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

Pavlou, A. T.; Betzler, B. R.; Burke, T. P.

Uncertainties in the composition and fabrication of fuel compacts for the Fort St. Vrain (FSV) high temperature gas reactor have been studied by performing eigenvalue sensitivity studies that represent the key uncertainties for the FSV neutronic analysis. The uncertainties for the TRISO fuel kernels were addressed by developing a suite of models for an 'average' FSV fuel compact that models the fuel as (1) a mixture of two different TRISO fuel particles representing fissile and fertile kernels, (2) a mixture of four different TRISO fuel particles representing small and large fissile kernels and small and large fertile kernels and (3)more » a stochastic mixture of the four types of fuel particles where every kernel has its diameter sampled from a continuous probability density function. All of the discrete diameter and continuous diameter fuel models were constrained to have the same fuel loadings and packing fractions. For the non-stochastic discrete diameter cases, the MCNP compact model arranged the TRISO fuel particles on a hexagonal honeycomb lattice. This lattice-based fuel compact was compared to a stochastic compact where the locations (and kernel diameters for the continuous diameter cases) of the fuel particles were randomly sampled. Partial core configurations were modeled by stacking compacts into fuel columns containing graphite. The differences in eigenvalues between the lattice-based and stochastic models were small but the runtime of the lattice-based fuel model was roughly 20 times shorter than with the stochastic-based fuel model. (authors)« less

Establishing an EGFR mutation screening service for non-small cell lung cancer - sample quality criteria and candidate histological predictors.

PubMed

Leary, Alexandra F; Castro, David Gonzalez de; Nicholson, Andrew G; Ashley, Sue; Wotherspoon, Andrew; O'Brien, Mary E R; Popat, Sanjay

2012-01-01

EGFR screening requires good quality tissue, sensitivity and turn-around time (TAT). We report our experience of routine screening, describing sample type, TAT, specimen quality (cellularity and DNA yield), histopathological description, mutation result and clinical outcome. Non-small cell lung cancer (NSCLC) sections were screened for EGFR mutations (M+) in exons 18-21. Clinical, pathological and screening outcome data were collected for year 1 of testing. Screening outcome alone was collected for year 2. In year 1, 152 samples were tested, most (72%) were diagnostic. TAT was 4.9 days (95%confidence interval (CI)=4.5-5.5). EGFR-M+ prevalence was 11% and higher (20%) among never-smoking women with adenocarcinomas (ADCs), but 30% of mutations occurred in current/ex-smoking men. EGFR-M+ tumours were non-mucinous ADCs and 100% thyroid transcription factor (TTF1+). No mutations were detected in poorly differentiated NSCLC-not otherwise specified (NOS). There was a trend for improved overall survival (OS) among EGFR-M+ versus EGFR-M- patients (median OS=78 versus 17 months). In year 1, test failure rate was 19%, and associated with scant cellularity and low DNA concentrations. However 75% of samples with poor cellularity but representative of tumour were informative and mutation prevalence was 9%. In year 2, 755 samples were tested; mutation prevalence was 13% and test failure only 5.4%. Although samples with low DNA concentration (<2 ng/μL) had more test failures (30% versus 3.9% for [DNA]>2.2 ng/μL), the mutation rate was 9.2%. Routine epidermal growth factor receptor (EGFR) screening using diagnostic samples is fast and feasible even on samples with poor cellularity and DNA content. Mutations tend to occur in better-differentiated non-mucinous TTF1+ ADCs. Whether these histological criteria may be useful to select patients for EGFR testing merits further investigation. Copyright © 2011 Elsevier Ltd. All rights reserved.

Semi-Supervised Sparse Representation Based Classification for Face Recognition With Insufficient Labeled Samples

NASA Astrophysics Data System (ADS)

Gao, Yuan; Ma, Jiayi; Yuille, Alan L.

2017-05-01

This paper addresses the problem of face recognition when there is only few, or even only a single, labeled examples of the face that we wish to recognize. Moreover, these examples are typically corrupted by nuisance variables, both linear (i.e., additive nuisance variables such as bad lighting, wearing of glasses) and non-linear (i.e., non-additive pixel-wise nuisance variables such as expression changes). The small number of labeled examples means that it is hard to remove these nuisance variables between the training and testing faces to obtain good recognition performance. To address the problem we propose a method called Semi-Supervised Sparse Representation based Classification (S$^3$RC). This is based on recent work on sparsity where faces are represented in terms of two dictionaries: a gallery dictionary consisting of one or more examples of each person, and a variation dictionary representing linear nuisance variables (e.g., different lighting conditions, different glasses). The main idea is that (i) we use the variation dictionary to characterize the linear nuisance variables via the sparsity framework, then (ii) prototype face images are estimated as a gallery dictionary via a Gaussian Mixture Model (GMM), with mixed labeled and unlabeled samples in a semi-supervised manner, to deal with the non-linear nuisance variations between labeled and unlabeled samples. We have done experiments with insufficient labeled samples, even when there is only a single labeled sample per person. Our results on the AR, Multi-PIE, CAS-PEAL, and LFW databases demonstrate that the proposed method is able to deliver significantly improved performance over existing methods.

Supercritical fluid extraction of the non-polar organic compounds in meteorites

NASA Astrophysics Data System (ADS)

Sephton, M. A.; Pillinger, C. T.; Gilmour, I.

2001-01-01

The carbonaceous chondrite meteorites contain a variety of extraterrestrial organic molecules. These organic components provide a valuable insight into the formation and evolution of the solar system. Attempts at obtaining and interpreting this information source are hampered by the small sample sizes available for study and the interferences from terrestrial contamination. Supercritical fluid extraction represents an efficient and contamination-free means of isolating extraterrestrial molecules. Gas chromatography-mass spectrometry analyses of extracts from Orgueil and Cold Bokkeveld reveal a complex mixture of free non-polar organic molecules which include normal alkanes, isoprenoid alkanes, tetrahydronaphthalenes and aromatic hydrocarbons. These organic assemblages imply contributions from both terrestrial and extraterrestrial sources.

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

Cook, David L.; Schönbächler, Maria, E-mail: david.cook@erdw.ethz.ch

We report non-mass-dependent Fe isotopic data for troilite (FeS) inclusions from 10 iron meteorites, representing both non-magmatic (IAB) and magmatic groups (IIAB, IIIAB, IVA). No resolvable variations are present in the most neutron-rich isotope ({sup 58}Fe), but small deficits (≈−0.1 ε ) in {sup 56}Fe were observed in several inclusions. With the exception of several Ca–Al-rich inclusions in primitive meteorites, these are the first reported non-mass-dependent variations in Fe isotopes for material formed in the early solar system. Nucleosynthetic variations in Ni isotopes were previously reported in these same samples. The effects in Fe isotopes are not correlated with thosemore » in Ni, which suggests that the origins of the isotopic variations are decoupled from one another. The {sup 56}Fe deficits may represent incomplete mixing of the precursor dust in the protoplanetary disk. Alternatively, a parent body process (e.g., irradiation by galactic cosmic rays) may have modified the Fe isotopic compositions of some inclusions, which initially had homogeneous Fe isotopic compositions.« less

Raman spectroscopy for forensic examination of β-ketophenethylamine "legal highs": reference and seized samples of cathinone derivatives.

PubMed

Stewart, Samantha P; Bell, Steven E J; Fletcher, Nicholas C; Bouazzaoui, Samira; Ho, Yen Cheng; Speers, S James; Peters, K Laota

2012-01-20

Raman spectra of a representative range of β-ketophenethylamine (β-KP), the rapidly growing family of cathinone-related "legal high" recreational drugs, have been recorded. These spectra showed characteristic changes that were associated with the pattern of substitution on the aromatic rings, for example, the compounds carrying substituents at the 4- position could be distinguished from 3,4-methylenedioxy "ecstasy" derivatives. They also showed small but detectable changes with differences in substitution on the ethylamine substituent. These features allowed the β-KPs present in seized casework samples to be identified. The seized samples typically contained only small amounts of bulking agents, which meant that the band intensities of these components within averaged data were very small. In contrast, grid sampling normally gave at least some spectra which had a higher than average proportion of the bulking agent(s), which allowed them to also be identified. This study therefore demonstrates that Raman spectroscopy can be used both to provide a rapid, non-destructive technique for identification of this class of drugs in seized samples and to detect minor constituents, giving a composition profile which can be used for drugs intelligence work. Crown Copyright © 2011. Published by Elsevier B.V. All rights reserved.

Recruitment for Occupational Research: Using Injured Workers as the Point of Entry into Workplaces

PubMed Central

Koehoorn, Mieke; Trask, Catherine M.; Teschke, Kay

2013-01-01

Objective To investigate the feasibility, costs and sample representativeness of a recruitment method that used workers with back injuries as the point of entry into diverse working environments. Methods Workers' compensation claims were used to randomly sample workers from five heavy industries and to recruit their employers for ergonomic assessments of the injured worker and up to 2 co-workers. Results The final study sample included 54 workers from the workers’ compensation registry and 72 co-workers. This sample of 126 workers was based on an initial random sample of 822 workers with a compensation claim, or a ratio of 1 recruited worker to approximately 7 sampled workers. The average recruitment cost was CND$262/injured worker and CND$240/participating worksite including co-workers. The sample was representative of the heavy industry workforce, and was successful in recruiting the self-employed (8.2%), workers from small employers (<20 workers, 38.7%), and workers from diverse working environments (49 worksites, 29 worksite types, and 51 occupations). Conclusions The recruitment rate was low but the cost per participant reasonable and the sample representative of workers in small worksites. Small worksites represent a significant portion of the workforce but are typically underrepresented in occupational research despite having distinct working conditions, exposures and health risks worthy of investigation. PMID:23826387

Grey literature in systematic reviews: a cross-sectional study of the contribution of non-English reports, unpublished studies and dissertations to the results of meta-analyses in child-relevant reviews.

PubMed

Hartling, Lisa; Featherstone, Robin; Nuspl, Megan; Shave, Kassi; Dryden, Donna M; Vandermeer, Ben

2017-04-19

Systematic reviews (SRs) are an important source of information about healthcare interventions. A key component of a well-conducted SR is a comprehensive literature search. There is limited evidence on the contribution of non-English reports, unpublished studies, and dissertations and their impact on results of meta-analyses. Our sample included SRs from three Cochrane Review Groups: Acute Respiratory Infections (ARI), Infectious Diseases (ID), Developmental Psychosocial and Learning Problems (DPLP) (n = 129). Outcomes included: 1) proportion of reviews that searched for and included each study type; 2) proportion of relevant studies represented by each study type; and 3) impact on results and conclusions of the primary meta-analysis for each study type. Most SRs searched for non-English studies; however, these were included in only 12% of reviews and represented less than 5% of included studies. There was a change in results in only four reviews (total sample = 129); in two cases the change did not have an impact on the statistical or clinical significance of results. Most SRs searched for unpublished studies but the majority did not include these (only 6%) and they represented 2% of included studies. In most cases the impact of including unpublished studies was small; a substantial impact was observed in one case that relied solely on unpublished data. Few reviews in ARI (9%) and ID (3%) searched for dissertations compared to 65% in DPLP. Overall, dissertations were included in only nine SRs and represented less than 2% of included studies. In the majority of cases the change in results was negligible or small; in the case where a large change was noted, the estimate was more conservative without dissertations. The majority of SRs searched for non-English and unpublished studies; however, these represented a small proportion of included studies and rarely impacted the results and conclusions of the review. Inclusion of these study types may have an impact in situations where there are few relevant studies, or where there are questionable vested interests in the published literature. We found substantial variation in whether SRs searched for dissertations; in most reviews that included dissertations, these had little impact on results.

Infectious agent screening in canine blood donors in the United Kingdom.

PubMed

Crawford, K; Walton, J; Lewis, D; Tasker, S; Warman, S M

2013-08-01

Transfusion of blood products is an important component of veterinary emergency medicine. Donors must be carefully selected to minimise risk of transmission of blood-borne infectious agents. This study was devised to assess the prevalence of such agents in healthy, non-travelled UK dogs screened as prospective donors. Ethylenediaminetetraacetic acid blood samples from dogs donating blood between August 2007 and January 2012 were screened by polymerase chain reaction for haemotropic mycoplasmas, Bartonella, Babesia, Leishmania, Ehrlichia and Anaplasma spp. Dogs with positive or inconclusive results underwent repeat polymerase chain reaction testing. Four of 262 dogs had positive or inconclusive results at initial screening. Repeat polymerase chain reaction testing in each dog was negative, and none of the dogs developed clinical signs of disease. The positive results on initial screening may have represented false positives from sample contamination or amplification of non-target DNA. It is also possible that dogs were infected at initial sampling but successfully cleared infection before repeat testing. The low number of positive results obtained suggests that prevalence of these agents in a population of healthy UK dogs is low and that use of blood products is unlikely to represent a significant risk of transmission of these diseases. © 2013 British Small Animal Veterinary Association.

Coiled-coil domain-containing protein 8 inhibits the invasiveness and migration of non-small cell lung cancer cells.

PubMed

Jiang, Gui-Yang; Zhang, Xiu-Peng; Zhang, Yong; Xu, Hong-Tao; Wang, Liang; Li, Qing-Chang; Wang, En-Hua

2016-10-01

Lung cancer has always been the leading cause of death among patients with malignant tumors, and the majority of these patients die because of cancer cell invasion and metastasis. Previous studies have implicated coiled-coil domain-containing protein 8 (CCDC8) as a tumor suppressor in several types of cancer, such as breast and prostate cancers. However, the expression levels or functions of CCDC8 in lung cancer have not been elucidated. Here, we used immunohistochemical staining to measure CCDC8 expression in 147 samples from tumors and 30 samples from the adjacent normal lung tissues of patients with non-small cell lung cancer. CCDC8 was shown to be located predominantly in the cytoplasm and partially on the cell membrane, and its expression level was significantly lower in lung cancer samples than that in the adjacent normal lung tissues (P=.001). CCDC8 expression was closely related to tumor differentiation (P=.039), tumor-node-metastasis stage (P=.009), lymph node metastasis (P=.038), and prognosis (P=.043) of lung cancer. Transfection of A549 cells with CCDC8 significantly reduced cell invasion and migration (P<.05), whereas the invasiveness and migration capacity in CCDC8-knockdown A549 cells were significantly increased in comparison with the control cells (P<.05). Furthermore, we demonstrated that CCDC8 can downregulate the expression of Snail and upregulate the expression of E-cadherin by inhibiting p-P38 and p-IκBα. Collectively, CCDC8 may suppress the invasion and metastasis of lung cancer cells, and it may represent a promising therapeutic target for non-small cell lung cancer. Copyright © 2016 Elsevier Inc. All rights reserved.

The descriptive epidemiology of house dust mite-specific and total immunoglobin E in England using a nationally representative sample.

PubMed

Court, C S; Cook, D G; Strachan, D P

2002-07-01

Previous studies have shown that IgE levels vary according to factors such as age, gender and smoking but most studies have been small and none have been based on a nationally representative sample. To investigate the influence of epidemiological factors on serum total IgE and house dust mite-specific IgE levels. An interviewer-led questionnaire was carried out and blood samples taken from 24 952 people aged 11 and over as part of the 1995 and 1996 Health Surveys for England. Serum total IgE and house dust mite-specific IgE were measured. Both total and house dust mite-specific IgE were more frequently raised in men and in younger age groups. After adjusting for age and sex, raised total IgE was more common in current smokers and non-white ethnic groups and was not related to social class. The higher levels in non-white ethnic groups was not explained by smoking, urban living or being born outside the UK. Whilst total IgE levels declined in older age groups in non-smokers, among smokers they increased across successive age groups from 50 years onwards. In contrast, following adjustment for age and sex, raised house dust mite IgE was more common in non-manual workers and in some non-white ethnic groups but was not related to smoking. This large nationwide study provides further confirmation of differing epidemiological patterns for total serum IgE and allergen-specific sensitization. Indicative ranges for 'usual' values for a wide range of ages among men and women in England are given.

A universal method for the mutational analysis of K-ras and p53 gene in non-small-cell lung cancer using formalin-fixed paraffin-embedded tissue.

PubMed

Sarkar, F H; Valdivieso, M; Borders, J; Yao, K L; Raval, M M; Madan, S K; Sreepathi, P; Shimoyama, R; Steiger, Z; Visscher, D W

1995-12-01

The p53 tumor suppressor gene has been found to be altered in almost all human solid tumors, whereas K-ras gene mutations have been observed in a limited number of human cancers (adenocarcinoma of colon, pancreas, and lung). Studies of mutational inactivation for both genes in the same patient's sample on non-small-cell lung cancer have been limited. In an effort to perform such an analysis, we developed and compared methods (for the mutational detection of p53 and K-ras gene) that represent a modified and universal protocol, in terms of DNA extraction, polymerase chain reaction (PCR) amplification, and nonradioisotopic PCR-single-strand conformation polymorphism (PCR-SSCP) analysis, which is readily applicable to either formalin-fixed, paraffin-embedded tissues or frozen tumor specimens. We applied this method to the evaluation of p53 (exons 5-8) and K-ras (codon 12 and 13) gene mutations in 55 cases of non-small-cell lung cancer. The mutational status in the p53 gene was evaluated by radioisotopic PCR-SSCP and compared with PCR-SSCP utilizing our standardized nonradioisotopic detection system using a single 6-microns tissue section. The mutational patterns observed by PCR-SSCP were subsequently confirmed by PCR-DNA sequencing. The mutational status in the K-ras gene was similarly evaluated by PCR-SSCP, and the specific mutation was confirmed by Southern slot-blot hybridization using 32P-labeled sequence-specific oligonucleotide probes for codons 12 and 13. Mutational changes in K-ras (codon 12) were found in 10 of 55 (18%) of non-small-cell lung cancers. Whereas adenocarcinoma showed K-ras mutation in 33% of the cases at codon 12, only one mutation was found at codon 13. As expected, squamous cell carcinoma samples (25 cases) did not show K-ras mutations. Mutations at exons 5-8 of the p53 gene were documented in 19 of 55 (34.5%) cases. Ten of the 19 mutations were single nucleotide point mutations, leading to amino acid substitution. Six showed insertional mutation, and three showed deletion mutations. Only three samples showed mutations of both K-ras and p53 genes. We conclude that although K-ras and p53 gene mutations are frequent in non-small-cell lung cancer, mutations of both genes in the same patient's samples are not common. We also conclude that this universal nonradioisotopic method is superior to other similar methods and is readily applicable to the rapid screening of large numbers of formalin-fixed, paraffin-embedded or frozen samples for the mutational analysis of multiple genes.

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

PubMed

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

2015-09-01

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

Fast, exact k-space sample density compensation for trajectories composed of rotationally symmetric segments, and the SNR-optimized image reconstruction from non-Cartesian samples.

PubMed

Mitsouras, Dimitris; Mulkern, Robert V; Rybicki, Frank J

2008-08-01

A recently developed method for exact density compensation of non uniformly arranged samples relies on the analytically known cross-correlations of Fourier basis functions corresponding to the traced k-space trajectory. This method produces a linear system whose solution represents compensated samples that normalize the contribution of each independent element of information that can be expressed by the underlying trajectory. Unfortunately, linear system-based density compensation approaches quickly become computationally demanding with increasing number of samples (i.e., image resolution). Here, it is shown that when a trajectory is composed of rotationally symmetric interleaves, such as spiral and PROPELLER trajectories, this cross-correlations method leads to a highly simplified system of equations. Specifically, it is shown that the system matrix is circulant block-Toeplitz so that the linear system is easily block-diagonalized. The method is described and demonstrated for 32-way interleaved spiral trajectories designed for 256 image matrices; samples are compensated non iteratively in a few seconds by solving the small independent block-diagonalized linear systems in parallel. Because the method is exact and considers all the interactions between all acquired samples, up to a 10% reduction in reconstruction error concurrently with an up to 30% increase in signal to noise ratio are achieved compared to standard density compensation methods. (c) 2008 Wiley-Liss, Inc.

Modified-Symbol Digit Modalities Test for African Americans, Caribbean Black Americans and Non-Latino Whites: Nationally Representative Normative Data from the National Survey of American Life

PubMed Central

González, Hector M.; Whitfield, Keith E.; West, Brady T.; Williams, David R.; Lichtenberg, Peter; Jackson, James S.

2007-01-01

Normative neuropsychological data for U.S. racial/ethnic minorities is limited. Extant norms are based on small, regional groups that may not be nationally representative. The objectives of this study were to 1) provide norms for a modified Symbol Digit Modalities Test (M-SDMT) based on a nationally representative sample of African Americans, Caribbean Blacks and non-Latino Whites (NLW) living in areas with large populations of Blacks, and 2) determine significant correlates of M-SDMT performance. The M-SDMT was administered to a subset of respondents from the National Survey of American Life in standard, face-to-face interviews. M-SDMT performance was influenced by race/ethnicity, age, education, and gender. African Americans and NLW groups had similar M-SDMT performances, which differed from Caribbean Blacks. The Black ethnic differences in M-SDMT were not explained by the sociodemographic factors considered in this study. Unlike previous work, this study supports the consideration of Black ethnicity when evaluating Black neuropsychological test performance. PMID:17493782

Diversity and Impacts of Mining on the Non-Volant Small Mammal Communities of Two Vegetation Types in the Brazilian Amazon.

PubMed

Ardente, Natália Carneiro; Ferreguetti, Átilla Colombo; Gettinger, Donald; Leal, Pricila; Mendes-Oliveira, Ana Cristina; Martins-Hatano, Fernanda; Bergallo, Helena Godoy

2016-01-01

The Carajás National Forest contains some of the largest iron ore deposits in the world. The majority of the minerals are found below a plant community known as Savana Metalófila, or "Canga", which represents only 3% of the landscape within the Carajás National Forest (CNF). The aim of our study was to understand the diversity of community of non-volant small mammals in the two predominant vegetation types: Ombrophilous Forest and Canga, and to examine how mining impacts these communities. Sampling was conducted from January 2010 to August 2011 in 11 sampling sites divided by the total area of Canga and 12 sampling sites in the forest, totalizing 23 sites. Of these, 12 sites (Canga and Forest) were considered impacted areas located close to the mine (< 900 meters) and 11 sites (Canga and Forest), serving as controls, which were at least 7,000 meters from the mine. We recorded 28 species, 11 from the Order Didelphimorphia and 17 from the Order Rodentia. The two forest types shared 68.42% of the species found in the CNF. A gradient analysis (Non-metric multidimensional scaling) revealed that the first axis clearly separated the non-flying small mammal communities by vegetation type. Occupancy models showed that the detectability of species was affected by the distance from the mining activities. Of all the small mammals analyzed, 10 species were positively affected by the distance from mining in areas impacted (e.g. more likely to be detected farther from mining areas) and detectability was lower in impacted areas. However, three species were negatively affected by the distance from mining, with higher detectability in the impacted areas, and seven species showed no effect of their proximity to mining operations. To date, there are no studies in Brazil about the impact of mining on mammals or other vertebrates. This study reveals that the effect of mining may go beyond the forest destruction caused by the opening of the mining pits, but also may negatively affect sensitive wildlife species.

Diversity and Impacts of Mining on the Non-Volant Small Mammal Communities of Two Vegetation Types in the Brazilian Amazon

PubMed Central

Ardente, Natália Carneiro; Ferreguetti, Átilla Colombo; Gettinger, Donald; Leal, Pricila; Mendes-Oliveira, Ana Cristina; Martins-Hatano, Fernanda; Bergallo, Helena Godoy

2016-01-01

The Carajás National Forest contains some of the largest iron ore deposits in the world. The majority of the minerals are found below a plant community known as Savana Metalófila, or “Canga”, which represents only 3% of the landscape within the Carajás National Forest (CNF). The aim of our study was to understand the diversity of community of non-volant small mammals in the two predominant vegetation types: Ombrophilous Forest and Canga, and to examine how mining impacts these communities. Sampling was conducted from January 2010 to August 2011 in 11 sampling sites divided by the total area of Canga and 12 sampling sites in the forest, totalizing 23 sites. Of these, 12 sites (Canga and Forest) were considered impacted areas located close to the mine (<< 900 meters) and 11 sites (Canga and Forest), serving as controls, which were at least 7,000 meters from the mine. We recorded 28 species, 11 from the Order Didelphimorphia and 17 from the Order Rodentia. The two forest types shared 68.42% of the species found in the CNF. A gradient analysis (Non-metric multidimensional scaling) revealed that the first axis clearly separated the non-flying small mammal communities by vegetation type. Occupancy models showed that the detectability of species was affected by the distance from the mining activities. Of all the small mammals analyzed, 10 species were positively affected by the distance from mining in areas impacted (e.g. more likely to be detected farther from mining areas) and detectability was lower in impacted areas. However, three species were negatively affected by the distance from mining, with higher detectability in the impacted areas, and seven species showed no effect of their proximity to mining operations. To date, there are no studies in Brazil about the impact of mining on mammals or other vertebrates. This study reveals that the effect of mining may go beyond the forest destruction caused by the opening of the mining pits, but also may negatively affect sensitive wildlife species. PMID:27893798

Expression of vascular endothelial growth factor mRNA in non-small-cell lung carcinomas

PubMed Central

Fontanini, G; Boldrini, L; Chinè, S; Pisaturo, F; Basolo, F; Calcinai, A; Lucchi, M; Mussi, A; Angeletti, C A; Bevilacqua, G

1999-01-01

The vascular endothelial growth factor (VEGF) has been shown to be strictly related to vascular permeability and endothelial cell growth under physiological and pathological conditions. In tumour development and progression, VEGF plays a pivotal role in the development of the tumoral vascular network, and useful information in the progression of human cancer can be obtained by analysing the vascular endothelial growth factor expression of the tumours. In this study, we investigated the vascular endothelial growth factor transcript expression in non-small-cell lung carcinomas to evaluate the significance of this factor in a group of cancers in which the vascular pattern has been shown to significantly affect progression. Surgical samples of 42 patients with NSCLC were studied using reverse transcription polymerase chain reaction (PCR) analysis and in situ hybridization. Thirty-three out of 42 cases (78.6%) showed VEGF transcript expression predominantly as transcripts for the secretory forms of VEGF (isoforms 121 and 165). In situ hybridization, performed on 24 out of 42 samples, showed that the VEGF transcript expression was in several cases present in the cytoplasm both of neoplastic and normal cells, even if the VEGF mRNA was less expressed in the corresponding non-tumoral part. The VEGF 121 expression was associated with hilar and/or mediastinal nodal involvement (P = 0.02), and, taken together, the VEGF isoforms were shown to significantly influence overall (P = 0.02) and disease-free survival (P = 0.03). As a regulator of tumour angiogenesis, VEGF may represent a useful indicator of progression and poor prognosis in non-small-cell lung carcinomas. © 1999 Cancer Research Campaign PMID:9888482

Liquid biopsy based biomarkers in non-small cell lung cancer for diagnosis and treatment monitoring.

PubMed

Pérez-Callejo, David; Romero, Atocha; Provencio, Mariano; Torrente, María

2016-10-01

Advances in the knowledge of the biology of non-small cell lung cancer (NSCLC) have revealed molecular information used for systemic cancer therapy targeting metastatic disease, with an important impact on patients overall survival (OS) and quality of life. However, a biopsy of overt metastases is an invasive procedure limited to certain locations and not easily acceptable in the clinic. Moreover, a single biopsy cannot reflect the clonal heterogeneity of the tumor. The analysis of peripheral blood samples of cancer patients represents a new source of cancer-derived material, known as liquid biopsy, and its components can be obtained from almost all body fluids. These components have shown to reflect characteristics of the status of both the primary and metastatic diseases, helping the clinicians to move towards a personalized medicine. The present review focuses on the liquid biopsy components: circulating tumor cells (CTCS), circulating free DNA (cfDNA), exosomes and tumor-educated platelets (TEP); the isolation technologies used and their potential use for non-invasive screening, early diagnosis, prognosis, response to treatment and real time monitoring of the disease, in NSCLC patients.

Liquid biopsy based biomarkers in non-small cell lung cancer for diagnosis and treatment monitoring

PubMed Central

Pérez-Callejo, David; Provencio, Mariano

2016-01-01

Advances in the knowledge of the biology of non-small cell lung cancer (NSCLC) have revealed molecular information used for systemic cancer therapy targeting metastatic disease, with an important impact on patients overall survival (OS) and quality of life. However, a biopsy of overt metastases is an invasive procedure limited to certain locations and not easily acceptable in the clinic. Moreover, a single biopsy cannot reflect the clonal heterogeneity of the tumor. The analysis of peripheral blood samples of cancer patients represents a new source of cancer-derived material, known as liquid biopsy, and its components can be obtained from almost all body fluids. These components have shown to reflect characteristics of the status of both the primary and metastatic diseases, helping the clinicians to move towards a personalized medicine. The present review focuses on the liquid biopsy components: circulating tumor cells (CTCS), circulating free DNA (cfDNA), exosomes and tumor-educated platelets (TEP); the isolation technologies used and their potential use for non-invasive screening, early diagnosis, prognosis, response to treatment and real time monitoring of the disease, in NSCLC patients. PMID:27826527

Sampling in epidemiological research: issues, hazards and pitfalls.

PubMed

Tyrer, Stephen; Heyman, Bob

2016-04-01

Surveys of people's opinions are fraught with difficulties. It is easier to obtain information from those who respond to text messages or to emails than to attempt to obtain a representative sample. Samples of the population that are selected non-randomly in this way are termed convenience samples as they are easy to recruit. This introduces a sampling bias. Such non-probability samples have merit in many situations, but an epidemiological enquiry is of little value unless a random sample is obtained. If a sufficient number of those selected actually complete a survey, the results are likely to be representative of the population. This editorial describes probability and non-probability sampling methods and illustrates the difficulties and suggested solutions in performing accurate epidemiological research.

Sampling in epidemiological research: issues, hazards and pitfalls

PubMed Central

Tyrer, Stephen; Heyman, Bob

2016-01-01

Surveys of people's opinions are fraught with difficulties. It is easier to obtain information from those who respond to text messages or to emails than to attempt to obtain a representative sample. Samples of the population that are selected non-randomly in this way are termed convenience samples as they are easy to recruit. This introduces a sampling bias. Such non-probability samples have merit in many situations, but an epidemiological enquiry is of little value unless a random sample is obtained. If a sufficient number of those selected actually complete a survey, the results are likely to be representative of the population. This editorial describes probability and non-probability sampling methods and illustrates the difficulties and suggested solutions in performing accurate epidemiological research. PMID:27087985

Screening and staging for non-small cell lung cancer by serum laser Raman spectroscopy.

PubMed

Wang, Hong; Zhang, Shaohong; Wan, Limei; Sun, Hong; Tan, Jie; Su, Qiucheng

2018-08-05

Lung cancer is the leading cause of cancer-related death worldwide. Current clinical screening methods to detect lung cancer are expensive and associated with many complications. Raman spectroscopy is a spectroscopic technique that offers a convenient method to gain molecular information about biological samples. In this study, we measured the serum Raman spectral intensity of healthy volunteers and patients with different stages of non-small cell lung cancer. The purpose of this study was to evaluate the application of serum laser Raman spectroscopy as a low cost alternative method in the screening and staging of non-small cell lung cancer (NSCLC). The Raman spectra of the sera of peripheral venous blood were measured with a LabRAM HR 800 confocal Micro Raman spectrometer for individuals from five groups including 14 healthy volunteers (control group), 23 patients with stage I NSCLC (stage I group), 24 patients with stage II NSCLC (stage II group), 19 patients with stage III NSCLC (stage III group), 11 patients with stage IV NSCLC (stage IV group). Each serum sample was measured 3 times at different spots and the average spectra represented the signal of Raman spectra in each case. The Raman spectrum signal data of the five groups were statistically analyzed by analysis of variance (ANOVA), principal component analysis (PCA), linear discriminant analysis (LDA), and cross-validation. Raman spectral intensity was sequentially reduced in serum samples from control group, stage I group, stage II group and stage III/IV group. The strongest peak intensity was observed in the control group, and the weakest one was found in the stage III/IV group at bands of 848 cm -1 , 999 cm -1 , 1152 cm -1 , 1446 cm -1 and 1658 cm -1 (P < 0.05). Linear discriminant analysis showed that the sensitivity to identify healthy people, stage I, stage II, and stage III/IV NSCLC was 86%, 65%, 75%, and 87%, respectively; the specificity was 95%, 94%, 88%, and 93%, respectively; and the overall accuracy rate was 92% (71/77). The laser Raman spectroscopy can effectively identify patients with stage I, stage II or stage III/IV Non-Small Cell Lung cancer using patient serum samples. Copyright © 2018 Elsevier B.V. All rights reserved.

Variation in the shape and mechanical performance of the lower jaws in ceratopsid dinosaurs (Ornithischia, Ceratopsia).

PubMed

Maiorino, Leonardo; Farke, Andrew A; Kotsakis, Tassos; Teresi, Luciano; Piras, Paolo

2015-11-01

Ceratopsidae represents a group of quadrupedal herbivorous dinosaurs that inhabited western North America and eastern Asia during the Late Cretaceous. Although horns and frills of the cranium are highly variable across species, the lower jaw historically has been considered to be relatively conservative in morphology. Here, the lower jaws from 58 specimens representing 21 ceratopsoid taxa were sampled, using geometric morphometrics and 2D finite element analysis (FEA) to explore differences in morphology and mechanical performance across Ceratopsoidea (the clade including Ceratopsidae, Turanoceratops and Zuniceratops). Principal component analyses and non-parametric permuted manovas highlight Triceratopsini as a morphologically distinct clade within the sample. A relatively robust and elongate dentary, a larger and more elongated coronoid process, and a small and dorso-ventrally compressed angular characterize this clade, as well as the absolutely larger size. By contrast, non-triceratopsin chasmosaurines, Centrosaurini and Pachyrhinosaurini have similar morphologies to each other. Zuniceratops and Avaceratops are distinct from other taxa. No differences in size between Pachyrhinosaurini and Centrosaurini are recovered using non-parametric permuted anovas. Structural performance, as evaluated using a 2D FEA, is similar across all groups as measured by overall stress, with the exception of Triceratopsini. Shape, size and stress are phylogenetically constrained. A longer dentary as well as a long coronoid process result in a lower jaw that is reconstructed as relatively much more stressed in triceratopsins. © 2015 Anatomical Society.

Survey on the treatment of non-small-cell lung cancer in Italy.

PubMed

Alexanian, A; Torri, V

2000-07-01

The results of the Italian part of an international survey on therapeutic preferences and opinions about prognosis of patients affected by non-small-cell lung cancer (NSCLC) are shown. The investigation was conducted by the means of a postal questionnaire aiming to gather information on preferences about treatment and beliefs about survival of three hypothetical patients affected by NSCLC in different stages (T2N1M0, T2N3M0, M1); three sources of Italian physicians potentially treating patients affected by NSCLC were the target population: participants in the Adjuvant Lung Project Italy (Alpi) trial, a 20% random sample of the Italian Medical Oncology Association (AIOM) and representatives of almost all the pneumology wards in Italy. Overall, there were 287 evaluable responses, 89% of respondents were males, mean age was 46 years, years from graduation 21 and charge of patients per clinician 82. The most important result is the wide variation of answers both about therapy and prognosis. Expectations about size of prognosis improvement with a new chemotherapy seem to be excessive. The results are discussed in relation to the twin surveys of Canada and England and Wales and to the meta-analyses on the efficacy of chemotherapy as an adjunct to primary treatment and on postoperative radiotherapy in non-small-cell lung cancer.

Reduction in training time of a deep learning model in detection of lesions in CT

NASA Astrophysics Data System (ADS)

Makkinejad, Nazanin; Tajbakhsh, Nima; Zarshenas, Amin; Khokhar, Ashfaq; Suzuki, Kenji

2018-02-01

Deep learning (DL) emerged as a powerful tool for object detection and classification in medical images. Building a well-performing DL model, however, requires a huge number of images for training, and it takes days to train a DL model even on a cutting edge high-performance computing platform. This study is aimed at developing a method for selecting a "small" number of representative samples from a large collection of training samples to train a DL model for the could be used to detect polyps in CT colonography (CTC), without compromising the classification performance. Our proposed method for representative sample selection (RSS) consists of a K-means clustering algorithm. For the performance evaluation, we applied the proposed method to select samples for the training of a massive training artificial neural network based DL model, to be used for the classification of polyps and non-polyps in CTC. Our results show that the proposed method reduce the training time by a factor of 15, while maintaining the classification performance equivalent to the model trained using the full training set. We compare the performance using area under the receiveroperating- characteristic curve (AUC).

Basin Visual Estimation Technique (BVET) and Representative Reach Approaches to Wadeable Stream Surveys: Methodological Limitations and Future Directions

Treesearch

Lance R. Williams; Melvin L. Warren; Susan B. Adams; Joseph L. Arvai; Christopher M. Taylor

2004-01-01

Basin Visual Estimation Techniques (BVET) are used to estimate abundance for fish populations in small streams. With BVET, independent samples are drawn from natural habitat units in the stream rather than sampling "representative reaches." This sampling protocol provides an alternative to traditional reach-level surveys, which are criticized for their lack...

[Arf6, RalA and BIRC5 protein expression in non small cell lung cancer].

PubMed

Knizhnik, A V; Kovaleva, O B; Laktionov, K K; Mochal'nikova, V V; Komel'kov, A V; Chevkina, E M; Zborovskaia, I B

2011-01-01

Evaluation of tumor markers expression pattern which determines individual progression parameters is one of the major topics in molecular oncopathology research. This work presents research on expression analysis of several Ras-Ral associated signal transduction pathway proteins (Arf6, RalA and BIRC5) in accordance with clinical criteria in non small cell lung cancer patients. Using Western-blot analysis and RT-PCR Arf6, RalA and BIRC5 expression has been analyzed in parallel in 53 non small cell lung cancer samples of different origin. Arf6 protein expression was elevated in 55% non small cell lung cancer tumor samples in comparison with normal tissue. In the group of squamous cell lung cancer Arf6 expression elevation was observed more often. RalA protein expression was decreased in comparison to normal tissue samples in 64% of non small cell lung cancer regardless to morphological structure. Correlation between RalA protein expression decrease and absence of regional metastases was revealed for squamous cell lung cancer. BIRC5 protein expression in tumor samples versus corresponding normal tissue was 1.3 times more often elevated in the squamous cell lung cancer group (in 76% tumor samples). At the same time elevation of BIRC5 expression was fixed only in 63% of adenocarcinoma tumor samples. A statistically significant decrease (p = 0.0158) of RalA protein expression and increase (p = 0.0498) of Arf6 protein expression in comparison with normal tissue was found for T1-2N0M0 and T1-2N1-2M0 groups of squamous cell lung cancer correspondingly.

Characterization of microplastic litter from oceans by an innovative approach based on hyperspectral imaging.

PubMed

Serranti, Silvia; Palmieri, Roberta; Bonifazi, Giuseppe; Cózar, Andrés

2018-06-01

An innovative approach, based on HyperSpectral Imaging (HSI), was developed in order to set up an efficient method to analyze marine microplastic litter. HSI was applied to samples collected by surface-trawling plankton nets from several parts of the world (i.e. Arctic, Mediterranean, South Atlantic and North Pacific). Reliable information on abundance, size, shape and polymer type for the whole ensemble of plastic particles in each sample was retrieved from single hyperspectral images. The simultaneous characterization of the polymeric composition of the plastic debris represents an important analytical advantage considering that this information, and even the validation of the plastic nature of the small debris, is a common flaw in the analysis of marine microplastic pollution. HSI was revealed as a rapid, non-invasive, non-destructive and reliable technology for the characterization of the microplastic waste, opening a promising way for improving the plastic pollution monitoring. Copyright © 2018 Elsevier Ltd. All rights reserved.

Utilization of breast cancer screening methods in a developing nation: results from a nationally representative sample of Malaysian households.

PubMed

Dunn, Richard A; Tan, Andrew K G

2011-01-01

As is the case in many developing nations, previous studies of breast cancer screening behavior in Malaysia have used relatively small samples that are not nationally representative, thereby limiting the generalizability of results. Therefore, this study uses nationally representative data from the Malaysia Non-Communicable Disease Surveillance-1 to investigate the role of socio-economic status on breast cancer screening behavior in Malaysia, particularly differences in screening behaviour between ethnic groups. The decisions of 816 women above age 40 in Malaysia to screen for breast cancer using mammography, clinical breast exams (CBE), and breast self-exams (BSE) are modeled using logistic regression. Results indicate that after adjusting for differences in age, education, household income, marital status, and residential location, Malay women are less likely than Chinese and Indian women to utilize mammography, but more likely to perform BSE. Education level and urban residence are positively associated with utilization of each method, but these relationships vary across ethnicity. Higher education levels are strongly related to using each screening method among Chinese women, but have no statistically significant relationship to screening among Malays. © 2011 Wiley Periodicals, Inc.

Likelihood inference of non-constant diversification rates with incomplete taxon sampling.

PubMed

Höhna, Sebastian

2014-01-01

Large-scale phylogenies provide a valuable source to study background diversification rates and investigate if the rates have changed over time. Unfortunately most large-scale, dated phylogenies are sparsely sampled (fewer than 5% of the described species) and taxon sampling is not uniform. Instead, taxa are frequently sampled to obtain at least one representative per subgroup (e.g. family) and thus to maximize diversity (diversified sampling). So far, such complications have been ignored, potentially biasing the conclusions that have been reached. In this study I derive the likelihood of a birth-death process with non-constant (time-dependent) diversification rates and diversified taxon sampling. Using simulations I test if the true parameters and the sampling method can be recovered when the trees are small or medium sized (fewer than 200 taxa). The results show that the diversification rates can be inferred and the estimates are unbiased for large trees but are biased for small trees (fewer than 50 taxa). Furthermore, model selection by means of Akaike's Information Criterion favors the true model if the true rates differ sufficiently from alternative models (e.g. the birth-death model is recovered if the extinction rate is large and compared to a pure-birth model). Finally, I applied six different diversification rate models--ranging from a constant-rate pure birth process to a decreasing speciation rate birth-death process but excluding any rate shift models--on three large-scale empirical phylogenies (ants, mammals and snakes with respectively 149, 164 and 41 sampled species). All three phylogenies were constructed by diversified taxon sampling, as stated by the authors. However only the snake phylogeny supported diversified taxon sampling. Moreover, a parametric bootstrap test revealed that none of the tested models provided a good fit to the observed data. The model assumptions, such as homogeneous rates across species or no rate shifts, appear to be violated.

Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs.

PubMed

Saunders, Christopher T; Wong, Wendy S W; Swamy, Sajani; Becq, Jennifer; Murray, Lisa J; Cheetham, R Keira

2012-07-15

Whole genome and exome sequencing of matched tumor-normal sample pairs is becoming routine in cancer research. The consequent increased demand for somatic variant analysis of paired samples requires methods specialized to model this problem so as to sensitively call variants at any practical level of tumor impurity. We describe Strelka, a method for somatic SNV and small indel detection from sequencing data of matched tumor-normal samples. The method uses a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, while leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. We demonstrate that the method has superior accuracy and sensitivity on impure samples compared with approaches based on either diploid genotype likelihoods or general allele-frequency tests. The Strelka workflow source code is available at ftp://strelka@ftp.illumina.com/. csaunders@illumina.com

Comparison of the prevalence of KRAS-LCS6 polymorphism (rs61764370) within different tumour types (colorectal, breast, non-small cell lung cancer and brain tumours). A study of the Czech population.

PubMed

Uvirova, Magdalena; Simova, Jarmila; Kubova, Barbora; Dvorackova, Nina; Tomaskova, Hana; Sedivcova, Monika; Dite, Petr

2015-09-01

A germline SNP (rs61764370) is located in a let-7 complementary site (LCS6) in the 3'UTR of KRAS oncogene, and it was found to alter the binding capability of the mature let-7 microRNA to the KRAS mRNA. The aim of the study was to evaluate the frequency of the KRAS-LCS6 variant allele in different cancer types that included patients with colorectal cancer (CRC), breast cancer (BC), non-small cell lung cancer (NSCLC) and brain tumour patient subgroups from the Czech Republic. The occurrence of this genetic variant was correlated with the presence of selected somatic mutations representing predictive biomarkers in the respective tumours. DNA of tumour tissues was isolated from 428 colorectal cancer samples, 311 non-small cell lung cancer samples, 195 breast cancer samples and 151 samples with brain tumour. Analysis of SNP (rs61764370) was performed by the PCR+RFLP method and direct sequencing. KRAS, BRAF and EGFR mutation status was assessed using real-time PCR. The status of the HER2 gene was assessed using the FISH method. The KRAS-LCS6 TG genotype has been detected in 16.4% (32/195) of breast cancer cases (in HER2 positive breast cancer 3.3%, in HER2 negative breast cancer 20.1%), in 12.4% (53/428) of CRC cases (KRAS/BRAF wild type CRC in 10.6%, KRAS mutant CRC in 10.1%, BRAF V600E mutant CRC in 18.5%), in 13.2% (41/311) of NSCLC samples, (EGFR mutant NSCLC patients in 8%, EGFR wild type NSCLC in 12.9%), and 17.9% (27/151) of brain tumour cases. The KRAS-LCS6 TG genotype was not significantly different across the studied tumours. In our study, the GG genotype has not been found among the cancer samples. Based on the findings, it is concluded that the occurrence of the KRAS-LCS6 TG genotype was statistically significantly different in association with status of the HER2 gene in breast cancer. Furthermore, significant association between the mutation status of analysed somatic variants in genes of the EGFR signalling pathway (KRAS, BRAF, EGFR) and the KRAS-LCS6 genotype in colorectal cancer and NSCLC has not been established.

Reporting Rape in a National Sample of College Women

PubMed Central

Wolitzky-Taylor, Kate B.; Resnick, Heidi S.; Amstadter, Ananda B.; McCauley, Jenna L.; Ruggiero, Kenneth J.; Kilpatrick, Dean G.

2011-01-01

Introduction Studies indicate that a small percentage of rapes are reported to law enforcement officials. Research also suggests that rapes perpetrated by a stranger are more likely to be reported and that rapes involving drugs and/or alcohol are less likely to be reported. College women represent a unique and understudied population with regard to reporting rape. Methods In the current study, we interviewed a national sample of 2,000 college women about rape experiences in 2006. Results Only 11.5% of college women in the sample reported their most recent/only rape experience to authorities, with only 2.7% of rapes involving drugs and/or alcohol reported. Minority status (i.e., non-white race) was associated with lower likelihood of reporting, whereas sustaining injuries during the rape was associated with increased likelihood of reporting. Discussion Reporting, particularly for rapes involving drugs and alcohol, is low among college women. Implications for policy are discussed. PMID:21823952

REPRESENTATIVE SAMPLING AND ANALYSIS OF HETEROGENEOUS SOILS

EPA Science Inventory

Standard sampling and analysis methods for hazardous substances in contaminated soils currently are available and routinely employed. Standard methods inherently assume a homogeneous soil matrix and contaminant distribution; therefore only small sample quantities typically are p...

Neighbourhood non-employment and daily smoking: a population-based study of women and men in Sweden.

PubMed

Ohlander, Emma; Vikström, Max; Lindström, Martin; Sundquist, Kristina

2006-02-01

To examine whether neighbourhood non-employment is associated with daily smoking after adjustment for individual characteristics, such as employment status. Cross-sectional study of a simple, random sample of 31,164 women and men aged 25-64, representative of the entire population in Sweden. Data were collected from the years 1993-2000. The individual variables included age, sex, employment status, occupation and housing tenure. Logistic regression was used in the analysis with neighbourhood non-employment rates measured at small area market statistics level. There was a significant association between neighbourhood non-employment rates and daily smoking for both women and men. After adjustment for employment status and housing tenure the odds ratios of daily smoking were 1.39 (95% CI = 1.22-1.58) for women and 1.41 (95% CI = 1.23-1.61) for men living in neighbourhoods with the highest non-employment rates. The individual variables of unemployment, low occupational level and renting were associated with daily smoking. Neighbourhood non-employment is associated with daily smoking. Smoking prevention in primary health care should address both individuals and neighbourhoods.

Testing non-inferiority of a new treatment in three-arm clinical trials with binary endpoints.

PubMed

Tang, Nian-Sheng; Yu, Bin; Tang, Man-Lai

2014-12-18

A two-arm non-inferiority trial without a placebo is usually adopted to demonstrate that an experimental treatment is not worse than a reference treatment by a small pre-specified non-inferiority margin due to ethical concerns. Selection of the non-inferiority margin and establishment of assay sensitivity are two major issues in the design, analysis and interpretation for two-arm non-inferiority trials. Alternatively, a three-arm non-inferiority clinical trial including a placebo is usually conducted to assess the assay sensitivity and internal validity of a trial. Recently, some large-sample approaches have been developed to assess the non-inferiority of a new treatment based on the three-arm trial design. However, these methods behave badly with small sample sizes in the three arms. This manuscript aims to develop some reliable small-sample methods to test three-arm non-inferiority. Saddlepoint approximation, exact and approximate unconditional, and bootstrap-resampling methods are developed to calculate p-values of the Wald-type, score and likelihood ratio tests. Simulation studies are conducted to evaluate their performance in terms of type I error rate and power. Our empirical results show that the saddlepoint approximation method generally behaves better than the asymptotic method based on the Wald-type test statistic. For small sample sizes, approximate unconditional and bootstrap-resampling methods based on the score test statistic perform better in the sense that their corresponding type I error rates are generally closer to the prespecified nominal level than those of other test procedures. Both approximate unconditional and bootstrap-resampling test procedures based on the score test statistic are generally recommended for three-arm non-inferiority trials with binary outcomes.

Design and Weighting Methods for a Nationally Representative Sample of HIV-infected Adults Receiving Medical Care in the United States-Medical Monitoring Project

PubMed Central

Iachan, Ronaldo; H. Johnson, Christopher; L. Harding, Richard; Kyle, Tonja; Saavedra, Pedro; L. Frazier, Emma; Beer, Linda; L. Mattson, Christine; Skarbinski, Jacek

2016-01-01

Background: Health surveys of the general US population are inadequate for monitoring human immunodeficiency virus (HIV) infection because the relatively low prevalence of the disease (<0.5%) leads to small subpopulation sample sizes. Objective: To collect a nationally and locally representative probability sample of HIV-infected adults receiving medical care to monitor clinical and behavioral outcomes, supplementing the data in the National HIV Surveillance System. This paper describes the sample design and weighting methods for the Medical Monitoring Project (MMP) and provides estimates of the size and characteristics of this population. Methods: To develop a method for obtaining valid, representative estimates of the in-care population, we implemented a cross-sectional, three-stage design that sampled 23 jurisdictions, then 691 facilities, then 9,344 HIV patients receiving medical care, using probability-proportional-to-size methods. The data weighting process followed standard methods, accounting for the probabilities of selection at each stage and adjusting for nonresponse and multiplicity. Nonresponse adjustments accounted for differing response at both facility and patient levels. Multiplicity adjustments accounted for visits to more than one HIV care facility. Results: MMP used a multistage stratified probability sampling design that was approximately self-weighting in each of the 23 project areas and nationally. The probability sample represents the estimated 421,186 HIV-infected adults receiving medical care during January through April 2009. Methods were efficient (i.e., induced small, unequal weighting effects and small standard errors for a range of weighted estimates). Conclusion: The information collected through MMP allows monitoring trends in clinical and behavioral outcomes and informs resource allocation for treatment and prevention activities. PMID:27651851

Relationship between hyperemesis gravidarum and small-for-gestational-age in the Japanese population: the Japan Environment and Children's Study (JECS).

PubMed

Morokuma, Seiichi; Shimokawa, Mototsugu; Kato, Kiyoko; Sanefuji, Masafumi; Shibata, Eiji; Tsuji, Mayumi; Senju, Ayako; Kawamoto, Toshihiro; Kusuhara, Koichi

2016-08-26

Small-for-gestational-age in infancy is a known risk factor not only for short-term prognosis but also for several long-term outcomes, such as neurological and metabolic disorders in adulthood. Previous research has shown that severe nausea and vomiting in early pregnancy (NVP) and hyperemesis gravidarum, which is an extreme form of NVP, represent risk factors for small-for-gestational-age birth. However, there is no clear consensus on this association. Thus, in the present study, we investigated the correlation between hyperemesis gravidarum and NVP on the one hand, and infant birth weight on the other, using data from the Japan Environment and Children's Study (JECS). The data utilized in the present study were obtained from the JECS, an ongoing cohort study that began in January 2011. Our sample size was 8635 parent-child pairs. The presence or absence of severe NVP, hyperemesis gravidarum, and potential confounding factors were noted. A multivariable regression analysis was used to estimate risks for small-for-gestational-age birth, and the results were expressed as risk ratios and 95 % confidence intervals. The risk ratios of small-for-gestational-age birth (95 % confidence interval) for mothers with severe NVP and those with hyperemesis gravidarum were 0.86 (0.62-1.19) and 0.81 (0.39-1.66), respectively, which represents a non-significant result. In our analysis of JECS data, neither severe NVP nor hyperemesis gravidarum was associated with increased risk for small-for-gestational-age birth.

Human Resource Development in Small Business: An Application of Brethower's Performance Principles to on the Job Training

ERIC Educational Resources Information Center

Twyford, Devon; Alagaraja, Meera; Shuck, Brad

2016-01-01

Small businesses provide economic infrastructure in which communities develop and thrive and, in the United States alone, currently represent 99.7 percent of all employer firms. However, many small businesses fail to thrive past the first two years of establishment. Of the reasons small businesses fail, limited or non-existent employee training…

Optimized Heart Sampling and Systematic Evaluation of Cardiac Therapies in Mouse Models of Ischemic Injury: Assessment of Cardiac Remodeling and Semi-Automated Quantification of Myocardial Infarct Size.

PubMed

Valente, Mariana; Araújo, Ana; Esteves, Tiago; Laundos, Tiago L; Freire, Ana G; Quelhas, Pedro; Pinto-do-Ó, Perpétua; Nascimento, Diana S

2015-12-02

Cardiac therapies are commonly tested preclinically in small-animal models of myocardial infarction. Following functional evaluation, post-mortem histological analysis is essential to assess morphological and molecular alterations underlying the effectiveness of treatment. However, non-methodical and inadequate sampling of the left ventricle often leads to misinterpretations and variability, making direct study comparisons unreliable. Protocols are provided for representative sampling of the ischemic mouse heart followed by morphometric analysis of the left ventricle. Extending the use of this sampling to other types of in situ analysis is also illustrated through the assessment of neovascularization and cellular engraftment in a cell-based therapy setting. This is of interest to the general cardiovascular research community as it details methods for standardization and simplification of histo-morphometric evaluation of emergent heart therapies. © 2015 by John Wiley & Sons, Inc. Copyright © 2015 John Wiley & Sons, Inc.

