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Sample records for sample study reveals

  1. Using Negative Emotions to Trace the Experience of Borderline Personality Pathology: Interconnected Relationships Revealed in an Experience Sampling Study.

    Science.gov (United States)

    Law, Mary Kate; Fleeson, William; Arnold, Elizabeth Mayfield; Furr, R Michael

    2016-02-01

    While emotional difficulties are highly implicated in borderline personality disorder (BPD), the dynamic relationships between emotions and BPD symptoms that occur in everyday life are unknown. The current paper examined the function of negative emotions as they relate to BPD symptoms in real time. Experience sampling methodology with 281 participants measured negative emotions and borderline symptoms, expressed as a spectrum of experiences, five times daily for two weeks. Overall, having a BDP diagnosis was associated with experiencing more negative emotions. Multilevel modeling supported positive concurrent relationships between negative emotions and BPD symptoms. Lagged models showed that even after 3 hours negative emotions and several symptoms continued to influence each other. Therefore, results indicated that negative emotions and BPD symptoms are intricately related; some evidenced long-lasting relationships. This research supports emotion-symptom contingencies within BPD and provides insight regarding the reactivity and functionality of negative emotions in borderline pathology.

  2. Using negative emotions to trace the experience of borderline personality pathology: Interconnected relationships revealed in an experience sampling study

    Science.gov (United States)

    Law, Mary Kate; Fleeson, William; Arnold, Elizabeth Mayfield; Furr, R. Michael

    2015-01-01

    While emotional difficulties are highly implicated in borderline personality disorder (BPD), the dynamic relationships between emotions and BPD symptoms that occur in everyday life are unknown. The current paper examined the function of negative emotions as they relate to BPD symptoms in real time. Experience sampling methodology with 281 participants measured negative emotions and borderline symptoms, expressed as a spectrum of experiences, five times daily for two weeks. Overall, having a BDP diagnosis was associated with experiencing more negative emotions. Multilevel modeling supported positive concurrent relationships between negative emotions and BPD symptoms. Lagged models showed that even after three hours negative emotions and several symptoms continued to influence each other. Therefore, results indicated that negative emotions and BPD symptoms are intricately related; some evidenced long-lasting relationships. This research supports emotion-symptom contingencies within BPD and provides insight regarding the reactivity and functionality of negative emotions in borderline pathology. PMID:25710731

  3. Longitudinal Study of Hepatitis A Infection by Saliva Sampling: The Kinetics of HAV Markers in Saliva Revealed the Application of Saliva Tests for Hepatitis A Study

    Science.gov (United States)

    Amado Leon, Luciane Almeida; de Almeida, Adilson José; de Paula, Vanessa Salete; Tourinho, Renata Santos; Villela, Daniel Antunes Maciel; Gaspar, Ana Maria Coimbra; Lewis-Ximenez, Lia Laura; Pinto, Marcelo Alves

    2015-01-01

    Despite the increasing numbers of studies investigating hepatitis A diagnostic through saliva, the frequency and the pattern of hepatitis A virus (HAV) markers in this fluid still remains unknown. To address this issue, we carried on a longitudinal study to examine the kinetics of HAV markers in saliva, in comparison with serum samples. The present study followed-up ten patients with acute hepatitis A infection during 180 days post diagnosis (dpd). Total anti-HAV was detected in paired serum and saliva samples until the end of the follow-up, showing a peak titer at 90th. However, total anti-HAV level was higher in serum than in saliva samples. This HAV marker showed a probability of 100% to be detected in both serum and saliva during 180 dpd. The IgM anti-HAV could be detected in saliva up to 150 dpd, showing the highest frequency at 30th, when it was detected in all individuals. During the first month of HAV infection, this acute HAV marker showed a detection probability of 100% in paired samples. The detection of IgM anti-HAV in saliva was not dependent on its level in serum, HAV-RNA detection and/or viral load, since no association was found between IgM anti-HAV positivity in saliva and any of these parameter (p>0.05). Most of the patients (80%) were found to contain HAV-RNA in saliva, mainly at early acute phase (30th day). However, it was possible to demonstrate the HAV RNA presence in paired samples for more than 90 days, even after seroconversion. No significant relationship was observed between salivary HAV-RNA positivity and serum viral load, demonstrating that serum viral load is not predictive of HAV-RNA detection in saliva. Similar viral load was seen in paired samples (on average 104 copies/mL). These data demonstrate that the best diagnostic coverage can be achieved by salivary anti-HAV antibodies and HAV-RNA tests during 30–90 dpd. The long detection and high probability of specific-HAV antibodies positivity in saliva samples make the assessment of

  4. Longitudinal Study of Hepatitis A Infection by Saliva Sampling: The Kinetics of HAV Markers in Saliva Revealed the Application of Saliva Tests for Hepatitis A Study.

    Science.gov (United States)

    Amado Leon, Luciane Almeida; de Almeida, Adilson José; de Paula, Vanessa Salete; Tourinho, Renata Santos; Villela, Daniel Antunes Maciel; Gaspar, Ana Maria Coimbra; Lewis-Ximenez, Lia Laura; Pinto, Marcelo Alves

    2015-01-01

    Despite the increasing numbers of studies investigating hepatitis A diagnostic through saliva, the frequency and the pattern of hepatitis A virus (HAV) markers in this fluid still remains unknown. To address this issue, we carried on a longitudinal study to examine the kinetics of HAV markers in saliva, in comparison with serum samples. The present study followed-up ten patients with acute hepatitis A infection during 180 days post diagnosis (dpd). Total anti-HAV was detected in paired serum and saliva samples until the end of the follow-up, showing a peak titer at 90th. However, total anti-HAV level was higher in serum than in saliva samples. This HAV marker showed a probability of 100% to be detected in both serum and saliva during 180 dpd. The IgM anti-HAV could be detected in saliva up to 150 dpd, showing the highest frequency at 30th, when it was detected in all individuals. During the first month of HAV infection, this acute HAV marker showed a detection probability of 100% in paired samples. The detection of IgM anti-HAV in saliva was not dependent on its level in serum, HAV-RNA detection and/or viral load, since no association was found between IgM anti-HAV positivity in saliva and any of these parameter (p>0.05). Most of the patients (80%) were found to contain HAV-RNA in saliva, mainly at early acute phase (30th day). However, it was possible to demonstrate the HAV RNA presence in paired samples for more than 90 days, even after seroconversion. No significant relationship was observed between salivary HAV-RNA positivity and serum viral load, demonstrating that serum viral load is not predictive of HAV-RNA detection in saliva. Similar viral load was seen in paired samples (on average 104 copies/mL). These data demonstrate that the best diagnostic coverage can be achieved by salivary anti-HAV antibodies and HAV-RNA tests during 30-90 dpd. The long detection and high probability of specific-HAV antibodies positivity in saliva samples make the assessment of

  5. Longitudinal Study of Hepatitis A Infection by Saliva Sampling: The Kinetics of HAV Markers in Saliva Revealed the Application of Saliva Tests for Hepatitis A Study.

    Directory of Open Access Journals (Sweden)

    Luciane Almeida Amado Leon

    Full Text Available Despite the increasing numbers of studies investigating hepatitis A diagnostic through saliva, the frequency and the pattern of hepatitis A virus (HAV markers in this fluid still remains unknown. To address this issue, we carried on a longitudinal study to examine the kinetics of HAV markers in saliva, in comparison with serum samples. The present study followed-up ten patients with acute hepatitis A infection during 180 days post diagnosis (dpd. Total anti-HAV was detected in paired serum and saliva samples until the end of the follow-up, showing a peak titer at 90th. However, total anti-HAV level was higher in serum than in saliva samples. This HAV marker showed a probability of 100% to be detected in both serum and saliva during 180 dpd. The IgM anti-HAV could be detected in saliva up to 150 dpd, showing the highest frequency at 30th, when it was detected in all individuals. During the first month of HAV infection, this acute HAV marker showed a detection probability of 100% in paired samples. The detection of IgM anti-HAV in saliva was not dependent on its level in serum, HAV-RNA detection and/or viral load, since no association was found between IgM anti-HAV positivity in saliva and any of these parameter (p>0.05. Most of the patients (80% were found to contain HAV-RNA in saliva, mainly at early acute phase (30th day. However, it was possible to demonstrate the HAV RNA presence in paired samples for more than 90 days, even after seroconversion. No significant relationship was observed between salivary HAV-RNA positivity and serum viral load, demonstrating that serum viral load is not predictive of HAV-RNA detection in saliva. Similar viral load was seen in paired samples (on average 104 copies/mL. These data demonstrate that the best diagnostic coverage can be achieved by salivary anti-HAV antibodies and HAV-RNA tests during 30-90 dpd. The long detection and high probability of specific-HAV antibodies positivity in saliva samples make the

  6. Biological Sampling Variability Study

    Energy Technology Data Exchange (ETDEWEB)

    Amidan, Brett G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hutchison, Janine R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-11-08

    There are many sources of variability that exist in the sample collection and analysis process. This paper addresses many, but not all, sources of variability. The main focus of this paper was to better understand and estimate variability due to differences between samplers. Variability between days was also studied, as well as random variability within each sampler. Experiments were performed using multiple surface materials (ceramic and stainless steel), multiple contaminant concentrations (10 spores and 100 spores), and with and without the presence of interfering material. All testing was done with sponge sticks using 10-inch by 10-inch coupons. Bacillus atrophaeus was used as the BA surrogate. Spores were deposited using wet deposition. Grime was coated on the coupons which were planned to include the interfering material (Section 3.3). Samples were prepared and analyzed at PNNL using CDC protocol (Section 3.4) and then cultured and counted. Five samplers were trained so that samples were taken using the same protocol. Each sampler randomly sampled eight coupons each day, four coupons with 10 spores deposited and four coupons with 100 spores deposited. Each day consisted of one material being tested. The clean samples (no interfering materials) were run first, followed by the dirty samples (coated with interfering material). There was a significant difference in recovery efficiency between the coupons with 10 spores deposited (mean of 48.9%) and those with 100 spores deposited (mean of 59.8%). There was no general significant difference between the clean and dirty (containing interfering material) coupons or between the two surface materials; however, there was a significant interaction between concentration amount and presence of interfering material. The recovery efficiency was close to the same for coupons with 10 spores deposited, but for the coupons with 100 spores deposited, the recovery efficiency for the dirty samples was significantly larger (65

  7. Increased genome sampling reveals novel insights into vertebrate molecular evolution

    OpenAIRE

    Doherty, Aoife

    2012-01-01

    In this thesis, increased vertebrate genome sampling and recent methodological advancements were combined to address three distinct questions pertaining to vertebrate molecular evolution. Gene duplicability is the tendency to retain multiple gene copies after a duplication event. Various factors correlate with gene duplicability, such as protein function and timing of expression during development. The position of a gene’s encoded product in the protein-protein interaction n...

  8. Historical sampling reveals dramatic demographic changes in western gorilla populations

    Directory of Open Access Journals (Sweden)

    Guschanski Katerina

    2011-04-01

    Full Text Available Abstract Background Today many large mammals live in small, fragmented populations, but it is often unclear whether this subdivision is the result of long-term or recent events. Demographic modeling using genetic data can estimate changes in long-term population sizes while temporal sampling provides a way to compare genetic variation present today with that sampled in the past. In order to better understand the dynamics associated with the divergences of great ape populations, these analytical approaches were applied to western gorillas (Gorilla gorilla and in particular to the isolated and Critically Endangered Cross River gorilla subspecies (G. g. diehli. Results We used microsatellite genotypes from museum specimens and contemporary samples of Cross River gorillas to infer both the long-term and recent population history. We find that Cross River gorillas diverged from the ancestral western gorilla population ~17,800 years ago (95% HDI: 760, 63,245 years. However, gene flow ceased only ~420 years ago (95% HDI: 200, 16,256 years, followed by a bottleneck beginning ~320 years ago (95% HDI: 200, 2,825 years that caused a 60-fold decrease in the effective population size of Cross River gorillas. Direct comparison of heterozygosity estimates from museum and contemporary samples suggests a loss of genetic variation over the last 100 years. Conclusions The composite history of western gorillas could plausibly be explained by climatic oscillations inducing environmental changes in western equatorial Africa that would have allowed gorilla populations to expand over time but ultimately isolate the Cross River gorillas, which thereafter exhibited a dramatic population size reduction. The recent decrease in the Cross River population is accordingly most likely attributable to increasing anthropogenic pressure over the last several hundred years. Isolation of diverging populations with prolonged concomitant gene flow, but not secondary admixture, appears

  9. Historical sampling reveals dramatic demographic changes in western gorilla populations

    Science.gov (United States)

    2011-01-01

    Background Today many large mammals live in small, fragmented populations, but it is often unclear whether this subdivision is the result of long-term or recent events. Demographic modeling using genetic data can estimate changes in long-term population sizes while temporal sampling provides a way to compare genetic variation present today with that sampled in the past. In order to better understand the dynamics associated with the divergences of great ape populations, these analytical approaches were applied to western gorillas (Gorilla gorilla) and in particular to the isolated and Critically Endangered Cross River gorilla subspecies (G. g. diehli). Results We used microsatellite genotypes from museum specimens and contemporary samples of Cross River gorillas to infer both the long-term and recent population history. We find that Cross River gorillas diverged from the ancestral western gorilla population ~17,800 years ago (95% HDI: 760, 63,245 years). However, gene flow ceased only ~420 years ago (95% HDI: 200, 16,256 years), followed by a bottleneck beginning ~320 years ago (95% HDI: 200, 2,825 years) that caused a 60-fold decrease in the effective population size of Cross River gorillas. Direct comparison of heterozygosity estimates from museum and contemporary samples suggests a loss of genetic variation over the last 100 years. Conclusions The composite history of western gorillas could plausibly be explained by climatic oscillations inducing environmental changes in western equatorial Africa that would have allowed gorilla populations to expand over time but ultimately isolate the Cross River gorillas, which thereafter exhibited a dramatic population size reduction. The recent decrease in the Cross River population is accordingly most likely attributable to increasing anthropogenic pressure over the last several hundred years. Isolation of diverging populations with prolonged concomitant gene flow, but not secondary admixture, appears to be a typical

  10. Constrained sampling experiments reveal principles of detection in natural scenes.

    Science.gov (United States)

    Sebastian, Stephen; Abrams, Jared; Geisler, Wilson S

    2017-07-11

    A fundamental everyday visual task is to detect target objects within a background scene. Using relatively simple stimuli, vision science has identified several major factors that affect detection thresholds, including the luminance of the background, the contrast of the background, the spatial similarity of the background to the target, and uncertainty due to random variations in the properties of the background and in the amplitude of the target. Here we use an experimental approach based on constrained sampling from multidimensional histograms of natural stimuli, together with a theoretical analysis based on signal detection theory, to discover how these factors affect detection in natural scenes. We sorted a large collection of natural image backgrounds into multidimensional histograms, where each bin corresponds to a particular luminance, contrast, and similarity. Detection thresholds were measured for a subset of bins spanning the space, where a natural background was randomly sampled from a bin on each trial. In low-uncertainty conditions, both the background bin and the amplitude of the target were fixed, and, in high-uncertainty conditions, they varied randomly on each trial. We found that thresholds increase approximately linearly along all three dimensions and that detection accuracy is unaffected by background bin and target amplitude uncertainty. The results are predicted from first principles by a normalized matched-template detector, where the dynamic normalizing gain factor follows directly from the statistical properties of the natural backgrounds. The results provide an explanation for classic laws of psychophysics and their underlying neural mechanisms.

  11. Proteomics Analysis of Tissue Samples Reveals Changes in Mitochondrial Protein Levels in Parathyroid Hyperplasia over Adenoma.

    Science.gov (United States)

    Akpinar, Gurler; Kasap, Murat; Canturk, Nuh Zafer; Zulfigarova, Mehin; Islek, Eylül Ece; Guler, Sertac Ata; Simsek, Turgay; Canturk, Zeynep

    2017-01-01

    To unveil the pathophysiology of primary hyperparathyroidism, molecular details of parathyroid hyperplasia and adenoma have to be revealed. Such details will provide the tools necessary for differentiation of these two look-alike diseases. Therefore, in the present study, a comparative proteomic study using postoperative tissue samples from the parathyroid adenoma and parathyroid hyperplasia patients was performed. Protein extracts were prepared from tissue samples (n=8 per group). Protein pools were created for each group and subjected to DIGE and conventional 2DE. Following image analysis, spots representing the differentially regulated proteins were excised from the and used for identification via MALDI-TOF/TOF analysis. The identities of 40 differentially-expressed proteins were revealed. Fourteen of these proteins were over-expressed in the hyperplasia while 26 of them were over-expressed in the adenoma. Most proteins found to be over-expressed in the hyperplasia samples were mitochondrial, underlying the importance of the mitochondrial activity as a potential biomarker for differentiation of parathyroid hyperplasia from adenoma. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  12. Transgenic zebrafish reveal tissue-specific differences in estrogen signaling in response to environmental water samples

    Science.gov (United States)

    Gorelick, Daniel A.; Iwanowicz, Luke R.; Hung, Alice L.; Blazer, Vicki; Halpern, Marnie E.

    2014-01-01

    Background: Environmental endocrine disruptors (EED) are exogenous chemicals that mimic endogenous hormones, such as estrogens. Previous studies using a zebrafish transgenic reporter demonstrated that the EEDs bisphenol A and genistein preferentially activate estrogen receptors (ER) in the larval heart compared to the liver. However, it was not known whether the transgenic zebrafish reporter was sensitive enough to detect estrogens from environmental samples, whether environmental estrogens would exhibit similar tissue-specific effects as BPA and genistein or why some compounds preferentially target receptors in the heart. Methods: We tested surface water samples using a transgenic zebrafish reporter with tandem estrogen response elements driving green fluorescent protein expression (5xERE:GFP). Reporter activation was colocalized with tissue-specific expression of estrogen receptor genes by RNA in situ hybridization. Results: Selective patterns of ER activation were observed in transgenic fish exposed to river water samples from the Mid-Atlantic United States, with several samples preferentially activating receptors in embryonic and larval heart valves. We discovered that tissue-specificity in ER activation is due to differences in the expression of estrogen receptor subtypes. ERα is expressed in developing heart valves but not in the liver, whereas ERβ2 has the opposite profile. Accordingly, subtype-specific ER agonists activate the reporter in either the heart valves or the liver. Conclusion: The use of 5xERE:GFP transgenic zebrafish has revealed an unexpected tissue-specific difference in the response to environmentally relevant estrogenic compounds. Exposure to estrogenic EEDs in utero is associated with adverse health effects, with the potentially unanticipated consequence of targeting developing heart valves.

  13. Sample size in usability studies

    NARCIS (Netherlands)

    Schmettow, Martin

    2012-01-01

    Usability studies are important for developing usable, enjoyable products, identifying design flaws (usability problems) likely to compromise the user experience. Usability testing is recommended for improving interactive design, but discovery of usability problems depends on the number of users

  14. Reveal Salmonella 2.0 test for detection of Salmonella spp. in foods and environmental samples. Performance Tested Method 960801.

    Science.gov (United States)

    Hoerner, Rebecca; Feldpausch, Jill; Gray, R Lucas; Curry, Stephanie; Islam, Zahidul; Goldy, Tim; Klein, Frank; Tadese, Theodros; Rice, Jennifer; Mozola, Mark

    2011-01-01

    Reveal Salmonella 2.0 is an improved version of the original Reveal Salmonella lateral flow immunoassay and is applicable to the detection of Salmonella enterica serogroups A-E in a variety of food and environmental samples. A Performance Tested Method validation study was conducted to compare performance of the Reveal 2.0 method with that of the U.S. Department of Agriculture-Food Safety and Inspection Service or U.S. Food and Drug Administration/Bacteriological Analytical Manual reference culture methods for detection of Salmonella spp. in chicken carcass rinse, raw ground turkey, raw ground beef, hot dogs, raw shrimp, a ready-to-eat meal product, dry pet food, ice cream, spinach, cantaloupe, peanut butter, stainless steel surface, and sprout irrigation water. In a total of 17 trials performed internally and four trials performed in an independent laboratory, there were no statistically significant differences in performance of the Reveal 2.0 and reference culture procedures as determined by Chi-square analysis, with the exception of one trial with stainless steel surface and one trial with sprout irrigation water where there were significantly more positive results by the Reveal 2.0 method. Considering all data generated in testing food samples using enrichment procedures specifically designed for the Reveal method, overall sensitivity of the Reveal method relative to the reference culture methods was 99%. In testing environmental samples, sensitivity of the Reveal method relative to the reference culture method was 164%. For select foods, use of the Reveal test in conjunction with reference method enrichment resulted in overall sensitivity of 92%. There were no unconfirmed positive results on uninoculated control samples in any trials for specificity of 100%. In inclusivity testing, 102 different Salmonella serovars belonging to serogroups A-E were tested and 99 were consistently positive in the Reveal test. In exclusivity testing of 33 strains of non

  15. Culture-independent genome sequencing of clinical samples reveals an unexpected heterogeneity of infections by Chlamydia pecorum.

    Science.gov (United States)

    Bachmann, Nathan L; Sullivan, Mitchell J; Jelocnik, Martina; Myers, Garry S A; Timms, Peter; Polkinghorne, Adam

    2015-05-01

    Chlamydia pecorum is an important global pathogen of livestock, and it is also a significant threat to the long-term survival of Australia's koala populations. This study employed a culture-independent DNA capture approach to sequence C. pecorum genomes directly from clinical swab samples collected from koalas with chlamydial disease as well as from sheep with arthritis and conjunctivitis. Investigations into single-nucleotide polymorphisms within each of the swab samples revealed that a portion of the reads in each sample belonged to separate C. pecorum strains, suggesting that all of the clinical samples analyzed contained mixed populations of genetically distinct C. pecorum isolates. This observation was independent of the anatomical site sampled and the host species. Using the genomes of strains identified in each of these samples, whole-genome phylogenetic analysis revealed that a clade containing a bovine and a koala isolate is distinct from other clades comprised of livestock or koala C. pecorum strains. Providing additional evidence to support exposure of koalas to Australian livestock strains, two minor strains assembled from the koala swab samples clustered with livestock strains rather than koala strains. Culture-independent probe-based genome capture and sequencing of clinical samples provides the strongest evidence yet to suggest that naturally occurring chlamydial infections are comprised of multiple genetically distinct strains. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  16. Sample size in qualitative interview studies

    DEFF Research Database (Denmark)

    Malterud, Kirsti; Siersma, Volkert Dirk; Guassora, Ann Dorrit Kristiane

    2016-01-01

    Sample sizes must be ascertained in qualitative studies like in quantitative studies but not by the same means. The prevailing concept for sample size in qualitative studies is “saturation.” Saturation is closely tied to a specific methodology, and the term is inconsistently applied. We propose...... the concept “information power” to guide adequate sample size for qualitative studies. Information power indicates that the more information the sample holds, relevant for the actual study, the lower amount of participants is needed. We suggest that the size of a sample with sufficient information power...... depends on (a) the aim of the study, (b) sample specificity, (c) use of established theory, (d) quality of dialogue, and (e) analysis strategy. We present a model where these elements of information and their relevant dimensions are related to information power. Application of this model in the planning...

  17. Phootprint - A Phobos sample return mission study

    Science.gov (United States)

    Koschny, Detlef; Svedhem, Håkan; Rebuffat, Denis

    Introduction ESA is currently studying a mission to return a sample from Phobos, called Phootprint. This study is performed as part of ESA’s Mars Robotic Exploration Programme. Part of the mission goal is to prepare technology needed for a sample return mission from Mars itself; the mission should also have a strong scientific justification, which is described here. 1. Science goal The main science goal of this mission will be to Understand the formation of the Martian moons Phobos and put constraints on the evolution of the solar system. Currently, there are several possibilities for explaining the formation of the Martian moons: (a) co-formation with Mars (b) capture of objects coming close to Mars (c) Impact of a large body onto Mars and formation from the impact ejecta The main science goal of this mission is to find out which of the three scenarios is the most probable one. To do this, samples from Phobos would be returned to Earth and analyzed with extremely high precision in ground-based laboratories. An on-board payload is foreseen to provide information to put the sample into the necessary geological context. 2. Mission Spacecraft and payload will be based on experience gained from previous studies to Martian moons and asteroids. In particular the Marco Polo and MarcoPolo-R asteroid sample return mission studies performed at ESA were used as a starting point. Currently, industrial studies are ongoing. The initial starting assumption was to use a Soyuz launcher. Uunlike the initial Marco Polo and MarcoPolo-R studies to an asteroid, a transfer stage will be needed. Another main difference to an asteroid mission is the fact that the spacecraft actually orbits Mars, not Phobos or Deimos. It is possible to select a spacecraft orbit, which in a Phobos- or Deimos-centred reference system would give an ellipse around the moon. The following model payload is currently foreseen: - Wide Angle Camera, - Narrow Angle Camera, - Close-Up Camera, - Context camera for

  18. Designing a sampling scheme to reveal correlations between weeds and soil properties at multiple spatial scales.

    Science.gov (United States)

    Metcalfe, H; Milne, A E; Webster, R; Lark, R M; Murdoch, A J; Storkey, J

    2016-02-01

    Weeds tend to aggregate in patches within fields, and there is evidence that this is partly owing to variation in soil properties. Because the processes driving soil heterogeneity operate at various scales, the strength of the relations between soil properties and weed density would also be expected to be scale-dependent. Quantifying these effects of scale on weed patch dynamics is essential to guide the design of discrete sampling protocols for mapping weed distribution. We developed a general method that uses novel within-field nested sampling and residual maximum-likelihood (reml) estimation to explore scale-dependent relations between weeds and soil properties. We validated the method using a case study of Alopecurus myosuroides in winter wheat. Using reml, we partitioned the variance and covariance into scale-specific components and estimated the correlations between the weed counts and soil properties at each scale. We used variograms to quantify the spatial structure in the data and to map variables by kriging. Our methodology successfully captured the effect of scale on a number of edaphic drivers of weed patchiness. The overall Pearson correlations between A. myosuroides and soil organic matter and clay content were weak and masked the stronger correlations at >50 m. Knowing how the variance was partitioned across the spatial scales, we optimised the sampling design to focus sampling effort at those scales that contributed most to the total variance. The methods have the potential to guide patch spraying of weeds by identifying areas of the field that are vulnerable to weed establishment.

  19. Widespread sampling biases in herbaria revealed from large-scale digitization.

    Science.gov (United States)

    Daru, Barnabas H; Park, Daniel S; Primack, Richard B; Willis, Charles G; Barrington, David S; Whitfeld, Timothy J S; Seidler, Tristram G; Sweeney, Patrick W; Foster, David R; Ellison, Aaron M; Davis, Charles C

    2018-01-01

    Nonrandom collecting practices may bias conclusions drawn from analyses of herbarium records. Recent efforts to fully digitize and mobilize regional floras online offer a timely opportunity to assess commonalities and differences in herbarium sampling biases. We determined spatial, temporal, trait, phylogenetic, and collector biases in c. 5 million herbarium records, representing three of the most complete digitized floras of the world: Australia (AU), South Africa (SA), and New England, USA (NE). We identified numerous shared and unique biases among these regions. Shared biases included specimens collected close to roads and herbaria; specimens collected more frequently during biological spring and summer; specimens of threatened species collected less frequently; and specimens of close relatives collected in similar numbers. Regional differences included overrepresentation of graminoids in SA and AU and of annuals in AU; and peak collection during the 1910s in NE, 1980s in SA, and 1990s in AU. Finally, in all regions, a disproportionately large percentage of specimens were collected by very few individuals. We hypothesize that these mega-collectors, with their associated preferences and idiosyncrasies, shaped patterns of collection bias via 'founder effects'. Studies using herbarium collections should account for sampling biases, and future collecting efforts should avoid compounding these biases to the extent possible. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  20. Comprehensive genotyping in two homogeneous Graves' disease samples reveals major and novel HLA association alleles.

    Directory of Open Access Journals (Sweden)

    Pei-Lung Chen

    Full Text Available BACKGROUND: Graves' disease (GD is the leading cause of hyperthyroidism and thyroid eye disease inherited as a complex trait. Although geoepidemiology studies showed relatively higher prevalence of GD in Asians than in Caucasians, previous genetic studies were contradictory concerning whether and/or which human leukocyte antigen (HLA alleles are associated with GD in Asians. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a case-control association study (499 unrelated GD cases and 504 controls and a replication in an independent family sample (419 GD individuals and their 282 relatives in 165 families. To minimize genetic and phenotypic heterogeneity, we included only ethnic Chinese Han population in Taiwan and excluded subjects with hypothyroidism. We performed direct and comprehensive genotyping of six classical HLA loci (HLA-A, -B, -C, -DPB1, -DQB1 and -DRB1 to 4-digit resolution. Combining the data of two sample populations, we found that B*46:01 (odds ratio under dominant model [OR]  = 1.33, Bonferroni corrected combined P [P(Bc]  = 1.17 x 10⁻², DPB1*05:01 (OR  = 2.34, P(Bc = 2.58 x 10⁻¹⁰, DQB1*03:02 (OR  = 0.62, P(Bc  = 1.97 x 10⁻², DRB1*15:01 (OR  = 1.68, P(Bc = 1.22 x 10⁻² and DRB1*16:02 (OR  = 2.63, P(Bc  = 1.46 x 10⁻⁵ were associated with GD. HLA-DPB1*05:01 is the major gene of GD in our population and singly accounts for 48.4% of population-attributable risk. CONCLUSIONS/SIGNIFICANCE: These GD-associated alleles we identified in ethnic Chinese Hans, and those identified in other Asian studies, are totally distinct from the known associated alleles in Caucasians. Identification of population-specific association alleles is the critical first step for individualized medicine. Furthermore, comparison between different susceptibility/protective alleles across populations could facilitate generation of novel hypothesis about GD pathophysiology and indicate a new direction for future

  1. Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics.

    Science.gov (United States)

    von Wulffen, Joachim; Ulmer, Andreas; Jäger, Günter; Sawodny, Oliver; Feuer, Ronny

    2017-02-28

    Escherichia coli is able to shift between anaerobic and aerobic metabolism by adapting its gene expression, e.g., of metabolic genes, to the new environment. The dynamics of gene expression that result from environmental shifts are limited, amongst others, by the time needed for regulation and transcription elongation. In this study, we examined gene expression dynamics after an anaerobic-to-aerobic shift on a short time scale (0.5, 1, 2, 5, and 10 min) by RNA sequencing with emphasis on delay times and transcriptional elongation rates (TER). Transient expression patterns and timing of differential expression, characterized by delay and elongation, were identified as key features of the dataset. Gene ontology enrichment analysis revealed early upregulation of respiratory and iron-related gene sets. We inferred specific TERs of 89 operons with a mean TER of 42.0 nt/s and mean delay time of 22.4 s. TERs correlate with sequence features, such as codon bias, whereas delay times correlate with the involvement of regulators. The presented data illustrate that at very short times after a shift in oxygenation, extensional changes of the transcriptome, such as temporary responses, can be observed. Besides regulation, TERs contribute to the dynamics of gene expression.

  2. Temporal genetic variation as revealed by a microsatellite analysis of European sardine ( Sardina pilchardus) archived samples

    DEFF Research Database (Denmark)

    Ruggeri, Paolo; Splendiani, Andrea; Bonanomi, Sara

    2012-01-01

    ) that explain the genetic diversity variation, while the same parameters turned out to be more stable in the southern samples. In addition, we detected the presence of a genetic bottleneck and low effective population size ( Ne) values in several northern samples. Even if the northern and southern Adriatic...... of otoliths and scales from sampling locations of northern (Chioggia) and southern (Vieste) Adriatic Sea, with the aim to investigate the genetic effects of these stock biomass fluctuations. The northern samples showed significant reduction in observed heterozygosity ( HO) and mean number of alleles ( Na...... sardine samples belong to the same genetic stock, the more pronounced decrease in genetic variability recorded in the northern sample led us to speculate that a more intensive fishing pressure and a more pronounced oceanographic isolation of this area could have accentuated the effects of the genetic...

  3. Changes in cancer cell metabolism revealed by direct sample analysis with MALDI mass spectrometry.

    Directory of Open Access Journals (Sweden)

    David A Pirman

    Full Text Available Biomarker discovery using mass spectrometry (MS has recently seen a significant increase in applications, mainly driven by the rapidly advancing field of metabolomics. Instrumental and data handling advancements have allowed for untargeted metabolite analyses which simultaneously interrogate multiple biochemical pathways to elucidate disease phenotypes and therapeutic mechanisms. Although most MS-based metabolomic approaches are coupled with liquid chromatography, a few recently published studies used matrix-assisted laser desorption (MALDI, allowing for rapid and direct sample analysis with minimal sample preparation. We and others have reported that prostaglandin E3 (PGE3, derived from COX-2 metabolism of the omega-3 fatty acid eicosapentaenoic acid (EPA, inhibited the proliferation of human lung, colon and pancreatic cancer cells. However, how PGE3 metabolism is regulated in cancer cells, particularly human non-small cell lung cancer (NSCLC cells, is not fully understood. Here, we successfully used MALDI to identify differences in lipid metabolism between two human non-small-cell lung cancer (NSCLC cell lines, A549 and H596, which could contribute to their differential response to EPA treatment. Analysis by MALDI-MS showed that the level of EPA incorporated into phospholipids in H596 cells was 4-fold higher than A549 cells. Intriguingly, H596 cells produced much less PGE3 than A549 cells even though the expression of COX-2 was similar in these two cell lines. This appears to be due to the relatively lower expression of cytosolic phospholipase A2 (cPLA2 in H596 cells than that of A549 cells. Additionally, the MALDI-MS approach was successfully used on tumor tissue extracts from a K-ras transgenic mouse model of lung cancer to enhance our understanding of the mechanism of action of EPA in the in vivo model. These results highlight the utility of combining a metabolomics workflow with MALDI-MS to identify the biomarkers that may regulate the

  4. On the nature of rainfall intermittency as revealed by different metrics and sampling approaches

    Directory of Open Access Journals (Sweden)

    G. Mascaro

    2013-01-01

    Full Text Available A general consensus on the concept of rainfall intermittency has not yet been reached, and intermittency is often attributed to different aspects of rainfall variability, including the fragmentation of the rainfall support (i.e., the alternation of wet and dry intervals and the strength of intensity fluctuations and bursts. To explore these different aspects, a systematic analysis of rainfall intermittency properties in the time domain is presented using high-resolution (1-min data recorded by a network of 201 tipping-bucket gauges covering the entire island of Sardinia (Italy. Four techniques, including spectral and scale invariance analysis, and computation of clustering and intermittency exponents, are applied to quantify the contribution of the alternation of dry and wet intervals (i.e., the rainfall support fragmentation, and the fluctuations of intensity amplitudes, to the overall intermittency of the rainfall process. The presence of three ranges of scaling regimes between 1 min to ~ 45 days is first demonstrated. In accordance with past studies, these regimes can be associated with a range dominated by single storms, a regime typical of frontal systems, and a transition zone. The positions of the breaking points separating these regimes change with the applied technique, suggesting that different tools explain different aspects of rainfall variability. Results indicate that the intermittency properties of rainfall support are fairly similar across the island, while metrics related to rainfall intensity fluctuations are characterized by significant spatial variability, implying that the local climate has a significant effect on the amplitude of rainfall fluctuations and minimal influence on the process of rainfall occurrence. In addition, for each analysis tool, evidence is shown of spatial patterns of the scaling exponents computed in the range of frontal systems. These patterns resemble the main pluviometric regimes observed on the

  5. Customized high resolution CGH-array for clinical diagnosis reveals additional genomic imbalances in previous well-defined pathological samples.

    Science.gov (United States)

    Vallespín, Elena; Palomares Bralo, María; Mori, M Ángeles; Martín, Rubén; García-Miñaúr, Sixto; Fernández, Luis; de Torres, M Luisa; García-Santiago, Fe; Mansilla, Elena; Santos, Fernando; M-Montaño, Victoria E; Crespo, M Carmen; Martín, Sol; Martínez-Glez, Victor; Delicado, Alicia; Lapunzina, Pablo; Nevado, Julián

    2013-08-01

    High-resolution array comparative genomic hybridization (aCGH) is a powerful molecular cytogenetic tool that is being adopted for diagnostic evaluation of genomic imbalances and study disease mechanisms and pathogenesis. We report on the design and use, of a custom whole-genome oligonucleotide-based array (called KaryoArray®v3.0; Agilent-based 8 × 60 K) for diagnostic setting, which was able to detect new and unexpected rearrangements in 11/63 (~17.5%) of previous known pathological cases associated with known genetic disorders, and in the second step it identified at least one causal genomic imbalance responsible of the phenotype in ~20% of patients with psychomotor development delay and/or intellectual disability. To validate the array, first; we blindly tested 120 samples; 63 genomic imbalances that had previously been detected by karyotyping, FISH and/or MLPA, and 57 sex-matched control samples from healthy individuals; secondly a prospective study of 540 patients with intellectual disabilities, autism spectrum disorder and multiple congenital anomalies were evaluated to confirm the utility of the tool. These data indicate that implementation of array technologies as the first-tier test may reveal that additional genomic imbalances could co-exist in patients with trisomies and classical del/dup syndromes, suggesting that aCGH may also be indicated in these individuals, at least when phenotype does not match completely with genotype. Copyright © 2013 Wiley Periodicals, Inc.

  6. GASOLINE VEHICLE EXHAUST PARTICLE SAMPLING STUDY

    Energy Technology Data Exchange (ETDEWEB)

    Kittelson, D; Watts, W; Johnson, J; Zarling, D Schauer,J Kasper, K; Baltensperger, U; Burtscher, H

    2003-08-24

    The University of Minnesota collaborated with the Paul Scherrer Institute, the University of Wisconsin (UWI) and Ricardo, Inc to physically and chemically characterize the exhaust plume from recruited gasoline spark ignition (SI) vehicles. The project objectives were: (1) Measure representative particle size distributions from a set of on-road SI vehicles and compare these data to similar data collected on a small subset of light-duty gasoline vehicles tested on a chassis dynamometer with a dilution tunnel using the Unified Drive Cycle, at both room temperature (cold start) and 0 C (cold-cold start). (2) Compare data collected from SI vehicles to similar data collected from Diesel engines during the Coordinating Research Council E-43 project. (3) Characterize on-road aerosol during mixed midweek traffic and Sunday midday periods and determine fleet-specific emission rates. (4) Characterize bulk- and size-segregated chemical composition of the particulate matter (PM) emitted in the exhaust from the gasoline vehicles. Particle number concentrations and size distributions are strongly influenced by dilution and sampling conditions. Laboratory methods were evaluated to dilute SI exhaust in a way that would produce size distributions that were similar to those measured during laboratory experiments. Size fractionated samples were collected for chemical analysis using a nano-microorifice uniform deposit impactor (nano-MOUDI). In addition, bulk samples were collected and analyzed. A mixture of low, mid and high mileage vehicles were recruited for testing during the study. Under steady highway cruise conditions a significant particle signature above background was not measured, but during hard accelerations number size distributions for the test fleet were similar to modern heavy-duty Diesel vehicles. Number emissions were much higher at high speed and during cold-cold starts. Fuel specific number emissions range from 1012 to 3 x 1016 particles/kg fuel. A simple

  7. Screening of a long-term sample set reveals two Ranavirus lineages in British herpetofauna.

    Directory of Open Access Journals (Sweden)

    Stephen J Price

    Full Text Available Reports of severe disease outbreaks in amphibian communities in mainland Europe due to strains of the common midwife toad virus (CMTV-like clade of Ranavirus are increasing and have created concern due to their considerable population impacts. In Great Britain, viruses in another clade of Ranavirus-frog virus 3 (FV3-like-have caused marked declines of common frog (Rana temporaria populations following likely recent virus introductions. The British public has been reporting mortality incidents to a citizen science project since 1992, with carcasses submitted for post-mortem examination, resulting in a long-term tissue archive spanning 25 years. We screened this archive for ranavirus (458 individuals from 228 incidents using molecular methods and undertook preliminary genotyping of the ranaviruses detected. In total, ranavirus was detected in 90 individuals from 41 incidents focused in the north and south of England. The majority of detections involved common frogs (90% but also another anuran, a caudate and a reptile. Most incidents were associated with FV3-like viruses but two, separated by 300 km and 16 years, involved CMTV-like viruses. These British CMTV-like viruses were more closely related to ranaviruses from mainland Europe than to each other and were estimated to have diverged at least 458 years ago. This evidence of a CMTV-like virus in Great Britain in 1995 represents the earliest confirmed case of a CMTV associated with amphibians and raises important questions about the history of ranavirus in Great Britain and the epidemiology of CMTV-like viruses. Despite biases present in the opportunistic sample used, this study also demonstrates the role of citizen science projects in generating resources for research and the value of maintaining long-term wildlife tissue archives.

  8. Screening of a long-term sample set reveals two Ranavirus lineages in British herpetofauna.

    Science.gov (United States)

    Price, Stephen J; Wadia, Alexandra; Wright, Owen N; Leung, William T M; Cunningham, Andrew A; Lawson, Becki

    2017-01-01

    Reports of severe disease outbreaks in amphibian communities in mainland Europe due to strains of the common midwife toad virus (CMTV)-like clade of Ranavirus are increasing and have created concern due to their considerable population impacts. In Great Britain, viruses in another clade of Ranavirus-frog virus 3 (FV3)-like-have caused marked declines of common frog (Rana temporaria) populations following likely recent virus introductions. The British public has been reporting mortality incidents to a citizen science project since 1992, with carcasses submitted for post-mortem examination, resulting in a long-term tissue archive spanning 25 years. We screened this archive for ranavirus (458 individuals from 228 incidents) using molecular methods and undertook preliminary genotyping of the ranaviruses detected. In total, ranavirus was detected in 90 individuals from 41 incidents focused in the north and south of England. The majority of detections involved common frogs (90%) but also another anuran, a caudate and a reptile. Most incidents were associated with FV3-like viruses but two, separated by 300 km and 16 years, involved CMTV-like viruses. These British CMTV-like viruses were more closely related to ranaviruses from mainland Europe than to each other and were estimated to have diverged at least 458 years ago. This evidence of a CMTV-like virus in Great Britain in 1995 represents the earliest confirmed case of a CMTV associated with amphibians and raises important questions about the history of ranavirus in Great Britain and the epidemiology of CMTV-like viruses. Despite biases present in the opportunistic sample used, this study also demonstrates the role of citizen science projects in generating resources for research and the value of maintaining long-term wildlife tissue archives.

  9. The Study on Mental Health at Work: Design and sampling.

    Science.gov (United States)

    Rose, Uwe; Schiel, Stefan; Schröder, Helmut; Kleudgen, Martin; Tophoven, Silke; Rauch, Angela; Freude, Gabriele; Müller, Grit

    2017-08-01

    The Study on Mental Health at Work (S-MGA) generates the first nationwide representative survey enabling the exploration of the relationship between working conditions, mental health and functioning. This paper describes the study design, sampling procedures and data collection, and presents a summary of the sample characteristics. S-MGA is a representative study of German employees aged 31-60 years subject to social security contributions. The sample was drawn from the employment register based on a two-stage cluster sampling procedure. Firstly, 206 municipalities were randomly selected from a pool of 12,227 municipalities in Germany. Secondly, 13,590 addresses were drawn from the selected municipalities for the purpose of conducting 4500 face-to-face interviews. The questionnaire covers psychosocial working and employment conditions, measures of mental health, work ability and functioning. Data from personal interviews were combined with employment histories from register data. Descriptive statistics of socio-demographic characteristics and logistic regressions analyses were used for comparing population, gross sample and respondents. In total, 4511 face-to-face interviews were conducted. A test for sampling bias revealed that individuals in older cohorts participated more often, while individuals with an unknown educational level, residing in major cities or with a non-German ethnic background were slightly underrepresented. There is no indication of major deviations in characteristics between the basic population and the sample of respondents. Hence, S-MGA provides representative data for research on work and health, designed as a cohort study with plans to rerun the survey 5 years after the first assessment.

  10. Microsatellite DNA reveals population genetic differentiation among sprat (Sprattus sprattus) sampled throughout the Northeast Atlantic, including Norwegian fjords

    DEFF Research Database (Denmark)

    Glover, Kevin A.; Skaala, Øystein; Limborg, Morten

    2011-01-01

    Glover, K. A., Skaala, Ø., Limborg, M., Kvamme, C., and Torstensen, E. Microsatellite DNA reveals population genetic differentiation among sprat (Sprattus sprattus) sampled throughout the Northeast Atlantic, including Norwegian fjords. – ICES Journal of Marine Science, 68: 2145–2151. Sprat (Sprat...... display population genetic differentiation throughout the Northeast Atlantic, and there may be limited connectivity between Norwegian fjord and sea-going populations....

  11. Ficolin-2 reveals different analytical and biological properties dependent on different sample handling procedures

    DEFF Research Database (Denmark)

    Hein, Estrid; Bay, Jakob T; Munthe-Fog, Lea

    2013-01-01

    mediated formation of the terminal complement complex was observed under the applied assay conditions. In conclusion, our results show that Ficolin-2 is a promiscuous molecule and that care should be taken during sampling, handling and matrix chosen for measurement of Ficolin-2 levels and activity....

  12. Comparative Study of element composition of some honey samples ...

    African Journals Online (AJOL)

    The study was carried out at the Federal College of Forestry, Ibadan with seven honey samples were randomly selected within Ibadan metropolis, labeled as: Sample A (Forestry Honey), Sample B(Pure Honey), Sample C (Mr. Honey), Sample D (Taraba Honey), Sample E (Sokoto Honey), Sample F (Saki Honey), and ...

  13. Variability Study of the S5 Sample

    Indian Academy of Sciences (India)

    2016-01-27

    Jan 27, 2016 ... We present the results of flux density monitoring of the S5 sample at 5GHz with the Urumqi 25-m radio telescope during Dec. 2008 and Nov. 2009. Most sources exhibited > 2% rms variation in our one-year monitoring. Twenty-five highly variable sources were detected at a confidence level of 99%. Weaker ...

  14. Ultradeep 16S rRNA sequencing analysis of geographically similar but diverse unexplored marine samples reveal varied bacterial community composition.

    Directory of Open Access Journals (Sweden)

    Chairmandurai Aravindraja

    Full Text Available BACKGROUND: Bacterial community composition in the marine environment differs from one geographical location to another. Reports that delineate the bacterial diversity of different marine samples from geographically similar location are limited. The present study aims to understand whether the bacterial community compositions from different marine samples harbour similar bacterial diversity since these are geographically related to each other. METHODS AND PRINCIPAL FINDINGS: In the present study, 16S rRNA deep sequencing analysis targeting V3 region was performed using Illumina bar coded sequencing. A total of 22.44 million paired end reads were obtained from the metagenomic DNA of Marine sediment, Rhizosphere sediment, Seawater and the epibacterial DNA of Seaweed and Seagrass. Diversity index analysis revealed that Marine sediment has the highest bacterial diversity and the least bacterial diversity was observed in Rhizosphere sediment. Proteobacteria, Actinobacteria and Bacteroidetes were the dominant taxa present in all the marine samples. Nearly 62-71% of rare species were identified in all the samples and most of these rare species were unique to a particular sample. Further taxonomic assignment at the phylum and genus level revealed that the bacterial community compositions differ among the samples. CONCLUSION: This is the first report that supports the fact that, bacterial community composition is specific for specific samples irrespective of its similar geographical location. Existence of specific bacterial community for each sample may drive overall difference in bacterial structural composition of each sample. Further studies like whole metagenomic sequencing will throw more insights to the key stone players and its interconnecting metabolic pathways. In addition, this is one of the very few reports that depicts the unexplored bacterial diversity of marine samples (Marine sediment, Rhizosphere sediment, Seawater and the host associated

  15. Ultradeep 16S rRNA sequencing analysis of geographically similar but diverse unexplored marine samples reveal varied bacterial community composition.

    Science.gov (United States)

    Aravindraja, Chairmandurai; Viszwapriya, Dharmaprakash; Karutha Pandian, Shunmugiah

    2013-01-01

    Bacterial community composition in the marine environment differs from one geographical location to another. Reports that delineate the bacterial diversity of different marine samples from geographically similar location are limited. The present study aims to understand whether the bacterial community compositions from different marine samples harbour similar bacterial diversity since these are geographically related to each other. In the present study, 16S rRNA deep sequencing analysis targeting V3 region was performed using Illumina bar coded sequencing. A total of 22.44 million paired end reads were obtained from the metagenomic DNA of Marine sediment, Rhizosphere sediment, Seawater and the epibacterial DNA of Seaweed and Seagrass. Diversity index analysis revealed that Marine sediment has the highest bacterial diversity and the least bacterial diversity was observed in Rhizosphere sediment. Proteobacteria, Actinobacteria and Bacteroidetes were the dominant taxa present in all the marine samples. Nearly 62-71% of rare species were identified in all the samples and most of these rare species were unique to a particular sample. Further taxonomic assignment at the phylum and genus level revealed that the bacterial community compositions differ among the samples. This is the first report that supports the fact that, bacterial community composition is specific for specific samples irrespective of its similar geographical location. Existence of specific bacterial community for each sample may drive overall difference in bacterial structural composition of each sample. Further studies like whole metagenomic sequencing will throw more insights to the key stone players and its interconnecting metabolic pathways. In addition, this is one of the very few reports that depicts the unexplored bacterial diversity of marine samples (Marine sediment, Rhizosphere sediment, Seawater) and the host associated marine samples (Seaweed and Seagrass) at higher depths from

  16. Exhaustive sampling of docking poses reveals binding hypotheses for propafenone type inhibitors of P-glycoprotein

    National Research Council Canada - National Science Library

    Klepsch, Freya; Chiba, Peter; Ecker, Gerhard F

    2011-01-01

    .... Therefore, structure-based design studies have to rely on protein homology models. In order to identify binding hypotheses for propafenone-type P-gp inhibitors, five different propafenone derivatives with known structure-activity relationship (SAR...

  17. Temporal Sampling of White Band Disease Infected Corals Reveals Complex and Dynamic Bacterial Communities

    Science.gov (United States)

    Gignoux-Wolfsohn, S.; Vollmer, S. V.; Aronson, F. M.

    2016-02-01

    White band disease (WBD) is a coral disease that is currently decimating populations of the endangered staghorn coral, Acropora cervicornis and elkhorn coral, A. palmata across the Caribbean. Since it was first reported in 1979, WBD has killed 95% of these critical reef-building Caribbean corals. WBD is infectious; it can be transmitted through the water column or by a corallivorous snail. While previous research shows that WBD is likely caused by bacteria, identification of a specific pathogen or pathogens has remained elusive. Much of the difficulty of understanding the etiology of the disease comes from a lack of information about how existing bacterial communities respond to disease and separating initial from secondary colonizers. In order to address this lack of information, we performed a fully-crossed tank infection experiment. We exposed healthy corals from two different sites to disease and healthy (control) homogenates from both sites, replicating genotype across tanks. We sampled every coral at three time points: before inoculation with the homogenate, after inoculation, and when the coral showed signs of disease. We then performed 16S rRNA gene sequencing on the Illumina HiSeq 2000. We saw significant differences between time points and disease state. Interestingly, at the first time point (time one) we observed differences between genotypes: every fragment from some genotypes was dominated by Endozoicomonas, while other genotypes were not dominated by one family. At time two we saw an increase in abundance of Alteromonadaceae and Flavobacteriaceae in all corals, and a larger increase in disease-exposed corals. At time three, we saw another increase in Flavobacteriaceae abundance in diseased corals, as well as an introduction of Francisella to diseased corals. While Flavobacteriaceae and Francisella were proposed as potential pathogens, their increase at time three suggests they may be secondary colonizers or opportunists. In genotypes that were

  18. Monitoring studies should consider temporal variability to reveal relations between cyanobacterial abundance and environmental variables

    Directory of Open Access Journals (Sweden)

    JULIANA WOJCIECHOWSKI

    2015-09-01

    Full Text Available One of the main goals of monitoring cyanobacteria blooms in aquatic environments is to reveal the relationship between cyanobacterial abundance and environmental variables. Studies typically correlate data that were simultaneously sampled. However, samplings occur sparsely over time and may not reveal the short-term responses of cyanobacterial abundance to environmental changes. In this study, we tested the hypothesis that stronger cyanobacteria x environment relationships in monitoring are found when the temporal variability of sampling points is incorporated in the statistical analyses. To this end, we investigated relationships between cyanobacteria and seven environmental variables that were sampled twice yearly for three years across 11 reservoirs, and data from an intensive monitoring in one of these reservoirs. Poor correlations were obtained when correlating data simultaneously sampled. In fact, the 'highly recurrent' role of phosphorus in cyanobacteria blooms is not properly observed in all sampling periods. On the other hand, the strongest correlation values for the total phosphorus x cyanobacteria relationship were observed when we used the variation of sampling points. We have also shown that environment variables better explain cyanobacteria when a time lag is considered. We conclude that, in cyanobacteria monitoring, the best approach to reveal determinants of cyanobacteria blooms is to consider environmental variability.

  19. Erosion patterns in the Changjiang (Yangtze River) catchment revealed by bulk-sample versus single-mineral provenance budgets

    Science.gov (United States)

    Vezzoli, Giovanni; Garzanti, Eduardo; Limonta, Mara; Andò, Sergio; Yang, Shouye

    2016-05-01

    The Changjiang, the fourth longest river on Earth and the largest in Eurasia, has a complex sediment-routing system presently interrupted by the Three Gorges Dam, the world's largest hydroelectric engineering project. To study sediment-generation processes in the huge catchment and compare the different erosion patterns obtained by different methodological approaches, high-resolution petrographic and heavy-mineral analyses were performed on sands from the trunk river and its major tributaries. The frequency distributions of diverse groups of detrital amphiboles were also investigated. Rigorous statistical methods were used to define end-members, evaluate mineralogical variability, assess similarities among samples, and eventually calculate the relative contributions from each major tributary to the trunk river by forward end-member modelling of integrated compositional data. The litho-quartzose sand with few heavy minerals generated in Tibetan headwaters evolves downstream to feldspatho-litho-quartzose with medium-rank metamorphic rock fragments and moderately rich amphibole-epidote suites. Sand across the Sichuan basin and as far as the Three Gorges Dam is enriched in mafic volcanic, clinopyroxene, and carbonate grains eroded from Permian basalts and Paleozoic strata of the South China Block. The final (Yangtze) tract is characterized by litho-feldspatho-quartzose sand with moderately poor, amphibole-dominated suites with epidote, clinopyroxene, and garnet. The orogenic compositional signature acquired in the upper part of the basin is thus carried all the way to the Chinese passive margin, as observed also for the Yellow River in the north. Even after long-distance transport across wide continental areas, detrital modes thus reveal the tectonic character of the source rather than the geodynamic environment of the sink. Quantitative provenance analysis indicates that left-bank tributaries draining the Longmen and Qinlin mountains supply most of the sand reaching

  20. Replicating studies in which samples of participants respond to samples of stimuli.

    Science.gov (United States)

    Westfall, Jacob; Judd, Charles M; Kenny, David A

    2015-05-01

    In a direct replication, the typical goal is to reproduce a prior experimental result with a new but comparable sample of participants in a high-powered replication study. Often in psychology, the research to be replicated involves a sample of participants responding to a sample of stimuli. In replicating such studies, we argue that the same criteria should be used in sampling stimuli as are used in sampling participants. Namely, a new but comparable sample of stimuli should be used to ensure that the original results are not due to idiosyncrasies of the original stimulus sample, and the stimulus sample must often be enlarged to ensure high statistical power. In support of the latter point, we discuss the fact that in experiments involving samples of stimuli, statistical power typically does not approach 1 as the number of participants goes to infinity. As an example of the importance of sampling new stimuli, we discuss the bygone literature on the risky shift phenomenon, which was almost entirely based on a single stimulus sample that was later discovered to be highly unrepresentative. We discuss the use of both resampled and expanded stimulus sets, that is, stimulus samples that include the original stimuli plus new stimuli. © The Author(s) 2015.

  1. Sampling

    CERN Document Server

    Thompson, Steven K

    2012-01-01

    Praise for the Second Edition "This book has never had a competitor. It is the only book that takes a broad approach to sampling . . . any good personal statistics library should include a copy of this book." —Technometrics "Well-written . . . an excellent book on an important subject. Highly recommended." —Choice "An ideal reference for scientific researchers and other professionals who use sampling." —Zentralblatt Math Features new developments in the field combined with all aspects of obtaining, interpreting, and using sample data Sampling provides an up-to-date treat

  2. Evidentials and advertising: a sample study

    Directory of Open Access Journals (Sweden)

    Laura Cruz García

    2017-07-01

    Full Text Available This paper explores the use of evidential devices in press adverts in English in a compilation of original advertisements. Due to the appellative nature of advertising discourse, I think that these texts are likely to convey source of knowledge through evidentials as an advertising strategy in order to pragmatically manifest a higher level of credibility and reliability of the information presented concerning the products and the brands. The selected corpus of adverts will allow us to focus special attention on this particular genre and on how evidentials are used, in the fashion of other works carried out in other textual genres (cf. Fox, 2001; Kaplan, 2007; Marín-Arrese, 2004, 2007; Ortega-Barrera and Torres-Ramírez, 2010. Evidentials are studied as part of a set of persuasion strategies used by different linguistic communities in the discourse of advertising (Block de Behar, 1992; Cook, 1992; Cortés de los Ríos, 2001; Pavitt, 2000; Rein, 1982. Conclusions will report on how evidentials are used in print adverts, and whether a type of evidential device prevails over the rest.

  3. Spectrum of Cytogenomic Abnormalities Revealed by Array Comparative Genomic Hybridization on Products of Conception Culture Failure and Normal Karyotype Samples.

    Science.gov (United States)

    Zhou, Qinghua; Wu, Shen-Yin; Amato, Katherine; DiAdamo, Autumn; Li, Peining

    2016-03-20

    Approximately 30% of pregnancies after implantation end up in spontaneous abortions, and 50% of them are caused by chromosomal abnormalities. However, the spectrum of genomic copy number variants (CNVs) in products of conception (POC) and the underlying gene-dosage-sensitive mechanisms causing spontaneous abortions remain largely unknown. In this study, array comparative genomic hybridization (aCGH) analysis was performed as a salvage procedure for 128 POC culture failure (POC-CF) samples and as a supplemental procedure for 106 POC normal karyotype (POC-NK) samples. Chromosomal abnormalities were detected in 10% of POC-CF and pathogenic CNVs were detected in 3.9% of POC-CF and 5.7% of POC-NK samples. Compiled results from this study and relevant case series through a literature review demonstrated an abnormality detection rate (ADR) of 35% for chromosomal abnormalities in POC-CF samples, 3.7% for pathogenic CNVs in POC-CF samples, and 4.6% for pathogenic CNVs in POC-NK samples. Ingenuity Pathway Analysis (IPA) was performed on the genes from pathogenic CNVs found in POC samples. The denoted primary gene networks suggested that apoptosis and cell proliferation pathways are involved in miscarriage. In summary, a similar spectrum of cytogenomic abnormalities was observed in POC culture success and POC-CF samples. A threshold effect correlating the number of dosage-sensitive genes in a chromosome with the observed frequency of autosomal trisomy is proposed. A rationalized approach using firstly fluorescence in situ hybridization (FISH) testing with probes of chromosomes X/Y/18, 13/21, and 15/16/22 for common aneuploidies and polyploidies and secondly aCGH for other cytogenomic abnormalities is recommended for POC-CF samples. Copyright © 2016 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

  4. Assessment of minimum sample sizes required to adequately represent diversity reveals inadequacies in datasets of domestic dog mitochondrial DNA.

    Science.gov (United States)

    Webb, Kristen; Allard, Marc

    2010-02-01

    Evolutionary and forensic studies commonly choose the mitochondrial control region as the locus for which to evaluate the domestic dog. However, the number of dogs that need to be sampled in order to represent the control region variation present in the worldwide population is yet to be determined. Following the methods of Pereira et al. (2004), we have demonstrated the importance of surveying the complete control region rather than only the popular left domain. We have also evaluated sample saturation in terms of the haplotype number and the number of polymorphisms within the control region. Of the most commonly cited evolutionary research, only a single study has adequately surveyed the domestic dog population, while all forensic studies have failed to meet the minimum values. We recommend that future studies consider dataset size when designing experiments and ideally sample both domains of the control region in an appropriate number of domestic dogs.

  5. [Respondent-Driven Sampling: a new sampling method to study visible and hidden populations].

    Science.gov (United States)

    Mantecón, Alejandro; Juan, Montse; Calafat, Amador; Becoña, Elisardo; Román, Encarna

    2008-01-01

    The paper introduces a variant of chain-referral sampling: respondent-driven sampling (RDS). This sampling method shows that methods based on network analysis can be combined with the statistical validity of standard probability sampling methods. In this sense, RDS appears to be a mathematical improvement of snowball sampling oriented to the study of hidden populations. However, we try to prove its validity with populations that are not within a sampling frame but can nonetheless be contacted without difficulty. The basics of RDS are explained through our research on young people (aged 14 to 25) who go clubbing, consume alcohol and other drugs, and have sex. Fieldwork was carried out between May and July 2007 in three Spanish regions: Baleares, Galicia and Comunidad Valenciana. The presentation of the study shows the utility of this type of sampling when the population is accessible but there is a difficulty deriving from the lack of a sampling frame. However, the sample obtained is not a random representative one in statistical terms of the target population. It must be acknowledged that the final sample is representative of a 'pseudo-population' that approximates to the target population but is not identical to it.

  6. Comparative Studies of Gasoline Samples Used in Nigeria | Faruq ...

    African Journals Online (AJOL)

    Comparative analysis was carried out on five samples of gasoline in the Nigerian market based on octane number, sulphur content, Reid vapour pressure, specific gravity, boiling point characteristics and chemical content. The result revealed that, Nigerian and Kuwait gasolines have low octane numbers in comparison to ...

  7. Do Research Findings Apply to My Students? Examining Study Samples and Sampling

    Science.gov (United States)

    Cook, Bryan G.; Cook, Lysandra

    2017-01-01

    Special educators are urged to use research findings to inform their instruction in order to improve student outcomes. However, it can be difficult to tell whether and how research findings apply to one's own students. In this article, we discuss how special educators can consider the samples and the sampling methods in studies to examine the…

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

    Science.gov (United States)

    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.

  9. Microdialysis Sampling from Wound Fluids Enables Quantitative Assessment of Cytokines, Proteins, and Metabolites Reveals Bone Defect-Specific Molecular Profiles.

    Science.gov (United States)

    Förster, Yvonne; Schmidt, Johannes R; Wissenbach, Dirk K; Pfeiffer, Susanne E M; Baumann, Sven; Hofbauer, Lorenz C; von Bergen, Martin; Kalkhof, Stefan; Rammelt, Stefan

    2016-01-01

    Bone healing involves a variety of different cell types and biological processes. Although certain key molecules have been identified, the molecular interactions of the healing progress are not completely understood. Moreover, a clinical routine for predicting the quality of bone healing after a fracture in an early phase is missing. This is mainly due to a lack of techniques to comprehensively screen for cytokines, growth factors and metabolites at their local site of action. Since all soluble molecules of interest are present in the fracture hematoma, its in-depth assessment could reveal potential markers for the monitoring of bone healing. Here, we describe an approach for sampling and quantification of cytokines and metabolites by using microdialysis, combined with solid phase extractions of proteins from wound fluids. By using a control group with an isolated soft tissue wound, we could reveal several bone defect-specific molecular features. In bone defect dialysates the neutrophil chemoattractants CXCL1, CXCL2 and CXCL3 were quantified with either a higher or earlier response compared to dialysate from soft tissue wound. Moreover, by analyzing downstream adaptions of the cells on protein level and focusing on early immune response, several proteins involved in the immune cell migration and activity could be identified to be specific for the bone defect group, e.g. immune modulators, proteases and their corresponding inhibitors. Additionally, the metabolite screening revealed different profiles between the bone defect group and the control group. In summary, we identified potential biomarkers to indicate imbalanced healing progress on all levels of analysis.

  10. Microdialysis Sampling from Wound Fluids Enables Quantitative Assessment of Cytokines, Proteins, and Metabolites Reveals Bone Defect-Specific Molecular Profiles.

    Directory of Open Access Journals (Sweden)

    Yvonne Förster

    Full Text Available Bone healing involves a variety of different cell types and biological processes. Although certain key molecules have been identified, the molecular interactions of the healing progress are not completely understood. Moreover, a clinical routine for predicting the quality of bone healing after a fracture in an early phase is missing. This is mainly due to a lack of techniques to comprehensively screen for cytokines, growth factors and metabolites at their local site of action. Since all soluble molecules of interest are present in the fracture hematoma, its in-depth assessment could reveal potential markers for the monitoring of bone healing. Here, we describe an approach for sampling and quantification of cytokines and metabolites by using microdialysis, combined with solid phase extractions of proteins from wound fluids. By using a control group with an isolated soft tissue wound, we could reveal several bone defect-specific molecular features. In bone defect dialysates the neutrophil chemoattractants CXCL1, CXCL2 and CXCL3 were quantified with either a higher or earlier response compared to dialysate from soft tissue wound. Moreover, by analyzing downstream adaptions of the cells on protein level and focusing on early immune response, several proteins involved in the immune cell migration and activity could be identified to be specific for the bone defect group, e.g. immune modulators, proteases and their corresponding inhibitors. Additionally, the metabolite screening revealed different profiles between the bone defect group and the control group. In summary, we identified potential biomarkers to indicate imbalanced healing progress on all levels of analysis.

  11. Genotyping of samples from German patients with ocular, cerebral and systemic toxoplasmosis reveals a predominance of Toxoplasma gondii type II.

    Science.gov (United States)

    Herrmann, Daland C; Maksimov, Pavlo; Hotop, Andrea; Groß, Uwe; Däubener, Walter; Liesenfeld, Oliver; Pleyer, Uwe; Conraths, Franz J; Schares, Gereon

    2014-10-01

    Toxoplasmosis is an important zoonosis transmitted from animals to humans world-wide. In order to determine Toxoplasma gondii genotypes in individuals living in Germany and to compare findings with those in animals, we analysed nine independent and unlinked genetic markers (nSAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico) by PCR-RFLP in 83 archived T. gondii-positive DNA samples from patients with ocular toxoplasmosis (n=35), toxoplasmic encephalitis (n=32), systemic toxoplasmosis after bone-marrow transplantation (n=15) and congenital toxoplasmosis (n=1). In 46 of these 83 samples the presence of T. gondii DNA was confirmed by conventional end-point PCR. Among these, 17 T. gondii-positive samples were typed at all nine loci. The majority (15/17, 88.2%) of these samples were of T. gondii type II (i.e., including both, the Apico type II and Apico type I variants). In addition, in one sample a T. gondii type II/type III allele combination and in another sample a T. gondii genotype displaying type III alleles at all markers was observed. In the remaining 11 samples, in which T. gondii could only be partially typed, exclusively type II (n=10) or type III (n=1) alleles were observed. Results of the present study suggest that the majority of patients in Germany are infected with type II T. gondii regardless of the clinical manifestation of toxoplasmosis. This finding is in accord with the predominance of type II T. gondii in oocysts isolated from cats and in tissues of other intermediate hosts in Germany. Copyright © 2014 Elsevier GmbH. All rights reserved.

  12. Considerations in determining sample size for pilot studies.

    Science.gov (United States)

    Hertzog, Melody A

    2008-04-01

    There is little published guidance concerning how large a pilot study should be. General guidelines, for example using 10% of the sample required for a full study, may be inadequate for aims such as assessment of the adequacy of instrumentation or providing statistical estimates for a larger study. This article illustrates how confidence intervals constructed around a desired or anticipated value can help determine the sample size needed. Samples ranging in size from 10 to 40 per group are evaluated for their adequacy in providing estimates precise enough to meet a variety of possible aims. General sample size guidelines by type of aim are offered.

  13. Metabolomics study of cereal grains reveals the discriminative metabolic markers associated with anatomical compartments

    Directory of Open Access Journals (Sweden)

    A.A. Moazzami

    2015-06-01

    Full Text Available This study used NMR-based metabolomics to compare the metabolic profile of different anatomical compartments of cereal grains i.e. bran and endosperm in order to gain further insightsinto their possible role in the beneficial health effects of whole grain products (WG. Polar watersoluble metabolites in 64 bran and endosperm, samples from rye and wheat were observed using600 MHz NMR. Bran samples had higher contents of 12 metabolites than endosperm samples. A comparative approach revealed higher contents of azelaic acid and sebacic acid in bran than in endosperm. In a pilot study, the consumption of WG rye bread (485 g caused NMR signals in 24h urine corresponding to azelaic acid. The relatively high abundance, anatomical specificity, patternof metabolism, urinary excretion in human, antibacterial, and anticancer activities suggest further studying of azelaic acid when exposure to WG or beneficial effects of WG are investigated.

  14. Sample Size and Statistical Power Calculation in Genetic Association Studies

    Directory of Open Access Journals (Sweden)

    Eun Pyo Hong

    2012-06-01

    Full Text Available A sample size with sufficient statistical power is critical to the success of genetic association studies to detect causal genes of human complex diseases. Genome-wide association studies require much larger sample sizes to achieve an adequate statistical power. We estimated the statistical power with increasing numbers of markers analyzed and compared the sample sizes that were required in case-control studies and case-parent studies. We computed the effective sample size and statistical power using Genetic Power Calculator. An analysis using a larger number of markers requires a larger sample size. Testing a single-nucleotide polymorphism (SNP marker requires 248 cases, while testing 500,000 SNPs and 1 million markers requires 1,206 cases and 1,255 cases, respectively, under the assumption of an odds ratio of 2, 5% disease prevalence, 5% minor allele frequency, complete linkage disequilibrium (LD, 1:1 case/control ratio, and a 5% error rate in an allelic test. Under a dominant model, a smaller sample size is required to achieve 80% power than other genetic models. We found that a much lower sample size was required with a strong effect size, common SNP, and increased LD. In addition, studying a common disease in a case-control study of a 1:4 case-control ratio is one way to achieve higher statistical power. We also found that case-parent studies require more samples than case-control studies. Although we have not covered all plausible cases in study design, the estimates of sample size and statistical power computed under various assumptions in this study may be useful to determine the sample size in designing a population-based genetic association study.

  15. Genetic analysis of historic western Great Lakes region wolf samples reveals early Canis lupus/lycaon hybridization.

    Science.gov (United States)

    Wheeldon, Tyler; White, Bradley N

    2009-02-23

    The genetic status of wolves in the western Great Lakes region has received increased attention following the decision to remove them from protection under the US Endangered Species Act. A recent study of mitochondrial DNA has suggested that the recovered wolf population is not genetically representative of the historic population. We present microsatellite genotype data on three historic samples and compare them with extant populations, and interpret published genetic data to show that the pre-recovery population was admixed over a century ago by eastern wolf (Canis lycaon) and grey wolf (Canis lupus) hybridization. The DNA profiles of the historic samples are similar to those of extant animals in the region, suggesting that the current Great Lakes wolves are representative of the historic population.

  16. Benchmarking sample preparation/digestion protocols reveals tube-gel being a fast and repeatable method for quantitative proteomics.

