for pubertal characteristics are influenced by genetic, geographic, dietary and socioeconomic factors. Therefore, the aim of this study was to establish age-specific reference intervals of glucose and lipid levels among local school children. This was cross-sectional study, conducted among Saudi school children. Fasting blood samples were collected from 2149 children, 1138 (53%) boys and 1011 (47%) girls, aged 6 to 18 years old. Samples were analyzed on the Architect c8000 Chemistry System (Abbott Diagnostics, USA) for glucose, cholesterol, triglycerides, HDL and LDL. Reference intervals were established by nonparametric methods between the 2.5th and 97.5th percentiles. Significant differences were observed between boys and girls for cholesterol and triglycerides levels in all age groups (P < 0.02). Only at age 6-7 years and at adolescents, HDL and LDL levels were found to be significant (P < 0.001). No significant differences were seen in glucose levels except at age 12 to 13 years. Saudi children have comparable serum cholesterol levels than their Western counterparts. This may reflect changing dietary habits and increasing affluence in Saudi Arabia. Increased lipid screening is anticipated, and these reference intervals will aid in the early assessment of cardiovascular and diabetes risk in Saudi pediatric populations.

Community exposure to hazardous site remediation in rural New Zealand: an exposed-referent study of serum dioxins and health effects.

PubMed

McBride, David; Lovelock, Kirsten; Shepherd, Daniel; Dirks, Kim; Welch, David; Gray, Andrew

2016-10-01

The New Zealand Ministry of Health responded to community concern about dioxin exposure during on-site remediation of a pesticide-contaminated rural area by commissioning this exposed-referent study of serum dioxins and health in local residents. All 200 residents were eligible, with age and sex matching to demographically comparable referents. Face-to-face interviews included questions on health status, health-related quality of life (HRQOL) and perceptions about community consultation. Thirty serum samples were obtained, eligibility being based on likelihood of exposure and age. Both HRQOL and serum outcomes were analysed by the appropriate regression methods. Of 200 eligible residents, 139 (69.5%) participated, with 139 matched referents. Mapua residents had lower physical and psychological HRQOL scores, but no difference in health status. 2,3,7,8 TCDD was below the limit of detection in the majority of all serum samples, with some congeners being higher in referents. Perceptions of the communication process were equivocal. Both dioxin levels and measures of health did not differ significantly between the exposed community and controls. Implications for public health: The results suggest neither significant dioxin exposure nor community health effects. Oversight by expert panel with health expertise, allied to sound communication, may have helped the community understand the risks. © 2016 Public Health Association of Australia.

Selection of internal reference genes for normalization of reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis in the rumen epithelium.

PubMed

Die, Jose V; Baldwin, Ransom L; Rowland, Lisa J; Li, Robert; Oh, Sunghee; Li, Congjun; Connor, Erin E; Ranilla, Maria-Jose

2017-01-01

The rumen is lined on the luminal side by a stratified squamous epithelium that is responsible for not only absorption, but also transport, extensive short-chain fatty acid (SCFA) metabolism and protection. Butyrate has been demonstrated to initiate the differentiation of the tissue following introduction of solid feed to the weaning neonate as well as affecting the metabolism of other nutrients and absorption of nutrients in in vitro experiments. The objective of the present study was to validate expression stability of eight putative reference genes bovine rumen, considering the intrinsic heterogeneity of bovine rumen with regard to different luminal characteristics due to direct infusion of butyrate to double the intra-ruminal content of the rumen liquor. Our focus was on identifying stable reference genes which are suitable to normalize real-time RT-qPCR experiments from rumen samples collected from clinical assays, irrespective of localization within the organ and the across physiological state. The most stably expressed genes included: ACTB, UXT, DBNDD2, RPS9, DDX54 and HMBS. Their high stability values suggest these reference genes will facilitate better evaluation of variation of across an array of conditions including: localization within the rumen, differences among cattle fed an array of rations, as well as response to development in the weaning animal. Moreover, we anticipate these reference genes may be useful for expression studies in other ruminants.

Background Mole Fractions of Hydrocarbons in North America Determined from NOAA Global Reference Network Data

NASA Astrophysics Data System (ADS)

Mielke-Maday, I.

2015-12-01

The National Oceanic and Atmospheric Administration (NOAA) Global Monitoring Division (GMD) maintains a global reference network for over 50 trace gas species and analyzes discrete air samples collected by this network throughout the world at the Earth System Research Laboratory in Boulder, Colorado. In particular, flask samples are analyzed for a number of hydrocarbons with policy and health relevance such as ozone precursors, greenhouse gases, and hazardous air pollutants. Because this global network's sites are remote and therefore minimally influenced by local anthropogenic emissions, these data yield information about background ambient mole fractions and can provide a context for observations collected in intensive field campaigns, such as the Front Range Air Pollution and Photochemistry Experiment (FRAPPE), the Southeast Nexus (SENEX) study, and the DISCOVER-AQ deployments. Information about background mole fractions during field campaigns is critical for calculating hydrocarbon enhancements in the region of study and for assessing the extent to which a particular region's local emissions sources contribute to these enhancements. Understanding the geographic variability of the background and its contribution to regional ambient mole fractions is also crucial for the development of realistic regulations. We present background hydrocarbon mole fractions and their ratios in North America using data from air samples collected in the planetary boundary layer at tall towers and aboard aircraft from 2008 to 2014. We discuss the spatial and seasonal variability in these data. We present trends over the time period of measurements and propose possible explanations for these trends.

Kalman/Map filtering-aided fast normalized cross correlation-based Wi-Fi fingerprinting location sensing.

PubMed

Sun, Yongliang; Xu, Yubin; Li, Cheng; Ma, Lin

2013-11-13

A Kalman/map filtering (KMF)-aided fast normalized cross correlation (FNCC)-based Wi-Fi fingerprinting location sensing system is proposed in this paper. Compared with conventional neighbor selection algorithms that calculate localization results with received signal strength (RSS) mean samples, the proposed FNCC algorithm makes use of all the on-line RSS samples and reference point RSS variations to achieve higher fingerprinting accuracy. The FNCC computes efficiently while maintaining the same accuracy as the basic normalized cross correlation. Additionally, a KMF is also proposed to process fingerprinting localization results. It employs a new map matching algorithm to nonlinearize the linear location prediction process of Kalman filtering (KF) that takes advantage of spatial proximities of consecutive localization results. With a calibration model integrated into an indoor map, the map matching algorithm corrects unreasonable prediction locations of the KF according to the building interior structure. Thus, more accurate prediction locations are obtained. Using these locations, the KMF considerably improves fingerprinting algorithm performance. Experimental results demonstrate that the FNCC algorithm with reduced computational complexity outperforms other neighbor selection algorithms and the KMF effectively improves location sensing accuracy by using indoor map information and spatial proximities of consecutive localization results.

Kalman/Map Filtering-Aided Fast Normalized Cross Correlation-Based Wi-Fi Fingerprinting Location Sensing

PubMed Central

Sun, Yongliang; Xu, Yubin; Li, Cheng; Ma, Lin

2013-01-01

A Kalman/map filtering (KMF)-aided fast normalized cross correlation (FNCC)-based Wi-Fi fingerprinting location sensing system is proposed in this paper. Compared with conventional neighbor selection algorithms that calculate localization results with received signal strength (RSS) mean samples, the proposed FNCC algorithm makes use of all the on-line RSS samples and reference point RSS variations to achieve higher fingerprinting accuracy. The FNCC computes efficiently while maintaining the same accuracy as the basic normalized cross correlation. Additionally, a KMF is also proposed to process fingerprinting localization results. It employs a new map matching algorithm to nonlinearize the linear location prediction process of Kalman filtering (KF) that takes advantage of spatial proximities of consecutive localization results. With a calibration model integrated into an indoor map, the map matching algorithm corrects unreasonable prediction locations of the KF according to the building interior structure. Thus, more accurate prediction locations are obtained. Using these locations, the KMF considerably improves fingerprinting algorithm performance. Experimental results demonstrate that the FNCC algorithm with reduced computational complexity outperforms other neighbor selection algorithms and the KMF effectively improves location sensing accuracy by using indoor map information and spatial proximities of consecutive localization results. PMID:24233027

Magnetotellurics with long distance remote reference to reject DC railway noise

NASA Astrophysics Data System (ADS)

Hanstein, T.; Jiang, J.; Strack, K.; Ritter, O.

2014-12-01

Some parts of railway network in Europe is electrified by DC current. The return current in the ground is varying in space, time and power when the train is moving. Since the train traffic is active 24 hours, there is no quite time. The train signal is dominating for periods longer than 1 s and is a near field source. The transfer function of the magnetotelluric sounding (MT) is influenced by this near field source, the phase is going to zero and amplitude increase with slope 1 for longer periods. Since this dominating noise is present all day robust magnetotelluric processing technique to identify and remove outliers are not applicable and sufficient. The remote reference technique has successfully been applied for magnetotelluric soundings Combining an disturbed local MT data set with the data of the remote station, which is recording simultaneously the horizontal magnetic fields, can improve the data quality. Finding a good remote station during field survey is difficult and expensive. There is a permanent MT remote reference station in Germany. The set up and maintance is done by the GFZ - Helmholtz Centre Potsdam - GFZ German Research Centre for Geosciences. The location is near Wittstock and has good signal-to-noise-ratio with low cutural noise, the ground is almost lD and recording since May 2010. The electric and magnetic field is continously recorded with 250 Hz sampling and induction coils. The magnetic field is also recorded with fluxgate magnetometers and 5 Hz sampling. The distance to the local MT site is about 600 km.

Changes in hydrogen isotope ratios in sequential plumage stages: an implication for the creation of isotope-base maps for tracking migratory birds.

PubMed

Duxbury, J M; Holroyd, G L; Muehlenbachs, K

2003-09-01

Accurate reference maps are important in the use of stable-isotopes to track the movements of migratory birds. Reference maps created by the analysis of samples collected from young at the nest site are more accurate than simply referring to naturally occurring patterns of hydrogen isotope ratios created by precipitation cycles. Ratios of hydrogen isotopes in the nutrients incorporated early in the development of young birds can be derived from endogenous, maternal sources. Base-maps should be created with the analysis of tissue samples from hatchlings after local the isotopic signature of exogenous nutrients is dominant. Migratory species such as Peregrine Falcons are known to use endogenous sources in the creation of their eggs, therefore knowledge of what plumage stage best represents the local hydrogen ratios would assist in the planning of nest visits. We conducted diet manipulation experiments involving Japanese Quail and Peregrine Falcons to determine the plumage stage when hydrogen isotope ratios were indicative of a switch in their food source. The natal down of both the quail and falcons reflected the diet of breeding adult females. The hydrogen isotope ratios of a new food source were dominant in the juvenile down of the young falcons, although a further shift was detected in the final juvenile plumage. The juvenile plumage is grown during weeks 3-4 after hatch on Peregrine Falcons. Nest visits for the purpose of collecting feathers for isotope-base-map creation should be made around 4 weeks after the presumed hatch of the young falcons.

Parasite fauna of Etheostoma nigrum (Percidae: Etheostomatinae) in localities of varying pollution stress in the St. Lawrence River, Quebec, Canada.

PubMed

Krause, Rachel J; McLaughlin, J Daniel; Marcogliese, David J

2010-07-01

Parasite communities were examined in johnny darters (Etheostoma nigrum) collected from five localities in the St. Lawrence River in southwestern Quebec: two reference localities, one polluted locality upstream of the Island of Montreal and downstream of industrial and agricultural activity, and two polluted localities downstream of the Island of Montreal in the plume from the wastewater treatment facility. Twenty-four helminth species were found. Fish from the upstream polluted locality had the highest parasite species richness and total parasite numbers, and fish from the downstream polluted localities the lowest. Nonmetric multivariate analyses were conducted using square-root-transformed Bray-Curtis dissimilarity index. An analysis of similarity, dendrogram of centroids, and a permutational multivariate analysis of variance with contrasts all showed that fish from the reference localities had different parasite community composition than those from the polluted localities, and fish from the upstream polluted locality had different parasite communities than fish from the downstream polluted localities. Differences between reference and polluted localities were mainly due to higher abundances of the brain-encysting trematode, Ornithodiplostomum sp., at the reference localities. Differences between upstream and downstream polluted localities were mainly due to a higher diversity and abundance of trematodes in fish at the upstream locality.

Field substitution of nonresponders can maintain sample size and structure without altering survey estimates-the experience of the Italian behavioral risk factors surveillance system (PASSI).

PubMed

Baldissera, Sandro; Ferrante, Gianluigi; Quarchioni, Elisa; Minardi, Valentina; Possenti, Valentina; Carrozzi, Giuliano; Masocco, Maria; Salmaso, Stefania

2014-04-01

Field substitution of nonrespondents can be used to maintain the planned sample size and structure in surveys but may introduce additional bias. Sample weighting is suggested as the preferable alternative; however, limited empirical evidence exists comparing the two methods. We wanted to assess the impact of substitution on surveillance results using data from Progressi delle Aziende Sanitarie per la Salute in Italia-Progress by Local Health Units towards a Healthier Italy (PASSI). PASSI is conducted by Local Health Units (LHUs) through telephone interviews of stratified random samples of residents. Nonrespondents are replaced with substitutes randomly preselected in the same LHU stratum. We compared the weighted estimates obtained in the original PASSI sample (used as a reference) and in the substitutes' sample. The differences were evaluated using a Wald test. In 2011, 50,697 units were selected: 37,252 were from the original sample and 13,445 were substitutes; 37,162 persons were interviewed. The initially planned size and demographic composition were restored. No significant differences in the estimates between the original and the substitutes' sample were found. In our experience, field substitution is an acceptable method for dealing with nonresponse, maintaining the characteristics of the original sample without affecting the results. This evidence can support appropriate decisions about planning and implementing a surveillance system. Copyright © 2014 Elsevier Inc. All rights reserved.

Additions to Mars Global Reference Atmospheric Model (MARS-GRAM)

NASA Technical Reports Server (NTRS)

Justus, C. G.; James, Bonnie

1992-01-01

Three major additions or modifications were made to the Mars Global Reference Atmospheric Model (Mars-GRAM): (1) in addition to the interactive version, a new batch version is available, which uses NAMELIST input, and is completely modular, so that the main driver program can easily be replaced by any calling program, such as a trajectory simulation program; (2) both the interactive and batch versions now have an option for treating local-scale dust storm effects, rather than just the global-scale dust storms in the original Mars-GRAM; and (3) the Zurek wave perturbation model was added, to simulate the effects of tidal perturbations, in addition to the random (mountain wave) perturbation model of the original Mars-GRAM. A minor modification was also made which allows heights to go 'below' local terrain height and return 'realistic' pressure, density, and temperature, and not the surface values, as returned by the original Mars-GRAM. This feature will allow simulations of Mars rover paths which might go into local 'valley' areas which lie below the average height of the present, rather coarse-resolution, terrain height data used by Mars-GRAM. Sample input and output of both the interactive and batch versions of Mars-GRAM are presented.

Additions to Mars Global Reference Atmospheric Model (Mars-GRAM)

NASA Technical Reports Server (NTRS)

Justus, C. G.

1991-01-01

Three major additions or modifications were made to the Mars Global Reference Atmospheric Model (Mars-GRAM): (1) in addition to the interactive version, a new batch version is available, which uses NAMELIST input, and is completely modular, so that the main driver program can easily be replaced by any calling program, such as a trajectory simulation program; (2) both the interactive and batch versions now have an option for treating local-scale dust storm effects, rather than just the global-scale dust storms in the original Mars-GRAM; and (3) the Zurek wave perturbation model was added, to simulate the effects of tidal perturbations, in addition to the random (mountain wave) perturbation model of the original Mars-GRAM. A minor modification has also been made which allows heights to go below local terrain height and return realistic pressure, density, and temperature (not the surface values) as returned by the original Mars-GRAM. This feature will allow simulations of Mars rover paths which might go into local valley areas which lie below the average height of the present, rather coarse-resolution, terrain height data used by Mars-GRAM. Sample input and output of both the interactive and batch version of Mars-GRAM are presented.

Population-based pediatric reference intervals for general clinical chemistry analytes on the Abbott Architect ci8200 instrument.

PubMed

Ridefelt, Peter; Aldrimer, Mattias; Rödöö, Per-Olof; Niklasson, Frank; Jansson, Leif; Gustafsson, Jan; Hellberg, Dan

2012-02-29

Reference intervals are crucial decision-making tools aiding clinicians in differentiating between healthy and diseased populations. However, for children such values often are lacking or incomplete. Blood samples were obtained from 692 healthy children, aged 6 months to 18 years, recruited in daycare centers and schools. Twelve common general clinical chemistry analytes were measured on the Abbott Architect ci8200 platform; sodium, potassium, chloride, calcium, albumin-adjusted calcium, phosphate, magnesium, creatinine (Jaffe and enzymatic), cystatin C, urea and uric acid. Age- and gender specific pediatric reference intervals were defined by calculating the 2.5th and 97.5th percentiles. The data generated is primarily applicable to a Caucasian population when using the Abbott Architect platform, but could be used by any laboratory if validated for the local patient population.

230 s room-temperature storage time and 1.14 eV hole localization energy in In{sub 0.5}Ga{sub 0.5}As quantum dots on a GaAs interlayer in GaP with an AlP barrier

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

Bonato, Leo, E-mail: leo.bonato@tu-berlin.de; Sala, Elisa M.; Stracke, Gernot

2015-01-26

A GaP n{sup +}p-diode containing In{sub 0.5}Ga{sub 0.5}As quantum dots (QDs) and an AlP barrier is characterized electrically, together with two reference samples: a simple n{sup +}p-diode and an n{sup +}p-diode with AlP barrier. Localization energy, capture cross-section, and storage time for holes in the QDs are determined using deep-level transient spectroscopy. The localization energy is 1.14(±0.04) eV, yielding a storage time at room temperature of 230(±60) s, which marks an improvement of 2 orders of magnitude compared to the former record value in QDs. Alternative material systems are proposed for still higher localization energies and longer storage times.

Local patient dose diagnostic reference levels in pediatric interventional cardiology in Chile using age bands and patient weight values

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

Ubeda, Carlos, E-mail: cubeda@uta.cl; Miranda, Patricia; Vano, Eliseo

Purpose: To present the results of a patient dose evaluation program in pediatric cardiology and propose local diagnostic reference levels (DRLs) for different types of procedure and age range, in addition to suggesting approaches to correlate patient dose values with patient weight. This study was the first conducted in Latin America for pediatric interventional cardiology under the auspices of the International Atomic Energy Agency. Methods: Over three years, the following data regarding demographic and patient dose values were collected: age, gender, weight, height, number of cine series, total number of cine frames, fluoroscopy time (FT), and two dosimetric quantities, dose-areamore » product (DAP) and cumulative dose (CD), at the patient entrance reference point. The third quartile values for FT, DAP, CD, number of cine series, and the DAP/body weight ratio were proposed as the set of quantities to use as local DRLs. Results: Five hundred and seventeen patients were divided into four age groups. Sample sizes by age group were 120 for <1 yr; 213 for 1 to <5 yr; 82 for 5 to <10 yr; and 102 for 10 to <16 yr. The third quartile values obtained for DAP by diagnostic and therapeutic procedures and age range were 1.17 and 1.11 Gy cm{sup 2} for <1 yr; 1.74 and 1.90 Gy cm{sup 2} for 1 to <5 yr; 2.83 and 3.22 Gy cm{sup 2} for 5 to <10 yr; and 7.34 and 8.68 Gy cm{sup 2} for 10 to <16 yr, respectively. The third quartile value obtained for the DAP/body weight ratio for the full sample of procedures was 0.17 (Gy cm{sup 2}/kg) for diagnostic and therapeutic procedures. Conclusions: The data presented in this paper are an initial attempt at establishing local DRLs in pediatric interventional cardiology, from a large sample of procedures for the standard age bands used in Europe, complemented with the values of the ratio between DAP and patient weight. This permits a rough estimate of DRLs for different patient weights and the refining of these values for the age bands when there may be large differences in child size. These DRLs were obtained at the largest pediatric hospital in Chile, with an active optimization program, and could be used by other hospitals in the Latin America region to compare their current patient dose values and determine whether corrective action is appropriate.« less

Local patient dose diagnostic reference levels in pediatric interventional cardiology in Chile using age bands and patient weight values.

PubMed

Ubeda, Carlos; Miranda, Patricia; Vano, Eliseo

2015-02-01

To present the results of a patient dose evaluation program in pediatric cardiology and propose local diagnostic reference levels (DRLs) for different types of procedure and age range, in addition to suggesting approaches to correlate patient dose values with patient weight. This study was the first conducted in Latin America for pediatric interventional cardiology under the auspices of the International Atomic Energy Agency. Over three years, the following data regarding demographic and patient dose values were collected: age, gender, weight, height, number of cine series, total number of cine frames, fluoroscopy time (FT), and two dosimetric quantities, dose-area product (DAP) and cumulative dose (CD), at the patient entrance reference point. The third quartile values for FT, DAP, CD, number of cine series, and the DAP/body weight ratio were proposed as the set of quantities to use as local DRLs. Five hundred and seventeen patients were divided into four age groups. Sample sizes by age group were 120 for <1 yr; 213 for 1 to <5 yr; 82 for 5 to <10 yr; and 102 for 10 to <16 yr. The third quartile values obtained for DAP by diagnostic and therapeutic procedures and age range were 1.17 and 1.11 Gy cm 2 for <1 yr; 1.74 and 1.90 Gy cm 2 for 1 to <5 yr; 2.83 and 3.22 Gy cm 2 for 5 to <10 yr; and 7.34 and 8.68 Gy cm 2 for 10 to <16 yr, respectively. The third quartile value obtained for the DAP/body weight ratio for the full sample of procedures was 0.17 (Gy cm 2 /kg) for diagnostic and therapeutic procedures. The data presented in this paper are an initial attempt at establishing local DRLs in pediatric interventional cardiology, from a large sample of procedures for the standard age bands used in Europe, complemented with the values of the ratio between DAP and patient weight. This permits a rough estimate of DRLs for different patient weights and the refining of these values for the age bands when there may be large differences in child size. These DRLs were obtained at the largest pediatric hospital in Chile, with an active optimization program, and could be used by other hospitals in the Latin America region to compare their current patient dose values and determine whether corrective action is appropriate. © 2015 American Association of Physicists in Medicine.

Factors influencing leaf litter decomposition: An intersite decomposition experiment across China

USGS Publications Warehouse

Zhou, G.; Guan, L.; Wei, X.; Tang, X.; Liu, S.; Liu, J.; Zhang, Dongxiao; Yan, J.

2008-01-01

The Long-Term Intersite Decomposition Experiment in China (hereafter referred to as LTIDE-China) was established in 2002 to study how substrate quality and macroclimate factors affect leaf litter decomposition. The LTIDE-China includes a wide variety of natural and managed ecosystems, consisting of 12 forest types (eight regional broadleaf forests, three needle-leaf plantations and one broadleaf plantation) at eight locations across China. Samples of mixed leaf litter from the south subtropical evergreen broadleaf forest in Dinghushan (referred to as the DHS sample) were translocated to all 12 forest types. The leaf litter from each of other 11 forest types was placed in its original forest to enable comparison of decomposition rates of DHS and local litters. The experiment lasted for 30 months, involving collection of litterbags from each site every 3 months. Our results show that annual decomposition rate-constants, as represented by regression fitted k-values, ranged from 0.169 to 1.454/year. Climatic factors control the decomposition rate, in which mean annual temperature and annual actual evapotranspiration are dominant and mean annual precipitation is subordinate. Initial C/N and N/P ratios were demonstrated to be important factors of regulating litter decomposition rate. Decomposition process may apparently be divided into two phases controlled by different factors. In our study, 0.75 years is believed to be the dividing line of the two phases. The fact that decomposition rates of DHS litters were slower than those of local litters may have been resulted from the acclimation of local decomposer communities to extraneous substrate. ?? 2008 Springer Science+Business Media B.V.

Regional soil geochemistry in the Ojailen Valley: a realm dominated by the industrial and mining city of Puertollano (South Central Spain)

NASA Astrophysics Data System (ADS)

López-Berdonces, Miguel; Fernandez-Calderón, Sergio; Higueras, Pablo; María Esbrí, Jose; Gonzalez-Corrochano, Beatríz; García-Noguero, Eva Mª; Martínez-Coronado, Alba; García-Noguero, Carolina

2013-04-01

Regional soil geochemistry in the Ojailén Valley: a realm dominated by the industrial and mining city of Puertollano (South Central Spain). Authors: Miguel A. López-Berdonces¹; Sergio Fernández Calderón¹; Pablo Higueras¹; José María Esbrí¹; Beatriz González-Corrochano¹; Eva Mª García-Noguero¹; Alba Martínez-Coronado¹; Carolina García Noguero¹ ¹Instituto de Geología Aplicada, Universidad de Castilla La Mancha, Almadén 13400 (Spain). Ojailén Valley is situated in South Central of Spain, an area where livestock, agriculture, mining and industry coexist. This work tries to assess the relationships between these activities and local environmental compartments: water, soils and heavy metal contents, and establish the most appropriate methodology of sample treatment and analytical techniques that can be employed on this kind of studies. For soil geochemistry, 152 samples were taken at two different depths, one at surface layer and another at 20 cm depth, and establish relationships between them and the possible sources. For this purpose, we determine soil parameters (pH, conductivity and organic matter) and total metal contents by Energy Dispersion of X Ray Fluorescence (EDXRF). Samples with higher nickel contents were analyzed with Inductive Coupled Plasma Spectroscopy (ICP-OES) after acid digestion. The study of surface waters includes 18 samples along the river and tributaries near mining and industrial areas. Water analysis was performed by ICP-OES. Soil samples shows pH between 6 and 8.5, highest located near on the east part of the valley, in the vicinity of petrochemical complex. Conductivity values show higher levels (1600 µS cm¯¹) in the vicinity of Puertollano and the industrial sites. Local reference value (LRV) for contaminated soils were determined according to the methodology proposed by Jimenez-Ballesta et al. (2010), using the equation: LRV=GM + 2SD, where LRV: Local Reference Value, GM: Geometric Mean, SD: Standard Deviation. Trace metals values are significantly higher than calculated LRV, especially for Zn, Pb, (Average content: 230 mg kg¯¹ and 249.9 mg kg¯¹ respectively), probable due to Pb-Zn mining in the nearest Alcudia valley. Other elements seem to be influenced by petrochemical industry (Ni, V, and Cu) with LRV: 199.9 mg kg¯¹, 39.2 mg kg¯¹ and 184.2 mg kg¯¹ respectively. Most water samples have metal contents higher than levels for drinking water (WHO, 2006), especially Fe and Pb with 20 µg l¯¹ and 10 µg l¯¹ respectively. Higher metal contents were located on three different sites: downstream an open-pit coal mine, in stagnant water where we can find an old sewage treatment plant, and downstream a photovoltaic plant built in 2008. We can consider that Ojailén Valley is not an area with high contents in heavy metals in the environment, but Puertollano and its petrochemical complex have contents in Pb, Zn, Cu, As, Ni above the LRV. A comparison of results obtained by ICP-MS and XRF related to Pb, Zn, Cr, Ni in thirty-four selected samples, we can conclude that both techniques are qualitatively agree, although XRF cannot be considered suitable for establishing reference legal limits. References Jiménez-Ballesta, R; Conde-Bueno,P; Martin-Rubí,J.A.; García-Jímenez,R. 2010. Geochemical baseline contents levels and soil quality reference values of trace elements in soils from the Mediterranean (Castilla-La Mancha, Spain). Central European Journal of Geosciences 2, 441-454. WHO2006. Guidelines for drinking- water quality, Vol.1, 3rd edition incorporating 1st and 2nd addenda. (http//www.who.int/entity/water_sanitation_health/dwq/fulltext.pdf) Geneve, Suiza.

Subjective Social Status and Well-Being: The Role of Referent Abstraction.

PubMed

Haught, Heather M; Rose, Jason; Geers, Andrew; Brown, Jill A

2015-01-01

Subjective social status (SSS) has been shown to predict well-being and mental health, above and beyond objective social status (OSS). However, little is known about the factors that moderate this relationship. Two studies explored whether the link between SSS and well-being varied depending upon the referent used for comparison in SSS judgments. Participants judged their well-being and SSS in comparison to referents that varied in abstraction. A confirmatory factor analysis on SSS judgments yielded two factors: (a) SSS perceptions toward global referents and (b) SSS perceptions toward local referents. SSS relative to a global referent was a better predictor of depression (Studies 1 and 2), life satisfaction (Studies 1 and 2), and self-esteem (Study 2) than SSS relative to a local referent. These findings have theoretical implications for understanding how people differentiate between local vs. global referents and practical implications for status-related health disparities.

Uptake of Elements From Aerosols by Humans ~ A Case Study From Delhi & Bangalore Cities

NASA Astrophysics Data System (ADS)

Anand, S.; Yadav, S.; Jain, V. K.

2006-05-01

Aerosol research has gained tremendous importance globally due to the cumulative effects of increasing industrialization and urbanization on aerosol production which can have an alarming impact on the climate of the planet as well as the health of its inhabitants. Therefore, there is an increasing need to study aerosols for all of their physicochemical and biological aspects on both local and global scales. World over extensive research has gone into studying the physical and the chemical aspects of aerosols. However, little information is yet available on the health impacts of aerosols particularly in the Asian context. Here we report uptake of various elements that are concentrated in aerosols by the human body in Delhi and Bangalore cities and their possible health effects. In many urban areas, for example in Delhi, inhalable fractions of aerosols are known to have high concentrations of elements such as Cu, Zn, Pb, Ba, Ni and Cr (Yadav and Rajamani 2004). Also aerosols in the North West part of India seem to be particularly enriched in these elements. If so, there is a high possibility of these elements getting into the human system either directly or indirectly through water and food. To determine the concentrations of these elements that are present in significant concentrations in the inhalable fractions of aerosols, human hair and blood samples are used as proxies. Both these regions have contrasting geographic and climatic conditions. Delhi (altitude : 213-305m above MSL) located on the fringes of the Thar desert which supplies considerable amount of dust, is semi-arid with annual rainfall of 60-80 cms & temperatures varying between 1° - 45°. Bangalore (altitude of 900m above MSL) receives a high annual rainfall of 80-100 cms and being located on the fringes of tropical forests of the Sahyadri Mountains (Western Ghats) receives little crustal contribution to the aerosols. Samples from least polluted mountainous areas of Himalayas (Gangothri) and Sahyadri (Ooty) were also collected as reference samples. All the samples were digested in a microwave system. Elemental analyses were carried out using both ICP-MS and ICP-AES methods using multi-element standard solutions from Merck. The elements analyzed include Al, Ca, Mg, Ni, Cu, Ba, Zn, Pb, Cr, Sr, K, Na, Si, and P in about 100 samples of blood and hair. Preliminary results indicate a possible human uptake of elements from the aerosols. In comparison to the international reference and local background values (Gangothri), Delhi and Bangalore samples of human hair and blood show significant enrichment of these elements. Samples from Gangothri are comparable to those of the international reference values. Delhi samples have much higher concentrations of several elements, especially Al, Zn, Pb and Cu. Although the Bangalore samples are also enriched compared to the reference values, they are much less enriched relative to the Delhi samples. Bangalore samples have negligible contributions from the crustal aerosols as compared to the Delhi samples where the crustal contributions seem to be very high. Elements enriched in the PM 10 aerosols or the respirable fractions include Ca, Mg, Al (crustal) and Ba, Zn,Cu, Pb, Ni, Cr (anthropogenic). In all the samples, hair seems to be a better long term indicator of elemental uptake compared to blood. The health effect of aerosols can be several as indicated by studies elsewhere and will be discussed.

Local earthquake interferometry of the IRIS Community Wavefield Experiment, Grant County, Oklahoma

NASA Astrophysics Data System (ADS)

Eddy, A. C.; Harder, S. H.

2017-12-01

The IRIS Community Wavefield Experiment was deployed in Grant County, located in north central Oklahoma, from June 21 to July 27, 2016. Data from all nodes were recorded at 250 samples per second between June 21 and July 20 along three lines. The main line was 12.5 km long oriented east-west and consisted of 129 nodes. The other two lines were 5.5 km long north-south oriented with 49 nodes each. During this time, approximately 150 earthquakes of magnitude 1.0 to 4.4 were recorded in the surrounding counties of Oklahoma and Kansas. Ideally, sources for local earthquake interferometry should be near surface events that produce high frequency body waves. Unlike ambient noise seismic interferometry (ANSI), which uses days, weeks, or even months of continuously recorded seismic data, local earthquake interferometry uses only short segments ( 2 min.) of data. Interferometry in this case is based on the cross-correlation of body wave surface multiples where the event source is translated to a reference station in the array, which acts as a virtual source. Multiples recorded between the reference station and all other stations can be cross-correlated to produce a clear seismic trace. This process will be repeated with every node acting as the reference station for all events. The resulting shot gather will then be processed and analyzed for quality and accuracy. Successful application of local earthquake interferometry will produce a crustal image with identifiable sedimentary and basement reflectors and possibly a Moho reflection. Economically, local earthquake interferometry could lower the time and resource cost of active and passive seismic surveys while improving subsurface image quality in urban settings or areas of limited access. The applications of this method can potentially be expanded with the inclusion of seismic events with a magnitude of 1.0 or lower.

Digital Fresnel reflection holography for high-resolution 3D near-wall flow measurement.

PubMed

Kumar, S Santosh; Hong, Jiarong

2018-05-14

We propose a novel backscatter holographic imaging system, as a compact and effective tool for 3D near-wall flow diagnostics at high resolutions, utilizing light reflected at the solid-liquid interface as a reference beam. The technique is fully calibrated, and is demonstrated in a densely seeded channel to achieve a spatial resolution of near-wall flows equivalent to or exceeding prior digital inline holographic measurements using local tracer seeding technique. Additionally, we examined the effects of seeding concentration and laser coherence on the measurement resolution and sample volume resolved, demonstrating the potential to manipulate sample domain by tuning the laser coherence profile.

Common computational properties found in natural sensory systems

NASA Astrophysics Data System (ADS)

Brooks, Geoffrey

2009-05-01

Throughout the animal kingdom there are many existing sensory systems with capabilities desired by the human designers of new sensory and computational systems. There are a few basic design principles constantly observed among these natural mechano-, chemo-, and photo-sensory systems, principles that have been proven by the test of time. Such principles include non-uniform sampling and processing, topological computing, contrast enhancement by localized signal inhibition, graded localized signal processing, spiked signal transmission, and coarse coding, which is the computational transformation of raw data using broadly overlapping filters. These principles are outlined here with references to natural biological sensory systems as well as successful biomimetic sensory systems exploiting these natural design concepts.

Metal concentrations in aquatic environments of Puebla River basin, Mexico: natural and industrial influences.

PubMed

Morales-García, S S; Rodríguez-Espinosa, P F; Shruti, V C; Jonathan, M P; Martínez-Tavera, E

2017-01-01

The rapid urban expansion and presence of volcanoes in the premises of Puebla River basin in central Mexico exert significant influences over its aquatic environments. Twenty surface sediment samples from Puebla River basin consisting of R. Alseseca, R. Atoyac, and Valsequillo dam were collected during September 2009 and analyzed for major (Al, Fe, Mg, Ba, Ca, and K) and trace elements (As, Cd, Co, Cr, Cu, Mn, Ni, Pb, Sr, V, and Zn) in order to identify the metal concentrations and their enrichment. R. Atoyac sediments presented higher concentrations of Ba (1193.8 μg g -1 ) and Pb (27.1 μg g -1 ) in comparison with the local reference sample values. All the metal concentrations except Sr for R. Alseseca sediments were within the range of local reference sample values indicating no significant external influence, whereas Valsequillo dam sediments had elevated concentrations of all the metals suggesting both natural and external influences in the study region. The magnitude of metal contamination was assessed using several indices such as geoaccumulation index (I geo ), enrichment factor (EF), degree of contamination (C d ), and pollution load index (PLI). The results suggest that As, Pb, and Zn were predominantly enriched in the Puebla River basin sediments. Comparing with sediment quality guidelines and ecotoxicological values, it is revealed that Cd, Cr, Cu, and Ni have possible harmful effects on the biological community. The present study provides an outlook of metal enrichment in Puebla River basin sediments, highlighting the necessity to conserve this river ecosystem for the near future.

Paleomagnetism of the Todos Santos Formation in the Maya Block, Chiapas, Mexico: Preliminary Results

NASA Astrophysics Data System (ADS)

Godinez-Urban, A.; Molina-Garza, R. S.; Iriondo, A.; Geissman, J. W.

2008-12-01

Preliminary results of a paleomagnetic study on jurassic volcanic rocks (U-Pb 188.8 +/- 3.2Ma) locally interbedded with red beds assigned to the Todos Santos Formation, sampled in the Homoclinal Tectonic Province of the Neogene Fold Belt, Chiapas-Mexico, reveal multi component magnetizations acquired during pre- and post- folding of these rocks. The samples responded well to thermal demagnetization, but not so to AF demagnetization, suggesting that a high coercivity mineral phase like hematite is the main remanence carrier. The post-folding B-component direction of Dec=174.3 Inc=-30.6 (k=46; alpha95=13.6; N=4) represents a recent Tertiary? overprint; while the pre-folding C-component direction of Dec=329.9 Inc=7.8 (k=12.5; alpha95=16.3; N=8) is in agreement with a previously reported small data set for the Todos Santos Formation. When compared to the North American reference direction (Jurassic Kayenta Formation) the observed direction indicates a counterclockwise rotation of 35.9 +/- 16.6 degrees, and moderate north to south latitudinal displacement. If a reference pole from NE North America is used, the amount of counterclockwise rotation and latitudinal displacement are both slightly reduced. If the assumption that Jurassic strata in Chiapas reflect displacement of the Maya Block, then these data are consistent with reconstructions of the Maya Block in the Gulf of Mexico region. Other sites sampled in Jurassic strata suggest that in addition to the interpreted regional rotation, local (vertical-axis) rotations may have affected the region in more recent times.

Population genetic structure and tolerance to dioxin-like compounds of a migratory marine fish (Menidia menidia) at polychlorinated biphenyl-contaminated and reference sites.

PubMed

Roark, Shaun A; Kelble, Mary A; Nacci, Diane; Champlin, Denise; Coiro, Laura; Guttman, Sheldon I

2005-03-01

The present study was conducted to evaluate evidence of genetic adaptation to local contaminants in populations of the migratory marine fish Menidia menidia residing seasonally in reference sites or an industrial harbor contaminated with dioxin-like compounds (DLCs). For this purpose, we compared DLC sensitivity and genetic patterns of populations sampled from sites both inside and outside New Bedford Harbor (NBH; MA, USA), a U.S. Environmental Protection Agency Superfund site with extreme polychlorinated biphenyl (PCB) contamination. Offspring of M. menidia collected from NBH were significantly less sensitive regarding embryonic exposure to the dioxin-like PCB congener 3,3',4,4',5-pentachlorobiphenyl (PCB 126) than offspring of M. menidia from a reference site. Analysis of 10 polymorphic enzymatic loci indicated little genetic differentiation among populations in the study area. However, genotype frequencies of juveniles from both NBH and an adjacent site in Massachusetts exhibited significant deviations from Hardy-Weinberg equilibrium expectations at one locus, phosphoglucomutase (PGM*). Genetic analysis of survivors of embryonic laboratory exposure to PCB 126 indicated that genotypes at PGM* were related to survivorship. Although a relationship was identified between DLC tolerance and PGM* genotype, regional mixing of M. menidia populations during migration and absence of multigeneration exposure at contaminated sites may limit localized adaptation.

Error assessment of local tie vectors in space geodesy

NASA Astrophysics Data System (ADS)

Falkenberg, Jana; Heinkelmann, Robert; Schuh, Harald

2014-05-01

For the computation of the ITRF, the data of the geometric space-geodetic techniques on co-location sites are combined. The combination increases the redundancy and offers the possibility to utilize the strengths of each technique while mitigating their weaknesses. To enable the combination of co-located techniques each technique needs to have a well-defined geometric reference point. The linking of the geometric reference points enables the combination of the technique-specific coordinate to a multi-technique site coordinate. The vectors between these reference points are called "local ties". The realization of local ties is usually reached by local surveys of the distances and or angles between the reference points. Identified temporal variations of the reference points are considered in the local tie determination only indirectly by assuming a mean position. Finally, the local ties measured in the local surveying network are to be transformed into the ITRF, the global geocentric equatorial coordinate system of the space-geodetic techniques. The current IERS procedure for the combination of the space-geodetic techniques includes the local tie vectors with an error floor of three millimeters plus a distance dependent component. This error floor, however, significantly underestimates the real accuracy of local tie determination. To fullfill the GGOS goals of 1 mm position and 0.1 mm/yr velocity accuracy, an accuracy of the local tie will be mandatory at the sub-mm level, which is currently not achievable. To assess the local tie effects on ITRF computations, investigations of the error sources will be done to realistically assess and consider them. Hence, a reasonable estimate of all the included errors of the various local ties is needed. An appropriate estimate could also improve the separation of local tie error and technique-specific error contributions to uncertainties and thus access the accuracy of space-geodetic techniques. Our investigations concern the simulation of the error contribution of each component of the local tie definition and determination. A closer look into the models of reference point definition, of accessibility, of measurement, and of transformation is necessary to properly model the error of the local tie. The effect of temporal variations on the local ties will be studied as well. The transformation of the local survey into the ITRF can be assumed to be the largest error contributor, in particular the orientation of the local surveying network to the ITRF.

Accelerated construction of a regional DNA-barcode reference library: Caddisflies (Trichoptera) in the Great Smoky Mountains National Park

USGS Publications Warehouse

Zhou, X.; Robinson, J.L.; Geraci, C.J.; Parker, C.R.; Flint, O.S.; Etnier, D.A.; Ruiter, D.; DeWalt, R.E.; Jacobus, L.M.; Hebert, P.D.N.

2011-01-01

Deoxyribonucleic acid (DNA) barcoding is an effective tool for species identification and lifestage association in a wide range of animal taxa. We developed a strategy for rapid construction of a regional DNA-barcode reference library and used the caddisflies (Trichoptera) of the Great Smoky Mountains National Park (GSMNP) as a model. Nearly 1000 cytochrome c oxidase subunit I (COI) sequences, representing 209 caddisfly species previously recorded from GSMNP, were obtained from the global Trichoptera Barcode of Life campaign. Most of these sequences were collected from outside the GSMNP area. Another 645 COI sequences, representing 80 species, were obtained from specimens collected in a 3-d bioblitz (short-term, intense sampling program) in GSMNP. The joint collections provided barcode coverage for 212 species, 91% of the GSMNP fauna. Inclusion of samples from other localities greatly expedited construction of the regional DNA-barcode reference library. This strategy increased intraspecific divergence and decreased average distances to nearest neighboring species, but the DNA-barcode library was able to differentiate 93% of the GSMNP Trichoptera species examined. Global barcoding projects will aid construction of regional DNA-barcode libraries, but local surveys make crucial contributions to progress by contributing rare or endemic species and full-length barcodes generated from high-quality DNA. DNA taxonomy is not a goal of our present work, but the investigation of COI divergence patterns in caddisflies is providing new insights into broader biodiversity patterns in this group and has directed attention to various issues, ranging from the need to re-evaluate species taxonomy with integrated morphological and molecular evidence to the necessity of an appropriate interpretation of barcode analyses and its implications in understanding species diversity (in contrast to a simple claim for barcoding failure).

Monitoring for airborne allergens

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

Burge, H.A.

1992-07-01

Monitoring for allergens can provide some information on the kinds and levels of exposure experienced by local patient populations, providing volumetric methods are used for sample collection and analysis is accurate and consistent. Such data can also be used to develop standards for the specific environment and to begin to develop predictive models. Comparing outdoor allergen aerosols between different monitoring sites requires identical collection and analysis methods and some kind of rational standard, whether arbitrary, or based on recognized health effects.32 references.

Community-level response of fishes and aquatic macroinvertebrates to stream restoration in a third-order tributary of the Potomac River, USA

USGS Publications Warehouse

Selego, S.M.; Rose, C.L.; Merovich, G.T.; Welsh, S.A.; Anderson, James T.

2012-01-01

Natural stream channel design principles and riparian restoration practices were applied during spring 2010 to an agriculturally impaired reach of the Cacapon River, a tributary of the Potomac River which flows into the Chesapeake Bay. Aquatic macroinvertebrates and fishes were sampled from the restoration reach, two degraded control, and two natural reference reaches prior to, concurrently with, and following restoration (2009 through 2010). Collector filterers and scrapers replaced collector gatherers as the dominant macroinvertebrate functional feeding groups in the restoration reach. Before restoration, based on indices of biotic integrity (IBI), the restoration reach fish and macroinvertebrate communities closely resembled those sampled from the control reaches, and after restoration more closely resembled those from the reference reaches. Although the macroinvertebrate community responded more favorably than the fish community, both communities recovered quickly from the temporary impairment caused by the disturbance of restoration procedures and suggest rapid improvement in local ecological conditions. Copyright ?? 2012 Stephen M. Selego et al.

Community-level response of fishes and aquatic macroinvertebrates to stream restoration in a third-order tributary of the Potomac River, USA

USGS Publications Warehouse

Selego, Stephen M.; Rose, Charnee L.; Merovich, George T.; Welsh, Stuart A.; Anderson, James T.

2012-01-01

Natural stream channel design principles and riparian restoration practices were applied during spring 2010 to an agriculturally impaired reach of the Cacapon River, a tributary of the Potomac River which flows into the Chesapeake Bay. Aquatic macroinvertebrates and fishes were sampled from the restoration reach, two degraded control, and two natural reference reaches prior to, concurrently with, and following restoration (2009 through 2010). Collector filterers and scrapers replaced collector gatherers as the dominant macroinvertebrate functional feeding groups in the restoration reach. Before restoration, based on indices of biotic integrity (IBI), the restoration reach fish and macroinvertebrate communities closely resembled those sampled from the control reaches, and after restoration more closely resembled those from the reference reaches. Although the macroinvertebrate community responded more favorably than the fish community, both communities recovered quickly from the temporary impairment caused by the disturbance of restoration procedures and suggest rapid improvement in local ecological conditions.

Survey of abdominal obesities in an adult urban population of Kinshasa, Democratic Republic of Congo

PubMed Central

Kasiam Lasi On’kin, JB; Longo-Mbenza, B; Okwe, A Nge; Kabangu, N Kangola

2007-01-01

Summary Background The prevalence of overweight/obesity, which is an important cardiovascular risk factor, is rapidly increasing worldwide. Abdominal obesity, a fundamental component of the metabolic syndrome, is not defined by appropriate cutoff points for sub-Saharan Africa. Objective To provide baseline and reference data on the anthropometry/body composition and the prevalence rates of obesity types and levels in the adult urban population of Kinshasa, DRC, Central Africa. Methods During this cross-sectional study carried out within a random sample of adults in Kinshasa town, body mass index, waist circumference and fatty mass were measured using standard methods. Their reference and local thresholds (cut-off points) were compared with those of WHO, NCEP and IFD to define the types and levels of obesity in the population. Results From this sample of 11 511 subjects (5 676 men and 5 835 women), the men presented with similar body mass index and fatty mass values to those of the women, but higher waist measurements. The international thresholds overestimated the prevalence of denutrition, but underscored that of general and abdominal obesity. The two types of obesity were more prevalent among women than men when using both international and local thresholds. Body mass index was negatively associated with age; but abdominal obesity was more frequent before 20 years of age and between 40 and 60 years old. Local thresholds of body mass index (≥ 23, ≥ 27 and ≥ 30 kg/m2) and waist measurement (≥ 80, ≥ 90 and ≥ 94 cm) defined epidemic rates of overweight/general obesity (52%) and abdominal obesity (40.9%). The threshold of waist circumference ≥ 94 cm (90th percentile) corresponding to the threshold of the body mass index ≥ 30 kg/m2 (90th percentile) was proposed as the specific threshold of definition of the metabolic syndrome, without reference to gender, for the cities of sub-Saharan Africa. Conclusion Further studies are required to define the optimal threshold of waist circumference in rural settings. The present local cut-off points of body mass index and waist circumference could be appropriate for the identification of Africans at risk of obesity-related disorders, and indicate the need to implement interventions to reverse increasing levels of obesity. PMID:17985031

Identification of Metal Oxide Nanoparticles in Histological Samples by Enhanced Darkfield Microscopy and Hyperspectral Mapping.

PubMed

Roth, Gary A; Sosa Peña, Maria del Pilar; Neu-Baker, Nicole M; Tahiliani, Sahil; Brenner, Sara A

2015-12-08

Nanomaterials are increasingly prevalent throughout industry, manufacturing, and biomedical research. The need for tools and techniques that aid in the identification, localization, and characterization of nanoscale materials in biological samples is on the rise. Currently available methods, such as electron microscopy, tend to be resource-intensive, making their use prohibitive for much of the research community. Enhanced darkfield microscopy complemented with a hyperspectral imaging system may provide a solution to this bottleneck by enabling rapid and less expensive characterization of nanoparticles in histological samples. This method allows for high-contrast nanoscale imaging as well as nanomaterial identification. For this technique, histological tissue samples are prepared as they would be for light-based microscopy. First, positive control samples are analyzed to generate the reference spectra that will enable the detection of a material of interest in the sample. Negative controls without the material of interest are also analyzed in order to improve specificity (reduce false positives). Samples can then be imaged and analyzed using methods and software for hyperspectral microscopy or matched against these reference spectra in order to provide maps of the location of materials of interest in a sample. The technique is particularly well-suited for materials with highly unique reflectance spectra, such as noble metals, but is also applicable to other materials, such as semi-metallic oxides. This technique provides information that is difficult to acquire from histological samples without the use of electron microscopy techniques, which may provide higher sensitivity and resolution, but are vastly more resource-intensive and time-consuming than light microscopy.

Morphometry, Microstructure, and Wear Pattern of Neornithischian Dinosaur Teeth From the Upper Cretaceous Iharkút Locality (Hungary).

PubMed

Virág, Attila; Ősi, Attila

2017-08-01

Teeth of iguanodontian ornithopods and ceratopsians could be remarkably similar, thus the referral of isolated dental material to particular neornithischian clades can be highly problematic. These groups are represented by the rhabdodontid Mochlodon vorosi and the basal coronosaurian Ajkaceratops kozmai in the Upper Cretaceous Csehbánya Formation at Iharkút (western Hungary). Whereas teeth of Mochlodon are common elements at the locality, no dental material belonging to Ajkaceratops was identified until now. Here we used mathematical statistical approaches, as well as tooth wear and dental microstructure analysis in order to decide whether the teeth previously referred to Mochlodon can be treated as a homogenous sample, or some remains belong rather to Ajkaceratops. According to our results, there was a striking morphological and structural convergence between the teeth of both taxa. However, the wear study revealed the existence of two different patterns within the sample. One is characterized by straight and parallel microstriations that suggest orthal movements during the jaw closure. This pattern was associated with Mochlodon. The other pattern appeared only on a few teeth, and it can be differentiated by its distinctive curved microstriations that indicate circumpalinal chewing. Because curved striations have never been described in ornithopods, but are found in several neoceratopsians, this pattern was associated here with Ajkaceratops. Here we present the first teeth that can provisionally be referred to the latter genus. We believe that the methodology discussed in this article will facilitate distinguishing ceratopsian and ornithopod teeth in other localities as well. Anat Rec, 300:1439-1463, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The local and referred pain from myofascial trigger points in the temporalis muscle contributes to pain profile in chronic tension-type headache.

PubMed

Fernández-de-Las-Peñas, César; Ge, Hong-You; Arendt-Nielsen, Lars; Cuadrado, Maria Luz; Pareja, Juan A

2007-01-01

To assess the local and referred pain areas and pain characteristics evoked from temporalis muscle trigger points (TrPs) in chronic tension-type headache (CTTH). Thirty CTTH patients and 30 age and sex-matched controls were studied. A headache diary was kept for 4 weeks to substantiate the diagnosis and record the pain history. Both temporalis muscles were examined for the presence of myofascial TrPs in a blinded fashion. The local and referred pain intensities, referred pain pattern, and pressure pain threshold were recorded. Referred pain was evoked in 87% and 54% on the dominant and nondominant sides in CTTH patients, which was significantly higher (P<0.001) than in controls (10% vs. 17%, respectively). Referred pain spread to the temple ipsilateral to the stimulated muscle in both patients and controls, with additional referral behind the eyes in most patients, but none in controls. CTTH patients reported a higher local [visual analog scale (VAS): 5.6+/-1.2 right side, 5.3+/-1.4 left side] and referred pain (VAS: 4.7+/-2 right side, 3.5+/-2.8 left side) intensity than healthy controls (VAS: 0.8+/-0.7 right side, 0.7+/-0.7 left side for local pain; and 0.3+/-0.2 right side, 0.4+/-0.3 left side for referred pain) in both temporalis muscles (both, P<0.001). The local and referred pain areas were larger in patients than in controls (P<0.001). Twenty-three out of 30 CTTH patients (77%) had active TrPs in the temporalis muscle leading to their usual headache (17 patients on the right side; 12 on the left side, whereas 6 with bilateral active TrPs). CTTH patients with active TrPs in either right or left temporalis muscle showed longer headache duration than those with latent TrPs (P=0.004). CTTH patients showed significantly (P<0.001) lower pressure pain threshold (1.1+/-0.2 right side, 1.2+/-0.3 left side) as compared with controls (2.5+/-0.5 right side, 2.6+/-0.4 left side). In CTTH patients, the evoked local and referred pain from active TrPs in the temporalis muscle and its sensory characteristics shared similar patterns as their habitual headache pain. Local and referred pain from active TrPs in the temporalis muscles may constitute one of the sources contributing to the pain profile of CTTH.

Effect of Spatial Locality Prefetching on Structural Locality

DTIC Science & Technology

1991-12-01

Pollution module calculates the SLC and CAM cache pollution percentages. And finally, the Generate Reference Frequency List module produces the output...3.2.5 Generate Reference Frequency List 3.2.6 Each program module in the structure chart is mapped into an Ada package. By performing this encapsulation...call routine to generate reference -- frequency list -- end if -- end loop -- close input, output, and reference files end Cache Simulator Figure 3.5

Challenges for conducting blood collection and biochemical analysis in a large multicenter school-based study with adolescents: lessons from ERICA in Brazil.

PubMed

Cureau, Felipe Vogt; Bloch, Katia Vergetti; Henz, Aline; Schaan, Camila W; Klein, Carlos Henrique; Oliveira, Cecília Lacroix de; Giannini, Denise Tavares; Leon, Elisa Brosina de; Abreu, Gabriela de Azevedo; Telo, Gabriela Heiden; Dias, Glauber Monteiro; Carvalho, Kênia Mara Baiocchi de; Barufaldi, Laura Augusta; Kuschnir, Maria Cristina Caetano; Szklo, Moyses; Montenegro, Renan; Silva, Thiago Luiz Nogueira da; Ekelund, Ulf; Schaan, Beatriz D

2017-05-18

The Study of Cardiovascular Risk in Adolescents (ERICA) is a pioneering study that aimed to assess the prevalence of cardiovascular risk factors, including metabolic syndrome components in Brazilian adolescents. This study aims to describe the methodological aspects related to blood collection as well as to report pertaining results of the preparation, transport, storage, and exams in ERICA. Exams in ERICA were performed in a single laboratory and blood samples were collected in schools in a standardized manner. Logistics involved air transportation of samples to the reference laboratory with controlled temperature since sample collection. The serum was stored in local biorepositories in four centers to be used in future analyses. During the study, 284,247 exams were performed and rate of participation in exams was 56.2%, thus involving 40,732 adolescents. From the total, 92.6% of the samples reached the reference laboratory maintaining the temperature between 0-10°C. No clinical significant changes in results due to temperature changes were identified. External quality control recorded satisfactory results in 98.7% of the evaluations. Four biorepositories with samples of 7,785 adolescents were created. Thus, we can consider that the logistics adopted in ERICA was fairly successful and description of this as well as the difficulties experienced in Brazil can inform and facilitate the planning of future studies, especially in developing countries.

Astronaut John Young on rim of Plum crater gathering lunar rock samples

NASA Technical Reports Server (NTRS)

1972-01-01

Astronaut John W. Young, commander of the Apollo 16 lunar landing mission, stands on the rim of Plum crater while collecting lunar rock samples at Station No.1 during the first Apollo 16 extravehicular activity (EVA-1) at the Descartes landing site. This scene, looking eastward, was photographed by Astronaut Charles M. Duke Jr., lunar module pilot. The small boulder in the center foreground was chip sampled by the crewmen. Plum crater is 40 meters in diameter and 10 meters deep. The Lunar Roving Vehicle is parked on the far rim of the crater. The gnomon, which is used as a photographic reference to establish local vertical sun angle, scale, and lunar color, is deployed in the center of the picture. Young holds a geological hammer in his right hand.

Processing Cones: A Computational Structure for Image Analysis.

DTIC Science & Technology

1981-12-01

image analysis applications, referred to as a processing cone, is described and sample algorithms are presented. A fundamental characteristic of the structure is its hierarchical organization into two-dimensional arrays of decreasing resolution. In this architecture, a protypical function is defined on a local window of data and applied uniformly to all windows in a parallel manner. Three basic modes of processing are supported in the cone: reduction operations (upward processing), horizontal operations (processing at a single level) and projection operations (downward

Humidity Effect on Nanoscale Electrochemistry in Solid Silver Ion Conductors and the Dual Nature of Its Locality

DOE PAGES

Yang, Sangmo; Strelcov, Evgheni; Paranthaman, Mariappan Parans; ...

2015-01-07

Scanning probe microscopy (SPM) is a powerful tool to investigate electrochemistry in nanoscale volumes. While most SPM-based studies have focused on reactions at the tip-surface junction, charge and mass conservation requires coupled and intrinsically non-local cathodic and anodic processes that can be significantly affected by ambient humidity. Here, we explore the role of water in both cathodic and anodic processes, associated charge transport, and topographic volume changes depending on the polarity of tip bias. The first-order reversal curve current-voltage technique combined with simultaneous detection of the sample topography, referred to as FORC-IVz, was applied to a silver solid ion conductor.more » We found that the protons generated from water affect silver ionic conduction, silver particle formation and dissolution, and mechanical integrity of the material. This work highlights the dual nature (simultaneously local and non-local) of electrochemical SPM studies, which should be considered for comprehensive understanding of nanoscale electrochemistry.« less

Ultrasonic slurry sampling electrothermal vaporization inductively coupled plasma mass spectrometry for the determination of Cr, Fe, Cu, Zn and Se in cereals

NASA Astrophysics Data System (ADS)

Huang, Shih-Yi; Jiang, Shiuh-Jen; Sahayam, A. C.

2014-11-01

Ultrasonic slurry sampling electrothermal vaporization inductively coupled plasma mass spectrometry (USS-ETV-ICP-MS) has been applied to determine Cr, Fe, Cu, Zn and Se in several cereal samples. Thioacetamide was used as the modifier to enhance the ion signals. The background ions at the masses of interest were reduced in intensity significantly by using 1.0 mL min- 1 methane (CH4) as reaction cell gas in the dynamic reaction cell (DRC). Since the sensitivities of Cr, Fe, Cu, Zn and Se in different matrices were quite different, standard addition and isotope dilution methods were used for the determination of Cr, Fe, Cu, Zn and Se in these cereal samples. The method detection limits estimated from standard addition curves were about 1, 10, 4, 12 and 2 ng g- 1 for Cr, Fe, Cu, Zn and Se, respectively, in original cereal samples. This procedure has been applied to the determination of Cr, Fe, Cu, Zn and Se whose concentrations are in μg g- 1 (except Cr and Se) in standard reference materials (SRM) of National institute of standards and technology (NIST), NIST SRM 1568a Rice Flour and NIST SRM 1567a Wheat Flour and two cereal samples purchased from a local market. The analysis results of reference materials agreed with certified values at 95% confidence level according to Student's T-test. The results for the real world cereal samples were also found to be in good agreement with the pneumatic nebulization DRC ICP-MS results of the sample solutions.

Estimating Sampling Selection Bias in Human Genetics: A Phenomenological Approach

PubMed Central

Risso, Davide; Taglioli, Luca; De Iasio, Sergio; Gueresi, Paola; Alfani, Guido; Nelli, Sergio; Rossi, Paolo; Paoli, Giorgio; Tofanelli, Sergio

2015-01-01

This research is the first empirical attempt to calculate the various components of the hidden bias associated with the sampling strategies routinely-used in human genetics, with special reference to surname-based strategies. We reconstructed surname distributions of 26 Italian communities with different demographic features across the last six centuries (years 1447–2001). The degree of overlapping between "reference founding core" distributions and the distributions obtained from sampling the present day communities by probabilistic and selective methods was quantified under different conditions and models. When taking into account only one individual per surname (low kinship model), the average discrepancy was 59.5%, with a peak of 84% by random sampling. When multiple individuals per surname were considered (high kinship model), the discrepancy decreased by 8–30% at the cost of a larger variance. Criteria aimed at maximizing locally-spread patrilineages and long-term residency appeared to be affected by recent gene flows much more than expected. Selection of the more frequent family names following low kinship criteria proved to be a suitable approach only for historically stable communities. In any other case true random sampling, despite its high variance, did not return more biased estimates than other selective methods. Our results indicate that the sampling of individuals bearing historically documented surnames (founders' method) should be applied, especially when studying the male-specific genome, to prevent an over-stratification of ancient and recent genetic components that heavily biases inferences and statistics. PMID:26452043

Estimating Sampling Selection Bias in Human Genetics: A Phenomenological Approach.

PubMed

Risso, Davide; Taglioli, Luca; De Iasio, Sergio; Gueresi, Paola; Alfani, Guido; Nelli, Sergio; Rossi, Paolo; Paoli, Giorgio; Tofanelli, Sergio

2015-01-01

This research is the first empirical attempt to calculate the various components of the hidden bias associated with the sampling strategies routinely-used in human genetics, with special reference to surname-based strategies. We reconstructed surname distributions of 26 Italian communities with different demographic features across the last six centuries (years 1447-2001). The degree of overlapping between "reference founding core" distributions and the distributions obtained from sampling the present day communities by probabilistic and selective methods was quantified under different conditions and models. When taking into account only one individual per surname (low kinship model), the average discrepancy was 59.5%, with a peak of 84% by random sampling. When multiple individuals per surname were considered (high kinship model), the discrepancy decreased by 8-30% at the cost of a larger variance. Criteria aimed at maximizing locally-spread patrilineages and long-term residency appeared to be affected by recent gene flows much more than expected. Selection of the more frequent family names following low kinship criteria proved to be a suitable approach only for historically stable communities. In any other case true random sampling, despite its high variance, did not return more biased estimates than other selective methods. Our results indicate that the sampling of individuals bearing historically documented surnames (founders' method) should be applied, especially when studying the male-specific genome, to prevent an over-stratification of ancient and recent genetic components that heavily biases inferences and statistics.

High-throughput SNP genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements.

PubMed

Lim, Haw Chuan; Braun, Michael J

2016-09-01

Sample availability limits population genetics research on many species, especially taxa from regions with high diversity. However, many such species are well represented in museum collections assembled before the molecular era. Development of techniques to recover genetic data from these invaluable specimens will benefit biodiversity science. Using a mixture of freshly preserved and historical tissue samples, and a sequence capture probe set targeting >5000 loci, we produced high-confidence genotype calls on thousands of single nucleotide polymorphisms (SNPs) in each of five South-East Asian bird species and their close relatives (N = 27-43). On average, 66.2% of the reads mapped to the pseudo-reference genome of each species. Of these mapped reads, an average of 52.7% was identified as PCR or optical duplicates. We achieved deeper effective sequencing for historical samples (122.7×) compared to modern samples (23.5×). The number of nucleotide sites with at least 8× sequencing depth was high, with averages ranging from 0.89 × 10(6)  bp (Arachnothera, modern samples) to 1.98 × 10(6)  bp (Stachyris, modern samples). Linear regression revealed that the amount of sequence data obtained from each historical sample (represented by per cent of the pseudo-reference genome recovered with ≥8× sequencing depth) was positively and significantly (P ≤ 0.013) related to how recently the sample was collected. We observed characteristic post-mortem damage in the DNA of historical samples. However, we were able to reduce the error rate significantly by truncating ends of reads during read mapping (local alignment) and conducting stringent SNP and genotype filtering. © 2016 John Wiley & Sons Ltd.

Resampling methods in Microsoft Excel® for estimating reference intervals

PubMed Central

Theodorsson, Elvar

2015-01-01

Computer- intensive resampling/bootstrap methods are feasible when calculating reference intervals from non-Gaussian or small reference samples. Microsoft Excel® in version 2010 or later includes natural functions, which lend themselves well to this purpose including recommended interpolation procedures for estimating 2.5 and 97.5 percentiles.
The purpose of this paper is to introduce the reader to resampling estimation techniques in general and in using Microsoft Excel® 2010 for the purpose of estimating reference intervals in particular.
Parametric methods are preferable to resampling methods when the distributions of observations in the reference samples is Gaussian or can transformed to that distribution even when the number of reference samples is less than 120. Resampling methods are appropriate when the distribution of data from the reference samples is non-Gaussian and in case the number of reference individuals and corresponding samples are in the order of 40. At least 500-1000 random samples with replacement should be taken from the results of measurement of the reference samples. PMID:26527366

Resampling methods in Microsoft Excel® for estimating reference intervals.

PubMed

Theodorsson, Elvar

2015-01-01

Computer-intensive resampling/bootstrap methods are feasible when calculating reference intervals from non-Gaussian or small reference samples. Microsoft Excel® in version 2010 or later includes natural functions, which lend themselves well to this purpose including recommended interpolation procedures for estimating 2.5 and 97.5 percentiles. 
The purpose of this paper is to introduce the reader to resampling estimation techniques in general and in using Microsoft Excel® 2010 for the purpose of estimating reference intervals in particular.
 Parametric methods are preferable to resampling methods when the distributions of observations in the reference samples is Gaussian or can transformed to that distribution even when the number of reference samples is less than 120. Resampling methods are appropriate when the distribution of data from the reference samples is non-Gaussian and in case the number of reference individuals and corresponding samples are in the order of 40. At least 500-1000 random samples with replacement should be taken from the results of measurement of the reference samples.

Assessment of exposure to heavy metals and health risks among residents near Tonglushan mine in Hubei, China.

PubMed

Cai, Li-Mei; Xu, Zhen-Cheng; Qi, Jian-Ying; Feng, Zhi-Zhou; Xiang, Ting-Sheng

2015-05-01

Heavy metal contamination due to mining activity is a global major concern because of its potential health risks to local inhabitants. In the present study, we investigated the levels of Cd, Cu, Pb and As in soil, crop, well water and fish samples collected from the vicinity of the Tonglushan mine in Hubei, China, and evaluated potential health risks among local residents. Results indicate that soils near the mine were heavily contaminated with Cd (2.59 mg kg(-1)), Cu (386 mg kg(-1)), Pb (120 mg kg(-1)) and As (35.4 mg kg(-1)), and exceeded the soil quality standard values of Cd and Cu contamination. The concentrations of Cd, Cu, Pb and As in crop samples grown in mine-affected soils were significantly higher than those of the reference soils. The concentrations of Cd and As in most vegetables grown in mine-affected soils exceeded the maximum allowable level (MAL). The Cd, Pb and As concentration in rice grain collected from mine-affected soils were 2.95, 1.85 and 2.07-fold higher than the MAL, respectively. The concentrations of Cd and As in fish muscle from the mine-affected area were above national MAL in 61% and 34% of analyzed samples, respectively. All measured heavy metals except Pb were significantly greater in well water in the mine-affected area than those in the reference areas. The average estimated daily intakes of Cd and As were beyond the provisional tolerable daily intake, respectively. The intake of rice was identified as a major contributor (⩾72%) to the estimated daily intake among the residents. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

PubMed

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

2013-05-01

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

Mobile robot motion estimation using Hough transform

NASA Astrophysics Data System (ADS)

Aldoshkin, D. N.; Yamskikh, T. N.; Tsarev, R. Yu

2018-05-01

This paper proposes an algorithm for estimation of mobile robot motion. The geometry of surrounding space is described with range scans (samples of distance measurements) taken by the mobile robot’s range sensors. A similar sample of space geometry in any arbitrary preceding moment of time or the environment map can be used as a reference. The suggested algorithm is invariant to isotropic scaling of samples or map that allows using samples measured in different units and maps made at different scales. The algorithm is based on Hough transform: it maps from measurement space to a straight-line parameters space. In the straight-line parameters, space the problems of estimating rotation, scaling and translation are solved separately breaking down a problem of estimating mobile robot localization into three smaller independent problems. The specific feature of the algorithm presented is its robustness to noise and outliers inherited from Hough transform. The prototype of the system of mobile robot orientation is described.