Trace elemental analysis of glass and paint samples of forensic interest by ICP-MS using laser ablation solid sample introduction

NASA Astrophysics Data System (ADS)

Almirall, Jose R.; Trejos, Tatiana; Hobbs, Andria; Furton, Kenneth G.

2003-09-01

The importance of small amounts of glass and paint evidence as a means to associate a crime event to a suspect or a suspect to another individual has been demonstrated in many cases. Glass is a fragile material that is often found at the scenes of crimes such as burglaries, hit-and-run accidents and violent crime offenses. Previous work has demonstrated the utility of elemental analysis by solution ICP-MS of small amounts of glass for the comparison between a fragment found at a crime scene to a possible source of the glass. The multi-element capability and the sensitivity of ICP-MS combined with the simplified sample introduction of laser ablation prior to ion detection provides for an excellent and relatively non-destructive technique for elemental analysis of glass fragments. The direct solid sample introduction technique of laser ablation (LA) is reported as an alternative to the solution method. Direct solid sampling provides several advantages over solution methods and shows great potential for a number of solid sample analyses in forensic science. The advantages of laser ablation include the simplification of sample preparation, thereby reducing the time and complexity of the analysis, the elimination of handling acid dissolution reagents such as HF and the reduction of sources of interferences in the ionization plasma. Direct sampling also provides for essentially "non-destructive" sampling due to the removal of very small amounts of sample needed for analysis. The discrimination potential of LA-ICP-MS is compared with previously reported solution ICP-MS methods using external calibration with internal standardization and a newly reported solution isotope dilution (ID) method. A total of ninety-one different glass samples were used for the comparison study using the techniques mentioned. One set consisted of forty-five headlamps taken from a variety of automobiles representing a range of twenty years of manufacturing dates. A second set consisted of forty-six automotive glasses (side windows and windshields) representing casework glass from different vehicle manufacturers over several years was also characterized by RI and elemental composition analysis. The solution sample introduction techniques (external calibration and isotope dilution) provide for excellent sensitivity and precision but have the disadvantages of destroying the sample and also involve complex sample preparation. The laser ablation method was simpler, faster and produced comparable discrimination to the EC-ICP-MS and ID-ICP-MS. LA-ICP-MS can provide for an excellent alternative to solution analysis of glass in forensic casework samples. Paints and coatings are frequently encountered as trace evidence samples submitted to forensic science laboratories. A LA-ICP-MS method has been developed to complement the commonly used techniques in forensic laboratories in order to better characterize these samples for forensic purposes. Time-resolved plots of each sample can be compared to associate samples to each other or to discriminate between samples. Additionally, the concentration of lead and the ratios of other elements have been determined in various automotive paints by the reported method. A sample set of eighteen (18) survey automotive paint samples have been analyzed with the developed method in order to determine the utility of LA-ICP-MS and to compare the method to the more commonly used scanning electron microscopy (SEM) method for elemental characterization of paint layers in forensic casework.

Comparing interval estimates for small sample ordinal CFA models

PubMed Central

Natesan, Prathiba

2015-01-01

Robust maximum likelihood (RML) and asymptotically generalized least squares (AGLS) methods have been recommended for fitting ordinal structural equation models. Studies show that some of these methods underestimate standard errors. However, these studies have not investigated the coverage and bias of interval estimates. An estimate with a reasonable standard error could still be severely biased. This can only be known by systematically investigating the interval estimates. The present study compares Bayesian, RML, and AGLS interval estimates of factor correlations in ordinal confirmatory factor analysis models (CFA) for small sample data. Six sample sizes, 3 factor correlations, and 2 factor score distributions (multivariate normal and multivariate mildly skewed) were studied. Two Bayesian prior specifications, informative and relatively less informative were studied. Undercoverage of confidence intervals and underestimation of standard errors was common in non-Bayesian methods. Underestimated standard errors may lead to inflated Type-I error rates. Non-Bayesian intervals were more positive biased than negatively biased, that is, most intervals that did not contain the true value were greater than the true value. Some non-Bayesian methods had non-converging and inadmissible solutions for small samples and non-normal data. Bayesian empirical standard error estimates for informative and relatively less informative priors were closer to the average standard errors of the estimates. The coverage of Bayesian credibility intervals was closer to what was expected with overcoverage in a few cases. Although some Bayesian credibility intervals were wider, they reflected the nature of statistical uncertainty that comes with the data (e.g., small sample). Bayesian point estimates were also more accurate than non-Bayesian estimates. The results illustrate the importance of analyzing coverage and bias of interval estimates, and how ignoring interval estimates can be misleading. Therefore, editors and policymakers should continue to emphasize the inclusion of interval estimates in research. PMID:26579002

Comparing interval estimates for small sample ordinal CFA models.

PubMed

Natesan, Prathiba

2015-01-01

Robust maximum likelihood (RML) and asymptotically generalized least squares (AGLS) methods have been recommended for fitting ordinal structural equation models. Studies show that some of these methods underestimate standard errors. However, these studies have not investigated the coverage and bias of interval estimates. An estimate with a reasonable standard error could still be severely biased. This can only be known by systematically investigating the interval estimates. The present study compares Bayesian, RML, and AGLS interval estimates of factor correlations in ordinal confirmatory factor analysis models (CFA) for small sample data. Six sample sizes, 3 factor correlations, and 2 factor score distributions (multivariate normal and multivariate mildly skewed) were studied. Two Bayesian prior specifications, informative and relatively less informative were studied. Undercoverage of confidence intervals and underestimation of standard errors was common in non-Bayesian methods. Underestimated standard errors may lead to inflated Type-I error rates. Non-Bayesian intervals were more positive biased than negatively biased, that is, most intervals that did not contain the true value were greater than the true value. Some non-Bayesian methods had non-converging and inadmissible solutions for small samples and non-normal data. Bayesian empirical standard error estimates for informative and relatively less informative priors were closer to the average standard errors of the estimates. The coverage of Bayesian credibility intervals was closer to what was expected with overcoverage in a few cases. Although some Bayesian credibility intervals were wider, they reflected the nature of statistical uncertainty that comes with the data (e.g., small sample). Bayesian point estimates were also more accurate than non-Bayesian estimates. The results illustrate the importance of analyzing coverage and bias of interval estimates, and how ignoring interval estimates can be misleading. Therefore, editors and policymakers should continue to emphasize the inclusion of interval estimates in research.

Characteristics associated with organizational independence in consumer-operated service organizations.

PubMed

Tanenbaum, Sandra J

2011-01-01

This research compares two types of consumer organizations in one state in order to explore the significance of organizational independence for internal structure/operations and external relationships. The first type, consumeroperated service organizations (COSOs), are independent and fully self-governing; the second are peer-support service organizations (PSSOs), which are part of larger non-consumer entities. Mail surveys were completed by COSO and PSSO directors of a geographically representative sample of organizations; telephone interviews were conducted with a sub-sample. Owing to small sample size, matched COSO-PSSO pairs were analyzed using non-parametric statistics. COSOs and PSSOs are similar in some ways, e.g., types of services provided, but significantly different on internal variables, such as budget size, and external variables, such as number of relationships with community groups. Organizational independence appears to be a significant characteristic for consumer service organizations and should be encouraged by funders and among participants. Funders might establish administrative and/or programmatic measures to support consumer organizations that are independent or moving toward independence; their participants would also benefit from the provision, by authorities or advocates, of materials to guide organizations toward, for example, 501(c)3 status.

Not Too Small To Care: Small Businesses and Child Care. National Advisory Panel Exchange #2.

ERIC Educational Resources Information Center

Eichman, Caroline; Reisman, Barbara

This report of the Child Care Action Committee's National Advisory Panel profiles 29 small businesses employing under 250 workers in 15 states which offer child care benefits to their employees. These businesses do not constitute a representative sample of small businesses. A series of factors for small businesses to consider when planning a child…

Next generation sequencing techniques in liquid biopsy: focus on non-small cell lung cancer patients.

PubMed

Malapelle, Umberto; Pisapia, Pasquale; Rocco, Danilo; Smeraglio, Riccardo; di Spirito, Maria; Bellevicine, Claudio; Troncone, Giancarlo

2016-10-01

The advent of genomic based personalized medicine has led to multiple advances in the molecular characterization of many tumor types, such as non-small cell lung cancer (NSCLC). NSCLC is diagnosed in most cases on small tissue samples that may be not always sufficient for EGFR mutational assessment to select patients for first and second generations' tyrosine kinase inhibitors (TKIs) therapy. In patients without tissue availability at presentation, the analysis of cell free DNA (cfDNA) derived from liquid biopsy samples, in particular from plasma, represent an established alternative to provide EGFR mutational testing for treatment decision making. In addition, a new paradigm for TKIs resistance management was recently approved by Food and Drug Administration, supporting the liquid biopsy based genotyping prior to tissue based genotyping for the detection of T790M mutation to select patients for third generation TKIs. In these settings, real time PCR (RT-PCR) and digital PCR 'targeted' methods, which detect known mutations by specific probes, have extensively been adopted. Taking into account the restricted reference range and the limited multiplexing power of these targeted methods, the performance of liquid biopsy analyses may be further improved by next generation sequencing (NGS). While most tissue based NGS genotyping is well established, liquid biopsy NGS application is challenging, requiring a careful validation of the whole process, from blood collection to variant calling. Here we review this evolving field, highlighting those methodological points that are crucial to accurately select NSCLC patients for TKIs treatment administration by NGS on cfDNA.

Determining the sample size required to establish whether a medical device is non-inferior to an external benchmark.

PubMed

Sayers, Adrian; Crowther, Michael J; Judge, Andrew; Whitehouse, Michael R; Blom, Ashley W

2017-08-28

The use of benchmarks to assess the performance of implants such as those used in arthroplasty surgery is a widespread practice. It provides surgeons, patients and regulatory authorities with the reassurance that implants used are safe and effective. However, it is not currently clear how or how many implants should be statistically compared with a benchmark to assess whether or not that implant is superior, equivalent, non-inferior or inferior to the performance benchmark of interest.We aim to describe the methods and sample size required to conduct a one-sample non-inferiority study of a medical device for the purposes of benchmarking. Simulation study. Simulation study of a national register of medical devices. We simulated data, with and without a non-informative competing risk, to represent an arthroplasty population and describe three methods of analysis (z-test, 1-Kaplan-Meier and competing risks) commonly used in surgical research. We evaluate the performance of each method using power, bias, root-mean-square error, coverage and CI width. 1-Kaplan-Meier provides an unbiased estimate of implant net failure, which can be used to assess if a surgical device is non-inferior to an external benchmark. Small non-inferiority margins require significantly more individuals to be at risk compared with current benchmarking standards. A non-inferiority testing paradigm provides a useful framework for determining if an implant meets the required performance defined by an external benchmark. Current contemporary benchmarking standards have limited power to detect non-inferiority, and substantially larger samples sizes, in excess of 3200 procedures, are required to achieve a power greater than 60%. It is clear when benchmarking implant performance, net failure estimated using 1-KM is preferential to crude failure estimated by competing risk models. © 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.

A Comparison of Basinwide and Representative Reach Habitat Survey Techniques in Three Southern Appalachian Watersheds

Treesearch

C. Andrew Dolloff; Holly E. Jennings

1997-01-01

We compared estimates of stream habitat at the watershed scale using the basinwide visual estimation technique (BVET) and the representative reach extrapolation technique (RRET) in three small watersheds in the Appalachian Mountains. Within each watershed, all habitat units were sampled by the BVET, in contrast, three or four 100-m reaches were sampled with the RRET....

ALK status testing in non-small-cell lung carcinoma by FISH on ThinPrep slides with cytology material.

PubMed

Minca, Eugen C; Lanigan, Christopher P; Reynolds, Jordan P; Wang, Zhen; Ma, Patrick C; Cicenia, Joseph; Almeida, Francisco A; Pennell, Nathan A; Tubbs, Raymond R

2014-04-01

Oncogenic anaplastic lymphoma kinase (ALK) gene rearrangements in non-small-cell lung carcinomas (NSCLC) provide the basis for targeted therapy with crizotinib and other specific ALK inhibitors. Treatment eligibility is conventionally determined by the Food and Drug Administration-approved companion diagnostic fluorescence in situ hybridization (FISH) assay on paraffin-embedded tissue (PET). On limited samples such as fine needle aspiration-derived cytoblocks, FISH for ALK is often uninformative. FISH performed on liquid-based ThinPrep slides (ThinPrep-FISH) may represent a robust alternative. Two hundred thirty cytology samples from 217 patients with advanced NSCLC, including a consecutive series of 179 specimens, were used to generate matched ThinPrep slides and paraffin cytoblocks. The same ThinPrep slides used for cytologic diagnosis were assessed by standard ALK break-apart two-color probe FISH, after etching of tumor areas. Ultrasensitive ALK immunohistochemistry (IHC) on corresponding cytoblocks [D5F3 antibody, OptiView signal amplification] served as the reference data set. ThinPrep-FISH ALK signals were robust in 228 of 230 cases and not compromised by nuclear truncation inherent in paraffin-embedded tissue-FISH; only two samples displayed no signals. Nine of 178 informative cases (5%) in the consecutive series and 18 of 228 informative cases (7.8%) overall were ALK rearranged by ThinPrep-FISH. In 154 informative matched ThinPrep-FISH and cytoblock-IHC samples, 152 were concordant (10, 6.5% ALK status positive; 142, 92.2% ALK status negative), and two (1.3%) were ThinPrep-FISH positive but IHC negative (sensitivity 100%, specificity 98.6%, overall agreement 98.7%). Detection of ALK gene rearrangements in liquid cytology ThinPrep slides derived from patients with NSCLC can be confidently used for clinical ALK molecular testing.

Analysis of oxidative stress biomarkers using a simultaneous competitive/non-competitive micromosaic immunoassay.

PubMed

Murphy, Brian M; Dandy, David S; Henry, Charles S

2009-04-27

Immunoassays represent a core workhorse methodology for many applications ranging from clinical diagnostics to environmental monitoring. In traditional formats such as the enzyme linked immunosorbent assay (ELISA), analytes are measured singly or in small sets. As more biomarkers are identified for disease states, there is a need to develop methods that can measure multiple markers simultaneously. Immunoaffinity arrays are one such chemistry that can achieve multi-marker screening. Most arrays are performed in either competitive or non-competitive formats, where the former are used predominantly for small molecules and the later for macromolecules. To date, ELISA and immunoaffinity array methods have relied exclusively on one of these formats and not the other. Here an immunoaffinity array method capable of performing simultaneous competitive and non-competitive analysis generated using micromosaic immunoassay techniques is introduced for the analysis of metabolites and proteins. In this report, three markers of oxidative stress were used as a model system. The method described here demonstrates the simultaneous analysis of 3-nitrotyrosine, by indirect competitive immunoassay while the enzymes catalase and superoxide dismutase are analyzed by non-competitive sandwich immunoassay. The method requires less than 1 microL sample and 45 min for completion. Logistic curve fits and LOD (limits of detection) statistical analysis of the binding results are presented and show good agreement with published data for these antibody-antigen systems.

Comparison of Grab, Air, and Surface Results for Radiation Site Characterization

NASA Astrophysics Data System (ADS)

Glassford, Eric Keith

2011-12-01

The use of proper sampling methods and sample types for evaluating sites believed to be contaminated with radioactive materials is necessary to avoid misrepresenting conditions at the site. This study was designed to investigate if the site characterization, based upon uranium contamination measured in different types of samples, is dependent upon the mass of the sample collected. A bulk sample of potentially contaminated interior dirt was collected from an abandoned metal processing mill that rolled uranium between 1948 and 1956. The original mill dates from 1910 and has a dirt floor. The bulk sample was a mixture of dirt, black and yellow particles of metal dust, and small fragments of natural debris. Small mass (approximately 0.75 grams (g)) and large mass (approximately 70g) grab samples were prepared from the bulk sample material to simulate collection of a "grab" type sample. Air sampling was performed by re-suspending a portion of the bulk sample material using a vibration table to simulate airborne contamination that might be present during site remediation. Additionally, samples of removable contaminated surface dust were collected on 47 mm diameter filter paper by wiping the surfaces of the exposure chamber used to resuspend the bulk material. Certified reference materials, one containing a precisely known quantity of U 3O8 and one containing a known quantity of natural uranium, were utilized to calibrate the gamma spectrometry measurement system. Non-destructive gamma spectrometry measurements were used to determine the content of uranium-235 (235U) at 185 keV and 143 keV, thorium-234 (234Th) at 63 keV, and protactinium-234m (234mPa) at 1001 keV in each sample. Measurement of natural uranium in small, 1 g samples is usually accomplished by radiochemical analysis in order to measure alpha particles emitted by 238U, 235U, and 234U. However, uranium in larger bulk samples can also be measured non-destructively using gamma spectrometry to detect the low energy photons from 234Th and 234mPa, the short-lived decay products of 238U, and 235U. Two sided t-tests and coefficient of variation were used to compare sampling types. The large grab samples had the lowest calculated coefficient of variation results for activity and atom percentage. The wipe samples had the highest calculated coefficient of variation of mean specific activity (dis/sec/g) for all three energies. The air filter samples had the highest coefficient of variation calculation for mean atom percentage, for both uranium isotopes examined. The data indicated that the large mass sample was the most effective at characterizing the rolling mill radioactive site conditions, since this would indicate which samples had the smallest variations compared to the mean. Additionally, measurement results of natural uranium in the samples indicate that the distribution of radioactive contamination at the sampling location is most likely non-homogeneous and that the size of the sample collected and analyzed must be sufficiently large to insure that the analytical results are truly representative of the activity present.

Sample Preparation Techniques for Grain Boundary Characterization of Annealed TRISO-Coated Particles

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

Dunzik-Gougar, M. L.; van Rooyen, I. J.; Hill, C. M.

Crystallographic information about chemical vapor deposition layers of silicon carbide (SiC) is essential to understanding layer performance, especially when the layers are in non planar geometries, such as spherical. We performed electron Back Scatter Diffraction (EBSD) analysis of spherical SiC layers using a different approach to sample focus ion beam milling technique to avoid the negative impacts of traditional sample polishing and to address the need of very small samples of irradiated materials for analysis. Mechanical and chemical grinding and polishing of sample surfaces can introduce lattice strains and result in unequal removal of SiC and surrounding layers of differentmore » material due to the hardness differences of these materials. The nature of layer interfaces is thought to play a key role in performance of the SiC; therefore, analysis of representative samples at these interfacial areas is crucial. In work reported here, a focused ion beam (FIB) was employed in a novel manner to prepare a more representative sample for EBSD analysis from TRISO layers free of effects introduced by mechanical and chemical preparation methods. In addition, the difficulty of handling neutron irradiated microscopic samples such as those analyzed in this work has been simplified with pre tilted mounting stages. Our study showed that although the average grain size of samples may be similar, the grain boundary characteristics may differ significantly. It was also found that low angle grain boundaries, comprises 25% in the FIB-prepared sample vs only 1-2% in the polished sample measured in the same particle. From this study it was determined that results of FIB prepared sample will provide more repeatable results, as the role of sample preparation is eliminated.« less

Sample Preparation Techniques for Grain Boundary Characterization of Annealed TRISO-Coated Particles

DOE PAGES

Dunzik-Gougar, M. L.; van Rooyen, I. J.; Hill, C. M.; ...

2016-08-25

Crystallographic information about chemical vapor deposition layers of silicon carbide (SiC) is essential to understanding layer performance, especially when the layers are in non planar geometries, such as spherical. We performed electron Back Scatter Diffraction (EBSD) analysis of spherical SiC layers using a different approach to sample focus ion beam milling technique to avoid the negative impacts of traditional sample polishing and to address the need of very small samples of irradiated materials for analysis. Mechanical and chemical grinding and polishing of sample surfaces can introduce lattice strains and result in unequal removal of SiC and surrounding layers of differentmore » material due to the hardness differences of these materials. The nature of layer interfaces is thought to play a key role in performance of the SiC; therefore, analysis of representative samples at these interfacial areas is crucial. In work reported here, a focused ion beam (FIB) was employed in a novel manner to prepare a more representative sample for EBSD analysis from TRISO layers free of effects introduced by mechanical and chemical preparation methods. In addition, the difficulty of handling neutron irradiated microscopic samples such as those analyzed in this work has been simplified with pre tilted mounting stages. Our study showed that although the average grain size of samples may be similar, the grain boundary characteristics may differ significantly. It was also found that low angle grain boundaries, comprises 25% in the FIB-prepared sample vs only 1-2% in the polished sample measured in the same particle. From this study it was determined that results of FIB prepared sample will provide more repeatable results, as the role of sample preparation is eliminated.« less

A population-based nested case control study on recurrent pneumonias in children with severe generalized cerebral palsy: ethical considerations of the design and representativeness of the study sample.

PubMed

Veugelers, Rebekka; Calis, Elsbeth A C; Penning, Corine; Verhagen, Arianne; Bernsen, Roos; Bouquet, Jan; Benninga, Marc A; Merkus, Peter J F M; Arets, Hubertus G M; Tibboel, Dick; Evenhuis, Heleen M

2005-07-19

In children with severe generalized cerebral palsy, pneumonias are a major health issue. Malnutrition, dysphagia, gastro-oesophageal reflux, impaired respiratory function and constipation are hypothesized risk factors. Still, no data are available on the relative contribution of these possible risk factors in the described population. This paper describes the initiation of a study in 194 children with severe generalized cerebral palsy, on the prevalence and on the impact of these hypothesized risk factors of recurrent pneumonias. A nested case-control design with 18 months follow-up was chosen. Dysphagia, respiratory function and constipation will be assessed at baseline, malnutrition and gastro-oesophageal reflux at the end of the follow-up. The study population consists of a representative population sample of children with severe generalized cerebral palsy. Inclusion was done through care-centres in a predefined geographical area and not through hospitals. All measurements will be done on-site which sets high demands on all measurements. If these demands were not met in "gold standard" methods, other methods were chosen. Although the inclusion period was prolonged, the desired sample size of 300 children was not met. With a consent rate of 33%, nearly 10% of all eligible children in The Netherlands are included (n = 194). The study population is subtly different from the non-participants with regard to severity of dysphagia and prevalence rates of pneumonias and gastro-oesophageal reflux. Ethical issues complicated the study design. Assessment of malnutrition and gastro-oesophageal reflux at baseline was considered unethical, since these conditions can be easily treated. Therefore, we postponed these diagnostics until the end of the follow-up. In order to include a representative sample, all eligible children in a predefined geographical area had to be contacted. To increase the consent rate, on-site measurements are of first choice, but timely inclusion is jeopardized. The initiation of this first study among children with severe neurological impairment led to specific, unexpected problems. Despite small differences between participants and non-participating children, our sample is as representative as can be expected from any population-based study and will provide important, new information to bring us further towards effective interventions to prevent pneumonias in this population.

A comparison of confidence/credible interval methods for the area under the ROC curve for continuous diagnostic tests with small sample size.

PubMed

Feng, Dai; Cortese, Giuliana; Baumgartner, Richard

2017-12-01

The receiver operating characteristic (ROC) curve is frequently used as a measure of accuracy of continuous markers in diagnostic tests. The area under the ROC curve (AUC) is arguably the most widely used summary index for the ROC curve. Although the small sample size scenario is common in medical tests, a comprehensive study of small sample size properties of various methods for the construction of the confidence/credible interval (CI) for the AUC has been by and large missing in the literature. In this paper, we describe and compare 29 non-parametric and parametric methods for the construction of the CI for the AUC when the number of available observations is small. The methods considered include not only those that have been widely adopted, but also those that have been less frequently mentioned or, to our knowledge, never applied to the AUC context. To compare different methods, we carried out a simulation study with data generated from binormal models with equal and unequal variances and from exponential models with various parameters and with equal and unequal small sample sizes. We found that the larger the true AUC value and the smaller the sample size, the larger the discrepancy among the results of different approaches. When the model is correctly specified, the parametric approaches tend to outperform the non-parametric ones. Moreover, in the non-parametric domain, we found that a method based on the Mann-Whitney statistic is in general superior to the others. We further elucidate potential issues and provide possible solutions to along with general guidance on the CI construction for the AUC when the sample size is small. Finally, we illustrate the utility of different methods through real life examples.

Characterization of the Fecal Microbiome from Non-Human Wild Primates Reveals Species Specific Microbial Communities

PubMed Central

Yildirim, Suleyman; Yeoman, Carl J.; Sipos, Maksim; Torralba, Manolito; Wilson, Brenda A.; Goldberg, Tony L.; Stumpf, Rebecca M.; Leigh, Steven R.; White, Bryan A.; Nelson, Karen E.

2010-01-01

Background Host-associated microbes comprise an integral part of animal digestive systems and these interactions have a long evolutionary history. It has been hypothesized that the gastrointestinal microbiome of humans and other non-human primates may have played significant roles in host evolution by facilitating a range of dietary adaptations. We have undertaken a comparative sequencing survey of the gastrointestinal microbiomes of several non-human primate species, with the goal of better understanding how these microbiomes relate to the evolution of non-human primate diversity. Here we present a comparative analysis of gastrointestinal microbial communities from three different species of Old World wild monkeys. Methodology/Principal Findings We analyzed fecal samples from three different wild non-human primate species (black-and-white colobus [Colubus guereza], red colobus [Piliocolobus tephrosceles], and red-tailed guenon [Cercopithecus ascanius]). Three samples from each species were subjected to small subunit rRNA tag pyrosequencing. Firmicutes comprised the vast majority of the phyla in each sample. Other phyla represented were Bacterioidetes, Proteobacteria, Spirochaetes, Actinobacteria, Verrucomicrobia, Lentisphaerae, Tenericutes, Planctomycetes, Fibrobacateres, and TM7. Bray-Curtis similarity analysis of these microbiomes indicated that microbial community composition within the same primate species are more similar to each other than to those of different primate species. Comparison of fecal microbiota from non-human primates with microbiota of human stool samples obtained in previous studies revealed that the gut microbiota of these primates are distinct and reflect host phylogeny. Conclusion/Significance Our analysis provides evidence that the fecal microbiomes of wild primates co-vary with their hosts, and that this is manifested in higher intraspecies similarity among wild primate species, perhaps reflecting species specificity of the microbiome in addition to dietary influences. These results contribute to the limited body of primate microbiome studies and provide a framework for comparative microbiome analysis between human and non-human primates as well as a comparative evolutionary understanding of the human microbiome. PMID:21103066

Evaluating hepatocellular carcinoma cell lines for tumour samples using within-sample relative expression orderings of genes.

PubMed

Ao, Lu; Guo, You; Song, Xuekun; Guan, Qingzhou; Zheng, Weicheng; Zhang, Jiahui; Huang, Haiyan; Zou, Yi; Guo, Zheng; Wang, Xianlong

2017-11-01

Concerns are raised about the representativeness of cell lines for tumours due to the culture environment and misidentification. Liver is a major metastatic destination of many cancers, which might further confuse the origin of hepatocellular carcinoma cell lines. Therefore, it is of crucial importance to understand how well they can represent hepatocellular carcinoma. The HCC-specific gene pairs with highly stable relative expression orderings in more than 99% of hepatocellular carcinoma but with reversed relative expression orderings in at least 99% of one of the six types of cancer, colorectal carcinoma, breast carcinoma, non-small-cell lung cancer, gastric carcinoma, pancreatic carcinoma and ovarian carcinoma, were identified. With the simple majority rule, the HCC-specific relative expression orderings from comparisons with colorectal carcinoma and breast carcinoma could exactly discriminate primary hepatocellular carcinoma samples from both primary colorectal carcinoma and breast carcinoma samples. Especially, they correctly classified more than 90% of liver metastatic samples from colorectal carcinoma and breast carcinoma to their original tumours. Finally, using these HCC-specific relative expression orderings from comparisons with six cancer types, we identified eight of 24 hepatocellular carcinoma cell lines in the Cancer Cell Line Encyclopedia (Huh-7, Huh-1, HepG2, Hep3B, JHH-5, JHH-7, C3A and Alexander cells) that are highly representative of hepatocellular carcinoma. Evaluated with a REOs-based prognostic signature for hepatocellular carcinoma, all these eight cell lines showed the same metastatic properties of the high-risk metastatic hepatocellular carcinoma tissues. Caution should be taken for using hepatocellular carcinoma cell lines. Our results should be helpful to select proper hepatocellular carcinoma cell lines for biological experiments. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Comparison of microbial populations in the small intestine, large intestine and feces of healthy horses using terminal restriction fragment length polymorphism

PubMed Central

2013-01-01

Background The composition of the microbiota of the equine intestinal tract is complex. Determining whether the microbial composition of fecal samples is representative of proximal compartments of the digestive tract could greatly simplify future studies. The objectives of this study were to compare the microbial populations of the duodenum, ileum, cecum, colon and rectum (feces) within and between healthy horses, and to determine whether rectal (fecal) samples are representative of proximal segments of the gastrointestinal tract. Intestinal samples were collected from ten euthanized horses. 16S rRNA gene PCR-based TRFLP was used to investigate microbiota richness in various segments of the gastrointestinal tract, and dice similarity indices were calculated to compare the samples. Results Within horses large variations of microbial populations along the gastrointestinal tract were seen. The microbiota in rectal samples was only partially representative of other intestinal compartments. The highest similarity was obtained when feces were compared to the cecum. Large compartmental variations were also seen when microbial populations were compared between six horses with similar dietary and housing management. Conclusion Rectal samples were not entirely representative of intestinal compartments in the small or large intestine. This should be taken into account when designing studies using fecal sampling to assess other intestinal compartments. Similarity between horses with similar dietary and husbandry management was also limited, suggesting that parts of the intestinal microbiota were unique to each animal in this study. PMID:23497580

2005 9th Annual Army Small Business Conference

DTIC Science & Technology

2005-11-03

field commanders who conduct acquisitions. All the Army’s major commands located in the United States will be represented. The conference...Engineer Squad Vehicle i r i l Mobile Gun System il yst Medical Evacuation Vehicle i l v ti i l Reconnaissance Vehicle iss i l Mortar Carrier rt r rri r...Manned Systems Unmanned Air Vehicles Class I ARV-A (L) Small (Manpackable) UGV Non-Line of Sight Cannon Non-Line of Sight Mortar Medical Treatment and

Polytopic vector analysis in igneous petrology: Application to lunar petrogenesis

NASA Technical Reports Server (NTRS)

Shervais, John W.; Ehrlich, R.

1993-01-01

Lunar samples represent a heterogeneous assemblage of rocks with complex inter-relationships that are difficult to decipher using standard petrogenetic approaches. These inter-relationships reflect several distinct petrogenetic trends as well as thermomechanical mixing of distinct components. Additional complications arise from the unequal quality of chemical analyses and from the fact that many samples (e.g., breccia clasts) are too small to be representative of the system from which they derived. Polytopic vector analysis (PVA) is a multi-variate procedure used as a tool for exploratory data analysis. PVA allows the analyst to classify samples and clarifies relationships among heterogenous samples with complex petrogenetic histories. It differs from orthogonal factor analysis in that it uses non-orthogonal multivariate sample vectors to extract sample endmember compositions. The output from a Q-mode (sample based) factor analysis is the initial step in PVA. The Q-mode analysis, using criteria established by Miesch and Klovan and Miesch, is used to determine the number of endmembers in the data system. The second step involves determination of endmembers and mixing proportions with all output expressed in the same geochemical variable as the input. The composition of endmembers is derived by analysis of the variability of the data set. Endmembers need not be present in the data set, nor is it necessary for their composition to be known a priori. A set of any endmembers defines a 'polytope' or classification figure (triangle for a three component system, tetrahedron for a four component system, a 'five-tope' in four dimensions for five component system, et cetera).

Native microflora in fresh-cut processing plants and their potentials of biofilm formation

USDA-ARS?s Scientific Manuscript database

Representative food contact and non-food contact surfaces in two mid-sized fresh cut processing facilities were sampled for microbiological analyses post routine daily sanitization. Mesophilic and psychrotrophic bacteria on the sampled surfaces were isolated by plating on non-selective bacterial med...

Composition and Longitudinal Patterns of Aquatic Insect Emergence in Small Rivers of Palawan Island, the Philippines

NASA Astrophysics Data System (ADS)

Freitag, Hendrik

2004-09-01

This study presents the first emergence trap samples from streams in the Philippines and Greater Sunda. Aquatic insect emergence from two small rivers and longitudinal patterns including estuaries are compared. A decline of total emergence towards estuaries was observed, affecting all major orders. Diptera, namely Chironomidae, dominated all sites. High abundances in Ceratopogonidae, Odonata, and Coleoptera were found, compared to other emergence studies from tropical and temperate latitudes. Ephemeroptera displayed a highly variable contribution to the emergence from Palawan as well as in other comparative studies either supported by the appropriate conditions for certain functional groups or limited by environmental variables such as pH. Trichoptera are likely to tolerate a wider range of environmental conditions and they are consequently able to fill further niches where Ephemeroptera are under-represented. Except for scarce abundances of Plecoptera observed in this and other studies from the tropics, no substantial differences in emergence composition at order level existed between temperate and tropical rivers, however, with a remarkable local variation. Components of riparian and non-aquatic insects and non-emergent fauna contributing to the collections are discussed based on trap features. (

[Mechanism and Prospect of Radiotherapy Combined with Apotatinib
in the Treatment of Non-small Cell Lung Cancer].

PubMed

Liu, Guohui; Wang, Chunbo; E, Mingyan

2017-12-20

Non-small cell lung cancer is one of the most commom malignant tumor being harmful to people's life and health. Most of the patients have developed to the last stage which not suitable for surgical indications, so radiation and chemotherapy is the main treatment strategy. In recent years, with the theory of anti-angiogenesis therapy for malignant tumors, apatinib as a promising novel medicine to treat malignant tumors, represents synergistic antitumor effects in combination with radiotherapy. The underlying mechanisms may include make blood vessel normalization, alleviating inner hypoxia, and angiogenic factors regulation. Apatinib in combination with radiotherapy may become a new and effective treatment strategy of non-small cell lung cancer.

Inheritance of Properties of Normal and Non-Normal Distributions after Transformation of Scores to Ranks

ERIC Educational Resources Information Center

Zimmerman, Donald W.

2011-01-01

This study investigated how population parameters representing heterogeneity of variance, skewness, kurtosis, bimodality, and outlier-proneness, drawn from normal and eleven non-normal distributions, also characterized the ranks corresponding to independent samples of scores. When the parameters of population distributions from which samples were…

US EPA Base Study Standard Operating Procedure for Sampling and Characterization of Viable and Non-Viable Bioaerosols in Indoor Air

EPA Pesticide Factsheets

The objective of the procedure is to collect a representative sample concentration of total airborne fungal spores (viable and non-viable) that may be present in indoor air and in the outdoor air supplied to the space tested.

A tree-like Bayesian structure learning algorithm for small-sample datasets from complex biological model systems.

PubMed

Yin, Weiwei; Garimalla, Swetha; Moreno, Alberto; Galinski, Mary R; Styczynski, Mark P

2015-08-28

There are increasing efforts to bring high-throughput systems biology techniques to bear on complex animal model systems, often with a goal of learning about underlying regulatory network structures (e.g., gene regulatory networks). However, complex animal model systems typically have significant limitations on cohort sizes, number of samples, and the ability to perform follow-up and validation experiments. These constraints are particularly problematic for many current network learning approaches, which require large numbers of samples and may predict many more regulatory relationships than actually exist. Here, we test the idea that by leveraging the accuracy and efficiency of classifiers, we can construct high-quality networks that capture important interactions between variables in datasets with few samples. We start from a previously-developed tree-like Bayesian classifier and generalize its network learning approach to allow for arbitrary depth and complexity of tree-like networks. Using four diverse sample networks, we demonstrate that this approach performs consistently better at low sample sizes than the Sparse Candidate Algorithm, a representative approach for comparison because it is known to generate Bayesian networks with high positive predictive value. We develop and demonstrate a resampling-based approach to enable the identification of a viable root for the learned tree-like network, important for cases where the root of a network is not known a priori. We also develop and demonstrate an integrated resampling-based approach to the reduction of variable space for the learning of the network. Finally, we demonstrate the utility of this approach via the analysis of a transcriptional dataset of a malaria challenge in a non-human primate model system, Macaca mulatta, suggesting the potential to capture indicators of the earliest stages of cellular differentiation during leukopoiesis. We demonstrate that by starting from effective and efficient approaches for creating classifiers, we can identify interesting tree-like network structures with significant ability to capture the relationships in the training data. This approach represents a promising strategy for inferring networks with high positive predictive value under the constraint of small numbers of samples, meeting a need that will only continue to grow as more high-throughput studies are applied to complex model systems.

Evaluation of EML4-ALK Fusion Proteins in Non-Small Cell Lung Cancer Using Small Molecule Inhibitors12

PubMed Central

Li, Yongjun; Ye, Xiaofen; Liu, Jinfeng; Zha, Jiping; Pei, Lin

2011-01-01

The echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK) fusion gene resulting from an inversion within chromosome 2p occurs in approximately 5% of non-small cell lung cancer and is mutually exclusive with Ras and EGFR mutations. In this study, we have used a potent and selective ALK small molecule inhibitor, NPV-TAE684, to assess the oncogenic role of EML4-ALK in non-small cell lung cancer (NSCLC). We show here that TAE684 inhibits proliferation and induces cell cycle arrest, apoptosis, and tumor regression in two NSCLC models that harbor EML4-ALK fusions. TAE684 inhibits EML4-ALK activation and its downstream signaling including ERK, AKT, and STAT3. We used microarray analysis to carry out targeted pathway studies of gene expression changes in H2228 NSCLC xenograft model after TAE684 treatment and identified a gene signature of EML4-ALK inhibition. The gene signature represents 1210 known human genes, and the top biologic processes represented by these genes are cell cycle, DNA synthesis, cell proliferation, and cell death. We also compared the effect of TAE684 with PF2341066, a c-Met and ALK small molecule inhibitor currently in clinical trial in cancers harboring ALK fusions, and demonstrated that TAE684 is a much more potent inhibitor of EML4-ALK. Our data demonstrate that EML4-ALK plays an important role in the pathogenesis of a subset of NSCLC and provides insight into the mechanism of EML4-ALK inhibition by a small molecule inhibitor. PMID:21245935

Metagenomes of the Picoalga Bathycoccus from the Chile Coastal Upwelling

PubMed Central

Vaulot, Daniel; Lepère, Cécile; Toulza, Eve; De la Iglesia, Rodrigo; Poulain, Julie; Gaboyer, Frédéric; Moreau, Hervé; Vandepoele, Klaas; Ulloa, Osvaldo; Gavory, Frederick; Piganeau, Gwenael

2012-01-01

Among small photosynthetic eukaryotes that play a key role in oceanic food webs, picoplanktonic Mamiellophyceae such as Bathycoccus, Micromonas, and Ostreococcus are particularly important in coastal regions. By using a combination of cell sorting by flow cytometry, whole genome amplification (WGA), and 454 pyrosequencing, we obtained metagenomic data for two natural picophytoplankton populations from the coastal upwelling waters off central Chile. About 60% of the reads of each sample could be mapped to the genome of Bathycoccus strain from the Mediterranean Sea (RCC1105), representing a total of 9 Mbp (sample T142) and 13 Mbp (sample T149) of non-redundant Bathycoccus genome sequences. WGA did not amplify all regions uniformly, resulting in unequal coverage along a given chromosome and between chromosomes. The identity at the DNA level between the metagenomes and the cultured genome was very high (96.3% identical bases for the three larger chromosomes over a 360 kbp alignment). At least two to three different genotypes seemed to be present in each natural sample based on read mapping to Bathycoccus RCC1105 genome. PMID:22745802

ReprDB and panDB: minimalist databases with maximal microbial representation.

PubMed

Zhou, Wei; Gay, Nicole; Oh, Julia

2018-01-18

Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes. We report pipelines that efficiently traverse all open access microbial genomes and assemble non-redundant genomic information. The pipelines result in two species-resolution microbial reference databases of relatively small sizes: reprDB, which assembles microbial representative or reference genomes, and panDB, for which we developed a novel iterative alignment algorithm to identify and assemble non-redundant genomic regions in multiple sequenced strains. With the databases, we managed to assign taxonomic labels and genome positions to the majority of metagenomic reads from human skin and gut microbiomes, demonstrating a significant improvement over a previous database-guided analysis on the same datasets. reprDB and panDB leverage the rapid increases in the number of open access microbial genomes to more fully profile metagenomic samples. Additionally, the databases exclude redundant sequence information to avoid inflated storage or memory space and indexing or analyzing time. Finally, the novel iterative alignment algorithm significantly increases efficiency in pan-genome identification and can be useful in comparative genomic analyses.

High-definition imaging of circulating tumor cells and associated cellular events in non-small cell lung cancer patients: a longitudinal analysis.

PubMed

Nieva, Jorge; Wendel, Marco; Luttgen, Madelyn S; Marrinucci, Dena; Bazhenova, Lyudmila; Kolatkar, Anand; Santala, Roger; Whittenberger, Brock; Burke, James; Torrey, Melissa; Bethel, Kelly; Kuhn, Peter

2012-02-01

Sampling circulating tumor cells (CTCs) from peripheral blood is ideally accomplished using assays that detect high numbers of cells and preserve them for downstream characterization. We sought to evaluate a method using enrichment free fluorescent labeling of CTCs followed by automated digital microscopy in patients with non-small cell lung cancer. Twenty-eight patients with non-small cell lung cancer and hematogenously seeded metastasis were analyzed with multiple blood draws. We detected CTCs in 68% of analyzed samples and found a propensity for increased CTC detection as the disease progressed in individual patients. CTCs were present at a median concentration of 1.6 CTCs ml⁻¹ of analyzed blood in the patient population. Higher numbers of detected CTCs were associated with an unfavorable prognosis.

The Immune Landscape of Non-Small Cell Lung Cancer: Utility of Cytologic and Histologic Samples Obtained Through Minimally Invasive Pulmonary Procedures.

PubMed

Beattie, Jason; Yarmus, Lonny; Wahidi, Momen M; Rivera, M Patricia; Gilbert, Christopher; Maldonado, Fabien; Czarnecka, Kasia; Argento, Angela; Chen, Alexander; Herth, Felix; Sterman, Daniel H

2018-05-14

The success of immune checkpoint inhibitors and the discovery of useful biomarkers to predict response to these agents is shifting much of the focus of personalized care for non-small cell lung cancer towards harnessing the immune response. With further advancement, more effective immunotherapy options will emerge along with more useful biomarkers. Paradoxically, minimally invasive small biopsy and cytology specimens have become the primary method for diagnosis of patients with advanced disease, as well for initial diagnosis and staging in earlier stage disease. For the benefit of these patients, we will continue to learn how to do more with less. In this perspective, we review aspects of immunobiology that underlie the current state of the art of existing and emerging immunologic biomarkers that hold potential to enhance the care of patients with non-small cell lung cancer. We address practical considerations for acquiring patient samples that accurately reflect disease immune status. We also propose a paradigm shift wherein the most important sample types that need to be proven in pioneering basic science and translation work and subsequent clinical trials are the specimens most often obtained clinically.

Engaging workplace representatives in research: what recruitment strategies work best?

PubMed

Coole, C; Nouri, F; Narayanasamy, M; Baker, P; Khan, S; Drummond, A

2018-05-23

Workplaces are key stakeholders in work and health but little is known about the methods used to recruit workplace representatives (WRs), including managers, occupational health advisers and colleagues, to externally funded healthcare research studies. To detail the strategies used in recruiting WRs from three areas of the UK to a qualitative study concerning their experience of employees undergoing hip or knee replacement, to compare the strategies and inform recruitment methods for future studies. Six strategies were used to recruit WRs from organizations of different sizes and sectors. Data on numbers approached and responses received were analysed descriptively. Twenty-five WRs were recruited. Recruitment had to be extended outside the main three study areas, and took several months. It proved more difficult to recruit from non-service sectors and small- and medium-sized enterprises. The most successful strategies were approaching organizations that had participated in previous research studies, or known professionally or personally to team members. Recruiting a diverse sample of WRs to healthcare research requires considerable resources and persistence, and a range of strategies. Recruitment is easier where local relationships already exist; the importance of building and maintaining these relationships cannot be underestimated. However, the potential risks of bias and participant fatigue need to be acknowledged and managed. Further studies are needed to explore how WRs can be recruited to health research, and to identify the researcher effort and costs involved in achieving unbiased and representative samples.

Salivary Cortisol as a Biomarker of Stress in Mothers and their Low Birth Weight Infants and Sample Collecting Challenges

PubMed Central

Vujičić, Ana Đorđević; Đukić, Svjetlana Maglajić

2016-01-01

Summary Background Salivary cortisol measurement is a non-invasive method suitable for use in neonatal research. Mother-infant separation after birth represents stress and skin-to-skin contact (SSC) has numerous benefits. The aim of the study was to measure salivary cortisol in mothers and newborns before and after SSC in order to assess the effect of SSC on mothers’ and infants’ stress and to estimate the efficacy of collecting small saliva samples in newborns. Methods Salivary cortisol was measured in 35 mother-infant pairs before and after the first and the fifth SSC in small saliva samples (50 μL) using the high sensitivity Quantitative ELISA-Kit (0.0828 nmol/L) for low cortisol levels detection. Samples were collected with eye sponge during 3 to 5 minutes. Results Cortisol level in mothers decreased after SSC: the highest levels were measured before and the lowest after SSC and the differences in values were significant during both the first (p<0.001) and the fifth SSC (p<0.001). During the first SSC the cortisol level decrease was detected in 14 (40%) and an increase in 21 (60%) newborns, and during the fifth SSC a decrease was detected in 16 (45.7%) and an increase in 19 (54.3%) newborns, without confirmed significance of the difference. Saliva sampling efficacy using eye sponge was 75%. Conclusions Cortisol level decrease in mothers proves the stress reduction during SSC, while variable cortisol levels in infants do not indicate stress reduction and imply the need for further research. The used sampling method appeared to be one of the most optimal considering the sample volume, sampling time and efficacy. PMID:28356870

Comparison of EGFR signaling pathway somatic DNA mutations derived from peripheral blood and corresponding tumor tissue of patients with advanced non-small-cell lung cancer using liquidchip technology.

PubMed

Zhang, Hui; Liu, Deruo; Li, Shanqing; Zheng, Yongqing; Yang, Xinjie; Li, Xi; Zhang, Quan; Qin, Na; Lu, Jialin; Ren-Heidenreich, Lifen; Yang, Huiyi; Wu, Yuhua; Zhang, Xinyong; Nong, Jingying; Sun, Yifen; Zhang, Shucai

2013-11-01

Somatic DNA mutations affecting the epidermal growth factor receptor (EGFR) signaling pathway are known to predict responsiveness to EGFR-tyrosine kinase inhibitor drugs in patients with advanced non-small-cell lung cancers. We evaluated a sensitive liquidchip platform for detecting EGFR, KRAS (alias Ki-ras), proto-oncogene B-Raf, and phosphatidylinositol 3-kinase CA mutations in plasma samples, which were highly correlated with matched tumor tissues from 86 patients with advanced non-small-cell lung cancers. Either EGFR exon 19 or 21 mutations were detected in 36 patients: 23 of whom had identical mutations in both their blood and tissue samples; whereas mutations in the remaining 13 were found only in their tumor samples. These EGFR mutations occurred at a significantly higher frequency in females, never-smokers, and in patients with adenocarcinomas (P ≤ 0.001). The EGFR exon 20 T790M mutation was detected in only one of the paired samples [100% (95% CI, 96% to 100%) agreement]. For KRAS, proto-oncogene B-Raf, and phosphatidylinositol 3-kinase CA mutations, the overall agreements were 97% (95% CI, 90% to 99%), 98% (95% CI, 92% to 99%), and 97% (95% CI, 90% to 99%), respectively, and these were not associated with age, sex, smoking history, or histopathologic type. In conclusion, mutations detected in plasma correlated strongly with mutation profiles in each respective tumor sample, suggesting that this liquidchip platform may offer a rapid and noninvasive method for predicting tumor responsiveness to EGFR-tyrosine kinase inhibitor drugs in patients with advanced non-small-cell lung cancers. Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Bias of health estimates obtained from chronic disease and risk factor surveillance systems using telephone population surveys in Australia: results from a representative face-to-face survey in Australia from 2010 to 2013.

PubMed

Dal Grande, Eleonora; Chittleborough, Catherine R; Campostrini, Stefano; Taylor, Anne W

2016-04-18

Emerging communication technologies have had an impact on population-based telephone surveys worldwide. Our objective was to examine the potential biases of health estimates in South Australia, a state of Australia, obtained via current landline telephone survey methodologies and to report on the impact of mobile-only household on household surveys. Data from an annual multi-stage, systematic, clustered area, face-to-face population survey, Health Omnibus Survey (approximately 3000 interviews annually), included questions about telephone ownership to assess the population that were non-contactable by current telephone sampling methods (2006 to 2013). Univariable analyses (2010 to 2013) and trend analyses were conducted for sociodemographic and health indicator variables in relation to telephone status. Relative coverage biases (RCB) of two hypothetical telephone samples was undertaken by examining the prevalence estimates of health status and health risk behaviours (2010 to 2013): directory-listed numbers, consisting mainly of landline telephone numbers and a small proportion of mobile telephone numbers; and a random digit dialling (RDD) sample of landline telephone numbers which excludes mobile-only households. Telephone (landline and mobile) coverage in South Australia is very high (97%). Mobile telephone ownership increased slightly (7.4%), rising from 89.7% in 2006 to 96.3% in 2013; mobile-only households increased by 431% over the eight year period from 5.2% in 2006 to 27.6% in 2013. Only half of the households have either a mobile or landline number listed in the telephone directory. There were small differences in the prevalence estimates for current asthma, arthritis, diabetes and obesity between the hypothetical telephone samples and the overall sample. However, prevalence estimate for diabetes was slightly underestimated (RCB value of -0.077) in 2013. Mixed RCB results were found for having a mental health condition for both telephone samples. Current smoking prevalence was lower for both hypothetical telephone samples in absolute differences and RCB values: -0.136 to -0.191 for RDD landline samples and -0.129 to -0.313 for directory-listed samples. These findings suggest landline-based sampling frames used in Australia, when appropriately weighted, produce reliable representative estimates for some health indicators but not for all. Researchers need to be aware of their limitations and potential biased estimates.

Predictors of patient non-attendance at Improving Access to Psychological Therapy services demonstration sites

PubMed Central

Di Bona, Laura; Saxon, David; Barkham, Michael; Dent-Brown, Kim; Parry, Glenys

2014-01-01

Background Improving Access to Psychological Therapy (IAPT) services have increased the number of people with common mental health disorders receiving psychological therapy in England, but concerns remain about how equitably these services are accessed. Method Using cohort patient data (N=363) collected as part of the independent evaluation of the two demonstration sites, logistic regression was utilised to identify socio-demographic, clinical and service factors predictive of IAPT non-attendance. Results Significant predictors of IAPT first session non-attendance by patients were: lower non-risk score on the Clinical Outcomes in Routine Evaluation-Outcome Measure (CORE-OM); more frequent thoughts of “being better off dead” (derived from the CORE-OM); either a very recent onset of common mental health disorder (1 month or less) or a long term condition (more than 2 years); and site. Limitations The small sample and low response rate are limitations, as the sample may not be representative of all those referred to IAPT services. The predictive power of the logistic regression model is limited and suggests other variables not available in the dataset may also be important predictors. Conclusions The clinical characteristics of risk to self, severity of emotional distress, and illness duration, along with site, were more predictive of IAPT non-attendance than socio-demographic characteristics. Further testing of the relationship between these variables and IAPT non-attendance is recommended. Clinicians should monitor IAPT uptake in those they refer and implement strategies to increase their engagement with services, particularly when referring people presenting with suicidal ideation or more chronic illness. PMID:25194784

Hospital days, hospitalization costs, and inpatient mortality among patients with mucormycosis: a retrospective analysis of US hospital discharge data

PubMed Central

2014-01-01

Background Mucormycosis is a rare and potentially fatal fungal infection occurring primarily in severely immunosuppressed patients. Because it is so rare, reports in the literature are mainly limited to case reports or small case series. The aim of this study was to evaluate inpatient mortality, length of stay (LOS), and costs among a matched sample of high-risk patients with and without mucormycosis in a large nationally representative database. Methods We conducted a retrospective analysis using the 2003–2010 Healthcare Cost and Utilization Project – Nationwide Inpatient Sample (HCUP-NIS). The NIS is a nationally representative 20% sample of hospitalizations from acute care United States (US) hospitals, with survey weights available to compute national estimates. We classified hospitalizations into four mutually exclusive risk categories for mucormycosis: A- severely immunocompromised, B- critically ill, C- mildly/moderately immunocompromised, D- major surgery or pneumonia. Mucormycosis hospitalizations (“cases”) were identified by ICD-9-CM code 117.7. Non-mucormycosis hospitalizations (“non-cases”) were propensity-score matched to cases 3:1. We examined demographics, clinical characteristics, and hospital outcomes (mortality, LOS, costs). Weighted results were reported. Results From 319,366,817 total hospitalizations, 5,346 cases were matched to 15,999 non-cases. Cases and non-cases did not differ significantly in age (49.6 vs. 49.7 years), female sex (40.5% vs. 41.0%), White race (53.3% vs. 55.9%) or high-risk group (A-49.1% vs. 49.0%, B-20.0% vs. 21.8%, C-25.5% vs. 23.8%, D-5.5% vs. 5.4%). Cases experienced significantly higher mortality (22.1% vs. 4.4%, P < 0.001), with mean LOS and total costs more than 3-fold higher (24.5 vs. 8.0 days and $90,272 vs. $25,746; both P < 0.001). Conclusions In a national hospital database, hospitalizations with mucormycosis had significantly higher inpatient mortality, LOS, and hospital costs than matched hospitalizations without mucormycosis. Findings suggest that interventions to prevent or more effectively treat mucormycosis are needed. PMID:24903188

Impact of spatial variability and sampling design on model performance

NASA Astrophysics Data System (ADS)

Schrape, Charlotte; Schneider, Anne-Kathrin; Schröder, Boris; van Schaik, Loes

2017-04-01

Many environmental physical and chemical parameters as well as species distributions display a spatial variability at different scales. In case measurements are very costly in labour time or money a choice has to be made between a high sampling resolution at small scales and a low spatial cover of the study area or a lower sampling resolution at the small scales resulting in local data uncertainties with a better spatial cover of the whole area. This dilemma is often faced in the design of field sampling campaigns for large scale studies. When the gathered field data are subsequently used for modelling purposes the choice of sampling design and resulting data quality influence the model performance criteria. We studied this influence with a virtual model study based on a large dataset of field information on spatial variation of earthworms at different scales. Therefore we built a virtual map of anecic earthworm distributions over the Weiherbach catchment (Baden-Württemberg in Germany). First of all the field scale abundance of earthworms was estimated using a catchment scale model based on 65 field measurements. Subsequently the high small scale variability was added using semi-variograms, based on five fields with a total of 430 measurements divided in a spatially nested sampling design over these fields, to estimate the nugget, range and standard deviation of measurements within the fields. With the produced maps, we performed virtual samplings of one up to 50 random points per field. We then used these data to rebuild the catchment scale models of anecic earthworm abundance with the same model parameters as in the work by Palm et al. (2013). The results of the models show clearly that a large part of the non-explained deviance of the models is due to the very high small scale variability in earthworm abundance: the models based on single virtual sampling points on average obtain an explained deviance of 0.20 and a correlation coefficient of 0.64. With increasing sampling points per field, we averaged the measured abundance of the sampling within each field to obtain a more representative value of the field average. Doubling the samplings per field strongly improved the model performance criteria (explained deviance 0.38 and correlation coefficient 0.73). With 50 sampling points per field the performance criteria were 0.91 and 0.97 respectively for explained deviance and correlation coefficient. The relationship between number of samplings and performance criteria can be described with a saturation curve. Beyond five samples per field the model improvement becomes rather small. With this contribution we wish to discuss the impact of data variability at sampling scale on model performance and the implications for sampling design and assessment of model results as well as ecological inferences.