    Science.gov (United States)

    Muller, Leslie; Fornecker, Luc; Van Dorsselaer, Alain; Cianférani, Sarah; Carapito, Christine

    2016-12-01

    Sample preparation, typically by in-solution or in-gel approaches, has a strong influence on the accuracy and robustness of quantitative proteomics workflows. The major benefit of in-gel procedures is their compatibility with detergents (such as SDS) for protein solubilization. However, SDS-PAGE is a time-consuming approach. Tube-gel (TG) preparation circumvents this drawback as it involves directly trapping the sample in a polyacrylamide gel matrix without electrophoresis. We report here the first global label-free quantitative comparison between TG, stacking gel (SG), and basic liquid digestion (LD). A series of UPS1 standard mixtures (at 0.5, 1, 2.5, 5, 10, and 25 fmol) were spiked in a complex yeast lysate background. TG preparation allowed more yeast proteins to be identified than did the SG and LD approaches, with mean numbers of 1979, 1788, and 1323 proteins identified, respectively. Furthermore, the TG method proved equivalent to SG and superior to LD in terms of the repeatability of the subsequent experiments, with mean CV for yeast protein label-free quantifications of 7, 9, and 10%. Finally, known variant UPS1 proteins were successfully detected in the TG-prepared sample within a complex background with high sensitivity. All the data from this study are accessible on ProteomeXchange (PXD003841). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Sample size computation for association studies using case–parents ...

    Indian Academy of Sciences (India)

    sample size for case–control association studies is discussed. Materials and methods. Parameter settings. We consider a candidate locus with two alleles A and a where. A is putatively associated with the disease status (increasing. Keywords. sample size; association tests; genotype relative risk; power; autism. Journal of ...

  18. Metagenomic analysis of a sample from a patient with respiratory tract infection reveals the presence of a γ-papillomavirus

    Directory of Open Access Journals (Sweden)

    Marta eCanuti

    2014-07-01

    Full Text Available Previously unknown or unexpected pathogens may be responsible for that proportion of respiratory diseases in which a causative agent cannot be identified. The application of broad-spectrum, sequence independent virus discovery techniques may be useful to reduce this proportion and widen our knowledge about respiratory pathogens. Thanks to the availability of high throughput sequencing (HTS technology, it became today possible to detect viruses which are present at a very low load, but the clinical relevance of those viruses must be investigated. In this study we used VIDISCA-454, a restriction enzyme based virus discovery method that utilizes Roche 454 HTS system, on a nasal swab collected from a subject with respiratory complaints. A γ-papillomavirus was detected (complete genome: 7142 bp and its role in disease was investigated. Respiratory samples collected both during the acute phase of the illness and two weeks after full recovery contained the virus. The patient presented antibodies directed against the virus but there was no difference between IgG levels in blood samples collected during the acute phase and two weeks after full recovery. We therefore concluded that the detected γ-papillomavirus is unlikely to be the causative agent of the respiratory complaints and its presence in the nose of the patient is not related to the disease. Although HTS based virus discovery techniques proved their great potential as a tool to clarify the aetiology of some infectious diseases, the obtained information must be subjected to cautious interpretations. This study underlines the crucial importance of performing careful investigations on viruses identified when applying sensitive virus discovery techniques, since the mere identification of a virus and its presence in a clinical sample are not satisfactory proofs to establish a causative link with a disease.

  19. Faecal microbiota study reveals specific dysbiosis in spondyloarthritis.

    Science.gov (United States)

    Breban, Maxime; Tap, Julien; Leboime, Ariane; Said-Nahal, Roula; Langella, Philippe; Chiocchia, Gilles; Furet, Jean-Pierre; Sokol, Harry

    2017-09-01

    Altered microbiota composition or dysbiosis is suspected to be implicated in the pathogenesis of chronic inflammatory diseases, such as spondyloarthritis (SpA) and rheumatoid arthritis (RA). 16S ribosomal RNA gene sequencing was performed on faecal DNA isolated from stool samples in two consecutive cross-sectional cohorts, each comprising three groups of adult volunteers: SpA, RA and healthy controls (HCs). In the second study, HCs comprised a majority of aged-matched siblings of patients with known HLA-B27 status. Alpha and beta diversities were assessed using QIIME, and comparisons were performed using linear discriminant analysis effect size to examine differences between groups. In both cohorts, dysbiosis was evidenced in SpA and RA, as compared with HCs, and was disease specific. A restriction of microbiota biodiversity was detected in both disease groups. The most striking change was a twofold to threefold increased abundance of Ruminococcus gnavus in SpA, as compared with both RA and HCs that was significant in both studies and positively correlated with disease activity in patients having a history of inflammatory bowel disease (IBD). Among HCs, significant difference in microbiota composition were also detected between HLA-B27+ and HLA-B27 negative siblings, suggesting that genetic background may influence gut microbiota composition. Our results suggest that distinctive dysbiosis characterise both SpA and RA and evidence a reproducible increase in R. gnavus that appears specific for SpA and a marker of disease activity. This observation is consistent with the known proinflammatory role of this bacteria and its association with IBD. It may provide an explanation for the link that exists between SpA and IBD. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  20. Astronaut Neil Armstrong studies rock samples during geological field trip

    Science.gov (United States)

    1969-01-01

    Astronaut Neil Armstrong, commander of the Apollo 11 lunar landing mission, studies rock samples during a geological field trip to the Quitman Mountains area near the Fort Quitman ruins in far west Texas.

  1. Study of kissing molars in Turkish population sample | Yanik ...

    African Journals Online (AJOL)

    Study of kissing molars in Turkish population sample. ... refers to contacting occlusal surfaces of the impacted mandibular second and third molars. ... was to report the incidence of kissing molars (KMs), classification, incorporated pathologies, ...

  2. Ocular-following responses to white noise stimuli in humans reveal a novel nonlinearity that results from temporal sampling.

    Science.gov (United States)

    Sheliga, Boris M; Quaia, Christian; FitzGibbon, Edmond J; Cumming, Bruce G

    2016-01-01

    White noise stimuli are frequently used to study the visual processing of broadband images in the laboratory. A common goal is to describe how responses are derived from Fourier components in the image. We investigated this issue by recording the ocular-following responses (OFRs) to white noise stimuli in human subjects. For a given speed we compared OFRs to unfiltered white noise with those to noise filtered with band-pass filters and notch filters. Removing components with low spatial frequency (SF) reduced OFR magnitudes, and the SF associated with the greatest reduction matched the SF that produced the maximal response when presented alone. This reduction declined rapidly with SF, compatible with a winner-take-all operation. Removing higher SF components increased OFR magnitudes. For higher speeds this effect became larger and propagated toward lower SFs. All of these effects were quantitatively well described by a model that combined two factors: (a) an excitatory drive that reflected the OFRs to individual Fourier components and (b) a suppression by higher SF channels where the temporal sampling of the display led to flicker. This nonlinear interaction has an important practical implication: Even with high refresh rates (150 Hz), the temporal sampling introduced by visual displays has a significant impact on visual processing. For instance, we show that this distorts speed tuning curves, shifting the peak to lower speeds. Careful attention to spectral content, in the light of this nonlinearity, is necessary to minimize the resulting artifact when using white noise patterns undergoing apparent motion.

  3. Protocol for fir tree sampling for provenance studies

    Science.gov (United States)

    Meisel, Thomas; Bandoniene, Donata; Zettl, Daniela

    2014-05-01

    Isotopic (stable and radiogenic) as well as trace element fingerprinting methods used for tracing the geographical origin, rely on databases, that need to contain data sets representative of the measurands of the individual samples for a specific geographic entity. Through this work, we want to assess different sampling strategies for obtaining representative sample of fir trees (Abies sp.). Motivation for this work is the protection of the local Austrian Christmas tree market from wrongly tagged trees of non-Austrian origin. In particular, we studied three typical Christmas trees the most common species sold as Christmas tree, namely Abies nordmanniana (Nordmann Fir), from the same locality in lower Austria. For the initial tests we applied the elemental fingerprinting method, to study the suitability of the different parts of the tree applying ICP-MS analysis after complete acid digestion in a high pressure asher system (HPA-S).Needle samples from each year of life of the tree and stem wood from three different heights were analyzed for their trace element content to prove the repeatability and to find the best sampling protocol. For the analysis of the needles, the natural wax coating had to be removed in order to get reproducible results. For the analysis of stem wood only the bark was removed. As expected the data of all three trees allowed the differentiation of the individual needle ages, but interestingly enough also between the three sampling heights of the needs. Both needles and wood proved to be suitable for successful fingerprinting, but importantly, provided that sample of the same type and ages are compared. The same samples for the three trees will also be used for isotopic analysis studies to better understand the influence of age and sampling height on the representativeness of fir tree samples. Based on elemental fingerprinting alone, a successful discrimination between local (Austrian) and foreign (Danish, Irish) Christmas trees was possible.

  4. Biopsies of cicatricial conjunctivitis cases reveal highly variable sampling practice among ophthalmologists: time for national and international standardisation.

    Science.gov (United States)

    Mudhar, Hardeep Singh

    2016-06-01

    There has been no in-depth study examining the preanalytical direct immunofluorescence (DIF) biopsy phase for patients with cicatricial conjunctivitis. 90 patients with cicatricial conjunctivitis had biopsies taken for DIF. The study examined the following biopsy and clinical parameters: Age and sex of patient, unilateral or bilateral involvement, unilateral or bilateral biopsy, site of biopsy, nature of biopsy site (normal or diseased), number of biopsies per eye, size of biopsy, medium in which biopsy sent, whether buccal mucosa biopsied, whether tissue biopsied for histology (fixed in formalin) DIF results for conjunctival and buccal biopsies and final clinicopathological diagnosis. Most cases had unilateral sampling despite many cases showing bilateral disease. 15/90 cases had buccal biopsies. The conjunctival site for biopsy was not consistent from case to case. The mean maximum biopsy size was 3.3 mm length, 1 mm depth. No case was inadequate for DIF. Biopsies were obtained from conjunctiva with varying disease activity. 80/90 cases were sent in an appropriate medium permitting DIF. DIF+ biopsy rates were not affected by biopsy site disease activity. Five cases of bilateral involvement and bilateral biopsies showed only unilateral DIF+. In five cases, the conjunctival biopsies were DIF+ and the buccal biopsy was DIF-. Five cases showed in situ and invasive carcinoma seen on the accompanying formalin-fixed biopsy. DIF biopsies for cicatricial conjunctivitis showed highly variable preanalytical phase sampling practice that requires national and international standardisation to facilitate prompt diagnosis, treatment, research and audit. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  5. Adaptation of image cytometry methodology for DNA ploidy analysis of cervical epithelium samples: A pilot study

    Directory of Open Access Journals (Sweden)

    Christiane Eliza Motta Duarte

    2014-06-01

    Conclusion: Image cytometry of the cervical specimens revealed DNA aneuploidy, most probably resulting from chromosomal alterations and appearing as precancerous lesions in 65% of the cases. The adaptations implemented in this study, enabled the DNA-image cytometry to become more accessible, enhancing its extended use as an adjuvant strategy for the early screening of the cervical epithelium samples during routine analyses.

  6. Using re-sampling methods in mortality studies.

    Directory of Open Access Journals (Sweden)

    Igor Itskovich

    Full Text Available Traditional methods of computing standardized mortality ratios (SMR in mortality studies rely upon a number of conventional statistical propositions to estimate confidence intervals for obtained values. Those propositions include a common but arbitrary choice of the confidence level and the assumption that observed number of deaths in the test sample is a purely random quantity. The latter assumption may not be fully justified for a series of periodic "overlapping" studies. We propose a new approach to evaluating the SMR, along with its confidence interval, based on a simple re-sampling technique. The proposed method is most straightforward and requires neither the use of above assumptions nor any rigorous technique, employed by modern re-sampling theory, for selection of a sample set. Instead, we include all possible samples that correspond to the specified time window of the study in the re-sampling analysis. As a result, directly obtained confidence intervals for repeated overlapping studies may be tighter than those yielded by conventional methods. The proposed method is illustrated by evaluating mortality due to a hypothetical risk factor in a life insurance cohort. With this method used, the SMR values can be forecast more precisely than when using the traditional approach. As a result, the appropriate risk assessment would have smaller uncertainties.

  7. Sample size and power calculation for molecular biology studies.

    Science.gov (United States)

    Jung, Sin-Ho

    2010-01-01

    Sample size calculation is a critical procedure when designing a new biological study. In this chapter, we consider molecular biology studies generating huge dimensional data. Microarray studies are typical examples, so that we state this chapter in terms of gene microarray data, but the discussed methods can be used for design and analysis of any molecular biology studies involving high-dimensional data. In this chapter, we discuss sample size calculation methods for molecular biology studies when the discovery of prognostic molecular markers is performed by accurately controlling false discovery rate (FDR) or family-wise error rate (FWER) in the final data analysis. We limit our discussion to the two-sample case.

  8. Neuromuscular dose-response studies: determining sample size.

    Science.gov (United States)

    Kopman, A F; Lien, C A; Naguib, M

    2011-02-01

    Investigators planning dose-response studies of neuromuscular blockers have rarely used a priori power analysis to determine the minimal sample size their protocols require. Institutional Review Boards and peer-reviewed journals now generally ask for this information. This study outlines a proposed method for meeting these requirements. The slopes of the dose-response relationships of eight neuromuscular blocking agents were determined using regression analysis. These values were substituted for γ in the Hill equation. When this is done, the coefficient of variation (COV) around the mean value of the ED₅₀ for each drug is easily calculated. Using these values, we performed an a priori one-sample two-tailed t-test of the means to determine the required sample size when the allowable error in the ED₅₀ was varied from ±10-20%. The COV averaged 22% (range 15-27%). We used a COV value of 25% in determining the sample size. If the allowable error in finding the mean ED₅₀ is ±15%, a sample size of 24 is needed to achieve a power of 80%. Increasing 'accuracy' beyond this point requires increasing greater sample sizes (e.g. an 'n' of 37 for a ±12% error). On the basis of the results of this retrospective analysis, a total sample size of not less than 24 subjects should be adequate for determining a neuromuscular blocking drug's clinical potency with a reasonable degree of assurance.

  9. Active versus Passive Sample Attrition: The Health and Retirement Study

    OpenAIRE

    Honggao Cao; Daniel H. Hill

    2005-01-01

    This paper investigates sample attrition in the Health and Retirement Study (HRS). We compare attrition behavior in two of the HRS cohorts: original HRS cohort and AHEAD cohort. We distinguish attrition due to death (passive attrition) from attrition due to other causes (active attrition), examining potential effects of different attrition modes on the representativeness of the remaining samples. This distinction is justified based on a specification test on a multinomial logistic regression ...

  10. Sample phenotype clusters in high-density oligonucleotide microarray data sets are revealed using Isomap, a nonlinear algorithm

    Directory of Open Access Journals (Sweden)

    Malyj Wasyl

    2005-08-01

    Full Text Available Abstract Background Life processes are determined by the organism's genetic profile and multiple environmental variables. However the interaction between these factors is inherently non-linear 1. Microarray data is one representation of the nonlinear interactions among genes and genes and environmental factors. Still most microarray studies use linear methods for the interpretation of nonlinear data. In this study, we apply Isomap, a nonlinear method of dimensionality reduction, to analyze three independent large Affymetrix high-density oligonucleotide microarray data sets. Results Isomap discovered low-dimensional structures embedded in the Affymetrix microarray data sets. These structures correspond to and help to interpret biological phenomena present in the data. This analysis provides examples of temporal, spatial, and functional processes revealed by the Isomap algorithm. In a spinal cord injury data set, Isomap discovers the three main modalities of the experiment – location and severity of the injury and the time elapsed after the injury. In a multiple tissue data set, Isomap discovers a low-dimensional structure that corresponds to anatomical locations of the source tissues. This model is capable of describing low- and high-resolution differences in the same model, such as kidney-vs.-brain and differences between the nuclei of the amygdala, respectively. In a high-throughput drug screening data set, Isomap discovers the monocytic and granulocytic differentiation of myeloid cells and maps several chemical compounds on the two-dimensional model. Conclusion Visualization of Isomap models provides useful tools for exploratory analysis of microarray data sets. In most instances, Isomap models explain more of the variance present in the microarray data than PCA or MDS. Finally, Isomap is a promising new algorithm for class discovery and class prediction in high-density oligonucleotide data sets.

  11. Serum Dried Samples to Detect Dengue Antibodies: A Field Study

    Directory of Open Access Journals (Sweden)

    Angelica Maldonado-Rodríguez

    2017-01-01

    Full Text Available Background. Dried blood and serum samples are useful resources for detecting antiviral antibodies. The conditions for elution of the sample need to be optimized for each disease. Dengue is a widespread disease in Mexico which requires continuous surveillance. In this study, we standardized and validated a protocol for the specific detection of dengue antibodies from dried serum spots (DSSs. Methods. Paired serum and DSS samples from 66 suspected cases of dengue were collected in a clinic in Veracruz, Mexico. Samples were sent to our laboratory, where the conditions for optimal elution of DSSs were established. The presence of anti-dengue antibodies was determined in the paired samples. Results. DSS elution conditions were standardized as follows: 1 h at 4°C in 200 µl of DNase-, RNase-, and protease-free PBS (1x. The optimal volume of DSS eluate to be used in the IgG assay was 40 µl. Sensitivity of 94%, specificity of 93.3%, and kappa concordance of 0.87 were obtained when comparing the antidengue reactivity between DSSs and serum samples. Conclusion. DSS samples are useful for detecting anti-dengue IgG antibodies in the field.

  12. Appearance Investment and Everyday Interpersonal Functioning: An Experience Sampling Study

    Science.gov (United States)

    Forand, Nicholas R.; Gunthert, Kathleen C.; German, Ramaris E.; Wenze, Susan J.

    2010-01-01

    Several studies have shown that body satisfaction affects interpersonal functioning. However, few have studied the specific interpersonal correlates of another important body image dimension, appearance investment--that is, the importance a woman places on appearance. We used an experience sampling design with PDA (personal digital assistant)…

  13. Virome profiling of bats from Myanmar by metagenomic analysis of tissue samples reveals more novel Mammalian viruses.

    Directory of Open Access Journals (Sweden)

    Biao He

    Full Text Available Bats are reservoir animals harboring many important pathogenic viruses and with the capability of transmitting these to humans and other animals. To establish an effective surveillance to monitor transboundary spread of bat viruses between Myanmar and China, complete organs from the thorax and abdomen from 853 bats of six species from two Myanmar counties close to Yunnan province, China, were collected and tested for their virome through metagenomics by Solexa sequencing and bioinformatic analysis. In total, 3,742,314 reads of 114 bases were generated, and over 86% were assembled into 1,649,512 contigs with an average length of 114 bp, of which 26,698 (2% contigs were recognizable viral sequences belonging to 24 viral families. Of the viral contigs 45% (12,086/26,698 were related to vertebrate viruses, 28% (7,443/26,698 to insect viruses, 27% (7,074/26,698 to phages and 95 contigs to plant viruses. The metagenomic results were confirmed by PCR of selected viruses in all bat samples followed by phylogenetic analysis, which has led to the discovery of some novel bat viruses of the genera Mamastrovirus, Bocavirus, Circovirus, Iflavirus and Orthohepadnavirus and to their prevalence rates in two bat species. In conclusion, the present study aims to present the bat virome in Myanmar, and the results obtained further expand the spectrum of viruses harbored by bats.

  14. Gender differences in the structural connectome of the teenage brain revealed by generalized q-sampling MRI

    Directory of Open Access Journals (Sweden)

    Yeu-Sheng Tyan

    2017-01-01

    Full Text Available The question of whether there are biological differences between male and female brains is a fraught one, and political positions and prior expectations seem to have a strong influence on the interpretation of scientific data in this field. This question is relevant to issues of gender differences in the prevalence of psychiatric conditions, including autism, attention deficit hyperactivity disorder (ADHD, Tourette's syndrome, schizophrenia, dyslexia, depression, and eating disorders. Understanding how gender influences vulnerability to these conditions is significant. Diffusion magnetic resonance imaging (dMRI provides a non-invasive method to investigate brain microstructure and the integrity of anatomical connectivity. Generalized q-sampling imaging (GQI has been proposed to characterize complicated fiber patterns and distinguish fiber orientations, providing an opportunity for more accurate, higher-order descriptions through the water diffusion process. Therefore, we aimed to investigate differences in the brain's structural network between teenage males and females using GQI. This study included 59 (i.e., 33 males and 26 females age- and education-matched subjects (age range: 13 to 14 years. The structural connectome was obtained by graph theoretical and network-based statistical (NBS analyses. Our findings show that teenage male brains exhibit better intrahemispheric communication, and teenage female brains exhibit better interhemispheric communication. Our results also suggest that the network organization of teenage male brains is more local, more segregated, and more similar to small-world networks than teenage female brains. We conclude that the use of an MRI study with a GQI-based structural connectomic approach like ours presents novel insights into network-based systems of the brain and provides a new piece of the puzzle regarding gender differences.

  15. Representative regional sampling of carbon dioxide and methane concentrations in hemiboreal headwater streams reveal underestimates in less systematic approaches

    National Research Council Canada - National Science Library

    Wallin, Marcus B; Löfgren, Stefan; Erlandsson, Martin; Bishop, Kevin

    2014-01-01

    .... The use of a headspace sampling method focusing on GHGs in combination with a statistically representative selection of more than 200 streams across two regions in Sweden was the basis for defining...

  16. Metabolomics reveals dose effects of low-dose chronic exposure to uranium in rats: identification of candidate biomarkers in urine samples.

    Science.gov (United States)

    Grison, Stéphane; Favé, Gaëlle; Maillot, Matthieu; Manens, Line; Delissen, Olivia; Blanchardon, Éric; Dublineau, Isabelle; Aigueperse, Jocelyne; Bohand, Sandra; Martin, Jean-Charles; Souidi, Maâmar

    2016-01-01

    Data are sparse about the potential health risks of chronic low-dose contamination of humans by uranium (natural or anthropogenic) in drinking water. Previous studies report some molecular imbalances but no clinical signs due to uranium intake. In a proof-of-principle study, we reported that metabolomics is an appropriate method for addressing this chronic low-dose exposure in a rat model (uranium dose: 40 mg L(-1); duration: 9 months, n = 10). In the present study, our aim was to investigate the dose-effect pattern and identify additional potential biomarkers in urine samples. Compared to our previous protocol, we doubled the number of rats per group (n = 20), added additional sampling time points (3 and 6 months) and included several lower doses of natural uranium (doses used: 40, 1.5, 0.15 and 0.015 mg L(-1)). LC-MS metabolomics was performed on urine samples and statistical analyses were made with SIMCA-P+ and R packages. The data confirmed our previous results and showed that discrimination was both dose and time related. Uranium exposure was revealed in rats contaminated for 9 months at a dose as low as 0.15 mg L(-1). Eleven features, including the confidently identified N1-methylnicotinamide, N1-methyl-2-pyridone-5-carboxamide and 4-hydroxyphenylacetylglycine, discriminated control from contaminated rats with a specificity and a sensitivity ranging from 83 to 96 %, when combined into a composite score. These findings show promise for the elucidation of underlying radiotoxicologic mechanisms and the design of a diagnostic test to assess exposure in urine, in a dose range experimentally estimated to be above a threshold between 0.015 and 0.15 mg L(-1).

  17. WRAP Module 1 sampling strategy and waste characterization alternatives study

    Energy Technology Data Exchange (ETDEWEB)

    Bergeson, C.L.

    1994-09-30

    The Waste Receiving and Processing Module 1 Facility is designed to examine, process, certify, and ship drums and boxes of solid wastes that have a surface dose equivalent of less than 200 mrem/h. These wastes will include low-level and transuranic wastes that are retrievably stored in the 200 Area burial grounds and facilities in addition to newly generated wastes. Certification of retrievably stored wastes processing in WRAP 1 is required to meet the waste acceptance criteria for onsite treatment and disposal of low-level waste and mixed low-level waste and the Waste Isolation Pilot Plant Waste Acceptance Criteria for the disposal of TRU waste. In addition, these wastes will need to be certified for packaging in TRUPACT-II shipping containers. Characterization of the retrievably stored waste is needed to support the certification process. Characterization data will be obtained from historical records, process knowledge, nondestructive examination nondestructive assay, visual inspection of the waste, head-gas sampling, and analysis of samples taken from the waste containers. Sample characterization refers to the method or methods that are used to test waste samples for specific analytes. The focus of this study is the sample characterization needed to accurately identify the hazardous and radioactive constituents present in the retrieved wastes that will be processed in WRAP 1. In addition, some sampling and characterization will be required to support NDA calculations and to provide an over-check for the characterization of newly generated wastes. This study results in the baseline definition of WRAP 1 sampling and analysis requirements and identifies alternative methods to meet these requirements in an efficient and economical manner.

  18. Practical recommendations for population PK studies with sampling time errors.

    Science.gov (United States)

    Choi, Leena; Crainiceanu, Ciprian M; Caffo, Brian S

    2013-12-01

    Population pharmacokinetic (PK) data collected from routine clinical practice offers a rich source of valuable information. However, in observational population PK data, accurate time information for blood samples is often missing, resulting in measurement errors (ME) in the sampling time variable. The goal of this study was to investigate the effects on model parameters when a scheduled time is used instead of the actual blood sampling time, and to propose ME correction methods. Simulation studies were conducted based on two major factors: the curvature in PK profiles and the size of ME. As ME correction methods, transform both sides (TBS) models were developed with application of Box-Cox power transformation and Taylor expansion. The TBS models were compared to a conventional population PK model using simulations. The most important determinant of bias due to time ME was the degree of curvature (nonlinearity) in PK profiles; the smaller the curvature around sampling times, the smaller the associated bias. The second important determinant was the magnitude of ME; the larger the ME, the larger the bias. The proposed TBS models performed better than a conventional population PK modeling when curvature and ME were substantial. Time ME in sampling time can lead to bias on the parameter estimators. The following practical recommendations are provided: 1) when the curvature of PK profiles is small, conventional population PK modeling is robust to even large ME; and 2) when the curvature is moderate or large, the proposed methodology reduces bias in parameter estimates.

  19. Astronauts Armstrong and Aldrin study rock samples during field trip

    Science.gov (United States)

    1969-01-01

    Astronaut Neil Armstrong, commander of the Apollo 11 lunar landing mission, and Astronaut Edwin Aldrin, Lunar module pilot for Apollo 11, study rock samples during a geological field trip to the Quitman Mountains area near the Fort Quitman ruins in far west Texas.

  20. Genesis Solar Wind Collector Cleaning Assessment: 60366 Sample Case Study

    Science.gov (United States)

    Goreva, Y. S.; Gonzalez, C. P.; Kuhlman, K. R.; Burnett, D. S.; Woolum, D.; Jurewicz, A. J.; Allton, J. H.; Rodriguez, M. C.; Burkett, P. J.

    2014-01-01

    In order to recognize, localize, characterize and remove particle and thin film surface contamination, a small subset of Genesis mission collector fragments are being subjected to extensive study via various techniques [1-5]. Here we present preliminary results for sample 60336, a Czochralski silicon (Si-CZ) based wafer from the bulk array (B/C).

  1. Sampling challenges in a study examining refugee resettlement

    Directory of Open Access Journals (Sweden)

    Thompson Sandra C

    2011-03-01

    Full Text Available Abstract Background As almost half of all refugees currently under United Nations protection are from Afghanistan or Iraq and significant numbers have already been resettled outside the region of origin, it is likely that future research will examine their resettlement needs. A number of methodological challenges confront researchers working with culturally and linguistically diverse groups; however, few detailed articles are available to inform other studies. The aim of this paper is to outline challenges with sampling and recruitment of socially invisible refugee groups, describing the method adopted for a mixed methods exploratory study assessing mental health, subjective wellbeing and resettlement perspectives of Afghan and Kurdish refugees living in New Zealand and Australia. Sampling strategies used in previous studies with similar refugee groups were considered before determining the approach to recruitment Methods A snowball approach was adopted for the study, with multiple entry points into the communities being used to choose as wide a range of people as possible to provide further contacts and reduce selection bias. Census data was used to assess the representativeness of the sample. Results A sample of 193 former refugee participants was recruited in Christchurch (n = 98 and Perth (n = 95, 47% were of Afghan and 53% Kurdish ethnicity. A good gender balance (males 52%, females 48% was achieved overall, mainly as a result of the sampling method used. Differences in the demographic composition of groups in each location were observed, especially in relation to the length of time spent in a refugee situation and time since arrival, reflecting variations in national humanitarian quota intakes. Although some measures were problematic, Census data comparison to assess reasonable representativeness of the study sample was generally reassuring. Conclusions Snowball sampling, with multiple initiation points to reduce selection bias, was

  2. Study Reveals Brain Biology behind Self-Control

    Science.gov (United States)

    Sparks, Sarah D.

    2011-01-01

    A new neuroscience twist on a classic psychology study offers some clues to what makes one student able to buckle down for hours of homework before a test while his classmates party. The study published in the September 2011 edition of "Proceedings of the National Academy of Science," suggests environmental cues may "hijack" the brain's mechanisms…

  3. Highlight: Pioneering study reveals importance of land tenure in ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    2016-04-14

    Apr 14, 2016 ... The findings of a pioneering study linking services to justice and land tenure were presented in Nairobi on February 5, 2015. The study, carried out by multiple stakeholders, shows that land tenure is critical to improving basic services and access to justice in informal settlements in Nairobi, Kenya.

  4. Implementing Japanese Lesson Study in Foreign Countries: Misconceptions Revealed

    Science.gov (United States)

    Fujii, Toshiakira

    2014-01-01

    This paper is based on data gathered during visits to Uganda and Malawi, conducted by the International Math-teacher Professionalization Using Lesson Study (IMPULS) project and the Japanese International Cooperation Agency (JICA). The author's observations and experiences highlighted misconceptions about lesson study. The paper concludes that some…

  5. Off-road sampling reveals a different grassland bird community than roadside sampling: implications for survey design and estimates to guide conservation

    Directory of Open Access Journals (Sweden)

    Troy I. Wellicome

    2014-06-01

    concern. Our results highlight the need to develop appropriate corrections for bias in estimates derived from roadside sampling, and the need to design surveys that sample bird communities across a more representative cross-section of the landscape, both near and far from roads.

  6. Multiscale study for stochastic characterization of shale samples

    Science.gov (United States)

    Tahmasebi, Pejman; Javadpour, Farzam; Sahimi, Muhammad; Piri, Mohammad

    2016-03-01

    Characterization of shale reservoirs, which are typically of low permeability, is very difficult because of the presence of multiscale structures. While three-dimensional (3D) imaging can be an ultimate solution for revealing important complexities of such reservoirs, acquiring such images is costly and time consuming. On the other hand, high-quality 2D images, which are widely available, also reveal useful information about shales' pore connectivity and size. Most of the current modeling methods that are based on 2D images use limited and insufficient extracted information. One remedy to the shortcoming is direct use of qualitative images, a concept that we introduce in this paper. We demonstrate that higher-order statistics (as opposed to the traditional two-point statistics, such as variograms) are necessary for developing an accurate model of shales, and describe an efficient method for using 2D images that is capable of utilizing qualitative and physical information within an image and generating stochastic realizations of shales. We then further refine the model by describing and utilizing several techniques, including an iterative framework, for removing some possible artifacts and better pattern reproduction. Next, we introduce a new histogram-matching algorithm that accounts for concealed nanostructures in shale samples. We also present two new multiresolution and multiscale approaches for dealing with distinct pore structures that are common in shale reservoirs. In the multiresolution method, the original high-quality image is upscaled in a pyramid-like manner in order to achieve more accurate global and long-range structures. The multiscale approach integrates two images, each containing diverse pore networks - the nano- and microscale pores - using a high-resolution image representing small-scale pores and, at the same time, reconstructing large pores using a low-quality image. Eventually, the results are integrated to generate a 3D model. The methods

  7. Study of β-NMR for Liquid Biological Samples

    CERN Document Server

    Beattie, Caitlin

    2017-01-01

    β-NMR is an exotic form of NMR spectroscopy that allows for the characterization of matter based on the anisotropic β-decay of radioactive probe nuclei. This has been shown to be an effective spectroscopic technique for many different compounds, but its use for liquid biological samples is relatively unexplored. The work at the VITO line of ISOLDE seeks to employ this technique to study such samples. Currently, preparations are being made for an experiment to characterize DNA G-quadruplexes and their interactions with stabilizing cations. More specifically, the work in which I engaged as a summer student focused on the experiment’s liquid handling system and the stability of the relevant biological samples under vacuum.

  8. Sample size considerations for clinical research studies in nuclear cardiology.

    Science.gov (United States)

    Chiuzan, Cody; West, Erin A; Duong, Jimmy; Cheung, Ken Y K; Einstein, Andrew J

    2015-12-01

    Sample size calculation is an important element of research design that investigators need to consider in the planning stage of the study. Funding agencies and research review panels request a power analysis, for example, to determine the minimum number of subjects needed for an experiment to be informative. Calculating the right sample size is crucial to gaining accurate information and ensures that research resources are used efficiently and ethically. The simple question "How many subjects do I need?" does not always have a simple answer. Before calculating the sample size requirements, a researcher must address several aspects, such as purpose of the research (descriptive or comparative), type of samples (one or more groups), and data being collected (continuous or categorical). In this article, we describe some of the most frequent methods for calculating the sample size with examples from nuclear cardiology research, including for t tests, analysis of variance (ANOVA), non-parametric tests, correlation, Chi-squared tests, and survival analysis. For the ease of implementation, several examples are also illustrated via user-friendly free statistical software.

  9. Detailed longitudinal sampling of glioma stem cells in situ reveals Chr7 gain and Chr10 loss as repeated events in primary tumor formation and recurrence.

    Science.gov (United States)

    Baysan, Mehmet; Woolard, Kevin; Cam, Margaret C; Zhang, Wei; Song, Hua; Kotliarova, Svetlana; Balamatsias, Demosthenes; Linkous, Amanda; Ahn, Susie; Walling, Jennifer; Belova, Galina I; Fine, Howard A

    2017-11-15

    Intratumoral heterogeneity at the genetic, epigenetic, transcriptomic, and morphologic levels is a commonly observed phenomenon in many aggressive cancer types. Clonal evolution during tumor formation and in response to therapeutic intervention can be predicted utilizing reverse engineering approaches on detailed genomic snapshots of heterogeneous patient tumor samples. In this study, we developed an extensive dataset for a GBM case via the generation of polyclonal and monoclonal glioma stem cell lines from initial diagnosis, and from multiple sections of distant tumor locations of the deceased patient's brain following tumor recurrence. Our analyses revealed the tissue-wide expansion of a new clone in the recurrent tumor and chromosome 7 gain and chromosome 10 loss as repeated genomic events in primary and recurrent disease. Moreover, chromosome 7 gain and chromosome 10 loss produced similar alterations in mRNA expression profiles in primary and recurrent tumors despite possessing other highly heterogeneous and divergent genomic alterations between the tumors. We identified ETV1 and CDK6 as putative candidate genes, and NFKB (complex), IL1B, IL6, Akt and VEGF as potential signaling regulators, as potentially central downstream effectors of chr7 gain and chr10 loss. Finally, the differences caused by the transcriptomic shift following gain of chromosome 7 and loss of chromosome 10 were consistent with those generally seen in GBM samples compared to normal brain in large-scale patient-tumor data sets. © 2017 UICC.

  10. Developmental palaeontology of Reptilia as revealed by histological studies.

    Science.gov (United States)

    Scheyer, Torsten M; Klein, Nicole; Sander, P Martin

    2010-06-01

    Among the fossilized ontogenetic series known for tetrapods, only more basal groups like temnospondyl amphibians have been used extensively in developmental studies, whereas reptilian and synapsid data have been largely neglected so far. However, before such ontogenetic series can be subject to study, the relative age and affiliation of putative specimens within a series has to be verified. Bone histology has a long-standing tradition as being a source of palaeobiological and growth history data in fossil amniotes and indeed, the analysis of bone microstructures still remains the most important and most reliable tool for determining the absolute ontogenetic age of fossil vertebrates. It is also the only direct way to reconstruct life histories and growth strategies for extinct animals. Herein the record of bone histology among Reptilia and its application to elucidate and expand fossilized ontogenies as a source of developmental data are reviewed. (c) 2009 Elsevier Ltd. All rights reserved.

  11. A phylogenomic study of birds reveals their evolutionary history.

    Science.gov (United States)

    Hackett, Shannon J; Kimball, Rebecca T; Reddy, Sushma; Bowie, Rauri C K; Braun, Edward L; Braun, Michael J; Chojnowski, Jena L; Cox, W Andrew; Han, Kin-Lan; Harshman, John; Huddleston, Christopher J; Marks, Ben D; Miglia, Kathleen J; Moore, William S; Sheldon, Frederick H; Steadman, David W; Witt, Christopher C; Yuri, Tamaki

    2008-06-27

    Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined approximately 32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds.

  12. Controlled samples for silicon defect and impurity studies

    Energy Technology Data Exchange (ETDEWEB)

    Ciszek, T.F. [National Renewable Energy Lab., Golden, CO (United States)

    1995-08-01

    Because of the diverse defects and impurities that are present in any given sample of silicon material, it can be extremely difficult to conduct a controlled experiment to study the influence of any particular defect or impurity on photovoltaic properties such as minority charge carrier lifetime {tau} or solar cell efficiency q. For example, the influence of iron may be different if boron is present, or the influence of silicon self interstitial clusters may be different if oxygen is present. It thus becomes important to conduct such studies on controlled samples where the influence of secondary effects is minimized. At NREL, over the past several years, we have focused on using the high-purity float-zone (FZ) growth method to obtain controlled samples. Because the silicon melt is not in contact with a container, and no heated components are in the growth region, very high purities and low defect levels can be achieved in baseline material. The baseline can be controllably perturbed by introduction of specific defects or impurities. The chart shown below lists some of the types of defect and impurity. combinations that can be studied in this way. The boxes marked with an {open_quotes}x{close_quotes} represent combinations we have studied to some extent.

  13. Sampling pig farms at the abattoir in a cross-sectional study - Evaluation of a sampling method.

    Science.gov (United States)

    Birkegård, Anna Camilla; Halasa, Tariq; Toft, Nils

    2017-09-15

    A cross-sectional study design is relatively inexpensive, fast and easy to conduct when compared to other study designs. Careful planning is essential to obtaining a representative sample of the population, and the recommended approach is to use simple random sampling from an exhaustive list of units in the target population. This approach is rarely feasible in practice, and other sampling procedures must often be adopted. For example, when slaughter pigs are the target population, sampling the pigs on the slaughter line may be an alternative to on-site sampling at a list of farms. However, it is difficult to sample a large number of farms from an exact predefined list, due to the logistics and workflow of an abattoir. Therefore, it is necessary to have a systematic sampling procedure and to evaluate the obtained sample with respect to the study objective. We propose a method for 1) planning, 2) conducting, and 3) evaluating the representativeness and reproducibility of a cross-sectional study when simple random sampling is not possible. We used an example of a cross-sectional study with the aim of quantifying the association of antimicrobial resistance and antimicrobial consumption in Danish slaughter pigs. It was not possible to visit farms within the designated timeframe. Therefore, it was decided to use convenience sampling at the abattoir. Our approach was carried out in three steps: 1) planning: using data from meat inspection to plan at which abattoirs and how many farms to sample; 2) conducting: sampling was carried out at five abattoirs; 3) evaluation: representativeness was evaluated by comparing sampled and non-sampled farms, and the reproducibility of the study was assessed through simulated sampling based on meat inspection data from the period where the actual data collection was carried out. In the cross-sectional study samples were taken from 681 Danish pig farms, during five weeks from February to March 2015. The evaluation showed that the sampling

  14. Microanalysis study of archaeological mural samples containing Maya blue pigment

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez del Rio, M. [ESRF, BP220, F-38043 Grenoble (France)]. E-mail: srio@esrf.fr; Martinetto, P. [Laboratoire de Cristallographie, CNRS, BP166 F-30842 Grenoble (France); Somogyi, A. [ESRF, BP220, F-38043 Grenoble (France); Reyes-Valerio, C. [INAH, Mexico DF (Mexico); Dooryhee, E. [Laboratoire de Cristallographie, CNRS, BP166 F-30842 Grenoble (France); Peltier, N. [Laboratoire de Cristallographie, CNRS, BP166 F-30842 Grenoble (France); Alianelli, L. [INFM-OGG c/o ESRF, BP220, F-38043 Grenoble Cedex (France); Moignard, B. [C2RMF, 6 Rue des Pyramides, F-75041 Paris Cedex 01 (France); Pichon, L. [C2RMF, 6 Rue des Pyramides, F-75041 Paris Cedex 01 (France); Calligaro, T. [C2RMF, 6 Rue des Pyramides, F-75041 Paris Cedex 01 (France); Dran, J.-C. [C2RMF, 6 Rue des Pyramides, F-75041 Paris Cedex 01 (France)

    2004-10-08

    Elemental analysis by X-ray fluorescence and particle induced X-ray emission is applied to the study of several Mesoamerican mural samples containing blue pigments. The most characteristic blue pigment is Maya blue, a very stable organo-clay complex original from Maya culture and widely used in murals, pottery and sculptures in a vast region of Mesoamerica during the pre-hispanic time (from VIII century) and during the colonization until 1580. The mural samples come from six different archaeological sites (four pre-hispanic and two from XVI century colonial convents). The correlation between the presence of some elements and the pigment colour is discussed. From the comparative study of the elemental concentration, some conclusions are drawn on the nature of the pigments and the technology used.

  15. Pubertal control mechanisms as revealed from human studies.

    Science.gov (United States)

    Chipman, J J

    1980-05-15

    Human puberty is thought to be regulated by a central nervous system (CNS) program. Strong presumptive evidence for this thesis has been drawn from the augmented gonadotropin secretion that occurs synchronously with sleep in early puberty and serves as a biologic index to CNS puberty. In response to wake/sleep gonadotropin patterns, sex steroids are also secreted in circadian-like patterns during puberty. In disorders such as precocious puberty, anorexia nervosa, and gonadal dysgenesis, the physiological mechanisms that control wake/sleep differences in gonadotropin secretion appear to be intact. Studies in such patients suggest that the primary sex hormones have a quantitative but not qualitative modulating effect on the CNS program. Possible additional control mechanisms include adrenal androgen secretion and body composition.

  16. Studies of heterogeneous samples and material composition by fluorescence XAFS

    Science.gov (United States)

    Tannazi, Firouzeh

    X-ray Absorption Fine Structure (XAFS) Spectroscopy has proven to be an important tool for studying the composition and structure of materials. One benefit of XAFS is that it can be applied to a wide variety of systems, including complex real-world samples such as those found in biology and the environment. Determination of the chemical speciation of toxic elements in the environment currently is an active area of research. This dissertation describes my application of XAFS to chemical speciation in environmental soil samples as well as synthetic samples. In situ experimental XAFS measurements of metal speciation in soil core samples were made and the results were correlated with speciation results from chemical extraction. Several numerical approaches were implemented and tested. A novel approach to determining speciation by a Linear Programming algorithm was developed and found to be the most successful method for dilute samples of small particle size, i.e. in the linear regime. However, discrepancies between the in situ speciation results and other methods led to a fundamental investigation of x-ray transport in heterogeneous samples in which the observed fluorescence spectrum no longer is a linear combination of the spectra of the constituents. Useful theoretical models of x-ray propagation through heterogeneous media were found in older x-ray spectrometry literature, corrected, adapted for the first time to XAFS spectra. A Monte Carlo method was developed to calculate the effect on spectra of the shape, size, and orientation of particles of arbitrary convex shape, and the results are parameterized so that the loss factors can be easily calculated. Combining these models permits one to compute the fluorescence from arbitrary randomly heterogeneous particulate samples. This work demonstrates that the particle size distribution and the solid packing fraction have an important effect on the resulting spectra, which, if neglected, can introduce significant errors

  17. TRU Waste Sampling Program: Volume II. Gas generation studies

    Energy Technology Data Exchange (ETDEWEB)

    Clements, T.L. Jr.; Kudera, D.E.

    1985-09-01

    Volume II of the TRU Waste Sampling Program report contains the data generated from evaluating the adequacy of venting/filtering devices for maintaining safe hydrogen levels in plutonium contaminated waste drums. Additional studies reported in this volume include gas generation rates, selected waste form monitoring, and evaluation of hydrogen migration from sealed 90-mil rigid polyethylene drum liners containing /sup 238/Pu-contaminated wastes. All wastes used in the studies were newly-generated, and the waste drums were under controlled, experimental conditions. Studies using /sup 239/Pu-contaminated wastes were conducted at the Rocky Flats Plant. Studies using /sup 238/Pu-contaminated wastes were conducted at the Los Alamos National Laboratory.

  18. Dynamics of Prochlorococcus and Synechococcus at Station ALOHA Revealed through Flow Cytometry and High-Resolution Vertical Sampling

    Directory of Open Access Journals (Sweden)

    Ger J. van den Engh

    2017-11-01

    Full Text Available The fluorescence and scattering properties of Prochlorococcus and Synechococcus at Station ALOHA as measured by flow cytometry (termed the FCM phenotype vary with depth and over a variety of time scales. The variation in FCM phenotypes may reflect population selection or physiological acclimation to local conditions. Observations before, during, and after a storm with deep water mixing show a short-term homogenization of the FCM phenotypes with depth, followed by a return to the stable pattern over the time span of a few days. These dynamics indicate that, within the upper mixed-layer, the FCM phenotype distribution represents acclimation to ambient light. The populations in the pycnocline (around 100 m and below, remain stable and are invariant with light conditions. In samples where both cyanobacteria coexist, fluorescence properties of Prochlorococcus and Synechococcus are tightly correlated providing further evidence that FCM phenotype variability is caused by a common environmental factor or factors. Measurements of the dynamics of FCM phenotypes provide insights into phytoplankton physiology and adaptation. Alternatively, FCM phenotype census of a water mass may provide information about its origin and illumination history.

  19. Salivary gland tumours in a Mexican sample. A retrospective study.

    Science.gov (United States)

    Ledesma-Montes, C; Garces-Ortiz, M

    2002-01-01

    Salivary gland tumours are an important part of the Oral and Maxillofacial Pathology, unfortunately, only few studies on these tumours have been done in Latin-American population. The aim of this study was to compare demographic data on salivary gland tumours in a Mexican sample with those previously published from Latin American and non-Latin American countries. All cases of salivary gland tumours or lesions diagnosed in our service were reviewed. Of the reviewed cases,67 were confirmed as salivary gland tumours. Out of these 64.2% were benign neoplasms, 35.8% were malignant and a slight female predominance (56.7%) was found. The most common location was palate followed by lips and floor of the mouth. Mean age for benign tumours was 40.6 years with female predominance (60.5%). Mean age for malignant tumours was 41 years and female predominance was found again. Palate followed by retromolar area were the usual locations. Pleomorphic adenoma (58.2%), mucoepidermoid carcinoma (17.9%) and adenoid cystic carcinoma (11.9%) were the more frequent neoplasms. All retromolar cases were malignant and all submandibular gland tumours were benign. We found a high proportion of salivary gland neoplasms in children. Our results showed that differences of the studied tumours among our sample and previously reported series exist. These differences can be related to race and geographical location.

  20. Saliva sampling in global clinical studies: the impact of low sampling volume on performance of DNA in downstream genotyping experiments

    Science.gov (United States)

    2013-01-01

    Background The collection of viable DNA samples is an essential element of any genetics research programme. Biological samples for DNA purification are now routinely collected in many studies with a variety of sampling methods available. Initial observation in this study suggested a reduced genotyping success rate of some saliva derived DNA samples when compared to blood derived DNA samples prompting further investigation. Methods Genotyping success rate was investigated to assess the suitability of using saliva samples in future safety and efficacy pharmacogenetics experiments. The Oragene® OG-300 DNA Self-Collection kit was used to collect and extract DNA from saliva from 1468 subjects enrolled in global clinical studies. Statistical analysis evaluated the impact of saliva sample volume of collection on the quality, yield, concentration and performance of saliva DNA in genotyping assays. Results Across 13 global clinical studies that utilized the Oragene® OG-300 DNA Self-Collection kit there was variability in the volume of saliva sample collection with ~31% of participants providing 0.5 mL of saliva, rather than the recommended 2 mL. While the majority of saliva DNA samples provided high quality genotype data, collection of 0.5 mL volumes of saliva contributed to DNA samples being significantly less likely to pass genotyping quality control standards. Assessment of DNA sample characteristics that may influence genotyping outcomes indicated that saliva sample volume, DNA purity and turbidity were independently associated with sample genotype pass rate, but that saliva collection volume had the greatest effect. Conclusion When employing saliva sampling to obtain DNA, it is important to encourage all study participants to provide sufficient sample to minimize potential loss of data in downstream genotyping experiments. PMID:23759220

  1. Sample size requirement in analytical studies for similarity assessment.

    Science.gov (United States)

    Chow, Shein-Chung; Song, Fuyu; Bai, He

    2017-01-01

    For the assessment of biosimilar products, the FDA recommends a stepwise approach for obtaining the totality-of-the-evidence for assessing biosimilarity between a proposed biosimilar product and its corresponding innovative biologic product. The stepwise approach starts with analytical studies for assessing similarity in critical quality attributes (CQAs), which are relevant to clinical outcomes at various stages of the manufacturing process. For CQAs that are the most relevant to clinical outcomes, the FDA requires an equivalence test be performed for similarity assessment based on an equivalence acceptance criterion (EAC) that is obtained using a single test value of some selected reference lots. In practice, we often have extremely imbalanced numbers of reference and test lots available for the establishment of EAC. In this case, to assist the sponsors, the FDA proposed an idea for determining the number of reference lots and the number of test lots required in order not to have imbalanced sample sizes when establishing EAC for the equivalence test based on extensive simulation studies. Along this line, this article not only provides statistical justification of Dong, Tsong, and Weng's proposal, but also proposes an alternative method for sample size requirement for the Tier 1 equivalence test.

  2. Studies on natural recovery from alcohol dependence: sample selection bias by media solicitation?

    Science.gov (United States)

    Rumpf, H J; Bischof, G; Hapke, U; Meyer, C; John, U

    2000-05-01

    To assess the selection bias of recruiting participants in studies on natural recovery from alcohol dependence through media solicitation. Two samples with different recruitment strategies are compared. Media solicitation and general population. Sample 1 consists of 176 alcohol-dependent individuals remitted without formal help and recruited through media solicitation, sample 2 consists of 32 natural remitters derived from a representative general population study with a sample size of 4075 respondents and a response rate of 70.2%. Several triggering mechanisms and maintenance factors of remission were assessed in a personal interview using standardized questionnaires. Results of logistic regression analyses show that media-solicited subjects were more often abstinent in the last 12 months, were more severely dependent, were less satisfied with eight life domains prior to remission and showed higher scores in a coping behaviour measure. Besides these major differences from the multivariate analysis, media subjects revealed more health problems prior to remission, experienced more social pressure to change drinking behaviour, and showed differences in reasons for not seeking help. Media solicitation leads to a sample selection bias in research on natural recovery from alcohol dependence. When measures to foster self-change are derived from such studies, findings from representative samples have to be considered.

  3. Whole-genome sequencing of Campylobacter jejuni isolated from Danish routine human stool samples reveals surprising degree of clustering

    DEFF Research Database (Denmark)

    Joensen, K G; Kuhn, K G; Müller, L

    2018-01-01

    OBJECTIVES: Outbreaks of Campylobacter are traditionally considered to be rare, however rather than being the true nature of the disease, this may reflect our present inability to detect them. The aim of this study was to determine the genetic and epidemiological degree of clustering among...

  4. Study population, questionnaire, data management and sample description.

    Science.gov (United States)

    de Waure, Chiara; Poscia, Andrea; Virdis, Andrea; Di Pietro, Maria Luisa; Ricciardi, Walter

    2015-01-01

    This article describes methodological issues of the "Sportello Salute Giovani" project ("Youth Health Information Desk"), a multicenter study aimed at assessing the health status and attitudes and behaviours of university students in Italy. The questionnaire used to carry out the study was adapted from the Italian health behaviours in school-aged children (HBSC) project and consisted of 93 items addressing: demographics; nutritional habits and status; physical activity; lifestyles; reproductive and preconception health; health and satisfaction of life; attitudes and behaviours toward academic study and new technologies. The questionnaire was administered to a pool of 12 000 students from 18 to 30 years of age who voluntary decided to participate during classes held at different Italian faculties or at the three "Sportello Salute Giovani" centers which were established in the three sites of the Università Cattolica del Sacro Cuore (Catholic University of the Sacred Heart of Rome). The final study sample was composed by 8516 university students. The mean age of responders was 22.2 (Standard Deviation 2.0) and 5702 (67.0%) were females. According to the distribution in age classes, 3601 (43.3%) belonged to the 18-21 one, 3796 (44.5%) to the 22-24 class and 1019 (12.2%) to the 25-30 class. With respect to socio-economic status, data were available for 8410 responders and showed that 50.3% of students belonged to the middle class. The project took into consideration a large number of individuals from different regions of the country and therefore may be considered representative of the general population of Italian university students. Furthermore, it is the first to address, at the same time, several issues, in particular attitudes and behaviours toward health, in Italian university students. The analysis of data from such a large sample of university students sets the basis for identifying the most appropriate interventions in order to address the specific needs of

  5. Revealing pathologies in the liquid crystalline structures of the brain by polarimetric studies (Presentation Recording)

    Science.gov (United States)

    Bakhshetyan, Karen; Melkonyan, Gurgen G.; Galstian, Tigran V.; Saghatelyan, Armen

    2015-10-01

    Natural or "self" alignment of molecular complexes in living tissue represents many similarities with liquid crystals (LC), which are anisotropic liquids. The orientational characteristics of those complexes may be related to many important functional parameters and their study may reveal important pathologies. The know-how, accumulated thanks to the study of LC materials, may thus be used to this end. One of the traditionally used methods, to characterize those materials, is the polarized light imaging (PLI) that allows for label-free analysis of anisotropic structures in the brain tissue and can be used, for example, for the analysis of myelinated fiber bundles. In the current work, we first attempted to apply the PLI on the mouse histological brain sections to create a map of anisotropic structures using cross-polarizer transmission light. Then we implemented the PLI for comparative study of histological sections of human postmortem brain samples under normal and pathological conditions, such as Parkinson's disease (PD). Imaging the coronal, sagittal and horizontal sections of mouse brain allowed us to create a false color-coded fiber orientation map under polarized light. In human brain datasets for both control and PD groups we measured the pixel intensities in myelin-rich subregions of internal capsule and normalized these to non-myelinated background signal from putamen and caudate nucleus. Quantification of intensities revealed a statistically significant reduction of fiber intensity of PD compared to control subjects (2.801 +/- 0.303 and 3.724 +/- 0.07 respectively; *p < 0.05). Our study confirms the validity of PLI method for visualizing myelinated axonal fibers. This relatively simple technique can become a promising tool for study of neurodegenerative diseases where labeling-free imaging is an important benefit.

  6. Social Studies Teachers' Viewpoints of the Social Studies Lesson "Sample of Turkey and Afghanistan"

    Science.gov (United States)

    Sonmez, Omer Faruk

    2014-01-01

    This study was conducted to reveal the perceptions of history, geography and social studies teachers giving the social studies lesson at primary schools in Turkey and Afghanistan towards the social studies lesson. The working group of the study involves history, geography and social studies teachers rendering service in Tokat and Kayseri provinces…

  7. Metabolomic profiling of urine samples from mice exposed to protons reveals radiation quality and dose specific differences.

    Science.gov (United States)

    Laiakis, Evagelia C; Trani, Daniela; Moon, Bo-Hyun; Strawn, Steven J; Fornace, Albert J

    2015-04-01

    As space travel is expanding to include private tourism and travel beyond low-Earth orbit, so is the risk of exposure to space radiation. Galactic cosmic rays and solar particle events have the potential to expose space travelers to significant doses of radiation that can lead to increased cancer risk and other adverse health consequences. Metabolomics has the potential to assess an individual's risk by exploring the metabolic perturbations in a biofluid or tissue. In this study, C57BL/6 mice were exposed to 0.5 and 2 Gy of 1 GeV/nucleon of protons and the levels of metabolites were evaluated in urine at 4 h after radiation exposure through liquid chromatography coupled to time-of-flight mass spectrometry. Significant differences were identified in metabolites that map to the tricarboxylic acid (TCA) cycle and fatty acid metabolism, suggesting that energy metabolism is severely impacted after exposure to protons. Additionally, various pathways of amino acid metabolism (tryptophan, tyrosine, arginine and proline and phenylalanine) were affected with potential implications for DNA damage repair and cognitive impairment. Finally, presence of products of purine and pyrimidine metabolism points to direct DNA damage or increased apoptosis. Comparison of these metabolomic data to previously published data from our laboratory with gamma radiation strongly suggests a more pronounced effect on metabolism with protons. This is the first metabolomics study with space radiation in an easily accessible biofluid such as urine that further investigates and exemplifies the biological differences at early time points after exposure to different radiation qualities.

  8. Sampling pig farms at the abattoir in a cross-sectional study − Evaluation of a sampling method

    DEFF Research Database (Denmark)

    Birkegård, Anna Camilla; Hisham Beshara Halasa, Tariq; Toft, Nils

    2017-01-01

    A cross-sectional study design is relatively inexpensive, fast and easy to conduct when compared to other study designs. Careful planning is essential to obtaining a representative sample of the population, and the recommended approach is to use simple random sampling from an exhaustive list of u...

  9. Study population, questionnaire, data management and sample description

    Directory of Open Access Journals (Sweden)

    Chiara de Waure

    2015-06-01

    Full Text Available INTRODUCTION: This article describes methodological issues of the "Sportello Salute Giovani" project ("Youth Health Information Desk", a multicenter study aimed at assessing the health status and attitudes and behaviours of university students in Italy. MATERIALS AND METHODS: The questionnaire used to carry out the study was adapted from the Italian health behaviours in school-aged children (HBSC project and consisted of 93 items addressing: demographics; nutritional habits and status; physical activity; lifestyles; reproductive and preconception health; health and satisfaction of life; attitudes and behaviours toward academic study and new technologies. The questionnaire was administered to a pool of 12 000 students from 18 to 30 years of age who voluntary decided to participate during classes held at different Italian faculties or at the three "Sportello Salute Giovani" centers which were established in the three sites of the Università Cattolica del Sacro Cuore (Catholic University of the Sacred Heart of Rome. RESULTS: The final study sample was composed by 8516 university students. The mean age of responders was 22.2 (Standard Deviation 2.0 and 5702 (67.0% were females. According to the distribution in age classes, 3601 (43.3% belonged to the 18-21 one, 3796 (44.5% to the 22-24 class and 1019 (12.2% to the 25-30 class. With respect to socio-economic status, data were available for 8410 responders and showed that 50.3% of students belonged to the middle class. DISCUSSION: The project took into consideration a large number of individuals from different regions of the country and therefore may be considered representative of the general population of Italian university students. Furthermore, it is the first to address, at the same time, several issues, in particular attitudes and behaviours toward health, in Italian university students. CONCLUSION: The analysis of data from such a large sample of university students sets the basis for

  10. Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales

    Science.gov (United States)

    Campagna, Leonardo; Van Coeverden de Groot, Peter J; Saunders, Brenda L; Atkinson, Stephen N; Weber, Diana S; Dyck, Markus G; Boag, Peter T; Lougheed, Stephen C

    2013-01-01

    As global warming accelerates the melting of Arctic sea ice, polar bears (Ursus maritimus) must adapt to a rapidly changing landscape. This process will necessarily alter the species distribution together with population dynamics and structure. Detailed knowledge of these changes is crucial to delineating conservation priorities. Here, we sampled 361 polar bears from across the center of the Canadian Arctic Archipelago spanning the Gulf of Boothia (GB) and M'Clintock Channel (MC). We use DNA microsatellites and mitochondrial control region sequences to quantify genetic differentiation, estimate gene flow, and infer population history. Two populations, roughly coincident with GB and MC, are significantly differentiated at both nuclear (FST = 0.01) and mitochondrial (ΦST = 0.47; FST = 0.29) loci, allowing Bayesian clustering analyses to assign individuals to either group. Our data imply that the causes of the mitochondrial and nuclear genetic patterns differ. Analysis of mtDNA reveals the matrilineal structure dates at least to the Holocene, and is common to individuals throughout the species’ range. These mtDNA differences probably reflect both genetic drift and historical colonization dynamics. In contrast, the differentiation inferred from microsatellites is only on the scale of hundreds of years, possibly reflecting contemporary impediments to gene flow. Taken together, our data suggest that gene flow is insufficient to homogenize the GB and MC populations and support the designation of GB and MC as separate polar bear conservation units. Our study also provide a striking example of how nuclear DNA and mtDNA capture different aspects of a species demographic history. PMID:24102001

  11. Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales.

    Science.gov (United States)

    Campagna, Leonardo; Van Coeverden de Groot, Peter J; Saunders, Brenda L; Atkinson, Stephen N; Weber, Diana S; Dyck, Markus G; Boag, Peter T; Lougheed, Stephen C

    2013-09-01

    As global warming accelerates the melting of Arctic sea ice, polar bears (Ursus maritimus) must adapt to a rapidly changing landscape. This process will necessarily alter the species distribution together with population dynamics and structure. Detailed knowledge of these changes is crucial to delineating conservation priorities. Here, we sampled 361 polar bears from across the center of the Canadian Arctic Archipelago spanning the Gulf of Boothia (GB) and M'Clintock Channel (MC). We use DNA microsatellites and mitochondrial control region sequences to quantify genetic differentiation, estimate gene flow, and infer population history. Two populations, roughly coincident with GB and MC, are significantly differentiated at both nuclear (F ST = 0.01) and mitochondrial (ΦST = 0.47; F ST = 0.29) loci, allowing Bayesian clustering analyses to assign individuals to either group. Our data imply that the causes of the mitochondrial and nuclear genetic patterns differ. Analysis of mtDNA reveals the matrilineal structure dates at least to the Holocene, and is common to individuals throughout the species' range. These mtDNA differences probably reflect both genetic drift and historical colonization dynamics. In contrast, the differentiation inferred from microsatellites is only on the scale of hundreds of years, possibly reflecting contemporary impediments to gene flow. Taken together, our data suggest that gene flow is insufficient to homogenize the GB and MC populations and support the designation of GB and MC as separate polar bear conservation units. Our study also provide a striking example of how nuclear DNA and mtDNA capture different aspects of a species demographic history.

  12. Pyrosequencing of 16S rRNA genes in fecal samples reveals high diversity of hindgut microflora in horses and potential links to chronic laminitis

    Directory of Open Access Journals (Sweden)

    Steelman Samantha M

    2012-11-01

    Full Text Available Abstract Background The nutrition and health of horses is closely tied to their gastrointestinal microflora. Gut bacteria break down plant structural carbohydrates and produce volatile fatty acids, which are a major source of energy for horses. Bacterial communities are also essential for maintaining gut homeostasis and have been hypothesized to contribute to various diseases including laminitis. We performed pyrosequencing of 16S rRNA bacterial genes isolated from fecal material to characterize hindgut bacterial communities in healthy horses and those with chronic laminitis. Results Fecal samples were collected from 10 normal horses and 8 horses with chronic laminitis. Genomic DNA was extracted and the V4-V5 segment of the 16S rRNA gene was PCR amplified and sequenced on the 454 platform generating a mean of 2,425 reads per sample after quality trimming. The bacterial communities were dominated by Firmicutes (69.21% control, 56.72% laminitis and Verrucomicrobia (18.13% control, 27.63% laminitis, followed by Bacteroidetes, Proteobacteria, and Spirochaetes. We observed more OTUs per individual in the laminitis group than the control group (419.6 and 355.2, respectively, P = 0.019 along with a difference in the abundance of two unassigned Clostridiales genera (P = 0.03 and P = 0.01. The most abundant bacteria were Streptococcus spp., Clostridium spp., and Treponema spp.; along with unassigned genera from Subdivision 5 of Verrucomicrobia, Ruminococcaceae, and Clostridiaceae, which together constituted ~ 80% of all OTUs. There was a high level of individual variation across all taxonomic ranks. Conclusions Our exploration of the equine fecal microflora revealed higher bacterial diversity in horses with chronic laminitis and identification of two Clostridiales genera that differed in abundance from control horses. There was large individual variation in bacterial communities that was not explained in our study. The core hindgut microflora was

  13. A comparative study of sampling techniques for monitoring carcass contamination

    NARCIS (Netherlands)

    Snijders, J.M.A.; Janssen, M.H.W.; Gerats, G.E.; Corstiaensen, G.P.

    1984-01-01

    Four bacteriological sampling techniques i.e. the excision, double swab, agar contract and modified agar contact techniques were compared by sampling pig carcasses before and after chilling. As well as assessing the advantages and disadvantages of the techniques particular attention was paid to

  14. On combining revealed and stated preferences to forecast customer behaviour: three case studies

    OpenAIRE

    Franses, Philip Hans; Verhoef, Peter

    2002-01-01

    textabstractMany companies collect stated preference data (SP) like intentions and satisfaction as well as revealed preference data (RP) like actual purchasing behavior. It seems relevant to examine the predictive usefulness of this information for future revealed preferences, that is, customer behavior. In this paper we address this issue by considering three case studies.

  15. Genetic studies revealed differences between European and North American populations of Calypogeia azurea

    Directory of Open Access Journals (Sweden)

    Buczkowska Katarzyna

    2016-06-01

    Full Text Available Calypogeia azurea, a widespread, subboreal-montane liverwort species, is one of a few representatives of the Calypogeia genus that are characterized by the occurrence of blue oil bodies. The aim of the study was to investigate the genetic variation and population structure of C. azurea originating from different parts of its distribution range (Europe and North America. Plants of C. azurea were compared with C. peruviana, another Calypogeia species with blue oil bodies. In general, 339 gametophytes from 15 populations of C. azurea were examined. Total gene diversity (HT estimated on the basis of nine isozyme loci of C. azurea at the species level was 0.201. The mean Nei’s genetic distance between European populations was equal to 0.083, whereas the mean genetic distance between populations originating from Europe and North America was 0.413. The analysis of molecular variance (AMOVA showed that 69% of C. azurea genetic variation was distributed among regions (Europe and North America, 15% - among populations within regions, and 16% - within populations. Our study revealed that C. azurea showed genetic diversity within its geographic distribution. All examined samples classified as C. azurea differed in respect of isozyme patterns from C. peruviana.

  16. Preliminary mass spectrometry characterization studies of galectin-3 samples, prior to carbohydrate-binding studies using Affinity mass spectrometry.

    Science.gov (United States)

    Jovanović, Marko; Peter-Katalinić, Jasna

    2017-01-15

    Investigation of non-covalent complexes of proteins using Affinity Mass Spectrometry (AMS) represents a major challenge in modern biomedical research. However, many experimental obstacles can make AMS data analysis complex. Additionally, sample purity and size of the protein may still pose significant challenges. Matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) was used for initial mapping of protein samples. nanoESI (electrospray ionization) quadrupole-time-of-flight (QTOF) MS was used for mapping of protein samples under native conditions and subsequent AMS studies. The human galectin-3 protein sample was expressed in E. coli. Full length galectin-3 was difficult to work with, due to several truncated forms observed after the purification procedures. On the other hand, galectin-3C produced excellent quality nanoESI-MS spectra. A covalent adduct of lactose was found to be located on residue Lys 176. Functional AMS control studies indicated that galectin-3 interactions with oligosaccharides may be dependent on its charge. Mass spectrometry represents a valuable tool that can be efficiently used for structural characterization of protein samples prior to functional analyses. By means of accurate mass measurements, many protein truncations can be identified based on mass alone. Analysis of covalent adducts is more challenging. Finally, for AMS studies, careful use of controls may reveal charge-dependence of protein-oligosaccharide interactions. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  17. Study of probe-sample distance for biomedical spectra measurement

    Directory of Open Access Journals (Sweden)

    Li Lei

    2011-11-01

    Full Text Available Abstract Background Fiber-based optical spectroscopy has been widely used for biomedical applications. However, the effect of probe-sample distance on the collection efficiency has not been well investigated. Method In this paper, we presented a theoretical model to maximize the illumination and collection efficiency in designing fiber optic probes for biomedical spectra measurement. This model was in general applicable to probes with single or multiple fibers at an arbitrary incident angle. In order to demonstrate the theory, a fluorescence spectrometer was used to measure the fluorescence of human finger skin at various probe-sample distances. The fluorescence spectrum and the total fluorescence intensity were recorded. Results The theoretical results show that for single fiber probes, contact measurement always provides the best results. While for multi-fiber probes, there is an optimal probe distance. When a 400- μm excitation fiber is used to deliver the light to the skin and another six 400- μm fibers surrounding the excitation fiber are used to collect the fluorescence signal, the experimental results show that human finger skin has very strong fluorescence between 475 nm and 700 nm under 450 nm excitation. The fluorescence intensity is heavily dependent on the probe-sample distance and there is an optimal probe distance. Conclusions We investigated a number of probe-sample configurations and found that contact measurement could be the primary choice for single-fiber probes, but was very inefficient for multi-fiber probes. There was an optimal probe-sample distance for multi-fiber probes. By carefully choosing the probe-sample distance, the collection efficiency could be enhanced by 5-10 times. Our experiments demonstrated that the experimental results of the probe-sample distance dependence of collection efficiency in multi-fiber probes were in general agreement with our theory.

  18. Feasibility study of spectral pattern recognition reveals distinct classes of volcanic tremor

    Science.gov (United States)

    Unglert, K.; Jellinek, A. M.

    2017-04-01

    Systematic investigations of the similarities and differences among volcanic tremor at a range of volcano types may hold crucial information about the plausibility of inferred source mechanisms, which, in turn, may be important for eruption forecasting. However, such studies are rare, in part because of an intrinsic difficulty with identifying tremor signals within very long time series of volcano seismic data. Accordingly, we develop an efficient tremor detection algorithm and identify over 12,000h of volcanic tremor on 24 stations at Kīlauea, Okmok, Pavlof, and Redoubt volcanoes. We estimate spectral content over 5-minute tremor windows, and apply a novel combination of Principal Component Analysis (PCA) and hierarchical clustering to identify patterns in the tremor spectra. Analyzing several stations from a given volcano together reveals different styles of tremor within individual volcanic settings. In addition to identifying tremor properties common to all stations in a given network, we find localized tremor signals including those related to processes such as lahars or dike intrusions that are only observed on some of the stations within a network. Subsequent application of our analysis to a combination of stations from the different volcanoes reveals that at least three main tremor classes can be detected across all settings. Whereas a regime with a ridge of high power distributed over 1-2Hz and a gradual decay of spectral power towards higher frequencies is observed dominantly at three volcanoes (Kīlauea, Okmok, Redoubt) with magma reservoirs centered at less than 5km below sea level (b.s.l.), a spectrum with a steeper slope and a narrower peak at 1-2Hz is observed only in association with open vents (Kīlauea and Pavlof). A third regime with a peak at approximately 3Hz is confined to two stratovolcanoes (Pavlof and Redoubt). These observations suggest generic relationships between the spectral character of the observed signals and volcano

  19. Fear, Anger, and Risk Preference Reversals: An Experimental Study on a Chinese Sample

    Directory of Open Access Journals (Sweden)

    Shengxiang She

    2017-08-01

    Full Text Available Fear and anger are basic emotions of the same valence which differ in terms of their certainty and control dimensions according to the Appraisal Tendency Framework, a theory addressing the relationship between specific emotions, and judgments and choices. Past research based on the Appraisal Theory revealed contradictory results for risky choice decision-making. However, these conclusions were drawn from Western samples (e.g., North American. Considering potential cultural differences, the present study aims to investigate whether the Appraisal Tendency hypothesis yields the same results in a Chinese sample. Our first study explores how dispositional fear and anger influence risk preferences through a classic virtual “Asia Disease Problem” task and the second study investigates how induced fear and anger influence risk preferences through an incentive-compatible task. Consistent with previous research, our results reveal that induced fear and anger have differential effects on risky decisions: angry participants prefer the risk-seeking option, whereas fearful participants prefer a risk-averse option. However, we find no associations between dispositional fear (or anger and risky decisions.