Calibrated work function mapping by Kelvin probe force microscopy

NASA Astrophysics Data System (ADS)

Fernández Garrillo, Pablo A.; Grévin, Benjamin; Chevalier, Nicolas; Borowik, Łukasz

2018-04-01

We propose and demonstrate the implementation of an alternative work function tip calibration procedure for Kelvin probe force microscopy under ultrahigh vacuum, using monocrystalline metallic materials with known crystallographic orientation as reference samples, instead of the often used highly oriented pyrolytic graphite calibration sample. The implementation of this protocol allows the acquisition of absolute and reproducible work function values, with an improved uncertainty with respect to unprepared highly oriented pyrolytic graphite-based protocols. The developed protocol allows the local investigation of absolute work function values over nanostructured samples and can be implemented in electronic structures and devices characterization as demonstrated over a nanostructured semiconductor sample presenting Al0.7Ga0.3As and GaAs layers with variable thickness. Additionally, using our protocol we find that the work function of annealed highly oriented pyrolytic graphite is equal to 4.6 ± 0.03 eV.

Metabolic syndrome in children and adolescents from Mérida city, Venezuela: Comparison of results using local and international reference values (CREDEFAR study).

PubMed

Villalobos Reyes, Marjorie; Mederico, Maracelly; Paoli de Valeri, Mariela; Briceño, Yajaira; Zerpa, Yajaira; Gómez-Pérez, Roald; Camacho, Nolis; Martínez, José Luis; Valeri, Lenín; Arata-Bellabarba, Gabriela

2014-11-01

To obtain local reference values for blood lipids and blood pressure (BP), and to determine the prevalence of metabolic syndrome (MS) in children and adolescents from Mérida, Venezuela, and to compare results using local and international cut-off values. The study enrolled 916 participants of both sexes aged 9-18 years of age from educational institutions. Demographic, anthropometric, and BP data were collected. Fasting blood glucose and lipid profile were measured. Percentile distribution of lipid and BP values was done by age group and sex. Prevalence of MS was estimated based on the NCEP-ATPIII classification (as modified by Cook et al.) and the classification of the International Diabetes Federation, using percentiles of Mérida and the USA as cut-off points. Agreement between both classifications was estimated using the kappa test (κ). Prevalence of MS was 2.2% by Cook-Merida percentiles, as compared to 1.8% by Cook-USA percentiles, a moderate agreement (κ=0.54). Agreement between Cook et al. and IDF using Merida percentiles was weak (κ=0.28). There was a higher frequency of abdominal obesity, hypertriglyceridemia and hypertension, and a lower frequency of low HDL-C using Mérida percentiles. The risk (odds ratio) of having MS is greater if abdominal obesity exists (OR: 98.63, CI: 22.45-433.35, p=0.0001). MS was significantly more common in obese subjects (18.3%, p=0.0001). Prevalence of MS in this sample of children and adolescents was 2.2%. Lipid and BP values were lower in Venezuelan as compared to US, European, and Asian children and adolescents, and similar to those in Latin-American references. Own reference values are required for accurate diagnosis of MS, as well as a worldwide consensus on its diagnostic criteria. Copyright © 2014 SEEN. Published by Elsevier Espana. All rights reserved.

Impact of iron and steel industry and waste incinerators on human exposure to dioxins, PCBs, and heavy metals: results of a cross-sectional study in Belgium.

PubMed

Fierens, Sébastien; Mairesse, Hélène; Heilier, Jean-François; Focant, Jean-François; Eppe, Gauthier; De Pauw, Edwin; Bernard, Alfred

2007-02-01

We evaluated the impact of two iron and steel plants and two municipal solid waste incinerators (MSWI) in Wallonia (Belgium) on the exposure of residents to dioxins, polychlorinated biphenyls (PCBs), and heavy metals. In total, 142 volunteers living around these facilities were recruited and compared with 63 referents from a rural area with no industrial source of pollution. Information about smoking habits, dietary habits, anthropometric characteristics, residential history, and health status was obtained from a self-administered questionnaire. The volunteers provided blood under fasting conditions in order to evaluate the body burden of dioxins (17 polychlorinated dibenzo-p-dioxins/dibenzofurans [PCDD/Fs] congeners) and PCBs. Samples of blood and urine were also taken for the determination of cadmium, mercury, and lead. After adjustment for covariates, concentrations of cadmium, mercury, and lead in urine or blood were not increased in subjects living in the vicinity of MSWIs or sinter plants by comparison with referents. Residents around the sinter plants and the MSWI located in the industrial area had concentrations of dioxins and PCBs in serum similar to that of referents. By contrast, subjects living in the vicinity of the MSWI in the rural area showed significantly higher serum levels of dioxins (geometric mean, 38 vs. 24 pg TEQ/g fat) and coplanar PCBs (geometric mean, 10.8 vs. 7.0 pg TEQ/g fat). Although age-adjusted dioxin levels in referents did not vary with local animal fat consumption, concentrations of dioxins in subjects living around the incinerators correlated positively with their intake of local animal fat, with almost a doubling in subjects with the highest fat intake. These results indicate that dioxins and coplanar PCBs emitted by MSWIs can indeed accumulate in the body of residents who regularly consume animal products of local origin.

HERUS: the far-IR/submm spectral energy distributions of local ULIRGs and photometric atlas

NASA Astrophysics Data System (ADS)

Clements, D. L.; Pearson, C.; Farrah, D.; Greenslade, J.; Bernard-Salas, Jeronimo; González-Alfonso, E.; Afonso, J.; Efstathiou, A.; Rigopoulou, D.; Lebouteiller, V.; Hurley, P. D.; Spoon, H.

2018-04-01

We present the Herschel-SPIRE photometric atlas for a complete flux limited sample of 43 local ultraluminous infrared galaxies (ULIRGs), selected at 60 μm by IRAS, as part of the HERschel ULIRG Survey (HERUS). Photometry observations were obtained using the SPIRE instrument at 250, 350, and 500 μm. We describe these observations, present the results, and combine the new observations with data from IRAS to examine the far-infrared spectral energy distributions (SEDs) of these sources. We fit the observed SEDs of HERUS objects with a simple parametrized modified blackbody model, where temperature and emissivity β are free parameters. We compare the fitted values to those of non-ULIRG local galaxies, and find, in agreement with earlier results, that HERUS ULIRGs have warmer dust (median temperature T = 37.9 ± 4.7 K compared to 21.3 ± 3.4 K) but a similar β distribution (median β = 1.7 compared to 1.8) to the Herschel reference sample (HRS, Cortese et al. 2014) galaxies. Dust masses are found to be in the range of 107.5-109 M⊙, significantly higher than that of HRS sources. We compare our results for local ULIRGs with higher redshift samples selected at 250 and 850 μm. These latter sources generally have cooler dust and/or redder 100-to-250 μm colours than our 60 μm-selected ULIRGs. We show that this difference may in part be the result of the sources being selected at different wavelengths rather than being a simple indication of rapid evolution in the properties of the population.

An Integrated Tiered Service Delivery Model (ITSDM) Based on Local CD4 Testing Demands Can Improve Turn-Around Times and Save Costs whilst Ensuring Accessible and Scalable CD4 Services across a National Programme

PubMed Central

Glencross, Deborah K.; Coetzee, Lindi M.; Cassim, Naseem

2014-01-01

Background The South African National Health Laboratory Service (NHLS) responded to HIV treatment initiatives with two-tiered CD4 laboratory services in 2004. Increasing programmatic burden, as more patients access anti-retroviral therapy (ART), has demanded extending CD4 services to meet increasing clinical needs. The aim of this study was to review existing services and develop a service-model that integrated laboratory-based and point-of-care testing (POCT), to extend national coverage, improve local turn-around/(TAT) and contain programmatic costs. Methods NHLS Corporate Data Warehouse CD4 data, from 60–70 laboratories and 4756 referring health facilities was reviewed for referral laboratory workload, respective referring facility volumes and related TAT, from 2009–2012. Results An integrated tiered service delivery model (ITSDM) is proposed. Tier-1/POCT delivers CD4 testing at single health-clinics providing ART in hard-to-reach areas (<5 samples/day). Laboratory-based testing is extended with Tier-2/POC-Hubs (processing ≤30–40 CD4 samples/day), consolidating POCT across 8–10 health-clinics with other HIV-related testing and Tier-3/‘community’ laboratories, serving ≤40 health-clinics, processing ≤150 samples/day. Existing Tier-4/‘regional’ laboratories serve ≤100 facilities and process <350 samples/day; Tier-5 are high-volume ‘metro’/centralized laboratories (>350–1500 tests/day, serving ≥200 health-clinics). Tier-6 provides national support for standardisation, harmonization and quality across the organization. Conclusion The ITSDM offers improved local TAT by extending CD4 services into rural/remote areas with new Tier-3 or Tier-2/POC-Hub services installed in existing community laboratories, most with developed infrastructure. The advantage of lower laboratory CD4 costs and use of existing infrastructure enables subsidization of delivery of more expensive POC services, into hard-to-reach districts without reasonable access to a local CD4 laboratory. Full ITSDM implementation across 5 service tiers (as opposed to widespread implementation of POC testing to extend service) can facilitate sustainable ‘full service coverage’ across South Africa, and save>than R125 million in HIV/AIDS programmatic costs. ITSDM hierarchical parental-support also assures laboratory/POC management, equipment maintenance, quality control and on-going training between tiers. PMID:25490718

Estrogen and progesterone receptor testing in breast carcinoma: concordance of results between local and reference laboratories in Brazil.

PubMed

Wludarski, Sheila Cristina Lordelo; Lopes, Lisandro Ferreira; Duarte, Ivison Xavier; Carvalho, Filomena Marino; Weiss, Lawrence; Bacchi, Carlos Eduardo

2011-01-01

Breast cancer accounts for approximately one quarter of all cancers in females. Estrogen and progesterone receptor testing has become an essential part of the clinical evaluation of breast carcinoma patients, and accurate results are critical in identifying patients who may benefit from hormone therapy. The present study had the aim of investigating the concordance of the results from hormone receptor tests between a reference laboratory and local (or community) laboratories in Brazil. Retrospective study at a reference pathology laboratory. The concordance in the results from hormone receptor tests between a reference laboratory and 146 local laboratories in Brazil was compared in relation to 500 invasive breast carcinoma cases, using immunohistochemistry. There was concordance in 89.4% (447/500 cases) and 85.0% (425/500 cases) of the results from estrogen (κ = 0.744, P < 0.001) and progesterone (κ = 0.688, P < 0.001) receptor tests, respectively, between local and reference laboratories. This was similar to findings in other countries. The false negative rates from estrogen and progesterone receptor tests in local laboratories were 8.7% and 14.4%, respectively. The false positive rates from estrogen and progesterone receptor tests in local laboratories were 15.5% and 16.0%, respectively. Technical and result interpretation issues may explain most of the discordances in hormone receptor testing in local laboratories. Validation of estrogen and progesterone receptor tests at local laboratories, with rigorous quality control measures, is strongly recommended in order to avoid erroneous treatment of breast cancer patients.

HEMATOLOGY AND PLASMA CHEMISTRY OF THE PLOUGHSHARE TORTOISE (ASTROCHELYS YNIPHORA) IN A CAPTIVE BREEDING PROGRAM.

PubMed

López, Javier; Waters, Michael; Routh, Andrew; Rakotonanahary, Tsanta F; Woolaver, Lance; Thomasson, Ann; Holmes, Emma; Steinmetz, Hanspeter W

2017-03-01

Blood samples from 172 captive and 40 wild, healthy, juvenile and adult, ploughshare tortoises ( Astrochelys yniphora ) were analyzed to determine hematological and biochemical reference intervals. Hematological analytes included packed cell volume (PCV), white blood cell count (WBC), and WBC differential estimates. Biochemical analysis included total protein measured by photometry (TP) and by refractometry (TPr), albumin (ALB), creatine kinase (CK), aspartate aminotransferase (AST), glutamate dehydrogenase (GLDH), bile acids (BA), calcium (Ca), phosphorus (P), urea (UREA), and uric acid (UA). The jugular vein was identified as the preferred venipuncture site as subcarapacial vein venipuncture resulted in regular hemodilution. In due consideration of small sample sizes in some of the groups studied, adult tortoises had significantly higher plasma GLDH activity and TPr, TP, ALB, BA, and UREA concentrations and significantly lower AST activity and P concentration than juveniles. Captivity had a significant influence in some reference intervals, with captive adults presenting significantly higher WBC, and estimated counts of all white cell types as well as UREA and TPr than wild counterparts. Captive juveniles also showed significantly higher estimated monocyte and lower estimated eosinophil and basophil counts. Although these differences most likely reflect local environmental or dietary differences, without representing pathology or a deviation from the normal, they question the applicability of reference values from captive animals to wild animals and vice versa. Significant sex differences were only observed for PCV and UA. The reported reference intervals may serve as benchmarks for clinical assessment and conservation of this critically endangered species.

EnEx-RANGE - Robust autonomous Acoustic Navigation in Glacial icE

NASA Astrophysics Data System (ADS)

Heinen, Dirk; Eliseev, Dmitry; Henke, Christoph; Jeschke, Sabina; Linder, Peter; Reuter, Sebastian; Schönitz, Sebastian; Scholz, Franziska; Weinstock, Lars Steffen; Wickmann, Stefan; Wiebusch, Christopher; Zierke, Simon

2017-03-01

Within the Enceladus Explorer Initiative of the DLR Space Administration navigation technologies for a future space mission are in development. Those technologies are the basis for the search for extraterrestrial life on the Saturn moon Enceladus. An autonomous melting probe, the EnEx probe, aims to extract a liquid sample from a water reservoir below the icy crust. A first EnEx probe was developed and demonstrated in a terrestrial scenario at the Bloodfalls, Taylor Glacier, Antarctica in November 2014. To enable navigation in glacier ice two acoustic systems were integrated into the probe in addition to conventional navigation technologies. The first acoustic system determines the position of the probe during the run based on propagation times of acoustic signals from emitters at reference positions at the glacier surface to receivers in the probe. The second system provides information about the forefield of the probe. It is based on sonographic principles with phased array technology integrated in the probe's melting head. Information about obstacles or sampling regions in the probe's forefield can be acquired. The development of both systems is now continued in the project EnEx-RANGE. The emitters of the localization system are replaced by a network of intelligent acoustic enabled melting probes. These localize each other by means of acoustic signals and create the reference system for the EnEx probe. This presentation includes the discussion of the intelligent acoustic network, the acoustic navigation systems of the EnEx probe and results of terrestrial tests.

[Volatile organic compounds of the tap water in the Watarase, Tone and Edo River system].

PubMed

Ohmichi, Kimihide; Ohmichi, Masayoshi; Machida, Kazuhiko

2004-01-01

The chlorination of river water in purification plants is known to produce carcinogens such as trihalomethanes (THMs). We studied the river system of the Watarase, Tone, and Edo Rivers in regard to the formation of THMs. This river system starts from the base of the Ashio copper mine and ends at Tokyo Bay. Along the rivers, there are 14 local municipalities in Gunma, Saitama, Ibaragi and Chiba Prefectures, as well as Tokyo. This area is the center of the Kanto plain and includes the main sources of water pollution from human activities. We also analyzed various chemicals in river water and tap water to clarify the status of the water environment, and we outline the problems of the water environment in the research area (Fig. 1). Water samples were taken from 18 river sites and 42 water faucets at public facilities in 14 local municipalities. We analyzed samples for volatile organic compounds such as THMs, by gas chromatography mass spectrometry (GC-MS), and evaluations of chemical oxygen demand (COD) were made with reference to Japanese drinking water quality standards. Concentrations of THMs in the downstream tap water samples were higher than those in the samples from the upperstream. This tendency was similar to the COD of the river water samples, but no correlation between the concentration of THMs in tap water and the COD in tap water sources was found. In tap water of local government C, trichloroethylene was detected. The current findings suggest that the present water filtration plant procedures are not sufficient to remove some hazardous chemicals from the source water. Moreover, it was confirmed that the water filtration produced THMs. Also, trichloroethylene was detected from the water environment in the research area, suggesting that pollution of the water environment continues.

Evaluation of locally established reference intervals for hematology and biochemistry parameters in Western Kenya.

PubMed

Odhiambo, Collins; Oyaro, Boaz; Odipo, Richard; Otieno, Fredrick; Alemnji, George; Williamson, John; Zeh, Clement

2015-01-01

Important differences have been demonstrated in laboratory parameters from healthy persons in different geographical regions and populations, mostly driven by a combination of genetic, demographic, nutritional, and environmental factors. Despite this, European and North American derived laboratory reference intervals are used in African countries for patient management, clinical trial eligibility, and toxicity determination; which can result in misclassification of healthy persons as having laboratory abnormalities. An observational prospective cohort study known as the Kisumu Incidence Cohort Study (KICoS) was conducted to estimate the incidence of HIV seroconversion and identify determinants of successful recruitment and retention in preparation for an HIV vaccine/prevention trial among young adults and adolescents in western Kenya. Laboratory values generated from the KICoS were compared to published region-specific reference intervals and the 2004 NIH DAIDS toxicity tables used for the trial. About 1106 participants were screened for the KICoS between January 2007 and June 2010. Nine hundred and fifty-three participants aged 16 to 34 years, HIV-seronegative, clinically healthy, and non-pregnant were selected for this analysis. Median and 95% reference intervals were calculated for hematological and biochemistry parameters. When compared with both published region-specific reference values and the 2004 NIH DAIDS toxicity table, it was shown that the use of locally established reference intervals would have resulted in fewer participants classified as having abnormal hematological or biochemistry values compared to US derived reference intervals from DAIDS (10% classified as abnormal by local parameters vs. >40% by US DAIDS). Blood urea nitrogen was most often out of range if US based intervals were used: <10% abnormal by local intervals compared to >83% by US based reference intervals. Differences in reference intervals for hematological and biochemical parameters between western and African populations highlight importance of developing local reference intervals for clinical care and trials in Africa.

The Spitzer/IRAC Star Formation Reference Survey

NASA Astrophysics Data System (ADS)

Fazio, Giovanni; Ashby, Matthew; Ashby, Matthew L. N.; Barmby, Pauline; Chakrabarti, Sukanya; Gonzalez-Alfonso, Eduardo; Huang, Jia-Sheng; Madden, Suzanne; Noeske, Kai; Pahre, Michael; Papovich, Casey; Robitaille, Thomas; Smith, Howard; Sturm, Eckhard; Surace, Jason; Wang, Zhong; Whitney, Barbara; Willner, Steven; Wu, Hong; Zezas, Andreas

2008-03-01

We propose a statistically robust study of 380 nearby, bright star-forming galaxies of all types to better understand the nature of star formation. The goal of this IRAC reference survey will be to measure total star formation rates via 8.0 micron PAH emission, with an emphasis on quantitative comparisons of multiple global star formation indicators including ultraviolet emission, H-alpha, and radio continuum measurements. The sample is selected to be fully representative of the entire ranges of infrared luminosity, dust temperature, and stellar mass exhibited by star-forming galaxies in the local universe: the sample galaxies exhibit all existing combinations of these properties with the minimum overall number, selected in a manner that allows results to be applied to the entire local galaxy population. Here we propose four-band Spitzer/IRAC photometry for the 275 out of 380 objects which lack suitable observations in the Spitzer archive. All sample galaxies already have extensive complementary data available including global ugrizJHK photometry plus radio continuum intensities. Most also have GALEX imaging; in addition we have already begun a ground-based campaign to acquire global H-alpha imaging for the complete sample. We are submitting this IRAC proposal in the context of a larger campaign that includes a GTO proposal to complete the MIPS 24 micron imaging, and a GO proposal to acquire the IRS low-resolution spectroscopy. Although these companion proposals will significantly increase the scientific return of our survey program, the success of this proposal is not contingent in any way on any other Spitzer proposal. Our international team is dedicated, experienced, and has adequate manpower and institutional resources, with expertise in all the relevant disciplines to ensure the success of this undertaking. PI Fazio believes this proposal to be the most important element of his extragalactic GTO program, and requests that it be assigned first priority.

Mobile Communication Devices, Ambient Noise, and Acoustic Voice Measures.

PubMed

Maryn, Youri; Ysenbaert, Femke; Zarowski, Andrzej; Vanspauwen, Robby

2017-03-01

The ability to move with mobile communication devices (MCDs; ie, smartphones and tablet computers) may induce differences in microphone-to-mouth positioning and use in noise-packed environments, and thus influence reliability of acoustic voice measurements. This study investigated differences in various acoustic voice measures between six recording equipments in backgrounds with low and increasing noise levels. One chain of continuous speech and sustained vowel from 50 subjects with voice disorders (all separated by silence intervals) was radiated and re-recorded in an anechoic chamber with five MCDs and one high-quality recording system. These recordings were acquired in one condition without ambient noise and in four conditions with increased ambient noise. A total of 10 acoustic voice markers were obtained in the program Praat. Differences between MCDs and noise condition were assessed with Friedman repeated-measures test and posthoc Wilcoxon signed-rank tests, both for related samples, after Bonferroni correction. (1) Except median fundamental frequency and seven nonsignificant differences, MCD samples have significantly higher acoustic markers than clinical reference samples in minimal environmental noise. (2) Except median fundamental frequency, jitter local, and jitter rap, all acoustic measures on samples recorded with the reference system experienced significant influence from room noise levels. Fundamental frequency is resistant to recording system, environmental noise, and their combination. All other measures, however, were impacted by both recording system and noise condition, and especially by their combination, often already in the reference/baseline condition without added ambient noise. Caution is therefore warranted regarding implementation of MCDs as clinical recording tools, particularly when applied for treatment outcomes assessments. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

A comparison of endoscopic localization error rate between operating surgeons and referring endoscopists in colorectal cancer.

PubMed

Azin, Arash; Saleh, Fady; Cleghorn, Michelle; Yuen, Andrew; Jackson, Timothy; Okrainec, Allan; Quereshy, Fayez A

2017-03-01

Colonoscopy for colorectal cancer (CRC) has a localization error rate as high as 21 %. Such errors can have substantial clinical consequences, particularly in laparoscopic surgery. The primary objective of this study was to compare accuracy of tumor localization at initial endoscopy performed by either the operating surgeon or non-operating referring endoscopist. All patients who underwent surgical resection for CRC at a large tertiary academic hospital between January 2006 and August 2014 were identified. The exposure of interest was the initial endoscopist: (1) surgeon who also performed the definitive operation (operating surgeon group); and (2) referring gastroenterologist or general surgeon (referring endoscopist group). The outcome measure was localization error, defined as a difference in at least one anatomic segment between initial endoscopy and final operative location. Multivariate logistic regression was used to explore the association between localization error rate and the initial endoscopist. A total of 557 patients were included in the study; 81 patients in the operating surgeon cohort and 476 patients in the referring endoscopist cohort. Initial diagnostic colonoscopy performed by the operating surgeon compared to referring endoscopist demonstrated statistically significant lower intraoperative localization error rate (1.2 vs. 9.0 %, P = 0.016); shorter mean time from endoscopy to surgery (52.3 vs. 76.4 days, P = 0.015); higher tattoo localization rate (32.1 vs. 21.0 %, P = 0.027); and lower preoperative repeat endoscopy rate (8.6 vs. 40.8 %, P < 0.001). Initial endoscopy performed by the operating surgeon was protective against localization error on both univariate analysis, OR 7.94 (95 % CI 1.08-58.52; P = 0.016), and multivariate analysis, OR 7.97 (95 % CI 1.07-59.38; P = 0.043). This study demonstrates that diagnostic colonoscopies performed by an operating surgeon are independently associated with a lower localization error rate. Further research exploring the factors influencing localization accuracy and why operating surgeons have lower error rates relative to non-operating endoscopists is necessary to understand differences in care.

Are captive tortoises a reservoir for conservation? An assessment of genealogical affiliation of captive Gopherus agassizii to local, wild populations

USGS Publications Warehouse

Berry, Kristin H.; Edwards, Taylor

2013-01-01

The conservation of tortoises poses a unique situation because several threatened species are commonly kept as pets within their native ranges. Thus, there is potential for captive populations to be a reservoir for repatriation efforts. We assess the utility of captive populations of the threatened Agassiz’s desert tortoise (Gopherus agassizii) for recovery efforts based on genetic affinity to local areas. We collected samples from 130 captive desert tortoises from three desert communities: two in California (Ridgecrest and Joshua Tree) and the Desert Tortoise Conservation Center (Las Vegas) in Nevada. We tested all samples for 25 short tandem repeats and sequenced 1,109 bp of the mitochondrial genome. We compared captive genotypes to a database of 1,258 Gopherus samples, including 657 wild caught G. agassizii spanning the full range of the species. We conducted population assignment tests to determine the genetic origins of the captive individuals. For our total sample set, only 44 % of captive individuals were assigned to local populations based on genetic units derived from the reference database. One individual from Joshua Tree, California, was identified as being a Morafka’s desert tortoise, G. morafkai, a cryptic species which is not native to the Mojave Desert. Our data suggest that captive desert tortoises kept within the native range of G. agassizii cannot be presumed to have a genealogical affiliation to wild tortoises in their geographic proximity. Precautions should be taken before considering the release of captive tortoises into the wild as a management tool for recovery.

Provenancing Archaeological Wool Textiles from Medieval Northern Europe by Light Stable Isotope Analysis (δ13C, δ15N, δ2H)

PubMed Central

von Holstein, Isabella C. C.; Walton Rogers, Penelope; Craig, Oliver E.; Penkman, Kirsty E. H.; Newton, Jason; Collins, Matthew J.

2016-01-01

We investigate the origin of archaeological wool textiles preserved by anoxic waterlogging from seven medieval archaeological deposits in north-western Europe (c. 700–1600 AD), using geospatial patterning in carbon (δ13C), nitrogen (δ15N) and non-exchangeable hydrogen (δ2H) composition of modern and ancient sheep proteins. δ13C, δ15N and δ2H values from archaeological wool keratin (n = 83) and bone collagen (n = 59) from four sites were interpreted with reference to the composition of modern sheep wool from the same regions. The isotopic composition of wool and bone collagen samples clustered strongly by settlement; inter-regional relationships were largely parallel in modern and ancient samples, though landscape change was also significant. Degradation in archaeological wool samples, examined by elemental and amino acid composition, was greater in samples from Iceland (Reykholt) than in samples from north-east England (York, Newcastle) or northern Germany (Hessens). A nominal assignment approach was used to classify textiles into local/non-local at each site, based on maximal estimates of isotopic variability in modern sheep wool. Light element stable isotope analysis provided new insights into the origins of wool textiles, and demonstrates that isotopic provenancing of keratin preserved in anoxic waterlogged contexts is feasible. We also demonstrate the utility of δ2H analysis to understand the location of origin of archaeological protein samples. PMID:27764106

Mobility of plume-derived volcanogenic elements in meteoric water at Nyiragongo volcano (Congo) inferred from the chemical composition of single rainfall events

NASA Astrophysics Data System (ADS)

Liotta, Marcello; Shamavu, Patient; Scaglione, Sarah; D'Alessandro, Walter; Bobrowski, Nicole; Bruno Giuffrida, Giovanni; Tedesco, Dario; Calabrese, Sergio

2017-11-01

The chemical composition of single rainfall events was investigated at Nyiragongo volcano (Democratic Republic of Congo) with the aim of determining the relative contributions of plume-derived elements. The different locations of the sampling sites allowed both plume-affected samples (hereafter referred to as ;fumigated samples;) and samples representative of the local background to be collected. The chemical composition of the local background reflects the peculiar geographic features of the area, being influenced by biomass burning, geogenic dust, and biological activity. Conversely, fumigated samples contain large amounts of volcanogenic elements that can be clearly distinguished from the local background. These elements are released into the atmosphere from the persistently boiling lava lake of the Nyiragongo crater and from the neonate lava lake of Nyamulagira. These emissions result in a volcanic plume that includes solid particles, acidic droplets, and gaseous species. The chemical signature of the volcanic emissions appears in falling raindrops as they interact with the plume. HCl and HBr readily dissolve in water, and so their ratio in rain samples reflects that of the volcanic plume. The transport of HF is mediated by the large amount of silicate particles generated at the magma-air interface. SO2 is partially converted into SO42- that dissolves in water. The refractory elements dissolved in rain samples derive from the dissolution of silicate particles, and most of them (Al, Mg, Ca, and Sr) are present at exactly the same molar ratios as in the rocks. In contrast, elements such as Na, K, Rb, Cu, and Pb are enriched relative to the whole-rock composition, suggesting that they are volatilized during magma degassing. After correcting for the dissolution of silicate particles, we can define that the volatility of the elements decreases in the following order: Pb ≫ Rb > K > Na. This finding, which is the first for a volcanic plume, is consistent with previous measurements in high-temperature fumaroles at other volcanic areas.

Five years' experience of classical swine fever polymerase chain reaction ring trials in France.

PubMed

Po, F; Le Dimna, M; Le Potier, M F

2011-12-01

Since 2004, the French National Reference Laboratory for classical swine fever (CSF) has conducted an annual proficiency test (PT) to evaluate the ability of local veterinary laboratories to perform real-time polymerase chain reaction (PCR) for CSF virus. The results of five years of testing (2004-2008) are described here. The PT was conducted under blind conditions on 20 samples. The same batch of samples was used for all five years. The number of laboratories that analysed the samples increased from four in 2004 to 13 in 2008. The results of the PT showed the following: cross-contamination between samples and deficiencies in RNA preparation can occur even in experienced laboratories; sample homogeneity should be checked carefully before selection; samples stored at-80 degrees C for several years remain stable; and poor shipment conditions do not damage the samples with regard to detection of CSF virus genome. These results will enable redesign of the panel to improve the overall quality of the PT, which will encourage laboratories to check and improve their PCR procedures and expertise. This is an excellent way to determine laboratory performance.

True non-contact atomic force microscopy imaging of heterogeneous biological samples in liquids: topography and material contrast.

PubMed

Almonte, Lisa; Colchero, Jaime

2017-02-23

The present work analyses how the tip-sample interaction signals critically determine the operation of an Atomic Force Microscope (AFM) set-up immersed in liquid. On heterogeneous samples, the conservative tip-sample interaction may vary significantly from point to point - in particular from attractive to repulsive - rendering correct feedback very challenging. Lipid membranes prepared on a mica substrate are analyzed as reference samples which are locally heterogeneous (material contrast). The AFM set-up is operated dynamically at low oscillation amplitude and all available experimental data signals - the normal force, as well as the amplitude and frequency - are recorded simultaneously. From the analysis of how the dissipation (oscillation amplitude) and the conservative interaction (normal force and resonance frequency) vary with the tip-sample distance we conclude that dissipation is the only appropriate feedback source for stable and correct topographic imaging. The normal force and phase then carry information about the sample composition ("chemical contrast"). Dynamic AFM allows imaging in a non-contact regime where essentially no forces are applied, rendering dynamic AFM a truly non-invasive technique.

A milliKelvin scanning Hall probe microscope for high resolution magnetic imaging

NASA Astrophysics Data System (ADS)

Khotkevych, V. V.; Bending, S. J.

2009-02-01

The design and performance of a novel scanning Hall probe microscope for milliKelvin magnetic imaging with submicron lateral resolution is presented. The microscope head is housed in the vacuum chamber of a commercial 3He-refrigerator and operates between room temperature and 300 mK in magnetic fields up to 10 T. Mapping of the local magnetic induction at the sample surface is performed by a micro-fabricated 2DEG Hall probe equipped with an integrated STM tip. The latter provides a reliable mechanism of surface tracking by sensing and controlling the tunnel currents. We discuss the results of tests of the system and illustrate its potential with images of suitable reference samples captured in different modes of operation.

Estimation of reference intervals from small samples: an example using canine plasma creatinine.

PubMed

Geffré, A; Braun, J P; Trumel, C; Concordet, D

2009-12-01

According to international recommendations, reference intervals should be determined from at least 120 reference individuals, which often are impossible to achieve in veterinary clinical pathology, especially for wild animals. When only a small number of reference subjects is available, the possible bias cannot be known and the normality of the distribution cannot be evaluated. A comparison of reference intervals estimated by different methods could be helpful. The purpose of this study was to compare reference limits determined from a large set of canine plasma creatinine reference values, and large subsets of this data, with estimates obtained from small samples selected randomly. Twenty sets each of 120 and 27 samples were randomly selected from a set of 1439 plasma creatinine results obtained from healthy dogs in another study. Reference intervals for the whole sample and for the large samples were determined by a nonparametric method. The estimated reference limits for the small samples were minimum and maximum, mean +/- 2 SD of native and Box-Cox-transformed values, 2.5th and 97.5th percentiles by a robust method on native and Box-Cox-transformed values, and estimates from diagrams of cumulative distribution functions. The whole sample had a heavily skewed distribution, which approached Gaussian after Box-Cox transformation. The reference limits estimated from small samples were highly variable. The closest estimates to the 1439-result reference interval for 27-result subsamples were obtained by both parametric and robust methods after Box-Cox transformation but were grossly erroneous in some cases. For small samples, it is recommended that all values be reported graphically in a dot plot or histogram and that estimates of the reference limits be compared using different methods.

Millstone: software for multiplex microbial genome analysis and engineering

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

Goodman, Daniel B.; Kuznetsov, Gleb; Lajoie, Marc J.

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. Here, we describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Millstone: software for multiplex microbial genome analysis and engineering.

PubMed

Goodman, Daniel B; Kuznetsov, Gleb; Lajoie, Marc J; Ahern, Brian W; Napolitano, Michael G; Chen, Kevin Y; Chen, Changping; Church, George M

2017-05-25

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Millstone: software for multiplex microbial genome analysis and engineering

DOE PAGES

Goodman, Daniel B.; Kuznetsov, Gleb; Lajoie, Marc J.; ...

2017-05-25

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. Here, we describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

PMAG: Relational Database Definition

NASA Astrophysics Data System (ADS)

Keizer, P.; Koppers, A.; Tauxe, L.; Constable, C.; Genevey, A.; Staudigel, H.; Helly, J.

2002-12-01

The Scripps center for Physical and Chemical Earth References (PACER) was established to help create databases for reference data and make them available to the Earth science community. As part of these efforts PACER supports GERM, REM and PMAG and maintains multiple online databases under the http://earthref.org umbrella website. This website has been built on top of a relational database that allows for the archiving and electronic access to a great variety of data types and formats, permitting data queries using a wide range of metadata. These online databases are designed in Oracle 8.1.5 and they are maintained at the San Diego Supercomputer Center. They are directly available via http://earthref.org/databases/. A prototype of the PMAG relational database is now operational within the existing EarthRef.org framework under http://earthref.org/databases/PMAG/. As will be shown in our presentation, the PMAG design focuses around the general workflow that results in the determination of typical paleo-magnetic analyses. This ensures that individual data points can be traced between the actual analysis and the specimen, sample, site, locality and expedition it belongs to. These relations guarantee traceability of the data by distinguishing between original and derived data, where the actual (raw) measurements are performed on the specimen level, and data on the sample level and higher are then derived products in the database. These relations may also serve to recalculate site means when new data becomes available for that locality. The PMAG data records are extensively described in terms of metadata. These metadata are used when scientists search through this online database in order to view and download their needed data. They minimally include method descriptions for field sampling, laboratory techniques and statistical analyses. They also include selection criteria used during the interpretation of the data and, most importantly, critical information about the site location (latitude, longitude, elevation), geography (continent, country, region), geological setting (lithospheric plate or block, tectonic setting), geological age (age range, timescale name, stratigraphic position) and materials (rock type, classification, alteration state). Each data point and method description is also related to its peer-reviewed reference [citation ID] as archived in the EarthRef Reference Database (ERR). This guarantees direct traceability all the way to its original source, where the user can find the bibliography of each PMAG reference along with every abstract, data table, technical note and/or appendix that are available in digital form and that can be downloaded as PDF/JPEG images and Microsoft Excel/Word data files. This may help scientists and teachers in performing their research since they have easy access to all the scientific data. It also allows for checking potential errors during the digitization process. Please visit the PMAG website at http://earthref.org/PMAG/ for more information.

Pixel-based absorption correction for dual-tracer fluorescence imaging of receptor binding potential

PubMed Central

Kanick, Stephen C.; Tichauer, Kenneth M.; Gunn, Jason; Samkoe, Kimberley S.; Pogue, Brian W.

2014-01-01

Ratiometric approaches to quantifying molecular concentrations have been used for decades in microscopy, but have rarely been exploited in vivo until recently. One dual-tracer approach can utilize an untargeted reference tracer to account for non-specific uptake of a receptor-targeted tracer, and ultimately estimate receptor binding potential quantitatively. However, interpretation of the relative dynamic distribution kinetics is confounded by differences in local tissue absorption at the wavelengths used for each tracer. This study simulated the influence of absorption on fluorescence emission intensity and depth sensitivity at typical near-infrared fluorophore wavelength bands near 700 and 800 nm in mouse skin in order to correct for these tissue optical differences in signal detection. Changes in blood volume [1-3%] and hemoglobin oxygen saturation [0-100%] were demonstrated to introduce substantial distortions to receptor binding estimates (error > 30%), whereas sampled depth was relatively insensitive to wavelength (error < 6%). In response, a pixel-by-pixel normalization of tracer inputs immediately post-injection was found to account for spatial heterogeneities in local absorption properties. Application of the pixel-based normalization method to an in vivo imaging study demonstrated significant improvement, as compared with a reference tissue normalization approach. PMID:25360349

Phenotypic characteristics of local cattle in Madura Island

NASA Astrophysics Data System (ADS)

Maylinda, Sucik; Nugroho, H.; Busono, W.

2017-05-01

The aim of the research is to (1) analyze phenotypic variance both qualitative and quantitative characters in Madura cattle, (2) to analyze the relationship between that characters and body weight. Cattle studied were located in Waru and Pademawu subdistrict, Pamekasan district, Indonesia. The sampling technique was accidental sampling. Subject animals were 8-20 month-old cows, grouped into 2 age groups of <1 and >1 years old. Both qualitative and quantitative phenotypic characteristics were recorded. Qualitative characteristics were the color of the body, white color in bottom and leg, black color at the back, and the presence of horns. Quantitative characteristics were the head index, body weight, chest girth (CG), body height (BH), body length (BL), and body condition score (BCS). Data were analyzed with correlation and regression analyses. Results showed that qualitative characteristics of the Madura local cattle were all those of the reference Madura cattle standard, such as the white color of leg and bottom, with small head indexes. We found that (1) most of Madura Local cattle had the standard Madura cattle characteristics in both sexes, and (2) the best cattle, in terms of body weight, can be selected based on chest girth rather than other measurements, which is advantageous because measuring the chest circumference is quicker and easier than directly measuring cattle weight in rural villages.

Pediatric reference value distributions and covariate-stratified reference intervals for 29 endocrine and special chemistry biomarkers on the Beckman Coulter Immunoassay Systems: a CALIPER study of healthy community children.

PubMed

Karbasy, Kimiya; Lin, Danny C C; Stoianov, Alexandra; Chan, Man Khun; Bevilacqua, Victoria; Chen, Yunqi; Adeli, Khosrow

2016-04-01

The CALIPER program is a national research initiative aimed at closing the gaps in pediatric reference intervals. CALIPER previously reported reference intervals for endocrine and special chemistry markers on Abbott immunoassays. We now report new pediatric reference intervals for immunoassays on the Beckman Coulter Immunoassay Systems and assess platform-specific differences in reference values. A total of 711 healthy children and adolescents from birth to <19 years of age were recruited from the community. Serum samples were collected for measurement of 29 biomarkers on the Beckman Coulter Immunoassay Systems. Statistically relevant age and/or gender-based partitions were determined, outliers removed, and reference intervals calculated in accordance with Clinical and Laboratory Standards Institute (CLSI) EP28-A3c guidelines. Complex profiles were observed for all 29 analytes, necessitating unique age and/or sex-specific partitions. Overall, changes in analyte concentrations observed over the course of development were similar to trends previously reported, and are consistent with biochemical and physiological changes that occur during childhood. Marked differences were observed for some assays including progesterone, luteinizing hormone and follicle-stimulating hormone where reference intervals were higher than those reported on Abbott immunoassays and parathyroid hormone where intervals were lower. This study highlights the importance of determining reference intervals specific for each analytical platform. The CALIPER Pediatric Reference Interval database will enable accurate diagnosis and laboratory assessment of children monitored by Beckman Coulter Immunoassay Systems in health care institutions worldwide. These reference intervals must however be validated by individual labs for the local pediatric population as recommended by CLSI.

Biological and environmental reference materials in CENAM.

PubMed

Arvizu-Torres, R; Perez-Castorena, A; Salas-Tellez, J A; Mitani-Nakanishi, Y

2001-06-01

Since 1994, when the NIST/NOAA Quality Assurance Program in Chemical Measurements was discussed in Queretaro, CENAM, the National Measurement Institute (NMI) of Mexico, has become involved in the development of reference materials. In the field of biological and environmental reference materials, in particular, the NORAMET collaboration program with NIST and NRC, and the North-American Environmental Cooperation signed among three free-trade treaty organizations, have greatly helped the development of the materials metrology program in the newly established CENAM. This paper describes some particularly significant efforts of CENAM in the development of biological and environmental reference materials, on the basis of inter-comparison studies organized with local and governmental environmental agencies of Mexico. In the field of water pollution CENAM has developed a practical proficiency testing (PT) scheme for field laboratories, as a part of registration by local government in the metropolitan area, according to the Mexican Ecological Regulation. The results from these eight PTs in the last 5 years have demonstrated that this scheme has helped ensure the reliability of analytical capability of more than 50 field laboratories in three states, Mexico, D.F., and the States of Mexico and Queretaro. Similar experience has been obtained for more than 70 service units of stack emission measurements in the three states in 1998 and 1999, as a result of the design of a PT scheme for reference gas mixtures. This PT scheme has been accomplished successfully by 30 analytical laboratories who provide monitoring services and perform research on toxic substances (Hg, methylmercury, PCB, etc.) in Mexico. To support these activities, reference samples have been produced through the NIST SRMs, and efforts have been made to increase CENAM's capability in the preparation of primary reference materials in spectrometric solutions and gas mixtures. Collaboration among NMIs has also successfully overcome the inability of CENAM to prepare biological tissue for mercury assessment and marine sediments for analysis of trace metals. The importance of international collaboration is stressed not only in the NORAMET region but also in the SIM, to provide help for each other and achieve mutual recognition among member countries of the region.

Study of galaxies in the Lynx-Cancer void - VII. New oxygen abundances

NASA Astrophysics Data System (ADS)

Pustilnik, S. A.; Perepelitsyna, Y. A.; Kniazev, A. Y.

2016-11-01

We present new or improved oxygen abundances (O/H) for the nearby Lynx-Cancer void updated galaxy sample. They are obtained via the SAO 6-m telescope spectroscopy (25 objects), or derived from the Sloan Digital Sky Survey spectra (14 galaxies, of which for seven objects O/H values were unknown). For eight galaxies with detected [O III] λ4363 line, O/H values are derived via the direct (Te) method. For the remaining objects, O/H was estimated via semi-empirical and empirical methods. For all accumulated O/H data for 81 galaxies of this void (with 40 of them derived via Te method), their relation `O/H versus MB' is compared with that for similar late-type galaxies from denser environments (the Local Volume `reference sample'). We confirm our previous conclusion derived for a subsample of 48 objects: void galaxies show systematically reduced O/H for the same luminosity with respect to the reference sample, in average by 0.2 dex, or by a factor of ˜1.6. Moreover, we confirm the fraction of ˜20 per cent of strong outliers, with O/H of two to four times lower than the typical values for the `reference' sample. The new data are consistent with the conclusion on the slower evolution of the main void galaxy population. We obtained Hα velocity for the faint optical counterpart of the most gas-rich (M(H I)/LB = 25) void object J0723+3624, confirming its connection with the respective H I blob. For similar extremely gas-rich dwarf J0706+3020, we give a tentative O/H ˜(O/H)⊙/45. In Appendix A, we present the results of calibration of semi-empirical method by Izotov & Thuan and of empirical calibrators by Pilyugin & Thuan and Yin et al. on the sample of ˜150 galaxies from the literature with O/H measured by Te method.

Intra prediction using face continuity in 360-degree video coding

NASA Astrophysics Data System (ADS)

Hanhart, Philippe; He, Yuwen; Ye, Yan

2017-09-01

This paper presents a new reference sample derivation method for intra prediction in 360-degree video coding. Unlike the conventional reference sample derivation method for 2D video coding, which uses the samples located directly above and on the left of the current block, the proposed method considers the spherical nature of 360-degree video when deriving reference samples located outside the current face to which the block belongs, and derives reference samples that are geometric neighbors on the sphere. The proposed reference sample derivation method was implemented in the Joint Exploration Model 3.0 (JEM-3.0) for the cubemap projection format. Simulation results for the all intra configuration show that, when compared with the conventional reference sample derivation method, the proposed method gives, on average, luma BD-rate reduction of 0.3% in terms of the weighted spherical PSNR (WS-PSNR) and spherical PSNR (SPSNR) metrics.

Automatic HTS force measurement instrument

DOEpatents

Sanders, Scott T.; Niemann, Ralph C.

1999-01-01

A device for measuring the levitation force of a high temperature superconductor sample with respect to a reference magnet includes a receptacle for holding several high temperature superconductor samples each cooled to superconducting temperature. A rotatable carousel successively locates a selected one of the high temperature superconductor samples in registry with the reference magnet. Mechanism varies the distance between one of the high temperature superconductor samples and the reference magnet, and a sensor measures levitation force of the sample as a function of the distance between the reference magnet and the sample. A method is also disclosed.

Laser Spectroscopy Monitoring of 13C18O16O and 12C17O16O of Atmospheric Carbon Dioxide

NASA Astrophysics Data System (ADS)

Shorter, J. H.; Nelson, D. D.; Ono, S.; McManus, J. B.; Zahniser, M. S.

2017-12-01

One of the main challenges to making accurate predictions of future changes in CO2 concentration is the capability to determine what fraction of human produced CO2 remains in the atmosphere. We present our progress in the application of Tunable Infrared Laser Direct Absorption Spectroscopy (TILDAS) to the measurement of the primary clumped (13C18O16O) as well as 17O (12C17O16O) isotopologues of atmospheric CO2, as a tracer of its sources and sinks. We expect unique isotopologue signals in CO2 from high-temperature combustion sources, plants, soils, and air-sea exchange processes. High sampling frequency (a few minutes for each sample vs. reference cycle) achieved by a TILDAS instrument is expected to enable us to document local heterogeneous sources and temporal variations. The TILDAS is equipped with a newly developed 400-meter absorption cell. We designed a dual pressure measurement technique in which the clumped isotopologue, 13C18O16O, and 13C16O16O are first measured at 30 torr cell pressure. This is followed by measurement of 12C17O16O, 12C18O16O and 12C16O16O at lower ( 5 torr) cell pressure. Isotopologue ratios are compared between reference and sample gases. Preliminary tests demonstrated a precision approaching 0.03 ‰ for the ratio 13C18O16O/13C16O16O and 0.08‰ for Δ13C18O16O value (1σ repeatability for 4 min sample vs. reference cycle). Sample size for a single analysis is approximately 100 mL of air (1.6μmol of CO2). Given the previously observed range of variations for Δ13C18O16O and Δ17O values as large as 0.6 to 0.3 ‰, respectively, TILDAS offers a novel approach for real time monitoring of atmospheric CO2 isotopologues. It was found that achieving better than 0.1‰ requires careful matching of CO2 mixing ratios between reference and sample air. A primary cause of pressure and mixing ratio dependence is inaccurate baseline fitting (analogous to abundance sensitivity or pressure baseline for IRMS). Given that mixing ratios of atmospheric CO2 can vary as much as 50% or more, a dynamic dilution scheme, where sample air is diluted by CO2 free air to match the reference mixing ratio, is being developed. An in-line calibration source of hot, equilibrated CO2 isotopologues is also being tested. We will discuss the current instrument performance, areas for improvement, and project future applications.

Impact of seaweed beachings on dynamics of δ(15)N isotopic signatures in marine macroalgae.

PubMed

Lemesle, Stéphanie; Mussio, Isabelle; Rusig, Anne-Marie; Menet-Nédélec, Florence; Claquin, Pascal

2015-08-15

A fine-scale survey of δ(15)N, δ(13)C, tissue-N in seaweeds was conducted using samples from 17 sampling points at two sites (Grandcamp-Maisy (GM), Courseulles/Mer (COU)) along the French coast of the English Channel in 2012 and 2013. Partial triadic analysis was performed on the parameter data sets and revealed the functioning of three areas: one estuary (EstA) and two rocky areas (GM(∗), COU(∗)). In contrast to oceanic and anthropogenic reference points similar temporal dynamics characterized δ(15)N signatures and N contents at GM(∗) and COU(∗). Nutrient dynamics were similar: the N-concentrations in seawater originated from the River Seine and local coastal rivers while P-concentrations mainly from these local rivers. δ(15)N at GM(∗) were linked to turbidity suggesting inputs of autochthonous organic matter from large-scale summer seaweed beachings made up of a mixture of Rhodophyta, Phaeophyta and Chlorophyta species. This study highlights the coupling between seaweed beachings and nitrogen sources of intertidal macroalgae. Copyright © 2015 Elsevier Ltd. All rights reserved.

Assessment of oxidative stress indices in a marine macro brown alga Padina tetrastromatica (Hauck) from comparable polluted coastal regions of the Arabian Sea, west coast of India.

PubMed

Maharana, Dusmant; Jena, Karmabeer; Pise, Navnath M; Jagtap, Tanaji G

2010-01-01

Oxidative stress and antioxidant defence systems were assessed in a marine brown alga Padina tetrastromatica, commonly occurring from the tropics. Lipid peroxidation (LPX) and H2O2 were measured as oxidative stress markers, and antioxidant defences were measured as catalase (CAT), glutathione S-transferase (GST) and ascorbic acid (AsA), in order to understand their dissimilarity with respect to pollution levels from selective locations along the central west coast of India. A significant increased levels of LPX, H2O2, CAT and GST were observed in samples from relatively polluted localities (Colaba and Karwar) when compared to less polluted locality (Anjuna), while AsA concentration was higher in algal samples from worst polluted region of Colaba. Heavy metals such as Cd and Pb were also higher in the vicinity of polluted areas compared to reference area. Variation of oxidative stress indices in response to accumulation of heavy metals within P. tetrastromatica could be used as molecular biomarkers in assessment and monitoring environmental quality of ecologically sensitive marine habitats.

Metal and metalloid distribution in different environmental compartments of the middle Xingu River in the Amazon, Brazil.

PubMed

Ribeiro, Danielle Regina Gomes; Faccin, Henrique; Molin, Thaís Ramos Dal; de Carvalho, Leandro Machado; Amado, Lílian Lund

2017-12-15

Concentrations of As, Cd, Cu, Cr, Pb, Hg, and Ni were analyzed during rainy and dry seasons in water, sediment, soil, and two fish species. The analysis took place at four points in the Xingu River, one point in the Fresco River, and two mining pits in the southeastern area of the Eastern Amazon, Brazil. In the water, the total concentration of As (>0.14μg/L) was higher than the local reference values at all sampling points and in both seasons. Ordination analysis (PCA) highlighted As and Cu elements in the water. PERMANOVA showed that the metals behaved differently in the water throughout the monitored season and between sampling points. The sites with mining activity were the regions that were the most contaminated by metals. Samples of sediment (Ni>18mg/kg and Cr>37.30mg/kg) and soil (Pb>72mg/kg, Cr>75mg/kg and Ni>30mg/Kg) showed concentrations above the recommended by local legislation. Metal values in the muscle of both fish species were relatively low at all sampling points and in both monitored seasons. Concentrations in water, sediment, and soil showed that some points of the Xingu River, Fresco River and mining pits are contaminated by trace elements, mainly As, Hg, Cr, Pb, and Ni. This was the first study about trace elements in the Middle Xingu River, which leads us to conclude that rainfall and cassiterite mining activities strongly influence the mobilization of metals, especially in abiotic compartments. However, the fish analyzed did not exhibit relevant levels of contamination. This indicates low risk for human consumption. Additionally, results highlight the need to establish local criteria to define contamination limits for different metals while taking into account local geochemistry particularities and biome diversity. Copyright © 2017 Elsevier B.V. All rights reserved.

Comparison of essential and toxic elements in esophagus, lung, mouth and urinary bladder male cancer patients with related to controls.

PubMed

Kazi, Tasneem Gul; Wadhwa, Sham Kumar; Afridi, Hassan Imran; Talpur, Farah Naz; Tuzen, Mustafa; Baig, Jameel Ahmed

2015-05-01

There is a compelling evidence in support of negative associations between essential trace and toxic elements in different types of cancer. The aim of the present study was to investigate the relationship between carcinogenic (As, Cd, Ni) and anti-carcinogenic (Se, Zn) trace elements in scalp hair samples of different male cancerous patients (esophagus, lung, mouth, and urinary bladder). For comparative purposes, the scalp hair samples of healthy males of the same age group (ranged 35-65 years) as controls were analyzed. Both controls and patients have the same socioeconomic status, localities, dietary habits, and smoking locally made cigarette. The scalp hair samples were oxidized by 65% nitric acid: 30% hydrogen peroxide (2:1) ratio in microwave oven followed by atomic absorption spectrometry. The validity and accuracy of the methodology were checked using certified reference material of human hair BCR 397. The mean concentrations of As, Cd, and Ni were found to be significantly higher in scalp hair samples of patients having different cancers as compared to the controls, while reverse results were obtained in the case of Se and Zn levels (p < 0.01). The study revealed that the carcinogenic processes are significantly affecting the trace elements burden and mutual interaction of essential trace and toxic elements in the cancerous patients.

Validating Reference Equations for Impulse Oscillometry in Healthy Mexican Children.

PubMed

Gochicoa-Rangel, Laura; Del Río-Hidalgo, Rodrigo; Hernández-Ruiz, Juana; Rodríguez-Moreno, Luis; Martínez-Briseño, David; Mora-Romero, Uri; Cid-Juárez, Silvia; García-Sancho, Cecilia; Torre-Bouscoulet, Luis

2017-09-01

The impulse oscillometry system (IOS) measures the impedance (Z) of the respiratory system, but proper interpretation of its results requires adequate reference values. The objectives of this work were: (1) to validate the reference equations for the IOS published previously by our group and (2) to compare the adjustment of new available reference equations for the IOS from different countries in a sample of healthy children. Subjects were healthy 4-15-y-old children from the metropolitan area of Mexico City, who performed an IOS test. The functional IOS parameters obtained were compared with the predicted values from 12 reference equations determined in studies of different ethnic groups. The validation methods applied were: analysis of the differences between measured and predicted values for each reference equation; correlation and concordance coefficients; adjustment by Z-score values; percentage of predicted value; and the percentage of patients below the lower limit of normality or above the upper limit of normality. Of the 224 participants, 117 (52.3%) were girls, and the mean age was 8.6 ± 2.3 y. The equations that showed the best adjustment for the different parameters were those from the studies by Nowowiejska et al (2008) and Gochicoa et al (2015). The equations proposed by Frei et al (2005), Hellinckx et al (1998), Kalhoff et al (2011), Klug and Bisgaard (1998), de Assumpção et al (2016), and Dencker et al (2006) overestimated the airway resistance of the children in our sample, whereas the equation of Amra et al (2008) underestimated it. In the analysis of the lower and upper limits of normality, Gochicoa et al equation was the closest, since 5% of subjects were below or above percentiles 5 and 95, respectively. The study found that, in general, all of the equations showed greater error at the extremes of the age distribution. Because of the robust adjustment of the present study reference equations for the IOS, it can be recommended for both clinical and research purposes in our population. The differential adjustment of other equations underlines the need to obtain local reference values. Copyright © 2017 by Daedalus Enterprises.

Communication: Estimating the initial biasing potential for λ-local-elevation umbrella-sampling (λ-LEUS) simulations via slow growth

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

Bieler, Noah S.; Hünenberger, Philippe H., E-mail: phil@igc.phys.chem.ethz.ch

2014-11-28

In a recent article [Bieler et al., J. Chem. Theory Comput. 10, 3006–3022 (2014)], we introduced a combination of the λ-dynamics (λD) approach for calculating alchemical free-energy differences and of the local-elevation umbrella-sampling (LEUS) memory-based biasing method to enhance the sampling along the alchemical coordinate. The combined scheme, referred to as λ-LEUS, was applied to the perturbation of hydroquinone to benzene in water as a test system, and found to represent an improvement over thermodynamic integration (TI) in terms of sampling efficiency at equivalent accuracy. However, the preoptimization of the biasing potential required in the λ-LEUS method requires “filling up”more » all the basins in the potential of mean force. This introduces a non-productive pre-sampling time that is system-dependent, and generally exceeds the corresponding equilibration time in a TI calculation. In this letter, a remedy is proposed to this problem, termed the slow growth memory guessing (SGMG) approach. Instead of initializing the biasing potential to zero at the start of the preoptimization, an approximate potential of mean force is estimated from a short slow growth calculation, and its negative used to construct the initial memory. Considering the same test system as in the preceding article, it is shown that of the application of SGMG in λ-LEUS permits to reduce the preoptimization time by about a factor of four.« less

Communication: Estimating the initial biasing potential for λ-local-elevation umbrella-sampling (λ-LEUS) simulations via slow growth

NASA Astrophysics Data System (ADS)

Bieler, Noah S.; Hünenberger, Philippe H.

2014-11-01

In a recent article [Bieler et al., J. Chem. Theory Comput. 10, 3006-3022 (2014)], we introduced a combination of the λ-dynamics (λD) approach for calculating alchemical free-energy differences and of the local-elevation umbrella-sampling (LEUS) memory-based biasing method to enhance the sampling along the alchemical coordinate. The combined scheme, referred to as λ-LEUS, was applied to the perturbation of hydroquinone to benzene in water as a test system, and found to represent an improvement over thermodynamic integration (TI) in terms of sampling efficiency at equivalent accuracy. However, the preoptimization of the biasing potential required in the λ-LEUS method requires "filling up" all the basins in the potential of mean force. This introduces a non-productive pre-sampling time that is system-dependent, and generally exceeds the corresponding equilibration time in a TI calculation. In this letter, a remedy is proposed to this problem, termed the slow growth memory guessing (SGMG) approach. Instead of initializing the biasing potential to zero at the start of the preoptimization, an approximate potential of mean force is estimated from a short slow growth calculation, and its negative used to construct the initial memory. Considering the same test system as in the preceding article, it is shown that of the application of SGMG in λ-LEUS permits to reduce the preoptimization time by about a factor of four.

Stratigraphic sections of the phosphoria formation in Utah, 1949-1951

USGS Publications Warehouse

Cheney, T.M.; Smart, R.A.; Waring, R.G.; Warner, M.A.

1953-01-01

As part of a comprehensive investigation of the phosphate deposits of the western field begun in 1947, the U.S. Geological Survey has measured and sampled the full thickness of the Permian Phosphoria formation and its partial correlative, the Park City formation, at many localities in Utah and other states. Although these data will not be fully analyzed for several years, segments of the data, accompanied by little or no interpretation, are published as preliminary reports as they are assembled. This report, which contains abstracts of the sections measured in northeastern Utah in 1949, 1950, and 1951, is one of this series and the second report of data gathered in Utah. The field and laboratory procedures adopted in these investigations are described rather fully in a previous report (McKelvey and others, 1953a). Many people have taken part in this investigation. The program which this work is a part was organized by V. E. McKelvey and the field program was supervised by R. W. Swanson. R. P. Sheldon assisted in the location and selection of sample localities and F. J. Anderson, McKelvey, Sheldon, and H. W. Peirce participated in the description of strata and the collection of samples referred to in this report. T. K. Rigby assisted in the preparation of trenches and the crushing and splitting of samples in the field. The laboratory preparation of samples for chemical analysis was done in Denver, Colo., under the direction of W. P. Huleatt.

Application of SERS spectroscopy to the identification of (3,4-methylenedioxy)amphetamine in forensic samples utilizing matrix stabilized silver halides.

PubMed

Sägmüller, B; Schwarze, B; Brehm, G; Schneider, S

2001-11-01

A method based on surface-enhanced Raman scattering (SERS) spectroscopy was developed to meet the need for the reliable and rapid identification of illicit drugs such as the 'designer drug' XTC, preferably to increase the security of legal certificates. A matrix stabilized silver halide dispersion on a microtiter plate is used as the SERS-active substrate, providing an easy to use system for sample preparation and probing by means of a Raman microscope. The potential of the method is demonstrated by applying it to the identification of the psychoactive ingredients of drug containing tablets which were confiscated by the local police at techno-music events. The samples of interest were 26 different brands of XTC tablets and several pieces of evidence (powders) containing amphetamine. For reference, we show SERS and Raman spectra of pristine amphetamine, methamphetamine, 3,4-methylenedioxyamphetamine, 3,4-methylenedioxymethamphetamine (MDMA) and 3,4-methylenedioxyethamphetamine.

Flux-limited sample of Galactic carbon stars

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

Claussen, M.J.; Kleinmann, S.G.; Joyce, R.R.

Published observational data (including IRAS observations) for a flux-limited sample of 215 Galactic carbon stars (CSs) selected from the 2-micron sky survey of Neugebauer and Leighton (1969) are compiled in extensive tables and graphs and analyzed statistically. The sample is found to penetrate a volume of radius 1.5 kpc, and the local CS space density and surface density are calculated as log rho0 (per cu kpc) = 2.0 + or - 0.4 and log N (per sq kpc) = 1.6 + or - 0.2, respectively. The total Galactic mass-return rate from these CSs is estimated as 0.013 solar mass/yr, implyingmore » a time scale of 0.1-1 Myr for the CS evolutionary phase and a mass of 1.2-1.6 solar mass for the (probably F-type) main-seqence progenitors of CSs. 81 references.« less

Assessment of exposure to lead in humans and turtles living in an industrial site in Coatzacoalcos Veracruz, Mexico.

PubMed

Pelallo-Martínez, N A; Ilizaliturri-Hernández, C A; Espinosa-Reyes, G; Carrizales-Yáñez, L; González-Mille, D J

2011-06-01

The intake of lead from the environment may occur thru various receptors. In order to measure lead levels absorbed, samples were taken from Children who live in three localities surrounding an industrial complex in Coatzacoalcos, Veracruz. Samples were also taken from turtles. Samples were analyzed and results were compared against the general population. In children tested, over 75% of all values were determined to be above CDC's safety levels of (10 μg/dL). The geometric mean lead concentration was 11.4 μg/dL, which is clearly higher around the industrial complex than in the general population. In turtles, lead blood levels in the exposed population were 2-fold above (24.2 μg/dL) those of turtles in the reference population (10.1 μg/dL). Lead levels observed represent a risk for both human and fauna health.

Performance of serological tests for syphilis in sexually transmitted diseases clinics in Guangxi Autonomous Region, China: implications for syphilis surveillance and control.

PubMed

Yin, Yue-Ping; Wei, Wan-Hui; Wang, Hong-Chun; Zhu, Bang-Yong; Yu, Yan-Hua; Chen, Xiang-Sheng; Peeling, Rosanna W; Cohen, Myron S

2009-03-01

China is experiencing a growing syphilis epidemic. Individuals are currently screened and cases are confirmed using traditional serological testing methods. A total of 11 558 serum specimens from patients at 14 sexually transmitted diseases (STD) clinics at provincial, prefecture and county levels in Guangxi Autonomous Region were tested at local clinics using the toluidine red unheated serum test (TRUST) and the SD Bioline Syphilis 3.0 Treponema Pallidum (SD-TP) test and then transported to the National STD Reference Laboratory for TRUST and confirmatory Treponema pallidum particle assay (TPPA) testing. In local clinics, 13.2% of specimens were TRUST positive and 12.8% were TRUST and SD-TP positive. At the Reference Laboratory, 15.4% of specimens were TRUST positive and 11.8% were TRUST and TPPA positive. Local clinics showed a significantly higher prevalence of active syphilis compared with results from the Reference Laboratory (12.8 v. 11.8%, chi(2) = 4.59, P = 0.03). The local TRUST tests had consistent results with Reference Laboratory tests qualitatively among 96.2% of the specimens and quantitatively among 95.5% of the specimens. The algorithm of TRUST screening and then SD-TP confirmation among positive TRUST specimens at local STD clinics had 96.6% sensitivity and 99.3% specificity in diagnosing active syphilis compared with the 'gold standard' based on TRUST and TPPA positivity at the Reference Laboratory (positive predictive value 95.1% and negative predictive value 99.5%). The TRUST screening and SD-TP confirmation in combination can be used at local STD clinics for the efficient diagnosis of serologically active syphilis. However, continuing capacity building and quality assurance remain critical in ensuring the quality of syphilis diagnosis at local clinics.

Incorporating geographical factors with artificial neural networks to predict reference values of erythrocyte sedimentation rate

PubMed Central

2013-01-01

Background The measurement of the Erythrocyte Sedimentation Rate (ESR) value is a standard procedure performed during a typical blood test. In order to formulate a unified standard of establishing reference ESR values, this paper presents a novel prediction model in which local normal ESR values and corresponding geographical factors are used to predict reference ESR values using multi-layer feed-forward artificial neural networks (ANN). Methods and findings Local normal ESR values were obtained from hospital data, while geographical factors that include altitude, sunshine hours, relative humidity, temperature and precipitation were obtained from the National Geographical Data Information Centre in China. The results show that predicted values are statistically in agreement with measured values. Model results exhibit significant agreement between training data and test data. Consequently, the model is used to predict the unseen local reference ESR values. Conclusions Reference ESR values can be established with geographical factors by using artificial intelligence techniques. ANN is an effective method for simulating and predicting reference ESR values because of its ability to model nonlinear and complex relationships. PMID:23497145

Incorporating geographical factors with artificial neural networks to predict reference values of erythrocyte sedimentation rate.

PubMed

Yang, Qingsheng; Mwenda, Kevin M; Ge, Miao

2013-03-12

The measurement of the Erythrocyte Sedimentation Rate (ESR) value is a standard procedure performed during a typical blood test. In order to formulate a unified standard of establishing reference ESR values, this paper presents a novel prediction model in which local normal ESR values and corresponding geographical factors are used to predict reference ESR values using multi-layer feed-forward artificial neural networks (ANN). Local normal ESR values were obtained from hospital data, while geographical factors that include altitude, sunshine hours, relative humidity, temperature and precipitation were obtained from the National Geographical Data Information Centre in China.The results show that predicted values are statistically in agreement with measured values. Model results exhibit significant agreement between training data and test data. Consequently, the model is used to predict the unseen local reference ESR values. Reference ESR values can be established with geographical factors by using artificial intelligence techniques. ANN is an effective method for simulating and predicting reference ESR values because of its ability to model nonlinear and complex relationships.