Genotypic Analyses of Shiga Toxin-Producing Escherichia coli O157 and Non-O157 Recovered from Feces of Domestic Animals on Rural Farms in Mexico

PubMed Central

Amézquita-López, Bianca A.; Quiñones, Beatriz; Cooley, Michael B.; León-Félix, Josefina; Castro-del Campo, Nohelia; Mandrell, Robert E.; Jiménez, Maribel; Chaidez, Cristóbal

2012-01-01

Shiga toxin-producing Escherichia coli (STEC) are zoonotic enteric pathogens associated with human gastroenteritis worldwide. Cattle and small ruminants are important animal reservoirs of STEC. The present study investigated animal reservoirs for STEC in small rural farms in the Culiacan Valley, an important agricultural region located in Northwest Mexico. A total of 240 fecal samples from domestic animals were collected from five sampling sites in the Culiacan Valley and were subjected to an enrichment protocol followed by either direct plating or immunomagnetic separation before plating on selective media. Serotype O157:H7 isolates with the virulence genes stx2, eae, and ehxA were identified in 40% (26/65) of the recovered isolates from cattle, sheep and chicken feces. Pulse-field gel electrophoresis (PFGE) analysis grouped most O157:H7 isolates into two clusters with 98.6% homology. The use of multiple-locus variable-number tandem repeat analysis (MLVA) differentiated isolates that were indistinguishable by PFGE. Analysis of the allelic diversity of MLVA loci suggested that the O157:H7 isolates from this region were highly related. In contrast to O157:H7 isolates, a greater genotypic diversity was observed in the non-O157 isolates, resulting in 23 PFGE types and 14 MLVA types. The relevant non-O157 serotypes O8:H19, O75:H8, O111:H8 and O146:H21 represented 35.4% (23/65) of the recovered isolates. In particular, 18.5% (12/65) of all the isolates were serotype O75:H8, which was the most variable serotype by both PFGE and MLVA. The non-O157 isolates were predominantly recovered from sheep and were identified to harbor either one or two stx genes. Most non-O157 isolates were ehxA-positive (86.5%, 32/37) but only 10.8% (4/37) harbored eae. These findings indicate that zoonotic STEC with genotypes associated with human illness are present in animals on small farms within rural communities in the Culiacan Valley and emphasize the need for the development of control measures to decrease risks associated with zoonotic STEC. PMID:23251577

Genotypic analyses of shiga toxin-producing Escherichia coli O157 and non-O157 recovered from feces of domestic animals on rural farms in Mexico.

PubMed

Amézquita-López, Bianca A; Quiñones, Beatriz; Cooley, Michael B; León-Félix, Josefina; Castro-del Campo, Nohelia; Mandrell, Robert E; Jiménez, Maribel; Chaidez, Cristóbal

2012-01-01

Shiga toxin-producing Escherichia coli (STEC) are zoonotic enteric pathogens associated with human gastroenteritis worldwide. Cattle and small ruminants are important animal reservoirs of STEC. The present study investigated animal reservoirs for STEC in small rural farms in the Culiacan Valley, an important agricultural region located in Northwest Mexico. A total of 240 fecal samples from domestic animals were collected from five sampling sites in the Culiacan Valley and were subjected to an enrichment protocol followed by either direct plating or immunomagnetic separation before plating on selective media. Serotype O157:H7 isolates with the virulence genes stx2, eae, and ehxA were identified in 40% (26/65) of the recovered isolates from cattle, sheep and chicken feces. Pulse-field gel electrophoresis (PFGE) analysis grouped most O157:H7 isolates into two clusters with 98.6% homology. The use of multiple-locus variable-number tandem repeat analysis (MLVA) differentiated isolates that were indistinguishable by PFGE. Analysis of the allelic diversity of MLVA loci suggested that the O157:H7 isolates from this region were highly related. In contrast to O157:H7 isolates, a greater genotypic diversity was observed in the non-O157 isolates, resulting in 23 PFGE types and 14 MLVA types. The relevant non-O157 serotypes O8:H19, O75:H8, O111:H8 and O146:H21 represented 35.4% (23/65) of the recovered isolates. In particular, 18.5% (12/65) of all the isolates were serotype O75:H8, which was the most variable serotype by both PFGE and MLVA. The non-O157 isolates were predominantly recovered from sheep and were identified to harbor either one or two stx genes. Most non-O157 isolates were ehxA-positive (86.5%, 32/37) but only 10.8% (4/37) harbored eae. These findings indicate that zoonotic STEC with genotypes associated with human illness are present in animals on small farms within rural communities in the Culiacan Valley and emphasize the need for the development of control measures to decrease risks associated with zoonotic STEC.

Theory of mind development in Chinese children: a meta-analysis of false-belief understanding across cultures and languages.

PubMed

Liu, David; Wellman, Henry M; Tardif, Twila; Sabbagh, Mark A

2008-03-01

Theory of mind is claimed to develop universally among humans across cultures with vastly different folk psychologies. However, in the attempt to test and confirm a claim of universality, individual studies have been limited by small sample sizes, sample specificities, and an overwhelming focus on Anglo- European children. The current meta-analysis of children's false-belief performance provides the most comprehensive examination to date of theory-of-mind development in a population of non-Western children speaking non-Indo-European languages (i.e., Mandarin and Cantonese). The meta-analysis consisted of 196 Chinese conditions (127 from mainland China and 69 from Hong Kong), representing responses from more than 3,000 children, compared with 155 similar North American conditions (83 conditions from the United States and 72 conditions from Canada). The findings show parallel developmental trajectories of false-belief understanding for children in China and North America coupled with significant differences in the timing of development across communities-children's false-belief performance varied across different locales by as much as 2 or more years. These data support the importance of both universal trajectories and specific experiential factors in the development of theory of mind.

Stream salamanders as indicators of stream quality in Maryland, USA

USGS Publications Warehouse

Southerland, M.T.; Jung, R.E.; Baxter, D.P.; Chellman, I.C.; Mercurio, G.; Volstad, J.H.

2004-01-01

Biological indicators are critical to the protection of small, headwater streams and the ecological values they provide. Maryland and other state monitoring programs have determined that fish indicators are ineffective in small streams, where stream salamanders may replace fish as top predators. Because of their life history, physiology, abundance, and ubiquity, stream salamanders are likely representative of biological integrity in these streams. The goal of this study was to determine whether stream salamanders are effective indicators of ecological conditions across biogeographic regions and gradients of human disturbance. During the summers of 2001 and 2002, we intensively surveyed for stream salamanders at 76 stream sites located west of the Maryland Coastal Plain, sites also monitored by the Maryland Biological Stream Survey (MBSS) and City of Gaithersburg. We found 1,584 stream salamanders, including all eight species known in Maryland, using two 15 ? 2 m transects and two 4 m2 quadrats that spanned both stream bank and channel. We performed removal sampling on transects to estimate salamander species detection probabilities, which ranged from 0.67-0.85. Stepwise regressions identified 15 of 52 non-salamander variables, representing water quality, physical habitat, land use, and biological conditions, which best predicted salamander metrics. Indicator development involved (1) identifying reference (non-degraded) and degraded sites (using percent forest, shading, riparian buffer width, aesthetic rating, and benthic macroinvertebrate and fish indices of biotic integrity); (2) testing 12 candidate salamander metrics (representing species richness and composition, abundance, species tolerance, and reproductive function) for their ability to distinguish reference from degraded sites; and (3) combining metrics into an index that effectively discriminated sites according to known stream conditions. Final indices for Highlands, Piedmont, and Non-Coastal Plain regions comprised four metrics: number of species, number of salamanders, number of intolerant salamanders, and number of adult salamanders, producing classification efficiencies between 87% and 90%. Partial validation of these indices was obtained when a test of the number of salamanders metric produced an 82% correct classification of 618 MBSS sites surveyed in 1995-97. This study supports the use of stream salamander monitoring and a composite stream salamander index of biotic integrity (SS-IBI) to determine stream quality in Maryland.

Occupancy Modeling Species-Environment Relationships with Non-ignorable Survey Designs.

PubMed

Irvine, Kathryn M; Rodhouse, Thomas J; Wright, Wilson J; Olsen, Anthony R

2018-05-26

Statistical models supporting inferences about species occurrence patterns in relation to environmental gradients are fundamental to ecology and conservation biology. A common implicit assumption is that the sampling design is ignorable and does not need to be formally accounted for in analyses. The analyst assumes data are representative of the desired population and statistical modeling proceeds. However, if datasets from probability and non-probability surveys are combined or unequal selection probabilities are used, the design may be non ignorable. We outline the use of pseudo-maximum likelihood estimation for site-occupancy models to account for such non-ignorable survey designs. This estimation method accounts for the survey design by properly weighting the pseudo-likelihood equation. In our empirical example, legacy and newer randomly selected locations were surveyed for bats to bridge a historic statewide effort with an ongoing nationwide program. We provide a worked example using bat acoustic detection/non-detection data and show how analysts can diagnose whether their design is ignorable. Using simulations we assessed whether our approach is viable for modeling datasets composed of sites contributed outside of a probability design Pseudo-maximum likelihood estimates differed from the usual maximum likelihood occu31 pancy estimates for some bat species. Using simulations we show the maximum likelihood estimator of species-environment relationships with non-ignorable sampling designs was biased, whereas the pseudo-likelihood estimator was design-unbiased. However, in our simulation study the designs composed of a large proportion of legacy or non-probability sites resulted in estimation issues for standard errors. These issues were likely a result of highly variable weights confounded by small sample sizes (5% or 10% sampling intensity and 4 revisits). Aggregating datasets from multiple sources logically supports larger sample sizes and potentially increases spatial extents for statistical inferences. Our results suggest that ignoring the mechanism for how locations were selected for data collection (e.g., the sampling design) could result in erroneous model-based conclusions. Therefore, in order to ensure robust and defensible recommendations for evidence-based conservation decision-making, the survey design information in addition to the data themselves must be available for analysts. Details for constructing the weights used in estimation and code for implementation are provided. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

pH-Responsive Hydrogels with Dispersed Hydrophobic Nanoparticles for the Oral Delivery of Chemotherapeutics

PubMed Central

Schoener, Cody A.; Hutson, Heather N.; Peppas, Nicholas A.

2012-01-01

Amphiphilic polymer carriers were formed by polymerizing a hydrophilic, pH-responsive hydrogel composed of poly(methacrylic – grafted – ethylene glycol) (P(MAA-g-EG)) in the presence of hydrophobic PMMA nanoparticles. These polymer carriers were varied in PMMA nanoparticle content to elicit a variety of physiochemical properties which would preferentially load doxorubicin, a hydrophobic chemotherapeutic, and release doxorubicin locally in the colon for the treatment of colon cancers. Loading levels ranged from 49% to 64% and increased with increasing nanoparticle content. Doxorubicin loaded polymers were released in a physiological model where low pH was used to simulate the stomach and then stepped to more neutral conditions to simulate the upper small intestine. P(MAA-g-EG) containing nanoparticles were less mucoadhesive as determined using a tensile tester, polymer samples, and fresh porcine small intestine. The cytocompatibility of the polymer materials were assessed using cell lines representing the GI tract and colon cancer and were non-cytotoxic at varying concentrations and exposure times. PMID:23281185

Computational discovery of pathway-level genetic vulnerabilities in non-small-cell lung cancer | Office of Cancer Genomics

Cancer.gov

Novel approaches are needed for discovery of targeted therapies for non-small-cell lung cancer (NSCLC) that are specific to certain patients. Whole genome RNAi screening of lung cancer cell lines provides an ideal source for determining candidate drug targets. Unsupervised learning algorithms uncovered patterns of differential vulnerability across lung cancer cell lines to loss of functionally related genes. Such genetic vulnerabilities represent candidate targets for therapy and are found to be involved in splicing, translation and protein folding.

Hookah use among college students: prevalence, drug use, and mental health.

PubMed

Goodwin, Renee D; Grinberg, Alice; Shapiro, Jack; Keith, Diana; McNeil, Michael P; Taha, Farah; Jiang, Bianca; Hart, Carl L

2014-08-01

There is consistent evidence that hookah use is as, if not more, harmful than cigarette use. Yet, hookah users underestimate the potential deleterious effects of hookah use. This study examined the rates of hookah use and associated demographic characteristics in a sample of undergraduates at a small Northeastern university. This study also examined the relationships between hookah use and other substance use, mental health problems, and perceived levels of stress. Data were drawn from the Spring 2009 American Health Association-National College Health Assessment (ACHA-NCHA) at one small, Northeastern university (N=1799). The relationships between hookah use and other substance use, mental health problems, and perceived stress levels were examined using logistic regression analyses. Hookah use (in the past month) was reported among 14.1% (253/1799) of this sample of undergraduates. Hookah users were more likely to use other substances, including cigarettes, cannabis, alcohol, cocaine, and amphetamines. The strongest associations emerged between hookah use and alcohol and cigarette use. There were no significant associations found between hookah use and any mental health problems or perceived stress levels. Hookah users are significantly more likely to use other substances, including alcohol, cigarettes, cannabis, cocaine, and amphetamines compared with non-hookah users. In contrast to cigarette smoking, hookah use does not appear to be associated with mental health problems or perceived stress levels in this sample of undergraduates. Further investigation into the prevalence and correlates of hookah use is needed in representative population samples. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Ceritinib for the treatment of patients with anaplastic lymphoma kinase (ALK)-positive metastatic non-small cell lung cancer.

PubMed

Landi, Lorenza; Cappuzzo, Federico

2016-01-01

Non-small cell lung cancer (NSCLC) represents the paradigm of personalized treatment of human cancer. Several oncogenic druggable alterations have been so far identified, with anaplastic lymphoma kinase (ALK) gene rearrangements representing one of the newest and most appealing. Crizotinib is now recognized as the standard of care in ALK-positive NSCLC due to the positive results of recently published trials. Unfortunately, resistance inevitably occurs within the first year of treatment. Overcoming resistance is the major challenge in clinical oncology, and novel potent ALK inhibitors are currently under evaluation, including ceritinib. Ceritinib is an oral, potent, second-generation ALK inhibitor demonstrating activity in patients who develop resistance to crizotinib. Recent data also suggested efficacy in ALK-inhibitor-naive population, thus supporting investigation of the drug in front-line setting.

[Relevance of long non-coding RNAs in tumour biology].

PubMed

Nagy, Zoltán; Szabó, Diána Rita; Zsippai, Adrienn; Falus, András; Rácz, Károly; Igaz, Péter

2012-09-23

The discovery of the biological relevance of non-coding RNA molecules represents one of the most significant advances in contemporary molecular biology. It has turned out that a major fraction of the non-coding part of the genome is transcribed. Beside small RNAs (including microRNAs) more and more data are disclosed concerning long non-coding RNAs of 200 nucleotides to 100 kb length that are implicated in the regulation of several basic molecular processes (cell proliferation, chromatin functioning, microRNA-mediated effects, etc.). Some of these long non-coding RNAs have been associated with human tumours, including H19, HOTAIR, MALAT1, etc., the different expression of which has been noted in various neoplasms relative to healthy tissues. Long non-coding RNAs may represent novel markers of molecular diagnostics and they might even turn out to be targets of therapeutic intervention.

Biases in the OSSOS Detection of Large Semimajor Axis Trans-Neptunian Objects

NASA Astrophysics Data System (ADS)

Gladman, Brett; Shankman, Cory; OSSOS Collaboration

2017-10-01

The accumulating but small set of large semimajor axis trans-Neptunian objects (TNOs) shows an apparent clustering in the orientations of their orbits. This clustering must either be representative of the intrinsic distribution of these TNOs, or else have arisen as a result of observation biases and/or statistically expected variations for such a small set of detected objects. The clustered TNOs were detected across different and independent surveys, which has led to claims that the detections are therefore free of observational bias. This apparent clustering has led to the so-called “Planet 9” hypothesis that a super-Earth currently resides in the distant solar system and causes this clustering. The Outer Solar System Origins Survey (OSSOS) is a large program that ran on the Canada-France-Hawaii Telescope from 2013 to 2017, discovering more than 800 new TNOs. One of the primary design goals of OSSOS was the careful determination of observational biases that would manifest within the detected sample. We demonstrate the striking and non-intuitive biases that exist for the detection of TNOs with large semimajor axes. The eight large semimajor axis OSSOS detections are an independent data set, of comparable size to the conglomerate samples used in previous studies. We conclude that the orbital distribution of the OSSOS sample is consistent with being detected from a uniform underlying angular distribution.

OSSOS. VI. Striking Biases in the Detection of Large Semimajor Axis Trans-Neptunian Objects

NASA Astrophysics Data System (ADS)

Shankman, Cory; Kavelaars, J. J.; Bannister, Michele T.; Gladman, Brett J.; Lawler, Samantha M.; Chen, Ying-Tung; Jakubik, Marian; Kaib, Nathan; Alexandersen, Mike; Gwyn, Stephen D. J.; Petit, Jean-Marc; Volk, Kathryn

2017-08-01

The accumulating but small set of large semimajor axis trans-Neptunian objects (TNOs) shows an apparent clustering in the orientations of their orbits. This clustering must either be representative of the intrinsic distribution of these TNOs, or else have arisen as a result of observation biases and/or statistically expected variations for such a small set of detected objects. The clustered TNOs were detected across different and independent surveys, which has led to claims that the detections are therefore free of observational bias. This apparent clustering has led to the so-called “Planet 9” hypothesis that a super-Earth currently resides in the distant solar system and causes this clustering. The Outer Solar System Origins Survey (OSSOS) is a large program that ran on the Canada–France–Hawaii Telescope from 2013 to 2017, discovering more than 800 new TNOs. One of the primary design goals of OSSOS was the careful determination of observational biases that would manifest within the detected sample. We demonstrate the striking and non-intuitive biases that exist for the detection of TNOs with large semimajor axes. The eight large semimajor axis OSSOS detections are an independent data set, of comparable size to the conglomerate samples used in previous studies. We conclude that the orbital distribution of the OSSOS sample is consistent with being detected from a uniform underlying angular distribution.

School Readiness in Children Living in Non-Parental Care: Impacts of Head Start

ERIC Educational Resources Information Center

Lipscomb, Shannon T.; Pratt, Megan E.; Schmitt, Sara A.; Pears, Katherine C.; Kim, Hyoun K.

2013-01-01

The current study examines the effects of Head Start on the development of school readiness outcomes for children living in non-parental care. Data were obtained from the Head Start Impact Study, a randomized controlled trial of Head Start conducted with a nationally representative sample of Head Start programs and families. The sample included…

Speeding Up Non-Parametric Bootstrap Computations for Statistics Based on Sample Moments in Small/Moderate Sample Size Applications

PubMed Central

Chaibub Neto, Elias

2015-01-01

In this paper we propose a vectorized implementation of the non-parametric bootstrap for statistics based on sample moments. Basically, we adopt the multinomial sampling formulation of the non-parametric bootstrap, and compute bootstrap replications of sample moment statistics by simply weighting the observed data according to multinomial counts instead of evaluating the statistic on a resampled version of the observed data. Using this formulation we can generate a matrix of bootstrap weights and compute the entire vector of bootstrap replications with a few matrix multiplications. Vectorization is particularly important for matrix-oriented programming languages such as R, where matrix/vector calculations tend to be faster than scalar operations implemented in a loop. We illustrate the application of the vectorized implementation in real and simulated data sets, when bootstrapping Pearson’s sample correlation coefficient, and compared its performance against two state-of-the-art R implementations of the non-parametric bootstrap, as well as a straightforward one based on a for loop. Our investigations spanned varying sample sizes and number of bootstrap replications. The vectorized bootstrap compared favorably against the state-of-the-art implementations in all cases tested, and was remarkably/considerably faster for small/moderate sample sizes. The same results were observed in the comparison with the straightforward implementation, except for large sample sizes, where the vectorized bootstrap was slightly slower than the straightforward implementation due to increased time expenditures in the generation of weight matrices via multinomial sampling. PMID:26125965

A Geology Sampling System for Small Bodies

NASA Technical Reports Server (NTRS)

Hood, A. D.; Naids, A. J.; Graff, T.; Abell, P.

2015-01-01

Human exploration of Small Bodies is being investigated as a precursor to a Mars surface mission. Asteroids, comets, dwarf planets, and the moons of Mars all fall into this Small Bodies category and some are being discussed as potential mission tar-gets. Obtaining geological samples for return to Earth will be a major objective for any mission to a Small Body. Currently the knowledge base for geology sampling in microgravity is in its infancy. Furthermore, humans interacting with non-engineered surfaces in a microgravity environment poses unique challenges. In preparation for such missions, a team at the National Aeronautics and Space Administration (NASA) John-son Space Center (JSC) has been working to gain experience on how to safely obtain numerous sample types in such an environment. This abstract briefly summarizes the type of samples the science community is interested in, discusses an integrated geology sampling solution, and highlights some of the unique challenges associated with this type of exploration.

Diversity of human small intestinal Streptococcus and Veillonella populations.

PubMed

van den Bogert, Bartholomeus; Erkus, Oylum; Boekhorst, Jos; de Goffau, Marcus; Smid, Eddy J; Zoetendal, Erwin G; Kleerebezem, Michiel

2013-08-01

Molecular and cultivation approaches were employed to study the phylogenetic richness and temporal dynamics of Streptococcus and Veillonella populations in the small intestine. Microbial profiling of human small intestinal samples collected from four ileostomy subjects at four time points displayed abundant populations of Streptococcus spp. most affiliated with S. salivarius, S. thermophilus, and S. parasanguinis, as well as Veillonella spp. affiliated with V. atypica, V. parvula, V. dispar, and V. rogosae. Relative abundances varied per subject and time of sampling. Streptococcus and Veillonella isolates were cultured using selective media from ileostoma effluent samples collected at two time points from a single subject. The richness of the Streptococcus and Veillonella isolates was assessed at species and strain level by 16S rRNA gene sequencing and genetic fingerprinting, respectively. A total of 160 Streptococcus and 37 Veillonella isolates were obtained. Genetic fingerprinting differentiated seven Streptococcus lineages from ileostoma effluent, illustrating the strain richness within this ecosystem. The Veillonella isolates were represented by a single phylotype. Our study demonstrated that the small intestinal Streptococcus populations displayed considerable changes over time at the genetic lineage level because only representative strains of a single Streptococcus lineage could be cultivated from ileostoma effluent at both time points. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Quantitation of mycotoxins using direct analysis in real time (DART)-mass spectrometry (MS)

USDA-ARS?s Scientific Manuscript database

Ambient ionization represents a new generation of mass spectrometry ion sources which is used for rapid ionization of small molecules under ambient conditions. The combination of ambient ionization and mass spectrometry allows analyzing multiple food samples with simple or no sample treatment, or in...

Status Variations in Alcohol Use among Young Adults: Results from the 1984 National Longitudinal Surveys of Youth.

ERIC Educational Resources Information Center

Crowley, Joan E.

This document gives descriptive results on alcohol use patterns among young adults from the 1984 National Longitudinal Survey of Labor Market of Youth, a survey of a large, nationally representative sample supplemented by samples of blacks, Hispanics, and economically disadvantaged non-black, non-Hispanic youth and covering the entire range of…

Measuring sperm backflow following female orgasm: a new method

PubMed Central

King, Robert; Dempsey, Maria; Valentine, Katherine A.

2016-01-01

Background Human female orgasm is a vexed question in the field while there is credible evidence of cryptic female choice that has many hallmarks of orgasm in other species. Our initial goal was to produce a proof of concept for allowing females to study an aspect of infertility in a home setting, specifically by aligning the study of human infertility and increased fertility with the study of other mammalian fertility. In the latter case - the realm of oxytocin-mediated sperm retention mechanisms seems to be at work in terms of ultimate function (differential sperm retention) while the proximate function (rapid transport or cervical tenting) remains unresolved. Method A repeated measures design using an easily taught technique in a natural setting was used. Participants were a small (n=6), non-representative sample of females. The introduction of a sperm-simulant combined with an orgasm-producing technique using a vibrator/home massager and other easily supplied materials. Results The sperm flowback (simulated) was measured using a technique that can be used in a home setting. There was a significant difference in simulant retention between the orgasm (M=4.08, SD=0.17) and non-orgasm (M=3.30, SD=0.22) conditions; t (5)=7.02, p=0.001. Cohen's d=3.97, effect size r=0.89. This indicates a medium to small effect size. Conclusions This method could allow females to test an aspect of sexual response that has been linked to lowered fertility in a home setting with minimal training. It needs to be replicated with a larger sample size. PMID:27799082

Three Rounds of External Quality Assessment in France to Evaluate the Performance of 28 Platforms for Multiparametric Molecular Testing in Metastatic Colorectal and Non-Small Cell Lung Cancer.

PubMed

Dequeker, Elisabeth M C; Keppens, Cleo; Egele, Caroline; Delen, Sofie; Lamy, Aude; Lemoine, Antoinette; Sabourin, Jean-Christophe; Andrieu, Catherine; Ligtenberg, Marjolijn; Fetique, Dominique; Tops, Bastiaan; Descarpentries, Clotilde; Blons, Hélène; Denoux, Yves; Aube, Cécile; Penault-Llorca, Frederique; Hofman, Paul; Leroy, Karen; Le Marechal, Cédric; Doucet, Laurent; Duranton-Tanneur, Valérie; Pedeutour, Florence; Soubeyran, Isabelle; Côté, Jean-François; Emile, Jean-François; Vignaud, Jean-Michel; Monhoven, Nathalie; Haddad, Véronique; Laurent-Puig, Pierre; van Krieken, Han; Nowak, Frederique; Lonchamp, Etienne; Bellocq, Jean-Pierre; Rouleau, Etienne

2016-03-01

Personalized medicine has gained increasing importance in clinical oncology, and several clinically important biomarkers are implemented in routine practice. In an effort to guarantee high quality of molecular testing in France, three subsequent external quality assessment rounds were organized at the initiative of the National Cancer Institute between 2012 and 2014. The schemes included clinically relevant biomarkers for metastatic colorectal (KRAS, NRAS, BRAF, PIK3CA, microsatellite instability) and non-small cell lung cancer (EGFR, KRAS, BRAF, PIK3CA, ERBB2), and they represent the first multigene/multicancer studies throughout Europe. In total, 56 laboratories coordinated by 28 regional molecular centers participated in the schemes. Laboratories received formalin-fixed, paraffin-embedded samples and were asked to use routine methods for molecular testing to predict patient response to targeted therapies. They were encouraged to return results within 14 calendar days after sample receipt. Both genotyping and reporting were evaluated separately. During the three external quality assessment rounds, mean genotype scores were all above the preset standard of 90% for all biomarkers. Participants were mainly challenged in case of rare insertions or deletions. Assessment of the written reports showed substantial progress between the external quality assessment schemes on multiple criteria. Several essential elements such as the clinical interpretation of test results and the reason for testing still require improvement by continued external quality assessment education. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Measuring sperm backflow following female orgasm: a new method.

PubMed

King, Robert; Dempsey, Maria; Valentine, Katherine A

2016-01-01

Human female orgasm is a vexed question in the field while there is credible evidence of cryptic female choice that has many hallmarks of orgasm in other species. Our initial goal was to produce a proof of concept for allowing females to study an aspect of infertility in a home setting, specifically by aligning the study of human infertility and increased fertility with the study of other mammalian fertility. In the latter case - the realm of oxytocin-mediated sperm retention mechanisms seems to be at work in terms of ultimate function (differential sperm retention) while the proximate function (rapid transport or cervical tenting) remains unresolved. A repeated measures design using an easily taught technique in a natural setting was used. Participants were a small (n=6), non-representative sample of females. The introduction of a sperm-simulant combined with an orgasm-producing technique using a vibrator/home massager and other easily supplied materials. The sperm flowback (simulated) was measured using a technique that can be used in a home setting. There was a significant difference in simulant retention between the orgasm (M=4.08, SD=0.17) and non-orgasm (M=3.30, SD=0.22) conditions; t (5)=7.02, p=0.001. Cohen's d=3.97, effect size r=0.89. This indicates a medium to small effect size. This method could allow females to test an aspect of sexual response that has been linked to lowered fertility in a home setting with minimal training. It needs to be replicated with a larger sample size.

Non-destructive controlled single-particle light scattering measurement

NASA Astrophysics Data System (ADS)

Maconi, G.; Penttilä, A.; Kassamakov, I.; Gritsevich, M.; Helander, P.; Puranen, T.; Salmi, A.; Hæggström, E.; Muinonen, K.

2018-01-01

We present a set of light scattering data measured from a millimeter-sized extraterrestrial rock sample. The data were acquired by our novel scatterometer, which enables accurate multi-wavelength measurements of single-particle samples whose position and orientation are controlled by ultrasonic levitation. The measurements demonstrate a non-destructive approach to derive optical properties of small mineral samples. This enables research on valuable materials, such as those returned from space missions or rare meteorites.

Demonstration/Validation of Incremental Sampling at Two Diverse Military Ranges and Development of an Incremental Sampling Tool

DTIC Science & Technology

2010-06-01

Sampling (MIS)? • Technique of combining many increments of soil from a number of points within exposure area • Developed by Enviro Stat (Trademarked...Demonstrating a reliable soil sampling strategy to accurately characterize contaminant concentrations in spatially extreme and heterogeneous...into a set of decision (exposure) units • One or several discrete or small- scale composite soil samples collected to represent each decision unit

The socio-economic patterning of survey participation and non-response error in a multilevel study of food purchasing behaviour: area- and individual-level characteristics.

PubMed

Turrell, Gavin; Patterson, Carla; Oldenburg, Brian; Gould, Trish; Roy, Marie-Andree

2003-04-01

To undertake an assessment of survey participation and non-response error in a population-based study that examined the relationship between socio-economic position and food purchasing behaviour. The study was conducted in Brisbane City (Australia) in 2000. The sample was selected using a stratified two-stage cluster design. Respondents were recruited using a range of strategies that attempted to maximise the involvement of persons from disadvantaged backgrounds: respondents were contacted by personal visit and data were collected using home-based face-to-face interviews; multiple call-backs on different days and at different times were used; and a financial gratuity was provided. Non-institutionalised residents of private dwellings located in 50 small areas that differed in their socio-economic characteristics. Rates of survey participation - measured by non-contacts, exclusions, dropped cases, response rates and completions - were similar across areas, suggesting that residents of socio-economically advantaged and disadvantaged areas were equally likely to be recruited. Individual-level analysis, however, showed that respondents and non-respondents differed significantly in their sociodemographic and food purchasing characteristics: non-respondents were older, less educated and exhibited different purchasing behaviours. Misclassification bias probably accounted for the inconsistent pattern of association between the area- and individual-level results. Estimates of bias due to non-response indicated that although respondents and non-respondents were qualitatively different, the magnitude of error associated with this differential was minimal. Socio-economic position measured at the individual level is a strong and consistent predictor of survey non-participation. Future studies that set out to examine the relationship between socio-economic position and diet need to adopt sampling strategies and data collection methods that maximise the likelihood of recruiting participants from all points on the socio-economic spectrum, and particularly persons from disadvantaged backgrounds. Study designs that are not sensitive to the difficulties associated with recruiting a socio-economically representative sample are likely to produce biased estimates (underestimates) of socio-economic differences in the dietary outcome being investigated.

Drinking Water Intake Is Associated with Higher Diet Quality among French Adults

PubMed Central

Gazan, Rozenn; Sondey, Juliette; Maillot, Matthieu; Guelinckx, Isabelle; Lluch, Anne

2016-01-01

This study aimed to examine the association between drinking water intake and diet quality, and to analyse the adherence of French men and women to the European Food Safety Authority 2010 Adequate Intake (EFSA AI). A representative sample of French adults (≥18) from the Individual and National Survey on Food Consumption (INCA2) was classified, by sex, into small, medium, and large drinking water consumers. Diet quality was assessed with several nutritional indices (mean adequacy ratio (MAR), mean excess ratio (MER), probability of adequate intakes (PANDiet), and solid energy density (SED)). Of the total sample, 72% of men and 46% of women were below the EFSA AI. This percentage of non-adherence decreased from the small to the large drinking water consumers (from 95% to 34% in men and from 81% to 9% in women). For both sexes, drinking water intake was associated with higher diet quality (greater MAR and PANDiet). This association remained significant independently of socio-economic status for women only. Low drinking water consumers did not compensate with other sources (beverages and food moisture) and a high drinking water intake was not a guarantee for reaching the EFSA AI, meaning that increasing consumption of water should be encouraged in France. PMID:27809236

Drinking Water Intake Is Associated with Higher Diet Quality among French Adults.

PubMed

Gazan, Rozenn; Sondey, Juliette; Maillot, Matthieu; Guelinckx, Isabelle; Lluch, Anne

2016-10-31

This study aimed to examine the association between drinking water intake and diet quality, and to analyse the adherence of French men and women to the European Food Safety Authority 2010 Adequate Intake (EFSA AI). A representative sample of French adults (≥18) from the Individual and National Survey on Food Consumption (INCA2) was classified, by sex, into small, medium, and large drinking water consumers. Diet quality was assessed with several nutritional indices (mean adequacy ratio (MAR), mean excess ratio (MER), probability of adequate intakes (PANDiet), and solid energy density (SED)). Of the total sample, 72% of men and 46% of women were below the EFSA AI. This percentage of non-adherence decreased from the small to the large drinking water consumers (from 95% to 34% in men and from 81% to 9% in women). For both sexes, drinking water intake was associated with higher diet quality (greater MAR and PANDiet). This association remained significant independently of socio-economic status for women only. Low drinking water consumers did not compensate with other sources (beverages and food moisture) and a high drinking water intake was not a guarantee for reaching the EFSA AI, meaning that increasing consumption of water should be encouraged in France.

Photoacoustic sensor for medical diagnostics

NASA Astrophysics Data System (ADS)

Wolff, Marcus; Groninga, Hinrich G.; Harde, Hermann

2004-03-01

The development of new optical sensor technologies has a major impact on the progress of diagnostic methods. Of the permanently increasing number of non-invasive breath tests, the 13C-Urea Breath Test (UBT) for the detection of Helicobacter pylori is the most prominent. However, many recent developments, like the detection of cancer by breath test, go beyond gastroenterological applications. We present a new detection scheme for breath analysis that employs an especially compact and simple set-up. Photoacoustic Spectroscopy (PAS) represents an offset-free technique that allows for short absorption paths and small sample cells. Using a single-frequency diode laser and taking advantage of acoustical resonances of the sample cell, we performed extremely sensitive and selective measurements. The smart data processing method contributes to the extraordinary sensitivity and selectivity as well. Also, the reasonable acquisition cost and low operational cost make this detection scheme attractive for many biomedical applications. The experimental set-up and data processing method, together with exemplary isotope-selective measurements on carbon dioxide, are presented.

Childhood Reports of Food Neglect and Impulse Control Problems and Violence in Adulthood

PubMed Central

Vaughn, Michael G.; Salas-Wright, Christopher P.; Naeger, Sandra; Huang, Jin; Piquero, Alex R.

2016-01-01

Food insecurity and hunger during childhood are associated with an array of developmental problems in multiple domains, including impulse control problems and violence. Unfortunately, extant research is based primarily on small convenience samples and an epidemiological assessment of the hunger-violence link is lacking. The current study employed data from Wave 1 (2001–2002) and Wave 2 (2004–2005) of the National Epidemiologic Survey on Alcohol and Related Conditions (NESARC). The NESARC is a nationally representative sample of non-institutionalized U.S. residents aged 18 years and older. Participants who experienced frequent hunger during childhood had significantly greater impulsivity, worse self-control, and greater involvement in several forms of interpersonal violence. These effects were stronger among whites, Hispanics, and males. The findings support general theoretical models implicating impulse control problems as a key correlate of crime and violence and add another facet to the importance of ameliorating food neglect in the United States. PMID:27043598

A Comparison of Techniques for Scheduling Earth-Observing Satellites

NASA Technical Reports Server (NTRS)

Globus, Al; Crawford, James; Lohn, Jason; Pryor, Anna

2004-01-01

Scheduling observations by coordinated fleets of Earth Observing Satellites (EOS) involves large search spaces, complex constraints and poorly understood bottlenecks, conditions where evolutionary and related algorithms are often effective. However, there are many such algorithms and the best one to use is not clear. Here we compare multiple variants of the genetic algorithm: stochastic hill climbing, simulated annealing, squeaky wheel optimization and iterated sampling on ten realistically-sized EOS scheduling problems. Schedules are represented by a permutation (non-temperal ordering) of the observation requests. A simple deterministic scheduler assigns times and resources to each observation request in the order indicated by the permutation, discarding those that violate the constraints created by previously scheduled observations. Simulated annealing performs best. Random mutation outperform a more 'intelligent' mutator. Furthermore, the best mutator, by a small margin, was a novel approach we call temperature dependent random sampling that makes large changes in the early stages of evolution and smaller changes towards the end of search.

The York Gospels: a 1000-year biological palimpsest

PubMed Central

Fiddyment, Sarah; Vnouček, Jiří; Mattiangeli, Valeria; Speller, Camilla; Binois, Annelise; Carver, Martin; Dand, Catherine; Newfield, Timothy P.; Webb, Christopher C.; Bradley, Daniel G.; Collins, Matthew J.

2017-01-01

Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA, we report a cost-effective and simple-to-use biomolecular sampling technique for parchment. We apply this combined methodology to document for the first time a rich palimpsest of biological information contained within the York Gospels, which has accumulated over the 1000-year lifespan of this cherished object that remains an active participant in the life of York Minster. These biological data provide insights into the decisions made in the selection of materials, the construction of the codex and the use history of the object. PMID:29134095

Factual knowledge about AIDS and dating practices among high school students from selected schools.

PubMed

Nyachuru-Sihlangu, R H; Ndlovu, J

1992-06-01

Following various educational strategies by governmental and non-governmental organisations to educate youths and school teachers about HIV infection and prevention, this KABP survey was one attempt to evaluate the results. The study sample of 478 high school students was drawn from four randomly selected schools in Mashonaland and Matabeleland including high and low density, government and mission co-educational schools. The sample was randomly selected and stratified to represent sex and grade level. The KABP self administered questionnaire was used. The paper analyses the relationship between the knowledge and dating patterns. Generally, respondents demonstrated a 50pc to 80pc accuracy of factual knowledge. Of the 66pc Forms I through IV pupils who dated, 30pc preferred only sexually involved relationships and a small number considered the possibility of HIV/AIDS infection. A theoretically based tripartite coalition involving the school, the family health care services for education, guidance and support to promote responsible behaviour throughout childhood was suggested.

A Propensity Score Matching Analysis of the Effects of Special Education Services

PubMed Central

Morgan, Paul L.; Frisco, Michelle; Farkas, George; Hibel, Jacob

2013-01-01

We sought to quantify the effectiveness of special education services as naturally delivered in U.S. schools. Specifically, we examined whether children receiving special education services displayed (a) greater reading or mathematics skills, (b) more frequent learning-related behaviors, or (c) less frequent externalizing or internalizing problem behaviors than closely matched peers not receiving such services. To do so, we used propensity score matching techniques to analyze data from the Early Childhood Longitudinal—Study Kindergarten Cohort, 1998–1999, a large scale, nationally representative sample of U.S. schoolchildren. Collectively, results indicate that receipt of special education services has either a negative or statistically non-significant impact on children’s learning or behavior. However, special education services do yield a small, positive effect on children’s learning-related behaviors. PMID:23606759

A Maximum Entropy Method for Particle Filtering

NASA Astrophysics Data System (ADS)

Eyink, Gregory L.; Kim, Sangil

2006-06-01

Standard ensemble or particle filtering schemes do not properly represent states of low priori probability when the number of available samples is too small, as is often the case in practical applications. We introduce here a set of parametric resampling methods to solve this problem. Motivated by a general H-theorem for relative entropy, we construct parametric models for the filter distributions as maximum-entropy/minimum-information models consistent with moments of the particle ensemble. When the prior distributions are modeled as mixtures of Gaussians, our method naturally generalizes the ensemble Kalman filter to systems with highly non-Gaussian statistics. We apply the new particle filters presented here to two simple test cases: a one-dimensional diffusion process in a double-well potential and the three-dimensional chaotic dynamical system of Lorenz.

A Propensity Score Matching Analysis of the Effects of Special Education Services.

PubMed

Morgan, Paul L; Frisco, Michelle; Farkas, George; Hibel, Jacob

2010-02-01

We sought to quantify the effectiveness of special education services as naturally delivered in U.S. schools. Specifically, we examined whether children receiving special education services displayed (a) greater reading or mathematics skills, (b) more frequent learning-related behaviors, or (c) less frequent externalizing or internalizing problem behaviors than closely matched peers not receiving such services. To do so, we used propensity score matching techniques to analyze data from the Early Childhood Longitudinal-Study Kindergarten Cohort, 1998-1999, a large scale, nationally representative sample of U.S. schoolchildren. Collectively, results indicate that receipt of special education services has either a negative or statistically non-significant impact on children's learning or behavior. However, special education services do yield a small, positive effect on children's learning-related behaviors.

Strengths and weaknesses of temporal stability analysis for monitoring and estimating grid-mean soil moisture in a high-intensity irrigated agricultural landscape

NASA Astrophysics Data System (ADS)

Ran, Youhua; Li, Xin; Jin, Rui; Kang, Jian; Cosh, Michael H.

2017-01-01

Monitoring and estimating grid-mean soil moisture is very important for assessing many hydrological, biological, and biogeochemical processes and for validating remotely sensed surface soil moisture products. Temporal stability analysis (TSA) is a valuable tool for identifying a small number of representative sampling points to estimate the grid-mean soil moisture content. This analysis was evaluated and improved using high-quality surface soil moisture data that were acquired by a wireless sensor network in a high-intensity irrigated agricultural landscape in an arid region of northwestern China. The performance of the TSA was limited in areas where the representative error was dominated by random events, such as irrigation events. This shortcoming can be effectively mitigated by using a stratified TSA (STSA) method, proposed in this paper. In addition, the following methods were proposed for rapidly and efficiently identifying representative sampling points when using TSA. (1) Instantaneous measurements can be used to identify representative sampling points to some extent; however, the error resulting from this method is significant when validating remotely sensed soil moisture products. Thus, additional representative sampling points should be considered to reduce this error. (2) The calibration period can be determined from the time span of the full range of the grid-mean soil moisture content during the monitoring period. (3) The representative error is sensitive to the number of calibration sampling points, especially when only a few representative sampling points are used. Multiple sampling points are recommended to reduce data loss and improve the likelihood of representativeness at two scales.

Integrated molecular portrait of non-small cell lung cancers

PubMed Central

2013-01-01

Background Non-small cell lung cancer (NSCLC), a leading cause of cancer deaths, represents a heterogeneous group of neoplasms, mostly comprising squamous cell carcinoma (SCC), adenocarcinoma (AC) and large-cell carcinoma (LCC). The objectives of this study were to utilize integrated genomic data including copy-number alteration, mRNA, microRNA expression and candidate-gene full sequencing data to characterize the molecular distinctions between AC and SCC. Methods Comparative genomic hybridization followed by mutational analysis, gene expression and miRNA microarray profiling were performed on 123 paired tumor and non-tumor tissue samples from patients with NSCLC. Results At DNA, mRNA and miRNA levels we could identify molecular markers that discriminated significantly between the various histopathological entities of NSCLC. We identified 34 genomic clusters using aCGH data; several genes exhibited a different profile of aberrations between AC and SCC, including PIK3CA, SOX2, THPO, TP63, PDGFB genes. Gene expression profiling analysis identified SPP1, CTHRC1and GREM1 as potential biomarkers for early diagnosis of the cancer, and SPINK1 and BMP7 to distinguish between AC and SCC in small biopsies or in blood samples. Using integrated genomics approach we found in recurrently altered regions a list of three potential driver genes, MRPS22, NDRG1 and RNF7, which were consistently over-expressed in amplified regions, had wide-spread correlation with an average of ~800 genes throughout the genome and highly associated with histological types. Using a network enrichment analysis, the targets of these potential drivers were seen to be involved in DNA replication, cell cycle, mismatch repair, p53 signalling pathway and other lung cancer related signalling pathways, and many immunological pathways. Furthermore, we also identified one potential driver miRNA hsa-miR-944. Conclusions Integrated molecular characterization of AC and SCC helped identify clinically relevant markers and potential drivers, which are recurrent and stable changes at DNA level that have functional implications at RNA level and have strong association with histological subtypes. PMID:24299561

The role of CD133 in the identification and characterisation of tumour-initiating cells in non-small-cell lung cancer.

PubMed

Tirino, Virginia; Camerlingo, Rosa; Franco, Renato; Malanga, Donatella; La Rocca, Antonello; Viglietto, Giuseppe; Rocco, Gaetano; Pirozzi, Giuseppe

2009-09-01

Emerging evidence suggests that specific sub-populations of cancer cells with stem cell characteristics within the bulk of tumours are implicated in the pathogenesis of heterogeneous malignant tumours. The cells that drive tumour growth have been denoted cancer-initiating cells or cancer stem cells (hereafter CSCs). CSCs have been isolated initially from leukaemias and subsequently from several solid tumours including brain, breast, prostate, colon and lung cancer. This study aimed at isolating and characterising the population of tumour-initiating cells in non-small-cell lung cancer (NSCLC). Specimens of NSCLC obtained from 89 patients undergoing tumour resection at the Cancer National Institute of Naples were analysed. Three methods to isolate the tumour-initiating cells were used: (1) flow cytometry analysis for identification of positive cells for surface markers such as CD24, CD29, CD31, CD34, CD44, CD133 and CD326; (2) Hoechst 33342 dye exclusion test for the identification of a side-population characteristic for the presence of stem cells; (3) non-adherent culture condition able to form spheres with stem cell-like characteristics. Definition of the tumourigenic potential of the cells through soft agar assay and injection into NOD/SCID mice were used to functionally define (in vitro and in vivo) putative CSCs isolated from NSCLC samples. Upon flow cytometry analysis of NSCLC samples, CD133-positive cells were found in 72% of 89 fresh specimens analysed and, on average, represented 6% of the total cells. Moreover, the number of CD133-positive cells increased markedly when the cells, isolated from NSCLC specimens, were grown as spheres in non-adherent culture conditions. Cells from NSCLC, grown as spheres, when assayed in soft agar, give rise to a 3.8-fold larger number of colonies in culture and are more tumourigenic in non-obese diabetic (NOD)/severe combined immunodeficiency (SCID) mice compared with the corresponding adherent cells. We have isolated and characterised a population of CD133-positive cells from NSCLC that is able to give rise to spheres and can act as tumour-initiating cells.

Small Bowel Volvulus in the Adult Populace of the United States: Results From a Population-Based Study

PubMed Central

Coe, Taylor M.; Chang, David C.; Sicklick, Jason K.

2015-01-01

Background Small bowel volvulus is a rare entity in Western adults. Greater insight into epidemiology and outcomes may be gained from a national database inquiry. Methods The Nationwide Inpatient Sample (1998–2010), a 20% stratified sample of United States hospitals, was retrospectively reviewed for small bowel volvulus cases (ICD-9 560.2 excluding gastric/colonic procedures) in patients ≥18-years old. Results There were 2,065,599 hospitalizations for bowel obstruction (ICD-9 560.x). Of those, there were 20,680 (1.00%) small bowel volvulus cases; 169 were attributable to intestinal malrotation. Most cases presented emergently (89.24%) and operative management was employed more frequently than non-operative (65.21% vs. 34.79%, P<0.0001). Predictors of mortality included age >50-years, Charlson comorbidity index ≥1, emergent admission, peritonitis, acute vascular insufficiency, coagulopathy, and non-operative management (P<0.0001). Conclusions As the first population-based epidemiological study of small bowel volvulus, our findings provide a robust representation of this rare cause of small bowel obstruction in American adults. PMID:26002189

Semi-Supervised Projective Non-Negative Matrix Factorization for Cancer Classification.

PubMed

Zhang, Xiang; Guan, Naiyang; Jia, Zhilong; Qiu, Xiaogang; Luo, Zhigang

2015-01-01

Advances in DNA microarray technologies have made gene expression profiles a significant candidate in identifying different types of cancers. Traditional learning-based cancer identification methods utilize labeled samples to train a classifier, but they are inconvenient for practical application because labels are quite expensive in the clinical cancer research community. This paper proposes a semi-supervised projective non-negative matrix factorization method (Semi-PNMF) to learn an effective classifier from both labeled and unlabeled samples, thus boosting subsequent cancer classification performance. In particular, Semi-PNMF jointly learns a non-negative subspace from concatenated labeled and unlabeled samples and indicates classes by the positions of the maximum entries of their coefficients. Because Semi-PNMF incorporates statistical information from the large volume of unlabeled samples in the learned subspace, it can learn more representative subspaces and boost classification performance. We developed a multiplicative update rule (MUR) to optimize Semi-PNMF and proved its convergence. The experimental results of cancer classification for two multiclass cancer gene expression profile datasets show that Semi-PNMF outperforms the representative methods.

The Demographics of Alcohol Use among Young Americans: Results from the 1983 National Longitudinal Survey of Labor Market Experience of Youth.

ERIC Educational Resources Information Center

Crowley, Joan E.

This document gives results of research on alcohol use by young Americans from the 1983 National Longitudinal Survey of Labor Market Experience of Youth, a survey of a large, nationally representative sample supplemented by samples of blacks, Hispanics, and economically disadvantaged non-black, non-Hispanic youth and covering the entire range of…

Improvement of core drill methods

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

Gatz, J.L.

1975-07-01

This report documents results of a program to evaluate effectiveness of more or less conventional subsurface samplers in obtaining representative and undisturbed samples of noncohesive alluvial materials containing large quantities of gravels and cobbles. This is the first phase of a research program to improve core drill methods. Samplers evaluated consisted of the Lawrence Livermore Laboratory membrane sampler, 4-in. Denison sampler, 6-in. Dension sampler, 5-in. Modified Denison sampler, and 3-in. thinwall drive tube. Small representative samples were obtained with the Dension samplers; no undisturbed samples were obtained. The field work was accomplished in the Rhodes Canyon area, White Sands Misslemore » Range, New Mexico.« less

AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees.

PubMed

Zhou, Chan; Mao, Fenglou; Yin, Yanbin; Huang, Jinling; Gogarten, Johann Peter; Xu, Ying

2014-01-01

A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php.

AST: An Automated Sequence-Sampling Method for Improving the Taxonomic Diversity of Gene Phylogenetic Trees

PubMed Central

Zhou, Chan; Mao, Fenglou; Yin, Yanbin; Huang, Jinling; Gogarten, Johann Peter; Xu, Ying

2014-01-01

A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php. PMID:24892935

Chemical Characterization of an Envelope A Sample from Hanford Tank 241-AN-103

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

Hay, M.S.

2000-08-23

A whole tank composite sample from Hanford waste tank 241-AN-103 was received at the Savannah River Technology Center (SRTC) and chemically characterized. Prior to characterization the sample was diluted to {approximately}5 M sodium concentration. The filtered supernatant liquid, the total dried solids of the diluted sample, and the washed insoluble solids obtained from filtration of the diluted sample were analyzed. A mass balance calculation of the three fractions of the sample analyzed indicate the analytical results appear relatively self-consistent for major components of the sample. However, some inconsistency was observed between results where more than one method of determination wasmore » employed and for species present in low concentrations. A direct comparison to previous analyses of material from tank 241-AN-103 was not possible due to unavailability of data for diluted samples of tank 241-AN-103 whole tank composites. However, the analytical data for other types of samples from 241-AN-103 we re mathematically diluted and compare reasonably with the current results. Although the segments of the core samples used to prepare the sample received at SRTC were combined in an attempt to produce a whole tank composite, determination of how well the results of the current analysis represent the actual composition of the Hanford waste tank 241-AN-103 remains problematic due to the small sample size and the large size of the non-homogenized waste tank.« less

Genome-wide identification of Hami melon miRNAs with putative roles during fruit development

PubMed Central

Wang, Guangzhi; Ma, Xinli; Li, Meihua; Wu, Haibo; Fu, Qiushi; Zhang, Yi; Yi, Hongping

2017-01-01

MicroRNAs represent a family of small endogenous, non-coding RNAs that play critical regulatory roles in plant growth, development, and environmental stress responses. Hami melon is famous for its attractive flavor and excellent nutritional value, however, the mechanisms underlying the fruit development and ripening remains largely unknown. Here, we performed small RNA sequencing to investigate the roles of miRNAs during Hami melon fruit development. Two batches of flesh samples were collected at four fruit development stages. Small RNA sequencing yielded a total of 54,553,424 raw reads from eight libraries. 113 conserved miRNAs belonging to 30 miRNA families and nine novel miRNAs comprising nine miRNA families were identified. The expression of 42 conserved miRNAs and three Hami melon-specific miRNAs significantly changed during fruit development. Furthermore, 484 and 124 melon genes were predicted as putative targets of 29 conserved and nine Hami melon-specific miRNA families, respectively. GO enrichment analysis were performed on target genes, “transcription, DNA-dependent”, “rRNA processing”, “oxidation reduction”, “signal transduction”, “regulation of transcription, DNA-dependent”, and “metabolic process” were the over-represented biological process terms. Cleavage sites of six target genes were validated using 5’ RACE. Our results present a comprehensive set of identification and characterization of Hami melon fruit miRNAs and their potential targets, which provide valuable basis towards understanding the regulatory mechanisms in programmed process of normal Hami fruit development and ripening. Specific miRNAs could be selected for further research and applications in breeding practices. PMID:28742088

Degradation analysis in the estimation of photometric redshifts from non-representative training sets

NASA Astrophysics Data System (ADS)

Rivera, J. D.; Moraes, B.; Merson, A. I.; Jouvel, S.; Abdalla, F. B.; Abdalla, M. C. B.