  20. Mind Wandering in Chinese Daily Lives – An Experience Sampling Study

    Science.gov (United States)

    Song, Xiaolan; Wang, Xiao

    2012-01-01

    Mind wandering has recently received extensive research because it reveals an important characteristic of our consciousness: conscious experience can arise internally and involuntarily. As the first attempt to examine mind wandering in a non-western population, the present study used experience-sampling method to collect the daily momentary mind wandering episodes in a Chinese sample. The results showed that mind wandering was also a ubiquitous experience among the Chinese population, and, instead of emerging out of nowhere, it was often elicited by external or internal cues. Furthermore, most of the mind wandering episodes involved prospective thinking and were closely related to one’s personal life. Finally, the frequency of mind wandering was influenced by some contextual factors. These results taken together suggest that mind wandering plays an important role in helping people to maintain a continuous feeling of “self” and to prepare them to cope with the upcoming events. PMID:22957071

  1. Study of gastric cancer samples using terahertz techniques

    Science.gov (United States)

    Wahaia, Faustino; Kasalynas, Irmantas; Seliuta, Dalius; Molis, Gediminas; Urbanowicz, Andrzej; Carvalho Silva, Catia D.; Carneiro, Fatima; Valusis, Gintaras; Granja, Pedro L.

    2014-08-01

    In the present work, samples of healthy and adenocarcinoma-affected human gastric tissue were analyzed using transmission time-domain THz spectroscopy (THz-TDS) and spectroscopic THz imaging at 201 and 590 GHz. The work shows that it is possible to distinguish between normal and cancerous regions in dried and paraffin-embedded samples. Plots of absorption coefficient α and refractive index n of normal and cancer affected tissues, as well as 2-D transmission THz images are presented and the conditions for discrimination between normal and affected tissues are discussed.

  2. GY SAMPLING THEORY IN ENVIRONMENTAL STUDIES 2: SUBSAMPLING ERROR MEASUREMENTS

    Science.gov (United States)

    Sampling can be a significant source of error in the measurement process. The characterization and cleanup of hazardous waste sites require data that meet site-specific levels of acceptable quality if scientifically supportable decisions are to be made. In support of this effort,...

  3. Planning Longitudinal Field Studies: Considerations in Determining Sample Size.

    Science.gov (United States)

    St.Pierre, Robert G.

    1980-01-01

    Factors that influence the sample size necessary for longitudinal evaluations include the nature of the evaluation questions, nature of available comparison groups, consistency of the treatment in different sites, effect size, attrition rate, significance level for statistical tests, and statistical power. (Author/GDC)

  4. Sampling considerations for demographic and habitat studies of Northern Goshawks

    Science.gov (United States)

    Richard T. Reynolds; J. David Wiens; Suzanne M. Joy; Susan R. Salafsky

    2005-01-01

    We used mark-recapture methods to monitor Northern Goshawks (Accipiter gentilis) and their nests over 12 yr in an increasing sample of breeding territories (37 in 1991 to 121 in 2002) in northern Arizona. As many as 8 yr of repeated nest searching were required to identify the population of breeders, as individuals skipped egg-laying on territories...

  5. Strip transect sampling and analysis for avian habitat studies

    Science.gov (United States)

    Richard N. Conner; James G. Dickson

    1980-01-01

    Censusing procedures that detect effects of habitat treatment on birds are outlined. We suggest that only relative values of bird species diversity, equitability, abundance, and species richness need be obtained. We also suggest that 4, 250-m strip transects per treatment and 8-10 trips over each transect are adequate. Aspects of sampling design that affect within-...

  6. Sample Size Calculations for Population Size Estimation Studies Using Multiplier Methods With Respondent-Driven Sampling Surveys.

    Science.gov (United States)

    Fearon, Elizabeth; Chabata, Sungai T; Thompson, Jennifer A; Cowan, Frances M; Hargreaves, James R

    2017-09-14

    While guidance exists for obtaining population size estimates using multiplier methods with respondent-driven sampling surveys, we lack specific guidance for making sample size decisions. To guide the design of multiplier method population size estimation studies using respondent-driven sampling surveys to reduce the random error around the estimate obtained. The population size estimate is obtained by dividing the number of individuals receiving a service or the number of unique objects distributed (M) by the proportion of individuals in a representative survey who report receipt of the service or object (P). We have developed an approach to sample size calculation, interpreting methods to estimate the variance around estimates obtained using multiplier methods in conjunction with research into design effects and respondent-driven sampling. We describe an application to estimate the number of female sex workers in Harare, Zimbabwe. There is high variance in estimates. Random error around the size estimate reflects uncertainty from M and P, particularly when the estimate of P in the respondent-driven sampling survey is low. As expected, sample size requirements are higher when the design effect of the survey is assumed to be greater. We suggest a method for investigating the effects of sample size on the precision of a population size estimate obtained using multipler methods and respondent-driven sampling. Uncertainty in the size estimate is high, particularly when P is small, so balancing against other potential sources of bias, we advise researchers to consider longer service attendance reference periods and to distribute more unique objects, which is likely to result in a higher estimate of P in the respondent-driven sampling survey.

  7. Survey of traditional Dai medicine reveals species confusion and potential safety concerns: a case study on Radix Clerodendri Japonicum.

    Science.gov (United States)

    Duan, Bao-Zhong; Fang, Hai-Lan; Li, Xi-Wen; Huang, Lin-Fang; Ping, Wang; Chen, Shi-Lin

    2017-06-01

    The adulteration of herbal products is a threat to consumer safety. In the present study, we surveyed the species composition of commercial Radix Clerodendri Japonicum products using DNA barcoding as a supervisory method. A reference database for plant-material DNA-barcode was successfully constructed with 48 voucher samples from 12 Clerodendrum species. The database was used to identify 27 Radix Clerodendri Japonicum decoction piece samples purchased from drug stores and hospitals. The DNA sequencing results revealed that only 1 decoction piece (3.70%) was authentic C. japonicum, as recorded in the Dai Pharmacopeia, whereas the other samples were all adulterants, indicating a potential safety issue. The results indicate that decoction pieces that are available in the market have complex origins and that DNA barcoding is a suitable tool for regulation of Dai medicines. Copyright © 2017 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.

  8. Whose sample is it anyway? Widespread misannotation of samples in transcriptomics studies [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Lilah Toker

    2016-08-01

    Full Text Available Concern about the reproducibility and reliability of biomedical research has been rising. An understudied issue is the prevalence of sample mislabeling, one impact of which would be invalid comparisons. We studied this issue in a corpus of human transcriptomics studies by comparing the provided annotations of sex to the expression levels of sex-specific genes. We identified apparent mislabeled samples in 46% of the datasets studied, yielding a 99% confidence lower-bound estimate for all studies of 33%. In a separate analysis of a set of datasets concerning a single cohort of subjects, 2/4 had mislabeled samples, indicating laboratory mix-ups rather than data recording errors. While the number of mixed-up samples per study was generally small, because our method can only identify a subset of potential mix-ups, our estimate is conservative for the breadth of the problem. Our findings emphasize the need for more stringent sample tracking, and that re-users of published data must be alert to the possibility of annotation and labelling errors.

  9. Study of an RF Direct Sampling Technique for Geodetic VLBI

    Science.gov (United States)

    Takefuji, K.; Kondo, T.; Sekido, M.; Ichikawa, R.; Kurihara, S.; Kokado, K.; Kawabata, R.

    2012-12-01

    Recently some digital samplers, which involve high RF frequency sensitivity, have been developed. We installed such samplers (sensitivity up to 24 GHz) at the Kashima 11-m station and the Tsukuba 32-m station (about 50 km baseline) in Japan and directly sampled X-band without any frequency conversion such as analog mixers. After the correlation process, we successfully detected first fringes at X-band. For the purpose of observing geodetic VLBI, we mixed signals of the S-band and the X-band just after the low noise amplifier. The mixed signal became overlapped and aliased baseband signals after 1024 MHz, 2-bit sampling. We could obtain four fringes (one from S-band and three from X-band), which came from the overlapped baseband signals, and successfully determined the baseline length.

  10. Multiwavelength studies of X-ray selected extragalactic sample

    OpenAIRE

    Mickaelian, A. M.; Paronyan, G. M.; Harutyunyan, G. S.; Abrahamyan, H. V.; Gyulzadyan, M. V.

    2015-01-01

    The joint catalogue of Active Galactic Nuclei selected from optical identifications of X-ray sources was created as a combination of two samples: Hamburg-ROSAT Catalogue (HRC) and Byurakan-Hamburg-ROSAT Catalogue (BHRC). Both are based on optical identifications of X-ray sources from ROSAT catalogues using low-dispersion spectra of Hamburg Quasar Survey (HQS). However, HRC and BHRC contain a number of misidentifications and using the recent optical and multiwavelength (MW) catalogues we have ...

  11. Interstitial water studies on small core samples, Leg 9

    Science.gov (United States)

    Sayles, F.L.; Waterman, L.S.; Manheim, F. T.

    1972-01-01

    The chemistry of the pore fluids obtained on Leg 9 is remarkable primarily in its constancy. Excepting silicon and strontium, only at one site do the concentrations of the major and minor constituents deviate notably from sea water concentrations (see Tables 1 and 2). The trends, or lack of them, seen in these samples have been discussed previously and only references will be given here. The constancy of composition and similarity to sea water is particularly noteworthy, as the sediments at all of the 9 sites are thought to be intruded by the basal basalt. The pore fluid chemistry exhibits no evidence of intrusion except possibly at Site 84.

  12. Random Sampling of Squamate Reptiles in Spanish Natural Reserves Reveals the Presence of Novel Adenoviruses in Lacertids (Family Lacertidae) and Worm Lizards (Amphisbaenia).

    Science.gov (United States)

    Szirovicza, Leonóra; López, Pilar; Kopena, Renáta; Benkő, Mária; Martín, José; Pénzes, Judit J

    2016-01-01

    Here, we report the results of a large-scale PCR survey on the prevalence and diversity of adenoviruses (AdVs) in samples collected randomly from free-living reptiles. On the territories of the Guadarrama Mountains National Park in Central Spain and of the Chafarinas Islands in North Africa, cloacal swabs were taken from 318 specimens of eight native species representing five squamate reptilian families. The healthy-looking animals had been captured temporarily for physiological and ethological examinations, after which they were released. We found 22 AdV-positive samples in representatives of three species, all from Central Spain. Sequence analysis of the PCR products revealed the existence of three hitherto unknown AdVs in 11 Carpetane rock lizards (Iberolacerta cyreni), nine Iberian worm lizards (Blanus cinereus), and two Iberian green lizards (Lacerta schreiberi), respectively. Phylogeny inference showed every novel putative virus to be a member of the genus Atadenovirus. This is the very first description of the occurrence of AdVs in amphisbaenian and lacertid hosts. Unlike all squamate atadenoviruses examined previously, two of the novel putative AdVs had A+T rich DNA, a feature generally deemed to mirror previous host switch events. Our results shed new light on the diversity and evolution of atadenoviruses.

  13. Sampling Key Populations for HIV Surveillance: Results From Eight Cross-Sectional Studies Using Respondent-Driven Sampling and Venue-Based Snowball Sampling.

    Science.gov (United States)

    Rao, Amrita; Stahlman, Shauna; Hargreaves, James; Weir, Sharon; Edwards, Jessie; Kochelani, Duncan; Kochelani, Duncan; Mavimbela, Mpumelelo; Baral, Stefan

    2017-10-20

    In using regularly collected or existing surveillance data to characterize engagement in human immunodeficiency virus (HIV) services among marginalized populations, differences in sampling methods may produce different pictures of the target population and may therefore result in different priorities for response. The objective of this study was to use existing data to evaluate the sample distribution of eight studies of female sex workers (FSW) and men who have sex with men (MSM), who were recruited using different sampling approaches in two locations within Sub-Saharan Africa: Manzini, Swaziland and Yaoundé, Cameroon. MSM and FSW participants were recruited using either respondent-driven sampling (RDS) or venue-based snowball sampling. Recruitment took place between 2011 and 2016. Participants at each study site were administered a face-to-face survey to assess sociodemographics, along with the prevalence of self-reported HIV status, frequency of HIV testing, stigma, and other HIV-related characteristics. Crude and RDS-adjusted prevalence estimates were calculated. Crude prevalence estimates from the venue-based snowball samples were compared with the overlap of the RDS-adjusted prevalence estimates, between both FSW and MSM in Cameroon and Swaziland. RDS samples tended to be younger (MSM aged 18-21 years in Swaziland: 47.6% [139/310] in RDS vs 24.3% [42/173] in Snowball, in Cameroon: 47.9% [99/306] in RDS vs 20.1% [52/259] in Snowball; FSW aged 18-21 years in Swaziland 42.5% [82/325] in RDS vs 8.0% [20/249] in Snowball; in Cameroon 15.6% [75/576] in RDS vs 8.1% [25/306] in Snowball). They were less educated (MSM: primary school completed or less in Swaziland 42.6% [109/310] in RDS vs 4.0% [7/173] in Snowball, in Cameroon 46.2% [138/306] in RDS vs 14.3% [37/259] in Snowball; FSW: primary school completed or less in Swaziland 86.6% [281/325] in RDS vs 23.9% [59/247] in Snowball, in Cameroon 87.4% [520/576] in RDS vs 77.5% [238/307] in Snowball) than the snowball

  14. n4Studies: Sample Size Calculation for an Epidemiological Study on a Smart Device

    Directory of Open Access Journals (Sweden)

    Chetta Ngamjarus

    2016-05-01

    Full Text Available Objective: This study was to develop a sample size application (called “n4Studies” for free use on iPhone and Android devices and to compare sample size functions between n4Studies with other applications and software. Methods: Objective-C programming language was used to create the application for the iPhone OS (operating system while javaScript, jquery mobile, PhoneGap and jstat were used to develop it for Android phones. Other sample size applications were searched from the Apple app and Google play stores. The applications’ characteristics and sample size functions were collected. Spearman’s rank correlation was used to investigate the relationship between number of sample size functions and price. Results: “n4Studies” provides several functions for sample size and power calculations for various epidemiological study designs. It can be downloaded from the Apple App and Google play store. Comparing n4Studies with other applications, it covers several more types of epidemiological study designs, gives similar results for estimation of infinite/finite population mean and infinite/finite proportion from GRANMO, for comparing two independent means from BioStats, for comparing two independent proportions from EpiCal application. When using the same parameters, n4Studies gives similar results to STATA, epicalc package in R, PS, G*Power, and OpenEpi. Conclusion: “n4Studies” can be an alternative tool for calculating the sample size. It may be useful to students, lecturers and researchers in conducting their research projects.

  15. Quantification of Leishmania (Viannia) Kinetoplast DNA in Ulcers of Cutaneous Leishmaniasis Reveals Inter-site and Inter-sampling Variability in Parasite Load.

    Science.gov (United States)

    Suárez, Milagros; Valencia, Braulio M; Jara, Marlene; Alba, Milena; Boggild, Andrea K; Dujardin, Jean-Claude; Llanos-Cuentas, Alejandro; Arevalo, Jorge; Adaui, Vanessa

    2015-01-01

    Cutaneous leishmaniasis (CL) is a skin disease caused by the protozoan parasite Leishmania. Few studies have assessed the influence of the sample collection site within the ulcer and the sampling method on the sensitivity of parasitological and molecular diagnostic techniques for CL. Sensitivity of the technique can be dependent upon the load and distribution of Leishmania amastigotes in the lesion. We applied a quantitative real-time PCR (qPCR) assay for Leishmania (Viannia) minicircle kinetoplast DNA (kDNA) detection and parasite load quantification in biopsy and scraping samples obtained from 3 sites within each ulcer (border, base, and center) as well as in cytology brush specimens taken from the ulcer base and center. A total of 248 lesion samples from 31 patients with laboratory confirmed CL of recent onset (≤3 months) were evaluated. The kDNA-qPCR detected Leishmania DNA in 97.6% (242/248) of the examined samples. Median parasite loads were significantly higher in the ulcer base and center than in the border in biopsies (PLeishmania amastigotes in acute CL ulcers, with higher parasite loads in the ulcer base and center, which has implications for bedside collection of diagnostic specimens. The use of scrapings and cytology brushes is recommended instead of the more invasive biopsy.

  16. NMR-based metabonomic studies reveal changes in the biochemical profile of plasma and urine from pigs fed high fibre rye bread

    DEFF Research Database (Denmark)

    Bertram, Hanne C.; Bach Knudsen, Knud E.; Serena, Anja

    2006-01-01

    This study presents an NMR-based metabonomic approach to elucidate the overall endogenous biochemical effects of a wholegrain diet. Two diets with similar levels of dietary fibre and macronutrients, but with contrasting levels of wholegrain ingredients, were prepared from wholegrain rye (wholegrain...... to a significantly higher content of betaine in WGD plasma samples compared with NWD samples. In an identical study with the same diets, urine samples were collected, and 1H NMR spectra were acquired on these. PLS-DA on spectra obtained for urine samples revealed changes in the intensities of spectral regions, which...

  17. Assessing the precision of a time-sampling-based study among GPs: balancing sample size and measurement frequency.

    Science.gov (United States)

    van Hassel, Daniël; van der Velden, Lud; de Bakker, Dinny; van der Hoek, Lucas; Batenburg, Ronald

    2017-12-04

    Our research is based on a technique for time sampling, an innovative method for measuring the working hours of Dutch general practitioners (GPs), which was deployed in an earlier study. In this study, 1051 GPs were questioned about their activities in real time by sending them one SMS text message every 3 h during 1 week. The required sample size for this study is important for health workforce planners to know if they want to apply this method to target groups who are hard to reach or if fewer resources are available. In this time-sampling method, however, standard power analyses is not sufficient for calculating the required sample size as this accounts only for sample fluctuation and not for the fluctuation of measurements taken from every participant. We investigated the impact of the number of participants and frequency of measurements per participant upon the confidence intervals (CIs) for the hours worked per week. Statistical analyses of the time-use data we obtained from GPs were performed. Ninety-five percent CIs were calculated, using equations and simulation techniques, for various different numbers of GPs included in the dataset and for various frequencies of measurements per participant. Our results showed that the one-tailed CI, including sample and measurement fluctuation, decreased from 21 until 3 h between one and 50 GPs. As a result of the formulas to calculate CIs, the increase of the precision continued and was lower with the same additional number of GPs. Likewise, the analyses showed how the number of participants required decreased if more measurements per participant were taken. For example, one measurement per 3-h time slot during the week requires 300 GPs to achieve a CI of 1 h, while one measurement per hour requires 100 GPs to obtain the same result. The sample size needed for time-use research based on a time-sampling technique depends on the design and aim of the study. In this paper, we showed how the precision of the

  18. Northeast Cooperative Research Study Fleet (SF) Program Biological Sampling Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Northeast Cooperative Research Study Fleet (SF) Program partners with a subset of commercial fishermen to collect high quality, high resolution, haul by haul...

  19. Study population, questionnaire, data management and sample description

    OpenAIRE

    Chiara de Waure; Andrea Poscia; Andrea Virdis; Maria Luisa Di Pietro; Walter Ricciardi

    2015-01-01

    INTRODUCTION: This article describes methodological issues of the "Sportello Salute Giovani" project ("Youth Health Information Desk"), a multicenter study aimed at assessing the health status and attitudes and behaviours of university students in Italy. MATERIALS AND METHODS: The questionnaire used to carry out the study was adapted from the Italian health behaviours in school-aged children (HBSC) project and consisted of 93 items addressing: demographics; nutritional habits and status; phys...

  20. Environmental sampling of Ceratonia siliqua (carob) trees in Spain reveals the presence of the rare Cryptococcus gattii genotype AFLP7/VGIV.

    Science.gov (United States)

    Linares, Carlos; Colom, María Francisca; Torreblanca, Marina; Esteban, Violeta; Romera, Álvaro; Hagen, Ferry

    2015-01-01

    Cryptococcus gattii is a pathogenic basidiomycetous yeast that is emerging in temperate climate zones worldwide. C. gattii has repetitively been isolated from numerous tree species. Ongoing environmental sampling and molecular characterization is essential to understand the presence of this primary pathogenic microorganism in the Mediterranean environment. To report the first isolation of the rare C. gattii genotype AFLP7/VGIV from the environment in Europe. Samples were collected from woody debris of carob trees (Ceratonia siliqua) and olive trees (Olea europaea) in El Perelló, Tarragona, Spain. Cryptococcus species were further characterized by using URA5-RFLP, MALDI-TOF, AFLP and MLST. The antifungal susceptibility profile to amphotericin B, 5-fluorocytosine, fluconazole, itraconazole, posaconazole and voriconazole was determined using Sensititre Yeast One and E-test. Cultures from one carob tree revealed the presence of ten Cryptococcus-like colonies. One colony was identified as C. gattii, and subsequent molecular characterization showed that it was an α mating-type that belonged to the rare genotype AFLP7/VGIV. Antifungal susceptibility testing showed values within the range of sensitivity described for other isolates of the same genotype and within the epidemiological cutoff values for this species. The isolation of the rare C. gattii genotype AFLP7/VGIV in Spain is the first report in the European environment, implying the possible presence in other regions of the Mediterranean area, and underlines that clinicians must be aware for C. gattii infections in healthy individuals. Copyright © 2014 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  1. Improvising in music: A learning biography study to reveal skill acquisition

    NARCIS (Netherlands)

    Wopereis, Iwan; Van Merriënboer, Jeroen; Kirschner, Paul A.

    2010-01-01

    Wopereis, I. G. J. H., Van Merriënboer, J. J. G., & Kirschner, P. A. (2010). Improvising in music: A learning biography study to reveal skill acquisition. In K. Gomez, L. Lyons, & J. Radinsky (Eds.), Proceedings of the 9th International Conference of the Learning Sciences: Vol. 2 (pp. 419-420).

  2. Practical Approaches For Determination Of Sample Size In Paired Case-Control Studies

    OpenAIRE

    Demirel, Neslihan; Ozlem EGE ORUC; Gurler, Selma

    2016-01-01

    Objective: Cross-over design or paired case control studies that are using in clinical studies are the methods of design of experiments which requires dependent samples. The problem of sample size determination is generally difficult step of planning the statistical design. The aim of this study is to provide the researchers a practical approach for determining the sample size in paired control studies. Material and Methods: In this study, determination of sample size is mentioned in detail i...

  3. Thermoluminescent properties studies of spodumene lilac sample to dosimetric applications

    Science.gov (United States)

    Lima, L. L.; Oliveira, R. A. P.; Lima, H. R. B. R.; Santos, H. N.; Santos, J. O.; Lima, A. F.; Souza, S. O.

    2010-11-01

    This work investigates the thermoluminescent (TL) dosimetric properties in natural spodumene, LiAlSi2O6, called kunzite, from Minas Gerais State, Brazil. The mineralogical and chemical composition of this material was identified by means X-ray fluorescence and X-ray diffraction. Some dosimetric properties were studied, such as thermoluminescent emission curves as function of gamma dose. The glow curves of annealed kunzite presented two very intense TL peaks at 215 °C (peak II) and 350 °C (peak III), after gamma irradiation, being both of first kinetic order. These two most prominent peaks analyzed do not presented a linear growth in the range of 50 to 5000 Gy in the range of doses studied. The peak II also presented a very short calculated lifetime, which means it is hardly can be used in dosimetry, while the peak III has a longer lifetime and could be used in some applications for high doses dosimetry.

  4. The Aggression Questionnaire: a validation study in student samples.

    Science.gov (United States)

    García-León, Ana; Reyes, Gustavo A; Vila, Jaime; Pérez, Nieves; Robles, Humbelina; Ramos, Manuel M

    2002-05-01

    The goal of this study was to examine the psychometric properties of the Aggression Questionnaire (AQ) in Spain. The AQ is a 29-item instrument designed to measure the different dimensions of the hostility/anger/aggression construct. It consists of 4 subscales that assess: (a) anger, (b) hostility, (c) verbal aggression, and (d) physical aggression. In Study 1, reliability, construct validity, and convergent validity were evaluated in a group of 384 male and female university students. Test-retest reliability was evaluated using a group of 154 male and female university students. The results of the factor analysis were similar to the scale structure claimed for this instrument. The subscales also showed internal consistency and stability over time. The AQ and its subscales were also compared with the scales and subscales of the Spielberger State-Trait Anger Expression Inventory (STAXI), the Cook-Medley Hostility Scale (Ho), the Buss-Durkee Hostility Inventory (BDHI), and the Jenkins Activity Survey-Form H (JASE-H). The results show that the AQ evaluates some aspects of anger, such as Anger-Trait and Anger-Out, rather than other elements, such as Anger-In or Anger-State. In Study 2, two new male groups were used to evaluate the criterion validity of the AQ: 57 prison inmates and 93 university students, finding that this instrument discriminated between the scores obtained by common offenders and university students.

  5. Situational runaway adolescents. A study on risk factors from a Turkish sample.

    Science.gov (United States)

    Ulusoy, Demet M; Demir, Nilüfer Ozcan

    2006-01-01

    Drawing on a sample of 726 non-clinical adolescents (aged 17-18 years) from high schools in Ankara, Turkey, this paper primarily aims to identify the risk factors related to situational run away behavior. This study was based on an ecological risk factors model and tried to discover the associations for runaways. Run away behavior is one of the problematic behaviors very commonly seen among Turkish adolescents. Regression analyses revealed that predictors for runaway behavior differed due to gender; while, delinquency, sexual intercourse, substance use, parental separation and suicidal ideation were the significant predictors for girl adolescent runaway behaviors, while lack of parental support and depression were the significant predictors for boy adolescent runaway behavior.

  6. Molecular detection methods and serotyping performed directly on clinical samples improve diagnostic sensitivity and reveal increased incidence of invasive disease by Streptococcus pneumoniae in Italian children.

    Science.gov (United States)

    Azzari, Chiara; Moriondo, Maria; Indolfi, Giuseppe; Massai, Cristina; Becciolini, Laura; de Martino, Maurizio; Resti, Massimo

    2008-10-01

    The aims of this study were to evaluate the incidence of invasive pneumococcal disease (IPD) in Italian children and perform serotyping by PCR-based assays directly on clinical samples. A 1-year paediatric (0-14 years) population-based surveillance study was designed to evaluate the incidence of IPD in the province of Florence, Italy, by cultural and molecular methods. Among 92 children (80 with pneumonia, 8 with meningitis/sepsis, 4 with arthritis), 4 cases of IPD were diagnosed both by culture and real-time PCR and 18 cases exclusively by molecular methods. The sensitivity of molecular methods was significantly higher than that of cultural methods (Cohen's kappa 0.41; McNemar P=0.000008). The incidence of IPD in children below 2 years of age was 11.5/100,000 and 51.8/100,000 by cultural and molecular methods, respectively. Pneumococcal serotyping by multiplex sequential PCR was obtained in 19/22 samples. Real-time PCR and multiplex sequential PCR can be used directly on biological samples, improving the ability to diagnose IPD. The incidence of IPD appears 5-10 times higher by PCR than by cultural methods.

  7. Oral leukoplakia in a South African sample: a clinicopathological study.

    Science.gov (United States)

    Chandran, R; Meer, S; Feller, L

    2013-09-01

    This study analysed differences in clinicopathological features of oral leukoplakia in different racial groups in the greater Johannesburg area of South Africa, with emphasis on the black population. The retrospective review included cases diagnosed clinically as oral leukoplakia and histologically as hyperkeratosis without dysplasia, hyperkeratosis with mild, moderate or severe dysplasia, and carcinoma in situ from 1990 to 2010. Age, gender, ethnicity, clinical appearance, site of lesion and tobacco smoking habit were recorded. Fourteen per cent of oral leukoplakia occurred in black South Africans compared with 80% in white South Africans. In contrast to whites, blacks were diagnosed with oral leukoplakia at a younger age; there were more men affected than women; and the proportion of idiopathic leukoplakia was greater. There were significantly more blacks (23%) than whites (13%) with non-homogenous leukoplakia and significantly more whites (51%) than blacks (23%) with dysplastic oral leukoplakia. This study suggests that oral leukoplakia, especially non-homogenous and idiopathic forms affects South African blacks less frequently than white South Africans; and in the former, it occurs more in men and at a younger age. These findings may provide some guidance in establishing screening policies for oral cancer, particularly suited for blacks. © 2012 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  8. Thermoluminescent properties studies of spodumene lilac sample to dosimetric applications

    Energy Technology Data Exchange (ETDEWEB)

    Lima, L L; Oliveira, R A P; Lima, H R B R; Santos, H N; Santos, J O; Lima, A F; Souza, S O, E-mail: sosouza@fisica.ufs.b

    2010-11-01

    This work investigates the thermoluminescent (TL) dosimetric properties in natural spodumene, LiAlSi{sub 2}O{sub 6}, called kunzite, from Minas Gerais State, Brazil. The mineralogical and chemical composition of this material was identified by means X-ray fluorescence and X-ray diffraction. Some dosimetric properties were studied, such as thermoluminescent emission curves as function of gamma dose. The glow curves of annealed kunzite presented two very intense TL peaks at 215 {sup 0}C (peak II) and 350 {sup 0}C (peak III), after gamma irradiation, being both of first kinetic order. These two most prominent peaks analyzed do not presented a linear growth in the range of 50 to 5000 Gy in the range of doses studied. The peak II also presented a very short calculated lifetime, which means it is hardly can be used in dosimetry, while the peak III has a longer lifetime and could be used in some applications for high doses dosimetry.

  9. Effectiveness of quadrat sampling on terrestrial cave fauna survey - a case study in a Neotropical cave

    OpenAIRE

    Maria Elina Bichuette; Luiza Bertelli Simões; Diego Monteiro von Schimonsky; Jonas Eduardo Gallão

    2015-01-01

    Quadrat sampling is a method used for a long time in plant ecology studies but only recently it has been used with focus on fauna. For the cave fauna samplings, there are rare works applying this methodology. The present study compared the methods of quadrat sampling with direct search qualitative for terrestrial cave fauna. For this, we conducted five sampling collections in a limestone cave in central Brazil. Quadrat sampling contributed with 121 exclusive species and 716 specimens and dire...

  10. [A comparative study of different sampling designs in fish community estimation].

    Science.gov (United States)

    Zhao, Jing; Zhang, Shou-Yu; Lin, Jun; Zhou, Xi-Jie

    2014-04-01

    The study of fishery community ecology depends on quality and quantity of data collected from well-designed sampling programs. The optimal sampling design must be cost-efficient, and the sampling results have been recognized as a significant factor affecting resources management. In this paper, the performances of stationary sampling, simple random sampling and stratified random sampling in estimating fish community were compared based on computer simulation by design effect (De), relative error (REE) and relative bias (RB). The results showed that, De of stationary sampling (average De was 3.37) was worse than simple random sampling and stratified random sampling (average De was 0.961). Stratified random sampling performed best among the three designs in terms of De, REE and RB. With the sample size increased, the design effect of stratified random sampling decreased but the precision and accuracy increased.

  11. Study of interaction between croscarmellose and escitalopram during sample preparation.

    Science.gov (United States)

    Larsen, Jesper; Melander, Claes

    2012-10-01

    During routine analysis of an escitalopram tablet formulation, it was seen that there was a systematic deviation between content uniformity (CU - one tablet analysis) and assay analysis (ten pooled tablets). In the presence of the excipients from the tablet, it was found that the extraction of the active pharmaceutical ingredient (API) was incomplete. It was shown that the commonly used tablet disintegrant croscarmellose sodium (crosslinked carboxy-methyl cellulose) had a significant interaction with escitalopram. This was later found to be the explanation for the lower extraction during assay testing. Under normal conditions, the extraction took place in acidic medium which caused protonation of the amine and thereby the interaction of charged species in solution. The interaction of API was studied further with pure croscarmellose and the entire tablet matrix. A range of conditions was considered, including altering extraction volumes, organic solvents, pH of the extraction solvent, and addition of competitive binder in various concentrations. It was seen that arginine was the most effective cationic competitive binder of those tested and that adding it at a suitable concentration level could significantly improve the analytical methods. In the present case, an improvement in recovery was from 98.5% to almost 100% was achieved.

  12. Table 1. Description of samples used for simulation study with S1, 2 ...

    Indian Academy of Sciences (India)

    priyanka

    Description of samples used for simulation study with S1, 2, 3. Sample name Treatment_time Treatment_agent Sample source. GEO sample. (GSM) file Ids. 1. Lm_Adult1. 0 h. Listeria monocytogenes. Peripheral blood. GSM1467819. 2 h. GSM1467820. 6 h. GSM1467821. 2. Lm_Adult2. 0 h. Peripheral blood. GSM1467822.

  13. Low incidence of clonality in cold water corals revealed through the novel use of standardized protocol adapted to deep sea sampling

    Science.gov (United States)

    Becheler, Ronan; Cassone, Anne-Laure; Noel, Philippe; Mouchel, Olivier; Morrison, Cheryl L.; Arnaud-Haond, Sophie

    2017-01-01

    Sampling in the deep sea is a technical challenge, which has hindered the acquisition of robust datasets that are necessary to determine the fine-grained biological patterns and processes that may shape genetic diversity. Estimates of the extent of clonality in deep-sea species, despite the importance of clonality in shaping the local dynamics and evolutionary trajectories, have been largely obscured by such limitations. Cold-water coral reefs along European margins are formed mainly by two reef-building species, Lophelia pertusa and Madrepora oculata. Here we present a fine-grained analysis of the genotypic and genetic composition of reefs occurring in the Bay of Biscay, based on an innovative deep-sea sampling protocol. This strategy was designed to be standardized, random, and allowed the georeferencing of all sampled colonies. Clonal lineages discriminated through their Multi-Locus Genotypes (MLG) at 6–7 microsatellite markers could thus be mapped to assess the level of clonality and the spatial spread of clonal lineages. High values of clonal richness were observed for both species across all sites suggesting a limited occurrence of clonality, which likely originated through fragmentation. Additionally, spatial autocorrelation analysis underlined the possible occurrence of fine-grained genetic structure in several populations of both L. pertusa and M. oculata. The two cold-water coral species examined had contrasting patterns of connectivity among canyons, with among-canyon genetic structuring detected in M. oculata, whereas L. pertusa was panmictic at the canyon scale. This study exemplifies that a standardized, random and georeferenced sampling strategy, while challenging, can be applied in the deep sea, and associated benefits outlined here include improved estimates of fine grained patterns of clonality and dispersal that are comparable across sites and among species.

  14. Low incidence of clonality in cold water corals revealed through the novel use of a standardized protocol adapted to deep sea sampling

    Science.gov (United States)

    Becheler, Ronan; Cassone, Anne-Laure; Noël, Philippe; Mouchel, Olivier; Morrison, Cheryl L.; Arnaud-Haond, Sophie

    2017-11-01

    Sampling in the deep sea is a technical challenge, which has hindered the acquisition of robust datasets that are necessary to determine the fine-grained biological patterns and processes that may shape genetic diversity. Estimates of the extent of clonality in deep-sea species, despite the importance of clonality in shaping the local dynamics and evolutionary trajectories, have been largely obscured by such limitations. Cold-water coral reefs along European margins are formed mainly by two reef-building species, Lophelia pertusa and Madrepora oculata. Here we present a fine-grained analysis of the genotypic and genetic composition of reefs occurring in the Bay of Biscay, based on an innovative deep-sea sampling protocol. This strategy was designed to be standardized, random, and allowed the georeferencing of all sampled colonies. Clonal lineages discriminated through their Multi-Locus Genotypes (MLG) at 6-7 microsatellite markers could thus be mapped to assess the level of clonality and the spatial spread of clonal lineages. High values of clonal richness were observed for both species across all sites suggesting a limited occurrence of clonality, which likely originated through fragmentation. Additionally, spatial autocorrelation analysis underlined the possible occurrence of fine-grained genetic structure in several populations of both L. pertusa and M. oculata. The two cold-water coral species examined had contrasting patterns of connectivity among canyons, with among-canyon genetic structuring detected in M. oculata, whereas L. pertusa was panmictic at the canyon scale. This study exemplifies that a standardized, random and georeferenced sampling strategy, while challenging, can be applied in the deep sea, and associated benefits outlined here include improved estimates of fine grained patterns of clonality and dispersal that are comparable across sites and among species.

  15. High Throughput qPCR Expression Profiling of Circulating MicroRNAs Reveals Minimal Sex- and Sample Timing-Related Variation in Plasma of Healthy Volunteers.

    Science.gov (United States)

    Mooney, Catherine; Raoof, Rana; El-Naggar, Hany; Sanz-Rodriguez, Amaya; Jimenez-Mateos, Eva M; Henshall, David C

    2015-01-01

    MicroRNAs are a class of small non-coding RNA that regulate gene expression at a post-transcriptional level. MicroRNAs have been identified in various body fluids under normal conditions and their stability as well as their dysregulation in disease opens up a new field for biomarker study. However, diurnal and day-to-day variation in plasma microRNA levels, and differential regulation between males and females, may affect biomarker stability. A QuantStudio 12K Flex Real-Time PCR System was used to profile plasma microRNA levels using OpenArray in male and female healthy volunteers, in the morning and afternoon, and at four time points over a one month period. Using this system we were able to run four OpenArray plates in a single run, the equivalent of 32 traditional 384-well qPCR plates or 12,000 data points. Up to 754 microRNAs can be identified in a single plasma sample in under two hours. 108 individual microRNAs were identified in at least 80% of all our samples which compares favourably with other reports of microRNA profiles in serum or plasma in healthy adults. Many of these microRNAs, including miR-16-5p, miR-17-5p, miR-19a-3p, miR-24-3p, miR-30c-5p, miR-191-5p, miR-223-3p and miR-451a are highly expressed and consistent with previous studies using other platforms. Overall, microRNA levels were very consistent between individuals, males and females, and time points and we did not detect significant differences in levels of microRNAs. These results suggest the suitability of this platform for microRNA profiling and biomarker discovery and suggest minimal confounding influence of sex or sample timing. However, the platform has not been subjected to rigorous validation which must be demonstrated in future biomarker studies where large differences may exist between disease and control samples.

  16. High Throughput qPCR Expression Profiling of Circulating MicroRNAs Reveals Minimal Sex- and Sample Timing-Related Variation in Plasma of Healthy Volunteers.

    Directory of Open Access Journals (Sweden)

    Catherine Mooney

    Full Text Available MicroRNAs are a class of small non-coding RNA that regulate gene expression at a post-transcriptional level. MicroRNAs have been identified in various body fluids under normal conditions and their stability as well as their dysregulation in disease opens up a new field for biomarker study. However, diurnal and day-to-day variation in plasma microRNA levels, and differential regulation between males and females, may affect biomarker stability. A QuantStudio 12K Flex Real-Time PCR System was used to profile plasma microRNA levels using OpenArray in male and female healthy volunteers, in the morning and afternoon, and at four time points over a one month period. Using this system we were able to run four OpenArray plates in a single run, the equivalent of 32 traditional 384-well qPCR plates or 12,000 data points. Up to 754 microRNAs can be identified in a single plasma sample in under two hours. 108 individual microRNAs were identified in at least 80% of all our samples which compares favourably with other reports of microRNA profiles in serum or plasma in healthy adults. Many of these microRNAs, including miR-16-5p, miR-17-5p, miR-19a-3p, miR-24-3p, miR-30c-5p, miR-191-5p, miR-223-3p and miR-451a are highly expressed and consistent with previous studies using other platforms. Overall, microRNA levels were very consistent between individuals, males and females, and time points and we did not detect significant differences in levels of microRNAs. These results suggest the suitability of this platform for microRNA profiling and biomarker discovery and suggest minimal confounding influence of sex or sample timing. However, the platform has not been subjected to rigorous validation which must be demonstrated in future biomarker studies where large differences may exist between disease and control samples.

  17. The effect of a biological explanation on attitudes towards homosexual persons. A Swedish national sample study.

    Science.gov (United States)

    Landén, Mikael; Innala, Sune

    2002-01-01

    Studies assessing attitudes towards homosexuals have revealed widespread homophobia. The first aim of this study was to assess potential changes in public attitudes after important legislative changes related to homosexuals in Sweden. The second aim was to test whether the attitudes differ: 1) between people who believe in biological vs. people who believe in psychological theories in explanation of homosexuality, 2) between men and women, and 3) between the older and younger age groups. To this end, a questionnaire survey of a representative, randomly selected, national sample of 992 adult Swedish residents was carried out. The response rate was 67%, which is considered high in this context. In conclusion, this study demonstrates a clear-cut change towards more tolerant attitudes towards homosexual men and women compared to earlier studies. The reasons for this change is discussed; among factors of importance are anti-discrimination legislation, increased visibility of homosexual people, and that more people currently regard homosexuality as a biologically determined, natural variant of human sexuality than was the case 10 years ago. In accordance, this study gave further support to the notion that those who believe that homosexuality is caused by biological factors have a less restrictive view on homosexuality than do people who hold a psychological view.

  18. Selenium isotope studies in plants. Development and validation of a novel geochemical tool and its application to organic samples

    Energy Technology Data Exchange (ETDEWEB)

    Banning, Helena

    2016-03-12

    Selenium (Se), being an essential nutrient and a toxin, enters the food chain mainly via plants. Selenium isotope signatures were proved to be an excellent redox tracer, making it a promising tool for the exploration of the Se cycle in plants. The analytical method is sensitive on organic samples and requires particular preparation methods, which were developed and validated in this study. Plant cultivation setups revealed the applicability of these methods to trace plant internal processes.

  19. An integrated multi-omics study revealed metabolic alterations underlying the effects of coffee consumption.

    Directory of Open Access Journals (Sweden)

    Shoko Takahashi

    Full Text Available Many epidemiological studies have indicated that coffee consumption may reduce the risks of developing obesity and diabetes, but the underlying mechanisms of these effects are poorly understood. Our previous study revealed the changes on gene expression profiles in the livers of C57BL/6J mice fed a high-fat diet containing three types of coffee (caffeinated, decaffeinated and green unroasted coffee, using DNA microarrays. The results revealed remarkable alterations in lipid metabolism-related molecules which may be involved in the anti-obesity effects of coffee. We conducted the present study to further elucidate the metabolic alterations underlying the effects of coffee consumption through comprehensive proteomic and metabolomic analyses. Proteomics revealed an up-regulation of isocitrate dehydrogenase (a key enzyme in the TCA cycle and its related proteins, suggesting increased energy generation. The metabolomics showed an up-regulation of metabolites involved in the urea cycle, with which the transcriptome data were highly consistent, indicating accelerated energy expenditure. The TCA cycle and the urea cycle are likely be accelerated in a concerted manner, since they are directly connected by mutually providing each other's intermediates. The up-regulation of these pathways might result in a metabolic shift causing increased ATP turnover, which is related to the alterations of lipid metabolism. This mechanism may play an important part in the suppressive effects of coffee consumption on obesity, inflammation, and hepatosteatosis. This study newly revealed global metabolic alterations induced by coffee intake, providing significant insights into the association between coffee intake and the prevention of type 2 diabetes, utilizing the benefits of multi-omics analyses.

  20. An integrated multi-omics study revealed metabolic alterations underlying the effects of coffee consumption.

    Science.gov (United States)

    Takahashi, Shoko; Saito, Kenji; Jia, Huijuan; Kato, Hisanori

    2014-01-01

    Many epidemiological studies have indicated that coffee consumption may reduce the risks of developing obesity and diabetes, but the underlying mechanisms of these effects are poorly understood. Our previous study revealed the changes on gene expression profiles in the livers of C57BL/6J mice fed a high-fat diet containing three types of coffee (caffeinated, decaffeinated and green unroasted coffee), using DNA microarrays. The results revealed remarkable alterations in lipid metabolism-related molecules which may be involved in the anti-obesity effects of coffee. We conducted the present study to further elucidate the metabolic alterations underlying the effects of coffee consumption through comprehensive proteomic and metabolomic analyses. Proteomics revealed an up-regulation of isocitrate dehydrogenase (a key enzyme in the TCA cycle) and its related proteins, suggesting increased energy generation. The metabolomics showed an up-regulation of metabolites involved in the urea cycle, with which the transcriptome data were highly consistent, indicating accelerated energy expenditure. The TCA cycle and the urea cycle are likely be accelerated in a concerted manner, since they are directly connected by mutually providing each other's intermediates. The up-regulation of these pathways might result in a metabolic shift causing increased ATP turnover, which is related to the alterations of lipid metabolism. This mechanism may play an important part in the suppressive effects of coffee consumption on obesity, inflammation, and hepatosteatosis. This study newly revealed global metabolic alterations induced by coffee intake, providing significant insights into the association between coffee intake and the prevention of type 2 diabetes, utilizing the benefits of multi-omics analyses.

  1. Revealing Praxis: A Study of Professional Learning and Development as a Beginning Social Studies Teacher Educator

    Science.gov (United States)

    Ritter, Jason K.

    2010-01-01

    This self-study reports on the professional learning and development of a beginning social studies teacher educator via an examination of the evolving relationship between the author's beliefs and practices during his first three years preparing social studies teachers. Throughout this time data were systematically collected in the form of written…

  2. Optical Methods for Identifying Hard Clay Core Samples During Petrophysical Studies

    Science.gov (United States)

    Morev, A. V.; Solovyeva, A. V.; Morev, V. A.

    2018-01-01

    X-ray phase analysis of the general mineralogical composition of core samples from one of the West Siberian fields was performed. Electronic absorption spectra of the clay core samples with an added indicator were studied. The speed and availability of applying the two methods in petrophysical laboratories during sample preparation for standard and special studies were estimated.

  3. Work Sampling Study of an Engineering Professor during a Regular Contract Period

    Science.gov (United States)

    Brink, Jan; McDonald, Dale B.

    2015-01-01

    Work sampling is a technique that has been employed in industry and fields such as healthcare for some time. It is a powerful technique, and an alternative to conventional stop watch time studies, used by industrial engineers to focus upon random work sampling observations. This study applies work sampling to the duties performed by an individual…

  4. Self-sampling is appropriate for detection of Staphylococcus aureus: a validation study

    Directory of Open Access Journals (Sweden)

    van Cleef Brigitte AGL

    2012-11-01

    Full Text Available Abstract Background Studies frequently use nasal swabs to determine Staphylococcus aureus carriage. Self-sampling would be extremely useful in an outhospital research situation, but has not been studied in a healthy population. We studied the similarity of self-samples and investigator-samples in nares and pharynxes of healthy study subjects (hospital staff in the Netherlands. Methods One hundred and five nursing personnel members were sampled 4 times in random order after viewing an instruction paper: 1 nasal self-sample, 2 pharyngeal self-sample, 3 nasal investigator-sample, and 4 pharyngeal investigator-sample. Results For nasal samples, agreement is 93% with a kappa coefficient of 0.85 (95% CI 0.74-0.96, indicating excellent agreement, for pharyngeal samples agreement is 83% and the kappa coefficient is 0.60 (95% CI 0.43-0.76, indicating good agreement. In both sampling sites self-samples even detected more S. aureus than investigator-samples. Conclusions This means that self-samples are appropriate for detection of Staphylococcus aureus and methicillin-resistant Staphylococcus aureus.

  5. A molecular study of the tardigrade Echiniscus testudo (Echiniscidae reveals low DNA sequence diversity over a large geographical area

    Directory of Open Access Journals (Sweden)

    Aslak JØRGENSEN

    2007-09-01

    Full Text Available In the present study we investigate the genetic diversity within the asexually reproducing tardigrade Echiniscus testudo. The present study is the first to sample a tardigrade species for comparison of DNA sequence diversity between widely separated samples. Echiniscus testudo was sampled at 13 localities spanning three continents. DNA sequences of the mitochondrial COI gene and the nuclear ITS2 sequence were used to investigate the genetic diversity and phylogeographic structure of the various asexual lineages. Terrestrial tardigrades with the capability of entering a cryptobiotic state are assumed to have a high passive dispersal potential through airborne transport. Our results show moderate (ITS2 to high (COI haplotype diversity and low sequence diversity that indicate evolution of haplotypes within distinct asexual lineages and a high dispersal potential. No isolation by distance was detected by Mantel tests. Different phylogeny inference methods (neighbor-joining, maximum parsimony, maximum likelihood and Bayesian inference revealed little topological resolution, but minimum spanning networks showed some phylogeographic patterns. The COI and ITS2 minimum spanning networks show patterns that indicate dispersal of several haplotypes from founding populations. In conclusion our data show a low genetic diversity and a relatively high haplotype diversity indicating that E. testudo is a young species with a high dispersal potential.

  6. Grab vs. composite sampling of particulate materials with significant spatial heterogeneity--a simulation study of "correct sampling errors".

    Science.gov (United States)

    Minkkinen, Pentti O; Esbensen, Kim H

    2009-10-19

    Sampling errors can be divided into two classes, incorrect sampling and correct sampling errors. Incorrect sampling errors arise from incorrectly designed sampling equipment or procedures. Correct sampling errors are due to the heterogeneity of the material in sampling targets. Excluding the incorrect sampling errors, which can all be eliminated in practice although informed and diligent work is often needed, five factors dominate sampling variance: two factors related to material heterogeneity (analyte concentration; distributional heterogeneity) and three factors related to the sampling process itself (sample type, sample size, sampling modus). Due to highly significant interactions, a comprehensive appreciation of their combined effects is far from trivial and has in fact never been illustrated in detail. Heterogeneous materials can be well characterized by the two first factors, while all essential sampling process characteristics can be summarized by combinations of the latter three. We here present simulations based on an experimental design that varies all five factors. Within the framework of the Theory of Sampling, the empirical Total Sampling Error is a function of the fundamental sampling error and the grouping and segregation error interacting with a specific sampling process. We here illustrate absolute and relative sampling variance levels resulting from a wide array of simulated repeated samplings and express the effects by pertinent lot mean estimates and associated Root Mean Squared Errors/sampling variances, covering specific combinations of materials' heterogeneity and typical sampling procedures as used in current science, technology and industry. Factors, levels and interactions are varied within limits selected to match realistic materials and sampling situations that mimic, e.g., sampling for genetically modified organisms; sampling of geological drill cores; sampling during off-loading 3-dimensional lots (shiploads, railroad cars, truckloads

  7. Religious Studies and Transcultural Studies: : Revealing a Cosmos Not Known Before?

    OpenAIRE

    Berg, Esther; Rakow, K.

    2016-01-01

    Drawing on our research on Pentecostal Christianity in Singapore, the article introduces the transcultural approach and discusses its possible contributions to the academic study of religions. After a short overview of the history of the discipline, the article introduces our understanding of the transcultural approach and a discussion of similar or related approaches in Religious Studies, which emphasize relationality and polyvocality in the study of religious practices and discourses. The f...

  8. Comparative Study of the Effect of Sample Pretreatment and Extraction on the Determination of Flavonoids from Lemon (Citrus limon)

    Science.gov (United States)

    Ledesma-Escobar, Carlos A.; Priego-Capote, Feliciano; Luque de Castro, María D.

    2016-01-01

    Background Flavonoids have shown to exert multiple beneficial effects on human health, being also appreciated by both food and pharmaceutical industries. Citrus fruits are a key source of flavonoids, thus promoting studies to obtain them. Characteristics of these studies are the discrepancies among sample pretreatments and among extraction methods, and also the scant number of comparative studies developed so far. Objective Evaluate the effect of both the sample pretreatment and the extraction method on the profile of flavonoids isolated from lemon. Results Extracts from fresh, lyophilized and air-dried samples obtained by shaking extraction (SE), ultrasound-assisted extraction (USAE), microwave-assisted extraction (MAE) and superheated liquid extraction (SHLE) were analyzed by LC–QTOF MS/MS, and 32 flavonoids were tentatively identified using MS/MS information. ANOVA applied to the data from fresh and dehydrated samples and from extraction by the different methods revealed that 26 and 32 flavonoids, respectively, were significant (p≤0.01). The pairwise comparison (Tukey HSD; p≤0.01) showed that lyophilized samples are more different from fresh samples than from air-dried samples; also, principal component analysis (PCA) showed a clear discrimination among sample pretreatment strategies and suggested that such differences are mainly created by the abundance of major flavonoids. On the other hand, pairwise comparison of extraction methods revealed that USAE and MAE provided quite similar extracts, being SHLE extracts different from the other two. In this case, PCA showed a clear discrimination among extraction methods, and their position in the scores plot suggests a lower abundance of flavonoids in the extracts from SHLE. In the two PCA the loadings plots revealed a trend to forming groups according to flavonoid aglycones. Conclusions The present study shows clear discrimination caused by both sample pretreatments and extraction methods. Under the studied

  9. Comparative Study of the Effect of Sample Pretreatment and Extraction on the Determination of Flavonoids from Lemon (Citrus limon).

    Science.gov (United States)

    Ledesma-Escobar, Carlos A; Priego-Capote, Feliciano; Luque de Castro, María D

    2016-01-01

    Flavonoids have shown to exert multiple beneficial effects on human health, being also appreciated by both food and pharmaceutical industries. Citrus fruits are a key source of flavonoids, thus promoting studies to obtain them. Characteristics of these studies are the discrepancies among sample pretreatments and among extraction methods, and also the scant number of comparative studies developed so far. Evaluate the effect of both the sample pretreatment and the extraction method on the profile of flavonoids isolated from lemon. Extracts from fresh, lyophilized and air-dried samples obtained by shaking extraction (SE), ultrasound-assisted extraction (USAE), microwave-assisted extraction (MAE) and superheated liquid extraction (SHLE) were analyzed by LC-QTOF MS/MS, and 32 flavonoids were tentatively identified using MS/MS information. ANOVA applied to the data from fresh and dehydrated samples and from extraction by the different methods revealed that 26 and 32 flavonoids, respectively, were significant (p≤0.01). The pairwise comparison (Tukey HSD; p≤0.01) showed that lyophilized samples are more different from fresh samples than from air-dried samples; also, principal component analysis (PCA) showed a clear discrimination among sample pretreatment strategies and suggested that such differences are mainly created by the abundance of major flavonoids. On the other hand, pairwise comparison of extraction methods revealed that USAE and MAE provided quite similar extracts, being SHLE extracts different from the other two. In this case, PCA showed a clear discrimination among extraction methods, and their position in the scores plot suggests a lower abundance of flavonoids in the extracts from SHLE. In the two PCA the loadings plots revealed a trend to forming groups according to flavonoid aglycones. The present study shows clear discrimination caused by both sample pretreatments and extraction methods. Under the studied conditions, liophilization provides extracts

  10. Comparative Study of the Effect of Sample Pretreatment and Extraction on the Determination of Flavonoids from Lemon (Citrus limon.

    Directory of Open Access Journals (Sweden)

    Carlos A Ledesma-Escobar

    Full Text Available Flavonoids have shown to exert multiple beneficial effects on human health, being also appreciated by both food and pharmaceutical industries. Citrus fruits are a key source of flavonoids, thus promoting studies to obtain them. Characteristics of these studies are the discrepancies among sample pretreatments and among extraction methods, and also the scant number of comparative studies developed so far.Evaluate the effect of both the sample pretreatment and the extraction method on the profile of flavonoids isolated from lemon.Extracts from fresh, lyophilized and air-dried samples obtained by shaking extraction (SE, ultrasound-assisted extraction (USAE, microwave-assisted extraction (MAE and superheated liquid extraction (SHLE were analyzed by LC-QTOF MS/MS, and 32 flavonoids were tentatively identified using MS/MS information. ANOVA applied to the data from fresh and dehydrated samples and from extraction by the different methods revealed that 26 and 32 flavonoids, respectively, were significant (p≤0.01. The pairwise comparison (Tukey HSD; p≤0.01 showed that lyophilized samples are more different from fresh samples than from air-dried samples; also, principal component analysis (PCA showed a clear discrimination among sample pretreatment strategies and suggested that such differences are mainly created by the abundance of major flavonoids. On the other hand, pairwise comparison of extraction methods revealed that USAE and MAE provided quite similar extracts, being SHLE extracts different from the other two. In this case, PCA showed a clear discrimination among extraction methods, and their position in the scores plot suggests a lower abundance of flavonoids in the extracts from SHLE. In the two PCA the loadings plots revealed a trend to forming groups according to flavonoid aglycones.The present study shows clear discrimination caused by both sample pretreatments and extraction methods. Under the studied conditions, liophilization provides

  11. The dynamics of attachment insecurity and paranoid thoughts: An experience sampling study.

    Science.gov (United States)

    Sitko, Katarzyna; Varese, Filippo; Sellwood, William; Hammond, Amy; Bentall, Richard

    2016-12-30

    It has been proposed that insecure attachment can have adverse effects on the course of psychosis once symptoms have emerged. There is longitudinal evidence that increased insecure attachment is associated with increased severity of psychotic symptoms. The present study examined whether in the flow of daily life attachment insecurity fluctuates, whether elevated stress precedes the occurrence of attachment insecurity, and whether elevated attachment insecurity precedes the occurrence of paranoia. Twenty clinical participants with a psychosis-spectrum diagnosis and twenty controls were studied over six consecutive days using the experience sampling method (ESM). The findings revealed that fluctuations in attachment insecurity were significantly higher in the clinical group, that elevated stress predicted a subsequent increase in attachment insecurity, and that elevated attachment insecurity predicted a subsequent increase in paranoia; this effect was not observed in auditory hallucinations once co-occurring symptoms were controlled for. Finally, although previous ESM studies have shown that low self-esteem precedes the occurrence of paranoia, attachment insecurity continued to predict paranoia even when self-esteem was controlled for. The findings suggest that attachment security may be associated with a lower risk of paranoia, and that psychological interventions should address attachment beliefs and work towards establishing a sense of attachment security. Copyright © 2016. Published by Elsevier Ireland Ltd.

  12. MarcoPolo-R: Near Earth Asteroid Sample Return Mission in ESA assessment study phase

    Science.gov (United States)

    Barucci, M. A.; Michel, P.; Cheng, A.; Böhnhardt, H.; Brucato, J. R.; Dotto, E.; Ehrenfreund, P.; Franchi, I. A.; Green, S. F.; Lara, L. M.; Marty, B.; Koschny, D.

    2012-04-01

    MarcoPolo-R is a sample return mission to a primitive Near-Earth Asteroid (NEA) selected in February 2011 for the Assessment Study Phase in the framework of ESA's Cosmic Vision 2 program. MarcoPolo-R is a European-led mission with a proposed NASA contribution. MarcoPolo-R takes advantage of three industrial studies completed as part of the previous Marco Polo mission (see ESA/SRE (2009)3). The aim of the new Assessment Study is to reduce the cost of the mission while maintaining its high science level, on the basis of advanced studies and technologies, optimization of the mission, and consolidation of the collaboration with other partners (NASA, AEB…). The main goal of the MarcoPolo-R mission is to return unaltered NEA material for detailed analysis in ground-based laboratories. The limited sampling provided by meteorites does not offer the most primitive material available in near-Earth space. More primitive material, having experienced less alteration on the asteroid, will be more friable and would not survive atmospheric entry in any discernible amount. Only in Earth laboratories can instruments measure the individual components of the complex mixture of materials that forms an asteroid regolith with the necessary precision and sensitivity to determine their precise chemical and isotopic composition. Such measurements are vital for revealing the evidence of stellar, interstellar medium, pre-solar nebula and parent body processes that are retained in primitive asteroidal material, unaltered by atmospheric entry or terrestrial contamination. It is no surprise therefore that sample return missions are considered a priority by a number of the leading space agencies. MarcoPolo-R will rendezvous with a unique kind of target, a primitive binary NEA, scientifically characterize it at multiple scales, and return a unique pristine sample to Earth unaltered by the atmospheric entry process or terrestrial weathering. The baseline target of MarcoPolo-R is the primitive

  13. Evolutionary Meta-Analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery

    Science.gov (United States)

    Dudley, Joel T.; Chen, Rong; Sanderford, Maxwell; Butte, Atul J.; Kumar, Sudhir

    2012-01-01

    Genome-wide disease association studies contrast genetic variation between disease cohorts and healthy populations to discover single nucleotide polymorphisms (SNPs) and other genetic markers revealing underlying genetic architectures of human diseases. Despite scores of efforts over the past decade, many reproducible genetic variants that explain substantial proportions of the heritable risk of common human diseases remain undiscovered. We have conducted a multispecies genomic analysis of 5,831 putative human risk variants for more than 230 disease phenotypes reported in 2,021 studies. We find that the current approaches show a propensity for discovering disease-associated SNPs (dSNPs) at conserved genomic positions because the effect size (odds ratio) and allelic P value of genetic association of an SNP relates strongly to the evolutionary conservation of their genomic position. We propose a new measure for ranking SNPs that integrates evolutionary conservation scores and the P value (E-rank). Using published data from a large case-control study, we demonstrate that E-rank method prioritizes SNPs with a greater likelihood of bona fide and reproducible genetic disease associations, many of which may explain greater proportions of genetic variance. Therefore, long-term evolutionary histories of genomic positions offer key practical utility in reassessing data from existing disease association studies, and in the design and analysis of future studies aimed at revealing the genetic basis of common human diseases. PMID:22389448

  14. What about N? A methodological study of sample-size reporting in focus group studies

    Science.gov (United States)

    2011-01-01

    Background Focus group studies are increasingly published in health related journals, but we know little about how researchers use this method, particularly how they determine the number of focus groups to conduct. The methodological literature commonly advises researchers to follow principles of data saturation, although practical advise on how to do this is lacking. Our objectives were firstly, to describe the current status of sample size in focus group studies reported in health journals. Secondly, to assess whether and how researchers explain the number of focus groups they carry out. Methods We searched PubMed for studies that had used focus groups and that had been published in open access journals during 2008, and extracted data on the number of focus groups and on any explanation authors gave for this number. We also did a qualitative assessment of the papers with regard to how number of groups was explained and discussed. Results We identified 220 papers published in 117 journals. In these papers insufficient reporting of sample sizes was common. The number of focus groups conducted varied greatly (mean 8.4, median 5, range 1 to 96). Thirty seven (17%) studies attempted to explain the number of groups. Six studies referred to rules of thumb in the literature, three stated that they were unable to organize more groups for practical reasons, while 28 studies stated that they had reached a point of saturation. Among those stating that they had reached a point of saturation, several appeared not to have followed principles from grounded theory where data collection and analysis is an iterative process until saturation is reached. Studies with high numbers of focus groups did not offer explanations for number of groups. Too much data as a study weakness was not an issue discussed in any of the reviewed papers. Conclusions Based on these findings we suggest that journals adopt more stringent requirements for focus group method reporting. The often poor and

  15. What about N? A methodological study of sample-size reporting in focus group studies.

    Science.gov (United States)

    Carlsen, Benedicte; Glenton, Claire

    2011-03-11

    Focus group studies are increasingly published in health related journals, but we know little about how researchers use this method, particularly how they determine the number of focus groups to conduct. The methodological literature commonly advises researchers to follow principles of data saturation, although practical advise on how to do this is lacking. Our objectives were firstly, to describe the current status of sample size in focus group studies reported in health journals. Secondly, to assess whether and how researchers explain the number of focus groups they carry out. We searched PubMed for studies that had used focus groups and that had been published in open access journals during 2008, and extracted data on the number of focus groups and on any explanation authors gave for this number. We also did a qualitative assessment of the papers with regard to how number of groups was explained and discussed. We identified 220 papers published in 117 journals. In these papers insufficient reporting of sample sizes was common. The number of focus groups conducted varied greatly (mean 8.4, median 5, range 1 to 96). Thirty seven (17%) studies attempted to explain the number of groups. Six studies referred to rules of thumb in the literature, three stated that they were unable to organize more groups for practical reasons, while 28 studies stated that they had reached a point of saturation. Among those stating that they had reached a point of saturation, several appeared not to have followed principles from grounded theory where data collection and analysis is an iterative process until saturation is reached. Studies with high numbers of focus groups did not offer explanations for number of groups. Too much data as a study weakness was not an issue discussed in any of the reviewed papers. Based on these findings we suggest that journals adopt more stringent requirements for focus group method reporting. The often poor and inconsistent reporting seen in these

  16. What about N? A methodological study of sample-size reporting in focus group studies

    Directory of Open Access Journals (Sweden)

    Glenton Claire

    2011-03-01

    Full Text Available Abstract Background Focus group studies are increasingly published in health related journals, but we know little about how researchers use this method, particularly how they determine the number of focus groups to conduct. The methodological literature commonly advises researchers to follow principles of data saturation, although practical advise on how to do this is lacking. Our objectives were firstly, to describe the current status of sample size in focus group studies reported in health journals. Secondly, to assess whether and how researchers explain the number of focus groups they carry out. Methods We searched PubMed for studies that had used focus groups and that had been published in open access journals during 2008, and extracted data on the number of focus groups and on any explanation authors gave for this number. We also did a qualitative assessment of the papers with regard to how number of groups was explained and discussed. Results We identified 220 papers published in 117 journals. In these papers insufficient reporting of sample sizes was common. The number of focus groups conducted varied greatly (mean 8.4, median 5, range 1 to 96. Thirty seven (17% studies attempted to explain the number of groups. Six studies referred to rules of thumb in the literature, three stated that they were unable to organize more groups for practical reasons, while 28 studies stated that they had reached a point of saturation. Among those stating that they had reached a point of saturation, several appeared not to have followed principles from grounded theory where data collection and analysis is an iterative process until saturation is reached. Studies with high numbers of focus groups did not offer explanations for number of groups. Too much data as a study weakness was not an issue discussed in any of the reviewed papers. Conclusions Based on these findings we suggest that journals adopt more stringent requirements for focus group method

  17. Religious Studies and Transcultural Studies: : Revealing a Cosmos Not Known Before?

    NARCIS (Netherlands)

    Berg, Esther; Rakow, K.

    2016-01-01

    Drawing on our research on Pentecostal Christianity in Singapore, the article introduces the transcultural approach and discusses its possible contributions to the academic study of religions. After a short overview of the history of the discipline, the article introduces our understanding of the

  18. Sampling estimators of total mill receipts for use in timber product output studies

    Science.gov (United States)

    John P. Brown; Richard G. Oderwald

    2012-01-01

    Data from the 2001 timber product output study for Georgia was explored to determine new methods for stratifying mills and finding suitable sampling estimators. Estimators for roundwood receipts totals comprised several types: simple random sample, ratio, stratified sample, and combined ratio. Two stratification methods were examined: the Dalenius-Hodges (DH) square...

  19. The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation.

    Science.gov (United States)

    Shao, Qiang; Gao, Yi Qin

    2011-10-07

    Molecular dynamics simulations using the integrated tempering sampling method were performed for the folding of wild-type B domain of protein A (BdpA). Starting from random and stretched structures, these simulations allow us to fold this protein into the native-like structure frequently, achieving very small backbone (1.7 Å) and all heavy-atom root-mean-square deviation (2.6 Å). Therefore, the method used here increases the efficiency of configuration sampling and thermodynamics characterization by molecular dynamics simulation. Although inconsistency exists between the calculation and experiments for the absolute stabilities, as a limitation of the force field parameters, the calculated order of helix stability (H3 > H2 > H1) is consistent with that determined by experiments for individual separate helices. The lowest free energy folding pathway of BdpA was found to start with a barrierless and non-cooperative structural collapse from the entirely extended (E) state, which leads to a physiologically unfolded (P) state consisting of multiple stable structures with few native inter-helical hydrophobic interactions formed. In the P state, only H3 is fully structured. The final formation of H1 (and to a lesser extent, H2) in the folded (F) state requires the packing of the inter-helical hydrophobic contacts. In addition, it was found that stabilities of backbone hydrogen bonds are significantly affected by their positions relative to the inter-helical hydrophobic core. As temperature increases, the stability of the hydrogen bonds exposed to the solvent tends to increase while that of the hydrogen bonds buried within the hydrophobic core decreases. Finally, we discuss implications of this study on the general folding mechanism of proteins. © 2011 American Institute of Physics

  20. Insights into antiviral innate immunity revealed by studying hepatitis C virus.

    Science.gov (United States)

    Horner, Stacy M

    2015-08-01

    Experimental studies on the interactions of the positive strand RNA virus hepatitis C virus (HCV) with the host have contributed to several discoveries in the field of antiviral innate immunity. These include revealing the antiviral sensing pathways that lead to the induction of type I interferon (IFN) during HCV infection and also the importance of type III IFNs in the antiviral immune response to HCV. These studies on HCV/host interactions have contributed to our overall understanding of viral sensing and viral evasion of the antiviral intracellular innate immune response. In this review, I will highlight how these studies of HCV/host interactions have led to new insights into antiviral innate immunity. Overall, I hope to emphasize that studying antiviral immunity in the context of virus infection is necessary to fully understand antiviral immunity and how it controls the outcome of viral infection. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Concept study for a low cost near-term Mars surface sample return mission

    Science.gov (United States)

    Draper, C.; Kemble, S.; Parkinson, R.; Smith, M.; Thatcher, J.; Reedman, T.; Sallaberger, C.; Pillinger, C.; Sims, M.

    Man has always had a fascination with the red planet and the quest to reveal its secrets. Although in the past this ques t has been confined to observation from afar and in-situ analysis by dated technology, the chance now exists to extract far more from the Martian surface than ever before - by bringing it home. The idea of a Mars Sample Return mission is not a new phenomenon and plans have been in existence for the last 30 years. The trouble is that these have always been restricted on the grounds of technology, politics and, more predominantly, cost. Many such missions have been estimated at well over 1billion, with huge development times and multiple launches for various mission stages. Plans for direct return missions from the Martian surface had the drawbacks of (a) being too expensive in terms of the launch costs required to lift the propellant needed for return and (b) being too slow if an in-situ resource propellant production technique was used. The alternative solution was to return via a rendezvous in Mars orbit, thus reducing the mass to be transported to and from the Martian surface. The most popular of the orbital rendezvous options involved the launch of a combined Mars Ascent Vehicle/Mars Rover mission to gather samples in readiness for a subsequent return to Earth via a second mission that would deliver an Earth Return Vehicle into Mars orbit with which to transport the samples back. This method had the disadvantages of incurring large costs from the prolonged stay at Mars and high launch costs due to the necessity of two separate launches. The concept of this study is to utilise the orbital rendezvous method but incorporate each of the elements into a single mission (i.e. one launch) using mature and affordable lander technology to return a small regolith core sample. This not only reduces launch and development costs, making the mission more `affordable', but also lowers the risk of mission failure compared to the two-launch method. An

  2. Parametric and nonparametric two-sample tests for feature screening in class comparison: a simulation study

    Directory of Open Access Journals (Sweden)

    Elena Landoni

    2016-06-01

    Full Text Available Background. The identification of a location-, scale- and shape-sensitive test to detect differentially expressed features between two comparison groups represents a key point in high dimensional studies. The most commonly used tests refer to differences in location, but general distributional discrepancies might be important to reveal differential biological processes.                                                         Methods. A simulation study was conducted to compare the performance of a set of two-sample tests, i.e. Student's t, Welch's t, Wilcoxon-Mann-Whitney, Podgor-Gastwirth PG2, Cucconi, Kolmogorov-Smirnov (KS, Cramer-von Mises (CvM, Anderson-Darling (AD and Zhang tests (ZK, ZC and ZA which were investigated under different distributional patterns. We applied the same tests to a real data example.                   Results. AD, CvM, ZA and ZC tests proved to be the most sensitive tests in mixture distribution patterns, while still maintaining a high power in normal distribution patterns. At best, the AD test showed a loss in power of ~ 2% in the comparison of two normal distributions, but a gain of ~ 32% with mixture distributions respect to the parametric tests. Accordingly, the AD test detected the greatest number of differentially expressed features in the real data application.   Conclusion. The tests for the general two-sample problem introduce a more general concept of 'differential expression', thus overcoming the limitations of the other tests restricted to specific moments of the feature distributions. In particular, the AD test should be considered as a powerful alternative to the parametric tests for feature screening in order to keep as many discriminative features as possible for the class prediction analysis.