Validating the Center for Epidemiological Studies Depression Scale for Children in Rwanda

PubMed Central

Betancourt, Theresa; Scorza, Pamela; Meyers-Ohki, Sarah; Mushashi, Christina; Kayiteshonga, Yvonne; Binagwaho, Agnes; Stulac, Sara; Beardslee, William R.

2017-01-01

Objective We assessed the validity of the Center for Epidemiological Studies Depression Scale for Children (CES-DC) as a screen for depression in Rwandan children and adolescents. Although the CES-DC is widely used for depression screening in high-income countries, its validity in low-income and culturally diverse settings, including sub-Saharan Africa, is unknown. Method The CES-DC was selected based on alignment with local expressions of depression-like problems in Rwandan children and adolescents. To examine criterion validity, we compared CES-DC scores to depression diagnoses on a structured diagnostic interview, the Mini International Neuropsychiatric Interview for Children (MINI KID), in a sample of 367 Rwandan children and adolescents aged 10 through 17 years. Caregiver and child or adolescent self-reports endorsing the presence of local depression-like problems agahinda kenshi (persistent sorrow) and kwiheba (severe hopelessness) were also examined for agreement with MINI KID diagnosis. Results The CES-DC exhibited good internal reliability (α = .86) and test-retest reliability (r = .85). The area under the receiver operating characteristic curve for the CES-DC was 0.825 when compared to MINI KID diagnoses, indicating a strong ability to distinguish between depressed and nondepressed children and adolescents in Rwanda. A cut point of ≥ 30 corresponded with a sensitivity of 81.9% and a specificity of 71.9% in this referred sample. MINI KID diagnosis was well aligned with local expressions of depression-like problems. Conclusion The CES-DC demonstrates good psychometric properties for clinical screening and evaluation in Rwanda, and should be considered for use in this and other low-resource settings. Population samples are needed to determine a generalizable cut point in nonreferred samples. PMID:23200285

Scale problems in assessment of hydrogeological parameters of groundwater flow models

NASA Astrophysics Data System (ADS)

Nawalany, Marek; Sinicyn, Grzegorz

2015-09-01

An overview is presented of scale problems in groundwater flow, with emphasis on upscaling of hydraulic conductivity, being a brief summary of the conventional upscaling approach with some attention paid to recently emerged approaches. The focus is on essential aspects which may be an advantage in comparison to the occasionally extremely extensive summaries presented in the literature. In the present paper the concept of scale is introduced as an indispensable part of system analysis applied to hydrogeology. The concept is illustrated with a simple hydrogeological system for which definitions of four major ingredients of scale are presented: (i) spatial extent and geometry of hydrogeological system, (ii) spatial continuity and granularity of both natural and man-made objects within the system, (iii) duration of the system and (iv) continuity/granularity of natural and man-related variables of groundwater flow system. Scales used in hydrogeology are categorised into five classes: micro-scale - scale of pores, meso-scale - scale of laboratory sample, macro-scale - scale of typical blocks in numerical models of groundwater flow, local-scale - scale of an aquifer/aquitard and regional-scale - scale of series of aquifers and aquitards. Variables, parameters and groundwater flow equations for the three lowest scales, i.e., pore-scale, sample-scale and (numerical) block-scale, are discussed in detail, with the aim to justify physically deterministic procedures of upscaling from finer to coarser scales (stochastic issues of upscaling are not discussed here). Since the procedure of transition from sample-scale to block-scale is physically well based, it is a good candidate for upscaling block-scale models to local-scale models and likewise for upscaling local-scale models to regional-scale models. Also the latest results in downscaling from block-scale to sample scale are briefly referred to.

Exposures to volatile organic compounds (VOCs) and associated health risks of socio-economically disadvantaged population in a "hot spot" in Camden, New Jersey

NASA Astrophysics Data System (ADS)

Wu, Xiangmei (May); Fan, Zhihua (Tina); Zhu, Xianlei; Jung, Kyung Hwa; Ohman-Strickland, Pamela; Weisel, Clifford P.; Lioy, Paul J.

2012-09-01

To address disparities in health risks associated with ambient air pollution for racial/ethnic minority groups, this study characterized personal and ambient concentrations of volatile organic compounds (VOCs) in a suspected hot spot of air pollution - the Village of Waterfront South (WFS), and an urban reference community - the Copewood/Davis Streets (CDS) neighborhood in Camden, New Jersey. Both are minority-dominant, impoverished communities. We collected 24-h integrated personal air samples from 54 WFS residents and 53 CDS residents, with one sample on a weekday and one on a weekend day during the summer and winter seasons of 2004-2006. Ambient air samples from the center of each community were also collected simultaneously during personal air sampling. Toluene, ethylbenzene, and xylenes (TEX) presented higher (p < 0.05) ambient levels in WFS than in CDS, particularly during weekdays. A stronger association between personal and ambient concentrations of MTBE and TEX was found in WFS than in CDS. Fourteen to forty-two percent of the variation in personal MTBE, hexane, benzene, and TEX was explained by local outdoor air pollution. These observations indicated that local sources impacted the community air pollution and personal exposure in WFS. The estimated cancer risks resulting from two locally emitted VOCs, benzene and ethylbenzene, and non-cancer neurological and respiratory effects resulting from hexane, benzene, toluene, and xylenes exceeded the US EPA risk benchmarks in both communities. These findings emphasized the need to address disparity in health risks associated with ambient air pollution for the socio-economically disadvantaged groups. This study also demonstrated that air pollution hot spots similar to WFS can provide robust setting to investigate health effects of ambient air pollution.

Clinical chemistry reference intervals of healthy adult populations in Gojjam Zones of Amhara National Regional State, Northwest Ethiopia.

PubMed

Mekonnen, Zewdie; Amuamuta, Asmare; Mulu, Wondemagegn; Yimer, Mulat; Zenebe, Yohannes; Adem, Yesuf; Abera, Bayeh; Gebeyehu, Wondemu; Gebregziabher, Yakob

2017-01-01

Reference interval is crucial for disease screening, diagnosis, monitoring, progression and treatment efficacy. Due to lack of locally derived reference values for the parameters, clinicians use reference intervals derived from western population. But, studies conducted in different African countries have indicated differences between locally and western derived reference values. Different studies also indicated considerable variation in clinical chemistry reference intervals by several variables such as age, sex, geographical location, environment, lifestyle and genetic variation. This study aimed to determine the reference intervals of common clinical chemistry parameters of the community of Gojjam Zones, Northwest Ethiopia. Population based cross-sectional study was conducted from November 2015 to December 2016 in healthy adult populations of Gojjam zone. Data such as, medical history, physical examination and socio-demographic data were collected. In addition, laboratory investigations were undertaken to screen the population. Clinical chemistry parameters were measured using Mindray BS 200 clinical chemistry autoanalyzer as per the manufacturer's instructions. Descriptive statistics was used to calculate mean, median and 95th percentiles. Independent sample T-test and one way ANOVA were used to see association between variables. After careful screening of a total of 799 apparently healthy adults who were consented for this study, complete data from 446 (224 females and 222 males) were included for the analysis. The mean age of both the study participants was 28.8 years. Males had high (P<0.05) mean and 2.5th-97.5th percentile ranges of ALT, AST, ALP, creatinine and direct bilirubin. The reference intervals of amylase, LDH, total protein and total bilirubin were not significantly different between the two sex groups (P>0.05). Mean, median, 95% percentile values of AST, ALP, amylase, LDH, creatinine, total protein, total bilirubin, and direct bilirubin across all age groups of participants were similar (P>0.05). But, there was a significant difference in the value of ALT (P<0.05). The reference intervals of ALT, total protein and creatinine were significantly (P<0.05) high in people having monthly income >1500 ETB compared to those with low monthly income. Significant (P<0.05) higher values of the ALT, ALP and total protein were observed in people living in high land compared to low land residences. The study showed that some of the common clinical chemistry parameters reference intervals of healthy adults in Gojjam zones were higher than the reference intervals generated from developed countries. Therefore, strict adherence to the reference values generated in developed countries could lead to inappropriate diagnosis and treatment of patients. There was also variation of reference interval values based on climate, gender, age, monthly income and geographical locations. Therefore, further study is required to establish reference intervals for Ethiopian population.

Identification of beer spoilage microorganisms using the MALDI Biotyper platform.

PubMed

Turvey, Michelle Elizabeth; Weiland, Florian; Meneses, Jon; Sterenberg, Nick; Hoffmann, Peter

2016-03-01

Beer spoilage microorganisms present a major risk for the brewing industry and can lead to cost-intensive recall of contaminated products and damage to brand reputation. The applicability of molecular profiling using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) in combination with Biotyper software was investigated for the identification of beer spoilage microorganisms from routine brewery quality control samples. Reference mass spectrum profiles for three of the most common bacterial beer spoilage microorganisms (Lactobacillus lindneri, Lactobacillus brevis and Pediococcus damnosus), four commercially available brewing yeast strains (top- and bottom-fermenting) and Dekkera/Brettanomyces bruxellensis wild yeast were established, incorporated into the Biotyper reference library and validated by successful identification after inoculation into beer. Each bacterial species could be accurately identified and distinguished from one another and from over 5600 other microorganisms present in the Biotyper database. In addition, wild yeast contaminations were rapidly detected and distinguished from top- and bottom-fermenting brewing strains. The applicability and integration of mass spectrometry profiling using the Biotyper platform into existing brewery quality assurance practices within industry were assessed by analysing routine microbiology control samples from a local brewery, where contaminating microorganisms could be reliably identified. Brewery-isolated microorganisms not present in the Biotyper database were further analysed for identification using LC-MS/MS methods. This renders the Biotyper platform a promising candidate for biological quality control testing within the brewing industry as a more rapid, high-throughput and cost-effective technology that can be tailored for the detection of brewery-specific spoilage organisms from the local environment.

Comparison of radioactivity data measured in PM10 aerosol samples at two elevated stations in northern Italy during the Fukushima event.

PubMed

Tositti, Laura; Brattich, Erika; Cinelli, Giorgia; Previti, Alberto; Mostacci, Domiziano

2012-12-01

The follow-up of Fukushima radioactive plume resulting from the 11th March 2011 devastating tsunami is discussed for two Italian stations in the northern Apennines: Mt. Cimone (Modena) and Montecuccolino (Bologna). Radioactivity data collected at both stations are described, including comparison between local natural background of airborne particulate and artificial radioactivity referable to the arrival of the radioactive plume and its persistence and evolution. Analysis of back-trajectories was used to confirm the arrival of artificial radionuclides following atmospheric transport and processing. The Fukushima plume was first detected on 3rd April 2011 when high volume sampling revealed the presence of the artificial radionuclides (131)I, (137)Cs and (134)Cs. The highest activity concentrations of these nuclides were detected on 5th April 2011 at the Montecuccolino site. Fukushima radioactivity data at the two stations were usually comparable, suggesting a good vertical mixing of the plume; discrepancies were occasional and attributed to different occurrence of wet removal, typically characterized by a scattered spatial pattern. To understand the relevance to the local population of the extra dose due to the Fukushima plume, atmospheric activities of the related artificial nuclides were compared to those of the main natural radionuclides in ambient particulate, and found to be lower by over one order of magnitude. Radiation doses referable to Fukushima, maximized for a whole year occurrence at the highest activity level observed at our stations in the weeks affected by the Japanese plume, were estimated at 1.1 μSv/year. Copyright © 2012 Elsevier Ltd. All rights reserved.

A multi-scale evaluation of pack stock effects on subalpine meadow plant communities in the Sierra Nevada

USGS Publications Warehouse

Lee, Steven R.; Berlow, Eric L.; Ostoja, Steven M.; Brooks, Matthew L.; Génin, Alexandre; Matchett, John R.; Hart, Stephen C.

2017-01-01

We evaluated the influence of pack stock (i.e., horse and mule) use on meadow plant communities in Sequoia and Yosemite National Parks in the Sierra Nevada of California. Meadows were sampled to account for inherent variability across multiple scales by: 1) controlling for among-meadow variability by using remotely sensed hydro-climatic and geospatial data to pair stock use meadows with similar non-stock (reference) sites, 2) accounting for within-meadow variation in the local hydrology using in-situ soil moisture readings, and 3) incorporating variation in stock use intensity by sampling across the entire available gradient of pack stock use. Increased cover of bare ground was detected only within “dry” meadow areas at the two most heavily used pack stock meadows (maximum animals per night per hectare). There was no difference in plant community composition for any level of soil moisture or pack stock use. Increased local-scale spatial variability in plant community composition (species dispersion) was detected in “wet” meadow areas at the two most heavily used meadows. These results suggest that at the meadow scale, plant communities are generally resistant to the contemporary levels of recreational pack stock use. However, finer-scale within-meadow responses such as increased bare ground or spatial variability in the plant community can be a function of local-scale hydrological conditions. Wilderness managers can improve monitoring of disturbance in Sierra Nevada meadows by adopting multiple plant community indices while simultaneously considering local moisture regimes.

Role of adrenal vein sampling in primary aldosteronism: Impact of imaging, localization, and age.

PubMed

Wachtel, Heather; Zaheer, Salman; Shah, Parth K; Trerotola, Scott O; Karakousis, Giorgos C; Roses, Robert E; Cohen, Debbie L; Fraker, Douglas L

2016-04-01

The role of adrenal vein sampling (AVS) has been debated, with some authorities advocating selective use in younger patients (≤40 years), and those localized by preoperative imaging. We examined our experience to determine the impact of AVS in patients who routinely underwent AVS with a high success rate. A retrospective cohort study was performed using a prospectively maintained database of patients referred for evaluation of PA (1997-2013). Patients were classified as localized (L) if a unilateral mass was identified on imaging, and non-localized (NL) otherwise. Of 367 patients, 94% (n = 345) underwent successful AVS. Seventy-two percent (n = 265) were L; AVS was lateralizing 58% (n = 214). AVS changed management in 43% of patients (n = 158). In patients ≤40 years, AVS changed management in 30% (n = 15). In patients ≤40 years with a ≥1 cm adrenal mass, 12% (n = 3) would have undergone unnecessary surgery based on imaging results alone; in patients >40 years with a ≥1 cm adrenal mass, 3% (n = 5) would have undergone wrong-side surgery, and 30% (n = 50) would have undergone unnecessary surgery based on imaging. AVS changed management in a significant minority of patients regardless of age and imaging findings. AVS should be routinely recommended in all patients with PA, to direct operative therapy. J. Surg. Oncol. 2016;113:532-537. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Spatial Standard Observer

NASA Technical Reports Server (NTRS)

Watson, Andrw B. (Inventor)

2010-01-01

The present invention relates to devices and methods for the measurement and/or for the specification of the perceptual intensity of a visual image. or the perceptual distance between a pair of images. Grayscale test and reference images are processed to produce test and reference luminance images. A luminance filter function is convolved with the reference luminance image to produce a local mean luminance reference image . Test and reference contrast images are produced from the local mean luminance reference image and the test and reference luminance images respectively, followed by application of a contrast sensitivity filter. The resulting images are combined according to mathematical prescriptions to produce a Just Noticeable Difference, JND value, indicative of a Spatial Standard Observer. SSO. Some embodiments include masking functions. window functions. special treatment for images lying on or near border and pre-processing of test images.

Spatial Standard Observer

NASA Technical Reports Server (NTRS)

Watson, Andrew B. (Inventor)

2012-01-01

The present invention relates to devices and methods for the measurement and/or for the specification of the perceptual intensity of a visual image, or the perceptual distance between a pair of images. Grayscale test and reference images are processed to produce test and reference luminance images. A luminance filter function is convolved with the reference luminance image to produce a local mean luminance reference image. Test and reference contrast images are produced from the local mean luminance reference image and the test and reference luminance images respectively, followed by application of a contrast sensitivity filter. The resulting images are combined according to mathematical prescriptions to produce a Just Noticeable Difference, JND value, indicative of a Spatial Standard Observer, SSO. Some embodiments include masking functions, window functions, special treatment for images lying on or near borders and pre-processing of test images.

Mineral occurrences of New York State with selected references to each locality

USGS Publications Warehouse

Luedke, Elaine M.; Wrucke, Chester T.; Graham, John A.

1959-01-01

References and locations were compiled for more than 1,000 mineral occurrences in New York State. Each occurrence is shown on an accompanying map and is given by commodity and county in a locality list. Fuels, sand and gravel, and clay are not included in this report.

Estimating A Reference Standard Segmentation With Spatially Varying Performance Parameters: Local MAP STAPLE

PubMed Central

Commowick, Olivier; Akhondi-Asl, Alireza; Warfield, Simon K.

2012-01-01

We present a new algorithm, called local MAP STAPLE, to estimate from a set of multi-label segmentations both a reference standard segmentation and spatially varying performance parameters. It is based on a sliding window technique to estimate the segmentation and the segmentation performance parameters for each input segmentation. In order to allow for optimal fusion from the small amount of data in each local region, and to account for the possibility of labels not being observed in a local region of some (or all) input segmentations, we introduce prior probabilities for the local performance parameters through a new Maximum A Posteriori formulation of STAPLE. Further, we propose an expression to compute confidence intervals in the estimated local performance parameters. We carried out several experiments with local MAP STAPLE to characterize its performance and value for local segmentation evaluation. First, with simulated segmentations with known reference standard segmentation and spatially varying performance, we show that local MAP STAPLE performs better than both STAPLE and majority voting. Then we present evaluations with data sets from clinical applications. These experiments demonstrate that spatial adaptivity in segmentation performance is an important property to capture. We compared the local MAP STAPLE segmentations to STAPLE, and to previously published fusion techniques and demonstrate the superiority of local MAP STAPLE over other state-of-the- art algorithms. PMID:22562727

Sample size of the reference sample in a case-augmented study.

PubMed

Ghosh, Palash; Dewanji, Anup

2017-05-01

The case-augmented study, in which a case sample is augmented with a reference (random) sample from the source population with only covariates information known, is becoming popular in different areas of applied science such as pharmacovigilance, ecology, and econometrics. In general, the case sample is available from some source (for example, hospital database, case registry, etc.); however, the reference sample is required to be drawn from the corresponding source population. The required minimum size of the reference sample is an important issue in this regard. In this work, we address the minimum sample size calculation and discuss related issues. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Large-aperture interferometer using local reference beam

NASA Technical Reports Server (NTRS)

Howes, W. L.

1982-01-01

A large-aperture interferometer was devised by adding a local-reference-beam-generating optical system to a schlieren system. Two versions of the interferometer are demonstrated, one employing 12.7 cm (5 in.) diameter schlieren optics, the other employing 30.48 cm (12 in.) diameter parabolic mirrors in an off-axis system. In the latter configuration a cylindrical lens is introduced near the light source to correct for astigmatism. A zone plate is a satisfactory decollimating element in the reference-beam arm of the interferometer. Attempts to increase the flux and uniformity of irradiance in the reference beam by using a diffuser are discussed.

Automatic HTS force measurement instrument

DOEpatents

Sanders, S.T.; Niemann, R.C.

1999-03-30

A device is disclosed for measuring the levitation force of a high temperature superconductor sample with respect to a reference magnet includes a receptacle for holding several high temperature superconductor samples each cooled to superconducting temperature. A rotatable carousel successively locates a selected one of the high temperature superconductor samples in registry with the reference magnet. Mechanism varies the distance between one of the high temperature superconductor samples and the reference magnet, and a sensor measures levitation force of the sample as a function of the distance between the reference magnet and the sample. A method is also disclosed. 3 figs.

Spectral multivariate calibration without laboratory prepared or determined reference analyte values.

PubMed

Ottaway, Josh; Farrell, Jeremy A; Kalivas, John H

2013-02-05

An essential part to calibration is establishing the analyte calibration reference samples. These samples must characterize the sample matrix and measurement conditions (chemical, physical, instrumental, and environmental) of any sample to be predicted. Calibration usually requires measuring spectra for numerous reference samples in addition to determining the corresponding analyte reference values. Both tasks are typically time-consuming and costly. This paper reports on a method named pure component Tikhonov regularization (PCTR) that does not require laboratory prepared or determined reference values. Instead, an analyte pure component spectrum is used in conjunction with nonanalyte spectra for calibration. Nonanalyte spectra can be from different sources including pure component interference samples, blanks, and constant analyte samples. The approach is also applicable to calibration maintenance when the analyte pure component spectrum is measured in one set of conditions and nonanalyte spectra are measured in new conditions. The PCTR method balances the trade-offs between calibration model shrinkage and the degree of orthogonality to the nonanalyte content (model direction) in order to obtain accurate predictions. Using visible and near-infrared (NIR) spectral data sets, the PCTR results are comparable to those obtained using ridge regression (RR) with reference calibration sets. The flexibility of PCTR also allows including reference samples if such samples are available.

Hg soil pollution around a decommissioned and unrestored Chlor-alkali plant: Jodar, Jaén province, SE Spain. Incidence in other environmental compartments.

NASA Astrophysics Data System (ADS)

López-Berdonces, Miguel Angel; María Esbrí, José; Lorenzo, Saturnino; Higueras, Pablo

2014-05-01

Data from soil pollution and its consequences around a decommissioned chlor-alkali plant are presented in this communication. The plant was active in the period 1977-1991, producing during these years a heavily pollution of Guadalquivir River and hidrargirism in more than local 45 workers. It is located at 7 km South of Jódar, a locality with some 12,120 inhabitants. Mercury usage was general in this type of plants, but at present it is being replaced by other types of technologies, due to the risks of mercury usage in personal and environment. A soil geochemistry survey was carried out in the area, together with the analysis of olive-tree leaves from the same area. 75 soil samples were taken at two different depths (0-15 cm. and 15-30 cm), together with 75 olive tree samples, 5 water samples. Besides, two monitoring surveys for total gaseous mercury in the atmosphere were performed. Mercury content of geologic and biologic samples was determined by means of Atomic Absorption Spectrometry with Zeeman Effect, using a Lumex RA-915+ device with the RP-91C pyrolysis attachment. Air surveys were carried our using a RA-915M Lumex portable analytical device, with GPS georreferenciation of the analysis points. Soil mercury contents were higher in topsoil than in the deeper soil samples, indicating that incorporation of mercury was due to dry and wet deposition of mercury vapors emitted from the plant. A local reference level was calculated as GM + 2SD (where GM is the geometric mean and SD the standard deviation). With this reference level it was possible to delimitate a contaminated soil area centered on the decommissioned chlor-alkali plant. A high affinity of local olive trees to accumulate mercury from the contaminated soil was also found, with a calculated maximum mercury content of 243.5 ng g-1. This maximum level is slightly higher than tolerable level for agronomic crops. Total mercury content in the analyzed waters was slightly higher than the chronic exposure level for aquatic life. Atmospheric mercury levels registered on the study area were much lower than most restrictive levels for chronic exposure. The area of influence of the facility (in terms of mercury content in air) was restricted to distances between 100 and 200 meters, depending on meteorological conditions. Main conclusions of this research work are the following: i) The Jódar decommissioned chlor-alkali plant is still a mercury source 20 years after its cease of activities without any reclamation measures; ii) The activity of the plant has produced an important dissemination of mercury in the surrounding environment; and iii) The corresponding pollution levels, in particular in soils, may suppose a risk to the main crops of the area (olive trees).

Investigation of Parent Austenite Grains from Martensite Structure Using EBSD in a Wear Resistant Steel

PubMed Central

Gyhlesten Back, Jessica; Engberg, Göran

2017-01-01

Crystallographic reconstruction of parent austenite grain boundaries from the martensitic microstructure in a wear resistant steel was carried out using electron backscattered diffraction (EBSD). The present study mainly aims to investigate the parent austenite grains from the martensitic structure in an as-rolled (reference) steel sample and samples obtained by quenching at different cooling rates with corresponding dilatometry. Subsequently, this study is to correlate the nearest cooling rate by the dilatometer which yields a similar orientation relationship and substructure as the reference sample. The Kurdjumov-Sachs orientation relationship was used to reconstruct the parent austenite grain boundaries from the martensite boundaries in both reference and dilatometric samples using EBSD crystallographic data. The parent austenite grain boundaries were successfully evaluated from the EBSD data and the corresponding grain sizes were measured. The parent austenite grain boundaries of the reference sample match the sample quenched at 100 °C/s (CR100). Also the martensite substructures and crystallographic textures are similar in these two samples. The results from hardness measurements show that the reference sample exhibits higher hardness than the CR100 sample due to the presence of carbides in the reference sample. PMID:28772813

Investigation of Parent Austenite Grains from Martensite Structure Using EBSD in a Wear Resistant Steel.

PubMed

Gyhlesten Back, Jessica; Engberg, Göran

2017-04-26

Crystallographic reconstruction of parent austenite grain boundaries from the martensitic microstructure in a wear resistant steel was carried out using electron backscattered diffraction (EBSD). The present study mainly aims to investigate the parent austenite grains from the martensitic structure in an as-rolled (reference) steel sample and samples obtained by quenching at different cooling rates with corresponding dilatometry. Subsequently, this study is to correlate the nearest cooling rate by the dilatometer which yields a similar orientation relationship and substructure as the reference sample. The Kurdjumov-Sachs orientation relationship was used to reconstruct the parent austenite grain boundaries from the martensite boundaries in both reference and dilatometric samples using EBSD crystallographic data. The parent austenite grain boundaries were successfully evaluated from the EBSD data and the corresponding grain sizes were measured. The parent austenite grain boundaries of the reference sample match the sample quenched at 100 °C/s (CR100). Also the martensite substructures and crystallographic textures are similar in these two samples. The results from hardness measurements show that the reference sample exhibits higher hardness than the CR100 sample due to the presence of carbides in the reference sample.

RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference

PubMed Central

Maples, Brian K.; Gravel, Simon; Kenny, Eimear E.; Bustamante, Carlos D.

2013-01-01

Local-ancestry inference is an important step in the genetic analysis of fully sequenced human genomes. Current methods can only detect continental-level ancestry (i.e., European versus African versus Asian) accurately even when using millions of markers. Here, we present RFMix, a powerful discriminative modeling approach that is faster (∼30×) and more accurate than existing methods. We accomplish this by using a conditional random field parameterized by random forests trained on reference panels. RFMix is capable of learning from the admixed samples themselves to boost performance and autocorrect phasing errors. RFMix shows high sensitivity and specificity in simulated Hispanics/Latinos and African Americans and admixed Europeans, Africans, and Asians. Finally, we demonstrate that African Americans in HapMap contain modest (but nonzero) levels of Native American ancestry (∼0.4%). PMID:23910464

Analytical evaluation of three enzymatic assays for measuring total bile acids in plasma using a fully-automated clinical chemistry platform.

PubMed

Danese, Elisa; Salvagno, Gian Luca; Negrini, Davide; Brocco, Giorgio; Montagnana, Martina; Lippi, Giuseppe

2017-01-01

Although the clinical significance of measuring bile acids concentration in plasma or serum has been recognized for long in patients with hepatobiliary disease and/or bile acid malabsorption, the reference separation techniques are expensive and mostly unsuitable for early diagnosis and for measuring large volumes of samples. Therefore, this study was aimed to evaluate the analytical performance of three commercial enzymatic techniques for measuring total bile acids in plasma using a fully-automated clinical chemistry platform. Three commercial enzymatic assays (from Diazyme, Randox and Sentinel) were adapted for use on a Cobas Roche c501. We performed imprecision and linearity studies, and we compared results with those obtained using a reference liquid chromatography-mass spectrometry (LC-MS) technique on an identical set of lithium-heparin plasma samples. Total imprecision was optimal, always equal or lower than 3%. All assays had optimal linearity between 3-138 μmol/L. The comparison studies showed good correlation with LC-MS data (Spearman's correlation coefficients always >0.92), but all plasma samples values were significantly underestimated using the commercial enzymatic assays (-44% for Diazyme, -16% for Randox and -12% for Sentinel). The agreement at the 10 and 40 μmol/L diagnostic thresholds of total bile acids in plasma ranged between 86-92%. This discrepancy was found to be mainly attributable to a heterogeneous composition in terms of bile acids content of the three assay calibrators. This study suggests that the analytical performance of the three commercial enzymatic assays is excellent, thus confirming that automation of this important test by means of enzymatic assessment may be feasible, practical, reliable and supposedly cheap. Nevertheless, the underestimation of values compared to the reference LC-MS also suggests that the local definition and validation of reference ranges according to the combination between the specific enzymatic assay and the different clinical chemistry platforms may be advisable.

Point cloud registration from local feature correspondences-Evaluation on challenging datasets.

PubMed

Petricek, Tomas; Svoboda, Tomas

2017-01-01

Registration of laser scans, or point clouds in general, is a crucial step of localization and mapping with mobile robots or in object modeling pipelines. A coarse alignment of the point clouds is generally needed before applying local methods such as the Iterative Closest Point (ICP) algorithm. We propose a feature-based approach to point cloud registration and evaluate the proposed method and its individual components on challenging real-world datasets. For a moderate overlap between the laser scans, the method provides a superior registration accuracy compared to state-of-the-art methods including Generalized ICP, 3D Normal-Distribution Transform, Fast Point-Feature Histograms, and 4-Points Congruent Sets. Compared to the surface normals, the points as the underlying features yield higher performance in both keypoint detection and establishing local reference frames. Moreover, sign disambiguation of the basis vectors proves to be an important aspect in creating repeatable local reference frames. A novel method for sign disambiguation is proposed which yields highly repeatable reference frames.

Strategies Typically Developing Writers Use for Translating Thought into the Next Sentence and Evolving Text: Implications for Assessment and Instruction

PubMed Central

Jones, Jasmin Niedo; Berninger, Virginia Wise

2016-01-01

Three new approaches to writing assessment are introduced. First, strategies for generating the very next sentence are assessed in reference to the local level as well as the evolving text level of composing in progress. Second, strategies for translating thought into written language are coded with transcription (spelling) skill—low, average, or high—held constant. Third, instead of describing composing skill in reference to a single normed score for age or grade in a standardization sample at a static time in development, translation is studied longitudinally when children are in grades 1, 3, and 5 (ages 6, 8, 10) or grades 3, 5, and 7 (ages 8, 10, 12). Applications of the results are discussed for assessment and instruction grounded in levels and generativity of written language and normal variation in typically developing writers. PMID:28127525

Mental health epidemiological research in South America: recent findings

PubMed Central

Silva de Lima, Maurício; Garcia de Oliveira Soares, Bernardo; de Jesus Mari, Jair

2004-01-01

This paper aims to review the recent mental health epidemiological research conducted in South America. The Latin American and the Caribbean (LILACS) database was searched from 1999 to 2003 using a specific strategy for identification of cohort, case-control and cross-sectional population-based studies in South America. The authors screened references and identified relevant studies. Further studies were obtained contacting local experts in epidemiology. 140 references were identified, and 12 studies were selected. Most selected studies explored the prevalence and risk factors for common mental disorders, and several of them used sophisticated methods of sample selection and analysis. There is a need for improving the quality of psychiatric journals in Latin America, and for increasing the distribution and access to research data. Regionally relevant problems such as violence and substance abuse should be considered in designing future investigations in this area. PMID:16633474

Correcting intensity loss errors in the absence of texture-free reference samples during pole figure measurement

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

Saleh, Ahmed A., E-mail: asaleh@uow.edu.au

Even with the use of X-ray polycapillary lenses, sample tilting during pole figure measurement results in a decrease in the recorded X-ray intensity. The magnitude of this error is affected by the sample size and/or the finite detector size. These errors can be typically corrected by measuring the intensity loss as a function of the tilt angle using a texture-free reference sample (ideally made of the same alloy as the investigated material). Since texture-free reference samples are not readily available for all alloys, the present study employs an empirical procedure to estimate the correction curve for a particular experimental configuration.more » It involves the use of real texture-free reference samples that pre-exist in any X-ray diffraction laboratory to first establish the empirical correlations between X-ray intensity, sample tilt and their Bragg angles and thereafter generate correction curves for any Bragg angle. It will be shown that the empirically corrected textures are in very good agreement with the experimentally corrected ones. - Highlights: •Sample tilting during X-ray pole figure measurement leads to intensity loss errors. •Texture-free reference samples are typically used to correct the pole figures. •An empirical correction procedure is proposed in the absence of reference samples. •The procedure relies on reference samples that pre-exist in any texture laboratory. •Experimentally and empirically corrected textures are in very good agreement.« less

An improved artifact removal in exposure fusion with local linear constraints

NASA Astrophysics Data System (ADS)

Zhang, Hai; Yu, Mali

2018-04-01

In exposure fusion, it is challenging to remove artifacts because of camera motion and moving objects in the scene. An improved artifact removal method is proposed in this paper, which performs local linear adjustment in artifact removal progress. After determining a reference image, we first perform high-dynamic-range (HDR) deghosting to generate an intermediate image stack from the input image stack. Then, a linear Intensity Mapping Function (IMF) in each window is extracted based on the intensities of intermediate image and reference image, the intensity mean and variance of reference image. Finally, with the extracted local linear constraints, we reconstruct a target image stack, which can be directly used for fusing a single HDR-like image. Some experiments have been implemented and experimental results demonstrate that the proposed method is robust and effective in removing artifacts especially in the saturated regions of the reference image.

Array-based comparative genomic hybridization-guided identification of reference genes for normalization of real-time quantitative polymerase chain reaction assay data for lymphomas, histiocytic sarcomas, and osteosarcomas of dogs.

PubMed

Tsai, Pei-Chien; Breen, Matthew

2012-09-01

To identify suitable reference genes for normalization of real-time quantitative PCR (RT-qPCR) assay data for common tumors of dogs. Malignant lymph node (n = 8), appendicular osteosarcoma (9), and histiocytic sarcoma (12) samples and control samples of various nonneoplastic canine tissues. Array-based comparative genomic hybridization (aCGH) data were used to guide selection of 9 candidate reference genes. Expression stability of candidate reference genes and 4 commonly used reference genes was determined for tumor samples with RT-qPCR assays and 3 software programs. LOC611555 was the candidate reference gene with the highest expression stability among the 3 tumor types. Of the commonly used reference genes, expression stability of HPRT was high in histiocytic sarcoma samples, and expression stability of Ubi and RPL32 was high in osteosarcoma samples. Some of the candidate reference genes had higher expression stability than did the commonly used reference genes. Data for constitutively expressed genes with high expression stability are required for normalization of RT-qPCR assay results. Without such data, accurate quantification of gene expression in tumor tissue samples is difficult. Results of the present study indicated LOC611555 may be a useful RT-qPCR assay reference gene for multiple tissue types. Some commonly used reference genes may be suitable for normalization of gene expression data for tumors of dogs, such as lymphomas, osteosarcomas, or histiocytic sarcomas.

Optically coupled methods for microwave impedance microscopy

NASA Astrophysics Data System (ADS)

Johnston, Scott R.; Ma, Eric Yue; Shen, Zhi-Xun

2018-04-01

Scanning Microwave Impedance Microscopy (MIM) measurement of photoconductivity with 50 nm resolution is demonstrated using a modulated optical source. The use of a modulated source allows for the measurement of photoconductivity in a single scan without a reference region on the sample, as well as removing most topographical artifacts and enhancing signal to noise as compared with unmodulated measurement. A broadband light source with a tunable monochrometer is then used to measure energy resolved photoconductivity with the same methodology. Finally, a pulsed optical source is used to measure local photo-carrier lifetimes via MIM, using the same 50 nm resolution tip.

The Magellan Evolution of Galaxies Spectroscopic and Ultraviolet Reference Atlas (MegaSaura). I. The Sample and the Spectra

NASA Astrophysics Data System (ADS)

Rigby, J. R.; Bayliss, M. B.; Sharon, K.; Gladders, M. D.; Chisholm, J.; Dahle, H.; Johnson, T.; Paterno-Mahler, R.; Wuyts, E.; Kelson, D. D.

2018-03-01

We introduce Project MEGaSaURA: the Magellan Evolution of Galaxies Spectroscopic and Ultraviolet Reference Atlas. MEGaSaURA comprises medium-resolution, rest-frame ultraviolet spectroscopy of N = 15 bright gravitationally lensed galaxies at redshifts of 1.68 < z < 3.6, obtained with the MagE spectrograph on the Magellan telescopes. The spectra cover the observed-frame wavelength range 3200 < λ o < 8280 Å the average spectral resolving power is R = 3300. The median spectrum has a signal-to-noise ratio (S/N) = 21 per resolution element at 5000 Å. As such, the MEGaSaURA spectra have superior S/N and wavelength coverage compared to what COS/HST provides for starburst galaxies in the local universe. This paper describes the sample, the observations, and the data reduction. We compare the measured redshifts for the stars, the ionized gas as traced by nebular lines, and the neutral gas as traced by absorption lines; we find the expected bulk outflow of the neutral gas, and no systemic offset between the redshifts measured from nebular lines and the redshifts measured from the stellar continuum. We provide the MEGaSaURA spectra to the astronomical community through a data release.

CellAtlasSearch: a scalable search engine for single cells.

PubMed

Srivastava, Divyanshu; Iyer, Arvind; Kumar, Vibhor; Sengupta, Debarka

2018-05-21

Owing to the advent of high throughput single cell transcriptomics, past few years have seen exponential growth in production of gene expression data. Recently efforts have been made by various research groups to homogenize and store single cell expression from a large number of studies. The true value of this ever increasing data deluge can be unlocked by making it searchable. To this end, we propose CellAtlasSearch, a novel search architecture for high dimensional expression data, which is massively parallel as well as light-weight, thus infinitely scalable. In CellAtlasSearch, we use a Graphical Processing Unit (GPU) friendly version of Locality Sensitive Hashing (LSH) for unmatched speedup in data processing and query. Currently, CellAtlasSearch features over 300 000 reference expression profiles including both bulk and single-cell data. It enables the user query individual single cell transcriptomes and finds matching samples from the database along with necessary meta information. CellAtlasSearch aims to assist researchers and clinicians in characterizing unannotated single cells. It also facilitates noise free, low dimensional representation of single-cell expression profiles by projecting them on a wide variety of reference samples. The web-server is accessible at: http://www.cellatlassearch.com.

Exploiting the locality of periodic subsystem density-functional theory: efficient sampling of the Brillouin zone.

PubMed

Genova, Alessandro; Pavanello, Michele

2015-12-16

In order to approximately satisfy the Bloch theorem, simulations of complex materials involving periodic systems are made n(k) times more complex by the need to sample the first Brillouin zone at n(k) points. By combining ideas from Kohn-Sham density-functional theory (DFT) and orbital-free DFT, for which no sampling is needed due to the absence of waves, subsystem DFT offers an interesting middle ground capable of sizable theoretical speedups against Kohn-Sham DFT. By splitting the supersystem into interacting subsystems, and mapping their quantum problem onto separate auxiliary Kohn-Sham systems, subsystem DFT allows an optimal topical sampling of the Brillouin zone. We elucidate this concept with two proof of principle simulations: a water bilayer on Pt[1 1 1]; and a complex system relevant to catalysis-a thiophene molecule physisorbed on a molybdenum sulfide monolayer deposited on top of an α-alumina support. For the latter system, a speedup of 300% is achieved against the subsystem DTF reference by using an optimized Brillouin zone sampling (600% against KS-DFT).

High Frequency of Human Blood in Triatoma dimidiata Captured Inside Dwellings in a Rural Community in the Yucatan Peninsula, Mexico, but Low Antibody Seroprevalence and Electrocardiographic Findings Compatible with Chagas Disease in Humans

PubMed Central

Monteon, Victor; Alducin, César; Hernández, Jorge; Ramos-Ligonio, Angel; Lopez, Ruth

2013-01-01

We studied a small rural community of 411 inhabitants localized in the state of Campeche in the Yucatan Peninsula, Mexico. In 44 collected triatomines captured inside the houses, human feeding source was revealed in 23 of 44 (52%) samples, and chicken feeding source was revealed in 16 of 44 (36%) samples. In a set of 29 triatomines, mouse was the feeding source in 13 (44%) samples, and dog was the feeding source in 7 (24%) samples. Infection index with Trypanosoma cruzi in collected triatomines was 38%, and all parasites belonged to discrete type unit I. Inhabitants referred high contact with triatomine's bite in 60 of 128 (47%) samples, but seroprevalence was 2.3% (3/128). Evidence of electrocardiographic alteration compatible with Chagas disease was observed only in one asymptomatic seropositive subject. In conclusion, Triatoma dimidiata in this region are preferentially infected with T. cruzi I and feed on human beings with relative high frequency, but seroprevalence and Chagas disease in humans is relatively low. PMID:23296447

Pesticide Residues in Commercial Lettuce, Onion, and Potato Samples From Bolivia-A Threat to Public Health?

PubMed

Skovgaard, Marlene; Encinas, Susana Renjel; Jensen, Olaf Chresten; Andersen, Jens Hinge; Condarco, Guido; Jørs, Erik

2017-01-01

Bolivia does not have a surveillance program for pesticide residues in food. The few published studies have suggested that pesticide contamination in food may present a public health problem. Data are lacking for all foods except tomatoes and breast milk. In this study 10 potato, 10 onion, and 10 lettuce samples from La Paz were sampled on August 15, 2015 at a local market and screened for 283 pesticides. Residues of cypermethrin, chlorpyrifos, difenoconazol, or/and λ-cyhalothrin were detected in 50% of the lettuce samples, whereas no pesticides were found in potatoes and onions. In 20% of the lettuce samples, the measurements were above the maximum residue limits, and 2 or 3 pesticides were identified simultaneously. Washing almost halved the pesticide levels, but still 20% of the samples showed measurements above the limits. No samples contained concentrations of pesticides which alone or together would lead to exposures that exceeded the acceptable daily intake or the acute reference dose. To protect consumers from pesticide poisonings and chronic effects, the development of measures for prevention, control, and monitoring of food contamination by pesticides in Bolivia is suggested.

Thermal shock behaviour of H and H/He-exposed tungsten at high temperature

NASA Astrophysics Data System (ADS)

Lemahieu, N.; Greuner, H.; Linke, J.; Maier, H.; Pintsuk, G.; Wirtz, M.; Van Oost, G.; Noterdaeme, J.-M.

2016-02-01

Polycrystalline tungsten samples were characterized and exposed to a pure H beam or mixed H/He beam containing 6% He in GLADIS at a surface temperature of 600 °C, 1000 °C, or 1500 °C. After 5400 s of exposure time with a heat flux of 10.5 MW m-2, the total accumulated fluence of 2 × 1025 m-2 was reached. Thereafter, edge localized mode (ELM)-like thermal shocks with a duration of 1 ms and an absorbed power density of 190 MW m-2 and 380 MW m-2 were applied on the samples in JUDITH 1. During the thermal shocks, the base temperature was kept at 1000 °C. The ELM-experiments with the lowest transient power density did not result in any detected damage. The other tests showed the beginning of crack formation for every sample, except the sample pre-exposed with the pure H-beam at 1500 °C in GLADIS. This sample was roughened, but did not show any crack initiation. With exception to the roughened sample, the category of ELM-induced damage for the pre-exposed samples is identical to the reference tests without pre-exposure to a particle flux.

Pesticide Residues in Commercial Lettuce, Onion, and Potato Samples From Bolivia—A Threat to Public Health?

PubMed Central

Skovgaard, Marlene; Renjel Encinas, Susana; Jensen, Olaf Chresten; Andersen, Jens Hinge; Condarco, Guido; Jørs, Erik

2017-01-01

Bolivia does not have a surveillance program for pesticide residues in food. The few published studies have suggested that pesticide contamination in food may present a public health problem. Data are lacking for all foods except tomatoes and breast milk. In this study 10 potato, 10 onion, and 10 lettuce samples from La Paz were sampled on August 15, 2015 at a local market and screened for 283 pesticides. Residues of cypermethrin, chlorpyrifos, difenoconazol, or/and λ-cyhalothrin were detected in 50% of the lettuce samples, whereas no pesticides were found in potatoes and onions. In 20% of the lettuce samples, the measurements were above the maximum residue limits, and 2 or 3 pesticides were identified simultaneously. Washing almost halved the pesticide levels, but still 20% of the samples showed measurements above the limits. No samples contained concentrations of pesticides which alone or together would lead to exposures that exceeded the acceptable daily intake or the acute reference dose. To protect consumers from pesticide poisonings and chronic effects, the development of measures for prevention, control, and monitoring of food contamination by pesticides in Bolivia is suggested. PMID:28469451

Effects of new motorway infrastructure on active travel in the local population: a retrospective repeat cross-sectional study in Glasgow, Scotland.

PubMed

Olsen, Jonathan R; Mitchell, Richard; Ogilvie, David

2016-07-07

Promoting active travel is an important part of increasing population physical activity, which has both physical and mental health benefits. A key benefit described by the then Scottish Government of the five-mile M74 motorway extension, which opened during June 2011 in the south of Glasgow, was that the forecast reduction in motor traffic on local streets would make these streets safer for walking and cycling, thus increasing active travel by the local population. The aim of the study was to evaluate the impact of new motorway infrastructure on the proportion of journey stages made actively (cycling or on foot) by individuals travelling in and out of the local area. Data for the periods 2009-10 and 2012-13 were extracted from the Scottish Household Survey (SHS) travel diaries, which record each journey stage made during the previous day by a representative sample of the Scottish population aged 16 and over. Each individual journey stage was assigned to one of the following study areas surrounding existing and new transport infrastructure: (1) an area surrounding the new M74 motorway extension (n = 435 (2009-10), 543 (2012-13)), (2) a comparator area surrounding an existing motorway (n = 477 (2009-10), 560 (2012-13)), and (3) a control area containing no comparable motorway infrastructure (n = 541 (2009-10), 593 (2012-13)). Multivariable, multi-level regression analysis was performed to determine any between-area differences in change in active travel over time, which might indicate an intervention effect. Reference populations were defined using two alternative definitions, (1) Glasgow City and (2) Glasgow and surrounding local authorities. The results showed an increase in the proportion of journey stages using active travel in all study areas compared to both reference populations. However, there were no significant between-area differences to suggest an effect attributable the M74 motorway extension. There was no clear evidence that the M74 motorway extension either increased or decreased active travel in the local area. The anticipation by policy makers that reduced motorised traffic on local streets might increase journeys walked or cycled appears to have been unfounded.

Assessment of Soil-Gas, Surface-Water, and Soil Contamination at the Installation Railhead, Fort Gordon, Georgia, 2008-2009

USGS Publications Warehouse

Landmeyer, James E.; Harrelson, Larry G.; Ratliff, W. Hagan; Wellborn, John B.

2010-01-01

The U.S. Geological Survey, in cooperation with the U.S. Department of the Army Environmental and Natural Resources Management Office of the U.S. Army Signal Center and Fort Gordon, assessed soil gas, surface water, and soil for contaminants at the Installation Railhead (IR) at Fort Gordon, Georgia, from October 2008 to September 2009. The assessment included delineation of organic contaminants present in soil-gas samples beneath the IR, and in a surface-water sample collected from an unnamed tributary to Marcum Branch in the western part of the IR. Inorganic contaminants were determined in a surface-water sample and in soil samples. This assessment was conducted to provide environmental contamination data to Fort Gordon personnel pursuant to requirements of the Resource Conservation and Recovery Act Part B Hazardous Waste Permit process. Soil-gas samples collected within a localized area on the western part of the IR contained total petroleum hydrocarbons; benzene, toluene, ethylbenzene, and total xylenes (referred to as BTEX); and naphthalene above the method detection level. These soil-gas samples were collected where buildings had previously stood. Soil-gas samples collected within a localized area contained perchloroethylene (PCE). These samples were collected where buildings 2410 and 2405 had been. Chloroform and toluene were detected in a surface-water sample collected from an unnamed tributary to Marcum Branch but at concentrations below the National Primary Drinking Water Standard maximum contaminant level (MCL) for each compound. Iron was detected in the surface-water sample at 686 micrograms per liter (ug/L) and exceeded the National Secondary Drinking Water Standard MCL for iron. Metal concentrations in composite soil samples collected at three locations from land surface to a depth of 6 inches did not exceed the U.S. Environmental Protection Agency Regional Screening Levels for industrial soil.

Actual distribution of Cronobacter spp. in industrial batches of powdered infant formula and consequences for performance of sampling strategies.

PubMed

Jongenburger, I; Reij, M W; Boer, E P J; Gorris, L G M; Zwietering, M H

2011-11-15

The actual spatial distribution of microorganisms within a batch of food influences the results of sampling for microbiological testing when this distribution is non-homogeneous. In the case of pathogens being non-homogeneously distributed, it markedly influences public health risk. This study investigated the spatial distribution of Cronobacter spp. in powdered infant formula (PIF) on industrial batch-scale for both a recalled batch as well a reference batch. Additionally, local spatial occurrence of clusters of Cronobacter cells was assessed, as well as the performance of typical sampling strategies to determine the presence of the microorganisms. The concentration of Cronobacter spp. was assessed in the course of the filling time of each batch, by taking samples of 333 g using the most probable number (MPN) enrichment technique. The occurrence of clusters of Cronobacter spp. cells was investigated by plate counting. From the recalled batch, 415 MPN samples were drawn. The expected heterogeneous distribution of Cronobacter spp. could be quantified from these samples, which showed no detectable level (detection limit of -2.52 log CFU/g) in 58% of samples, whilst in the remainder concentrations were found to be between -2.52 and 2.75 log CFU/g. The estimated average concentration in the recalled batch was -2.78 log CFU/g and a standard deviation of 1.10 log CFU/g. The estimated average concentration in the reference batch was -4.41 log CFU/g, with 99% of the 93 samples being below the detection limit. In the recalled batch, clusters of cells occurred sporadically in 8 out of 2290 samples of 1g taken. The two largest clusters contained 123 (2.09 log CFU/g) and 560 (2.75 log CFU/g) cells. Various sampling strategies were evaluated for the recalled batch. Taking more and smaller samples and keeping the total sampling weight constant, considerably improved the performance of the sampling plans to detect such a type of contaminated batch. Compared to random sampling, stratified random sampling improved the probability to detect the heterogeneous contamination. Copyright © 2011 Elsevier B.V. All rights reserved.

Development of non-destructive examination techniques for CFC-metal joints in annular geometry and their application to the manufacturing of plasma-facing components

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

Di Pietro, E.; Visca, E.; Orsini, A.

1995-12-31

The design of plasma-facing components for ITER, as for any of the envisaged next-step machines, relies heavily on the use of brazed junctions to couple armour materials to the heat sink and cooling tubes. Moreover, the typical number of brazed components and the envisaged effects of local overheating due to failure in a single brazed junction stress the importance of having a set of NDE techniques developed that can ensure the flawless quality of the joint. The qualification and application of two NDE techniques (ultrasonic and thermographic analysis) for inspection of CFC-to-metal joints is described with particular regard to themore » annular geometry typical of macroblock/monoblock solutions for divertor high-heat-flux components. The results of the eddy current inspection are not reported. The development has been focused specifically on the joint between carbon-fiber composite and TZM molybdenum alloy; techniques for the production of reference defect samples have been devised and a set of reference defect samples produced. The comparative results of the NDE inspections are reported and discussed, also on the basis of the destructive examination of the samples. The nature and size of relevant and detectable defects are discussed together with hints for a possible NDE strategy for divertor high-heat-flux components.« less

Avoidance of pseudogene interference in the detection of 3' deletions in PMS2.

PubMed

Vaughn, Cecily P; Hart, Kimberly J; Samowitz, Wade S; Swensen, Jeffrey J

2011-09-01

Lynch syndrome is characterized by mutations in the mismatch repair genes MLH1, MSH2, MSH6, and PMS2. In PMS2, detection of mutations is confounded by numerous pseudogenes. Detection of 3' deletions is particularly complicated by the pseudogene PMS2CL, which has strong similarity to PMS2 exons 9 and 11-15, due to extensive gene conversion. A newly designed multiplex ligation-dependent probe amplification (MLPA) kit incorporates probes for variants found in both PMS2 and PMS2CL. This provides detection of deletions, but does not allow localization of deletions to the gene or pseudogene. To address this, we have developed a methodology incorporating reference samples with known copy numbers of variants, and paired MLPA results with sequencing of PMS2 and PMS2CL. We tested a subset of clinically indicated samples for which mutations were either unidentified or not fully characterized using existing methods. We identified eight unrelated patients with deletions encompassing exons 9-15, 11-15, 13-15, 14-15, and 15. By incorporating specific, characterized reference samples and sequencing the gene and pseudogene it is possible to identify deletions in this region of PMS2 and provide clinically relevant results. This methodology represents a significant advance in the diagnosis of patients with Lynch syndrome caused by PMS2 mutations. © 2011 Wiley-Liss, Inc.

Method of remotely estimating a rest or best lock frequency of a local station receiver using telemetry

NASA Technical Reports Server (NTRS)

Fielhauer, Karl B. (Inventor); Jensen, James R. (Inventor)

2007-01-01

A system includes a remote station and a local station having a receiver. The receiver operates in an unlocked state corresponding to its best lock frequency (BLF). The local station derives data indicative of a ratio of the BLF to a reference frequency of the receiver, and telemeters the data to the remote station. The remote station estimates the BLF based on (i) the telemetered data, and (ii) a predetermined estimate of the reference frequency.

A VLA Search for Radio Signals from M31 and M33

NASA Astrophysics Data System (ADS)

Gray, Robert H.; Mooley, Kunal

2017-03-01

Observing nearby galaxies would facilitate the search for artificial radio signals by sampling several billions of stars simultaneously, but few efforts have been made to exploit this opportunity. An added attraction is that the Milky Way is the second largest member of the Local Group, so our galaxy might be a probable target for hypothetical broadcasters in nearby galaxies. We present the first relatively high spectral resolution (<1 kHz) 21 cm band search for intelligent radio signals of complete galaxies in the Local Group with the Jansky VLA, observing the galaxies M31 (Andromeda) and M33 (Triangulum)—the first and third largest members of the group, respectively—sampling more stars than any prior search of this kind. We used 122 Hz channels over a 1 MHz spectral window in the target galaxy velocity frame of reference, and 15 Hz channels over a 125 kHz window in our local standard of rest. No narrowband signals were detected above a signal-to-noise ratio of 7, suggesting the absence of continuous narrowband flux greater than approximately 0.24 and 1.33 Jy in the respective spectral windows illuminating our part of the Milky Way during our observations in 2014 December and 2015 January. This is also the first study in which the upgraded VLA has been used for SETI.

Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data

PubMed Central

Kosugi, Shunichi; Natsume, Satoshi; Yoshida, Kentaro; MacLean, Daniel; Cano, Liliana; Kamoun, Sophien; Terauchi, Ryohei

2013-01-01

Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in ‘targeted’ alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/. PMID:24116042

Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions

NASA Astrophysics Data System (ADS)

He, Jianbin; Zhang, Zhiyong; Shi, Yunyu; Liu, Haiyan

2003-08-01

We describe a method for efficient sampling of the energy landscape of a protein in atomic molecular dynamics simulations. A simulation is divided into alternatively occurring relaxation phases and excitation phases. In the relaxation phase (conventional simulation), we use a frequently updated reference structure and deviations from this reference structure to mark whether the system has been trapped in a local minimum. In that case, the simulation enters the excitation phase, during which a few slow collective modes of the system are coupled to a higher temperature bath. After the system has escaped from the minimum (also judged by deviations from the reference structure) the simulation reenters the relaxation phase. The collective modes are obtained from a coarse-grained Gaussian elastic network model. The scheme, which we call ACM-AME (amplified collective motion-assisted minimum escaping), is compared with conventional simulations as well as an alternative scheme that elevates the temperature of all degrees of freedom during the excitation phase (amplified overall motion-assisted minimum escaping, or AOM-AME). Comparison is made using simulations on four peptides starting from non-native extended or all helical structures. In terms of sampling low energy conformations and continuously sampling new conformations throughout a simulation, the ACM-AME scheme demonstrates very good performance while the AOM-AME scheme shows little improvement upon conventional simulations. Limited success is achieved in producing structures close to the native structures of the peptides: for an S-peptide analog, the ACM-AME approach is able to reproduce its native helical structure, and starting from an all-helical structure of the villin headpiece subdomain (HP-36) in implicit solvent, two out of three 150 ns ACM-AME runs are able to sample structures with 3-4 Å backbone root-mean-square deviations from the nuclear magnetic resonance structure of the protein.

The chemical response of particle-associated contaminants in aquatic sediments to urbanization in New England, U.S.A.

NASA Astrophysics Data System (ADS)

Chalmers, A. T.; Van Metre, P. C.; Callender, E.

2007-04-01

Relations between urbanization and particle-associated contaminants in New England were evaluated using a combination of samples from sediment cores, streambed sediments, and suspended stream sediments. Concentrations of PAHs, PCBs, DDT, and seven trace metals (Cd, Cr, Cu, Hg, Ni, Pb, Zn) were correlated strongly with urbanization, with the strongest relations to percentage commercial, industrial, and transportation (CIT) land use. Average PAH and metal concentrations in the most urbanized watersheds were approximately 30 and 6 times the reference concentrations, respectively, in remote, undeveloped watersheds. One-quarter to one-half of sampling sites had concentrations of PAHs, Cu, Pb, or Zn above the probable effects concentration, a set of sediment quality guidelines for adverse effects to aquatic biota, and sediments were predicted to be toxic, on average, when CIT land use exceeded about 10%. Trends in metals in cores from urban watersheds were dominantly downward, whereas trends in PAHs in a suburban watershed were upward. A regional atmospheric-fallout gradient was indicated by as much as order-of-magnitude-greater concentrations and accumulation rates of contaminants in cores from an undeveloped reference lake in Boston compared to those from remote reference watersheds. Contaminant accumulation rates in the lakes with urbanization in their watersheds, however, were 1-3 orders of magnitude greater than those of reference lakes, which indicate the dominance of local sources and fluvial transport of contaminants to urban lakes. These analyses demonstrate the magnitude of urban contamination of aquatic systems and air sheds, and suggest that, despite reductions in contaminant emissions in urban settings, streams and lakes will decline in quality as urbanization of their watersheds takes place.

The chemical response of particle-associated contaminants in aquatic sediments to urbanization in New England, U.S.A.

USGS Publications Warehouse

Chalmers, A.T.; Van Metre, P.C.; Callender, E.

2007-01-01

Relations between urbanization and particle-associated contaminants in New England were evaluated using a combination of samples from sediment cores, streambed sediments, and suspended stream sediments. Concentrations of PAHs, PCBs, DDT, and seven trace metals (Cd, Cr, Cu, Hg, Ni, Pb, Zn) were correlated strongly with urbanization, with the strongest relations to percentage commercial, industrial, and transportation (CIT) land use. Average PAH and metal concentrations in the most urbanized watersheds were approximately 30 and 6 times the reference concentrations, respectively, in remote, undeveloped watersheds. One-quarter to one-half of sampling sites had concentrations of PAHs, Cu, Pb, or Zn above the probable effects concentration, a set of sediment quality guidelines for adverse effects to aquatic biota, and sediments were predicted to be toxic, on average, when CIT land use exceeded about 10%. Trends in metals in cores from urban watersheds were dominantly downward, whereas trends in PAHs in a suburban watershed were upward. A regional atmospheric-fallout gradient was indicated by as much as order-of-magnitude-greater concentrations and accumulation rates of contaminants in cores from an undeveloped reference lake in Boston compared to those from remote reference watersheds. Contaminant accumulation rates in the lakes with urbanization in their watersheds, however, were 1-3 orders of magnitude greater than those of reference lakes, which indicate the dominance of local sources and fluvial transport of contaminants to urban lakes. These analyses demonstrate the magnitude of urban contamination of aquatic systems and air sheds, and suggest that, despite reductions in contaminant emissions in urban settings, streams and lakes will decline in quality as urbanization of their watersheds takes place. ?? 2006 Elsevier B.V. All rights reserved.

Uptake of community-based, self-collected HPV testing vs. visual inspection with acetic acid for cervical cancer screening in Kampala, Uganda: preliminary results of a randomised controlled trial.

PubMed

Moses, Erin; Pedersen, Heather N; Mitchell, Sheona M; Sekikubo, Musa; Mwesigwa, David; Singer, Joel; Biryabarema, Christine; Byamugisha, Josaphat K; Money, Deborah M; Ogilvie, Gina S

2015-10-01

To compare two cervical cancer screening methods: community-based self-collection of high-risk human papillomavirus (HR-HPV) testing and visual inspection with acetic acid (VIA). Pilot randomised controlled trial of 500 women aged 30-65 in the community of Kisenyi, Uganda. Women randomised to self-collection-based HR-HPV testing provided a cervico-vaginal swab for HR-HPV, and results were provided by phone after laboratory testing. Women who tested HPV positive were referred for VIA at the local health unit. Women randomised to VIA underwent screening at the local health unit, where women who tested positive with VIA were provided cryotherapy at time of screening, as per local standard of care. Women were referred for colposcopy when indicated. Outcome measures were uptake of screening, HR-HPV prevalence, VIA result and treatment rates. In the HR-HPV arm, 248 of 250 (p < 0.01) women provided samples, while in the VIA arm, 121 of 250 (48.4%) women attended screening. Among the 73 of 248 HR-HPV-positive women, 45.2% (N = 33) attended VIA screening for follow-up, 21.2% (N = 7) of whom screened positive; five received treatment and two were missing clinical follow-up records. Of the 121 women in the VIA arm who attended screening, 13.2% (N = 16) screened positive; seven received cryotherapy, three refused treatment, five were referred to colposcopy; and one woman had suspected cervical cancer and received treatment after confirmatory testing. This pilot study demonstrated trial feasibility and willingness of the women to participate and be randomised successfully into the two arms. Self-collection-based cervical cancer screening had a higher uptake than VIA. © 2015 John Wiley & Sons Ltd.

Design and Development of the SMAP Microwave Radiometer Electronics

NASA Technical Reports Server (NTRS)

Piepmeier, Jeffrey R.; Medeiros, James J.; Horgan, Kevin A.; Brambora, Clifford K.; Estep, Robert H.

2014-01-01

The SMAP microwave radiometer will measure land surface brightness temperature at L-band (1413 MHz) in the presence of radio frequency interference (RFI) for soil moisture remote sensing. The radiometer design was driven by the requirements to incorporate internal calibration, to operate synchronously with the SMAP radar, and to mitigate the deleterious effects of RFI. The system design includes a highly linear super-heterodyne microwave receiver with internal reference loads and noise sources for calibration and an innovative digital signal processor and detection system. The front-end comprises a coaxial cable-based feed network, with a pair of diplexers and a coupled noise source, and radiometer front-end (RFE) box. Internal calibration is provided by reference switches and a common noise source inside the RFE. The RF back-end (RBE) downconverts the 1413 MHz channel to an intermediate frequency (IF) of 120 MHz. The IF signals are then sampled and quantized by high-speed analog-to-digital converters in the radiometer digital electronics (RDE) box. The RBE local oscillator and RDE sampling clocks are phase-locked to a common reference to ensure coherency between the signals. The RDE performs additional filtering, sub-band channelization, cross-correlation for measuring third and fourth Stokes parameters, and detection and integration of the first four raw moments of the signals. These data are packetized and sent to the ground for calibration and further processing. Here we discuss the novel features of the radiometer hardware particularly those influenced by the need to mitigate RFI.

Tracing the genomic ancestry of Peruvians reveals a major legacy of pre-Columbian ancestors.

PubMed

Sandoval, Jose R; Salazar-Granara, Alberto; Acosta, Oscar; Castillo-Herrera, Wilder; Fujita, Ricardo; Pena, Sergio D J; Santos, Fabricio R

2013-09-01

In order to investigate the underlying genetic structure and genomic ancestry proportions of Peruvian subpopulations, we analyzed 551 human samples of 25 localities from the Andean, Amazonian, and Coastal regions of Peru with a set of 40 ancestry informative insertion-deletion polymorphisms. Using genotypes of reference populations from different continents for comparison, our analysis indicated that populations from all 25 Peruvian locations had predominantly Amerindian genetic ancestry. Among populations from the Titicaca Lake islands of Taquile, Amantani, Anapia, and Uros, and the Yanque locality from the southern Peruvian Andes, there was no significant proportion of non-autochthonous genomes, indicating that their genetic background is effectively derived from the first settlers of South America. However, the Andean populations from San Marcos, Cajamarca, Characato and Chogo, and coastal populations from Lambayeque and Lima displayed a low but significant European ancestry proportion. Furthermore, Amazonian localities of Pucallpa, Lamas, Chachapoyas, and Andean localities of Ayacucho and Huancayo displayed intermediate levels of non-autochthonous ancestry, mostly from Europe. These results are in close agreement with the documented history of post-Columbian immigrations in Peru and with several reports suggesting a larger effective size of indigenous inhabitants during the formation of the current country's population.

Celestial reference frames and the gauge freedom in the post-Newtonian mechanics of the Earth-Moon system

NASA Astrophysics Data System (ADS)

Kopeikin, Sergei; Xie, Yi

2010-11-01

We introduce the Jacobi coordinates adopted to the advanced theoretical analysis of the relativistic Celestial Mechanics of the Earth-Moon system. Theoretical derivation utilizes the relativistic resolutions on reference frames adopted by the International Astronomical Union (IAU) in 2000. The resolutions assume that the Solar System is isolated and space-time is asymptotically flat at infinity and the primary reference frame covers the entire space-time, has its origin at the Solar System barycenter (SSB) with spatial axes stretching up to infinity. The SSB frame is not rotating with respect to a set of distant quasars that are assumed to be at rest on the sky forming the International Celestial Reference Frame (ICRF). The second reference frame has its origin at the Earth-Moon barycenter (EMB). The EMB frame is locally inertial and is not rotating dynamically in the sense that equation of motion of a test particle moving with respect to the EMB frame, does not contain the Coriolis and centripetal forces. Two other local frames—geocentric and selenocentric—have their origins at the center of mass of Earth and Moon respectively and do not rotate dynamically. Each local frame is subject to the geodetic precession both with respect to other local frames and with respect to the ICRF because of their relative motion with respect to each other. Theoretical advantage of the dynamically non-rotating local frames is in a more simple mathematical description of the metric tensor and relative equations of motion of the Moon with respect to Earth. Each local frame can be converted to kinematically non-rotating one after alignment with the axes of ICRF by applying the matrix of the relativistic precession as recommended by the IAU resolutions. The set of one global and three local frames is introduced in order to decouple physical effects of gravity from the gauge-dependent effects in the equations of relative motion of the Moon with respect to Earth.

Norovirus contamination of a drinking water supply at a hotel resort.

PubMed

Jack, Susan; Bell, Derek; Hewitt, Joanne

2013-12-13

To investigate a waterborne gastroenteritis outbreak and consider wider environmental contamination concerns. An acute gastroenteritis outbreak was investigated through interviews, analysis of faecal samples, drinking water and environmental water samples. A total of 53 cases reported an illness of acute gastroenteritis following stays and/or dining at a hotel or neighbouring resort in southern New Zealand over a 1-month period in early spring 2012. The consumption of table or tap water was strongly associated with the illness. Faecal samples were positive for norovirus (NoV) genogroup I and II (GI and GII). Drinking tap water samples were positive for NoV GI and GII but negative for Escherichia coli (E. coli). Wider environmental water testing at local drinking water sources, around the sewage disposal field and at the nearby river showed the presence of NoV GI and GII. Voluntary boil water notices were issued and implemented with no further cases following this action. Additional treatment of drinking water supplies has been implemented and sewerage disposal concerns referred to local government. Investigation of this gastroenteritis outbreak revealed contamination of both drinking water and the wider environment with NoV. Bacterial indicators do not adequately cover contamination by viruses but due to costs, frequent virus monitoring programmes are currently impractical. A strategy to decrease environmental contamination of drinking water supplies in this busy tourist location through improved management of sewage disposal and drinking water is urgently required.