2018-07-01

We perform an analysis of photometric redshifts estimated by using a non-representative training sets in magnitude space. We use the ANNz2 and GPz algorithms to estimate the photometric redshift both in simulations and in real data from the Sloan Digital Sky Survey (DR12). We show that for the representative case, the results obtained by using both algorithms have the same quality, using either magnitudes or colours as input. In order to reduce the errors when estimating the redshifts with a non-representative training set, we perform the training in colour space. We estimate the quality of our results by using a mock catalogue which is split samples cuts in the r band between 19.4 < r < 20.8. We obtain slightly better results with GPz on single point z-phot estimates in the complete training set case, however the photometric redshifts estimated with ANNz2 algorithm allows us to obtain mildly better results in deeper r-band cuts when estimating the full redshift distribution of the sample in the incomplete training set case. By using a cumulative distribution function and a Monte Carlo process, we manage to define a photometric estimator which fits well the spectroscopic distribution of galaxies in the mock testing set, but with a larger scatter. To complete this work, we perform an analysis of the impact on the detection of clusters via density of galaxies in a field by using the photometric redshifts obtained with a non-representative training set.

Degradation analysis in the estimation of photometric redshifts from non-representative training sets

NASA Astrophysics Data System (ADS)

Rivera, J. D.; Moraes, B.; Merson, A. I.; Jouvel, S.; Abdalla, F. B.; Abdalla, M. C. B.

2018-04-01

We perform an analysis of photometric redshifts estimated by using a non-representative training sets in magnitude space. We use the ANNz2 and GPz algorithms to estimate the photometric redshift both in simulations as well as in real data from the Sloan Digital Sky Survey (DR12). We show that for the representative case, the results obtained by using both algorithms have the same quality, either using magnitudes or colours as input. In order to reduce the errors when estimating the redshifts with a non-representative training set, we perform the training in colour space. We estimate the quality of our results by using a mock catalogue which is split samples cuts in the r-band between 19.4 < r < 20.8. We obtain slightly better results with GPz on single point z-phot estimates in the complete training set case, however the photometric redshifts estimated with ANNz2 algorithm allows us to obtain mildly better results in deeper r-band cuts when estimating the full redshift distribution of the sample in the incomplete training set case. By using a cumulative distribution function and a Monte-Carlo process, we manage to define a photometric estimator which fits well the spectroscopic distribution of galaxies in the mock testing set, but with a larger scatter. To complete this work, we perform an analysis of the impact on the detection of clusters via density of galaxies in a field by using the photometric redshifts obtained with a non-representative training set.

RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse

PubMed Central

Hüttenhofer, Alexander; Kiefmann, Martin; Meier-Ewert, Sebastian; O’Brien, John; Lehrach, Hans; Bachellerie, Jean-Pierre; Brosius, Jürgen

2001-01-01

In mouse brain cDNA libraries generated from small RNA molecules we have identified a total of 201 different expressed RNA sequences potentially encoding novel small non-messenger RNA species (snmRNAs). Based on sequence and structural motifs, 113 of these RNAs can be assigned to the C/D box or H/ACA box subclass of small nucleolar RNAs (snoRNAs), known as guide RNAs for rRNA. While 30 RNAs represent mouse homologues of previously identified human C/D or H/ACA snoRNAs, 83 correspond to entirely novel snoRNAs. Among these, for the first time, we identified four C/D box snoRNAs and four H/ACA box snoRNAs predicted to direct modifications within U2, U4 or U6 small nuclear RNAs (snRNAs). Furthermore, 25 snoRNAs from either class lacked antisense elements for rRNAs or snRNAs. Therefore, additional snoRNA targets have to be considered. Surprisingly, six C/D box snoRNAs and one H/ACA box snoRNA were expressed exclusively in brain. Of the 88 RNAs not belonging to either snoRNA subclass, at least 26 are probably derived from truncated heterogeneous nuclear RNAs (hnRNAs) or mRNAs. Short interspersed repetitive elements (SINEs) are located on five RNA sequences and may represent rare examples of transcribed SINEs. The remaining RNA species could not as yet be assigned either to any snmRNA class or to a part of a larger hnRNA/mRNA. It is likely that at least some of the latter will represent novel, unclassified snmRNAs. PMID:11387227

Non-Crop Host Sampling Yields Insights into Small-Scale Population Dynamics of Drosophila suzukii (Matsumura)

PubMed Central

Loeb, Gregory M.

2018-01-01

Invasive, polyphagous crop pests subsist on a number of crop and non-crop resources. While knowing the full range of host species is important, a seasonal investigation into the use of non-crop plants adjacent to cropping systems provide key insights into some of the factors determining local population dynamics. This study investigated the infestation of non-crop plants by the invasive Drosophila suzukii (Matsumura), a pest of numerous economically important stone and small fruit crops, by sampling fruit-producing non-crop hosts adjacent to commercial plantings weekly from June through November in central New York over a two-year period. We found D. suzukii infestation rates (number of flies emerged/kg fruit) peaked mid-August through early September, with Rubus allegheniensis Porter and Lonicera morrowii Asa Gray showing the highest average infestation in both years. Interannual infestation patterns were similar despite a lower number of adults caught in monitoring traps the second year, suggesting D. suzukii host use may be density independent. PMID:29301358

Mutation patterns in small cell and non-small cell lung cancer patients suggest a different level of heterogeneity between primary and metastatic tumors.

PubMed

Saber, Ali; Hiltermann, T Jeroen N; Kok, Klaas; Terpstra, M Martijn; de Lange, Kim; Timens, Wim; Groen, Harry J M; van den Berg, Anke

2017-02-01

Several studies have shown heterogeneity in lung cancer, with parallel existence of multiple subclones characterized by their own specific mutational landscape. The extent to which minor clones become dominant in distinct metastasis is not clear. The aim of our study was to gain insight in the evolution pattern of lung cancer by investigating genomic heterogeneity between primary tumor and its distant metastases. Whole exome sequencing (WES) was performed on 24 tumor and five normal samples of two small cell lung carcinoma (SCLC) and three non-SCLC (NSCLC) patients. Validation of somatic variants in these 24 and screening of 33 additional samples was done by single primer enrichment technology. For each of the three NSCLC patients, about half of the mutations were shared between all tumor samples, whereas for SCLC patients, this percentage was around 95. Independent validation of the non-ubiquitous mutations confirmed the WES data for the vast majority of the variants. Phylogenetic trees indicated more distance between the tumor samples of the NSCLC patients as compared to the SCLC patients. Analysis of 30 independent DNA samples of 16 biopsies used for WES revealed a low degree of intra-tumor heterogeneity of the selected sets of mutations. In the primary tumors of all five patients, variable percentages (19-67%) of the seemingly metastases-specific mutations were present albeit at low read frequencies. Patients with advanced NSCLC have a high percentage of non-ubiquitous mutations indicative of branched evolution. In contrast, the low degree of heterogeneity in SCLC suggests a parallel and linear model of evolution. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

NON-REGULATED WATER CONTAMINANTS: EMERGING RESEARCH

EPA Science Inventory

Those chemical pollutants that are regulated under various international, federal, and state programs represent but a small fraction of the universe of chemicals that occur in the environment as a result of both natural processes and human influence. Although this galaxy of targe...

Universal calibration of Raman spectroscopy for the analysis of volatiles in glasses of variable composition

NASA Astrophysics Data System (ADS)

Schiavi, Federica; Bolfan-Casanova, Nathalie

2017-04-01

The amount and distribution of volatiles (water, carbon dioxide …) in magmas represent key parameters for the understanding of magma processes and dynamics within volcanic plumbing systems. Micro-Raman spectroscopy is an excellent technique for accurate determination of volatile contents in magmas, as it combines several advantages. The technique is non-destructive and requires minimal sample preparation before the analysis. Its high lateral and in-depth spatial resolution is crucial for the study of small objects and samples that are chemically and texturally heterogeneous at the small scale (microns). Moreover, the high confocality allows analysis of sample regions not exposed to the surface and 3D mapping. We present a universal calibration of Raman spectroscopy for quantification of volatiles in silicate glasses. The proposed method is based on internal calibration, i.e., on the correlation between the glass water content and the ratio between the areas of the water and silicate Raman bands. Synthetic glasses with variable major element compositions (basaltic, andesitic, rhyolitic, dacitic ..) bearing different H2O (up to 7 wt%) and CO2 contents are used as standard glasses. Natural silicate glasses, mainly in the form of melt inclusions, are used to test the goodness of the proposed method. In addition to quantification of volatiles in glass, in bubble-bearing melt inclusions we perform micro-Raman spectroscopy investigation of gas-bearing bubbles for accurate determination of total volatile contents in melt inclusions.

Prevalence and risk factors for foot and mouth disease infection in small ruminants in Israel.

PubMed

Elnekave, Ehud; van Maanen, Kees; Shilo, Hila; Gelman, Boris; Storm, Nick; Berdenstain, Svetlane; Berke, Olaf; Klement, Eyal

2016-03-01

During the last decade, 27% of the foot and mouth disease (FMD) outbreaks in Israel affected small ruminant (SR) farms. FMD outbreaks reoccur in Israel despite vaccination of all livestock and application of control measures. We performed a cross-sectional serological study, aimed at estimating the prevalence of FMD infection in SR in Israel and the possible risk factors for infection. Overall, 2305 samples of adult sheep (n=1948) and goats (n=357) were collected during 2011-14 in two separate surveys. One survey was based on random sampling of intensive management system farms and the other was originally aimed at the detection of Brucella melitensis at extensive and semi-intensive management system farms. Sera were tested by NS blocking ELISA (PrioCHECK(®)). The serological prevalence of antibodies against non structural proteins (NSP) of FMD virus was estimated at 3.7% (95% confidence interval (CI95%)=3.0% -4.5%). Additionally, a significantly lower infection prevalence (p value=0.049) of 1.0% (CI95%=0.1%-3.6%) was found in a small sample (197 sera) of young SR, collected during 2012. The positive samples from adult SR were scattered all over Israel, though two significant infection clusters were found by the spatial scan statistic. Occurrence of an outbreak on a non-SR farm within 5km distance was associated with a fifteen times increase in the risk of FMD infection of SR in the univariable analysis. Yet, this variable was not included in the multivariable analysis due to collinearities with the other independent variables. Multivariable logistic regression modeling found significantly negative associations (P value<0.05) of grazing and being in a herd larger than 500 animals with risk of infection. Grazing herds and herds larger than 500 animals, both represent farms that are intensively or semi-intensively managed. Higher maintenance of bio-safety, fewer introductions of new animals and higher vaccination compliance in these farms may explain their lower risk of infection by FMD virus. We conclude that despite the wide distribution of infection among SR farms, low farm level prevalence indicates that in Israel SR pose only limited role in the transmission and dissemination of FMD. This conclusion may be applicable for other endemic countries in which, similar to Israel, all livestock are vaccinated against FMD. Copyright © 2016 Elsevier B.V. All rights reserved.

An efficient reliability algorithm for locating design point using the combination of importance sampling concepts and response surface method

NASA Astrophysics Data System (ADS)

Shayanfar, Mohsen Ali; Barkhordari, Mohammad Ali; Roudak, Mohammad Amin

2017-06-01

Monte Carlo simulation (MCS) is a useful tool for computation of probability of failure in reliability analysis. However, the large number of required random samples makes it time-consuming. Response surface method (RSM) is another common method in reliability analysis. Although RSM is widely used for its simplicity, it cannot be trusted in highly nonlinear problems due to its linear nature. In this paper, a new efficient algorithm, employing the combination of importance sampling, as a class of MCS, and RSM is proposed. In the proposed algorithm, analysis starts with importance sampling concepts and using a represented two-step updating rule of design point. This part finishes after a small number of samples are generated. Then RSM starts to work using Bucher experimental design, with the last design point and a represented effective length as the center point and radius of Bucher's approach, respectively. Through illustrative numerical examples, simplicity and efficiency of the proposed algorithm and the effectiveness of the represented rules are shown.

The first liquid biopsy test approved. Is it a new era of mutation testing for non-small cell lung cancer?

PubMed Central

2017-01-01

Specific mutations in epidermal growth factor receptor (EGFR) gene are predictive for response to the EGFR tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer patients (NSCLC). According to international guidelines, the molecular testing in patients with advanced NSCLC of a non-squamous subtype is recommended. However, obtain a tissue sample could be challenging. Liquid biopsy allows to determine patients suitable for EGFR-targeted therapy by analysis of circulating-free tumor DNA (cfDNA) in peripheral blood samples and might replace tissue biopsy. It allows to acquire a material in convenient minimally invasive manner, is easily repeatable, could be used for molecular identification and molecular changes monitoring. Many studies show a high concordance rate between tissue and plasma samples testing. When U.S. Food and Drug Administration (FDA) approved the first liquid biopsy test, analysis of driver gene mutation from cfDNA becomes a reality in clinical practice for patients with NSCLC. PMID:28251125

A High-Sensitivity Hydraulic Load Cell for Small Kitchen Appliances

PubMed Central

Pačnik, Roman; Novak, Franc

2010-01-01

In this paper we present a hydraulic load cell made from hydroformed metallic bellows. The load cell was designed for a small kitchen appliance with the weighing function integrated into the composite control and protection of the appliance. It is a simple, low-cost solution with small dimensions and represents an alternative to the existing hydraulic load cells in industrial use. A good non-linearity and a small hysteresis were achieved. The influence of temperature leads to an error of 7.5%, which can be compensated for by software to meet the requirements of the target application. PMID:22163665

A high-sensitivity hydraulic load cell for small kitchen appliances.

PubMed

Pačnik, Roman; Novak, Franc

2010-01-01

In this paper we present a hydraulic load cell made from hydroformed metallic bellows. The load cell was designed for a small kitchen appliance with the weighing function integrated into the composite control and protection of the appliance. It is a simple, low-cost solution with small dimensions and represents an alternative to the existing hydraulic load cells in industrial use. A good non-linearity and a small hysteresis were achieved. The influence of temperature leads to an error of 7.5%, which can be compensated for by software to meet the requirements of the target application.

Identification of Species and Sources of Cryptosporidium Oocysts in Storm Waters with a Small-Subunit rRNA-Based Diagnostic and Genotyping Tool

PubMed Central

Xiao, Lihua; Alderisio, Kerri; Limor, Josef; Royer, Michael; Lal, Altaf A.

2000-01-01

The identification of Cryptosporidium oocysts in environmental samples is largely made by the use of an immunofluorescent assay. In this study, we have used a small-subunit rRNA-based PCR-restriction fragment length polymorphism technique to identify species and sources of Cryptosporidium oocysts present in 29 storm water samples collected from a stream in New York. A total of 12 genotypes were found in 27 positive samples; for 4 the species and probable origins were identified by sequence analysis, whereas the rest represent new genotypes from wildlife. Thus, this technique provides an alternative method for the detection and differentiation of Cryptosporidium parasites in environmental samples. PMID:11097935

Multiscale Roughness Influencing on Transport Behavior of Passive Solute through a Single Self-affine Fracture

NASA Astrophysics Data System (ADS)

Dou, Z.

2017-12-01

In this study, the influence of multi-scale roughness on transport behavior of the passive solute through the self-affine fracture was investigated. The single self-affine fracture was constructed by the successive random additions (SRA) and the fracture roughness was decomposed into two different scales (i.e. large-scale primary roughness and small-scale secondary roughness) by the Wavelet analysis technique. The fluid flow in fractures, which was characterized by the Forchheimer's law, showed the non-linear flow behaviors such as eddies and tortuous streamlines. The results indicated that the small-scale secondary roughness was primarily responsible for the non-linear flow behaviors. The direct simulations of asymptotic passive solute transport represented the Non-Fickian transport characteristics (i.e. early arrivals and long tails) in breakthrough curves (BTCs) and residence time distributions (RTDs) with and without consideration of the secondary roughness. Analysis of multiscale BTCs and RTDs showed that the small-scale secondary roughness played a significant role in enhancing the Non-Fickian transport characteristics. We found that removing small-scale secondary roughness led to the lengthening arrival and shortening tail. The peak concentration in BTCs decreased as the secondary roughness was removed, implying that the secondary could also enhance the solute dilution. The estimated BTCs by the Fickian advection-dispersion equation (ADE) yielded errors which decreased with the small-scale secondary roughness being removed. The mobile-immobile model (MIM) was alternatively implemented to characterize the Non-Fickian transport. We found that the MIM was more capable of estimating Non-Fickian BTCs. The small-scale secondary roughness resulted in the decreasing mobile domain fraction and the increasing mass exchange rate between immobile and mobile domains. The estimated parameters from the MIM could provide insight into the inherent mechanism of roughness-induced Non-Fickian transport behaviors.

Differential expression analysis for RNAseq using Poisson mixed models

PubMed Central

Sun, Shiquan; Hood, Michelle; Scott, Laura; Peng, Qinke; Mukherjee, Sayan; Tung, Jenny

2017-01-01

Abstract Identifying differentially expressed (DE) genes from RNA sequencing (RNAseq) studies is among the most common analyses in genomics. However, RNAseq DE analysis presents several statistical and computational challenges, including over-dispersed read counts and, in some settings, sample non-independence. Previous count-based methods rely on simple hierarchical Poisson models (e.g. negative binomial) to model independent over-dispersion, but do not account for sample non-independence due to relatedness, population structure and/or hidden confounders. Here, we present a Poisson mixed model with two random effects terms that account for both independent over-dispersion and sample non-independence. We also develop a scalable sampling-based inference algorithm using a latent variable representation of the Poisson distribution. With simulations, we show that our method properly controls for type I error and is generally more powerful than other widely used approaches, except in small samples (n <15) with other unfavorable properties (e.g. small effect sizes). We also apply our method to three real datasets that contain related individuals, population stratification or hidden confounders. Our results show that our method increases power in all three data compared to other approaches, though the power gain is smallest in the smallest sample (n = 6). Our method is implemented in MACAU, freely available at www.xzlab.org/software.html. PMID:28369632

Psychometric Properties of the Penn State Worry Questionnaire for Children in a Large Clinical Sample

ERIC Educational Resources Information Center

Pestle, Sarah L.; Chorpita, Bruce F.; Schiffman, Jason

2008-01-01

The Penn State Worry Questionnaire for Children (PSWQ-C; Chorpita, Tracey, Brown, Collica, & Barlow, 1997) is a 14-item self-report measure of worry in children and adolescents. Although the PSWQ-C has demonstrated favorable psychometric properties in small clinical and large community samples, this study represents the first psychometric…

EBUS-TBNA Provides Highest RNA Yield for Multiple Biomarker Testing from Routinely Obtained Small Biopsies in Non-Small Cell Lung Cancer Patients - A Comparative Study of Three Different Minimal Invasive Sampling Methods

PubMed Central

Schmid-Bindert, Gerald; Wang, Yongsheng; Jiang, Hongbin; Sun, Hui; Henzler, Thomas; Wang, Hao; Pilz, Lothar R.; Ren, Shengxiang; Zhou, Caicun

2013-01-01

Background Multiple biomarker testing is necessary to facilitate individualized treatment of lung cancer patients. More than 80% of lung cancers are diagnosed based on very small tumor samples. Often there is not enough tissue for molecular analysis. We compared three minimal invasive sampling methods with respect to RNA quantity for molecular testing. Methods 106 small biopsies were prospectively collected by three different methods forceps biopsy, endobronchial ultrasound (EBUS) guided transbronchial needle aspiration (TBNA), and CT-guided core biopsy. Samples were split into two halves. One part was formalin fixed and paraffin embedded for standard pathological evaluation. The other part was put in RNAlater for immediate RNA/DNA extraction. If the pathologist confirmed the diagnosis of non-small cell lung cancer(NSCLC), the following molecular markers were tested: EGFR mutation, ERCC1, RRM1 and BRCA1. Results Overall, RNA-extraction was possible in 101 out of 106 patients (95.3%). We found 49% adenocarcinomas, 38% squamouscarcinomas, and 14% non-otherwise-specified(NOS). The highest RNA yield came from endobronchial ultrasound guided needle aspiration, which was significantly higher than bronchoscopy (37.74±41.09 vs. 13.74±15.53 ng respectively, P = 0.005) and numerically higher than CT-core biopsy (37.74±41.09 vs. 28.72±44.27 ng respectively, P = 0.244). EGFR mutation testing was feasible in 100% of evaluable patients and its incidence was 40.8%, 7.9% and 14.3% in adenocarcinomas, squamouscarcinomas and NSCLC NOS subgroup respectively. There was no difference in the feasibility of molecular testing between the three sampling methods with feasibility rates for ERCC1, RRM1 and BRCA1 of 91%, 87% and 81% respectively. Conclusion All three methods can provide sufficient tumor material for multiple biomarkers testing from routinely obtained small biopsies in lung cancer patients. In our study EBUS guided needle aspiration provided the highest amount of tumor RNA compared to bronchoscopy or CT guided core biopsy. Thus EBUS should be considered as an acceptable option for tissue acquisition for molecular testing. PMID:24205040

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

Castelle, Cindy; Wrighton, Kelly C.; Thomas, Brian C.

Domain Archaea is currently represented by one phylum (Euryarchaeota) and two superphyla (TACK and DPANN). However, gene surveys indicate the existence of a vast diversity of uncultivated archaea for which metabolic information is lacking. We sequenced DNA from complex sediment- and groundwater-associated microbial communities sampled prior to and during an acetate biostimulation field experiment to investigate the diversity and physiology of uncultivated subsurface archaea. We sampled 15 genomes that improve resolution of a new phylum within the TACK superphylum and 119 DPANN genomes that highlight a major subdivision within the archaeal domain that separates DPANN from TACK/Euryarchaeota lineages. Within themore » DPANN superphylum, which lacks any isolated representatives, we defined two new phyla using sequences from 100 newly sampled genomes. The first new phylum, for which we propose the name Woesearchaeota, was defined using 54 new sequences. We reconstructed a complete (finished) genome for an archaeon from this phylum that is only 0.8 Mb in length and lacks almost all core biosynthetic pathways, but has genes encoding enzymes predicted to interact with bacterial cell walls, consistent with a symbiotic lifestyle. The second new phylum, for which we propose the name Pacearchaeota, was defined based on 46 newly sampled archaeal genomes. This phylum includes the first non-methanogen with an intermediate Type II/III RuBisCO. We also reconstructed a complete (1.24 Mb) genome for another DPANN archaeon, a member of the Diapherotrites phylum. Metabolic prediction and transcriptomic data indicate that this organism has a fermentation-based lifestyle. In fact, genomic analyses consistently indicate lack of recognizable pathways for sulfur, nitrogen, methane, oxygen, and metal cycling, and suggest that symbiotic and fermentation-based lifestyles are widespread across the DPANN superphylum. Thus, as for a recently identified superphylum of bacteria with small genomes and no cultivated representatives, the biogeochemical impacts of this major radiation of archaea are primarily through anaerobic carbon and hydrogen cycling.« less

Online video game addiction: identification of addicted adolescent gamers.

PubMed

Van Rooij, Antonius J; Schoenmakers, Tim M; Vermulst, Ad A; Van den Eijnden, Regina J J M; Van de Mheen, Dike

2011-01-01

To provide empirical data-driven identification of a group of addicted online gamers. Repeated cross-sectional survey study, comprising a longitudinal cohort, conducted in 2008 and 2009. Secondary schools in the Netherlands.   Two large samples of Dutch schoolchildren (aged 13-16 years). Compulsive internet use scale, weekly hours of online gaming and psychosocial variables. This study confirms the existence of a small group of addicted online gamers (3%), representing about 1.5% of all children aged 13-16 years in the Netherlands. Although these gamers report addiction-like problems, relationships with decreased psychosocial health were less evident. The identification of a small group of addicted online gamers supports efforts to develop and validate questionnaire scales aimed at measuring the phenomenon of online video game addiction. The findings contribute to the discussion on the inclusion of non-substance addictions in the proposed unified concept of 'Addiction and Related Disorders' for the DSM-V by providing indirect identification and validation of a group of suspected online video game addicts. © 2010 The Authors, Addiction © 2010 Society for the Study of Addiction.

Biochar-attenuated desorption of heavy metals in small arms range soils

USDA-ARS?s Scientific Manuscript database

Stabilization (capping/solidification) and dilution (e.g., washing, chelate-assisted phytoremediation) represent non-removal and removal remediation technologies for heavy metal contaminated soils. Biochar is stable in soil, and contains carboxyl and other surface ligands; these properties are usef...

32 CFR 536.15 - Claims policies.

Code of Federal Regulations, 2014 CFR

2014-07-01

... payable claims nor did it intend that small non-meritous claims be paid. Practically any claim, regardless... fair analysis should be paramount. Personal contact with claimants or their representatives is... will publish written interpretations of this part. Interpretations will have the same force and effect...

32 CFR 536.15 - Claims policies.

Code of Federal Regulations, 2013 CFR

2013-07-01

... payable claims nor did it intend that small non-meritous claims be paid. Practically any claim, regardless... fair analysis should be paramount. Personal contact with claimants or their representatives is... will publish written interpretations of this part. Interpretations will have the same force and effect...

32 CFR 536.15 - Claims policies.

Code of Federal Regulations, 2012 CFR

2012-07-01

... payable claims nor did it intend that small non-meritous claims be paid. Practically any claim, regardless... fair analysis should be paramount. Personal contact with claimants or their representatives is... will publish written interpretations of this part. Interpretations will have the same force and effect...

Coding and small non-coding transcriptional landscape of tuberous sclerosis complex cortical tubers: implications for pathophysiology and treatment.

PubMed

Mills, James D; Iyer, Anand M; van Scheppingen, Jackelien; Bongaarts, Anika; Anink, Jasper J; Janssen, Bart; Zimmer, Till S; Spliet, Wim G; van Rijen, Peter C; Jansen, Floor E; Feucht, Martha; Hainfellner, Johannes A; Krsek, Pavel; Zamecnik, Josef; Kotulska, Katarzyna; Jozwiak, Sergiusz; Jansen, Anna; Lagae, Lieven; Curatolo, Paolo; Kwiatkowski, David J; Pasterkamp, R Jeroen; Senthilkumar, Ketharini; von Oerthel, Lars; Hoekman, Marco F; Gorter, Jan A; Crino, Peter B; Mühlebner, Angelika; Scicluna, Brendon P; Aronica, Eleonora

2017-08-14

Tuberous Sclerosis Complex (TSC) is a rare genetic disorder that results from a mutation in the TSC1 or TSC2 genes leading to constitutive activation of the mechanistic target of rapamycin complex 1 (mTORC1). TSC is associated with autism, intellectual disability and severe epilepsy. Cortical tubers are believed to represent the neuropathological substrates of these disabling manifestations in TSC. In the presented study we used high-throughput RNA sequencing in combination with systems-based computational approaches to investigate the complexity of the TSC molecular network. Overall we detected 438 differentially expressed genes and 991 differentially expressed small non-coding RNAs in cortical tubers compared to autopsy control brain tissue. We observed increased expression of genes associated with inflammatory, innate and adaptive immune responses. In contrast, we observed a down-regulation of genes associated with neurogenesis and glutamate receptor signaling. MicroRNAs represented the largest class of over-expressed small non-coding RNA species in tubers. In particular, our analysis revealed that the miR-34 family (including miR-34a, miR-34b and miR-34c) was significantly over-expressed. Functional studies demonstrated the ability of miR-34b to modulate neurite outgrowth in mouse primary hippocampal neuronal cultures. This study provides new insights into the TSC transcriptomic network along with the identification of potential new treatment targets.

Safe Schools? Transgender Youth's School Experiences and Perceptions of School Climate.

PubMed

Day, Jack K; Perez-Brumer, Amaya; Russell, Stephen T

2018-06-01

The magnitude of gender identity-related disparities in school-based outcomes is unknown because of a lack of representative studies that include measures of gender identity. By utilizing a representative sample generalizable to a broader population, this study elucidates the size of gender identity-related disparities, independent of sexual orientation, in school experiences associated with school connectedness and perceptions of school climate. Additionally, the inclusion of and comparison to results of a large non-representative sample allows for more direct comparisons to previous studies of the school experiences of transgender youth. The analyses in this study primarily draw on a sample of 31,896 youth representative of the middle and high school population in California who participated in the 2013-2015 California Student Survey (a subsample of the California Healthy Kids Survey, which includes the largest known sample of transgender youth). Over half the sample identified their sex as female (51.3%), and 398 identified as transgender (1.0%). The sample was racially and ethnically diverse: 30.7% identified as multiracial, 33.0% as White, 11.1% as Asian, 7.4% as Black, and 52.9% as Hispanic. Findings from multilevel analyses show that relative to non-transgender youth, transgender youth were more likely to be truant from school, to experience victimization and bias-based bullying, and to report more negative perceptions of school climate, though did not differ in self-reported grades. The findings have implications for improving school policies and practices to create safer and more supportive school climates for all youth.

Three-dimensional spatial localization of thin fluorophore-filled capillaries in thick scattering media

NASA Astrophysics Data System (ADS)

Desrochers, Johanne; Vermette, Patrick; Fontaine, Réjean; Bérubé-Lauzière, Yves

2008-06-01

Fluorescence optical diffuse tomography (fDOT) is of much interest in molecular imaging to retrieve information from fluorescence signals emitted from specifically targeted bioprocesses deep within living tissues. An exciting application of fDOT is in the growing field of tissue engineering, where 3D non-invasive imaging techniques are required to ultimately grow 3D engineered tissues. Via appropriate labelling strategies and fluorescent probes, fDOT has the potential to monitor culture environment and cells viability non-destructively directly within the bioreactor environment where tissues are to be grown. Our ultimate objective is to image the formation of blood vessels in bioreactor conditions. Herein, we use a non-contact setup for small animal fDOT imaging designed for 3D light collection around the sample. We previously presented a time of flight approach using a numerical constant fraction discrimination technique to assign an early photons arrival time to every fluorescence time point-spread function collected around the sample. Towards bioreactor in-situ imaging, we have shown the capability of our approach to localize a fluorophore-filled 500 μm capillary immersed coaxially in a cylindrically shaped bioreactor phantom containing an absorbing/scattering medium representative of experiments on real tissue cultures. Here, we go one step further, and present results for the 3D localization of thinner indocyanine green labelled capillaries (250 μm and 360 μm inner diameter) immersed in the same phantom conditions and geometry but with different spatial configurations (10° and 30° capillary inclination).

Comparison of non-landslide sampling strategies to counteract inventory-based biases within national-scale statistical landslide susceptibility models

NASA Astrophysics Data System (ADS)

Lima, Pedro; Steger, Stefan; Glade, Thomas

2017-04-01

Landslides can represent a significant threat for people and infrastructure in hilly and mountainous landscapes worldwide. The understanding and prediction of those geomorphic processes is crucial to avoid economic loses or even casualties to people and their properties. Statistical based landslide susceptibility models are well known for being highly reliant on the quality, representativeness and availability of input data. In this context, several studies indicate that the landslide inventory represents the most important input data. However each landslide mapping technique or data collection has its drawbacks. Consequently, biased landslide inventories may be commonly introduced into statistical models, especially at regional or even national scale. It remains to the researcher to be aware of potential limitations and design strategies to avoid or reduce the potential propagation of input data errors and biases influences on the modelling outcomes. Previous studies have proven that such erroneous landslide inventories may lead to unrealistic landslide susceptibility maps. We assume that one possibility to tackle systematic landslide inventory-based biases might be a concentration on sampling strategies that focus on the distribution of non-landslide locations. For this purpose, we test an approach for the Austrian territory that concentrates on a modified non-landslide sampling strategy, instead the traditional applied random sampling. It is expected that the way non-landslide locations are represented (e.g. equally over the area or within those areas where mapping campaigns have been conducted) is important to reduce a potential over- or underestimation of landslide susceptibility within specific areas caused by bias. As presumably each landslide inventory is known to be systematically incomplete, especially in those areas where no mapping campaign was previously conducted. This is also applicable to the one currently available for the Austrian territory, composed by 14,519 shallow landslides. Within this study, we introduce the following explanatory variables to test the effect of different non-landslide strategies: Lithological units, grouped by their geotechnical properties and topographic parameters such as aspect, elevation, slope gradient and the topographic position. Landslide susceptibility maps will be derived by applying logistic regression, while systematic comparisons will be carried out based on models created by different non-landslide sampling strategies. Models generated by the conventional random sampling are presented against models based on stratified and clustered sampling strategies. The modelling results will be compared in terms of their prediction performance measured by the AUROC (Area Under the Receiver Operating Characteristic Curve) obtained by means of a k-fold cross-validation and also by the spatial pattern of the maps. The outcomes of this study are intended to contribute to the understanding on how landslide-inventory based biases may be counteracted.

Influence of various water quality sampling strategies on load estimates for small streams

USGS Publications Warehouse

Robertson, Dale M.; Roerish, Eric D.

1999-01-01

Extensive streamflow and water quality data from eight small streams were systematically subsampled to represent various water‐quality sampling strategies. The subsampled data were then used to determine the accuracy and precision of annual load estimates generated by means of a regression approach (typically used for big rivers) and to determine the most effective sampling strategy for small streams. Estimation of annual loads by regression was imprecise regardless of the sampling strategy used; for the most effective strategy, median absolute errors were ∼30% based on the load estimated with an integration method and all available data, if a regression approach is used with daily average streamflow. The most effective sampling strategy depends on the length of the study. For 1‐year studies, fixed‐period monthly sampling supplemented by storm chasing was the most effective strategy. For studies of 2 or more years, fixed‐period semimonthly sampling resulted in not only the least biased but also the most precise loads. Additional high‐flow samples, typically collected to help define the relation between high streamflow and high loads, result in imprecise, overestimated annual loads if these samples are consistently collected early in high‐flow events.

Evaluation of respondent-driven sampling.

PubMed

McCreesh, Nicky; Frost, Simon D W; Seeley, Janet; Katongole, Joseph; Tarsh, Matilda N; Ndunguse, Richard; Jichi, Fatima; Lunel, Natasha L; Maher, Dermot; Johnston, Lisa G; Sonnenberg, Pam; Copas, Andrew J; Hayes, Richard J; White, Richard G

2012-01-01

Respondent-driven sampling is a novel variant of link-tracing sampling for estimating the characteristics of hard-to-reach groups, such as HIV prevalence in sex workers. Despite its use by leading health organizations, the performance of this method in realistic situations is still largely unknown. We evaluated respondent-driven sampling by comparing estimates from a respondent-driven sampling survey with total population data. Total population data on age, tribe, religion, socioeconomic status, sexual activity, and HIV status were available on a population of 2402 male household heads from an open cohort in rural Uganda. A respondent-driven sampling (RDS) survey was carried out in this population, using current methods of sampling (RDS sample) and statistical inference (RDS estimates). Analyses were carried out for the full RDS sample and then repeated for the first 250 recruits (small sample). We recruited 927 household heads. Full and small RDS samples were largely representative of the total population, but both samples underrepresented men who were younger, of higher socioeconomic status, and with unknown sexual activity and HIV status. Respondent-driven sampling statistical inference methods failed to reduce these biases. Only 31%-37% (depending on method and sample size) of RDS estimates were closer to the true population proportions than the RDS sample proportions. Only 50%-74% of respondent-driven sampling bootstrap 95% confidence intervals included the population proportion. Respondent-driven sampling produced a generally representative sample of this well-connected nonhidden population. However, current respondent-driven sampling inference methods failed to reduce bias when it occurred. Whether the data required to remove bias and measure precision can be collected in a respondent-driven sampling survey is unresolved. Respondent-driven sampling should be regarded as a (potentially superior) form of convenience sampling method, and caution is required when interpreting findings based on the sampling method.

Frequency of Cannabis Use and Medical Cannabis Use Among Persons Living With HIV in the United States: Findings From a Nationally Representative Sample.

PubMed

Pacek, Lauren R; Towe, Sheri L; Hobkirk, Andrea L; Nash, Denis; Goodwin, Renee D

2018-04-01

Little is known about cannabis use frequency, medical cannabis use, or correlates of use among persons living with HIV (PLWH) in United States nationally representative samples. Data came from 626 PLWH from the 2005-2015 National Survey on Drug Use and Health. Logistic regression identified characteristics associated with frequency of cannabis use. Chi-squares identified characteristics associated with medial cannabis use. Non-daily and daily cannabis use was reported by 26.9% and 8.0%. Greater perceived risk of cannabis use was negatively associated with daily and non-daily use. Younger age, substance use, and binge drinking were positively associated with non-daily cannabis use. Smoking and depression were associated with non-daily and daily use. One-quarter reported medical cannabis use. Medical users were more likely to be White, married, and nondrinkers. Cannabis use was common among PLWH. Findings help to differentiate between cannabis users based on frequency of use and medical versus recreational use.

Genome-wide combination profiling of DNA copy number and methylation for deciphering biomarkers in non-small cell lung cancer patients.

PubMed

Son, Ji Woong; Jeong, Kang Jin; Jean, Woo-Sean; Park, Soon Young; Jheon, Sanghoon; Cho, Hyun Min; Park, Chang Gyo; Lee, Hoi Young; Kang, Jaeku

2011-12-01

Early detection of lung cancer provides the highest potential for saving lives. To date, no routine screening method enabling early detection is available, which is a key factor in the disease's high mortality rate. Copy number changes and DNA methylation alterations are good indicators of carcinogenesis and cancer prognosis. In this study, we attempted to combine profiles of DNA copy number and methylation patterns in 20 paired cancerous and noncancerous tissue samples from non-small cell lung cancer (NSCLC) patients, and we detected several clinically important genes with genetic and epigenetic relationships. Using array comparative genomic hybridization (aCGH), statistically significant differences were observed across the histological subtypes for gains at 1p31.1, 3q26.1, and 3q26.31-3q29 as well as for losses at 1p21.1, 2q33.3, 2q37.3, 3p12.3, 4q35.2, and 13q34 in squamous cell carcinoma (SQ) patients, and losses at 12q24.33 were measured in adenocarcinoma (AD) patients (p < 0.05). In an analysis of DNA methylation at 1505 autosomal CpG loci that are associated with 807 cancer-related genes, we identified six and nine loci with higher and lower DNA methylation levels, respectively, in tumor tissue compared to non-tumor lung tissues from AD patients. In addition, three loci with higher and seven loci with lower DNA methylation levels were identified in tumor tissue from SQ patients compared to non-tumor lung tissue. Subsequently, we searched for regions exhibiting concomitant hypermethylation and genomic loss in both ADs and SQs. One clone representing 7p15.2 (which includes candidate genes such as HOXA9 and HOXA11) and one target ID representing HOXA9_E252_R were detected. Quantitative real-time PCR identified the potential candidate gene HOXA9 as being down-regulated in the majority of NSCLC patients. Moreover, following HOXA9 over-expression, the invasion of representative cell lines, A549 and HCC95, were significantly inhibited. Taken together, our results show that the combined profiling analysis technique is a useful tool for identifying biomarkers in lung cancer and that HOXA9 might be a potential candidate gene for the pathogenesis and diagnosis of NSCLC patients. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Small area estimation (SAE) model: Case study of poverty in West Java Province

NASA Astrophysics Data System (ADS)

Suhartini, Titin; Sadik, Kusman; Indahwati

2016-02-01

This paper showed the comparative of direct estimation and indirect/Small Area Estimation (SAE) model. Model selection included resolve multicollinearity problem in auxiliary variable, such as choosing only variable non-multicollinearity and implemented principal component (PC). Concern parameters in this paper were the proportion of agricultural venture poor households and agricultural poor households area level in West Java Province. The approach for estimating these parameters could be performed based on direct estimation and SAE. The problem of direct estimation, three area even zero and could not be conducted by directly estimation, because small sample size. The proportion of agricultural venture poor households showed 19.22% and agricultural poor households showed 46.79%. The best model from agricultural venture poor households by choosing only variable non-multicollinearity and the best model from agricultural poor households by implemented PC. The best estimator showed SAE better then direct estimation both of the proportion of agricultural venture poor households and agricultural poor households area level in West Java Province. The solution overcame small sample size and obtained estimation for small area was implemented small area estimation method for evidence higher accuracy and better precision improved direct estimator.

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades.

PubMed

Friedländer, Marc R; Mackowiak, Sebastian D; Li, Na; Chen, Wei; Rajewsky, Nikolaus

2012-01-01

microRNAs (miRNAs) are a large class of small non-coding RNAs which post-transcriptionally regulate the expression of a large fraction of all animal genes and are important in a wide range of biological processes. Recent advances in high-throughput sequencing allow miRNA detection at unprecedented sensitivity, but the computational task of accurately identifying the miRNAs in the background of sequenced RNAs remains challenging. For this purpose, we have designed miRDeep2, a substantially improved algorithm which identifies canonical and non-canonical miRNAs such as those derived from transposable elements and informs on high-confidence candidates that are detected in multiple independent samples. Analyzing data from seven animal species representing the major animal clades, miRDeep2 identified miRNAs with an accuracy of 98.6-99.9% and reported hundreds of novel miRNAs. To test the accuracy of miRDeep2, we knocked down the miRNA biogenesis pathway in a human cell line and sequenced small RNAs before and after. The vast majority of the >100 novel miRNAs expressed in this cell line were indeed specifically downregulated, validating most miRDeep2 predictions. Last, a new miRNA expression profiling routine, low time and memory usage and user-friendly interactive graphic output can make miRDeep2 useful to a wide range of researchers.

Using the Properties of Broad Absorption Line Quasars to Illuminate Quasar Structure

NASA Astrophysics Data System (ADS)

Yong, Suk Yee; King, Anthea L.; Webster, Rachel L.; Bate, Nicholas F.; O'Dowd, Matthew J.; Labrie, Kathleen

2018-06-01

A key to understanding quasar unification paradigms is the emission properties of broad absorption line quasars (BALQs). The fact that only a small fraction of quasar spectra exhibit deep absorption troughs blueward of the broad permitted emission lines provides a crucial clue to the structure of quasar emitting regions. To learn whether it is possible to discriminate between the BALQ and non-BALQ populations given the observed spectral properties of a quasar, we employ two approaches: one based on statistical methods and the other supervised machine learning classification, applied to quasar samples from the Sloan Digital Sky Survey. The features explored include continuum and emission line properties, in particular the absolute magnitude, redshift, spectral index, line width, asymmetry, strength, and relative velocity offsets of high-ionisation C IV λ1549 and low-ionisation Mg II λ2798 lines. We consider a complete population of quasars, and assume that the statistical distributions of properties represent all angles where the quasar is viewed without obscuration. The distributions of the BALQ and non-BALQ sample properties show few significant differences. None of the observed continuum and emission line features are capable of differentiating between the two samples. Most published narrow disk-wind models are inconsistent with these observations, and an alternative disk-wind model is proposed. The key feature of the proposed model is a disk-wind filling a wide opening angle with multiple radial streams of dense clumps.

Non-Gaussian Multi-resolution Modeling of Magnetosphere-Ionosphere Coupling Processes

NASA Astrophysics Data System (ADS)

Fan, M.; Paul, D.; Lee, T. C. M.; Matsuo, T.

2016-12-01

The most dynamic coupling between the magnetosphere and ionosphere occurs in the Earth's polar atmosphere. Our objective is to model scale-dependent stochastic characteristics of high-latitude ionospheric electric fields that originate from solar wind magnetosphere-ionosphere interactions. The Earth's high-latitude ionospheric electric field exhibits considerable variability, with increasing non-Gaussian characteristics at decreasing spatio-temporal scales. Accurately representing the underlying stochastic physical process through random field modeling is crucial not only for scientific understanding of the energy, momentum and mass exchanges between the Earth's magnetosphere and ionosphere, but also for modern technological systems including telecommunication, navigation, positioning and satellite tracking. While a lot of efforts have been made to characterize the large-scale variability of the electric field in the context of Gaussian processes, no attempt has been made so far to model the small-scale non-Gaussian stochastic process observed in the high-latitude ionosphere. We construct a novel random field model using spherical needlets as building blocks. The double localization of spherical needlets in both spatial and frequency domains enables the model to capture the non-Gaussian and multi-resolutional characteristics of the small-scale variability. The estimation procedure is computationally feasible due to the utilization of an adaptive Gibbs sampler. We apply the proposed methodology to the computational simulation output from the Lyon-Fedder-Mobarry (LFM) global magnetohydrodynamics (MHD) magnetosphere model. Our non-Gaussian multi-resolution model results in characterizing significantly more energy associated with the small-scale ionospheric electric field variability in comparison to Gaussian models. By accurately representing unaccounted-for additional energy and momentum sources to the Earth's upper atmosphere, our novel random field modeling approach will provide a viable remedy to the current numerical models' systematic biases resulting from the underestimation of high-latitude energy and momentum sources.

Sediment deposition and production in SE-Asia seagrass meadows

NASA Astrophysics Data System (ADS)

Gacia, E.; Duarte, C. M.; Marbà, N.; Terrados, J.; Kennedy, H.; Fortes, M. D.; Tri, N. H.

2003-04-01

Seagrass meadows play an important role in the trapping and binding of particles in coastal sediments. Yet seagrass may also contribute to sediment production directly, through the deposition of detritus and also the deposition of the associated mineral particles. This study aims at estimating the contribution of different seagrass species growing across an extensive range of deposition to inorganic (carbonate and non-carbonate) and organic sediment production. Total daily deposition measured with sediment traps varied from 18.8 (±2.0) g DW m -2 d -1 in Silaqui (Philippines) to 681.1 (±102) g DW m -2 d -1 in Bay Tien (Vietnam). These measurements correspond to a single sampling event and represent sedimentation conditions during the dry season in SE-Asia coastal areas. Enhalus acoroides was the most common species in the seagrass meadows visited and, together with Thalassia hemprichii, was present at sites from low to very high deposition. Halodule uninervis and Cymodocea species were present in sites from low to medium deposition. The mineral load in seagrass leaves increased with age, and was high in E. acoroides because it had the largest and long-lived leaves (up to 417 mg calcium carbonate per leaf and 507 mg non-carbonate minerals per leaf) and low in H. uninervis with short-lived leaves (4 mg calcium carbonate per leaf and 2 mg non-carbonate minerals per leaf). In SE-Asia seagrass meadows non-carbonate minerals accumulate at slower rates than the production of calcium carbonate by the epiphytic community, consequently the final loads supported by fully grown leaves were, as average, lower than calcium carbonate loads. Our results show that organic and inorganic production of the seagrasses in SE-Asia represents a small contribution (maximum of 15%) of the materials sedimented on a daily base by the water column during the sampling period. The contribution of the carbonate fraction can be locally significant (i.e. 34% in Silaqui) in areas where the depositional flux is low, but is minor (<1%) in sites were siltation is significant (i.e. Umalagan and all the visited sites in Vietnam).

Stochastic voyages into uncharted chemical space produce a representative library of all possible drug-like compounds

PubMed Central

Virshup, Aaron M.; Contreras-García, Julia; Wipf, Peter; Yang, Weitao; Beratan, David N.

2013-01-01

The “small molecule universe” (SMU), the set of all synthetically feasible organic molecules of 500 Daltons molecular weight or less, is estimated to contain over 1060 structures, making exhaustive searches for structures of interest impractical. Here, we describe the construction of a “representative universal library” spanning the SMU that samples the full extent of feasible small molecule chemistries. This library was generated using the newly developed Algorithm for Chemical Space Exploration with Stochastic Search (ACSESS). ACSESS makes two important contributions to chemical space exploration: it allows the systematic search of the unexplored regions of the small molecule universe, and it facilitates the mining of chemical libraries that do not yet exist, providing a near-infinite source of diverse novel compounds. PMID:23548177

Prevalence of Female Urinary Incontinence in the General Population According to Different Definitions and Study Designs.

PubMed

Bedretdinova, Dina; Fritel, Xavier; Panjo, Henri; Ringa, Virginie

2016-02-01

Estimates of the prevalence of female urinary incontinence (UI) vary widely. To estimate UI prevalence among women in France using data from five national surveys and analyse prevalence differences among the surveys according to their design (representative sample or not, survey focused on UI or not) and UI definition (based on symptoms or disease perception). Data came from two representative telephone surveys, Fecond (5017 women aged 15-49 yr) and Barometer (3089 women aged 40-85 yr), general and urinary postal surveys of the GAZEL cohort (3098 women aged 54-69 yr), and the web-based NutriNet survey (85,037 women aged 18-87 yr). Definitions of UI based on the International Conference on Incontinence Questionnaire UI short form (ICIQ-UI-SF) and on a list of health problems were considered. We compared age-adjusted prevalence rates among studies via logistic regression and generalised linear models. Overall, 13% of the women in Fecond, 24% in Barometer, 15% in the GAZEL general survey, 39% in the GAZEL urinary survey, and 1.5% in the NutriNet survey reported any UI. Prevalence rates in representative samples with the same UI definition (ICIQ-UI-SF) were concordant. UI prevalence in the representative samples was 17%. The estimated number of women in France with UI was 5.35 million (95% confidence interval [CI] 5.34-5.36 million) for any UI and 1.54 million (95% CI 1.53-1.55 million) for daily UI. For the GAZEL sample, UI prevalence was lower but UI severity was greater for responses to a questionnaire with the list-based UI definition rather than to a questionnaire with the ICIQ-UI-SF-based definition. In all surveys, information about UI was self-reported and was not validated by objective measurements. UI definitions and sampling strategies influence estimates of UI prevalence among women. Precise estimates of UI prevalence should be based on non-UI-focused surveys among representative samples and using a validated standardised symptom-based questionnaire. We looked at estimates of urinary incontinence (UI) prevalence in studies with different designs and different UI definitions in a large population of French women. We found that estimates varied with the definition and the design. We conclude that the most precise estimates of UI prevalence are obtained in studies of representative populations that are not focused on UI and use a validated international standard questionnaire with sufficient details to allow grading of UI severity. Most women reported rare urine leakages involving small amounts of urine with little impact on their quality of life. Copyright © 2015 European Association of Urology. Published by Elsevier B.V. All rights reserved.

Electronic gaming and psychosocial adjustment.

PubMed

Przybylski, Andrew K

2014-09-01

The rise of electronic games has driven both concerns and hopes regarding their potential to influence young people. Existing research identifies a series of isolated positive and negative effects, yet no research to date has examined the balance of these potential effects in a representative sample of children and adolescents. The objective of this study was to explore how time spent playing electronic games accounts for significant variation in positive and negative psychosocial adjustment using a representative cohort of children aged 10 to 15 years. A large sample of children and adolescents aged 10 to 15 years completed assessments of psychosocial adjustment and reported typical daily hours spent playing electronic games. Relations between different levels of engagement and indicators of positive and negative psychosocial adjustment were examined, controlling for participant age and gender and weighted for population representativeness. Low levels (<1 hour daily) as well as high levels (>3 hours daily) of game engagement was linked to key indicators of psychosocial adjustment. Low engagement was associated with higher life satisfaction and prosocial behavior and lower externalizing and internalizing problems, whereas the opposite was found for high levels of play. No effects were observed for moderate play levels when compared with non-players. The links between different levels of electronic game engagement and psychosocial adjustment were small (<1.6% of variance) yet statistically significant. Games consistently but not robustly associated with children's adjustment in both positive and negative ways, findings that inform policy-making as well as future avenues for research in the area. Copyright © 2014 by the American Academy of Pediatrics.

Comparison of Metabolomics Approaches for Evaluating the Variability of Complex Botanical Preparations: Green Tea (Camellia sinensis) as a Case Study.

PubMed

Kellogg, Joshua J; Graf, Tyler N; Paine, Mary F; McCune, Jeannine S; Kvalheim, Olav M; Oberlies, Nicholas H; Cech, Nadja B

2017-05-26

A challenge that must be addressed when conducting studies with complex natural products is how to evaluate their complexity and variability. Traditional methods of quantifying a single or a small range of metabolites may not capture the full chemical complexity of multiple samples. Different metabolomics approaches were evaluated to discern how they facilitated comparison of the chemical composition of commercial green tea [Camellia sinensis (L.) Kuntze] products, with the goal of capturing the variability of commercially used products and selecting representative products for in vitro or clinical evaluation. Three metabolomic-related methods-untargeted ultraperformance liquid chromatography-mass spectrometry (UPLC-MS), targeted UPLC-MS, and untargeted, quantitative 1 HNMR-were employed to characterize 34 commercially available green tea samples. Of these methods, untargeted UPLC-MS was most effective at discriminating between green tea, green tea supplement, and non-green-tea products. A method using reproduced correlation coefficients calculated from principal component analysis models was developed to quantitatively compare differences among samples. The obtained results demonstrated the utility of metabolomics employing UPLC-MS data for evaluating similarities and differences between complex botanical products.

Comparison of Metabolomics Approaches for Evaluating the Variability of Complex Botanical Preparations: Green Tea (Camellia sinensis) as a Case Study

PubMed Central

2017-01-01

A challenge that must be addressed when conducting studies with complex natural products is how to evaluate their complexity and variability. Traditional methods of quantifying a single or a small range of metabolites may not capture the full chemical complexity of multiple samples. Different metabolomics approaches were evaluated to discern how they facilitated comparison of the chemical composition of commercial green tea [Camellia sinensis (L.) Kuntze] products, with the goal of capturing the variability of commercially used products and selecting representative products for in vitro or clinical evaluation. Three metabolomic-related methods—untargeted ultraperformance liquid chromatography–mass spectrometry (UPLC-MS), targeted UPLC-MS, and untargeted, quantitative 1HNMR—were employed to characterize 34 commercially available green tea samples. Of these methods, untargeted UPLC-MS was most effective at discriminating between green tea, green tea supplement, and non-green-tea products. A method using reproduced correlation coefficients calculated from principal component analysis models was developed to quantitatively compare differences among samples. The obtained results demonstrated the utility of metabolomics employing UPLC-MS data for evaluating similarities and differences between complex botanical products. PMID:28453261

The AL 333-160 fourth metatarsal from Hadar compared to that of humans, great apes, baboons and proboscis monkeys: non-conclusive evidence for pedal arches or obligate bipedality in Hadar hominins.