  3. How many is enough? Determining optimal sample sizes for normative studies in pediatric neuropsychology.

    Science.gov (United States)

    Bridges, Ana J; Holler, Karen A

    2007-11-01

    The purpose of this investigation was to determine how confidence intervals (CIs) for pediatric neuropsychological norms vary as a function of sample size, and to determine optimal sample sizes for normative studies. First, the authors calculated 95% CIs for a set of published pediatric norms for four commonly used neuropsychological instruments. Second, 95% CIs were calculated for varying sample size (from n = 5 to n = 500). Results suggest that some pediatric norms have unacceptably wide CIs, and normative studies ought optimally to use 50 to 75 participants per cell. Smaller sample sizes may lead to overpathologizing results, while the cost of obtaining larger samples may not be justifiable.

  4. Definitions of love in a sample of British women: an empirical study using Q methodology.

    Science.gov (United States)

    Watts, Simon; Stenner, Paul

    2014-09-01

    Social psychological research has increasingly acknowledged that any pretensions to a singular theory of love should be replaced with a concern about its affirmation and what people actually say and do in love's name. Lee's (1977) love styles research and Sternberg's (1995) theory of love as a story are prime examples. Despite traditional definitions of love in western cultures being dominated by feminine images and tales of gender difference, however, the personal definitions and experiences of women have received comparatively little empirical attention, particularly in recent years and despite some well-documented changes in their cultural circumstances. This study remedies that situation through presentation of a Q methodological study in which a convenience sample of 59 British women were asked to Q sort 54 single-word descriptors of love to define love as they had experienced it. Factor analysis of the resulting Q sorts revealed six distinct definitions of love, interpreted as 'attraction, passion & romance', 'unconditional love', 'sex & fun', 'friendship & spirituality', 'a permanent commitment', and 'separate people, separate lives'. The six definitions are then discussed in terms of their allegiance to traditionally feminine and/or masculine values and as a means of highlighting the changing face of Britain's relational culture. © 2013 The British Psychological Society.

  5. Fungal diversity of "Tomme d'Orchies" cheese during the ripening process as revealed by a metagenomic study.

    Science.gov (United States)

    Ceugniez, Alexandre; Taminiau, Bernard; Coucheney, Françoise; Jacques, Philippe; Delcenserie, Véronique; Daube, Georges; Drider, Djamel

    2017-10-03

    Tomme d'Orchies is an artisanal pressed and uncooked cheese produced and marketed in the north of France. This study aimed at showing the fungal microbiota evolution of this cheese using a metagenetic based Illumina technology targeting the ITS2 domain of 5.8S fungal rDNAs. To this end, samples were taken from the rind and the core of different cheeses, after 0, 1, 3, 7, 14 and 21days of ripening. The data underpinned the prevalence of Yarrowia lipolytica and Galactomyces geotrichum for both microbiotas. Unusual species including Clavispora lusitaniae, Kazachstania unispora and Cladosporium cladosporioides were also detected, but their origins remain to be ascertained. The metagenomic revealed also the presence of Kluyveromyces and Debaryomyces species. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Comparative Morphology, Transcription, and Proteomics Study Revealing the Key Molecular Mechanism of Camphor on the Potato Tuber Sprouting Effect

    Directory of Open Access Journals (Sweden)

    Li-Qin Li

    2017-10-01

    Full Text Available Sprouting regulation in potato tubers is important for improving commercial value and producing new plants. Camphor shows flexible inhibition of tuber sprouting and prolongs the storage period of potato, but its underlying mechanism remains unknown. The results of the present study suggest that camphor inhibition caused bud growth deformities and necrosis, but after moving to more ventilated conditions, new sprouts grew from the bud eye of the tuber. Subsequently, the sucrose and fructose contents as well as polyphenol oxidase (PPO activity were assessed after camphor inhibition. Transcription and proteomics data from dormancy (D, sprouting (S, camphor inhibition (C, and recovery sprouting (R samples showed changes in the expression levels of approximately 4000 transcripts, and 700 proteins showed different abundances. KEGG (Kyoto encyclopaedia of genes and genomes pathway analysis of the transcription levels indicated that phytohormone synthesis and signal transduction play important roles in tuber sprouting. Camphor inhibited these processes, particularly for gibberellic acid, brassinosteroids, and ethylene, leading to dysregulation of physiological processes such as cutin, suberine and wax biosynthesis, fatty acid elongation, phenylpropanoid biosynthesis, and starch and sucrose metabolism, resulting in bud necrosis and prolonged storage periods. The KEGG pathway correlation between transcripts and proteins revealed that terpenoid backbone biosynthesis and plant–pathogen interaction pathways showed significant differences in D vs. S samples, but 13 pathways were remarkably different in the D vs. C groups, as camphor inhibition significantly increased both the transcription levels and protein abundance of pathogenesis-related protein PR-10a (or STH-2, the pathogenesis-related P2-like precursor protein, and the kirola-like protein as compared to sprouting. In recovery sprouting, these genes and proteins were decreased at both the

  7. Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C.

    Science.gov (United States)

    Ramos-González, Pedro Luis; Chabi-Jesus, Camila; Guerra-Peraza, Orlene; Breton, Michèle Claire; Arena, Gabriella Dias; Nunes, Maria Andreia; Kitajima, Elliot Watanabe; Machado, Marcos Antonio; Freitas-Astúa, Juliana

    2016-06-06

    Citrus leprosis virus C (CiLV-C) causes a severe disease affecting citrus orchards in the Western hemisphere. This study reveals the molecular variability of the virus by analyzing four genomic regions (p29, p15, MP and RNA2-intergenic region) distributed over its two RNAs. Nucleotide diversity (π) values were relatively low but statistically different over the analyzed genes and subpopulations, indicating their distinct evolutionary history. Values of πp29 and πMP were higher than those of πp15 and πRNA2-IR, whereas πMP was increased due to novel discovered isolates phylogenetically clustered in a divergent clade that we called SJP. Isolate BR_SP_SJP_01 RNA1 and RNA2 sequences, clade SJP, showed an identity of 85.6% and 88.4%, respectively, with those corresponding to CiLV-C, the type member of the genus Cilevirus, and its RNA2 5'-proximal region was revealed as a minor donor in a putative inter-clade recombination event. In addition to citrus, BR_SP_SJP_01 naturally infects the weed Commelina benghalensis and is efficiently transmitted by Brevipalpus yothersi mites. Our data demonstrated that negative selection was the major force operating in the evaluated viral coding regions and defined amino acids putatively relevant for the biological function of cilevirus proteins. This work provides molecular tools and sets up a framework for further epidemiological studies.

  8. Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C

    Directory of Open Access Journals (Sweden)

    Pedro Luis Ramos-González

    2016-06-01

    Full Text Available Citrus leprosis virus C (CiLV-C causes a severe disease affecting citrus orchards in the Western hemisphere. This study reveals the molecular variability of the virus by analyzing four genomic regions (p29, p15, MP and RNA2-intergenic region distributed over its two RNAs. Nucleotide diversity (π values were relatively low but statistically different over the analyzed genes and subpopulations, indicating their distinct evolutionary history. Values of πp29 and πMP were higher than those of πp15 and πRNA2–IR, whereas πMP was increased due to novel discovered isolates phylogenetically clustered in a divergent clade that we called SJP. Isolate BR_SP_SJP_01 RNA1 and RNA2 sequences, clade SJP, showed an identity of 85.6% and 88.4%, respectively, with those corresponding to CiLV-C, the type member of the genus Cilevirus, and its RNA2 5′-proximal region was revealed as a minor donor in a putative inter-clade recombination event. In addition to citrus, BR_SP_SJP_01 naturally infects the weed Commelina benghalensis and is efficiently transmitted by Brevipalpus yothersi mites. Our data demonstrated that negative selection was the major force operating in the evaluated viral coding regions and defined amino acids putatively relevant for the biological function of cilevirus proteins. This work provides molecular tools and sets up a framework for further epidemiological studies.

  9. Memory retrieval of smoking-related images induce greater insula activation as revealed by an fMRI-based delayed matching to sample task.

    Science.gov (United States)

    Janes, Amy C; Ross, Robert S; Farmer, Stacey; Frederick, Blaise B; Nickerson, Lisa D; Lukas, Scott E; Stern, Chantal E

    2015-03-01

    Nicotine dependence is a chronic and difficult to treat disorder. While environmental stimuli associated with smoking precipitate craving and relapse, it is unknown whether smoking cues are cognitively processed differently than neutral stimuli. To evaluate working memory differences between smoking-related and neutral stimuli, we conducted a delay-match-to-sample (DMS) task concurrently with functional magnetic resonance imaging (fMRI) in nicotine-dependent participants. The DMS task evaluates brain activation during the encoding, maintenance and retrieval phases of working memory. Smoking images induced significantly more subjective craving, and greater midline cortical activation during encoding in comparison to neutral stimuli that were similar in content yet lacked a smoking component. The insula, which is involved in maintaining nicotine dependence, was active during the successful retrieval of previously viewed smoking versus neutral images. In contrast, neutral images required more prefrontal cortex-mediated active maintenance during the maintenance period. These findings indicate that distinct brain regions are involved in the different phases of working memory for smoking-related versus neutral images. Importantly, the results implicate the insula in the retrieval of smoking-related stimuli, which is relevant given the insula's emerging role in addiction. © 2013 Society for the Study of Addiction.

  10. Non–invasive sampling of endangered neotropical river otters reveals high levels of dispersion in the Lacantun River System of Chiapas, Mexico

    Directory of Open Access Journals (Sweden)

    Ortega, J.

    2012-01-01

    Full Text Available Patterns of genetic dispersion, levels of population genetic structure, and movement of the neotropical river otter (Lontra longicaudis were investigated by screening eight polymorphic microsatellites from DNA extracted from fecal samples, collected in a hydrologic system of the Lacandon rainforest in Chiapas, Mexico. A total of 34 unique genotypes were detected from our surveys along six different rivers, and the effect of landscape genetic structure was studied. We recovered 16 of the 34 individuals in multiple rivers at multiple times. We found high levels of dispersion and low levels of genetic differentiation among otters from the six surveyed rivers (P > 0.05, except for the pairwise comparison among the Lacantún and José rivers (P < 0.05. We recommend that conservation management plans for the species consider the entire Lacantún River System and its tributaries as a single management unit to ensure the maintenance of current levels of population genetic diversity, because the population analyzed seems to follow a source–sink dynamic mainly determined by the existence of the major river.

  11. Is it really theoretical? A review of sampling in grounded theory studies in nursing journals.

    Science.gov (United States)

    McCrae, Niall; Purssell, Edward

    2016-10-01

    Grounded theory is a distinct method of qualitative research, where core features are theoretical sampling and constant comparative analysis. However, inconsistent application of these activities has been observed in published studies. This review assessed the use of theoretical sampling in grounded theory studies in nursing journals. An adapted systematic review was conducted. Three leading nursing journals (2010-2014) were searched for studies stating grounded theory as the method. Sampling was assessed using a concise rating tool. A high proportion (86%) of the 134 articles described an iterative process of data collection and analysis. However, half of the studies did not demonstrate theoretical sampling, with many studies declaring or indicating a purposive sampling approach throughout. Specific reporting guidelines for grounded theory studies should be developed to ensure that study reports describe an iterative process of fieldwork and theoretical development. © 2016 John Wiley & Sons Ltd.

  12. Children with dyslexia reveal abnormal native language representations: evidence from a study of mismatch negativity.

    Science.gov (United States)

    Bruder, Jennifer; Leppänen, Paavo H T; Bartling, Jürgen; Csépe, Valéria; Démonet, Jean-Francois; Schulte-Körne, Gerd

    2011-08-01

    Although a deficit perceiving phonemes, as indexed by the mismatch negativity (MMN), is apparent in developmental dyslexia (DD), studies have not yet addressed whether this deficit might be a result of deficient native language speech representations. The present study examines how a native-vowel prototype and an atypical vowel are discriminated by 9-year-old children with (n = 14) and without (n = 12) DD. MMN was elicited in all conditions in both groups. The control group revealed enhanced MMN to the native-vowel prototype in comparison to the atypical vowel. Children with DD did not show enhanced MMN amplitude to the native-vowel prototype, suggesting impaired tuning to native language speech representations. Furthermore, higher MMN amplitudes to the native-vowel prototype correlated with more advanced reading (r = - .47) and spelling skills (r = - .52). Copyright © 2011 Society for Psychophysiological Research.

  13. Age and perceived effects of erotica-pornography: a national sample study.

    Science.gov (United States)

    Merritt, C G; Gerstl, J E; LoSciuto, L A

    1975-11-01

    In the spring of 1970, a national sample survey of 2486 adults (aged 20-80) was studied to ascertain U.S. public attitudes toward and experience with erotic materials. Twelve items measured whether or not those interviewed believed that looking at or reading sexual materials had certain effects on themselves or others. Initial description of the results revealed a considerable diversity of opinion. This report provides a multistage typology of those item responses, beginning with characterization of items as positive, neutral, or negative in effect. Striking age gradients were observed at each stage in the typology formation. At first glance, these results are hardly surprising, yet introduction of controls for level of education, gender, and reported previous levels of actual exposure to erotica did not appreciably change the age-graded response pattern. The last stage in the typology contained four levels and showed an attribute solely desirable and/or neutral effects to erotica. Those who expressed neutral and mixed (strongly positive and negative) views were somewhat older. The next age norms about explicit sexual materials took on a perception of no effects or a position of uncertainty. Finally, those who believed that pornography has largely or solely undesirable effects on its consumers were oldest. The replicability of the pattern suggests a specific order in the underlying process of change in values (historical and/or intraindividual).

  14. Stable RNA markers for identification of blood and saliva stains revealed from whole genome expression analysis of time-wise degraded samples

    NARCIS (Netherlands)

    D. Zubakov (Dmitry); E.E. Hanekamp (Eline); M. Kokshoorn (Mieke); W.F.J. van IJcken (Wilfred); M.H. Kayser (Manfred)

    2008-01-01

    textabstractHuman body fluids such as blood and saliva represent the most common source of biological material found at a crime scene. Reliable tissue identification in forensic science can reveal significant insights into crime scene reconstruction and can thus contribute toward solving crimes.

  15. Talaromyces marneffei Genomic, Transcriptomic, Proteomic and Metabolomic Studies Reveal Mechanisms for Environmental Adaptations and Virulence

    Directory of Open Access Journals (Sweden)

    Susanna K. P. Lau

    2017-06-01

    Full Text Available Talaromyces marneffei is a thermally dimorphic fungus causing systemic infections in patients positive for HIV or other immunocompromised statuses. Analysis of its ~28.9 Mb draft genome and additional transcriptomic, proteomic and metabolomic studies revealed mechanisms for environmental adaptations and virulence. Meiotic genes and genes for pheromone receptors, enzymes which process pheromones, and proteins involved in pheromone response pathway are present, indicating its possibility as a heterothallic fungus. Among the 14 Mp1p homologs, only Mp1p is a virulence factor binding a variety of host proteins, fatty acids and lipids. There are 23 polyketide synthase genes, one for melanin and two for mitorubrinic acid/mitorubrinol biosynthesis, which are virulence factors. Another polyketide synthase is for biogenesis of the diffusible red pigment, which consists of amino acid conjugates of monascorubin and rubropunctatin. Novel microRNA-like RNAs (milRNAs and processing proteins are present. The dicer protein, dcl-2, is required for biogenesis of two milRNAs, PM-milR-M1 and PM-milR-M2, which are more highly expressed in hyphal cells. Comparative transcriptomics showed that tandem repeat-containing genes were overexpressed in yeast phase, generating protein polymorphism among cells, evading host’s immunity. Comparative proteomics between yeast and hyphal cells revealed that glyceraldehyde-3-phosphate dehydrogenase, up-regulated in hyphal cells, is an adhesion factor for conidial attachment.

  16. Nutrition and health - the association between eating behavior and various health parameters: a matched sample study.

    Directory of Open Access Journals (Sweden)

    Nathalie T Burkert

    Full Text Available Population-based studies have consistently shown that our diet has an influence on health. Therefore, the aim of our study was to analyze differences between different dietary habit groups in terms of health-related variables. The sample used for this cross-sectional study was taken from the Austrian Health Interview Survey AT-HIS 2006/07. In a first step, subjects were matched according to their age, sex, and socioeconomic status (SES. After matching, the total number of subjects included in the analysis was 1320 (N = 330 for each form of diet - vegetarian, carnivorous diet rich in fruits and vegetables, carnivorous diet less rich in meat, and carnivorous diet rich in meat. Analyses of variance were conducted controlling for lifestyle factors in the following domains: health (self-assessed health, impairment, number of chronic conditions, vascular risk, health care (medical treatment, vaccinations, preventive check-ups, and quality of life. In addition, differences concerning the presence of 18 chronic conditions were analyzed by means of Chi-square tests. Overall, 76.4% of all subjects were female. 40.0% of the individuals were younger than 30 years, 35.4% between 30 and 49 years, and 24.0% older than 50 years. 30.3% of the subjects had a low SES, 48.8% a middle one, and 20.9% had a high SES. Our results revealed that a vegetarian diet is related to a lower BMI and less frequent alcohol consumption. Moreover, our results showed that a vegetarian diet is associated with poorer health (higher incidences of cancer, allergies, and mental health disorders, a higher need for health care, and poorer quality of life. Therefore, public health programs are needed in order to reduce the health risk due to nutritional factors.

  17. In silico studies revealed multiple neurological targets for the antidepressant molecule ursolic acid.

    Science.gov (United States)

    Singla, Rajeev K; Scotti, Luciana; Dubey, Ashok K

    2016-12-29

    Ursolic acid, a bioactive pentacyclic triterpenoid had been evaluated for its interaction with the neurological targets associated with antidepressant drugs. Current study was to mechanistically analyze the probable site of action for ursolic acid on the target proteins. Ursolic acid has been docked with monoamine oxidase isoforms: MAO-A and MAO-B, LeuT (homologue of SERT, NET, DAT) and Human C-terminal CAP1 using GRIP docking methodology. Results revealed its non-selective antidepressant action with strong binding affinity towards LeuT and MAO-A proteins, which was found to be comparable with the reference ligands like chlorgyline, clomipramine, sertraline and deprenyl / selegiline. Significant binding affinity of ursolic acid was seen with MAO-A, which indicated its potential role in other neurological disorders, for example, Alzheimer's disease and Parkinson disease besides depression.

  18. Genetic diversity study of the yeast Saccharomyces bayanus var. uvarum reveals introgressed subtelomeric Saccharomyces cerevisiae genes.

    Science.gov (United States)

    Naumova, Elena S; Naumov, Gennadi I; Michailova, Yulia V; Martynenko, Nikolay N; Masneuf-Pomarède, Isabelle

    2011-01-01

    Intraspecies polymorphism of the yeast Saccharomyces bayanus var. uvarum was studied using the polymerase chain reaction with a microsatellite primer (GTG)(5). Sixty-nine strains of different origins were analyzed. There existed a correlation between PCR patterns of the strains and the source of their isolation: the type of wine and the particular winemaking region. Southern hybridization analysis revealed for the first time introgression between Saccharomyces cerevisiae and S. bayanus var. uvarum. Two strains isolated from alcoholic beverages in Hungary and identified by genetic analysis as S. bayanus var. uvarum were found to harbor a number of S. cerevisiae subtelomeric sequences: Y', SUC, RTM and MAL. Copyright © 2010 Institut Pasteur. Published by Elsevier SAS. All rights reserved.

  19. Surface phenomena revealed by in situ imaging: studies from adhesion, wear and cutting

    Science.gov (United States)

    Viswanathan, Koushik; Mahato, Anirban; Yeung, Ho; Chandrasekar, Srinivasan

    2017-03-01

    Surface deformation and flow phenomena are ubiquitous in mechanical processes. In this work we present an in situ imaging framework for studying a range of surface mechanical phenomena at high spatial resolution and across a range of time scales. The in situ framework is capable of resolving deformation and flow fields quantitatively in terms of surface displacements, velocities, strains and strain rates. Three case studies are presented demonstrating the power of this framework for studying surface deformation. In the first, the origin of stick-slip motion in adhesive polymer interfaces is investigated, revealing a intimate link between stick-slip and surface wave propagation. Second, the role of flow in mediating formation of surface defects and wear particles in metals is analyzed using a prototypical sliding process. It is shown that conventional post-mortem observation and inference can lead to erroneous conclusions with regard to formation of surface cracks and wear particles. The in situ framework is shown to unambiguously capture delamination wear in sliding. Third, material flow and surface deformation in a typical cutting process is analyzed. It is shown that a long-standing problem in the cutting of annealed metals is resolved by the imaging, with other benefits such as estimation of energy dissipation and power from the flow fields. In closure, guidelines are provided for profitably exploiting in situ observations to study large-strain deformation, flow and friction phenomena at surfaces that display a variety of time-scales.

  20. Storage and shipping of tissue samples for DNA analyses: A case study on earthworms ?

    OpenAIRE

    Straube, Daniela; Juen, Anita

    2013-01-01

    Nowadays, molecular analyses play an important role in studies of soil dwelling animals, for example in taxonomy, phylogeography or food web analyses. The quality of the DNA, used for later molecular analyses, is an important factor and depends on collection and preservation of samples prior to DNA extraction. Ideally, DNA samples are frozen immediately upon collection, but if samples are collected in the field, suitable preservation methods might be limited due to unavailability of resources...

  1. Long-stay psychiatric patients: a prospective study revealing persistent antipsychotic-induced movement disorder.

    Directory of Open Access Journals (Sweden)

    P Roberto Bakker

    Full Text Available OBJECTIVE: The purpose of this study was to assess the frequency of persistent drug-induced movement disorders namely, tardive dyskinesia (TD, parkinsonism, akathisia and tardive dystonia in a representative sample of long-stay patients with chronic severe mental illness. METHOD: Naturalistic study of 209, mainly white, antipsychotic-treated patients, mostly diagnosed with psychotic disorder. Of this group, the same rater examined 194 patients at least two times over a 4-year period, with a mean follow-up time of 1.1 years, with validated scales for TD, parkinsonism, akathisia, and tardive dystonia. RESULTS: The frequencies of persistent movement disorders in the sample were 28.4% for TD, 56.2% for parkinsonism, 4.6% for akathisia and 5.7% for tardive dystonia. Two-thirds of the participants displayed at least one type of persistent movement disorder. CONCLUSIONS: Persistent movement disorder continues to be the norm for long-stay patients with chronic mental illness and long-term antipsychotic treatment. Measures are required to remedy this situation.

  2. In silico sampling reveals the effect of clustering and shows that the log-normal rank abundance curve is an artefact

    NARCIS (Netherlands)

    Neuteboom, J.H.; Struik, P.C.

    2005-01-01

    The impact of clustering on rank abundance, species-individual (S-N)and species-area curves was investigated using a computer programme for in silico sampling. In a rank abundance curve the abundances of species are plotted on log-scale against species sequence. In an S-N curve the number of species

  3. Mitochondrial DNA from archived tissue samples kept in formalin for forensic odontology studies.

    Science.gov (United States)

    Pandey, Rahul; Mehrotra, Divya; Kowtal, Pradnya; Mahdi, Abbas Ali; Sarin, Rajiv

    2014-01-01

    Samples used for DNA isolation to be used for forensic odontology studies are often limited. The possibility to use tissue samples stored in formalin for a prolonged period, which contains nucleic acids of questionable quality, opens exciting possibilities for genetic and molecular biology studies useful in speciality of forensic odontology. The present study defines substantial modification of existing protocols for total genomic isolation including mitochondrial DNA and proves the utility of such obtained mitochondrial DNA in microsatellite analyses. 50 dental tissue samples which were kept in neutral buffered formalin liquid bottles were taken for DNA isolation and subsequent analysis. For the isolation of total genomic DNA from tissue samples, a new protocol with substantial modifications from routine ones was adopted by us. Total genomic DNA from matched blood samples were extracted using standard phenol-chloroform extraction method. Polymerase Chain Reaction and Sequencing of such extracted DNA samples for mitochondrial D loop region were successful and the results were comparable with DNA extracted from normal sources of samples. The present study reports for the first time that nucleic acids extracted from human dental tissue samples under prolonged formalin fixation times can be used for forensic odontology studies using the described methodology.

  4. Sampling strategies for tropical forest nutrient cycling studies: a case study in São Paulo, Brazil

    Directory of Open Access Journals (Sweden)

    G. Sparovek

    1997-12-01

    Full Text Available The precise sampling of soil, biological or micro climatic attributes in tropical forests, which are characterized by a high diversity of species and complex spatial variability, is a difficult task. We found few basic studies to guide sampling procedures. The objective of this study was to define a sampling strategy and data analysis for some parameters frequently used in nutrient cycling studies, i. e., litter amount, total nutrient amounts in litter and its composition (Ca, Mg, Κ, Ν and P, and soil attributes at three depths (organic matter, Ρ content, cation exchange capacity and base saturation. A natural remnant forest in the West of São Paulo State (Brazil was selected as study area and samples were collected in July, 1989. The total amount of litter and its total nutrient amounts had a high spatial independent variance. Conversely, the variance of litter composition was lower and the spatial dependency was peculiar to each nutrient. The sampling strategy for the estimation of litter amounts and the amount of nutrient in litter should be different than the sampling strategy for nutrient composition. For the estimation of litter amounts and the amount of nutrients in litter (related to quantity a large number of randomly distributed determinations are needed. Otherwise, for the estimation of litter nutrient composition (related to quality a smaller amount of spatially located samples should be analyzed. The determination of sampling for soil attributes differed according to the depth. Overall, surface samples (0-5 cm showed high short distance spatial dependent variance, whereas, subsurface samples exhibited spatial dependency in longer distances. Short transects with sampling interval of 5-10 m are recommended for surface sampling. Subsurface samples must also be spatially located, but with transects or grids with longer distances between sampling points over the entire area. Composite soil samples would not provide a complete

  5. Genome-wide association study (GWAS) reveals the genetic architecture of four husk traits in maize.

    Science.gov (United States)

    Cui, Zhenhai; Luo, Jinhong; Qi, Chuangye; Ruan, Yanye; Li, Jing; Zhang, Ao; Yang, Xiaohong; He, Yan

    2016-11-21

    Maize (Zea mays) husk referring to the leafy outer enclosing the ear, plays an important role in grain production by directly contributing photosynthate and protecting ear from pathogen infection. Although the physiological functions related to husk have been extensively studied, little is known about its morphological variation and genetic basis in natural population. Here we utilized a maize association panel including 508 inbred lines with tropical, subtropical and temperate backgrounds to decipher the genetic architecture attributed to four husk traits, i.e. number of layers, length, width and thickness. Evaluating the phenotypic diversity at two different environments showed that four traits exhibit broadly natural variations and moderate levels of heritability with 0.64, 0.74, 0.49 and 0.75 for number, length, width and thickness, respectively. Diversity analysis indicated that different traits have dissimilar responses to subpopulation effects. A series of significantly positive or negative correlations between husk phenotypes and other agronomic traits were identified, indicating that husk growth is coordinated with other developmental processes. Combining husk traits with about half of a million of single nucleotide polymorphisms (SNPs) via genome-wide association study revealed a total of 9 variants significantly associated with traits at P husk development, and further studies on identified candidate genes facilitate to illuminate molecular pathways regulating maize husk growth.

  6. Randomized controlled trials 5: Determining the sample size and power for clinical trials and cohort studies.

    Science.gov (United States)

    Greene, Tom

    2015-01-01

    Performing well-powered randomized controlled trials is of fundamental importance in clinical research. The goal of sample size calculations is to assure that statistical power is acceptable while maintaining a small probability of a type I error. This chapter overviews the fundamentals of sample size calculation for standard types of outcomes for two-group studies. It considers (1) the problems of determining the size of the treatment effect that the studies will be designed to detect, (2) the modifications to sample size calculations to account for loss to follow-up and nonadherence, (3) the options when initial calculations indicate that the feasible sample size is insufficient to provide adequate power, and (4) the implication of using multiple primary endpoints. Sample size estimates for longitudinal cohort studies must take account of confounding by baseline factors.

  7. Municipal solid waste composition: Sampling methodology, statistical analyses, and case study evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Edjabou, Maklawe Essonanawe, E-mail: vine@env.dtu.dk [Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby (Denmark); Jensen, Morten Bang; Götze, Ramona; Pivnenko, Kostyantyn [Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby (Denmark); Petersen, Claus [Econet AS, Omøgade 8, 2.sal, 2100 Copenhagen (Denmark); Scheutz, Charlotte; Astrup, Thomas Fruergaard [Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby (Denmark)

    2015-02-15

    Highlights: • Tiered approach to waste sorting ensures flexibility and facilitates comparison of solid waste composition data. • Food and miscellaneous wastes are the main fractions contributing to the residual household waste. • Separation of food packaging from food leftovers during sorting is not critical for determination of the solid waste composition. - Abstract: Sound waste management and optimisation of resource recovery require reliable data on solid waste generation and composition. In the absence of standardised and commonly accepted waste characterisation methodologies, various approaches have been reported in literature. This limits both comparability and applicability of the results. In this study, a waste sampling and sorting methodology for efficient and statistically robust characterisation of solid waste was introduced. The methodology was applied to residual waste collected from 1442 households distributed among 10 individual sub-areas in three Danish municipalities (both single and multi-family house areas). In total 17 tonnes of waste were sorted into 10–50 waste fractions, organised according to a three-level (tiered approach) facilitating comparison of the waste data between individual sub-areas with different fractionation (waste from one municipality was sorted at “Level III”, e.g. detailed, while the two others were sorted only at “Level I”). The results showed that residual household waste mainly contained food waste (42 ± 5%, mass per wet basis) and miscellaneous combustibles (18 ± 3%, mass per wet basis). The residual household waste generation rate in the study areas was 3–4 kg per person per week. Statistical analyses revealed that the waste composition was independent of variations in the waste generation rate. Both, waste composition and waste generation rates were statistically similar for each of the three municipalities. While the waste generation rates were similar for each of the two housing types (single

  8. Who Are We Studying? Sample Diversity in Teaching of Psychology Research

    Science.gov (United States)

    Richmond, Aaron S.; Broussard, Kristin A.; Sterns, Jillian L.; Sanders, Kristina K.; Shardy, Justin C.

    2015-01-01

    The purpose of the current study was to examine the sample diversity of empirical articles published in four premier teaching of psychology journals from 2008 to 2013. We investigated which demographic information was commonly reported and if samples were ethnically representative and whether gender was representative compared to National…

  9. The mouthwash : A non-invasive sampling method to study cytokine gene polymorphisms

    NARCIS (Netherlands)

    Laine, ML; Farre, MA; Crusius, JBA; van Winkelhoff, AJ; Pena, AS

    Background: We describe a simple, non-invasive mouthwash sampling method for rapid DNA isolation to detect cytokine gene polymorphisms. In the present paper, interleukin-1 beta (IL-1B) and interleukin-1 receptor antagonist (IL-1RN) gene polymorphisms were studied. Methods: Two mouthwash samples and

  10. Chlamydia trachomatis antibody detection in home-collected blood samples for use in epidemiological studies.

    Science.gov (United States)

    Hoenderboom, B M; van Ess, E F; van den Broek, I V F; van Loo, I H M; Hoebe, C J P A; Ouburg, S; Morré, S A

    2018-01-01

    Capillary blood collected in serum tubes was subjected to centrifugation delay while stored at room temperature. Chlamydia trachomatis (CT) IgG concentrations in aliquoted serum of these blood samples remained stable for seven days after collection. CT IgG concentrations can reliably be measured in mailed blood samples in epidemiological studies. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Statistical considerations for plot design, sampling procedures, analysis, and quality assurance of ozone injury studies

    Science.gov (United States)

    Michael Arbaugh; Larry Bednar

    1996-01-01

    The sampling methods used to monitor ozone injury to ponderosa and Jeffrey pines depend on the objectives of the study, geographic and genetic composition of the forest, and the source and composition of air pollutant emissions. By using a standardized sampling methodology, it may be possible to compare conditions within local areas more accurately, and to apply the...

  12. Protected sampling is preferable in bronchoscopic studies of the airway microbiome

    Directory of Open Access Journals (Sweden)

    Rune Grønseth

    2017-08-01

    Full Text Available The aim was to evaluate susceptibility of oropharyngeal contamination with various bronchoscopic sampling techniques. 67 patients with obstructive lung disease and 58 control subjects underwent bronchoscopy with small-volume lavage (SVL through the working channel, protected bronchoalveolar lavage (PBAL and bilateral protected specimen brush (PSB sampling. Subjects also provided an oral wash (OW sample, and negative control samples were gathered for each bronchoscopy procedure. DNA encoding bacterial 16S ribosomal RNA was sequenced and bioinformatically processed to cluster into operational taxonomic units (OTU, assign taxonomy and obtain measures of diversity. The proportion of Proteobacteria increased, whereas Firmicutes diminished in the order OW, SVL, PBAL, PSB (p<0.01. The alpha-diversity decreased in the same order (p<0.01. Also, beta-diversity varied by sampling method (p<0.01, and visualisation of principal coordinates analyses indicated that differences in diversity were smaller between OW and SVL and OW and PBAL samples than for OW and the PSB samples. The order of sampling (left versus right first did not influence alpha- or beta-diversity for PSB samples. Studies of the airway microbiota need to address the potential for oropharyngeal contamination, and protected sampling might represent an acceptable measure to minimise this problem.

  13. Successful Sampling Strategy Advances Laboratory Studies of NMR Logging in Unconsolidated Aquifers

    DEFF Research Database (Denmark)

    Behroozmand, Ahmad A.; Knight, Rosemary; Müller-Petke, Mike

    2017-01-01

    , as is typically done in the petroleum industry. However, the challenge has been obtaining high-quality laboratory samples from unconsolidated aquifers. At a study site in Denmark, we employed sonic drilling, which minimizes the disturbance of the surrounding material, and extracted twelve 7.6-cm diameter samples...... for laboratory measurements. We present a detailed comparison of the acquired laboratory- and logging-NMR data. The agreement observed between the laboratory and logging data suggests that the methodologies proposed in this study provide good conditions for studying NMR measurements of unconsolidated near......-surface aquifers. Finally, we show how laboratory sample size and condition impact the NMR measurements....

  14. Treatability studies on different refinery wastewater samples using high-throughput microbial electrolysis cells (MECs)

    KAUST Repository

    Ren, Lijiao

    2013-05-01

    High-throughput microbial electrolysis cells (MECs) were used to perform treatability studies on many different refinery wastewater samples all having appreciably different characteristics, which resulted in large differences in current generation. A de-oiled refinery wastewater sample from one site (DOW1) produced the best results, with 2.1±0.2A/m2 (maximum current density), 79% chemical oxygen demand removal, and 82% headspace biological oxygen demand removal. These results were similar to those obtained using domestic wastewater. Two other de-oiled refinery wastewater samples also showed good performance, with a de-oiled oily sewer sample producing less current. A stabilization lagoon sample and a stripped sour wastewater sample failed to produce appreciable current. Electricity production, organics removal, and startup time were improved when the anode was first acclimated to domestic wastewater. These results show mini-MECs are an effective method for evaluating treatability of different wastewaters. © 2013 Elsevier Ltd.

  15. Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales

    OpenAIRE

    Campagna, Leonardo; Van Coeverden de Groot, Peter J.; Saunders, Brenda L; Atkinson, Stephen N; Weber, Diana S.; Dyck, Markus G; Boag, Peter T; Lougheed, Stephen C.

    2013-01-01

    As global warming accelerates the melting of Arctic sea ice, polar bears (Ursus maritimus) must adapt to a rapidly changing landscape. This process will necessarily alter the species distribution together with population dynamics and structure. Detailed knowledge of these changes is crucial to delineating conservation priorities. Here, we sampled 361 polar bears from across the center of the Canadian Arctic Archipelago spanning the Gulf of Boothia (GB) and M'Clintock Channel (MC). We use DNA ...

  16. Pseudomonas aeruginosa variants obtained from veterinary clinical samples reveal a role for cyclic di-GMP in biofilm formation and colony morphology.

    Science.gov (United States)

    Brock, Maria T; Fedderly, Galya C; Borlee, Grace I; Russell, Michael M; Filipowska, Liliana K; Hyatt, Doreene R; Ferris, Ryan A; Borlee, Bradley R

    2017-10-16

    Overuse of antibiotics is contributing to an emerging antimicrobial resistance crisis. To better understand how bacteria adapt tolerance and resist antibiotic treatment, Pseudomonas aeruginosa isolates obtained from infection sites sampled from companion animals were collected and evaluated for phenotypic differences. Selected pairs of clonal isolates were obtained from individual infection samples and were assessed for antibiotic susceptibility, cyclic di-GMP levels, biofilm production, motility and genetic-relatedness. A total of 18 samples from equine, feline and canine origin were characterized. A sample from canine otitis media produced a phenotypically heterogeneous pair of P. aeruginosa isolates, 42121A and 42121B, which during growth on culture medium respectively exhibited hyper dye-binding small colony morphology and wild-type phenotypes. Antibiotic susceptibility to gentamicin and ciprofloxacin also differed between this pair of clonal isolates. Sequence analysis of gyrA, a gene known to be involved in ciprofloxacin resistance, indicated that 42121A and 42121B both contained mutations that confer ciprofloxacin resistance, but this did not explain the differences in ciprofloxacin resistance that were observed. Cyclic di-GMP levels also varied between this pair of isolates and were shown to contribute to the observed colony morphology variation and ability to form a biofilm. Our results demonstrate the role of cyclic di-GMP in generating the observed morphological phenotypes that are known to contribute to biofilm-mediated antibiotic tolerance. The generation of phenotypic diversity may go unnoticed during standard diagnostic evaluation, which potentially impacts the therapeutic strategy chosen to treat the corresponding infection and may contribute to the spread of antibiotic resistance.

  17. Genome-wide association study reveals two new risk loci for bipolar disorder.

    Science.gov (United States)

    Mühleisen, Thomas W; Leber, Markus; Schulze, Thomas G; Strohmaier, Jana; Degenhardt, Franziska; Treutlein, Jens; Mattheisen, Manuel; Forstner, Andreas J; Schumacher, Johannes; Breuer, René; Meier, Sandra; Herms, Stefan; Hoffmann, Per; Lacour, André; Witt, Stephanie H; Reif, Andreas; Müller-Myhsok, Bertram; Lucae, Susanne; Maier, Wolfgang; Schwarz, Markus; Vedder, Helmut; Kammerer-Ciernioch, Jutta; Pfennig, Andrea; Bauer, Michael; Hautzinger, Martin; Moebus, Susanne; Priebe, Lutz; Czerski, Piotr M; Hauser, Joanna; Lissowska, Jolanta; Szeszenia-Dabrowska, Neonila; Brennan, Paul; McKay, James D; Wright, Adam; Mitchell, Philip B; Fullerton, Janice M; Schofield, Peter R; Montgomery, Grant W; Medland, Sarah E; Gordon, Scott D; Martin, Nicholas G; Krasnow, Valery; Chuchalin, Alexander; Babadjanova, Gulja; Pantelejeva, Galina; Abramova, Lilia I; Tiganov, Alexander S; Polonikov, Alexey; Khusnutdinova, Elza; Alda, Martin; Grof, Paul; Rouleau, Guy A; Turecki, Gustavo; Laprise, Catherine; Rivas, Fabio; Mayoral, Fermin; Kogevinas, Manolis; Grigoroiu-Serbanescu, Maria; Propping, Peter; Becker, Tim; Rietschel, Marcella; Nöthen, Markus M; Cichon, Sven

    2014-03-11

    Bipolar disorder (BD) is a common and highly heritable mental illness and genome-wide association studies (GWAS) have robustly identified the first common genetic variants involved in disease aetiology. The data also provide strong evidence for the presence of multiple additional risk loci, each contributing a relatively small effect to BD susceptibility. Large samples are necessary to detect these risk loci. Here we present results from the largest BD GWAS to date by investigating 2.3 million single-nucleotide polymorphisms (SNPs) in a sample of 24,025 patients and controls. We detect 56 genome-wide significant SNPs in five chromosomal regions including previously reported risk loci ANK3, ODZ4 and TRANK1, as well as the risk locus ADCY2 (5p15.31) and a region between MIR2113 and POU3F2 (6q16.1). ADCY2 is a key enzyme in cAMP signalling and our finding provides new insights into the biological mechanisms involved in the development of BD.

  18. Sampling strategies to measure the prevalence of common recurrent infections in longitudinal studies

    Directory of Open Access Journals (Sweden)

    Luby Stephen P

    2010-08-01

    Full Text Available Abstract Background Measuring recurrent infections such as diarrhoea or respiratory infections in epidemiological studies is a methodological challenge. Problems in measuring the incidence of recurrent infections include the episode definition, recall error, and the logistics of close follow up. Longitudinal prevalence (LP, the proportion-of-time-ill estimated by repeated prevalence measurements, is an alternative measure to incidence of recurrent infections. In contrast to incidence which usually requires continuous sampling, LP can be measured at intervals. This study explored how many more participants are needed for infrequent sampling to achieve the same study power as frequent sampling. Methods We developed a set of four empirical simulation models representing low and high risk settings with short or long episode durations. The model was used to evaluate different sampling strategies with different assumptions on recall period and recall error. Results The model identified three major factors that influence sampling strategies: (1 the clustering of episodes in individuals; (2 the duration of episodes; (3 the positive correlation between an individual's disease incidence and episode duration. Intermittent sampling (e.g. 12 times per year often requires only a slightly larger sample size compared to continuous sampling, especially in cluster-randomized trials. The collection of period prevalence data can lead to highly biased effect estimates if the exposure variable is associated with episode duration. To maximize study power, recall periods of 3 to 7 days may be preferable over shorter periods, even if this leads to inaccuracy in the prevalence estimates. Conclusion Choosing the optimal approach to measure recurrent infections in epidemiological studies depends on the setting, the study objectives, study design and budget constraints. Sampling at intervals can contribute to making epidemiological studies and trials more efficient, valid

  19. Oxidation mechanism of chalcopyrite revealed by X-ray photoelectron spectroscopy and first principles studies

    Science.gov (United States)

    Xiong, Xiaolu; Hua, Xiaoming; Zheng, Yongfei; Lu, Xionggang; Li, Shenggang; Cheng, Hongwei; Xu, Qian

    2018-01-01

    X-ray photoelectron spectroscopic (XPS) studies revealed that the iron site on the chalcopyrite (CuFeS2) surface was preferably oxidized to the Cu site when exposed to an oxidizing environment. Extensive density functional theory calculations were performed to investigate the surface structure of chalcopyrite and its reaction with both molecular oxygen (O2) and water. The adsorption and dissociation of a single O2 molecule, a single H2O molecule, as well as both molecules at the Fe and Cu sites on the CuFeS2 (001) surface were studied. Consistent with our experimental observation, the Fe site was found to be preferred for the adsorption and dissociation of O2 due to its lower energy barrier and greater exothermicity. The dissociation of H2O on the CuFeS2 (001) surface by itself was found to be unfavorable both thermodynamically and kinetically. However, the surface formed upon O2 dissociation was predicted to be much more reactive with H2O, which was attributed to favorable hydrogen transfer to the O site formed upon O2 dissociation to hydrogen transfer to the S site due to the much weaker Ssbnd H bond than the Osbnd H bond.

  20. A second life for old data: global patterns in pollution ecology revealed from published observational studies.

    Science.gov (United States)

    Kozlov, Mikhail V; Zvereva, Elena L

    2011-05-01

    A synthesis of research on the responses of terrestrial biota (1095 effect sizes) to industrial pollution (206 point emission sources) was conducted to reveal regional and global patterns from small-scale observational studies. A meta-analysis, in combination with other statistical methods, showed that the effects of pollution depend on characteristics of the specific polluter (type, amount of emission, duration of impact on biota), the affected organism (trophic group, life history), the level at which the response was measured (organism, population, community), and the environment (biome, climate). In spite of high heterogeneity in responses, we have detected several general patterns. We suggest that the development of evolutionary adaptations to pollution is a common phenomenon and that the harmful effects of pollution on terrestrial ecosystems are likely to increase as the climate warms. We argue that community- and ecosystem-level responses to pollution should be explored directly, rather than deduced from organism-level studies. Copyright © 2010 Elsevier Ltd. All rights reserved.

  1. Fish gut-liver immunity during homeostasis or inflammation revealed by integrative transcriptome and proteome studies

    Science.gov (United States)

    Wu, Nan; Song, Yu-Long; Wang, Bei; Zhang, Xiang-Yang; Zhang, Xu-Jie; Wang, Ya-Li; Cheng, Ying-Yin; Chen, Dan-Dan; Xia, Xiao-Qin; Lu, Yi-Shan; Zhang, Yong-An

    2016-11-01

    The gut-associated lymphoid tissue, connected with liver via bile and blood, constructs a local immune environment of both defense and tolerance. The gut-liver immunity has been well-studied in mammals, yet in fish remains largely unknown, even though enteritis as well as liver and gallbladder syndrome emerged as a limitation in aquaculture. In this study, we performed integrative bioinformatic analysis for both transcriptomic (gut and liver) and proteomic (intestinal mucus and bile) data, in both healthy and infected tilapias. We found more categories of immune transcripts in gut than liver, as well as more adaptive immune in gut meanwhile more innate in liver. Interestingly reduced differential immune transcripts between gut and liver upon inflammation were also revealed. In addition, more immune proteins in bile than intestinal mucus were identified. And bile probably providing immune effectors to intestinal mucus upon inflammation was deduced. Specifically, many key immune transcripts in gut or liver as well as key immune proteins in mucus or bile were demonstrated. Accordingly, we proposed a hypothesized profile of fish gut-liver immunity, during either homeostasis or inflammation. Current data suggested that fish gut and liver may collaborate immunologically while keep homeostasis using own strategies, including potential unique mechanisms.

  2. Estrogenic activity of commercial milk as revealed in immature hamster uterotrophic assay – pilot study

    Science.gov (United States)

    Radko, Lidia; Minta, Maria; Stypuła-Trębas, Sylwia

    The risk for public health posed by endocrine disruptors present in food is relatively new issue. Our current understanding of human exposure is mainly based on the residue analysis of selected compounds. With such approach potential, effects of mixtures, including so-far unidentified compounds are not taken into consideration. Therefore, the knowledge of overall hormonal activity in food samples is of big importance. Milk and dairy products are a rich source of estrogens but very rarely undergo testing for estrogenic activity. For this reason the rodent uterotrophic bioassay is one of the most useful tool. This preliminary study was conducted in immature hamsters to assess commercially available milk. The endpoint measured was uterine weight increase. Fifteen-day old females received ad libitum throughout 7 days commercially available milk i.e. raw goat’s, raw cow’s, processed 3.2% UHT, and for comparison soy milk. The animals of negative control group received water but positive control group got 17β - estradiol (E2) at the concentration of 100 ng/ml. All samples of milk showed estrogenic activity as follow: goat’s >cow’s >soy >processed milk. Significant increase of uteri weights were recorded in goat’s (pmilk (pmilk experimental groups ranged from 0.112% to 0.153% and in positive control this value was 0.493%. The results suggest that commercially available milk has a weak uterotrophic activity. Further in vivo and in vitro studies are warranted to gain more insight into the estrogenic risk from milk and other dairy products.

  3. Statistical methods for genetic association studies with response-selective sampling designs

    NARCIS (Netherlands)

    Balliu, Brunilda

    2015-01-01

    This dissertation describes new statistical methods designed to improve the power of genetic association studies. Of particular interest are studies with a response-selective sampling design, i.e. case-control studies of unrelated individuals and case-control studies of family members. The

  4. Relations among questionnaire and experience sampling measures of inner speech: a smartphone app study

    National Research Council Canada - National Science Library

    Alderson-Day, Ben; Fernyhough, Charles

    2015-01-01

    ... (which involve collecting data at random timepoints). The present study compared self-reporting of inner speech collected via a general questionnaire and experience sampling, using data from a custom-made smartphone app (Inner Life...

  5. Clinical trials with nested subgroups: Analysis, sample size determination and internal pilot studies.

    Science.gov (United States)

    Placzek, Marius; Friede, Tim

    2017-01-01

    The importance of subgroup analyses has been increasing due to a growing interest in personalized medicine and targeted therapies. Considering designs with multiple nested subgroups and a continuous endpoint, we develop methods for the analysis and sample size determination. First, we consider the joint distribution of standardized test statistics that correspond to each (sub)population. We derive multivariate exact distributions where possible, providing approximations otherwise. Based on these results, we present sample size calculation procedures. Uncertainties about nuisance parameters which are needed for sample size calculations make the study prone to misspecifications. We discuss how a sample size review can be performed in order to make the study more robust. To this end, we implement an internal pilot study design where the variances and prevalences of the subgroups are reestimated in a blinded fashion and the sample size is recalculated accordingly. Simulations show that the procedures presented here do not inflate the type I error significantly and maintain the prespecified power as long as the sample size of the smallest subgroup is not too small. We pay special attention to the case of small sample sizes and attain a lower boundary for the size of the internal pilot study.

  6. Tick (Ixodes ricinus) abundance and seasonality at recreational sites in the UK: hazards in relation to fine-scale habitat types revealed by complementary sampling methods.

    Science.gov (United States)

    Dobson, Andrew D M; Taylor, Jennifer L; Randolph, Sarah E

    2011-06-01

    The seasonal risk to humans of picking up Ixodes ricinus ticks in different habitats at 3 recreational sites in the UK was assessed. A comprehensive range of vegetation types was sampled at 3-weekly intervals for 2 years, using standard blanket-dragging complemented by woollen leggings and square 'heel flags'. Ticks were found in all vegetation types sampled, including short grass close to car parks, but highest densities were consistently found in plots with trees present. Blankets picked up the greatest number of ticks, but heel flags provided important complementary counts of the immature stages in bracken plots; they showed clearly that the decline in tick numbers on blankets in early summer was due to the seasonal growth of vegetation that lifted the blanket clear of the typical questing height, but in reality ticks remained abundant through the summer. Leggings picked up only 11% of the total nymphs and 22% of total adults counted, but this still represented a significant hazard to humans. These results should prompt a greater awareness of the fine-scale distribution of this species in relation to human activities that determines the most likely zones of contact between humans and ticks. Risk communication may then be designed accordingly. Copyright © 2011 Elsevier GmbH. All rights reserved.

  7. Individual differences in fluid intelligence predicts inattentional blindness in a sample of older adults: a preliminary study.

    Science.gov (United States)

    O'Shea, Deirdre M; Fieo, Robert A

    2015-07-01

    Previous research has shown that aging increases susceptibility to inattentional blindness (Graham and Burke, Psychol Aging 26:162, 2011) as well as individual differences in cognitive ability related to working memory and executive functions in separate studies. Therefore, the present study was conducted in an attempt to bridge a gap that involved investigating 'age-sensitive' cognitive abilities that may predict inattentional blindness in a sample of older adults. We investigated whether individual differences in general fluid intelligence and speed of processing would predict inattentional blindness in our sample of older adults. Thirty-six healthy older adults took part in the study. Using the inattentional blindness paradigm developed by Most et al. (Psychol Rev 112:217, 2005), we investigated whether rates of inattentional blindness could be predicted by participant's performance on the Raven's Advanced Progressive Matrices and a choice-reaction time task. A Mann-Whitney U test revealed that a higher score on the Raven's Advanced Progressive Matrices was significantly associated with lower incidences of inattentional blindness. However, a t test revealed that choice-reaction times were not significantly associated with inattentional blindness. Preliminary results from the present study suggest that individual differences in general fluid intelligence are predictive of inattentional blindness in older adults but not speed of processing. Moreover, our findings are consistent with previous studies that have suggested executive attention control may be the source of these individual differences. These findings also highlight the association between attention and general fluid intelligence and how it may impact environmental awareness. Future research would benefit from repeating these analyses in a larger sample and also including a younger comparison group.

  8. Whole brain white matter changes revealed by multiple diffusion metrics in multiple sclerosis: A TBSS study

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yaou, E-mail: asiaeurope80@gmail.com [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Duan, Yunyun, E-mail: xiaoyun81.love@163.com [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); He, Yong, E-mail: yong.h.he@gmail.com [State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875 (China); Yu, Chunshui, E-mail: csyuster@gmail.com [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Wang, Jun, E-mail: jun_wang@bnu.edu.cn [State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875 (China); Huang, Jing, E-mail: sainthj@126.com [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Ye, Jing, E-mail: jingye.2007@yahoo.com.cn [Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Parizel, Paul M., E-mail: paul.parizel@ua.ac.be [Department of Radiology, Antwerp University Hospital and University of Antwerp, Wilrijkstraat 10, 2650 Edegem, 8 Belgium (Belgium); Li, Kuncheng, E-mail: kunchengli55@gmail.com [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Shu, Ni, E-mail: nshu55@gmail.com [State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875 (China)

    2012-10-15

    Objective: To investigate whole brain white matter changes in multiple sclerosis (MS) by multiple diffusion indices, we examined patients with diffusion tensor imaging and utilized tract-based spatial statistics (TBSS) method to analyze the data. Methods: Forty-one relapsing-remitting multiple sclerosis (RRMS) patients and 41 age- and gender-matched normal controls were included in this study. Diffusion weighted images were acquired by employing a single-shot echo planar imaging sequence on a 1.5 T MR scanner. Voxel-wise analyses of multiple diffusion metrics, including fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD) and radial diffusivity (RD) were performed with TBSS. Results: The MS patients had significantly decreased FA (9.11%), increased MD (8.26%), AD (3.48%) and RD (13.17%) in their white matter skeletons compared with the controls. Through TBSS analyses, we found abnormal diffusion changes in widespread white matter regions in MS patients. Specifically, decreased FA, increased MD and increased RD were involved in whole-brain white matter, while several regions exhibited increased AD. Furthermore, white matter regions with significant correlations between the diffusion metrics and the clinical variables (the EDSS scores, disease durations and white matter lesion loads) in MS patients were identified. Conclusion: Widespread white matter abnormalities were observed in MS patients revealed by multiple diffusion metrics. The diffusion changes and correlations with clinical variables were mainly attributed to increased RD, implying the predominant role of RD in reflecting the subtle pathological changes in MS.

  9. Structural Studies Reveal the Functional Modularity of the Scc2-Scc4 Cohesin Loader

    Directory of Open Access Journals (Sweden)

    William C.H. Chao

    2015-08-01

    Full Text Available The remarkable accuracy of eukaryotic cell division is partly maintained by the cohesin complex acting as a molecular glue to prevent premature sister chromatid separation. The loading of cohesin onto chromosomes is catalyzed by the Scc2-Scc4 loader complex. Here, we report the crystal structure of Scc4 bound to the N terminus of Scc2 and show that Scc4 is a tetratricopeptide repeat (TPR superhelix. The Scc2 N terminus adopts an extended conformation and is entrapped by the core of the Scc4 superhelix. Electron microscopy (EM analysis reveals that the Scc2-Scc4 loader complex comprises three domains: a head, body, and hook. Deletion studies unambiguously assign the Scc2N-Scc4 as the globular head domain, whereas in vitro cohesin loading assays show that the central body and the hook domains are sufficient to catalyze cohesin loading onto circular DNA, but not chromatinized DNA in vivo, suggesting a possible role for Scc4 as a chromatin adaptor.

  10. Quartz grains reveal sedimentary palaeoenvironment and past storm events: A case study from eastern Baltic

    Science.gov (United States)

    Kalińska-Nartiša, Edyta; Stivrins, Normunds; Grudzinska, Ieva

    2018-01-01

    Sediment record collected from the coastal lake serves as a powerful tool for reconstructing changes in palaeoenvironment and understanding the potential signals of past storminess. In this study, we use several proxies from sediment of the Holocene Thermal Maximum at coastal Lake Lilaste, Latvia. We focus on surface texture of quartz grains from the mineral inorganic fraction as indicators of depositional environments. We then use this as a proxy for potential storm transport and combine with information on granulometry, diatom stratigraphy and chronology to answer the question whether flux of quartz grains in the lake originated from the sea or from the land. Analyses in a binocular and scanning electron microscope reveal that most of the investigated quartz grains originate from dwelling in the seawater and wave action in the nearshore zone. Grains representing very energetic subaqueous environment similar to storm events are also present. Terrestrial record is of minor significance and visible through occurrence of aeolian quartz grains. During drier and colder conditions, an influx of sand with aeolian imprint was delivered to the lake between 8500 and 7800 cal yr BP. Marine and terrestrial conditions alternated between 7800 and 6000 cal yr BP. Storm-induced grains were likely deposited three times: at 7300 cal yr BP, 6600-6400 cal yr BP, and 6200-6000 cal yr BP. Overall stable marine environmental conditions prevailed between 6000 and 4000 cal yr BP except of the last portion of terrestrial-induced sediment at 4100 cal yr BP.

  11. Metagenomic study of red biofilms from Diamante Lake reveals ancient arsenic bioenergetics in haloarchaea.

    Science.gov (United States)

    Rascovan, Nicolás; Maldonado, Javier; Vazquez, Martín P; Eugenia Farías, María

    2016-02-01

    Arsenic metabolism is proposed to be an ancient mechanism in microbial life. Different bacteria and archaea use detoxification processes to grow under high arsenic concentration. Some of them are also able to use arsenic as a bioenergetic substrate in either anaerobic arsenate respiration or chemolithotrophic growth on arsenite. However, among the archaea, bioenergetic arsenic metabolism has only been found in the Crenarchaeota phylum. Here we report the discovery of haloarchaea (Euryarchaeota phylum) biofilms forming under the extreme environmental conditions such as high salinity, pH and arsenic concentration at 4589 m above sea level inside a volcano crater in Diamante Lake, Argentina. Metagenomic analyses revealed a surprisingly high abundance of genes used for arsenite oxidation (aioBA) and respiratory arsenate reduction (arrCBA) suggesting that these haloarchaea use arsenic compounds as bioenergetics substrates. We showed that several haloarchaea species, not only from this study, have all genes required for these bioenergetic processes. The phylogenetic analysis of aioA showed that haloarchaea sequences cluster in a novel and monophyletic group, suggesting that the origin of arsenic metabolism in haloarchaea is ancient. Our results also suggest that arsenite chemolithotrophy likely emerged within the archaeal lineage. Our results give a broad new perspective on the haloarchaea metabolism and shed light on the evolutionary history of arsenic bioenergetics.

  12. Abnormal affective decision making revealed in adolescent binge drinkers using a functional magnetic resonance imaging study.

    Science.gov (United States)

    Xiao, Lin; Bechara, Antoine; Gong, Qiyong; Huang, Xiaoqi; Li, Xiangrui; Xue, Gui; Wong, Savio; Lu, Zhong-Lin; Palmer, Paula; Wei, Yonglan; Jia, Yong; Johnson, C Anderson

    2013-06-01

    The goal of this study was to investigate the neural correlates of affective decision making, as measured by the Iowa Gambling Task (IGT), which are associated with adolescent binge drinking. Fourteen adolescent binge drinkers (16-18 years of age) and 14 age-matched adolescents who had never consumed alcohol--never drinkers--were recruited from local high schools in Chengdu, China. Questionnaires were used to assess academic performance, drinking experience, and urgency. Brain regions activated by the IGT performance were identified with functional magnetic resonance imaging. Results showed that, compared to never drinkers, binge drinkers performed worse on the IGT and showed higher activity in the subcomponents of the decision-making neural circuitry implicated in the execution of emotional and incentive-related behaviors, namely, the left amygdala and insula bilaterally. Moreover, measures of the severity of drinking problems in real life, as well as high urgency scores, were associated with increased activity within the insula, combined with decreased activity within the orbitofrontal cortex. These results suggest that hyperreactivity of a neural system implicated in the execution of emotional and incentive-related behaviors can be associated with socially undesirable behaviors, such as binge drinking, among adolescents. These findings have social implications because they potentially reveal underlying neural mechanisms for making poor decisions, which may increase an individual's risk and vulnerability for alcoholism. 2013 APA, all rights reserved

  13. Mechanisms of skeletal muscle injury and repair revealed by gene expression studies in mouse models.

    Science.gov (United States)

    Warren, Gordon L; Summan, Mukesh; Gao, Xin; Chapman, Rebecca; Hulderman, Tracy; Simeonova, Petia P

    2007-07-15

    Common acute injuries to skeletal muscle can lead to significant pain and disability. The current therapeutic approaches for treating muscle injuries are dependent on the clinical severity but not on the type of injury. In the present studies, the pathophysiology and molecular pathways associated with two different types of skeletal muscle injury, one induced by direct destruction of muscle tissue (i.e. FI) and the other induced by a contractile overload (more specifically high-force eccentric contractions, i.e. CI) were compared side by side. Histopathological evaluation and measurements of muscle strength were accompanied by analyses of expression for 12 488 known genes at four time points ranging from 6 h to 7 days after injury. Real-time RT-PCR was used to confirm some of the injury type differences in the temporal profiles of gene expression. Our data revealed several pools of genes, including early induction of transcription, myogenic and stress-responsive factors, common for both types of injury as well as pools of genes expressed specifically with one of the injury types. Only CI activated a set of genes associated with the repair of impaired proteins and structures including genes related to apoptosis, whereas FI uniquely activated gene sets involved in extensive inflammatory responses, tissue remodelling, angiogenesis and myofibre/extracellular matrix synthesis. In conclusion, knowledge of the sets of genes associated specifically with the nature of the injury may have application for development of new strategies for acceleration of the recovery process in injured skeletal muscle.

  14. (Sample) size matters! An examination of sample size from the SPRINT trial study to prospectively evaluate reamed intramedullary nails in patients with tibial fractures

    NARCIS (Netherlands)

    Bhandari, Mohit; Tornetta, Paul; Rampersad, Shelly-Ann; Sprague, Sheila; Heels-Ansdell, Diane; Sanders, David W.; Schemitsch, Emil H.; Swiontkowski, Marc; Walter, Stephen; Guyatt, Gordon; Buckingham, Lisa; Leece, Pamela; Viveiros, Helena; Mignott, Tashay; Ansell, Natalie; Sidorkewicz, Natalie; Agel, Julie; Bombardier, Claire; Berlin, Jesse A.; Bosse, Michael; Browner, Bruce; Gillespie, Brenda; O'Brien, Peter; Poolman, Rudolf; Macleod, Mark D.; Carey, Timothy; Leitch, Kellie; Bailey, Stuart; Gurr, Kevin; Konito, Ken; Bartha, Charlene; Low, Isolina; MacBean, Leila V.; Ramu, Mala; Reiber, Susan; Strapp, Ruth; Tieszer, Christina; Kreder, Hans; Stephen, David J. G.; Axelrod, Terry S.; Yee, Albert J. M.; Richards, Robin R.; Finkelstein, Joel; Holtby, Richard M.; Cameron, Hugh; Cameron, John; Gofton, Wade; Murnaghan, John; Schatztker, Joseph; Bulmer, Beverly; Conlan, Lisa; Laflamme, Yves; Berry, Gregory; Beaumont, Pierre; Ranger, Pierre; Laflamme, Georges-Henri; Jodoin, Alain; Renaud, Eric; Gagnon, Sylvain; Maurais, Gilles; Malo, Michel; Fernandes, Julio; Latendresse, Kim; Poirier, Marie-France; Daigneault, Gina; McKee, Michael M.; Waddell, James P.; Bogoch, Earl R.; Daniels, Timothy R.; McBroom, Robert R.; Vicente, Milena R.; Storey, Wendy; Wild, Lisa M.; McCormack, Robert; Perey, Bertrand; Goetz, Thomas J.; Pate, Graham; Penner, Murray J.; Panagiotopoulos, Kostas; Pirani, Shafique; Dommisse, Ian G.; Loomer, Richard L.; Stone, Trevor; Moon, Karyn; Zomar, Mauri; Webb, Lawrence X.; Teasdall, Robert D.; Birkedal, John Peter; Martin, David Franklin; Ruch, David S.; Kilgus, Douglas J.; Pollock, David C.; Harris, Mitchel Brion; Wiesler, Ethan Ron; Ward, William G.; Shilt, Jeffrey Scott; Koman, Andrew L.; Poehling, Gary G.; Kulp, Brenda; Creevy, William R.; Stein, Andrew B.; Bono, Christopher T.; Einhorn, Thomas A.; Brown, T. Desmond; Pacicca, Donna; Sledge, John B.; Foster, Timothy E.; Voloshin, Ilva; Bolton, Jill; Carlisle, Hope; Shaughnessy, Lisa; Ombremsky, William T.; LeCroy, C. Michael; Meinberg, Eric G.; Messer, Terry M.; Craig, William L.; Dirschl, Douglas R.; Caudle, Robert; Harris, Tim; Elhert, Kurt; Hage, William; Jones, Robert; Piedrahita, Luis; Schricker, Paul O.; Driver, Robin; Godwin, Jean; Hansley, Gloria; Obremskey, William Todd; Kregor, Philip James; Tennent, Gregory; Truchan, Lisa M.; Sciadini, Marcus; Shuler, Franklin D.; Driver, Robin E.; Nading, Mary Alice; Neiderstadt, Jacky; Vap, Alexander R.; Vallier, Heather A.; Patterson, Brendan M.; Wilber, John H.; Wilber, Roger G.; Sontich, John K.; Moore, Timothy Alan; Brady, Drew; Cooperman, Daniel R.; Davis, John A.; Cureton, Beth Ann; Mandel, Scott; Orr, R. Douglas; Sadler, John T. S.; Hussain, Tousief; Rajaratnam, Krishan; Petrisor, Bradley; Drew, Brian; Bednar, Drew A.; Kwok, Desmond C. H.; Pettit, Shirley; Hancock, Jill; Cole, Peter A.; Smith, Joel J.; Brown, Gregory A.; Lange, Thomas A.; Stark, John G.; Levy, Bruce; Swiontkowski, Marc F.; Garaghty, Mary J.; Salzman, Joshua G.; Schutte, Carol A.; Tastad, Linda Toddie; Vang, Sandy; Seligson, David; Roberts, Craig S.; Malkani, Arthur L.; Sanders, Laura; Gregory, Sharon Allen; Dyer, Carmen; Heinsen, Jessica; Smith, Langan; Madanagopal, Sudhakar; Coupe, Kevin J.; Tucker, Jeffrey J.; Criswell, Allen R.; Buckle, Rosemary; Rechter, Alan Jeffrey; Sheth, Dhiren Shaskikant; Urquart, Brad; Trotscher, Thea; Anders, Mark J.; Kowalski, Joseph M.; Fineberg, Marc S.; Bone, Lawrence B.; Phillips, Matthew J.; Rohrbacher, Bernard; Stegemann, Philip; Mihalko, William M.; Buyea, Cathy; Augustine, Stephen J.; Jackson, William Thomas; Solis, Gregory; Ero, Sunday U.; Segina, Daniel N.; Berrey, Hudson B.; Agnew, Samuel G.; Fitzpatrick, Michael; Campbell, Lakina C.; Derting, Lynn; McAdams, June; Goslings, J. Carel; Ponsen, Kees Jan; Luitse, Jan; Kloen, Peter; Joosse, Pieter; Winkelhagen, Jasper; Duivenvoorden, Raphaël; Teague, David C.; Davey, Joseph; Sullivan, J. Andy; Ertl, William J. J.; Puckett, Timothy A.; Pasque, Charles B.; Tompkins, John F.; Gruel, Curtis R.; Kammerlocher, Paul; Lehman, Thomas P.; Puffinbarger, William R.; Carl, Kathy L.; Weber, Donald W.; Jomha, Nadr M.; Goplen, Gordon R.; Masson, Edward; Beaupre, Lauren A.; Greaves, Karen E.; Schaump, Lori N.; Jeray, Kyle J.; Goetz, David R.; Westberry, Davd E.; Broderick, J. Scott; Moon, Bryan S.; Tanner, Stephanie L.; Powell, James N.; Buckley, Richard E.; Elves, Leslie; Connolly, Stephen; Abraham, Edward P.; Eastwood, Donna; Steele, Trudy; Ellis, Thomas; Herzberg, Alex; Brown, George A.; Crawford, Dennis E.; Hart, Robert; Hayden, James; Orfaly, Robert M.; Vigland, Theodore; Vivekaraj, Maharani; Bundy, Gina L.; Miclau, Theodore; Matityahu, Amir; Coughlin, R. Richard; Kandemir, Utku; McClellan, R. Trigg; Lin, Cindy Hsin-Hua; Karges, David; Cramer, Kathryn; Watson, J. Tracy; Moed, Berton; Scott, Barbara; Beck, Dennis J.; Orth, Carolyn; Puskas, David; Clark, Russell; Jones, Jennifer; Egol, Kenneth A.; Paksima, Nader; France, Monet; Wai, Eugene K.; Johnson, Garth; Wilkinson, Ross; Gruszczynski, Adam T.; Vexler, Liisa

    2013-01-01

    Inadequate sample size and power in randomized trials can result in misleading findings. This study demonstrates the effect of sample size in a large clinical trial by evaluating the results of the Study to Prospectively evaluate Reamed Intramedullary Nails in Patients with Tibial fractures (SPRINT)

  15. cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies

    Science.gov (United States)

    Chase, John H.; Bolyen, Evan; Rideout, Jai Ram

    2015-01-01

    ABSTRACT The number of samples in high-throughput comparative “omics” studies is increasing rapidly due to declining experimental costs. To keep sample data and metadata manageable and to ensure the integrity of scientific results as the scale of these projects continues to increase, it is essential that we transition to better-designed sample identifiers. Ideally, sample identifiers should be globally unique across projects, project teams, and institutions; short (to facilitate manual transcription); correctable with respect to common types of transcription errors; opaque, meaning that they do not contain information about the samples; and compatible with existing standards. We present cual-id, a lightweight command line tool that creates, or mints, sample identifiers that meet these criteria without reliance on centralized infrastructure. cual-id allows users to assign universally unique identifiers, or UUIDs, that are globally unique to their samples. UUIDs are too long to be conveniently written on sampling materials, such as swabs or microcentrifuge tubes, however, so cual-id additionally generates human-friendly 4- to 12-character identifiers that map to their UUIDs and are unique within a project. By convention, we use “cual-id” to refer to the software, “CualID” to refer to the short, human-friendly identifiers, and “UUID” to refer to the globally unique identifiers. CualIDs are used by humans when they manually write or enter identifiers, while the longer UUIDs are used by computers to unambiguously reference a sample. Finally, cual-id optionally generates printable label sticker sheets containing Code 128 bar codes and CualIDs for labeling of sample collection and processing materials. IMPORTANCE The adoption of identifiers that are globally unique, correctable, and easily handwritten or manually entered into a computer will be a major step forward for sample tracking in comparative omics studies. As the fields transition to more

  16. A simulation study provided sample size guidance for differential item functioning (DIF) studies using short scales.

    Science.gov (United States)

    Scott, Neil W; Fayers, Peter M; Aaronson, Neil K; Bottomley, Andrew; de Graeff, Alexander; Groenvold, Mogens; Gundy, Chad; Koller, Michael; Petersen, Morten A; Sprangers, Mirjam A G

    2009-03-01

    Differential item functioning (DIF) analyses are increasingly used to evaluate health-related quality of life (HRQoL) instruments, which often include relatively short subscales. Computer simulations were used to explore how various factors including scale length affect analysis of DIF by ordinal logistic regression. Simulated data, representative of HRQoL scales with four-category items, were generated. The power and type I error rates of the DIF method were then investigated when, respectively, DIF was deliberately introduced and when no DIF was added. The sample size, scale length, floor effects (FEs) and significance level were varied. When there was no DIF, type I error rates were close to 5%. Detecting moderate uniform DIF in a two-item scale required a sample size of 300 per group for adequate (>80%) power. For longer scales, a sample size of 200 was adequate. Considerably larger sample sizes were required to detect nonuniform DIF, when there were extreme FEs or when a reduced type I error rate was required. The impact of the number of items in the scale was relatively small. Ordinal logistic regression successfully detects DIF for HRQoL instruments with short scales. Sample size guidelines are provided.