Molecular analysis of faecal samples from birds to identify potential crop pests and useful biocontrol agents in natural areas.

PubMed

King, R A; Symondson, W O C; Thomas, R J

2015-06-01

Wild habitats adjoining farmland are potentially valuable sources of natural enemies, but also of pests. Here we tested the utility of birds as 'sampling devices', to identify the diversity of prey available to predators and particularly to screen for pests and natural enemies using natural ecosystems as refugia. Here we used PCR to amplify prey DNA from three sympatric songbirds foraging on small invertebrates in Phragmites reedbed ecosystems, namely the Reed Warbler (Acrocephalus scirpaceus), Sedge Warbler (Acrocephalus schoenobaenus) and Cetti's Warbler (Cettia cetti). A recently described general invertebrate primer pair was used for the first time to analyse diets. Amplicons were cloned and sequenced, then identified by reference to the Barcoding of Life Database and to our own sequences obtained from fresh invertebrates. Forty-five distinct prey DNA sequences were obtained from 11 faecal samples, of which 39 could be identified to species or genus. Targeting three warbler species ensured that species-specific differences in prey choice broadened the range of prey taken. Amongst the prey found in reedbeds were major pests (including the tomato moth Lacanobia oleracea) as well as many potentially valuable natural enemies including aphidophagous hoverflies and braconid wasps. Given the mobility of birds, this approach provides a practical way of sampling a whole habitat at once, providing growers with information on possible invasion by locally resident pests and the colonization potential of natural enemies from local natural habitats.

Review of geochemical reference sample programs since G-1 and W-1: progress to date and remaining challenges

USGS Publications Warehouse

Kane, J.S.

1991-01-01

A brief history of programs to develop geochemical reference samples and certified reference samples for use in geochemical analysis is presented. While progress has been made since G-1 and W-1 were issued, many challenges remain. ?? 1991.

US Fish and Wildlife Service biomonitoring operations manual, Appendices A--K

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

Gianotto, D.F.; Rope, R.C.; Mondecar, M.

1993-04-01

Volume 2 contains Appendices and Summary Sheets for the following areas: A-Legislative Background and Key to Relevant Legislation, B- Biomonitoring Operations Workbook, C-Air Monitoring, D-Introduction to the Flora and Fauna for Biomonitoring, E-Decontamination Guidance Reference Field Methods, F-Documentation Guidance, Sample Handling, and Quality Assurance/Quality Control Standard Operating Procedures, G-Field Instrument Measurements Reference Field Methods, H-Ground Water Sampling Reference Field Methods, I-Sediment Sampling Reference Field Methods, J-Soil Sampling Reference Field Methods, K-Surface Water Reference Field Methods. Appendix B explains how to set up strategy to enter information on the ``disk workbook``. Appendix B is enhanced by DE97006389, an on-line workbook formore » users to be able to make revisions to their own biomonitoring data.« less

Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation

PubMed Central

Pasaniuc, Bogdan; Sankararaman, Sriram; Torgerson, Dara G.; Gignoux, Christopher; Zaitlen, Noah; Eng, Celeste; Rodriguez-Cintron, William; Chapela, Rocio; Ford, Jean G.; Avila, Pedro C.; Rodriguez-Santana, Jose; Chen, Gary K.; Le Marchand, Loic; Henderson, Brian; Reich, David; Haiman, Christopher A.; Gonzàlez Burchard, Esteban; Halperin, Eran

2013-01-01

Motivation: Local ancestry analysis of genotype data from recently admixed populations (e.g. Latinos, African Americans) provides key insights into population history and disease genetics. Although methods for local ancestry inference have been extensively validated in simulations (under many unrealistic assumptions), no empirical study of local ancestry accuracy in Latinos exists to date. Hence, interpreting findings that rely on local ancestry in Latinos is challenging. Results: Here, we use 489 nuclear families from the mainland USA, Puerto Rico and Mexico in conjunction with 3204 unrelated Latinos from the Multiethnic Cohort study to provide the first empirical characterization of local ancestry inference accuracy in Latinos. Our approach for identifying errors does not rely on simulations but on the observation that local ancestry in families follows Mendelian inheritance. We measure the rate of local ancestry assignments that lead to Mendelian inconsistencies in local ancestry in trios (MILANC), which provides a lower bound on errors in the local ancestry estimates. We show that MILANC rates observed in simulations underestimate the rate observed in real data, and that MILANC varies substantially across the genome. Second, across a wide range of methods, we observe that loci with large deviations in local ancestry also show enrichment in MILANC rates. Therefore, local ancestry estimates at such loci should be interpreted with caution. Finally, we reconstruct ancestral haplotype panels to be used as reference panels in local ancestry inference and show that ancestry inference is significantly improved by incoroprating these reference panels. Availability and implementation: We provide the reconstructed reference panels together with the maps of MILANC rates as a public resource for researchers analyzing local ancestry in Latinos at http://bogdanlab.pathology.ucla.edu. Contact: bpasaniuc@mednet.ucla.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23572411

Sunlight Intensity Based Global Positioning System for Near-Surface Underwater Sensors

PubMed Central

Gómez, Javier V.; Sandnes, Frode E.; Fernández, Borja

2012-01-01

Water monitoring is important in domains including documenting climate change, weather prediction and fishing. This paper presents a simple and energy efficient localization strategy for near surface buoy based sensors. Sensors can be dropped randomly in the ocean and thus self-calibrate in terms of geographic location such that geo-tagged observations of water quality can be made without the need for costly and energy consuming GPS-hardware. The strategy is based on nodes with an accurate clock and light sensors that can regularly sample the level of light intensity. The measurements are fitted into a celestial model of the earth motion around the sun. By identifying the trajectory of the sun across the skies one can accurately determine sunrise and sunset times, and thus extract the longitude and latitude of the sensor. Unlike previous localization techniques for underwater sensors, the current approach does not rely on stationary or mobile reference points. PMID:22438746

Sunlight intensity based global positioning system for near-surface underwater sensors.

PubMed

Gómez, Javier V; Sandnes, Frode E; Fernández, Borja

2012-01-01

Water monitoring is important in domains including documenting climate change, weather prediction and fishing. This paper presents a simple and energy efficient localization strategy for near surface buoy based sensors. Sensors can be dropped randomly in the ocean and thus self-calibrate in terms of geographic location such that geo-tagged observations of water quality can be made without the need for costly and energy consuming GPS-hardware. The strategy is based on nodes with an accurate clock and light sensors that can regularly sample the level of light intensity. The measurements are fitted into a celestial model of the earth motion around the sun. By identifying the trajectory of the sun across the skies one can accurately determine sunrise and sunset times, and thus extract the longitude and latitude of the sensor. Unlike previous localization techniques for underwater sensors, the current approach does not rely on stationary or mobile reference points.

Clinical chemistry reference intervals of healthy adult populations in Gojjam Zones of Amhara National Regional State, Northwest Ethiopia

PubMed Central

Amuamuta, Asmare; Mulu, Wondemagegn; Yimer, Mulat; Zenebe, Yohannes; Adem, Yesuf; Abera, Bayeh; Gebeyehu, Wondemu; Gebregziabher, Yakob

2017-01-01

Background Reference interval is crucial for disease screening, diagnosis, monitoring, progression and treatment efficacy. Due to lack of locally derived reference values for the parameters, clinicians use reference intervals derived from western population. But, studies conducted in different African countries have indicated differences between locally and western derived reference values. Different studies also indicated considerable variation in clinical chemistry reference intervals by several variables such as age, sex, geographical location, environment, lifestyle and genetic variation. Objective This study aimed to determine the reference intervals of common clinical chemistry parameters of the community of Gojjam Zones, Northwest Ethiopia. Method Population based cross-sectional study was conducted from November 2015 to December 2016 in healthy adult populations of Gojjam zone. Data such as, medical history, physical examination and socio-demographic data were collected. In addition, laboratory investigations were undertaken to screen the population. Clinical chemistry parameters were measured using Mindray BS 200 clinical chemistry autoanalyzer as per the manufacturer’s instructions. Descriptive statistics was used to calculate mean, median and 95th percentiles. Independent sample T-test and one way ANOVA were used to see association between variables. Results After careful screening of a total of 799 apparently healthy adults who were consented for this study, complete data from 446 (224 females and 222 males) were included for the analysis. The mean age of both the study participants was 28.8 years. Males had high (P<0.05) mean and 2.5th-97.5th percentile ranges of ALT, AST, ALP, creatinine and direct bilirubin. The reference intervals of amylase, LDH, total protein and total bilirubin were not significantly different between the two sex groups (P>0.05). Mean, median, 95% percentile values of AST, ALP, amylase, LDH, creatinine, total protein, total bilirubin, and direct bilirubin across all age groups of participants were similar (P>0.05). But, there was a significant difference in the value of ALT (P<0.05). The reference intervals of ALT, total protein and creatinine were significantly (P<0.05) high in people having monthly income >1500 ETB compared to those with low monthly income. Significant (P<0.05) higher values of the ALT, ALP and total protein were observed in people living in high land compared to low land residences. Conclusion The study showed that some of the common clinical chemistry parameters reference intervals of healthy adults in Gojjam zones were higher than the reference intervals generated from developed countries. Therefore, strict adherence to the reference values generated in developed countries could lead to inappropriate diagnosis and treatment of patients. There was also variation of reference interval values based on climate, gender, age, monthly income and geographical locations. Therefore, further study is required to establish reference intervals for Ethiopian population. PMID:28886191

Strong Spatial Influence on Colonization Rates in a Pioneer Zooplankton Metacommunity

PubMed Central

Frisch, Dagmar; Cottenie, Karl; Badosa, Anna; Green, Andy J.

2012-01-01

The magnitude of community-wide dispersal is central to metacommunity models, yet dispersal is notoriously difficult to quantify in passive and cryptic dispersers such as many freshwater invertebrates. By overcoming the problem of quantifying dispersal rates, colonization rates into new habitats can provide a useful estimate of the magnitude of effective dispersal. Here we study the influence of spatial and local processes on colonization rates into new ponds that indicate differential dispersal limitation of major zooplankton taxa, with important implications for metacommunity dynamics. We identify regional and local factors that affect zooplankton colonization rates and spatial patterns in a large-scale experimental system. Our study differs from others in the unique setup of the experimental pond area by which we were able to test spatial and environmental variables at a large spatial scale. We quantified colonization rates separately for the Copepoda, Cladocera and Rotifera from samples collected over a period of 21 months in 48 newly constructed temporary ponds of 0.18–2.95 ha distributed in a restored wetland area of 2,700 ha in Doñana National Park, Southern Spain. Species richness upon initial sampling of new ponds was about one third of that in reference ponds, although the rate of detection of new species from thereon were not significantly different, probably owing to high turnover in the dynamic, temporary reference ponds. Environmental heterogeneity had no detectable effect on colonization rates in new ponds. In contrast, connectivity, space (based on latitude and longitude) and surface area were key determinants of colonization rates for copepods and cladocerans. This suggests dispersal limitation in cladocerans and copepods, but not in rotifers, possibly due to differences in propagule size and abundance. PMID:22792241

Strong spatial influence on colonization rates in a pioneer zooplankton metacommunity.

PubMed

Frisch, Dagmar; Cottenie, Karl; Badosa, Anna; Green, Andy J

2012-01-01

The magnitude of community-wide dispersal is central to metacommunity models, yet dispersal is notoriously difficult to quantify in passive and cryptic dispersers such as many freshwater invertebrates. By overcoming the problem of quantifying dispersal rates, colonization rates into new habitats can provide a useful estimate of the magnitude of effective dispersal. Here we study the influence of spatial and local processes on colonization rates into new ponds that indicate differential dispersal limitation of major zooplankton taxa, with important implications for metacommunity dynamics. We identify regional and local factors that affect zooplankton colonization rates and spatial patterns in a large-scale experimental system. Our study differs from others in the unique setup of the experimental pond area by which we were able to test spatial and environmental variables at a large spatial scale. We quantified colonization rates separately for the Copepoda, Cladocera and Rotifera from samples collected over a period of 21 months in 48 newly constructed temporary ponds of 0.18-2.95 ha distributed in a restored wetland area of 2,700 ha in Doñana National Park, Southern Spain. Species richness upon initial sampling of new ponds was about one third of that in reference ponds, although the rate of detection of new species from thereon were not significantly different, probably owing to high turnover in the dynamic, temporary reference ponds. Environmental heterogeneity had no detectable effect on colonization rates in new ponds. In contrast, connectivity, space (based on latitude and longitude) and surface area were key determinants of colonization rates for copepods and cladocerans. This suggests dispersal limitation in cladocerans and copepods, but not in rotifers, possibly due to differences in propagule size and abundance.

A multi-scale evaluation of pack stock effects on subalpine meadow plant communities in the Sierra Nevada

PubMed Central

Berlow, Eric L.; Ostoja, Steven M.; Brooks, Matthew L.; Génin, Alexandre; Matchett, John R.; Hart, Stephen C.

2017-01-01

We evaluated the influence of pack stock (i.e., horse and mule) use on meadow plant communities in Sequoia and Yosemite National Parks in the Sierra Nevada of California. Meadows were sampled to account for inherent variability across multiple scales by: 1) controlling for among-meadow variability by using remotely sensed hydro-climatic and geospatial data to pair stock use meadows with similar non-stock (reference) sites, 2) accounting for within-meadow variation in the local hydrology using in-situ soil moisture readings, and 3) incorporating variation in stock use intensity by sampling across the entire available gradient of pack stock use. Increased cover of bare ground was detected only within “dry” meadow areas at the two most heavily used pack stock meadows (maximum animals per night per hectare). There was no difference in plant community composition for any level of soil moisture or pack stock use. Increased local-scale spatial variability in plant community composition (species dispersion) was detected in “wet” meadow areas at the two most heavily used meadows. These results suggest that at the meadow scale, plant communities are generally resistant to the contemporary levels of recreational pack stock use. However, finer-scale within-meadow responses such as increased bare ground or spatial variability in the plant community can be a function of local-scale hydrological conditions. Wilderness managers can improve monitoring of disturbance in Sierra Nevada meadows by adopting multiple plant community indices while simultaneously considering local moisture regimes. PMID:28609464

32 CFR 1602.15 - Local board of jurisdiction.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 32 National Defense 6 2010-07-01 2010-07-01 false Local board of jurisdiction. 1602.15 Section... DEFINITIONS § 1602.15 Local board of jurisdiction. The local board of jurisdiction is the local board to which... determine his claim or to issue to him an order. His local board and registrant's local board refer to the...

32 CFR 1602.15 - Local board of jurisdiction.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 32 National Defense 6 2011-07-01 2011-07-01 false Local board of jurisdiction. 1602.15 Section... DEFINITIONS § 1602.15 Local board of jurisdiction. The local board of jurisdiction is the local board to which... determine his claim or to issue to him an order. His local board and registrant's local board refer to the...

Comparative Accuracy Evaluation of Fine-Scale Global and Local Digital Surface Models: The Tshwane Case Study I

NASA Astrophysics Data System (ADS)

Breytenbach, A.

2016-10-01

Conducted in the City of Tshwane, South Africa, this study set about to test the accuracy of DSMs derived from different remotely sensed data locally. VHR digital mapping camera stereo-pairs, tri-stereo imagery collected by a Pléiades satellite and data detected from the Tandem-X InSAR satellite configuration were fundamental in the construction of seamless DSM products at different postings, namely 2 m, 4 m and 12 m. The three DSMs were sampled against independent control points originating from validated airborne LiDAR data. The reference surfaces were derived from the same dense point cloud at grid resolutions corresponding to those of the samples. The absolute and relative positional accuracies were computed using well-known DEM error metrics and accuracy statistics. Overall vertical accuracies were also assessed and compared across seven slope classes and nine primary land cover classes. Although all three DSMs displayed significantly more vertical errors where solid waterbodies, dense natural and/or alien woody vegetation and, in a lesser degree, urban residential areas with significant canopy cover were encountered, all three surpassed their expected positional accuracies overall.

Acoustic Impedance Inversion of Seismic Data Using Genetic Algorithm

NASA Astrophysics Data System (ADS)

Eladj, Said; Djarfour, Noureddine; Ferahtia, Djalal; Ouadfeul, Sid-Ali

2013-04-01

The inversion of seismic data can be used to constrain estimates of the Earth's acoustic impedance structure. This kind of problem is usually known to be non-linear, high-dimensional, with a complex search space which may be riddled with many local minima, and results in irregular objective functions. We investigate here the performance and the application of a genetic algorithm, in the inversion of seismic data. The proposed algorithm has the advantage of being easily implemented without getting stuck in local minima. The effects of population size, Elitism strategy, uniform cross-over and lower mutation are examined. The optimum solution parameters and performance were decided as a function of the testing error convergence with respect to the generation number. To calculate the fitness function, we used L2 norm of the sample-to-sample difference between the reference and the inverted trace. The cross-over probability is of 0.9-0.95 and mutation has been tested at 0.01 probability. The application of such a genetic algorithm to synthetic data shows that the inverted acoustic impedance section was efficient. Keywords: Seismic, Inversion, acoustic impedance, genetic algorithm, fitness functions, cross-over, mutation.

Geodetic measurement of deformation in California. Ph.D. Thesis - Massachusetts Inst. of Technology

NASA Technical Reports Server (NTRS)

Sauber, Jeanne

1989-01-01

The very long baseline interferometry (VLBI) measurements made in the western U.S. since 1979 as part of the NASA Crustal Dynamics Project provide discrete samples of the temporal and spatial deformation field. The interpretation of the VLBI-derived rates of deformation requires an examination of geologic information and more densely sampled ground-based geodetic data. In the first two of three related studies, triangulation and trilateration data measured on two regional networks, one in the central Mojave Desert and one in the Coast Ranges east of the San Andreas fault, have been processed. At the spatial scales spanned by these local geodetic networks, auxiliary geologic and geophysical data have been utilized to examine the relation between measured incremental strain and the accommodation of strain seen in local geological structures, strain release in earthquakes, and principal stress directions inferred from in situ measurements. In a third study, the geocentric position vectors from a set of 77 VLBI experiments beginning in October 1982 have been used to estimate the tangential rate of change of station positions in the western U.S. in a North-America-Fixed reference frame.

A Collaborative Secure Localization Algorithm Based on Trust Model in Underwater Wireless Sensor Networks

PubMed Central

Han, Guangjie; Liu, Li; Jiang, Jinfang; Shu, Lei; Rodrigues, Joel J.P.C.

2016-01-01

Localization is one of the hottest research topics in Underwater Wireless Sensor Networks (UWSNs), since many important applications of UWSNs, e.g., event sensing, target tracking and monitoring, require location information of sensor nodes. Nowadays, a large number of localization algorithms have been proposed for UWSNs. How to improve location accuracy are well studied. However, few of them take location reliability or security into consideration. In this paper, we propose a Collaborative Secure Localization algorithm based on Trust model (CSLT) for UWSNs to ensure location security. Based on the trust model, the secure localization process can be divided into the following five sub-processes: trust evaluation of anchor nodes, initial localization of unknown nodes, trust evaluation of reference nodes, selection of reference node, and secondary localization of unknown node. Simulation results demonstrate that the proposed CSLT algorithm performs better than the compared related works in terms of location security, average localization accuracy and localization ratio. PMID:26891300

Bias Assessment of General Chemistry Analytes using Commutable Samples.

PubMed

Koerbin, Gus; Tate, Jillian R; Ryan, Julie; Jones, Graham Rd; Sikaris, Ken A; Kanowski, David; Reed, Maxine; Gill, Janice; Koumantakis, George; Yen, Tina; St John, Andrew; Hickman, Peter E; Simpson, Aaron; Graham, Peter

2014-11-01

Harmonisation of reference intervals for routine general chemistry analytes has been a goal for many years. Analytical bias may prevent this harmonisation. To determine if analytical bias is present when comparing methods, the use of commutable samples, or samples that have the same properties as the clinical samples routinely analysed, should be used as reference samples to eliminate the possibility of matrix effect. The use of commutable samples has improved the identification of unacceptable analytical performance in the Netherlands and Spain. The International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) has undertaken a pilot study using commutable samples in an attempt to determine not only country specific reference intervals but to make them comparable between countries. Australia and New Zealand, through the Australasian Association of Clinical Biochemists (AACB), have also undertaken an assessment of analytical bias using commutable samples and determined that of the 27 general chemistry analytes studied, 19 showed sufficiently small between method biases as to not prevent harmonisation of reference intervals. Application of evidence based approaches including the determination of analytical bias using commutable material is necessary when seeking to harmonise reference intervals.

Development and characterization of sub-monolayer coatings as novel calibration samples for X-ray spectroscopy

NASA Astrophysics Data System (ADS)

Hönicke, Philipp; Krämer, Markus; Lühl, Lars; Andrianov, Konstantin; Beckhoff, Burkhard; Dietsch, Rainer; Holz, Thomas; Kanngießer, Birgit; Weißbach, Danny; Wilhein, Thomas

2018-07-01

With the advent of both modern X-ray fluorescence (XRF) methods and improved analytical reliability requirements the demand for suitable reference samples has increased. Especially in nanotechnology with the very low areal mass depositions, quantification becomes considerably more difficult. However, the availability of suited reference samples is drastically lower than the demand. Physical vapor deposition techniques have been enhanced significantly in the last decade driven by the need for extremely precise film parameters in multilayer production. We have applied those techniques for the development of layer-like reference samples with mass depositions in the ng-range and well below for Ca, Cu, Pb, Mo, Pd, Pb, La, Fe and Ni. Numerous other elements would also be possible. Several types of reference samples were fabricated: multi-elemental layer and extremely low (sub-monolayer) samples for various applications in XRF and total-reflection XRF analysis. Those samples were characterized and compared at three different synchrotron radiation beamlines at the BESSY II electron storage ring employing the reference-free XRF approach based on physically calibrated instrumentation. In addition, the homogeneity of the multi-elemental coatings was checked at the P04 beamline at DESY. The measurements demonstrate the high precision achieved in the manufacturing process as well as the versatility of application fields for the presented reference samples.

Improved imputation accuracy in Hispanic/Latino populations with larger and more diverse reference panels: applications in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

PubMed Central

Nelson, Sarah C.; Stilp, Adrienne M.; Papanicolaou, George J.; Taylor, Kent D.; Rotter, Jerome I.; Thornton, Timothy A.; Laurie, Cathy C.

2016-01-01

Imputation is commonly used in genome-wide association studies to expand the set of genetic variants available for analysis. Larger and more diverse reference panels, such as the final Phase 3 of the 1000 Genomes Project, hold promise for improving imputation accuracy in genetically diverse populations such as Hispanics/Latinos in the USA. Here, we sought to empirically evaluate imputation accuracy when imputing to a 1000 Genomes Phase 3 versus a Phase 1 reference, using participants from the Hispanic Community Health Study/Study of Latinos. Our assessments included calculating the correlation between imputed and observed allelic dosage in a subset of samples genotyped on a supplemental array. We observed that the Phase 3 reference yielded higher accuracy at rare variants, but that the two reference panels were comparable at common variants. At a sample level, the Phase 3 reference improved imputation accuracy in Hispanic/Latino samples from the Caribbean more than for Mainland samples, which we attribute primarily to the additional reference panel samples available in Phase 3. We conclude that a 1000 Genomes Project Phase 3 reference panel can yield improved imputation accuracy compared with Phase 1, particularly for rare variants and for samples of certain genetic ancestry compositions. Our findings can inform imputation design for other genome-wide association studies of participants with diverse ancestries, especially as larger and more diverse reference panels continue to become available. PMID:27346520

Optical distribution of local oscillators in future telecommunication satellite payloads

NASA Astrophysics Data System (ADS)

Benazet, Benoît; Sotom, Michel; Maignan, Michel; Berthon, Jacques

2017-11-01

The distribution of high spectral purity reference signals over optical fibre in future telecommunication satellite payloads is presented. Several types of applications are considered, including the distribution of a reference frequency at 10 MHz (Ultra-Stable Reference Oscillator) as well as the distribution of a radiofrequency oscillator around 800 MHz (Master Local Oscillator). The results of both experimental and theoretical studies are reported. In order to meet phase noise requirements for the USRO distribution, the use of an optimised receiver circuit based on an optically synchronised oscillator is investigated. Finally, the optical distribution of microwave local oscillators at frequencies exceeding 20 GHz is described. Such a scheme paves the way to more advanced sub-systems involving optical frequency-mixing and optical transmission of microwave signals, with applications to multiple-beam active antennas.

Radiofrequency energy deposition and radiofrequency power requirements in parallel transmission with increasing distance from the coil to the sample.

PubMed

Deniz, Cem M; Vaidya, Manushka V; Sodickson, Daniel K; Lattanzi, Riccardo

2016-01-01

We investigated global specific absorption rate (SAR) and radiofrequency (RF) power requirements in parallel transmission as the distance between the transmit coils and the sample was increased. We calculated ultimate intrinsic SAR (UISAR), which depends on object geometry and electrical properties but not on coil design, and we used it as the reference to compare the performance of various transmit arrays. We investigated the case of fixing coil size and increasing the number of coils while moving the array away from the sample, as well as the case of fixing coil number and scaling coil dimensions. We also investigated RF power requirements as a function of lift-off, and tracked local SAR distributions associated with global SAR optima. In all cases, the target excitation profile was achieved and global SAR (as well as associated maximum local SAR) decreased with lift-off, approaching UISAR, which was constant for all lift-offs. We observed a lift-off value that optimizes the balance between global SAR and power losses in coil conductors. We showed that, using parallel transmission, global SAR can decrease at ultra high fields for finite arrays with a sufficient number of transmit elements. For parallel transmission, the distance between coils and object can be optimized to reduce SAR and minimize RF power requirements associated with homogeneous excitation. © 2015 Wiley Periodicals, Inc.

Radioactivity levels in the mostly local foodstuff consumed by residents of the high level natural radiation areas of Ramsar, Iran.

PubMed

Fathabadi, Nasrin; Salehi, Ali Akbar; Naddafi, Kazem; Kardan, Mohammad Reza; Yunesian, Masud; Nodehi, Ramin Nabizadeh; Deevband, Mohammad Reza; Shooshtari, Molood Gooniband; Hosseini, Saeedeh Sadat; Karimi, Mahtab

2017-04-01

Among High Level Natural Radiation Areas (HLNRAs) all over the world, the northern coastal city of Ramsar has been considered enormously important. Many studies have measured environmental radioactivity in Ramsar, however, no survey has been undertaken to measure concentrations in the diets of residents. This study determined the 226 Ra activity concentration in the daily diet of people of Ramsar. The samples were chosen from both normal and high level natural radiation areas and based on the daily consumption patterns of residents. About 150 different samples, which all are local and have the highest consumption, were collected during the four seasons. In these samples, after washing and drying and pretreatment, the radionuclide was determined by α-spectrometry. The mean radioactivity concentration of 226 Ra ranged between 5 ± 1 mBq kg -1 wet weight (chino and meat) to 725 ± 480 mBq kg -1 for tea dry leaves. The 226 Ra activity concentrations compared with the reference values of UNSCEAR appear to be higher in leafy vegetables, milk and meat product. Of the total daily dietary 226 Ra exposure for adults in Ramsar, the largest percentage was from eggs. The residents consuming eggs from household chickens may receive an elevated dose in the diet. Copyright © 2016. Published by Elsevier Ltd.

GIS multimedia view of local politics

NASA Astrophysics Data System (ADS)

Muddam, Sandeep Reddy

The abstract mainly focuses on describing the prototype of the "GIS Multimedia View of Local Politics" of San Diego County. This project puts the local political information on a website which helps school children to learn about the structure of a political body and how it is organized, how the representatives are elected. It also puts up the statistics of the elections previously held. So for this, past and present election statistics have been collected. The shape files of San Diego county, congressional districts, council districts, supervisor districts have been collected. A sample community college districts is also presented. With these shape files we can show the information in an interactive map application which is based on GIS. Poll Watcher: A candidate, political party or political committee may ask someone to go to a polling place or early voting area and observe. This person is known as a poll watcher. The poll watcher observes the election process to see if any violation of the election laws occurs. If a violation occurs, the poll watcher is to refer the violation to the clerk of the election board.

Local effects of redundant terrestrial and GPS-based tie vectors in ITRF-like combinations

NASA Astrophysics Data System (ADS)

Abbondanza, Claudio; Altamimi, Zuheir; Sarti, Pierguido; Negusini, Monia; Vittuari, Luca

2009-11-01

Tie vectors (TVs) between co-located space geodetic instruments are essential for combining terrestrial reference frames (TRFs) realised using different techniques. They provide relative positioning between instrumental reference points (RPs) which are part of a global geodetic network such as the international terrestrial reference frame (ITRF). This paper gathers the set of very long baseline interferometry (VLBI)-global positioning system (GPS) local ties performed at the observatory of Medicina (Northern Italy) during the years 2001-2006 and discusses some important aspects related to the usage of co-location ties in the combinations of TRFs. Two measurement approaches of local survey are considered here: a GPS-based approach and a classical approach based on terrestrial observations (i.e. angles, distances and height differences). The behaviour of terrestrial local ties, which routinely join combinations of space geodetic solutions, is compared to that of GPS-based local ties. In particular, we have performed and analysed different combinations of satellite laser ranging (SLR), VLBI and GPS long term solutions in order to (i) evaluate the local effects of the insertion of the series of TVs computed at Medicina, (ii) investigate the consistency of GPS-based TVs with respect to space geodetic solutions, (iii) discuss the effects of an imprecise alignment of TVs from a local to a global reference frame. Results of ITRF-like combinations show that terrestrial TVs originate the smallest residuals in all the three components. In most cases, GPS-based TVs fit space geodetic solutions very well, especially in the horizontal components (N, E). On the contrary, the estimation of the VLBI RP Up component through GPS technique appears to be awkward, since the corresponding post fit residuals are considerably larger. Besides, combination tests including multi-temporal TVs display local effects of residual redistribution, when compared to those solutions where Medicina TVs are added one at a time. Finally, the combination of TRFs turns out to be sensitive to the orientation of the local tie into the global frame.

A soil sampling reference site: the challenge in defining reference material for sampling.

PubMed

de Zorzi, Paolo; Barbizzi, Sabrina; Belli, Maria; Fajgelj, Ales; Jacimovic, Radojko; Jeran, Zvonka; Sansone, Umberto; van der Perk, Marcel

2008-11-01

In the frame of the international SOILSAMP project, funded and coordinated by the Italian Environmental Protection Agency, an agricultural area was established as a reference site suitable for performing soil sampling inter-comparison exercises. The reference site was characterized for trace element content in soil, in terms of the spatial and temporal variability of their mass fraction. Considering that the behaviour of long-lived radionuclides in soil can be expected to be similar to that of some stable trace elements and that the distribution of these trace elements in soil can simulate the distribution of radionuclides, the reference site characterised in term of trace elements, can be also used to compare the soil sampling strategies developed for radionuclide investigations.

Unsupervised Segmentation of Head Tissues from Multi-modal MR Images for EEG Source Localization.

PubMed

Mahmood, Qaiser; Chodorowski, Artur; Mehnert, Andrew; Gellermann, Johanna; Persson, Mikael

2015-08-01

In this paper, we present and evaluate an automatic unsupervised segmentation method, hierarchical segmentation approach (HSA)-Bayesian-based adaptive mean shift (BAMS), for use in the construction of a patient-specific head conductivity model for electroencephalography (EEG) source localization. It is based on a HSA and BAMS for segmenting the tissues from multi-modal magnetic resonance (MR) head images. The evaluation of the proposed method was done both directly in terms of segmentation accuracy and indirectly in terms of source localization accuracy. The direct evaluation was performed relative to a commonly used reference method brain extraction tool (BET)-FMRIB's automated segmentation tool (FAST) and four variants of the HSA using both synthetic data and real data from ten subjects. The synthetic data includes multiple realizations of four different noise levels and several realizations of typical noise with a 20% bias field level. The Dice index and Hausdorff distance were used to measure the segmentation accuracy. The indirect evaluation was performed relative to the reference method BET-FAST using synthetic two-dimensional (2D) multimodal magnetic resonance (MR) data with 3% noise and synthetic EEG (generated for a prescribed source). The source localization accuracy was determined in terms of localization error and relative error of potential. The experimental results demonstrate the efficacy of HSA-BAMS, its robustness to noise and the bias field, and that it provides better segmentation accuracy than the reference method and variants of the HSA. They also show that it leads to a more accurate localization accuracy than the commonly used reference method and suggest that it has potential as a surrogate for expert manual segmentation for the EEG source localization problem.

Low-temperature positron annihilation study of B+-ion implanted PMMA

NASA Astrophysics Data System (ADS)

Kavetskyy, T. S.; Tsmots, V. M.; Voloshanska, S. Ya.; Šauša, O.; Nuzhdin, V. I.; Valeev, V. F.; Osin, Y. N.; Stepanov, A. L.

2014-08-01

Temperature dependent positron annihilation lifetime spectroscopy (PALS) measurements in the range of 50-300 K are carried out to study positronium formation in 40 KeV B+-ion implanted polymethylmethacrylate (B:PMMA) with two ion doses of 3.13 × 1015 and 3.75 × 1016 ions/cm2. The investigated samples show the various temperature trends of ortho-positronium (o-Ps) lifetime τ3 and intensity I3 in PMMA before and after ion implantation. Two transitions in the vicinity of ˜150 and ˜250 K, ascribed to γ and β transitions, respectively, are observed in the PMMA and B:PMMA samples in consistent with reference data for pristine sample. The obtained results are compared with room temperature PALS study of PMMA with different molecular weight (Mw) which known from literature. It is found that B+-ion implantation leads to decreasing Mw in PMMA at lower ion dose. At higher ion dose the local destruction of polymeric structure follows to broadening of lifetime distribution (hole size distribution).

Heavy metals in emergent trees and pioneers from tropical forest with special reference to forest fires and local pollution sources in Sarawak, Malaysia.

PubMed

Breulman, G; Markert, B; Weckert, V; Herpin, U; Yoneda, R; Ogino, K

2002-02-21

Leaf samples of tropical trees, i.e. Dryobalanops lanceolata (Kapur paji), Dipterocarpaceae and Macaranga spp. (Mahang), Euphorbiaceae were analyzed for 21 chemical elements. The pioneer Macaranga spp. exhibited higher concentrations for the majority of elements compared to the emergent species of Dryobalanops lanceolata, which was attributed to the higher physiological activity of the fast growing pioneer species compared to emergent trees. Lead showed rather high concentrations in several samples from the Bakam re-forestation site. This is suggested to be caused by emissions through brick manufacturing and related activities in the vicinity. A comparison of Dryobalanops lanceolata samples collected in 1993, 1995 and 1997 in the Lambir Hills National Park revealed that certain heavy metals, i.e. Co, Cu, Mn, Ni, Pb and Ti showed higher values in 1997 compared to the previous years, which could indicate an atmospheric input from the haze caused by the extensive forest fires raging in Borneo and other parts of Southeast Asia.

Development of internal forest soil reference samples and testing of digestion methods

Treesearch

J.E. Hislop; J.W. Hornbeck; S.W. Bailey; R.A. Hallett

1998-01-01

Our research requires determinations of total elemental concentrations of forest soils. The lack of certified forest soil reference materials led us to develop internal reference samples. Samples were collected from three soil horizons (Oa, B, and C) at three locations having forested, acidic soils similar to those we commonly analyze. A shatterbox was used to...

Abundances of disk and bulge giants from high-resolution optical spectra. I. O, Mg, Ca, and Ti in the solar neighborhood and Kepler field samples

NASA Astrophysics Data System (ADS)

Jönsson, H.; Ryde, N.; Nordlander, T.; Pehlivan Rhodin, A.; Hartman, H.; Jönsson, P.; Eriksson, K.

2017-02-01

Context. The Galactic bulge is an intriguing and significant part of our Galaxy, but it is hard to observe because it is both distant and covered by dust in the disk. Therefore, there are not many high-resolution optical spectra of bulge stars with large wavelength coverage, whose determined abundances can be compared with nearby, similarly analyzed stellar samples. Aims: We aim to determine the diagnostically important alpha elements of a sample of bulge giants using high-resolution optical spectra with large wavelength coverage. The abundances found are compared to similarly derived abundances from similar spectra of similar stars in the local thin and thick disks. In this first paper we focus on the solar neighborhood reference sample. Methods: We used spectral synthesis to derive the stellar parameters as well as the elemental abundances of both the local and bulge samples of giants. We took special care to benchmark our method of determining stellar parameters against independent measurements of effective temperatures from angular diameter measurements and surface gravities from asteroseismology. Results: In this first paper we present the method used to determine the stellar parameters and elemental abundances, evaluate them, and present the results for our local disk sample of 291 giants. Conclusions: When comparing our determined spectroscopic temperatures to those derived from angular diameter measurements, we reproduce these with a systematic difference of +10 K and a standard deviation of 53 K. The spectroscopic gravities reproduce those determined from asteroseismology with a systematic offset of +0.10 dex and a standard deviation of 0.12 dex. When it comes to the abundance trends, our sample of local disk giants closely follows trends found in other works analyzing solar neighborhood dwarfs, showing that the much brighter giant stars are as good abundance probes as the often used dwarfs. Based on observations made with the Nordic Optical Telescope (programs 51-018 and 53-002), operated by the Nordic Optical Telescope Scientific Association at the Observatorio del Roque de los Muchachos, La Palma, Spain, of the Instituto de Astrofisica de Canarias, and on spectral data retrieved from PolarBase at Observatoire Midi Pyrénées.Full Tables A.1 and A.3 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/598/A100

Language in Context: MEG Evidence for Modality-General and -Specific Responses to Reference Resolution

PubMed Central

2016-01-01

Abstract Successful language comprehension critically depends on our ability to link linguistic expressions to the entities they refer to. Without reference resolution, newly encountered language cannot be related to previously acquired knowledge. The human experience includes many different types of referents, some visual, some auditory, some very abstract. Does the neural basis of reference resolution depend on the nature of the referents, or do our brains use a modality-general mechanism for linking meanings to referents? Here we report evidence for both. Using magnetoencephalography (MEG), we varied both the modality of referents, which consisted either of visual or auditory objects, and the point at which reference resolution was possible within sentences. Source-localized MEG responses revealed brain activity associated with reference resolution that was independent of the modality of the referents, localized to the medial parietal lobe and starting ∼415 ms after the onset of reference resolving words. A modality-specific response to reference resolution in auditory domains was also found, in the vicinity of auditory cortex. Our results suggest that referential language processing cannot be reduced to processing in classical language regions and representations of the referential domain in modality-specific neural systems. Instead, our results suggest that reference resolution engages medial parietal cortex, which supports a mechanism for referential processing regardless of the content modality. PMID:28058272

Selection of reference genes for tissue/organ samples on day 3 fifth-instar larvae in silkworm, Bombyx mori.

PubMed

Wang, Genhong; Chen, Yanfei; Zhang, Xiaoying; Bai, Bingchuan; Yan, Hao; Qin, Daoyuan; Xia, Qingyou

2018-06-01

The silkworm, Bombyx mori, is one of the world's most economically important insect. Surveying variations in gene expression among multiple tissue/organ samples will provide clues for gene function assignments and will be helpful for identifying genes related to economic traits or specific cellular processes. To ensure their accuracy, commonly used gene expression quantification methods require a set of stable reference genes for data normalization. In this study, 24 candidate reference genes were assessed in 10 tissue/organ samples of day 3 fifth-instar B. mori larvae using geNorm and NormFinder. The results revealed that, using the combination of the expression of BGIBMGA003186 and BGIBMGA008209 was the optimum choice for normalizing the expression data of the B. mori tissue/organ samples. The most stable gene, BGIBMGA003186, is recommended if just one reference gene is used. Moreover, the commonly used reference gene encoding cytoplasmic actin was the least appropriate reference gene of the samples investigated. The reliability of the selected reference genes was further confirmed by evaluating the expression profiles of two cathepsin genes. Our results may be useful for future studies involving the quantification of relative gene expression levels of different tissue/organ samples in B. mori. © 2018 Wiley Periodicals, Inc.

Mahan excitons in degenerate wurtzite InN: Photoluminescence spectroscopy and reflectivity measurements

NASA Astrophysics Data System (ADS)

Feneberg, Martin; Däubler, Jürgen; Thonke, Klaus; Sauer, Rolf; Schley, Pascal; Goldhahn, Rüdiger

2008-06-01

Unintentionally degenerately doped n -type hexagonal wurtzite InN samples were studied by using Fourier-transform photoluminescence spectroscopy and reflectivity measurements. We found in luminescence overlapping band acceptor (e,A0) transitions related to two different acceptors with a strong enhancement of their intensities close to the Fermi energy of the electrons recombining with the localized holes. Our explanation is in terms of a Fermi-edge singularity of the electrons due to strongly increased electron-hole scattering. Electron-hole pairs with such resonantly enhanced oscillator strengths have been referred to as Mahan excitons. Temperature-dependent reflectivity measurements confirm this interpretation.

Comparison of low cost measurement techniques for long-term monitoring of atmospheric ammonia.

PubMed

Sutton, M A; Miners, B; Tang, Y S; Milford, C; Wyers, G P; Duyzer, J H; Fowler, D

2001-10-01

An inter-comparison of techniques for long-term sampling of atmospheric ammonia (NH3) was conducted with a view to establishing a national network with > 50 sites. Key requirements were for: a low cost system, simplicity and durability to enable a postal exchange with local site operators, a precision of < +/- 20% for monthly sampling at expected NH3 concentrations of 1-2 micrograms m-3, a detection limit sufficient to resolve the small NH3 concentrations (< 0.2 microgram m-3) expected in remote parts of the UK, and a quantitative means to establish quality control. Five sampling methods were compared: A, a commercially available membrane diffusion tube (exposed in triplicate), with membranes removed immediately after sampling; B, the above method, with the membranes left in place until analysis; C, open-ended diffusion tubes (exposed with 4 replicates); D, a new active sampling diffusion denuder system; and E, an active sampling bubbler system. Method D consisted of two 0.1 m acid coated glass denuders in series with sampling at approximately 0.3 l min-1. These methods were deployed at 6 locations in the UK and the Netherlands and compared against reference estimates. Method D was the most precise and sensitive of the techniques compared, with a detection limit of < 0.1 microgram m-3. The bubbler provided a less precise estimate of NH3 concentration, and also suffered several practical drawbacks. The diffusion tubes were found to correlate with the reference at high concentrations (> 3 micrograms m-3), but were less precise and overestimated NH3 at smaller concentrations. Of the passive methods, A was the most precise and C the least precise. On the basis of the results, method D has been implemented in the national network, together with application of method A to explore spatial variability in regions with expected high NH3 concentrations.

The role of local terminologies in electronic health records. The HEGP experience.

PubMed

Daniel-Le Bozec, Christel; Steichen, Olivier; Dart, Thierry; Jaulent, Marie-Christine

2007-01-01

Despite decades of work, there is no universally accepted standard medical terminology and no generally usable terminological tools have yet emerged. The local dictionary of concepts of the Georges Pompidou European Hospital (HEGP) is a Terminological System (TS) designed to support clinical data entry. It covers 93 data entry forms and contains definitions and synonyms of more than 5000 concepts, sometimes linked to reference terminologies such as ICD-10. In this article, we evaluate to which extend SNOMED CT could fully replace or rather be mapped to the local terminology system. We first describe the local dictionary of concepts of HEGP according to some published TS characterization framework. Then we discuss the specific role that a local terminology system plays with regards to reference terminologies.

Inequality measures perform differently in global and local assessments: An exploratory computational experiment

NASA Astrophysics Data System (ADS)

Chiang, Yen-Sheng

2015-11-01

Inequality measures are widely used in both the academia and public media to help us understand how incomes and wealth are distributed. They can be used to assess the distribution of a whole society-global inequality-as well as inequality of actors' referent networks-local inequality. How different is local inequality from global inequality? Formalizing the structure of reference groups as a network, the paper conducted a computational experiment to see how the structure of complex networks influences the difference between global and local inequality assessed by a selection of inequality measures. It was found that local inequality tends to be higher than global inequality when population size is large; network is dense and heterophilously assorted, and income distribution is less dispersed. The implications of the simulation findings are discussed.

Pharmacokinetic characterization of three novel 4-mg nicotine lozenges
.

PubMed

Sukhija, Manpreet; Srivastava, Reena; Kaushik, Aditya

2018-03-01

Nicotine replacement therapy (NRT) increases the probability of smoking cessation. This study was conducted to determine if three prototype 4-mg nicotine lozenges produced locally in India were bioequivalent to a globally marketed reference product, Nicorette® 4-mg nicotine lozenge. Healthy adult smokers (N = 39) were treated with three prototype 4-mg nicotine lozenges in comparison with a reference 4-mg lozenge in this single-center, randomized, open-label, single-dose, 4-way crossover study. Pharmacokinetic sampling was obtained to test for bioequivalence using maximal plasma concentration (Cmax) and extent of absorption (AUC0-t). Secondarily, AUC;0-∞, time to maximal plasma concentration (tmax), half-life (T1/2), elimination rate constant (Kel), and safety of the prototype lozenges versus the reference lozenge were compared. Each prototype 4-mg nicotine lozenge was found to be bioequivalent to the reference 4-mg nicotine lozenge based on the ratio of geometric means and 90% confidence intervals for Cmax, AUC0-t, and AUC;0-∞. Although tmax; was significantly longer for prototype III, all four lozenges achieved maximum plasma nicotine concentrations at a median of 1.5 hours. The safety profiles of the three prototype 4-mg lozenges did not differ from that of the 4-mg reference product. Each prototype 4-mg nicotine lozenge was bioequivalent to the reference 4-mg nicotine lozenge and was well tolerated. Furthermore, as these bioequivalent prototypes differed in in-vitro dissolution profiles, these data suggest that performance from the in -vitro method deployed is not a firm predictor of pharmacokinetic behavior.
.

MicroRNA Expression in Formalin-fixed Paraffin-embedded Cancer Tissue: Identifying Reference MicroRNAs and Variability.

PubMed

Boisen, Mogens Karsbøl; Dehlendorff, Christian; Linnemann, Dorte; Schultz, Nicolai Aagaard; Jensen, Benny Vittrup; Høgdall, Estrid Vilma Solyom; Johansen, Julia Sidenius

2015-12-29

Archival formalin-fixed paraffin-embedded (FFPE) cancer tissue samples are a readily available resource for microRNA (miRNA) biomarker identification. No established standard for reference miRNAs in FFPE tissue exists. We sought to identify stable reference miRNAs for normalization of miRNA expression in FFPE tissue samples from patients with colorectal (CRC) and pancreatic (PC) cancer and to quantify the variability associated with sample age and fixation. High-throughput miRNA profiling results from 203 CRC and 256 PC FFPE samples as well as from 37 paired frozen/FFPE samples from nine other CRC tumors (methodological samples) were used. Candidate reference miRNAs were identified by their correlation with global mean expression. The stability of reference genes was analyzed according to published methods. The association between sample age and global mean miRNA expression was tested using linear regression. Variability was described using correlation coefficients and linear mixed effects models. Normalization effects were determined by changes in standard deviation and by hierarchical clustering. We created lists of 20 miRNAs with the best correlation to global mean expression in each cancer type. Nine of these miRNAs were present in both lists, and miR-103a-3p was the most stable reference miRNA for both CRC and PC FFPE tissue. The optimal number of reference miRNAs was 4 in CRC and 10 in PC. Sample age had a significant effect on global miRNA expression in PC (50% reduction over 20 years) but not in CRC. Formalin fixation for 2-6 days decreased miRNA expression 30-65%. Normalization using global mean expression reduced variability for technical and biological replicates while normalization using the expression of the identified reference miRNAs reduced variability only for biological replicates. Normalization only had a minor impact on clustering results. We identified suitable reference miRNAs for future miRNA expression experiments using CRC- and PC FFPE tissue samples. Formalin fixation decreased miRNA expression considerably, while the effect of increasing sample age was estimated to be negligible in a clinical setting.

Validation of reference genes for RT-qPCR studies of gene expression in banana fruit under different experimental conditions.

PubMed

Chen, Lei; Zhong, Hai-ying; Kuang, Jian-fei; Li, Jian-guo; Lu, Wang-jin; Chen, Jian-ye

2011-08-01

Reverse transcription quantitative real-time PCR (RT-qPCR) is a sensitive technique for quantifying gene expression, but its success depends on the stability of the reference gene(s) used for data normalization. Only a few studies on validation of reference genes have been conducted in fruit trees and none in banana yet. In the present work, 20 candidate reference genes were selected, and their expression stability in 144 banana samples were evaluated and analyzed using two algorithms, geNorm and NormFinder. The samples consisted of eight sample sets collected under different experimental conditions, including various tissues, developmental stages, postharvest ripening, stresses (chilling, high temperature, and pathogen), and hormone treatments. Our results showed that different suitable reference gene(s) or combination of reference genes for normalization should be selected depending on the experimental conditions. The RPS2 and UBQ2 genes were validated as the most suitable reference genes across all tested samples. More importantly, our data further showed that the widely used reference genes, ACT and GAPDH, were not the most suitable reference genes in many banana sample sets. In addition, the expression of MaEBF1, a gene of interest that plays an important role in regulating fruit ripening, under different experimental conditions was used to further confirm the validated reference genes. Taken together, our results provide guidelines for reference gene(s) selection under different experimental conditions and a foundation for more accurate and widespread use of RT-qPCR in banana.

Towards generalised reference condition models for environmental assessment: a case study on rivers in Atlantic Canada.

PubMed

Armanini, D G; Monk, W A; Carter, L; Cote, D; Baird, D J

2013-08-01

Evaluation of the ecological status of river sites in Canada is supported by building models using the reference condition approach. However, geography, data scarcity and inter-operability constraints have frustrated attempts to monitor national-scale status and trends. This issue is particularly true in Atlantic Canada, where no ecological assessment system is currently available. Here, we present a reference condition model based on the River Invertebrate Prediction and Classification System approach with regional-scale applicability. To achieve this, we used biological monitoring data collected from wadeable streams across Atlantic Canada together with freely available, nationally consistent geographic information system (GIS) environmental data layers. For the first time, we demonstrated that it is possible to use data generated from different studies, even when collected using different sampling methods, to generate a robust predictive model. This model was successfully generated and tested using GIS-based rather than local habitat variables and showed improved performance when compared to a null model. In addition, ecological quality ratio data derived from the model responded to observed stressors in a test dataset. Implications for future large-scale implementation of river biomonitoring using a standardised approach with global application are presented.

National Survey of Adult and Pediatric Reference Intervals in Clinical Laboratories across Canada: A Report of the CSCC Working Group on Reference Interval Harmonization.

PubMed

Adeli, Khosrow; Higgins, Victoria; Seccombe, David; Collier, Christine P; Balion, Cynthia M; Cembrowski, George; Venner, Allison A; Shaw, Julie

2017-11-01

Reference intervals are widely used decision-making tools in laboratory medicine, serving as health-associated standards to interpret laboratory test results. Numerous studies have shown wide variation in reference intervals, even between laboratories using assays from the same manufacturer. Lack of consistency in either sample measurement or reference intervals across laboratories challenges the expectation of standardized patient care regardless of testing location. Here, we present data from a national survey conducted by the Canadian Society of Clinical Chemists (CSCC) Reference Interval Harmonization (hRI) Working Group that examines variation in laboratory reference sample measurements, as well as pediatric and adult reference intervals currently used in clinical practice across Canada. Data on reference intervals currently used by 37 laboratories were collected through a national survey to examine the variation in reference intervals for seven common laboratory tests. Additionally, 40 clinical laboratories participated in a baseline assessment by measuring six analytes in a reference sample. Of the seven analytes examined, alanine aminotransferase (ALT), alkaline phosphatase (ALP), and creatinine reference intervals were most variable. As expected, reference interval variation was more substantial in the pediatric population and varied between laboratories using the same instrumentation. Reference sample results differed between laboratories, particularly for ALT and free thyroxine (FT4). Reference interval variation was greater than test result variation for the majority of analytes. It is evident that there is a critical lack of harmonization in laboratory reference intervals, particularly for the pediatric population. Furthermore, the observed variation in reference intervals across instruments cannot be explained by the bias between the results obtained on instruments by different manufacturers. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

SU-E-P-10: Establishment of Local Diagnostic Reference Levels of Routine Exam in Computed Tomography

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

Yeh, M; Wang, Y; Weng, H

Introduction National diagnostic reference levels (NDRLs) can be used as a reference dose of radiological examination can provide radiation dose as the basis of patient dose optimization. Local diagnostic reference levels (LDRLs) by periodically view and check doses, more efficiency to improve the way of examination. Therefore, the important first step is establishing a diagnostic reference level. Computed Tomography in Taiwan had been built up the radiation dose limit value,in addition, many studies report shows that CT scan contributed most of the radiation dose in different medical. Therefore, this study was mainly to let everyone understand DRL’s international status. Formore » computed tomography in our hospital to establish diagnostic reference levels. Methods and Materials: There are two clinical CT scanners (a Toshiba Aquilion and a Siemens Sensation) were performed in this study. For CT examinations the basic recommended dosimetric quantity is the Computed Tomography Dose Index (CTDI). Each exam each different body part, we collect 10 patients at least. Carried out the routine examinations, and all exposure parameters have been collected and the corresponding CTDIv and DLP values have been determined. Results: The majority of patients (75%) were between 60–70 Kg of body weight. There are 25 examinations in this study. Table 1 shows the LDRL of each CT routine examination. Conclusions: Therefore, this study would like to let everyone know DRL’s international status, but also establishment of computed tomography of the local reference levels for our hospital, and providing radiation reference, as a basis for optimizing patient dose.« less

Comparison of the quality of patient referrals from physicians, physician assistants, and nurse practitioners.

PubMed

Lohr, Robert H; West, Colin P; Beliveau, Margaret; Daniels, Paul R; Nyman, Mark A; Mundell, William C; Schwenk, Nina M; Mandrekar, Jayawant N; Naessens, James M; Beckman, Thomas J

2013-11-01

To compare the quality of referrals of patients with complex medical problems from nurse practitioners (NPs), physician assistants (PAs), and physicians to general internists. We conducted a retrospective comparison study involving regional referrals to an academic medical center from January 1, 2009, through December 31, 2010. All 160 patients referred by NPs and PAs combined and a random sample of 160 patients referred by physicians were studied. Five experienced physicians blinded to the source of referral used a 7-item instrument to assess the quality of referrals. Internal consistency, interrater reliability, and dimensionality of item scores were determined. Differences between item scores for patients referred by physicians and those for patients referred by NPs and PAs combined were analyzed by using multivariate ordinal logistical regression adjusted for patient age, sex, distance of the referral source from Mayo Clinic, and Charlson Index. Factor analysis revealed a 1-dimensional measure of the quality of patient referrals. Interrater reliability (intraclass correlation coefficient for individual items: range, 0.77-0.93; overall, 0.92) and internal consistency for items combined (Cronbach α=0.75) were excellent. Referrals from physicians were scored higher (percentage of agree/strongly agree responses) than were referrals from NPs and PAs for each of the following items: referral question clearly articulated (86.3% vs 76.0%; P=.0007), clinical information provided (72.6% vs 54.1%; P=.003), documented understanding of the patient's pathophysiology (51.0% vs 30.3%; P<.0001), appropriate evaluation performed locally (60.3% vs 39.0%; P<.0001), appropriate management performed locally (53.5% vs 24.1%; P<.0001), and confidence returning patient to referring health care professional (67.8% vs 41.4%; P<.0001). Referrals from physicians were also less likely to be evaluated as having been unnecessary (30.1% vs 56.2%; P<.0001). The quality of referrals to an academic medical center was higher for physicians than for NPs and PAs regarding the clarity of the referral question, understanding of pathophysiology, and adequate prereferral evaluation and documentation. Copyright © 2013 Mayo Foundation for Medical Education and Research. Published by Elsevier Inc. All rights reserved.

Fixation, description and DNA barcode of a neotype for Botryllus schlosseri (Pallas, 1766) (Tunicata, Ascidiacea).

PubMed

Brunetti, Riccardo; Manni, Lucia; Mastrototaro, Francesco; Gissi, Carmela; Gasparini, Fabio

2017-11-22

Botryllus schlosseri is a widespread colonial ascidian commonly considered cosmopolitan and amply used as model for researches ranging from developmental biology to immunobiology. Recently, molecular data lead to hypothesize that the species named B. schlosseri may consist of more than a single taxon. Indeed, five highly divergent clades, named A-E, have been genetically identified and are referred as cryptic species. In this context, and lacking both a type and a detailed morphological description, we believe that it is necessary, as a taxonomic reference point, to designate a neotype and re-describe the species. Therefore, a sample from the Lagoon of Venice (Adriatic Sea, Italy) was deposited as neotype in the Natural History Museum of Venice (Italy), preserved both in formalin and in 90% ethanol. Here we provide a morphological description of the suggested neotype of B. schlosseri that takes into account several developmental stages (oozooid, zooid of first blastogenic generations, and mature zooid) and is carefully compared with the previous descriptions of samples coming from other European and non-European localities. Finally, we associate our morphological description to a "DNA barcode", consisting in a long fragment of the mitochondrial COI gene. Our description is associated to clade A, although at now we cannot guarantee that this association is univocal.

Managing a cluster outbreak of psittacosis in Belgium linked to a pet shop visit in The Netherlands.

PubMed

DE Boeck, C; Dehollogne, C; Dumont, A; Spierenburg, M; Heijne, M; Gyssens, I; VAN DER Hilst, J; Vanrompay, D

2016-06-01

In July 2013, a Belgian couple were admitted to hospital because of pneumonia. Medical history revealed contact with birds. Eleven days earlier, they had purchased a lovebird in a pet shop in The Netherlands. The bird became ill, with respiratory symptoms. The couple's daughter who accompanied them to the pet shop, reported similar symptoms, but was travelling abroad. On the suspicion of psittacosis, pharyngeal swabs from the couple were taken and sent to the Belgian reference laboratory for psittacosis. Culture and nested polymerase chain reaction (PCR) tests were positive for the presence of Chlamydia psittaci, and ompA genotyping indicated genotype A in both patients. The patients were treated with doxycycline and the daughter started quinolone therapy; all three recovered promptly. Psittacosis is a notifiable disease in Belgium and therefore local healthcare authorities were informed. They contacted their Dutch colleagues, who visited the pet shop. Seven pooled faecal samples were taken and analysed using PCR by the Dutch national reference laboratory for notifiable animal diseases for the presence of Chlamydia psittaci. Four (57%) samples tested positive, genotyping revealed genotype A. Enquiring about exposure to pet birds is essential when patients present with pneumonia. Reporting to health authorities, even across borders, is warranted to prevent further spread.

Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations

PubMed Central

Fogolari, Federico; Corazza, Alessandra; Fortuna, Sara; Soler, Miguel Angel; VanSchouwen, Bryan; Brancolini, Giorgia; Corni, Stefano; Melacini, Giuseppe; Esposito, Gennaro

2015-01-01

Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements;the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state;backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy);the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic. PMID:26177039

Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations.

PubMed

Fogolari, Federico; Corazza, Alessandra; Fortuna, Sara; Soler, Miguel Angel; VanSchouwen, Bryan; Brancolini, Giorgia; Corni, Stefano; Melacini, Giuseppe; Esposito, Gennaro

2015-01-01

Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements;the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state;backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy);the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic.

Biomonitoring of urinary metals in a population living in the vicinity of industrial sources: a comparison with the general population of Andalusia, Spain.

PubMed

Aguilera, Inmaculada; Daponte, Antonio; Gil, Fernando; Hernández, Antonio F; Godoy, Patricia; Pla, Antonio; Ramos, Juan Luis

2008-12-15

The Ria of Huelva (south-west Spain) is one of the most polluted fluvial-estuarine systems in the world. Industrial activity delivers huge amounts of pollutants to the local environment, particularly heavy metals and arsenic. Here we aimed to determine urinary levels of As, Cd, Cr, Cu and Ni in a representative sample (n=857) of adults living in the Ria of Huelva. Levels were compared to those from a representative sample of 861 adults of the general urban population of Andalusia (southern Spain) and multiple regression models were developed to identify individual factors associated with urinary levels of these elements. Arsenic levels were significantly higher in the Ria of Huelva as compared to other Andalusian cities, whereas Cd and Ni levels were significantly lower. Despite these differences, levels in both groups were similar to the reference values reported in previous studies for general population. Age, gender, diet and lifestyle were the major factors contributing to the interindividual variation in urinary metals. In conclusion, despite living in a highly polluted area, the population of the Ria of Huelva failed to show higher urinary levels of the studied metals as compared to a reference urban population of the same region.

[Saarland Growth Study: sampling design].

PubMed

Danker-Hopfe, H; Zabransky, S

2000-01-01

The use of reference data to evaluate the physical development of children and adolescents is part of the daily routine in the paediatric ambulance. The construction of such reference data is based on the collection of extensive reference data. There are different kinds of reference data: cross sectional references, which are based on data collected from a big representative cross-sectional sample of the population, longitudinal references, which are based on follow-up surveys of usually smaller samples of individuals from birth to maturity, and mixed longitudinal references, which are a combination of longitudinal and cross-sectional reference data. The advantages and disadvantages of the different methods of data collection and the resulting reference data are discussed. The Saarland Growth Study was conducted for several reasons: growth processes are subject to secular changes, there are no specific reference data for children and adolescents from this part of the country and the growth charts in use in the paediatric praxis are possibly not appropriate any more. Therefore, the Saarland Growth Study served two purposes a) to create actual regional reference data and b) to create a database for future studies on secular trends in growth processes of children and adolescents from Saarland. The present contribution focusses on general remarks on the sampling design of (cross-sectional) growth surveys and its inferences for the design of the present study.

An Application of the A* Search to Trajectory Optimization

DTIC Science & Technology

1990-05-11

linearized model of orbital motion called the Clohessy - Wiltshire Equations and a node search technique called A*. The planner discussed in this thesis starts...states while transfer time is left unspecified. 13 Chapter 2. Background HILL’S ( CLOHESSY - WILTSHIRE ) EQUATIONS The Euler-Hill equations describe... Clohessy - Wiltshire equations. The coordinate system used in this thesis is commonly referred to as Local Vertical, Local Horizontal or LVLH reference frame

Creating an open access cal/val repository via the LACO-Wiki online validation platform

NASA Astrophysics Data System (ADS)

Perger, Christoph; See, Linda; Dresel, Christopher; Weichselbaum, Juergen; Fritz, Steffen

2017-04-01

There is a major gap in the amount of in-situ data available on land cover and land use, either as field-based ground truth information or from image interpretation, both of which are used for the calibration and validation (cal/val) of products derived from Earth Observation. Although map producers generally publish their confusion matrices and the accuracy measures associated with their land cover and land use products, the cal/val data (also referred to as reference data) are rarely shared in an open manner. Although there have been efforts in compiling existing reference datasets and making them openly available, e.g. through the GOFC/GOLD (Global Observation for Forest Cover and Land Dynamics) portal or the European Commission's Copernicus Reference Data Access (CORDA), this represents a tiny fraction of the reference data collected and stored locally around the world. Moreover, the validation of land cover and land use maps is usually undertaken with tools and procedures specific to a particular institute or organization due to the lack of standardized validation procedures; thus, there are currently no incentives to share the reference data more broadly with the land cover and land use community. In an effort to provide a set of standardized, online validation tools and to build an open repository of cal/val data, the LACO-Wiki online validation portal has been developed, which will be presented in this paper. The portal contains transparent, documented and reproducible validation procedures that can be applied to local as well as global products. LACO-Wiki was developed through a user consultation process that resulted in a 4-step wizard-based workflow, which supports the user from uploading the map product for validation, through to the sampling process and the validation of these samples, until the results are processed and a final report is created that includes a range of commonly reported accuracy measures. One of the design goals of LACO-Wiki has been to simplify the workflows as much as possible so that the tool can be used both professionally and in an educational or non-expert context. By using the tool for validation, the user agrees to share their validation samples and therefore contribute to an open access cal/val repository. Interest in the use of LACO-Wiki for validation of national land cover or related products has already been expressed, e.g. by national stakeholders under the umbrella of the European Environment Agency (EEA), and for global products by GOFC/GOLD and the Group on Earth Observation (GEO). Thus, LACO-Wiki has the potential to become the focal point around which an international land cover validation community could be built, and could significantly advance the state-of-the-art in land cover cal/val, particularly given recent developments in opening up of the Landsat archive and the open availability of Sentinel imagery. The platform will also offer open access to crowdsourced in-situ data, for example, from the recently developed LACO-Wiki mobile smartphone app, which can be used to collect additional validation information in the field, as well as to validation data collected via its partner platform, Geo-Wiki, where an already established community of citizen scientists collect land cover and land use data for different research applications.

Method and Apparatus for Measuring Near-Angle Scattering of Mirror Coatings

NASA Technical Reports Server (NTRS)

Chipman, Russell A. (Inventor); Daugherty, Brian J. (Inventor); McClain, Stephen C. (Inventor); Macenka, Steven A. (Inventor)

2013-01-01

Disclosed herein is a method of determining the near angle scattering of a sample reflective surface comprising the steps of: a) splitting a beam of light having a coherence length of greater than or equal to about 2 meters into a sample beam and a reference beam; b) frequency shifting both the sample beam and the reference beam to produce a fixed beat frequency between the sample beam and the reference beam; c) directing the sample beam through a focusing lens and onto the sample reflective surface, d) reflecting the sample beam from the sample reflective surface through a detection restriction disposed on a movable stage; e) recombining the sample beam with the reference beam to form a recombined beam, followed by f) directing the recombined beam to a detector and performing heterodyne analysis on the recombined beam to measure the near-angle scattering of the sample reflective surface, wherein the position of the detection restriction relative to the sample beam is varied to occlude at least a portion of the sample beam to measure the near-angle scattering of the sample reflective surface. An apparatus according to the above method is also disclosed.

Controls on water vapor isotopes over Roorkee, India: Impact of convective activities and depression systems

NASA Astrophysics Data System (ADS)

Saranya, P.; Krishan, Gopal; Rao, M. S.; Kumar, Sudhir; Kumar, Bhishm

2018-02-01

The study evaluates the water vapor isotopic compositions and its controls with special reference to Indian Summer Monsoon (ISM) season at Roorkee, India. Precipitation is usually a discrete event spatially and temporally in this part of the country, therefore, the information provided is limited, while, the vapors have all time availability and have a significant contribution in the hydrological cycle locally or over a regional scale. Hence for understanding the processes altering the various sources, its isotopic signatures were studied. The Isotope Water Vapour Line (Iso Val) was drawn together with the Global Meteoric Water Line (GMWL) and the best fit line was δD = 5.42 * δ18O + 27.86. The precipitation samples were also collected during the study period and were best fitted with δD = 8.20(±0.18) * δ18O + 9.04(±1.16) in the Local Meteoric Water Line (LMWL). From the back trajectory analysis of respective vapor samples, it is unambiguous that three major sources viz; local vapor, western disturbance and monsoon vapor are controlling the fate of moisture over Roorkee. The d-excess in ground-level vapor (GLV) reveals the supply of recycled moisture from continental water bodies and evapo-transpiration as additional moisture sources to the study area. The intensive depletion in isotopic ratios was associated with the large-scale convective activity and low-pressure/cyclonic/depression systems formed over Bay of Bengal.

Characterization of etch pits found on a large-grain bulk niobium superconducting radio-frequency resonant cavity

DOE PAGES

Zhao, Xin; Ciovati, G.; Bieler, T. R.