PubMed

Mitchell, P J; Sarmiento, E E; Meldrum, D J

2012-10-01

Based on comparisons to non-statistically representative samples of humans and two great ape species (i.e. common chimpanzees Pan troglodytes and lowland gorillas Gorilla gorilla), Ward et al. (2011) concluded that a complete hominin fourth metatarsal (4th MT) from Hadar, AL 333-160, belonged to a committed terrestrial biped with fixed transverse and longitudinal pedal arches, which was no longer under selection favoring substantial arboreal behaviors. According to Ward et al., the Hadar 4th MT had (1) a torsion value indicating a transverse arch, (2) sagittal plane angles between the diaphyseal long axis and the planes of the articular surfaces indicating a longitudinal arch, and (3) a narrow mediolateral to dorsoplantar base ratio, an ectocuneiform facet, and tarsal articular surface contours all indicating a rigid foot without an ape-like mid-tarsal break. Comparisons of the Hadar 4th MT characters to those of statistically representative samples of humans, all five great ape species, baboons and proboscis monkeys show that none of the correlations Ward et al. make to localized foot function were supported by this analysis. The Hadar 4th MT characters are common to catarrhines that have a midtarsal break and lack fixed transverse or longitudinal arches. Further comparison of the AL 333-160 4th MT length, and base, midshaft and head circumferences to those of catarrhines with field collected body weights show that this bone is uniquely short with a large base. Its length suggests the AL 333-160 individual was a poor leaper with limited arboreal behaviors and lacked a longitudinal arch, i.e. its 4th MT long axis was usually held perpendicular to gravity. Its large base implies cuboid-4th MT joint mobility. A relatively short 4th MT head circumference indicates AL 333-160 had small proximal phalanges with a restricted range of mobility. Overall, AL 333-160 is most similar to the 4th MT of eastern gorillas, a slow moving quadruped that sacrifices arboreal behaviors for terrestrial ones. This study highlights evolutionary misconceptions underlying the practice of using localized anatomy and/or a single bony element to reconstruct overall locomotor behaviors and of summarizing great ape structure and behavior based on non-statistically representative samples of only a few living great ape species. Copyright © 2012. Published by Elsevier GmbH.

Prematurity and School Readiness in a Nationally Representative Sample of Australian Children: Does Typically Occurring Preschool Moderate the Relationship?

PubMed Central

Chen, Jen-Hao; Claessens, Amy; Msall, Michael E.

2013-01-01

OBJECTIVE To examine the relationship between indicators of prematurity and children’s cognitive and behavioral school readiness in a nationally representative sample and to investigate whether typically occurring preschool enrollment moderates this relationship, particularly for children from disadvantaged families in Australia. METHODS The Longitudinal Study of Australian Children is a nationally representative prospective sample of two cohorts of children with sequentially obtained indicators of child health and developmental outcomes. We analyzed information on 8,060 children age 4–5 years who had complete data on birth weight, gestational age, prenatal risks, social factors, and cognitive and behavioral outcomes of school readiness. Multivariate regressions were used to relate three indicators of prematurity (low birth weight, preterm birth, and small for gestational age) to cognitive and behavioral school readiness. RESULTS Children born preterm, small for gestational age, or with low birth weight have significantly lower cognitive school readiness after controlling for social factors and prenatal risks. None of the premature indicators was associated with behavioral school readiness. All children benefited from attending preschool. Yet, preschool enrollment did not moderate the relationship between prematurity and school readiness. The only exception is for small for gestational age survivors with low educated mothers. Preschool enrollment was associated with an increase in cognitive school readiness skills. CONCLUSIONS Prematurity was associated with lower cognitive school readiness skills. Typical occurring preschool did not eliminate this association. Findings suggest that simply expanding the preschool enrollment is inadequate to address the developmental needs of premature children from disadvantaged backgrounds. PMID:24401664

Health of US parents with and without disabilities.

PubMed

Li, Henan; Parish, Susan L; Mitra, Monika; Nicholson, Joanne

2017-04-01

The health of parents with disabilities is not well understood. Existing research has used small, non-representative samples. The lack of research using national representative data has hindered advocacy and policy-making efforts. In the present study, we used nationally-representative data to examine the prevalence rates of chronic physical health conditions among parents with disabilities and compared them to parents without disabilities. We analyzed pooled and linked data from the 2007-2011 Medical Expenditure Panel Survey and the corresponding National Health Interview Survey. We conducted logistic regression analyses to examine age-adjusted health differences of US parents with and without disabilities, controlling for covariates. Outcome measures included obesity, arthritis, asthma, cancer, heart disease, diabetes, emphysema, high cholesterol, hypertension, and stroke. After controlling for all model covariates and adjusting for age, parents with disabilities had significantly higher odds (aOR ranging from 1.69 to 4.82) of having each of the chronic conditions (P < 0.001). Parents with disabilities also have significant higher odds of having 2 conditions (aOR = 1.63), 3 conditions (aOR = 2.44), and 4 or more conditions (aOR = 5.56). Parents with disabilities have significantly poorer health than parents without disabilities. Copyright © 2016 Elsevier Inc. All rights reserved.

Post-sampling mortality and non-response patterns in the English Cancer Patient Experience Survey: Implications for epidemiological studies based on surveys of cancer patients.

PubMed

Abel, Gary A; Saunders, Catherine L; Lyratzopoulos, Georgios

2016-04-01

Surveys of the experience of cancer patients are increasingly being introduced in different countries and used in cancer epidemiology research. Sampling processes, post-sampling mortality and survey non-response can influence the representativeness of cancer patient surveys. We examined predictors of post-sampling mortality and non-response among patients initially included in the sampling frame of the English Cancer Patient Experience Survey. We also compared the respondents' diagnostic case-mix to other relevant populations of cancer patients, including incident and prevalent cases. Of 109,477 initially sampled cancer patients, 6273 (5.7%) died between sampling and survey mail-out. Older age and diagnosis of brain, lung and pancreatic cancer were associated with higher risk of post-sampling mortality. The overall response rate was 67% (67,713 respondents), being >70% for the most affluent patients and those diagnosed with colon or breast cancer and <50% for Asian or Black patients, those under 35 and those diagnosed with brain cancer. The diagnostic case-mix of respondents varied substantially from incident or prevalent cancer cases. Respondents to the English Cancer Patient Experience Survey represent a population of recently treated cancer survivors. Although patient survey data can provide unique insights for improving cancer care quality, features of survey populations need to be acknowledged when analysing and interpreting findings from studies using such data. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Reactive flow modeling of small scale detonation failure experiments for a baseline non-ideal explosive

NASA Astrophysics Data System (ADS)

Kittell, David E.; Cummock, Nick R.; Son, Steven F.

2016-08-01

Small scale characterization experiments using only 1-5 g of a baseline ammonium nitrate plus fuel oil (ANFO) explosive are discussed and simulated using an ignition and growth reactive flow model. There exists a strong need for the small scale characterization of non-ideal explosives in order to adequately survey the wide parameter space in sample composition, density, and microstructure of these materials. However, it is largely unknown in the scientific community whether any useful or meaningful result may be obtained from detonation failure, and whether a minimum sample size or level of confinement exists for the experiments. In this work, it is shown that the parameters of an ignition and growth rate law may be calibrated using the small scale data, which is obtained from a 35 GHz microwave interferometer. Calibration is feasible when the samples are heavily confined and overdriven; this conclusion is supported with detailed simulation output, including pressure and reaction contours inside the ANFO samples. The resulting shock wave velocity is most likely a combined chemical-mechanical response, and simulations of these experiments require an accurate unreacted equation of state (EOS) in addition to the calibrated reaction rate. Other experiments are proposed to gain further insight into the detonation failure data, as well as to help discriminate between the role of the EOS and reaction rate in predicting the measured outcome.

Reactive flow modeling of small scale detonation failure experiments for a baseline non-ideal explosive

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

Kittell, David E.; Cummock, Nick R.; Son, Steven F.

2016-08-14

Small scale characterization experiments using only 1–5 g of a baseline ammonium nitrate plus fuel oil (ANFO) explosive are discussed and simulated using an ignition and growth reactive flow model. There exists a strong need for the small scale characterization of non-ideal explosives in order to adequately survey the wide parameter space in sample composition, density, and microstructure of these materials. However, it is largely unknown in the scientific community whether any useful or meaningful result may be obtained from detonation failure, and whether a minimum sample size or level of confinement exists for the experiments. In this work, itmore » is shown that the parameters of an ignition and growth rate law may be calibrated using the small scale data, which is obtained from a 35 GHz microwave interferometer. Calibration is feasible when the samples are heavily confined and overdriven; this conclusion is supported with detailed simulation output, including pressure and reaction contours inside the ANFO samples. The resulting shock wave velocity is most likely a combined chemical-mechanical response, and simulations of these experiments require an accurate unreacted equation of state (EOS) in addition to the calibrated reaction rate. Other experiments are proposed to gain further insight into the detonation failure data, as well as to help discriminate between the role of the EOS and reaction rate in predicting the measured outcome.« less

One practice's experiment in refusing detail rep visits.

PubMed

Evans, David V; Hartung, Daniel M; Andeen, Gabriel; Mahler, Jo; Haxby, Dean G; Kraemer, Dale F; Fagnan, Lyle J

2011-08-01

The physician-pharmaceutical industry relationship has come under increasing scrutiny. Little guidance exists concerning how smaller practices should manage this relationship.In 2006, Madras Medical Group, a small family practice in rural Oregon, implemented a policy prohibiting visits from representatives of the pharmaceutical industry and the acceptance of drug samples. This qualitative study documents the attitudes of clinic personnel in response to this policy. Semistructured interviews were conducted using standardized questions related to 4 areas of policy perception: verification of policy decision, impact on clinic operations,influence of pharmaceutical industry, and lessons to share. Common themes were identified. Three physicians and 3 nurses participated in the study. There was consensus on the existence and effectiveness of the clinic policy. Key themes identified from both groups of interviewees included the perception of enhanced clinic operation after eliminating interruptions from pharmaceutical representatives, positive response from the public, and reduced diversion of samples for personal use. Clinicians interviewed agreed that samples were of questionable benefit,that information obtained from industry representatives was incomplete or of questionable veracity or objectivity, and that it was helpful to substitute other drug information sources and clinic-sponsored lunches for past industry offerings. In this case study, a policy prohibiting pharmaceutical representatives from a small family practice was well accepted and a source of pride among physicians and nurses. Other clinics wishing to enact a similar policy may wish to supplement their efforts by proactively using other sources of drug information.

Experimental light scattering by ultrasonically controlled small particles - Implications for Planetary Science

NASA Astrophysics Data System (ADS)

Gritsevich, M.; Penttilä, A.; Maconi, G.; Kassamakov, I.; Markkanen, J.; Martikainen, J.; Väisänen, T.; Helander, P.; Puranen, T.; Salmi, A.; Hæggström, E.; Muinonen, K.

2017-09-01

We present the results obtained with our newly developed 3D scatterometer - a setup for precise multi-angular measurements of light scattered by mm- to µm-sized samples held in place by sound. These measurements are cross-validated against the modeled light-scattering characteristics of the sample, i.e., the intensity and the degree of linear polarization of the reflected light, calculated with state-of-the-art electromagnetic techniques. We demonstrate a unique non-destructive approach to derive the optical properties of small grain samples which facilitates research on highly valuable planetary materials, such as samples returned from space missions or rare meteorites.

A Behavior-Genetic Study of Parenting Quality, Infant Attachment Security, and Their Covariation in a Nationally Representative Sample

ERIC Educational Resources Information Center

Roisman, Glenn I.; Fraley, R. Chris

2008-01-01

A number of relatively small-sample, genetically sensitive studies of infant attachment security have been published in the past several years that challenge the view that all psychological phenotypes are heritable and that environmental influences on child development--to the extent that they can be detected--serve to make siblings dissimilar.…

A Hands-On Exercise Improves Understanding of the Standard Error of the Mean

ERIC Educational Resources Information Center

Ryan, Robert S.

2006-01-01

One of the most difficult concepts for statistics students is the standard error of the mean. To improve understanding of this concept, 1 group of students used a hands-on procedure to sample from small populations representing either a true or false null hypothesis. The distribution of 120 sample means (n = 3) from each population had standard…

High-resolution non-destructive three-dimensional imaging of integrated circuits

NASA Astrophysics Data System (ADS)

Holler, Mirko; Guizar-Sicairos, Manuel; Tsai, Esther H. R.; Dinapoli, Roberto; Müller, Elisabeth; Bunk, Oliver; Raabe, Jörg; Aeppli, Gabriel

2017-03-01

Modern nanoelectronics has advanced to a point at which it is impossible to image entire devices and their interconnections non-destructively because of their small feature sizes and the complex three-dimensional structures resulting from their integration on a chip. This metrology gap implies a lack of direct feedback between design and manufacturing processes, and hampers quality control during production, shipment and use. Here we demonstrate that X-ray ptychography—a high-resolution coherent diffractive imaging technique—can create three-dimensional images of integrated circuits of known and unknown designs with a lateral resolution in all directions down to 14.6 nanometres. We obtained detailed device geometries and corresponding elemental maps, and show how the devices are integrated with each other to form the chip. Our experiments represent a major advance in chip inspection and reverse engineering over the traditional destructive electron microscopy and ion milling techniques. Foreseeable developments in X-ray sources, optics and detectors, as well as adoption of an instrument geometry optimized for planar rather than cylindrical samples, could lead to a thousand-fold increase in efficiency, with concomitant reductions in scan times and voxel sizes.

Cerebellar development in childhood onset schizophrenia and non-psychotic siblings

PubMed Central

Greenstein, Deanna; Lenroot, Rhoshel; Clausen, Liv; Gogtay, Nitin; Rapoport, Judith

2011-01-01

We explored regional and total volumetric cerebellar differences in probands and their unaffected full siblings relative to typically developing participants. Participants included 94 (51 males) patients diagnosed with childhood onset schizophrenia (COS), 80 related non-psychotic siblings (37 males) and 110 (64 males) typically developing participants scanned longitudinally. The sample mean age was 16.87(SD=4.7; range 6.5 to 29). We performed mixed model regressions to examine group differences in trajectory and volume. The COS group had smaller bilateral anterior lobes and anterior and total vermis volumes than controls. The COS group diverged from controls over time in total, left, right, and bilateral posterior inferior cerebellum. Siblings did not have any fixed volumetric differences relative to controls but differed from controls in developmental trajectories of total and right cerebellum, left inferior posterior, left superior posterior, and superior vermis. Results are consistent with previous COS findings and several reports of decreased cerebellar volume in adult onset schizophrenia. Sibling trajectories may represent a trait marker, although the effect size for volumetric differences in early adulthood may be small. PMID:21803550

High-resolution non-destructive three-dimensional imaging of integrated circuits.

PubMed

Holler, Mirko; Guizar-Sicairos, Manuel; Tsai, Esther H R; Dinapoli, Roberto; Müller, Elisabeth; Bunk, Oliver; Raabe, Jörg; Aeppli, Gabriel

2017-03-15

Modern nanoelectronics has advanced to a point at which it is impossible to image entire devices and their interconnections non-destructively because of their small feature sizes and the complex three-dimensional structures resulting from their integration on a chip. This metrology gap implies a lack of direct feedback between design and manufacturing processes, and hampers quality control during production, shipment and use. Here we demonstrate that X-ray ptychography-a high-resolution coherent diffractive imaging technique-can create three-dimensional images of integrated circuits of known and unknown designs with a lateral resolution in all directions down to 14.6 nanometres. We obtained detailed device geometries and corresponding elemental maps, and show how the devices are integrated with each other to form the chip. Our experiments represent a major advance in chip inspection and reverse engineering over the traditional destructive electron microscopy and ion milling techniques. Foreseeable developments in X-ray sources, optics and detectors, as well as adoption of an instrument geometry optimized for planar rather than cylindrical samples, could lead to a thousand-fold increase in efficiency, with concomitant reductions in scan times and voxel sizes.

Towards a system level understanding of non-model organisms sampled from the environment: a network biology approach.

PubMed

Williams, Tim D; Turan, Nil; Diab, Amer M; Wu, Huifeng; Mackenzie, Carolynn; Bartie, Katie L; Hrydziuszko, Olga; Lyons, Brett P; Stentiford, Grant D; Herbert, John M; Abraham, Joseph K; Katsiadaki, Ioanna; Leaver, Michael J; Taggart, John B; George, Stephen G; Viant, Mark R; Chipman, Kevin J; Falciani, Francesco

2011-08-01

The acquisition and analysis of datasets including multi-level omics and physiology from non-model species, sampled from field populations, is a formidable challenge, which so far has prevented the application of systems biology approaches. If successful, these could contribute enormously to improving our understanding of how populations of living organisms adapt to environmental stressors relating to, for example, pollution and climate. Here we describe the first application of a network inference approach integrating transcriptional, metabolic and phenotypic information representative of wild populations of the European flounder fish, sampled at seven estuarine locations in northern Europe with different degrees and profiles of chemical contaminants. We identified network modules, whose activity was predictive of environmental exposure and represented a link between molecular and morphometric indices. These sub-networks represented both known and candidate novel adverse outcome pathways representative of several aspects of human liver pathophysiology such as liver hyperplasia, fibrosis, and hepatocellular carcinoma. At the molecular level these pathways were linked to TNF alpha, TGF beta, PDGF, AGT and VEGF signalling. More generally, this pioneering study has important implications as it can be applied to model molecular mechanisms of compensatory adaptation to a wide range of scenarios in wild populations.

Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach

PubMed Central

Williams, Tim D.; Turan, Nil; Diab, Amer M.; Wu, Huifeng; Mackenzie, Carolynn; Bartie, Katie L.; Hrydziuszko, Olga; Lyons, Brett P.; Stentiford, Grant D.; Herbert, John M.; Abraham, Joseph K.; Katsiadaki, Ioanna; Leaver, Michael J.; Taggart, John B.; George, Stephen G.; Viant, Mark R.; Chipman, Kevin J.; Falciani, Francesco

2011-01-01

The acquisition and analysis of datasets including multi-level omics and physiology from non-model species, sampled from field populations, is a formidable challenge, which so far has prevented the application of systems biology approaches. If successful, these could contribute enormously to improving our understanding of how populations of living organisms adapt to environmental stressors relating to, for example, pollution and climate. Here we describe the first application of a network inference approach integrating transcriptional, metabolic and phenotypic information representative of wild populations of the European flounder fish, sampled at seven estuarine locations in northern Europe with different degrees and profiles of chemical contaminants. We identified network modules, whose activity was predictive of environmental exposure and represented a link between molecular and morphometric indices. These sub-networks represented both known and candidate novel adverse outcome pathways representative of several aspects of human liver pathophysiology such as liver hyperplasia, fibrosis, and hepatocellular carcinoma. At the molecular level these pathways were linked to TNF alpha, TGF beta, PDGF, AGT and VEGF signalling. More generally, this pioneering study has important implications as it can be applied to model molecular mechanisms of compensatory adaptation to a wide range of scenarios in wild populations. PMID:21901081

Accounting for parameter uncertainty in the definition of parametric distributions used to describe individual patient variation in health economic models.

PubMed

Degeling, Koen; IJzerman, Maarten J; Koopman, Miriam; Koffijberg, Hendrik

2017-12-15

Parametric distributions based on individual patient data can be used to represent both stochastic and parameter uncertainty. Although general guidance is available on how parameter uncertainty should be accounted for in probabilistic sensitivity analysis, there is no comprehensive guidance on reflecting parameter uncertainty in the (correlated) parameters of distributions used to represent stochastic uncertainty in patient-level models. This study aims to provide this guidance by proposing appropriate methods and illustrating the impact of this uncertainty on modeling outcomes. Two approaches, 1) using non-parametric bootstrapping and 2) using multivariate Normal distributions, were applied in a simulation and case study. The approaches were compared based on point-estimates and distributions of time-to-event and health economic outcomes. To assess sample size impact on the uncertainty in these outcomes, sample size was varied in the simulation study and subgroup analyses were performed for the case-study. Accounting for parameter uncertainty in distributions that reflect stochastic uncertainty substantially increased the uncertainty surrounding health economic outcomes, illustrated by larger confidence ellipses surrounding the cost-effectiveness point-estimates and different cost-effectiveness acceptability curves. Although both approaches performed similar for larger sample sizes (i.e. n = 500), the second approach was more sensitive to extreme values for small sample sizes (i.e. n = 25), yielding infeasible modeling outcomes. Modelers should be aware that parameter uncertainty in distributions used to describe stochastic uncertainty needs to be reflected in probabilistic sensitivity analysis, as it could substantially impact the total amount of uncertainty surrounding health economic outcomes. If feasible, the bootstrap approach is recommended to account for this uncertainty.

Promotional methods used by representatives of drug companies: A prospective survey in general practice

PubMed Central

Schramm, Jesper; Andersen, Morten; Vach, Kirstin; Kragstrup, Jakob; Peter Kampmann, Jens; Søndergaard, Jens

2007-01-01

Objective To examine the extent and composition of pharmaceutical industry representatives’ marketing techniques with a particular focus on drug sampling in relation to drug age. Design A group of 47 GPs prospectively collected data on drug promotional activities during a six-month period, and a sub-sample of 10 GPs furthermore recorded the representatives’ marketing techniques in detail. Setting Primary healthcare. Subjects General practitioners in the County of Funen, Denmark. Main outcome measures. Promotional visits and corresponding marketing techniques. Results The 47 GPs recorded 1050 visits corresponding to a median of 19 (range 3 to 63) per GP in the six months. The majority of drugs promoted (52%) were marketed more than five years ago. There was a statistically significant decline in the proportion of visits where drug samples were offered with drug age, but the decline was small OR 0.97 (95% CI 0.95;0.98) per year. Leaflets (68%), suggestions on how to improve therapy for a specific patient registered with the practice (53%), drug samples (48%), and gifts (36%) were the most frequently used marketing techniques. Conclusion Drug-industry representatives use a variety of promotional methods. The tendency to hand out drug samples was statistically significantly associated with drug age, but the decline was small. PMID:17497486

A gel-based visual immunoassay for non-instrumental detection of chloramphenicol in food samples.

PubMed

Yuan, Meng; Sheng, Wei; Zhang, Yan; Wang, Junping; Yang, Yijin; Zhang, Shuguang; Goryacheva, Irina Yu; Wang, Shuo

2012-11-02

A gel-based non-instrumental immuno-affinity assay was developed for the rapid screening of chloramphenicol (CAP) in food samples with the limit of detection (LOD) of 1 μg L(-1). The immuno-affinity test column (IATC) consisted of a test layer containing anti-CAP antibody coupled gel, and a control layer with anti-HRP antibody coupled gel. Based on the direct competitive immuno-reaction and the horseradish peroxidase enzymatic reaction, the test results could be evaluated visually. Basically, blue color development represented the negative results, while the absence of color development represented the positive results. In this study, CAP spiked samples of raw milk, pasteurized milk, UHT milk, skimmed milk powder, acacia honey, date honey, fish and shrimp were tested. Little or none sample pretreatment was required for this assay. The whole procedure was completed within 10min. In conclusion, the gel-based immuno-affinity test is a simple, rapid, and promising on-site screening method for CAP residues in food samples, with no instrumental requirement. Copyright © 2012 Elsevier B.V. All rights reserved.

A Study of Non-Native English Speakers' Academic Performance at Santa Ana College.

ERIC Educational Resources Information Center

Slark, Julie; Bateman, Harold

A study was conducted in 1980-81 at Santa Ana College (SAC) to collect data on the English communication skills of non-native English speakers and to determine if a relationship existed between these skills and student's educational success. A sample of 22 classes, with an enrollment of at least 50% non-native English speakers and representing a…

Analysis of small sample size studies using nonparametric bootstrap test with pooled resampling method.

PubMed

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.

Interpreting survival data from clinical trials of surgery versus stereotactic body radiation therapy in operable Stage I non-small cell lung cancer patients.

PubMed

Samson, Pamela; Keogan, Kathleen; Crabtree, Traves; Colditz, Graham; Broderick, Stephen; Puri, Varun; Meyers, Bryan

2017-01-01

To identify the variability of short- and long-term survival outcomes among closed Phase III randomized controlled trials with small sample sizes comparing SBRT (stereotactic body radiation therapy) and surgical resection in operable clinical Stage I non-small cell lung cancer (NSCLC) patients. Clinical Stage I NSCLC patients who underwent surgery at our institution meeting the inclusion/exclusion criteria for STARS (Randomized Study to Compare CyberKnife to Surgical Resection in Stage I Non-small Cell Lung Cancer), ROSEL (Trial of Either Surgery or Stereotactic Radiotherapy for Early Stage (IA) Lung Cancer), or both were identified. Bootstrapping analysis provided 10,000 iterations to depict 30-day mortality and three-year overall survival (OS) in cohorts of 16 patients (to simulate the STARS surgical arm), 27 patients (to simulate the pooled surgical arms of STARS and ROSEL), and 515 (to simulate the goal accrual for the surgical arm of STARS). From 2000 to 2012, 749/873 (86%) of clinical Stage I NSCLC patients who underwent resection were eligible for STARS only, ROSEL only, or both studies. When patients eligible for STARS only were repeatedly sampled with a cohort size of 16, the 3-year OS rates ranged from 27 to 100%, and 30-day mortality varied from 0 to 25%. When patients eligible for ROSEL or for both STARS and ROSEL underwent bootstrapping with n=27, the 3-year OS ranged from 46 to 100%, while 30-day mortality varied from 0 to 15%. Finally, when patients eligible for STARS were repeatedly sampled in groups of 515, 3-year OS narrowed to 70-85%, with 30-day mortality varying from 0 to 4%. Short- and long-term survival outcomes from trials with small sample sizes are extremely variable and unreliable for extrapolation. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Rural Values and Concensus(sic).

ERIC Educational Resources Information Center

England, J. Lynn; And Others

Sample populations from 15 Intermountain West communities (representative of population, ethnic, and employment variety) were surveyed to test the following hypotheses: (1) there is a greater degree of consensus in rural than in non-rural communities; (2) there are differences between values in rural and non-rural communities; (3) a model…

Status of Aquatic Non-indigenous Species in the St. Louis River System

EPA Science Inventory

As part of a study to develop recommendations for aquatic non-indigenous species (NIS) monitoring in Great Lakes areas at risk of invasion, we conducted comprehensive, multi-gear sampling in the lower St. Louis River in 2005-2007. This effort represents the most spatially and ta...

Metabolic profiling of human lung cancer blood plasma using 1H NMR spectroscopy

NASA Astrophysics Data System (ADS)

Kokova, Daria; Dementeva, Natalia; Kotelnikov, Oleg; Ponomaryova, Anastasia; Cherdyntseva, Nadezhda; Kzhyshkowska, Juliya

2017-11-01

Lung cancer (both small cell and non-small cell) is the second most common cancer in both men and women. The article represents results of evaluating of the plasma metabolic profiles of 100 lung cancer patients and 100 controls to investigate significant metabolites using 400 MHz 1H NMR spectrometer. The results of multivariate statistical analysis show that a medium-field NMR spectrometer can obtain the data which are already sufficient for clinical metabolomics.

Identification of Soldier Behaviors Associated with Search and Target Acquisition (STA)

DTIC Science & Technology

2010-05-01

specifically concentrated on representing Soldier and small unit behavior engaging "non-acquired" targets and "non-standard" entities, such as: muzzle ...Forces Are Targeting (e.g., weapon orientation, bullet impacts) Area Where Fire Coming From (e.g., muzzle Flash) Target Handoff...Surveys Cue Average Sum* Participants Muzzle Flash 7.51 34 Hostile Behaviors 7.35 40 Outgoing Fire 7.22 18 Suspicious Behaviors/Activities 6.91

Inhibition of protein translocation at the endoplasmic reticulum promotes activation of the unfolded protein response

PubMed Central

McKibbin, Craig; Mares, Alina; Piacenti, Michela; Williams, Helen; Roboti, Peristera; Puumalainen, Marjo; Callan, Anna C.; Lesiak-Mieczkowska, Karolina; Linder, Stig; Harant, Hanna; High, Stephen; Flitsch, Sabine L.; Whitehead, Roger C.; Swanton, Eileithyia

2011-01-01

Selective small-molecule inhibitors represent powerful tools for the dissection of complex biological processes. ESI (eeyarestatin I) is a novel modulator of ER (endoplasmic reticulum) function. In the present study, we show that in addition to acutely inhibiting ERAD (ER-associated degradation), ESI causes production of mislocalized polypeptides that are ubiquitinated and degraded. Unexpectedly, our results suggest that these non-translocated polypeptides promote activation of the UPR (unfolded protein response), and indeed we can recapitulate UPR activation with an alternative and quite distinct inhibitor of ER translocation. These results suggest that the accumulation of non-translocated proteins in the cytosol may represent a novel mechanism that contributes to UPR activation. PMID:22145777

Differential expression analysis for RNAseq using Poisson mixed models.

PubMed

Sun, Shiquan; Hood, Michelle; Scott, Laura; Peng, Qinke; Mukherjee, Sayan; Tung, Jenny; Zhou, Xiang

2017-06-20

Identifying differentially expressed (DE) genes from RNA sequencing (RNAseq) studies is among the most common analyses in genomics. However, RNAseq DE analysis presents several statistical and computational challenges, including over-dispersed read counts and, in some settings, sample non-independence. Previous count-based methods rely on simple hierarchical Poisson models (e.g. negative binomial) to model independent over-dispersion, but do not account for sample non-independence due to relatedness, population structure and/or hidden confounders. Here, we present a Poisson mixed model with two random effects terms that account for both independent over-dispersion and sample non-independence. We also develop a scalable sampling-based inference algorithm using a latent variable representation of the Poisson distribution. With simulations, we show that our method properly controls for type I error and is generally more powerful than other widely used approaches, except in small samples (n <15) with other unfavorable properties (e.g. small effect sizes). We also apply our method to three real datasets that contain related individuals, population stratification or hidden confounders. Our results show that our method increases power in all three data compared to other approaches, though the power gain is smallest in the smallest sample (n = 6). Our method is implemented in MACAU, freely available at www.xzlab.org/software.html. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Selecting the most appropriate time points to profile in high-throughput studies

PubMed Central

Kleyman, Michael; Sefer, Emre; Nicola, Teodora; Espinoza, Celia; Chhabra, Divya; Hagood, James S; Kaminski, Naftali; Ambalavanan, Namasivayam; Bar-Joseph, Ziv

2017-01-01

Biological systems are increasingly being studied by high throughput profiling of molecular data over time. Determining the set of time points to sample in studies that profile several different types of molecular data is still challenging. Here we present the Time Point Selection (TPS) method that solves this combinatorial problem in a principled and practical way. TPS utilizes expression data from a small set of genes sampled at a high rate. As we show by applying TPS to study mouse lung development, the points selected by TPS can be used to reconstruct an accurate representation for the expression values of the non selected points. Further, even though the selection is only based on gene expression, these points are also appropriate for representing a much larger set of protein, miRNA and DNA methylation changes over time. TPS can thus serve as a key design strategy for high throughput time series experiments. Supporting Website: www.sb.cs.cmu.edu/TPS DOI: http://dx.doi.org/10.7554/eLife.18541.001 PMID:28124972

Holographic entanglement entropy and entanglement thermodynamics of 'black' non-susy D3 brane

NASA Astrophysics Data System (ADS)

Bhattacharya, Aranya; Roy, Shibaji

2018-06-01

Like BPS D3 brane, the non-supersymmetric (non-susy) D3 brane of type IIB string theory is also known to have a decoupling limit and leads to a non-supersymmetric AdS/CFT correspondence. The throat geometry in this case represents a QFT which is neither conformal nor supersymmetric. The 'black' version of the non-susy D3 brane in the decoupling limit describes a QFT at finite temperature. Here we first compute the entanglement entropy for small subsystem of such QFT from the decoupled geometry of 'black' non-susy D3 brane using holographic technique. Then we study the entanglement thermodynamics for the weakly excited states of this QFT from the asymptotically AdS geometry of the decoupled 'black' non-susy D3 brane. We observe that for small subsystem this background indeed satisfies a first law like relation with a universal (entanglement) temperature inversely proportional to the size of the subsystem and an (entanglement) pressure normal to the entangling surface. Finally we show how the entanglement entropy makes a cross-over to the thermal entropy at high temperature.

Genetic stock identification of Russian honey bees.

PubMed

Bourgeois, Lelania; Sheppard, Walter S; Sylvester, H Allen; Rinderer, Thomas E

2010-06-01

A genetic stock certification assay was developed to distinguish Russian honey bees from other European (Apis mellifera L.) stocks that are commercially produced in the United States. In total, 11 microsatellite and five single-nucleotide polymorphism loci were used. Loci were selected for relatively high levels of homogeneity within each group and for differences in allele frequencies between groups. A baseline sample consisted of the 18 lines of Russian honey bees released to the Russian Bee Breeders Association and bees from 34 queen breeders representing commercially produced European honey bee stocks. Suitability tests of the baseline sample pool showed high levels of accuracy. The probability of correct assignment was 94.2% for non-Russian bees and 93.3% for Russian bees. A neighbor-joining phenogram representing genetic distance data showed clear distinction of Russian and non-Russian honey bee stocks. Furthermore, a test of appropriate sample size showed a sample of eight bees per colony maximizes accuracy and consistency of the results. An additional 34 samples were tested as blind samples (origin unknown to those collecting data) to determine accuracy of individual assignment tests. Only one of these samples was incorrectly assigned. The 18 current breeding lines were represented among the 2009 blind sampling, demonstrating temporal stability of the genetic stock identification assay. The certification assay will be used through services provided by a service laboratory, by the Russian Bee Breeders Association to genetically certify their stock. The genetic certification will be used in conjunction with continued selection for favorable traits, such as honey production and varroa and tracheal mite resistance.

TNO/Centaurs grouping tested with asteroid data sets

NASA Astrophysics Data System (ADS)

Fulchignoni, M.; Birlan, M.; Barucci, M. A.

2001-11-01

Recently, we have discussed the possible subdivision in few groups of a sample of 22 TNO and Centaurs for which the BVRIJ photometry were available (Barucci et al., 2001, A&A, 371,1150). We obtained this results using the multivariate statistics adopted to define the current asteroid taxonomy, namely the Principal Components Analysis and the G-mode method (Tholen & Barucci, 1989, in ASTEROIDS II). How these methods work with a very small statistical sample as the TNO/Centaurs one? Theoretically, the number of degrees of freedom of the sample is correct. In fact it is 88 in our case and have to be larger then 50 to cope with the requirements of the G-mode. Does the random sampling of the small number of members of a large population contain enough information to reveal some structure in the population? We extracted several samples of 22 asteroids out of a data-base of 86 objects of known taxonomic type for which BVRIJ photometry is available from ECAS (Zellner et al. 1985, ICARUS 61, 355), SMASS II (S.W. Bus, 1999, PhD Thesis, MIT), and the Bell et al. Atlas of the asteroid infrared spectra. The objects constituting the first sample were selected in order to give a good representation of the major asteroid taxonomic classes (at least three samples each class): C,S,D,A, and G. Both methods were able to distinguish all these groups confirming the validity of the adopted methods. The S class is hard to individuate as a consequence of the choice of I and J variables, which imply a lack of information on the absorption band at 1 micron. The other samples were obtained by random choice of the objects. Not all the major groups were well represented (less than three samples per groups), but the general trend of the asteroid taxonomy has been always obtained. We conclude that the quoted grouping of TNO/Centaurs is representative of some physico-chemical structure of the outer solar system small body population.

Non-wadeable river bioassessment: spatial variation of benthic diatom assemblages in Pacific Northwest rivers, USA

EPA Science Inventory

Current bioassessment efforts are focused on small wadeable streams, at least partly because assessing ecological conditions in non-wadeable large rivers poses many additional challenges. In this study, we sampled 20 sites in each of seven large rivers in the Pacific Northwest, U...

Validating DNA barcodes: A non-destructive extraction protocol enables simultaneous vouchering of DNA and morphological vouchers

USDA-ARS?s Scientific Manuscript database

Morphology-based keys support accurate identification of many taxa. However, identification can be difficult for taxa that are not well studied, very small, members of cryptic species complexes, or represented by immature stages. For such cases, DNA barcodes may provide diagnostic characters. Ecolog...

Suspect Screening and Non-Targeted Analysis of Drinking Water Using Point-Of-Use Filters

EPA Science Inventory

Monitored contaminants in drinking water represent a small portion of the total compounds present, many of which may be relevant to human health. To understand the totality of human exposure to compounds in drinking water, broader monitoring methods are imperative. In an effort t...

Validity of thermally-driven small-scale ventilated filling box models

NASA Astrophysics Data System (ADS)

Partridge, Jamie L.; Linden, P. F.

2013-11-01

The majority of previous work studying building ventilation flows at laboratory scale have used saline plumes in water. The production of buoyancy forces using salinity variations in water allows dynamic similarity between the small-scale models and the full-scale flows. However, in some situations, such as including the effects of non-adiabatic boundaries, the use of a thermal plume is desirable. The efficacy of using temperature differences to produce buoyancy-driven flows representing natural ventilation of a building in a small-scale model is examined here, with comparison between previous theoretical and new, heat-based, experiments.

Comparison of Sample Size by Bootstrap and by Formulas Based on Normal Distribution Assumption.

PubMed

Wang, Zuozhen

2018-01-01

Bootstrapping technique is distribution-independent, which provides an indirect way to estimate the sample size for a clinical trial based on a relatively smaller sample. In this paper, sample size estimation to compare two parallel-design arms for continuous data by bootstrap procedure are presented for various test types (inequality, non-inferiority, superiority, and equivalence), respectively. Meanwhile, sample size calculation by mathematical formulas (normal distribution assumption) for the identical data are also carried out. Consequently, power difference between the two calculation methods is acceptably small for all the test types. It shows that the bootstrap procedure is a credible technique for sample size estimation. After that, we compared the powers determined using the two methods based on data that violate the normal distribution assumption. To accommodate the feature of the data, the nonparametric statistical method of Wilcoxon test was applied to compare the two groups in the data during the process of bootstrap power estimation. As a result, the power estimated by normal distribution-based formula is far larger than that by bootstrap for each specific sample size per group. Hence, for this type of data, it is preferable that the bootstrap method be applied for sample size calculation at the beginning, and that the same statistical method as used in the subsequent statistical analysis is employed for each bootstrap sample during the course of bootstrap sample size estimation, provided there is historical true data available that can be well representative of the population to which the proposed trial is planning to extrapolate.

Maternal Responsiveness Predicts Child Language at Ages 3 and 4 in a Community-Based Sample of Slow-to-Talk Toddlers

ERIC Educational Resources Information Center

Hudson, Sophie; Levickis, Penny; Down, Kate; Nicholls, Ruth; Wake, Melissa

2015-01-01

Background: Maternal responsiveness has been shown to predict child language outcomes in clinical samples of children with language delay and non-representative samples of typically developing children. An effective and timely measure of maternal responsiveness for use at the population level has not yet been established. Aims: To determine…

Taxonomic Characterization of Honey Bee (Apis mellifera) Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci.

PubMed

Cornman, R Scott; Otto, Clint R V; Iwanowicz, Deborah; Pettis, Jeffery S

2015-01-01

Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5' of ITS1 and the 3' of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower "read2" quality, further protocol optimization and/or a modest reduction in multiplex scale should offset this difficulty. As small quantities of pollen are sufficient for amplification, our approach might be extendable to other questions or species for which large pollen samples are not available.

Taxonomic Characterization of Honey Bee (Apis mellifera) Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci

PubMed Central

Cornman, R. Scott; Otto, Clint R. V.; Iwanowicz, Deborah; Pettis, Jeffery S.

2015-01-01

Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5’ of ITS1 and the 3’ of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower “read2” quality, further protocol optimization and/or a modest reduction in multiplex scale should offset this difficulty. As small quantities of pollen are sufficient for amplification, our approach might be extendable to other questions or species for which large pollen samples are not available. PMID:26700168

Taxonomic characterization of honey bee (Apis mellifera) pollen foraging based on non-overlapping paired-end sequencing of nuclear ribosomal loci

USGS Publications Warehouse

Cornman, Robert S.; Otto, Clint R.; Iwanowicz, Deborah; Pettis, Jeffery S

2015-01-01

Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5’ of ITS1 and the 3’ of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower “read2” quality, further protocol optimization and/or a modest reduction in multiplex scale should offset this difficulty. As small quantities of pollen are sufficient for amplification, our approach might be extendable to other questions or species for which large pollen samples are not available.

Pre-operative intra-articular deep tissue sampling with novel retrograde forceps improves the diagnostics in periprosthetic joint infection.

PubMed

Wimmer, Matthias D; Ploeger, Milena M; Friedrich, Max J; Hügle, Thomas; Gravius, Sascha; Randau, Thomas M

2017-07-01

Histopathological tissue analysis is a key parameter within the diagnostic algorithm for suspected periprosthetic joint infections (PJIs), conventionally acquired in open surgery. In 2014, Hügle and co-workers introduced novel retrograde forceps for retrograde synovial biopsy with simultaneous fluid aspiration of the knee joint. We hypothesised that tissue samples acquired by retrograde synovial biopsy are equal to intra-operatively acquired deep representative tissue samples regarding bacterial detection and differentiation of periprosthetic infectious membranes. Thirty patients (male n = 15, 50%; female n = 15, 50%) with 30 suspected PJIs in painful total hip arthroplasties (THAs) were included in this prospective, controlled, non-blinded trial. The results were compared with intra-operatively obtained representative deep tissue samples. In summary, 27 out of 30 patients were diagnosed correctly as infected (17/17) or non-infected (10/13). The sensitivity to predict a PJI using the Retroforce® sampling forceps in addition to standard diagnostics was 85%, the specificity 100%. Retrograde synovial biopsy is a new and rapid diagnostic procedure under local anaesthesia in patients with painful THAs with similar histological results compared to deep tissue sampling.

A comparison of the male customers of female street prostitutes with national samples of men.

PubMed

Monto, Martin A; McRee, Nick

2005-10-01

Previous research on customers of prostitutes has relied on small samples and qualitative interviews. Conceptions of customers have tended toward either the "every man" perspective, which implies customers are no different than other men, or the "peculiar man" perspective, which implies customers are characterized by stark differences or psychological inadequacies. This study compares a large sample of men (N = 1672) arrested for trying to hire street prostitutes with nationally representative samples of men. Customers were less likely to be married, less likely to be happily married if married, and more likely to report being unhappy in general than men in the national samples. Customers also expressed greater sexual liberalism and reported thinking about sex, masturbating, and participating in other aspects of the sex industry more frequently than men in general. Most differences were small, indicating customers as a category differ from other men in degree rather than quality.

Nonlinear rescaling of control values simplifies fuzzy control

NASA Technical Reports Server (NTRS)

Vanlangingham, H.; Tsoukkas, A.; Kreinovich, V.; Quintana, C.

1993-01-01

Traditional control theory is well-developed mainly for linear control situations. In non-linear cases there is no general method of generating a good control, so we have to rely on the ability of the experts (operators) to control them. If we want to automate their control, we must acquire their knowledge and translate it into a precise control strategy. The experts' knowledge is usually represented in non-numeric terms, namely, in terms of uncertain statements of the type 'if the obstacle is straight ahead, the distance to it is small, and the velocity of the car is medium, press the brakes hard'. Fuzzy control is a methodology that translates such statements into precise formulas for control. The necessary first step of this strategy consists of assigning membership functions to all the terms that the expert uses in his rules (in our sample phrase these words are 'small', 'medium', and 'hard'). The appropriate choice of a membership function can drastically improve the quality of a fuzzy control. In the simplest cases, we can take the functions whose domains have equally spaced endpoints. Because of that, many software packages for fuzzy control are based on this choice of membership functions. This choice is not very efficient in more complicated cases. Therefore, methods have been developed that use neural networks or generic algorithms to 'tune' membership functions. But this tuning takes lots of time (for example, several thousands iterations are typical for neural networks). In some cases there are evident physical reasons why equally space domains do not work: e.g., if the control variable u is always positive (i.e., if we control temperature in a reactor), then negative values (that are generated by equal spacing) simply make no sense. In this case it sounds reasonable to choose another scale u' = f(u) to represent u, so that equal spacing will work fine for u'. In the present paper we formulate the problem of finding the best rescaling function, solve this problem, and show (on a real-life example) that after an optimal rescaling, the un-tuned fuzzy control can be as good as the best state-of-art traditional non-linear controls.

Serum peptide expression and treatment responses in patients with advanced non-small-cell lung cancer

PubMed Central

An, Juan; Tang, Chuan-Hao; Wang, Na; Liu, Yi; Lv, Jin; Xu, Bin; Li, Xiao-Yan; Guo, Wan-Feng; Gao, Hong-Jun; He, Kun; Liu, Xiao-Qing

2018-01-01

Epidermal growth factor receptor (EGFR) mutation is an important predictor for response to personalized treatments of patients with advanced non-small-cell lung cancer (NSCLC). However its usage is limited due to the difficult of obtaining tissue specimens. A novel prediction system using matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been reported to be a perspective tool in European countries to identify patients who are likely to benefit from EGFR tyrosine kinase inhibitor (TKI) treatment. In the present study, MALDI-TOF MS was used on pretreatment serum samples of patients with advanced non-small-cell lung cancer to discriminate the spectra between disease control and disease progression groups in one cohort of Chinese patients. The candidate features for classification were subsequently validated in a blinded fashion in another set of patients. The correlation between plasma EGFR mutation status and the intensities of representative spectra for classification was evaluated. A total of 103 patients that were treated with EGFR-TKIs were included. It was determined that 8 polypeptides peaks were significant different between the disease control and disease progression group. A total of 6 polypeptides were established in the classification algorithm. The sensitivity of the algorithm to predict treatment responses was 76.2% (16/21) and the specificity was 81.8% (18/22). The accuracy rate of the algorithm was 79.1% (34/43). A total of 3 polypeptides were significantly correlated with EGFR mutations (P=0.04, P=0.03 and P=0.04, respectively). The present study confirmed that MALDI-TOF MS analysis can be used to predict responses to EGFR-TKI treatment of the Asian population where the EGFR mutation status differs from the European population. Furthermore, the expression intensities of the three polypeptides in the classification model were associated with EGFR mutation. PMID:29844828

Evaluation of Pleistocene groundwater flow through fractured tuffs using a U-series disequilibrium approach, Pahute Mesa, Nevada, USA

USGS Publications Warehouse

Paces, James B.; Nichols, Paul J.; Neymark, Leonid A.; Rajaram, Harihar

2013-01-01

Groundwater flow through fractured felsic tuffs and lavas at the Nevada National Security Site represents the most likely mechanism for transport of radionuclides away from underground nuclear tests at Pahute Mesa. To help evaluate fracture flow and matrix–water exchange, we have determined U-series isotopic compositions on more than 40 drill core samples from 5 boreholes that represent discrete fracture surfaces, breccia zones, and interiors of unfractured core. The U-series approach relies on the disruption of radioactive secular equilibrium between isotopes in the uranium-series decay chain due to preferential mobilization of 234U relative to 238U, and U relative to Th. Samples from discrete fractures were obtained by milling fracture surfaces containing thin secondary mineral coatings of clays, silica, Fe–Mn oxyhydroxides, and zeolite. Intact core interiors and breccia fragments were sampled in bulk. In addition, profiles of rock matrix extending 15 to 44 mm away from several fractures that show evidence of recent flow were analyzed to investigate the extent of fracture/matrix water exchange. Samples of rock matrix have 234U/238U and 230Th/238U activity ratios (AR) closest to radioactive secular equilibrium indicating only small amounts of groundwater penetrated unfractured matrix. Greater U mobility was observed in welded-tuff matrix with elevated porosity and in zeolitized bedded tuff. Samples of brecciated core were also in secular equilibrium implying a lack of long-range hydraulic connectivity in these cases. Samples of discrete fracture surfaces typically, but not always, were in radioactive disequilibrium. Many fractures had isotopic compositions plotting near the 230Th-234U 1:1 line indicating a steady-state balance between U input and removal along with radioactive decay. Numerical simulations of U-series isotope evolution indicate that 0.5 to 1 million years are required to reach steady-state compositions. Once attained, disequilibrium 234U/238U and 230Th/238U AR values can be maintained indefinitely as long as hydrological and geochemical processes remain stable. Therefore, many Pahute Mesa fractures represent stable hydrologic pathways over million-year timescales. A smaller number of samples have non-steady-state compositions indicating transient conditions in the last several hundred thousand years. In these cases, U mobility is dominated by overall gains rather than losses of U.

Sampling Methods in Cardiovascular Nursing Research: An Overview.

PubMed

Kandola, Damanpreet; Banner, Davina; O'Keefe-McCarthy, Sheila; Jassal, Debbie

2014-01-01

Cardiovascular nursing research covers a wide array of topics from health services to psychosocial patient experiences. The selection of specific participant samples is an important part of the research design and process. The sampling strategy employed is of utmost importance to ensure that a representative sample of participants is chosen. There are two main categories of sampling methods: probability and non-probability. Probability sampling is the random selection of elements from the population, where each element of the population has an equal and independent chance of being included in the sample. There are five main types of probability sampling including simple random sampling, systematic sampling, stratified sampling, cluster sampling, and multi-stage sampling. Non-probability sampling methods are those in which elements are chosen through non-random methods for inclusion into the research study and include convenience sampling, purposive sampling, and snowball sampling. Each approach offers distinct advantages and disadvantages and must be considered critically. In this research column, we provide an introduction to these key sampling techniques and draw on examples from the cardiovascular research. Understanding the differences in sampling techniques may aid nurses in effective appraisal of research literature and provide a reference pointfor nurses who engage in cardiovascular research.

Succession and regulation factors of small eukaryote community composition in a lacustrine ecosystem (Lake Pavin).

PubMed

Lepère, Cécile; Boucher, Delphine; Jardillier, Ludwig; Domaizon, Isabelle; Debroas, Didier

2006-04-01

The structure and dynamics of small eukaryotes (cells with a diameter less than 5 microm) were studied over two consecutive years in an oligomesotrophic lake (Lake Pavin in France). Water samples were collected at 5 and 30 m below the surface; when the lake was stratified, these depths corresponded to the epilimnion and hypolimnion. Changes in small-eukaryote structure were analyzed using terminal restriction fragment length polymorphism (T-RFLP) and cloning and sequencing of the 18S rRNA genes. Terminal restriction fragments from clones were used to reveal the dominant taxa in T-RFLP profiles of the environmental samples. Spumella-like cells (Chrysophyceae) did not dominate the small eukaryote community identified by molecular techniques in lacustrine ecosystems. Small eukaryotes appeared to be dominated by heterotrophic cells, particularly Cercozoa, which represented nearly half of the identified phylotypes, followed by the Fungi-LKM11 group (25%), choanoflagellates (10.3%) and Chrysophyceae (8.9%). Bicosoecida, Cryptophyta, and ciliates represented less than 9% of the community studied. No seasonal reproducibility in temporal evolution of the small-eukaryote community was observed from 1 year to the next. The T-RFLP patterns were related to bottom-up (resources) and top-down (grazing) variables using canonical correspondence analysis. The results showed a strong top-down regulation of small eukaryotes by zooplankton, more exactly, by cladocerans at 5 m and copepods at 30 m. Among bottom-up factors, temperature had a significant effect at both depths. The concentrations of nitrogenous nutrients and total phosphorus also had an effect on small-eukaryote dynamics at 5 m, whereas bacterial abundance and dissolved oxygen played a more important structuring role in the deeper zone.

Nanoparticle functionalised small-core suspended-core fibre - a novel platform for efficient sensing.

PubMed

Doherty, Brenda; Csáki, Andrea; Thiele, Matthias; Zeisberger, Matthias; Schwuchow, Anka; Kobelke, Jens; Fritzsche, Wolfgang; Schmidt, Markus A

2017-02-01

Detecting small quantities of specific target molecules is of major importance within bioanalytics for efficient disease diagnostics. One promising sensing approach relies on combining plasmonically-active waveguides with microfluidics yielding an easy-to-use sensing platform. Here we introduce suspended-core fibres containing immobilised plasmonic nanoparticles surrounding the guiding core as a concept for an entirely integrated optofluidic platform for efficient refractive index sensing. Due to the extremely small optical core and the large adjacent microfluidic channels, over two orders of magnitude of nanoparticle coverage densities have been accessed with millimetre-long sample lengths showing refractive index sensitivities of 170 nm/RIU for aqueous analytes where the fibre interior is functionalised by gold nanospheres. Our concept represents a fully integrated optofluidic sensing system demanding small sample volumes and allowing for real-time analyte monitoring, both of which are highly relevant within invasive bioanalytics, particularly within molecular disease diagnostics and environmental science.

Diverse papillomaviruses identified in Weddell seals.

PubMed

Smeele, Zoe E; Burns, Jennifer M; Van Doorsaler, Koenraad; Fontenele, Rafaela S; Waits, Kara; Stainton, Daisy; Shero, Michelle R; Beltran, Roxanne S; Kirkham, Amy L; Berngartt, Rachel; Kraberger, Simona; Varsani, Arvind

2018-04-01

Papillomaviridae is a diverse family of circular, double-stranded DNA (dsDNA) viruses that infect a broad range of mammalian, avian and fish hosts. While papillomaviruses have been characterized most extensively in humans, the study of non-human papillomaviruses has contributed greatly to our understanding of their pathogenicity and evolution. Using high-throughput sequencing approaches, we identified 7 novel papillomaviruses from vaginal swabs collected from 81 adult female Weddell seals (Leptonychotes weddellii) in the Ross Sea of Antarctica between 2014-2017. These seven papillomavirus genomes were amplified from seven individual seals, and six of the seven genomes represented novel species with distinct evolutionary lineages. This highlights the diversity of papillomaviruses among the relatively small number of Weddell seal samples tested. Viruses associated with large vertebrates are poorly studied in Antarctica, and this study adds information about papillomaviruses associated with Weddell seals and contributes to our understanding of the evolutionary history of papillomaviruses.

Simulation of Wind Profile Perturbations for Launch Vehicle Design

NASA Technical Reports Server (NTRS)

Adelfang, S. I.