  17. Case study: Curation and publication of physical samples using persistent identifiers

    Science.gov (United States)

    Golodoniuc, Pavel; Devaraju, Anusuriya; Klump, Jens

    2017-04-01

    Physical samples are important observational units in Earth and Space sciences. Samples and their derived data play vital role in scientific validation and reproducibility. Systematic practices and technical solutions are required to curate and publish samples and their data on the Web. Persistent identifiers ensure unambiguous identification, and enable linkage and citation of samples and associated data sets. The International Geo Sample Number (IGSN) is a persistent and globally unique identifier for physical samples and sample collections. IGSNs are allocated to clients (e.g., laboratories, projects, individual users) through agents. Agents are institutions that represent the IGSN e.V., the IGSN Implementation Organization. For example, CSIRO, Geoscience Australia and Curtin University are IGSN allocating agents in Australia. Clients register IGSNs for samples through the respective agent's registration services. The Discovery research program of CSIRO is conducting research in the prolific metallogenic provinces of the Capricorn Orogen - a regional study aimed to define distal footprints of covered ore systems. In CSIRO, the Capricorn Distal Footprints (CAPDF) project is one of the early adopters of the IGSN in its sample curation. The project involves collection of various samples, including water, rock, sediment, vegetation and regolith, which are collected by different researchers. The application of IGSN requires not only the supporting infrastructure and tools (e.g., user interface, service, metadata model) but also systematic workflows to cater different users, i.e., practices of laboratories or individual researchers. We present the application of the IGSN in the context of the CAPDF project as a sample inventory management system, samples identification in publications and sample discovery through a web portal. We describe workflows that demonstrate IGSN integration into existing sample curation practices and highlight challenges and benefits of such a

  18. Effectiveness of quadrat sampling on terrestrial cave fauna survey - a case study in a Neotropical cave

    Directory of Open Access Journals (Sweden)

    Maria Elina Bichuette

    2015-07-01

    Full Text Available Quadrat sampling is a method used for a long time in plant ecology studies but only recently it has been used with focus on fauna. For the cave fauna samplings, there are rare works applying this methodology. The present study compared the methods of quadrat sampling with direct search qualitative for terrestrial cave fauna. For this, we conducted five sampling collections in a limestone cave in central Brazil. Quadrat sampling contributed with 121 exclusive species and 716 specimens and direct search qualitative method contributed with 91 exclusive species and 355 specimens. Mann-Whitney test evidenced significant differences between the two methods. We demonstrated that quadrat sampling method was slightly more efficient to analyze the species richness and much more effective to assess the abundance than the use of only direct search qualitative method, mainly considering tiny and/or cryptobiotic invertebrates (e.g., earth worms, symphylans, psocopterans, trichopterans, dipterans, small spiders, and small isopods. We recommend the association of different methods to test patterns in cave fauna, since incomplete sampling may lead to erroneous estimates and equivocated decisions about management, impact studies and cave conservation.

  19. Does host plant richness explain diversity of ectomycorrhizal fungi? Re-evaluation of Gao et al. (2013) data sets reveals sampling effects.

    Science.gov (United States)

    Tedersoo, Leho; Bahram, Mohammad; Dickie, Ian A

    2014-03-01

    The generally positive relationship between biodiversity of groups of directly or indirectly interacting organisms is one of the most important ecological concepts (Gaston, 2000 Nature, 405, 220-227; Scherber C, Eisenhauer N, Weisser WW et al., 2010 Nature, 468, 553-556). In a recent issue of Molecular Ecology, Gao C, Shi N-N, Liu Y-X et al. (2013: 22, 3403-3414) reported that the richness of plants and ectomycorrhizal fungi is positively correlated both at local and at global scales. Here, we challenge these findings by re-analysis of data and ascribe the reported results to sampling effect and poor data compilation. © 2014 John Wiley & Sons Ltd.

  20. Screening sourdough samples for gliadin-degrading activity revealed Lactobacillus casei strains able to individually metabolize the coeliac-disease-related 33-mer peptide.

    Science.gov (United States)

    Alvarez-Sieiro, Patricia; Redruello, Begoña; Ladero, Victor; Martín, Maria Cruz; Fernández, María; Alvarez, Miguel A

    2016-05-01

    A selective culture medium containing acid-hydrolyzed gliadins as the sole nitrogen source was used in the search for sourdough-indigenous lactic acid bacteria (LAB) with gliadin-metabolizing activity. Twenty gliadin-degrading LAB strains were isolated from 10 sourdoughs made in different ways and from different geographical regions. Fifteen of the 20 isolated strains were identified as Lactobacillus casei, a species usually reported as subdominant in sourdough populations. The other 5 gliadin-degrading strains belonged to the more commonly encountered sourdough species Leuconostoc mesenteroides and Lactobacillus plantarum. All these strains were shown to be safe in terms of their resistance to antimicrobial agents. When individually incubated with the α2-gliadin-derived immunotoxic 33-mer peptide (97.5 ppm), half of the L. casei strains metabolized at least 50% of it within 24 h. One strain metabolized 82% of the 33-mer peptide within 8 h and made it fully disappear within 12 h. These results reveal for the first time the presence in sourdough of proteolytic L. casei strains with the capacity to individually metabolize the coeliac-disease-related 33-mer peptide.

  1. Quantitative Study on Exact Reconstruction Sampling Condition in Limited-view CT

    CERN Document Server

    Yan, Bin; Li, Lei; Zhang, Hanming; Wang, Linyuan

    2016-01-01

    In limited-view computed tomography reconstruction, iterative image reconstruction with sparsity-exploiting methods, such as total variation (TV) minimization, inspired by compressive sensing, potentially claims large reductions in sampling requirements. However, a quantitative notion of this claim is non-trivial because of the ill-defined reduction in sampling achieved by the sparsity-exploiting method. In this paper, exact reconstruction sampling condition for limited-view problem is studied by verifying the uniqueness of solution in TV minimization model. Uniqueness is tested by solving a convex optimization problem derived from the sufficient and necessary condition of solution uniqueness. Through this method, the sufficient sampling number of exact reconstruction is quantified for any fixed phantom and settled geometrical parameter in the limited-view problem. This paper provides a reference to quantify the sampling condition. Using Shepp-Logan phantom as an example, the experiment results show the quant...

  2. Alternaria and Fusarium in Norwegian grains of reduced quality - a matched pair sample study

    DEFF Research Database (Denmark)

    Kosiak, B.; Torp, M.; Skjerve, E.

    2004-01-01

    The occurrence and geographic distribution of species belonging to the genera Alternaria and Fusarium in grains of reduced and of acceptable quality were studied post-harvest in 1997 and 1998. A total of 260 grain samples of wheat, barley and oats was analysed. The distribution of Alternaria...... and Fusarium spp. varied significantly in samples of reduced quality compared with acceptable samples. Alternaria spp. dominated in the acceptable samples with A. infectoria group as the most frequently isolated and most abundant species group of this genus while Fusarium spp. dominated in samples of reduced...... of reduced quality. The results indicated a negative interaction between E graminearum and Alternaria spp. as well as between F graminearum and other Fusarium spp....

  3. A Qualitative Study Revealing the Relationship Between Cultural Indicators and Attitudes Toward the Ads

    Directory of Open Access Journals (Sweden)

    Emine Sahin

    2014-12-01

    Full Text Available The companies, in International markets, are required to examine the attitudes and the behaviours to recognize the consumer to be able to make their products preferable under constantly growing competitive conditions. Therefore, it is of great importance to know cultural values of the customers in the country's where global brands compete and to shape ads which is one of the marketing communication tools in this direction. In this respect, knowing the cultural similarities or differences of the countries where the ads are used (such as that country's religion, language, norms and cultural values gains importance. The consumer attitudes towards the ads change in accordance with their cultural similarities or dissimilarities and this attitude change determines the tendency of shopping. According to Geert Hofstede, social anthropologist who analyzes the cultural levels and the relationships among them the basic elements of the culture consists of symbols, heroes, rituals and values underlying them. Thorough symbols, a number of cultural values are conveyed to ads. The problem of this study which was carried out in order to determine attitude change towards the ads including cultural differences is “Is there a difference in the attitudes towards the ads including different cultural symbols? How it is distributed according to gender differences?" In this study, a qualitative research method was applied and interviewed with 20 test subject. 20 students studying in one of the universities in Turkey were selected with formal sampling, they were asked questions, and it was tried to determine the difference between the ad of Doğuş Çay-a tea brand which uses the symbols and local accent of Black sea region in Turkey in its ads- and the ad of Lipton which is an international British tea brand. At the end of the study, it was found out that sample’s the attitude was positive towards ad of Doğuş Çay, not Lipton.

  4. Evaluation of Legionella Air Contamination in Healthcare Facilities by Different Sampling Methods: An Italian Multicenter Study

    Directory of Open Access Journals (Sweden)

    Maria Teresa Montagna

    2017-06-01

    Full Text Available Healthcare facilities (HF represent an at-risk environment for legionellosis transmission occurring after inhalation of contaminated aerosols. In general, the control of water is preferred to that of air because, to date, there are no standardized sampling protocols. Legionella air contamination was investigated in the bathrooms of 11 HF by active sampling (Surface Air System and Coriolis®μ and passive sampling using settling plates. During the 8-hour sampling, hot tap water was sampled three times. All air samples were evaluated using culture-based methods, whereas liquid samples collected using the Coriolis®μ were also analyzed by real-time PCR. Legionella presence in the air and water was then compared by sequence-based typing (SBT methods. Air contamination was found in four HF (36.4% by at least one of the culturable methods. The culturable investigation by Coriolis®μ did not yield Legionella in any enrolled HF. However, molecular investigation using Coriolis®μ resulted in eight HF testing positive for Legionella in the air. Comparison of Legionella air and water contamination indicated that Legionella water concentration could be predictive of its presence in the air. Furthermore, a molecular study of 12 L. pneumophila strains confirmed a match between the Legionella strains from air and water samples by SBT for three out of four HF that tested positive for Legionella by at least one of the culturable methods. Overall, our study shows that Legionella air detection cannot replace water sampling because the absence of microorganisms from the air does not necessarily represent their absence from water; nevertheless, air sampling may provide useful information for risk assessment. The liquid impingement technique appears to have the greatest capacity for collecting airborne Legionella if combined with molecular investigations.

  5. Evaluation of Legionella Air Contamination in Healthcare Facilities by Different Sampling Methods: An Italian Multicenter Study.

    Science.gov (United States)

    Montagna, Maria Teresa; De Giglio, Osvalda; Cristina, Maria Luisa; Napoli, Christian; Pacifico, Claudia; Agodi, Antonella; Baldovin, Tatjana; Casini, Beatrice; Coniglio, Maria Anna; D'Errico, Marcello Mario; Delia, Santi Antonino; Deriu, Maria Grazia; Guida, Marco; Laganà, Pasqualina; Liguori, Giorgio; Moro, Matteo; Mura, Ida; Pennino, Francesca; Privitera, Gaetano; Romano Spica, Vincenzo; Sembeni, Silvia; Spagnolo, Anna Maria; Tardivo, Stefano; Torre, Ida; Valeriani, Federica; Albertini, Roberto; Pasquarella, Cesira

    2017-06-22

    Healthcare facilities (HF) represent an at-risk environment for legionellosis transmission occurring after inhalation of contaminated aerosols. In general, the control of water is preferred to that of air because, to date, there are no standardized sampling protocols. Legionella air contamination was investigated in the bathrooms of 11 HF by active sampling (Surface Air System and Coriolis(®)μ) and passive sampling using settling plates. During the 8-hour sampling, hot tap water was sampled three times. All air samples were evaluated using culture-based methods, whereas liquid samples collected using the Coriolis(®)μ were also analyzed by real-time PCR. Legionella presence in the air and water was then compared by sequence-based typing (SBT) methods. Air contamination was found in four HF (36.4%) by at least one of the culturable methods. The culturable investigation by Coriolis(®)μ did not yield Legionella in any enrolled HF. However, molecular investigation using Coriolis(®)μ resulted in eight HF testing positive for Legionella in the air. Comparison of Legionella air and water contamination indicated that Legionella water concentration could be predictive of its presence in the air. Furthermore, a molecular study of 12 L. pneumophila strains confirmed a match between the Legionella strains from air and water samples by SBT for three out of four HF that tested positive for Legionella by at least one of the culturable methods. Overall, our study shows that Legionella air detection cannot replace water sampling because the absence of microorganisms from the air does not necessarily represent their absence from water; nevertheless, air sampling may provide useful information for risk assessment. The liquid impingement technique appears to have the greatest capacity for collecting airborne Legionella if combined with molecular investigations.

  6. Meta-GWAS and Meta-Analysis of Exome Array Studies Do Not Reveal Genetic Determinants of Serum Hepcidin.

    Science.gov (United States)

    Galesloot, Tessel E; Verweij, Niek; Traglia, Michela; Barbieri, Caterina; van Dijk, Freerk; Geurts-Moespot, Anneke J; Girelli, Domenico; Kiemeney, Lambertus A L M; Sweep, Fred C G J; Swertz, Morris A; van der Meer, Peter; Camaschella, Clara; Toniolo, Daniela; Vermeulen, Sita H; van der Harst, Pim; Swinkels, Dorine W

    2016-01-01

    Serum hepcidin concentration is regulated by iron status, inflammation, erythropoiesis and numerous other factors, but underlying processes are incompletely understood. We studied the association of common and rare single nucleotide variants (SNVs) with serum hepcidin in one Italian study and two large Dutch population-based studies. We genotyped common SNVs with genome-wide association study (GWAS) arrays and subsequently performed imputation using the 1000 Genomes reference panel. Cohort-specific GWAS were performed for log-transformed serum hepcidin, adjusted for age and gender, and results were combined in a fixed-effects meta-analysis (total N 6,096). Six top SNVs (p<5x10-6) were genotyped in 3,821 additional samples, but associations were not replicated. Furthermore, we meta-analyzed cohort-specific exome array association results of rare SNVs with serum hepcidin that were available for two of the three cohorts (total N 3,226), but no exome-wide significant signal (p<1.4x10-6) was identified. Gene-based meta-analyses revealed 19 genes that showed significant association with hepcidin. Our results suggest the absence of common SNVs and rare exonic SNVs explaining a large proportion of phenotypic variation in serum hepcidin. We recommend extension of our study once additional substantial cohorts with hepcidin measurements, GWAS and/or exome array data become available in order to increase power to identify variants that explain a smaller proportion of hepcidin variation. In addition, we encourage follow-up of the potentially interesting genes that resulted from the gene-based analysis of low-frequency and rare variants.

  7. Meta-GWAS and Meta-Analysis of Exome Array Studies Do Not Reveal Genetic Determinants of Serum Hepcidin.

    Directory of Open Access Journals (Sweden)

    Tessel E Galesloot

    Full Text Available Serum hepcidin concentration is regulated by iron status, inflammation, erythropoiesis and numerous other factors, but underlying processes are incompletely understood. We studied the association of common and rare single nucleotide variants (SNVs with serum hepcidin in one Italian study and two large Dutch population-based studies. We genotyped common SNVs with genome-wide association study (GWAS arrays and subsequently performed imputation using the 1000 Genomes reference panel. Cohort-specific GWAS were performed for log-transformed serum hepcidin, adjusted for age and gender, and results were combined in a fixed-effects meta-analysis (total N 6,096. Six top SNVs (p<5x10-6 were genotyped in 3,821 additional samples, but associations were not replicated. Furthermore, we meta-analyzed cohort-specific exome array association results of rare SNVs with serum hepcidin that were available for two of the three cohorts (total N 3,226, but no exome-wide significant signal (p<1.4x10-6 was identified. Gene-based meta-analyses revealed 19 genes that showed significant association with hepcidin. Our results suggest the absence of common SNVs and rare exonic SNVs explaining a large proportion of phenotypic variation in serum hepcidin. We recommend extension of our study once additional substantial cohorts with hepcidin measurements, GWAS and/or exome array data become available in order to increase power to identify variants that explain a smaller proportion of hepcidin variation. In addition, we encourage follow-up of the potentially interesting genes that resulted from the gene-based analysis of low-frequency and rare variants.

  8. Long-Term Field Study Reveals Subtle Effects of the Invasive Alga Sargassum muticum upon the Epibiota of Zostera marina.

    Science.gov (United States)

    DeAmicis, Stacey; Foggo, Andrew

    2015-01-01

    Invasive species can alter coastal ecosystems both directly, e.g. through competition for substratum and nutrients, and indirectly. Indirect effects may be mediated by creation of dissimilar or inimical habitats, changes in predator and/or prey assemblages, alterations in associated biota, and perturbations of water movement and thermal regimes. Previous studies have shown that invasive algae can modify native habitat architecture, disrupt intricately linked food webs and alter epibiotic assemblages. In the UK, the seagrass Zostera marina supports a diverse epibiotic assemblage, influencing key factors such as sediment dynamics, depositional regime and trophic linkages. Increasing encroachment of the invasive alga Sargassum muticum into seagrass meadows changes the physical and chemical characteristics of the local environment and creates the potential for changes in the epibionts associated with the seagrass blades, threatening the integrity of the seagrass ecosystem. We investigated the effects of S. muticum invasion upon the epibiota of Z. marina in a drowned river valley in SW England seasonally from spring to autumn over four years in an in-situ manipulative experiment, comparing permanent quadrats with and without artificially introduced S. muticum. Epibiota were weighed, identified to the most detailed operational taxonomic unit (OTU) possible, and unitary organisms were enumerated. Multivariate PERMANOVA+ analysis revealed significant differences in epibiont assemblages between Sargassum treatments. Linear mixed effects models indicated that differences in epibiota assemblage composition were not reflected as significant differences in mean biomass per sample, or number of epibiont OTUs per sample. We conclude that S. muticum invasion into Z. marina meadows may significantly alter the species composition and abundance distribution of epibiotic assemblages found on the blades of the seagrass. Thus S. muticum invasion could have more wide-reaching effects on

  9. Long-Term Field Study Reveals Subtle Effects of the Invasive Alga Sargassum muticum upon the Epibiota of Zostera marina.

    Directory of Open Access Journals (Sweden)

    Stacey DeAmicis

    Full Text Available Invasive species can alter coastal ecosystems both directly, e.g. through competition for substratum and nutrients, and indirectly. Indirect effects may be mediated by creation of dissimilar or inimical habitats, changes in predator and/or prey assemblages, alterations in associated biota, and perturbations of water movement and thermal regimes. Previous studies have shown that invasive algae can modify native habitat architecture, disrupt intricately linked food webs and alter epibiotic assemblages. In the UK, the seagrass Zostera marina supports a diverse epibiotic assemblage, influencing key factors such as sediment dynamics, depositional regime and trophic linkages. Increasing encroachment of the invasive alga Sargassum muticum into seagrass meadows changes the physical and chemical characteristics of the local environment and creates the potential for changes in the epibionts associated with the seagrass blades, threatening the integrity of the seagrass ecosystem. We investigated the effects of S. muticum invasion upon the epibiota of Z. marina in a drowned river valley in SW England seasonally from spring to autumn over four years in an in-situ manipulative experiment, comparing permanent quadrats with and without artificially introduced S. muticum. Epibiota were weighed, identified to the most detailed operational taxonomic unit (OTU possible, and unitary organisms were enumerated. Multivariate PERMANOVA+ analysis revealed significant differences in epibiont assemblages between Sargassum treatments. Linear mixed effects models indicated that differences in epibiota assemblage composition were not reflected as significant differences in mean biomass per sample, or number of epibiont OTUs per sample. We conclude that S. muticum invasion into Z. marina meadows may significantly alter the species composition and abundance distribution of epibiotic assemblages found on the blades of the seagrass. Thus S. muticum invasion could have more wide

  10. Small sample sizes in the study of ontogenetic allometry; implications for palaeobiology.

    Science.gov (United States)

    Brown, Caleb Marshall; Vavrek, Matthew J

    2015-01-01

    Quantitative morphometric analyses, particularly ontogenetic allometry, are common methods used in quantifying shape, and changes therein, in both extinct and extant organisms. Due to incompleteness and the potential for restricted sample sizes in the fossil record, palaeobiological analyses of allometry may encounter higher rates of error. Differences in sample size between fossil and extant studies and any resulting effects on allometric analyses have not been thoroughly investigated, and a logical lower threshold to sample size is not clear. Here we show that studies based on fossil datasets have smaller sample sizes than those based on extant taxa. A similar pattern between vertebrates and invertebrates indicates this is not a problem unique to either group, but common to both. We investigate the relationship between sample size, ontogenetic allometric relationship and statistical power using an empirical dataset of skull measurements of modern Alligator mississippiensis. Across a variety of subsampling techniques, used to simulate different taphonomic and/or sampling effects, smaller sample sizes gave less reliable and more variable results, often with the result that allometric relationships will go undetected due to Type II error (failure to reject the null hypothesis). This may result in a false impression of fewer instances of positive/negative allometric growth in fossils compared to living organisms. These limitations are not restricted to fossil data and are equally applicable to allometric analyses of rare extant taxa. No mathematically derived minimum sample size for ontogenetic allometric studies is found; rather results of isometry (but not necessarily allometry) should not be viewed with confidence at small sample sizes.

  11. Outpatient Tinnitus Clinic, Self-Help Web Platform, or Mobile Application to Recruit Tinnitus Study Samples?

    Science.gov (United States)

    Probst, Thomas; Pryss, Rüdiger C; Langguth, Berthold; Spiliopoulou, Myra; Landgrebe, Michael; Vesala, Markku; Harrison, Stephen; Schobel, Johannes; Reichert, Manfred; Stach, Michael; Schlee, Winfried

    2017-01-01

    For understanding the heterogeneity of tinnitus, large samples are required. However, investigations on how samples recruited by different methods differ from each other are lacking. In the present study, three large samples each recruited by different means were compared: N = 5017 individuals registered at a self-help web platform for tinnitus (crowdsourcing platform Tinnitus Talk), N = 867 users of a smart mobile application for tinnitus (crowdsensing platform TrackYourTinnitus), and N = 3786 patients contacting an outpatient tinnitus clinic (Tinnitus Center of the University Hospital Regensburg). The three samples were compared regarding age, gender, and duration of tinnitus (month or years perceiving tinnitus; subjective report) using chi-squared tests. The three samples significantly differed from each other in age, gender and tinnitus duration (p platform were younger, users of the Tinnitus Talk crowdsourcing platform had more often female gender, and users of both newer technologies (crowdsourcing and crowdsensing) had more frequently acute/subacute tinnitus (20 years). The implications of these findings for clinical research are that newer technologies such as crowdsourcing and crowdsensing platforms offer the possibility to reach individuals hard to get in contact with at an outpatient tinnitus clinic. Depending on the aims and the inclusion/exclusion criteria of a given study, different recruiting strategies (clinic and/or newer technologies) offer different advantages and disadvantages. In general, the representativeness of study results might be increased when tinnitus study samples are recruited in the clinic as well as via crowdsourcing and crowdsensing.

  12. Genotyping faecal samples of Bengal tiger Panthera tigris tigris for population estimation: A pilot study

    Science.gov (United States)

    Bhagavatula, Jyotsna; Singh, Lalji

    2006-01-01

    Background Bengal tiger Panthera tigris tigris the National Animal of India, is an endangered species. Estimating populations for such species is the main objective for designing conservation measures and for evaluating those that are already in place. Due to the tiger's cryptic and secretive behaviour, it is not possible to enumerate and monitor its populations through direct observations; instead indirect methods have always been used for studying tigers in the wild. DNA methods based on non-invasive sampling have not been attempted so far for tiger population studies in India. We describe here a pilot study using DNA extracted from faecal samples of tigers for the purpose of population estimation. Results In this study, PCR primers were developed based on tiger-specific variations in the mitochondrial cytochrome b for reliably identifying tiger faecal samples from those of sympatric carnivores. Microsatellite markers were developed for the identification of individual tigers with a sibling Probability of Identity of 0.005 that can distinguish even closely related individuals with 99.9% certainty. The effectiveness of using field-collected tiger faecal samples for DNA analysis was evaluated by sampling, identification and subsequently genotyping samples from two protected areas in southern India. Conclusion Our results demonstrate the feasibility of using tiger faecal matter as a potential source of DNA for population estimation of tigers in protected areas in India in addition to the methods currently in use. PMID:17044939

  13. Genotyping faecal samples of Bengal tiger Panthera tigris tigris for population estimation: A pilot study

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    Singh Lalji

    2006-10-01

    Full Text Available Abstract Background Bengal tiger Panthera tigris tigris the National Animal of India, is an endangered species. Estimating populations for such species is the main objective for designing conservation measures and for evaluating those that are already in place. Due to the tiger's cryptic and secretive behaviour, it is not possible to enumerate and monitor its populations through direct observations; instead indirect methods have always been used for studying tigers in the wild. DNA methods based on non-invasive sampling have not been attempted so far for tiger population studies in India. We describe here a pilot study using DNA extracted from faecal samples of tigers for the purpose of population estimation. Results In this study, PCR primers were developed based on tiger-specific variations in the mitochondrial cytochrome b for reliably identifying tiger faecal samples from those of sympatric carnivores. Microsatellite markers were developed for the identification of individual tigers with a sibling Probability of Identity of 0.005 that can distinguish even closely related individuals with 99.9% certainty. The effectiveness of using field-collected tiger faecal samples for DNA analysis was evaluated by sampling, identification and subsequently genotyping samples from two protected areas in southern India. Conclusion Our results demonstrate the feasibility of using tiger faecal matter as a potential source of DNA for population estimation of tigers in protected areas in India in addition to the methods currently in use.

  14. Genotyping faecal samples of Bengal tiger Panthera tigris tigris for population estimation: a pilot study.

    Science.gov (United States)

    Bhagavatula, Jyotsna; Singh, Lalji

    2006-10-17

    Bengal tiger Panthera tigris tigris the National Animal of India, is an endangered species. Estimating populations for such species is the main objective for designing conservation measures and for evaluating those that are already in place. Due to the tiger's cryptic and secretive behaviour, it is not possible to enumerate and monitor its populations through direct observations; instead indirect methods have always been used for studying tigers in the wild. DNA methods based on non-invasive sampling have not been attempted so far for tiger population studies in India. We describe here a pilot study using DNA extracted from faecal samples of tigers for the purpose of population estimation. In this study, PCR primers were developed based on tiger-specific variations in the mitochondrial cytochrome b for reliably identifying tiger faecal samples from those of sympatric carnivores. Microsatellite markers were developed for the identification of individual tigers with a sibling Probability of Identity of 0.005 that can distinguish even closely related individuals with 99.9% certainty. The effectiveness of using field-collected tiger faecal samples for DNA analysis was evaluated by sampling, identification and subsequently genotyping samples from two protected areas in southern India. Our results demonstrate the feasibility of using tiger faecal matter as a potential source of DNA for population estimation of tigers in protected areas in India in addition to the methods currently in use.

  15. Impact of repeated measures and sample selection on genome-wide association studies of fasting glucose

    Science.gov (United States)

    Rasmussen-Torvik, Laura J.; Alonso, Alvaro; Li, Man; Kao, Wen; Köttgen, Anna; Yan, Yuer; Couper, David; Boerwinkle, Eric; Bielinski, Suzette J.; Pankow, James S.

    2010-01-01

    Although GWAS have been performed in longitudinal studies, most used only a single trait measure. GWAS of fasting glucose have generally included only normoglycemic individuals. We examined the impact of both repeated measures and sample selection on GWAS in ARIC, a study which obtained four longitudinal measures of fasting glucose and included both individuals with and without prevalent diabetes. The sample included Caucasians and the Affymetrix 6.0 chip was used for genotyping. Sample sizes for GWAS analyses ranged from 8372 (first study visit) to 5782 (average fasting glucose). Candidate SNP analyses with SNPs identified through fasting glucose or diabetes GWAS were conducted in 9133 individuals, including 761 with prevalent diabetes. For a constant sample size, smaller p-values were obtained for the average measure of fasting glucose compared to values at any single visit, and two additional significant GWAS signals were detected. For four candidate SNPs (rs780094, rs10830963, rs7903146, and rs4607517), the strength of association between genotype and glucose was significantly (p-interaction fasting glucose candidate SNPs (rs780094, rs10830963, rs560887, rs4607517, rs13266634) the association with measured fasting glucose was more significant in the smaller sample without prevalent diabetes than in the larger combined sample of those with and without diabetes. This analysis demonstrates the potential utility of averaging trait values in GWAS studies and explores the advantage of using only individuals without prevalent diabetes in GWAS of fasting glucose. PMID:20839289

  16. Comparative study of different Portuguese samples of propolis: pollinic, sensorial, physicochemical, microbiological characterization and antibacterial activity.

    Science.gov (United States)

    Dias, Luís G; Pereira, Ana Paula; Estevinho, Leticia M

    2012-12-01

    The aim of this work was to study four propolis samples from Trás-os-Montes region of Portugal. The propolis samples' color was different, which pollen analysis showed to be due to different botanical sources: Populus sp., Pinus sp., Quercus sp. and Castanea sativa. The data from physicochemical analysis (moisture, soluble and insoluble solids content, pH, conductivity, ash content, wax, total phenolics and flavonoids content) was treated using multivariate statistical tools as cluster heat map, principal components analysis and linear discriminant analysis with the purpose of classifying the sample accordingly to the botanical/geographical origin. The discriminant analysis was applied with stepwise to select the variables that most contribute to sample identification accordingly to pollinic profile. The cross-validation technique was applied, using the leave-one-out procedure, which showed good prediction capabilities of the samples. Microbiologically, the commercial quality was satisfactory, since the samples didn't contain deterioration or pathogenic microorganisms. All the samples studied presented antimicrobial activity against Methicillin-resistant Staphylococcus aureus, in a dose dependent way. The antimicrobial activity was strictly related to the physicochemical composition. This work will allow connecting a particular chemical propolis type to a specific type of biological activity, what is essential for the use in therapeutic applications. Copyright © 2012 Elsevier Ltd. All rights reserved.

  17. Adaptive autonomous sampling toward the study of microbial carbon and energy fluxes in a dynamic estuary

    Science.gov (United States)

    Herfort, L.; Seaton, C. M.; Wilkin, M.; Baptista, A. M.; Roman, B.; Preston, C. M.; Scholin, C. A.; Melançon, C.; Simon, H. M.

    2013-12-01

    An autonomous microbial sampling device was integrated with a long-term (endurance) environmental sensor system to investigate variation in microbial composition and activities related to complex estuarine dynamics. This integration was a part of ongoing efforts in the Center for Coastal Margin Observation and Prediction (CMOP) to study estuarine carbon and nitrogen cycling using an observation and prediction system (SATURN, http://www.stccmop.org/saturn) as foundational infrastructure. The two endurance stations fitted with physical and biogeochemical sensors that were used in this study are located in the SATURN observation network. The microbial sampler is the Environmental Sample Processor (ESP), a commercially available electromechanical/fluidic system designed for automated collection, preservation and in situ analyses of marine water samples. The primary goal of the integration was to demonstrate that the ESP, developed for sampling of pelagic oceanic environments, could be successfully deployed for autonomous sample acquisition in the highly dynamic and turbid Columbia River estuary. The ability of the ESP to collect material at both pre-determined times and automatically in response to local conditions was tested. Pre-designated samples were acquired at specific times to capture variability in the tidal cycle. Autonomous, adaptive sampling was triggered when conditions associated with specific water masses were detected in real-time by the SATURN station's sensors and then communicated to the ESP via the station computer to initiate sample collection. Triggering criteria were based on our understanding of estuary dynamics, as provided by the analysis of extensive archives of high-resolution, long-term SATURN observations and simulations. In this manner, we used the ESP to selectively sample various microbial consortia in the estuary to facilitate the study of ephemeral microbial-driven processes. For example, during the summer of 2013 the adaptive sampling

  18. Genetic and genomic diversity studies of Acacia symbionts in Senegal reveal new species of Mesorhizobium with a putative geographical pattern.

    Directory of Open Access Journals (Sweden)

    Fatou Diouf

    Full Text Available Acacia senegal (L Willd. and Acacia seyal Del. are highly nitrogen-fixing and moderately salt tolerant species. In this study we focused on the genetic and genomic diversity of Acacia mesorhizobia symbionts from diverse origins in Senegal and investigated possible correlations between the genetic diversity of the strains, their soil of origin, and their tolerance to salinity. We first performed a multi-locus sequence analysis on five markers gene fragments on a collection of 47 mesorhizobia strains of A. senegal and A. seyal from 8 localities. Most of the strains (60% clustered with the M. plurifarium type strain ORS 1032T, while the others form four new clades (MSP1 to MSP4. We sequenced and assembled seven draft genomes: four in the M. plurifarium clade (ORS3356, ORS3365, STM8773 and ORS1032T, one in MSP1 (STM8789, MSP2 (ORS3359 and MSP3 (ORS3324. The average nucleotide identities between these genomes together with the MLSA analysis reveal three new species of Mesorhizobium. A great variability of salt tolerance was found among the strains with a lack of correlation between the genetic diversity of mesorhizobia, their salt tolerance and the soils samples characteristics. A putative geographical pattern of A. senegal symbionts between the dryland north part and the center of Senegal was found, reflecting adaptations to specific local conditions such as the water regime. However, the presence of salt does not seem to be an important structuring factor of Mesorhizobium species.

  19. Impact of community-acquired paediatric rotavirus gastroenteritis on family life: data from the REVEAL study.

    Science.gov (United States)

    Van der Wielen, Marie; Giaquinto, Carlo; Gothefors, Leif; Huelsse, Christel; Huet, Frédéric; Littmann, Martina; Maxwell, Melanie; Talayero, José M P; Todd, Peter; Vila, Miguel T; Cantarutti, Luigi; Van Damme, Pierre

    2010-03-15

    Rotavirus is the leading cause of acute gastroenteritis (AGE) and the most frequent cause of severe diarrhoea in children aged less than 5 years. Although the epidemiology of rotavirus gastroenteritis (RVGE) is well documented, there are few data on the impact of RVGE on the families of affected children. Data associated with the burden of RVGE, including number of working days lost, levels of parental stress, the need for alternative childcare arrangements and additional nappies used, were extracted from questionnaires completed by parents of children participating in a prospective, multicentre, observational study (Rotavirus gastroenteritis Epidemiology and Viral types in Europe Accounting for Losses in public health and society, REVEAL), conducted during 2004-2005 in selected areas of Belgium, France, Germany, Italy, Spain, Sweden, and the United Kingdom to estimate the incidence of RVGE in children aged less than 5 years seeking medical care as a result of AGE. 1102 children with RVGE were included in the present analysis. The proportion of RVGE cases that required at least one parent or other person to be absent from work was 39%-91% in the hospital setting, 44%-64% in the emergency department, and 20%-64% in primary care. Self-reported levels of parental stress were generally high (mean stress levels, > or = 5 on a 10-point visual analogue scale). Additional childcare arrangements were required in up to 21% of RVGE episodes. The mean number of nappies used per day during RVGE episodes was approximately double that used when the child was not ill. Paediatric RVGE cases cause disruption to families and parental stress. The burden of RVGE on children and their families could be substantially reduced by routine rotavirus vaccination of infants.

  20. Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplications

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    Huang Yong

    2009-11-01

    Full Text Available Abstract Background Gene and genome duplication is the principle creative force in evolution. Recently, protein subcellular relocalization, or neolocalization was proposed as one of the mechanisms responsible for the retention of duplicated genes. This hypothesis received support from the analysis of yeast genomes, but has not been tested thoroughly on animal genomes. In order to evaluate the importance of subcellular relocalizations for retention of duplicated genes in animal genomes, we systematically analyzed nuclear encoded mitochondrial proteins in the human genome by reconstructing phylogenies of mitochondrial multigene families. Results The 456 human mitochondrial proteins selected for this study were clustered into 305 gene families including 92 multigene families. Among the multigene families, 59 (64% consisted of both mitochondrial and cytosolic (non-mitochondrial proteins (mt-cy families while the remaining 33 (36% were composed of mitochondrial proteins (mt-mt families. Phylogenetic analyses of mt-cy families revealed three different scenarios of their neolocalization following gene duplication: 1 relocalization from mitochondria to cytosol, 2 from cytosol to mitochondria and 3 multiple subcellular relocalizations. The neolocalizations were most commonly enabled by the gain or loss of N-terminal mitochondrial targeting signals. The majority of detected subcellular relocalization events occurred early in animal evolution, preceding the evolution of tetrapods. Mt-mt protein families showed a somewhat different pattern, where gene duplication occurred more evenly in time. However, for both types of protein families, most duplication events appear to roughly coincide with two rounds of genome duplications early in vertebrate evolution. Finally, we evaluated the effects of inaccurate and incomplete annotation of mitochondrial proteins and found that our conclusion of the importance of subcellular relocalization after gene duplication on

  1. Impact of community-acquired paediatric rotavirus gastroenteritis on family life: data from the REVEAL study

    Directory of Open Access Journals (Sweden)

    Talayero José MP

    2010-03-01

    Full Text Available Abstract Background Rotavirus is the leading cause of acute gastroenteritis (AGE and the most frequent cause of severe diarrhoea in children aged less than 5 years. Although the epidemiology of rotavirus gastroenteritis (RVGE is well documented, there are few data on the impact of RVGE on the families of affected children. Methods Data associated with the burden of RVGE, including number of working days lost, levels of parental stress, the need for alternative childcare arrangements and additional nappies used, were extracted from questionnaires completed by parents of children participating in a prospective, multicentre, observational study (Rotavirus gastroenteritis Epidemiology and Viral types in Europe Accounting for Losses in public health and society, REVEAL, conducted during 2004-2005 in selected areas of Belgium, France, Germany, Italy, Spain, Sweden, and the United Kingdom to estimate the incidence of RVGE in children aged less than 5 years seeking medical care as a result of AGE. Results 1102 children with RVGE were included in the present analysis. The proportion of RVGE cases that required at least one parent or other person to be absent from work was 39%-91% in the hospital setting, 44%-64% in the emergency department, and 20%-64% in primary care. Self-reported levels of parental stress were generally high (mean stress levels, ≥ 5 on a 10-point visual analogue scale. Additional childcare arrangements were required in up to 21% of RVGE episodes. The mean number of nappies used per day during RVGE episodes was approximately double that used when the child was not ill. Conclusions Paediatric RVGE cases cause disruption to families and parental stress. The burden of RVGE on children and their families could be substantially reduced by routine rotavirus vaccination of infants.

  2. Field studies reveal strong postmating isolation between ecologically divergent butterfly populations.

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    Carolyn S McBride

    2010-10-01

    Full Text Available Gene flow between populations that are adapting to distinct environments may be restricted if hybrids inherit maladaptive, intermediate phenotypes. This phenomenon, called extrinsic postzygotic isolation (EPI, is thought to play a critical role in the early stages of speciation. However, despite its intuitive appeal, we know surprisingly little about the strength and prevalence of EPI in nature, and even less about the specific phenotypes that tend to cause problems for hybrids. In this study, we searched for EPI among allopatric populations of the butterfly Euphydryas editha that have specialized on alternative host plants. These populations recall a situation thought typical of the very early stages of speciation. They lack consistent host-associated genetic differentiation at random nuclear loci and show no signs of reproductive incompatibility in the laboratory. However, they do differ consistently in diverse host-related traits. For each of these traits, we first asked whether hybrids between populations that use different hosts (different-host hybrids were intermediate to parental populations and to hybrids between populations that use the same host (same-host hybrids. We then conducted field experiments to estimate the effects of intermediacy on fitness in nature. Our results revealed strong EPI under field conditions. Different-host hybrids exhibited an array of intermediate traits that were significantly maladaptive, including four behaviors. Intermediate foraging height slowed the growth of larvae, while intermediate oviposition preference, oviposition site height, and clutch size severely reduced the growth and survival of the offspring of adult females. We used our empirical data to construct a fitness surface on which different-host hybrids can be seen to fall in an adaptive valley between two peaks occupied by same-host hybrids. These findings demonstrate how ecological selection against hybrids can create a strong barrier to gene

  3. Molecular dynamics simulation study reveals potential substrate entry path into γ-secretase/presenilin-1.

    Science.gov (United States)

    Kong, Ren; Chang, Shan; Xia, Weiming; Wong, Stephen T C

    2015-08-01

    Presenilin 1 (PS1) is the catalytic unit of γ-secretase which cleaves more than one hundred substrates. Among them, amyloid precursor protein (APP) and Notch are notable for their pivotal role in the pathogenesis of Alzheimer's disease (AD) and certain types of cancer. The hydrolysis process occurring inside the hydrophobic lipid bilayer remains unclear. With the aim to understand the mechanism of intramembrane proteolysis by γ-secretase, we constructed a homology model of human PS1 and performed molecular dynamics simulation in explicit membrane phospholipids with different components. During the simulation, TM9 was found to exhibit a high level of flexibility that involved in "gate-open" movement of TM2 and TM6, and thus partially exposed the catalytic residues. The highly conserved PALP motif acts as an anchor to mediate the conformation changes of TM6 induced by TM9. Moreover, direct interactions were observed between 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) and the active site of γ-secretase, indicating that the lipid molecules have the potential to modulate γ-secretase by contacting with the catalytic residues, i.e., ASP 257 and ASP 385 of PS1. The intermediate states indicate a potential substrate penetration pathway through the interface of TM2 and TM6, which may be induced by changes of TM9. To our knowledge, this is the first molecular simulation study that reveals dynamic behavior of the human PS1 structure in the lipid bilayer and provides insight into the substrate entry path for subsequent intramembrane hydrolysis, which is critical information required for new strategy development of γ-secretase modulators to alleviate devastating AD. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Revealing And Studying Super-massive Black Holes In The Universe With EXIST

    Science.gov (United States)

    Della Ceca, Roberto; Tagliaferri, G.; Ghisellini, G.; Coppi, P.; De Rosa, A.; Foschini, L.; Grindlay, J. E.; Natalucci, L.; Panessa, F.; Pareschi, G.; Ubertini, P.; Tavecchio, F.

    2010-03-01

    Active Galactic Nuclei (AGN) emit over the entire electromagnetic spectrum and are widely believed to be powered by accretion of matter onto a Supermassive (million to billion) Black Hole (SMBH). Besides being sites of "extreme" physics, AGN are likely leading actors in the formation and evolution of galaxies. Fully understanding the history of galaxy formation thus requires us to find when, where, and how SMBH grow and interact with their surroundings. With its large collection area, broad-band energy coverage from optical/NIR to soft/hard X-ray (˜ 0.1 to 600 keV), all-sky monitoring capability, and on-board follow-up, the proposed EXIST mission provides an unrivaled census of SMBH activity especially in the local (zEXIST's all-sky survey and monitoring capabilities and the factor 20 increase in hard X-ray sensitivity compared to current and prior X-ray missions. In particular, EXIST will enable major progress in understanding: i) when and where SMBH are active in the Universe (by revealing and measuring heavily obscured accretion including the one occurring in rare, local or luminous objects), ii) the physics of accretion around SMBH (by studying their broad-band X-ray spectra and variability), and iii) the link between accretion power and jet/outflow power (by using observations of blazars). Last but not least EXIST's ability to find powerful but very rare blazars enables it to probe the appearance of the very first SMBH in the Universe, allowing us to derive the black hole mass function of distant (z>4) radio loud AGN.

  5. The impact of sample size and marker selection on the study of haplotype structures

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    Sun Xiao

    2004-03-01

    Full Text Available Abstract Several studies of haplotype structures in the human genome in various populations have found that the human chromosomes are structured such that each chromosome can be divided into many blocks, within which there is limited haplotype diversity. In addition, only a few genetic markers in a putative block are needed to capture most of the diversity within a block. There has been no systematic empirical study of the effects of sample size and marker set on the identified block structures and representative marker sets, however. The purpose of this study was to conduct a detailed empirical study to examine such impacts. Towards this goal, we have analysed three representative autosomal regions from a large genome-wide study of haplotypes with samples consisting of African-Americans and samples consisting of Japanese and Chinese individuals. For both populations, we have found that the sample size and marker set have significant impact on the number of blocks and the total number of representative markers identified. The marker set in particular has very strong impacts, and our results indicate that the marker density in the original datasets may not be adequate to allow a meaningful characterisation of haplotype structures. In general, we conclude that we need a relatively large sample size and a very dense marker panel in the study of haplotype structures in human populations.

  6. Using Environmental Variables for Studying of the Quality of Sampling in Soil Mapping

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    A. Jafari

    2016-02-01

    Full Text Available Introduction: Methods of soil survey are generally empirical and based on the mental development of the surveyor, correlating soil with underlying geology, landforms, vegetation and air-photo interpretation. Since there are no statistical criteria for traditional soil sampling; this may lead to bias in the areas being sampled. In digital soil mapping, soil samples may be used to elaborate quantitative relationships or models between soil attributes and soil covariates. Because the relationships are based on the soil observations, the quality of the resulting soil map depends also on the soil observation quality. An appropriate sampling design for digital soil mapping depends on how much data is available and where the data is located. Some statistical methods have been developed for optimizing data sampling for soil surveys. Some of these methods deal with the use of ancillary information. The purpose of this study was to evaluate the quality of sampling of existing data. Materials and Methods: The study area is located in the central basin of the Iranian plateau (Figure 1. The geologic infrastructure of the area is mainly Cretaceous limestone, Mesozoic shale and sandstone. Air photo interpretation (API was used to differentiate geomorphic patterns based on their formation processes, general structure and morphometry. The patterns were differentiated through a nested geomorphic hierarchy (Fig. 2. A four-level geomorphic hierarchy is used to breakdown the complexity of different landscapes of the study area. In the lower level of the hierarchy, the geomorphic surfaces, which were formed by a unique process during a specific geologic time, were defined. A stratified sampling scheme was designed based on geomorphic mapping. In the stratified simple random sampling, the area was divided into sub-areas referred to as strata based on geomorphic surfaces, and within each stratum, sampling locations were randomly selected (Figure 2. This resulted in 191

  7. Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies

    OpenAIRE

    Passamonti Marco; Ferrucci Ronald R; Plazzi Federico

    2010-01-01

    Abstract Background Taxon sampling is a major concern in phylogenetic studies. Incomplete, biased, or improper taxon sampling can lead to misleading results in reconstructing evolutionary relationships. Several theoretical methods are available to optimize taxon choice in phylogenetic analyses. However, most involve some knowledge about the genetic relationships of the group of interest (i.e., the ingroup), or even a well-established phylogeny itself; these data are not always available in ge...

  8. A comparative study of extraction and purification methods for environmental DNA from soil and sludge samples

    OpenAIRE

    Roh, Changhyun; Villatte, Francois; Kim, Byung-Gee; Schmid, Rolf D.

    2006-01-01

    An important prerequisite for a successful metagenome library construction is an efficient extraction procedure for DNA out of environmental samples. In this study we compared three indirect and four direct extraction methods, including a commercial kit, in terms of DNA yield, purity and time requirement. A special focus was set on methods which are appropriate for the extraction of environmental DNA (eDNA) from very limited sample sizes (0.1 g) to enable a highly parallel approach. Direct ex...

  9. Relations among questionnaire and experience sampling measures of inner speech: a smartphone app study

    OpenAIRE

    Ben eAlderson-Day; Charles eFernyhough

    2015-01-01

    Inner speech is often reported to be a common and central part of inner experience, but its true prevalence is unclear. Many questionnaire-based measures appear to lack convergent validity and it has been claimed that they overestimate inner speech in comparison to experience sampling methods (which involve collecting data at random timepoints). The present study compared self-reporting of inner speech collected via a general questionnaire and experience sampling, using data from a custom-mad...

  10. Kinetic studies in solid state reactions by sample-controlled methods and advanced analysis procedures

    OpenAIRE

    Pérez-Maqueda, Luis A.; Criado, J. M.; Sánchez-Jiménez, P.E.; Perejón, Antonio

    2013-01-01

    A comparative study of both conventional rising temperature and sample-controlled methods, like constant rate thermal analysis (CRTA), is carried out after analyzing a set of solid state reactions using both methods. It is shown that CRTA avoids the influence of heat and mass transfer phenomena for a wide range of sample sizes leading to reliable kinetic parameters. On the other hand, conventional rising temperature methods yield α–T plots dependent on experimental conditions, even when using...

  11. The Effect of Small Sample Size on Measurement Equivalence of Psychometric Questionnaires in MIMIC Model: A Simulation Study

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    Jamshid Jamali

    2017-01-01

    Full Text Available Evaluating measurement equivalence (also known as differential item functioning (DIF is an important part of the process of validating psychometric questionnaires. This study aimed at evaluating the multiple indicators multiple causes (MIMIC model for DIF detection when latent construct distribution is nonnormal and the focal group sample size is small. In this simulation-based study, Type I error rates and power of MIMIC model for detecting uniform-DIF were investigated under different combinations of reference to focal group sample size ratio, magnitude of the uniform-DIF effect, scale length, the number of response categories, and latent trait distribution. Moderate and high skewness in the latent trait distribution led to a decrease of 0.33% and 0.47% power of MIMIC model for detecting uniform-DIF, respectively. The findings indicated that, by increasing the scale length, the number of response categories and magnitude DIF improved the power of MIMIC model, by 3.47%, 4.83%, and 20.35%, respectively; it also decreased Type I error of MIMIC approach by 2.81%, 5.66%, and 0.04%, respectively. This study revealed that power of MIMIC model was at an acceptable level when latent trait distributions were skewed. However, empirical Type I error rate was slightly greater than nominal significance level. Consequently, the MIMIC was recommended for detection of uniform-DIF when latent construct distribution is nonnormal and the focal group sample size is small.

  12. Patients' nursing records revealing opportunities for interprofessional workplace learning in primary care: a chart review study.

    Science.gov (United States)

    Pype, Peter; Wens, Johan; Stes, Ann; Grypdonck, Maria; Eynden, Bart Vanden; Deveugele, Myriam

    2014-01-01

    Working and learning go hand in hand during interprofessional collaborative practice. Patients' nursing records are designed to record patient care and health status. It is not known whether these records are also used to keep track of interprofessional contacts or interprofessional learning between team members. This study explored the usefulness of patients' nursing records in optimising interprofessional workplace learning for general practitioners. We utilized a descriptive retrospective chart review. All palliative home care teams of the Dutch speaking part of Belgium were involved. Throughout the year 2010, a representative sample of patient charts was selected. Characteristics of encounters between general practitioners and palliative care nurses were extracted from the charts. Detailed accounts of interprofessional contacts were found in the charts. Palliative care nurses recorded number and type of contacts, topics discussed during contacts and general practitioner's learning activities. Palliative care nurses are sensitive and open towards the general practitioners' learning needs. Patients' nursing records provide useful information for interprofessional team discussions on workplace learning. Healthcare professionals should be trained to respond to each other's learning needs.

  13. Storage and shipping of tissue samples for DNA analyses: A case study on earthworms☆

    Science.gov (United States)

    Straube, Daniela; Juen, Anita

    2013-01-01

    Nowadays, molecular analyses play an important role in studies of soil dwelling animals, for example in taxonomy, phylogeography or food web analyses. The quality of the DNA, used for later molecular analyses, is an important factor and depends on collection and preservation of samples prior to DNA extraction. Ideally, DNA samples are frozen immediately upon collection, but if samples are collected in the field, suitable preservation methods might be limited due to unavailability of resources or remote field sites. Moreover, shipping samples over long distances can cause loss of DNA quality e.g. by thawing or leaking of preservation liquid. In this study we use earthworms, a key organism in soil research, to compare three different DNA preservation methods – freezing at −20 °C, storing in 75% ethanol, and freeze drying. Samples were shipped from the United States of America to Austria. The DNA of the samples was extracted using two different extraction methods, peqGOLD™ and Chelex® 100. The DNA amplification success was determined by amplifying four DNA fragments of different length. The PCR amplification success is significantly influenced by preservation method and extraction method and differed significantly depending on the length of the DNA fragment. Freeze drying samples was the best preservation method when samples were extracted using the silica based extraction method peqGOLD™. For samples that were extracted with Chelex® 100, storage in ethanol was the best preservation method. However, the overall amplification success was significantly lower for the extraction procedure based on Chelex® 100. The detection of the small DNA fragments was higher and independent from the extraction method, while the amplification success was significantly reduced for the longer DNA fragments. We recommend freeze drying of DNA samples, especially when they have to be shipped for longer distances. No special packaging or declaration is needed for freeze dried

  14. Storage and shipping of tissue samples for DNA analyses: A case study on earthworms.

    Science.gov (United States)

    Straube, Daniela; Juen, Anita

    2013-07-01

    Nowadays, molecular analyses play an important role in studies of soil dwelling animals, for example in taxonomy, phylogeography or food web analyses. The quality of the DNA, used for later molecular analyses, is an important factor and depends on collection and preservation of samples prior to DNA extraction. Ideally, DNA samples are frozen immediately upon collection, but if samples are collected in the field, suitable preservation methods might be limited due to unavailability of resources or remote field sites. Moreover, shipping samples over long distances can cause loss of DNA quality e.g. by thawing or leaking of preservation liquid. In this study we use earthworms, a key organism in soil research, to compare three different DNA preservation methods - freezing at -20 °C, storing in 75% ethanol, and freeze drying. Samples were shipped from the United States of America to Austria. The DNA of the samples was extracted using two different extraction methods, peqGOLD™ and Chelex® 100. The DNA amplification success was determined by amplifying four DNA fragments of different length. The PCR amplification success is significantly influenced by preservation method and extraction method and differed significantly depending on the length of the DNA fragment. Freeze drying samples was the best preservation method when samples were extracted using the silica based extraction method peqGOLD™. For samples that were extracted with Chelex® 100, storage in ethanol was the best preservation method. However, the overall amplification success was significantly lower for the extraction procedure based on Chelex® 100. The detection of the small DNA fragments was higher and independent from the extraction method, while the amplification success was significantly reduced for the longer DNA fragments. We recommend freeze drying of DNA samples, especially when they have to be shipped for longer distances. No special packaging or declaration is needed for freeze dried

  15. Planning considerations for a Mars Sample Receiving Facility: summary and interpretation of three design studies.

    Science.gov (United States)

    Beaty, David W; Allen, Carlton C; Bass, Deborah S; Buxbaum, Karen L; Campbell, James K; Lindstrom, David J; Miller, Sylvia L; Papanastassiou, Dimitri A

    2009-10-01

    It has been widely understood for many years that an essential component of a Mars Sample Return mission is a Sample Receiving Facility (SRF). The purpose of such a facility would be to take delivery of the flight hardware that lands on Earth, open the spacecraft and extract the sample container and samples, and conduct an agreed-upon test protocol, while ensuring strict containment and contamination control of the samples while in the SRF. Any samples that are found to be non-hazardous (or are rendered non-hazardous by sterilization) would then be transferred to long-term curation. Although the general concept of an SRF is relatively straightforward, there has been considerable discussion about implementation planning. The Mars Exploration Program carried out an analysis of the attributes of an SRF to establish its scope, including minimum size and functionality, budgetary requirements (capital cost, operating costs, cost profile), and development schedule. The approach was to arrange for three independent design studies, each led by an architectural design firm, and compare the results. While there were many design elements in common identified by each study team, there were significant differences in the way human operators were to interact with the systems. In aggregate, the design studies provided insight into the attributes of a future SRF and the complex factors to consider for future programmatic planning.

  16. Laboratory Studies on Surface Sampling of Bacillus anthracis Contamination: Summary, Gaps, and Recommendations

    Energy Technology Data Exchange (ETDEWEB)

    Piepel, Gregory F.; Amidan, Brett G.; Hu, Rebecca

    2011-11-28

    This report summarizes previous laboratory studies to characterize the performance of methods for collecting, storing/transporting, processing, and analyzing samples from surfaces contaminated by Bacillus anthracis or related surrogates. The focus is on plate culture and count estimates of surface contamination for swab, wipe, and vacuum samples of porous and nonporous surfaces. Summaries of the previous studies and their results were assessed to identify gaps in information needed as inputs to calculate key parameters critical to risk management in biothreat incidents. One key parameter is the number of samples needed to make characterization or clearance decisions with specified statistical confidence. Other key parameters include the ability to calculate, following contamination incidents, the (1) estimates of Bacillus anthracis contamination, as well as the bias and uncertainties in the estimates, and (2) confidence in characterization and clearance decisions for contaminated or decontaminated buildings. Gaps in knowledge and understanding identified during the summary of the studies are discussed and recommendations are given for future studies.

  17. Successful Sampling Strategy Advances Laboratory Studies of NMR Logging in Unconsolidated Aquifers

    Science.gov (United States)

    Behroozmand, Ahmad A.; Knight, Rosemary; Müller-Petke, Mike; Auken, Esben; Barfod, Adrian A. S.; Ferré, Ty P. A.; Vilhelmsen, Troels N.; Johnson, Carole D.; Christiansen, Anders V.

    2017-11-01

    The nuclear magnetic resonance (NMR) technique has become popular in groundwater studies because it responds directly to the presence and mobility of water in a porous medium. There is a need to conduct laboratory experiments to aid in the development of NMR hydraulic conductivity models, as is typically done in the petroleum industry. However, the challenge has been obtaining high-quality laboratory samples from unconsolidated aquifers. At a study site in Denmark, we employed sonic drilling, which minimizes the disturbance of the surrounding material, and extracted twelve 7.6 cm diameter samples for laboratory measurements. We present a detailed comparison of the acquired laboratory and logging NMR data. The agreement observed between the laboratory and logging data suggests that the methodologies proposed in this study provide good conditions for studying NMR measurements of unconsolidated near-surface aquifers. Finally, we show how laboratory sample size and condition impact the NMR measurements.

  18. Bayesian sample size determination for cost-effectiveness studies with censored data.

    Directory of Open Access Journals (Sweden)

    Daniel P Beavers

    Full Text Available Cost-effectiveness models are commonly utilized to determine the combined clinical and economic impact of one treatment compared to another. However, most methods for sample size determination of cost-effectiveness studies assume fully observed costs and effectiveness outcomes, which presents challenges for survival-based studies in which censoring exists. We propose a Bayesian method for the design and analysis of cost-effectiveness data in which costs and effectiveness may be censored, and the sample size is approximated for both power and assurance. We explore two parametric models and demonstrate the flexibility of the approach to accommodate a variety of modifications to study assumptions.

  19. A comparative study of general intelligence in Spanish and Moroccan samples.

    Science.gov (United States)

    Diaz, Amelia; Sellami, Khadija; Infanzón, Eugenia; Lanzón, Teresa; Lynn, Richard

    2012-07-01

    The aim of this study is to fill a gap in intelligence research by presenting data for the average IQ in Morocco and for a comparable sample in Spain. Adult samples were administered the Raven Standard Progressive Matrices (SPM) (Raven, Court, & Raven, 2001) and scored for the total test and for the three sub-factors of gestalt continuation, verbal-analytical reasoning and visuospatial ability identified by Lynn, Allik, and Irwing (2004). The total test and the three factors have shown satisfactory reliability. Our results for the Moroccan sample show significant relationship between general intelligence factor, gestalt continuation and visuospatial ability with education level and income. Conversely, these variables have been shown to be independent for the Spanish sample. This sample obtained significantly higher scores for the four factors assessed than the Moroccan one. These differences have been found also comparing samples with the same education levels. Finally, the errors percentage for Moroccans has been higher than for Spaniards in all the items, suggesting that the level of difficulty was higher for the Moroccan sample.

  20. A preliminary study on identification of Thai rice samples by INAA and statistical analysis

    Science.gov (United States)

    Kongsri, S.; Kukusamude, C.

    2017-09-01

    This study aims to investigate the elemental compositions in 93 Thai rice samples using instrumental neutron activation analysis (INAA) and to identify rice according to their types and rice cultivars using statistical analysis. As, Mg, Cl, Al, Br, Mn, K, Rb and Zn in Thai jasmine rice and Sung Yod rice samples were successfully determined by INAA. The accuracy and precision of the INAA method were verified by SRM 1568a Rice Flour. All elements were found to be in a good agreement with the certified values. The precisions in term of %RSD were lower than 7%. The LODs were obtained in range of 0.01 to 29 mg kg-1. The concentration of 9 elements distributed in Thai rice samples was evaluated and used as chemical indicators to identify the type of rice samples. The result found that Mg, Cl, As, Br, Mn, K, Rb, and Zn concentrations in Thai jasmine rice samples are significantly different but there was no evidence that Al is significantly different from concentration in Sung Yod rice samples at 95% confidence interval. Our results may provide preliminary information for discrimination of rice samples and may be useful database of Thai rice.

  1. A Study on Primary and Secondary School Students' Misconceptions about Greenhouse Effect (Erzurum Sampling)

    Science.gov (United States)

    Gul, Seyda; Yesilyurt, Selami

    2011-01-01

    The aim of this study is to determine what level of primary and secondary school students' misconceptions related to greenhouse effect is. Study group consists of totally 280 students attended to totally 8 primary and secondary schools (4 primary school, 4 secondary school) which were determined with convenient sampling method from center of…

  2. Assessment of dust sampling methods for the study of cultivable-microorganism exposure in stables.

    NARCIS (Netherlands)

    Normand, A.C.; Vacheyrou, M.; Sudre, B.; Heederik, D.|info:eu-repo/dai/nl/072910542; Piarroux, R.

    2009-01-01

    Studies have shown a link between living on a farm, exposure to microbial components (e.g., endotoxins or beta-d-glucans), and a lower risk for allergic diseases and asthma. Due to the lack of validated sampling methods, studies of asthma and atopy have not relied on exposure assessment based on

  3. Experimental Study and Mathematical Modeling of Asphaltene Deposition Mechanism in Core Samples

    Directory of Open Access Journals (Sweden)

    Jafari Behbahani T.

    2015-11-01

    Full Text Available In this work, experimental studies were conducted to determine the effect of asphaltene deposition on the permeability reduction and porosity reduction of carbonate, sandstone and dolomite rock samples using an Iranian bottom hole live oil sample which is close to reservoir conditions, whereas in the majority of previous work, a mixture of recombined oil (a mixture of dead oil and associated gas was injected into a core sample which is far from reservoir conditions. The effect of the oil injection rate on asphaltene deposition and permeability reduction was studied. The experimental results showed that an increase in the oil injection flow rate can result in an increase in asphaltene deposition and permeability reduction. Also, it can be observed that at lower injection flow rates, a monotonic decrease in permeability of the rock samples can be attained upon increasing the injection flow rate, while at higher injection rates, after a decrease in rock permeability, an increasing trend is observed before a steady-state condition can be reached. The experimental results also showed that the rock type can affect the amount of asphaltene deposition, and the asphaltene deposition has different mechanisms in sandstone and carbonate core samples. It can be seen that the adsorption and plugging mechanisms have a more important role in asphaltene deposition in carbonate core samples than sandstone core samples. From the results, it can be observed that the pore volumes of the injected crude oil are higher for sandstone cores compared with the carbonate cores. Also, it can be inferred that three depositional types may take place during the crude oil injection, i.e., continuous deposition for low-permeability cores, slow, steady plugging for high-permeability cores and steady deposition for medium-permeability cores. It can be seen from the experimental results that damage to the core samples was found to increase when the production pressures were

  4. Opening the Big Black Box: European study reveals visitors' impressions of science laboratories

    CERN Multimedia

    2004-01-01

    "On 29 - 30 March the findings of 'Inside the Big Black Box'- a Europe-wide science and society project - will be revealed during a two-day seminar hosted by CERN*. The principle aim of Inside the Big Black Box (IN3B) is to determine whether a working scientific laboratory can capture the curiosity of the general public through visits" (1 page)

  5. Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies.

    Science.gov (United States)

    Plazzi, Federico; Ferrucci, Ronald R; Passamonti, Marco

    2010-04-27

    Taxon sampling is a major concern in phylogenetic studies. Incomplete, biased, or improper taxon sampling can lead to misleading results in reconstructing evolutionary relationships. Several theoretical methods are available to optimize taxon choice in phylogenetic analyses. However, most involve some knowledge about the genetic relationships of the group of interest (i.e., the ingroup), or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications. We propose a new method to assess taxon sampling developing Clarke and Warwick statistics. This method aims to measure the "phylogenetic representativeness" of a given sample or set of samples and it is based entirely on the pre-existing available taxonomy of the ingroup, which is commonly known to investigators. Moreover, our method also accounts for instability and discordance in taxonomies. A Python-based script suite, called PhyRe, has been developed to implement all analyses we describe in this paper. We show that this method is sensitive and allows direct discrimination between representative and unrepresentative samples. It is also informative about the addition of taxa to improve taxonomic coverage of the ingroup. Provided that the investigators' expertise is mandatory in this field, phylogenetic representativeness makes up an objective touchstone in planning phylogenetic studies.

  6. Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies

    Directory of Open Access Journals (Sweden)

    Passamonti Marco

    2010-04-01

    Full Text Available Abstract Background Taxon sampling is a major concern in phylogenetic studies. Incomplete, biased, or improper taxon sampling can lead to misleading results in reconstructing evolutionary relationships. Several theoretical methods are available to optimize taxon choice in phylogenetic analyses. However, most involve some knowledge about the genetic relationships of the group of interest (i.e., the ingroup, or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications. Results We propose a new method to assess taxon sampling developing Clarke and Warwick statistics. This method aims to measure the "phylogenetic representativeness" of a given sample or set of samples and it is based entirely on the pre-existing available taxonomy of the ingroup, which is commonly known to investigators. Moreover, our method also accounts for instability and discordance in taxonomies. A Python-based script suite, called PhyRe, has been developed to implement all analyses we describe in this paper. Conclusions We show that this method is sensitive and allows direct discrimination between representative and unrepresentative samples. It is also informative about the addition of taxa to improve taxonomic coverage of the ingroup. Provided that the investigators' expertise is mandatory in this field, phylogenetic representativeness makes up an objective touchstone in planning phylogenetic studies.

  7. Estimating sample size for landscape-scale mark-recapture studies of North American migratory tree bats

    Science.gov (United States)

    Ellison, Laura E.; Lukacs, Paul M.

    2014-01-01

    Concern for migratory tree-roosting bats in North America has grown because of possible population declines from wind energy development. This concern has driven interest in estimating population-level changes. Mark-recapture methodology is one possible analytical framework for assessing bat population changes, but sample size requirements to produce reliable estimates have not been estimated. To illustrate the sample sizes necessary for a mark-recapture-based monitoring program we conducted power analyses using a statistical model that allows reencounters of live and dead marked individuals. We ran 1,000 simulations for each of five broad sample size categories in a Burnham joint model, and then compared the proportion of simulations in which 95% confidence intervals overlapped between and among years for a 4-year study. Additionally, we conducted sensitivity analyses of sample size to various capture probabilities and recovery probabilities. More than 50,000 individuals per year would need to be captured and released to accurately determine 10% and 15% declines in annual survival. To detect more dramatic declines of 33% or 50% survival over four years, then sample sizes of 25,000 or 10,000 per year, respectively, would be sufficient. Sensitivity analyses reveal that increasing recovery of dead marked individuals may be more valuable than increasing capture probability of marked individuals. Because of the extraordinary effort that would be required, we advise caution should such a mark-recapture effort be initiated because of the difficulty in attaining reliable estimates. We make recommendations for what techniques show the most promise for mark-recapture studies of bats because some techniques violate the assumptions of mark-recapture methodology when used to mark bats.

  8. The 4-vessel Sampling Approach to Integrative Studies of Human Placental Physiology In Vivo.

    Science.gov (United States)

    Holme, Ane M; Holm, Maia B; Roland, Marie C P; Horne, Hildegunn; Michelsen, Trond M; Haugen, Guttorm; Henriksen, Tore

    2017-08-02

    The human placenta is highly inaccessible for research while still in utero. The current understanding of human placental physiology in vivo is therefore largely based on animal studies, despite the high diversity among species in placental anatomy, hemodynamics and duration of the pregnancy. The vast majority of human placenta studies are ex vivo perfusion studies or in vitro trophoblast studies. Although in vitro studies and animal models are essential, extrapolation of the results from such studies to the human placenta in vivo is uncertain. We aimed to study human placenta physiology in vivo at term, and present a detailed protocol of the method. Exploiting the intraabdominal access to the uterine vein just before the uterine incision during planned cesarean section, we collect blood samples from the incoming and outgoing vessels on the maternal and fetal sides of the placenta. When combining concentration measurements from blood samples with volume blood flow measurements, we are able to quantify placental and fetal uptake and release of any compound. Furthermore, placental tissue samples from the same mother-fetus pairs can provide measurements of transporter density and activity and other aspects of placental functions in vivo. Through this integrative use of the 4-vessel sampling method we are able to test some of the current concepts of placental nutrient transfer and metabolism in vivo, both in normal and pathological pregnancies. Furthermore, this method enables the identification of substances secreted by the placenta to the maternal circulation, which could be an important contribution to the search for biomarkers of placenta dysfunction.

  9. APPLICATION OF ULTRAVIOLET RADIATION TO CONTROL MICROBIOLOGICALLY INFLUENCED CORROSION: A CASE STUDY ON SOIL SAMPLE FROM MANGROVE

    Directory of Open Access Journals (Sweden)

    MUHAMMAD KHAIROOL FAHMY BIN MOHD ALI

    2016-12-01

    Full Text Available Microbiologically influenced corrosion (MIC is significant to the presence of microorganisms such as sulfate reducing bacteria (SRB in the deterioration of metallic and non-metallic materials. Bacterial chemical biocides are commonly used to disinfect microorganism effectively. Yet, the practice has some negative impact on the environment since the chemical content may cause pollution. A laboratory experimental investigation was conducted to explore the performance of Ultraviolet (UV radiation in exterminating SRB as an option to replace biocides usage. The morphologies of the isolated Sg. Ular SRB used in this study were related to Desulfovibrio species. An experimental work was conducted in determining the optimum pH and temperature for the SRB to grow before disinfection purposes. The experimental result showed optimum growth for respective SRB were at pH of 8.5 with temperature recorded at 37˚C. UV radiation with wavelength of 254 nm was utilised to disinfect the microorganism. SRB samples were exposed to UV radiation for one hour and left incubated for 21 days. It was found that the percentage of metal loss in a sample exposed to UV radiation was lower compared with untreated sample. Results from the study revealed that UV has a potential as a viable option for SRB disinfection purposes and may be further developed to reduce the consumption of chemical biocides in pipeline maintenance scheme.