2010-12-15

The performance of superconducting radio-frequency (SRF) resonant cavities made of bulk niobium is limited by nonlinear localized effects. Surface analysis of regions of higher power dissipation is thus of intense interest. Such areas (referred to as “hotspots”) were identified in a large-grain single-cell cavity that had been buffered-chemical polished and dissected for examination by high resolution electron microscopy, electron backscattered diffraction microscopy (EBSD), and optical microscopy. Pits with clearly discernible crystal facets were observed in both “hotspot” and “coldspot” specimens. The pits were found in-grain, at bicrystal boundaries, and on tricrystal junctions. They are interpreted as etch pits induced bymore » crystal defects (e.g. dislocations). All coldspots examined had a qualitatively lower density of etch pits or relatively smooth tricrystal boundary junctions. EBSD mapping revealed the crystal orientation surrounding the pits. Locations with high pit density are correlated with higher mean values of the local average misorientation angle distributions, indicating a higher geometrically necessary dislocation content. In addition, a survey of the samples by energy dispersive x-ray analysis did not show any significant contamination of the samples’ surface. In conclusion, the local magnetic field enhancement produced by the sharp-edge features observed on the samples is not sufficient to explain the observed degradation of the cavity quality factor, which starts at peak surface magnetic field as low as 20 mT.« less

Local sensitivity of per-recruit fishing mortality reference points.

PubMed

Cadigan, N G; Wang, S

2016-12-01

We study the sensitivity of fishery management per-recruit harvest rates which may be part of a quantitative harvest strategy designed to achieve some objective for catch or population size. We use a local influence sensitivity analysis to derive equations that describe how these reference harvest rates are affected by perturbations to productivity processes. These equations give a basic theoretical understanding of sensitivity that can be used to predict what the likely impacts of future changes in productivity will be. Our results indicate that per-recruit reference harvest rates are more sensitive to perturbations when the equilibrium catch or population size per recruit, as functions of the harvest rate, have less curvature near the reference point. Overall our results suggest that per recruit reference points will, with some exceptions, usually increase if (1) growth rates increase, (2) natural mortality rates increase, or (3) fishery selectivity increases to an older age.

Evaluation of Skin Surface as an Alternative Source of Reference DNA Samples: A Pilot Study.

PubMed

Albujja, Mohammed H; Bin Dukhyil, Abdul Aziz; Chaudhary, Abdul Rauf; Kassab, Ahmed Ch; Refaat, Ahmed M; Babu, Saranya Ramesh; Okla, Mohammad K; Kumar, Sachil

2018-01-01

An acceptable area for collecting DNA reference sample is a part of the forensic DNA analysis development. The aim of this study was to evaluate skin surface cells (SSC) as an alternate source of reference DNA sample. From each volunteer (n = 10), six samples from skin surface areas (forearm and fingertips) and two traditional samples (blood and buccal cells) were collected. Genomic DNA was extracted and quantified then genotyped using standard techniques. The highest DNA concentration of SSC samples was collected using the tape/forearm method of collection (2.1 ng/μL). Cotton swabs moistened with ethanol yielded higher quantities of DNA than swabs moistened with salicylic acid, and it gave the highest percentage of full STR profiles (97%). This study supports the use of SSC as a noninvasive sampling technique and as a extremely useful source of DNA reference samples among certain cultures where the use of buccal swabs can be considered socially unacceptable. © 2017 American Academy of Forensic Sciences.

26 CFR 1.164-4 - Taxes for local benefits.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 26 Internal Revenue 2 2013-04-01 2013-04-01 false Taxes for local benefits. 1.164-4 Section 1.164... local benefits. (a) So-called taxes for local benefits referred to in paragraph (g) of § 1.164-2, more properly assessments, paid for local benefits such as street, sidewalk, and other like improvements...

Characterization of the spatial variability of soil available zinc at various sampling densities using grouped soil type information.

PubMed

Song, Xiao-Dong; Zhang, Gan-Lin; Liu, Feng; Li, De-Cheng; Zhao, Yu-Guo

2016-11-01

The influence of anthropogenic activities and natural processes involved high uncertainties to the spatial variation modeling of soil available zinc (AZn) in plain river network regions. Four datasets with different sampling densities were split over the Qiaocheng district of Bozhou City, China. The difference of AZn concentrations regarding soil types was analyzed by the principal component analysis (PCA). Since the stationarity was not indicated and effective ranges of four datasets were larger than the sampling extent (about 400 m), two investigation tools, namely F3 test and stationarity index (SI), were employed to test the local non-stationarity. Geographically weighted regression (GWR) technique was performed to describe the spatial heterogeneity of AZn concentrations under the non-stationarity assumption. GWR based on grouped soil type information (GWRG for short) was proposed so as to benefit the local modeling of soil AZn within each soil-landscape unit. For reference, the multiple linear regression (MLR) model, a global regression technique, was also employed and incorporated the same predictors as in the GWR models. Validation results based on 100 times realization demonstrated that GWRG outperformed MLR and can produce similar or better accuracy than the GWR approach. Nevertheless, GWRG can generate better soil maps than GWR for limit soil data. Two-sample t test of produced soil maps also confirmed significantly different means. Variogram analysis of the model residuals exhibited weak spatial correlation, rejecting the use of hybrid kriging techniques. As a heuristically statistical method, the GWRG was beneficial in this study and potentially for other soil properties.

Respiratory effects in people exposed to arsenic via the drinking water and tobacco smoking in southern part of Pakistan.

PubMed

Arain, Muhammad Balal; Kazi, Tasneem Gul; Baig, Jameel Ahmed; Jamali, Muhammad Khan; Afridi, Hassan Imran; Jalbani, Nusrat; Sarfraz, Raja Adil; Shah, Abdul Qadir; Kandhro, Ghulam Abbas

2009-10-15

In this study, a survey has been conducted during 2005-2007 on surface and groundwater arsenic (As) contamination and its impact on the health of local population, of villages located on the banks of Manchar lake, southern part of Sindh, Pakistan. We have also assessed the relationship between arsenic exposure through respiratory disorders in male subjects with drinking water and smoking cigarettes made from tobacco grown in agricultural land irrigated with As contaminated lake water. The biological samples (blood and scalp hair) were collected from As exposed subjects (100% smokers) and age matched healthy male subjects (40.2% smoker and 59.8% non smokers) belong to unexposed areas for comparison purposes. The As concentration in drinking water (surface and underground water), agricultural soil, cigarette tobacco and biological samples were determined by electrothermal atomic absorption spectrometry. The range of As concentrations in lake water was 35.2-158 microg/L (average 97.5 microg/L), which is 3-15 folds higher than permissible limit of World Health Organization (WHO, 2004). While the As level in local cigarette tobacco was found to be 3-6 folds higher than branded cigarettes (0.37-0.79 microg/g). Arsenic exposed subjects (with and without RD) had significantly elevated levels of As in their biological samples as compared to referent male subject of unexposed area. These respiratory effects were more pronounced in individuals who had also As induced skin lesions. The linear regressions showed good correlations between As concentrations in water versus hair and blood samples of exposed subjects with and without respiratory problems.

Imaging whole mouse brains with a dual resolution serial swept-source optical coherence tomography scanner

NASA Astrophysics Data System (ADS)

Lefebvre, Joël.; Castonguay, Alexandre; Lesage, Frédéric

2018-02-01

High resolution imaging of whole rodent brains using serial OCT scanners is a promising method to investigate microstructural changes in tissue related to the evolution of neuropathologies. Although micron to sub-micron sampling resolution can be obtained by using high numerical aperture objectives and dynamic focusing, such an imaging system is not adapted to whole brain imaging. This is due to the large amount of data it generates and the significant computational resources required for reconstructing such volumes. To address this limitation, a dual resolution serial OCT scanner was developed. The optical setup consists in a swept-source OCT made of two sample and reference arms, each arm being coupled with different microscope objectives (3X / 40X). Motorized flip mirrors were used to switch between each OCT arm, thus allowing low and high resolution acquisitions within the same sample. The low resolution OCT volumes acquired with the 3X arm were stitched together, providing a 3D map of the whole mouse brain. This brain can be registered to an OCT brain template to enable neurological structures localization. The high resolution volumes acquired with the 40X arm were also stitched together to create local high resolution 3D maps of the tissue microstructure. The 40X data can be acquired at any arbitrary location in the sample, thus limiting storage-heavy high resolution data to application restricted to specific regions of interest. By providing dual-resolution OCT data, this setup can be used to validate diffusion MRI with tissue microstructure derived metrics measured at any location in ex vivo brains.

Chroma Shift and Gamut Shape: Going Beyond Average Color Fidelity and Gamut Area

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

Royer, Michael P.; Houser, Kevin W.; David, Aurélien

Though sometimes referred to as a two-measure system for evaluating color rendition, IES TM-30-15 includes other key components that go beyond the high-level average values IES Rf and IES Rg. This article focuses on the Color Vector Graphic and Local Chroma Shift (IES Rcs,hj), discussing the calculation methods for these evaluation tools and providing context for the interpretation of the values. It also presents alternatives for quantifying the same characteristics, which can inform the development of future measures. The Color Vector Graphic (CVG) is a visual representation of hue and chroma shifts across different hues. It quickly communicates complex informationmore » about how object colors will be rendered by a light source, although it is difficult or impossible to use for writing a specification. CVGs demonstrate that increases in chroma for certain hues sometimes means a decrease in chroma for other hues, and illustrates hue shifts for intermediate colors. The combination of shifts over different hues can be referred to as gamut shape. Complementing this information are the IES Rcs,hj values, which quantify the average relative chroma shift for samples in each of the 16 hue-angle bins (j) specified in IES TM-30-15. Unlike measures of average color fidelity and gamut area, gamut shape and hue-specific chroma shift are new concepts with no directly-comparable historical references. It will be critical to incorporate the Color Vector Graphic and Local Chroma Shift values into practice because they capture information about color rendition that is impossible to describe with average measures (such as CIE Ra, IES Rf, or IES Rg), but that is critical to understanding human evaluations of color quality in architectural environments.« less

Travel time tomography with local image regularization by sparsity constrained dictionary learning

NASA Astrophysics Data System (ADS)

Bianco, M.; Gerstoft, P.

2017-12-01

We propose a regularization approach for 2D seismic travel time tomography which models small rectangular groups of slowness pixels, within an overall or `global' slowness image, as sparse linear combinations of atoms from a dictionary. The groups of slowness pixels are referred to as patches and a dictionary corresponds to a collection of functions or `atoms' describing the slowness in each patch. These functions could for example be wavelets.The patch regularization is incorporated into the global slowness image. The global image models the broad features, while the local patch images incorporate prior information from the dictionary. Further, high resolution slowness within patches is permitted if the travel times from the global estimates support it. The proposed approach is formulated as an algorithm, which is repeated until convergence is achieved: 1) From travel times, find the global slowness image with a minimum energy constraint on the pixel variance relative to a reference. 2) Find the patch level solutions to fit the global estimate as a sparse linear combination of dictionary atoms.3) Update the reference as the weighted average of the patch level solutions.This approach relies on the redundancy of the patches in the seismic image. Redundancy means that the patches are repetitions of a finite number of patterns, which are described by the dictionary atoms. Redundancy in the earth's structure was demonstrated in previous works in seismics where dictionaries of wavelet functions regularized inversion. We further exploit redundancy of the patches by using dictionary learning algorithms, a form of unsupervised machine learning, to estimate optimal dictionaries from the data in parallel with the inversion. We demonstrate our approach on densely, but irregularly sampled synthetic seismic images.

A universal reference sample derived from clone vector for improved detection of differential gene expression

PubMed Central

Khan, Rishi L; Gonye, Gregory E; Gao, Guang; Schwaber, James S

2006-01-01

Background Using microarrays by co-hybridizing two samples labeled with different dyes enables differential gene expression measurements and comparisons across slides while controlling for within-slide variability. Typically one dye produces weaker signal intensities than the other often causing signals to be undetectable. In addition, undetectable spots represent a large problem for two-color microarray designs and most arrays contain at least 40% undetectable spots even when labeled with reference samples such as Stratagene's Universal Reference RNAs™. Results We introduce a novel universal reference sample that produces strong signal for all spots on the array, increasing the average fraction of detectable spots to 97%. Maximizing detectable spots on the reference image channel also decreases the variability of microarray data allowing for reliable detection of smaller differential gene expression changes. The reference sample is derived from sequence contained in the parental EST clone vector pT7T3D-Pac and is called vector RNA (vRNA). We show that vRNA can also be used for quality control of microarray printing and PCR product quality, detection of hybridization anomalies, and simplification of spot finding and segmentation tasks. This reference sample can be made inexpensively in large quantities as a renewable resource that is consistent across experiments. Conclusion Results of this study show that vRNA provides a useful universal reference that yields high signal for almost all spots on a microarray, reduces variation and allows for comparisons between experiments and laboratories. Further, it can be used for quality control of microarray printing and PCR product quality, detection of hybridization anomalies, and simplification of spot finding and segmentation tasks. This type of reference allows for detection of small changes in differential expression while reference designs in general allow for large-scale multivariate experimental designs. vRNA in combination with reference designs enable systems biology microarray experiments of small physiologically relevant changes. PMID:16677381

Comparison of soil pollution concentrations determined using AAS and portable XRF techniques.

PubMed

Radu, Tanja; Diamond, Dermot

2009-11-15

Past mining activities in the area of Silvermines, Ireland, have resulted in heavily polluted soils. The possibility of spreading pollution to the surrounding areas through dust blow-offs poses a potential threat for the local communities. Conventional environmental soil and dust analysis techniques are very slow and laborious and consequently there is a need for fast and accurate analytical methods, which can provide real-time in situ pollution mapping. Laboratory-based aqua regia acid digestion of the soil samples collected in the area followed by the atomic absorption spectrophotometry (AAS) analysis confirmed very high pollution, especially by Pb, As, Cu, and Zn. In parallel, samples were analyzed using portable X-ray fluorescence radioisotope and miniature tube powered (XRF) NITON instruments and their performance was compared. Overall, the portable XRF instrument gave excellent correlation with the laboratory-based reference AAS method.

An outbreak of locally acquired Plasmodium vivax malaria among migrant workers in Oman

PubMed Central

Simon, Bruno; Sow, Fatimata; Al Mukhaini, Said K.; Al-Abri, Seif; Ali, Osama A.M.; Bonnot, Guillaume; Bienvenu, Anne-Lise; Petersen, Eskild; Picot, Stéphane

2017-01-01

Plasmodium vivax is the most widely distributed human malaria parasite. Outside sub-Saharan Africa, the proportion of P. vivax malaria is rising. A major cause for concern is the re-emergence of Plasmodium vivax in malaria-free areas. Oman, situated in the south-eastern corner of the Arabian Peninsula, has long been an area of vivax malaria transmission but no locally acquired cases were reported in 2004. However, local transmission has been registered in small outbreaks since 2007. In this study, a local outbreak of 54 cases over 50 days in 2014 was analyzed retrospectively and stained blood slides have been obtained for parasite identification and genotyping. The aim of this study was to identify the geographical origin of these cases, in an attempt to differentiate between imported cases and local transmission. Using circumsporozoite protein (csp), merozoite surface protein 1 (msp1), and merozoite surface protein 3 (msp3) markers for genotyping of parasite DNA obtained by scrapping off the surface of smears, genetic diversity and phylogenetic analysis were performed. The study found that the samples had very low genetic diversity, a temperate genotype, and a high genetic distance, with most of the reference strains coming from endemic countries. We conclude that a small outbreak of imported malaria is not associated with re-emergence of malaria transmission in Oman, as no new cases have been seen since the outbreak ended. PMID:28695821

Assessment of existing local houses condition as analysis tools for shore housing improvement program in Weriagar district, Bintuni Bay

NASA Astrophysics Data System (ADS)

Firmansyah, F.; Fernando, A.; Allo, I. P. R.

2018-01-01

The housing assessment is a part of the pre-feasibility study inThe Shore Housing Improvement Program in Weriagar District, West Papua. The housing assessment was conducted to identify the physical condition of existing houses. The parameters of assessment formulated from local references, practices and also national building regulation that covers each building system components, such as building structure/frame, building floor, building cover, and building roof. This study aims to explains lessons from local practices and references, used as the formula to generate assessment parameter, elaborate with Indonesia building regulation. The result of housing assessment were used as a basis to develop the house improvement strategy, the design alternative for housing improvement and further planning recommendations. The local knowledges involved in housing improvement program expected that the local-based approach could respect to the local build culture, respect the local environment, and the most important can offer best suitable solutions for functional utility and livability.

New craniodental fossils of papionin monkeys from Cooper's D, South Africa.

PubMed

Folinsbee, Kaila E; Reisz, Robert R

2013-08-01

Papionin monkey fossils are common in the Plio-Pleistocene aged karst cave deposits northwest of Johannesburg in South Africa. These deposits have yielded important primate and other vertebrate fauna since their discovery in the early part of the 20th century. In this article, we describe new primate cranial and dental specimens from excavations at the site of Cooper's D in the Sterkfontein Valley that date to around 1.5 million years ago. Unlike other localities in southern Africa, most of the new fossils are referred to Theropithecus oswaldi oswaldi, an extinct gramnivorous monkey related to the living gelada. Diagnostic features of T. o. oswaldi crania and teeth include large, thickly enameled molars with tall, columnar cusps, and high molar relief, an upright mandibular ramus, postorbital constriction, and anterior fusion of temporal lines. Also present in the new sample are teeth referred to Papio sp., which show low crowned bunodont molars, and a number of indeterminate papionin teeth and skull fragments. The presence of T. o. oswaldi at Cooper's D extends the list of known localities where the taxon is found, and may indicate the presence of an open, grassland environment in the area during the early Pleistocene. The abundance of theropith fossils at Cooper's suggests that Papio was not consistently the most common papionin in southern Africa over the past three million years. Copyright © 2013 Wiley Periodicals, Inc.

PROPOSALS FOR THE ESTABLISHMENT OF NATIONAL DIAGNOSTIC REFERENCE LEVELS FOR RADIOGRAPHY FOR ADULT PATIENTS BASED ON REGIONAL DOSE SURVEYS IN RUSSIAN FEDERATION.

PubMed

Vodovatov, A V; Balonov, M I; Golikov, V Yu; Shatsky, I G; Chipiga, L A; Bernhardsson, C

2017-04-01

In 2009-2014, dose surveys aimed to collect adult patient data and parameters of most common radiographic examinations were performed in six Russian regions. Typical patient doses were estimated for the selected examinations both in entrance surface dose and in effective dose. 75%-percentiles of typical patient effective dose distributions were proposed as preliminary regional diagnostic reference levels (DRLs) for radiography. Differences between the 75%-percentiles of regional typical patient dose distributions did not exceed 30-50% for the examinations with standardized clinical protocols (skull, chest and thoracic spine) and a factor of 1.5 for other examinations. Two different approaches for establishing national DRLs were evaluated: as a 75%-percentile of a pooled regional sample of patient typical doses (pooled method) and as a median of 75%-percentiles of regional typical patient dose distributions (median method). Differences between pooled and median methods for effective dose did not exceed 20%. It was proposed to establish Russian national DRLs in effective dose using a pooled method. In addition, the local authorities were granted an opportunity to establish regional DRLs if the local radiological practice and typical patient dose distributions are significantly different. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A mixture model with a reference-based automatic selection of components for disease classification from protein and/or gene expression levels

PubMed Central

2011-01-01

Background Bioinformatics data analysis is often using linear mixture model representing samples as additive mixture of components. Properly constrained blind matrix factorization methods extract those components using mixture samples only. However, automatic selection of extracted components to be retained for classification analysis remains an open issue. Results The method proposed here is applied to well-studied protein and genomic datasets of ovarian, prostate and colon cancers to extract components for disease prediction. It achieves average sensitivities of: 96.2 (sd = 2.7%), 97.6% (sd = 2.8%) and 90.8% (sd = 5.5%) and average specificities of: 93.6% (sd = 4.1%), 99% (sd = 2.2%) and 79.4% (sd = 9.8%) in 100 independent two-fold cross-validations. Conclusions We propose an additive mixture model of a sample for feature extraction using, in principle, sparseness constrained factorization on a sample-by-sample basis. As opposed to that, existing methods factorize complete dataset simultaneously. The sample model is composed of a reference sample representing control and/or case (disease) groups and a test sample. Each sample is decomposed into two or more components that are selected automatically (without using label information) as control specific, case specific and not differentially expressed (neutral). The number of components is determined by cross-validation. Automatic assignment of features (m/z ratios or genes) to particular component is based on thresholds estimated from each sample directly. Due to the locality of decomposition, the strength of the expression of each feature across the samples can vary. Yet, they will still be allocated to the related disease and/or control specific component. Since label information is not used in the selection process, case and control specific components can be used for classification. That is not the case with standard factorization methods. Moreover, the component selected by proposed method as disease specific can be interpreted as a sub-mode and retained for further analysis to identify potential biomarkers. As opposed to standard matrix factorization methods this can be achieved on a sample (experiment)-by-sample basis. Postulating one or more components with indifferent features enables their removal from disease and control specific components on a sample-by-sample basis. This yields selected components with reduced complexity and generally, it increases prediction accuracy. PMID:22208882

Usefulness of molecular markers in the diagnosis of occupational and recreational histoplasmosis outbreaks.

PubMed

Frías-De-León, María Guadalupe; Ramírez-Bárcenas, José Antonio; Rodríguez-Arellanes, Gabriela; Velasco-Castrejón, Oscar; Taylor, Maria Lucia; Reyes-Montes, María Del Rocío

2017-03-01

Histoplasmosis is considered the most important systemic mycosis in Mexico, and its diagnosis requires fast and reliable methodologies. The present study evaluated the usefulness of PCR using Hcp100 and 1281-1283 (220) molecular markers in detecting Histoplasma capsulatum in occupational and recreational outbreaks. Seven clinical serum samples of infected individuals from three different histoplasmosis outbreaks were processed by enzyme-linked immunosorbent assay (ELISA) to titre anti-H. capsulatum antibodies and to extract DNA. Fourteen environmental samples were also processed for H. capsulatum isolation and DNA extraction. Both clinical and environmental DNA samples were analysed by PCR with Hcp100 and 1281-1283 (220) markers. Antibodies to H. capsulatum were detected by ELISA in all serum samples using specific antigens, and in six of these samples, the PCR products of both molecular markers were amplified. Four environmental samples amplified one of the two markers, but only one sample amplified both markers and an isolate of H. capsulatum was cultured from this sample. All PCR products were sequenced, and the sequences for each marker were analysed using the Basic Local Alignment Search Tool (BLASTn), which revealed 95-98 and 98-100 % similarities with the reference sequences deposited in the GenBank for Hcp100 and 1281-1283 (220) , respectively. Both molecular markers proved to be useful in studying histoplasmosis outbreaks because they are matched for pathogen detection in either clinical or environmental samples.

A Catalog of Visually Classified Galaxies in the Local (z ∼ 0.01) Universe

NASA Astrophysics Data System (ADS)

Ann, H. B.; Seo, Mira; Ha, D. K.

2015-04-01

The morphological types of 5836 galaxies were classified by a visual inspection of color images using the Sloan Digital Sky Survey Data Release 7 to produce a morphology catalog of a representative sample of local galaxies with z\\lt 0.01. The sample galaxies are almost complete for galaxies brighter than {{r}pet}=17.77. Our classification system is basically the same as that of the Third Reference Catalog of Bright Galaxies with some simplifications for giant galaxies. On the other hand, we distinguish the fine features of dwarf elliptical (dE)-like galaxies to classify five subtypes: dE, blue-cored dwarf ellipticals, dwarf spheroidals (dSph), blue dwarf ellipticals (dEblue), and dwarf lenticulars (dS0). In addition, we note the presence of nucleation in dE, dSph, and dS0. Elliptical galaxies and lenticular galaxies contribute only ∼ 1.5 and ∼ 4.9% of local galaxies, respectively, whereas spirals and irregulars contribute ∼ 32.1 and ∼ 42.8%, respectively. The dEblue galaxies, which are a recently discovered population of galaxies, contribute a significant fraction of dwarf galaxies. There seem to be structural differences between dSph and dE galaxies. The dSph galaxies are fainter and bluer with a shallower surface brightness gradient than dE galaxies. They also have a lower fraction of galaxies with small axis ratios (b/a≲ 0.4) than dE galaxies. The mean projected distance to the nearest neighbor galaxy is ∼260 kpc. About 1% of local galaxies have no neighbors with comparable luminosity within a projected distance of 2 Mpc.

Model-based local density sharpening of cryo-EM maps

PubMed Central

Jakobi, Arjen J; Wilmanns, Matthias

2017-01-01

Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by amplitude scaling against the radially averaged local falloff estimated from a windowed reference model. By testing the procedure using six cryo-EM structures of TRPV1, β-galactosidase, γ-secretase, ribosome-EF-Tu complex, 20S proteasome and RNA polymerase III, we illustrate how local sharpening can increase interpretability of density maps in particular in cases of resolution variation and facilitates model building and atomic model refinement. PMID:29058676

SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries.

PubMed

Wu, Jemma X; Song, Xiaomin; Pascovici, Dana; Zaw, Thiri; Care, Natasha; Krisp, Christoph; Molloy, Mark P

2016-07-01

The use of data-independent acquisition methods such as SWATH for mass spectrometry based proteomics is usually performed with peptide MS/MS assay libraries which enable identification and quantitation of peptide peak areas. Reference assay libraries can be generated locally through information dependent acquisition, or obtained from community data repositories for commonly studied organisms. However, there have been no studies performed to systematically evaluate how locally generated or repository-based assay libraries affect SWATH performance for proteomic studies. To undertake this analysis, we developed a software workflow, SwathXtend, which generates extended peptide assay libraries by integration with a local seed library and delivers statistical analysis of SWATH-quantitative comparisons. We designed test samples using peptides from a yeast extract spiked into peptides from human K562 cell lysates at three different ratios to simulate protein abundance change comparisons. SWATH-MS performance was assessed using local and external assay libraries of varying complexities and proteome compositions. These experiments demonstrated that local seed libraries integrated with external assay libraries achieve better performance than local assay libraries alone, in terms of the number of identified peptides and proteins and the specificity to detect differentially abundant proteins. Our findings show that the performance of extended assay libraries is influenced by the MS/MS feature similarity of the seed and external libraries, while statistical analysis using multiple testing corrections increases the statistical rigor needed when searching against large extended assay libraries. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries*

PubMed Central

Wu, Jemma X.; Song, Xiaomin; Pascovici, Dana; Zaw, Thiri; Care, Natasha; Krisp, Christoph; Molloy, Mark P.

2016-01-01

The use of data-independent acquisition methods such as SWATH for mass spectrometry based proteomics is usually performed with peptide MS/MS assay libraries which enable identification and quantitation of peptide peak areas. Reference assay libraries can be generated locally through information dependent acquisition, or obtained from community data repositories for commonly studied organisms. However, there have been no studies performed to systematically evaluate how locally generated or repository-based assay libraries affect SWATH performance for proteomic studies. To undertake this analysis, we developed a software workflow, SwathXtend, which generates extended peptide assay libraries by integration with a local seed library and delivers statistical analysis of SWATH-quantitative comparisons. We designed test samples using peptides from a yeast extract spiked into peptides from human K562 cell lysates at three different ratios to simulate protein abundance change comparisons. SWATH-MS performance was assessed using local and external assay libraries of varying complexities and proteome compositions. These experiments demonstrated that local seed libraries integrated with external assay libraries achieve better performance than local assay libraries alone, in terms of the number of identified peptides and proteins and the specificity to detect differentially abundant proteins. Our findings show that the performance of extended assay libraries is influenced by the MS/MS feature similarity of the seed and external libraries, while statistical analysis using multiple testing corrections increases the statistical rigor needed when searching against large extended assay libraries. PMID:27161445

Local television news reporting of kidney disease.

PubMed

Jaffery, Jonathan B; Jacobson, Lynn M; Goldstein, Kenneth M; Pribble, James M

2006-12-01

Local television is the primary news source for the majority of Americans. This study aims to describe how local news reports on kidney disease. Using our searchable database of health-related late local news segments from 2002, we identified stories with the key words kidney, hypertension, blood pressure, or diabetes. This database is a representative sample of the late local news on 122 stations in the 50 largest US media markets, comprising 60% of the population. The content of each identified story was reviewed to determine whether it mentioned: (1) chronic kidney disease (CKD), (2) screening for kidney disease, or (3) kidney disease as a potential complication (for blood pressure- or diabetes-related stories). Only 2 of 1,799 database news stories (0.11%) included "kidney" as a summary key word; neither referred to CKD, screening, or complications of other diseases. Of 19 stories about hypertension or blood pressure (1.06% of all stories) and the 14 stories about diabetes (0.78% of all stories), none mentioned these criteria. Despite efforts to increase public awareness of and screening for CKD, local television news (the most important news source for a majority of Americans) did little to help achieve these goals. Further work will be needed to confirm whether this paucity of coverage varies over time and determine why so little attention is given to CKD. Educating physicians and public relations personnel who advocate for kidney disease about journalists' needs may be an important step to help advance public awareness of CKD.

Apparatus and method for detecting gamma radiation

DOEpatents

Sigg, Raymond A.

1994-01-01

A high efficiency radiation detector for measuring X-ray and gamma radiation from small-volume, low-activity liquid samples with an overall uncertainty better than 0.7% (one sigma SD). The radiation detector includes a hyperpure germanium well detector, a collimator, and a reference source. The well detector monitors gamma radiation emitted by the reference source and a radioactive isotope or isotopes in a sample source. The radiation from the reference source is collimated to avoid attenuation of reference source gamma radiation by the sample. Signals from the well detector are processed and stored, and the stored data is analyzed to determine the radioactive isotope(s) content of the sample. Minor self-attenuation corrections are calculated from chemical composition data.

Towards a unified description of the charge transport mechanisms in conductive atomic force microscopy studies of semiconducting polymers.

PubMed

Moerman, D; Sebaihi, N; Kaviyil, S E; Leclère, P; Lazzaroni, R; Douhéret, O

2014-09-21

In this work, conductive atomic force microscopy (C-AFM) is used to study the local electrical properties in thin films of self-organized fibrillate poly(3-hexylthiophene) (P3HT), as a reference polymer semiconductor. Depending on the geometrical confinement in the transport channel, the C-AFM current is shown to be governed either by the charge transport in the film or by the carrier injection at the tip-sample contact, leading to either bulk or local electrical characterization of the semiconducting polymer, respectively. Local I-V profiles allow discrimination of the different dominating electrical mechanisms, i.e., resistive in the transport regime and space charge limited current (SCLC) in the local regime. A modified Mott-Gurney law is analytically derived for the contact regime, taking into account the point-probe geometry of the contact and the radial injection of carriers. Within the SCLC regime, the probed depth is shown to remain below 12 nm with a lateral electrical resolution below 5 nm. This confirms that high resolution is reached in those C-AFM measurements, which therefore allows for the analysis of single organic semiconducting nanostructures. The carrier density and mobility in the volume probed under the tip under steady-state conditions are also determined in the SCLC regime.

Comparison of three light doses in the photodynamic treatment of actinic keratosis using mathematical modeling

NASA Astrophysics Data System (ADS)

Vignion-Dewalle, Anne-Sophie; Betrouni, Nacim; Tylcz, Jean-Baptiste; Vermandel, Maximilien; Mortier, Laurent; Mordon, Serge

2015-05-01

Photodynamic therapy (PDT) is an emerging treatment modality for various diseases, especially for cancer therapy. Although high efficacy is demonstrated for PDT using standardized protocols in nonhyperkeratotic actinic keratoses, alternative light doses expected to increase efficiency, to reduce adverse effects or to expand the use of PDT, are still being evaluated and refined. We propose a comparison of the three most common light doses in the treatment of actinic keratosis with 5-aminolevulinic acid PDT through mathematical modeling. The proposed model is based on an iterative procedure that involves determination of the local fluence rate, updating of the local optical properties, and estimation of the local damage induced by the therapy. This model was applied on a simplified skin sample model including an actinic keratosis lesion, with three different light doses (red light dose, 37 J/cm2, 75 mW/cm2, 500 s blue light dose, 10 J/cm2, 10 mW/cm2, 1000 s and daylight dose, 9000 s). Results analysis shows that the three studied light doses, although all efficient, lead to variable local damage. Defining reference damage enables the nonoptimal parameters for the current light doses to be refined and the treatment to be more suitable.

Commutability of food microbiology proficiency testing samples.

PubMed

Abdelmassih, M; Polet, M; Goffaux, M-J; Planchon, V; Dierick, K; Mahillon, J

2014-03-01

Food microbiology proficiency testing (PT) is a useful tool to assess the analytical performances among laboratories. PT items should be close to routine samples to accurately evaluate the acceptability of the methods. However, most PT providers distribute exclusively artificial samples such as reference materials or irradiated foods. This raises the issue of the suitability of these samples because the equivalence-or 'commutability'-between results obtained on artificial vs. authentic food samples has not been demonstrated. In the clinical field, the use of noncommutable PT samples has led to erroneous evaluation of the performances when different analytical methods were used. This study aimed to provide a first assessment of the commutability of samples distributed in food microbiology PT. REQUASUD and IPH organized 13 food microbiology PTs including 10-28 participants. Three types of PT items were used: genuine food samples, sterile food samples and reference materials. The commutability of the artificial samples (reference material or sterile samples) was assessed by plotting the distribution of the results on natural and artificial PT samples. This comparison highlighted matrix-correlated issues when nonfood matrices, such as reference materials, were used. Artificially inoculated food samples, on the other hand, raised only isolated commutability issues. In the organization of a PT-scheme, authentic or artificially inoculated food samples are necessary to accurately evaluate the analytical performances. Reference materials, used as PT items because of their convenience, may present commutability issues leading to inaccurate penalizing conclusions for methods that would have provided accurate results on food samples. For the first time, the commutability of food microbiology PT samples was investigated. The nature of the samples provided by the organizer turned out to be an important factor because matrix effects can impact on the analytical results. © 2013 The Society for Applied Microbiology.

Improved Compressive Sensing of Natural Scenes Using Localized Random Sampling

PubMed Central

Barranca, Victor J.; Kovačič, Gregor; Zhou, Douglas; Cai, David

2016-01-01

Compressive sensing (CS) theory demonstrates that by using uniformly-random sampling, rather than uniformly-spaced sampling, higher quality image reconstructions are often achievable. Considering that the structure of sampling protocols has such a profound impact on the quality of image reconstructions, we formulate a new sampling scheme motivated by physiological receptive field structure, localized random sampling, which yields significantly improved CS image reconstructions. For each set of localized image measurements, our sampling method first randomly selects an image pixel and then measures its nearby pixels with probability depending on their distance from the initially selected pixel. We compare the uniformly-random and localized random sampling methods over a large space of sampling parameters, and show that, for the optimal parameter choices, higher quality image reconstructions can be consistently obtained by using localized random sampling. In addition, we argue that the localized random CS optimal parameter choice is stable with respect to diverse natural images, and scales with the number of samples used for reconstruction. We expect that the localized random sampling protocol helps to explain the evolutionarily advantageous nature of receptive field structure in visual systems and suggests several future research areas in CS theory and its application to brain imaging. PMID:27555464

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.

A parent-report Gender Identity Questionnaire for Children: A cross-national, cross-clinic comparative analysis.

PubMed

Cohen-Kettenis, Peggy T; Wallien, Madeleine; Johnson, Laurel L; Owen-Anderson, Allison F H; Bradley, Susan J; Zucker, Kenneth J

2006-07-01

A one-factor, 14-item parent-report Gender Identity Questionnaire for Children (GIQC) was developed in a sample of 325 clinic-referred children with gender identity problems and 504 controls from Toronto, Canada (Johnson et al., 2004). In this study, we report a cross-national, cross-clinic comparative analysis of the GIQC on gender-referred children (N = 338) from Toronto and gender-referred children (N = 175) from Utrecht, The Netherlands. Across clinics, the results showed both similarities and differences. Gender-referred boys from Utrecht had a significantly higher total score (indicating more cross-gender behavior) than did gender-referred boys from Toronto, but there was no significant difference for girls. In the Toronto sample, the gender-referred girls had a significantly higher total score than the gender-referred boys, but there was no significant sex difference in the Utrecht sample. Across both clinics, gender-referred children who met the complete DSM criteria for gender identity disorder (GID) had a significantly higher cross-gender score than the gender-referred children who were subthreshold for GID (Cohen's d = 1.11). The results of this study provide the first empirical evidence of relative similarity in cross-gender behavior in a sample of gender-referred children from western Europe when compared to North American children. The results also provide some support for cross-clinic consistency in clinician-based diagnosis of GID.

Assessment of fracture risk: value of random population-based samples--the Geelong Osteoporosis Study.

PubMed

Henry, M J; Pasco, J A; Seeman, E; Nicholson, G C; Sanders, K M; Kotowicz, M A

2001-01-01

Fracture risk is determined by bone mineral density (BMD). The T-score, a measure of fracture risk, is the position of an individual's BMD in relation to a reference range. The aim of this study was to determine the magnitude of change in the T-score when different sampling techniques were used to produce the reference range. Reference ranges were derived from three samples, drawn from the same region: (1) an age-stratified population-based random sample, (2) unselected volunteers, and (3) a selected healthy subset of the population-based sample with no diseases or drugs known to affect bone. T-scores were calculated using the three reference ranges for a cohort of women who had sustained a fracture and as a group had a low mean BMD (ages 35-72 yr; n = 484). For most comparisons, the T-scores for the fracture cohort were more negative using the population reference range. The difference in T-scores reached 1.0 SD. The proportion of the fracture cohort classified as having osteoporosis at the spine was 26, 14, and 23% when the population, volunteer, and healthy reference ranges were applied, respectively. The use of inappropriate reference ranges results in substantial changes to T-scores and may lead to inappropriate management.

Nonlinear Spatial Inversion Without Monte Carlo Sampling

NASA Astrophysics Data System (ADS)

Curtis, A.; Nawaz, A.

2017-12-01

High-dimensional, nonlinear inverse or inference problems usually have non-unique solutions. The distribution of solutions are described by probability distributions, and these are usually found using Monte Carlo (MC) sampling methods. These take pseudo-random samples of models in parameter space, calculate the probability of each sample given available data and other information, and thus map out high or low probability values of model parameters. However, such methods would converge to the solution only as the number of samples tends to infinity; in practice, MC is found to be slow to converge, convergence is not guaranteed to be achieved in finite time, and detection of convergence requires the use of subjective criteria. We propose a method for Bayesian inversion of categorical variables such as geological facies or rock types in spatial problems, which requires no sampling at all. The method uses a 2-D Hidden Markov Model over a grid of cells, where observations represent localized data constraining the model in each cell. The data in our example application are seismic properties such as P- and S-wave impedances or rock density; our model parameters are the hidden states and represent the geological rock types in each cell. The observations at each location are assumed to depend on the facies at that location only - an assumption referred to as `localized likelihoods'. However, the facies at a location cannot be determined solely by the observation at that location as it also depends on prior information concerning its correlation with the spatial distribution of facies elsewhere. Such prior information is included in the inversion in the form of a training image which represents a conceptual depiction of the distribution of local geologies that might be expected, but other forms of prior information can be used in the method as desired. The method provides direct (pseudo-analytic) estimates of posterior marginal probability distributions over each variable, so these do not need to be estimated from samples as is required in MC methods. On a 2-D test example the method is shown to outperform previous methods significantly, and at a fraction of the computational cost. In many foreseeable applications there are therefore no serious impediments to extending the method to 3-D spatial models.

Bounded Linear Stability Analysis - A Time Delay Margin Estimation Approach for Adaptive Control

NASA Technical Reports Server (NTRS)

Nguyen, Nhan T.; Ishihara, Abraham K.; Krishnakumar, Kalmanje Srinlvas; Bakhtiari-Nejad, Maryam

2009-01-01

This paper presents a method for estimating time delay margin for model-reference adaptive control of systems with almost linear structured uncertainty. The bounded linear stability analysis method seeks to represent the conventional model-reference adaptive law by a locally bounded linear approximation within a small time window using the comparison lemma. The locally bounded linear approximation of the combined adaptive system is cast in a form of an input-time-delay differential equation over a small time window. The time delay margin of this system represents a local stability measure and is computed analytically by a matrix measure method, which provides a simple analytical technique for estimating an upper bound of time delay margin. Based on simulation results for a scalar model-reference adaptive control system, both the bounded linear stability method and the matrix measure method are seen to provide a reasonably accurate and yet not too conservative time delay margin estimation.

Genotype Imputation with Millions of Reference Samples

PubMed Central

Browning, Brian L.; Browning, Sharon R.

2016-01-01

We present a genotype imputation method that scales to millions of reference samples. The imputation method, based on the Li and Stephens model and implemented in Beagle v.4.1, is parallelized and memory efficient, making it well suited to multi-core computer processors. It achieves fast, accurate, and memory-efficient genotype imputation by restricting the probability model to markers that are genotyped in the target samples and by performing linear interpolation to impute ungenotyped variants. We compare Beagle v.4.1 with Impute2 and Minimac3 by using 1000 Genomes Project data, UK10K Project data, and simulated data. All three methods have similar accuracy but different memory requirements and different computation times. When imputing 10 Mb of sequence data from 50,000 reference samples, Beagle’s throughput was more than 100× greater than Impute2’s throughput on our computer servers. When imputing 10 Mb of sequence data from 200,000 reference samples in VCF format, Minimac3 consumed 26× more memory per computational thread and 15× more CPU time than Beagle. We demonstrate that Beagle v.4.1 scales to much larger reference panels by performing imputation from a simulated reference panel having 5 million samples and a mean marker density of one marker per four base pairs. PMID:26748515

Reference surfaces for bridge scour depths

USGS Publications Warehouse

Landers, Mark N.; Mueller, David S.; ,

1993-01-01

Depth of scour is measured as the vertical distance between scoured channel geometry and a measurement reference surface. A scour depth measurement can have a wide range depending on the method used to establish the reference surface. A consistent method to establish reference surfaces for bridge scour measurements is needed to facilitate transferability of scour data an scour analyses. This paper describes and evaluates techniques for establishing reference surfaces from which local and contraction scour are measured.

Proposing an Empirically Justified Reference Threshold for Blood Culture Sampling Rates in Intensive Care Units

PubMed Central

Castell, Stefanie; Schwab, Frank; Geffers, Christine; Bongartz, Hannah; Brunkhorst, Frank M.; Gastmeier, Petra; Mikolajczyk, Rafael T.

2014-01-01

Early and appropriate blood culture sampling is recommended as a standard of care for patients with suspected bloodstream infections (BSI) but is rarely taken into account when quality indicators for BSI are evaluated. To date, sampling of about 100 to 200 blood culture sets per 1,000 patient-days is recommended as the target range for blood culture rates. However, the empirical basis of this recommendation is not clear. The aim of the current study was to analyze the association between blood culture rates and observed BSI rates and to derive a reference threshold for blood culture rates in intensive care units (ICUs). This study is based on data from 223 ICUs taking part in the German hospital infection surveillance system. We applied locally weighted regression and segmented Poisson regression to assess the association between blood culture rates and BSI rates. Below 80 to 90 blood culture sets per 1,000 patient-days, observed BSI rates increased with increasing blood culture rates, while there was no further increase above this threshold. Segmented Poisson regression located the threshold at 87 (95% confidence interval, 54 to 120) blood culture sets per 1,000 patient-days. Only one-third of the investigated ICUs displayed blood culture rates above this threshold. We provided empirical justification for a blood culture target threshold in ICUs. In the majority of the studied ICUs, blood culture sampling rates were below this threshold. This suggests that a substantial fraction of BSI cases might remain undetected; reporting observed BSI rates as a quality indicator without sufficiently high blood culture rates might be misleading. PMID:25520442

Variability of 137Cs inventory at a reference site in west-central Iran.

PubMed

Bazshoushtari, Nasim; Ayoubi, Shamsollah; Abdi, Mohammad Reza; Mohammadi, Mohammad

2016-12-01

137 Cs technique has been widely used for the evaluation rates and patterns of soil erosion and deposition. This technique requires an accurate estimate of the values of 137 Cs inventory at the reference site. This study was conducted to evaluate the variability of the inventory of 137 Cs regarding to the sampling program including sample size, distance and sampling method at a reference site located in vicinity of Fereydan district in Isfahan province, west-central Iran. Two 3 × 8 grids were established comprising large grid (35 m length and 8 m width), and small grid (24 m length and 6 m width). At each grid intersection two soil samples were collected from 0 to 15 cm and 15-30 cm depths, totally 96 soil samples from 48 sampling points. Coefficients of variation for 137 Cs inventory in the soil samples was relatively low (CV = 15%), and the sampling distance and methods used did not significantly affect the 137 Cs inventories across the studied reference site. To obtain a satisfactory estimate of the mean 137 Cs activity in the reference sites, particularly those located in the semiarid regions, it is recommended to collect at least four samples along in a grid pattern 3 m apart. Copyright © 2016 Elsevier Ltd. All rights reserved.

Micron-Scale Differential Scanning Calorimeter on a Chip

DOEpatents

Cavicchi, Richard E; Poirier, Gregory Ernest; Suehle, John S; Gaitan, Michael; Tea, Nim H

1998-06-30

A differential scanning microcalorimeter produced on a silicon chip enables microscopic scanning calorimetry measurements of small samples and thin films. The chip may be fabricated using standard CMOS processes. The microcalorimeter includes a reference zone and a sample zone. The reference and sample zones may be at opposite ends of a suspended platform or may reside on separate platforms. An integrated polysilicon heater provides heat to each zone. A thermopile consisting of a succession of thermocouple junctions generates a voltage representing the temperature difference between the reference and sample zones. Temperature differences between the zones provide information about the chemical reactions and phase transitions that occur in a sample placed in the sample zone.

The limits of boundaries: unpacking localization and cognitive mapping relative to a boundary.

PubMed

Zhou, Ruojing; Mou, Weimin

2018-05-01

Previous research (Zhou, Mou, Journal of Experimental Psychology: Learning, Memory and Cognition 42(8):1316-1323, 2016) showed that learning individual locations relative to a single landmark, compared to learning relative to a boundary, led to more accurate inferences of inter-object spatial relations (cognitive mapping of multiple locations). Following our past findings, the current study investigated whether the larger number of reference points provided by a homogeneous circular boundary, as well as less accessible knowledge of direct spatial relations among the multiple reference points, would lead to less effective cognitive mapping relative to the boundary. Accordingly, we manipulated (a) the number of primary reference points (one segment drawn from a circular boundary, four such segments, vs. the complete boundary) available when participants were localizing four objects sequentially (Experiment 1) and (b) the extendedness of each of the four segments (Experiment 2). The results showed that cognitive mapping was the least accurate in the whole boundary condition. However, expanding each of the four segments did not affect the accuracy of cognitive mapping until the four were connected to form a continuous boundary. These findings indicate that when encoding locations relative to a homogeneous boundary, participants segmented the boundary into differentiated pieces and subsequently chose the most informative local part (i.e., the segment closest in distance to one location) as the primary reference point for a particular location. During this process, direct spatial relations among the reference points were likely not attended to. These findings suggest that people might encode and represent bounded space in a fragmented fashion when localizing within a homogeneous boundary.

Quality assessment program for EuroFlow protocols: summary results of four-year (2010-2013) quality assurance rounds.

PubMed

Kalina, Tomas; Flores-Montero, Juan; Lecrevisse, Quentin; Pedreira, Carlos E; van der Velden, Vincent H J; Novakova, Michaela; Mejstrikova, Ester; Hrusak, Ondrej; Böttcher, Sebastian; Karsch, Dennis; Sędek, Łukasz; Trinquand, Amelie; Boeckx, Nancy; Caetano, Joana; Asnafi, Vahid; Lucio, Paulo; Lima, Margarida; Helena Santos, Ana; Bonaccorso, Paola; van der Sluijs-Gelling, Alita J; Langerak, Anton W; Martin-Ayuso, Marta; Szczepański, Tomasz; van Dongen, Jacques J M; Orfao, Alberto

2015-02-01

Flow cytometric immunophenotyping has become essential for accurate diagnosis, classification, and disease monitoring in hemato-oncology. The EuroFlow Consortium has established a fully standardized "all-in-one" pipeline consisting of standardized instrument settings, reagent panels, and sample preparation protocols and software for data analysis and disease classification. For its reproducible implementation, parallel development of a quality assurance (QA) program was required. Here, we report on the results of four consecutive annual rounds of the novel external QA EuroFlow program. The novel QA scheme aimed at monitoring the whole flow cytometric analysis process (cytometer setting, sample preparation, acquisition and analysis) by reading the median fluorescence intensities (MedFI) of defined lymphocytes' subsets. Each QA participant applied the predefined reagents' panel on blood cells of local healthy donors. A uniform gating strategy was applied to define lymphocyte subsets and to read MedFI values per marker. The MedFI values were compared with reference data and deviations from reference values were quantified using performance score metrics. In four annual QA rounds, we analyzed 123 blood samples from local healthy donors on 14 different instruments in 11 laboratories from nine European countries. The immunophenotype of defined cellular subsets appeared sufficiently standardized to permit unified (software) data analysis. The coefficient of variation of MedFI for 7 of 11 markers performed repeatedly below 30%, average MedFI in each QA round ranged from 86 to 125% from overall median. Calculation of performance scores was instrumental to pinpoint standardization failures and their causes. Overall, the new EuroFlow QA system for the first time allowed to quantify the technical variation that is introduced in the measurement of fluorescence intensities in a multicentric setting over an extended period of time. EuroFlow QA is a proficiency test specific for laboratories that use standardized EuroFlow protocols. It may be used to complement, but not replace, established proficiency tests. © 2014 International Society for Advancement of Cytometry. © 2014 International Society for Advancement of Cytometry.

Molecular identification and genetic diversity of open reading frame 7 field isolated porcine reproductive and respiratory syndrome in North Sumatera, Indonesia, in the period of 2008-2014.

PubMed

Faisal, Faisal; Widayanti, Rini; Haryanto, Aris; Tabu, Charles Rangga

2015-07-01

Molecular identification and genetic diversity of open reading frame 7 (ORF7) of field isolated porcine reproductive and respiratory syndrome virus (PRRSV) in North Sumatera, Indonesia, in the period of 2008-2014. A total of 47 PRRSV samples were collected from the death case of pigs. The samples were collected from different districts in the period of 2008-2014 from North Sumatera province. Two pairs of primer were designed to amplify ORF7 of Type 1 and 2 PRRSV based on the sequence of reference viruses VR2332 and Lelystad. Viral RNAs were extracted from samples using PureLink™ micro-to-Midi total RNA purification system (Invitrogen). To amplify the ORF7 of PRRSV, the synthesis cDNA and DNA amplification were performed by reverse transcription polymerase chain reaction (RT-PCR) and nested PCR method. Then the DNA sequencing of PCR products and phylogenetic analysis were accomplished by molecular evolutionary genetics analysis version 6.0 software program. RT-: PCR and nested PCR used in this study had successfully detected of 18 samples positive PRRS virus with the amplification products at 703bp and 508bp, respectively. Sequencing of the ORF7 shows that 18 PRRS viruses isolated from North Sumatera belonged to North American (NA). JXA1 Like and classic NA type viruses. Several mutations were detected, particularly in the area of nuclear localization signal (NLS1) and in NLS2. In the local viruses, which were related closed to JXA1 virus; there are two differences in amino acids in position 12 and 43 of ORF7. Our tested viruses showed that the amino acid positions 12 and 43 are Asparagine and Arginine, while the reference virus (VR2332, Lelystad, and JXA1) occupied both by Lysine. Based on differences in two amino acids at position 12 and 43 showed that viruses from North Sumatera has its own uniqueness and related closed to highly pathogenic PRRS (HP-PRRS) virus (JXA1). The results demonstrated that North Sumatera type PRRS virus has caused PRRS outbreaks in pig in North Sumatera between 2008 and 2014. The JAX1 like viruses had unique amino acid residue in position 12 and 43 of asparagine and lysine, and these were genetic determinants of North Sumatera viruses compared to other PRRS viruses.

Mapping South African allied health primary care clinical guideline activity: establishing a stakeholder reference sample.

PubMed

Dizon, Janine Margarita; Grimmer, Karen; Machingaidze, Shingai; McLaren, Pam; Louw, Quinette

2016-10-10

Little is known about allied health (AH) clinical practice guideline (CPG) activity in South Africa, and particularly in relation to primary health care (PHC). This paper reports on a scoping study undertaken to establish a reference framework, from which a comprehensive maximum variation sample could be selected. This was required to underpin robust sampling for a qualitative study aimed at understanding South African primary care AH therapy CPG activities. This paper builds on findings from the South African Guidelines Evaluation (Project SAGE) Flagship grant. South African government websites were searched for structures of departments and portfolios, and available CPGs. Professional AH association websites were searched for CPGs, purposively-identified key informants were interviewed, and CPGs previously identified for priority South African primary care conditions were critiqued for AH therapy involvement. Key informants described potentially complex relationships between players who may be engaged in South African AH CPGs, in both public and private sectors. There were disability/rehabilitation portfolios at national and provincial governments, but no uniformity in provincial government organisation of, or support for, PHC AH services. There were no AH primary care therapy CPGs on government websites, although there was 'clinical guidance' in various forms on professional association websites. Only two CPGs of priority South African PHC conditions included mention of any AH therapy (physiotherapy for adult asthma and chronic obstructive pulmonary disease). A comprehensive and wide-reaching stakeholder reference framework would be required in order to capture the heterogeneity of AH primary care CPG activity in South Africa. This should involve the voices of national and purposively-selected provincial governments, academic institutions, consultants, public sector managers and clinicians, private practitioners, professional associations, and private sector insurers. Provincial governments should be selected to reflect heterogeneity in local economics, population demographics and availability of university AH training programs. This investigation should aim to determine the areas of PHC in which AH are engaged.

Long-Term Impacts on Macroinvertebrates Downstream of Reclaimed Mountaintop Mining Valley Fills in Central Appalachia

NASA Astrophysics Data System (ADS)

Pond, Gregory J.; Passmore, Margaret E.; Pointon, Nancy D.; Felbinger, John K.; Walker, Craig A.; Krock, Kelly J. G.; Fulton, Jennifer B.; Nash, Whitney L.

2014-10-01

Recent studies have documented adverse effects to biological communities downstream of mountaintop coal mining and valley fills (VF), but few data exist on the longevity of these impacts. We sampled 15 headwater streams with VFs reclaimed 11-33 years prior to 2011 and sampled seven local reference sites that had no VFs. We collected chemical, habitat, and benthic macroinvertebrate data in April 2011; additional chemical samples were collected in September 2011. To assess ecological condition, we compared VF and reference abiotic and biotic data using: (1) ordination to detect multivariate differences, (2) benthic indices (a multimetric index and an observed/expected predictive model) calibrated to state reference conditions to detect impairment, and (3) correlation and regression analysis to detect relationships between biotic and abiotic data. Although VF sites had good instream habitat, nearly 90 % of these streams exhibited biological impairment. VF sites with higher index scores were co-located near unaffected tributaries; we suggest that these tributaries were sources of sensitive taxa as drifting colonists. There were clear losses of expected taxa across most VF sites and two functional feeding groups (% scrapers and %shredders) were significantly altered. Percent VF and forested area were related to biological quality but varied more than individual ions and specific conductance. Within the subset of VF sites, other descriptors (e.g., VF age, site distance from VF, the presence of impoundments, % forest) had no detectable relationships with biological condition. Although these VFs were constructed pursuant to permits and regulatory programs that have as their stated goals that (1) mined land be reclaimed and restored to its original use or a use of higher value, and (2) mining does not cause or contribute to violations of water quality standards, we found sustained ecological damage in headwaters streams draining VFs long after reclamation was completed.

Post-Newtonian Reference Frames for Advanced Theory of the Lunar Motion and a New Generation of Lunar Laser Ranging

NASA Astrophysics Data System (ADS)

Xie, Yi; Kopeikin, Sergei Affiliaiton: AB(Department of Physics and Astronomy, University of Missouri, USA kopeikins@missouri.edu)

2010-08-01

We overview a set of post-Newtonian reference frames for a comprehensive study of the orbital dynamics and rotational motion of Moon and Earth by means of lunar laser ranging (LLR). We employ a scalar-tensor theory of gravity depending on two post-Newtonian parameters, and , and utilize the relativistic resolutions on reference frames adopted by the International Astronomical Union (IAU) in 2000. We assume that the solar system is isolated and space-time is asymptotically flat at infinity. The primary reference frame covers the entire space-time, has its origin at the solar-system barycenter (SSB) and spatial axes stretching up to infinity. The SSB frame is not rotating with respect to a set of distant quasars that are forming the International Celestial Reference Frame (ICRF). The secondary reference frame has its origin at the Earth-Moon barycenter (EMB). The EMB frame is locally-inertial and is not rotating dynamically in the sense that equation of motion of a test particle moving with respect to the EMB frame, does not contain the Coriolis and centripetal forces. Two other local frames geocentric (GRF) and selenocentric (SRF) have their origins at the center of mass of Earth and Moon respectively and do not rotate dynamically. Each local frame is subject to the geodetic precession both with respect to other local frames and with respect to the ICRF because of their relative motion with respect to each other. Theoretical advantage of the dynamically non-rotating local frames is in a more simple mathematical description. Each local frame can be aligned with the axes of ICRF after applying the matrix of the relativistic precession. The set of one global and three local frames is introduced in order to fully decouple the relative motion of Moon with respect to Earth from the orbital motion of the Earth-Moon barycenter as well as to connect the coordinate description of the lunar motion, an observer on Earth, and a retro-reflector on Moon to directly measurable quantities such as the proper time and the round-trip laser-light distance. We solve the gravity field equations and find out the metric tensor and the scalar field in all frames which description includes the post-Newtonian multipole moments of the gravitational field of Earth and Moon. We also derive the post-Newtonian coordinate transformations between the frames and analyze the residual gauge freedom.

The Worldwide Marine Radiocarbon Reservoir Effect: Definitions, Mechanisms, and Prospects

NASA Astrophysics Data System (ADS)

Alves, Eduardo Q.; Macario, Kita; Ascough, Philippa; Bronk Ramsey, Christopher

2018-03-01

When a carbon reservoir has a lower radiocarbon content than the atmosphere, this is referred to as a reservoir effect. This is expressed as an offset between the radiocarbon ages of samples from the two reservoirs at a single point in time. The marine reservoir effect (MRE) has been a major concern in the radiocarbon community, as it introduces an additional source of error that is often difficult to accurately quantify. For this reason, researchers are often reluctant to date marine material where they have another option. The influence of this phenomenon makes the study of the MRE important for a broad range of applications. The advent of Accelerator Mass Spectrometry (AMS) has reduced sample size requirements and increased measurement precision, in turn increasing the number of studies seeking to measure marine samples. These studies rely on overcoming the influence of the MRE on marine radiocarbon dates through the worldwide quantification of the local parameter ΔR, that is, the local variation from the global average MRE. Furthermore, the strong dependence on ocean dynamics makes the MRE a useful indicator for changes in oceanic circulation, carbon exchange between reservoirs, and the fate of atmospheric CO2, all of which impact Earth's climate. This article explores data from the Marine Reservoir Database and reviews the place of natural radiocarbon in oceanic records, focusing on key questions (e.g., changes in ocean dynamics) that have been answered by MRE studies and on their application to different subjects.

Merging parallel tempering with sequential geostatistical resampling for improved posterior exploration of high-dimensional subsurface categorical fields

NASA Astrophysics Data System (ADS)

Laloy, Eric; Linde, Niklas; Jacques, Diederik; Mariethoz, Grégoire

2016-04-01

The sequential geostatistical resampling (SGR) algorithm is a Markov chain Monte Carlo (MCMC) scheme for sampling from possibly non-Gaussian, complex spatially-distributed prior models such as geologic facies or categorical fields. In this work, we highlight the limits of standard SGR for posterior inference of high-dimensional categorical fields with realistically complex likelihood landscapes and benchmark a parallel tempering implementation (PT-SGR). Our proposed PT-SGR approach is demonstrated using synthetic (error corrupted) data from steady-state flow and transport experiments in categorical 7575- and 10,000-dimensional 2D conductivity fields. In both case studies, every SGR trial gets trapped in a local optima while PT-SGR maintains an higher diversity in the sampled model states. The advantage of PT-SGR is most apparent in an inverse transport problem where the posterior distribution is made bimodal by construction. PT-SGR then converges towards the appropriate data misfit much faster than SGR and partly recovers the two modes. In contrast, for the same computational resources SGR does not fit the data to the appropriate error level and hardly produces a locally optimal solution that looks visually similar to one of the two reference modes. Although PT-SGR clearly surpasses SGR in performance, our results also indicate that using a small number (16-24) of temperatures (and thus parallel cores) may not permit complete sampling of the posterior distribution by PT-SGR within a reasonable computational time (less than 1-2 weeks).

Designing image segmentation studies: Statistical power, sample size and reference standard quality.

PubMed

Gibson, Eli; Hu, Yipeng; Huisman, Henkjan J; Barratt, Dean C

2017-12-01

Segmentation algorithms are typically evaluated by comparison to an accepted reference standard. The cost of generating accurate reference standards for medical image segmentation can be substantial. Since the study cost and the likelihood of detecting a clinically meaningful difference in accuracy both depend on the size and on the quality of the study reference standard, balancing these trade-offs supports the efficient use of research resources. In this work, we derive a statistical power calculation that enables researchers to estimate the appropriate sample size to detect clinically meaningful differences in segmentation accuracy (i.e. the proportion of voxels matching the reference standard) between two algorithms. Furthermore, we derive a formula to relate reference standard errors to their effect on the sample sizes of studies using lower-quality (but potentially more affordable and practically available) reference standards. The accuracy of the derived sample size formula was estimated through Monte Carlo simulation, demonstrating, with 95% confidence, a predicted statistical power within 4% of simulated values across a range of model parameters. This corresponds to sample size errors of less than 4 subjects and errors in the detectable accuracy difference less than 0.6%. The applicability of the formula to real-world data was assessed using bootstrap resampling simulations for pairs of algorithms from the PROMISE12 prostate MR segmentation challenge data set. The model predicted the simulated power for the majority of algorithm pairs within 4% for simulated experiments using a high-quality reference standard and within 6% for simulated experiments using a low-quality reference standard. A case study, also based on the PROMISE12 data, illustrates using the formulae to evaluate whether to use a lower-quality reference standard in a prostate segmentation study. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

[Errors in Peruvian medical journals references].

PubMed

Huamaní, Charles; Pacheco-Romero, José

2009-01-01

References are fundamental in our studies; an adequate selection is asimportant as an adequate description. To determine the number of errors in a sample of references found in Peruvian medical journals. We reviewed 515 scientific papers references selected by systematic randomized sampling and corroborated reference information with the original document or its citation in Pubmed, LILACS or SciELO-Peru. We found errors in 47,6% (245) of the references, identifying 372 types of errors; the most frequent were errors in presentation style (120), authorship (100) and title (100), mainly due to spelling mistakes (91). References error percentage was high, varied and multiple. We suggest systematic revision of references in the editorial process as well as to extend the discussion on this theme. references, periodicals, research, bibliometrics.

Apparatus and method for detecting gamma radiation

DOEpatents

Sigg, R.A.

1994-12-13

A high efficiency radiation detector is disclosed for measuring X-ray and gamma radiation from small-volume, low-activity liquid samples with an overall uncertainty better than 0.7% (one sigma SD). The radiation detector includes a hyperpure germanium well detector, a collimator, and a reference source. The well detector monitors gamma radiation emitted by the reference source and a radioactive isotope or isotopes in a sample source. The radiation from the reference source is collimated to avoid attenuation of reference source gamma radiation by the sample. Signals from the well detector are processed and stored, and the stored data is analyzed to determine the radioactive isotope(s) content of the sample. Minor self-attenuation corrections are calculated from chemical composition data. 4 figures.

Molecular typing of the recently expanding subtype B HIV-1 epidemic in Romania: evidence for local spread among MSMs in Bucharest area.

PubMed

Paraschiv, Simona; Otelea, Dan; Batan, Ionelia; Baicus, Cristian; Magiorkinis, Gkikas; Paraskevis, Dimitrios

2012-07-01

HIV-1 subtype B is predominant in Europe except in some countries from Eastern Europe which are characterized by a high prevalence of non-B subtypes and circulating recombinant forms (CRFs). Romania is a particular case: the HIV-1 epidemic started with subtype F1 which is still the most prevalent. Previous studies have shown an increasing prevalence of subtype B which is the second most frequent one among the newly diagnosed individuals, followed by subtype C and several CRFs as well as unique recombinant forms (URFs). Our objective was to analyze in detail the characteristics (way of dispersal, association with transmission risk groups) of the subtype B infections in Romania by means of phylogenetic analysis. Among all the individuals sampled during 2003-2010, 71 out of 1127 patients (6.3%) have been identified to be infected with subtype B strains. The most frequent route of infection identified in HIV-1 subtype B patients in Romania was MSM transmission (39.6%), followed by the heterosexual route (35.2%). Many of the patients acquired the infection abroad, mainly in Western European countries. Phylogenetic analysis indicated the existence of a local transmission network (monophyletic clade) including 14 patients, mainly MSM living in the Bucharest area. We estimate the origin of the local transmission network that dates at the beginning of the 90s; the introduction of the F1 and C subtypes occurred earlier. The rest of the sequences were intermixed with reference strains sampled across Europe suggesting that single infection were not followed by subsequent dispersal within the local population. Although HIV-1 subtype B epidemic in Romania is recent, there is evidence for local spread among the MSMs, in addition to multiple introductions. Copyright © 2012 Elsevier B.V. All rights reserved.

Estimating local noise power spectrum from a few FBP-reconstructed CT scans

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

Zeng, Rongping, E-mail: rongping.zeng@fda.hhs.gov; Gavrielides, Marios A.; Petrick, Nicholas

Purpose: Traditional ways to estimate 2D CT noise power spectrum (NPS) involve an ensemble average of the power spectrums of many noisy scans. When only a few scans are available, regions of interest are often extracted from different locations to obtain sufficient samples to estimate the NPS. Using image samples from different locations ignores the nonstationarity of CT noise and thus cannot accurately characterize its local properties. The purpose of this work is to develop a method to estimate local NPS using only a few fan-beam CT scans. Methods: As a result of FBP reconstruction, the CT NPS has themore » same radial profile shape for all projection angles, with the magnitude varying with the noise level in the raw data measurement. This allows a 2D CT NPS to be factored into products of a 1D angular and a 1D radial function in polar coordinates. The polar separability of CT NPS greatly reduces the data requirement for estimating the NPS. The authors use this property and derive a radial NPS estimation method: in brief, the radial profile shape is estimated from a traditional NPS based on image samples extracted at multiple locations. The amplitudes are estimated by fitting the traditional local NPS to the estimated radial profile shape. The estimated radial profile shape and amplitudes are then combined to form a final estimate of the local NPS. We evaluate the accuracy of the radial NPS method and compared it to traditional NPS methods in terms of normalized mean squared error (NMSE) and signal detectability index. Results: For both simulated and real CT data sets, the local NPS estimated with no more than six scans using the radial NPS method was very close to the reference NPS, according to the metrics of NMSE and detectability index. Even with only two scans, the radial NPS method was able to achieve a fairly good accuracy. Compared to those estimated using traditional NPS methods, the accuracy improvement was substantial when a few scans were available. Conclusions: The radial NPS method was shown to be accurate and efficient in estimating the local NPS of FBP-reconstructed 2D CT images. It presents strong advantages over traditional NPS methods when the number of scans is limited and can be extended to estimate the in-plane NPS of cone-beam CT and multislice helical CT scans.« less

Influence of population selection on the 99th percentile reference value for cardiac troponin assays.