2004-01-01

Ideally, a statistically representative sample of measured high-resolution wind profiles with wavelengths as small as tens of meters is required in design studies to establish aerodynamic load indicator dispersions and vehicle control system capability. At most potential launch sites, high- resolution wind profiles may not exist. Representative samples of Rawinsonde wind profiles to altitudes of 30 km are more likely to be available from the extensive network of measurement sites established for routine sampling in support of weather observing and forecasting activity. Such a sample, large enough to be statistically representative of relatively large wavelength perturbations, would be inadequate for launch vehicle design assessments because the Rawinsonde system accurately measures wind perturbations with wavelengths no smaller than 2000 m (1000 m altitude increment). The Kennedy Space Center (KSC) Jimsphere wind profiles (150/month and seasonal 2 and 3.5-hr pairs) are the only adequate samples of high resolution profiles approx. 150 to 300 m effective resolution, but over-sampled at 25 m intervals) that have been used extensively for launch vehicle design assessments. Therefore, a simulation process has been developed for enhancement of measured low-resolution Rawinsonde profiles that would be applicable in preliminary launch vehicle design studies at launch sites other than KSC.

Multi-source recruitment strategies for advancing addiction recovery research beyond treated samples

PubMed Central

Subbaraman, Meenakshi Sabina; Laudet, Alexandre B.; Ritter, Lois A.; Stunz, Aina; Kaskutas, Lee Ann

2014-01-01

Background The lack of established sampling frames makes reaching individuals in recovery from substance problems difficult. Although general population studies are most generalizable, the low prevalence of individuals in recovery makes this strategy costly and inefficient. Though more efficient, treatment samples are biased. Aims To describe multi-source recruitment for capturing participants from heterogeneous pathways to recovery; assess which sources produced the most respondents within subgroups; and compare treatment and non-treatment samples to address generalizability. Results Family/friends, Craigslist, social media and non-12-step groups produced the most respondents from hard-to-reach groups, such as racial minorities and treatment-naïve individuals. Recovery organizations yielded twice as many African-Americans and more rural dwellers, while social media yielded twice as many young people than other sources. Treatment samples had proportionally fewer females and older individuals compared to non-treated samples. Conclusions Future research on recovery should utilize previously neglected recruiting strategies to maximize the representativeness of samples. PMID:26166909

Simultaneous Multiparameter Cellular Energy Metabolism Profiling of Small Populations of Cells.

PubMed

Kelbauskas, Laimonas; Ashili, Shashaanka P; Lee, Kristen B; Zhu, Haixin; Tian, Yanqing; Meldrum, Deirdre R

2018-03-12

Functional and genomic heterogeneity of individual cells are central players in a broad spectrum of normal and disease states. Our knowledge about the role of cellular heterogeneity in tissue and organism function remains limited due to analytical challenges one encounters when performing single cell studies in the context of cell-cell interactions. Information based on bulk samples represents ensemble averages over populations of cells, while data generated from isolated single cells do not account for intercellular interactions. We describe a new technology and demonstrate two important advantages over existing technologies: first, it enables multiparameter energy metabolism profiling of small cell populations (<100 cells)-a sample size that is at least an order of magnitude smaller than other, commercially available technologies; second, it can perform simultaneous real-time measurements of oxygen consumption rate (OCR), extracellular acidification rate (ECAR), and mitochondrial membrane potential (MMP)-a capability not offered by any other commercially available technology. Our results revealed substantial diversity in response kinetics of the three analytes in dysplastic human epithelial esophageal cells and suggest the existence of varying cellular energy metabolism profiles and their kinetics among small populations of cells. The technology represents a powerful analytical tool for multiparameter studies of cellular function.

Sample types applied for molecular diagnosis of therapeutic management of advanced non-small cell lung cancer in the precision medicine.

PubMed

Han, Yanxi; Li, Jinming

2017-10-26

In this era of precision medicine, molecular biology is becoming increasingly significant for the diagnosis and therapeutic management of non-small cell lung cancer. The specimen as the primary element of the whole testing flow is particularly important for maintaining the accuracy of gene alteration testing. Presently, the main sample types applied in routine diagnosis are tissue and cytology biopsies. Liquid biopsies are considered as the most promising alternatives when tissue and cytology samples are not available. Each sample type possesses its own strengths and weaknesses, pertaining to the disparity of sampling, preparation and preservation procedures, the heterogeneity of inter- or intratumors, the tumor cellularity (percentage and number of tumor cells) of specimens, etc., and none of them can individually be a "one size to fit all". Therefore, in this review, we summarized the strengths and weaknesses of different sample types that are widely used in clinical practice, offered solutions to reduce the negative impact of the samples and proposed an optimized strategy for choice of samples during the entire diagnostic course. We hope to provide valuable information to laboratories for choosing optimal clinical specimens to achieve comprehensive functional genomic landscapes and formulate individually tailored treatment plans for NSCLC patients that are in advanced stages.

Short-term monitoring of benzene air concentration in an urban area: a preliminary study of application of Kruskal-Wallis non-parametric test to assess pollutant impact on global environment and indoor.

PubMed

Mura, Maria Chiara; De Felice, Marco; Morlino, Roberta; Fuselli, Sergio

2010-01-01

In step with the need to develop statistical procedures to manage small-size environmental samples, in this work we have used concentration values of benzene (C6H6), concurrently detected by seven outdoor and indoor monitoring stations over 12 000 minutes, in order to assess the representativeness of collected data and the impact of the pollutant on indoor environment. Clearly, the former issue is strictly connected to sampling-site geometry, which proves critical to correctly retrieving information from analysis of pollutants of sanitary interest. Therefore, according to current criteria for network-planning, single stations have been interpreted as nodes of a set of adjoining triangles; then, a) node pairs have been taken into account in order to estimate pollutant stationarity on triangle sides, as well as b) node triplets, to statistically associate data from air-monitoring with the corresponding territory area, and c) node sextuplets, to assess the impact probability of the outdoor pollutant on indoor environment for each area. Distributions from the various node combinations are all non-Gaussian, in the consequently, Kruskal-Wallis (KW) non-parametric statistics has been exploited to test variability on continuous density function from each pair, triplet and sextuplet. Results from the above-mentioned statistical analysis have shown randomness of site selection, which has not allowed a reliable generalization of monitoring data to the entire selected territory, except for a single "forced" case (70%); most important, they suggest a possible procedure to optimize network design.

Urinary metabolomic study of non-small cell lung carcinoma based on ultra high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry.

PubMed

Wu, Qian; Wang, Yan; Gu, Xue; Zhou, Junyi; Zhang, Huiping; Lv, Wang; Chen, Zhe; Yan, Chao

2014-07-01

Metabolic profiles from human urine reveal the significant difference of carnitine and acylcarnitines levels between non-small cell lung carcinoma patients and healthy controls. Urine samples from cancer patients and healthy individuals were assayed in this metabolomic study using ultra high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. The data were normalized by the sum of all intensities and creatinine calibration, respectively, before orthogonal partial least squares discriminant analysis. Twenty differential metabolites were identified based on standard compounds or tandem mass spectrometry fragments. Among them, some medium-/long-chain acylcarnitines, for example, cis-3,4-methylene heptanoylcarnitine, were found to be downregulated while carnitine was upregulated in urine samples from the cancer group compared to the control group. Receiver operating characteristic analysis of the two groups showed that the area under curve for the combination of carnitine and 11 selected acylcarnitines was 0.958. This study suggests that the developed carnitine and acylcarnitines profiling method has the potential to be used for screening non-small cell lung carcinoma. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Trace element contamination in feather and tissue samples from Anna’s hummingbirds

USGS Publications Warehouse

Mikoni, Nicole A.; Poppenga, Robert H.; Ackerman, Joshua T.; Foley, Janet E.; Hazlehurst, Jenny; Purdin, Güthrum; Aston, Linda; Hargrave, Sabine; Jelks, Karen; Tell, Lisa A.

2017-01-01

Trace element contamination (17 elements; Be, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Mo, Cd, Ba, Hg, Tl, and Pb) of live (feather samples only) and deceased (feather and tissue samples) Anna's hummingbirds (Calypte anna) was evaluated. Samples were analyzed using inductively coupled plasma-mass spectrometry (ICP-MS; 17 elements) and atomic absorption spectrophotometry (Hg only). Mean plus one standard deviation (SD) was considered the benchmark, and concentrations above the mean + 1 SD were considered elevated above normal. Contour feathers were sampled from live birds of varying age, sex, and California locations. In order to reduce thermal impacts, minimal feathers were taken from live birds, therefore a novel method was developed for preparation of low mass feather samples for ICP-MS analysis. The study found that the novel feather preparation method enabled small mass feather samples to be analyzed for trace elements using ICP-MS. For feather samples from live birds, all trace elements, with the exception of beryllium, had concentrations above the mean + 1 SD. Important risk factors for elevated trace element concentrations in feathers of live birds were age for iron, zinc, and arsenic, and location for iron, manganese, zinc, and selenium. For samples from deceased birds, ICP-MS results from body and tail feathers were correlated for Fe, Zn, and Pb, and feather concentrations were correlated with renal (Fe, Zn, Pb) or hepatic (Hg) tissue concentrations. Results for AA spectrophotometry analyzed samples from deceased birds further supported the ICP-MS findings where a strong correlation between mercury concentrations in feather and tissue (pectoral muscle) samples was found. These study results support that sampling feathers from live free-ranging hummingbirds might be a useful, non-lethal sampling method for evaluating trace element exposure and provides a sampling alternative since their small body size limits traditional sampling of blood and tissues. The results from this study provide a benchmark for the distribution of trace element concentrations in feather and tissue samples from hummingbirds and suggests a reference mark for exceeding normal. Lastly, pollinating avian species are minimally represented in the literature as bioindicators for environmental trace element contamination. Given that trace elements can move through food chains by a variety of routes, our study indicates that hummingbirds are possible bioindicators of environmental trace element contamination.

Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples.

PubMed

Zhao, Qi; Liu, Yuanning; Zhang, Ning; Hu, Menghan; Zhang, Hao; Joshi, Trupti; Xu, Dong

2018-01-01

In recent years, an increasing number of studies have reported the presence of plant miRNAs in human samples, which resulted in a hypothesis asserting the existence of plant-derived exogenous microRNA (xenomiR). However, this hypothesis is not widely accepted in the scientific community due to possible sample contamination and the small sample size with lack of rigorous statistical analysis. This study provides a systematic statistical test that can validate (or invalidate) the plant-derived xenomiR hypothesis by analyzing 388 small RNA sequencing data from human samples in 11 types of body fluids/tissues. A total of 166 types of plant miRNAs were found in at least one human sample, of which 14 plant miRNAs represented more than 80% of the total plant miRNAs abundance in human samples. Plant miRNA profiles were characterized to be tissue-specific in different human samples. Meanwhile, the plant miRNAs identified from microbiome have an insignificant abundance compared to those from humans, while plant miRNA profiles in human samples were significantly different from those in plants, suggesting that sample contamination is an unlikely reason for all the plant miRNAs detected in human samples. This study also provides a set of testable synthetic miRNAs with isotopes that can be detected in situ after being fed to animals.

Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

NASA Astrophysics Data System (ADS)

Morard, Raphaël; Lejzerowicz, Franck; Darling, Kate F.; Lecroq-Bennet, Béatrice; Winther Pedersen, Mikkel; Orlando, Ludovic; Pawlowski, Jan; Mulitza, Stefan; de Vargas, Colomban; Kucera, Michal

2017-06-01

Deep-sea sediments constitute a unique archive of ocean change, fueled by a permanent rain of mineral and organic remains from the surface ocean. Until now, paleo-ecological analyses of this archive have been mostly based on information from taxa leaving fossils. In theory, environmental DNA (eDNA) in the sediment has the potential to provide information on non-fossilized taxa, allowing more comprehensive interpretations of the fossil record. Yet, the process controlling the transport and deposition of eDNA onto the sediment and the extent to which it preserves the features of past oceanic biota remains unknown. Planktonic foraminifera are the ideal taxa to allow an assessment of the eDNA signal modification during deposition because their fossils are well preserved in the sediment and their morphological taxonomy is documented by DNA barcodes. Specifically, we re-analyze foraminiferal-specific metabarcodes from 31 deep-sea sediment samples, which were shown to contain a small fraction of sequences from planktonic foraminifera. We confirm that the largest portion of the metabarcode originates from benthic bottom-dwelling foraminifera, representing the in situ community, but a small portion (< 10 %) of the metabarcodes can be unambiguously assigned to planktonic taxa. These organisms live exclusively in the surface ocean and the recovered barcodes thus represent an allochthonous component deposited with the rain of organic remains from the surface ocean. We take advantage of the planktonic foraminifera portion of the metabarcodes to establish to what extent the structure of the surface ocean biota is preserved in sedimentary eDNA. We show that planktonic foraminifera DNA is preserved in a range of marine sediment types, the composition of the recovered eDNA metabarcode is replicable and that both the similarity structure and the diversity pattern are preserved. Our results suggest that sedimentary eDNA could preserve the ecological structure of the entire pelagic community, including non-fossilized taxa, thus opening new avenues for paleoceanographic and paleoecological studies.

High-throughput analysis using non-depletive SPME: challenges and applications to the determination of free and total concentrations in small sample volumes.

PubMed

Boyacı, Ezel; Bojko, Barbara; Reyes-Garcés, Nathaly; Poole, Justen J; Gómez-Ríos, Germán Augusto; Teixeira, Alexandre; Nicol, Beate; Pawliszyn, Janusz

2018-01-18

In vitro high-throughput non-depletive quantitation of chemicals in biofluids is of growing interest in many areas. Some of the challenges facing researchers include the limited volume of biofluids, rapid and high-throughput sampling requirements, and the lack of reliable methods. Coupled to the above, growing interest in the monitoring of kinetics and dynamics of miniaturized biosystems has spurred the demand for development of novel and revolutionary methodologies for analysis of biofluids. The applicability of solid-phase microextraction (SPME) is investigated as a potential technology to fulfill the aforementioned requirements. As analytes with sufficient diversity in their physicochemical features, nicotine, N,N-Diethyl-meta-toluamide, and diclofenac were selected as test compounds for the study. The objective was to develop methodologies that would allow repeated non-depletive sampling from 96-well plates, using 100 µL of sample. Initially, thin film-SPME was investigated. Results revealed substantial depletion and consequent disruption in the system. Therefore, new ultra-thin coated fibers were developed. The applicability of this device to the described sampling scenario was tested by determining the protein binding of the analytes. Results showed good agreement with rapid equilibrium dialysis. The presented method allows high-throughput analysis using small volumes, enabling fast reliable free and total concentration determinations without disruption of system equilibrium.

Non-parametric methods for cost-effectiveness analysis: the central limit theorem and the bootstrap compared.

PubMed

Nixon, Richard M; Wonderling, David; Grieve, Richard D

2010-03-01

Cost-effectiveness analyses (CEA) alongside randomised controlled trials commonly estimate incremental net benefits (INB), with 95% confidence intervals, and compute cost-effectiveness acceptability curves and confidence ellipses. Two alternative non-parametric methods for estimating INB are to apply the central limit theorem (CLT) or to use the non-parametric bootstrap method, although it is unclear which method is preferable. This paper describes the statistical rationale underlying each of these methods and illustrates their application with a trial-based CEA. It compares the sampling uncertainty from using either technique in a Monte Carlo simulation. The experiments are repeated varying the sample size and the skewness of costs in the population. The results showed that, even when data were highly skewed, both methods accurately estimated the true standard errors (SEs) when sample sizes were moderate to large (n>50), and also gave good estimates for small data sets with low skewness. However, when sample sizes were relatively small and the data highly skewed, using the CLT rather than the bootstrap led to slightly more accurate SEs. We conclude that while in general using either method is appropriate, the CLT is easier to implement, and provides SEs that are at least as accurate as the bootstrap. (c) 2009 John Wiley & Sons, Ltd.

The analysis of ALK gene rearrangement by fluorescence in situ hybridization in non-small cell lung cancer patients

PubMed Central

Krawczyk, Paweł Adam; Ramlau, Rodryg Adam; Szumiło, Justyna; Kozielski, Jerzy; Kalinka-Warzocha, Ewa; Bryl, Maciej; Knopik-Dąbrowicz, Alina; Spychalski, Łukasz; Szczęsna, Aleksandra; Rydzik, Ewelina; Milanowski, Janusz

2013-01-01

Introduction ALK gene rearrangement is observed in a small subset (3–7%) of non-small cell lung cancer (NSCLC) patients. The efficacy of crizotinib was shown in lung cancer patients harbouring ALK rearrangement. Nowadays, the analysis of ALK gene rearrangement is added to molecular examination of predictive factors. Aim of the study The frequency of ALK gene rearrangement as well as the type of its irregularity was analysed by fluorescence in situ hybridisation (FISH) in tissue samples from NSCLC patients. Material and methods The ALK gene rearrangement was analysed in 71 samples including 53 histological and 18 cytological samples. The analysis could be performed in 56 cases (78.87%), significantly more frequently in histological than in cytological materials. The encountered problem with ALK rearrangement diagnosis resulted from the scarcity of tumour cells in cytological samples, high background fluorescence noises and fragmentation of cell nuclei. Results The normal ALK copy number without gene rearrangement was observed in 26 (36.62%) patients ALK gene polysomy without gene rearrangement was observed in 25 (35.21%) samples while in 3 (4.23%) samples ALK gene amplification was found. ALK gene rearrangement was observed in 2 (2.82%) samples from males, while in the first case the rearrangement coexisted with ALK amplification. In the second case, signet-ring tumour cells were found during histopathological examination and this patient was successfully treated with crizotinib with partial remission lasting 16 months. Conclusions FISH is a useful technique for ALK gene rearrangement analysis which allows us to specify the type of gene irregularities. ALK gene examination could be performed in histological as well as cytological (cellblocks) samples, but obtaining a reliable result in cytological samples depends on the cellularity of examined materials. PMID:24592134

Post-traumatic stress disorder in older adults: a systematic review of the psychotherapy treatment literature.

PubMed

Dinnen, Stephanie; Simiola, Vanessa; Cook, Joan M

2015-01-01

Older adults represent the fastest growing segment of the US and industrialized populations. However, older adults have generally not been included in randomized clinical trials of psychotherapy for post-traumatic stress disorder (PTSD). This review examined reports of psychological treatment for trauma-related problems, primarily PTSD, in studies with samples of at least 50% adults aged 55 and older using standardized measures. A systematic review of the literature was conducted on psychotherapy for PTSD with older adults using PubMed, Medline, PsychInfo, CINAHL, PILOTS, and Google Scholar. A total of 42 studies were retrieved for full review; 22 were excluded because they did not provide at least one outcome measure or results were not reported by age in the case of mixed-age samples. Of the 20 studies that met review criteria, there were: 13 case studies or series, three uncontrolled pilot studies, two randomized clinical trials, one non-randomized concurrent control study and one post hoc effectiveness study. Significant methodological limitations in the current older adult PTSD treatment outcome literature were found reducing its internal validity and generalizability, including non-randomized research designs, lack of comparison conditions and small sample sizes. Select evidence-based interventions validated in younger and middle-aged populations appear acceptable and efficacious with older adults. There are few treatment studies on subsets of the older adult population including cultural and ethnic minorities, women, the oldest old (over 85), and those who are cognitively impaired. Implications for clinical practice and future research directions are discussed.

75 FR 15492 - Paperwork Reduction Act of 1995, as Amended by Public Law 104-13; Proposed Collection, Comment...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-29

.... James W. Sample, Director of CyberSecurity. [FR Doc. 2010-6904 Filed 3-26-10; 8:45 am] BILLING CODE 8120...: Individuals or households, state or local governments, farms, businesses, or other for-profit Federal agencies or employees, non-profit institutions, small businesses or organizations. Small Businesses or...

75 FR 34534 - Paperwork Reduction Act of 1995, as Amended by Public Law 104-13; Proposed Collection, Comment...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-17

... published in 18 CFR part 1304. James W. Sample, Director of CyberSecurity. [FR Doc. 2010-14560 Filed 6-16-10... Affected Public: Individuals or households, state or local governments, farms, businesses, or other for-profit Federal agencies or employees, non-profit institutions, small businesses or organizations. Small...

Collateral Information for Equating in Small Samples: A Preliminary Investigation

ERIC Educational Resources Information Center

Kim, Sooyeon; Livingston, Samuel A.; Lewis, Charles

2011-01-01

This article describes a preliminary investigation of an empirical Bayes (EB) procedure for using collateral information to improve equating of scores on test forms taken by small numbers of examinees. Resampling studies were done on two different forms of the same test. In each study, EB and non-EB versions of two equating methods--chained linear…

Value of information methods to design a clinical trial in a small population to optimise a health economic utility function.

PubMed

Pearce, Michael; Hee, Siew Wan; Madan, Jason; Posch, Martin; Day, Simon; Miller, Frank; Zohar, Sarah; Stallard, Nigel

2018-02-08

Most confirmatory randomised controlled clinical trials (RCTs) are designed with specified power, usually 80% or 90%, for a hypothesis test conducted at a given significance level, usually 2.5% for a one-sided test. Approval of the experimental treatment by regulatory agencies is then based on the result of such a significance test with other information to balance the risk of adverse events against the benefit of the treatment to future patients. In the setting of a rare disease, recruiting sufficient patients to achieve conventional error rates for clinically reasonable effect sizes may be infeasible, suggesting that the decision-making process should reflect the size of the target population. We considered the use of a decision-theoretic value of information (VOI) method to obtain the optimal sample size and significance level for confirmatory RCTs in a range of settings. We assume the decision maker represents society. For simplicity we assume the primary endpoint to be normally distributed with unknown mean following some normal prior distribution representing information on the anticipated effectiveness of the therapy available before the trial. The method is illustrated by an application in an RCT in haemophilia A. We explicitly specify the utility in terms of improvement in primary outcome and compare this with the costs of treating patients, both financial and in terms of potential harm, during the trial and in the future. The optimal sample size for the clinical trial decreases as the size of the population decreases. For non-zero cost of treating future patients, either monetary or in terms of potential harmful effects, stronger evidence is required for approval as the population size increases, though this is not the case if the costs of treating future patients are ignored. Decision-theoretic VOI methods offer a flexible approach with both type I error rate and power (or equivalently trial sample size) depending on the size of the future population for whom the treatment under investigation is intended. This might be particularly suitable for small populations when there is considerable information about the patient population.

Learning in later life: participation in formal, non-formal and informal activities in a nationally representative Spanish sample.

PubMed

Villar, Feliciano; Celdrán, Montserrat

2013-06-01

This article examines the participation of Spanish older people in formal, non-formal and informal learning activities and presents a profile of participants in each kind of learning activity. We used data from a nationally representative sample of Spanish people between 60 and 75 years old ( n  = 4,703). The data were extracted from the 2007 Encuesta sobre la Participación de la Población Adulta en Actividades de Aprendizaje (EADA, Survey on Adult Population Involvement in Learning Activities). Overall, only 22.8 % of the sample participated in a learning activity. However, there was wide variation in the participation rates for the different types of activity. Informal activities were far more common than formal ones. Multivariate logistic regression indicated that education level and involvement in social and cultural activities were associated with likelihood of participating, regardless of the type of learning activity. When these variables were taken into account, age did not predict decreasing participation, at least in non-formal and informal activities. Implications for further research, future trends and policies to promote older adult education are discussed.

Observer-based output feedback control of networked control systems with non-uniform sampling and time-varying delay

NASA Astrophysics Data System (ADS)

Meng, Su; Chen, Jie; Sun, Jian

2017-10-01

This paper investigates the problem of observer-based output feedback control for networked control systems with non-uniform sampling and time-varying transmission delay. The sampling intervals are assumed to vary within a given interval. The transmission delay belongs to a known interval. A discrete-time model is first established, which contains time-varying delay and norm-bounded uncertainties coming from non-uniform sampling intervals. It is then converted to an interconnection of two subsystems in which the forward channel is delay-free. The scaled small gain theorem is used to derive the stability condition for the closed-loop system. Moreover, the observer-based output feedback controller design method is proposed by utilising a modified cone complementary linearisation algorithm. Finally, numerical examples illustrate the validity and superiority of the proposed method.

NON-REGULATED CONTAMINANTS EMERGING RESEARCH, EXISTING AND FUTURE POLLUTANTS IN WATER SUPPLIES: OLD POLLUTANTS, NEW CONCERNS - NEW POLLUTANTS, UNKNOWN ISSUES

EPA Science Inventory

Those chemical pollutants that are regulated under various international, federal, and state programs represent but a small fraction of the universe of chemicals that occur in the environment as a result of both natural processes and human influence. Although this galaxy of targe...

Er-doped YVO4 amplifier diode pumped at 976 nm

NASA Astrophysics Data System (ADS)

Newburgh, G. A.; Dubinskii, Mark

2016-05-01

We report on the use of a 976 nm diode pumped Er:YVO4 slab for the amplification of 1603 nm laser radiation with a small signal gain of 2.1. To the best of our knowledge, this represents the first use of Er:YVO4 as a non-resonantly pumped amplifier.

Treatment modalities for advanced ALK-rearranged non-small-cell lung cancer.

PubMed

Sullivan, Ivana; Planchard, David

2016-04-01

The ALK gene plays a key role in the pathogenesis of non-small-cell lung cancer (NSCLC). Patients with NSCLC harboring an ALK-rearrangement represent the second oncogene addiction to be identified in this disease. Crizotinib was the first ALK inhibitor showing pronounced clinical activity, and is now a reference treatment for ALK-positive NSCLC disease. However, despite initial impressive responses to crizotinib, acquired resistance almost invariably develops within 12 months. The pressing need for effective second-line agents has prompted the rapid development of next-generation ALK inhibitors. These agents, notably ceritinib and alectinib as the most developed, have a higher potency against ALK than crizotinib, along with activity against tumors harboring crizotinib-resistant mutations and potentially improved CNS penetration.

FUSION-Guided Hypothesis Development Leads to the Identification of N6,N6-Dimethyladenosine, a Marine-Derived AKT Pathway Inhibitor

PubMed Central

Vaden, Rachel M.; Oswald, Nathaniel W.; Potts, Malia B.; MacMillan, John B.; White, Michael A.

2017-01-01

Chemicals found in nature have evolved over geological time scales to productively interact with biological molecules, and thus represent an effective resource for pharmaceutical development. Marine-derived bacteria are rich sources of chemically diverse, bioactive secondary metabolites, but harnessing this diversity for biomedical benefit is limited by challenges associated with natural product purification and determination of biochemical mechanism. Using Functional Signature Ontology (FUSION), we report the parallel isolation and characterization of a marine-derived natural product, N6,N6-dimethyladenosine, that robustly inhibits AKT signaling in a variety of non-small cell lung cancer cell lines. Upon validation of the elucidated structure by comparison with a commercially available sample, experiments were initiated to understand the small molecule’s breadth of effect in a biological setting. One such experiment, a reverse phase protein array (RPPA) analysis of >50 kinases, indicated a specific cellular response to treatment. In all, leveraging the FUSION platform allowed for the rapid generation and validation of a biological mechanism of action hypothesis for an unknown natural product and permitted accelerated purification of the bioactive component from a chemically complex fraction. PMID:28294973

Non-phytoseiid Mesostigmata within citrus orchards in Florida: species distribution, relative and seasonal abundance within trees, associated vines and ground cover plants and additional collection records of mites in citrus orchards.

PubMed

Childers, Carl C; Ueckermann, Eduard A

2015-03-01

Seven citrus orchards on reduced- to no-pesticide spray programs in central and south central Florida were sampled for non-phytoseiid mesostigmatid mites. Inner and outer canopy leaves, fruits, twigs and trunk scrapings were sampled monthly between August 1994 and January 1996. Open flowers were sampled in March from five of the sites. A total of 431 samples from one or more of 82 vine or ground cover plants were sampled monthly in five of the seven orchards. Two of the seven orchards (Mixon I and II) were on full herbicide programs and vines and ground cover plants were absent. A total of 2,655 mites (26 species) within the families: Ascidae, Blattisociidae, Laelapidae, Macrochelidae, Melicharidae, Pachylaelapidae and Parasitidae were identified. A total of 685 mites in the genus Asca (nine species: family Ascidae) were collected from within tree samples, 79 from vine or ground cover plants. Six species of Blattisociidae were collected: Aceodromus convolvuli, Blattisocius dentriticus, B. keegani, Cheiroseius sp. near jamaicensis, Lasioseius athiashenriotae and L. dentatus. A total of 485 Blattisociidae were collected from within tree samples compared with 167 from vine or ground cover plants. Low numbers of Laelapidae and Macrochelidae were collected from within tree samples. One Zygoseius furciger (Pachylaelapidae) was collected from Eleusine indica. Four species of Melicharidae were identified from 34 mites collected from within tree samples and 1,190 from vine or ground cover plants: Proctolaelaps lobatus was the most abundant species with 1,177 specimens collected from seven ground cover plants. One Phorytocarpais fimetorum (Parasitidae) was collected from inner leaves and four from twigs. Species of Ascidae, Blattisociidae, Melicharidae, Laelapidae and Pachylaelapidae were collected from 31 of the 82 vine or ground cover plants sampled, representing only a small fraction of the total number of Phytoseiidae collected from the same plants. Including the collection records of Martin Muma prior to 1975, a total of 69 species of Ascidae, Blattisociidae, Laelapidae, Macrochelidae, Melicharidae, Pachylaelapidae and Parasitidae have now been reported from citrus in Florida.

Microbial agents in macroscopically healthy mammary gland tissues of small ruminants.

PubMed

Spuria, Liliana; Biasibetti, Elena; Bisanzio, Donal; Biasato, Ilaria; De Meneghi, Daniele; Nebbia, Patrizia; Robino, Patrizia; Bianco, Paolo; Lamberti, Michele; Caruso, Claudio; Di Blasio, Alessia; Peletto, Simone; Masoero, Loretta; Dondo, Alessandro; Capucchio, Maria Teresa

2017-01-01

Health of mammary glands is fundamental for milk and dairy products hygiene and quality, with huge impacts on consumers welfare. This study aims to investigate the microbial agents (bacteria, fungi and lentiviruses) isolated from 89 macroscopically healthy udders of regularly slaughtered small ruminants (41 sheep, 48 goats), also correlating their presence with the histological findings. Multinomial logistic regression was applied to evaluate the association between lesions and positivity for different microbial isolates, animal age and bacteria. Twenty-five samples were microbiologically negative; 138 different bacteria were isolated in 64 positive udders. Coagulase-negative staphylococci were the most prevalent bacteria isolated (46.42%), followed by environmental opportunists (34.76%), others (10.14%) and pathogens (8.68%). Most mammary glands showed coinfections (75%). Lentiviruses were detected in 39.3% of samples. Histologically, chronic non-suppurative mastitis was observed in 45/89 glands, followed by chronic mixed mastitis (12/89) and acute suppurative mastitis (4/89). Only 28 udders were normal. Histological lesions were significantly associated with the animal species and lentiviruses and coagulase-negative staphylococci infections. Goats had significantly higher risk to show chronic mixed mastitis compared to sheep. Goats showed a significantly lower risk (OR = 0.26; 95% CI [0.06-0.71]) of being infected by environmental opportunists compared to sheep, but higher risk (OR = 10.87; 95% CI [3.69-37.77]) of being infected with lentiviruses. The results of the present study suggest that macroscopically healthy glands of small ruminants could act as a reservoir of microbial agents for susceptible animals, representing a potential risk factor for the widespread of acute or chronic infection in the flock.

Retrospective MicroRNA Sequencing: Complementary DNA Library Preparation Protocol Using Formalin-fixed Paraffin-embedded RNA Specimens.

PubMed

Loudig, Olivier; Liu, Christina; Rohan, Thomas; Ben-Dov, Iddo Z

2018-05-05

-Archived, clinically classified formalin-fixed paraffin-embedded (FFPE) tissues can provide nucleic acids for retrospective molecular studies of cancer development. By using non-invasive or pre-malignant lesions from patients who later develop invasive disease, gene expression analyses may help identify early molecular alterations that predispose to cancer risk. It has been well described that nucleic acids recovered from FFPE tissues have undergone severe physical damage and chemical modifications, which make their analysis difficult and generally requires adapted assays. MicroRNAs (miRNAs), however, which represent a small class of RNA molecules spanning only up to ~18-24 nucleotides, have been shown to withstand long-term storage and have been successfully analyzed in FFPE samples. Here we present a 3' barcoded complementary DNA (cDNA) library preparation protocol specifically optimized for the analysis of small RNAs extracted from archived tissues, which was recently demonstrated to be robust and highly reproducible when using archived clinical specimens stored for up to 35 years. This library preparation is well adapted to the multiplex analysis of compromised/degraded material where RNA samples (up to 18) are ligated with individual 3' barcoded adapters and then pooled together for subsequent enzymatic and biochemical preparations prior to analysis. All purifications are performed by polyacrylamide gel electrophoresis (PAGE), which allows size-specific selections and enrichments of barcoded small RNA species. This cDNA library preparation is well adapted to minute RNA inputs, as a pilot polymerase chain reaction (PCR) allows determination of a specific amplification cycle to produce optimal amounts of material for next-generation sequencing (NGS). This approach was optimized for the use of degraded FFPE RNA from specimens archived for up to 35 years and provides highly reproducible NGS data.

IP-FCM measures physiologic protein-protein interactions modulated by signal transduction and small-molecule drug inhibition.

PubMed

Smith, Stephen E P; Bida, Anya T; Davis, Tessa R; Sicotte, Hugues; Patterson, Steven E; Gil, Diana; Schrum, Adam G

2012-01-01

Protein-protein interactions (PPI) mediate the formation of intermolecular networks that control biological signaling. For this reason, PPIs are of outstanding interest in pharmacology, as they display high specificity and may represent a vast pool of potentially druggable targets. However, the study of physiologic PPIs can be limited by conventional assays that often have large sample requirements and relatively low sensitivity. Here, we build on a novel method, immunoprecipitation detected by flow cytometry (IP-FCM), to assess PPI modulation during either signal transduction or pharmacologic inhibition by two different classes of small-molecule compounds. First, we showed that IP-FCM can detect statistically significant differences in samples possessing a defined PPI change as low as 10%. This sensitivity allowed IP-FCM to detect a PPI that increases transiently during T cell signaling, the antigen-inducible interaction between ZAP70 and the T cell antigen receptor (TCR)/CD3 complex. In contrast, IP-FCM detected no ZAP70 recruitment when T cells were stimulated with antigen in the presence of the src-family kinase inhibitor, PP2. Further, we tested whether IP-FCM possessed sufficient sensitivity to detect the effect of a second, rare class of compounds called SMIPPI (small-molecule inhibitor of PPI). We found that the first-generation non-optimized SMIPPI, Ro-26-4550, inhibited the IL-2:CD25 interaction detected by IP-FCM. This inhibition was detectable using either a recombinant CD25-Fc chimera or physiologic full-length CD25 captured from T cell lysates. Thus, we demonstrate that IP-FCM is a sensitive tool for measuring physiologic PPIs that are modulated by signal transduction and pharmacologic inhibition.

Dynamics of multiple resistance mechanisms in plasma DNA during EGFR-targeted therapies in non-small cell lung cancer.

PubMed

Tsui, Dana Wai Yi; Murtaza, Muhammed; Wong, Alvin Seng Cheong; Rueda, Oscar M; Smith, Christopher G; Chandrananda, Dineika; Soo, Ross A; Lim, Hong Liang; Goh, Boon Cher; Caldas, Carlos; Forshew, Tim; Gale, Davina; Liu, Wei; Morris, James; Marass, Francesco; Eisen, Tim; Chin, Tan Min; Rosenfeld, Nitzan

2018-06-01

Tumour heterogeneity leads to the development of multiple resistance mechanisms during targeted therapies. Identifying the dominant driver(s) is critical for treatment decision. We studied the relative dynamics of multiple oncogenic drivers in longitudinal plasma of 50 EGFR -mutant non-small-cell lung cancer patients receiving gefitinib and hydroxychloroquine. We performed digital PCR and targeted sequencing on samples from all patients and shallow whole-genome sequencing on samples from three patients who underwent histological transformation to small-cell lung cancer. In 43 patients with known EGFR mutations from tumour, we identified them accurately in plasma of 41 patients (95%, 41/43). We also found additional mutations, including EGFR T790M (31/50, 62%), TP53 (23/50, 46%), PIK3CA (7/50, 14%) and PTEN (4/50, 8%). Patients with both TP53 and EGFR mutations before treatment had worse overall survival than those with only EGFR Patients who progressed without T790M had worse PFS during TKI continuation and developed alternative alterations, including small-cell lung cancer-associated copy number changes and TP53 mutations, that tracked subsequent treatment responses. Longitudinal plasma analysis can help identify dominant resistance mechanisms, including non-druggable genetic information that may guide clinical management. © 2018 The Authors. Published under the terms of the CC BY 4.0 license.

Paranuclear blue inclusions in metastatic undifferentiated small cell carcinoma in the bone marrow.

PubMed

Wittchow, R; Laszewski, M; Walker, W; Dick, F

1992-09-01

Paranuclear blue inclusions (PBIs) are frequently identified within metastatic undifferentiated small cell carcinoma (SCC) cells on air-dried bone marrow aspirates stained with Wright's stain. To determine the sensitivity and specificity of this finding, 116 bone marrow aspirates containing metastatic neoplasms were evaluated for the presence and frequency of PBIs. Bone marrow specimens included 47 cases of metastatic SCC of the lung, 13 cases of large cell lymphoma, 19 cases of neuroblastoma, five cases of small, noncleaved cell lymphoma, seven cases of rhabdomyosarcoma, three cases of Ewing's sarcoma, three cases of other sarcomas, and 19 cases of non-small cell carcinoma (adenocarcinoma). PBIs were identified in 40 of 47 (85%) cases of SCC and their frequency varied from 0 to 24% of tumor cells among different cases. In approximately half the cases of SCC, PBIs were identified in 1 to 4% tumor cells; and in eight cases, PBIs were present in 5% or more of tumor cells. PBIs were also identified in two of seven (29%) cases of rhabdomyosarcoma and one case of malignant peripheral nerve sheath tumor, but they were not seen in Ewing's sarcoma, small non-cleaved cell lymphoma, large cell lymphoma, neuroblastoma, or non-small cell carcinoma. In addition, PBIs were not seen in alcohol-fixed, Papanicolaou-stained cytology specimens containing SCC. Ultrastructurally, PBIs may represent phagocytized nuclear/cellular material. PBIs are a feature of small cell carcinoma on air-dried, cytologic material stained with Romanowsky type stains. Their presence may provide diagnostic information with regard to the differential diagnosis of metastatic SCC in the bone marrow. Future studies evaluating non-bone marrow Wright's stained fine-needle aspiration specimens are needed to determine if PBIs are useful in distinguishing SCC from other poorly differentiated tumors in the cytology laboratory.

Determination of Small Animal Long Bone Properties Using Densitometry

NASA Technical Reports Server (NTRS)

Breit, Gregory A.; Goldberg, BethAnn K.; Whalen, Robert T.; Hargens, Alan R. (Technical Monitor)

1996-01-01

Assessment of bone structural property changes due to loading regimens or pharmacological treatment typically requires destructive mechanical testing and sectioning. Our group has accurately and non-destructively estimated three dimensional cross-sectional areal properties (principal moments of inertia, Imax and Imin, and principal angle, Theta) of human cadaver long bones from pixel-by-pixel analysis of three non-coplanar densitometry scans. Because the scanner beam width is on the order of typical small animal diapbyseal diameters, applying this technique to high-resolution scans of rat long bones necessitates additional processing to minimize errors induced by beam smearing, such as dependence on sample orientation and overestimation of Imax and Imin. We hypothesized that these errors are correctable by digital image processing of the raw scan data. In all cases, four scans, using only the low energy data (Hologic QDR-1000W, small animal mode), are averaged to increase image signal-to-noise ratio. Raw scans are additionally processed by interpolation, deconvolution by a filter derived from scanner beam characteristics, and masking using a variable threshold based on image dynamic range. To assess accuracy, we scanned an aluminum step phantom at 12 orientations over a range of 180 deg about the longitudinal axis, in 15 deg increments. The phantom dimensions (2.5, 3.1, 3.8 mm x 4.4 mm; Imin/Imax: 0.33-0.74) were comparable to the dimensions of a rat femur which was also scanned. Cross-sectional properties were determined at 0.25 mm increments along the length of the phantom and femur. The table shows average error (+/- SD) from theory of Imax, Imin, and Theta) over the 12 orientations, calculated from raw and fully processed phantom images, as well as standard deviations about the mean for the femur scans. Processing of phantom scans increased agreement with theory, indicating improved accuracy. Smaller standard deviations with processing indicate increased precision and repeatability. Standard deviations for the femur are consistent with those of the phantom. We conclude that in conjunction with digital image enhancement, densitometry scans are suitable for non-destructive determination of areal properties of small animal bones of comparable size to our phantom, allowing prediction of Imax and Imin within 2.5% and Theta within a fraction of a degree. This method represents a considerable extension of current methods of analyzing bone tissue distribution in small animal bones.

Field application of passive SBSE for the monitoring of pesticides in surface waters.

PubMed

Assoumani, A; Coquery, M; Liger, L; Mazzella, N; Margoum, C

2015-03-01

Spot sampling lacks representativeness for monitoring organic contaminants in most surface waters. Passive sampling has emerged as a cost-effective complementary sampling technique. We recently developed passive stir bar sorptive extraction (passive SBSE), with Twister from Gerstel, for monitoring moderately hydrophilic to hydrophobic pesticides (2.18 < log K ow < 5.11) in surface water. The aims of the present study were to assess this new passive sampler for the determination of representative average concentrations and to evaluate the contamination levels of two French rivers. Passive SBSE was evaluated for the monitoring of 16 pesticides in two rivers located in a small vineyard watershed during two 1-month field campaigns in spring 2010 and spring 2011. Passive SBSE was applied for periods of 1 or 2 weeks during the field campaigns and compared with spot sampling and weekly average automated sampling. The results showed that passive SBSE could achieve better time-representativeness than spot sampling and lower limits of quantification than automated sampling coupled with analytical SBSE for the pesticides studied. Finally, passive SBSE proved useful for revealing spatial and temporal variations in pesticide contamination of both rivers and the impact of rainfall and runoff on the river water quality.

Selective inhibitors of trypanosomal uridylyl transferase RET1 establish druggability of RNA post-transcriptional modifications

PubMed Central

Cording, Amy; Gormally, Michael; Bond, Peter J.; Carrington, Mark; Balasubramanian, Shankar; Miska, Eric A.; Thomas, Beth

2017-01-01

ABSTRACT Non-coding RNAs are crucial regulators for a vast array of cellular processes and have been implicated in human disease. These biological processes represent a hitherto untapped resource in our fight against disease. In this work we identify small molecule inhibitors of a non-coding RNA uridylylation pathway. The TUTase family of enzymes is important for modulating non-coding RNA pathways in both human cancer and pathogen systems. We demonstrate that this new class of drug target can be accessed with traditional drug discovery techniques. Using the Trypanosoma brucei TUTase, RET1, we identify TUTase inhibitors and lay the groundwork for the use of this new target class as a therapeutic opportunity for the under-served disease area of African Trypanosomiasis. In a broader sense this work demonstrates the therapeutic potential for targeting RNA post-transcriptional modifications with small molecules in human disease. PMID:26786754

Selective inhibitors of trypanosomal uridylyl transferase RET1 establish druggability of RNA post-transcriptional modifications.

PubMed

Cording, Amy; Gormally, Michael; Bond, Peter J; Carrington, Mark; Balasubramanian, Shankar; Miska, Eric A; Thomas, Beth

2017-05-04

Non-coding RNAs are crucial regulators for a vast array of cellular processes and have been implicated in human disease. These biological processes represent a hitherto untapped resource in our fight against disease. In this work we identify small molecule inhibitors of a non-coding RNA uridylylation pathway. The TUTase family of enzymes is important for modulating non-coding RNA pathways in both human cancer and pathogen systems. We demonstrate that this new class of drug target can be accessed with traditional drug discovery techniques. Using the Trypanosoma brucei TUTase, RET1, we identify TUTase inhibitors and lay the groundwork for the use of this new target class as a therapeutic opportunity for the under-served disease area of African Trypanosomiasis. In a broader sense this work demonstrates the therapeutic potential for targeting RNA post-transcriptional modifications with small molecules in human disease.

A Religious Experience? Personal, Parental, and Peer Religiosity and the Academic Success of Sexual-Minority Youth Using Nationally Representative Samples

ERIC Educational Resources Information Center

Gottfried, Michael A.; Polikoff, Morgan S.

2012-01-01

Using nationally representative transcript data, this study is the first to include a discussion of religiosity in the context of sexual-minority students' academic achievement. This study examines the issue in three capacities: first, by comparing school success of sexual-minority youth to a non-sexual-minority reference group; second, by…

Biological variation in a large sample of mouse lemurs from Amboasary, Madagascar: implications for interpreting variation in primate biology and paleobiology.

PubMed

Cuozzo, Frank P; Rasoazanabary, Emilienne; Godfrey, Laurie R; Sauther, Michelle L; Youssouf, Ibrahim Antho; LaFleur, Marni M

2013-01-01

A thorough knowledge of biological variation in extant primates is imperative for interpreting variation, and for delineating species in primate biology and paleobiology. This is especially the case given the recent, rapid taxonomic expansion in many primate groups, notably among small-bodied nocturnal forms. Here we present data on dental, cranial, and pelage variation in a single-locality museum sample of mouse lemurs from Amboasary, Madagascar. To interpret these data, we include comparative information from other museum samples, and from a newly collected mouse lemur skeletal sample from the Beza Mahafaly Special Reserve (BMSR), Madagascar. We scored forty dental traits (n = 126) and three pelage variants (n = 19), and collected 21 cranial/dental measures. Most dental traits exhibit variable frequencies, with some only rarely present. Individual dental variants include misshapen and supernumerary teeth. All Amboasary pelage specimens display a "reversed V" on the cap, and a distinct dorsal median stripe on the back. All but two displayed the dominant gray-brown pelage coloration typical of Microcebus griseorufus. Cranial and dental metric variability are each quite low, and craniometric variation does not illustrate heteroscedasticity. To assess whether this sample represents a single species, we compared dental and pelage variation to a documented, single-species M. griseorufus sample from BMSR. As at Amboasary, BMSR mouse lemurs display limited odontometric variation and wide variation in non-metric dental traits. In contrast, BMSR mouse lemurs display diverse pelage, despite reported genetic homogeneity. Ranges of dental and pelage variation at BMSR and Amboasary overlap. Thus, we conclude that the Amboasary mouse lemurs represent a single species - most likely (in the absence of genetic data to the contrary) M. griseorufus, and we reject their previous allocation to Microcebus murinus. Patterns of variation in the Amboasary sample provide a comparative template for recognizing the degree of variation manifested in a single primate population, and by implication, they provide minimum values for this species' intraspecific variation. Finally, discordance between different biological systems in our mouse lemur samples illustrates the need to examine multiple systems when conducting taxonomic analyses among living or fossil primates. Copyright © 2012 Elsevier Ltd. All rights reserved.

COMPARISON OF PERFLUORINATED CHLOROFORMATES AS DIRECT AQUEOUS SAMPLE DERIVATIZING AGENTS FOR HIGHLY HYDROPHILIC ANALYTES

EPA Science Inventory

Strong oxidants are supposed to produce quite extensive cleavage of the hydrocarbon backbone of natural organic matter, resulting in the release of partly oxidized organic molecules. The identification and detection of these small and highly polar compounds represents a challengi...

Advances in statistics

Treesearch

Howard Stauffer; Nadav Nur

2005-01-01

The papers included in the Advances in Statistics section of the Partners in Flight (PIF) 2002 Proceedings represent a small sample of statistical topics of current importance to Partners In Flight research scientists: hierarchical modeling, estimation of detection probabilities, and Bayesian applications. Sauer et al. (this volume) examines a hierarchical model...

Skills and Training in the Non-Profit Sector. CPRN Research Series on Human Resources in the Non-Profit Sector.

ERIC Educational Resources Information Center

McMullen. Kathryn; Schellenberg, Grant

Training in Canada's nonprofit sector was examined through a review of data from Canada's Workplace and Employer Survey, which collected data from a nationally representative sample of Canadian workplaces and paid employees in those workplaces. Overall, 61% of employees in nonprofit organizations considered a postsecondary credential necessary to…

The Role of Traumatic Event History in Non-Medical Use of Prescription Drugs among a Nationally Representative Sample of US Adolescents

ERIC Educational Resources Information Center

McCauley, Jenna L.; Danielson, Carla Kmett; Amstadter, Ananda B.; Ruggiero, Kenneth J.; Resnick, Heidi S.; Hanson, Rochelle F.; Smith, Daniel W.; Saunders, Benjamin E.; Kilpatrick, Dean G.

2010-01-01

Background: Building on previous research with adolescents that examined demographic variables and other forms of substance abuse in relation to non-medical use of prescription drugs (NMUPD), the current study examined potentially traumatic events, depression, posttraumatic stress disorder (PTSD), other substance use, and delinquent behavior as…

Voltage control of magnetic single domains in Ni discs on ferroelectric BaTiO3

NASA Astrophysics Data System (ADS)

Ghidini, M.; Zhu, B.; Mansell, R.; Pellicelli, R.; Lesaine, A.; Moya, X.; Crossley, S.; Nair, B.; Maccherozzi, F.; Barnes, C. H. W.; Cowburn, R. P.; Dhesi, S. S.; Mathur, N. D.

2018-06-01

For 1 µm-diameter Ni discs on a BaTiO3 substrate, the local magnetization direction is determined by ferroelectric domain orientation as a consequence of growth strain, such that single-domain discs lie on single ferroelectric domains. On applying a voltage across the substrate, ferroelectric domain switching yields non-volatile magnetization rotations of 90°, while piezoelectric effects that are small and continuous yield non-volatile magnetization reversals that are non-deterministic. This demonstration of magnetization reversal without ferroelectric domain switching implies reduced fatigue, and therefore represents a step towards applications.

Reaching Asian Americans: sampling strategies and incentives.

PubMed

Lee, Soo-Kyung; Cheng, Yu-Yao

2006-07-01

Reaching and recruiting representative samples of minority populations is often challenging. This study examined in Chinese and Korean Americans: 1) whether using two different sampling strategies (random sampling vs. convenience sampling) significantly affected characteristics of recruited participants and 2) whether providing different incentives in the mail survey produced different response rates. We found statistically significant, however mostly not remarkable, differences between random and convenience samples. Offering monetary incentives in the mail survey improved response rates among Chinese Americans, while offering a small gift did not improve response rates among either Chinese or Korean Americans. This information will be useful for researchers and practitioners working with Asian Americans.

Anaphylaxis Imaging: Non-Invasive Measurement of Surface Body Temperature and Physical Activity in Small Animals

PubMed Central

Manzano-Szalai, Krisztina; Pali-Schöll, Isabella; Krishnamurthy, Durga; Stremnitzer, Caroline; Flaschberger, Ingo; Jensen-Jarolim, Erika

2016-01-01

In highly sensitized patients, the encounter with a specific allergen from food, insect stings or medications may rapidly induce systemic anaphylaxis with potentially lethal symptoms. Countless animal models of anaphylaxis, most often in BALB/c mice, were established to understand the pathophysiology and to prove the safety of different treatments. The most common symptoms during anaphylactic shock are drop of body temperature and reduced physical activity. To refine, improve and objectify the currently applied manual monitoring methods, we developed an imaging method for the automated, non-invasive measurement of the whole-body surface temperature and, at the same time, of the horizontal and vertical movement activity of small animals. We tested the anaphylaxis imaging in three in vivo allergy mouse models for i) milk allergy, ii) peanut allergy and iii) egg allergy. These proof-of-principle experiments suggest that the imaging technology represents a reliable non-invasive method for the objective monitoring of small animals during anaphylaxis over time. We propose that the method will be useful for monitoring diseases associated with both, changes in body temperature and in physical behaviour. PMID:26963393

A Geology Sampling System for Small Bodies

NASA Technical Reports Server (NTRS)

Naids, Adam J.; Hood, Anthony D.; Abell, Paul; Graff, Trevor; Buffington, Jesse

2016-01-01

Human exploration of microgravity bodies is being investigated as a precursor to a Mars surface mission. Asteroids, comets, dwarf planets, and the moons of Mars all fall into this microgravity category and some are being discussed as potential mission targets. Obtaining geological samples for return to Earth will be a major objective for any mission to a small body. Currently, the knowledge base for geology sampling in microgravity is in its infancy. Humans interacting with non-engineered surfaces in microgravity environment pose unique challenges. In preparation for such missions a team at the NASA Johnson Space Center has been working to gain experience on how to safely obtain numerous sample types in such an environment. This paper describes the type of samples the science community is interested in, highlights notable prototype work, and discusses an integrated geology sampling solution.

Salt- and pH-induced desorption: Comparison between non-aggregated and aggregated mussel adhesive protein, Mefp-1, and a synthetic cationic polyelectrolyte.

PubMed

Krivosheeva, Olga; Dedinaite, Andra; Claesson, Per M

2013-10-15

Mussel adhesive proteins are of great interest in many applications due to their ability to bind strongly to many types of surfaces under water. Effective use such proteins, for instance the Mytilus edulis foot protein - Mefp-1, for surface modification requires achievement of a large adsorbed amount and formation of a layer that is resistant towards desorption under changing conditions. In this work we compare the adsorbed amount and layer properties obtained by using a sample containing small Mefp-1 aggregates with that obtained by using a non-aggregated sample. We find that the use of the sample containing small aggregates leads to higher adsorbed amount, larger layer thickness and similar water content compared to what can be achieved with a non-aggregated sample. The layer formed by the aggregated Mefp-1 was, after removal of the protein from bulk solution, exposed to aqueous solutions with high ionic strength (up to 1M NaCl) and to solutions with low pH in order to reduce the electrostatic surface affinity. It was found that the preadsorbed Mefp-1 layer under all conditions explored was significantly more resistant towards desorption than a layer built by a synthetic cationic polyelectrolyte with similar charge density. These results suggest that the non-electrostatic surface affinity for Mefp-1 is larger than for the cationic polyelectrolyte. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Novel insights from NMR spectroscopy into seasonal changes in the composition of dissolved organic matter exported to the Bering Sea by the Yukon River

NASA Astrophysics Data System (ADS)

Cao, Xiaoyan; Aiken, George R.; Spencer, Robert G. M.; Butler, Kenna; Mao, Jingdong; Schmidt-Rohr, Klaus

2016-05-01

Seasonal (spring freshet, summer-autumn, and winter) variability in the chemical composition of dissolved organic matter (DOM) from the Yukon River was determined using advanced one- and two-dimensional (2D) solid-state NMR spectroscopy, coupled with isotopic measurements and UV-visible spectroscopy. Analyses were performed on two major DOM fractions, the hydrophobic organic acid (HPOA) and transphilic organic acid (TPIA) fractions obtained using XAD resins. Together these two fractions comprised 64-74% of the total DOM. Carboxyl-rich alicyclic molecules (CRAM) accounted for the majority of carbon atoms in the HPOA (63-77%) and TPIA (54-78%) samples, and more so in winter and summer than in spring samples. 2D and selective NMR data revealed association of abundant nonprotonated O-alkyl and quaternary alkyl C (OCnp, OCnpO and Cq, 13-17% of HPOA and 15-20% of TPIA) and isolated O-CH structures with CRAM, which were not recognized in previous studies. Spectral editing and 2D NMR allowed for the discrimination of carbohydrate-like O-alkyl C from non-carbohydrate O-alkyl C. Whereas two spring freshet TPIA samples contained carbohydrate clusters such as carboxylated carbohydrates (16% and 26%), TPIA samples from other seasons or HPOA samples mostly had small amounts (<8%) of sugar rings dispersed in a nonpolar alkyl environment. Though nonprotonated aromatic C represented the largest fraction of aromatic C in all HPOA/TPIA isolates, only a small fraction (∼5% in HPOA and 3% in TPIA) was possibly associated with dissolved black carbon. Our results imply a relatively stable portion of DOM exported by the Yukon River across different seasons, due to the predominance of CRAM and their associated nonprotonated C-O and O-C-O structures, and elevated reactivity (bio- and photo-lability) of spring DOM due to the presence of terrestrial inputs enriched in carbohydrates and aromatic structures.