  10. CREDIT SCORING MODELING WITH STATE-DEPENDENT SAMPLE SELECTION: A COMPARISON STUDY WITH THE USUAL LOGISTIC MODELING

    Directory of Open Access Journals (Sweden)

    Paulo H. Ferreira

    2015-04-01

    Full Text Available Statistical methods have been widely employed to assess the capabilities of credit scoring classification models in order to reduce the risk of wrong decisions when granting credit facilities to clients. The predictive quality of a classification model can be evaluated based on measures such as sensitivity, specificity, predictive values, accuracy, correlation coefficients and information theoretical measures, such as relative entropy and mutual information. In this paper we analyze the performance of a naive logistic regression model, a logistic regression with state-dependent sample selection model and a bounded logistic regression model via a large simulation study. Also, as a case study, the methodology is illustrated on a data set extracted from a Brazilian retail bank portfolio. Our simulation results so far revealed that there is nostatistically significant difference in terms of predictive capacity among the naive logistic regression models, the logistic regression with state-dependent sample selection models and the bounded logistic regression models. However, there is difference between the distributions of the estimated default probabilities from these three statistical modeling techniques, with the naive logistic regression models and the boundedlogistic regression models always underestimating such probabilities, particularly in the presence of balanced samples. Which are common in practice.

  11. [Modeling and simulation activities to design sampling scheme for population pharmacokinetic study on amlodipine].

    Science.gov (United States)

    Zuo, Xiao-Cong; Yuan, Hong; Zhang, Bi-Kui; Ng, Chee M; Barrett, Jeff S; Yang, Guo-Ping; Huang, Zhi-Jun; Pei, Qi; Guo, Ren; Zhou, Ya-Nan; Jing, Ning-Ning; Di, Wu

    2012-07-01

    Reasonable sampling scheme is the important basis for establishing reliable population pharmacokinetic model. It is an effective method for estimation of population pharmacokinetic parameters with sparse data to perform population pharmacokinetic analysis using the nonlinear mixed-effects models. We designed the sampling scheme for amlodipine based on D-optimal sampling strategy and Bayesian estimation method. First, optimized sample scenarios were designed using WinPOPT software according to the aim, dosage regimen and visit schedule of the clinical study protocol, and the amlodipine population model reported by Rohatagi et al. Second, we created a NONMEM-formatted dataset (n = 400) for each sample scenario via Monte Carlo simulation. Third, the estimation of amlodipine pharmacokinetic parameters (clearance (CL/F), volume (V/F) and Ka) was based on the simulation results. All modeling and simulation exercises were conducted with NONMEM version 7.2. Finally, the accuracy and precision of the estimated parameters were evaluated using the mean prediction error (MPE) and the mean absolute error (MAPE), respectively. Among the 6 schemes, schemes 6 and 3 have good accuracy and precision. MPE is 0.1% for scheme 6 and -0.6% for scheme 3, respectively. MAPE is 0.7% for both schemes. There is no significant difference in MPE and MAPE of volume among them. Therefore, we select scheme 3 as the final sample scenario because it has good accuracy and precision and less sample points. This research aims to provide scientific and effective sampling scheme for population pharmacokinetic (PK) study of amlodipine in patients with renal impairment and hypertension, provide a scientific method for an optimum design in clinical population PK/PD (pharmacodynamics) research.

  12. High-risk human papillomavirus (HPV screening and detection in healthy patient saliva samples: a pilot study

    Directory of Open Access Journals (Sweden)

    Wang Robert C

    2011-10-01

    Full Text Available Abstract Background The human papillomaviruses (HPV are a large family of non-enveloped DNA viruses, mainly associated with cervical cancers. Recent epidemiologic evidence has suggested that HPV may be an independent risk factor for oropharyngeal cancers. Evidence now suggests HPV may modulate the malignancy process in some tobacco- and alcohol-induced oropharynx tumors, but might also be the primary oncogenic factor for inducing carcinogenesis among some non-smokers. More evidence, however, is needed regarding oral HPV prevalence among healthy adults to estimate risk. The goal of this study was to perform an HPV screening of normal healthy adults to assess oral HPV prevalence. Methods Healthy adult patients at a US dental school were selected to participate in this pilot study. DNA was isolated from saliva samples and screened for high-risk HPV strains HPV16 and HPV18 and further processed using qPCR for quantification and to confirm analytical sensitivity and specificity. Results Chi-square analysis revealed the patient sample was representative of the general clinic population with respect to gender, race and age (p Conclusions The successful recruitment and screening of healthy adult patients revealed HPV16, but not HPV18, was present in a small subset. These results provide new information about oral HPV status, which may help to contextualize results from other studies that demonstrate oral cancer rates have risen in the US among both females and minorities and in some geographic areas that are not solely explained by rates of tobacco and alcohol use. The results of this study may be of significant value to further our understanding of oral health and disease risk, as well as to help design future studies exploring the role of other factors that influence oral HPV exposure, as well as the short- and long-term consequences of oral HPV infection.

  13. [Sampling procedure for a survey of an interventional study on acute respiratory infections].

    Science.gov (United States)

    Ramón Bravo, J; González Ochoa, E

    1993-01-01

    A description is made of the methodology used for obtaining a sample made up of 500 children under 5 years and 500 adults 65 year old and more, in order to carry out an intervention study on acute respiratory tract infections in an urban zone in Havana City and in a rural zone in Matanzas province, where different intervention stops will be taken with regards sanitary education about management of acute respiratory tract infections for the population and training for primary care medical personnel. We show the way the selected sample fits was planned with a very homogeneous distribution in the 8 areas under study, which allows for great reliability in the results.

  14. Study design and sampling intensity for demographic analyses of bear populations

    Science.gov (United States)

    Harris, R.B.; Schwartz, C.C.; Mace, R.D.; Haroldson, M.A.

    2011-01-01

    The rate of population change through time (??) is a fundamental element of a wildlife population's conservation status, yet estimating it with acceptable precision for bears is difficult. For studies that follow known (usually marked) bears, ?? can be estimated during some defined time by applying either life-table or matrix projection methods to estimates of individual vital rates. Usually however, confidence intervals surrounding the estimate are broader than one would like. Using an estimator suggested by Doak et al. (2005), we explored the precision to be expected in ?? from demographic analyses of typical grizzly (Ursus arctos) and American black (U. americanus) bear data sets. We also evaluated some trade-offs among vital rates in sampling strategies. Confidence intervals around ?? were more sensitive to adding to the duration of a short (e.g., 3 yrs) than a long (e.g., 10 yrs) study, and more sensitive to adding additional bears to studies with small (e.g., 10 adult females/yr) than large (e.g., 30 adult females/yr) sample sizes. Confidence intervals of ?? projected using process-only variance of vital rates were only slightly smaller than those projected using total variances of vital rates. Under sampling constraints typical of most bear studies, it may be more efficient to invest additional resources into monitoring recruitment and juvenile survival rates of females already a part of the study, than to simply increase the sample size of study females. ?? 2011 International Association for Bear Research and Management.

  15. Numerical study of the lateral resolution in electrostatic force microscopy for dielectric samples

    Science.gov (United States)

    Riedel, C.; Alegría, A.; Schwartz, G. A.; Colmenero, J.; Sáenz, J. J.

    2011-07-01

    We present a study of the lateral resolution in electrostatic force microscopy for dielectric samples in both force and gradient modes. Whereas previous studies have reported expressions for metallic surfaces having potential heterogeneities (Kelvin probe force microscopy), in this work we take into account the presence of a dielectric medium. We introduce a definition of the lateral resolution based on the force due to a test particle being either a point charge or a polarizable particle on the dielectric surface. The behaviour has been studied over a wide range of typical experimental parameters: tip-sample distance (1-20) nm, sample thickness (0-5) µm and dielectric constant (1-20), using the numerical simulation of the equivalent charge method. For potential heterogeneities on metallic surfaces expressions are in agreement with the bibliography. The lateral resolution of samples having a dielectric constant of more than 10 tends to metallic behaviour. We found a characteristic thickness of 100 nm, above which the lateral resolution measured on the dielectric surface is close to that of an infinite medium. As previously reported, the lateral resolution is better in the gradient mode than in the force mode. Finally, we showed that for the same experimental conditions, the lateral resolution is better for a polarizable particle than for a charge, i.e. dielectric heterogeneities should always look 'sharper' (better resolved) than inhomogeneous charge distributions. This fact should be taken into account when interpreting images of heterogeneous samples.

  16. Studies on the Presence of Mycotoxins in Biological Samples: An Overview

    Science.gov (United States)

    Escrivá, Laura; Font, Guillermina; Manyes, Lara

    2017-01-01

    Mycotoxins are fungal secondary metabolites with bioaccumulation levels leading to their carry-over into animal fluids, organs, and tissues. As a consequence, mycotoxin determination in biological samples from humans and animals has been reported worldwide. Since most mycotoxins show toxic effects at low concentrations and considering the extremely low levels present in biological samples, the application of reliable detection methods is required. This review summarizes the information regarding the studies involving mycotoxin determination in biological samples over the last 10 years. Relevant data on extraction methodology, detection techniques, sample size, limits of detection, and quantitation are presented herein. Briefly, liquid-liquid extraction followed by LC-MS/MS determination was the most common technique. The most analyzed mycotoxin was ochratoxin A, followed by zearalenone and deoxynivalenol—including their metabolites, enniatins, fumonisins, aflatoxins, T-2 and HT-2 toxins. Moreover, the studies were classified by their purpose, mainly focused on the development of analytical methodologies, mycotoxin biomonitoring, and exposure assessment. The study of tissue distribution, bioaccumulation, carry-over, persistence and transference of mycotoxins, as well as, toxicokinetics and ADME (absorption, distribution, metabolism and excretion) were other proposed goals for biological sample analysis. Finally, an overview of risk assessment was discussed. PMID:28820481

  17. A review of blood sample handling and pre-processing for metabolomics studies.

    Science.gov (United States)

    Hernandes, Vinicius Veri; Barbas, Coral; Dudzik, Danuta

    2017-09-01

    Metabolomics has been found to be applicable to a wide range of clinical studies, bringing a new era for improving clinical diagnostics, early disease detection, therapy prediction and treatment efficiency monitoring. A major challenge in metabolomics, particularly untargeted studies, is the extremely diverse and complex nature of biological specimens. Despite great advances in the field there still exist fundamental needs for considering pre-analytical variability that can introduce bias to the subsequent analytical process and decrease the reliability of the results and moreover confound final research outcomes. Many researchers are mainly focused on the instrumental aspects of the biomarker discovery process, and sample related variables sometimes seem to be overlooked. To bridge the gap, critical information and standardized protocols regarding experimental design and sample handling and pre-processing are highly desired. Characterization of a range variation among sample collection methods is necessary to prevent results misinterpretation and to ensure that observed differences are not due to an experimental bias caused by inconsistencies in sample processing. Herein, a systematic discussion of pre-analytical variables affecting metabolomics studies based on blood derived samples is performed. Furthermore, we provide a set of recommendations concerning experimental design, collection, pre-processing procedures and storage conditions as a practical review that can guide and serve for the standardization of protocols and reduction of undesirable variation. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. A non-uniform sampling approach enables studies of dilute and unstable proteins.

    Science.gov (United States)

    Miljenović, Tomas; Jia, Xinying; Lavrencic, Peter; Kobe, Bostjan; Mobli, Mehdi

    2017-06-01

    NMR spectroscopy is a powerful method in structural and functional analysis of macromolecules and has become particularly prevalent in studies of protein structure, function and dynamics. Unique to NMR spectroscopy is the relatively low constraints on sample preparation and the high level of control of sample conditions. Proteins can be studied in a wide range of buffer conditions, e.g. different pHs and variable temperatures, allowing studies of proteins under conditions that are closer to their native environment compared to other structural methods such as X-ray crystallography and electron microscopy. The key disadvantage of NMR is the relatively low sensitivity of the method, requiring either concentrated samples or very lengthy data-acquisition times. Thus, proteins that are unstable or can only be studied in dilute solutions are often considered practically unfeasible for NMR studies. Here, we describe a general method, where non-uniform sampling (NUS) allows for signal averaging to be monitored in an iterative manner, enabling efficient use of spectrometer time, ultimately leading to savings in costs associated with instrument and isotope-labelled protein use. The method requires preparation of multiple aliquots of the protein sample that are flash-frozen and thawed just before acquisition of a short NMR experiments carried out while the protein is stable (12 h in the presented case). Non-uniform sampling enables sufficient resolution to be acquired for each short experiment. Identical NMR datasets are acquired and sensitivity is monitored after each co-added spectrum is reconstructed. The procedure is repeated until sufficient signal-to-noise is obtained. We discuss how maximum entropy reconstruction is used to process the data, and propose a variation on the previously described method of automated parameter selection. We conclude that combining NUS with iterative co-addition is a general approach, and particularly powerful when applied to unstable

  19. Statistical inferences for data from studies conducted with an aggregated multivariate outcome-dependent sample design.

    Science.gov (United States)

    Lu, Tsui-Shan; Longnecker, Matthew P; Zhou, Haibo

    2017-03-15

    Outcome-dependent sampling (ODS) scheme is a cost-effective sampling scheme where one observes the exposure with a probability that depends on the outcome. The well-known such design is the case-control design for binary response, the case-cohort design for the failure time data, and the general ODS design for a continuous response. While substantial work has been carried out for the univariate response case, statistical inference and design for the ODS with multivariate cases remain under-developed. Motivated by the need in biological studies for taking the advantage of the available responses for subjects in a cluster, we propose a multivariate outcome-dependent sampling (multivariate-ODS) design that is based on a general selection of the continuous responses within a cluster. The proposed inference procedure for the multivariate-ODS design is semiparametric where all the underlying distributions of covariates are modeled nonparametrically using the empirical likelihood methods. We show that the proposed estimator is consistent and developed the asymptotically normality properties. Simulation studies show that the proposed estimator is more efficient than the estimator obtained using only the simple-random-sample portion of the multivariate-ODS or the estimator from a simple random sample with the same sample size. The multivariate-ODS design together with the proposed estimator provides an approach to further improve study efficiency for a given fixed study budget. We illustrate the proposed design and estimator with an analysis of association of polychlorinated biphenyl exposure to hearing loss in children born to the Collaborative Perinatal Study. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  20. Environmental study of two significant solid samples: gravitation dust sediment and soil.

    Science.gov (United States)

    Remeteiová, Dagmar; Rusnák, Radoslav; Kucanová, Eva; Fióová, Beáta; Ružičková, Silvia; Fekete, Ilona; Horváth, Márk; Dirner, Vojtech

    2012-01-01

    In this work are presented results of the complex study of two significant solid environmental samples: gravitation dust sediments (industrial pollutants, potential source of risk elements input to soils) and soils (component of the environment, potential source of risk elements input to food web). The first phase of this study was focused on the study of the significant chemical properties (phase composition, content of organic and inorganic carbon) of the dust and soil samples. In the second phase, the fractionation analysis was used on the evaluation of the mobility of chosen risk elements (Cu, Ni, Pb, Zn) in the studied samples. The single-step extractions were applied in the order of the isolation of the element forms (fractions), with different mobilities during defined ecological conditions by utilization of the following reagents: 1 mol dm(-3) NH(4)NO(3) for isolation of the "mobile" fraction, 0.05 mol dm(-3) ethylenediaminetetraacetic acid and 0.43 mol dm(-3) CH(3)COOH for isolation of the "mobilizable" fraction, and 2 mol dm(-3) HNO(3) for isolation of all releasable forms. On the basis of the results obtained in this study, it is possible to state that different origins and positions of solid environmental samples in the environment reflect in different chemical properties of their matrix. The different properties of the sample matrix result in different mobilities of risk elements in these kinds of samples. The fractionation analysis with single-step extraction for isolation element fractions is the method most suitable for easy checking of environmental pollution and for evaluation of risk elements cycle in the environment.

  1. Enhanced procedural blank control for organic geochemical studies of critical sample material.

    Science.gov (United States)

    Leider, A; Schumacher, T C; Hallmann, C

    2016-09-01

    Organic contamination of sedimentary rocks can produce artefacts in studies of hydrocarbon composition, and this can have significant negative consequences for interpretations of the geobiological record. False positives - that is cases of non-syngenetic hydrocarbon biomarkers - are common in Precambrian studies, and significant challenges persist despite the intensive effort devoted to these studies. Efforts to standardize the 'burden of proof' for distinguishing between contamination and syngenetic material have to date failed to yield a simple or universal protocol, yet the need remains great, as both bitumen-lean rocks and bitumen-rich samples can be vulnerable to the accumulation of false-positive signals. In an effort to determine the best approach to quality control, we tested the capability of different blank materials to collect ambient contamination by assessing their capacity to adsorb hydrocarbons during storage in plastic bags and found that commonly used Quartz sand does not provide an adequate measure of storage- or laboratory-induced contamination. Brick blanks, having the advantage that they can parallel rock samples even during the sawing process, are characterized by similar poor adsorption properties. Primarily steered by mineralogy, organic carbon content and surface area, model-black shales can adsorb up to 20 times more contaminants than sand blanks and up to 200 times more contaminants than organic-free model-carbonates. This observation provides an explanation for reports and observations of seemingly systematic stratigraphic variation of contaminants, but mostly should raise awareness for the evaluation of procedural blanks, in particular of sample-to-blank ratios, when studying bitumen-lean rock samples of varying lithologies. Additionally, differences between the hydrocarbon profiles in plastic bags and the hydrocarbon signatures transferred to blank materials emphasize difficulties in the unequivocal detection of contamination sources

  2. Black Locust (Robinia pseudoacacia L. Root Cuttings: Diversity and Identity Revealed by SSR Genotyping: A Case Study

    Directory of Open Access Journals (Sweden)

    Maria Emilia Malvolti

    2015-10-01

    Full Text Available Background and Purpose: Black locust (Robinia pseudoacacia L. is a valuable species native to North America and today widely planted throughout the world for biomass production. In Hungary, where Robinia has great importance in the forest management, the clones have been selected for plantations on good, medium and poor quality sites. To conserve the identity, superior clones are vegetatively propagated by root cuttings. At times the collection of root cuttings can cause uncertainty for clonal identity because of the overlap of roots from neighboring plants. This can occur especially when the repository is damaged from severe environmental accidents and the planting layout has been lost. The aim of this study has been to verify by molecular markers the diversity or identity of black locust clones by root cuttings harvested in a damaged trial. Materials and Methods: Root cuttings of 91 clones belonging to five cultivars were collected in a trial severely damaged by storms and flooding periods. The obtained plantlets were analyzed with nine microsatellite (SSR markers and the genetic identity/diversity within and among the plants was tested using the software GenAlEx version 6. Results: Multilocus genotypes (MLG and the Paetkau’s assignation test (1985 revealed genetic variability among the samples: the analyzed plantlets were grouped in four classes instead of the five expected. In addition, 6 unique genotypes have been detected. Conclusions: This study remarks problems that may arise during the harvest of Robinia’s root cuttings, especially when the planting layout has been confused. Molecular analyses can be successfully used to control the germplasm before its sale as guaranty for nurseries, farmers and stakeholders.

  3. Comparative study of the human ficolins reveals unique features of Ficolin-3 (Hakata antigen)

    DEFF Research Database (Denmark)

    Hummelshoj, Tina; Fog, Lea Munthe; Madsen, Hans O

    2007-01-01

    features of the ficolins and MBL. We investigated the tissue distribution of the FCN1-3 and the MBL2 genes encoding the ficolins and MBL by quantitative PCR. Recombinant proteins were produced and structural and biological characteristics were investigated and compared. Our main findings were that FCN3 m......RNA was highly expressed in the liver and lung compared with the other genes revealing the lung as the tissue with the highest FCN3 expression pattern. Ficolin-3 revealed higher complement activating capacity compared with Ficolin-2, MBL and Ficolin-1 and was highly resistant to bacterial collagenase treatment......, which is different from the other ficolins and MBL. We discovered several unique properties of Ficolin-3 showing that FCN3 is the most highly expressed gene in liver and lung among the lectin complement pathway initiators. Moreover, Ficolin-3 has a high complement activating potential and is the only...

  4. Validation study of a multi-method integrity test in a Peruvian sample

    OpenAIRE

    Blumen, Sheyla; Bayona, Hugo; Givoli, Simon; Pecker, Gabriela; Fine, Saul

    2016-01-01

    The present study summarizes the validity of a multi-method integrity test developed to measure integrity and counterproductive work behaviors (CWB) in personnel selection of a Peruvian sample. This instrument has been thoroughly studied in other cultural contexts, establishing its validity in predicting counter-productive behaviors. In order to study external validity, two criteria were used: (a) The Counterproductive Work Behavior Checklist (CWB-C) and (b) a supervisor evaluation questionna...

  5. Sedative Drug Use among King Saud University Medical Students: A Cross-Sectional Sampling Study

    OpenAIRE

    Al-Sayed, Ahmed A.; Al-Rashoudi, Abdualltef H.; Al-Eisa, Abdulrhman A.; Addar, Abdullah M.; Al-Hargan, Abdullah H.; Al-Jerian, Albaraa A.; Al-Omair, Abdullah A.; Ahmed I. Al-Sheddi; Hussam I. Al-Nowaiser; Al-Kathiri, Omar A.; Al-Hassan, Abdullah H.

    2014-01-01

    Introduction. Medical students experience significant psychological stress and are therefore at higher risk of using sedatives. There are currently no studies describing the prevalence of sedative drug use among medical students in Saudi Arabia. The aim of this study was to evaluate the prevalence and factors associated with sedative drug use among medical students in Saudi Arabia. Materials and Methods. A cross-sectional convenience sampling study gathered data by anonymous questionnaire fro...

  6. Epidemiological Studies Based on Small Sample Sizes – A Statistician's Point of View

    OpenAIRE

    Ersbøll Annette; Ersbøll Bjarne

    2003-01-01

    We consider 3 basic steps in a study, which have relevance for the statistical analysis. They are: study design, data quality, and statistical analysis. While statistical analysis is often considered an important issue in the literature and the choice of statistical method receives much attention, less emphasis seems to be put on study design and necessary sample sizes. Finally, a very important step, namely assessment and validation of the quality of the data collected seems to be completel...

  7. Study of a twisted ATLAS SCT Barrel deformation as revealed by a photogrammetric survey

    CERN Document Server

    Dobson, E; Heinemann, F; Karagoz-Unel, M

    2007-01-01

    A photogrammetry survey on the SCT barrels was performed as an engineering check on the structure of the ATLAS Semiconductor Tracker (SCT) shortly after construction. Analysis of the data obtained revealed small scale elliptical deformation as well as a twist of the structure. The results of the survey are presented as well as interpolation of the measured targets to the module positions and a comparison with track based alignment measurements.

  8. Treatability studies on different refinery wastewater samples using high-throughput microbial electrolysis cells (MECs).

    Science.gov (United States)

    Ren, Lijiao; Siegert, Michael; Ivanov, Ivan; Pisciotta, John M; Logan, Bruce E

    2013-05-01

    High-throughput microbial electrolysis cells (MECs) were used to perform treatability studies on many different refinery wastewater samples all having appreciably different characteristics, which resulted in large differences in current generation. A de-oiled refinery wastewater sample from one site (DOW1) produced the best results, with 2.1±0.2 A/m(2) (maximum current density), 79% chemical oxygen demand removal, and 82% headspace biological oxygen demand removal. These results were similar to those obtained using domestic wastewater. Two other de-oiled refinery wastewater samples also showed good performance, with a de-oiled oily sewer sample producing less current. A stabilization lagoon sample and a stripped sour wastewater sample failed to produce appreciable current. Electricity production, organics removal, and startup time were improved when the anode was first acclimated to domestic wastewater. These results show mini-MECs are an effective method for evaluating treatability of different wastewaters. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. Patients' perspectives on providing a stool sample to their GP: a qualitative study.

    Science.gov (United States)

    Lecky, Donna M; Hawking, Meredith K D; McNulty, Cliodna A M

    2014-11-01

    Stool specimen collection is challenging and informal feedback has indicated that participants find the process difficult. Increasing stool specimen returns would improve the investigation of outbreaks of diarrhoeal and food-borne disease. To explore the barriers to stool sample collection and specimen return to ascertain which factors may help to improve the process. Qualitative patient interview study in Gloucester, UK. A two-stage purposive sampling process was used to identify patients who had either previous experience or no experience of collecting a stool sample. The interview schedule, based on the theory of planned behaviour, was used to facilitate interviews with 26 patients. Interview transcripts were analysed using a modified framework analysis. Barriers to collection included embarrassment, fear of results, concerns around hygiene and contamination, discretion and privacy, and lack of information. Personal gain was identified as the main incentive to collecting and returning a stool sample. The need for an information leaflet on stool collection was emphasised by most patients. GPs could make a number of small changes that could make a big difference for patients and potentially increase stool sample return. If they, rather than receptionists, distributed collection kits it may be easier for patients to ask any questions they had regarding collection. In addition, the provision of a stool-collection information leaflet could increase patients' confidence regarding collecting the sample, and providing drop-off boxes for specimens could help prevent patients' embarrassment regarding handing their stool over to a receptionist. © British Journal of General Practice 2014.

  10. Functional Characterization Reveals Novel Putative Coding Sequences in Prevotella ruminicola Genome Extracted from Rumen Metagenomic Studies.

    Science.gov (United States)

    Nathani, Neelam M; Kothari, Ramesh K; Patel, Amrutlal K; Joshi, Chaitanya G

    2015-01-01

    To reassemble Prevotella ruminicola genome from rumen metagenomic data of cattle and buffalo and compare with the published reference genome. Rumen microbial communities from Mehsani buffaloes (n = 8) and Kankrej cattle (n = 8), each adapted to different proportions of a dry or green roughage diet, were subjected to metagenomic sequencing by Ion Torrent PGM, and subsequent reads were analyzed by MG-RAST. Using reference-guided assembly of the sequences against the published P. ruminicola strain 23, draft genomes of 2.56 and 2.46 Mb were reconstructed from Mehsani buffalo and Kankrej cows, respectively. The genomes were annotated using the RAST Server and carbohydrate active enzyme (CAZyme) analysis. Taxonomic analysis by MG-RAST revealed P. ruminicola to be the most abundant species present among the rumen microflora. Functional annotation of reconstructed genomes using the RAST Server depicted the maximum assignment of coding sequences involved in the subsystems amino acid and derivatives and carbohydrate metabolism. CAZyme profiling revealed the glycoside hydrolases (GH) family to be the most abundant. GH family subclassification revealed that the extracted genomes had more sequence hits for GH2, GH3, GH92 and GH97 as compared to the reference. The results reflect the metabolic significance of rumen-adapted P. ruminicola in utilizing a coarse diet for animals based on acquisition of novel genetic elements. © 2015 S. Karger AG, Basel.

  11. Comprehensive study of unexpected microscope condensers formed in sample arrangements commonly used in optical microscopy.

    Science.gov (United States)

    Desai, Darshan B; Aldawsari, Mabkhoot Mudith S; Alharbi, Bandar Mohammed H; Sen, Sanchari; Grave de Peralta, Luis

    2015-09-01

    We show that various setups for optical microscopy which are commonly used in biomedical laboratories behave like efficient microscope condensers that are responsible for observed subwavelength resolution. We present a series of experiments and simulations that reveal how inclined illumination from such unexpected condensers occurs when the sample is perpendicularly illuminated by a microscope's built-in white-light source. In addition, we demonstrate an inexpensive add-on optical module that serves as an efficient and lightweight microscope condenser. Using such add-on optical module in combination with a low-numerical-aperture objective lens and Fourier plane imaging microscopy technique, we demonstrate detection of photonic crystals with a period nearly eight times smaller than the Rayleigh resolution limit.

  12. Study on a pattern classification method of soil quality based on simplified learning sample dataset

    Science.gov (United States)

    Zhang, Jiahua; Liu, S.; Hu, Y.; Tian, Y.

    2011-01-01

    Based on the massive soil information in current soil quality grade evaluation, this paper constructed an intelligent classification approach of soil quality grade depending on classical sampling techniques and disordered multiclassification Logistic regression model. As a case study to determine the learning sample capacity under certain confidence level and estimation accuracy, and use c-means algorithm to automatically extract the simplified learning sample dataset from the cultivated soil quality grade evaluation database for the study area, Long chuan county in Guangdong province, a disordered Logistic classifier model was then built and the calculation analysis steps of soil quality grade intelligent classification were given. The result indicated that the soil quality grade can be effectively learned and predicted by the extracted simplified dataset through this method, which changed the traditional method for soil quality grade evaluation. ?? 2011 IEEE.

  13. A case study of sample entropy analysis to the fault detection of bearing in wind turbine

    Directory of Open Access Journals (Sweden)

    Qing Ni

    2017-10-01

    Full Text Available Rolling bearing is an important and fragile component in the wind turbine transmission system. The failure of rolling bearing is one of the highest risk events which may result in unexpected economic loss. To give a proper condition assessment of rolling bearing, especially for early fault detection, is of great importance and become an urgent issue to the wind energy industry. In this paper, sample entropy is studied through the field data of wind turbine transmission system measured from Lu Nan Wind Farm in China. Compared with several frequently used statistical indicators, sample entropy features advantages in detecting and evaluating the progress of the early faults of the rolling bearing. The studies show that the sample entropy is an effective and practical tool for condition monitoring of rolling bearing for a wind turbine transmission system.

  14. Mars, Phobos, and Deimos Sample Return Enabled by ARRM Alternative Trade Study Spacecraft

    Science.gov (United States)

    Englander, Jacob A.; Vavrina, Matthew; Merrill, Raymond G.; Qu, Min; Naasz, Bo J.

    2014-01-01

    The Asteroid Robotic Redirect Mission (ARRM) has been the topic of many mission design studies since 2011. The reference ARRM spacecraft uses a powerful solar electric propulsion (SEP) system and a bag device to capture a small asteroid from an Earth-like orbit and redirect it to a distant retrograde orbit (DRO) around the moon. The ARRM Option B spacecraft uses the same propulsion system and multi-Degree of Freedom (DoF) manipulators device to retrieve a very large sample (thousands of kilograms) from a 100+ meter diameter farther-away Near Earth Asteroid (NEA). This study will demonstrate that the ARRM Option B spacecraft design can also be used to return samples from Mars and its moons - either by acquiring a large rock from the surface of Phobos or Deimos, and or by rendezvousing with a sample-return spacecraft launched from the surface of Mars.

  15. Accuracy of micro four-point probe measurements on inhomogeneous samples: A probe spacing dependence study

    DEFF Research Database (Denmark)

    Wang, Fei; Petersen, Dirch Hjorth; Østerberg, Frederik Westergaard

    2009-01-01

    In this paper, we discuss a probe spacing dependence study in order to estimate the accuracy of micro four-point probe measurements on inhomogeneous samples. Based on sensitivity calculations, both sheet resistance and Hall effect measurements are studied for samples (e.g. laser annealed samples......) with periodic variations of sheet resistance, sheet carrier density, and carrier mobility. With a variation wavelength of ¿, probe spacings from 0.0012 to 1002 have been applied to characterize the local variations. The calculations show that the measurement error is highly dependent on the probe spacing. When...... the probe spacing is smaller than 1/40 of the variation wavelength, micro four-point probes can provide an accurate record of local properties with less than 1% measurement error. All the calculations agree well with previous experimental results....

  16. Influence of the sampling period and time resolution on the PM source apportionment: Study based on the high time-resolution data and long-term daily data

    Science.gov (United States)

    Tian, Yingze; Xiao, Zhimei; Wang, Haiting; Peng, Xing; Guan, Liao; Huangfu, Yanqi; Shi, Guoliang; Chen, Kui; Bi, Xiaohui; Feng, Yinchang

    2017-09-01

    When planning short-term and long-term measurement campaigns of particulate matter (PM), parameters such as sampling period, time resolution, sampling number, etc. are vital. To study their influence and to provide suggestion for the sampling plan of PM source apportionment (SA), ambient and synthetic speciated datasets (including a high time-resolution dataset and a long-term daily dataset) were studied. First, aiming at studying the sampling period required to generate representative and reliable results for SA, high time-resolution ambient samples were collected by online instruments in a megacity in China. Datasets with different sampling periods (four months, two months, one month, two weeks and one week) were modeled by the Positive Matrix Factorization (PMF). Compared with four month results, AAEs (percent absolute errors between true and estimated contributions) ranged from 11.2 to 27.2% (two months), 19.8-44.5% (one month), 21.0-45.9% (two weeks) and 23.9-44.6% (one week), indicating that divergence increased with decreasing sampling periods. To systematically evaluate this problem and investigate if the increasing time resolutions in a short period could enhance the modeling performance, synthetic datasets were constructed. Results revealed that a sufficient sampling period is required to ensure stable results; without sufficient sampling period, the contributions cannot be reliably estimated, even if the number of samples is large. Then, to explore the influence of variability absences, long-term daily datasets with various variability absences were apportioned and compared. The summed AAEs were 102.2% (no winter), 73.6% (no weekend), 138.7% (no weekday) and 165.6% (no autumn, winter or weekends). This general increase of AAEs can indicate that uncertainty enhanced with the increase in variability absences. When planning short-term measurement campaigns, except for number of samples, sampling period that involves sufficient source cycles has significant

  17. Personality and Eating Disorders: A Longitudinal Study on a Non-Clinical Sample of Adolescents

    OpenAIRE

    De Caro, Elide Francesca; Di Blas, Lisa

    2014-01-01

    The present longitudinal study is aimed at analyzing how adolescents change their dysfunctional attitudes towards their body and eating behaviors in relation to personality characteristics across a six-month time span. Via multiple regression analyses we investigated whether MMPI-A Obsessiveness, Low Self-Esteem, Depression, Family Problems and Concern for health are temporal antecedents of EDI-2 eating disorders, and vice versa. Our main findings revealed a bidirectio...

  18. Outpatient Tinnitus Clinic, Self-Help Web Platform, or Mobile Application to Recruit Tinnitus Study Samples?

    Directory of Open Access Journals (Sweden)

    Thomas Probst

    2017-04-01

    Full Text Available For understanding the heterogeneity of tinnitus, large samples are required. However, investigations on how samples recruited by different methods differ from each other are lacking. In the present study, three large samples each recruited by different means were compared: N = 5017 individuals registered at a self-help web platform for tinnitus (crowdsourcing platform Tinnitus Talk, N = 867 users of a smart mobile application for tinnitus (crowdsensing platform TrackYourTinnitus, and N = 3786 patients contacting an outpatient tinnitus clinic (Tinnitus Center of the University Hospital Regensburg. The three samples were compared regarding age, gender, and duration of tinnitus (month or years perceiving tinnitus; subjective report using chi-squared tests. The three samples significantly differed from each other in age, gender and tinnitus duration (p < 0.05. Users of the TrackYourTinnitus crowdsensing platform were younger, users of the Tinnitus Talk crowdsourcing platform had more often female gender, and users of both newer technologies (crowdsourcing and crowdsensing had more frequently acute/subacute tinnitus (<3 months and 4–6 months as well as a very long tinnitus duration (>20 years. The implications of these findings for clinical research are that newer technologies such as crowdsourcing and crowdsensing platforms offer the possibility to reach individuals hard to get in contact with at an outpatient tinnitus clinic. Depending on the aims and the inclusion/exclusion criteria of a given study, different recruiting strategies (clinic and/or newer technologies offer different advantages and disadvantages. In general, the representativeness of study results might be increased when tinnitus study samples are recruited in the clinic as well as via crowdsourcing and crowdsensing.

  19. Analysis of family- and population-based samples in cohort genome-wide association studies.

    Science.gov (United States)

    Manichaikul, Ani; Chen, Wei-Min; Williams, Kayleen; Wong, Quenna; Sale, Michèle M; Pankow, James S; Tsai, Michael Y; Rotter, Jerome I; Rich, Stephen S; Mychaleckyj, Josyf C

    2012-02-01

    Cohort studies typically sample unrelated individuals from a population, although family members of index cases may also be recruited to investigate shared familial risk factors. Recruitment of family members may be incomplete or ancillary to the main cohort, resulting in a mixed sample of independent family units, including unrelated singletons and multiplex families. Multiple methods are available to perform genome-wide association (GWA) analysis of binary or continuous traits in families, but it is unclear whether methods known to perform well on ascertained pedigrees, sibships, or trios are appropriate in analysis of a mixed unrelated cohort and family sample. We present simulation studies based on Multi-Ethnic Study of Atherosclerosis (MESA) pedigree structures to compare the performance of several popular methods of GWA analysis for both quantitative and dichotomous traits in cohort studies. We evaluate approaches suitable for analysis of families, and combined the best performing methods with population-based samples either by meta-analysis, or by pooled analysis of family- and population-based samples (mega-analysis), comparing type 1 error and power. We further assess practical considerations, such as availability of software and ability to incorporate covariates in statistical modeling, and demonstrate our recommended approaches through quantitative and binary trait analysis of HDL cholesterol (HDL-C) in 2,553 MESA family- and population-based African-American samples. Our results suggest linear modeling approaches that accommodate family-induced phenotypic correlation (e.g., variance-component model for quantitative traits or generalized estimating equations for dichotomous traits) perform best in the context of combined family- and population-based cohort GWAS.

  20. The role of sample preparation in interpretation of trace element concentration variability in moss bioindication studies

    Science.gov (United States)

    Migaszewski, Z.M.; Lamothe, P.J.; Crock, J.G.; Galuszka, A.; Dolegowska, S.

    2011-01-01

    Trace element concentrations in plant bioindicators are often determined to assess the quality of the environment. Instrumental methods used for trace element determination require digestion of samples. There are different methods of sample preparation for trace element analysis, and the selection of the best method should be fitted for the purpose of a study. Our hypothesis is that the method of sample preparation is important for interpretation of the results. Here we compare the results of 36 element determinations performed by ICP-MS on ashed and on acid-digested (HNO3, H2O2) samples of two moss species (Hylocomium splendens and Pleurozium schreberi) collected in Alaska and in south-central Poland. We found that dry ashing of the moss samples prior to analysis resulted in considerably lower detection limits of all the elements examined. We also show that this sample preparation technique facilitated the determination of interregional and interspecies differences in the chemistry of trace elements. Compared to the Polish mosses, the Alaskan mosses displayed more positive correlations of the major rock-forming elements with ash content, reflecting those elements' geogenic origin. Of the two moss species, P. schreberi from both Alaska and Poland was also highlighted by a larger number of positive element pair correlations. The cluster analysis suggests that the more uniform element distribution pattern of the Polish mosses primarily reflects regional air pollution sources. Our study has shown that the method of sample preparation is an important factor in statistical interpretation of the results of trace element determinations. ?? 2010 Springer-Verlag.

  1. Anxiety and depression in Brazilian orthopaedics inpatients: a cross sectional study with a clinical sample comparison.

    Science.gov (United States)

    de Moraes, Vinícius Ynoe; Jorge, Miguel Roberto; Faloppa, Flávio; Belloti, João Carlos

    2010-03-01

    There are few studies on the development of anxiety and depression in orthopaedics and trauma (O&T) inpatients. We designed a cross-sectional study aimed at comparing the prevalence of depression and anxiety in 100 O&T inpatients and 100 clinical inpatients in the same hospital. O&T patients were divided into subgroups: trauma and non-trauma (arthroplasty, tumour, and infection sub grouping). We measured anxiety and depression by the Hospital Anxiety and Depression Scale and co-morbidities by the Charlson age-adjusted comorbidity index (CCI). For the trauma subgroup, AO/OTA fracture classification and Gustillo and Anderson grade of open fractures classification was applied. The prevalence of anxiety and depression was 35% and 28%, respectively for the clinical sample, and 44% and 33% for the O&T sample. Compared with the clinical sample, anxiety scores were higher in the O&T sample (p = .047), and in arthroplasty (p = .020) and trauma subgroups (p = .031). In the O&T sample, high CCI scores were associated with high anxiety scores (p = .033).

  2. DNA sampling from eggshells and microsatellite genotyping in rare tropical birds: Case study on Brazilian Merganser

    Directory of Open Access Journals (Sweden)

    Thais Augusta Maia

    2017-10-01

    Full Text Available Abstract This study shows that sampling maternal DNA from hatched and abandoned eggshells is a viable noninvasive strategy for studying the genetics of rare or endangered tropical birds, as exemplified here by the Brazilian Merganser (Mergus octosetaceus. Eighteen microsatellites were isolated from enriched libraries and nine heterologous loci from related species were tested. Seven loci were amplified successfully, with five of them being polymorphic. These loci exhibited amplicons ranging from 110 to 254 bp for 132 samples, with 60 from eggshells and 72 from blood or muscle samples. The number of alleles for M. octosetaceus ranged from one to six (mean = 3.71, which is low compared to M. merganser (1-15 alleles, a ‘least concern’ species. Genetic diversity did not differ significantly between noninvasive and invasive samples (Z(u = 0.31, p = 0.37. Thus, noninvasive sampling, as demonstrated here with eggshells, provides an efficient means to assess genetic diversity in tropical birds without the need to capture and handle them.

  3. Structural and magnetic properties evolution study method using a single ribbon-shaped sample

    Science.gov (United States)

    Moya, Javier A.

    2017-06-01

    A new type of study is presented for magnetic and structural characterization of amorphous or nanocrystalline metallic alloys in ribbon or wire-shaped samples. A single sample is subjecting to successive steps of flash isocurrent heat treatments with increasing duration in time, followed by a rapid cooling, while magneto-electric properties evolution are scanned in situ at room temperature. When one set of isocurrent heat treatments is finished, the annealing current is increased and a new set of isocurrent treatments starts. The properties studied were the saturation magnetization and the coercive field at 50 Hz, magnetic permeability at 100 kHz and electrical resistance from where we also obtained the crystalline fraction. The method was applied on two samples of Finemet-like alloys and the results were analyzed from the perspective of current literature. With the present method it is possible to obtain a general and meticulous understanding of the structural and magnetic evolution of the samples tested, with a considerable saving of time and samples.

  4. Woodbridge research facility remedial investigation/feasibility study. Sampling and analysis plan vol 1: Field sampling plan vol II: Quality assurance project plan. Addendum 1

    Energy Technology Data Exchange (ETDEWEB)

    Wisbeck, D.; Thompson, P.; Williams, T.; Ehlers, M.; Eliass, M.

    1996-09-01

    U.S. Army Woodbridge Research Facility (WRF) was used in the past as a major military communications center and a research and development laboratory where electromagnetic pulse energy was tested on military and other equipment. WRF is presently an inactive facility pursuant to the 1991 Base Realignment and Closure list. Past investigation activities indicate that polychlorinated biphenyl compounds (PCBs) are the primary chemicals of concern. This task calls for provision of the necessary staff and equipment to provide remedial investigation/feasibility study support for the USAEC BRAC Program investigation at WRF. This Sampling and Analysis Plan, Addendum 1, Field Sampling Plan presents the sample location and rationale for additional samples required to complete the RI/FS; and the Quality Assurance Project Plan presents any additional data quality objectives and proposed laboratory methods for chemical analysis of samples.

  5. Power and sample size calculations for Mendelian randomization studies using one genetic instrument.

    Science.gov (United States)

    Freeman, Guy; Cowling, Benjamin J; Schooling, C Mary

    2013-08-01

    Mendelian randomization, which is instrumental variable analysis using genetic variants as instruments, is an increasingly popular method of making causal inferences from observational studies. In order to design efficient Mendelian randomization studies, it is essential to calculate the sample sizes required. We present formulas for calculating the power of a Mendelian randomization study using one genetic instrument to detect an effect of a given size, and the minimum sample size required to detect effects for given levels of significance and power, using asymptotic statistical theory. We apply the formulas to some example data and compare the results with those from simulation methods. Power and sample size calculations using these formulas should be more straightforward to carry out than simulation approaches. These formulas make explicit that the sample size needed for Mendelian randomization study is inversely proportional to the square of the correlation between the genetic instrument and the exposure and proportional to the residual variance of the outcome after removing the effect of the exposure, as well as inversely proportional to the square of the effect size.

  6. Size Distributions and Characterization of Native and Ground Samples for Toxicology Studies

    Science.gov (United States)

    McKay, David S.; Cooper, Bonnie L.; Taylor, Larry A.

    2010-01-01

    This slide presentation shows charts and graphs that review the particle size distribution and characterization of natural and ground samples for toxicology studies. There are graphs which show the volume distribution versus the number distribution for natural occurring dust, jet mill ground dust, and ball mill ground dust.

  7. Required sample size for monitoring stand dynamics in strict forest reserves: a case study

    Science.gov (United States)

    Diego Van Den Meersschaut; Bart De Cuyper; Kris Vandekerkhove; Noel Lust

    2000-01-01

    Stand dynamics in European strict forest reserves are commonly monitored using inventory densities of 5 to 15 percent of the total surface. The assumption that these densities guarantee a representative image of certain parameters is critically analyzed in a case study for the parameters basal area and stem number. The required sample sizes for different accuracy and...

  8. Results for five sets of forensic genetic markers studied in a Greek population sample

    DEFF Research Database (Denmark)

    Tomas Mas, Carmen; Skitsa, I; Steinmeier, E

    2015-01-01

    A population sample of 223 Greek individuals was typed for five sets of forensic genetic markers with the kits NGM SElect™, SNPforID 49plex, DIPplex(®), Argus X-12 and PowerPlex(®) Y23. No significant deviation from Hardy-Weinberg expectations was observed for any of the studied markers after Holm...

  9. Anxiety in High-Functioning Autism: A Pilot Study of Experience Sampling Using a Mobile Platform

    Science.gov (United States)

    Hare, Dougal Julian; Gracey, Carolyn; Wood, Christopher

    2016-01-01

    Anxiety and stress are everyday issues for many people with high-functioning autism, and while cognitive-behavioural therapy is the treatment of choice for the management of anxiety, there are challenges in using it with people with high-functioning autism. This study used modified experience sampling techniques to examine everyday anxiety and…

  10. Risk Factors for Severe Inter-Sibling Violence: A Preliminary Study of a Youth Forensic Sample

    Science.gov (United States)

    Khan, Roxanne; Cooke, David J.

    2008-01-01

    The perpetration of severe inter-sibling violence (SISV) remains a largely unexplored area of family violence. This article describes an investigation of risk factors for intentional SISV perpetration. A sample of 111 young people under the care of the Scottish criminal justice or welfare systems was studied. A SISV perpetration interview schedule…

  11. Disadvantaged Youth Report Less Negative Emotion to Minor Stressors When with Peers: An Experience Sampling Study

    Science.gov (United States)

    Uink, Bep Norma; Modecki, Kathryn Lynn; Barber, Bonnie L.

    2017-01-01

    Previous Experience Sampling Method (ESM) studies demonstrate that adolescents' daily emotional states are heavily influenced by their immediate social context. However, despite adolescence being a risk period for exposure to daily stressors, research has yet to examine the influence of peers on adolescents' emotional responses to stressors…

  12. Detecting evidence for CO2 fertilization from tree ring studies: The potential role of sampling biases

    NARCIS (Netherlands)

    Brienen, R.J.W.; Gloor, E.; Zuidema, P.A.

    2012-01-01

    Tree ring analysis allows reconstructing historical growth rates over long periods. Several studies have reported an increasing trend in ring widths, often attributed to growth stimulation by increasing atmospheric CO2 concentration. However, these trends may also have been caused by sampling

  13. Evaluation of HDPE water sample bottles and PVC sampler tubing used in herbicide dissipation studies.

    Science.gov (United States)

    J. B. Fischer; J. L. Michael; H. L. Gibbs

    2009-01-01

    The recovery of six herbicides (triclopyr, triclopyr ester, sulfometuron methyl, metsulfuron methyl, imazapyr, and hexazinone) was evaluated in two stream water samples, one from Weogufka Creek in the Alabama Piedmont and one from a stagnant stream in the Escambia Experimental Forest near Florida. Simulated field study conditions were...

  14. Sample Size Determination in a Chi-Squared Test Given Information from an Earlier Study.

    Science.gov (United States)

    Gillett, Raphael

    1996-01-01

    A rigorous method is outlined for using information from a previous study and explicitly taking into account the variability of an effect size estimate when determining sample size for a chi-squared test. This approach assures that the average power of all experiments in a discipline attains the desired level. (SLD)

  15. Laboratory performance study for passive sampling of nonpolar chemicals in water

    NARCIS (Netherlands)

    Booij, K.; Smedes, F.; Crum, S.

    2017-01-01

    Two laboratory performance studies with 21 and 11 participants were carried out for passive sampling of nonpolar chemicals in water, using silicone samplers that were deployed for 7 wk and 13 wk at 2 river sites in the Netherlands. Target analytes were polychlorinated biphenyls, polycyclic aromatic

  16. Lymph node sampling in localized neuroblastoma: a Pediatric Oncology Group study.

    Science.gov (United States)

    Contador, M P; Johnston, S; Smith, E I; Shuster, J J; Hayes, F A; Castleberry, R P

    1999-06-01

    Lymph node (LN) sampling was required by the Pediatric Oncology Group (POG) staging for neuroblastoma and currently is required as a part of the International Neuroblastoma Staging System (INSS). This retrospective study of planned lymph node sampling in patients with localized neuroblastoma was carried out with the intent of assisting surgeons in carrying out this procedure. The report documents the POG experience where LN, both uninvolved and involved with tumor, were found based on site of primary. From 391 patients with localized neuroblastoma of the abdomen, chest, and neck, 238 patients had LN sampling at the primary operation, and these patients constitute the major part of the study. In addition, 89 patients had a carefully documented search for LN, and 64 had neither search nor biopsy. The operative note, pathology report, and surgical study sheet were used in the 238 patients based on the site of the primary tumor to determine which nodal groups or basins underwent biopsy, and in which groups tumor was found. The pattern of drainage, based on the primary site of abdominal tumors, favored an arterial rather than venous pathway. Primary tumors and metastatic LN were more numerous on the left side. The abdominal drainage followed three pathways: (1) infrarenal tumors from the left and midline were associated with paraaortic LN; (2) right infrarenal tumors were associated with LN in the paracaval basin; (3) with suprarenal primaries and with both adrenals, the superior mesenteric-portal-celiac basins were most productive for nodal sampling. Tumor was found most frequently in the left adrenal-renal basin and in the paraaortic basin. The actual number of LN sampled in a single case varied from 1 to 19 LN, with a mean number of LN based on stage and primary from one to seven LN. The tumor spread in LN was consistent with a "watershed" course, but this was not statistically significant. Patients for whom LN were sought had a better outcome, contrasting with the

  17. A non-destructive sampling protocol for field studies of seed dispersal by fishes.

    Science.gov (United States)

    Correa, S B; Anderson, J T

    2016-05-01

    This paper presents a standardized protocol for the non-lethal capture of fishes, sampling of stomach contents and quantification of seed dispersal efficiency by frugivorous fishes. Neotropical pacu Piaractus mesopotamicus individuals were collected with fruit-baited hooks. The diets of 110 fish were sampled using a lavage method, which retrieved >90% of stomach contents of both juveniles and adults and allowed individuals to recover within 5 min of treatment. The proportional volume of six food categories was similar for stomachs and whole digestive tracts retrieved by dissection. Fruit pulp was proportionally lower in the stomach. The abundance and species richness of intact seeds increased with fish size independent of whether only stomachs or whole digestive tracts were analysed. The analysis of stomach contents accounted for 62·5% of the total species richness of seeds dispersed by P. mesopotamicus and 96% of common seeds (seed species retrieved from more than one fish). Germination trials revealed that seed viability was similar for seeds collected from the stomach via lavage and seeds that passed through the entire digestive tract. Therefore, stomach contents provide an unbiased representation of the dietary patterns and seed dispersal of frugivorous fishes. © 2016 The Fisheries Society of the British Isles.

  18. Sorption-desorption studies on tuff. II. Continuation of studies with samples from Jackass Flats, Nevada and initial studies with samples from Yucca Mountain, Nevada

    Energy Technology Data Exchange (ETDEWEB)

    Vine, E.N.; Aguilar, R.D.; Bayhurst, B.P.

    1980-01-01

    Distruibution coefficients were determined by a static (batch) technique for sorption-desorption of radionuclides between tuffs from drill holes UE25a No. 1 and J-13 at the Nevada Test Site and water from well J-13. Measurements were performed under atmospheric and controlled atmosphere conditions. Under atmospheric conditions tuffs high in zeolite minerals had sorption ratios of {similar_to}10{sup 3} to 10{sup 4} ml/g with Sr, Cs, Ba, Ce, Eu, Am, and Pu. For tuffs similar mineralogically to a microgranite the sorption ratios were {similar_to}10{sup 2} to 10{sup 3} ml/g. Values for U and Tc were obtained under controlled atmosphere (< 0.2 ppM 0{sub 2}) conditions. Studies were also begun to measure distribution ratios by a dynamic (column) technique. The ratios obtained for the elements studied, Sr, Cs, and Ba, were similar to, although lower than, those obtained by batch methods.

  19. A Study of Micro Craters in Material Samples after Long Duration Exposure on ISS Komplast Panels

    Science.gov (United States)

    Shaevich, S. K.; Aleksandrov, N. G.; Shumov, A. E.; Novikov, L. S.; Chernik, V. N.; Samokhina, M. S.; Golden, J. L.; Graves, R. F.; Kravchenko, M.; Christiansen, E. L.; hide

    2012-01-01

    The Komplast materials experiment was designed by the Khrunichev State Research and Production Space Center, together with other Russian scientific institutes, and has been carried out by Mission Control Moscow since 1998. Komplast panels fitted with material samples and sensors were located on the International Space Station (ISS) Functional Cargo Block (FGB) module exterior surface. Within the framework of this experiment, the purpose was to study the effect of the low earth orbit (LEO) environment on exposed samples of various materials. The panels were sent into orbit with the FGB when it launched on November 20, 1998. .

  20. Studies on the true coincidence correction in measuring filter samples by gamma spectrometry

    CERN Document Server

    Lian Qi; Chang Yong Fu; Xia Bing

    2002-01-01

    The true coincidence correction in measuring filter samples has been studied by high efficiency HPGe gamma detectors. The true coincidence correction for a specific three excited levels de-excitation case has been analyzed, and the typical analytical expressions of true coincidence correction factors have been given. According to the measured relative efficiency on the detector surface with 8 'single' energy gamma emitters and efficiency of filter samples, the peak and total efficiency surfaces are fitted. The true coincidence correction factors of sup 6 sup 0 Co and sup 1 sup 5 sup 2 Eu calculated by the efficiency surfaces agree well with experimental results

  1. Cigarette smoking initiation during college predicts future alcohol involvement: A matched-samples study

    OpenAIRE

    Myers, MG; Doran, NM; Edland, SD; Amanda Schweizer, C; Wall, TL

    2013-01-01

    Objective: Little is known about the relationship between cigarette smoking initiation and subsequent alcohol involvement. To address this question, the present study compared alcohol use between students who initiated smoking during college and a matched sample of never-smoking students. We hypothesized greater increases in alcohol involvement among smoking initiators, mediated by exposure to cigarette use situations. Method: Included in the present study were 104 Chinese American and Korean...

  2. The importance of taxon sampling in genomic studies: an example from the cyclooxygenases of teleost fishes.

    Science.gov (United States)

    Havird, Justin C; Miyamoto, Michael M

    2010-07-01

    Comparative genomic studies must often rely on single model species and exemplars to represent the genetic variation both within and among different major groups, because of technological, financial, and time constraints. This study of the cyclooxygenases from teleost fishes serves as a reminder that caution is required in these cases, since such incomplete taxon sampling can lead to errors in the interpretation and prediction of genome evolution, function, and structure. Copyright 2010 Elsevier Inc. All rights reserved.

  3. Gridsampler – A Simulation Tool to Determine the Required Sample Size for Repertory Grid Studies

    Directory of Open Access Journals (Sweden)

    Mark Heckmann

    2017-01-01

    Full Text Available The repertory grid is a psychological data collection technique that is used to elicit qualitative data in the form of attributes as well as quantitative ratings. A common approach for evaluating multiple repertory grid data is sorting the elicited bipolar attributes (so called constructs into mutually exclusive categories by means of content analysis. An important question when planning this type of study is determining the sample size needed to a discover all attribute categories relevant to the field and b yield a predefined minimal number of attributes per category. For most applied researchers who collect multiple repertory grid data, programming a numeric simulation to answer these questions is not feasible. The gridsampler software facilitates determining the required sample size by providing a GUI for conducting the necessary numerical simulations. Researchers can supply a set of parameters suitable for the specific research situation, determine the required sample size, and easily explore the effects of changes in the parameter set.

  4. Age of the moon: An isotopic study of uranium-thorium-lead systematics of lunar samples

    Science.gov (United States)

    Tatsumoto, M.; Rosholt, J.N.

    1970-01-01

    Concentrations of U, Th, and Pb in Apollo 11 samples studied are low (U. 0.16 to 0.87; Th, 0.53 to 3.4; Pb, 0.29 to 1.7, in ppm) but the extremely radiogenic lead in samples allows radiometric dating. The fine dust and the breccia have a concordant age of 4.66 billion years on the basis of 207Pb/206Pb, 206Pb/238U, 207Pb/235U, and 208Pb/232Th ratios. This age is comparable with the age of meteorites and with the age generally accepted for the earth. Six crystalline and vesicular samples are distinctly younger than the dust and breccia. The 238U/235U ratio is the same as that in earth rocks, and 234U is in radioactive equilibrium with parent 238U.

  5. Preliminary study of Histamine in Rainbow trout (Oncorhynchus mykiss samples from fish markets in Tehran

    Directory of Open Access Journals (Sweden)

    Z Mashak

    2011-08-01

    Full Text Available Histidine is one of non-protein nitrogen extractives which found in fish such as Salmonidae family (trout is belonged this family.Members of this family has high amounts of Histidine compared to other foods. Some Salmon microbial flora can decarboxylated Histidine to Histamine and this metabolite is a hazard component for human. Evaluation of Histamine levels in Salmon via a fast and accurate method can be useful for decreasing the intensity of these hazards. In this study evaluated psychrophilic and mesophilic aerobic bacteria and also histamine level in purchased salmon samples from fish markets in Tehran by ELISA method (Rida Screen Histamine Kits. A total of 60 samples of Rainbow trout (Oncorhynchus mykiss purchased from fish markets and assayed for Histamine by using Rida Screen Histamine ELISA Kits. Bacterial enumeration was performed on 10-fold diluted samples at 25°C and 35°C for mesophilic and psychrophilic bacteria, respectively. The range of Histamine content was 4 to 28mg/100g (14.18mg/100g. 12.50 percent of samples had Histamine content above the international standard level (20mg/100g. Data achieved by bacterial enumeration and ELISA test were analyzed by Pearson correlation test indicated that direct relationship between histamine and the number of bacteria in fish samples is established (p

  6. Technical Basis for the Removal of Unremediated Nitrate Salt Sampling (UNS) to Support LANL Treatment Studies

    Energy Technology Data Exchange (ETDEWEB)

    Funk, David John [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-05-05

    The sampling of unremediated nitrate salts (UNS) was originally proposed by the U.S. Department of Energy (DOE) and Los Alamos National Security, LLC (LANS) (collectively, the Permittees) as a means to ensure adequate understanding and characterization of the problematic waste stream created when the Permittees remediated these nitrate salts-bearing waste with an organic absorbent. The proposal to sample the UNS was driven by a lack of understanding with respect to the radioactive contamination release that occurred within the underground repository at the Waste Isolation Pilot Plant (WIPP) in February 14, 2014, as well as recommendations made by a Peer Review Team. As discussed, the Permittees believe that current knowledge and understanding of the waste has sufficiently matured such that this additional sampling is not required. Perhaps more importantly, the risk of both chemical and radiological exposure to the workers sampling the UNS drum material is unwarranted. This memo provides the technical justification and rationale for excluding the UNS sampling from the treatment studies.

  7. Relations among questionnaire and experience sampling measures of inner speech: a smartphone app study.

    Science.gov (United States)

    Alderson-Day, Ben; Fernyhough, Charles

    2015-01-01

    Inner speech is often reported to be a common and central part of inner experience, but its true prevalence is unclear. Many questionnaire-based measures appear to lack convergent validity and it has been claimed that they overestimate inner speech in comparison to experience sampling methods (which involve collecting data at random timepoints). The present study compared self-reporting of inner speech collected via a general questionnaire and experience sampling, using data from a custom-made smartphone app (Inner Life). Fifty-one university students completed a generalized self-report measure of inner speech (the Varieties of Inner Speech Questionnaire, VISQ) and responded to at least seven random alerts to report on incidences of inner speech over a 2-week period. Correlations and pairwise comparisons were used to compare generalized endorsements and randomly sampled scores for each VISQ subscale. Significant correlations were observed between general and randomly sampled measures for only two of the four VISQ subscales, and endorsements of inner speech with evaluative or motivational characteristics did not correlate at all across different measures. Endorsement of inner speech items was significantly lower for random sampling compared to generalized self-report, for all VISQ subscales. Exploratory analysis indicated that specific inner speech characteristics were also related to anxiety and future-oriented thinking.

  8. Study on sampling of continuous linear system based on generalized Fourier transform

    Science.gov (United States)

    Li, Huiguang

    2003-09-01

    In the research of signal and system, the signal's spectrum and the system's frequency characteristic can be discussed through Fourier Transform (FT) and Laplace Transform (LT). However, some singular signals such as impulse function and signum signal don't satisfy Riemann integration and Lebesgue integration. They are called generalized functions in Maths. This paper will introduce a new definition -- Generalized Fourier Transform (GFT) and will discuss generalized function, Fourier Transform and Laplace Transform under a unified frame. When the continuous linear system is sampled, this paper will propose a new method to judge whether the spectrum will overlap after generalized Fourier transform (GFT). Causal and non-causal systems are studied, and sampling method to maintain system's dynamic performance is presented. The results can be used on ordinary sampling and non-Nyquist sampling. The results also have practical meaning on research of "discretization of continuous linear system" and "non-Nyquist sampling of signal and system." Particularly, condition for ensuring controllability and observability of MIMO continuous systems in references 13 and 14 is just an applicable example of this paper.

  9. Visualizing shear bands in 3-D using axisymmetric sample: An experimental study

    Directory of Open Access Journals (Sweden)

    W. Khraisat

    2017-07-01

    Full Text Available In this study a qualitative description of the occurrence of shear bands produced by a sudden impact on an axisymmetric specimen made of medium carbon steel 0.45% C is given. A simple experiment was developed aimed at producing a pinch shear stress in the front side of the test sample in order to visualize shear bands in 3-D. Curve fitting using MATLAB was employed based on the points taken from the images of the front section of the test sample. The predictions of the curve fitting suggests a hyperbolic section leading to the conclusion that within the sample there is a double cone region of material where the shear band region is located on its outer surface. The formation of the shear band is explained by the fact that the interaction of the stress wave front with the free surface of the test sample produces reflection waves that attenuate the incoming stress wave inwards leading to a stress gradient in the plane of the front side of the specimen that causes shear localization. Also, the progressively increasing cross sectional area of the test sample causes the expansion of the wave front, which also results in a stress gradient in the normal direction of the front side of the specimen. So the formation of shear bands depends not only on the impact momentum and strain rates but also on the sample’s geometry.

  10. Relations among questionnaire and experience sampling measures of inner speech: A smartphone app study

    Directory of Open Access Journals (Sweden)

    Ben eAlderson-Day

    2015-04-01

    Full Text Available Inner speech is often reported to be a common and central part of inner experience, but its true prevalence is unclear. Many questionnaire-based measures appear to lack convergent validity and it has been claimed that they overestimate inner speech in comparison to experience sampling methods (which involve collecting data at random timepoints. The present study compared self-reporting of inner speech collected via a general questionnaire and experience sampling, using data from a custom-made smartphone app (Inner Life. Fifty-one university students completed a generalized self-report measure of inner speech (the Varieties of Inner Speech Questionnaire, or VISQ and responded to at least 7 random alerts to report on incidences of inner speech over a 2-week period. Correlations and pairwise comparisons were used to compare generalized endorsements and randomly-sampled scores for each VISQ subscale. Significant correlations were observed between general and randomly sampled measures for only 2 of the 4 VISQ subscales, and endorsements of inner speech with evaluative or motivational characteristics did not correlate at all across different measures. Endorsement of inner speech items was significantly lower for random sampling compared to generalized self-report, for all VISQ subscales. Exploratory analysis indicated that specific inner speech characteristics were also related to anxiety and future-oriented thinking.

  11. Adaptive sampling in two-phase designs: a biomarker study for progression in arthritis

    Science.gov (United States)

    McIsaac, Michael A; Cook, Richard J

    2015-01-01

    Response-dependent two-phase designs are used increasingly often in epidemiological studies to ensure sampling strategies offer good statistical efficiency while working within resource constraints. Optimal response-dependent two-phase designs are difficult to implement, however, as they require specification of unknown parameters. We propose adaptive two-phase designs that exploit information from an internal pilot study to approximate the optimal sampling scheme for an analysis based on mean score estimating equations. The frequency properties of estimators arising from this design are assessed through simulation, and they are shown to be similar to those from optimal designs. The design procedure is then illustrated through application to a motivating biomarker study in an ongoing rheumatology research program. Copyright © 2015 © 2015 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd. PMID:25951124

  12. Advancing Research on Racial–Ethnic Health Disparities: Improving Measurement Equivalence in Studies with Diverse Samples

    Science.gov (United States)

    Landrine, Hope; Corral, Irma

    2014-01-01

    To conduct meaningful, epidemiologic research on racial–ethnic health disparities, racial–ethnic samples must be rendered equivalent on other social status and contextual variables via statistical controls of those extraneous factors. The racial–ethnic groups must also be equally familiar with and have similar responses to the methods and measures used to collect health data, must have equal opportunity to participate in the research, and must be equally representative of their respective populations. In the absence of such measurement equivalence, studies of racial–ethnic health disparities are confounded by a plethora of unmeasured, uncontrolled correlates of race–ethnicity. Those correlates render the samples, methods, and measures incomparable across racial–ethnic groups, and diminish the ability to attribute health differences discovered to race–ethnicity vs. to its correlates. This paper reviews the non-equivalent yet normative samples, methodologies and measures used in epidemiologic studies of racial–ethnic health disparities, and provides concrete suggestions for improving sample, method, and scalar measurement equivalence. PMID:25566524

  13. A Study on Learning Environments of Elementary School Students Taking Social Studies Course: Bursa Sample

    Science.gov (United States)

    Dogan, Yadigar; Sezer, Gonul Onur

    2011-01-01

    Schools as educational and instructional institutions are expected to be renewable ones where motivation is increased through establishing relationships between students' interests and needs, and subject matters of social studies lessons are derived from daily life and events. Finalizing any learning activity at school by realizing it as aimed and…

  14. Comparative study on production, purification of penicillin by Penicillium chrysogenum isolated from soil and citrus samples.

    Science.gov (United States)

    Dayalan, S Anto Jeya; Darwin, Pramod; Prakash, S

    2011-01-01

    To explore various unexplored locations where Penicillium spp. would be available and study the production of penicillin from the isolated Penicillium spp. in different media with altered carbohydrate source. The collected soil samples were screened for the isolation of Penicillium chrysogenum (P. chrysogenum) by soil dilution plate. The isolated Penicillium species were further grown in different production media with changes in the carbohydrate source. The extracted penicillin from various isolates was analyzed by HPLC for the efficacy of the product. Further the products were screened with various bacterial species including methicillin resistant Staphylococcus aureus (MRSA). And the work was extended to find the possible action on MRSA, along with characterization using other pathogens. From the various soil and citrus samples used for analysis, only the soil sample from Government General Hospital of Bangalore, India, and Sanjay Gandhi Hospital, Bangalore, India, showed some potential growth of the desired fungi P. chrysogenum. Different production media showed varied range of growth of Penicillium. Optimum production of penicillin was obtained in maltose which proved maximum zone of inhibition during assay. Characterization of penicillin on pathogens, like wild Escherichia coli strain, Klebsiella spp., and MRSA, gave quite interesting results such as no activity on the later strain as it is resistant. HPLC data provided the analytical and confirmation details of the penicillin produced. Accordingly, the penicillin produced from the soil sample of Government General Hospital had the high milli absorbance unit of 441.5 mAu compared with that of the penicillin produced from Sanjay Gandhi Hospital sample, 85.52 mAu. Therefore, there was a considerable change in quantity of the penicillin produced from both the samples. The Penicillium spp. could be possibly rich in hospital contaminants and its environments. This research focuses on various unexplored sources of

  15. Study of Organochlorinated Pesticide Residues and Polychlorinated Biphenyls in Soil Samples

    Directory of Open Access Journals (Sweden)

    MSc. Vlora Gashi

    2013-12-01

    Full Text Available This paper presents and discusses the data obtained for organochlorinated pesticides and their residues in the soil samples of agricultural areas. Soil contamination is one of most important factors influencing the quality of agricultural products. Usage of heavy farm equipment, the land drainage, an exces­sive application of agrochemicals, emissions originating from mining, metallurgical, and chemical and coal power plants and transport, all generate a number of undesired substances (nitric and sulphur oxides, PAHs, heavy metals, pesticides, which after deposition in soil may influence crop quality. Thus, input of these contaminants into the environment should be carefully monitored. Levels of organochlorinated pesticides contamination were evaluated in agriculture areas that are in use. 10 soil samples were taken in agricultural areas  Plane of  Dugagjini , Kosovo. Representa­tive soil samples were collected from 0-30 cm top layer of the soil. In the analytical method we combined ultrasonic bath extraction and a Florisil column for samples clean-up. The analysis of the organochlorinated pesticides in soil samples was performed by gas chromatography technique using electron capture detector (GC/ECD. Optima-5 (low/mid polarity, 5% phenyl methyl siloxane 60 m x 0.33 mm x 0.25μm film capillary column was used for isolation and determination of organochlorinated pesticides. Low concentrations of organochlorinated pesticide and their metabolites were found in the studied samples. The presence of organochlorinated pesticides and their residues is probably resulting of their previous uses for agricultural purposes.

  16. Preliminary study of the EChO data sampling and processing

    Science.gov (United States)

    Farina, M.; Di Giorgio, A. M.; Focardi, M.; Pace, E.; Micela, G.; Galli, E.; Giusi, G.; Liu, S. J.; Pezzuto, S.

    2014-08-01

    The EChO Payload is an integrated spectrometer with six different channels covering the spectral range from the visible up to the thermal infrared. A common Instrument Control Unit (ICU) implements all the instrument control and health monitoring functionalities as well as all the onboard science data processing. To implement an efficient design of the ICU on board software, separate analysis of the unit requirements are needed for the commanding and housekeeping collection as well as for the data acquisition, sampling and compression. In this work we present the results of the analysis carried out to optimize the EChO data acquisition and processing chain. The HgCdTe detectors used for EChO mission allow for non-destructive readout modes, such that the charge may be read without removing it after reading out. These modes can reduce the equivalent readout noise and the gain in signal to noise ratio can be computed using well known relations based on fundamental principles. In particular, we considered a multiaccumulation approach based on non-destructive reading of detector samples taken at equal time intervals. All detectors are periodically reset after a certain number of samples have been acquired and the length of the reset interval, as well as the number of samples and the sampling rate can be adapted to the brightness of the considered source. The estimation of the best set of parameters for the signal to noise ratio optimization and of the best sampling technique has been done by taking into account also the needs of mitigating the expected radiation effects on the acquired data. Cosmic rays can indeed be one of the major sources of data loss for a space observatory, and the studies made for the JWST mission allowed us to evaluate the actual need of the implementation of a dedicated deglitching procedure on board EChO.

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

    Science.gov (United States)

    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.