PubMed

Collinson, Paul O; Heung, Yen Ming; Gaze, David; Boa, Frances; Senior, Roxy; Christenson, Robert; Apple, Fred S

2012-01-01

We sought to determine the effect of patient selection on the 99th reference percentile of 2 sensitive and 1 high-sensitivity (hs) cardiac troponin assays in a well-defined reference population. Individuals>45 years old were randomly selected from 7 representative local community practices. Detailed information regarding the participants was collected via questionnaires. The healthy reference population was defined as individuals who had no history of vascular disease, hypertension, or heavy alcohol intake; were not receiving cardiac medication; and had blood pressure<140/90 mmHg, fasting blood glucose<110 mg/dL (approximately 6 mmol/L), estimated creatinine clearance>60 mL·min(-1)·(1.73 m2)(-1), and normal cardiac function according to results of echocardiography. Samples were stored at -70 °C until analysis for cardiac troponin I (cTnI) and cardiac troponin T (cTnT) and N-terminal pro-B-type natriuretic peptide. Application of progressively more stringent population selection strategies to the initial baseline population of 545 participants until the only individuals who remained were completely healthy according to the study criteria reduced the number of outliers seen and led to a progressive decrease in the 99th-percentile value obtained for the Roche hs-cTnT assay and the sensitive Beckman cTnI assay but not for the sensitive Siemens Ultra cTnI assay. Furthermore, a sex difference found in the baseline population for the hs-cTnT (P=0.0018) and Beckman cTnI assays (P<0.0001) progressively decreased with more stringent population selection criteria. The reference population selection strategy significantly influenced the 99th percentile reference values determined for troponin assays and the observed sex differences in troponin concentrations.

Radioiodine detector based on laser induced fluorescence

DOEpatents

McDonald, Jimmie R.; Baronavski, Andrew P.

1980-01-01

The invention involves the measurement of the concentration of the radioisotope .sup.129 I.sub.2 in the presence of a gas. The invention uses a laser to excite a sample of the .sup.129 I.sub.2 in a sample gas chamber and a reference sample of a known concentration of .sup.129 I.sub.2 in a reference gas chamber. The .sup.129 I.sub.2 in the sample and reference gas chamber each gives off fluorescence emissions which are received by photomultipliers which provide signals to a detector. The detector uses a ratioing technique to determine the concentration of .sup.129 I.sub.2 in the sample gas chamber.

Reference Value Advisor: a new freeware set of macroinstructions to calculate reference intervals with Microsoft Excel.

PubMed

Geffré, Anne; Concordet, Didier; Braun, Jean-Pierre; Trumel, Catherine

2011-03-01

International recommendations for determination of reference intervals have been recently updated, especially for small reference sample groups, and use of the robust method and Box-Cox transformation is now recommended. Unfortunately, these methods are not included in most software programs used for data analysis by clinical laboratories. We have created a set of macroinstructions, named Reference Value Advisor, for use in Microsoft Excel to calculate reference limits applying different methods. For any series of data, Reference Value Advisor calculates reference limits (with 90% confidence intervals [CI]) using a nonparametric method when n≥40 and by parametric and robust methods from native and Box-Cox transformed values; tests normality of distributions using the Anderson-Darling test and outliers using Tukey and Dixon-Reed tests; displays the distribution of values in dot plots and histograms and constructs Q-Q plots for visual inspection of normality; and provides minimal guidelines in the form of comments based on international recommendations. The critical steps in determination of reference intervals are correct selection of as many reference individuals as possible and analysis of specimens in controlled preanalytical and analytical conditions. Computing tools cannot compensate for flaws in selection and size of the reference sample group and handling and analysis of samples. However, if those steps are performed properly, Reference Value Advisor, available as freeware at http://www.biostat.envt.fr/spip/spip.php?article63, permits rapid assessment and comparison of results calculated using different methods, including currently unavailable methods. This allows for selection of the most appropriate method, especially as the program provides the CI of limits. It should be useful in veterinary clinical pathology when only small reference sample groups are available. ©2011 American Society for Veterinary Clinical Pathology.

Networking DEC and IBM computers

NASA Technical Reports Server (NTRS)

Mish, W. H.

1983-01-01

Local Area Networking of DEC and IBM computers within the structure of the ISO-OSI Seven Layer Reference Model at a raw signaling speed of 1 Mops or greater are discussed. After an introduction to the ISO-OSI Reference Model nd the IEEE-802 Draft Standard for Local Area Networks (LANs), there follows a detailed discussion and comparison of the products available from a variety of manufactures to perform this networking task. A summary of these products is presented in a table.

Children and adults exposed to electromagnetic fields at the ICNIRP reference levels: theoretical assessment of the induced peak temperature increase.

PubMed

Bakker, J F; Paulides, M M; Neufeld, E; Christ, A; Kuster, N; van Rhoon, G C

2011-08-07

To avoid potentially adverse health effects of electromagnetic fields (EMF), the International Commission on Non-Ionizing Radiation Protection (ICNIRP) has defined EMF reference levels. Restrictions on induced whole-body-averaged specific absorption rate (SAR(wb)) are provided to keep the whole-body temperature increase (T(body, incr)) under 1 °C during 30 min. Additional restrictions on the peak 10 g spatial-averaged SAR (SAR(10g)) are provided to prevent excessive localized tissue heating. The objective of this study is to assess the localized peak temperature increase (T(incr, max)) in children upon exposure at the reference levels. Finite-difference time-domain modeling was used to calculate T(incr, max) in six children and two adults exposed to orthogonal plane-wave configurations. We performed a sensitivity study and Monte Carlo analysis to assess the uncertainty of the results. Considering the uncertainties in the model parameters, we found that a peak temperature increase as high as 1 °C can occur for worst-case scenarios at the ICNIRP reference levels. Since the guidelines are deduced from temperature increase, we used T(incr, max) as being a better metric to prevent excessive localized tissue heating instead of localized peak SAR. However, we note that the exposure time should also be considered in future guidelines. Hence, we advise defining limits on T(incr, max) for specified durations of exposure.

Psychological Factors Predict Local and Referred Experimental Muscle Pain: A Cluster Analysis in Healthy Adults

PubMed Central

Lee, Jennifer E.; Watson, David; Frey-Law, Laura A.

2012-01-01

Background Recent studies suggest an underlying three- or four-factor structure explains the conceptual overlap and distinctiveness of several negative emotionality and pain-related constructs. However, the validity of these latent factors for predicting pain has not been examined. Methods A cohort of 189 (99F; 90M) healthy volunteers completed eight self-report negative emotionality and pain-related measures (Eysenck Personality Questionnaire-Revised; Positive and Negative Affect Schedule; State-Trait Anxiety Inventory; Pain Catastrophizing Scale; Fear of Pain Questionnaire; Somatosensory Amplification Scale; Anxiety Sensitivity Index; Whiteley Index). Using principal axis factoring, three primary latent factors were extracted: General Distress; Catastrophic Thinking; and Pain-Related Fear. Using these factors, individuals clustered into three subgroups of high, moderate, and low negative emotionality responses. Experimental pain was induced via intramuscular acidic infusion into the anterior tibialis muscle, producing local (infusion site) and/or referred (anterior ankle) pain and hyperalgesia. Results Pain outcomes differed between clusters (multivariate analysis of variance and multinomial regression), with individuals in the highest negative emotionality cluster reporting the greatest local pain (p = 0.05), mechanical hyperalgesia (pressure pain thresholds; p = 0.009) and greater odds (2.21 OR) of experiencing referred pain compared to the lowest negative emotionality cluster. Conclusion Our results provide support for three latent psychological factors explaining the majority of the variance between several pain-related psychological measures, and that individuals in the high negative emotionality subgroup are at increased risk for (1) acute local muscle pain; (2) local hyperalgesia; and (3) referred pain using a standardized nociceptive input. PMID:23165778

A method for atomic-level noncontact thermometry with electron energy distribution

NASA Astrophysics Data System (ADS)

Kinoshita, Ikuo; Tsukada, Chiharu; Ouchi, Kohei; Kobayashi, Eiichi; Ishii, Juntaro

2017-04-01

We devised a new method of determining the temperatures of materials with their electron-energy distributions. The Fermi-Dirac distribution convoluted with a linear combination of Gaussian and Lorentzian distributions was fitted to the photoelectron spectrum measured for the Au(110) single-crystal surface at liquid N2-cooled temperature. The fitting successfully determined the surface-local thermodynamic temperature and the energy resolution simultaneously from the photoelectron spectrum, without any preliminary results of other measurements. The determined thermodynamic temperature was 99 ± 2.1 K, which was in good agreement with the reference temperature of 98.5 ± 0.5 K measured using a silicon diode sensor attached to the sample holder.

Collagenous gastritis.

PubMed

Jin, Xiaoyi; Koike, Tomoyuki; Chiba, Takashi; Kondo, Yutaka; Ara, Nobuyuki; Uno, Kaname; Asano, Naoki; Iijima, Katsunori; Imatani, Akira; Watanabe, Mika; Shirane, Akio; Shimosegawa, Tooru

2013-09-01

In the present paper, we report a case of rare collagenous gastritis. The patient was a 25-year-old man who had experienced nausea, abdominal distention and epigastralgia since 2005. Esophagogastroduodenoscopy (EGD) carried out at initial examination by the patient's local doctor revealed an extensively discolored depression from the upper gastric body to the lower gastric body, mainly including the greater curvature, accompanied by residual mucosa with multiple islands and nodularity with a cobblestone appearance. Initial biopsies sampled from the nodules and accompanying atrophic mucosa were diagnosed as chronic gastritis. In August, 2011, the patient was referred to Tohoku University Hospital for observation and treatment. EGD at our hospital showed the same findings as those by the patient's local doctor. Pathological findings included a membranous collagen band in the superficial layer area of the gastric mucosa, which led to a diagnosis of collagenous gastritis. Collagenous gastritis is an extremely rare disease, but it is important to recognize its characteristic endoscopic findings to make a diagnosis. © 2012 The Authors. Digestive Endoscopy © 2012 Japan Gastroenterological Endoscopy Society.

Combining near-field scanning optical microscopy with spectral interferometry for local characterization of the optical electric field in photonic structures.

PubMed

Trägårdh, Johanna; Gersen, Henkjan

2013-07-15

We show how a combination of near-field scanning optical microscopy with crossed beam spectral interferometry allows a local measurement of the spectral phase and amplitude of light propagating in photonic structures. The method only requires measurement at the single point of interest and at a reference point, to correct for the relative phase of the interferometer branches, to retrieve the dispersion properties of the sample. Furthermore, since the measurement is performed in the spectral domain, the spectral phase and amplitude could be retrieved from a single camera frame, here in 70 ms for a signal power of less than 100 pW limited by the dynamic range of the 8-bit camera. The method is substantially faster than most previous time-resolved NSOM methods that are based on time-domain interferometry, which also reduced problems with drift. We demonstrate how the method can be used to measure the refractive index and group velocity in a waveguide structure.

Buckligami: Actuation of soft structures through mechanical instabilities

NASA Astrophysics Data System (ADS)

Lazarus, Arnaud; Reis, Pedro

2013-03-01

We present a novel mechanism for actuating soft structures, that is triggered through buckling. Our elastomeric samples are rapid-prototyped using digital fabrication and comprise of a cylindrical shell patterned with an array of voids, each of which is covered by a thin membrane. Decreasing the internal pressure of the structure induces local buckling of the ligaments of the pattern, resulting in controllable folding of the global structure. Using rigid inclusions to plug the voids in specific geometric arrangements allows us to excite a variety of different fundamental motions of the cylindrical shell, including flexure and twist. We refer to this new mechanism of buckling-induced folding as ``buckligami.'' Given that geometry, elasticity and buckling are the underlying ingredients of this local folding mechanism, the global actuation is scalable, reversible and repeatable. Characterization and rationalization of our experiments provide crucial fundamental understanding to aid the design of new scale-independent actuators, with potential implications in the field of soft robotics.

Humidity effect on nanoscale electrochemistry in solid silver ion conductors and the dual nature of its locality.

PubMed

Yang, Sang Mo; Strelcov, Evgheni; Paranthaman, M Parans; Tselev, Alexander; Noh, Tae Won; Kalinin, Sergei V

2015-02-11

Scanning probe microscopy (SPM) is a powerful tool to investigate electrochemistry in nanoscale volumes. While most SPM-based studies have focused on reactions at the tip-surface junction, charge and mass conservation requires coupled and intrinsically nonlocal cathodic and anodic processes that can be significantly affected by ambient humidity. Here, we explore the role of water in both cathodic and anodic processes, associated charge transport, and topographic volume changes depending on the polarity of tip bias. The first-order reversal curve current-voltage technique combined with simultaneous detection of the sample topography, referred to as FORC-IVz, was applied to a silver solid ion conductor. We found that the protons generated from water affect silver ionic conduction, silver particle formation and dissolution, and mechanical integrity of the material. This work highlights the dual nature (simultaneously local and nonlocal) of electrochemical SPM studies, which should be considered for comprehensive understanding of nanoscale electrochemistry.

SU-E-P-08: Establishment of Local Diagnostic Reference Levels of Routine Abdomen Exam in Computed Tomography According to Body Weight

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

Wang, H; Wang, Y; Weng, H

Purpose: The national diagnostic reference levels (NDRLs) is an efficient, concise and powerful standard for optimizing radiation protection of a patient. However, for each hospital the dose-reducing potential of focusing on establishment of local DRLs (LDRLs). A lot of study reported that Computed tomography exam contributed majority radiation dose in different medical modalities, therefore, routine abdomen CT exam was choose in initial pilot study in our study. Besides the mAs of routine abdomen CT exam was decided automatic exposure control by linear attenuation is relate to body shape of patient. In this study we would like to establish the localmore » diagnostic reference levels of routine abdomen exam in computed tomography according to body weight of patient. Methods and Materials: There are two clinical CT scanners (a Toshiba Aquilion and a Siemens Sensation) were performed in this study. For CT examinations the basic recommended dosimetric quantity is the Computed Tomography Dose Index (CTDI). The patient sample involved 82 adult patients of both sexes and divided into three groups by their body weight (50–60 kg, 60–70 kg, 70–80 kg).Carried out the routine abdomen examinations, and all exposure parameters have been collected and the corresponding CTDIv and DLP values have been determined. The average values were compared with the European DRLs. Results: The majority of patients (75%) were between 50–70 Kg of body weight, the numbers of patient in each group of weight were 40–50:7; 50–60:29; 60–70:33; 70–80:13. The LDRLs in each group were 10.81mGy, 14.46mGy, 20.27mGy and 21.04mGy, respectively. The DLP were 477mGy, 630mGy, 887mGy and 959mGy, respectively. No matter which group the LDRLs were lower than European DRLs. Conclusions: We would like to state that this was a pioneer work in local hospital in Chiayi. We hope that this may lead the way to further developments in Taiwan.« less

[Local Regression Algorithm Based on Net Analyte Signal and Its Application in Near Infrared Spectral Analysis].

PubMed

Zhang, Hong-guang; Lu, Jian-gang

2016-02-01

Abstract To overcome the problems of significant difference among samples and nonlinearity between the property and spectra of samples in spectral quantitative analysis, a local regression algorithm is proposed in this paper. In this algorithm, net signal analysis method(NAS) was firstly used to obtain the net analyte signal of the calibration samples and unknown samples, then the Euclidean distance between net analyte signal of the sample and net analyte signal of calibration samples was calculated and utilized as similarity index. According to the defined similarity index, the local calibration sets were individually selected for each unknown sample. Finally, a local PLS regression model was built on each local calibration sets for each unknown sample. The proposed method was applied to a set of near infrared spectra of meat samples. The results demonstrate that the prediction precision and model complexity of the proposed method are superior to global PLS regression method and conventional local regression algorithm based on spectral Euclidean distance.

Dual frequency optical carrier technique for transmission of reference frequencies in dispersive media

NASA Technical Reports Server (NTRS)

Maleki, Lutfollah (Inventor)

1993-01-01

Two different carrier frequencies modulated by a reference frequency are transmitted to each receiver to be synchronized therewith. Each receiver responds to local phase differences between the two received signals to correct the phase of one of them so as to maintain the corrected signal as a reliable synchronization reference.

A Pragmatic Approach to HIV-1 Drug Resistance Determination in Resource-Limited Settings by Use of a Novel Genotyping Assay Targeting the Reverse Transcriptase-Encoding Region Only

PubMed Central

Bronze, Michelle; Wallis, Carole L.; Stuyver, Lieven; Steegen, Kim; Balinda, Sheila; Kityo, Cissy; Stevens, Wendy; Rinke de Wit, Tobias F.; Schuurman, Rob

2013-01-01

In resource-limited settings (RLS), reverse transcriptase (RT) inhibitors form the backbone of first-line treatment regimens. We have developed a simplified HIV-1 drug resistance genotyping assay targeting the region of RT harboring all major RT inhibitor resistance mutation positions, thus providing all relevant susceptibility data for first-line failures, coupled with minimal cost and labor. The assay comprises a one-step RT-PCR amplification reaction, followed by sequencing using one forward and one reverse primer, generating double-stranded coverage of RT amino acids (aa) 41 to 238. The assay was optimized for all major HIV-1 group M subtypes in plasma and dried blood spot (DBS) samples using a panel of reference viruses for HIV-1 subtypes A to D, F to H, and circulating recombinant form 01_AE (CRF01_AE) and applied to 212 clinical plasma samples and 25 DBS samples from HIV-1-infected individuals from Africa and Europe. The assay was subsequently transferred to Uganda and applied locally on clinical plasma samples. All major HIV-1 subtypes could be detected with an analytical sensitivity of 5.00E+3 RNA copies/ml for plasma and DBS. Application of the assay on 212 clinical samples from African subjects comprising subtypes A to D, F to H (rare), CRF01_AE, and CRF02_AG at a viral load (VL) range of 6.71E+2 to 1.00E+7 (median, 1.48E+5) RNA copies/ml was 94.8% (n = 201) successful. Application on clinical samples in Uganda demonstrated a comparable success rate. Genotyping of clinical DBS samples, all subtype C with a VL range of 1.02E+3 to 4.49E+5 (median, 1.42E+4) RNA copies/ml, was 84.0% successful. The described assay greatly reduces hands-on time and the costs required for genotyping and is ideal for use in RLS, as demonstrated in a reference laboratory in Uganda and its successful application on DBS samples. PMID:23536405

Use of Naturally Available Reference Targets to Calibrate Airborne Laser Scanning Intensity Data

PubMed Central

Vain, Ants; Kaasalainen, Sanna; Pyysalo, Ulla; Krooks, Anssi; Litkey, Paula

2009-01-01

We have studied the possibility of calibrating airborne laser scanning (ALS) intensity data, using land targets typically available in urban areas. For this purpose, a test area around Espoonlahti Harbor, Espoo, Finland, for which a long time series of ALS campaigns is available, was selected. Different target samples (beach sand, concrete, asphalt, different types of gravel) were collected and measured in the laboratory. Using tarps, which have certain backscattering properties, the natural samples were calibrated and studied, taking into account the atmospheric effect, incidence angle and flying height. Using data from different flights and altitudes, a time series for the natural samples was generated. Studying the stability of the samples, we could obtain information on the most ideal types of natural targets for ALS radiometric calibration. Using the selected natural samples as reference, the ALS points of typical land targets were calibrated again and examined. Results showed the need for more accurate ground reference data, before using natural samples in ALS intensity data calibration. Also, the NIR camera-based field system was used for collecting ground reference data. This system proved to be a good means for collecting in situ reference data, especially for targets with inhomogeneous surface reflection properties. PMID:22574045

25 CFR 47.10 - How is the local educational financial plan developed?

Code of Federal Regulations, 2010 CFR

2010-04-01

... notes any problem with the plan, he or she must: (i) Notify the local board and local supervisor of the problem within two weeks of receiving the plan; (ii) Make arrangements to assist the local school supervisor and board to correct the problem; and (iii) Refer the problem to the Director of the Office of...

Uptake of non-invasive prenatal testing in Chinese women: money matters.

PubMed

Han, J; Zhen, L; Pan, M; Yang, X; Ou, Y-M; Liao, C; Li, D-Z

2015-12-01

To determine the influence of free invasive prenatal testing on the uptake of non-invasive prenatal testing (NIPT). Over a 2-year period at a Chinese tertiary prenatal diagnostic unit, women at risk of fetal trisomy were given the option of NIPT or invasive prenatal testing. Invasive prenatal testing was offered free of charge to women with a local Hukou (household registration); however, women without a local Hukou were charged for invasive prenatal testing. Both women with and without a local Hukou were charged for NIPT. During the first year, 2647 women with a positive trisomy 21 screening test were referred (474 women with a local Hukou and 2173 women without a local Hukou). Only 1.6% of the women with a local Hukou underwent NIPT, while this proportion was 20.6% in the women without a local Hukou. During the second year, the price of NIPT was reduced. The total number of women referred was 3047 (502 women with a local Hukou and 2545 women without a local Hukou). The uptake of NIPT in women without a local Hukou doubled, but the uptake of NIPT remained stable in women with a local Hukou. The financial impact on the uptake of NIPT should not be underestimated. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Genotype Imputation with Millions of Reference Samples.

PubMed

Browning, Brian L; Browning, Sharon R

2016-01-07

We present a genotype imputation method that scales to millions of reference samples. The imputation method, based on the Li and Stephens model and implemented in Beagle v.4.1, is parallelized and memory efficient, making it well suited to multi-core computer processors. It achieves fast, accurate, and memory-efficient genotype imputation by restricting the probability model to markers that are genotyped in the target samples and by performing linear interpolation to impute ungenotyped variants. We compare Beagle v.4.1 with Impute2 and Minimac3 by using 1000 Genomes Project data, UK10K Project data, and simulated data. All three methods have similar accuracy but different memory requirements and different computation times. When imputing 10 Mb of sequence data from 50,000 reference samples, Beagle's throughput was more than 100× greater than Impute2's throughput on our computer servers. When imputing 10 Mb of sequence data from 200,000 reference samples in VCF format, Minimac3 consumed 26× more memory per computational thread and 15× more CPU time than Beagle. We demonstrate that Beagle v.4.1 scales to much larger reference panels by performing imputation from a simulated reference panel having 5 million samples and a mean marker density of one marker per four base pairs. Copyright © 2016 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

USE OF NATURAL WATERS AS U. S. GEOLOGICAL SURVEY REFERENCE SAMPLES.

USGS Publications Warehouse

Janzer, Victor J.

1985-01-01

The U. S. Geological Survey conducts research and collects hydrologic data relating to the Nation's water resources. Seven types of natural matrix reference water samples are prepared for use in the Survey's quality assurance program. These include samples containing major constituents, trace metals, nutrients, herbicides, insecticides, trace metals in a water and suspended-sediment mixture, and precipitation (snowmelt). To prepare these reference samples, natural water is collected in plastic drums and the sediment is allowed to settle. The water is then filtered, selected constituents are added, and if necessary the water is acidified and sterilized by ultraviolet irradiation before bottling in plastic or glass. These reference samples are distributed twice yearly to more than 100 laboratories for chemical analysis. The most probable values for each constituent are determined by evaluating the data submitted by the laboratories using statistical techniques recommended by ASTM.

Global reference frame: Intercomparison of results (SLR, VLBI and GPS)

NASA Technical Reports Server (NTRS)

Ma, Chopo; Watkins, Michael M.; Heflin, M.

1994-01-01

The terrestrial reference frame (TRF) is realized by a set of positions and velocities derived from a combination of the three space geodetic techniques, SLR, VLBI and GPS. The standard International TRF is constructed by the International Earth Rotation Service in such a way that it is stable with time and the addition of new data. An adopted model for overall plate motion, NUVEL-1 NNR, defines the conceptual reference frame in which all the plates are moving. In addition to the measurements made between reference points within the space geodetic instruments, it is essential to have accurate, documented eccentricity measurements from the instrument reference points to ground monuments. Proper local surveys between the set of ground monuments at a site are also critical for the use of the space geodetic results. Eccentricities and local surveys are, in fact, the most common and vexing sources of error in the use of the TRF for such activities as collocation and intercomparison.

Determining optimal parameters of the self-referent encoding task: A large-scale examination of self-referent cognition and depression.

PubMed

Dainer-Best, Justin; Lee, Hae Yeon; Shumake, Jason D; Yeager, David S; Beevers, Christopher G

2018-06-07

Although the self-referent encoding task (SRET) is commonly used to measure self-referent cognition in depression, many different SRET metrics can be obtained. The current study used best subsets regression with cross-validation and independent test samples to identify the SRET metrics most reliably associated with depression symptoms in three large samples: a college student sample (n = 572), a sample of adults from Amazon Mechanical Turk (n = 293), and an adolescent sample from a school field study (n = 408). Across all 3 samples, SRET metrics associated most strongly with depression severity included number of words endorsed as self-descriptive and rate of accumulation of information required to decide whether adjectives were self-descriptive (i.e., drift rate). These metrics had strong intratask and split-half reliability and high test-retest reliability across a 1-week period. Recall of SRET stimuli and traditional reaction time (RT) metrics were not robustly associated with depression severity. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Determination of the platinum - Group elements (PGE) and gold (Au) in manganese nodule reference samples by nickel sulfide fire-assay and Te coprecipitation with ICP-MS

USGS Publications Warehouse

Balaram, V.; Mathur, R.; Banakar, V.K.; Hein, J.R.; Rao, C.R.M.; Gnaneswara, Rao T.; Dasaram, B.

2006-01-01

Platinum group elements (PGE) and Au data in polymetallic oceanic ferromanganese nodule reference samples and crust samples obtained by inductively coupled plasma mass spectrometry (ICP-MS), after separation and pre-concentration by nickel sulfide fire-assay and Te coprecipitation, are presented. By optimizing several critical parameters such as flux composition, matrix matching calibration, etc., best experimental conditions were established to develop a method suitable for routine analysis of manganese nodule samples for PGE and Au. Calibrations were performed using international PGE reference materials, WMG-1 and WMS-1. This improved procedure offers extremely low detection limits in the range of 0.004 to 0.016 ng/g. The results obtained in this study for the reference materials compare well with previously published data wherever available. New PGE data arc also provided on some international manganese nodule reference materials. The analytical methodology described here can be used for the routine analysis of manganese nodule and crust samples in marine geochemical studies.

Collaborative localization in wireless sensor networks via pattern recognition in radio irregularity using omnidirectional antennas.

PubMed

Jiang, Joe-Air; Chuang, Cheng-Long; Lin, Tzu-Shiang; Chen, Chia-Pang; Hung, Chih-Hung; Wang, Jiing-Yi; Liu, Chang-Wang; Lai, Tzu-Yun

2010-01-01

In recent years, various received signal strength (RSS)-based localization estimation approaches for wireless sensor networks (WSNs) have been proposed. RSS-based localization is regarded as a low-cost solution for many location-aware applications in WSNs. In previous studies, the radiation patterns of all sensor nodes are assumed to be spherical, which is an oversimplification of the radio propagation model in practical applications. In this study, we present an RSS-based cooperative localization method that estimates unknown coordinates of sensor nodes in a network. Arrangement of two external low-cost omnidirectional dipole antennas is developed by using the distance-power gradient model. A modified robust regression is also proposed to determine the relative azimuth and distance between a sensor node and a fixed reference node. In addition, a cooperative localization scheme that incorporates estimations from multiple fixed reference nodes is presented to improve the accuracy of the localization. The proposed method is tested via computer-based analysis and field test. Experimental results demonstrate that the proposed low-cost method is a useful solution for localizing sensor nodes in unknown or changing environments.

14 CFR 171.263 - Localizer automatic monitor system.

Code of Federal Regulations, 2012 CFR

2012-01-01

... (CONTINUED) NAVIGATIONAL FACILITIES NON-FEDERAL NAVIGATION FACILITIES Interim Standard Microwave Landing... provide an automatic monitor system that transmits a warning to designated local and remote control points... centerline equivalent to more than 0.015 DDM at the ISMLS reference datum. (2) For localizers in which the...

14 CFR 171.263 - Localizer automatic monitor system.

Code of Federal Regulations, 2014 CFR

2014-01-01

... (CONTINUED) NAVIGATIONAL FACILITIES NON-FEDERAL NAVIGATION FACILITIES Interim Standard Microwave Landing... provide an automatic monitor system that transmits a warning to designated local and remote control points... centerline equivalent to more than 0.015 DDM at the ISMLS reference datum. (2) For localizers in which the...

14 CFR 171.263 - Localizer automatic monitor system.

Code of Federal Regulations, 2010 CFR

2010-01-01

... (CONTINUED) NAVIGATIONAL FACILITIES NON-FEDERAL NAVIGATION FACILITIES Interim Standard Microwave Landing... provide an automatic monitor system that transmits a warning to designated local and remote control points... centerline equivalent to more than 0.015 DDM at the ISMLS reference datum. (2) For localizers in which the...

14 CFR 171.263 - Localizer automatic monitor system.

Code of Federal Regulations, 2011 CFR

2011-01-01

... (CONTINUED) NAVIGATIONAL FACILITIES NON-FEDERAL NAVIGATION FACILITIES Interim Standard Microwave Landing... provide an automatic monitor system that transmits a warning to designated local and remote control points... centerline equivalent to more than 0.015 DDM at the ISMLS reference datum. (2) For localizers in which the...

14 CFR 171.263 - Localizer automatic monitor system.

Code of Federal Regulations, 2013 CFR

2013-01-01

... (CONTINUED) NAVIGATIONAL FACILITIES NON-FEDERAL NAVIGATION FACILITIES Interim Standard Microwave Landing... provide an automatic monitor system that transmits a warning to designated local and remote control points... centerline equivalent to more than 0.015 DDM at the ISMLS reference datum. (2) For localizers in which the...

Anthropogenic influence on surface water quality of the Nhue and Day sub-river systems in Vietnam.

PubMed

Hanh, Pham Thi Minh; Sthiannopkao, Suthipong; Kim, Kyoung-Woong; Ba, Dang The; Hung, Nguyen Quang

2010-06-01

In order to investigate the temporal and spatial variations of 14 physical and chemical surface water parameters in the Nhue and Day sub-river systems of Vietnam, surface water samples were taken from 43 sampling sites during the dry and rainy seasons in 2007. The results were statistically examined by Mann-Whitney U-test and hierarchical cluster analysis. The results show that water quality of the Day River was significantly improved during the rainy season while this was not the case of the Nhue River. However, the river water did not meet the Vietnamese surface water quality standards for dissolved oxygen (DO), biological oxygen demand (BOD(5)), chemical oxygen demand (COD), nutrients, total coliform, and fecal coliform. This implies that the health of local communities using untreated river water for drinking purposes as well as irrigation of vegetables may be at risk. Forty-three sampling sites were grouped into four main clusters on the basis of water quality characteristics with particular reference to geographic location and land use and revealed the contamination levels from anthropogenic sources.

Spectroscopic diagnostics for bacteria in biologic sample

DOEpatents

El-Sayed, Mostafa A.; El-Sayed, Ivan H.

2002-01-01

A method to analyze and diagnose specific bacteria in a biologic sample using spectroscopy is disclosed. The method includes obtaining the spectra of a biologic sample of a non-infected patient for use as a reference, subtracting the reference from the spectra of an infected sample, and comparing the fingerprint regions of the resulting differential spectrum with reference spectra of bacteria in saline. Using this diagnostic technique, specific bacteria can be identified sooner and without culturing, bacteria-specific antibiotics can be prescribed sooner, resulting in decreased likelihood of antibiotic resistance and an overall reduction of medical costs.

Gene Expression Profile Analysis is Directly Affected by the Selected Reference Gene: The Case of Leaf-Cutting Atta Sexdens

PubMed Central

Máximo, Wesley P. F.; Zanetti, Ronald; Paiva, Luciano V.

2018-01-01

Although several ant species are important targets for the development of molecular control strategies, only a few studies focus on identifying and validating reference genes for quantitative reverse transcription polymerase chain reaction (RT-qPCR) data normalization. We provide here an extensive study to identify and validate suitable reference genes for gene expression analysis in the ant Atta sexdens, a threatening agricultural pest in South America. The optimal number of reference genes varies according to each sample and the result generated by RefFinder differed about which is the most suitable reference gene. Results suggest that the RPS16, NADH and SDHB genes were the best reference genes in the sample pool according to stability values. The SNF7 gene expression pattern was stable in all evaluated sample set. In contrast, when using less stable reference genes for normalization a large variability in SNF7 gene expression was recorded. There is no universal reference gene suitable for all conditions under analysis, since these genes can also participate in different cellular functions, thus requiring a systematic validation of possible reference genes for each specific condition. The choice of reference genes on SNF7 gene normalization confirmed that unstable reference genes might drastically change the expression profile analysis of target candidate genes. PMID:29419794

Metabarcoding of Fecal Samples to Determine Herbivore Diets: A Case Study of the Endangered Pacific Pocket Mouse

PubMed Central

Adams, Cynthia R.; Kohn, Joshua R.; Fisher, Robert N.; Brehme, Cheryl S.

2016-01-01

Understanding the diet of an endangered species illuminates the animal’s ecology, habitat requirements, and conservation needs. However, direct observation of diet can be difficult, particularly for small, nocturnal animals such as the Pacific pocket mouse (Heteromyidae: Perognathus longimembris pacificus). Very little is known of the dietary habits of this federally endangered rodent, hindering management and restoration efforts. We used a metabarcoding approach to identify source plants in fecal samples (N = 52) from the three remaining populations known. The internal transcribed spacers (ITS) of the nuclear ribosomal loci were sequenced following the Illumina MiSeq amplicon strategy and processed reads were mapped to reference databases. We evaluated a range of threshold mapping criteria and found the best-performing setting generally recovered two distinct mock communities in proportions similar to expectation. We tested our method on captive animals fed a known diet and recovered almost all plant sources, but found substantial heterogeneity among fecal pellets collected from the same individual at the same time. Observed richness did not increase with pooling of pellets from the same individual. In field-collected samples, we identified 4–14 plant genera in individual samples and 74 genera overall, but over 50 percent of reads mapped to just six species in five genera. We simulated the effects of sequencing error, variable read length, and chimera formation to infer taxon-specific rates of misassignment for the local flora, which were generally low with some exceptions. Richness at the species and genus levels did not reach a clear asymptote, suggesting that diet breadth remained underestimated in the current pool of samples. Large numbers of scat samples are therefore needed to make inferences about diet and resource selection in future studies of the Pacific pocket mouse. We conclude that our minimally invasive method is promising for determining herbivore diets given a library of sequences from local plants. PMID:27851756

Metabarcoding of Fecal Samples to Determine Herbivore Diets: A Case Study of the Endangered Pacific Pocket Mouse.

PubMed

Iwanowicz, Deborah D; Vandergast, Amy G; Cornman, Robert S; Adams, Cynthia R; Kohn, Joshua R; Fisher, Robert N; Brehme, Cheryl S

2016-01-01

Understanding the diet of an endangered species illuminates the animal's ecology, habitat requirements, and conservation needs. However, direct observation of diet can be difficult, particularly for small, nocturnal animals such as the Pacific pocket mouse (Heteromyidae: Perognathus longimembris pacificus). Very little is known of the dietary habits of this federally endangered rodent, hindering management and restoration efforts. We used a metabarcoding approach to identify source plants in fecal samples (N = 52) from the three remaining populations known. The internal transcribed spacers (ITS) of the nuclear ribosomal loci were sequenced following the Illumina MiSeq amplicon strategy and processed reads were mapped to reference databases. We evaluated a range of threshold mapping criteria and found the best-performing setting generally recovered two distinct mock communities in proportions similar to expectation. We tested our method on captive animals fed a known diet and recovered almost all plant sources, but found substantial heterogeneity among fecal pellets collected from the same individual at the same time. Observed richness did not increase with pooling of pellets from the same individual. In field-collected samples, we identified 4-14 plant genera in individual samples and 74 genera overall, but over 50 percent of reads mapped to just six species in five genera. We simulated the effects of sequencing error, variable read length, and chimera formation to infer taxon-specific rates of misassignment for the local flora, which were generally low with some exceptions. Richness at the species and genus levels did not reach a clear asymptote, suggesting that diet breadth remained underestimated in the current pool of samples. Large numbers of scat samples are therefore needed to make inferences about diet and resource selection in future studies of the Pacific pocket mouse. We conclude that our minimally invasive method is promising for determining herbivore diets given a library of sequences from local plants.

Metabarcoding of fecal samples to determine herbivore diets: A case study of the endangered Pacific pocket mouse

USGS Publications Warehouse

Iwanowicz, Deborah; Vandergast, Amy; Cornman, Robert S.; Adams, Cynthia; Kohn, Joshua R.; Fisher, Robert N.; Brehme, Cheryl S.

2016-01-01

Understanding the diet of an endangered species illuminates the animal’s ecology, habitat requirements, and conservation needs. However, direct observation of diet can be difficult, particularly for small, nocturnal animals such as the Pacific pocket mouse (Heteromyidae: Perognathus longimembris pacificus). Very little is known of the dietary habits of this federally endangered rodent, hindering management and restoration efforts. We used a metabarcoding approach to identify source plants in fecal samples (N = 52) from the three remaining populations known. The internal transcribed spacers (ITS) of the nuclear ribosomal loci were sequenced following the Illumina MiSeq amplicon strategy and processed reads were mapped to reference databases. We evaluated a range of threshold mapping criteria and found the best-performing setting generally recovered two distinct mock communities in proportions similar to expectation. We tested our method on captive animals fed a known diet and recovered almost all plant sources, but found substantial heterogeneity among fecal pellets collected from the same individual at the same time. Observed richness did not increase with pooling of pellets from the same individual. In field-collected samples, we identified 4–14 plant genera in individual samples and 74 genera overall, but over 50 percent of reads mapped to just six species in five genera. We simulated the effects of sequencing error, variable read length, and chimera formation to infer taxon-specific rates of misassignment for the local flora, which were generally low with some exceptions. Richness at the species and genus levels did not reach a clear asymptote, suggesting that diet breadth remained underestimated in the current pool of samples. Large numbers of scat samples are therefore needed to make inferences about diet and resource selection in future studies of the Pacific pocket mouse. We conclude that our minimally invasive method is promising for determining herbivore diets given a library of sequences from local plants.

Beyond the double banana: improved recognition of temporal lobe seizures in long-term EEG.

PubMed

Rosenzweig, Ivana; Fogarasi, András; Johnsen, Birger; Alving, Jørgen; Fabricius, Martin Ejler; Scherg, Michael; Neufeld, Miri Y; Pressler, Ronit; Kjaer, Troels W; van Emde Boas, Walter; Beniczky, Sándor

2014-02-01

To investigate whether extending the 10-20 array with 6 electrodes in the inferior temporal chain and constructing computed montages increases the diagnostic value of ictal EEG activity originating in the temporal lobe. In addition, the accuracy of computer-assisted spectral source analysis was investigated. Forty EEG samples were reviewed by 7 EEG experts in various montages (longitudinal and transversal bipolar, common average, source derivation, source montage, current source density, and reference-free montages) using 2 electrode arrays (10-20 and the extended one). Spectral source analysis used source montage to calculate density spectral array, defining the earliest oscillatory onset. From this, phase maps were calculated for localization. The reference standard was the decision of the multidisciplinary epilepsy surgery team on the seizure onset zone. Clinical performance was compared with the double banana (longitudinal bipolar montage, 10-20 array). Adding the inferior temporal electrode chain, computed montages (reference free, common average, and source derivation), and voltage maps significantly increased the sensitivity. Phase maps had the highest sensitivity and identified ictal activity at earlier time-point than visual inspection. There was no significant difference concerning specificity. The findings advocate for the use of these digital EEG technology-derived analysis methods in clinical practice.

[Climatic analysis of heavy metal concentration associated with urban road-deposited sediment].

PubMed

Zafra-Mejía, Carlos; Santamaría-Galindo, Diana M; Torres-Galindo, Cristian D

2015-05-01

Objective To climatically assess (daily) the concentration of heavy metals (Pb and Cu) in sediment deposited on road surfaces of the localities of Kennedy and Puente Aranda (Bogota, D.C., Colombia). Additionally, the detected concentrations are to be evaluated with respect to the legislation chosen as reference point for the protection of human health in urban areas. Methods The concentration was determined by flame atomic absorption spectrometry. The samples were previously digested in a mixture of hydrochloric and nitric acid (3:1; aqua regia). Results The results show, with respect to road sediment closest to the size that could be potentially inhaled from the point of view of public health (≤ 10 µm), that the metal concentrations on average tend to increase in dry weather (29 %). In this regard, the concentrations during these time periods are on average 1.69 times higher than the lowest limit value set by the reference legislation. However, it is suggested that the metal concentrations are mostly due to the use of the land rather than weather conditions. Conclusions The findings are a reference point in Colombia for the discussion and publication of environmental regulations associated with the protection of human health from heavy metals and for visualizing future lines of research about the effect of climate change on metal concentrations in urban environments.

Calibration-Free Laser-Induced Breakdown Spectroscopy (CF-LIBS) with Standard Reference Line for the Analysis of Stainless Steel.

PubMed

Fu, Hongbo; Dong, Fengzhong; Wang, Huadong; Jia, Junwei; Ni, Zhibo

2017-08-01

In this work, calibration-free laser-induced breakdown spectroscopy (CF-LIBS) is used to analyze a certified stainless steel sample. Due to self-absorption of the spectral lines from the major element Fe and the sparse lines of trace elements, it is usually not easy to construct the Boltzmann plots of all species. A standard reference line method is proposed here to solve this difficulty under the assumption of local thermodynamic equilibrium so that the same temperature value for all elements present into the plasma can be considered. Based on the concentration and rich spectral lines of Fe, the Stark broadening of Fe(I) 381.584 nm and Saha-Boltzmann plots of this element are used to calculate the electron density and the plasma temperature, respectively. In order to determine the plasma temperature accurately, which is seriously affected by self-absorption, a pre-selection procedure for eliminating those spectral lines with strong self-absorption is employed. Then, one spectral line of each element is selected to calculate its corresponding concentration. The results from the standard reference lines with and without self-absorption of Fe are compared. This method allows us to measure trace element content and effectively avoid the adverse effects due to self-absorption.

Eastern Baltic region vs. Western Europe: modelling age related changes in the pubic symphysis and the auricular surface.

PubMed

Jatautis, Šarūnas; Jankauskas, Rimantas

2018-02-01

Objectives. The present study addresses the following two main questions: a) Is the pattern of skeletal ageing observed in well-known western European reference collections applicable to modern eastern Baltic populations, or are population-specific standards needed? b) What are the consequences for estimating the age-at-death distribution in the target population when differences in the estimates from reference data are not taken into account? Materials and methods. The dataset consists of a modern Lithuanian osteological reference collection, which is the only collection of this type in the eastern Baltic countries (n = 381); and two major western European reference collections, Coimbra (n = 264) and Spitalfields (n = 239). The age-related changes were evaluated using the scoring systems of Suchey-Brooks (Brooks & Suchey 1990) and Lovejoy et al. (1985), and were modelled via regression models for multinomial responses. A controlled experiment based on simulations and the Rostock Manifesto estimation protocol (Wood et al. 2002) was then carried out to assess the effect of using estimates from different reference samples and different regression models on estimates of the age-at-death distribution in the hypothetical target population. Results. The following key results were obtained in this study. a) The morphological alterations in the pubic symphysis were much faster among women than among men at comparable ages in all three reference samples. In contrast, we found no strong evidence in any of the reference samples that sex is an important factor to explain rate of changes in the auricular surface. b) The rate of ageing in the pubic symphysis seems to be similar across the three reference samples, but there is little evidence of a similar pattern in the auricular surface. That is, the estimated rate of age-related changes in the auricular surface was much faster in the LORC and the Coimbra samples than in the Spitalfields sample. c) The results of simulations showed that the differences in the estimates from the reference data result in noticeably different age-at-death distributions in the target population. Thus, a degree bias may be expected if estimates from the western European reference data are used to collect information on ages at death in the eastern Baltic region based on the changes in the auricular surface. d) Moreover, the bias is expected to be more pronounced if the fitted regression model improperly describes the reference data. Conclusions. Differences in the timing of age-related changes in skeletal traits are to be expected among European reference samples, and cannot be ignored when seeking to reliably estimate an age-at-death distribution in the target population. This form of bias should be taken into consideration in further studies of skeletal samples from the eastern Baltic region.

Birefringence imaging in biological tissue using polarization sensitive optical coherent tomography

DOEpatents

De Boer, Johannes F.; Milner, Thomas E.; Nelson, J. Stuart

2001-01-01

Employing a low coherence Michelson interferometer, two dimensional images of optical birefringence in turbid samples as a function of depth are measured. Polarization sensitive detection of the signal formed by interference of backscattered light from the sample and a mirror or reference plane in the reference arm which defines a reference optical path length, give the optical phase delay between light propagating along the fast and slow axes of the birefringence sample. Images showing the change in birefringence in response to irradiation of the sample are produced as an example of the detection apparatus and methodology. The technique allow rapid, noncontact investigation of tissue or sample diagnostic imaging for various medical or materials procedures.

Implementation in Indonesia of the WHO Pocket Book of Hospital Care for Children.

PubMed

Li, Michelle Y; Puspita, Ratih; Duke, Trevor; Agung, Fransisca H; Hegar, Badriul; Pritasari, Kirana; Weber, Martin W

2014-05-01

Effective implementation of evidence-based practice guidelines has the potential to improve quality of hospital care for children. To achieve this in Indonesia, a locally adapted version of the WHO Pocket Book of Hospital Care for Children was published in 2009. To document implementation of the Pocket Book in Indonesia and to compare uptake in health facilities in which there has been a quality-improvement approach involving audit and feedback with uptake in settings in which there has been only passive dissemination. Indonesian district health offices, district hospitals, health centres with beds, and medical schools were surveyed by telephone, and an online and telephone survey of paediatricians was conducted. Health facilities in four provinces were visited, and key stakeholders were interviewed. Health facilities were assessed on availability of the guidelines, use by staff, and their incorporation into hospital procedures and activities. There was evidence of use of the Pocket Book across Indonesia, despite limited funding for implementation. Its distribution had reached all provinces; 61% (33/54) of health facilities surveyed had a copy of the guidelines. Hospitals involved in a related quality audit were more likely to report use of the guidelines than hospitals exposed to passive dissemination, although this difference was not significant. Of 150 paediatricians sampled, 109 (73%) reported referring to the guidelines in their clinical practice. The guidelines have been incorporated into the postgraduate paediatric curriculum in four of 13 universities sampled. There was encouraging evidence of uptake of the Pocket Book in Indonesia following local adaptation, nationwide mailing distribution and small-scale local implementation activities.

Vehicle Localization by LIDAR Point Correlation Improved by Change Detection

NASA Astrophysics Data System (ADS)

Schlichting, A.; Brenner, C.

2016-06-01

LiDAR sensors are proven sensors for accurate vehicle localization. Instead of detecting and matching features in the LiDAR data, we want to use the entire information provided by the scanners. As dynamic objects, like cars, pedestrians or even construction sites could lead to wrong localization results, we use a change detection algorithm to detect these objects in the reference data. If an object occurs in a certain number of measurements at the same position, we mark it and every containing point as static. In the next step, we merge the data of the single measurement epochs to one reference dataset, whereby we only use static points. Further, we also use a classification algorithm to detect trees. For the online localization of the vehicle, we use simulated data of a vertical aligned automotive LiDAR sensor. As we only want to use static objects in this case as well, we use a random forest classifier to detect dynamic scan points online. Since the automotive data is derived from the LiDAR Mobile Mapping System, we are able to use the labelled objects from the reference data generation step to create the training data and further to detect dynamic objects online. The localization then can be done by a point to image correlation method using only static objects. We achieved a localization standard deviation of about 5 cm (position) and 0.06° (heading), and were able to successfully localize the vehicle in about 93 % of the cases along a trajectory of 13 km in Hannover, Germany.

Highly sensitive measurement of whole blood chromium by inductively coupled plasma mass spectrometry.

PubMed

Cieslak, Wendy; Pap, Kathleen; Bunch, Dustin R; Reineks, Edmunds; Jackson, Raymond; Steinle, Roxanne; Wang, Sihe

2013-02-01

Chromium (Cr), a trace metal element, is implicated in diabetes and cardiovascular disease. A hypochromic state has been associated with poor blood glucose control and unfavorable lipid metabolism. Sensitive and accurate measurement of blood chromium is very important to assess the chromium nutritional status. However, interferents in biological matrices and contamination make the sensitive analysis challenging. The primary goal of this study was to develop a highly sensitive method for quantification of total Cr in whole blood by inductively coupled plasma mass spectrometry (ICP-MS) and to validate the reference interval in a local healthy population. This method was developed on an ICP-MS with a collision/reaction cell. Interference was minimized using both kinetic energy discrimination between the quadrupole and hexapole and a selective collision gas (helium). Reference interval was validated in whole blood samples (n=51) collected in trace element free EDTA tubes from healthy adults (12 males, 39 females), aged 19-64 years (38.8±12.6), after a minimum of 8 h fasting. Blood samples were aliquoted into cryogenic vials and stored at -70 °C until analysis. The assay linearity was 3.42 to 1446.59 nmol/L with an accuracy of 87.7 to 99.8%. The high sensitivity was achieved by minimization of interference through selective kinetic energy discrimination and selective collision using helium. The reference interval for total Cr using a non-parametric method was verified to be 3.92 to 7.48 nmol/L. This validated ICP-MS methodology is highly sensitive and selective for measuring total Cr in whole blood. Copyright © 2012 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved. Published by Elsevier Inc. All rights reserved.

Contaminant exposure and reproductive success of Ospreys (Pandion haliaetus) nesting in Chesapeake Bay regions of concern

USGS Publications Warehouse

Rattner, B.A.; McGowan, P.C.; Golden, N.H.; Hatfield, J.S.; Toschik, P.C.; Lukei, R.F.; Hale, R.C.; Schmitz-Afonso, I.; Rice, C.P.

2004-01-01

The Chesapeake Bay osprey population has more than doubled in size since restrictions were placed on the production and use of DDT and other toxic organochlorine contaminants in the 1970s. Ospreys are now nesting in the most highly polluted portions of the Bay. In 2000 and 2001, contaminant exposure and reproduction were monitored in ospreys nesting in regions of concern, including Baltimore Harbor and the Patapsco River, the Anacostia and middle Potomac rivers, and the Elizabeth River, and a presumed reference site consisting of the South, West, and Rhode rivers. A 'sample egg' from each study nest was collected for contaminant analysis, and the fate of eggs remaining in each nest (n = 14-16/site) was monitored at 7- to 10-day intervals from egg incubation through fledging of young. Ospreys fledged young in regions of concern (observed success: 0.88 -1.53 fledglings/active nest), although productivity was marginal for sustaining local populations in Baltimore Harbor and the Patapsco River and in the Anacostia and middle Potomac rivers. Concentrations of p,p'DDE and many other organochlorine pesticides or metabolites, total PCBs, some arylhydrocarbon receptor-active PCB congeners and polybrominated diphenyl ether congeners, and perfluorooctanesulfonate were often greater in sample eggs from regions of concern compared to the reference site. Nonetheless, logistic regression analyses did not provide evidence linking marginal productivity to p,p' -DDE, total PCBs, or arylhydrocarbon receptor-active PCB congener exposure in regions of concern. In view of the moderate concentrations of total PCBs in eggs from the reference site, concerns related to new and emerging toxicants, and the absence of ecotoxicological data for terrestrial vertebrates in many Bay tributaries, a more thorough spatial evaluation of contaminant exposure in ospreys throughout the Chesapeake may be warranted.

A cloud-based workflow to quantify transcript-expression levels in public cancer compendia

PubMed Central

Tatlow, PJ; Piccolo, Stephen R.

2016-01-01

Public compendia of sequencing data are now measured in petabytes. Accordingly, it is infeasible for researchers to transfer these data to local computers. Recently, the National Cancer Institute began exploring opportunities to work with molecular data in cloud-computing environments. With this approach, it becomes possible for scientists to take their tools to the data and thereby avoid large data transfers. It also becomes feasible to scale computing resources to the needs of a given analysis. We quantified transcript-expression levels for 12,307 RNA-Sequencing samples from the Cancer Cell Line Encyclopedia and The Cancer Genome Atlas. We used two cloud-based configurations and examined the performance and cost profiles of each configuration. Using preemptible virtual machines, we processed the samples for as little as $0.09 (USD) per sample. As the samples were processed, we collected performance metrics, which helped us track the duration of each processing step and quantified computational resources used at different stages of sample processing. Although the computational demands of reference alignment and expression quantification have decreased considerably, there remains a critical need for researchers to optimize preprocessing steps. We have stored the software, scripts, and processed data in a publicly accessible repository (https://osf.io/gqrz9). PMID:27982081

78 FR 22425 - Designation of Areas for Air Quality Planning Purposes; State of Nevada; Total Suspended Particulate

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-16

... carbon monoxide, hydrocarbons, nitrogen dioxide, photochemical oxidant, sulfur dioxide, and particulate... rely on local dust ordinances, completion of local road paving projects, and regulation of emissions from industrial processing activities. Among the local dust ordinances referred to in these four plans...

Community Air Sensor Network (CAIRSENSE) project ...

EPA Pesticide Factsheets

Advances in air pollution sensor technology have enabled the development of small and low cost systems to measure outdoor air pollution. The deployment of a large number of sensors across a small geographic area would have potential benefits to supplement traditional monitoring networks with additional geographic and temporal measurement resolution, if the data quality were sufficient. To understand the capability of emerging air sensor technology, the Community Air Sensor Network (CAIRSENSE) project deployed low cost, continuous and commercially-available air pollution sensors at a regulatory air monitoring site and as a local sensor network over a surrounding ~2 km area in Southeastern U.S. Co-location of sensors measuring oxides of nitrogen, ozone, carbon monoxide, sulfur dioxide, and particles revealed highly variable performance, both in terms of comparison to a reference monitor as well as whether multiple identical sensors reproduced the same signal. Multiple ozone, nitrogen dioxide, and carbon monoxide sensors revealed low to very high correlation with a reference monitor, with Pearson sample correlation coefficient (r) ranging from 0.39 to 0.97, -0.25 to 0.76, -0.40 to 0.82, respectively. The only sulfur dioxide sensor tested revealed no correlation (r 0.5), step-wise multiple linear regression was performed to determine if ambient temperature, relative humidity (RH), or age of the sensor in sampling days could be used in a correction algorihm to im

The Star Formation Reference Survey - II. Activity demographics and host-galaxy properties for infrared-selected galaxies

NASA Astrophysics Data System (ADS)

Maragkoudakis, A.; Zezas, A.; Ashby, M. L. N.; Willner, S. P.

2018-04-01

We present activity demographics and host-galaxy properties of infrared-selected galaxies in the local Universe, using the representative Star Formation Reference Survey (SFRS). Our classification scheme is based on a combination of optical emission-line diagrams (BPT) and infrared (IR)-colour diagnostics. Using the weights assigned to the SFRS galaxies based on its parent sample, a far-IR-selected sample comprises 71 per cent H II galaxies, 13 per cent Seyferts, 3 per cent transition objects (TOs), and 13 per cent low-ionization nuclear emission-line regions (LINERs). For the SFRS H II galaxies, we derive nuclear star formation rates and gas-phase metallicities. We measure host-galaxy metallicities for all galaxies with available long-slit spectroscopy and abundance gradients for a subset of 12 face-on galaxies. The majority of H II galaxies show a narrow range of metallicities, close to solar, and flat metallicity profiles. Based on their host-galaxy and nuclear properties, the dominant ionizing source in the far-infrared selected TOs is star-forming activity. LINERs are found mostly in massive hosts (median of 1010.5 M⊙), median L(60 μm) = 109 L⊙, median dust temperatures of F60/F100 = 0.36, and median LH α surface density of 1040.2 erg s-1kpc-2, indicating older stellar populations as their main ionizing source rather than active galactic nucleus activity.

Validation of reference genes for real-time quantitative PCR normalization in soybean developmental and germinating seeds.

PubMed

Li, Qing; Fan, Cheng-Ming; Zhang, Xiao-Mei; Fu, Yong-Fu

2012-10-01

Most of traditional reference genes chosen for real-time quantitative PCR normalization were assumed to be ubiquitously and constitutively expressed in vegetative tissues. However, seeds show distinct transcriptomes compared with the vegetative tissues. Therefore, there is a need for re-validation of reference genes in samples of seed development and germination, especially for soybean seeds. In this study, we aimed at identifying reference genes suitable for the quantification of gene expression level in soybean seeds. In order to identify the best reference genes for soybean seeds, 18 putative reference genes were tested with various methods in different seed samples. We combined the outputs of both geNorm and NormFinder to assess the expression stability of these genes. The reference genes identified as optimums for seed development were TUA5 and UKN2, whereas for seed germination they were novel reference genes Glyma05g37470 and Glyma08g28550. Furthermore, for total seed samples it was necessary to combine four genes of Glyma05g37470, Glyma08g28550, Glyma18g04130 and UKN2 [corrected] for normalization. Key message We identified several reference genes that stably expressed in soybean seed developmental and germinating processes.

MR-guided fine needle aspiration of breast lesions: Initial experience

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

Wald, D.S.; Weinreb, J.C.; Newstead, G.

1996-01-01

Fine needle aspiration (FNA) is a minimally invasive procedure that is used to obtain cytologic specimens of suspicious lesions in the breast. The goal of this study was to evaluate the logistics and limitations of MR-guided FNA using a prototype breast localization coil. MR-guided FNAs were attempted on 18 lesions (detected on mammography and/or palpation) in 16 patients. Patients were prone with their compressed mediolaterally between two plates in a circularly polarized RF coil. Lesion position was determined by reference to fiducial makers that corresponded to a grid of holes placed at 5 mm intervals in compression plate. FNA wasmore » performed with a 22G non-ferromagnetic needle. FNA was successful for 11 of 18 lesions (61%). Of the seven unsuccessful cases, there were four in which the lesions were too posteriorly placed to be accessed through the compression plate by the needle. Three cases were too anteriorly placed to be effectively immobilized and, although successfully localized, were insufficiently sampled by the FNA technique. MR-guided FNA is possible using a prototype breast localization device in a select group of patients. Current coil design limits its use in performing MR-guided FNA on the most anteriorly and posteriorly placed breast lesions. Unique requirements of FNA under MR guidance as compared to needle localization and biopsy have been identified. Modifications in localization hardware and cytology aspiration needles should overcome these restrictions. 15 refs., 3 figs.« less

An outbreak of locally acquired Plasmodium vivax malaria among migrant workers in Oman.

PubMed

Simon, Bruno; Sow, Fatimata; Al Mukhaini, Said K; Al-Abri, Seif; Ali, Osama A M; Bonnot, Guillaume; Bienvenu, Anne-Lise; Petersen, Eskild; Picot, Stéphane

2017-01-01

Plasmodium vivax is the most widely distributed human malaria parasite. Outside sub-Saharan Africa, the proportion of P. vivax malaria is rising. A major cause for concern is the re-emergence of Plasmodium vivax in malaria-free areas. Oman, situated in the south-eastern corner of the Arabian Peninsula, has long been an area of vivax malaria transmission but no locally acquired cases were reported in 2004. However, local transmission has been registered in small outbreaks since 2007. In this study, a local outbreak of 54 cases over 50 days in 2014 was analyzed retrospectively and stained blood slides have been obtained for parasite identification and genotyping. The aim of this study was to identify the geographical origin of these cases, in an attempt to differentiate between imported cases and local transmission. Using circumsporozoite protein (csp), merozoite surface protein 1 (msp1), and merozoite surface protein 3 (msp3) markers for genotyping of parasite DNA obtained by scrapping off the surface of smears, genetic diversity and phylogenetic analysis were performed. The study found that the samples had very low genetic diversity, a temperate genotype, and a high genetic distance, with most of the reference strains coming from endemic countries. We conclude that a small outbreak of imported malaria is not associated with re-emergence of malaria transmission in Oman, as no new cases have been seen since the outbreak ended. © B. Simon et al., published by EDP Sciences, 2017.

Change of reference frame for tactile localization during child development.

PubMed

Pagel, Birthe; Heed, Tobias; Röder, Brigitte

2009-11-01

Temporal order judgements (TOJ) for two tactile stimuli, one presented to the left and one to the right hand, are less precise when the hands are crossed over the midline than when the hands are uncrossed. This 'crossed hand' effect has been considered as evidence for a remapping of tactile input into an external reference frame. Since late, but not early, blind individuals show such remapping, it has been hypothesized that the use of an external reference frame develops during childhood. Five- to 10-year-old children were therefore tested with the tactile TOJ task, both with uncrossed and crossed hands. Overall performance in the TOJ task improved with age. While children older than 5 1/2 years displayed a crossed hand effect, younger children did not. Therefore the use of an external reference frame for tactile, and possibly multisensory, localization seems to be acquired at age 5.

Public health response to an incident of secondary chemical contamination at a beach in the United Kingdom

PubMed Central

Goodfellow, F; Murray, V; Ouki, S; Iversen, A; Sparks, A; Bartlett, T

2001-01-01

OBJECTIVES—To gather enough data from a large scale investigation involving two health authorities, to assess the possible concentrations and routes of exposure and the consequent health implications.To use the data to decide whether a polluted beach should remain open to the public. In Spring 1997, a chemical incident came to light at a beach on the south coast of England when a local resident reported a sulphurous smell, visible signs of oil, and reduced numbers of fishing bait. The beach was situated adjacent to a former gasworks site and was accessible to the public. The incident was reported to the local authority and was initially investigated by the Environment Agency and the local authority. An Environment Agency report confirmed contamination of the beach with cyanide, ammonia, and polycyclic aromatic hydrocarbons (PAHs) with associated potential health risks. The incident was then referred to the local health authorities for investigation.
METHODS—The investigation was carried out in four stages: comprehensive sampling and analysis to identify the extent of contamination, followed by an assessment of risk to health; establishment of a long term monitoring programme to identify any changes in contaminant concentrations; investigation of the effects of the contamination on shellfish; and review of the routine monitoring data and current sampling strategy.
RESULTS—The initial investigation confirmed that the beach was contaminated, with the most likely source being the adjacent former gasworks site. The level of contamination was not found to be likely to pose a hazard to users of the beach. However, subsequent investigation of shellfish in the area led to warning signs being erected on the beach to prevent human consumption of mussels contaminated with PAHs.
CONCLUSIONS—Several lessons can be learnt from this investigation, which can be applied to incident management more generally: the importance of collaboration and coordination; the need for early involvement of the health authority; and the importance of carrying out appropriate sampling and analysis as soon as possible, to assess the risk to health and the environment.


Keywords: public health; water pollutants; chemical; hydrocarbons; cyanides PMID:11245739

Using Electronic Data Interchange to Report Product Quality

DTIC Science & Technology

1993-03-01

Numbers 0 31.1 S........................ . . . . ........... .... . .--- . ... N/U 140 SPS Sampling Parameters for Summary Statistics 0 1 N/U 150 REF...DTM Date/Time Reference 0 1 N/U 190 REF Reference Numbers 021 .................................. .......... .. ... NAU 200 STA Statistics 0 1 N/U 210...Measurements 0 1 N/U 120 DTM Date/Time Reference 0 >1 N/U 130 REF Reference Numbers 0 >1 :LOOIV f-SPS N/U 140 SPS Sampling Parameters for Summary Statistics 0 1

Characterization of a Polymer Composite Section of Foreign Armor

DTIC Science & Technology

2000-03-01

Core Sample 8 6. ESEM From Owens - Corning S-2 Glass Reference 10 7. ESEM From Owens-Coming E Glass Reference 11 8. ESEM From Known Russian S...light element energy dispersive spectrometer. Samples of domestic Owens - Corning E and S-2 glass fibers were first analyzed for reference purposes...for comparison to the unknown Russian armor fiber. The two domestic reference fibers were Owens - Corning E and S-2 glass. Their spectra are shown in

Single point aerosol sampling: evaluation of mixing and probe performance in a nuclear stack.

PubMed

Rodgers, J C; Fairchild, C I; Wood, G O; Ortiz, C A; Muyshondt, A; McFarland, A R

1996-01-01

Alternative reference methodologies have been developed for sampling of radionuclides from stacks and ducts, which differ from the methods previously required by the United States Environmental Protection Agency. These alternative reference methodologies have recently been approved by the U.S. EPA for use in lieu of the current standard techniques. The standard EPA methods are prescriptive in selection of sampling locations and in design of sampling probes whereas the alternative reference methodologies are performance driven. Tests were conducted in a stack at Los Alamos National Laboratory to demonstrate the efficacy of some aspects of the alternative reference methodologies. Coefficients of variation of velocity, tracer gas, and aerosol particle profiles were determined at three sampling locations. Results showed that numerical criteria placed upon the coefficients of variation by the alternative reference methodologies were met at sampling stations located 9 and 14 stack diameters from the flow entrance, but not at a location that was 1.5 diameters downstream from the inlet. Experiments were conducted to characterize the transmission of 10 microns aerodynamic diameter liquid aerosol particles through three types of sampling probes. The transmission ratio (ratio of aerosol concentration at the probe exit plane to the concentration in the free stream) was 107% for a 113 L min-1 (4-cfm) anisokinetic shrouded probe, but only 20% for an isokinetic probe that follows the existing EPA standard requirements. A specially designed isokinetic probe showed a transmission ratio of 63%. The shrouded probe performance would conform to the alternative reference methodologies criteria; however, the isokinetic probes would not.

Recruiting Human Microbiome Shotgun Data to Site-Specific Reference Genomes

PubMed Central

Xie, Gary; Lo, Chien-Chi; Scholz, Matthew; Chain, Patrick S. G.

2014-01-01

The human body consists of innumerable multifaceted environments that predispose colonization by a number of distinct microbial communities, which play fundamental roles in human health and disease. In addition to community surveys and shotgun metagenomes that seek to explore the composition and diversity of these microbiomes, there are significant efforts to sequence reference microbial genomes from many body sites of healthy adults. To illustrate the utility of reference genomes when studying more complex metagenomes, we present a reference-based analysis of sequence reads generated from 55 shotgun metagenomes, selected from 5 major body sites, including 16 sub-sites. Interestingly, between 13% and 92% (62.3% average) of these shotgun reads were aligned to a then-complete list of 2780 reference genomes, including 1583 references for the human microbiome. However, no reference genome was universally found in all body sites. For any given metagenome, the body site-specific reference genomes, derived from the same body site as the sample, accounted for an average of 58.8% of the mapped reads. While different body sites did differ in abundant genera, proximal or symmetrical body sites were found to be most similar to one another. The extent of variation observed, both between individuals sampled within the same microenvironment, or at the same site within the same individual over time, calls into question comparative studies across individuals even if sampled at the same body site. This study illustrates the high utility of reference genomes and the need for further site-specific reference microbial genome sequencing, even within the already well-sampled human microbiome. PMID:24454771

Light escape cones in local reference frames of Kerr-de Sitter black hole spacetimes and related black hole shadows

NASA Astrophysics Data System (ADS)

Stuchlík, Zdeněk; Charbulák, Daniel; Schee, Jan

2018-03-01

We construct the light escape cones of isotropic spot sources of radiation residing in special classes of reference frames in the Kerr-de Sitter (KdS) black hole spacetimes, namely in the fundamental class of `non-geodesic' locally non-rotating reference frames (LNRFs), and two classes of `geodesic' frames, the radial geodesic frames (RGFs), both falling and escaping, and the frames related to the circular geodesic orbits (CGFs). We compare the cones constructed in a given position for the LNRFs, RGFs, and CGFs. We have shown that the photons locally counter-rotating relative to LNRFs with positive impact parameter and negative covariant energy are confined to the ergosphere region. Finally, we demonstrate that the light escaping cones govern the shadows of black holes located in front of a radiating screen, as seen by the observers in the considered frames. For shadows related to distant static observers the LNRFs are relevant.

Establishment of detailed reference values for luteinizing hormone, follicle stimulating hormone, estradiol, and progesterone during different phases of the menstrual cycle on the Abbott ARCHITECT analyzer.