Novel insights from NMR spectroscopy into seasonal changes in the composition of dissolved organic matter exported to the Bering Sea by the Yukon River

USGS Publications Warehouse

Cao, Xiaoyan; Aiken, George R.; Spencer, Robert G. M.; Butler, Kenna D.; Mao, Jingdong; Schmidt-Rohr, Klaus

2016-01-01

Seasonal (spring freshet, summer–autumn, and winter) variability in the chemical composition of dissolved organic matter (DOM) from the Yukon River was determined using advanced one- and two-dimensional (2D) solid-state NMR spectroscopy, coupled with isotopic measurements and UV–visible spectroscopy. Analyses were performed on two major DOM fractions, the hydrophobic organic acid (HPOA) and transphilic organic acid (TPIA) fractions obtained using XAD resins. Together these two fractions comprised 64–74% of the total DOM. Carboxyl-rich alicyclic molecules (CRAM) accounted for the majority of carbon atoms in the HPOA (63–77%) and TPIA (54–78%) samples, and more so in winter and summer than in spring samples. 2D and selective NMR data revealed association of abundant nonprotonated O-alkyl and quaternary alkyl C (OCnp, OCnpO and Cq, 13–17% of HPOA and 15–20% of TPIA) and isolated O–CH structures with CRAM, which were not recognized in previous studies. Spectral editing and 2D NMR allowed for the discrimination of carbohydrate-like O-alkyl C from non-carbohydrate O-alkyl C. Whereas two spring freshet TPIA samples contained carbohydrate clusters such as carboxylated carbohydrates (16% and 26%), TPIA samples from other seasons or HPOA samples mostly had small amounts (<8%) of sugar rings dispersed in a nonpolar alkyl environment. Though nonprotonated aromatic C represented the largest fraction of aromatic C in all HPOA/TPIA isolates, only a small fraction (∼5% in HPOA and 3% in TPIA) was possibly associated with dissolved black carbon. Our results imply a relatively stable portion of DOM exported by the Yukon River across different seasons, due to the predominance of CRAM and their associated nonprotonated C–O and O–C–O structures, and elevated reactivity (bio- and photo-lability) of spring DOM due to the presence of terrestrial inputs enriched in carbohydrates and aromatic structures.

Comparison of small biopsy specimens and surgical specimens for the detection of EGFR mutations and EML4-ALK in non-small-cell lung cancer.

PubMed

Xiao, DeSheng; Lu, Can; Zhu, Wei; He, QiuYan; Li, Yong; Fu, ChunYan; Zhou, JianHua; Liu, Shuang; Tao, YongGuang

2016-09-13

Epidermal growth factor receptor (EGFR) mutations and anaplastic lymphoma kinase (ALK) fusion genes represent novel oncogenes that are associated with non-small-cell lung cancers (NSCLC). The feasibility of detecting EGFR mutations and ALK fusion genes in small biopsy specimens or surgical specimens was determined. Of the 721 NSCLC patients, a total of 305 cases were positive for EGFR mutations (42.3%). The rate of EGFR mutations in women was significantly higher than that in men. Histologically, the EGFR mutation rate in adenocarcinomas was significantly higher than that in squamous cell carcinomas. No difference in the EGFR mutation rate was observed between surgical specimens (42.1%) and small biopsy specimens (42.4%), which indicated that the EGFR mutation ratios in surgical specimens and small biopsy specimens were not different. In 385 NSCLC patients, 26 cases were positive for EML4-ALK (6.8%). However, 11.7% of the surgical specimens were EML4-ALK-positive, whereas the positive proportion in the small biopsy specimens was only 4.7%, which indicated that EML4-ALK-positive rate in the surgical specimens was significantly higher than that in the small biopsy specimens. Detection of EGFR gene mutations was feasible in small biopsy specimens, and screening for EML4-ALK expression in small biopsy specimens can be used to guide clinical treatments.

Sampling versus systematic full lymphatic dissection in surgical treatment of non-small cell lung cancer.

PubMed

Koulaxouzidis, Georgios; Karagkiouzis, Grigorios; Konstantinou, Marios; Gkiozos, Ioannis; Syrigos, Konstantinos

2013-04-22

The extent of mediastinal lymph node assessment during surgery for non-small cell cancer remains controversial. Different techniques are used, ranging from simple visual inspection of the unopened mediastinum to an extended bilateral lymph node dissection. Furthermore, different terms are used to define these techniques. Sampling is the removal of one or more lymph nodes under the guidance of pre-operative findings. Systematic (full) nodal dissection is the removal of all mediastinal tissue containing the lymph nodes systematically within anatomical landmarks. A Medline search was conducted to identify articles in the English language that addressed the role of mediastinal lymph node resection in the treatment of non-small cell lung cancer. Opinions as to the reasons for favoring full lymphatic dissection include complete resection, improved nodal staging and better local control due to resection of undetected micrometastasis. Arguments against routine full lymphatic dissection are increased morbidity, increase in operative time, and lack of evidence of improved survival. For complete resection of non-small cell lung cancer, many authors recommend a systematic nodal dissection as the standard approach during surgery, and suggest that this provides both adequate nodal staging and guarantees complete resection. Whether extending the lymph node dissection influences survival or recurrence rate is still not known. There are valid arguments in favor in terms not only of an improved local control but also of an improved long-term survival. However, the impact of lymph node dissection on long-term survival should be further assessed by large-scale multicenter randomized trials.

Application of SAXS and SANS in evaluation of porosity, pore size distribution and surface area of coal

USGS Publications Warehouse

Radlinski, A.P.; Mastalerz, Maria; Hinde, A.L.; Hainbuchner, M.; Rauch, H.; Baron, M.; Lin, J.S.; Fan, L.; Thiyagarajan, P.

2004-01-01

This paper discusses the applicability of small angle X-ray scattering (SAXS) and small angle neutron scattering (SANS) techniques for determining the porosity, pore size distribution and internal specific surface area in coals. The method is noninvasive, fast, inexpensive and does not require complex sample preparation. It uses coal grains of about 0.8 mm size mounted in standard pellets as used for petrographic studies. Assuming spherical pore geometry, the scattering data are converted into the pore size distribution in the size range 1 nm (10 A??) to 20 ??m (200,000 A??) in diameter, accounting for both open and closed pores. FTIR as well as SAXS and SANS data for seven samples of oriented whole coals and corresponding pellets with vitrinite reflectance (Ro) values in the range 0.55% to 5.15% are presented and analyzed. Our results demonstrate that pellets adequately represent the average microstructure of coal samples. The scattering data have been used to calculate the maximum surface area available for methane adsorption. Total porosity as percentage of sample volume is calculated and compared with worldwide trends. By demonstrating the applicability of SAXS and SANS techniques to determine the porosity, pore size distribution and surface area in coals, we provide a new and efficient tool, which can be used for any type of coal sample, from a thin slice to a representative sample of a thick seam. ?? 2004 Elsevier B.V. All rights reserved.

Relationships fade with time: a meta-analysis of temporal trends in publication in ecology and evolution.

PubMed Central

Jennions, Michael D; Møller, Anders P

2002-01-01

Both significant positive and negative relationships between the magnitude of research findings (their 'effect size') and their year of publication have been reported in a few areas of biology. These trends have been attributed to Kuhnian paradigm shifts, scientific fads and bias in the choice of study systems. Here we test whether or not these isolated cases reflect a more general trend. We examined the relationship using effect sizes extracted from 44 peer-reviewed meta-analyses covering a wide range of topics in ecological and evolutionary biology. On average, there was a small but significant decline in effect size with year of publication. For the original empirical studies there was also a significant decrease in effect size as sample size increased. However, the effect of year of publication remained even after we controlled for sampling effort. Although these results have several possible explanations, it is suggested that a publication bias against non-significant or weaker findings offers the most parsimonious explanation. As in the medical sciences, non-significant results may take longer to publish and studies with both small sample sizes and non-significant results may be less likely to be published. PMID:11788035

Time-integrated sampling of fluvial suspended sediment: a simple methodology for small catchments

NASA Astrophysics Data System (ADS)

Phillips, J. M.; Russell, M. A.; Walling, D. E.

2000-10-01

Fine-grained (<62·5 µm) suspended sediment transport is a key component of the geochemical flux in most fluvial systems. The highly episodic nature of suspended sediment transport imposes a significant constraint on the design of sampling strategies aimed at characterizing the biogeochemical properties of such sediment. A simple sediment sampler, utilizing ambient flow to induce sedimentation by settling, is described. The sampler can be deployed unattended in small streams to collect time-integrated suspended sediment samples. In laboratory tests involving chemically dispersed sediment, the sampler collected a maximum of 71% of the input sample mass. However, under natural conditions, the existence of composite particles or flocs can be expected to increase significantly the trapping efficiency. Field trials confirmed that the particle size composition and total carbon content of the sediment collected by the sampler were representative statistically of the ambient suspended sediment.

Biochip-Based Detection of KRAS Mutation in Non-Small Cell Lung Cancer

PubMed Central

Kriegshäuser, Gernot; Fabjani, Gerhild; Ziegler, Barbara; Zöchbauer-Müller, Sabine; End, Adelheid; Zeillinger, Robert

2011-01-01

This study is aimed at evaluating the potential of a biochip assay to sensitively detect KRAS mutation in DNA from non-small cell lung cancer (NSCLC) tissue samples. The assay covers 10 mutations in codons 12 and 13 of the KRAS gene, and is based on mutant-enriched PCR followed by reverse-hybridization of biotinylated amplification products to an array of sequence-specific probes immobilized on the tip of a rectangular plastic stick (biochip). Biochip hybridization identified 17 (21%) samples to carry a KRAS mutation of which 16 (33%) were adenocarcinomas and 1 (3%) was a squamous cell carcinoma. All mutations were confirmed by DNA sequencing. Using 10 ng of starting DNA, the biochip assay demonstrated a detection limit of 1% mutant sequence in a background of wild-type DNA. Our results suggest that the biochip assay is a sensitive alternative to protocols currently in use for KRAS mutation testing on limited quantity samples. PMID:22272089

Identification of I1171N resistance mutation in ALK-positive non-small-cell lung cancer tumor sample and circulating tumor DNA.

PubMed

Johnson, Alison C; Dô, Pascal; Richard, Nicolas; Dubos, Catherine; Michels, Jean Jacques; Bonneau, Jessica; Gervais, Radj

2016-09-01

Anaplastic lymphoma kinase (ALK)-rearranged non-small cell lung cancer (NSCLC) is sensitive to ALK inhibitor therapy, but resistance invariably develops and can be mediated by certain secondary mutations. The detection of these mutations is useful to guide treatment decisions, but tumors are not always easily accessible to re-biopsy. We report the case of a patient with ALK-rearranged NSCLC who presented acquired resistance to crizotinib and then alectinib. Sequencing analyses of DNA from a liver metastasis biopsy sample and circulating tumor DNA both found the same I1171N ALK kinase domain mutation, known to confer resistance to certain ALK inhibitors. However, the patient then received ceritinib, a 2nd generation ALK inhibitor, and achieved another partial response. This case underlines how ALK resistance mutation detection in peripheral blood could be a reliable, safer, and less invasive alternative to tissue-based samples in NSCLC. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

ABCC3 as a marker for multidrug resistance in non-small cell lung cancer

PubMed Central

Zhao, Yanbin; Lu, Hailing; Yan, An; Yang, Yanmei; Meng, Qingwei; Sun, Lichun; Pang, Hui; Li, Chunhong; Dong, Xiaoqun; Cai, Li

2013-01-01

Multidrug resistance (MDR) contributes to the failure of chemotherapy and high mortality in non-small cell lung cancer (NSCLC). We aim to identify MDR genes that predict tumor response to chemotherapy. 199 NSCLC fresh tissue samples were tested for chemosensitivity by MTT assay. cDNA microarray was done with 5 samples with highest resistance and 6 samples with highest sensitivity. Expression of ABCC3 mRNA and protein was detected by real-time PCR and immunohistochemisty, respectively. The association between gene expression and overall survival (OS) was examined using Cox proportional hazard regression. 44 genes were upregulated and 168 downregulated in the chemotherapy-resistant group. ABCC3 was one of the most up-regulated genes in the resistant group. ABCC3-positive expression correlated with lymph node involvement, advanced TNM stage, more malignant histological type, multiple-resistance to anti-cancer drugs, and reduced OS. ABCC3 expression may serve as a marker for MDR and predictor for poor clinical outcome of NSCLC. PMID:24176985

Representative Sampling: Follow-up of Spring 1972 and Spring 1973 Students. TEX-SIS FOLLOW-UP SC3.

ERIC Educational Resources Information Center

Wilkinson, Larry; And Others

This report presents the findings of a research study, conducted by the College of the Mainland (COM) as a subcontractor for Project FOLLOW-UP, designed to test the accuracy of random sampling and to measure non-response bias in mail surveys. In 1975, a computer-generated random sample of 500 students was drawn from a population of 1,256 students…

Trends and college-level characteristics associated with the non-medical use of prescription drugs among US college students from 1993 to 2001

PubMed Central

McCabe, Sean Esteban; West, Brady T.; Wechsler, Henry

2007-01-01

Aims The present study examines the prevalence trends and college-level characteristics associated with the non-medical use of prescription drugs (i.e. amphetamines, opioids, sedatives, tranquilizers) and illicit drug use among US college students between 1993 and 2001. Design Data were collected from self-administered mail surveys, sent to independent cross-sectional samples of college students from a nationally representative sample of 119 colleges in 4 years between 1993 and 2001. Setting Nationally representative 4-year US colleges and universities in 1993, 1997, 1999 and 2001. Participants Representative samples of 15 282, 14 428, 13 953 and 10 904 randomly selected college students at these colleges in 1993, 1997, 1999 and 2001, respectively. Findings The results indicate that life-time and 12-month prevalence rates of non-medical use of prescription drugs (NMPD) increased between 1993 and 2001. Specific college-level characteristics were found to be correlated positively (marijuana use) and negatively (historically black college status and commuter status) with NMPD, consistently across the four cross-sectional samples. Significant between-college variation in terms of trajectories in the prevalence of NMPD over time was found in hierarchical linear models, and selected college-level characteristics were not found to explain all of the variation in the trajectories, suggesting the need for further investigation of what determines between-college variance in the prevalence trends. Conclusions The findings of the present study suggest that continued monitoring of NMPD and illicit drug use among college students is needed and collegiate substance prevention programs should include efforts to reduce these drug use behaviors. PMID:17298654

Spatio-temporal dynamics of processing non-symbolic number: An ERP source localization study

PubMed Central

Hyde, Daniel C.; Spelke, Elizabeth S.

2013-01-01

Coordinated studies with adults, infants, and nonhuman animals provide evidence for two distinct systems of non-verbal number representation. The ‘parallel individuation’ system selects and retains information about 1–3 individual entities and the ‘numerical magnitude’ system establishes representations of the approximate cardinal value of a group. Recent ERP work has demonstrated that these systems reliably evoke functionally and temporally distinct patterns of brain response that correspond to established behavioral signatures. However, relatively little is known about the neural generators of these ERP signatures. To address this question, we targeted known ERP signatures of these systems, by contrasting processing of small versus large non-symbolic numbers, and used a source localization algorithm (LORETA) to identify their cortical origins. Early processing of small numbers, showing the signature effects of parallel individuation on the N1 (∼150 ms), was localized primarily to extrastriate visual regions. In contrast, qualitatively and temporally distinct processing of large numbers, showing the signatures of approximate number representation on the mid-latency P2p (∼200–250 ms), was localized primarily to right intraparietal regions. In comparison, mid-latency small number processing was localized to the right temporal-parietal junction and left-lateralized intraparietal regions. These results add spatial information to the emerging ERP literature documenting the process by which we represent number. Furthermore, these results substantiate recent claims that early attentional processes determine whether a collection of objects will be represented through parallel individuation or as an approximate numerical magnitude by providing evidence that downstream processing diverges to distinct cortical regions. PMID:21830257

Plasma serotonin in horses undergoing surgery for small intestinal colic

PubMed Central

Torfs, Sara C.; Maes, An A.; Delesalle, Catherine J.; Pardon, Bart; Croubels, Siska M.; Deprez, Piet

2015-01-01

This study compared serotonin concentrations in platelet poor plasma (PPP) from healthy horses and horses with surgical small intestinal (SI) colic, and evaluated their association with postoperative ileus, strangulation and non-survival. Plasma samples (with EDTA) from 33 horses with surgical SI colic were collected at several pre- and post-operative time points. Serotonin concentrations were determined using liquid-chromatography tandem mass spectrometry. Results were compared with those for 24 healthy control animals. The serotonin concentrations in PPP were significantly lower (P < 0.01) in pre- and post-operative samples from surgical SI colic horses compared to controls. However, no association with postoperative ileus or non-survival could be demonstrated at any time point. In this clinical study, plasma serotonin was not a suitable prognostic factor in horses with SI surgical colic. PMID:25694668

A Model for Predicting Behavioural Sleep Problems in a Random Sample of Australian Pre-Schoolers

ERIC Educational Resources Information Center

Hall, Wendy A.; Zubrick, Stephen R.; Silburn, Sven R.; Parsons, Deborah E.; Kurinczuk, Jennifer J.

2007-01-01

Behavioural sleep problems (childhood insomnias) can cause distress for both parents and children. This paper reports a model describing predictors of high sleep problem scores in a representative population-based random sample survey of non-Aboriginal singleton children born in 1995 and 1996 (1085 girls and 1129 boys) in Western Australia.…

Childhood Trauma and Psychiatric Disorders as Correlates of School Dropout in a National Sample of Young Adults

ERIC Educational Resources Information Center

Porche, Michelle V.; Fortuna, Lisa R.; Lin, Julia; Alegria, Margarita

2011-01-01

The effect of childhood trauma, psychiatric diagnoses, and mental health services on school dropout among U.S.-born and immigrant youth is examined using data from the Collaborative Psychiatric Epidemiology Surveys, a nationally representative probability sample of African Americans, Afro-Caribbeans, Asians, Latinos, and non-Latino Whites,…

Choosing non-redundant representative subsets of protein sequence data sets using submodular optimization.

PubMed

Libbrecht, Maxwell W; Bilmes, Jeffrey A; Noble, William Stafford

2018-04-01

Selecting a non-redundant representative subset of sequences is a common step in many bioinformatics workflows, such as the creation of non-redundant training sets for sequence and structural models or selection of "operational taxonomic units" from metagenomics data. Previous methods for this task, such as CD-HIT, PISCES, and UCLUST, apply a heuristic threshold-based algorithm that has no theoretical guarantees. We propose a new approach based on submodular optimization. Submodular optimization, a discrete analogue to continuous convex optimization, has been used with great success for other representative set selection problems. We demonstrate that the submodular optimization approach results in representative protein sequence subsets with greater structural diversity than sets chosen by existing methods, using as a gold standard the SCOPe library of protein domain structures. In this setting, submodular optimization consistently yields protein sequence subsets that include more SCOPe domain families than sets of the same size selected by competing approaches. We also show how the optimization framework allows us to design a mixture objective function that performs well for both large and small representative sets. The framework we describe is the best possible in polynomial time (under some assumptions), and it is flexible and intuitive because it applies a suite of generic methods to optimize one of a variety of objective functions. © 2018 Wiley Periodicals, Inc.

49 CFR 173.461 - Demonstration of compliance with tests.

Code of Federal Regulations, 2010 CFR

2010-10-01

...) Performance of tests with prototypes or samples of the specimens representing LSA-III, special form Class 7... to be tested, must be prepared as normally presented for transport. The use of non-radioactive...

PCDD/F and PCB in human serum of differently exposed population groups of an Italian city.

PubMed

Turrio-Baldassarri, Luigi; Abate, Vittorio; Battistelli, Chiara Laura; Carasi, Sergio; Casella, Marialuisa; Iacovella, Nicola; Indelicato, Annamaria; La Rocca, Cinzia; Scarcella, Carmelo; Alivernini, Silvia

2008-08-01

A chemical plant located in Brescia, an industrial city in North-Western Italy, produced polychlorobiphenyls (PCBs) during a 30-50 year period, causing widespread pollution of the surrounding agricultural area. This area contains several small farms, which principally produce veal meat for private consumption of the farmers' families. The pollution went undiscovered for many years, during which period contaminated food was regularly consumed. This paper reports the polychlorodibenzodioxin (PCDD), polychlorodibenzofuran (PCDF) and PCB levels of a serum sample pooled from the consumers of contaminated food, compared to six population groups of the city of Brescia. Four of these groups were selected in order to represent, respectively, the local general population and the residents of three zones of the polluted area, while the last two groups represented, respectively, the present and the former workers of the plant. One human milk sample from one of the consumers of contaminated food was also analyzed. Results show that the consumers of the contaminated food and the former workers of the plant display considerably higher levels than all other groups. The levels of general population and of all other groups were generally similar both to each other and to the range of literature values for unexposed populations. The respective contribution of PCDDs, PCDFs, mono-ortho and non-ortho PCBs (dioxin-like PCBs) to (Toxicity Equivalents) TEQ of the population groups of this study were also compared to literature data: the two groups with a high contamination level, together with the human milk sample, displayed a higher incidence of mono-ortho PCBs and a lower contribution of PCDD, possibly correlated with the source of contamination.

Birth-Order Effects in the Academically Talented.

ERIC Educational Resources Information Center

Parker, Wayne D.

1998-01-01

Birth-order position was studied among 828 academically talented sixth-grade students. When compared to census data, the sample was disproportionately composed of first-born students. However, this effect was largely explained by the covariate of family size, with small families over represented among the gifted. Other findings indicated no…

Too Many Friends: Social Integration, Network Cohesion and Adolescent Depressive Symptoms

ERIC Educational Resources Information Center

Falci, Christina; McNeely, Clea

2009-01-01

Using a nationally representative sample of adolescents, we examine associations among social integration (network size), network cohesion (alter-density), perceptions of social relationships (e.g., social support) and adolescent depressive symptoms. We find that adolescents with either too large or too small a network have higher levels of…

SMALL-COLUMN MICROCOSM FOR ASSESSING METHANE-STIMULATED VINYL CHLORIDE TRANSFORMATION IN AQUIFER SAMPLES. (R825689C051)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Emergence of superconductivity and magnetic ordering tuned by Fe-vacancy in alkali-metal Fe chalcogenides RbxFe2-ySe2

NASA Astrophysics Data System (ADS)

Kobayashi, Yoshiaki; Kototani, Shouhei; Itoh, Masayuki; Sato, Masatoshi

2014-12-01

Samples of RbxFe2-ySe2 exhibiting superconductivity [superconducting (SC) samples] undergo a phase-separation into two phases, a Fe-vacancy ordered phase with antiferromagnetic (AFM) transition at TN1~500 K (AFM1 phase) and a phase with little Fe- vacancy and SC transition at Tc~30 K (SC phase). The samples of RbxFe2-ySe2 exhibiting no SC behaviour (non-SC samples) are phase-separated into three phases, the AFM1 phase, another AFM phase with TN2 ~150 K (AFM2 phase), and a paramagnetic phase with no SC transitions (paramagnetic non-SC phase). In this paper, we present the experimental results of magnetic susceptibility, electrical resistivity, and NMR measurements on single crystals of RbxFe2-ySe2 to reveal physical properties of these co-existing phases in the SC and non-SC samples. The 87Rb and 77Se NMR spectra show that the Fe vacancy concentration is very small in the Fe planes of the SC phase, whereas the AFM2 and paramagnetic non-SC phases in non-SC samples have larger amount of Fe vacancies. The randomness induced by the Fe vacancy in the non-SC samples makes the AFM2 and paramagnetic non-SC phases insulating/semiconducting and magnetically active, resulting in the absence of the superconductivity in RbxFe2-ySe2.

Concentrations of antifouling biocides in sediment and mussel samples collected from Otsuchi bay, Japan.

PubMed

Harino, Hiroya; Yamamoto, Yoshikazu; Eguchi, Sayaka; Kawai, Shini'chiro; Kurokawa, Yuko; Arai, Takaomi; Ohji, Madoka; Okamura, Hideo; Miyazaki, Nobuyuki

2007-02-01

Organotin compounds (OTs) and representative booster biocides were measured in sediment and mussels from Otsuchi Bay, Japan. The mean amounts of tributyltin (TBT) and triphenyltin (TPT) compounds in sediment were 13 microg kg(-1) dry and 3 microg kg(-1) dry, respectively. Representative booster biocides (Sea-Nine 211, Diuron, Dichlofluanid, Irgarol 1501, M1, which is a degradation compound of Irgarol 1051, and Copper pyrithione) were also detected in sediment from Otsuchi Bay. OT concentrations were higher than those of the measured booster biocides. Otsuchi Bay was divided into four parts by cluster analysis based on OT concentrations in sediment sampled from the bay. These areas included the vicinity of a shipyard, a small fishing port, the closed inner area of the bay, and the mouth of the bay. Higher concentrations of TBT and TPT and a higher ratio of TBT to total BTs were observed in the vicinity of the shipyard. A higher concentration of TPT in comparison with TBT was detected in a small fishing port. Furthermore, OT concentrations in the mouth of the bay were higher than those in the closed-off section. OT concentrations in mussels decreased with distance from the shipyard. Otsuchi Bay was then divided into three parts by cluster analysis based on the concentrations of representative booster biocides found in the bay's sediment. These areas included the vicinity of a shipyard, a small fishing port, and other sites. Concentrations of Diuron and Irgarol 1051 in the vicinity of a shipyard and a small fishing port were dramatically high in comparison with the other sites. Copper pyrithione and Dichlofluanid in addition to Diuron and Irgarol 1051 were also detected in the area of a small fishing port. The concentrations of antifouling biocides were highest in the water in front of the shipyard and showed a marked decrease with distance from the shipyard.

Intrapopulational body size variation and cranial capacity variation in Middle Pleistocene humans: the Sima de los Huesos sample (Sierra de Atapuerca, Spain).

PubMed

Lorenzo, C; Carretero, J M; Arsuaga, J L; Gracia, A; Martínez, I

1998-05-01

A sexual dimorphism more marked than in living humans has been claimed for European Middle Pleistocene humans, Neandertals and prehistoric modern humans. In this paper, body size and cranial capacity variation are studied in the Sima de los Huesos Middle Pleistocene sample. This is the largest sample of non-modern humans found to date from one single site, and with all skeletal elements represented. Since the techniques available to estimate the degree of sexual dimorphism in small palaeontological samples are all unsatisfactory, we have used the bootstraping method to asses the magnitude of the variation in the Sima de los Huesos sample compared to modern human intrapopulational variation. We analyze size variation without attempting to sex the specimens a priori. Anatomical regions investigated are scapular glenoid fossa; acetabulum; humeral proximal and distal epiphyses; ulnar proximal epiphysis; radial neck; proximal femur; humeral, femoral, ulnar and tibial shaft; lumbosacral joint; patella; calcaneum; and talar trochlea. In the Sima de los Huesos sample only the humeral midshaft perimeter shows an unusual high variation (only when it is expressed by the maximum ratio, not by the coefficient of variation). In spite of that the cranial capacity range at Sima de los Huesos almost spans the rest of the European and African Middle Pleistocene range. The maximum ratio is in the central part of the distribution of modern human samples. Thus, the hypothesis of a greater sexual dimorphism in Middle Pleistocene populations than in modern populations is not supported by either cranial or postcranial evidence from Sima de los Huesos.

Analog system for computing sparse codes

DOEpatents

Rozell, Christopher John; Johnson, Don Herrick; Baraniuk, Richard Gordon; Olshausen, Bruno A.; Ortman, Robert Lowell

2010-08-24

A parallel dynamical system for computing sparse representations of data, i.e., where the data can be fully represented in terms of a small number of non-zero code elements, and for reconstructing compressively sensed images. The system is based on the principles of thresholding and local competition that solves a family of sparse approximation problems corresponding to various sparsity metrics. The system utilizes Locally Competitive Algorithms (LCAs), nodes in a population continually compete with neighboring units using (usually one-way) lateral inhibition to calculate coefficients representing an input in an over complete dictionary.

Holocene monsoon variability as resolved in small complex networks from palaeodata

NASA Astrophysics Data System (ADS)

Rehfeld, K.; Marwan, N.; Breitenbach, S.; Kurths, J.

2012-04-01

To understand the impacts of Holocene precipitation and/or temperature changes in the spatially extensive and complex region of Asia, it is promising to combine the information from palaeo archives, such as e.g. stalagmites, tree rings and marine sediment records from India and China. To this end, complex networks present a powerful and increasingly popular tool for the description and analysis of interactions within complex spatially extended systems in the geosciences and therefore appear to be predestined for this task. Such a network is typically constructed by thresholding a similarity matrix which in turn is based on a set of time series representing the (Earth) system dynamics at different locations. Looking into the pre-instrumental past, information about the system's processes and thus its state is available only through the reconstructed time series which -- most often -- are irregularly sampled in time and space. Interpolation techniques are often used for signal reconstruction, but they introduce additional errors, especially when records have large gaps. We have recently developed and extensively tested methods to quantify linear (Pearson correlation) and non-linear (mutual information) similarity in presence of heterogeneous and irregular sampling. To illustrate our approach we derive small networks from significantly correlated, linked, time series which are supposed to capture the underlying Asian Monsoon dynamics. We assess and discuss whether and where links and directionalities in these networks from irregularly sampled time series can be soundly detected. Finally, we investigate the role of the Northern Hemispheric temperature with respect to the correlation patterns and find that those derived from warm phases (e.g. Medieval Warm Period) are significantly different from patterns found in cold phases (e.g. Little Ice Age).

Cartilage biomarkers in the osteoarthropathy of alkaptonuria reveal low turnover and accelerated ageing.

PubMed

Taylor, Adam M; Hsueh, Ming-Feng; Ranganath, Lakshminarayan R; Gallagher, James A; Dillon, Jane P; Huebner, Janet L; Catterall, Jon B; Kraus, Virginia B

2017-01-01

Alkaptonuria (AKU) is a rare autosomal recessive disease resulting from a single enzyme deficiency in tyrosine metabolism. As a result, homogentisic acid cannot be metabolized, causing systemic increases. Over time, homogentisic acid polymerizes and deposits in collagenous tissues, leading to ochronosis. Typically, this occurs in joint cartilages, leading to an early onset, rapidly progressing osteoarthropathy. The aim of this study was to examine tissue turnover in cartilage affected by ochronosis and its role in disease initiation and progression. With informed patient consent, hip and knee cartilages were obtained at surgery for arthropathy due to AKU (n = 6; 2 knees/4 hips) and OA (n = 12; 5 knees/7 hips); healthy non-arthritic (non-OA n = 6; 1 knee/5 hips) cartilages were obtained as waste from trauma surgery. We measured cartilage concentrations (normalized to dry weight) of racemized aspartate, GAG, COMP and deamidated COMP (D-COMP). Unpaired AKU, OA and non-OA samples were compared by non-parametric Mann-Whitney U test. Despite more extractable total protein being obtained from AKU cartilage than from OA or non-OA cartilage, there was significantly less extractable GAG, COMP and D-COMP in AKU samples compared with OA and non-OA comparators. Racemized Asx (aspartate and asparagine) was significantly enriched in AKU cartilage compared with in OA cartilage. These novel data represent the first examination of cartilage matrix components in a sample of patients with AKU, representing almost 10% of the known UK alkaptonuric population. Compared with OA and non-OA, AKU cartilage demonstrates a very low turnover state and has low levels of extractable matrix proteins. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Cartilage biomarkers in the osteoarthropathy of alkaptonuria reveal low turnover and accelerated ageing

PubMed Central

Hsueh, Ming-Feng; Ranganath, Lakshminarayan R.; Gallagher, James A.; Dillon, Jane P.; Huebner, Janet L.; Catterall, Jon B.; Kraus, Virginia B.

2017-01-01

Objective. Alkaptonuria (AKU) is a rare autosomal recessive disease resulting from a single enzyme deficiency in tyrosine metabolism. As a result, homogentisic acid cannot be metabolized, causing systemic increases. Over time, homogentisic acid polymerizes and deposits in collagenous tissues, leading to ochronosis. Typically, this occurs in joint cartilages, leading to an early onset, rapidly progressing osteoarthropathy. The aim of this study was to examine tissue turnover in cartilage affected by ochronosis and its role in disease initiation and progression. Methods. With informed patient consent, hip and knee cartilages were obtained at surgery for arthropathy due to AKU (n = 6; 2 knees/4 hips) and OA (n = 12; 5 knees/7 hips); healthy non-arthritic (non-OA n = 6; 1 knee/5 hips) cartilages were obtained as waste from trauma surgery. We measured cartilage concentrations (normalized to dry weight) of racemized aspartate, GAG, COMP and deamidated COMP (D-COMP). Unpaired AKU, OA and non-OA samples were compared by non-parametric Mann–Whitney U test. Results. Despite more extractable total protein being obtained from AKU cartilage than from OA or non-OA cartilage, there was significantly less extractable GAG, COMP and D-COMP in AKU samples compared with OA and non-OA comparators. Racemized Asx (aspartate and asparagine) was significantly enriched in AKU cartilage compared with in OA cartilage. Conclusions. These novel data represent the first examination of cartilage matrix components in a sample of patients with AKU, representing almost 10% of the known UK alkaptonuric population. Compared with OA and non-OA, AKU cartilage demonstrates a very low turnover state and has low levels of extractable matrix proteins. PMID:28028161

UNC-Utah NA-MIC framework for DTI fiber tract analysis.

PubMed

Verde, Audrey R; Budin, Francois; Berger, Jean-Baptiste; Gupta, Aditya; Farzinfar, Mahshid; Kaiser, Adrien; Ahn, Mihye; Johnson, Hans; Matsui, Joy; Hazlett, Heather C; Sharma, Anuja; Goodlett, Casey; Shi, Yundi; Gouttard, Sylvain; Vachet, Clement; Piven, Joseph; Zhu, Hongtu; Gerig, Guido; Styner, Martin

2014-01-01

Diffusion tensor imaging has become an important modality in the field of neuroimaging to capture changes in micro-organization and to assess white matter integrity or development. While there exists a number of tractography toolsets, these usually lack tools for preprocessing or to analyze diffusion properties along the fiber tracts. Currently, the field is in critical need of a coherent end-to-end toolset for performing an along-fiber tract analysis, accessible to non-technical neuroimaging researchers. The UNC-Utah NA-MIC DTI framework represents a coherent, open source, end-to-end toolset for atlas fiber tract based DTI analysis encompassing DICOM data conversion, quality control, atlas building, fiber tractography, fiber parameterization, and statistical analysis of diffusion properties. Most steps utilize graphical user interfaces (GUI) to simplify interaction and provide an extensive DTI analysis framework for non-technical researchers/investigators. We illustrate the use of our framework on a small sample, cross sectional neuroimaging study of eight healthy 1-year-old children from the Infant Brain Imaging Study (IBIS) Network. In this limited test study, we illustrate the power of our method by quantifying the diffusion properties at 1 year of age on the genu and splenium fiber tracts.

"Role magnets"? An empirical investigation of popularity trajectories for life-course persistent individuals during adolescence.

PubMed

Young, Jacob T N

2014-01-01

Recent scholarship has focused on the role of social status in peer groups to explain the fact that delinquency is disproportionately committed during adolescence. Yet, the precise mechanism linking adolescence, social status, and antisocial behavior is not well understood. Dual-taxonomy postulates a testable mechanism that links the sudden increase in risky behavior among adolescents to the social magnetism of a small group of persistently antisocial individuals, referred to here as the "role magnet" hypothesis. Using semi-parametric group-based trajectory modeling and growth-curve modeling, this study provides the first test of this hypothesis by examining physical violence and popularity trajectories for 1,845 male respondents age 11-32 from a nationally representative sample (54 % non-Hispanic White; 21 % non-Hispanic African American; 17 % Hispanic; 8 % Asian). Individuals assigned to a "chronic violence" trajectory group showed consistently lower average levels of popularity from 11 to 19. But, these same individuals experienced increases in popularity during early adolescence and subsequent declines in late adolescence. These findings are linked to current research examining social status as a mechanism generating antisocial behavior during adolescence and the consequences of delayed entry into adult roles.

UNC-Utah NA-MIC framework for DTI fiber tract analysis

PubMed Central

Verde, Audrey R.; Budin, Francois; Berger, Jean-Baptiste; Gupta, Aditya; Farzinfar, Mahshid; Kaiser, Adrien; Ahn, Mihye; Johnson, Hans; Matsui, Joy; Hazlett, Heather C.; Sharma, Anuja; Goodlett, Casey; Shi, Yundi; Gouttard, Sylvain; Vachet, Clement; Piven, Joseph; Zhu, Hongtu; Gerig, Guido; Styner, Martin

2014-01-01

Diffusion tensor imaging has become an important modality in the field of neuroimaging to capture changes in micro-organization and to assess white matter integrity or development. While there exists a number of tractography toolsets, these usually lack tools for preprocessing or to analyze diffusion properties along the fiber tracts. Currently, the field is in critical need of a coherent end-to-end toolset for performing an along-fiber tract analysis, accessible to non-technical neuroimaging researchers. The UNC-Utah NA-MIC DTI framework represents a coherent, open source, end-to-end toolset for atlas fiber tract based DTI analysis encompassing DICOM data conversion, quality control, atlas building, fiber tractography, fiber parameterization, and statistical analysis of diffusion properties. Most steps utilize graphical user interfaces (GUI) to simplify interaction and provide an extensive DTI analysis framework for non-technical researchers/investigators. We illustrate the use of our framework on a small sample, cross sectional neuroimaging study of eight healthy 1-year-old children from the Infant Brain Imaging Study (IBIS) Network. In this limited test study, we illustrate the power of our method by quantifying the diffusion properties at 1 year of age on the genu and splenium fiber tracts. PMID:24409141

Retrospective analysis of bevacizumab-induced hypertension and clinical outcome in patients with colorectal cancer and lung cancer.

PubMed

Nakaya, Aya; Kurata, Takayasu; Yokoi, Takashi; Iwamoto, Shigeyoshi; Torii, Yoshitaro; Katashiba, Yuichi; Ogata, Makoto; Hamada, Madoka; Kon, Masanori; Nomura, Shosaku

2016-07-01

Bevacizumab(Avastin(®) ), a humanized therapeutic monoclonal antibody that targets vascular endothelial growth factor, is widely used in cancer treatment. Patients who are treated with bevacizumab have an increased risk of developing systemic hypertension. However, the relationship between bevacizumab-induced hypertension and clinical outcome remains unclear. We aimed to evaluate the effect of bevacizumab-induced hypertension in terms of prognosis in patients with colorectal cancer and non-small cell lung cancer. The study included 632 patients, 317 patients with non-small cell lung cancer and 315 patients with colorectal cancer. All patients were treated with bevacizumab in combination with standard chemotherapy protocols, between April 2007 and December 2014. Blood pressure was measured before each treatment cycle. In the patient group with colorectal cancer, treated with bevacizumab, Grade 2-3 hypertension was present in 27.6%. In hypertensive patients with colorectal cancer, median overall survival was 42.6 months, compared with 20.6 months for normotensive patients in this group (P = 0.00071). In the patient group with non-small cell lung cancer, treated with bevacizumab, Grade 2-3 hypertension was present in 20.5%. In hypertensive patients with non-small cell lung cancer, median overall survival was 43.0 months, compared with 26.3 months for normotensive patients in this group (P = 0.00451). Patients who developed hypertension during treatment with bevacizumab for colorectal cancer and non-small cell lung cancer had significantly prolonged overall survival when compared with normotensive patients. Bevacizumab-induced hypertension may represent a biomarker for clinical benefit in cancer patients treated with bevacizumab. © 2016 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

A Research Communication Brief: Gluten Analysis in Beef Samples Collected Using a Rigorous, Nationally Representative Sampling Protocol Confirms That Grain-Finished Beef Is Naturally Gluten-Free.

PubMed

McNeill, Shalene H; Cifelli, Amy M; Roseland, Janet M; Belk, Keith E; Woerner, Dale R; Gehring, Kerri B; Savell, Jeffrey W; Brooks, J Chance; Thompson, Leslie D

2017-08-25

Knowing whether or not a food contains gluten is vital for the growing number of individuals with celiac disease and non-celiac gluten sensitivity. Questions have recently been raised about whether beef from conventionally-raised, grain-finished cattle may contain gluten. To date, basic principles of ruminant digestion have been cited in support of the prevailing expert opinion that beef is inherently gluten-free. For this study, gluten analysis was conducted in beef samples collected using a rigorous nationally representative sampling protocol to determine whether gluten was present. The findings of our research uphold the understanding of the principles of gluten digestion in beef cattle and corroborate recommendations that recognize beef as a naturally gluten-free food.

A nonlethal sampling method to obtain, generate and assemble whole blood transcriptomes from small, wild mammals.

PubMed

Huang, Zixia; Gallot, Aurore; Lao, Nga T; Puechmaille, Sébastien J; Foley, Nicole M; Jebb, David; Bekaert, Michaël; Teeling, Emma C

2016-01-01

The acquisition of tissue samples from wild populations is a constant challenge in conservation biology, especially for endangered species and protected species where nonlethal sampling is the only option. Whole blood has been suggested as a nonlethal sample type that contains a high percentage of bodywide and genomewide transcripts and therefore can be used to assess the transcriptional status of an individual, and to infer a high percentage of the genome. However, only limited quantities of blood can be nonlethally sampled from small species and it is not known if enough genetic material is contained in only a few drops of blood, which represents the upper limit of sample collection for some small species. In this study, we developed a nonlethal sampling method, the laboratory protocols and a bioinformatic pipeline to sequence and assemble the whole blood transcriptome, using Illumina RNA-Seq, from wild greater mouse-eared bats (Myotis myotis). For optimal results, both ribosomal and globin RNAs must be removed before library construction. Treatment of DNase is recommended but not required enabling the use of smaller amounts of starting RNA. A large proportion of protein-coding genes (61%) in the genome were expressed in the blood transcriptome, comparable to brain (65%), kidney (63%) and liver (58%) transcriptomes, and up to 99% of the mitogenome (excluding D-loop) was recovered in the RNA-Seq data. In conclusion, this nonlethal blood sampling method provides an opportunity for a genomewide transcriptomic study of small, endangered or critically protected species, without sacrificing any individuals. © 2015 John Wiley & Sons Ltd.

38 CFR 74.4 - Who does CVE consider to control a veteran-owned small business?

Code of Federal Regulations, 2010 CFR

2010-07-01

... the exception of a spouse or personal caregiver who represents a severely disabled veteran owner, no such non-veteran or immediate family member may: (1) Exercise actual control or have the power to... firm to an immediate family member within 2 years prior to the application and remain involved in the...

Vitamin D receptor gene and osteoporosis - author`s response

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

Looney, J.E.; Yoon, Hyun Koo; Fischer, M.

1996-04-01

We appreciate the comments of Dr. Nguyen et al. about our recent study, but we disagree with their suggestion that the lack of an association between low bone density and the BB VDR genotype, which we reported, is an artifact generated by the small sample size. Furthermore, our results are consistent with similar conclusions reached by a number of other investigators, as recently reported by Peacock. Peacock states {open_quotes}Taken as a whole, the results of studies outlined ... indicate that VDR alleles, cannot account for the major part of the heritable component of bone density as indicated by Morrison etmore » al.{close_quotes}. The majority of the 17 studies cited in this editorial could not confirm an association between the VDR genotype and the bone phenotype. Surely one cannot criticize this combined work as representing an artifact because of a too small sample size. We do not dispute the suggestion by Nguyen et al. that large sample sizes are required to analyze small biological effects. This is evident in both Peacock`s summary and in their own bone density studies. We did not design our study with a larger sample size because, based on the work of Morrison et al., we had hypothesized a large biological effect; large sample sizes are only needed for small biological effects. 4 refs.« less

SPR Biosensors in Direct Molecular Fishing: Implications for Protein Interactomics.

PubMed

Florinskaya, Anna; Ershov, Pavel; Mezentsev, Yuri; Kaluzhskiy, Leonid; Yablokov, Evgeniy; Medvedev, Alexei; Ivanov, Alexis

2018-05-18

We have developed an original experimental approach based on the use of surface plasmon resonance (SPR) biosensors, applicable for investigation of potential partners involved in protein⁻protein interactions (PPI) as well as protein⁻peptide or protein⁻small molecule interactions. It is based on combining a SPR biosensor, size exclusion chromatography (SEC), mass spectrometric identification of proteins (LC-MS/MS) and direct molecular fishing employing principles of affinity chromatography for isolation of potential partner proteins from the total lysate of biological samples using immobilized target proteins (or small non-peptide compounds) as ligands. Applicability of this approach has been demonstrated within the frame of the Human Proteome Project (HPP) and PPI regulation by a small non-peptide biologically active compound, isatin.

Marijuana and tobacco co-use among a nationally representative sample of US pregnant and non-pregnant women: 2005-2014 National Survey on Drug Use and Health findings.

PubMed

Coleman-Cowger, Victoria H; Schauer, Gillian L; Peters, Erica N

2017-08-01

Marijuana and tobacco are the most commonly used illicit and licit drugs during pregnancy. This study aimed to examine a nationally representative sample of US pregnant women and to: (1) determine the prevalence of past month marijuana and tobacco co-use, (2) identify characteristics that distinguish marijuana and tobacco co-users from users of marijuana only, tobacco only, or neither, and (3) compare characteristics that differ between pregnant and non-pregnant co-users of marijuana and tobacco. Data were obtained from 497,218 US women (8721 pregnant) ages 12-49 who participated in the 2005-2014 National Survey on Drug Use and Health. Prevalence and demographic and substance use characteristics were compared across groups using weighted estimates and chi-squared tests. Multinomial logistic regression identified demographic and substance use correlates of co-use. Co-use among pregnant and non-pregnant women was significantly more prevalent than marijuana-only use but was less common than tobacco-only use. In unadjusted frequencies, pregnant co-users significantly differed from non-pregnant co-users across several domains. Among pregnant women, multivariate correlates of co-use of tobacco and marijuana vs. tobacco-only use were ages 12-17, non-Hispanic black race, Hispanic ethnicity, and past month polytobacco, any alcohol, and other drug use (all adjusted odds ratios≥2.0). In this first examination of the prevalence and correlates of co-use of marijuana and tobacco among a nationally representative group of pregnant women, pregnant co-users were more likely to report other high risk behaviors compared with non-pregnant co-users and users of a single substance, suggesting disparities worthy of further investigation. Copyright © 2017 Elsevier B.V. All rights reserved.

Adaptive Importance Sampling for Control and Inference

NASA Astrophysics Data System (ADS)

Kappen, H. J.; Ruiz, H. C.

2016-03-01

Path integral (PI) control problems are a restricted class of non-linear control problems that can be solved formally as a Feynman-Kac PI and can be estimated using Monte Carlo sampling. In this contribution we review PI control theory in the finite horizon case. We subsequently focus on the problem how to compute and represent control solutions. We review the most commonly used methods in robotics and control. Within the PI theory, the question of how to compute becomes the question of importance sampling. Efficient importance samplers are state feedback controllers and the use of these requires an efficient representation. Learning and representing effective state-feedback controllers for non-linear stochastic control problems is a very challenging, and largely unsolved, problem. We show how to learn and represent such controllers using ideas from the cross entropy method. We derive a gradient descent method that allows to learn feed-back controllers using an arbitrary parametrisation. We refer to this method as the path integral cross entropy method or PICE. We illustrate this method for some simple examples. The PI control methods can be used to estimate the posterior distribution in latent state models. In neuroscience these problems arise when estimating connectivity from neural recording data using EM. We demonstrate the PI control method as an accurate alternative to particle filtering.

Radioactivity Registered With a Small Number of Events

NASA Astrophysics Data System (ADS)

Zlokazov, Victor; Utyonkov, Vladimir

2018-02-01

The synthesis of superheavy elements asks for the analysis of low statistics experimental data presumably obeying an unknown exponential distribution and to take the decision whether they originate from one source or have admixtures. Here we analyze predictions following from non-parametrical methods, employing only such fundamental sample properties as the sample mean, the median and the mode.

A non-destructive method for quantifying small-diameter woody biomass in southern pine forests

Treesearch

D. Andrew Scott; Rick Stagg; Morris Smith

2006-01-01

Quantifying the impact of silvicultural treatments on woody understory vegetation largely has been accomplished by destructive sampling or through estimates of frequency and coverage. In studies where repeated measures of understory biomass across large areas are needed, destructive sampling and percent cover estimates are not satisfactory. For example, estimates of...

Ellipsometer

NASA Technical Reports Server (NTRS)

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

1997-01-01

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

Importance of Religion and Spirituality in the Lives of African Americans, Caribbean Blacks and Non-Hispanic Whites

ERIC Educational Resources Information Center

Taylor, Robert Joseph; Chatters, Linda M.

2010-01-01

This study examined the importance of spirituality and religion in daily life (i.e., only religion, only spirituality, both religion and spirituality, and neither religion nor spirituality) among a nationally representative sample of African Americans, Caribbean Blacks and non-Hispanic Whites. A majority in each group felt they were both important…

Job Quality in Non-Profit Organizations. CPRN Research Series on Human Resources in the Non-Profit Sector.

ERIC Educational Resources Information Center

McMullen, Kathryn; Schellenberg, Grant

The quality of jobs in nonprofit organizations in Canada was examined through a review of data from Canada's Workplace and Employer Survey, which collected data from a nationally representative sample of Canadian workplaces and paid employees in those workplaces. Key findings of the analysis were as follows: (1) overall, compared to the for-profit…

Post-translational control of transcription factors: methylation ranks highly.

PubMed

Carr, Simon M; Poppy Roworth, A; Chan, Cheryl; La Thangue, Nicholas B

2015-12-01

Methylation of lysine and arginine residues on histones has long been known to determine both chromatin structure and gene expression. In recent years, the methylation of non-histone proteins has emerged as a prevalent modification which impacts on diverse processes such as cell cycle control, DNA repair, senescence, differentiation, apoptosis and tumourigenesis. Many of these non-histone targets represent transcription factors, cell signalling molecules and tumour suppressor proteins. Evidence now suggests that the dysregulation of methyltransferases, demethylases and reader proteins is involved in the development of many diseases, including cancer, and several of these proteins represent potential therapeutic targets for small molecule compounds, fuelling a recent surge in chemical inhibitor design. Such molecules will greatly help us to understand the role of methylation in both health and disease. © 2015 FEBS.

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

PubMed

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

2013-02-01

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

Discovery and Validation of Predictive Biomarkers of Survival for Non-small Cell Lung Cancer Patients Undergoing Radical Radiotherapy: Two Proteins With Predictive Value

PubMed Central

Walker, Michael J.; Zhou, Cong; Backen, Alison; Pernemalm, Maria; Williamson, Andrew J.K.; Priest, Lynsey J.C.; Koh, Pek; Faivre-Finn, Corinne; Blackhall, Fiona H.; Dive, Caroline; Whetton, Anthony D.

2015-01-01

Lung cancer is the most frequent cause of cancer-related death world-wide. Radiotherapy alone or in conjunction with chemotherapy is the standard treatment for locally advanced non-small cell lung cancer (NSCLC). Currently there is no predictive marker with clinical utility to guide treatment decisions in NSCLC patients undergoing radiotherapy. Identification of such markers would allow treatment options to be considered for more effective therapy. To enable the identification of appropriate protein biomarkers, plasma samples were collected from patients with non-small cell lung cancer before and during radiotherapy for longitudinal comparison following a protocol that carries sufficient power for effective discovery proteomics. Plasma samples from patients pre- and during radiotherapy who had survived > 18 mo were compared to the same time points from patients who survived < 14 mo using an 8 channel isobaric tagging tandem mass spectrometry discovery proteomics platform. Over 650 proteins were detected and relatively quantified. Proteins which showed a change during radiotherapy were selected for validation using an orthogonal antibody-based approach. Two of these proteins were verified in a separate patient cohort: values of CRP and LRG1 combined gave a highly significant indication of extended survival post one week of radiotherapy treatment. PMID:26425690

Screening Cereals Quality by Electronic Nose: the Example of Mycotoxins Naturally Contaminated Maize and Durum Wheat

NASA Astrophysics Data System (ADS)

Campagnoli, Anna; Dell'Orto, Vittorio; Savoini, Giovanni; Cheli, Federica

2009-05-01

Mycotoxins represent an heterogeneous group of toxic compounds from fungi metabolism. Due to the frequent occurrence of mycotoxins in cereals commodities the develop of cost/effective screening methods represent an important topic to ensure food and feed safety. In the presented study a commercial electronic nose constituted by ten MOS (Metal Oxide Sensors) was applied to verify the possibility of discriminating between mycotoxins contaminated and non-contaminated cereals. The described analytical approach was able to discriminate contaminated and non-contaminated samples both in the case of aflatoxins infected maize and deoxynivalenol infected durum wheat samples. In the case of maize data two sensors from the array revealed a partial relation with the level of aflatoxins. These results could be promising for a further improvement of electronic nose application in order to develop a semi-quantitative screening approach to mycotoxins contamination.

Non-invasive NMR stratigraphy of a multi-layered artefact: an ancient detached mural painting.