  18. Mercury levels in hair samples of dentists: A comparative study in Sri Lanka.

    Science.gov (United States)

    Wijesekara, Lumbini A; Usoof, Rinzee; Gamage, Sachindra S T; Jayasinghe, Ruwan; Gamage, Nandasena; De Silva, Dileep; Ekanayake, Sagarika

    2017-10-22

    Elemental mercury is widely used in dentistry as dental amalgam. Hair samples constitute preferred biomarkers to determine the index of mercury exposure. In the absence of any published studies, the aim of the present study was to ascertain the level of mercury in a selected sample of dentists and controls in Sri Lanka. Hair samples (.7 g) from dentists working in and around the Colombo district in Sri Lanka (n = 50) and controls (n = 50) were digested with sulfuric acid-potassium permanganate solution, and reduced to metallic mercury with stannous chloride. Digested samples were analyzed for mercury using an atomic absorption spectrophotometer. The average mercury contents of the test and control samples (n = 50 each) were 5.36 ± 2.64 ppb and 3.1 ± 1.99 ppb, respectively. Based on the estimated ratio of mercury in hair to blood in humans as 250:1, the average content of mercury in the blood of the two groups could be .02 ppb and .01 ppb, respectively. The number of years in dentistry and number of amalgam restorations performed within 1 week were not correlated with the hair concentration of mercury. As the values of both groups were well below 10 ng/mL (10 ppb), within the concentrations considered as normal, mercury use was not considered an occupational hazard for dentists. © 2017 John Wiley & Sons Australia, Ltd.

  19. Review of sample preparation strategies for MS-based metabolomic studies in industrial biotechnology.

    Science.gov (United States)

    Causon, Tim J; Hann, Stephan

    2016-09-28

    Fermentation and cell culture biotechnology in the form of so-called "cell factories" now play an increasingly significant role in production of both large (e.g. proteins, biopharmaceuticals) and small organic molecules for a wide variety of applications. However, associated metabolic engineering optimisation processes relying on genetic modification of organisms used in cell factories, or alteration of production conditions remain a challenging undertaking for improving the final yield and quality of cell factory products. In addition to genomic, transcriptomic and proteomic workflows, analytical metabolomics continues to play a critical role in studying detailed aspects of critical pathways (e.g. via targeted quantification of metabolites), identification of biosynthetic intermediates, and also for phenotype differentiation and the elucidation of previously unknown pathways (e.g. via non-targeted strategies). However, the diversity of primary and secondary metabolites and the broad concentration ranges encompassed during typical biotechnological processes means that simultaneous extraction and robust analytical determination of all parts of interest of the metabolome is effectively impossible. As the integration of metabolome data with transcriptome and proteome data is an essential goal of both targeted and non-targeted methods addressing production optimisation goals, additional sample preparation steps beyond necessary sampling, quenching and extraction protocols including clean-up, analyte enrichment, and derivatisation are important considerations for some classes of metabolites, especially those present in low concentrations or exhibiting poor stability. This contribution critically assesses the potential of current sample preparation strategies applied in metabolomic studies of industrially-relevant cell factory organisms using mass spectrometry-based platforms primarily coupled to liquid-phase sample introduction (i.e. flow injection, liquid

  20. Association study between the Taq1A (rs1800497 polymorphism and schizophrenia in a Brazilian sample

    Directory of Open Access Journals (Sweden)

    Quirino Cordeiro

    2014-08-01

    Full Text Available Schizophrenia is a severe psychotic disorder with recurrent relapse and functional impairment. It results from a poorly understood gene-environment interaction. The Taq1A polymorphism (located in the gene cluster NTAD is a likely candidate for schizophrenia. Its rs1800497 polymorphism was shown to be associated with DRD2 gene expression. Therefore the present work aims to investigate a possible association between schizophrenia and such polymorphism. The compared distribution of the alleles and genotypes of the studied polymorphism was investigated in a Brazilian sample of 235 patients and 834 controls. Genotypic frequencies were in Hardy-Weinberg equilibrium. There was a trend of allelic association between the Taq1A polymorphism (rs1800497 with schizophrenia in the studied sample. However no statistically differences were found between cases and controls when analyzed by gender or schizophrenia subtypes.

  1. Oxide Nanolayers in Stratified Samples Studied by X-Ray Resonant Raman Scattering at Grazing Incidence

    Directory of Open Access Journals (Sweden)

    Juan José Leani

    2015-01-01

    Full Text Available X-ray resonant Raman scattering is applied at grazing incidence conditions with the aim of discriminating and identifying chemical environment of iron in different layers of stratified materials using a low resolution energy dispersive system. The methodology allows for depth studies with nanometric resolution. Nanostratified samples of Fe oxides were studied at the Brazilian synchrotron facility (LNLS using monochromatic radiation and an EDS setup. The measurements were carried out in grazing incident regime with incident photon energy lower than and close to the Fe-K absorption edge. The result allowed for characterizing oxide nanolayers, not observable with conventional geometries, identifying the oxidation state present in a particular depth of a sample surface with nanometric, or even subnanometric, resolution using a low-resolution system.

  2. A multicenter study of viable PCR using propidium monoazide to detect Legionella in water samples.

    Science.gov (United States)

    Scaturro, Maria; Fontana, Stefano; Dell'eva, Italo; Helfer, Fabrizia; Marchio, Michele; Stefanetti, Maria Vittoria; Cavallaro, Mario; Miglietta, Marilena; Montagna, Maria Teresa; De Giglio, Osvalda; Cuna, Teresa; Chetti, Leonarda; Sabattini, Maria Antonietta Bucci; Carlotti, Michela; Viggiani, Mariagabriella; Stenico, Alberta; Romanin, Elisa; Bonanni, Emma; Ottaviano, Claudio; Franzin, Laura; Avanzini, Claudio; Demarie, Valerio; Corbella, Marta; Cambieri, Patrizia; Marone, Piero; Rota, Maria Cristina; Bella, Antonino; Ricci, Maria Luisa

    2016-07-01

    Legionella quantification in environmental samples is overestimated by qPCR. Combination with a viable dye, such as Propidium monoazide (PMA), could make qPCR (named then vPCR) very reliable. In this multicentre study 717 artificial water samples, spiked with fixed concentrations of Legionella and interfering bacterial flora, were analysed by qPCR, vPCR and culture and data were compared by statistical analysis. A heat-treatment at 55 °C for 10 minutes was also performed to obtain viable and not-viable bacteria. When data of vPCR were compared with those of culture and qPCR, statistical analysis showed significant differences (P 0.05). Overall this study provided a good experimental reproducibility of vPCR but also highlighted limits of PMA in the discriminating capability of dead and live bacteria, making vPCR not completely reliable. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Aluminum, iron, and lead content of respirable particulate samples from a personal monitoring study

    Energy Technology Data Exchange (ETDEWEB)

    Tosteson, T.D.; Spengler, J.D.; Weker, R.A.

    1982-01-01

    Samples of respirable particulate matter collected during a personal monitoring study in Topeka, KS, were analyzed for iron, aluminum, and lead content. The sampling protocol and instrumentation are described in detail. Lead indoor concentrations (median = 79 ng/m/sup 3/) were found to be less than both personal (median = 112 ng/m/sup 3/) and outdoor lead concentrations (median = 106 ng/m/sup 3/). The indoor, outdoor, and personal levels of iron and aluminum were not significantly different. In addition, it was determined that outdoor respirable particulate mass does not correlate well with the personal or indoor metal concentrations, and that the amount of time spent in motor vehicles is a relatively good indicator of lead exposures. The relationships between indoor, outdoor, and personal lead are discussed in greater detail, with references to supporting evidence from other studies.

  4. A STUDY OF THE DIVERSE T DWARF POPULATION REVEALED BY WISE

    Energy Technology Data Exchange (ETDEWEB)

    Mace, Gregory N.; Wright, Edward L.; McLean, Ian S. [Department of Physics and Astronomy, UCLA, 430 Portola Plaza, Box 951547, Los Angeles, CA 90095-1547 (United States); Davy Kirkpatrick, J.; Gelino, Christopher R.; Griffith, Roger L.; Mix, Katholeen; Beichman, Charles A.; Lowrance, Patrick J. [Infrared Processing and Analysis Center, MS 100-22, California Institute of Technology, Pasadena, CA 91125 (United States); Cushing, Michael C. [Department of Physics and Astronomy, MS 111, University of Toledo, 2801 W. Bancroft St., Toledo, OH 43606-3328 (United States); Skrutskie, Michael F. [Department of Astronomy, University of Virginia, Charlottesville, VA 22904 (United States); Marsh, Kenneth A. [School of Physics and Astronomy, Cardiff University, Cardiff CF24 3AA (United Kingdom); Eisenhardt, Peter R. [NASA Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, CA 91109 (United States); Thompson, Maggie A. [Department of Astrophysical Sciences, Princeton University, Peyton Hall, 4 Ivy Lane, Princeton, NJ 08544-1001 (United States); Bailey, Vanessa; Hinz, Philip M.; Knox, Russell P. [Steward Observatory, The University of Arizona, 933 N. Cherry Ave., Tucson, AZ 85721 (United States); Bloom, Joshua S. [Department of Astronomy, University of California, Berkeley, CA 94720 (United States); Burgasser, Adam J. [Department of Physics, University of California, San Diego, CA 92093 (United States); Fortney, Jonathan J., E-mail: gmace@astro.ucla.edu [Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA 95064 (United States); and others

    2013-03-01

    We report the discovery of 87 new T dwarfs uncovered with the Wide-field Infrared Survey Explorer (WISE) and 3 brown dwarfs with extremely red near-infrared colors that exhibit characteristics of both L and T dwarfs. Two of the new T dwarfs are likely binaries with L7 {+-} 1 primaries and mid-type T secondaries. In addition, our follow-up program has confirmed 10 previously identified T dwarfs and 4 photometrically selected L and T dwarf candidates in the literature. This sample, along with the previous WISE discoveries, triples the number of known brown dwarfs with spectral types later than T5. Using the WISE All-Sky Source Catalog we present updated color-color and color-type diagrams for all the WISE-discovered T and Y dwarfs. Near-infrared spectra of the new discoveries are presented along with spectral classifications. To accommodate later T dwarfs we have modified the integrated flux method of determining spectral indices to instead use the median flux. Furthermore, a newly defined J-narrow index differentiates the early-type Y dwarfs from late-type T dwarfs based on the J-band continuum slope. The K/J indices for this expanded sample show that 32% of late-type T dwarfs have suppressed K-band flux and are blue relative to the spectral standards, while only 11% are redder than the standards. Comparison of the Y/J and K/J index to models suggests diverse atmospheric conditions and supports the possible re-emergence of clouds after the L/T transition. We also discuss peculiar brown dwarfs and candidates that were found not to be substellar, including two young stellar objects and two active galactic nuclei. The substantial increase in the number of known late-type T dwarfs provides a population that will be used to test models of cold atmospheres and star formation. The coolest WISE-discovered brown dwarfs are the closest of their type and will remain the only sample of their kind for many years to come.

  5. Opportunity in our Ignorance: Urban Biodiversity Study Reveals 30 New Species and One New Nearctic Record for Megaselia (Diptera: Phoridae) in Los Angeles (California, USA).

    Science.gov (United States)

    Hartop, Emily A; Brown, Brian V; Disney, R Henry L

    2015-04-02

    An urban biodiversity study sampling primarily from private backyards in Los Angeles, California (USA), reveals the presence of fifty-six species of Megaselia within the first few months of sampling. Thirty of these are described as new to science: M. armstrongorum, M. bradyi, M. brejchaorum, M. carthayensis, M. ciancii, M. creasoni, M. defibaughorum, M. donahuei, M. francoae, M. fujiokai, M. hardingorum, M. heini, M. hentschkeae, M. hoffmanorum, M. hoggorum, M. hoguei, M. isaacmajorum, M. kelleri, M. lombardorum, M. marquezi, M. mikejohnsoni, M. oxboroughae, M. pisanoi, M. renwickorum, M. rodriguezorum, M. sacatelensis, M. seaverorum, M. sidneyae, M. steptoeae, and M. wiegmanae. M. largifrontalis is newly reported from the Nearctic Region. The implications these findings have for future taxonomic work in Megaselia, particularly in urban areas, are discussed.

  6. Microbial Safety of Low Water Activity Foods: Study of Simulated and Durban Household Samples

    OpenAIRE

    Ijabadeniyi, O. A.; Pillay, Y.

    2017-01-01

    Sixty household low water activity foods were examined and a simulative study was conducted in a high sugar, low aw almond and macadamia butter to determine the survival of Bacillus cereus and Staphylococcus aureus ATCC 25923. Results obtained from 60 low aw samples collected at household level had some significant differences (P≤0,05) within food categories amongst the various tests. Spices had the highest number of aerobic bacteria, aerobic spore-formers, anaerobic spore-formers, and S. aur...

  7. [Job satisfaction among a sample of Italian nurses: a questionnaire study].

    Science.gov (United States)

    Panella, Massimiliano; Cortes Sosa, Jamy Patricia; Vanhaecht, Kris

    2012-01-01

    Job satisfaction among staff nurses is an important issue in any healthcare organization because of its possible impact on the quality of patient care. A questionnaire study was performed to identify possible determinants of job satisfaction among a sample of 89 nurses in Piedmont (northern Italy). Participating nurses held jobs in various hospital and ambulatory care units of two local health authorities of the region. Findings indicate that perception of an excessive degree of paperwork is the main factor negatively affecting job satisfaction.

  8. INAPPROPRIATE CONFIDENCE AND RETIREMENT PLANNING: FOUR STUDIES WITH A NATIONAL SAMPLE

    OpenAIRE

    Parker, Andrew M.; de Bruin, Wändi Bruine; Yoong, Joanne; Willis, Robert

    2011-01-01

    Financial decisions about investing and saving for retirement are increasingly complex, requiring financial knowledge and confidence in that knowledge. Few studies have examined whether direct assessments of individuals’ confidence are related to the outcomes of their financial decisions. Here, we analyzed data from a national sample recruited through RAND’s American Life Panel (ALP), an internet panel of U.S. adults aged 18 to 88. We examined the relationship of confidence with self-reported...

  9. Desert Research and Technology Studies Exposure of Lotus Coated Electrodynamic Shield Samples

    Science.gov (United States)

    Rodriquez, Marcello; Peters, Wanda C.; Straka, Sharon A.; Jones, Craig B.

    2011-01-01

    The Lotus dust mitigation coating and the electrodynamic shield (EDS) are two new technologies currently being developed by NASA as countermeasures for addressing dust accumulation for long-duration human space exploration. These combined technologies were chosen by the Habitation Demonstration Unit (HDU) program for desert dust exposure at the Desert Research and Technologies Studies (D-RaTS) test site in Arizona. Characterization of these samples was performed prior to, during and post D-RaTS exposure.

  10. Gridsampler – A Simulation Tool to Determine the Required Sample Size for Repertory Grid Studies

    OpenAIRE

    Mark Heckmann; Lukas Burk

    2017-01-01

    The repertory grid is a psychological data collection technique that is used to elicit qualitative data in the form of attributes as well as quantitative ratings. A common approach for evaluating multiple repertory grid data is sorting the elicited bipolar attributes (so called constructs) into mutually exclusive categories by means of content analysis. An important question when planning this type of study is determining the sample size needed to a) discover all attribute categories relevant...

  11. Analysis of small sample size studies using nonparametric bootstrap test with pooled resampling method.

    Science.gov (United States)

    Dwivedi, Alok Kumar; Mallawaarachchi, Indika; Alvarado, Luis A

    2017-06-30

    Experimental studies in biomedical research frequently pose analytical problems related to small sample size. In such studies, there are conflicting findings regarding the choice of parametric and nonparametric analysis, especially with non-normal data. In such instances, some methodologists questioned the validity of parametric tests and suggested nonparametric tests. In contrast, other methodologists found nonparametric tests to be too conservative and less powerful and thus preferred using parametric tests. Some researchers have recommended using a bootstrap test; however, this method also has small sample size limitation. We used a pooled method in nonparametric bootstrap test that may overcome the problem related with small samples in hypothesis testing. The present study compared nonparametric bootstrap test with pooled resampling method corresponding to parametric, nonparametric, and permutation tests through extensive simulations under various conditions and using real data examples. The nonparametric pooled bootstrap t-test provided equal or greater power for comparing two means as compared with unpaired t-test, Welch t-test, Wilcoxon rank sum test, and permutation test while maintaining type I error probability for any conditions except for Cauchy and extreme variable lognormal distributions. In such cases, we suggest using an exact Wilcoxon rank sum test. Nonparametric bootstrap paired t-test also provided better performance than other alternatives. Nonparametric bootstrap test provided benefit over exact Kruskal-Wallis test. We suggest using nonparametric bootstrap test with pooled resampling method for comparing paired or unpaired means and for validating the one way analysis of variance test results for non-normal data in small sample size studies. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  12. Damage initiation in brittle and ductile materials as revealed from a fractoluminescence study

    Directory of Open Access Journals (Sweden)

    Alexandre Chmel

    2014-10-01

    Full Text Available A set of heterogeneous and homogeneous materials differing in their brittle and ductile characteristics (granite, marble, silica ceramics, silicon carbide, organic glass were subjected to impact damaging by a falling weight. Multiple chemical bond ruptures produced by elastic waves propagating from a damaged zone were accompanied by the photon emission generated throughout the sample (tribo- or fractoluminescence, FL. The statistical analysis of the FL time series detected with high resolution (10 ns showed that the energy release distributions in brittle solids follow the power law typical for the correlated nucleation of primary defects. At the same time, the formation of damaged sites in ductile materials (marble and organic glass was found to be fully random.

  13. Preparation of well-defined samples of AlPdMn quasicrystals for surface studies

    Science.gov (United States)

    Jenks, C. J.; Delaney, D. W.; Bloomer, T. E.; Chang, S.-L.; Lograsso, T. A.; Shen, Z.; Zhang, C.-M.; Thiel, P. A.

    1996-12-01

    We have developed a method for preparing single-grain, quasicrystalline AlPdMn samples for surface studies in ultrahigh vacuum. The main issues of concern are phase purity, the quality of the surface structure, and the surface, and the surface composition. Phase purity is enhanced by annealing the sample in ultra-pure Ar in a sealed quartz ampoule for several days before polishing. Polishing with colloidal silica allows secondary phases to be detected readily with an optical microscope. As a final precaution, phase purity can be checked sensitively with scanning Auger microscopy. After this stage, the sample can be cleaned in ultrahigh vacuum with ion bombardment. Annealing is required after bombardment to restore surface structure and to obtain a low-energy electron diffraction (LEED) pattern of an oriented sample. However, both ion bombardment and heating to temperatures above 870 K in vacuum, produce Pd-rich surfaces. As a final step, for the five-fold surface, we recommend heating briefly to 1050-1100 K and then annealing at 870 K for several hours. This produces both an excellent LEED pattern, and a surface composition close to that of the bulk.

  14. Preliminary study on element mass fraction determination on catfish samples from Paraguay

    Energy Technology Data Exchange (ETDEWEB)

    Moreira, Edson G.; Catharino, Marilia G.M.; Vasconcellos, Marina B.A., E-mail: emoreira@ipen.br, E-mail: mbvascon@ipen.br, E-mail: mariliasemmler@uol.com.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil); Frutos, Sixto A.; Insaurralde, Mario S., E-mail: tony8013@hotmail.com, E-mail: insaurraldemar9@hotmail.com [Universidad Nacional de Asuncion (FCV/UNA), San Lorenzo (Paraguay). Facultad de Ciencias Veterinarias. Departamento de Pesca y Acuicultura

    2013-07-01

    South American catfish (Pseudoplatystoma), commonly known in Spanish as atigrado or surubi and in Portuguese as surubim or pintado is a large fish that typically reaches 1 m long and weighs 60 kg to 80 kg and may be found at the basins of the Amazon, the Sao Francisco and de la Plata rivers, usually in riverbeds and deep wells. Being a much appreciated fish for human consumption, it is quite sought after by fishermen who have been contributing to the reduction of the stocks. This fact attracted the attention of the Paraguayan authorities to the point of imposing restrictions to free fishing and commercialization. This study aims to assist the conservation efforts towards this fish by investigating its exposure to possible pollutants. Preliminary results on element determination on six samples of catfish from Paraguayan rivers are presented. Cs, Co, Fe, Se and Zn were determined by applying an Instrumental Neutron Activation Analysis method. While these element levels were lower than the legislation for human consumption, the elements As, Cr e La were not detected in the samples as they are below the detection limit of the method employed. Atomic Absorption Spectrometry was used to investigate the presence of Cd, Hg and Pb in the samples. Hg was detected in the samples while Cd and Pb were below the detection limit of the method. (author)

  15. Identification and Correction of Sample Mix-Ups in Expression Genetic Data: A Case Study.

    Science.gov (United States)

    Broman, Karl W; Keller, Mark P; Broman, Aimee Teo; Kendziorski, Christina; Yandell, Brian S; Sen, Śaunak; Attie, Alan D

    2015-08-19

    In a mouse intercross with more than 500 animals and genome-wide gene expression data on six tissues, we identified a high proportion (18%) of sample mix-ups in the genotype data. Local expression quantitative trait loci (eQTL; genetic loci influencing gene expression) with extremely large effect were used to form a classifier to predict an individual's eQTL genotype based on expression data alone. By considering multiple eQTL and their related transcripts, we identified numerous individuals whose predicted eQTL genotypes (based on their expression data) did not match their observed genotypes, and then went on to identify other individuals whose genotypes did match the predicted eQTL genotypes. The concordance of predictions across six tissues indicated that the problem was due to mix-ups in the genotypes (although we further identified a small number of sample mix-ups in each of the six panels of gene expression microarrays). Consideration of the plate positions of the DNA samples indicated a number of off-by-one and off-by-two errors, likely the result of pipetting errors. Such sample mix-ups can be a problem in any genetic study, but eQTL data allow us to identify, and even correct, such problems. Our methods have been implemented in an R package, R/lineup. Copyright © 2015 Broman et al.

  16. Experiments Are Revealing a Foundation Species: A Case Study of Eastern Hemlock (Tsuga canadensis

    Directory of Open Access Journals (Sweden)

    Aaron M. Ellison

    2014-01-01

    Full Text Available Foundation species are species that create and define particular ecosystems; control in large measure the distribution and abundance of associated flora and fauna; and modulate core ecosystem processes, such as energy flux and biogeochemical cycles. However, whether a particular species plays a foundational role in a system is not simply asserted. Rather, it is a hypothesis to be tested, and such tests are best done with large-scale, long-term manipulative experiments. The utility of such experiments is illustrated through a review of the Harvard Forest Hemlock Removal Experiment (HF-HeRE, a multidecadal, multihectare experiment designed to test the foundational role of eastern hemlock, Tsuga canadensis, in eastern North American forests. Experimental removal of T. canadensis has revealed that after 10 years, this species has pronounced, long-term effects on associated flora and fauna, but shorter-term effects on energy flux and nutrient cycles. We hypothesize that on century-long scales, slower changes in soil microbial associates will further alter ecosystem processes in T. canadensis stands. HF-HeRE may indeed continue for >100 years, but at such time scales, episodic disturbances and changes in regional climate and land cover can be expected to interact in novel ways with these forests and their foundation species.

  17. Spirocyclic character of ixazomib citrate revealed by comprehensive XRD, NMR and DFT study

    Science.gov (United States)

    Skorepova, Eliska; Čerňa, Igor; Vlasáková, Růžena; Zvoníček, Vít; Tkadlecová, Marcela; Dušek, Michal

    2017-11-01

    Ixazomib citrate is a very recently approved anti-cancer drug. Until now, to the best of our knowledge, no one has been able to solve any crystal structures of this compound. In this work, we present the crystal structures of two isostructural solvates of ixazomib citrate. In all currently available literature, the molecule is characterized as containing a single optically active carbon atom and a borate cycle formed when ixazomib is reacted with citric acid to form a stabilized ixazomib citrate that can be administered orally. However, the crystal structures revealed that none of the up-to-date presented structural formulas of ixazomib citrate are fully accurate. In addition to the citrate ring, another 5-membered ring is formed. These two rings are connected by the boron atom, making this compound a spirocyclic borate. By spirocyclization, the boron atom becomes tetrahedral and therefore optically active. In the crystal structures, ixazomib citrate was found to be in forms of two RR and RS stereoisomers. The results are supported by solid-state and solution NMR and DFT quantum mechanical calculations.

  18. Revealing a room temperature ferromagnetism in cadmium oxide nanoparticles: An experimental and first-principles study

    KAUST Repository

    Bououdina, Mohamed

    2015-03-26

    We obtain a single cadmium oxide phase from powder synthesized by a thermal decomposition method of cadmium acetate dehydrate. The yielded powder is annealed in air, vacuum, and H2 gas in order to create point defects. Magnetization-field curves reveal the appearance of diamagnetic behavior with a ferromagnetic component for all the powders. Powder annealing under vacuum and H2 atmosphere leads to a saturation magnetization 1.15 memu g-1 and 1.2 memu g-1 respectively with an increase by 45% and 16% compared to the one annealed in air. We show that annealing in vacuum produces mainly oxygen vacancies while annealing in H2 gas creates mainly Cd vacancy leading to room temperature ferromagnetic (RTFM) component together with known diamagnetic properties. Ab initio calculations performed on the CdO nanoparticles show that the magnetism is governed by polarized hybrid states of the Cd d and O p orbitals together with the vacancy. © The Royal Society of Chemistry 2015.

  19. A family history study of male sexual orientation using three independent samples.

    Science.gov (United States)

    Bailey, J M; Pillard, R C; Dawood, K; Miller, M B; Farrer, L A; Trivedi, S; Murphy, R L

    1999-03-01

    Available evidence suggests that male homosexuality is both familial and somewhat heritable and that some cases may be caused by an X-linked gene. However, most studies have recruited subjects in a relatively unsystematic manner, typically via advertisements, and hence suffer from the potential methodological flaw of ascertainment bias due to volunteer self-selection. In the present study we assessed the familiality of male homosexuality using two carefully ascertained samples and attempted to replicate findings consistent with X-linkage in three samples. The percentage of siblings of the probands rated as either homosexual or bisexual, with a high degree of certainty, ranged from 7 to 10% for brothers and 3 to 4% for sisters. These estimates are higher than recent comparable population-based estimates of homosexuality, supporting the importance of familial factors for male homosexuality. Estimates of lambda s for male homosexuality ranged from 3.0 to 4.0. None of the samples showed a significantly greater proportion of maternal than paternal homosexual uncles or homosexual male maternal first cousins. Although our results differed significantly with those of some prior studies, they do not exclude the possibility of moderate X-linkage for male sexual orientation.

  20. Sampling design for the Study of Cardiovascular Risks in Adolescents (ERICA).

    Science.gov (United States)

    Vasconcellos, Mauricio Teixeira Leite de; Silva, Pedro Luis do Nascimento; Szklo, Moyses; Kuschnir, Maria Cristina Caetano; Klein, Carlos Henrique; Abreu, Gabriela de Azevedo; Barufaldi, Laura Augusta; Bloch, Katia Vergetti

    2015-05-01

    The Study of Cardiovascular Risk in Adolescents (ERICA) aims to estimate the prevalence of cardiovascular risk factors and metabolic syndrome in adolescents (12-17 years) enrolled in public and private schools of the 273 municipalities with over 100,000 inhabitants in Brazil. The study population was stratified into 32 geographical strata (27 capitals and five sets with other municipalities in each macro-region of the country) and a sample of 1,251 schools was selected with probability proportional to size. In each school three combinations of shift (morning and afternoon) and grade were selected, and within each of these combinations, one class was selected. All eligible students in the selected classes were included in the study. The design sampling weights were calculated by the product of the reciprocals of the inclusion probabilities in each sampling stage, and were later calibrated considering the projections of the numbers of adolescents enrolled in schools located in the geographical strata by sex and age.

  1. Exploring Stochastic Sampling in Nuclear Data Uncertainties Assessment for Reactor Physics Applications and Validation Studies

    Directory of Open Access Journals (Sweden)

    Alexander Vasiliev

    2016-12-01

    Full Text Available The quantification of uncertainties of various calculation results, caused by the uncertainties associated with the input nuclear data, is a common task in nuclear reactor physics applications. Modern computation resources and improved knowledge on nuclear data allow nowadays to significantly advance the capabilities for practical investigations. Stochastic sampling is the method which has received recently a high momentum for its use and exploration in the domain of reactor design and safety analysis. An application of a stochastic sampling based tool towards nuclear reactor dosimetry studies is considered in the given paper with certain exemplary test evaluations. The stochastic sampling not only allows the input nuclear data uncertainties propagation through the calculations, but also an associated correlation analysis performance with no additional computation costs and for any parameters of interest can be done. Thus, an example of assessment of the Pearson correlation coefficients for several models, used in practical validation studies, is shown here. As a next step, the analysis of the obtained information is proposed for discussion, with focus on the systems similarities assessment. The benefits of the employed method and tools with respect to practical reactor dosimetry studies are consequently outlined.

  2. Sampling design for the Study of Cardiovascular Risks in Adolescents (ERICA

    Directory of Open Access Journals (Sweden)

    Mauricio Teixeira Leite de Vasconcellos

    2015-05-01

    Full Text Available The Study of Cardiovascular Risk in Adolescents (ERICA aims to estimate the prevalence of cardiovascular risk factors and metabolic syndrome in adolescents (12-17 years enrolled in public and private schools of the 273 municipalities with over 100,000 inhabitants in Brazil. The study population was stratified into 32 geographical strata (27 capitals and five sets with other municipalities in each macro-region of the country and a sample of 1,251 schools was selected with probability proportional to size. In each school three combinations of shift (morning and afternoon and grade were selected, and within each of these combinations, one class was selected. All eligible students in the selected classes were included in the study. The design sampling weights were calculated by the product of the reciprocals of the inclusion probabilities in each sampling stage, and were later calibrated considering the projections of the numbers of adolescents enrolled in schools located in the geographical strata by sex and age.

  3. Whole genome transcript profiling from fingerstick blood samples: a comparison and feasibility study

    Directory of Open Access Journals (Sweden)

    Williams Adam R

    2009-12-01

    Full Text Available Abstract Background Whole genome gene expression profiling has revolutionized research in the past decade especially with the advent of microarrays. Recently, there have been significant improvements in whole blood RNA isolation techniques which, through stabilization of RNA at the time of sample collection, avoid bias and artifacts introduced during sample handling. Despite these improvements, current human whole blood RNA stabilization/isolation kits are limited by the requirement of a venous blood sample of at least 2.5 mL. While fingerstick blood collection has been used for many different assays, there has yet to be a kit developed to isolate high quality RNA for use in gene expression studies from such small human samples. The clinical and field testing advantages of obtaining reliable and reproducible gene expression data from a fingerstick are many; it is less invasive, time saving, more mobile, and eliminates the need of a trained phlebotomist. Furthermore, this method could also be employed in small animal studies, i.e. mice, where larger sample collections often require sacrificing the animal. In this study, we offer a rapid and simple method to extract sufficient amounts of high quality total RNA from approximately 70 μl of whole blood collected via a fingerstick using a modified protocol of the commercially available Qiagen PAXgene RNA Blood Kit. Results From two sets of fingerstick collections, about 70 uL whole blood collected via finger lancet and capillary tube, we recovered an average of 252.6 ng total RNA with an average RIN of 9.3. The post-amplification yields for 50 ng of total RNA averaged at 7.0 ug cDNA. The cDNA hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips had an average % Present call of 52.5%. Both fingerstick collections were highly correlated with r2 values ranging from 0.94 to 0.97. Similarly both fingerstick collections were highly correlated to the venous collection with r2 values ranging from 0.88 to 0

  4. The Brown Longitudinal Obsessive Compulsive Study: Clinical Features and Symptoms of the Sample at Intake

    Science.gov (United States)

    Pinto, Anthony; Mancebo, Maria C.; Eisen, Jane L.; Pagano, Maria E.; Rasmussen, Steve A.

    2012-01-01

    Objective This article describes the method and intake findings of the Brown Longitudinal Obsessive Compulsive Study, the first comprehensive prospective investigation of the naturalistic course of obsessive-compulsive disorder (OCD) in a large clinical sample using longitudinal research methodology. Method Intake data, collected between June 2001 and October 2004, are presented for 293 adult participants in a prospective, naturalistic study of OCD. Participants had a primary diagnosis of DSM-IV OCD and had sought treatment for the disorder. Results Our findings indicate that OCD typically has a gradual onset and a continuous course regardless of age at onset. There is a substantial lag between the onset of the disorder and initiation of treatment. OCD, which almost always coexists with other psychiatric symptoms, leads to serious social and occupational impairment. Compared with participants with late-onset OCD, early-onset participants had higher rates of lifetime panic disorder, eating disorders, and obsessive-compulsive personality disorder. The groups also differed on the types of obsessive-compulsive symptoms that were first noticed, as well as on rates of current obsessions and compulsions. Conclusion The demographics, clinical characteristics, comorbidity rates, and symptom presentation of the sample are consistent with those reported for cross-sectional studies of OCD, including the DSM-IV Field Trial. The current sample has a number of advantages over previously collected prospective samples of OCD in that it is large, diagnostically well characterized, recruited from multiple settings, and treatment seeking. This unique data set will contribute to the identification of meaningful phenotypes in OCD based on stability of symptom dimensions, prospective course patterns, and treatment response. PMID:16841619

  5. Chemical and geotechnical analyses of soil samples from Olkiluoto for studies on sorption in soils

    Energy Technology Data Exchange (ETDEWEB)

    Lusa, M.; Aemmaelae, K.; Hakanen, M.; Lehto, J. (Helsinki Univ., Dept. of Chemistry, Lab. of Radiochemistry (Finland)); Lahdenperae, A.-M. (Poeyry Environment Oy, Vantaa (Finland))

    2009-05-15

    The safety assessment of disposal of spent nuclear fuel will include an estimate on the behavior of nuclear waste nuclides in the biosphere. As a part of this estimate also the transfer of nuclear waste nuclides in the soil and sediments is to be considered. In this study soil samples were collected from three excavator pits in Olkiluoto and the geotechnical and chemical characteristics of the samples were determined. In later stage these results will be used in sorption tests. Aim of these tests is to determine the Kd-values for Cs, Tc and I and later for Mo, Nb and Cl. Results of these sorption tests will be reported later. The geotechnical characteristics studied included dry weight and organic matter content as well as grain size distribution and mineralogy analyses. Selective extractions were carried out to study the sorption of cations into different mineral types. The extractions included five steps in which the cations bound to exchangeable, carbonate, oxides of Fe and Mn, organic matter and residual fractions were determined. For all fractions ICPMS analyses were carried out. In these analyses Li, Na, Mg, K, Ca, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Sr, Mo, Cd, Cs and Pb were determined. In addition six profiles were taken from the surroundings of two excavator pits for the 137Cs determination. Besides the samples taken for the characterization of soil, supplement samples were taken from the same layers for the separation of soil water. From the soil water pH, DOC, anions (F, Cl, NO{sub 3}, SO{sub 4}) and cations (Na, Mg, K, Ca, Al, Cr, Mn, Fe, Ni, Cu, Zn, As, S, Cd, Cs, Pb, U) were determined. (orig.)

  6. Assessment of the occurrence and richness of arbuscular mycorrhizal fungal spores by direct analysis of field samples and trap culture - a comparative study.

    Science.gov (United States)

    Leal, Patrícia L; Carvalho, Teotonio S DE; Siqueira, José Oswaldo; Moreira, Fatima M S

    2017-08-07

    In this work, we hypothesized that two spore-based methods, direct analysis of field samples and trap cultures, simultaneously used for assessment of occurrence and species richness of arbuscular mycorrhizal fungi (AMF) may vary in their efficiency according to the environmental conditions and the total AMF species richness of the evaluated ecosystem. The performance of both methods was analyzed based on two datasets: 1) a complete site x species matrix compiled from two studies in different land uses in the Amazon using direct analysis of field samples and trap cultures. 2) Total number of AMF morphotypes detected by both methods in published manuscripts across several ecosystems. From dataset 1, direct analysis of field samples revealed 57 morphotypes, whereas only 21 of these were detected by trap culture. Community variation (beta diversity) analysis revealed that field samples are far more sensitive in detecting shifts in AMF community composition among land uses than trap cultures in the Amazon region, with the combined results of both methods being not better than that obtained only by direct analysis of field samples. Analysis of dataset 2 showed that the relative performance of trap cultures, using direct analysis of field sample as reference, was inversely related to the total observed AMF species richness.

  7. Can stature be estimated from tooth crown dimensions? A study in a sample of South-East Asians.

    Science.gov (United States)

    Hossain, Mohammad Zakir; Munawar, Khalil M M; Rahim, Zubaidah H A; Bakri, Marina Mohd

    2016-04-01

    Stature estimation is an important step during medico-legal and forensic examination. Difficulty arises when highly decomposed and mutilated dead bodies with fragmentary remains are brought for forensic identification like in mass disaster or airplane crash. The body remains could be just a jaw with some teeth. The objective of this study was to explore if the stature of an individual can be determined from the tooth crown dimensions. A total of 201 volunteers participated in this study. The stature and clinical crown dimensions (length, mesiodistal and labiolingual diameters) of maxillary anterior teeth were measured. Correlation between crown dimensions and stature was analyzed by Pearson correlation test. Regression analysis was used to get equations for estimation of stature from crown measurements. The regression equations were applied in the same sample of volunteers that was used to obtain the equations. The reliability and accuracy of the equations were checked in another sample of volunteers. Length and mesiodistal diameter of the crown of central incisors and canines showed significant albeit low to moderate correlations (0.35-0.45) with the stature. The correlation co-efficient values were higher (as high as 0.537) when summation of the measurements was taken for analysis. The regression equations when applied to the same and a test sample of volunteers revealed that differences between actual and estimated stature can be as low as 0.01 to as much as 16.50cm. The findings suggest that although there are some degrees of positive correlations between stature and tooth crown dimensions, stature estimation from the tooth crown dimensions cannot provide the accuracy of estimation as required in forensic situations. The stature estimation accuracy using tooth crown dimensions is comparable to that of cephalo-facial dimensions but inferior to that of long bones. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Genesis Solar Wind Collector Cleaning Assessment: Update on 60336 Sample Case Study

    Science.gov (United States)

    Goreva, Y. S.; Allums, K. K.; Gonzalez, C. P.; Jurewicz, A. J.; Burnett, D. S.; Allton, J. H.; Kuhlman, K. R.; Woolum, D.

    2015-01-01

    To maximize the scientific return of Genesis Solar Wind return mission it is necessary to characterize and remove a crash-derived particle and thin film surface contamination. A small subset of Genesis mission collector fragments are being subjected to extensive study via various techniques. Here we present an update on the sample 60336, a Czochralski silicon (Si-CZ) based wafer from the bulk array (B/C). This sample has undergone multiple cleaning steps (see the table below): UPW spin wash, aggressive chemical cleanings (including aqua regia, hot xylene and RCA1), as well as optical and chemical (EDS, ToF-SIMS) imaging. Contamination appeared on the surface of 60336 after the initial 2007 UPW cleaning. Aqua regia and hot xylene treatment (8/13/2013) did little to remove contaminants. The sample was UPW cleaned for the third time and imaged (9/16/13). The UPW removed the dark stains that were visible on the sample. However, some features, like "the Flounder" (a large, 100 micron feature in Fig. 1b) appeared largely intact, resisting all previous cleaning efforts. These features were likely from mobilized adhesive, derived from the Post-It notes used to stabilize samples for transport from Utah after the hard landing. To remove this contamination, an RCA step 1 organic cleaning (RCA1) was employed. Although we are still uncertain on the nature of the Flounder and why it is resistant to UPW and aqua regia/hot xylene treatment, we have found RCA1 to be suitable for its removal. It is likely that the glue from sticky pads used during collector recovery may have been a source for resistant organic contamination [9]; however [8] shows that UPW reaction with crash-derived organic contamination does not make particle removal more difficult.

  9. Free amino acids in the Arctic snow and ice core samples: Potential markers for paleoclimatic studies.

    Science.gov (United States)

    Barbaro, Elena; Spolaor, Andrea; Karroca, Ornela; Park, Ki-Tae; Martma, Tõnu; Isaksson, Elisabeth; Kohler, Jack; Gallet, Jean Charles; Bjorkman, Mats P; Cappelletti, David; Spreen, Gunnar; Zangrando, Roberta; Barbante, Carlo; Gambaro, Andrea

    2017-12-31

    The role of oceanic primary production on climate variability has long been debated. Defining changes in past oceanic primary production can help understanding of the important role that marine algae have in climate variability. In ice core research methanesulfonic acid is the chemical marker commonly used for assessing changes in past primary production. However, other organic compounds such as amino acids, can be produced and emitted into the atmosphere during a phytoplankton bloom. These species can be transported and deposited onto the ice cap in polar regions. Here we investigate the correlation between the concentration of chlorophyll-a, marker of marine primary production, and amino acids present in an ice core. For the first time, free l- and d-amino acids in Arctic snow and firn samples were determined by a sensitive and selective analytical method based on liquid chromatography coupled with tandem mass spectrometry. The new method for the determination of free amino acids concentrations was applied to firn core samples collected on April 2015 from the summit of the Holtedahlfonna glacier, Svalbard (N 79'08.424, E 13'23.639, 1120m a.s.l.). The main results of this work are summarized as follows: (1) glycine, alanine and proline, were detected and quantified in the firn core samples; (2) their concentration profiles, compared with that of the stable isotope δ18O ratio, show a seasonal cycling with the highest concentrations during the spring and summer time; (3) back-trajectories and Greenland Sea chlorophyll-a concentrations obtained by satellite measurements were compared with the amino acids profile obtained from ice core samples, this provided further insights into the present results. This study suggests that the amino acid concentrations in the ice samples collected from the Holtedahlfonna glaciers could reflect changes in oceanic phytoplankton abundance. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Plurality of Linguistic Communication as Revealed by Media Studies and a Social Differentiation Theory

    OpenAIRE

    柳瀬, 陽介

    2011-01-01

    With the use of unanalyzed terms, discourse on English Language Teaching in Japan is often too simplistic. The current paper examines media studies and sociological studies to establish an analytical framework for the discourse on ELT. Media studies provide six stages of language use: primary orality; proto-writing literacy; manuscript literacy; print literacy; second orality; and multitude-media literacy. Luhman's sociological theory distinguishes four types of differentiation: segmentary; c...

  11. Prevalence and predictors of Video Game Addiction: A study based on a national sample of Gamers.

    OpenAIRE

    Wittek, CT; Finserås, TR; Pallesen, S; Mentzoni, RA; Hanss, D; Griffiths, MD; Molde, H

    2015-01-01

    Video gaming has become a popular leisure activity in many parts of the world, and an increasing number of empirical studies examine the small minority that appears to develop problems as a result of excessive gaming. This study investigated prevalence rates and predictors of video game addiction in a sample of gamers, randomly selected from the National Population Registry of Norway (N?=?3389). Results showed there were 1.4 % addicted gamers, 7.3 % problem gamers, 3.9 % engaged gamers, and 8...

  12. Prediction accuracy of a sample-size estimation method for ROC studies.

    Science.gov (United States)

    Chakraborty, Dev P

    2010-05-01

    Sample-size estimation is an important consideration when planning a receiver operating characteristic (ROC) study. The aim of this work was to assess the prediction accuracy of a sample-size estimation method using the Monte Carlo simulation method. Two ROC ratings simulators characterized by low reader and high case variabilities (LH) and high reader and low case variabilities (HL) were used to generate pilot data sets in two modalities. Dorfman-Berbaum-Metz multiple-reader multiple-case (DBM-MRMC) analysis of the ratings yielded estimates of the modality-reader, modality-case, and error variances. These were input to the Hillis-Berbaum (HB) sample-size estimation method, which predicted the number of cases needed to achieve 80% power for 10 readers and an effect size of 0.06 in the pivotal study. Predictions that generalized to readers and cases (random-all), to cases only (random-cases), and to readers only (random-readers) were generated. A prediction-accuracy index defined as the probability that any single prediction yields true power in the 75%-90% range was used to assess the HB method. For random-case generalization, the HB-method prediction-accuracy was reasonable, approximately 50% for five readers and 100 cases in the pilot study. Prediction-accuracy was generally higher under LH conditions than under HL conditions. Under ideal conditions (many readers in the pilot study) the DBM-MRMC-based HB method overestimated the number of cases. The overestimates could be explained by the larger modality-reader variance estimates when reader variability was large (HL). The largest benefit of increasing the number of readers in the pilot study was realized for LH, where 15 readers were enough to yield prediction accuracy >50% under all generalization conditions, but the benefit was lesser for HL where prediction accuracy was approximately 36% for 15 readers under random-all and random-reader conditions. The HB method tends to overestimate the number of cases

  13. Bovine liver sample preparation and micro-homogeneity study for Cu and Zn determination by solid sampling electrothermal atomic absorption spectrometry

    Science.gov (United States)

    Nomura, Cassiana S.; Silva, Cíntia S.; Nogueira, Ana R. A.; Oliveira, Pedro V.

    2005-06-01

    This work describes a systematic study for the bovine liver sample preparation for Cu and Zn determination by solid sampling electrothermal atomic absorption spectrometry. The main parameters investigated were sample drying, grinding process, particle size, sample size, microsample homogeneity, and their relationship with the precision and accuracy of the method. A bovine liver sample was prepared using different drying procedures: (1) freeze drying, and (2) drying in a household microwave oven followed by drying in a stove at 60 °C until constant mass. Ball and cryogenic mills were used for grinding. Less sensitive wavelengths for Cu (216.5 nm) and Zn (307.6 nm), and Zeeman-based three-field background correction for Cu were used to diminish the sensitivities. The pyrolysis and atomization temperatures adopted were 1000 °C and 2300 °C for Cu, and 700 °C and 1700 °C for Zn, respectively. For both elements, it was possible to calibrate the spectrometer with aqueous solutions. The use of 250 μg of W + 200 μg of Rh as permanent chemical modifier was imperative for Zn. Under these conditions, the characteristic mass and detection limit were 1.4 ng and 1.6 ng for Cu, and 2.8 ng and 1.3 ng for Zn, respectively. The results showed good agreement (95% confidence level) for homogeneity of the entire material (> 200 mg) when the sample was dried in microwave/stove and ground in a cryogenic mill. The microsample homogeneity study showed that Zn is more dependent on the sample pretreatment than Cu. The bovine liver sample prepared in microwave/stove and ground in a cryogenic mill presented results with the lowest relative standard deviation for Cu than Zn. Good accuracy and precision were observed for bovine liver masses higher than 40 μg for Cu and 30 μg for Zn. The concentrations of Cu and Zn in the prepared bovine liver sample were 223 mg kg - 1 and 128 mg kg - 1, respectively. The relative standard deviations were lower than 6% ( n = 5). The accuracy of the entire

  14. The Predictive Validity of Four Intelligence Tests for School Grades: A Small Sample Longitudinal Study.

    Science.gov (United States)

    Gygi, Jasmin T; Hagmann-von Arx, Priska; Schweizer, Florine; Grob, Alexander

    2017-01-01

    Intelligence is considered the strongest single predictor of scholastic achievement. However, little is known regarding the predictive validity of well-established intelligence tests for school grades. We analyzed the predictive validity of four widely used intelligence tests in German-speaking countries: The Intelligence and Development Scales (IDS), the Reynolds Intellectual Assessment Scales (RIAS), the Snijders-Oomen Nonverbal Intelligence Test (SON-R 6-40), and the Wechsler Intelligence Scale for Children (WISC-IV), which were individually administered to 103 children (Mage = 9.17 years) enrolled in regular school. School grades were collected longitudinally after 3 years (averaged school grades, mathematics, and language) and were available for 54 children (Mage = 11.77 years). All four tests significantly predicted averaged school grades. Furthermore, the IDS and the RIAS predicted both mathematics and language, while the SON-R 6-40 predicted mathematics. The WISC-IV showed no significant association with longitudinal scholastic achievement when mathematics and language were analyzed separately. The results revealed the predictive validity of currently used intelligence tests for longitudinal scholastic achievement in German-speaking countries and support their use in psychological practice, in particular for predicting averaged school grades. However, this conclusion has to be considered as preliminary due to the small sample of children observed.

  15. The Predictive Validity of Four Intelligence Tests for School Grades: A Small Sample Longitudinal Study

    Science.gov (United States)

    Gygi, Jasmin T.; Hagmann-von Arx, Priska; Schweizer, Florine; Grob, Alexander

    2017-01-01

    Intelligence is considered the strongest single predictor of scholastic achievement. However, little is known regarding the predictive validity of well-established intelligence tests for school grades. We analyzed the predictive validity of four widely used intelligence tests in German-speaking countries: The Intelligence and Development Scales (IDS), the Reynolds Intellectual Assessment Scales (RIAS), the Snijders-Oomen Nonverbal Intelligence Test (SON-R 6-40), and the Wechsler Intelligence Scale for Children (WISC-IV), which were individually administered to 103 children (Mage = 9.17 years) enrolled in regular school. School grades were collected longitudinally after 3 years (averaged school grades, mathematics, and language) and were available for 54 children (Mage = 11.77 years). All four tests significantly predicted averaged school grades. Furthermore, the IDS and the RIAS predicted both mathematics and language, while the SON-R 6-40 predicted mathematics. The WISC-IV showed no significant association with longitudinal scholastic achievement when mathematics and language were analyzed separately. The results revealed the predictive validity of currently used intelligence tests for longitudinal scholastic achievement in German-speaking countries and support their use in psychological practice, in particular for predicting averaged school grades. However, this conclusion has to be considered as preliminary due to the small sample of children observed. PMID:28348543

  16. Comprehensive Pharmacogenomic Study Reveals an Important Role of UGT1A3 in Montelukast Pharmacokinetics.

    Science.gov (United States)

    Hirvensalo, Päivi; Tornio, Aleksi; Neuvonen, Mikko; Tapaninen, Tuija; Paile-Hyvärinen, Maria; Kärjä, Vesa; Männistö, Ville T; Pihlajamäki, Jussi; Backman, Janne T; Niemi, Mikko

    2017-09-23

    To identify the genetic basis of interindividual variability in montelukast exposure, we determined its pharmacokinetics and sequenced 379 pharmacokinetic genes in 191 healthy volunteers. An intronic single nucleotide variation (SNV), strongly linked with UGT1A3*2, associated with reduced area under the plasma concentration-time curve (AUC0-∞ ) of montelukast (by 18% per copy of the minor allele; P = 1.83 × 10(-10) ). UGT1A3*2 was associated with increased AUC0-∞ of montelukast acyl-glucuronide M1 and decreased AUC0-∞ of hydroxymetabolites M5R, M5S, and M6 (P montelukast. The found UGT1A3 and ABCC9 variants associated with increased expression of the respective genes in human liver samples. Montelukast and its hydroxymetabolites were glucuronidated by UGT1A3 in vitro. These results indicate that UGT1A3 plays an important role in montelukast pharmacokinetics, especially in UGT1A3*2 carriers. © 2017, The Authors Clinical Pharmacology & Therapeutics published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

  17. Microbial Safety of Low Water Activity Foods: Study of Simulated and Durban Household Samples

    Directory of Open Access Journals (Sweden)

    O. A. Ijabadeniyi

    2017-01-01

    Full Text Available Sixty household low water activity foods were examined and a simulative study was conducted in a high sugar, low aw almond and macadamia butter to determine the survival of Bacillus cereus and Staphylococcus aureus ATCC 25923. Results obtained from 60 low aw samples collected at household level had some significant differences (P≤0,05 within food categories amongst the various tests. Spices had the highest number of aerobic bacteria, aerobic spore-formers, anaerobic spore-formers, and S. aureus. Mean aerobic colony counts for nuts and spices were 2.30 log CFU/g and 4.40 log CFU/g, respectively. Pathogens such as Escherichia coli and Cronobacter sakazakii were present in nuts, whilst Salmonella spp. was present in chocolates. This implies that certain low aw foods may present a public health risk. In the simulative study, temperature and high sucrose concentrations played a significant role in the survival of B. cereus and S. aureus ATCC 25923. B. cereus was found to be more osmotolerant at both reduced and elevated temperatures (18°C and 25°C in the 12% sucrose sample in both butters, whilst S. aureus ATCC 25923 seemed to grow better in sucrose-free samples at both temperatures in both butters. This implies that certain low aw foods may present a public health risk. Also, B. cereus, being a spore-forming bacterium, can be osmotolerant at both reduced and elevated temperatures.

  18. Studies on spectral analysis of randomly sampled signals: Application to laser velocimetry data

    Science.gov (United States)

    Sree, David

    1992-01-01

    Spectral analysis is very useful in determining the frequency characteristics of many turbulent flows, for example, vortex flows, tail buffeting, and other pulsating flows. It is also used for obtaining turbulence spectra from which the time and length scales associated with the turbulence structure can be estimated. These estimates, in turn, can be helpful for validation of theoretical/numerical flow turbulence models. Laser velocimetry (LV) is being extensively used in the experimental investigation of different types of flows, because of its inherent advantages; nonintrusive probing, high frequency response, no calibration requirements, etc. Typically, the output of an individual realization laser velocimeter is a set of randomly sampled velocity data. Spectral analysis of such data requires special techniques to obtain reliable estimates of correlation and power spectral density functions that describe the flow characteristics. FORTRAN codes for obtaining the autocorrelation and power spectral density estimates using the correlation-based slotting technique were developed. Extensive studies have been conducted on simulated first-order spectrum and sine signals to improve the spectral estimates. A first-order spectrum was chosen because it represents the characteristics of a typical one-dimensional turbulence spectrum. Digital prefiltering techniques, to improve the spectral estimates from randomly sampled data were applied. Studies show that the spectral estimates can be increased up to about five times the mean sampling rate.

  19. Organic Compounds Detected in Deciduous Teeth: A Replication Study from Children with Autism in Two Samples

    Directory of Open Access Journals (Sweden)

    Raymond F. Palmer

    2015-01-01

    Full Text Available Biological samples are an important part of investigating toxic exposures and disease outcomes. However, blood, urine, saliva, or hair can only reflect relatively recent exposures. Alternatively, deciduous teeth have served as a biomarker of early developmental exposure to heavy metals, but little has been done to assess organic toxic exposures such as pesticides, plastics, or medications. The purpose of our study was to determine if organic chemicals previously detected in a sample of typically developing children could be detected in teeth from a sample of children with autism. Eighty-three deciduous teeth from children with autism spectrum disorders (ASD were chosen from our tooth repository. Organic compounds were assessed using liquid chromatography tandem mass spectrometry and gas chromatography methods. Consistent with a prior report from Camann et al., (2013, we have demonstrated that specific semivolatile organic chemicals relevant to autism etiology can be detected in deciduous teeth. This report provides evidence that teeth can be useful biomarkers of early life exposure for use in epidemiologic case-control studies seeking to identify differential unbiased exposures during development between those with and without specific disorders such as autism.

  20. A detailed study of the performance of the uranium-gas sampling calorimeter

    Energy Technology Data Exchange (ETDEWEB)

    Arefiev, A.; Burov, S.; Chumakov, M.; Galaktionov, Yu.; Gordeev, A.; Gorodkov, Yu.; Kamyshkov, Yu.; Klimentov, A.; Koutsenko, V.; Kunin, A.; Malinin, A.; Morgunov, V.; Plyaskin, V.; Pojidaev, V.; Rozhkov, A.; Savin, A.; Shevchenko, S.; Shevchenko, V.; Shmakov, K.; Shoutko, V.; Shumilov, E.; Tarkovsky, E.; Tchoudakov, V.; Vorobiev, I. (Institut Teoreticheskoj i Ehksperimental' noj Fiziki, Moscow (USSR)); Azemoon, T.; Bal, R.; Capell, M.; Goldfarb, S.; Jones, L.W.; Mills, G.B.; Roe, B.P. (Michigan Univ., Ann Arbor (USA)); Chen, H.S.; Lu, Y.S.; Tung, K.L. (Academia Sinica, Beijing (China). Inst. of High Energy Physics); Chen, M.; Ting, S.C.C. (Massachusetts Inst. of Tech., Cambridge (USA)); Gong, Z.F. (CCAST World Lab., Beijing, BJ (China) China Univ. of Science and Technology, Hefei, AH); Lecomte, P.; LeCoultre, P.; Lettry, J.; Lin, Z.R.; Spiess, B. (Eidgenoessische Technische Hochschule, Zurich (Switzerland)); Ulbricht, J. (Paul Scherrer Inst., Wuerenlingen (Switzerland)); L3 Collaboration

    1989-12-20

    Results of experimental studies of the performance of the uranium calorimeter with gas sampling detectors are presented. There is further evidence showing the importance of the contribution of the neutron component of a hadronic shower to the detected signal. The response and the resolution of the uranium calorimeter are measured in the momentum range 0.3-0.6 GeV/c for the different incident particles and different gases that are used in the detectors. For a calorimeter structure with double-gas-detector layers, the correlation between signals from two calorimeters formed by chambers filled with different gas mixtures is measured. The topics that are relevant to the performance of the L3 uranium-gas sampling calorimeter - such as its operation in the magnetic field, the energy dependence of muon response, the uranium noise, as well as the electronics optimization - are discussed. (orig.).

  1. Preparation of Samples for Leaf Architecture Studies, A Method for Mounting Cleared Leaves

    Directory of Open Access Journals (Sweden)

    Alejandra Vasco

    2014-09-01

    Full Text Available Premise of the study: Several recent waves of interest in leaf architecture have shown an expanding range of approaches and applications across a number of disciplines. Despite this increased interest, examination of existing archives of cleared and mounted leaves shows that current methods for mounting, in particular, yield unsatisfactory results and deterioration of samples over relatively short periods. Although techniques for clearing and staining leaves are numerous, published techniques for mounting leaves are scarce. Methods and Results: Here we present a complete protocol and recommendations for clearing, staining, and imaging leaves, and, most importantly, a method to permanently mount cleared leaves. Conclusions: The mounting protocol is faster than other methods, inexpensive, and straightforward; moreover, it yields clear and permanent samples that can easily be imaged, scanned, and stored. Specimens mounted with this method preserve well, with leaves that were mounted more than 35 years ago showing no signs of bubbling or discoloration.

  2. A study of high-redshift AGN feedback in SZ cluster samples

    Science.gov (United States)

    Bîrzan, L.; Rafferty, D. A.; Brüggen, M.; Intema, H. T.

    2017-10-01

    We present a study of active galactic nucleus (AGN) feedback at higher redshifts (0.3 HERGs) in massive clusters at z > 0.6, implying a transition from HERG-mode accretion to lower power low-excitation radio galaxy (LERG)-mode accretion at intermediate redshifts. Additionally, we use local radio-to-jet power scaling relations to estimate feedback power and find that half of the CF systems in our sample probably have enough heating to balance cooling. However, we postulate that the local relations are likely not well suited to predict feedback power in high-luminosity HERGs, as they are derived from samples composed mainly of lower luminosity LERGs.

  3. Municipal solid waste composition: Sampling methodology, statistical analyses, and case study evaluation

    DEFF Research Database (Denmark)

    Edjabou, Vincent Maklawe Essonanawe; Jensen, Morten Bang; Götze, Ramona

    2015-01-01

    stratification parameter. Separating food leftovers from food packaging during manual sorting of the sampled waste did not have significant influence on the proportions of food waste and packaging materials, indicating that this step may not be required. (C) 2014 Elsevier Ltd. All rights reserved.......Sound waste management and optimisation of resource recovery require reliable data on solid waste generation and composition. In the absence of standardised and commonly accepted waste characterisation methodologies, various approaches have been reported in literature. This limits both...... comparability and applicability of the results. In this study, a waste sampling and sorting methodology for efficient and statistically robust characterisation of solid waste was introduced. The methodology was applied to residual waste collected from 1442 households distributed among 10 individual sub...

  4. Study of carbon compounds in Apollo 12 and 14 lunar samples.

    Science.gov (United States)

    Holland, P. T.; Simoneit, B. R.; Wszolek, P. C.; Burlingame, A. L.

    1972-01-01

    The results of gas-chromatography and high-resolution mass spectroscopy studies of gases released on deuterium fluoride dissolution of Apollo 12 and 14 lunar samples are reported. The results confirm previous observations that CH4 and C2H6 are released as well as CD4, C2D4, C2D6, and higher deuterated hydrocarbons. The yields correlate with the total carbon content of the samples, and the CH4 and C2H6 released may be regarded as indigenous, while the deuterated products result from hydrolysis of carbide material. The results provide the first experimental confirmation of the hypothesis that the CH4 derives from solar wind interactions.

  5. A comparison of different estimation methods for simulation-based sample size determination in longitudinal studies

    Science.gov (United States)

    Bahçecitapar, Melike Kaya

    2017-07-01

    Determining sample size necessary for correct results is a crucial step in the design of longitudinal studies. Simulation-based statistical power calculation is a flexible approach to determine number of subjects and repeated measures of longitudinal studies especially in complex design. Several papers have provided sample size/statistical power calculations for longitudinal studies incorporating data analysis by linear mixed effects models (LMMs). In this study, different estimation methods (methods based on maximum likelihood (ML) and restricted ML) with different iterative algorithms (quasi-Newton and ridge-stabilized Newton-Raphson) in fitting LMMs to generated longitudinal data for simulation-based power calculation are compared. This study examines statistical power of F-test statistics for parameter representing difference in responses over time from two treatment groups in the LMM with a longitudinal covariate. The most common procedures in SAS, such as PROC GLIMMIX using quasi-Newton algorithm and PROC MIXED using ridge-stabilized algorithm are used for analyzing generated longitudinal data in simulation. It is seen that both procedures present similar results. Moreover, it is found that the magnitude of the parameter of interest in the model for simulations affect statistical power calculations in both procedures substantially.

  6. Electron cryotomography studies of maturing HIV-1 particles reveal the assembly pathway of the viral core.

    Science.gov (United States)

    Woodward, Cora L; Cheng, Sarah N; Jensen, Grant J

    2015-01-15

    To better characterize the assembly of the HIV-1 core, we have used electron cryotomography (ECT) to image infected cells and the viral particles cryopreserved next to them. We observed progressive stages of virus assembly and egress, including flower-like flat Gag lattice assemblies, hemispherical budding profiles, and virus buds linked to the plasma membrane via a thin membrane neck. The population of budded viral particles contains immature, maturation-intermediate, and mature core morphologies. Structural characteristics of the maturation intermediates suggest that the core assembly pathway involves the formation of a CA sheet that associates with the condensed ribonucleoprotein (RNP) complex. Our analysis also reveals a correlation between RNP localization within the viral particle and the formation of conical cores, suggesting that the RNP helps drive conical core assembly. Our findings support an assembly pathway for the HIV-1 core that begins with a small CA sheet that associates with the RNP to form the core base, followed by polymerization of the CA sheet along one side of the conical core toward the tip, and then closure around the body of the cone. During HIV-1 assembly and release, the Gag polyprotein is organized into a signature hexagonal lattice, termed the immature lattice. To become infectious, the newly budded virus must disassemble the immature lattice by proteolyzing Gag and then reassemble the key proteolytic product, the structural protein p24 (CA), into a distinct, mature hexagonal lattice during a process termed maturation. The mature HIV-1 virus contains a conical capsid that encloses the condensed viral genome at its wide base. Mutations or small molecules that interfere with viral maturation also disrupt viral infectivity. Little is known about the assembly pathway that results in the conical core and genome encapsidation. Here, we have used electron cryotomography to structurally characterize HIV-1 particles that are actively maturing

  7. Conditions Affecting the Accuracy of Classical Equating Methods for Small Samples under the NEAT Design: A Simulation Study

    Science.gov (United States)

    Sunnassee, Devdass

    2011-01-01

    Small sample equating remains a largely unexplored area of research. This study attempts to fill in some of the research gaps via a large-scale, IRT-based simulation study that evaluates the performance of seven small-sample equating methods under various test characteristic and sampling conditions. The equating methods considered are typically…

  8. Field and laboratory studies reveal interacting effects of stream oxygenation and warming on aquatic ectotherms.

    Science.gov (United States)

    Verberk, Wilco C E P; Durance, Isabelle; Vaughan, Ian P; Ormerod, Steve J

    2016-05-01

    Aquatic ecological responses to climatic warming are complicated by interactions between thermal effects and other environmental stressors such as organic pollution and hypoxia. Laboratory experiments have demonstrated how oxygen limitation can set heat tolerance for some aquatic ectotherms, but only at unrealistic lethal temperatures and without field data to assess whether oxygen shortages might also underlie sublethal warming effects. Here, we test whether oxygen availability affects both lethal and nonlethal impacts of warming on two widespread Eurasian mayflies, Ephemera danica, Müller 1764 and Serratella ignita (Poda 1761). Mayfly nymphs are often a dominant component of the invertebrate assemblage in streams, and play a vital role in aquatic and riparian food webs. In the laboratory, lethal impacts of warming were assessed under three oxygen conditions. In the field, effects of oxygen availability on nonlethal impacts of warming were assessed from mayfly occurrence in 42 293 UK stream samples where water temperature and biochemical oxygen demand were measured. Oxygen limitation affected both lethal and sublethal impacts of warming in each species. Hypoxia lowered lethal limits by 5.5 °C (±2.13) and 8.2 °C (±0.62) for E. danica and S. ignita respectively. Field data confirmed the importance of oxygen limitation in warmer waters; poor oxygenation drastically reduced site occupancy, and reductions were especially pronounced under warm water conditions. Consequently, poor oxygenation lowered optimal stream temperatures for both species. The broad concordance shown here between laboratory results and extensive field data suggests that oxygen limitation not only impairs survival at thermal extremes but also restricts species abundance in the field at temperatures well below upper lethal limits. Stream oxygenation could thus control the vulnerability of aquatic ectotherms to global warming. Improving water oxygenation and reducing pollution can provide

  9. An fMRI Study of Audiovisual Speech Perception Reveals Multisensory Interactions in Auditory Cortex

    National Research Council Canada - National Science Library

    Okada, Kayoko; Venezia, Jonathan H; Matchin, William; Saberi, Kourosh; Hickok, Gregory

    2013-01-01

    .... While previous audiovisual speech studies demonstrate that high-level multisensory interactions occur in pSTS, what remains unclear is how early in the processing hierarchy these multisensory interactions may occur...

  10. Landmark study reveals low national rate of frog abnormalities on Wildlife Refuges

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This U.S. Fish and Wildlife Service news releases announces the publication of an unprecedented 10-year-study of abnormal amphibians on U.S. National Wildlife...

  11. Psychometric properties of the Icelandic NEO-FFI in a general population sample compared to a sample recruited for a study on the genetics of addiction

    DEFF Research Database (Denmark)

    Bjornsdottir, Gyda; Jonsson, Fridrik H.; Hansdottir, Ingunn

    2014-01-01

    . Icelandic norms were compared to American norms and language translations selected for geographical and cultural proximity to Iceland. Multiple discriminant function analysis using NEO-FFI trait scores and gender as independent variables predicted membership in recruitment groups for 47.3% of addiction....... We present results of psychometric testing of the Icelandic NEO-FFI in a population sample (N= 657) and a sample recruited for a study on addiction genetics (N= 3804). The Icelandic NEO-FFI demonstrated internal consistency and temporal stability. Factor analyses supported the five-factor structure...

  12. Economic and Humanistic Burden of Osteoarthritis: A Systematic Review of Large Sample Studies.

    Science.gov (United States)

    Xie, Feng; Kovic, Bruno; Jin, Xuejing; He, Xiaoning; Wang, Mengxiao; Silvestre, Camila

    2016-11-01

    Osteoarthritis (OA) consumes a significant amount of healthcare resources, and impairs the health-related quality of life (HRQoL) of patients. Previous reviews have consistently found substantial variations in the costs of OA across studies and countries. The comparability between studies was poor and limited the detection of the true differences between these studies. To review large sample studies on measuring the economic and/or humanistic burden of OA published since May 2006. We searched MEDLINE and EMBASE databases using comprehensive search strategies to identify studies reporting economic burden and HRQoL of OA. We included large sample studies if they had a sample size ≥1000 and measured the cost and/or HRQoL of OA. Reviewers worked independently and in duplicate, performing a cross-check between groups to verify agreement. Within- and between-group consolidation was performed to resolve discrepancies, with outstanding discrepancies being resolved by an arbitrator. The Kappa statistic was reported to assess the agreement between the reviewers. All costs were adjusted in their original currency to year 2015 using published inflation rates for the country where the study was conducted, and then converted to 2015 US dollars. A total of 651 articles were screened by title and abstract, 94 were reviewed in full text, and 28 were included in the final review. The Kappa value was 0.794. Twenty studies reported direct costs and nine reported indirect costs. The total annual average direct costs varied from US$1442 to US$21,335, both in USA. The annual average indirect costs ranged from US$238 to US$29,935. Twelve studies measured HRQoL using various instruments. The Short Form 12 version 2 scores ranged from 35.0 to 51.3 for the physical component, and from 43.5 to 55.0 for the mental component. Health utilities varied from 0.30 for severe OA to 0.77 for mild OA. Per-patient OA costs are considerable and a patient's quality of life remains poor. Variations in

  13. Environmental monitoring study of linear alkylbenzene sulfonates and insoluble soap in Spanish sewage sludge samples.

    Science.gov (United States)

    Cantarero, Samuel; Zafra-Gómez, Alberto; Ballesteros, Oscar; Navalón, Alberto; Reis, Marco S; Saraiva, Pedro M; Vílchez, José L

    2011-01-01

    In this work we present a monitoring study of linear alkylbenzene sulfonates (LAS) and insoluble soap performed on Spanish sewage sludge samples. This work focuses on finding statistical relations between LAS concentrations and insoluble soap in sewage sludge samples and variables related to wastewater treatment plants such as water hardness, population and treatment type. It is worth to mention that 38 samples, collected from different Spanish regions, were studied. The statistical tool we used was Principal Component Analysis (PC), in order to reduce the number of response variables. The analysis of variance (ANOVA) test and a non-parametric test such as the Kruskal-Wallis test were also studied through the estimation of the p-value (probability of obtaining a test statistic at least as extreme as the one that was actually observed, assuming that the null hypothesis is true) in order to study possible relations between the concentration of both analytes and the rest of variables. We also compared LAS and insoluble soap behaviors. In addition, the results obtained for LAS (mean value) were compared with the limit value proposed by the future Directive entitled "Working Document on Sludge". According to the results, the mean obtained for soap and LAS was 26.49 g kg(-1) and 6.15 g kg(-1) respectively. It is worth noting that LAS mean was significantly higher than the limit value (2.6 g kg(-1)). In addition, LAS and soap concentrations depend largely on water hardness. However, only LAS concentration depends on treatment type.

  14. Observed mass distribution of spontaneous fission fragments from samples of lime - an SSNTD study

    CERN Document Server

    Paul, D; Ghose, D; Sastri, R C

    1999-01-01

    SSNTD is one of the most commonly used detectors in the studies involving nuclear phenomena. The ease of registration of the presence of alpha particles and fission fragments has made it particularly suitable in studies where stable long exposures are needed to extract reliable information. Studies on the presence of alpha emitting nuclides in the environment assume importance since they are found to be carcinogenic. Lime samples from Silchar in Assam of Eastern India have shown the presence of spontaneous fission fragments besides alphas. In the present study we look at the ratio of the average mass distribution of these fission fragments, that gives us an indication of the presence of the traces of transuranic elements.