PubMed

Stricker, Reto; Eberhart, Raphael; Chevailler, Marie-Christine; Quinn, Frank A; Bischof, Paul; Stricker, René

2006-01-01

During a normal menstrual cycle, serum levels of luteinizing hormone (LH), follicle-stimulating hormone (FSH), estradiol, and progesterone can vary widely between cycles for the same woman, as well as between different woman. Reliable reference values based on the local population are important for correct interpretation of laboratory results. The purpose of our study was to determine detailed reference values for these hormones throughout the menstrual cycle using the Abbott ARCHITECT system. From 20 volunteers (age 20-36 years) with normal cycles and no use of oral contraceptives, samples were taken every day during their cycle. Volunteers received three vaginal ultrasound examinations (days 10 and 13, and 1 or 2 days after ovulation) to measure follicular and corpus luteum development. Hormone levels were measured using the corresponding ARCHITECT assay and were synchronized to the LH peak. Median, and 5th and 95th percentile values were determined for each day of the cycle, as well as for early follicular (days -15 to -6), late follicular (days -5 to -1), LH peak (day 0), early luteal (+1 to +4), mid-luteal (days +5 to +9), and late luteal (days +10 to +14) phases of the cycle. Based on our data, we were able to establish detailed reference values for LH, FSH, estradiol, and progesterone, which should aid in the interpretation of results for these reproductive hormones in a variety of circumstances.

Linking multimetric and multivariate approaches to assess the ecological condition of streams.

PubMed

Collier, Kevin J

2009-10-01

Few attempts have been made to combine multimetric and multivariate analyses for bioassessment despite recognition that an integrated method could yield powerful tools for bioassessment. An approach is described that integrates eight macroinvertebrate community metrics into a Principal Components Analysis to develop a Multivariate Condition Score (MCS) from a calibration dataset of 511 samples. The MCS is compared to an Index of Biotic Integrity (IBI) derived using the same metrics based on the ratio to the reference site mean. Both approaches were highly correlated although the MCS appeared to offer greater potential for discriminating a wider range of impaired conditions. Both the MCS and IBI displayed low temporal variability within reference sites, and were able to distinguish between reference conditions and low levels of catchment modification and local habitat degradation, although neither discriminated among three levels of low impact. Pseudosamples developed to test the response of the metric aggregation approaches to organic enrichment, urban, mining, pastoral and logging stressor scenarios ranked pressures in the same order, but the MCS provided a lower score for the urban scenario and a higher score for the pastoral scenario. The MCS was calculated for an independent test dataset of urban and reference sites, and yielded similar results to the IBI. Although both methods performed comparably, the MCS approach may have some advantages because it removes the subjectivity of assigning thresholds for scoring biological condition, and it appears to discriminate a wider range of degraded conditions.

Police and public health partnerships: evidence from the evaluation of Vancouver's supervised injection facility.

PubMed

DeBeck, Kora; Wood, Evan; Zhang, Ruth; Tyndall, Mark; Montaner, Julio; Kerr, Thomas

2008-05-07

In various settings, drug market policing strategies have been found to have unintended negative effects on health service use among injection drug users (IDU). This has prompted calls for more effective coordination of policing and public health efforts. In Vancouver, Canada, a supervised injection facility (SIF) was established in 2003. We sought to determine if local police impacted utilization of the SIF. We used generalized estimating equations (GEE) to prospectively identify the prevalence and correlates of being referred by local police to Vancouver's SIF among IDU participating in the Scientific Evaluation of Supervised Injecting (SEOSI) cohort during the period of December 2003 to November 2005. Among 1090 SIF clients enrolled in SEOSI, 182 (16.7%) individuals reported having ever been referred to the SIF by local police. At baseline, 22 (2.0%) participants reported that they first learned of the SIF via police. In multivariate analyses, factors positively associated with being referred to the SIF by local police when injecting in public include: sex work (Adjusted Odds Ratio [AOR] = 1.80, 95%CI 1.28-2.53); daily cocaine injection (AOR = 1.54, 95%CI 1.14-2.08); and unsafe syringe disposal (AOR = 1.46, 95%CI 1.00-2.11). These findings indicate that local police are facilitating use of the SIF by IDU at high risk for various adverse health outcomes. We further found that police may be helping to address public order concerns by referring IDU who are more likely to discard used syringes in public spaces. Our study suggests that the SIF provides an opportunity to coordinate policing and public health efforts and thereby resolve some of the existing tensions between public order and health initiatives.

Determination of arsenic species in fish, crustacean and sediment samples from Thailand using high performance liquid chromatography (HPLC) coupled with inductively coupled plasma mass spectrometry (ICP-MS).

PubMed

Rattanachongkiat, S; Millward, G E; Foulkes, M E

2004-04-01

Suitable techniques have been developed for the extraction of arsenic species in a variety of biological and environmental samples from the Pak Pa-Nang Estuary and catchment, located in Southern Thailand, and for their determination using HPLC directly coupled with ICP-MS. The estuary catchment comprises a tin mining area and inhabitants of the region can suffer from various stages of arsenic poisoning. The important arsenic species, AsB, DMA, MMA, and inorganic arsenic (As III and V) have been determined in fish and crustacean samples to provide toxicological information on those fauna which contribute to the local diet. A Hamilton PRP-X100 anion-exchange HPLC system employing a step elution has been used successfully to achieve separation of the arsenic species. A nitric acid microwave digestion procedure, followed by carrier gas nitrogen addition- (N2)-ICP-MS analysis was used to measure total arsenic in sample digests and extracts. The arsenic speciation of the biological samples was preserved using a Trypsin enzymatic extraction procedure. Extraction efficiencies were high, with values of 82-102%(As) for fish and crustacean samples. Validation for these procedures was carried out using certified reference materials. Fish and crustacean samples from the Pak Pa-Nang Estuary showed a range for total arsenic concentration, up to 17 microg g(-1) dry mass. The major species of arsenic in all fauna samples taken was AsB, together with smaller quantities of DMA and, more importantly, inorganic As. For sediment samples, arsenic species were determined following phosphoric acid (1 M H3PO4) extraction in an open focused microwave system. A phosphate-based eluant, pH 6-7.5, with anion exchange HPLC coupled with ICP-MS was used for separation and detection of AsIII, AsV, MMA and DMA. The optimum conditions, identified using an estuarine sediment reference material (LGC), were achieved using 45 W power and a 20 minute heating period for extraction of 0.5 g sediment. The stability and recovery of arsenic species under the extraction conditions were also determined by a spiking procedure which included the estuarine sediment reference material. The results show good stability for all species after extraction with a variability of less than 10%. Total concentrations of arsenic in the sediments from the Pak Pa-Nang river catchment and the estuary covered the ranges 7-269 microg g(-1)and 4-20 [micro sign]g g(-1)(dry weight), respectively. AsV was the major species found in all the sediment samples with smaller quantities of AsIII. The presence of the more toxic inorganic forms of arsenic in both sediments and biota samples has implications for human health, particularly as they are readily 'available'.

Method for detection of dental caries and periodontal disease using optical imaging

DOEpatents

Nathel, Howard; Kinney, John H.; Otis, Linda L.

1996-01-01

A method for detecting the presence of active and inactive caries in teeth and diagnosing periodontal disease uses non-ionizing radiation with techniques for reducing interference from scattered light. A beam of non-ionizing radiation is divided into sample and reference beams. The region to be examined is illuminated by the sample beam, and reflected or transmitted radiation from the sample is recombined with the reference beam to form an interference pattern on a detector. The length of the reference beam path is adjustable, allowing the operator to select the reflected or transmitted sample photons that recombine with the reference photons. Thus radiation scattered by the dental or periodontal tissue can be prevented from obscuring the interference pattern. A series of interference patterns may be generated and interpreted to locate dental caries and periodontal tissue interfaces.

Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary

PubMed Central

Soboleva, Lyubov; Charlop-Powers, Zachary

2017-01-01

The difficulty of censusing marine animal populations hampers effective ocean management. Analyzing water for DNA traces shed by organisms may aid assessment. Here we tested aquatic environmental DNA (eDNA) as an indicator of fish presence in the lower Hudson River estuary. A checklist of local marine fish and their relative abundance was prepared by compiling 12 traditional surveys conducted between 1988–2015. To improve eDNA identification success, 31 specimens representing 18 marine fish species were sequenced for two mitochondrial gene regions, boosting coverage of the 12S eDNA target sequence to 80% of local taxa. We collected 76 one-liter shoreline surface water samples at two contrasting estuary locations over six months beginning in January 2016. eDNA was amplified with vertebrate-specific 12S primers. Bioinformatic analysis of amplified DNA, using a reference library of GenBank and our newly generated 12S sequences, detected most (81%) locally abundant or common species and relatively few (23%) uncommon taxa, and corresponded to seasonal presence and habitat preference as determined by traditional surveys. Approximately 2% of fish reads were commonly consumed species that are rare or absent in local waters, consistent with wastewater input. Freshwater species were rarely detected despite Hudson River inflow. These results support further exploration and suggest eDNA will facilitate fine-scale geographic and temporal mapping of marine fish populations at relatively low cost. PMID:28403183

iGRaND: an invariant frame for RGBD sensor feature detection and descriptor extraction with applications

NASA Astrophysics Data System (ADS)

Willis, Andrew R.; Brink, Kevin M.

2016-06-01

This article describes a new 3D RGBD image feature, referred to as iGRaND, for use in real-time systems that use these sensors for tracking, motion capture, or robotic vision applications. iGRaND features use a novel local reference frame derived from the image gradient and depth normal (hence iGRaND) that is invariant to scale and viewpoint for Lambertian surfaces. Using this reference frame, Euclidean invariant feature components are computed at keypoints which fuse local geometric shape information with surface appearance information. The performance of the feature for real-time odometry is analyzed and its computational complexity and accuracy is compared with leading alternative 3D features.

Spatially resolved imaging of opto-electrical property variations

DOEpatents

Nikiforov, Maxim; Darling, Seth B; Suzer, Ozgun; Guest, Jeffrey; Roelofs, Andreas

2014-09-16

Systems and methods for opto electric properties are provided. A light source illuminates a sample. A reference detector senses light from the light source. A sample detector receives light from the sample. A positioning fixture allows for relative positioning of the sample or the light source with respect to each other. An electrical signal device measures the electrical properties of the sample. The reference detector, sample detector and electrical signal device provide information that may be processed to determine opto-electric properties of the same.

State and Local Government Publications.

ERIC Educational Resources Information Center

Nakata, Yuri; Kopec, Karen

1980-01-01

Reviews trends in library programs for state and local government publications and documents the increased interest in microforms and databases. Discussion focuses on publication distribution and control, and efforts to support interstate networking. There are 28 references. (RAA)

Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface

PubMed Central

2012-01-01

Background Despite computational challenges, elucidating conformations that a protein system assumes under physiologic conditions for the purpose of biological activity is a central problem in computational structural biology. While these conformations are associated with low energies in the energy surface that underlies the protein conformational space, few existing conformational search algorithms focus on explicitly sampling low-energy local minima in the protein energy surface. Methods This work proposes a novel probabilistic search framework, PLOW, that explicitly samples low-energy local minima in the protein energy surface. The framework combines algorithmic ingredients from evolutionary computation and computational structural biology to effectively explore the subspace of local minima. A greedy local search maps a conformation sampled in conformational space to a nearby local minimum. A perturbation move jumps out of a local minimum to obtain a new starting conformation for the greedy local search. The process repeats in an iterative fashion, resulting in a trajectory-based exploration of the subspace of local minima. Results and conclusions The analysis of PLOW's performance shows that, by navigating only the subspace of local minima, PLOW is able to sample conformations near a protein's native structure, either more effectively or as well as state-of-the-art methods that focus on reproducing the native structure for a protein system. Analysis of the actual subspace of local minima shows that PLOW samples this subspace more effectively that a naive sampling approach. Additional theoretical analysis reveals that the perturbation function employed by PLOW is key to its ability to sample a diverse set of low-energy conformations. This analysis also suggests directions for further research and novel applications for the proposed framework. PMID:22759582

Assessment of the genetic diversity of the Tunisian citrus rootstock germplasm

PubMed Central

2012-01-01

Background Citrus represents a substantial income for farmers in the Mediterranean Basin. However, the Mediterranean citrus industry faces increasing biotic and abiotic constraints. Therefore the breeding and selection of new rootstocks are now of the utmost importance. In Tunisia, in addition to sour orange, the most widespread traditional rootstock of the Mediterranean area, other citrus rootstocks and well adapted to local environmental conditions, are traditionally used and should be important genetic resources for breeding. To characterize the diversity of Tunisian citrus rootstocks, two hundred and one local accessions belonging to four facultative apomictic species (C. aurantium, sour orange; C. sinensis, orange; C. limon, lemon; and C. aurantifolia, lime) were collected and genotyped using 20 nuclear SSR markers and four indel mitochondrial markers. Multi-locus genotypes (MLGs) were compared to references from French and Spanish collections. Results The differentiation of the four varietal groups was well-marked. The groups displayed a relatively high allelic diversity, primarily due to very high heterozygosity. Sixteen distinct MLGs were identified. Ten of these were noted in sour oranges. However, the majority of the analysed sour orange accessions corresponded with only two MLGs, differentiated by a single allele, likely due to a mutation. The most frequent MLG is shared with the reference sour oranges. No polymorphism was found within the sweet orange group. Two MLGs, differentiated by a single locus, were noted in lemon. The predominant MLG was shared with the reference lemons. Limes were represented by three genotypes. Two corresponded to the 'Mexican lime' and 'limonette de Marrakech' references. The MLG of 'Chiiri' lime was unique. Conclusions The Tunisian citrus rootstock genetic diversity is predominantly due to high heterozygosity and differentiation between the four varietal groups. The phenotypic diversity within the varietal groups has resulted from multiple introductions, somatic mutations and rare sexual recombination events. Finally, this diversity study enabled the identification of a core sample of accessions for further physiological and agronomical evaluations. These core accessions will be integrated into citrus rootstock breeding programs for the Mediterranean Basin. PMID:22429788

Comparison of water-quality samples collected by siphon samplers and automatic samplers in Wisconsin

USGS Publications Warehouse

Graczyk, David J.; Robertson, Dale M.; Rose, William J.; Steur, Jeffrey J.

2000-01-01

In small streams, flow and water-quality concentrations often change quickly in response to meteorological events. Hydrologists, field technicians, or locally hired stream ob- servers involved in water-data collection are often unable to reach streams quickly enough to observe or measure these rapid changes. Therefore, in hydrologic studies designed to describe changes in water quality, a combination of manual and automated sampling methods have commonly been used manual methods when flow is relatively stable and automated methods when flow is rapidly changing. Auto- mated sampling, which makes use of equipment programmed to collect samples in response to changes in stage and flow of a stream, has been shown to be an effective method of sampling to describe the rapid changes in water quality (Graczyk and others, 1993). Because of the high cost of automated sampling, however, especially for studies examining a large number of sites, alternative methods have been considered for collecting samples during rapidly changing stream conditions. One such method employs the siphon sampler (fig. 1). also referred to as the "single-stage sampler." Siphon samplers are inexpensive to build (about $25- $50 per sampler), operate, and maintain, so they are cost effective to use at a large number of sites. Their ability to collect samples representing the average quality of water passing though the entire cross section of a stream, however, has not been fully demonstrated for many types of stream sites.

Food adulteration analysis without laboratory prepared or determined reference food adulterant values.

PubMed

Kalivas, John H; Georgiou, Constantinos A; Moira, Marianna; Tsafaras, Ilias; Petrakis, Eleftherios A; Mousdis, George A

2014-04-01

Quantitative analysis of food adulterants is an important health and economic issue that needs to be fast and simple. Spectroscopy has significantly reduced analysis time. However, still needed are preparations of analyte calibration samples matrix matched to prediction samples which can be laborious and costly. Reported in this paper is the application of a newly developed pure component Tikhonov regularization (PCTR) process that does not require laboratory prepared or reference analysis methods, and hence, is a greener calibration method. The PCTR method requires an analyte pure component spectrum and non-analyte spectra. As a food analysis example, synchronous fluorescence spectra of extra virgin olive oil samples adulterated with sunflower oil is used. Results are shown to be better than those obtained using ridge regression with reference calibration samples. The flexibility of PCTR allows including reference samples and is generic for use with other instrumental methods and food products. Copyright © 2013 Elsevier Ltd. All rights reserved.

Local Implementation and Land Use Decision Making.

ERIC Educational Resources Information Center

Garlasco, Chris; And Others

This material includes student guide sheets, reference material, and tape script for the audio-tutorial unit on Local Implementation. An audio tape is used with the materials. The material is designed for use with Connecticut schools, but can be adapted to other localities. The material in this unit emphasizes the role of planning and zoning in…

What Talking about Them Reveals about Us: The Organization of Person Reference in Conversations about Family Photographs

ERIC Educational Resources Information Center

Mates, Andrea Wong

2009-01-01

Talking with friend about personal photographs is a recognizable as an activity in which people participate in the modern world. This dissertation presents three studies examining the locally initial person reference formulations used to refer to people in the photographs in such an activity. The first study shows how the speakers narrating the…

A 'Global Reference' Comparator for Biosimilar Development.

PubMed

Webster, Christopher J; Woollett, Gillian R

2017-08-01

Major drug regulators have indicated in guidance their flexibility to accept some development data for biosimilars generated with reference product versions licensed outside their own jurisdictions, but most authorities require new bridging studies between these versions and the versions of them licensed locally. The costs of these studies are not trivial in absolute terms and, due to the multiplier effect of required repetition by each biosimilar sponsor, their collective costs are substantial. Yet versions of biologics licensed in different jurisdictions usually share the same development data, and any manufacturing changes between versions have been justified by a rigorous comparability process. The fact that a biosimilar is usually expected to be licensed in multiple jurisdictions, in each case as similar to the local reference product, confirms that minor analytical differences between versions of reference biologics are typically inconsequential for clinical outcomes and licensing. A greatly simplified basis for selecting a reference comparator, that does not require conducting new bridging studies, is proposed and justified based on the shared data of the reference product versions as well as the proof offered where biosimilars have already been approved. The relevance of this proposal to the interchangeability designation available in the US is discussed.

Measurements of radiated elastic wave energy from dynamic tensile cracks

NASA Technical Reports Server (NTRS)

Boler, Frances M.

1990-01-01

The role of fracture-velocity, microstructure, and fracture-energy barriers in elastic wave radiation during a dynamic fracture was investigated in experiments in which dynamic tensile cracks of two fracture cofigurations of double cantilever beam geometry were propagating in glass samples. The first, referred to as primary fracture, consisted of fractures of intact glass specimens; the second configuration, referred to as secondary fracture, consisted of a refracture of primary fracture specimens which were rebonded with an intermittent pattern of adhesive to produce variations in fracture surface energy along the crack path. For primary fracture cases, measurable elastic waves were generated in 31 percent of the 16 fracture events observed; the condition for radiation of measurable waves appears to be a local abrupt change in the fracture path direction, such as occurs when the fracture intersects a surface flaw. For secondary fractures, 100 percent of events showed measurable elastic waves; in these fractures, the ratio of radiated elastic wave energy in the measured component to fracture surface energy was 10 times greater than for primary fracture.

The role of appeals to tradition in origin food marketing. A survey among Polish consumers.

PubMed

Bryła, Paweł

2015-08-01

The frequency of the use of tradition in marketing is growing. Appealing to tradition reflects the need to have reference points, trust and stability. The perceived authenticity of a product is strongly connected with its origin, which is expressed by the factors of time (history), place (area), socialisation (local community) and naturalness (raw materials). The paper aims to examine consumer attitudes, preferences and behaviours regarding origin food in Poland. We carried out a survey in a representative sample of 1000 Polish consumers. According to our respondents, the characteristics differentiating origin food from conventional food include links with tradition as well as sensory and health properties. Referring to the typology proposed by van der Meulen, traditionality and territoriality are the most important characteristics of origin food. The perceived authenticity of origin products depends to the largest extent on such factors as: natural taste, product quality, sale in the region of origin and labelling. The most important determinants of origin food selection include: traditional recipe, taste, and product uniqueness. Copyright © 2015 Elsevier Ltd. All rights reserved.

High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level

PubMed Central

Gong, Hui; Xu, Dongli; Yuan, Jing; Li, Xiangning; Guo, Congdi; Peng, Jie; Li, Yuxin; Schwarz, Lindsay A.; Li, Anan; Hu, Bihe; Xiong, Benyi; Sun, Qingtao; Zhang, Yalun; Liu, Jiepeng; Zhong, Qiuyuan; Xu, Tonghui; Zeng, Shaoqun; Luo, Qingming

2016-01-01

The precise annotation and accurate identification of neural structures are prerequisites for studying mammalian brain function. The orientation of neurons and neural circuits is usually determined by mapping brain images to coarse axial-sampling planar reference atlases. However, individual differences at the cellular level likely lead to position errors and an inability to orient neural projections at single-cell resolution. Here, we present a high-throughput precision imaging method that can acquire a co-localized brain-wide data set of both fluorescent-labelled neurons and counterstained cell bodies at a voxel size of 0.32 × 0.32 × 2.0 μm in 3 days for a single mouse brain. We acquire mouse whole-brain imaging data sets of multiple types of neurons and projections with anatomical annotation at single-neuron resolution. The results show that the simultaneous acquisition of labelled neural structures and cytoarchitecture reference in the same brain greatly facilitates precise tracing of long-range projections and accurate locating of nuclei. PMID:27374071

SAMSA2: a standalone metatranscriptome analysis pipeline.

PubMed

Westreich, Samuel T; Treiber, Michelle L; Mills, David A; Korf, Ian; Lemay, Danielle G

2018-05-21

Complex microbial communities are an area of growing interest in biology. Metatranscriptomics allows researchers to quantify microbial gene expression in an environmental sample via high-throughput sequencing. Metatranscriptomic experiments are computationally intensive because the experiments generate a large volume of sequence data and each sequence must be compared with reference sequences from thousands of organisms. SAMSA2 is an upgrade to the original Simple Annotation of Metatranscriptomes by Sequence Analysis (SAMSA) pipeline that has been redesigned for standalone use on a supercomputing cluster. SAMSA2 is faster due to the use of the DIAMOND aligner, and more flexible and reproducible because it uses local databases. SAMSA2 is available with detailed documentation, and example input and output files along with examples of master scripts for full pipeline execution. SAMSA2 is a rapid and efficient metatranscriptome pipeline for analyzing large RNA-seq datasets in a supercomputing cluster environment. SAMSA2 provides simplified output that can be examined directly or used for further analyses, and its reference databases may be upgraded, altered or customized to fit the needs of any experiment.

Estimating clinical chemistry reference values based on an existing data set of unselected animals.

PubMed

Dimauro, Corrado; Bonelli, Piero; Nicolussi, Paola; Rassu, Salvatore P G; Cappio-Borlino, Aldo; Pulina, Giuseppe

2008-11-01

In an attempt to standardise the determination of biological reference values, the International Federation of Clinical Chemistry (IFCC) has published a series of recommendations on developing reference intervals. The IFCC recommends the use of an a priori sampling of at least 120 healthy individuals. However, such a high number of samples and laboratory analysis is expensive, time-consuming and not always feasible, especially in veterinary medicine. In this paper, an alternative (a posteriori) method is described and is used to determine reference intervals for biochemical parameters of farm animals using an existing laboratory data set. The method used was based on the detection and removal of outliers to obtain a large sample of animals likely to be healthy from the existing data set. This allowed the estimation of reliable reference intervals for biochemical parameters in Sarda dairy sheep. This method may also be useful for the determination of reference intervals for different species, ages and gender.

Range imaging laser radar

DOEpatents

Scott, Marion W.

1990-01-01

A laser source is operated continuously and modulated periodically (typicy sinusoidally). A receiver imposes another periodic modulation on the received optical signal, the modulated signal being detected by an array of detectors of the integrating type. Range to the target determined by measuring the phase shift of the intensity modulation on the received optical beam relative to a reference. The receiver comprises a photoemitter for converting the reflected, periodically modulated, return beam to an accordingly modulated electron stream. The electron stream is modulated by a local demodulation signal source and subsequently converted back to a photon stream by a detector. A charge coupled device (CCD) array then averages and samples the photon stream to provide an electrical signal in accordance with the photon stream.

Range imaging laser radar

DOEpatents

Scott, M.W.

1990-06-19

A laser source is operated continuously and modulated periodically (typically sinusoidally). A receiver imposes another periodic modulation on the received optical signal, the modulated signal being detected by an array of detectors of the integrating type. Range to the target determined by measuring the phase shift of the intensity modulation on the received optical beam relative to a reference. The receiver comprises a photoemitter for converting the reflected, periodically modulated, return beam to an accordingly modulated electron stream. The electron stream is modulated by a local demodulation signal source and subsequently converted back to a photon stream by a detector. A charge coupled device (CCD) array then averages and samples the photon stream to provide an electrical signal in accordance with the photon stream. 2 figs.

Underdetermined blind separation of three-way fluorescence spectra of PAHs in water

NASA Astrophysics Data System (ADS)

Yang, Ruifang; Zhao, Nanjing; Xiao, Xue; Zhu, Wei; Chen, Yunan; Yin, Gaofang; Liu, Jianguo; Liu, Wenqing

2018-06-01

In this work, underdetermined blind decomposition method is developed to recognize individual components from the three-way fluorescent spectra of their mixtures by using sparse component analysis (SCA). The mixing matrix is estimated from the mixtures using fuzzy data clustering algorithm together with the scatters corresponding to local energy maximum value in the time-frequency domain, and the spectra of object components are recovered by pseudo inverse technique. As an example, using this method three and four pure components spectra can be blindly extracted from two samples of their mixture, with similarities between resolved and reference spectra all above 0.80. This work opens a new and effective path to realize monitoring PAHs in water by three-way fluorescence spectroscopy technique.

New approach to estimating variability in visual field data using an image processing technique.

PubMed Central

Crabb, D P; Edgar, D F; Fitzke, F W; McNaught, A I; Wynn, H P

1995-01-01

AIMS--A new framework for evaluating pointwise sensitivity variation in computerised visual field data is demonstrated. METHODS--A measure of local spatial variability (LSV) is generated using an image processing technique. Fifty five eyes from a sample of normal and glaucomatous subjects, examined on the Humphrey field analyser (HFA), were used to illustrate the method. RESULTS--Significant correlation between LSV and conventional estimates--namely, HFA pattern standard deviation and short term fluctuation, were found. CONCLUSION--LSV is not dependent on normals' reference data or repeated threshold determinations, thus potentially reducing test time. Also, the illustrated pointwise maps of LSV could provide a method for identifying areas of fluctuation commonly found in early glaucomatous field loss. PMID:7703196

Unification of height systems in the frame of GGOS

NASA Astrophysics Data System (ADS)

Sánchez, Laura

2015-04-01

Most of the existing vertical reference systems do not fulfil the accuracy requirements of modern Geodesy. They refer to local sea surface levels, are stationary (do not consider variations in time), realize different physical height types (orthometric, normal, normal-orthometric, etc.), and their combination in a global frame presents uncertainties at the metre level. To provide a precise geodetic infrastructure for monitoring the Earth system, the Global Geodetic Observing System (GGOS) of the International Association of Geodesy (IAG), promotes the standardization of the height systems worldwide. The main purpose is to establish a global gravity field-related vertical reference system that (1) supports a highly-precise (at cm-level) combination of physical and geometric heights worldwide, (2) allows the unification of all existing local height datums, and (3) guarantees vertical coordinates with global consistency (the same accuracy everywhere) and long-term stability (the same order of accuracy at any time). Under this umbrella, the present contribution concentrates on the definition and realization of a conventional global vertical reference system; the standardization of the geodetic data referring to the existing height systems; and the formulation of appropriate strategies for the precise transformation of the local height datums into the global vertical reference system. The proposed vertical reference system is based on two components: a geometric component consisting of ellipsoidal heights as coordinates and a level ellipsoid as the reference surface, and a physical component comprising geopotential numbers as coordinates and an equipotential surface defined by a conventional W0 value as the reference surface. The definition of the physical component is based on potential parameters in order to provide reference to any type of physical heights (normal, orthometric, etc.). The conversion of geopotential numbers into metric heights and the modelling of the reference surface (geoid or quasigeoid determination) are considered as steps of the realization. The vertical datum unification strategy is based on (1) the physical connection of height datums to determine their discrepancies, (2) joint analysis of satellite altimetry and tide gauge records to determine time variations of sea level at reference tide gauges, (3) combination of geometrical and physical heights in a well-distributed and high-precise reference frame to estimate the relationship between the individual vertical levels and the global one, and (4) analysis of GNSS time series at reference tide gauges to separate crustal movements from sea level changes. The final vertical transformation parameters are provided by the common adjustment of the observation equations derived from these methods.

Identification and Validation of Reference Genes for RT-qPCR Analysis in Non-Heading Chinese Cabbage Flowers

PubMed Central

Wang, Cheng; Cui, Hong-Mi; Huang, Tian-Hong; Liu, Tong-Kun; Hou, Xi-Lin; Li, Ying

2016-01-01

Non-heading Chinese cabbage (Brassica rapa ssp. chinensis Makino) is an important vegetable member of Brassica rapa crops. It exhibits a typical sporophytic self-incompatibility (SI) system and is an ideal model plant to explore the mechanism of SI. Gene expression research are frequently used to unravel the complex genetic mechanism and in such studies appropriate reference selection is vital. Validation of reference genes have neither been conducted in Brassica rapa flowers nor in SI trait. In this study, 13 candidate reference genes were selected and examined systematically in 96 non-heading Chinese cabbage flower samples that represent four strategic groups in compatible and self-incompatible lines of non-heading Chinese cabbage. Two RT-qPCR analysis software, geNorm and NormFinder, were used to evaluate the expression stability of these genes systematically. Results revealed that best-ranked references genes should be selected according to specific sample subsets. DNAJ, UKN1, and PP2A were identified as the most stable reference genes among all samples. Moreover, our research further revealed that the widely used reference genes, CYP and ACP, were the least suitable reference genes in most non-heading Chinese cabbage flower sample sets. To further validate the suitability of the reference genes identified in this study, the expression level of SRK and Exo70A1 genes which play important roles in regulating interaction between pollen and stigma were studied. Our study presented the first systematic study of reference gene(s) selection for SI study and provided guidelines to obtain more accurate RT-qPCR results in non-heading Chinese cabbage. PMID:27375663

RF-Based Location Using Interpolation Functions to Reduce Fingerprint Mapping

PubMed Central

Ezpeleta, Santiago; Claver, José M.; Pérez-Solano, Juan J.; Martí, José V.

2015-01-01

Indoor RF-based localization using fingerprint mapping requires an initial training step, which represents a time consuming process. This location methodology needs a database conformed with RSSI (Radio Signal Strength Indicator) measures from the communication transceivers taken at specific locations within the localization area. But, the real world localization environment is dynamic and it is necessary to rebuild the fingerprint database when some environmental changes are made. This paper explores the use of different interpolation functions to complete the fingerprint mapping needed to achieve the sought accuracy, thereby reducing the effort in the training step. Also, different distributions of test maps and reference points have been evaluated, showing the validity of this proposal and necessary trade-offs. Results reported show that the same or similar localization accuracy can be achieved even when only 50% of the initial fingerprint reference points are taken. PMID:26516862

Evidence for validity of five secondary data sources for enumerating retail food outlets in seven American Indian communities in North Carolina.

PubMed

Fleischhacker, Sheila E; Rodriguez, Daniel A; Evenson, Kelly R; Henley, Amanda; Gizlice, Ziya; Soto, Dolly; Ramachandran, Gowri

2012-11-22

Most studies on the local food environment have used secondary sources to describe the food environment, such as government food registries or commercial listings (e.g., Reference USA). Most of the studies exploring evidence for validity of secondary retail food data have used on-site verification and have not conducted analysis by data source (e.g., sensitivity of Reference USA) or by food outlet type (e.g., sensitivity of Reference USA for convenience stores). Few studies have explored the food environment in American Indian communities. To advance the science on measuring the food environment, we conducted direct, on-site observations of a wide range of food outlets in multiple American Indian communities, without a list guiding the field observations, and then compared our findings to several types of secondary data. Food outlets located within seven State Designated Tribal Statistical Areas in North Carolina (NC) were gathered from online Yellow Pages, Reference USA, Dun & Bradstreet, local health departments, and the NC Department of Agriculture and Consumer Services. All TIGER/Line 2009 roads (>1,500 miles) were driven in six of the more rural tribal areas and, for the largest tribe, all roads in two of its cities were driven. Sensitivity, positive predictive value, concordance, and kappa statistics were calculated to compare secondary data sources to primary data. 699 food outlets were identified during primary data collection. Match rate for primary data and secondary data differed by type of food outlet observed, with the highest match rates found for grocery stores (97%), general merchandise stores (96%), and restaurants (91%). Reference USA exhibited almost perfect sensitivity (0.89). Local health department data had substantial sensitivity (0.66) and was almost perfect when focusing only on restaurants (0.91). Positive predictive value was substantial for Reference USA (0.67) and moderate for local health department data (0.49). Evidence for validity was comparatively lower for Dun & Bradstreet, online Yellow Pages, and the NC Department of Agriculture. Secondary data sources both over- and under-represented the food environment; they were particularly problematic for identifying convenience stores and specialty markets. More attention is needed to improve the validity of existing data sources, especially for rural local food environments.

Evidence for validity of five secondary data sources for enumerating retail food outlets in seven American Indian Communities in North Carolina

PubMed Central

2012-01-01

Background Most studies on the local food environment have used secondary sources to describe the food environment, such as government food registries or commercial listings (e.g., Reference USA). Most of the studies exploring evidence for validity of secondary retail food data have used on-site verification and have not conducted analysis by data source (e.g., sensitivity of Reference USA) or by food outlet type (e.g., sensitivity of Reference USA for convenience stores). Few studies have explored the food environment in American Indian communities. To advance the science on measuring the food environment, we conducted direct, on-site observations of a wide range of food outlets in multiple American Indian communities, without a list guiding the field observations, and then compared our findings to several types of secondary data. Methods Food outlets located within seven State Designated Tribal Statistical Areas in North Carolina (NC) were gathered from online Yellow Pages, Reference USA, Dun & Bradstreet, local health departments, and the NC Department of Agriculture and Consumer Services. All TIGER/Line 2009 roads (>1,500 miles) were driven in six of the more rural tribal areas and, for the largest tribe, all roads in two of its cities were driven. Sensitivity, positive predictive value, concordance, and kappa statistics were calculated to compare secondary data sources to primary data. Results 699 food outlets were identified during primary data collection. Match rate for primary data and secondary data differed by type of food outlet observed, with the highest match rates found for grocery stores (97%), general merchandise stores (96%), and restaurants (91%). Reference USA exhibited almost perfect sensitivity (0.89). Local health department data had substantial sensitivity (0.66) and was almost perfect when focusing only on restaurants (0.91). Positive predictive value was substantial for Reference USA (0.67) and moderate for local health department data (0.49). Evidence for validity was comparatively lower for Dun & Bradstreet, online Yellow Pages, and the NC Department of Agriculture. Conclusions Secondary data sources both over- and under-represented the food environment; they were particularly problematic for identifying convenience stores and specialty markets. More attention is needed to improve the validity of existing data sources, especially for rural local food environments. PMID:23173781

Electron microscopy for ultrastructural analysis and protein localization in Saccharomyces cerevisiae

PubMed Central

Frankl, Andri; Mari, Muriel; Reggiori, Fulvio

2015-01-01

The yeast Saccharomyces cerevisiae is a key model system for studying of a multitude of cellular processes because of its amenability to genetics, molecular biology and biochemical procedures. Ultrastructural examinations of this organism, though, are traditionally difficult because of the presence of a thick cell wall and the high density of cytoplasmic proteins. A series of recent methodological and technical developments, however, has revived interest in morphological analyses of yeast (e.g. 123). Here we present a review of established and new methods, from sample preparation to imaging, for the ultrastructural analysis of S. cerevisiae. We include information for the use of different fixation methods, embedding procedures, approaches for contrast enhancement, and sample visualization techniques, with references to successful examples. The goal of this review is to guide researchers that want to investigate a particular process at the ultrastructural level in yeast by aiding in the selection of the most appropriate approach to visualize a specific structure or subcellular compartment. PMID:28357267

GREAT: a gradient-based color-sampling scheme for Retinex.

PubMed

Lecca, Michela; Rizzi, Alessandro; Serapioni, Raul Paolo

2017-04-01

Modeling the local color spatial distribution is a crucial step for the algorithms of the Milano Retinex family. Here we present GREAT, a novel, noise-free Milano Retinex implementation based on an image-aware spatial color sampling. For each channel of a color input image, GREAT computes a 2D set of edges whose magnitude exceeds a pre-defined threshold. Then GREAT re-scales the channel intensity of each image pixel, called target, by the average of the intensities of the selected edges weighted by a function of their positions, gradient magnitudes, and intensities relative to the target. In this way, GREAT enhances the input image, adjusting its brightness, contrast and dynamic range. The use of the edges as pixels relevant to color filtering is justified by the importance that edges play in human color sensation. The name GREAT comes from the expression "Gradient RElevAnce for ReTinex," which refers to the threshold-based definition of a gradient relevance map for edge selection and thus for image color filtering.

A pancultural perspective on the fading affect bias in autobiographical memory.

PubMed

Ritchie, Timothy D; Batteson, Tamzin J; Bohn, Annette; Crawford, Matthew T; Ferguson, Georgie V; Schrauf, Robert W; Vogl, Rodney J; Walker, W Richard

2015-01-01

The fading affect bias (FAB) refers to the negative affect associated with autobiographical events fading faster than the positive affect associated with such events, a reliable and valid valence effect established by researchers in the USA. The present study examined the idea that the FAB is a ubiquitous emotion regulating phenomenon in autobiographical memory that is present in people from a variety of cultures. We tested for evidence of the FAB by sampling more than 2400 autobiographical event descriptions from 562 participants in 10 cultures around the world. Using variations on a common method, each sample evidenced a FAB: positive affect faded slower than negative affect did. Results suggest that in tandem with local norms and customs, the FAB may foster recovery from negative life events and promote the retention of the positive emotions, within and outside of the USA. We discuss these findings in the context of Keltner and Haidt's levels of analysis theory of emotion and culture.

Results of the U. S. Geological Survey's analytical evaluation program for standard reference samples distributed in April 2001

USGS Publications Warehouse

Woodworth, M.T.; Connor, B.F.

2001-01-01

This report presents the results of the U.S. Geological Survey's analytical evaluation program for six standard reference samples -- T-165 (trace constituents), M-158 (major constituents), N-69 (nutrient constituents), N-70 (nutrient constituents), P-36 (low ionic-strength constituents), and Hg-32 (mercury) -- that were distributed in April 2001 to laboratories enrolled in the U.S. Geological Survey sponsored interlaboratory testing program. Analytical data received from 73 laboratories were evaluated with respect to overall laboratory performance and relative laboratory performance for each analyte in the six reference samples. Results of these evaluations are presented in tabular form. Also presented are tables and graphs summarizing the analytical data provided by each laboratory for each analyte in the six standard reference samples. The most probable value for each analyte was determined using nonparametric statistics.

Method for detection of dental caries and periodontal disease using optical imaging

DOEpatents

Nathel, H.; Kinney, J.H.; Otis, L.L.

1996-10-29

A method is disclosed for detecting the presence of active and inactive caries in teeth and diagnosing periodontal disease uses non-ionizing radiation with techniques for reducing interference from scattered light. A beam of non-ionizing radiation is divided into sample and reference beams. The region to be examined is illuminated by the sample beam, and reflected or transmitted radiation from the sample is recombined with the reference beam to form an interference pattern on a detector. The length of the reference beam path is adjustable, allowing the operator to select the reflected or transmitted sample photons that recombine with the reference photons. Thus radiation scattered by the dental or periodontal tissue can be prevented from obscuring the interference pattern. A series of interference patterns may be generated and interpreted to locate dental caries and periodontal tissue interfaces. 7 figs.

Results of the U. S. Geological Survey's Analytical Evaluation Program for Standard Reference Samples Distributed in March 2002

USGS Publications Warehouse

Woodworth, M.T.; Conner, B.F.

2002-01-01

This report presents the results of the U.S. Geological Survey's analytical evaluation program for six standard reference samples -- T- 169 (trace constituents), M- 162 (major constituents), N-73 (nutrient constituents), N-74 (nutrient constituents), P-38 (low ionic-strength constituents), and Hg-34 (mercury) -- that were distributed in March 2002 to laboratories enrolled in the U.S. Geological Survey sponsored intedaboratory testing program. Analytical data received from 93 laboratories were evaluated with respect to overall laboratory performance and relative laboratory performance for each analyte in the six reference samples. Results of these evaluations are presented in tabular form. Also presented are tables and graphs summarizing the analytical data provided by each laboratory for each analyte in the six standard reference samples. The most probable value for each analyte was determined using nonparametric statistics.

Results of the U.S. Geological Survey's analytical evaluation program for standard reference samples distributed in September 2002

USGS Publications Warehouse

Woodworth, Mark T.; Connor, Brooke F.

2003-01-01

This report presents the results of the U.S. Geological Survey's analytical evaluation program for six standard reference samples -- T-171 (trace constituents), M-164 (major constituents), N-75 (nutrient constituents), N-76 (nutrient constituents), P-39 (low ionic-strength constituents), and Hg-35 (mercury) -- that were distributed in September 2002 to laboratories enrolled in the U.S. Geological Survey sponsored interlaboratory testing program. Analytical data received from 102 laboratories were evaluated with respect to overall laboratory performance and relative laboratory performance for each analyte in the six reference samples. Results of these evaluations are presented in tabular form. Also presented are tables and graphs summarizing the analytical data provided by each laboratory for each analyte in the six standard reference samples. The most probable value for each analyte was determined using nonparametric statistics.

Results of the U.S. Geological Survey's analytical evaluation program for standard reference samples distributed in September 2001

USGS Publications Warehouse

Woodworth, Mark T.; Connor, Brooke F.

2002-01-01

This report presents the results of the U.S. Geological Survey's analytical evaluation program for six standard reference samples -- T-167 (trace constituents), M-160 (major constituents), N-71 (nutrient constituents), N-72 (nutrient constituents), P-37 (low ionic-strength constituents), and Hg-33 (mercury) -- that were distributed in September 2001 to laboratories enrolled in the U.S. Geological Survey sponsored interlaboratory testing program. Analytical data received from 98 laboratories were evaluated with respect to overall laboratory performance and relative laboratory performance for each analyte in the six reference samples. Results of these evaluations are presented in tabular form. Also presented are tables and graphs summarizing the analytical data provided by each laboratory for each analyte in the six standard reference samples. The most probable value for each analyte was determined using nonparametric statistics.

Results of the U.S. Geological Survey's Analytical Evaluation Program for Standard Reference Samples Distributed in March 2000

USGS Publications Warehouse

Farrar, Jerry W.; Copen, Ashley M.

2000-01-01

This report presents the results of the U.S. Geological Survey's analytical evaluation program for six standard reference samples -- T-161 (trace constituents), M-154 (major constituents), N-65 (nutrient constituents), N-66 nutrient constituents), P-34 (low ionic strength constituents), and Hg-30 (mercury) -- that were distributed in March 2000 to 144 laboratories enrolled in the U.S. Geological Survey sponsored interlaboratory testing program. Analytical data that were received from 132 of the laboratories were evaluated with respect to overall laboratory performance and relative laboratory performance for each analyte in the six reference samples. Results of these evaluations are presented in tabular form. Also presented are tables and graphs summarizing the analytical data provided by each laboratory for each analyte in the six standard reference samples. The most probable value for each analyte was determined using nonparametric statistics.

Results of the U.S. Geological Survey's analytical evaluation program for standard reference samples distributed in October 1999

USGS Publications Warehouse

Farrar, T.W.

2000-01-01

This report presents the results of the U.S. Geological Survey's analytical evaluation program for six standard reference samples -- T-159 (trace constituents), M-152 (major constituents), N-63 (nutrient constituents), N-64 (nutrient constituents), P-33 (low ionic strength constituents), and Hg-29 (mercury) -- that were distributed in October 1999 to 149 laboratories enrolled in the U.S. Geological Survey sponsored interlaboratory testing program. Analytical data that were received from 131 of the laboratories were evaluated with respect to overall laboratory performance and relative laboratory performance for each analyte in the six reference samples. Results of these evaluations are presented in tabular form. Also presented are tables and graphs summarizing the analytical data provided by each laboratory for each analyte in the six standard reference samples. The most probable value for each analyte was determined using nonparametric statistics.

Results of the U.S. Geological Survey's analytical evaluation program for standard reference samples distributed in March 2003

USGS Publications Warehouse

Woodworth, Mark T.; Connor, Brooke F.

2003-01-01

This report presents the results of the U.S. Geological Survey's analytical evaluation program for six standard reference samples -- T-173 (trace constituents), M-166 (major constituents), N-77 (nutrient constituents), N-78 (nutrient constituents), P-40 (low ionic-strength constituents), and Hg-36 (mercury) -- that were distributed in March 2003 to laboratories enrolled in the U.S. Geological Survey sponsored interlaboratory testing program. Analytical data received from 110 laboratories were evaluated with respect to overall laboratory performance and relative laboratory performance for each analyte in the six reference samples. Results of these evaluations are presented in tabular form. Also presented are tables and graphs summarizing the analytical data provided by each laboratory for each analyte in the six standard reference samples. The most probable value for each analyte was determined using nonparametric statistics.

Results of the U. S. Geological Survey's analytical evaluation program for standard reference samples distributed in October 2000

USGS Publications Warehouse

Connor, B.F.; Currier, J.P.; Woodworth, M.T.

2001-01-01

This report presents the results of the U.S. Geological Survey's analytical evaluation program for six standard reference samples -- T-163 (trace constituents), M-156 (major constituents), N-67 (nutrient constituents), N-68 (nutrient constituents), P-35 (low ionic strength constituents), and Hg-31 (mercury) -- that were distributed in October 2000 to 126 laboratories enrolled in the U.S. Geological Survey sponsored interlaboratory testing program. Analytical data that were received from 122 of the laboratories were evaluated with respect to overall laboratory performance and relative laboratory performance for each analyte in the six reference samples. Results of these evaluations are presented in tabular form. Also presented are tables and graphs summarizing the analytical data provided by each laboratory for each analyte in the six standard reference samples. The most probable value for each analyte was determined using nonparametric statistics.

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.

Evaluation of local electric fields generated by transcranial direct current stimulation with an extracephalic reference electrode based on realistic 3D body modeling

NASA Astrophysics Data System (ADS)

Im, Chang-Hwan; Park, Ji-Hye; Shim, Miseon; Chang, Won Hyuk; Kim, Yun-Hee

2012-04-01

In this study, local electric field distributions generated by transcranial direct current stimulation (tDCS) with an extracephalic reference electrode were evaluated to address extracephalic tDCS safety issues. To this aim, we generated a numerical model of an adult male human upper body and applied the 3D finite element method to electric current conduction analysis. In our simulations, the active electrode was placed over the left primary motor cortex (M1) and the reference electrode was placed at six different locations: over the right temporal lobe, on the right supraorbital region, on the right deltoid, on the left deltoid, under the chin, and on the right buccinator muscle. The maximum current density and electric field intensity values in the brainstem generated by the extracephalic reference electrodes were comparable to, or even less than, those generated by the cephalic reference electrodes. These results suggest that extracephalic reference electrodes do not lead to unwanted modulation of the brainstem cardio-respiratory and autonomic centers, as indicated by recent experimental studies. The volume energy density was concentrated at the neck area by the use of deltoid reference electrodes, but was still smaller than that around the active electrode locations. In addition, the distributions of elicited cortical electric fields demonstrated that the use of extracephalic reference electrodes might allow for the robust prediction of cortical modulations with little dependence on the reference electrode locations.

Liver Rapid Reference Set Application: Hiro Yamada - Wako (2011) — EDRN Public Portal

Cancer.gov

Measure clinical effectiveness of AFP-L3 and DCP for early detection of HCC in patient samples collected prospectively during surveillance. However since such samples are not readily available in the USA the reference set samples are well characterized and studied, gaining access to these samples will allow Wako to quickly measure clinical effectiveness of AFP-L3 and DCP in detecting early HCC.

Four reference soil and rock samples for measuring element availability in the Western Energy Regions

USGS Publications Warehouse

Crock, J.G.; Severson, R.C.

1980-01-01

Attaining acceptable precision in extractable element determinations is more difficult than in total element determinations. In total element determinations, dissolution of the sample is qualitatively checked by the clarity of the solution and the absence of residues. These criteria cannot be used for extracts. Possibilities for error are introduced in virtually every step in soil extractions. Therefore, the use of reference materials whose homogeneity and element content are reasonably well known is essential for determination of extractable elements. In this report, estimates of homogeneity and element content are presented for four reference samples. Bulk samples of about 100 kilograms of each sample were ground to pass an 80-mesh sieve. The samples were homogenized and split using a Jones-type splitter. Fourteen splits of each reference sample were analyzed for total content of Ca, Co, Cu, Fe, K, Mg, Mn, Na, and Zn; DTPA-extractable Cd, Co, Cu, Fe, Mn, Ni, Pb, and Zn; exchangeable Ca, Mg, K, and Na; cation exchange capacity water-saturation-extractable Ca, Mg, K, Na, C1, and SO4; soil pH; and hot-water-extractable boron. Error measured between splits was small, indicating that the samples were homogenized adequately and that the laboratory procedure provided reproducible results.

Local network assessment

NASA Astrophysics Data System (ADS)

Glen, D. V.

1985-04-01

Local networks, related standards activities of the Institute of Electrical and Electronics Engineers the American National Standards Institute and other elements are presented. These elements include: (1) technology choices such as topology, transmission media, and access protocols; (2) descriptions of standards for the 802 local area networks (LAN's); high speed local networks (HSLN's) and military specification local networks; and (3) intra- and internetworking using bridges and gateways with protocols Interconnection (OSI) reference model. The convergence of LAN/PBX technology is also described.

Body Weight, Length and Head Circumference at Birth in a Cohort of Turkish Newborns

PubMed Central

Kurtoğlu, Selim; Hatipoğlu, Nihal; Mazıcıoğlu, Mustafa Mümtaz; Akın, Mustafa Ali; Çoban, Dilek; Gökoğlu, Sonay; Baştuğ, Osman

2012-01-01

Objective: Intrauterine growth references are primarily useful indicators in the assessment of the general health status of newborn infants. Although Lubchenco’s references are still used in many neonatal care units, we believe that there is a need for up-to-date intrauterine growth references specific for different populations. To develop gestational age-and gender-specific national references for birth weight, birth length and head circumference. Methods: Data were collected from neonatal records of perinatology services of eleven hospitals from January to December 2009. The anthropometry of a total of 4750 singleton live births born between 28 and 41 weeks of gestation were recorded. Means and standard deviations were calculated, and percentiles for each gender and gestational week were produced using the LMS program. The results were compared with US infants and also with local data. Results: Gestational age- and gender-specific 3rd, 5th, 10th, 15th, 25th, 50th, 75th, 85th, 90th, 95th and 97th percentile values were produced. Comparison of the 10th, 50th and 90th percentile values showed that the boys were heavier and longer than the girls. Head circumference values were also higher in the boys. Proportions of small for gestational age (SGA), appropriate for gestational age (AGA) and large for gestational age (LGA) infants in the sample were 10.1%, 79.1% and 10.8%, respectively. Conclusion: These gender- and gestational age-specific references will be of use in clinical practice and also for research purposes until more comprehensive, reliable and accessible national data pertaining to the intrauterine growth of Turkish infants are produced. Conflict of interest:None declared. PMID:22664362

Example-Based Image Colorization Using Locality Consistent Sparse Representation.

PubMed

Bo Li; Fuchen Zhao; Zhuo Su; Xiangguo Liang; Yu-Kun Lai; Rosin, Paul L

2017-11-01

Image colorization aims to produce a natural looking color image from a given gray-scale image, which remains a challenging problem. In this paper, we propose a novel example-based image colorization method exploiting a new locality consistent sparse representation. Given a single reference color image, our method automatically colorizes the target gray-scale image by sparse pursuit. For efficiency and robustness, our method operates at the superpixel level. We extract low-level intensity features, mid-level texture features, and high-level semantic features for each superpixel, which are then concatenated to form its descriptor. The collection of feature vectors for all the superpixels from the reference image composes the dictionary. We formulate colorization of target superpixels as a dictionary-based sparse reconstruction problem. Inspired by the observation that superpixels with similar spatial location and/or feature representation are likely to match spatially close regions from the reference image, we further introduce a locality promoting regularization term into the energy formulation, which substantially improves the matching consistency and subsequent colorization results. Target superpixels are colorized based on the chrominance information from the dominant reference superpixels. Finally, to further improve coherence while preserving sharpness, we develop a new edge-preserving filter for chrominance channels with the guidance from the target gray-scale image. To the best of our knowledge, this is the first work on sparse pursuit image colorization from single reference images. Experimental results demonstrate that our colorization method outperforms the state-of-the-art methods, both visually and quantitatively using a user study.

Contamination from polycyclic aromatic hydrocarbons (PAHs) in the soil of a botanic garden localized next to a former manufacturing gas plant in Palermo (Italy).

PubMed

Orecchio, Santino

2010-08-15

The Botanical Garden lies within the city of Palermo, a few meters away from one of the largest unused Manufacturing Gas Plant in Sicily. The total concentrations of PAHs (23 compounds) in the soil of Botanical Garden ranged from 947 to 18,072 microg/kg. The wide range of PAH concentrations (RSD=84%) found in the soil samples indicates heterogeneous levels of contamination in the area and this can be explained by considering the different tree distributions which prevents the homogeneous deposition of pollutants on the soil. Soils collected in the Botanical Garden generally showed the highest PAH concentrations, being almost 2-3 times higher than the concentration samples obtained in the urban reference sites and about 20 times higher than those in the rural stations. The total PAH concentrations, in the Botanical Garden soil, resulted higher than the maximum concentrations allowed by the Italian legislation for the green areas. Perylene, was found in all the stations. From a careful study of the isomeric ratios, we can hypothesize that the soils of the Botanical Garden are mainly affected by localized MGP particulate deposition, suggesting that the partitioning between organic matter and PAHs is not the dominant process in the soils with higher organic matter content. Copyright 2010 Elsevier B.V. All rights reserved.

A DNA Barcoding Approach to Characterize Pollen Collected by Honeybees

PubMed Central

Bruni, Ilaria; Scaccabarozzi, Daniela; Sandionigi, Anna; Barbuto, Michela; Casiraghi, Maurizio; Labra, Massimo

2014-01-01

In the present study, we investigated DNA barcoding effectiveness to characterize honeybee pollen pellets, a food supplement largely used for human nutrition due to its therapeutic properties. We collected pollen pellets using modified beehives placed in three zones within an alpine protected area (Grigna Settentrionale Regional Park, Italy). A DNA barcoding reference database, including rbcL and trnH-psbA sequences from 693 plant species (104 sequenced in this study) was assembled. The database was used to identify pollen collected from the hives. Fifty-two plant species were identified at the molecular level. Results suggested rbcL alone could not distinguish among congeneric plants; however, psbA-trnH identified most of the pollen samples at the species level. Substantial variability in pollen composition was observed between the highest elevation locality (Alpe Moconodeno), characterized by arid grasslands and a rocky substrate, and the other two sites (Cornisella and Ortanella) at lower altitudes. Pollen from Ortanella and Cornisella showed the presence of typical deciduous forest species; however in samples collected at Ortanella, pollen of the invasive Lonicera japonica, and the ornamental Pelargonium x hortorum were observed. Our results indicated pollen composition was largely influenced by floristic local biodiversity, plant phenology, and the presence of alien flowering species. Therefore, pollen molecular characterization based on DNA barcoding might serve useful to beekeepers in obtaining honeybee products with specific nutritional or therapeutic characteristics desired by food market demands. PMID:25296114

A digital image-based method for determining of total acidity in red wines using acid-base titration without indicator.

PubMed

Tôrres, Adamastor Rodrigues; Lyra, Wellington da Silva; de Andrade, Stéfani Iury Evangelista; Andrade, Renato Allan Navarro; da Silva, Edvan Cirino; Araújo, Mário César Ugulino; Gaião, Edvaldo da Nóbrega

2011-05-15

This work proposes the use of digital image-based method for determination of total acidity in red wines by means of acid-base titration without using an external indicator or any pre-treatment of the sample. Digital images present the colour of the emergent radiation which is complementary to the radiation absorbed by anthocyanines present in wines. Anthocyanines change colour depending on the pH of the medium, and from the variation of colour in the images obtained during titration, the end point can be localized with accuracy and precision. RGB-based values were employed to build titration curves, and end points were localized by second derivative curves. The official method recommends potentiometric titration with a NaOH standard solution, and sample dilution until the pH reaches 8.2-8.4. In order to illustrate the feasibility of the proposed method, titrations of ten red wines were carried out. Results were compared with the reference method, and no statistically significant difference was observed between the results by applying the paired t-test at the 95% confidence level. The proposed method yielded more precise results than the official method. This is due to the trivariate nature of the measurements (RGB), associated with digital images. Copyright © 2011 Elsevier B.V. All rights reserved.

Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

PubMed Central

Wang, C-H; Zheng, X-M; Xu, Q; Yuan, X-P; Huang, L; Zhou, H-F; Wei, X-H; Ge, S

2014-01-01

Despite extensive studies on cultivated rice, the genetic structure and subdivision of this crop remain unclear at both global and local scales. Using 84 nuclear simple sequence repeat markers, we genotyped a panel of 153 global rice cultivars covering all previously recognized groups and 826 cultivars representing the diversity of Chinese rice germplasm. On the basis of model-based grouping, neighbour-joining tree and principal coordinate analysis, we confirmed the widely accepted five major groups of rice cultivars (indica, aus, aromatic, temperate japonica and tropical japonica), and demonstrated that rayada rice was unique in genealogy and should be treated as a new (the sixth) major group of rice germplasm. With reference to the global classification of rice cultivars, we identified three major groups (indica, temperate japonica and tropical japonica) in Chinese rice germplasm and showed that Chinese temperate japonica contained higher diversity than that of global samples, whereas Chinese indica and tropical japonica maintained slightly lower diversity than that present in the global samples. Particularly, we observed that all seasonal, drought-tolerant and endosperm types occurred within each of three major groups of Chinese cultivars, which does not support previous claims that seasonal differentiation exists in Indica and drought-tolerant differentiation is present in Japonica. It is most likely that differentiation of cultivar types arose multiple times stemming from artificial selection for adaptation to local environments. PMID:24326293

Improved Reference Sampling and Subtraction: A Technique for Reducing the Read Noise of Near-infrared Detector Systems

NASA Astrophysics Data System (ADS)

Rauscher, Bernard J.; Arendt, Richard G.; Fixsen, D. J.; Greenhouse, Matthew A.; Lander, Matthew; Lindler, Don; Loose, Markus; Moseley, S. H.; Mott, D. Brent; Wen, Yiting; Wilson, Donna V.; Xenophontos, Christos

2017-10-01

Near-infrared array detectors, like the James Webb Space Telescope (JWST) NIRSpec’s Teledyne’s H2RGs, often provide reference pixels and a reference output. These are used to remove correlated noise. Improved reference sampling and subtraction (IRS2) is a statistical technique for using this reference information optimally in a least-squares sense. Compared with the traditional H2RG readout, IRS2 uses a different clocking pattern to interleave many more reference pixels into the data than is otherwise possible. Compared with standard reference correction techniques, IRS2 subtracts the reference pixels and reference output using a statistically optimized set of frequency-dependent weights. The benefits include somewhat lower noise variance and much less obvious correlated noise. NIRSpec’s IRS2 images are cosmetically clean, with less 1/f banding than in traditional data from the same system. This article describes the IRS2 clocking pattern and presents the equations needed to use IRS2 in systems other than NIRSpec. For NIRSpec, applying these equations is already an option in the calibration pipeline. As an aid to instrument builders, we provide our prototype IRS2 calibration software and sample JWST NIRSpec data. The same techniques are applicable to other detector systems, including those based on Teledyne’s H4RG arrays. The H4RG’s interleaved reference pixel readout mode is effectively one IRS2 pattern.

Reconstructing a herbivore's diet using a novel rbcL DNA mini-barcode for plants.

PubMed

Erickson, David L; Reed, Elizabeth; Ramachandran, Padmini; Bourg, Norman A; McShea, William J; Ottesen, Andrea

2017-05-01

Next Generation Sequencing and the application of metagenomic analyses can be used to answer questions about animal diet choice and study the consequences of selective foraging by herbivores. The quantification of herbivore diet choice with respect to native versus exotic plant species is particularly relevant given concerns of invasive species establishment and their effects on ecosystems. While increased abundance of white-tailed deer ( Odocoileus virginianus ) appears to correlate with increased incidence of invasive plant species, data supporting a causal link is scarce. We used a metabarcoding approach (PCR amplicons of the plant rbc L gene) to survey the diet of white-tailed deer (fecal samples), from a forested site in Warren County, Virginia with a comprehensive plant species inventory and corresponding reference collection of plant barcode and chloroplast sequences. We sampled fecal pellet piles and extracted DNA from 12 individual deer in October 2014. These samples were compared to a reference DNA library of plant species collected within the study area. For 72 % of the amplicons, we were able to assign taxonomy at the species level, which provides for the first time-sufficient taxonomic resolution to quantify the relative frequency at which native and exotic plant species are being consumed by white-tailed deer. For each of the 12 individual deer we collected three subsamples from the same fecal sample, resulting in sequencing 36 total samples. Using Qiime, we quantified the plant DNA found in all 36 samples, and found that variance within samples was less than variance between samples ( F  = 1.73, P  = 0.004), indicating additional subsamples may not be necessary. Species level diversity ranged from 60 to 93 OTUs per individual and nearly 70 % of all plant sequences recovered were from native plant species. The number of species detected did reduce significantly (range 4-12) when we excluded species whose OTU composed <1 % of each sample's total. When compared to the abundance of native and non-natives plants inventoried in the local community, our results support the observation that white-tailed deer have strong foraging preferences, but these preferences were not consistent for species in either class. Deer forage behaviour may favour some exotic species, but not all.

Local synchronization of chaotic neural networks with sampled-data and saturating actuators.

PubMed

Wu, Zheng-Guang; Shi, Peng; Su, Hongye; Chu, Jian

2014-12-01

This paper investigates the problem of local synchronization of chaotic neural networks with sampled-data and actuator saturation. A new time-dependent Lyapunov functional is proposed for the synchronization error systems. The advantage of the constructed Lyapunov functional lies in the fact that it is positive definite at sampling times but not necessarily between sampling times, and makes full use of the available information about the actual sampling pattern. A local stability condition of the synchronization error systems is derived, based on which a sampled-data controller with respect to the actuator saturation is designed to ensure that the master neural networks and slave neural networks are locally asymptotically synchronous. Two optimization problems are provided to compute the desired sampled-data controller with the aim of enlarging the set of admissible initial conditions or the admissible sampling upper bound ensuring the local synchronization of the considered chaotic neural networks. A numerical example is used to demonstrate the effectiveness of the proposed design technique.

Requirements for the Development of Bacillus Anthracis Spore Reference Materials Used to Test Detection Systems

PubMed Central

Almeida, Jamie L.; Wang, Lili; Morrow, Jayne B.; Cole, Kenneth D.

2006-01-01

Bacillus anthracis spores have been used as biological weapons and the possibility of their further use requires surveillance systems that can accurately and reliably detect their presence in the environment. These systems must collect samples from a variety of matrices, process the samples, and detect the spores. The processing of the sample may include removal of inhibitors, concentration of the target, and extraction of the target in a form suitable for detection. Suitable reference materials will allow the testing of each of these steps to determine the sensitivity and specificity of the detection systems. The development of uniform and well-characterized reference materials will allow the comparison of different devices and technologies as well as assure the continued performance of detection systems. This paper discusses the special requirements of reference materials for Bacillus anthracis spores that could be used for testing detection systems. The detection of Bacillus anthracis spores is based on recognition of specific characteristics (markers) on either the spore surface or in the nucleic acids (DNA). We have reviewed the specific markers and their relevance to characterization of reference materials. We have also included the approach for the characterization of candidate reference materials that we are developing at the NIST laboratories. Additional applications of spore reference materials would include testing sporicidal treatments, techniques for sampling the environment, and remediation of spore-contaminated environments. PMID:27274929

Breast Reference Set Application: Chris Li-FHCRC (2015) — EDRN Public Portal

Cancer.gov

We propose to evaluate nine candidate biomarkers for ER+ breast cancer in samples from the EDRN Breast Cancer Reference Set. These biomarkers have been preliminarily validated in preclinical samples. The intended clinical applications of these markers are to: 1. Inform timing of a subsequent mammogram in women with a negative screening mammogram; 2. Inform continuation of mammographic screening among women 75-79 years; 3. Prioritize women who should be screened with mammography in areas with limited resources. Testing the reference samples would further expedite addressing these intended clinical applications by providing further validation data to support requests for samples from other sources for further Phase 3 evaluation (e.g., WHI, PLCO, and samples collected at the time of mammographic screening from the University of Toronto and UCSF).

Precision Thickness Variation Mapping Via One-Transducer Ultrasonic High Resolution Profilometry for Sample With Irregular or Rough Surface

NASA Technical Reports Server (NTRS)

Roth, Don J. (Inventor)

1996-01-01

An apparatus and method for determination of sample thickness and surface depression utilizing ultrasonic pulses is discussed. The sample is held in a predetermined position by a support member having a reference surface. Ultrasonic pulses travel through a medium of known velocity propagation and reflect off the reference surface and a sample surface. Time of flight data of surface echoes are converted to distances between sample surfaces to obtain computer-generated thickness profiles and surface mappings.

Quality-assurance results for routine water analyses in U.S. Geological Survey laboratories, water year 1998

USGS Publications Warehouse

Ludtke, Amy S.; Woodworth, Mark T.; Marsh, Philip S.

2000-01-01

The U.S. Geological Survey operates a quality-assurance program based on the analyses of reference samples for two laboratories: the National Water Quality Laboratory and the Quality of Water Service Unit. Reference samples that contain selected inorganic, nutrient, and low-level constituents are prepared and submitted to the laboratory as disguised routine samples. The program goal is to estimate precision and bias for as many analytical methods offered by the participating laboratories as possible. Blind reference samples typically are submitted at a rate of 2 to 5 percent of the annual environmental-sample load for each constituent. The samples are distributed to the laboratories throughout the year. The reference samples are subject to the identical laboratory handling, processing, and analytical procedures as those applied to environmental samples and, therefore, have been used as an independent source to verify bias and precision of laboratory analytical methods and ambient water-quality measurements. The results are stored permanently in the National Water Information System and the Blind Sample Project's data base. During water year 1998, 95 analytical procedures were evaluated at the National Water Quality Laboratory and 63 analytical procedures were evaluated at the Quality of Water Service Unit. An overall evaluation of the inorganic and low-level constituent data for water year 1998 indicated 77 of 78 analytical procedures at the National Water Quality Laboratory met the criteria for precision. Silver (dissolved, inductively coupled plasma-mass spectrometry) was determined to be imprecise. Five of 78 analytical procedures showed bias throughout the range of reference samples: chromium (dissolved, inductively coupled plasma-atomic emission spectrometry), dissolved solids (dissolved, gravimetric), lithium (dissolved, inductively coupled plasma-atomic emission spectrometry), silver (dissolved, inductively coupled plasma-mass spectrometry), and zinc (dissolved, inductively coupled plasma-mass spectrometry). At the National Water Quality Laboratory during water year 1998, lack of precision was indicated for 2 of 17 nutrient procedures: ammonia as nitrogen (dissolved, colorimetric) and orthophosphate as phosphorus (dissolved, colorimetric). Bias was indicated throughout the reference sample range for ammonia as nitrogen (dissolved, colorimetric, low level) and nitrate plus nitrite as nitrogen (dissolved, colorimetric, low level). All analytical procedures tested at the Quality of Water Service Unit during water year 1998 met the criteria for precision. One of the 63 analytical procedures indicated a bias throughout the range of reference samples: aluminum (whole-water recoverable, inductively coupled plasma-atomic emission spectrometry, trace).