  15. Study of microtip-based extraction and purification of DNA from human samples for portable devices

    Science.gov (United States)

    Fotouhi, Gareth

    DNA sample preparation is essential for genetic analysis. However, rapid and easy-to-use methods are a major challenge to obtaining genetic information. Furthermore, DNA sample preparation technology must follow the growing need for point-of-care (POC) diagnostics. The current use of centrifuges, large robots, and laboratory-intensive protocols has to be minimized to meet the global challenge of limited access healthcare by bringing the lab to patients through POC devices. To address these challenges, a novel extraction method of genomic DNA from human samples is presented by using heat-cured polyethyleneimine-coated microtips generating a high electric field. The microtip extraction method is based on recent work using an electric field and capillary action integrated into an automated device. The main challenges to the method are: (1) to obtain a stable microtip surface for the controlled capture and release of DNA and (2) to improve the recovery of DNA from samples with a high concentration of inhibitors, such as human samples. The present study addresses these challenges by investigating the heat curing of polyethyleneimine (PEI) coated on the surface of the microtip. Heat-cured PEI-coated microtips are shown to control the capture and release of DNA. Protocols are developed for the extraction and purification of DNA from human samples. Heat-cured PEI-coated microtip methods of DNA sample preparation are used to extract genomic DNA from human samples. It is discovered through experiment that heat curing of a PEI layer on a gold-coated surface below 150°C could inhibit the signal of polymerase chain reaction (PCR). Below 150°C, the PEI layer is not completely cured and dissolved off the gold-coated surface. Dissolved PEI binds with DNA to inhibit PCR. Heat curing of a PEI layer above 150°C on a gold-coated surface prevents inhibition to PCR and gel electrophoresis. In comparison to gold-coated microtips, the 225°C-cured PEI-coated microtips improve the

  16. A general method to determine sampling windows for nonlinear mixed effects models with an application to population pharmacokinetic studies.

    Science.gov (United States)

    Foo, Lee Kien; McGree, James; Duffull, Stephen

    2012-01-01

    Optimal design methods have been proposed to determine the best sampling times when sparse blood sampling is required in clinical pharmacokinetic studies. However, the optimal blood sampling time points may not be feasible in clinical practice. Sampling windows, a time interval for blood sample collection, have been proposed to provide flexibility in blood sampling times while preserving efficient parameter estimation. Because of the complexity of the population pharmacokinetic models, which are generally nonlinear mixed effects models, there is no analytical solution available to determine sampling windows. We propose a method for determination of sampling windows based on MCMC sampling techniques. The proposed method attains a stationary distribution rapidly and provides time-sensitive windows around the optimal design points. The proposed method is applicable to determine sampling windows for any nonlinear mixed effects model although our work focuses on an application to population pharmacokinetic models. Copyright © 2012 John Wiley & Sons, Ltd.

  17. Collection, storage, and filtration of in vivo study samples using 96-well filter plates to facilitate automated sample preparation and LC/MS/MS analysis.

    Science.gov (United States)

    Berna, M; Murphy, A T; Wilken, B; Ackermann, B

    2002-03-01

    The benefits of high-throughput bioanalysis within the pharmaceutical industry are well established. One of the most significant bottlenecks in bioanalysis is transferring in vivo-generated study samples from their collection tubes during sample preparation and extraction. In most cases, the plasma samples must be stored frozen prior to analysis, and the freeze/thaw (F/T) process introduces thrombin clots that are capable of plugging pipets and automated liquid-transfer systems. A new approach to dealing with this problem involves the use of Ansys Captiva 96-well 20-microm polypropylene filter plates to collect, store frozen, and filter plasma samples prior to bioanalysis. The samples are collected from the test subjects, and the corresponding plasma samples are placed directly into the wells of the filter plate. Two Duoseal (patent pending) covers are used to seal the top and bottom of the plate, and the plate is stored at down to -70 degrees C. Prior to sample analysis, the seals are removed and the plate is placed in a 96-well SPE manifold. As the plasma thaws, it passes (by gravity or mild vacuum) through the polypropylene filter into a 96-well collection plate. A multichannel pipet or automated liquid-transfer system is used to transfer sample aliquots without fear of plugging. A significant advantage of this approach is that, unlike other methods, issues related to incomplete pipetting are virtually eliminated. The entire process is rapid since thawing and filtering take place simultaneously, and if a second F/T cycle is required for reanalysis, it is not necessary to refilter the samples (additional clotting was not observed after three F/T cycles). This technique was tested using monkey, rat, and dog plasma and sodium heparin and EDTA anticoagulants. To assess the possibility of nonspecific binding to the polypropylene filter, a variety of drug candidates from diverse drug classes were studied. Validation data generated for two Lilly compounds from distinct

  18. Abortion experiences among Zanzibari women: a chain-referral sampling study.

    Science.gov (United States)

    Norris, Alison; Harrington, Bryna J; Grossman, Daniel; Hemed, Maryam; Hindin, Michelle J

    2016-03-11

    In Zanzibar, a semi-autonomous region of Tanzania, induced abortion is illegal but common, and fewer than 12% of married reproductive-aged women use modern contraception. As part of a multi-method study about contraception and consequences of unwanted pregnancies, the objective of this study was to understand the experiences of Zanzibari women who terminated pregnancies. The cross-sectional study was set in Zanzibar, Tanzania. Participants were a community-based sample of women who had terminated pregnancies. We carried out semi-structured interviews with 45 women recruited via chain-referral sampling. We report the characteristics of women who have had abortions, the reasons they had abortions, and the methods used to terminate their pregnancies. Women in Zanzibar terminate pregnancies that are unwanted for a range of reasons, at various points in their reproductive lives, and using multiple methods. While clinical methods were most effective, nearly half of our participants successfully terminated a pregnancy using non-clinical methods and very few had complications requiring post abortion care (PAC). Even in settings where abortion is illegal, some women experience illegal abortions without adverse health consequences, what we might call 'safer' unsafe abortions; these kinds of abortion experiences can be missed in studies about abortion conducted among women seeking PAC in hospitals.

  19. [Identification and sampling of people with migration background for epidemiological studies in Germany].

    Science.gov (United States)

    Reiss, K; Makarova, N; Spallek, J; Zeeb, H; Razum, O

    2013-06-01

    In 2009, 19.6% of the population of Germany either had migrated themselves or were the offspring of people with migration experience. Migrants differ from the autochthonous German population in terms of health status, health awareness and health behaviour. To further investigate the health situation of migrants in Germany, epidemiological studies are needed. Such studies can employ existing databases which provide detailed information on migration status. Otherwise, onomastic or toponomastic procedures can be applied to identify people with migration background. If migrants have to be recruited into an epidemiological study, this can be done register-based (e. g., data from registration offices or telephone lists), based on residential location (random-route or random-walk procedure), via snowball sampling (e. g., through key persons) or via settings (e. g., school entry examination). An oversampling of people with migration background is not sufficient to avoid systematic bias in the sample due to non-participation. Additional measures have to be taken to increase access and raise participation rates. Personal contacting, multilingual instruments, multilingual interviewers and extensive public relations increase access and willingness to participate. Empirical evidence on 'successful' recruitment strategies for studies with migrants is still lacking in epidemiology and health sciences in Germany. The choice of the recruitment strategy as well as the measures to raise accessibility and willingness to participate depend on the available resources, the research question and the specific migrant target group. © Georg Thieme Verlag KG Stuttgart · New York.

  20. The Study of Suicidal Behaviors Rates in the Community Sample of Karaj City in 2005

    Directory of Open Access Journals (Sweden)

    S.K. Malakouti

    2008-04-01

    Full Text Available Introduction & Objective: Although many studies have been conducted in Iran, but because of the importance of suicide problem in the mental health programs, it is still necessary to do some epidemiologic study. This study has addressed to suicidal behaviors rates in a community sample of Karaj city.Materials & Methods: Karaj with 1,000,000 population was selected as the environment of study. Our subjects (no=2300 were 15 years and older that were selected by randomized sampling. SUPRE-MISS questionnaire was employed in this survey.Results: 65% of the subjects were female, 57.2% of them were married , and most of them had high school level of education (48%. Housewife women were the most common category among occupational groups (43.3%. According to the results the prevalence of positive history for suicide behaviors (idea, plan, attempt were 12.7%, 6.2% & 3.3% respectively, and for current year were 5.7%, 2.9% & 1%.Conclusion: Suicidal behaviors in Iran, in spite of suicide leading to death, have similar prevalence to western countries.

  1. Comprehensive metabolomic study of platelets reveals the expression of discrete metabolic phenotypes during storage

    DEFF Research Database (Denmark)

    Paglia, Giuseppe; Sigurjónsson, Ólafur E; Rolfsson, Óttar

    2014-01-01

    BACKGROUND: Platelet (PLT) concentrates are routinely stored for 5 to 7 days. During storage they exhibit what has been termed PLT storage lesion (PSL), which is evident by a loss of hemostatic function when transfused into patients. The overall goal of this study was to obtain a comprehensive data...... set describing PLT metabolism during storage. STUDY DESIGN AND METHODS: The experimental approach adopted to achieve this goal combined a series of standard assays to monitor the quality of stored PLTs and a deep-coverage metabolomics study using liquid chromatography coupled with mass spectrometry...... not undergo a monotonic decay, but experienced systematic changes in metabolism reflected in three discrete metabolic phenotypes: The first (Days 0-3) was associated with active glycolysis, pentose phosphate pathway, and glutathione metabolism and down regulation of tricarboxylic acid (TCA) cycle. The second...

  2. Multi-study integration of brain cancer transcriptomes reveals organ-level molecular signatures.

    Directory of Open Access Journals (Sweden)

    Jaeyun Sung

    Full Text Available We utilized abundant transcriptomic data for the primary classes of brain cancers to study the feasibility of separating all of these diseases simultaneously based on molecular data alone. These signatures were based on a new method reported herein--Identification of Structured Signatures and Classifiers (ISSAC--that resulted in a brain cancer marker panel of 44 unique genes. Many of these genes have established relevance to the brain cancers examined herein, with others having known roles in cancer biology. Analyses on large-scale data from multiple sources must deal with significant challenges associated with heterogeneity between different published studies, for it was observed that the variation among individual studies often had a larger effect on the transcriptome than did phenotype differences, as is typical. For this reason, we restricted ourselves to studying only cases where we had at least two independent studies performed for each phenotype, and also reprocessed all the raw data from the studies using a unified pre-processing pipeline. We found that learning signatures across multiple datasets greatly enhanced reproducibility and accuracy in predictive performance on truly independent validation sets, even when keeping the size of the training set the same. This was most likely due to the meta-signature encompassing more of the heterogeneity across different sources and conditions, while amplifying signal from the repeated global characteristics of the phenotype. When molecular signatures of brain cancers were constructed from all currently available microarray data, 90% phenotype prediction accuracy, or the accuracy of identifying a particular brain cancer from the background of all phenotypes, was found. Looking forward, we discuss our approach in the context of the eventual development of organ-specific molecular signatures from peripheral fluids such as the blood.

  3. Impact of Freezing Delay Time on Tissue Samples for Metabolomic Studies.

    Science.gov (United States)

    Haukaas, Tonje H; Moestue, Siver A; Vettukattil, Riyas; Sitter, Beathe; Lamichhane, Santosh; Segura, Remedios; Giskeødegård, Guro F; Bathen, Tone F

    2016-01-01

    Metabolic profiling of intact tumor tissue by high-resolution magic angle spinning (HR MAS) MR spectroscopy (MRS) provides important biological information possibly useful for clinical diagnosis and development of novel treatment strategies. However, generation of high-quality data requires that sample handling from surgical resection until analysis is performed using systematically validated procedures. In this study, we investigated the effect of postsurgical freezing delay time on global metabolic profiles and stability of individual metabolites in intact tumor tissue. Tumor tissue samples collected from two patient-derived breast cancer xenograft models (n = 3 for each model) were divided into pieces that were snap-frozen in liquid nitrogen at 0, 15, 30, 60, 90, and 120 min after surgical removal. In addition, one sample was analyzed immediately, representing the metabolic profile of fresh tissue exposed neither to liquid nitrogen nor to room temperature. We also evaluated the metabolic effect of prolonged spinning during the HR MAS experiments in biopsies from breast cancer patients (n = 14). All samples were analyzed by proton HR MAS MRS on a Bruker Avance DRX600 spectrometer, and changes in metabolic profiles were evaluated using multivariate analysis and linear mixed modeling. Multivariate analysis showed that the metabolic differences between the two breast cancer models were more prominent than variation caused by freezing delay time. No significant changes in levels of individual metabolites were observed in samples frozen within 30 min of resection. After this time point, levels of choline increased, whereas ascorbate, creatine, and glutathione (GS) levels decreased. Freezing had a significant effect on several metabolites but is an essential procedure for research and biobank purposes. Furthermore, four metabolites (glucose, glycine, glycerophosphocholine, and choline) were affected by prolonged HR MAS experiment time possibly caused by

  4. Impact of freezing delay time on tissue samples for metabolomic studies

    Directory of Open Access Journals (Sweden)

    Tonje Husby Haukaas

    2016-01-01

    Full Text Available Introduction: Metabolic profiling of intact tumor tissue by high resolution magic angle spinning (HR MAS MR spectroscopy (MRS provides important biological information possibly useful for clinical diagnosis and development of novel treatment strategies. However, generation of high-quality data requires that sample handling from surgical resection until analysis is performed using systematically validated procedures. In this study, we investigated the effect of post-surgical freezing delay time on global metabolic profiles and stability of individual metabolites in intact tumor tissue.Materials and methods: Tumor tissue samples collected from two patient derived breast cancer xenograft models (n=3 for each model were divided into pieces that were snap-frozen in liquid nitrogen at 0, 15, 30, 60, 90, and 120 minutes after surgical removal. In addition, one sample was analysed immediately, representing the metabolic profile of fresh tissue exposed neither to liquid nitrogen nor to room temperature. We also evaluated the metabolic effect of prolonged spinning during the HR MAS experiments in biopsies from breast cancer patiens (n=14. All samples were analyzed by proton HR MAS MRS on a Bruker Avance DRX600 spectrometer, and changes in metabolic profiles were evaluated using multivariate analysis and linear mixed modeling (LMM. Results: Multivariate analysis showed that the metabolic differences between the two breast cancer models were more prominent than variation caused by freezing delay time. No significant changes in levels of individual metabolites were observed in samples frozen within 30 minutes of resection. After this time point, levels of choline increased whereas ascorbate, creatine and glutathione (GS levels decreased. Freezing had a significant effect on several metabolites, but is an essential procedure for research and biobank purposes. Furthermore, four metabolites (glucose, glycine, glycerophosphocholine and choline were affected by

  5. Magnetic Study on Environmental Samples from Guadalajara Mexico for Monitoring of Atmospheric Pollution

    Science.gov (United States)

    Aguilar, B.; Cejudo, R.; Bogalo, M. F.; Rosas-Elguera, J.; Quintana, P.; Bautista, F.; Gogichaishvili, A.; Morales, J.

    2013-05-01

    Guadalajara is the second bigger city in Mexico, catalogued as critical zone because of atmospheric pollution levels. The magnetic methodology has been largely used as an alternative way to evaluate the pollution levels as well as identify the critical points in a given area. In this work, results from chemical analyses and magnetic measurements are presented in order to show the correlation between magnetic signal and the pollution level. We analyzed three kinds of environmental samples: urban soils, urban dust and leaves from ficus benjamina. Samples were taken in 30 sites distributed along a main avenue and two secondary avenues, including three points with very poor traffic influence. We determined a ferromagnetic carrier in most of samples, magnetite probably, since the Tc calculated from the thermomagnetic curves is around 580 °C. The magnetic susceptibility (Xlf) as well as the Saturation Isothermal Remanent Magnetization (SIRM) correlate well with the heavy metals content, specially Pb in urban dusts. These results allowed us to identify the most affected points, by vehicular traffic and industrial emissions. Furthermore, the values obtained for these magnetic parameters are above of those found in other studies for polluted cities in Europe and Asia.

  6. Bosco: Boosting Corrections for Genome-Wide Association Studies With Imbalanced Samples.

    Science.gov (United States)

    Bao, Feng; Deng, Yue; Zhao, Yanyu; Suo, Jinli; Dai, Qionghai

    2017-01-01

    In genome-wide association studies (GWAS), the acquired sequential data may exhibit imbalance structure: abundant control vs. limited case samples. Such sample imbalance issue is particularly serious when investigating rare diseases or common diseases on rare populations. Conventional GWAS methods may suffer from severe statistic biases to the major group, leading to power losses in uncovering true suspicious loci. We introduce a boosting correction method termed as Bosco to deal with such imbalanced problem. Bosco is motivated by the boost learning theory in machine learning and is implemented in a coarse-to-fine learning framework: the coarse step assigns importance scores for all samples in the major group and the fine step calculates P -values by a weighted logistic regression. On simulated data sets, we demonstrate the proposed methods can dramatically improve the discovery power even on extremely imbalanced datasets, with well controlling the false positives. The Bosco is also applied to a genome-scale gastric cancer data set to conduct genome-wide analysis. Our method replicates existing reported findings (from the likelihood ratio test) with high statistical significance and shows the ability to identify new suspicious SNPs.

  7. Performance of a Brazilian population sample in the Boston Diagnostic Aphasia Examination: A pilot study

    Directory of Open Access Journals (Sweden)

    M. Radanovic

    2002-03-01

    Full Text Available Brazilian researchers and health professionals often face the challenge of having to use tests developed in foreign languages and standardized for populations of other countries, especially in the fields of Neuropsychology and Neurolinguistics. This fact promotes a feeling that some scoring systems may be inadequate for our sociocultural reality. In the present study, we describe the performance of a Brazilian population sample submitted to a translated and adapted version of the Boston Diagnostic Aphasia Examination (BDAE. Sixty normal volunteers (21 men and 39 women, all Portuguese native speakers, ranging in age from 15 to 78 years (average 43.7 and with an educational level of 2 to 16 years (average 9.9, were tested using a translated and adapted Portuguese version of the BDAE. Cut-off scores are suggested for our population and the performance of the Brazilian sample is compared to that of American and Colombian samples, with the results being closely similar in all tasks. We also performed a correlation analysis between age, gender and educational level and the influence of these variables on the performance of the subjects. We found no statistically significant differences between genders. Educational level correlated positively with performance, especially in the subtests involving reading and writing. There was a negative correlation between age and performance in two subtests (Visual Confrontation Naming and Sentences to Dictation, but a coexisting effect of educational level could not be ruled out.

  8. Performance of a Brazilian population sample in the Boston Diagnostic Aphasia Examination: a pilot study.

    Science.gov (United States)

    Radanovic, M; Mansur, L L

    2002-03-01

    Brazilian researchers and health professionals often face the challenge of having to use tests developed in foreign languages and standardized for populations of other countries, especially in the fields of Neuropsychology and Neurolinguistics. This fact promotes a feeling that some scoring systems may be inadequate for our sociocultural reality. In the present study, we describe the performance of a Brazilian population sample submitted to a translated and adapted version of the Boston Diagnostic Aphasia Examination (BDAE). Sixty normal volunteers (21 men and 39 women), all Portuguese native speakers, ranging in age from 15 to 78 years (average 43.7) and with an educational level of 2 to 16 years (average 9.9), were tested using a translated and adapted Portuguese version of the BDAE. Cut-off scores are suggested for our population and the performance of the Brazilian sample is compared to that of American and Colombian samples, with the results being closely similar in all tasks. We also performed a correlation analysis between age, gender and educational level and the influence of these variables on the performance of the subjects. We found no statistically significant differences between genders. Educational level correlated positively with performance, especially in the subtests involving reading and writing. There was a negative correlation between age and performance in two subtests (Visual Confrontation Naming and Sentences to Dictation), but a coexisting effect of educational level could not be ruled out.

  9. Conceptual study and key technology development for Mars Aeroflyby sample collection

    Science.gov (United States)

    Fujita, K.; Ozawa, T.; Okudaira, K.; Mikouchi, T.; Suzuki, T.; Takayanagi, H.; Tsuda, Y.; Ogawa, N.; Tachibana, S.; Satoh, T.

    2014-01-01

    Conceptual study of Mars Aeroflyby Sample Collection (MASC) is conducted as a part of the next Mars exploration mission currently entertained in Japan Aerospace Exploration Agency. In the mission scenario, an atmospheric entry vehicle is flown into the Martian atmosphere, collects the Martian dust particles as well as atmospheric gases during the guided hypersonic flight, exits the Martian atmosphere, and is inserted into a parking orbit from which a return system departs for the earth to deliver the dust and gas samples. In order to accomplish a controlled flight and a successful orbit insertion, aeroassist orbit transfer technologies are introduced into the guidance and control system. System analysis is conducted to assess the feasibility and to make a conceptual design, finding that the MASC system is feasible at the minimum system mass of 600 kg approximately. The aerogel, which is one of the candidates for the dust sample collector, is assessed by arcjet heating tests to examine its behavior when exposed to high-temperature gases, as well as by particle impingement tests to evaluate its dust capturing capability.

  10. Comparative study of the extracellular proteome of Sulfolobus species reveals limited secretion

    NARCIS (Netherlands)

    Ellen, Albert F.; Albers, Sonja-Verena; Driessen, Arnold J. M.

    Although a large number of potentially secreted proteins can be predicted on the basis of genomic distribution of signal sequence-bearing proteins, protein secretion in Archaea has barely been studied. A proteomic inventory and comparison of the growth medium proteins in three

  11. Trends that FCS Education Should Address: A Delphi Study Reveals Top 16

    Science.gov (United States)

    Alexander, Karen L.; Davis, Kimberlee

    2011-01-01

    This study used the Delphi method to identify trends of importance to family and consumer sciences (FCS) education. A panel of 21 FCS education experts identified 16 trends and evaluated them by importance, desirability, feasibility, and confidence in validity of the trend. Nutrition appeared as a top priority, followed by consumer economics. The…

  12. The neural substrates of script knowledge deficits as revealed by a PET study in Huntington's disease

    NARCIS (Netherlands)

    Allain, P.; Gaura, V.; Fasotti, L.; Chauvire, V.; Prundean, A.; Sherer-Gagou, C.; Bonneau, D.; Bachoud-Levi, A.C.; Dubas, F.; Remy, P.; Verny, C.

    2011-01-01

    Introduction Previous neuropsychological investigations have suggested that both the prefrontal cortex and the basal ganglia are involved in the management of script event knowledge required in planning behavior. Methods This study was designated to map, the correlations between resting-state brain

  13. The neural substrates of script knowledge deficits as revealed by a PET study in Huntington's disease

    NARCIS (Netherlands)

    Allain, P.; Gaura, V.; Fasotti, L.; Chauvire, V.; Prundean, A.; Sherer-Gagou, C.; Bonneau, D.; Bachoud-Levi, A.C.; Dubas, F.; Remy, P.; Verny, C.

    2011-01-01

    Introduction Previous neuropsychological investigations have suggested that both the prefrontal cortex and the basal ganglia are involved in the management of script event knowledge required in planning behavior. Methods This study was designated to map, the correlations between resting-state

  14. How Can We Explain Poverty? Case Study of Dee Reveals the Complexities

    Science.gov (United States)

    Seccombe, Karen

    2011-01-01

    Many theories have been offered to explain why people are impoverished. This article by Karen Seccombe uses the case study of "Dee," a newly single mother, to explore four of the most common: individualism, social structuralism, the culture of poverty, and fatalism. She concludes that poverty is a highly complex phenomenon, and it is likely that…

  15. The shady past of female boxers – what case studies in the USA reveal

    DEFF Research Database (Denmark)

    Pfister, Gertrud Ursula; Gems, Gerald

    2017-01-01

    This study attempts to rectify the invisibility of female boxers and to narrow a research gap by examining the careers of four prominent female champions who managed to excel in the sport despite the social, psychological and physical restrictions imposed by the gender order of American society...

  16. Four studies of economic behavior : integrating revealed and stated preferences data

    NARCIS (Netherlands)

    de Ree, J.J.

    2010-01-01

    This thesis estimates equivalence scales for Indonesia, proposes a new type of test of the life-cycle model, shows how important economic and demographic characteristics of Dutch households evolve over age, cohorts and time, and studies the decision problem to when and how much to work, save and

  17. The study of fkbp and ubiquitin reveals interesting aspects of Artemia stress history.

    Science.gov (United States)

    Maniatsi, Stefania; Farmaki, Theodora; Abatzopoulos, Theodore J

    2015-08-01

    Research on stress responses in animals has increased greatly during the last decades. Though most studies focus on the cellular and molecular bases of the stress response mechanisms, the ecological and evolutionary aspects of stress responses gain more and more interest. Here, we use species and parthenogenetic strains of the genus Artemia, an extremophile model organism, to study, for the first time, a protein well known for its chaperone activity and its involvement in stress responses. More specifically, transcription and protein accumulation of an FK506-Binding Protein (FKBP) homologue were investigated under heat and salt stresses. Additionally, the mRNA levels of ubiquitin, a heat-inducible protein related to the proteasomal pathway, were quantitated under these conditions. Biochemical and phylogenetic analyses showed that the studied FKBP orthologue is a typical representative of the family that clusters with other crustacean sequences. The expression was increased in both fkbp and ubiquitin genes after salt and heat stresses. However, our results in combination with the fact that Artemia species and parthenogenetic strains, selected for this study, exhibit different heat or salt tolerance provide useful hints about the evolutionary significance of FKBP and ubiquitin. Regarding FKBP, mRNA expression and protein accumulation seem to depend on the environmental conditions and the evolutionary history of each Artemia population while ubiquitin has a clear and more conserved role under heat shock. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. A comparative study of nucleostemin family members in zebrafish reveals specific roles in ribosome biogenesis

    NARCIS (Netherlands)

    Essers, Paul B; Pereboom, Tamara C; Goos, Yvonne J; Paridaen, Judith T; Macinnes, Alyson W

    2014-01-01

    Nucleostemin (NS) is an essential protein for the growth and viability of developmental stem cells. Its functions are multi-faceted, including important roles in ribosome biogenesis and in the p53-induced apoptosis pathway. While NS has been well studied, the functions of its family members GNL2 and

  19. SAMPLE SIZE DETERMINATION IN NON-RADOMIZED SURVIVAL STUDIES WITH NON-CENSORED AND CENSORED DATA

    Directory of Open Access Journals (Sweden)

    S FAGHIHZADEH

    2003-06-01

    Full Text Available Introduction: In survival analysis, determination of sufficient sample size to achieve suitable statistical power is important .In both parametric and non-parametric methods of classic statistics, randomn selection of samples is a basic condition. practically, in most clinical trials and health surveys randomn allocation is impossible. Fixed - effect multiple linear regression analysis covers this need and this feature could be extended to survival regression analysis. This paper is the result of sample size determination in non-randomnized surval analysis with censored and non -censored data. Methods: In non-randomnized survival studies, linear regression with fixed -effect variable could be used. In fact such a regression is conditional expectation of dependent variable, conditioned on independent variable. Likelihood fuction with exponential hazard constructed by considering binary variable for allocation of each subject to one of two comparing groups, stating the variance of coefficient of fixed - effect independent variable by determination coefficient , sample size determination formulas are obtained with both censored and non-cencored data. So estimation of sample size is not based on the relation of a single independent variable but it could be attain the required power for a test adjusted for effect of the other explanatory covariates. Since the asymptotic distribution of the likelihood estimator of parameter is normal, we obtained the variance of the regression coefficient estimator formula then by stating the variance of regression coefficient of fixed-effect variable, by determination coefficient we derived formulas for determination of sample size in both censored and non-censored data. Results: In no-randomnized survival analysis ,to compare hazard rates of two groups without censored data, we obtained an estimation of determination coefficient ,risk ratio and proportion of membership to each group and their variances from

  20. Ligand- and drug-binding studies of membrane proteins revealed through circular dichroism spectroscopy.

    Science.gov (United States)

    Siligardi, Giuliano; Hussain, Rohanah; Patching, Simon G; Phillips-Jones, Mary K

    2014-01-01

    A great number of membrane proteins have proven difficult to crystallise for use in X-ray crystallographic structural determination or too complex for NMR structural studies. Circular dichroism (CD) is a fast and relatively easy spectroscopic technique to study protein conformational behaviour. In this review examples of the applications of CD and synchrotron radiation CD (SRCD) to membrane protein ligand binding interaction studies are discussed. The availability of SRCD has been an important advancement in recent progress, most particularly because it can be used to extend the spectral region in the far-UV region (important for increasing the accuracy of secondary structure estimations) and for working with membrane proteins available in only small quantities for which SRCD has facilitated molecular recognition studies. Such studies have been accomplished by probing in the near-UV region the local tertiary structure of aromatic amino acid residues upon addition of chiral or non-chiral ligands using long pathlength cells of small volume capacity. In particular, this review describes the most recent use of the technique in the following areas: to obtain quantitative data on ligand binding (exemplified by the FsrC membrane sensor kinase receptor); to distinguish between functionally similar drugs that exhibit different mechanisms of action towards membrane proteins (exemplified by secretory phospholipase A2); and to identify suitable detergent conditions to observe membrane protein-ligand interactions using stabilised proteins (exemplified by the antiseptic transporter SugE). Finally, the importance of characterising in solution the conformational behaviour and ligand binding properties of proteins in both far- and near-UV regions is discussed. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding. © 2013.

  1. Importance of sampling design and analysis in animal population studies: a comment on Sergio et al

    Science.gov (United States)

    Kery, M.; Royle, J. Andrew; Schmid, Hans

    2008-01-01

    community studied and the sampling fraction among communities compared should be the same on average, otherwise formal estimation approaches must be applied to avoid misleading inference.

  2. Measurement of Beryllium in Biological Samples by Accelerator Mass Spectrometry: Applications for Studying Chronic Beryllium Disease

    Energy Technology Data Exchange (ETDEWEB)

    Chiarappa-Zucca, M L; Finkel, R C; Martinelli, R E; McAninch, J E; Nelson, D O; Turtletaub, K W

    2004-04-15

    A method using accelerator mass spectrometry (AMS) has been developed for quantifying attomoles of beryllium (Be) in biological samples. This method provides the sensitivity to trace Be in biological samples at very low doses with the purpose of identifying the molecular targets involved in chronic beryllium disease. Proof of the method was tested by administering 0.001, 0.05, 0.5 and 5.0 {micro}g {sup 9}Be and {sup 10}Be by intraperitoneal injection to male mice and removing spleen, liver, femurs, blood, lung, and kidneys after 24 h exposure. These samples were prepared for AMS analysis by tissue digestion in nitric acid, followed by further organic oxidation with hydrogen peroxide and ammonium persulfate and lastly, precipitation of Be with ammonium hydroxide, and conversion to beryllium oxide at 800 C. The {sup 10}Be/{sup 9}Be ratio of the extracted beryllium oxide was measured by AMS and Be in the original sample was calculated. Results indicate that Be levels were dose-dependent in all tissues and the highest levels were measured in the spleen and liver. The measured {sup 10}Be/{sup 9}Be ratios spanned 4 orders of magnitude, from 10{sup -10} to 10{sup -14}, with a detection limit of 3.0 x 10{sup -14}, which is equivalent to 0.8 attomoles of {sup 10}Be. These results show that routine quantification of nanogram levels of Be in tissues is possible and that AMS is a sensitive method that can be used in biological studies to understand the molecular dosimetry of Be and mechanisms of toxicity.

  3. Sampling design considerations for demographic studies: a case of colonial seabirds.

    Science.gov (United States)

    Kendall, William L; Converse, Sarah J; Doherty, Paul F; Naughton, Maura B; Anders, Angela; Hines, James E; Flint, Elizabeth

    2009-01-01

    For the purposes of making many informed conservation decisions, the main goal for data collection is to assess population status and allow prediction of the consequences of candidate management actions. Reducing the bias and variance of estimates of population parameters reduces uncertainty in population status and projections, thereby reducing the overall uncertainty under which a population manager must make a decision. In capture-recapture studies, imperfect detection of individuals, unobservable life-history states, local movement outside study areas, and tag loss can cause bias or precision problems with estimates of population parameters. Furthermore, excessive disturbance to individuals during capture-recapture sampling may be of concern because disturbance may have demographic consequences. We address these problems using as an example a monitoring program for Black-footed Albatross (Phoebastria nigripes) and Laysan Albatross (Phoebastria immutabilis) nesting populations in the northwestern Hawaiian Islands. To mitigate these estimation problems, we describe a synergistic combination of sampling design and modeling approaches. Solutions include multiple capture periods per season and multistate, robust design statistical models, dead recoveries and incidental observations, telemetry and data loggers, buffer areas around study plots to neutralize the effect of local movements outside study plots, and double banding and statistical models that account for band loss. We also present a variation on the robust capture-recapture design and a corresponding statistical model that minimizes disturbance to individuals. For the albatross case study, this less invasive robust design was more time efficient and, when used in combination with a traditional robust design, reduced the standard error of detection probability by 14% with only two hours of additional effort in the field. These field techniques and associated modeling approaches are applicable to studies of

  4. Sampling design considerations for demographic studies: a case of colonial seabirds

    Science.gov (United States)

    Kendall, William L.; Converse, Sarah J.; Doherty, Paul F.; Naughton, Maura B.; Anders, Angela; Hines, James E.; Flint, Elizabeth

    2009-01-01

    For the purposes of making many informed conservation decisions, the main goal for data collection is to assess population status and allow prediction of the consequences of candidate management actions. Reducing the bias and variance of estimates of population parameters reduces uncertainty in population status and projections, thereby reducing the overall uncertainty under which a population manager must make a decision. In capture-recapture studies, imperfect detection of individuals, unobservable life-history states, local movement outside study areas, and tag loss can cause bias or precision problems with estimates of population parameters. Furthermore, excessive disturbance to individuals during capture?recapture sampling may be of concern because disturbance may have demographic consequences. We address these problems using as an example a monitoring program for Black-footed Albatross (Phoebastria nigripes) and Laysan Albatross (Phoebastria immutabilis) nesting populations in the northwestern Hawaiian Islands. To mitigate these estimation problems, we describe a synergistic combination of sampling design and modeling approaches. Solutions include multiple capture periods per season and multistate, robust design statistical models, dead recoveries and incidental observations, telemetry and data loggers, buffer areas around study plots to neutralize the effect of local movements outside study plots, and double banding and statistical models that account for band loss. We also present a variation on the robust capture?recapture design and a corresponding statistical model that minimizes disturbance to individuals. For the albatross case study, this less invasive robust design was more time efficient and, when used in combination with a traditional robust design, reduced the standard error of detection probability by 14% with only two hours of additional effort in the field. These field techniques and associated modeling approaches are applicable to studies of

  5. Rugae pattern in a sample of population of Meerut - An institutional study.

    Science.gov (United States)

    Bhagwath, S; Chandra, L

    2014-05-01

    Many studies on rugae pattern have been done on various samples of population, but no study has so far been done to assess the rugae pattern of population of western Uttar radesh, especially Meerut. This study was aimed to assess the rugae pattern in males and females of a sample of population of Meerut, which may be an additional method of determining gender when dealing with any crime or with mutilated bodies that have undergone damage beyond recognition. A total of 100 Class I dentulous subjects, 50 male and 50 female patients reporting to the outpatient department of Kalka Dental College, Meerut, Uttar Pradesh were randomly selected with an age range between 20-30 years. Exclusion criteria were subjects >14 years of age, congenital malformations, previous orthognathic surgery, allergy to impression material, bony and soft tissue protuberances, active lesions, deformity or scars and trauma of the palate. Prior approval from the Institutional Ethical Committee was taken. Alginate impressions of palate of selected patients were poured in dental stone and rugae pattern was identified and analyzed by a single rater employing Thomas and Kotze's (1983) method. Two-sample t-test and Chi-Square tests were used for comparison of means and relationship between the attributes. A significance level of 5% was considered as critical value. No significant difference was noted in total number or length of rugae between the genders. However, statistically significant difference in the circular type in males and converge type in females was observed. Rugae pattern can be used as a method of differentiation between males and females to corroborate the findings of other methods such as anthropometric evaluation of the cranium and dental characteristics.

  6. Continuous acoustic studies of overwintering sprat Sprattus sprattus reveal flexible behavior

    KAUST Repository

    Solberg, I

    2012-09-19

    The clupeid fish Sprattus sprattus was studied in a 150 m deep Norwegian fjord throughout an entire overwintering period during which the fjord froze over and a major water renewal occurred. A bottom-mounted (upward-facing) echosounder provided continuous high-resolution data and enabled studies of swimming speed and behavior of individual sprat in addition to population behavior. The continuous acoustic studies were supplemented with intermittent field campaigns. The sprat displayed different behavioral modes with changing environmental conditions. During the first part of the winter, the majority of the population occurred in deep waters during both day and night, yet exhibited a shallower night-time distribution. Individual sprat swam alternately up and down, a ‘rise and sink’ behavior likely a compensation for negative buoyancy because of swim bladder compression. Because feeding was negligible in deep waters, the swimming pattern was not inferred as prey search behavior. Another part of the population schooled at shallower depths during the day and carried out vertical migration to upper waters at night. However, individuals were observed as they switched between these behavioral groups. A sudden change in both swimming behavior and vertical distribution occurred as the fjord became ice covered. Near-bottom ‘rise and sink’ swimming was replaced by schooling in mid-water during the day, and the sprat aggregated in dense layers near the surface at night. We suggest that the ice made the sprat shift their antipredator strategy from hiding at depth to hiding in schools in the darker waters below the ice. This long-term acoustic study has shown that sprat have a flexible behavioral repertoire, displaying different overwintering strategies within a population, depending on environmental conditions.

  7. Attitude towards computer-based learning: determinants as revealed by a controlled interventional study.

    Science.gov (United States)

    Hahne, Amina Katharina; Benndorf, Ralf; Frey, Peter; Herzig, Stefan

    2005-09-01

    Curriculum-wide implementation of computer-based learning (CBL) in undergraduate medical education remains elusive. Unlike many pilot tests of singular learning programmes, dropout rates are high and acceptance seems low in the long run. We studied the effect of a new CBL programme, suitable for curriculum-wide implementation, on Year 3 medical students' attitudes towards CBL. Students from 2 universities participating in a mandatory pharmacology course were given access to a CBL programme covering cardiovascular drug therapy in a controlled randomised study (n = 167). Learner properties and attitude towards CBL were measured using psychometric scales, and knowledge by multiple-choice questions (pre- and post-test). Attitude towards CBL worsened in the CBL group (n = 70). Individual learners' properties did not explain this effect. The perceived programme quality was rated only 'average', which may contribute to the lower post-test values of attitude towards CBL. Learning outcomes were similar between the control group (n = 97) and students using CBL (n = 44). Learning efforts were shifted from self-study towards CBL. The initial enthusiasm of students was not maintained when using a programme designed to complement or even replace traditional teaching. Curriculum-wide implementation of CBL might be hampered by the discouragement of users.

  8. Resistive Micromegas for sampling calorimetry, a study of charge-up effects

    Energy Technology Data Exchange (ETDEWEB)

    Chefdeville, M., E-mail: chefdevi@lapp.in2p3.fr [LAPP, Université de Savoie, CNRS/IN2P3, Annecy-Le-Vieux (France); Karyotakis, Y. [LAPP, Université de Savoie, CNRS/IN2P3, Annecy-Le-Vieux (France); Geralis, T. [INP, NCSR Demokritos, Athens (Greece); Titov, M. [IRFU, Saclay CEA, Gif-sur-Yvette (France)

    2016-07-11

    Micromegas, as a proportional and compact gaseous detector, is well suited for sampling calorimetry. The limitation of occasional sparking has now been lifted by means of resistive electrodes but at the cost of current-dependent charge-up effects. These effects are studied in this contribution, with an emphasis on gain variations during operation at high particle rate and under heavy ionisation. Results are reproduced by a simple model of charging-up which will be used for detector design optimisation in the future.

  9. Intercomparison NaI(Tl) and HPGe spectrometry to studies of natural radioactivity on geological samples.

    Science.gov (United States)

    Hung, Nguyen Quoc; Chuong, Huynh Dinh; Vuong, Le Quang; Thanh, Tran Thien; Tao, Chau Van

    2016-11-01

    In this study, in situ gamma spectra using NaI(Tl) detector have been compared with the laboratory measurements by using HPGe detector on geological samples. The results for measuring naturally occurring terrestrial gamma radiation of 40K and the decay series of 232Th and, 238U respectively of both detectors show a maximum deviation about 5%. The mass activities series from both detectors were checked for coherence using proficiency test procedure from the International Atomic Energy Agency. The reliability and precision pass for final scores for all the analytical determinations of are received "acceptable" for all radionuclides. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Intensity and prevalence of depressive states in cancer inpatients: a large sample descriptive study.

    Science.gov (United States)

    Muzzatti, B; Mella, S; Bomben, F; Flaiban, C; Gipponi, K; Piccinin, M; Busato, S; Annunziata, M A

    2016-06-30

    In cancer patients, depression causes suffering during the whole disease trajectory and it also influences the personal perception of well-being as well as treatment adherence. Consequently, its better definition is needed for planning more tailored supportive programmes. This study was aimed to provide information on depressive state intensity and prevalence in an heterogeneous sample of cancer inpatients. In addition, associations were studied between depressive state and different socio-demographic and clinical factors. A total of 1,147 consecutive adult cancer inpatients completed the Center for Epidemiologic Studies Scale on Depression together with a form for collecting socio-demographic and clinical data. The mean score of depression was 16.9 (SD = 9.3). There were differences in depression intensity associated with gender (p < .001), age (p = .001) and cancer type (p < .001), but not with education level (p = .282) or marital status (p = .436). Of the entire sample 13.9% had depressive states; this percentage raised to 26.2% if a less stringent criterion was used. These data reinforce the importance of a clinical and research focus on depression in oncology. As differences according to gender, age and diagnosis exist in depression prevalence and intensity, tailored supportive intervention should be planned and verified for effectiveness and efficacy. © 2016 John Wiley & Sons Ltd.

  11. Self-collected cervicovaginal sampling for site-of-care primary HPV-based cervical cancer screening: a pilot study in a rural underserved Greek population.

    Science.gov (United States)

    Chatzistamatiou, Kimon; Chatzaki, Εkaterini; Constantinidis, Τheocharis; Nena, Evangelia; Tsertanidou, Athena; Agorastos, Theodoros

    2017-11-01

    In the present pilot study, the feasibility of a site-of-care cervicovaginal self-sampling methodology for HPV-based screening was tested in 346 women residing in underserved rural areas of Northern Greece. These women provided self-collected cervicovaginal sample along with a study questionnaire. Following molecular testing, using the cobas® HPV Test, Roche®, HPV positive women, were referred to colposcopy and upon abnormal findings, to biopsy and treatment. Participation rate was 100%. Regular pap-test examination was reported for 17.1%. Among hrHPV testing, 11.9% were positive and colposcopy/biopsy revealed 2 CIN3 cases. Non-compliance was the most prevalent reason for no previous attendance. Most women reported non-difficulty and non-discomfort in self-sampling (77.6% and 82.4%, respectively). They would choose self-sampling over clinician-sampling (86.2%), and should self-sampling being available, they would test themselves more regularly (92.3%). In conclusion, self-sampling is feasible and well-accepted for HPV-based screening, and could increase population coverage in underserved areas, helping towards successful prevention.

  12. Ex post-facto study of long term stress in a sample of adoptees

    Directory of Open Access Journals (Sweden)

    Amelia Díaz

    2016-01-01

    Full Text Available In this work we study the impact of relinquishment and the adoption process in posttraumatic symptoms in a group of 55 adults that were adopted as children before 1970. The effects of institutionalization, maltreatment, traumatic revelation of the adopted status and stressful life events have also been studied. No significant differences were found between institutionalized and non-institutionalized adoptees in posttraumatic symptomatology. However, adoptees who suffered maltreatment, traumatic revelation and high level of stressful life events scored significantly higher in intrusion and arousal than those adoptees non-maltreated, without traumatic revelation and with low level of stressful life events respectively. Traumatic revelation, alone or in association with maltreatment, seems to play an important role in posttraumatic symptoms in the sample studied.

  13. Self-regulated learning and self-directed study in a pre-college sample.

    Science.gov (United States)

    Abar, Beau; Loken, Eric

    2010-02-01

    Self-regulated learning (SRL) is a multi-dimensional construct that has been difficult to operationalize using traditional, variable-centered methodologies. The current paper takes a person-centered approach to the study of SRL in a sample of 205 high-school students. Using latent profile analysis on self-reports of seven aspects of SRL, three groups were identified: high SRL, low SRL, and average SRL. Student self-reports of goal orientation were used as validation for the profile solution, with the high academic self- regulation group reporting the highest levels of mastery orientation while the low self-regulation group reported highest levels of avoidant orientation. Profiles were also compared on independently collected, behavioral measures of study behaviors, with the highly self-regulated group tending to study more material and for a longer time than less self-regulated individuals.

  14. Asynchronous dentofacial development and dental crowding: a cross-sectional study in a contemporary sample of children in France.

    Science.gov (United States)

    Yan-Vergnes, Wei; Vergnes, Jean-Noel; Dumoncel, Jean; Baron, Pascal; Marchal-Sixou, Christine; Braga, José

    2013-11-19

    The causes of dental crowding are not fully understood, but it may result from an evolutionary trend towards reduced facial volume, without a proportional reduction in tooth sizes. Most previous studies conducted among modern humans have revealed a very low or non-existent correlation between tooth size and jaw size. Cross-comparison between dental age and facial skeletal age could help to provide better knowledge of the dynamic process of dental crowding. The primary objective of this research was to study the synchronism of dental maturation and skeletal facial growth in a sample of modern children living in France. The secondary objective was to assess the link between dentofacial asynchronism and dental crowding. The random sample comprised 28 subjects (16 girls, 12 boys). Mean chronological age was 13.5 years (± 2.1; range 9.2-17.6). Mean dental age was 14.2 years (± 2.8; range 7.5-17) and mean facial skeletal age was 12.8 years (± 2.6, range 7-22). In the estimations of dental age and facial skeletal age, there was no evidence of systematic bias. There were 10 subjects (9 girls, 1 boy) with asynchronous dentofacial development. Finally, there were 13 subjects (8 girls, 5 boys) with dental crowding. A significant association was found between delayed facial skeletal growth/advanced dental maturation and dental crowding (P = 0.01). Dental maturation and facial growth are not necessarily synchronous. Further understanding of the interactions between dental maturation and facial growth could have crucial implications in biological anthropology, as well as for the clinical practice of orthodontists. From an anthropological perspective, this study suggests that asynchronous dentofacial development could, at least partially, explain the frequency of dental crowding in modern populations.

  15. In vitro studies reveal antiurolithic effect of Terminalia arjuna using quantitative morphological information from computerized microscopy

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    A. Mittal

    2015-10-01

    Full Text Available ABSTRACT Purpose: For most cases, urolithiasis is a condition where excessive oxalate is present in the urine. Many reports have documented free radical generation followed by hyperoxaluria as a consequence of which calcium oxalate (CaOx deposition occurs in the kidney tissue. The present study is aimed to exam the antilithiatic potency of the aqueous extract (AE of Terminalia arjuna (T. arjuna. Materials and Methods: The antilithiatic activity of Terminalia arjuna was investigated in vitro nucleation, aggregation and growth of the CaOx crystals as well as the morphology of CaOx crystals using the inbuilt software ‘Image-Pro Plus 7.0’ of Olympus upright microscope (BX53. Antioxidant activity of AE of Terminalia arjuna bark was also determined in vitro. Results: Terminalia arjuna extract exhibited a concentration dependent inhibition of nucleation and aggregation of CaOx crystals. The AE of Terminalia arjuna bark also inhibited the growth of CaOx crystals. At the same time, the AE also modified the morphology of CaOx crystals from hexagonal to spherical shape with increasing concentrations of AE and reduced the dimensions such as area, perimeter, length and width of CaOx crystals in a dose dependent manner. Also, the Terminalia arjuna AE scavenged the DPPH (2, 2-diphenyl-1-picrylhydrazyl radicals with an IC50 at 13.1µg/mL. Conclusions: The study suggests that Terminalia arjuna bark has the potential to scavenge DPPH radicals and inhibit CaOx crystallization in vitro. In the light of these studies, Terminalia arjuna can be regarded as a promising candidate from natural plant sources of antilithiatic and antioxidant activity with high value.

  16. Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links.

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    Rico Rueedi

    2014-02-01

    Full Text Available Metabolic traits are molecular phenotypes that can drive clinical phenotypes and may predict disease progression. Here, we report results from a metabolome- and genome-wide association study on (1H-NMR urine metabolic profiles. The study was conducted within an untargeted approach, employing a novel method for compound identification. From our discovery cohort of 835 Caucasian individuals who participated in the CoLaus study, we identified 139 suggestively significant (P<5×10(-8 and independent associations between single nucleotide polymorphisms (SNP and metabolome features. Fifty-six of these associations replicated in the TasteSensomics cohort, comprising 601 individuals from São Paulo of vastly diverse ethnic background. They correspond to eleven gene-metabolite associations, six of which had been previously identified in the urine metabolome and three in the serum metabolome. Our key novel findings are the associations of two SNPs with NMR spectral signatures pointing to fucose (rs492602, P = 6.9×10(-44 and lysine (rs8101881, P = 1.2×10(-33, respectively. Fine-mapping of the first locus pinpointed the FUT2 gene, which encodes a fucosyltransferase enzyme and has previously been associated with Crohn's disease. This implicates fucose as a potential prognostic disease marker, for which there is already published evidence from a mouse model. The second SNP lies within the SLC7A9 gene, rare mutations of which have been linked to severe kidney damage. The replication of previous associations and our new discoveries demonstrate the potential of untargeted metabolomics GWAS to robustly identify molecular disease markers.

  17. Proteomics study reveals the molecular mechanisms underlying water stress tolerance induced by Piriformospora indica in barley.

    Science.gov (United States)

    Ghabooli, Mehdi; Khatabi, Behnam; Ahmadi, Farajolah Shahriary; Sepehri, Mozhgan; Mirzaei, Mehdi; Amirkhani, Ardeshir; Jorrín-Novo, Jesús V; Salekdeh, Ghasem Hosseini

    2013-12-06

    Piriformospora indica is a mutualistic root endophytic fungus, which transfers several benefits to hosts including enhance plant growth and increase yield under both normal and stress conditions. It has been shown that P. indica root-colonization enhances water stress tolerance based on general and non-specific plant-species mechanism. To better understand the molecular mechanism of P. indica-mediated drought stress tolerance, we designed a set of comparative experiments to study the impact of P. indica on barely plants cultivar "Golden Promise" grown under different drought levels [Filed capacity (F.C.) and 25% F.C.]. P. indica enhanced root and shoot biomass of colonized plants under both well-watered and water-deficit conditions. Proteome analysis of P. indica-colonized barley leaves under well-treated and water-deficit conditions resulted in detection of 726 reproducibly protein spots. Mass spectrometry analysis resulted in the identification of 45 differentially accumulated proteins involved in photosynthesis, reactive oxygen scavenging, metabolisms, signal transduction, and plant defense responses. Interestingly, P. indica increased the level of proteins involved in photosynthesis, antioxidative defense system and energy transport. We propose that P. indica-mediated drought stress tolerance in barely is through photosynthesis stimulation, energy releasing and enhanced antioxidative capacity in colonized plants. Plant mutualistic symbionts offer long-term abiotic stress tolerance through the host adaptation to environmental stress. There have been a few published proteomic studies of plant symbionts to drought, and this is thought to be the first proteomic analysis, demonstrating the impact of endophyte on barley plant under drought stress. For some of identified proteins like TCTP and PCNA, a connection to physiological function in plants is novel, and can be the best candidates for sources of drought tolerance in future studies. © 2013.

  18. Transcriptome and Proteome Studies Reveal Candidate Attachment Genes during the Development of the Barnacle Amphibalanus Amphitrite

    KAUST Repository

    Al-Aqeel, Sarah

    2016-09-21

    The acorn barnacle, Balanus amphitrite, is the main biofouling organism in marine environments. In the present study we profiled the transcriptome and proteome of B. amphitrite at different life stages (nauplius II, nauplius VI, and cyprid) from the Red Sea, where the average water surface temperature is 34°C and the salinity reaches 41%. We identified 65,784 expressed contigs, and a total of 1387 expressed proteins measured by quantitative proteomics. We found that osmotic stress, salt stress, hyperosmotic response and the Wnt signaling pathway were strongly up-regulated during the planktonic stage, while the MAPK pathway, lipid metabolism, and cuticle development genes were down-regulated. In the transition stage between the nauplius VI and the cyprid, genes that are involved in blood coagulation, cuticle development and eggshell formation were highly up-regulated, while the nitric oxide pathway, which stimulates the swimming and feeding response in marine invertebrates, was down-regulated. We are able to report for the first time that sound sensory system proteins are highly abundant in the nauplius VI stage, implying that these proteins are good targets for the development of new antifouling compounds. The results presented here together with the new genome-wide datasets for a non-model specie represent an important resource for the study of biofouling and development. Proteomics data are available via ProteomeXchange with identifier PXD004679.

  19. Transcriptome and proteome studies reveal candidate attachment genes during the development of the barnacle Amphibalanus Amphitrite

    Directory of Open Access Journals (Sweden)

    Sarah Al-Aqeel

    2016-09-01

    Full Text Available The acorn barnacle, Balanus amphitrite, is the main biofouling organism in marine environments. In the present study we profiled the transcriptome and proteome of B. amphitrite at different life stages (nauplius II, nauplius VI and cyprid from the Red Sea, where the average water surface temperature is 34°C and the salinity reaches 41‰. We identified 65,784 expressed contigs, and a total of 1,387 expressed proteins measured by quantitative proteomics. We found that osmotic stress, salt stress, hyperosmotic response and the Wnt signaling pathway were strongly up-regulated during the planktonic stage, while the MAPK pathway, lipid metabolism, and cuticle development genes were down-regulated. In the transition stage between the nauplius VI and the cyprid, genes that are involved in blood coagulation, cuticle development and eggshell formation were highly up-regulated, while the nitric oxide pathway, which stimulates the swimming and feeding response in marine invertebrates, was down-regulated. We are able to report for the first time that sound sensory system proteins are highly abundant in the nauplius VI stage, implying that these proteins are good targets for the development of new antifouling compounds. The results presented here together with the new genome-wide datasets for a non-model specie represent an important resource for the study of biofouling and development.

  20. An fMRI Study of Audiovisual Speech Perception Reveals Multisensory Interactions in Auditory Cortex.

    Science.gov (United States)

    Okada, Kayoko; Venezia, Jonathan H; Matchin, William; Saberi, Kourosh; Hickok, Gregory

    2013-01-01

    Research on the neural basis of speech-reading implicates a network of auditory language regions involving inferior frontal cortex, premotor cortex and sites along superior temporal cortex. In audiovisual speech studies, neural activity is consistently reported in posterior superior temporal Sulcus (pSTS) and this site has been implicated in multimodal integration. Traditionally, multisensory interactions are considered high-level processing that engages heteromodal association cortices (such as STS). Recent work, however, challenges this notion and suggests that multisensory interactions may occur in low-level unimodal sensory cortices. While previous audiovisual speech studies demonstrate that high-level multisensory interactions occur in pSTS, what remains unclear is how early in the processing hierarchy these multisensory interactions may occur. The goal of the present fMRI experiment is to investigate how visual speech can influence activity in auditory cortex above and beyond its response to auditory speech. In an audiovisual speech experiment, subjects were presented with auditory speech with and without congruent visual input. Holding the auditory stimulus constant across the experiment, we investigated how the addition of visual speech influences activity in auditory cortex. We demonstrate that congruent visual speech increases the activity in auditory cortex.

  1. An fMRI Study of Audiovisual Speech Perception Reveals Multisensory Interactions in Auditory Cortex.

    Directory of Open Access Journals (Sweden)

    Kayoko Okada

    Full Text Available Research on the neural basis of speech-reading implicates a network of auditory language regions involving inferior frontal cortex, premotor cortex and sites along superior temporal cortex. In audiovisual speech studies, neural activity is consistently reported in posterior superior temporal Sulcus (pSTS and this site has been implicated in multimodal integration. Traditionally, multisensory interactions are considered high-level processing that engages heteromodal association cortices (such as STS. Recent work, however, challenges this notion and suggests that multisensory interactions may occur in low-level unimodal sensory cortices. While previous audiovisual speech studies demonstrate that high-level multisensory interactions occur in pSTS, what remains unclear is how early in the processing hierarchy these multisensory interactions may occur. The goal of the present fMRI experiment is to investigate how visual speech can influence activity in auditory cortex above and beyond its response to auditory speech. In an audiovisual speech experiment, subjects were presented with auditory speech with and without congruent visual input. Holding the auditory stimulus constant across the experiment, we investigated how the addition of visual speech influences activity in auditory cortex. We demonstrate that congruent visual speech increases the activity in auditory cortex.

  2. Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.

    Science.gov (United States)

    Inouye, Michael; Ripatti, Samuli; Kettunen, Johannes; Lyytikäinen, Leo-Pekka; Oksala, Niku; Laurila, Pirkka-Pekka; Kangas, Antti J; Soininen, Pasi; Savolainen, Markku J; Viikari, Jorma; Kähönen, Mika; Perola, Markus; Salomaa, Veikko; Raitakari, Olli; Lehtimäki, Terho; Taskinen, Marja-Riitta; Järvelin, Marjo-Riitta; Ala-Korpela, Mika; Palotie, Aarno; de Bakker, Paul I W

    2012-01-01

    Association testing of multiple correlated phenotypes offers better power than univariate analysis of single traits. We analyzed 6,600 individuals from two population-based cohorts with both genome-wide SNP data and serum metabolomic profiles. From the observed correlation structure of 130 metabolites measured by nuclear magnetic resonance, we identified 11 metabolic networks and performed a multivariate genome-wide association analysis. We identified 34 genomic loci at genome-wide significance, of which 7 are novel. In comparison to univariate tests, multivariate association analysis identified nearly twice as many significant associations in total. Multi-tissue gene expression studies identified variants in our top loci, SERPINA1 and AQP9, as eQTLs and showed that SERPINA1 and AQP9 expression in human blood was associated with metabolites from their corresponding metabolic networks. Finally, liver expression of AQP9 was associated with atherosclerotic lesion area in mice, and in human arterial tissue both SERPINA1 and AQP9 were shown to be upregulated (6.3-fold and 4.6-fold, respectively) in atherosclerotic plaques. Our study illustrates the power of multi-phenotype GWAS and highlights candidate genes for atherosclerosis.

  3. Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.

    Directory of Open Access Journals (Sweden)

    Michael Inouye

    Full Text Available Association testing of multiple correlated phenotypes offers better power than univariate analysis of single traits. We analyzed 6,600 individuals from two population-based cohorts with both genome-wide SNP data and serum metabolomic profiles. From the observed correlation structure of 130 metabolites measured by nuclear magnetic resonance, we identified 11 metabolic networks and performed a multivariate genome-wide association analysis. We identified 34 genomic loci at genome-wide significance, of which 7 are novel. In comparison to univariate tests, multivariate association analysis identified nearly twice as many significant associations in total. Multi-tissue gene expression studies identified variants in our top loci, SERPINA1 and AQP9, as eQTLs and showed that SERPINA1 and AQP9 expression in human blood was associated with metabolites from their corresponding metabolic networks. Finally, liver expression of AQP9 was associated with atherosclerotic lesion area in mice, and in human arterial tissue both SERPINA1 and AQP9 were shown to be upregulated (6.3-fold and 4.6-fold, respectively in atherosclerotic plaques. Our study illustrates the power of multi-phenotype GWAS and highlights candidate genes for atherosclerosis.

  4. Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides.

    Science.gov (United States)

    Fahrenkrog, Annette M; Neves, Leandro G; Resende, Márcio F R; Vazquez, Ana I; de Los Campos, Gustavo; Dervinis, Christopher; Sykes, Robert; Davis, Mark; Davenport, Ruth; Barbazuk, William B; Kirst, Matias

    2017-01-01

    Genome-wide association studies (GWAS) have been used extensively to dissect the genetic regulation of complex traits in plants. These studies have focused largely on the analysis of common genetic variants despite the abundance of rare polymorphisms in several species, and their potential role in trait variation. Here, we conducted the first GWAS in Populus deltoides, a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits, and common and low-frequency single-nucleotide polymorphisms detected by targeted resequencing of 18 153 genes in a population of 391 unrelated individuals. To increase power to detect associations with low-frequency variants, multiple-marker association tests were used in combination with single-marker association tests. Significant associations were discovered for all phenotypes and are indicative that low-frequency polymorphisms contribute to phenotypic variance of several bioenergy traits. Our results suggest that both common and low-frequency variants need to be considered for a comprehensive understanding of the genetic regulation of complex traits, particularly in species that carry large numbers of rare polymorphisms. These polymorphisms may be critical for the development of specialized plant feedstocks for bioenergy. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  5. An intercomparison study of analytical methods used for quantification of levoglucosan in ambient aerosol filter samples

    Science.gov (United States)

    Yttri, K. E.; Schnelle-Kreis, J.; Maenhaut, W.; Abbaszade, G.; Alves, C.; Bjerke, A.; Bonnier, N.; Bossi, R.; Claeys, M.; Dye, C.; Evtyugina, M.; García-Gacio, D.; Hillamo, R.; Hoffer, A.; Hyder, M.; Iinuma, Y.; Jaffrezo, J.-L.; Kasper-Giebl, A.; Kiss, G.; López-Mahia, P. L.; Pio, C.; Piot, C.; Ramirez-Santa-Cruz, C.; Sciare, J.; Teinilä, K.; Vermeylen, R.; Vicente, A.; Zimmermann, R.

    2015-01-01

    The monosaccharide anhydrides (MAs) levoglucosan, galactosan and mannosan are products of incomplete combustion and pyrolysis of cellulose and hemicelluloses, and are found to be major constituents of biomass burning (BB) aerosol particles. Hence, ambient aerosol particle concentrations of levoglucosan are commonly used to study the influence of residential wood burning, agricultural waste burning and wildfire emissions on ambient air quality. A European-wide intercomparison on the analysis of the three monosaccharide anhydrides was conducted based on ambient aerosol quartz fiber filter samples collected at a Norwegian urban background site during winter. Thus, the samples' content of MAs is representative for BB particles originating from residential wood burning. The purpose of the intercomparison was to examine the comparability of the great diversity of analytical methods used for analysis of levoglucosan, mannosan and galactosan in ambient aerosol filter samples. Thirteen laboratories participated, of which three applied high-performance anion-exchange chromatography (HPAEC), four used high-performance liquid chromatography (HPLC) or ultra-performance liquid chromatography (UPLC) and six resorted to gas chromatography (GC). The analytical methods used were of such diversity that they should be considered as thirteen different analytical methods. All of the thirteen laboratories reported levels of levoglucosan, whereas nine reported data for mannosan and/or galactosan. Eight of the thirteen laboratories reported levels for all three isomers. The accuracy for levoglucosan, presented as the mean percentage error (PE) for each participating laboratory, varied from -63 to 20%; however, for 62% of the laboratories the mean PE was within ±10%, and for 85% the mean PE was within ±20%. For mannosan, the corresponding range was -60 to 69%, but as for levoglucosan, the range was substantially smaller for a subselection of the laboratories; i.e. for 33% of the

  6. The neural substrates of script knowledge deficits as revealed by a PET study in Huntington's disease.

    Science.gov (United States)

    Allain, Philippe; Gaura, Véronique; Fasotti, Luciano; Chauviré, Valérie; Prundean, Adriana; Sherer-Gagou, Clarisse; Bonneau, Dominique; Bachoud-Levi, Anne-Catherine; Dubas, Frédéric; Remy, Philippe; Le Gall, Didier; Verny, Christophe

    2011-07-01

    Previous neuropsychological investigations have suggested that both the prefrontal cortex and the basal ganglia are involved in the management of script event knowledge required in planning behavior. This study was designated to map, the correlations between resting-state brain glucose utilization as measured by FDG-PET (positron emission tomography) and scores obtained by means of a series of script generation and script sorting tasks in 8 patients with early Huntington's disease. These patients exhibited a selectively greater impairment for the organizational aspects of scripts compared to the semantic aspects of scripts. We showed significant negative correlations between the number of sequencing, boundary, perseverative and intrusion errors and the metabolism of several cortical regions, not only including frontal, but also posterior regions. Our findings suggest that, within the fronto-striatal system, the cortical frontal regions are more crucial in script retrieval and script sequencing than the basal ganglia. Copyright © 2011 Elsevier Ltd. All rights reserved.

  7. Smartphones reveal angler behavior: A case study of a popular mobile fishing application in Alberta, Canada

    Science.gov (United States)

    Papenfuss, Jason T.; Phelps, Nicholas; Fulton, David C.; Venturelli, Paul A.

    2015-01-01

    Successfully managing fisheries and controlling the spread of invasive species depends on the ability to describe and predict angler behavior. However, finite resources restrict conventional survey approaches and tend to produce retrospective data that are limited in time or space and rely on intentions or attitudes rather than actual behavior. In this study, we used three years of angler data from a popular mobile fishing application in Alberta, Canada, to determine province-wide, seasonal patterns of (1) lake popularity that were consistent with conventional data and (2) anthropogenic lake connectivity that has not been widely described in North America. Our proof-of-concept analyses showed that mobile apps can be an inexpensive source of high-resolution, real-time data for managing fisheries and invasive species. We also identified key challenges that underscore the need for further research and development in this new frontier that combines big data with increased stakeholder interaction and cooperation.

  8. Identification of Promising Mutants Associated with Egg Production Traits Revealed by Genome-Wide Association Study.

    Science.gov (United States)

    Yuan, Jingwei; Sun, Congjiao; Dou, Taocun; Yi, Guoqiang; Qu, LuJiang; Qu, Liang; Wang, Kehua; Yang, Ning

    2015-01-01

    Egg number (EN), egg laying rate (LR) and age at first egg (AFE) are important production traits related to egg production in poultry industry. To better understand the knowledge of genetic architecture of dynamic EN during the whole laying cycle and provide the precise positions of associated variants for EN, LR and AFE, laying records from 21 to 72 weeks of age were collected individually for 1,534 F2 hens produced by reciprocal crosses between White Leghorn and Dongxiang Blue-shelled chicken, and their genotypes were assayed by chicken 600 K Affymetrix high density genotyping arrays. Subsequently, pedigree and SNP-based genetic parameters were estimated and a genome-wide association study (GWAS) was conducted on EN, LR and AFE. The heritability estimates were similar between pedigree and SNP-based estimates varying from 0.17 to 0.36. In the GWA analysis, we identified nine genome-wide significant loci associated with EN of the laying periods from 21 to 26 weeks, 27 to 36 weeks and 37 to 72 weeks. Analysis of GTF2A1 and CLSPN suggested that they influenced the function of ovary and uterus, and may be considered as relevant candidates. The identified SNP rs314448799 for accumulative EN from 21 to 40 weeks on chromosome 5 created phenotypic differences of 6.86 eggs between two homozygous genotypes, which could be potentially applied to the molecular breeding for EN selection. Moreover, our finding showed that LR was a moderate polygenic trait. The suggestive significant region on chromosome 16 for AFE suggested the relationship between sex maturity and immune in the current population. The present study comprehensively evaluates the role of genetic variants in the development of egg laying. The findings will be helpful to investigation of causative genes function and future marker-assisted selection and genomic selection in chickens.

  9. Identification of Promising Mutants Associated with Egg Production Traits Revealed by Genome-Wide Association Study.

    Directory of Open Access Journals (Sweden)

    Jingwei Yuan

    Full Text Available Egg number (EN, egg laying rate (LR and age at first egg (AFE are important production traits related to egg production in poultry industry. To better understand the knowledge of genetic architecture of dynamic EN during the whole laying cycle and provide the precise positions of associated variants for EN, LR and AFE, laying records from 21 to 72 weeks of age were collected individually for 1,534 F2 hens produced by reciprocal crosses between White Leghorn and Dongxiang Blue-shelled chicken, and their genotypes were assayed by chicken 600 K Affymetrix high density genotyping arrays. Subsequently, pedigree and SNP-based genetic parameters were estimated and a genome-wide association study (GWAS was conducted on EN, LR and AFE. The heritability estimates were similar between pedigree and SNP-based estimates varying from 0.17 to 0.36. In the GWA analysis, we identified nine genome-wide significant loci associated with EN of the laying periods from 21 to 26 weeks, 27 to 36 weeks and 37 to 72 weeks. Analysis of GTF2A1 and CLSPN suggested that they influenced the function of ovary and uterus, and may be considered as relevant candidates. The identified SNP rs314448799 for accumulative EN from 21 to 40 weeks on chromosome 5 created phenotypic differences of 6.86 eggs between two homozygous genotypes, which could be potentially applied to the molecular breeding for EN selection. Moreover, our finding showed that LR was a moderate polygenic trait. The suggestive significant region on chromosome 16 for AFE suggested the relationship between sex maturity and immune in the current population. The present study comprehensively evaluates the role of genetic variants in the development of egg laying. The findings will be helpful to investigation of causative genes function and future marker-assisted selection and genomic selection in chickens.

  10. Identification of Pleiotropic Cancer Susceptibility Variants from Genome-Wide Association Studies Reveals Functional Characteristics.

    Science.gov (United States)

    Wu, Yi-Hsuan; Graff, Rebecca E; Passarelli, Michael N; Hoffman, Joshua D; Ziv, Elad; Hoffmann, Thomas J; Witte, John S

    2018-01-01

    Background: There exists compelling evidence that some genetic variants are associated with the risk of multiple cancer sites (i.e., pleiotropy). However, the biological mechanisms through which the pleiotropic variants operate are unclear.Methods: We obtained all cancer risk associations from the National Human Genome Research Institute-European Bioinformatics Institute GWAS Catalog, and correlated cancer risk variants were clustered into groups. Pleiotropic variant groups and genes were functionally annotated. Associations of pleiotropic cancer risk variants with noncancer traits were also obtained.Results: We identified 1,431 associations between variants and cancer risk, comprised of 989 unique variants associated with 27 unique cancer sites. We found 20 pleiotropic variant groups (2.1%) composed of 33 variants (3.3%), including novel pleiotropic variants rs3777204 and rs56219066 located in the ELL2 gene. Relative to single-cancer risk variants, pleiotropic variants were more likely to be in genes (89.0% vs. 65.3%, P = 2.2 × 10-16), and to have somewhat larger risk allele frequencies (median RAF = 0.49 versus 0.39, P = 0.046). The 27 genes to which the pleiotropic variants mapped were suggestive for enrichment in response to radiation and hypoxia, alpha-linolenic acid metabolism, cell cycle, and extension of telomeres. In addition, we observed that 8 of 33 pleiotropic cancer risk variants were associated with 16 traits other than cancer.Conclusions: This study identified and functionally characterized genetic variants showing pleiotropy for cancer risk.Impact: Our findings suggest biological pathways common to different cancers and other diseases, and provide a basis for the study of genetic testing for multiple cancers and repurposing cancer treatments. Cancer Epidemiol Biomarkers Prev; 27(1); 75-85. ©2017 AACR. ©2017 American Association for Cancer Research.

  11. Pharmacoinformatic and molecular docking studies reveal potential novel antidepressants against neurodegenerative disorders by targeting HSPB8

    Directory of Open Access Journals (Sweden)

    Sehgal SA

    2016-05-01

    Full Text Available Sheikh Arslan Sehgal,1–4 Shazia Mannan,1 Sannia Ali1 1Department of Bioscience, COMSATS Institute of Information Technology, Sahiwal, Pakistan; 2State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, 3University of Chinese Academy of Sciences, Beijing, People’s Republic of China; 4Department of Bioinformatics and Bi