Reduction of measurement errors in OCT scanning

NASA Astrophysics Data System (ADS)

Morel, E. N.; Tabla, P. M.; Sallese, M.; Torga, J. R.

2018-03-01

Optical coherence tomography (OCT) is a non-destructive optical technique, which uses a light source with a wide band width that focuses on a point in the sample to determine the distance (strictly, the optical path difference, OPD) between this point and a reference surface. The point can be superficial or at an interior interface of the sample (transparent or semitransparent), allowing topographies and / or tomographies in different materials. The Michelson interferometer is the traditional experimental scheme for this technique, in which a beam of light is divided into two arms, one the reference and the other the sample. The overlap of reflected light in the sample and in the reference generates an interference signal that gives us information about the OPD between arms. In this work, we work on the experimental configuration in which the reference signal and the reflected signal in the sample travel on the same arm, improving the quality of the interference signal. Among the most important aspects of this improvement we can mention that the noise and errors produced by the relative reference-sample movement and by the dispersion of the refractive index are considerably reduced. It is thus possible to obtain 3D images of surfaces with a spatial resolution in the order of microns. Results obtained on the topography of metallic surfaces, glass and inks printed on paper are presented.

Hematology and serum clinical chemistry reference intervals for free-ranging Scandinavian gray wolves (Canis lupus).

PubMed

Thoresen, Stein I; Arnemo, Jon M; Liberg, Olof

2009-06-01

Scandinavian free-ranging wolves (Canis lupus) are endangered, such that laboratory data to assess their health status is increasingly important. Although wolves have been studied for decades, most biological information comes from captive animals. The objective of the present study was to establish reference intervals for 30 clinical chemical and 8 hematologic analytes in Scandinavian free-ranging wolves. All wolves were tracked and chemically immobilized from a helicopter before examination and blood sampling in the winter of 7 consecutive years (1998-2004). Seventy-nine blood samples were collected from 57 gray wolves, including 24 juveniles (24 samples), 17 adult females (25 samples), and 16 adult males (30 samples). Whole blood and serum samples were stored at refrigeration temperature for 1-3 days before hematologic analyses and for 1-5 days before serum biochemical analyses. Reference intervals were calculated as 95% confidence intervals except for juveniles where the minimum and maximum values were used. Significant differences were observed between adult and juvenile wolves for RBC parameters, alkaline phosphatase and amylase activities, and total protein, albumin, gamma-globulins, cholesterol, creatinine, calcium, chloride, magnesium, phosphate, and sodium concentrations. Compared with published reference values for captive wolves, reference intervals for free-ranging wolves reflected exercise activity associated with capture (higher creatine kinase activity, higher glucose concentration), and differences in nutritional status (higher urea concentration).

Books, Baths, and Burials: Notes on Certain Nineteenth Century Adoptive Acts

ERIC Educational Resources Information Center

Whiteman, Philip M.

1973-01-01

Early legislation relating to street lighting, baths and washhouses, burial of the dead, public libraries and public improvements in England and Wales, reflected Parliament's suspicion of local democracy and distrust of local authorities. (9 references) (Author)

LOCALIZING THE RANGELAND HEALTH METHOD FOR SOUTHEASTERN ARIZONA

EPA Science Inventory

The interagency manual Interpreting Indicators of Rangeland Health, Version 4 (Technical Reference 1734-6) provides a method for making rangeland health assessments. The manual recommends that the rangeland health assessment approach be adapted to local conditions. This technica...

How to Plug into Your Local Umbilical Cord.

ERIC Educational Resources Information Center

Bloch, David C.

1981-01-01

Briefly describes the development of cable television and how it is transmitted. Public benefit uses, refranchising, and getting a local franchise started are discussed, as well as resources to help set up such a system. References are included. (BK)

Mobile Robot Self-Localization by Matching Range Maps Using a Hausdorff Measure

NASA Technical Reports Server (NTRS)

Olson, C. F.

1997-01-01

This paper examines techniques for a mobile robot to perform self-localization in natural terrain by comparing a dense range map computed from stereo imagery to a range map in a known frame of reference.

Whisking mechanics and active sensing

PubMed Central

Bush, Nicholas E; Solla, Sara A

2017-01-01

We describe recent advances in quantifying the three-dimensional (3D) geometry and mechanics of whisking. Careful delineation of relevant 3D reference frames reveals important geometric and mechanical distinctions between the localization problem (‘where’ is an object) and the feature extraction problem (‘what’ is an object). Head-centered and resting-whisker reference frames lend themselves to quantifying temporal and kinematic cues used for object localization. The whisking-centered reference frame lends itself to quantifying the contact mechanics likely associated with feature extraction. We offer the ‘windowed sampling’ hypothesis for active sensing: that rats can estimate an object’s spatial features by integrating mechanical information across whiskers during brief (25–60 ms) windows of ‘haptic enclosure’ with the whiskers, a motion that resembles a hand grasp. PMID:27632212

Bringing together local culture and rural development: findings from Ireland, Pennsylvania and Alaska

Treesearch

M.A. Brennan; Courtney G. Flint; A.E. Luloff

2009-01-01

The developmental trajectories of communities are routinely explained by reference to economic history, human capital deficits, or the structure of local labour markets. The role of local culture in understanding community development or in interpreting empirical research has received less attention. We believe culture plays an important independent role in shaping...

Quantifying Local, Response Dependence between Two Polytomous Items Using the Rasch Model

ERIC Educational Resources Information Center

Andrich, David; Humphry, Stephen M.; Marais, Ida

2012-01-01

Models of modern test theory imply statistical independence among responses, generally referred to as "local independence." One violation of local independence occurs when the response to one item governs the response to a subsequent item. Expanding on a formulation of this kind of violation as a process in the dichotomous Rasch model,…

State and Local Responsibility for Promoting Learning Environments of Equity and Equality: A Conceptual Analysis.

ERIC Educational Resources Information Center

Willie, Charles V.

This paper presents a conceptual analysis of the different responsibilities that State and local levels should assume in promoting the purposes of education. It is their responsibility to provide learning environments that promote equity and equality. The problem for State and local authorities with reference to desegregated education is that of…

20 CFR 653.113 - Processing apparent violations.

Code of Federal Regulations, 2013 CFR

2013-04-01

... employee shall document the suspected violation and refer this information to the local office manager. (b) If the employer has filed a job order with the JS office within the past 12 months, the local office... agency in writing. (c) If the employer has not filed a job order with the local office during the past 12...

20 CFR 653.113 - Processing apparent violations.

Code of Federal Regulations, 2014 CFR

2014-04-01

... employee shall document the suspected violation and refer this information to the local office manager. (b) If the employer has filed a job order with the JS office within the past 12 months, the local office... agency in writing. (c) If the employer has not filed a job order with the local office during the past 12...

20 CFR 653.113 - Processing apparent violations.

Code of Federal Regulations, 2012 CFR

2012-04-01

... employee shall document the suspected violation and refer this information to the local office manager. (b) If the employer has filed a job order with the JS office within the past 12 months, the local office... agency in writing. (c) If the employer has not filed a job order with the local office during the past 12...

20 CFR 653.113 - Processing apparent violations.

Code of Federal Regulations, 2011 CFR

2011-04-01

... employee shall document the suspected violation and refer this information to the local office manager. (b) If the employer has filed a job order with the JS office within the past 12 months, the local office... agency in writing. (c) If the employer has not filed a job order with the local office during the past 12...

Adjustment of pesticide concentrations for temporal changes in analytical recovery, 1992–2010

USGS Publications Warehouse

Martin, Jeffrey D.; Eberle, Michael

2011-01-01

Recovery is the proportion of a target analyte that is quantified by an analytical method and is a primary indicator of the analytical bias of a measurement. Recovery is measured by analysis of quality-control (QC) water samples that have known amounts of target analytes added ("spiked" QC samples). For pesticides, recovery is the measured amount of pesticide in the spiked QC sample expressed as a percentage of the amount spiked, ideally 100 percent. Temporal changes in recovery have the potential to adversely affect time-trend analysis of pesticide concentrations by introducing trends in apparent environmental concentrations that are caused by trends in performance of the analytical method rather than by trends in pesticide use or other environmental conditions. This report presents data and models related to the recovery of 44 pesticides and 8 pesticide degradates (hereafter referred to as "pesticides") that were selected for a national analysis of time trends in pesticide concentrations in streams. Water samples were analyzed for these pesticides from 1992 through 2010 by gas chromatography/mass spectrometry. Recovery was measured by analysis of pesticide-spiked QC water samples. Models of recovery, based on robust, locally weighted scatterplot smooths (lowess smooths) of matrix spikes, were developed separately for groundwater and stream-water samples. The models of recovery can be used to adjust concentrations of pesticides measured in groundwater or stream-water samples to 100 percent recovery to compensate for temporal changes in the performance (bias) of the analytical method.

Incorporation of physical constraints in optimal surface search for renal cortex segmentation

NASA Astrophysics Data System (ADS)

Li, Xiuli; Chen, Xinjian; Yao, Jianhua; Zhang, Xing; Tian, Jie

2012-02-01

In this paper, we propose a novel approach for multiple surfaces segmentation based on the incorporation of physical constraints in optimal surface searching. We apply our new approach to solve the renal cortex segmentation problem, an important but not sufficiently researched issue. In this study, in order to better restrain the intensity proximity of the renal cortex and renal column, we extend the optimal surface search approach to allow for varying sampling distance and physical separation constraints, instead of the traditional fixed sampling distance and numerical separation constraints. The sampling distance of each vertex-column is computed according to the sparsity of the local triangular mesh. Then the physical constraint learned from a priori renal cortex thickness is applied to the inter-surface arcs as the separation constraints. Appropriate varying sampling distance and separation constraints were learnt from 6 clinical CT images. After training, the proposed approach was tested on a test set of 10 images. The manual segmentation of renal cortex was used as the reference standard. Quantitative analysis of the segmented renal cortex indicates that overall segmentation accuracy was increased after introducing the varying sampling distance and physical separation constraints (the average true positive volume fraction (TPVF) and false positive volume fraction (FPVF) were 83.96% and 2.80%, respectively, by using varying sampling distance and physical separation constraints compared to 74.10% and 0.18%, respectively, by using fixed sampling distance and numerical separation constraints). The experimental results demonstrated the effectiveness of the proposed approach.

Partitioning the components of maxillary tooth displacement by the comparison of data from three cephalometric superimpositions.

PubMed

Baumrind, S; Ben-Bassat, Y; Bravo, L A; Curry, S; Korn, E L

1996-01-01

Using roentgenographic cephalograms from a sample of subjects with metallic implants, appropriately superimposed tracings were used to distinguish developmental and treatment-associated displacements of the maxillary central incisor and first molar associated "local" changes within the periodontium from "secondary" changes which reflect sutural and appositional growth at more distant osseous loci. Tracings were superimposed on anterior cranial base (ACB), on the maxillary implants only (IMP_MAX), and according to the best fit of maxillary anatomic structures without reference to the implants (A_MAX). Using the IMP_MAX superimposition, one could measure total local displacement at any landmark taking into consideration the effects of all appositional and resorptive changes on the superior and anterior surfaces of the palate, whereas using the A_MAX superimposition one could measure local displacement without consideration of surface appositional and resorptive changes. If the second of these measurements were subtracted from the first, the result would be a direct measurement of the effects of surface appositional and resorptive changes as they are expressed at that particular landmark. This strategy has enabled us to quantify and report the amount of accommodation which occurs at the location of each dental landmark in association with the resorptive and appositional changes which occur through time on the superior and anterior surfaces of the hard palate.

Pollution-Induced Community Tolerance To Diagnose Hazardous Chemicals in Multiple Contaminated Aquatic Systems.

PubMed

Rotter, Stefanie; Gunold, Roman; Mothes, Sibylle; Paschke, Albrecht; Brack, Werner; Altenburger, Rolf; Schmitt-Jansen, Mechthild

2015-08-18

Aquatic ecosystems are often contaminated with large numbers of chemicals, which cannot be sufficiently addressed by chemical target analyses. Effect-directed analysis (EDA) enables the identification of toxicants in complex contaminated environmental samples. This study suggests pollution-induced community tolerance (PICT) as a confirmation tool for EDA to identify contaminants which actually impact on local communities. The effects of three phytotoxic compounds local periphyton communities, cultivated at a reference (R-site) and a polluted site (P-site), were assessed to confirm the findings of a former EDA study on sediments. The sensitivities of R- and P-communities to prometryn, tributyltin (TBT) and N-phenyl-2-naphthylamine (PNA) were quantified in short-term toxicity tests and exposure concentrations were determined. Prometryn and PNA concentrations were significantly higher at the P-site, whereas TBT concentrations were in the same range at both sites. Periphyton communities differed in biomass, but algal class composition and diatom diversity were similar. Community tolerance of P-communities was significantly enhanced for prometryn, but not for PNA and TBT, confirming site-specific effects on local periphyton for prometryn only. Thus, PICT enables in situ effect confirmation of phytotoxic compounds at the community level and seems to be suitable to support confirmation and enhance ecological realism of EDA.

A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline

PubMed Central

Rudnick, Paul A.; Markey, Sanford P.; Roth, Jeri; Mirokhin, Yuri; Yan, Xinjian; Tchekhovskoi, Dmitrii V.; Edwards, Nathan J.; Thangudu, Ratna R.; Ketchum, Karen A.; Kinsinger, Christopher R.; Mesri, Mehdi; Rodriguez, Henry; Stein, Stephen E.

2016-01-01

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has produced large proteomics datasets from the mass spectrometric interrogation of tumor samples previously analyzed by The Cancer Genome Atlas (TCGA) program. The availability of the genomic and proteomic data is enabling proteogenomic study for both reference (i.e., contained in major sequence databases) and non-reference markers of cancer. The CPTAC labs have focused on colon, breast, and ovarian tissues in the first round of analyses; spectra from these datasets were produced from 2D LC-MS/MS analyses and represent deep coverage. To reduce the variability introduced by disparate data analysis platforms (e.g., software packages, versions, parameters, sequence databases, etc.), the CPTAC Common Data Analysis Platform (CDAP) was created. The CDAP produces both peptide-spectrum-match (PSM) reports and gene-level reports. The pipeline processes raw mass spectrometry data according to the following: (1) Peak-picking and quantitative data extraction, (2) database searching, (3) gene-based protein parsimony, and (4) false discovery rate (FDR)-based filtering. The pipeline also produces localization scores for the phosphopeptide enrichment studies using the PhosphoRS program. Quantitative information for each of the datasets is specific to the sample processing, with PSM and protein reports containing the spectrum-level or gene-level (“rolled-up”) precursor peak areas and spectral counts for label-free or reporter ion log-ratios for 4plex iTRAQ™. The reports are available in simple tab-delimited formats and, for the PSM-reports, in mzIdentML. The goal of the CDAP is to provide standard, uniform reports for all of the CPTAC data, enabling comparisons between different samples and cancer types as well as across the major ‘omics fields. PMID:26860878

HapMap tagSNP transferability in multiple populations: general guidelines

PubMed Central

Xing, Jinchuan; Witherspoon, David J.; Watkins, W. Scott; Zhang, Yuhua; Tolpinrud, Whitney; Jorde, Lynn B.

2008-01-01

This PDF receipt will only be used as the basis for generating PubMed Central (PMC) documents. PMC documents will be made available for review after conversion (approx. 2–3 weeks time). Any corrections that need to be made will be done at that time. No materials will be released to PMC without the approval of an author. Only the PMC documents will appear on PubMed Central -- this PDF Receipt will not appear on PubMed Central. Linkage disequilibrium (LD) has received much recent attention because of its value in localizing disease-causing genes. Due to the extensive LD between neighboring loci in the human genome, it is believed that a subset of the single nucleotide polymorphisms in a region (tagSNPs) can be selected to capture most of the remaining SNP variants. In this study, we examined LD patterns and HapMap tagSNP transferability in more than 300 individuals. A South Indian and an African Mbuti Pygmy population sample were included to evaluate the performance of HapMap tagSNPs in geographically distinct and genetically isolated populations. Our results show that HapMap tagSNPs selected with r2 >= 0.8 can capture more than 85% of the SNPs in populations that are from the same continental group. Combined tagSNPs from HapMap CEU and CHB+JPT serve as the best reference for the Indian sample. The HapMap YRI are a sufficient reference for tagSNP selection in the Pygmy sample. In addition to our findings, we reviewed over 25 recent studies of tagSNP transferability and propose a general guideline for selecting tagSNPs from HapMap populations. PMID:18482828

Getting DNA copy numbers without control samples

PubMed Central

2012-01-01

Background The selection of the reference to scale the data in a copy number analysis has paramount importance to achieve accurate estimates. Usually this reference is generated using control samples included in the study. However, these control samples are not always available and in these cases, an artificial reference must be created. A proper generation of this signal is crucial in terms of both noise and bias. We propose NSA (Normality Search Algorithm), a scaling method that works with and without control samples. It is based on the assumption that genomic regions enriched in SNPs with identical copy numbers in both alleles are likely to be normal. These normal regions are predicted for each sample individually and used to calculate the final reference signal. NSA can be applied to any CN data regardless the microarray technology and preprocessing method. It also finds an optimal weighting of the samples minimizing possible batch effects. Results Five human datasets (a subset of HapMap samples, Glioblastoma Multiforme (GBM), Ovarian, Prostate and Lung Cancer experiments) have been analyzed. It is shown that using only tumoral samples, NSA is able to remove the bias in the copy number estimation, to reduce the noise and therefore, to increase the ability to detect copy number aberrations (CNAs). These improvements allow NSA to also detect recurrent aberrations more accurately than other state of the art methods. Conclusions NSA provides a robust and accurate reference for scaling probe signals data to CN values without the need of control samples. It minimizes the problems of bias, noise and batch effects in the estimation of CNs. Therefore, NSA scaling approach helps to better detect recurrent CNAs than current methods. The automatic selection of references makes it useful to perform bulk analysis of many GEO or ArrayExpress experiments without the need of developing a parser to find the normal samples or possible batches within the data. The method is available in the open-source R package NSA, which is an add-on to the aroma.cn framework. http://www.aroma-project.org/addons. PMID:22898240

Getting DNA copy numbers without control samples.

PubMed

Ortiz-Estevez, Maria; Aramburu, Ander; Rubio, Angel

2012-08-16

The selection of the reference to scale the data in a copy number analysis has paramount importance to achieve accurate estimates. Usually this reference is generated using control samples included in the study. However, these control samples are not always available and in these cases, an artificial reference must be created. A proper generation of this signal is crucial in terms of both noise and bias.We propose NSA (Normality Search Algorithm), a scaling method that works with and without control samples. It is based on the assumption that genomic regions enriched in SNPs with identical copy numbers in both alleles are likely to be normal. These normal regions are predicted for each sample individually and used to calculate the final reference signal. NSA can be applied to any CN data regardless the microarray technology and preprocessing method. It also finds an optimal weighting of the samples minimizing possible batch effects. Five human datasets (a subset of HapMap samples, Glioblastoma Multiforme (GBM), Ovarian, Prostate and Lung Cancer experiments) have been analyzed. It is shown that using only tumoral samples, NSA is able to remove the bias in the copy number estimation, to reduce the noise and therefore, to increase the ability to detect copy number aberrations (CNAs). These improvements allow NSA to also detect recurrent aberrations more accurately than other state of the art methods. NSA provides a robust and accurate reference for scaling probe signals data to CN values without the need of control samples. It minimizes the problems of bias, noise and batch effects in the estimation of CNs. Therefore, NSA scaling approach helps to better detect recurrent CNAs than current methods. The automatic selection of references makes it useful to perform bulk analysis of many GEO or ArrayExpress experiments without the need of developing a parser to find the normal samples or possible batches within the data. The method is available in the open-source R package NSA, which is an add-on to the aroma.cn framework. http://www.aroma-project.org/addons.

Plasma creatinine in dogs: intra- and inter-laboratory variation in 10 European veterinary laboratories

PubMed Central

2011-01-01

Background There is substantial variation in reported reference intervals for canine plasma creatinine among veterinary laboratories, thereby influencing the clinical assessment of analytical results. The aims of the study was to determine the inter- and intra-laboratory variation in plasma creatinine among 10 veterinary laboratories, and to compare results from each laboratory with the upper limit of its reference interval. Methods Samples were collected from 10 healthy dogs, 10 dogs with expected intermediate plasma creatinine concentrations, and 10 dogs with azotemia. Overlap was observed for the first two groups. The 30 samples were divided into 3 batches and shipped in random order by postal delivery for plasma creatinine determination. Statistical testing was performed in accordance with ISO standard methodology. Results Inter- and intra-laboratory variation was clinically acceptable as plasma creatinine values for most samples were usually of the same magnitude. A few extreme outliers caused three laboratories to fail statistical testing for consistency. Laboratory sample means above or below the overall sample mean, did not unequivocally reflect high or low reference intervals in that laboratory. Conclusions In spite of close analytical results, further standardization among laboratories is warranted. The discrepant reference intervals seem to largely reflect different populations used in establishing the reference intervals, rather than analytical variation due to different laboratory methods. PMID:21477356

Sample collection of ash and burned soils from the October 2007 southern California Wildfires

USGS Publications Warehouse

Hoefen, Todd M.; Kokaly, Raymond F.; Martin, Deborah A.; Rochester, Carlton J.; Plumlee, Geoffrey S.; Mendez, Greg; Reichard, Eric G.; Fisher, Robert N.

2009-01-01

Between November 2 through 9, 2007 scientists from the U.S. Geological Survey (USGS) collected samples of ash and burned soils from 28 sites in six areas burned as a result of the Southern California wildfires of October 2007, including the Harris, Witch, Santiago, Ammo, Canyon, and Grass Valley Fires. The primary goal of this sampling and analysis effort was to understand how differences in ash and burned soil composition relate to vegetation type, underlying bedrock geology, burn intensity, and residential versus wildland. Sampling sites were chosen with the input of local experts from the USGS Water Resources and Biological Resources Disciplines to help understand possible effects of the fires on water supplies, ecosystems, and endangered species. The sampling was also carried out in conjunction with detailed field analysis of the spectral reflectance characteristics of the ash, so that chemical and mineralogical characteristics of the field samples could be used to help interpret data collected as part of an airborne, hyperspectral remote-sensing survey of several of the burned areas in mid-late November, 2007.This report presents an overview of the field sampling methodologies used to collect the samples, includes representative photos of the sites sampled, and summarizes important characteristics of each of the collection sites. In this report we use the term “ash” to refer collectively to white mineral ash, which results from full combustion of vegetation and black charred organic matter from partial combustion of vegetation or other materials. These materials were found to be intermingled as a deposited residue on the soil surface following the Southern California fires of 2007.

The Pursuit of Word Meanings

PubMed Central

Stevens, Jon Scott; Gleitman, Lila R.; Trueswell, John C.; Yang, Charles

2016-01-01

We evaluate here the performance of four models of cross-situational word learning; two global models, which extract and retain multiple referential alternatives from each word occurrence; and two local models, which extract just a single referent from each occurrence. One of these local models, dubbed Pursuit, uses an associative learning mechanism to estimate word-referent probability but pursues and tests the best referent-meaning at any given time. Pursuit is found to perform as well as global models under many conditions extracted from naturalistic corpora of parent child-interactions, even though the model maintains far less information than global models. Moreover, Pursuit is found to best capture human experimental findings from several relevant cross-situational word-learning experiments, including those of Yu and Smith (2007), the paradigm example of a finding believed to support fully global cross-situational models. Implications and limitations of these results are discussed, most notably that the model characterizes only the earliest stages of word learning, when reliance on the co-occurring referent world is at its greatest. PMID:27666335

Scaling laws and accurate small-amplitude stationary solution for the motion of a planar vortex filament in the Cartesian form of the local induction approximation.

PubMed

Van Gorder, Robert A

2013-04-01

We provide a formulation of the local induction approximation (LIA) for the motion of a vortex filament in the Cartesian reference frame (the extrinsic coordinate system) which allows for scaling of the reference coordinate. For general monotone scalings of the reference coordinate, we derive an equation for the planar solution to the derivative nonlinear Schrödinger equation governing the LIA. We proceed to solve this equation perturbatively in small amplitude through an application of multiple-scales analysis, which allows for accurate computation of the period of the planar vortex filament. The perturbation result is shown to agree strongly with numerical simulations, and we also relate this solution back to the solution obtained in the arclength reference frame (the intrinsic coordinate system). Finally, we discuss nonmonotone coordinate scalings and their application for finding self-intersections of vortex filaments. These self-intersecting vortex filaments are likely unstable and collapse into other structures or dissipate completely.

Automation of Precise Time Reference Stations (PTRS)

NASA Astrophysics Data System (ADS)

Wheeler, P. J.

1985-04-01

The U.S. Naval Observatory is presently engaged in a program of automating precise time stations (PTS) and precise time reference stations (PTBS) by using a versatile mini-computer controlled data acquisition system (DAS). The data acquisition system is configured to monitor locally available PTTI signals such as LORAN-C, OMEGA, and/or the Global Positioning System. In addition, the DAS performs local standard intercomparison. Computer telephone communications provide automatic data transfer to the Naval Observatory. Subsequently, after analysis of the data, results and information can be sent back to the precise time reference station to provide automatic control of remote station timing. The DAS configuration is designed around state of the art standard industrial high reliability modules. The system integration and software are standardized but allow considerable flexibility to satisfy special local requirements such as stability measurements, performance evaluation and printing of messages and certificates. The DAS operates completely independently and may be queried or controlled at any time with a computer or terminal device (control is protected for use by authorized personnel only). Such DAS equipped PTS are operational in Hawaii, California, Texas and Florida.

Factors influencing humanitarian care and the treatment of local patients within the deployed military medical system: casualty referral limitations.

PubMed

Causey, Marlin; Rush, Robert M; Kjorstad, Randy J; Sebesta, James A

2012-05-01

Humanitarian medical care is an essential task of the deployed military health care system. The purpose of this study was to analyze referral acceptance in treating injured local national patients during Operation Enduring Freedom. A prospective observation study of local nationals who were referred for humanitarian trauma care in Afghanistan from March through August 2009. Sixty-six patients were referred for evacuation for suspected non-coalition-caused injuries. The bed status at the receiving hospital was defined as green (able to accept patients), amber (nearing capacity), and red (at capacity). The only factor associated with acceptance was the accepting hospital bed status (odds ratio = 1.57%, 95% confidence interval, 1.11-2.22; P = .009). Factors not significant were age, the province of origin, the type of referring facility, a prior operation before the request, patient status/affiliation, or the mechanism of injury. Humanitarian medical care is directly related to the capacity for high-acuity care because bed availability is the predominate reason for acceptance or rejection. Published by Elsevier Inc.

INNOVATIVE TECHNOLOGY EVALUATION REPORT ...

EPA Pesticide Factsheets

The Split Core Sampler for Submerged Sediments (Split Core Sampler) designed and fabricated by Arts Manufacturing & Supply, Inc., was demonstrated under the U.S. Environmental Protection Agency (EPA) Superfund Innovative Technology Evaluation Program in April and May 1999 at sites in EPA Regions 1 and 5, respectively. In addition to assessing ease of sampler operation, key objectives of the demonstration included evaluating the samplers ability to (1) consistently collect a given volume of sediment, (2) consistently collect sediment in a given depth interval, (3) collect samples with consistent characteristics from a homogenous layer of sediment, and (4) collect samples under a variety of site conditions. This report describes the demonstration results for the Split Core Sampler and two conventional samplers (the Hand Corer and Vibrocorer) used as reference samplers. During the demonstration, the Split Core Sampler performed as well as or better than the reference samplers. Based on visual observations, both the Split Core Sampler and reference samplers collected partially compressed samples of consolidated and unconsolidated sediments from the sediment surface downward; sample representativeness may be questionable because of core shortening and core compression. Sediment stratification was preserved for both consolidated and unconsolidated sediment samples collected by the Split Core Sampler and reference samplers. No sampler was able to collect samples

Spatial and temporal assessment of surface water quality in the Arka River, Akkar, Lebanon.

PubMed

Daou, Claude; Nabbout, Rony; Kassouf, Amine

2016-12-01

Surface water quality monitoring constitutes a crucial and important step in any water quality management system. Twenty-three physicochemical and microbiological parameters were assessed in surface water samples collected from the Arka River located in the Akkar District, north of Lebanon. Eight sampling locations were considered along the river and seven sampling campaigns were performed in order to evaluate spatial and temporal influences. The extraction of relevant information from this relatively large data set was done using principal component analysis (PCA), being a very well established chemometric tool in this field. In a first step, extracted PCA loadings revealed the implication of several physicochemical parameters in the discriminations and trends highlighted by PCA scores, mainly due to soil leaching and seawater intrusion. However, further investigations showed the implication of organic and bacterial parameters in the discrimination of stations in the Akkar flatland. These discriminations probably refer to anthropogenic pollution coming from the agricultural area and the surrounding villages. Specific ultraviolet absorption (SUVA) indices confirmed these findings since values decreased for samples collected across the villages and the flatland, indicating an increase in anthropogenic dissolved organic matter. This study will hopefully help the national and local authorities to ameliorate the surface water quality management, enabling its proper use for irrigation purposes.

Prevalence and distribution of Arcobacter spp. in raw milk and retail raw beef.

PubMed

Shah, A H; Saleha, A A; Murugaiyah, M; Zunita, Z; Memon, A A

2012-08-01

A total of 106 beef samples which consisted of local (n = 59) and imported (n = 47) beef and 180 milk samples from cows (n = 86) and goats (n = 94) were collected from Selangor, Malaysia. Overall, 30.2% (32 of 106) of beef samples were found positive for Arcobacter species. Imported beef was significantly more contaminated (46.80%) than local beef (16.9%). Arcobacter butzleri was the species isolated most frequently from imported (81.8%) and local (60%) beef, followed by Arcobacter cryaerophilus in local (33.3%) and imported (18.2%) beef samples. Only one local beef sample (10%) yielded Arcobacter skirrowii. Arcobacter species were detected from cow's milk (5.8%), with A. butzleri as the dominant species (60%), followed by A. cryaerophilus (40%), whereas none of the goat's milk samples were found positive for Arcobacter. This is the first report of the detection of Arcobacter in milk and beef in Malaysia.

Eddy-Current Reference Standard

NASA Technical Reports Server (NTRS)

Ambrose, H. H., Jr.

1985-01-01

Magnetic properties of metallic reference standards duplicated and stabilized for eddy-current coil measurements over long times. Concept uses precisely machined notched samples of known annealed materials as reference standards.

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.

Tip localization of an atomic force microscope in transmission microscopy with nanoscale precision

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

Baumann, Fabian; Pippig, Diana A., E-mail: diana.pippig@physik.uni-muenchen.de; Gaub, Hermann E.

Since the atomic force microscope (AFM) has evolved into a general purpose platform for mechanical experiments at the nanoscale, the need for a simple and generally applicable localization of the AFM cantilever in the reference frame of an optical microscope has grown. Molecular manipulations like in single molecule cut and paste or force spectroscopy as well as tip mediated nanolithography are prominent examples for the broad variety of applications implemented to date. In contrast to the different kinds of superresolution microscopy where fluorescence is used to localize the emitter, we, here, employ the absorbance of the tip to localize itsmore » position in transmission microscopy. We show that in a low aperture illumination, the tip causes a significant reduction of the intensity in the image plane of the microscope objective when it is closer than a few hundred nm. By independently varying the z-position of the sample slide, we could verify that this diffraction limited image of the tip is not caused by a near field effect but is rather caused by the absorbance of the transmitted light in the low apex needle-like tip. We localized the centroid position of this tip image with a precision of better than 6 nm and used it in a feedback loop to position the tip into nano-apertures of 110 nm radius. Single-molecule force spectroscopy traces on the unfolding of individual green fluorescent proteins within the nano-apertures showed that their center positions were repeatedly approached with very high fidelity leaving the specific handle chemistry on the tip’s surface unimpaired.« less

Report on the U.S. Geological Survey's evaluation program for standard reference samples distributed in October 1994 : T-131 (trace constituents), T-133 (trace constituents), M-132 (major constituents), N-43 (nutrients), N-44 (nutrients), P-23 (low ionic strength) and Hg-19 (mercury)

USGS Publications Warehouse

Long, H. Keith; Farrar, Jerry W.

1995-01-01

This report presents the results of the U.S. Geological Survey's analytical evaluation program for 7 standard reference samples--T-131 (trace constituents), T-133 (trace constituents), M-132 (major constituents), N-43 (nutrients), N-44 (nutrients), P-23 (low ionic strength), and Hg-19 (mercury). The samples were distributed in October 1994 to 131 laboratories registered in the U.S. Geological Survey sponsored interlaboratory testing program. Analytical data that were received from 121 of the laboratories were evaluated with respect to: overall laboratory performance and relative laboratory performance for each analyte in the seven reference samples. Results of these evaluations are presented in tabular form. Also presented are tables and graphs summarizing the analytical data provided by each laboratory for each analyte in the seven standard reference samples. The most probable value for each analyte was determined using nonparametric statistics.

Development of a candidate reference measurement procedure for the analysis of cortisol in human serum samples by isotope dilution-gas chromatography-mass spectrometry.

PubMed

Kawaguchi, Migaku; Takatsu, Akiko

2009-08-01

A candidate reference measurement procedure involving isotope dilution coupled with gas chromatography-mass spectrometry (GC-MS) has been developed and critically evaluated. An isotopically labeled internal standard, cortisol-d(2), was added to a serum sample. After equilibration, solid-phase extractions (SPE) for sample preparation and derivatization with heptafluorobutyric anhydride (HFBA) were performed for GC-MS analysis. The limit of detection (LOD) and the limit of quantification (LOQ) were 5 and 20 ng g(-1), respectively. The recovery of the added cortisol ranged from 99.8 to 101.0%. Excellent precision was obtained with a within-day variation (RSD) of 0.7% for GC-MS analysis. The accuracy of the measurement was evaluated by comparing of results of this reference measurement procedure on lyophilized human serum reference materials for cortisol (European Reference Materials (ERM)-DA 192) as Certified Reference Materials (CRMs). The results of this method for total cortisol agreed with the certified values within some uncertainty. This method, which demonstrates simply, easy, good accuracy, high precision, and is free from interferences from structural analogues, qualifies as a reference measurement procedure.

[Prevalence and severity of gingivitis among scholars (7-14 years): local conditions associated to bleeding on probing].

PubMed

Chambrone, Leandro; Macedo, Sergio Bassit; Ramalho, Francisco Cardoso; Trevizani Filho, Eduardo; Chambrone, Luiz Armando

2010-03-01

The objective of this study was to collect data about the prevalence and severity of gingivitis in a sample of scholars, as well as its relationship with possible local risk factors. Two hundred and six subjects were examined, 107 male and 99 female, with age ranging from 7 to 14 years, where data from their Plaque Index (IP), Gingival Index (IG), and Clinical Probing Depth (PCS) were collected. Among all the clinical parameters observed, the mean values found referent to PCS, IP and IG were 1.58 + 0.46, 1.12 + 0.49 and 0.89 + 0.32, respectively. Ninety five subjects (46.1%) presented a diagnostic of slight gingivitis and 111 (53.9%) of moderate gingivitis. Overall, male subjects presented statistically more dental plaque and more gingival inflammation than female subjects. Clinical signs of gingival inflammation were found in all the examined subjects. Gingivitis severity around permanent teeth was directly linked to the amount of dental plaque deposits and to the presence of bleeding on probing.

Solving the Mystery of Galaxy Bulges and Bulge Substructure

NASA Astrophysics Data System (ADS)

Erwin, Peter

2017-08-01

Understanding galaxy bulges is crucial for understanding galaxy evolution and the growth of supermassive black holes (SMBHs). Recent studies have shown that at least some - perhaps most - disk-galaxy bulges are actually composite structures, with both classical-bulge (spheroid) and pseudobulge (disky) components; this calls into question the standard practice of using simple, low-resolution bulge/disk decompositions to determine spheroid and SMBH mass functions. We propose WFC3 optical and near-IR imaging of a volume- and mass-limited sample of local disk galaxies to determine the full range of pure-classical, pure-pseudobulge, and composite-bulge frequencies and parameters, including stellar masses for classical bulges, disky pseudobulges, and boxy/peanut-shaped bulges. We will combine this with ground-based spectroscopy to determine the stellar-kinematic and population characteristics of the different substructures revealed by our WFC3 imaging. This will help resolve growing uncertainties about the status and nature of bulges and their relation to SMBH masses, and will provide an essential local-universe reference for understanding bulge (and SMBH) formation and evolution.

Reactive oxygen species alteration of immune cells in local residents at an electronic waste recycling site in northern China.

PubMed

Li, Ran; Yang, Qiaoyun; Qiu, Xinghua; Li, Keqiu; Li, Guang; Zhu, Ping; Zhu, Tong

2013-04-02

The health effects of exposure to pollutants from electronic waste (e-waste) pose an important issue. In this study, we explored the association between oxidative stress and blood levels of e-waste-related pollutants. Blood samples were collected from individuals living in the proximity of an e-waste recycling site located in northern China, and pollutants, as well as reactive oxygen species (ROS), were measured in comparison to a reference population. The geometric mean concentrations of PCBs, dechlorane plus, and 2,2',4,4',5,5'-hexabromobiphenyl in plasma from the exposure group were 60.4, 9.0, and 0.55 ng g(-1) lipid, respectively, which were 2.2, 3.2, and 2.2 times higher than the corresponding measurement in the reference group. Correspondingly, ROS levels in white blood cells, including in neutrophil granulocytes, from the exposure group were significantly higher than in those from the reference group, suggesting potential ROS related health effects for residents at the e-waste site. In contrast, fewer ROS were generated in the respiratory burst of neutrophil granulocytes for the exposure group, indicating a depressed innate immune function for the individuals living at the e-waste site. These findings suggest a potential linkage between exposure to pollutants from e-waste recycling and both elevated oxidative stress and altered immune function.

Comparative bioavailability and pharmacokinetics of two oral formulations of flurbiprofen: a single-dose, randomized, open-label, two-period, crossover study in Pakistani subjects.

PubMed

Qayyum, Aisha; Najmi, Muzammil Hasan; Abbas, Mateen

2013-11-01

Comparative bioavailability studies are conducted to establish the bioequivalence of generic formulation with that of branded reference formulation, providing confidence to clinicians to use these products interchangeably. This study was carried out to compare a locally manufactured formulation of flurbiprofen with that of a branded product. Twenty two healthy male adults received a single dose of flurbiprofen (100mg) either generic or branded product according to randomization scheme on each of 2 periods. Blood samples were collected and plasma flurbiprofen concentration was determined by a validated HPLC method. Pharmacokinetic parameters like AUC(0-t), AUC(0-oo), Cmax, Tmax, t½, Vd and clearance were determined. The 90% CI for the ratio of geometric means of test to reference product's pharmacokinetic variables was calculated. Pharmacokinetic parameters for two formulations were comparable. Ratio of means of AUC(0-24), AUC(0-oo) and Cmax for test to reference products and 90% CI for these ratios were within the acceptable range. The p-values calculated by TOST were much less than the specified value (p-0.05). ANOVA gave p-values which were more than the specified value (p-0.05) for sequence, subject, period and formulation. Test formulation of flurbiprofen (tablet Flurso) was found to meet the criteria for bioequivalence to branded product (tablet Ansaid) based on pharmacokinetic parameters.

Tracing the geographic origin of traded leopard body parts in the indian subcontinent with DNA-based assignment tests.

PubMed

Mondol, Samrat; Sridhar, Vanjulavalli; Yadav, Prasanjeet; Gubbi, Sanjay; Ramakrishnan, Uma

2015-04-01

Illicit trade in wildlife products is rapidly decimating many species across the globe. Such trade is often underestimated for wide-ranging species until it is too late for the survival of their remaining populations. Policing this trade could be vastly improved if one could reliably determine geographic origins of illegal wildlife products and identify areas where greater enforcement is needed. Using DNA-based assignment tests (i.e., samples are assigned to geographic locations), we addressed these factors for leopards (Panthera pardus) on the Indian subcontinent. We created geography-specific allele frequencies from a genetic reference database of 173 leopards across India to infer geographic origins of DNA samples from 40 seized leopard skins. Sensitivity analyses of samples of known geographic origins and assignments of seized skins demonstrated robust assignments for Indian leopards. We found that confiscated pelts seized in small numbers were not necessarily from local leopards. The geographic footprint of large seizures appeared to be bigger than the cumulative footprint of several smaller seizures, indicating widespread leopard poaching across the subcontinent. Our seized samples had male-biased sex ratios, especially the large seizures. From multiple seized sample assignments, we identified central India as a poaching hotspot for leopards. The techniques we applied can be used to identify origins of seized illegal wildlife products and trade routes at the subcontinent scale and beyond. © 2014 Society for Conservation Biology.

Rubidium distribution at atomic scale in high efficient Cu(In,Ga)Se2 thin-film solar cells

NASA Astrophysics Data System (ADS)

Vilalta-Clemente, Arantxa; Raghuwanshi, Mohit; Duguay, Sébastien; Castro, Celia; Cadel, Emmanuel; Pareige, Philippe; Jackson, Philip; Wuerz, Roland; Hariskos, Dimitrios; Witte, Wolfram

2018-03-01

The introduction of a rubidium fluoride post deposition treatment (RbF-PDT) for Cu(In,Ga)Se2 (CIGS) absorber layers has led to a record efficiency up to 22.6% for thin-film solar cell technology. In the present work, high efficiency CIGS samples with RbF-PDT have been investigated by atom probe tomography (APT) to reveal the atomic distribution of all alkali elements present in CIGS layers and compared with non-treated samples. A Scanning Electron Microscopy Dual beam station (Focused Ion Beam-Gas Injection System) as well as Transmission Kikuchi diffraction is used for atom probe sample preparation and localization of the grain boundaries (GBs) in the area of interest. The analysis of the 3D atomic scale APT reconstructions of CIGS samples with RbF-PDT shows that inside grains, Rb is under the detection limit, but the Na concentration is enhanced as compared to the reference sample without Rb. At the GBs, a high concentration of Rb reaching 1.5 at. % was found, and Na and K (diffusing from the glass substrate) are also segregated at GBs but at lower concentrations as compared to Rb. The intentional introduction of Rb leads to significant changes in the chemical composition of CIGS matrix and at GBs, which might contribute to improve device efficiency.

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS

PubMed Central

Röst, Hannes L; Ludwig, Christina; Buil, Alfonso; Bensimon, Ariel; Soste, Martin; Spector, Tim D; Dermitzakis, Emmanouil T; Collins, Ben C; Malmström, Lars; Aebersold, Ruedi

2017-01-01

The consistent detection and quantification of protein post-translational modifications (PTMs) across sample cohorts is an essential prerequisite for the functional analysis of biological processes. Data-independent acquisition (DIA), a bottom-up mass spectrometry based proteomic strategy, exemplified by SWATH-MS, provides complete precursor and fragment ion information of a sample and thus, in principle, the information to identify peptidoforms, the modified variants of a peptide. However, due to the convoluted structure of DIA data sets the confident and systematic identification and quantification of peptidoforms has remained challenging. Here we present IPF (Inference of PeptidoForms), a fully automated algorithm that uses spectral libraries to query, validate and quantify peptidoforms in DIA data sets. The method was developed on data acquired by SWATH-MS and benchmarked using a synthetic phosphopeptide reference data set and phosphopeptide-enriched samples. The data indicate that IPF reduced false site-localization by more than 7-fold in comparison to previous approaches, while recovering 85.4% of the true signals. IPF was applied to detect and quantify peptidoforms carrying ten different types of PTMs in DIA data acquired from more than 200 samples of undepleted blood plasma of a human twin cohort. The data approportioned, for the first time, the contribution of heritable, environmental and longitudinal effects on the observed quantitative variability of specific modifications in blood plasma of a human population. PMID:28604659

Reconstructing a herbivore’s diet using a novel rbcL DNA mini-barcode for plants

USGS Publications Warehouse

Erickson, David L.; Reed, Elizabeth; Ramachandran, Padmini; Bourg, Norman; McShea, William J.; Ottesen, Andrea

2017-01-01

Next Generation Sequencing and the application of metagenomic analyses can be used to answer questions about animal diet choice and study the consequences of selective foraging by herbivores. The quantification of herbivore diet choice with respect to native versus exotic plant species is particularly relevant given concerns of invasive species establishment and their effects on ecosystems. While increased abundance of white-tailed deer (Odocoileus virginianus) appears to correlate with increased incidence of invasive plant species, data supporting a causal link is scarce. We used a metabarcoding approach (PCR amplicons of the plant rbcL gene) to survey the diet of white-tailed deer (fecal samples), from a forested site in Warren County, Virginia with a comprehensive plant species inventory and corresponding reference collection of plant barcode and chloroplast sequences. We sampled fecal pellet piles and extracted DNA from 12 individual deer in October 2014. These samples were compared to a reference DNA library of plant species collected within the study area. For 72 % of the amplicons, we were able to assign taxonomy at the species level, which provides for the first time—sufficient taxonomic resolution to quantify the relative frequency at which native and exotic plant species are being consumed by white-tailed deer. For each of the 12 individual deer we collected three subsamples from the same fecal sample, resulting in sequencing 36 total samples. Using Qiime, we quantified the plant DNA found in all 36 samples, and found that variance within samples was less than variance between samples (F = 1.73, P = 0.004), indicating additional subsamples may not be necessary. Species level diversity ranged from 60 to 93 OTUs per individual and nearly 70 % of all plant sequences recovered were from native plant species. The number of species detected did reduce significantly (range 4–12) when we excluded species whose OTU composed <1 % of each sample’s total. When compared to the abundance of native and non-natives plants inventoried in the local community, our results support the observation that white-tailed deer have strong foraging preferences, but these preferences were not consistent for species in either class. Deer forage behaviour may favour some exotic species, but not all.

Reconstructing a herbivore’s diet using a novel rbcL DNA mini-barcode for plants

PubMed Central

Erickson, David L.; Reed, Elizabeth; Ramachandran, Padmini; Bourg, Norman A.; Ottesen, Andrea

2017-01-01

Abstract Next Generation Sequencing and the application of metagenomic analyses can be used to answer questions about animal diet choice and study the consequences of selective foraging by herbivores. The quantification of herbivore diet choice with respect to native versus exotic plant species is particularly relevant given concerns of invasive species establishment and their effects on ecosystems. While increased abundance of white-tailed deer (Odocoileus virginianus) appears to correlate with increased incidence of invasive plant species, data supporting a causal link is scarce. We used a metabarcoding approach (PCR amplicons of the plant rbcL gene) to survey the diet of white-tailed deer (fecal samples), from a forested site in Warren County, Virginia with a comprehensive plant species inventory and corresponding reference collection of plant barcode and chloroplast sequences. We sampled fecal pellet piles and extracted DNA from 12 individual deer in October 2014. These samples were compared to a reference DNA library of plant species collected within the study area. For 72 % of the amplicons, we were able to assign taxonomy at the species level, which provides for the first time—sufficient taxonomic resolution to quantify the relative frequency at which native and exotic plant species are being consumed by white-tailed deer. For each of the 12 individual deer we collected three subsamples from the same fecal sample, resulting in sequencing 36 total samples. Using Qiime, we quantified the plant DNA found in all 36 samples, and found that variance within samples was less than variance between samples (F = 1.73, P = 0.004), indicating additional subsamples may not be necessary. Species level diversity ranged from 60 to 93 OTUs per individual and nearly 70 % of all plant sequences recovered were from native plant species. The number of species detected did reduce significantly (range 4–12) when we excluded species whose OTU composed <1 % of each sample’s total. When compared to the abundance of native and non-natives plants inventoried in the local community, our results support the observation that white-tailed deer have strong foraging preferences, but these preferences were not consistent for species in either class. Deer forage behaviour may favour some exotic species, but not all. PMID:28533898

Seasonal climatology of CO2 across North America from aircraft measurements in the NOAA/ESRL Global Greenhouse Gas Reference Network

NASA Astrophysics Data System (ADS)

Sweeney, Colm; Karion, Anna; Wolter, Sonja; Newberger, Timothy; Guenther, Doug; Higgs, Jack A.; Andrews, Arlyn Elyzabeth; Lang, Patricia M.; Neff, Don; Dlugokencky, Edward; Miller, John B.; Montzka, Stephen A.; Miller, Ben R.; Masarie, Ken Alan; Biraud, Sebastien Christophe; Novelli, Paul C.; Crotwell, Molly; Crotwell, Andrew M.; Thoning, Kirk; Tans, Pieter P.

2015-05-01

Seasonal spatial and temporal gradients for the CO2 mole fraction over North America are examined by creating a climatology from data collected 2004-2013 by the NOAA/ESRL Global Greenhouse Gas Reference Network Aircraft Program relative to trends observed for CO2 at the Mauna Loa Observatory. The data analyzed are from measurements of air samples collected in specially fabricated flask packages at frequencies of days to months at 22 sites over continental North America and shipped back to Boulder, Colorado, for analysis. These measurements are calibrated relative to the CO2 World Meteorological Organization mole fraction scale. The climatologies of CO2 are compared to climatologies of CO, CH4, SF6, N2O (which are also measured from this sampling program), and winds to understand the dominant transport and chemical and biological processes driving changes in the spatial and temporal mole fractions of CO2 as air passes over continental North America. The measurements show that air masses coming off the Pacific on the west coast of North America are relatively homogeneous with altitude. As air masses flow eastward, the lower section from the surface to 4000 m above sea level (masl) becomes distinctly different from the 4000-8000 masl section of the column. This is due in part to the extent of the planetary boundary layer, which is directly impacted by continental sources and sinks, and to the vertical gradient in west-to-east wind speeds. The slowdown and southerly shift in winds at most sites during summer months amplify the summertime drawdown relative to what might be expected from local fluxes. This influence counteracts the dilution of summer time CO2 drawdown (known as the "rectifier effect") as well as changes the surface influence "footprint" for each site. An early start to the summertime drawdown, a pronounced seasonal cycle in the column mean (500 to 8000 masl), and small vertical gradients in CO2, CO, CH4, SF6, and N2O at high-latitude western sites such as Poker Flat, Alaska, suggest recent influence of transport from southern latitudes and not local processes. This transport pathway provides a significant contribution to the large seasonal cycle observed in the high latitudes at all altitudes sampled. A sampling analysis of the NOAA/ESRL CarbonTracker model suggests that the average sampling resolution of 22 days is sufficient to get a robust estimate of mean seasonal cycle of CO2 during this 10 year period but insufficient to detect interannual variability in emissions over North America.

Edge Triggered Apparatus and Method for Measuring Strain in Bragg Gratings

NASA Technical Reports Server (NTRS)

Froggatt, Mark E. (Inventor)

2003-01-01

An apparatus and method for measuring strain of gratings written into an optical fiber. Optical radiation is transmitted over one or more contiguous predetermined wavelength ranges into a reference optical fiber network and an optical fiber network under test to produce a plurality of reference interference fringes and measurement interference fringes, respectively. The reference and measurement fringes are detected, and the reference fringes trigger the sampling of the measurement fringes. This results in the measurement fringes being sampled at 2(pi) increments of the reference fringes. Each sampled measurement fringe of each wavelength sweep is transformed into a spatial domain waveform. The spatial domain waveforms are summed to form a summation spatial domain waveform that is used to determine location of each grating with respect to a reference reflector. A portion of each spatial domain waveform that corresponds to a particular grating is determined and transformed into a corresponding frequency spectrum representation. The strain on the grating at each wavelength of optical radiation is determined by determining the difference between the current wavelength and an earlier, zero-strain wavelength measurement.

Forecasting eruption size: what we know, what we don't know

NASA Astrophysics Data System (ADS)

Papale, Paolo

2017-04-01

Any eruption forecast includes an evaluation of the expected size of the forthcoming eruption, usually expressed as the probability associated to given size classes. Such evaluation is mostly based on the previous volcanic history at the specific volcano, or it is referred to a broader class of volcanoes constituting "analogues" of the one under specific consideration. In any case, use of knowledge from past eruptions implies considering the completeness of the reference catalogue, and most importantly, the existence of systematic biases in the catalogue, that may affect probability estimates and translate into biased volcanic hazard forecasts. An analysis of existing catalogues, with major reference to the catalogue from the Smithsonian Global Volcanism Program, suggests that systematic biases largely dominate at global, regional and local scale: volcanic histories reconstructed at individual volcanoes, often used as a reference for volcanic hazard forecasts, are the result of systematic loss of information with time and poor sample representativeness. That situation strictly requires the use of techniques to complete existing catalogues, as well as careful consideration of the uncertainties deriving from inadequate knowledge and model-dependent data elaboration. A reconstructed global eruption size distribution, obtained by merging information from different existing catalogues, shows a mode in the VEI 1-2 range, <0.1% incidence of eruptions with VEI 7 or larger, and substantial uncertainties associated with individual VEI frequencies. Even larger uncertainties are expected to derive from application to individual volcanoes or classes of analogue volcanoes, suggesting large to very large uncertainties associated to volcanic hazard forecasts virtually at any individual volcano worldwide.

A combined reference panel from the 1000 Genomes and UK10K projects improved rare variant imputation in European and Chinese samples

PubMed Central

Chou, Wen-Chi; Zheng, Hou-Feng; Cheng, Chia-Ho; Yan, Han; Wang, Li; Han, Fang; Richards, J. Brent; Karasik, David; Kiel, Douglas P.; Hsu, Yi-Hsiang

2016-01-01

Imputation using the 1000 Genomes haplotype reference panel has been widely adapted to estimate genotypes in genome wide association studies. To evaluate imputation quality with a relatively larger reference panel and a reference panel composed of different ethnic populations, we conducted imputations in the Framingham Heart Study and the North Chinese Study using a combined reference panel from the 1000 Genomes (N = 1,092) and UK10K (N = 3,781) projects. For rare variants with 0.01% < MAF ≤ 0.5%, imputation in the Framingham Heart Study with the combined reference panel increased well-imputed genotypes (with imputation quality score ≥0.4) from 62.9% to 76.1% when compared to imputation with the 1000 Genomes. For the North Chinese samples, imputation of rare variants with 0.01% < MAF ≤ 0.5% with the combined reference panel increased well-imputed genotypes by from 49.8% to 61.8%. The predominant European ancestry of the UK10K and the combined reference panels may explain why there was less of an increase in imputation success in the North Chinese samples. Our results underscore the importance and potential of larger reference panels to impute rare variants, while recognizing that increasing ethnic specific variants in reference panels may result in better imputation for genotypes in some ethnic groups. PMID:28004816

Dental age estimation in Japanese individuals combining permanent teeth and third molars.

PubMed

Ramanan, Namratha; Thevissen, Patrick; Fleuws, Steffen; Willems, G

2012-12-01

The study aim was, firstly, to verify the Willems et al. model on a Japanese reference sample. Secondly to develop a Japanese reference model based on the Willems et al. method and to verify it. Thirdly to analyze the age prediction performance adding tooth development information of third molars to permanent teeth. Retrospectively 1877 panoramic radiographs were selected in the age range between 1 and 23 years (1248 children, 629 sub-adults). Dental development was registered applying Demirjian 's stages of the mandibular left permanent teeth in children and Köhler stages on the third molars. The children's data were, firstly, used to validate the Willems et al. model (developed a Belgian reference sample), secondly, split ino a training and a test sample. On the training sample a Japanese reference model was developed based on the Willems method. The developed model and the Willems et al; model were verified on the test sample. Regression analysis was used to detect the age prediction performance adding third molar scores to permanent tooth scores. The validated Willems et al. model provided a mean absolute error of 0.85 and 0.75 years in females and males, respectively. The mean absolute error in the verified Willems et al. and the developed Japanese reference model was 0.85, 0.77 and 0.79, 0.75 years in females and males, respectively. On average a negligible change in root mean square error values was detected adding third molar scores to permanent teeth scores. The Belgian sample could be used as a reference model to estimate the age of the Japanese individuals. Combining information from the third molars and permanent teeth was not providing clinically significant improvement of age predictions based on permanent teeth information alone.

Multicomponent blood lipid analysis by means of near infrared spectroscopy, in geese.

PubMed

Bazar, George; Eles, Viktoria; Kovacs, Zoltan; Romvari, Robert; Szabo, Andras

2016-08-01

This study provides accurate near infrared (NIR) spectroscopic models on some laboratory determined clinicochemical parameters (i.e. total lipid (5.57±1.95 g/l), triglyceride (2.59±1.36 mmol/l), total cholesterol (3.81±0.68 mmol/l), high density lipoprotein (HDL) cholesterol (2.45±0.58 mmol/l)) of blood serum samples of fattened geese. To increase the performance of multivariate chemometrics, samples significantly deviating from the regression models implying laboratory error were excluded from the final calibration datasets. Reference data of excluded samples having outlier spectra in principal component analysis were not marked as false. Samples deviating from the regression models but having non outlier spectra in PCA were identified as having false reference constituent values. Based on the NIR selection methods, 5% of the reference measurement data were rated as doubtful. The achieved models reached R(2) of 0.864, 0.966, 0.850, 0.793, and RMSE of 0.639 g/l, 0.232 mmol/l, 0.210 mmol/l, 0.241 mmol/l for total lipid, triglyceride, total cholesterol and HDL cholesterol, respectively, during independent validation. Classical analytical techniques focus on single constituents and often require chemicals, time-consuming measurements, and experienced technicians. NIR technique provides a quick, cost effective, non-hazardous alternative method for analysis of several constituents based on one single spectrum of each sample, and it also offers the possibility for looking at the laboratory reference data critically. Evaluation of reference data to identify and exclude falsely analyzed samples can provide warning feedback to the reference laboratory, especially in the case of analyses where laboratory methods are not perfectly suited to the subjected material and there is an increased chance of laboratory error. Copyright © 2016 Elsevier B.V. All rights reserved.

Accurate and fiducial-marker-free correction for three-dimensional chromatic shift in biological fluorescence microscopy.

PubMed

Matsuda, Atsushi; Schermelleh, Lothar; Hirano, Yasuhiro; Haraguchi, Tokuko; Hiraoka, Yasushi

2018-05-15

Correction of chromatic shift is necessary for precise registration of multicolor fluorescence images of biological specimens. New emerging technologies in fluorescence microscopy with increasing spatial resolution and penetration depth have prompted the need for more accurate methods to correct chromatic aberration. However, the amount of chromatic shift of the region of interest in biological samples often deviates from the theoretical prediction because of unknown dispersion in the biological samples. To measure and correct chromatic shift in biological samples, we developed a quadrisection phase correlation approach to computationally calculate translation, rotation, and magnification from reference images. Furthermore, to account for local chromatic shifts, images are split into smaller elements, for which the phase correlation between channels is measured individually and corrected accordingly. We implemented this method in an easy-to-use open-source software package, called Chromagnon, that is able to correct shifts with a 3D accuracy of approximately 15 nm. Applying this software, we quantified the level of uncertainty in chromatic shift correction, depending on the imaging modality used, and for different existing calibration methods, along with the proposed one. Finally, we provide guidelines to choose the optimal chromatic shift registration method for any given situation.

Stability of selected serum proteins after long-term storage in the Janus Serum Bank.

PubMed

Gislefoss, Randi E; Grimsrud, Tom K; Mørkrid, Lars

2009-01-01

Human serum from biobanks is frequently used in prospective epidemiological studies. Long-term storage may modify its composition. A better understanding of the stability of the serum components may improve the interpretation of future studies. The concentrations of selected proteins; immunoglobulins, carrier proteins and enzymes in samples stored at -25 degrees C for 25 years and 2 years were compared with 1-month-old samples. For each length of storage time, 130 specimens were randomly selected from apparently healthy male blood donors aged 40-49 years. We examined the distribution of values, compared dispersion and localization of central tendency, and established reference intervals for each component. The study demonstrated non-significant or numerically small group differences in the concentrations of albumin, aspartate amino transferase, cystatin C, immunoglobulin E, immunoglobulin G, and sex hormone binding globulin. Mean values between fresh and 25-year-old samples suggested larger differences during storage for alanine amino transferase (-73.4%), creatinine kinase (-96.1%), insulin C-peptide (-98.7%), ferritin (-18.5%) and transferrin (+8.2%). The findings showed that long-term storage can introduce a considerable bias for vulnerable components.

Determination of mercury compounds in fish by microwave-assisted extraction and liquid chromatography-vapor generation-inductively coupled plasma mass spectrometry

NASA Astrophysics Data System (ADS)

Chiou, Chwei-Sheng; Jiang, Shiuh-Jen; Kumar Danadurai, K. Suresh

2001-07-01

A method employing a vapor generation system and LC combined with inductively coupled plasma mass spectrometry (LC-ICP-MS) is presented for the determination of mercury in biological tissues. An open vessel microwave digestion system was used to extract the mercury compounds from the sample matrix. The efficiency of the mobile phase, a mixture of L-cysteine and 2-mercaptoethanol, was evaluated for LC separation of inorganic mercury [Hg(II)], methylmercury (methyl-Hg) and ethylmercury (ethyl-Hg). The sensitivity, detection limits and repeatability of the liquid chromatography (LC) ICP-MS system with a vapor generator were comparable to, or better than, that of an LC-ICP-MS system with conventional pneumatic nebulization, or other sample introduction techniques. The experimental detection limits for various mercury species were in the range of 0.05-0.09 ng ml -1 Hg, based on peak height. The proposed method was successfully applied to the determination of mercury compounds in a swordfish sample purchased from the local market. The accuracy of the method was evaluated by analyzing a marine biological certified reference material (DORM-2, NRCC).

Development of a simple, sensitive and inexpensive ion-pairing cloud point extraction approach for the determination of trace inorganic arsenic species in spring water, beverage and rice samples by UV-Vis spectrophotometry.

PubMed

Gürkan, Ramazan; Kır, Ufuk; Altunay, Nail

2015-08-01

The determination of inorganic arsenic species in water, beverages and foods become crucial in recent years, because arsenic species are considered carcinogenic and found at high concentrations in the samples. This communication describes a new cloud-point extraction (CPE) method for the determination of low quantity of arsenic species in the samples, purchased from the local market by UV-Visible Spectrophotometer (UV-Vis). The method is based on selective ternary complex of As(V) with acridine orange (AOH(+)) being a versatile fluorescence cationic dye in presence of tartaric acid and polyethylene glycol tert-octylphenyl ether (Triton X-114) at pH 5.0. Under the optimized conditions, a preconcentration factor of 65 and detection limit (3S blank/m) of 1.14 μg L(-1) was obtained from the calibration curve constructed in the range of 4-450 μg L(-1) with a correlation coefficient of 0.9932 for As(V). The method is validated by the analysis of certified reference materials (CRMs). Copyright © 2015 Elsevier Ltd. All rights reserved.

Continuous Time Level Crossing Sampling ADC for Bio-Potential Recording Systems

PubMed Central

Tang, Wei; Osman, Ahmad; Kim, Dongsoo; Goldstein, Brian; Huang, Chenxi; Martini, Berin; Pieribone, Vincent A.

2013-01-01

In this paper we present a fixed window level crossing sampling analog to digital convertor for bio-potential recording sensors. This is the first proposed and fully implemented fixed window level crossing ADC without local DACs and clocks. The circuit is designed to reduce data size, power, and silicon area in future wireless neurophysiological sensor systems. We built a testing system to measure bio-potential signals and used it to evaluate the performance of the circuit. The bio-potential amplifier offers a gain of 53 dB within a bandwidth of 200 Hz-20 kHz. The input-referred rms noise is 2.8 µV. In the asynchronous level crossing ADC, the minimum delta resolution is 4 mV. The input signal frequency of the ADC is up to 5 kHz. The system was fabricated using the AMI 0.5 µm CMOS process. The chip size is 1.5 mm by 1.5 mm. The power consumption of the 4-channel system from a 3.3 V supply is 118.8 µW in the static state and 501.6 µW with a 240 kS/s sampling rate. The conversion efficiency is 1.6 nJ/conversion. PMID:24163640

The Impact of World Knowledge on the Processing of Mandarin Possessive Reflexive "Zijide"

ERIC Educational Resources Information Center

Li, Rui; Zhang, Zhiyi; Ni, Chuanbin

2017-01-01

It has long been considered that the Mandarin possessive reflexive "zijide" can be either locally bound or long distance bound, leading to ambiguity where it fails to exclusively refer back to either long distance binding NP or the local NP. In addition to syntactic factors such as the local versus long distance division, the present…

Compositional analysis and pollution impact assessment: A case study in the Gulfs of Naples and Salerno

NASA Astrophysics Data System (ADS)

Menghan, Wang; Stefano, Albanese; Annamaria, Lima; Claudia, Cannatelli; Antonio, Cosenza; Wanjun, Lu; Marco, Sacchi; Angela, Doherty; Benedetto, De Vivo

2015-07-01

This paper presents the results of an environmental geochemical investigation of the Gulfs of Naples and Salerno, near the Campania plain (Southern Italy). Surface marine sediment samples were collected during three field campaigns: 96 from the Gulfs of Naples and Salerno (NaSa); 123 from the Bagnoli site coastal area (BaSi); and 11 from the ports around the Gulf of Naples (PoNa). Elemental concentrations were determined and their interpolated distribution maps were compiled. Three geochemical sources (or processes) were determined associating elemental distribution with the results obtained from a R-mode factor analysis: 1) geogenic, 2) water kinetics and 3) anthropogenic. The results are presented as raw data single element distributions of eight potential toxic elements (PTEs) (As, Cd, Cr, Cu, Hg, Pb, Ni and Zn) in the forms of raw data and additive log-ratio transformed data. The latter showed advantages in revealing the actual distribution patterns. Geochemical background reference values of PTEs were determined from the median value of local background reference values. Based on these values, pollution impact analysis was carried out to both BaSi and PoNa samples, indicating most of BaSi and PoNa sediments were affected by moderate to strong Pb, Zn, Cd and Hg pollution. An ecological risk assessment was subsequently carried out on the entire database, pointing a toxic risk ranking in the order Pb > As > Ni > Cd > Hg > Cr.

Electron gun for a multiple beam klystron with magnetic compression of the electron beams

DOEpatents

Ives, R. Lawrence; Tran, Hien T; Bui, Thuc; Attarian, Adam; Tallis, William; David, John; Forstall, Virginia; Andujar, Cynthia; Blach, Noah T; Brown, David B; Gadson, Sean E; Kiley, Erin M; Read, Michael

2013-10-01

A multi-beam electron gun provides a plurality N of cathode assemblies comprising a cathode, anode, and focus electrode, each cathode assembly having a local cathode axis and also a central cathode point defined by the intersection of the local cathode axis with the emitting surface of the cathode. Each cathode is arranged with its central point positioned in a plane orthogonal to a device central axis, with each cathode central point an equal distance from the device axis and with an included angle of 360/N between each cathode central point. The local axis of each cathode has a cathode divergence angle with respect to the central axis which is set such that the diverging magnetic field from a solenoidal coil is less than 5 degrees with respect to the projection of the local cathode axis onto a cathode reference plane formed by the device axis and the central cathode point, and the local axis of each cathode is also set such that the angle formed between the cathode reference plane and the local cathode axis results in minimum spiraling in the path of the electron beams in a homogenous magnetic field region of the solenoidal field generator.