PubMed

Di Tullio, Valeria; Capitani, Donatella; Presciutti, Federica; Gentile, Gennaro; Brunetti, Brunetto Giovanni; Proietti, Noemi

2013-10-01

NMR stratigraphy was used to investigate in situ, non-destructively and non-invasively, the stratigraphy of hydrogen-rich layers of an ancient Nubian detached mural painting. Because of the detachment procedure, a complex multi-layered artefact was obtained, where, besides layers of the original mural painting, also the materials used during the procedure all became constitutive parts of the artefact. NMR measurements in situ enabled monitoring of the state of conservation of the artefact and planning of minimum representative sampling to validate results obtained in situ by solid-state NMR analysis of the samples. This analysis enabled chemical characterization of all organic materials. Use of reference compounds and prepared specimens assisted data interpretation.

Chemical Characterization of an Envelope B/D Sample from Hanford Tank 241-AZ-102

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

Hay, M.S.

2000-08-23

A sample from Hanford waste tank 241-AZ-102 was received at the Savannah River Technology Center (SRTC) and chemically characterized. The sample containing supernate and a small amount of sludge solids was analyzed as-received. The filtered supernatant liquid, the total dried solids of the sample, and the washed insoluble solids obtained from filtration of the sample were analyzed. A mass balance calculation of the three fractions of the sample analyzed indicate the analytical results appear relatively self-consistent for major components of the sample. However, some inconsistency was observed between results were more than one method of determination was employed and formore » species present in low concentrations. The actinides isotopes, plutonium, americium, and curium, present analytical challenges due to the low concentration of these species and the potential for introduction of small amounts of contamination during sampling handling resulting in large uncertainties. A direct comparison to previous analyses of material from tank 241-AZ-102 showed good agreement with the filtered supernatant liquid. However, the comparison of solids data showed poor agreement. The poor agreement shown between the current results for the solids samples and previous analyses most likely results from the uncertainties associated with obtaining small solids samples from a large non-homogenized waste tank.« less

Correction of Population Stratification in Large Multi-Ethnic Association Studies

PubMed Central

Serre, David; Montpetit, Alexandre; Paré, Guillaume; Engert, James C.; Yusuf, Salim; Keavney, Bernard; Hudson, Thomas J.; Anand, Sonia

2008-01-01

Background The vast majority of genetic risk factors for complex diseases have, taken individually, a small effect on the end phenotype. Population-based association studies therefore need very large sample sizes to detect significant differences between affected and non-affected individuals. Including thousands of affected individuals in a study requires recruitment in numerous centers, possibly from different geographic regions. Unfortunately such a recruitment strategy is likely to complicate the study design and to generate concerns regarding population stratification. Methodology/Principal Findings We analyzed 9,751 individuals representing three main ethnic groups - Europeans, Arabs and South Asians - that had been enrolled from 154 centers involving 52 countries for a global case/control study of acute myocardial infarction. All individuals were genotyped at 103 candidate genes using 1,536 SNPs selected with a tagging strategy that captures most of the genetic diversity in different populations. We show that relying solely on self-reported ethnicity is not sufficient to exclude population stratification and we present additional methods to identify and correct for stratification. Conclusions/Significance Our results highlight the importance of carefully addressing population stratification and of carefully “cleaning” the sample prior to analyses to obtain stronger signals of association and to avoid spurious results. PMID:18196181

Laser capture microdissection tailored to type 1 diabetes mellitus research.

PubMed

Szulawski, Robert; Nakazawa, Masato; McCall, Kelly D; James, Calvin B L; Schwartz, Frank L

2016-01-01

RNA isolation from pancreatic islets poses unique challenges. Here, we present a reproducible means of obtaining high-quality RNA from juvenile rodent islets in sufficient quantities for use in ex vivo expression studies. Tissue was extracted from female non-obese diabetic (NOD) toll-like receptor 3 (TLR3)(+/+) and (TLR3)(-/-) mice in the pre-diabetic stage. Samples were frozen in liquid nitrogen, sectioned, fixed in a highly alcoholic solution, and stained with an alcoholic cresyl violet (CV) solution. Rehydration of the fixed sections was minimized. Islets were identified visually and isolated with the Leica LMD6000 laser capture microdissection (LCM) system to yield samples highly enriched in islet RNA. Real time qPCR was performed on the islet cDNA using probes for CXC chemokine ligand 10 (CXCL10), an inflammatory marker that plays a critical role in the pathogenesis of type 1 diabetes mellitus (TIDM). This method represents an improvement over currently described LCM techniques for rodent pancreatic islets and makes feasible expression studies using small amounts of starting tissue without the need for RNA pre-amplification. This has immediate implications for ongoing TIDM studies using the NOD mouse.

Micron-Scale Differential Scanning Calorimeter on a Chip

DOEpatents

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

1998-06-30

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

Paleoecological Calibration In Central Guatemala: Modern Pollen Rain From Bryophyte Polsters And Surface Sediments

NASA Astrophysics Data System (ADS)

Finkelstein, S. A.; Avendano, C. E.; Cowling, S. A.

2009-05-01

Paleoecology requires understanding the correspondences between modern pollen rain and local-regional vegetation, in order to develop accurate paleovegetation reconstructions. Paleoecology in Guatemala has been developed largely over decades in the northern lowlands in close relationship with Classic Maya archaeology, where paleoenvironmental reconstructions have been made mainly through the use of fossil pollen. Scarcity of calibration studies in the Mesoamerican region however remains evident; nevertheless, they are necessary to produce reliable reconstructions. We present calibration pollen data from two locations in Central Guatemala: Lachua Lowlands and Purulha Highlands. Pollen spectra were analyzed from surface sediments samples (SS) from a lake and a small pond in Lachua, a river floodplain and a lake shore in Purulha. Bryophyte polsters samples (BP) were collected from the interior of minimally disturbed forests in both Lachua (rain forest) and Purulha (cloud forest). Pollen spectra between SS and BP differed in both locations. Analysis per location indicates that SS were more similar for Purulha, as compared to Lachua. Combined analysis of locations indicates that SS from both locations were related to anemophilous taxa - great production of pollen quantities that has high dispersion capacities-. This provides evidence that the pollen signal from SS is probably more regional than local. BP from Lachua and Purulha differed notably in their pollen signal, each location containing local taxa, tropical and temperate respectively. Some temperate anemophilous taxa were better represented in Lachua than in Purulha. Purulha SS were similar, and contained more taxa related to disturbance and anemophilous taxa. The arboreal pollen (AP) to non-arboreal (NAP) ratio (AP/NAP) of both SS and BP corresponded with the tree- prevalent landscape in Lachua. The SS AP/NAP ratio represented the deforested landscape of the river floodplain and lake environments in Purulha, while for BP the extensive forest cover from the cloud forest was represented. Comparison of SS with BP provides foundation to understand better the pollen signal recorded in the sedimentary record, since BP pollen signal bring information about what is not represented. The calibration analysis that we present brings in-depth exploration of pollen-vegetation relationships and represents an important contribution for paleoecological research in Guatemala.

Cognitive and Academic Abilities Associated with Symptoms of Attention-Deficit/Hyperactivity Disorder: A Comparison between Subtypes in a Greek Non-Clinical Sample

ERIC Educational Resources Information Center

Papaioannou, Sophia; Mouzaki, Angeliki; Sideridis, Georgios D.; Antoniou, Foteini; Padeliadu, Suzanna; Simos, Panagiotis G.

2016-01-01

The study assessed cognitive and academic performance of children demonstrating teacher-rated ADHD-related symptoms (Inattention [IA] and/or Hyperactivity/Impulsivity [H/I]) in a representative sample of, largely untreated, Greek elementary school students (N?=?923). A battery of tests assessing short-term memory (STM), sustained attention,…

Species composition, diversity and relative abundance of amphibians in forests and non-forest habitats on Langkawi Island, Peninsular Malaysia

NASA Astrophysics Data System (ADS)

Nur Johana, J.; Muzzneena, A. M.; Grismer, L. L.; Norhayati, A.

2016-11-01

Anurans on Langkawi Island, Peninsular Malaysia exhibit variation in their habits and forms, ranging from small (SVL < 25 mm) to large (SVL > 150 mm), and occupy a range of habitats, such as riverine forests, agricultural fields, peat swamps, and lowland and upland dipterocarp forests. These variations provide a platform to explore species diversity, distribution, abundance, microhabitat, and other ecological parameters to understand the distribution patterns and to facilitate conservation and management of sensitive or important species and areas. The objective of this study was to evaluate the diversity and distribution of anuran species in different types of habitat on Langkawi Island. Specimens were collected based on active sampling using the Visual Encounter Survey (VES) method. We surveyed anuran species inhabiting seven types of habitat, namely agriculture (AG), coastal (CL), forest (FT), pond (PD), mangrove (MG), riparian forest (RF) and river (RV). A total of 775 individuals were sampled from all localities, representing 23 species from 12 genera and included all six families of frogs in Malaysia. FT and RF showed high values of Shannon Index, H', 2.60 and 2.38, respectively, followed by the other types of habitat, CL (1.82), RV (1.71), MG (1.56), PD (1.54), and AG (1.53). AG had the highest abundance (156 individuals) compared to other habitat types. Based on Cluster Analysis by using Jaccard coefficient (UPGMA), two groups can be clearly seen and assigned as forested species group (FT and RF) and species associating with human activity (AG, CL, PD, MG and RV). Forest species group is more diverse compared to non-forest group. Nevertheless, non-forest species are found in abundance, highlighting the relevance of these disturbed habitats in supporting the amphibians.

State of the Art of Language Learning Design Using Mobile Technology: Sample Apps and Some Critical Reflection

ERIC Educational Resources Information Center

Bárcena, Elena; Read, Timothy; Underwood, Joshua; Obari, Hiroyuki; Cojocnean, Diana; Koyama, Toshiko; Pareja-Lora, Antonio; Calle, Cristina; Pomposo, Lourdes; Talaván, Noa; Ávila-Cabrera, José; Ibañez, Ana; Vermeulen, Anna; Jordano, María; Arús-Hita, Jorge; Rodríguez, Pilar; Castrillo, María Dolores; Kétyi, Andras; Selwood, Jaime; Gaved, Mark; Kukulska-Hulme, Agnes

2015-01-01

In this paper, experiences from different research groups illustrate the state-of-the-art of Mobile Assisted Language Learning (henceforth, MALL) in formal and non-formal education. These research samples represent recent and on-going progress made in the field of MALL at an international level and offer encouragement for practitioners who are…

The future of Stardust science

NASA Astrophysics Data System (ADS)

Westphal, A. J.; Bridges, J. C.; Brownlee, D. E.; Butterworth, A. L.; de Gregorio, B. T.; Dominguez, G.; Flynn, G. J.; Gainsforth, Z.; Ishii, H. A.; Joswiak, D.; Nittler, L. R.; Ogliore, R. C.; Palma, R.; Pepin, R. O.; Stephan, T.; Zolensky, M. E.

2017-09-01

Recent observations indicate that >99% of the small bodies in the solar system reside in its outer reaches—in the Kuiper Belt and Oort Cloud. Kuiper Belt bodies are probably the best-preserved representatives of the icy planetesimals that dominated the bulk of the solid mass in the early solar system. They likely contain preserved materials inherited from the protosolar cloud, held in cryogenic storage since the formation of the solar system. Despite their importance, they are relatively underrepresented in our extraterrestrial sample collections by many orders of magnitude ( 1013 by mass) as compared with the asteroids, represented by meteorites, which are composed of materials that have generally been strongly altered by thermal and aqueous processes. We have only begun to scratch the surface in understanding Kuiper Belt objects, but it is already clear that the very limited samples of them that we have in our laboratories hold the promise of dramatically expanding our understanding of the formation of the solar system. Stardust returned the first samples from a known small solar system body, the Jupiter-family comet 81P/Wild 2, and, in a separate collector, the first solid samples from the local interstellar medium. The first decade of Stardust research resulted in more than 142 peer-reviewed publications, including 15 papers in Science. Analyses of these amazing samples continue to yield unexpected discoveries and to raise new questions about the history of the early solar system. We identify nine high-priority scientific objectives for future Stardust analyses that address important unsolved problems in planetary science.

MicroRNA-1285-5p influences the proliferation and metastasis of non-small-cell lung carcinoma cells via downregulating CDH1 and Smad4.

PubMed

Zhou, Shixia; Zhang, Zhongmian; Zheng, Pengyuan; Zhao, Wenchao; Han, Na

2017-06-01

Abnormal expression of microRNAs has been reported to regulate gene expression and cancer cell growth, invasion, and migration. Recently, upregulation of hsa-miR-1285 was demonstrated in bronchoalveolar lavage fluid samples from patients with lung cancer and downregulation in plasma level of stage-I lung cancer patients. However, the function and the underlying mechanism of miR-1285 in non-small-cell lung carcinoma have not been elucidated. In this study, we found that miR-1285-5p, the mature form of miR-1285, was significantly upregulated in human non-small-cell lung carcinoma cell lines A549 and SK-MES-1. Additionally, cells transfected with the miR-1285-5p inhibitor LV-anti-miR-1285-5p demonstrated significantly inhibited proliferation and invasion and depressed migration. Further analysis demonstrated that the miR-1285-5p precursor LV-miR-1285-5p attenuated the expression of Smad4 and cadherin-1 (CDH1) but that LV-anti-miR-1285-5p showed opposite results. A luciferase reporter assay confirmed that miR-1285-5p targeted Smad4 and CDH1. Mechanism analyses revealed that silence of Smad4 and CDH1 significantly attenuated the inhibitory effects of LV-anti-miR-1285-5p on non-small-cell lung carcinoma growth and invasion. Taken together, our data suggest that miR-1285-5p functions as a tumor promoter in the development of non-small-cell lung carcinoma by targeting Smad4 and CDH1, indicating a novel therapeutic strategy for non-small-cell lung carcinoma patients.

Prevalence of second-hand smoke exposure after introduction of the Italian smoking ban: the Florence and Belluno survey.

PubMed

Gorini, Giuseppe; Gasparrini, Antonio; Tamang, Elizabeth; Nebot, Manel; Lopez, Maria José; Albertini, Marco; Marcolina, Daniela; Fernandez, Esteve

2008-01-01

A law banning smoking in enclosed public places was implemented in Italy on January 10, 2005. The aim of this paper is to present a cross-sectional survey on two representative samples of non-smokers of two Italian towns (Florence and Belluno), conducted one year after the introduction of the ban, in order to assess prevalence of second-hand smoke exposure, to record the attitudes towards the ban, and the perception about its compliance in a representative sample of non-smokers. Computer-assisted telephone interviews were carried out in March 2006, from a random sample of households from telephone registries. Respondents were 402 non-smokers from Belluno and 1,073 from Florence. About 12% of Florentines and 7% of Belluno respondents were exposed at home; 39% and 19%, respectively, at work; 10% and 5% in hospitality venues; 20% and 10% in cars. The smoke-free law was almost universally supported (about 98%) even if a smaller proportion of people (about 90%) had the perception that the ban was observed. Second-hand smoke exposure at home and in hospitality premises has dropped to < or = 10%, whereas exposure at work remained higher. These results suggest the need for more controls in workplaces other than hospitality venues.

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

Madronich, Sasha; Kleinman, Larry; Conley, Andrew

Gas-to-particle partitioning of organic aerosols (OA) is represented in most models by Raoult’s law, and depends on the existing mass of particles into which organic gases can dissolve. This raises the possibility of non-linear response of particle-phase OA to the emissions of precursor volatile organic compounds (VOCs) that contribute to this partitioning mass. Implications for air quality management are evident: A strong non-linear dependence would suggest that reductions in VOC emission would have a more-than-proportionate benefit in lowering ambient OA concentrations. Chamber measurements on simple VOC mixtures generally confirm the non-linear scaling between OA and VOCs, usually stated as amore » mass-dependence of the measured OA yields. However, for realistic ambient conditions including urban settings, no single component dominates the composition of the organic particles, and deviations from linearity are presumed to be small. Here we re-examine the linearity question using volatility spectra from several sources: (1) chamber studies of selected aerosols, (2) volatility inferred for aerosols sampled in two megacities, Mexico City and Paris, and (3) an explicit chemistry model (GECKO-A). These few available volatility distributions suggest that urban OA may be only slightly super-linear, with most values of the sensitivity exponent in the range 1.1-1.3, also substantially lower than seen in chambers for some specific aerosols. Furthermore, the rather low values suggest that OA concentrations in megacities are not an inevitable convergence of non-linear effects, but can be addressed (much like in smaller urban areas) by proportionate reductions in emissions.« less

A machine learning model with human cognitive biases capable of learning from small and biased datasets.

PubMed

Taniguchi, Hidetaka; Sato, Hiroshi; Shirakawa, Tomohiro

2018-05-09

Human learners can generalize a new concept from a small number of samples. In contrast, conventional machine learning methods require large amounts of data to address the same types of problems. Humans have cognitive biases that promote fast learning. Here, we developed a method to reduce the gap between human beings and machines in this type of inference by utilizing cognitive biases. We implemented a human cognitive model into machine learning algorithms and compared their performance with the currently most popular methods, naïve Bayes, support vector machine, neural networks, logistic regression and random forests. We focused on the task of spam classification, which has been studied for a long time in the field of machine learning and often requires a large amount of data to obtain high accuracy. Our models achieved superior performance with small and biased samples in comparison with other representative machine learning methods.

Phylloquinone (vitamin K₁) intake and pulse pressure as a measure of arterial stiffness in older adults.

PubMed

Vaccaro, Joan A; Huffman, Fatma G

2013-01-01

This study examined the relationships among ethnicity/race, lifestyle factors, phylloquinone (vitamin K₁) intake, and arterial pulse pressure in a nationally representative sample of older adults from four ethnic/racial groups: non-Hispanic Whites, non-Hispanic Blacks, Mexican Americans, and other Hispanics. This was a cross-sectional study of U.S. representative sample with data from the National Health and Nutrition Examination Surveys, 2007-2008 and 2009-2010 of adults aged 50 years and older (N = 5296). Vitamin K intake was determined by 24-hour recall. Pulse pressure was calculated as the difference between the averages of systolic blood pressure and diastolic blood pressure. Compared to White non-Hispanics, the other ethnic/racial groups were more likely to have inadequate vitamin K₁ intake. Inadequate vitamin K₁ intake was an independent predictor of high arterial pulse pressure. This was the first study that compared vitamin K₁ inadequacy with arterial pulse pressure across ethnicities/races in U.S. older adults. These findings suggest that vitamin K screening may be a beneficial marker for the health of older adults.

Assessment of real-time PCR method for detection of EGFR mutation using both supernatant and cell pellet of malignant pleural effusion samples from non-small-cell lung cancer patients.

PubMed

Shin, Saeam; Kim, Juwon; Kim, Yoonjung; Cho, Sun-Mi; Lee, Kyung-A

2017-10-26

EGFR mutation is an emerging biomarker for treatment selection in non-small-cell lung cancer (NSCLC) patients. However, optimal mutation detection is hindered by complications associated with the biopsy procedure, tumor heterogeneity and limited sensitivity of test methodology. In this study, we evaluated the diagnostic utility of real-time PCR using malignant pleural effusion samples. A total of 77 pleural fluid samples from 77 NSCLC patients were tested using the cobas EGFR mutation test (Roche Molecular Systems). Pleural fluid was centrifuged, and separated cell pellets and supernatants were tested in parallel. Results were compared with Sanger sequencing and/or peptide nucleic acid (PNA)-mediated PCR clamping of matched tumor tissue or pleural fluid samples. All samples showed valid real-time PCR results in one or more DNA samples extracted from cell pellets and supernatants. Compared with other molecular methods, the sensitivity of real-time PCR method was 100%. Concordance rate of real-time PCR and Sanger sequencing plus PNA-mediated PCR clamping was 98.7%. We have confirmed that real-time PCR using pleural fluid had a high concordance rate compared to conventional methods, with no failed samples. Our data demonstrated that the parallel real-time PCR testing using supernatant and cell pellet could offer reliable and robust surrogate strategy when tissue is not available.

To the non-local theory of cold nuclear fusion.

PubMed

Alexeev, Boris V

2014-10-01

In this paper, we revisit the cold fusion (CF) phenomenon using the generalized Bolzmann kinetics theory which can represent the non-local physics of this CF phenomenon. This approach can identify the conditions when the CF can take place as the soliton creation under the influence of the intensive sound waves. The vast mathematical modelling leads to affirmation that all parts of soliton move with the same velocity and with the small internal change of the pressure. The zone of the high density is shaped on the soliton's front. It means that the regime of the 'acoustic CF' could be realized from the position of the non-local hydrodynamics.

Cell block samples from malignant pleural effusion might be valid alternative samples for anaplastic lymphoma kinase detection in patients with advanced non-small-cell lung cancer.

PubMed

Zhou, Jianya; Yao, Hongtian; Zhao, Jing; Zhang, Shumeng; You, Qihan; Sun, Ke; Zou, Yinying; Zhou, Caicun; Zhou, Jianying

2015-06-01

To evaluate the clinical value of cell block samples from malignant pleural effusion (MPE) as alternative samples to tumour tissue for anaplastic lymphoma kinase (ALK) detection in patients with advanced non-small-cell lung cancer (NSCLC). Fifty-two matched samples were eligible for analysis. ALK status was detected by Ventana immunohistochemistry (IHC) (with the D5F3 clone), reverse transcription polymerase chain reaction (RT-PCR) and fluorescence in-situ hybridization (FISH) in MPE cell block samples, and by FISH in tumour tissue block samples. In total, ALK FISH results were obtained for 52 tumour tissue samples and 41 MPE cell block samples. Eight cases (15.4%) were ALK-positive in tumour tissue samples by FISH, and among matched MPE cell block samples, five were ALK-positive by FISH, seven were ALK-positive by RT-PCR, and eight were ALK-positive by Ventana IHC. The ALK status concordance rates between tumour tissue and MPE cell block samples were 78.9% by FISH, 98.1% by RT-PCR, and 100% by Ventana IHC. In MPE cell block samples, the sensitivity and specificity of Ventana IHC (100% and 100%) and RT-PCR (87.5% and 100%) were higher than those of FISH (62.5% and 100%). Malignant pleural effusion cell block samples had a diagnostic performance for ALK detection in advanced NSCLC that was comparable to that of tumour tissue samples. MPE cell block samples might be valid alternative samples for ALK detection when tissue is not available. Ventana IHC could be the most suitable method for ALK detection in MPE cell block samples. © 2014 John Wiley & Sons Ltd.

Neural correlates of sample-coding and reward-coding in the delay activity of neurons in the entopallium and nidopallium caudolaterale of pigeons (Columba livia).

PubMed

Johnston, Melissa; Anderson, Catrona; Colombo, Michael

2017-01-15

We recorded neuronal activity from the nidopallium caudolaterale, the avian equivalent of mammalian prefrontal cortex, and the entopallium, the avian equivalent of the mammalian visual cortex, in four birds trained on a differential outcomes delayed matching-to-sample procedure in which one sample stimulus was followed by reward and the other was not. Despite similar incidence of reward-specific and reward-unspecific delay cell types across the two areas, overall entopallium delay activity occurred following both rewarded and non-rewarded stimuli, whereas nidopallium caudolaterale delay activity tended to occur following the rewarded stimulus but not the non-rewarded stimulus. These findings are consistent with the view that delay activity in entopallium represents a code of the sample stimulus whereas delay activity in nidopallium caudolaterale represents a code of the possibility of an upcoming reward. However, based on the types of delay cells encountered, cells in NCL also code the sample stimulus and cells in ENTO are influenced by reward. We conclude that both areas support the retention of information, but that the activity in each area is differentially modulated by factors such as reward and attentional mechanisms. Copyright © 2016 Elsevier B.V. All rights reserved.

Methods for estimating population density in data-limited areas: evaluating regression and tree-based models in Peru.

PubMed

Anderson, Weston; Guikema, Seth; Zaitchik, Ben; Pan, William

2014-01-01

Obtaining accurate small area estimates of population is essential for policy and health planning but is often difficult in countries with limited data. In lieu of available population data, small area estimate models draw information from previous time periods or from similar areas. This study focuses on model-based methods for estimating population when no direct samples are available in the area of interest. To explore the efficacy of tree-based models for estimating population density, we compare six different model structures including Random Forest and Bayesian Additive Regression Trees. Results demonstrate that without information from prior time periods, non-parametric tree-based models produced more accurate predictions than did conventional regression methods. Improving estimates of population density in non-sampled areas is important for regions with incomplete census data and has implications for economic, health and development policies.

Methods for Estimating Population Density in Data-Limited Areas: Evaluating Regression and Tree-Based Models in Peru

PubMed Central

Anderson, Weston; Guikema, Seth; Zaitchik, Ben; Pan, William

2014-01-01

Obtaining accurate small area estimates of population is essential for policy and health planning but is often difficult in countries with limited data. In lieu of available population data, small area estimate models draw information from previous time periods or from similar areas. This study focuses on model-based methods for estimating population when no direct samples are available in the area of interest. To explore the efficacy of tree-based models for estimating population density, we compare six different model structures including Random Forest and Bayesian Additive Regression Trees. Results demonstrate that without information from prior time periods, non-parametric tree-based models produced more accurate predictions than did conventional regression methods. Improving estimates of population density in non-sampled areas is important for regions with incomplete census data and has implications for economic, health and development policies. PMID:24992657

Community Heavy Metal Exposure, San Francisco, California

NASA Astrophysics Data System (ADS)

Chavez, A.; Devine, M.; Ho, T.; Zapata, I.; Bissell, M.; Neiss, J.

2008-12-01

Heavy metals are natural elements that generally occur in minute concentrations in the earth's crust. While some of these elements, in small quantities, are vital to life, most are harmful in larger doses. Various industrial and agricultural processes can result in dangerously high concentrations of heavy metals in our environment. Consequently, humans can be exposed to unsafe levels of these elements via the air we breathe, the water and food we consume, and the many products we use. During a two week study we collected numerous samples of sediments, water, food, and household items from around the San Francisco Bay Area that represent industrial, agricultural, and urban/residential settings. We analyzed these samples for Mercury (Hg), Lead (Pb), and Arsenic (As). Our goal was to examine the extent of our exposure to heavy metals in our daily lives. We discovered that many of the common foods and materials in our lives have become contaminated with unhealthy concentrations of these metals. Of our food samples, many exceeded the EPA's Maximum Contaminant Levels (MCL) set for each metal. Meats (fish, chicken, and beef) had higher amounts of each metal than did non-meat items. Heavy metals were also prevalent in varying concentrations in the environment. While many of our samples exceeded the EPA's Sediment Screening Level (SSL) for As, only two other samples surpassed the SSL set for Pb, and zero of our samples exceeded the SSL for Hg. Because of the serious health effects that can result from over-exposure to heavy metals, the information obtained in this study should be used to influence our future dietary and recreational habits.

Physical and chemical characterization of representative samples of recycled rubber from end-of-life tires.

PubMed

Re Depaolini, Andrea; Bianchi, Giancarlo; Fornai, Daniele; Cardelli, Angela; Badalassi, Marco; Cardelli, Camillo; Davoli, Enrico

2017-10-01

A large number of end-of-life tires (ELTs) were sampled and classified by type, age and origin to obtain recycled rubber samples representative of the materials placed on the Italian market. The selected recycled tire rubber samples were physically and chemically characterized and a chemometric approach was used to determine correlations. The polycyclic aromatic hydrocarbons (PAHs) content was correlated to the aromaticity index and a model was built to establish the H-Bay aromaticity index (H-Bay) from the PAH concentrations. ELT of different origin and age produced in non-European countries generally had higher PAH content and a higher H-Bay index. H-Bay values of all the samples were lower than the REACH limits and old tires had higher aromatic content than recent ones, possibly due to the replacement of aromatic oils in tire production. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

The Groove of Growth: How Early Gains in Math Ability Influence Adolescent Achievement

ERIC Educational Resources Information Center

Watts, Tyler W.; Duncan, Greg J.; Siegler, Robert S.; Davis-Kean, Pamela E.

2014-01-01

A number of studies, both small scale and of nationally-representative student samples, have reported substantial associations between school entry math ability and later elementary school achievement. However, questions remain regarding the persistence of the association between early growth in math ability and later math achievement due to the…

Are We Talking about the Same Child? Parent-Teacher Ratings of Preschoolers' Social-Emotional Behaviors

ERIC Educational Resources Information Center

Major, Sofia O.; Seabra-Santos, Maria J.; Martin, Roy P.

2015-01-01

The parent-teacher agreement has become an important issue of children's psychological assessment. However, the amount of research available for preschool children is small and mainly based on one index of agreement with samples of modest size/representativeness. This study examined parent-teacher agreement (correlations) and discrepancies (t…

Training of polyp staging systems using mixed imaging modalities.

PubMed

Wimmer, Georg; Gadermayr, Michael; Kwitt, Roland; Häfner, Michael; Tamaki, Toru; Yoshida, Shigeto; Tanaka, Shinji; Merhof, Dorit; Uhl, Andreas

2018-05-04

In medical image data sets, the number of images is usually quite small. The small number of training samples does not allow to properly train classifiers which leads to massive overfitting to the training data. In this work, we investigate whether increasing the number of training samples by merging datasets from different imaging modalities can be effectively applied to improve predictive performance. Further, we investigate if the extracted features from the employed image representations differ between different imaging modalities and if domain adaption helps to overcome these differences. We employ twelve feature extraction methods to differentiate between non-neoplastic and neoplastic lesions. Experiments are performed using four different classifier training strategies, each with a different combination of training data. The specifically designed setup for these experiments enables a fair comparison between the four training strategies. Combining high definition with high magnification training data and chromoscopic with non-chromoscopic training data partly improved the results. The usage of domain adaptation has only a small effect on the results compared to just using non-adapted training data. Merging datasets from different imaging modalities turned out to be partially beneficial for the case of combining high definition endoscopic data with high magnification endoscopic data and for combining chromoscopic with non-chromoscopic data. NBI and chromoendoscopy on the other hand are mostly too different with respect to the extracted features to combine images of these two modalities for classifier training. Copyright © 2018 Elsevier Ltd. All rights reserved.

A sampling procedure to guide the collection of narrow-band, high-resolution spatially and spectrally representative reflectance data. [satellite imagery of earth resources

NASA Technical Reports Server (NTRS)

Brand, R. R.; Barker, J. L.

1983-01-01

A multistage sampling procedure using image processing, geographical information systems, and analytical photogrammetry is presented which can be used to guide the collection of representative, high-resolution spectra and discrete reflectance targets for future satellite sensors. The procedure is general and can be adapted to characterize areas as small as minor watersheds and as large as multistate regions. Beginning with a user-determined study area, successive reductions in size and spectral variation are performed using image analysis techniques on data from the Multispectral Scanner, orbital and simulated Thematic Mapper, low altitude photography synchronized with the simulator, and associated digital data. An integrated image-based geographical information system supports processing requirements.

FDATMOS16 non-linear partitioning and organic volatility distributions in urban aerosols

DOE PAGES

Madronich, Sasha; Kleinman, Larry; Conley, Andrew; ...

2015-12-17

Gas-to-particle partitioning of organic aerosols (OA) is represented in most models by Raoult’s law, and depends on the existing mass of particles into which organic gases can dissolve. This raises the possibility of non-linear response of particle-phase OA to the emissions of precursor volatile organic compounds (VOCs) that contribute to this partitioning mass. Implications for air quality management are evident: A strong non-linear dependence would suggest that reductions in VOC emission would have a more-than-proportionate benefit in lowering ambient OA concentrations. Chamber measurements on simple VOC mixtures generally confirm the non-linear scaling between OA and VOCs, usually stated as amore » mass-dependence of the measured OA yields. However, for realistic ambient conditions including urban settings, no single component dominates the composition of the organic particles, and deviations from linearity are presumed to be small. Here we re-examine the linearity question using volatility spectra from several sources: (1) chamber studies of selected aerosols, (2) volatility inferred for aerosols sampled in two megacities, Mexico City and Paris, and (3) an explicit chemistry model (GECKO-A). These few available volatility distributions suggest that urban OA may be only slightly super-linear, with most values of the sensitivity exponent in the range 1.1-1.3, also substantially lower than seen in chambers for some specific aerosols. Furthermore, the rather low values suggest that OA concentrations in megacities are not an inevitable convergence of non-linear effects, but can be addressed (much like in smaller urban areas) by proportionate reductions in emissions.« less

Small non coding RNAs in adipocyte biology and obesity.

PubMed

Amri, Ez-Zoubir; Scheideler, Marcel

2017-11-15

Obesity has reached epidemic proportions world-wide and constitutes a substantial risk factor for hypertension, type 2 diabetes, cardiovascular diseases and certain cancers. So far, regulation of energy intake by dietary and pharmacological treatments has met limited success. The main interest of current research is focused on understanding the role of different pathways involved in adipose tissue function and modulation of its mass. Whole-genome sequencing studies revealed that the majority of the human genome is transcribed, with thousands of non-protein-coding RNAs (ncRNA), which comprise small and long ncRNAs. ncRNAs regulate gene expression at the transcriptional and post-transcriptional level. Numerous studies described the involvement of ncRNAs in the pathogenesis of many diseases including obesity and associated metabolic disorders. ncRNAs represent potential diagnostic biomarkers and promising therapeutic targets. In this review, we focused on small ncRNAs involved in the formation and function of adipocytes and obesity. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis of chorioallantoic membranes to assess PCB accumulation in American alligators and Loggerhead sea turtles from the coast of South Carolina

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

Cobb, G.P.; Wood, P.D.; O`Quinn, M.

1995-12-31

Investigation of contaminant burdens in threatened and endangered species is difficult due to the small number of samples that can be collected. Many samples can be collected if the sampling methods are non-lethal and more specifically non-invasive. Analysis of chorioallantoic membranes is demonstrated for American alligators and Loggerhead sea turtles. Significant differences were found in PCB, uptake by alligators from the Ashepoo-Combahee-Edisto Basin reference site and a contaminated site in Winyah Bay. Intrasite and intersite differences in uptake and distribution of PCB homologues were noted. These data will be discussed as they relate to egg viability and embryo development.

The role of traumatic event history in non-medical use of prescription drugs among a nationally representative sample of US adolescents.

PubMed

McCauley, Jenna L; Danielson, Carla Kmett; Amstadter, Ananda B; Ruggiero, Kenneth J; Resnick, Heidi S; Hanson, Rochelle F; Smith, Daniel W; Saunders, Benjamin E; Kilpatrick, Dean G

2010-01-01

Building on previous research with adolescents that examined demographic variables and other forms of substance abuse in relation to non-medical use of prescription drugs (NMUPD), the current study examined potentially traumatic events, depression, posttraumatic stress disorder (PTSD), other substance use, and delinquent behavior as potential correlates of past-year non-medical use of prescription drugs. A nationally representative sample of 3,614 non-institutionalized, civilian, English-speaking adolescents (aged 12-17 years) residing in households with a telephone was selected. Demographic characteristics, traumatic event history, mental health, and substance abuse variables were assessed. NMUPD was assessed by asking if, in the past year, participants had used a prescription drug in a non-medical manner. Multivariable logistic regressions were conducted for each theoretically derived predictor set. Significant predictors from each set were then entered into a final multivariable logistic regression to determine significant predictors of past-year NMUPD. NMUPD was endorsed by 6.7% of the sample (n = 242). The final multivariable model showed that lifetime history of delinquent behavior, other forms of substance use/abuse, history of witnessed violence, and lifetime history of PTSD were significantly associated with increased likelihood of NMUPD. Risk reduction efforts targeting NMUPD among adolescents who have witnessed significant violence, endorsed abuse of other substances and delinquent behavior, and/or endorsed PTSD are warranted. Interventions for adolescents with history of violence exposure or PTSD, or those adjudicated for delinquent behavior, should include treatment or prevention modules that specifically address NMUPD.

[A Paired Case Controlled Study Comparing the Short-term Outcomes of Da Vinci RATS and VATS Approach for Non-small Cell Lung Cancer].

PubMed

Dai, Feng; Xu, Shiguang; Xu, Wei; Ding, Renquan; Liu, Bo; Meng, Hao; Kang, Yunteng; Meng, Xiangrui; Lin, Jie; Wang, Shumin

2018-03-20

Da Vinci Surgical System is one of the greatest inventions of the 20th century, which represents the development direction of the precise minimally invasive surgical techniques, the aim of this study was to comparing the short-term outcomes between da Vinci robot-assisted lobectomy and video-assisted thoracic surgery (VATS) lobectomy for non-small cell lung cancer. 45 pairs of non-small cell lung cancer patients underwent pulmonary lobectomy with da Vinci Robotic assisted thoracoscopic (RATS) and VATS approach during the same period from January 2014 to January 2017. The operative time, estimated blood loss (EBL), total number and total groups of dissected lymph nodes, postoperative duration of drainage, the first day volume of drainage, total volume of drainage were compared. No perioperative death and convertion to thoracotomy occured in both groups. There were significant difference between RATS group and VATS group in EBL [(50.30±32.33) mL vs (208.60±132.63) mL], the first day volume of drainage [(275.00±145.42) mL vs (347.60±125.80) mL], the dissected total number [(22.67±9.67) vs (15.51±5.41)] and total team [(6.31±1.43) vs (4.91±1.04)] of lymph node. There were no significant difference in other outcomes. RATS is safe and effective and took better short-outcomes than VATS in non-small cell lung cancer.

Normal Approximations to the Distributions of the Wilcoxon Statistics: Accurate to What "N"? Graphical Insights

ERIC Educational Resources Information Center

Bellera, Carine A.; Julien, Marilyse; Hanley, James A.

2010-01-01

The Wilcoxon statistics are usually taught as nonparametric alternatives for the 1- and 2-sample Student-"t" statistics in situations where the data appear to arise from non-normal distributions, or where sample sizes are so small that we cannot check whether they do. In the past, critical values, based on exact tail areas, were…

Quantitative Exposure Assessment of Various Chemical Substances in a Wafer Fabrication Industry Facility

PubMed Central

Jang, Jae-Kil; Shin, Jung-Ah

2011-01-01

Objectives This study was designed to evaluate exposure levels of various chemicals used in wafer fabrication product lines in the semiconductor industry where work-related leukemia has occurred. Methods The research focused on 9 representative wafer fabrication bays among a total of 25 bays in a semiconductor product line. We monitored the chemical substances categorized as human carcinogens with respect to leukemia as well as harmful chemicals used in the bays and substances with hematologic and reproductive toxicities to evaluate the overall health effect for semiconductor industry workers. With respect to monitoring, active and passive sampling techniques were introduced. Eight-hour long-term and 15-minute short-term sampling was conducted for the area as well as on personal samples. Results The results of the measurements for each substance showed that benzene, toluene, xylene, n-butyl acetate, 2-methoxyethanol, 2-heptanone, ethylene glycol, sulfuric acid, and phosphoric acid were non-detectable (ND) in all samples. Arsine was either "ND" or it existed only in trace form in the bay air. The maximum exposure concentration of fluorides was approximately 0.17% of the Korea occupational exposure limits, with hydrofluoric acid at about 0.2%, hydrochloric acid 0.06%, nitric acid 0.05%, isopropyl alcohol 0.4%, and phosphine at about 2%. The maximum exposure concentration of propylene glycol monomethyl ether acetate (PGMEA) was 0.0870 ppm, representing only 0.1% or less than the American Industrial Hygiene Association recommended standard (100 ppm). Conclusion Benzene, a known human carcinogen for leukemia, and arsine, a hematologic toxin, were not detected in wafer fabrication sites in this study. Among reproductive toxic substances, n-butyl acetate was not detected, but fluorides and PGMEA existed in small amounts in the air. This investigation was focused on the air-borne chemical concentrations only in regular working conditions. Unconditional exposures during spills and/or maintenance tasks and by-product chemicals were not included. Supplementary studies might be required. PMID:22953186

Polymorphism in magic-sized Au144(SR)60 clusters

NASA Astrophysics Data System (ADS)

Jensen, Kirsten M. Ø.; Juhas, Pavol; Tofanelli, Marcus A.; Heinecke, Christine L.; Vaughan, Gavin; Ackerson, Christopher J.; Billinge, Simon J. L.

2016-06-01

Ultra-small, magic-sized metal nanoclusters represent an important new class of materials with properties between molecules and particles. However, their small size challenges the conventional methods for structure characterization. Here we present the structure of ultra-stable Au144(SR)60 magic-sized nanoclusters obtained from atomic pair distribution function analysis of X-ray powder diffraction data. The study reveals structural polymorphism in these archetypal nanoclusters. In addition to confirming the theoretically predicted icosahedral-cored cluster, we also find samples with a truncated decahedral core structure, with some samples exhibiting a coexistence of both cluster structures. Although the clusters are monodisperse in size, structural diversity is apparent. The discovery of polymorphism may open up a new dimension in nanoscale engineering.

Masculinity and Social Class, Tradition and Change: The Production of "Young Christian Gentlemen" at an Elite Australian Boys' School

ERIC Educational Resources Information Center

Proctor, Helen

2011-01-01

High fee-charging non-government schools for boys comprise a small but significant sector of the Australian schooling market. In different ways in different historical periods these schools have represented themselves as being concerned with more than just an instrumental or utilitarian education, making both explicit and implicit claims about the…

Epidermal growth factor receptor and K-Ras in non-small cell lung cancer-molecular pathways involved and targeted therapies

PubMed Central

de Mello, Ramon Andrade; Marques, Dânia Sofia; Medeiros, Rui; Araújo, António MF

2011-01-01

Lung cancer is currently the leading cause of cancer death in Western nations. Non-small cell lung cancer (NSCLC) represents 80% of all lung cancers, and adenocarcinoma is the predominant histological type. Despite the intensive research carried out on this field and therapeutic advances, the overall prognosis of these patients remains unsatisfactory, with a 5-year overall survival rate of less than 15%. Nowadays, pharmacogenetics and pharmacogenomics represent the key to successful treatment. Recent studies suggest the existence of two distinct molecular pathways in the carcinogenesis of lung adenocarcinoma: one associated with smoking and activation of the K-Ras oncogene and the other not associated with smoking and activation of the epidermal growth factor receptor (EGFR). The K-ras mutation is mainly responsible for primary resistance to new molecules which inhibit tyrosine kinase EGFR (erlotinib and gefitinib) and most of the EGFR mutations are responsible for increased tumor sensitivity to these drugs. This article aims to conduct a systematic review of the literature regarding the molecular pathways involving the EGFR, K-Ras and EGFR targeted therapies in NSCLC tumor behavior. PMID:22087435

Atezolizumab for the treatment of non-small cell lung cancer.

PubMed

Santini, Fernando C; Rudin, Charles M

2017-09-01

The immune system can restrain or promote cancer development and growth. Antibodies targeting immune checkpoints have revolutionized cancer treatment. Among the best responses have been in non-small cell lung cancer (NSCLC) which is largely caused by chronic exposure to carcinogens; associated with high neoantigen creation and sensitization to immune recognition. Atezolizumab was the first approved antibody that targets the PD-1 ligand (PD-L1). Areas covered: This drug profile article covers the basics of the cancer-immunity cycle and reviews some aspects of innate and adaptive immunology. We discuss the discovery of PD-L1 and PD-L2 while highlight the potential differences in targeting PD-L1 versus PD-1. In addition, we briefly summarized the available pre-clinical and clinical data of atezolizumab use in NSCLC. A special section covers the challenges of PD-L1 immunohistochemistry assay. Expert commentary: PD-1:PD-L1 blockade has taken the lead in the immunotherapeutics field and represents the backbone of developing combination immunotherapies. Atezolizumab represents a step forward in the treatment of advanced NSCLC, nonetheless PD1:PD-L1 blockade in early-stage lung cancer is still a matter of debate.

Genetic diversity of small eukaryotes in lakes differing by their trophic status.

PubMed

Lefranc, Marie; Thénot, Aurélie; Lepère, Cécile; Debroas, Didier

2005-10-01

Small eukaryotes, cells with a diameter of less than 5 mum, are fundamental components of lacustrine planktonic systems. In this study, small-eukaryote diversity was determined by sequencing cloned 18S rRNA genes in three libraries from lakes of differing trophic status in the Massif Central, France: the oligotrophic Lake Godivelle, the oligomesotrophic Lake Pavin, and the eutrophic Lake Aydat. This analysis shows that the least diversified library was in the eutrophic lake (12 operational taxonomic units [OTUs]) and the most diversified was in the oligomesotrophic lake (26 OTUs). Certain groups were present in at least two ecosystems, while the others were specific to one lake on the sampling date. Cryptophyta, Chrysophyceae, and the strictly heterotrophic eukaryotes, Ciliophora and fungi, were identified in the three libraries. Among the small eukaryotes found only in two lakes, Choanoflagellida and environmental sequences (LKM11) were not detected in the eutrophic system whereas Cercozoa were confined to the oligomesotrophic and eutrophic lakes. Three OTUs, linked to the Perkinsozoa, were detected only in the Aydat library, where they represented 60% of the clones of the library. Chlorophyta and Haptophyta lineages were represented by a single clone and were present only in Godivelle and Pavin, respectively. Of the 127 clones studied, classical pigmented organisms (autotrophs and mixotrophs) represented only a low proportion regardless of the library's origin. This study shows that the small-eukaryote community composition may differ as a function of trophic status; certain lineages could be detected only in a single ecosystem.

A Research Communication Brief: Gluten Analysis in Beef Samples Collected Using a Rigorous, Nationally Representative Sampling Protocol Confirms That Grain-Finished Beef Is Naturally Gluten-Free

PubMed Central

McNeill, Shalene H.; Cifelli, Amy M.; Roseland, Janet M.; Belk, Keith E.; Gehring, Kerri B.; Brooks, J. Chance; Thompson, Leslie D.

2017-01-01

Knowing whether or not a food contains gluten is vital for the growing number of individuals with celiac disease and non-celiac gluten sensitivity. Questions have recently been raised about whether beef from conventionally-raised, grain-finished cattle may contain gluten. To date, basic principles of ruminant digestion have been cited in support of the prevailing expert opinion that beef is inherently gluten-free. For this study, gluten analysis was conducted in beef samples collected using a rigorous nationally representative sampling protocol to determine whether gluten was present. The findings of our research uphold the understanding of the principles of gluten digestion in beef cattle and corroborate recommendations that recognize beef as a naturally gluten-free food. PMID:28841165

Observational studies of patients in the emergency department: a comparison of 4 sampling methods.

PubMed

Valley, Morgan A; Heard, Kennon J; Ginde, Adit A; Lezotte, Dennis C; Lowenstein, Steven R

2012-08-01

We evaluate the ability of 4 sampling methods to generate representative samples of the emergency department (ED) population. We analyzed the electronic records of 21,662 consecutive patient visits at an urban, academic ED. From this population, we simulated different models of study recruitment in the ED by using 2 sample sizes (n=200 and n=400) and 4 sampling methods: true random, random 4-hour time blocks by exact sample size, random 4-hour time blocks by a predetermined number of blocks, and convenience or "business hours." For each method and sample size, we obtained 1,000 samples from the population. Using χ(2) tests, we measured the number of statistically significant differences between the sample and the population for 8 variables (age, sex, race/ethnicity, language, triage acuity, arrival mode, disposition, and payer source). Then, for each variable, method, and sample size, we compared the proportion of the 1,000 samples that differed from the overall ED population to the expected proportion (5%). Only the true random samples represented the population with respect to sex, race/ethnicity, triage acuity, mode of arrival, language, and payer source in at least 95% of the samples. Patient samples obtained using random 4-hour time blocks and business hours sampling systematically differed from the overall ED patient population for several important demographic and clinical variables. However, the magnitude of these differences was not large. Common sampling strategies selected for ED-based studies may affect parameter estimates for several representative population variables. However, the potential for bias for these variables appears small. Copyright © 2012. Published by Mosby, Inc.

Non-contact optoacoustic imaging by raster scanning a piezoelectric air-coupled transducer

NASA Astrophysics Data System (ADS)

Deán-Ben, X. Luís.; Pang, Genny A.; Montero de Espinosa, Francisco; Razansky, Daniel

2016-03-01

Optoacoustic techniques rely on ultrasound transmission between optical absorbers within tissues and the measurement location. Much like in echography, commonly used piezoelectric transducers require either direct contact with the tissue or through a liquid coupling medium. The contact nature of this detection approach then represents a disadvantage of standard optoacoustic systems with respect to other imaging modalities (including optical techniques) in applications where non-contact imaging is needed, e.g. in open surgeries or when burns or other lesions are present in the skin. Herein, non-contact optoacoustic imaging using raster-scanning of a spherically-focused piezoelectric air-coupled ultrasound transducer is demonstrated. When employing laser fluence levels not exceeding the maximal permissible human exposure, it is shown possible to attain detectable signals from objects as small as 1 mm having absorption properties representative of blood at near-infrared wavelengths with a relatively low number of averages. Optoacoustic images from vessel-mimicking tubes embedded in an agar phantom are further showcased. The initial results indicate that the air-coupled ultrasound detection approach can be potentially made suitable for non-contact biomedical imaging with optoacoustics.

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

DOE PAGES

Caskey, Christopher M.; Holder, Aaron; Shulda, Sarah; ...

2016-04-12

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experimentsmore » indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. Furthermore, this observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn 3N 4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.« less

Expression and prognostic relevance of MET and phospho-BAD in non-small cell lung cancer.

PubMed

Sun, Wenze; Ai, Ting; Gao, Ying; Zhang, Yingbing; Cui, Jie; Song, Liping

2013-01-01

MET is involved in the progression of several types of human cancers, while phospho-BAD(Ser-136) is a key molecule in apoptosis and might be regulated by MET. The aim of this study was to investigate the correlation between altered expression of MET and phospho-BAD in non-small cell lung cancer (NSCLC) and their association with clinicopathologic parameters and overall survival. MET and phospho-BAD(Ser-136) proteins were evaluated by immunohistochemical analysis in 183 paraffin-embedded specimens and were also assessed by Western blotting analysis in 12 frozen tumor tissue samples, which were representative examples of immunohistochemical staining. Positive expression of MET and phospho-BAD(Ser-136) occurred in 67.2% and 49.2% of the 183 cases of NSCLC, respectively. However, neither MET expression nor phospho-BAD(Ser-136) expression was associated with any clinicopathologic parameter. A significant correlation was found between MET and phospho-BAD(Ser-136) expression levels evaluated by immunohistochemistry (r = 0.268, P < 0.001). Overexpression of MET was significantly associated with shortened overall survival in univariate analysis (P < 0.001). Moreover, patients with a MET+/phospho-BAD(Ser-136)+ phenotype had a poorer prognosis than others (P < 0.001). Multivariate Cox proportional hazard analysis confirmed that MET expression is a prognostic factor for NSCLC. MET expression might be correlated with phospho-BAD(Ser-136) expression, and may be an adverse predictor for NSCLC. Activation of the MET/phospho-BAD(Ser-136) signaling pathway might play a role in the development and progression of NSCLC.

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

NASA Astrophysics Data System (ADS)

Caskey, Christopher M.; Holder, Aaron; Shulda, Sarah; Christensen, Steven T.; Diercks, David; Schwartz, Craig P.; Biagioni, David; Nordlund, Dennis; Kukliansky, Alon; Natan, Amir; Prendergast, David; Orvananos, Bernardo; Sun, Wenhao; Zhang, Xiuwen; Ceder, Gerbrand; Ginley, David S.; Tumas, William; Perkins, John D.; Stevanovic, Vladan; Pylypenko, Svitlana; Lany, Stephan; Richards, Ryan M.; Zakutayev, Andriy

2016-04-01

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn3N4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures.

PubMed

Caskey, Christopher M; Holder, Aaron; Shulda, Sarah; Christensen, Steven T; Diercks, David; Schwartz, Craig P; Biagioni, David; Nordlund, Dennis; Kukliansky, Alon; Natan, Amir; Prendergast, David; Orvananos, Bernardo; Sun, Wenhao; Zhang, Xiuwen; Ceder, Gerbrand; Ginley, David S; Tumas, William; Perkins, John D; Stevanovic, Vladan; Pylypenko, Svitlana; Lany, Stephan; Richards, Ryan M; Zakutayev, Andriy

2016-04-14

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn3N4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

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

Caskey, Christopher M.; Colorado School of Mines, Golden, Colorado 80401; Larix Chemical Science, Golden, Colorado 80401

2016-04-14

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experimentsmore » indicate that this novel material is N-deficient SnN with tin in the mixed II/IV valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn{sub 3}N{sub 4} spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.« less

Ultrasonic nondestructive testing of composite materials using disturbed coincidence conditions

NASA Astrophysics Data System (ADS)

Bause, F.; Olfert, S.; Schröder, A.; Rautenberg, J.; Henning, B.; Moritzer, E.

2012-05-01

In this contribution we present a new method detecting changes in the composite material's acoustic behavior by analyzing disturbed coincidence conditions on plate-like test samples. The coincidence condition for an undamaged GFRP test sample has been experimentally identified using Schlieren measurements. Disturbances of this condition follow from a disturbed acoustic behavior of the test sample which is an indicator for local damages in the region inspected. An experimental probe has been realized consisting of two piezoceramic elements adhered to the nonparallel sides of an isosceles trapezoidal body made of silicone. The base angles of the trapezoidal body have been chosen such that the incident wave meets pre-measured condition of coincidence. The receiving element receives the geometric reflection of the acoustic wave scattered at the test sample's surface which corresponds to the non-coupled part of the incident wave as send by the sending element. Analyzing the transfer function or impulse response of the electro-acoustic system (transmitter, scattering at test sample, receiver), it is possible to detect local disturbances with respect to Cramer's coincidence rule. Thus, it is possible to realize a very simple probe for local ultrasonic nondestructive testing of composite materials (as well as non-composite material) which can be integrated in a small practical device and is good for small size inspection areas.

Development of Preliminary Remediation Goals for Indoor Dust at the Colonie FUSRAP Site - 12273

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

Watters, David J.; Opdyke, Clifford P.; Moore, James T.

2012-07-01

The Colonie FUSRAP Site is located in the Town of Colonie, Albany County, New York. The U.S. Army Corps of Engineers is currently addressing environmental contamination associated with the Site under the Comprehensive Environmental Response, Compensation and Liability Act (CERCLA) process as part of the Formerly Utilized Sites Remedial Action Program (FUSRAP). Soil remediation activities have been substantially completed at the Colonie FUSRAP Site and its vicinity properties under the FUSRAP. A study unrelated to FUSRAP was recently performed by an independent party to establish the distribution of DU contamination in various media in the environs of the Site. Asmore » part of this study, dust samples were collected in residencies and businesses in the immediate vicinity of the Site. These samples were collected in non-living areas such as basement window sills and garages. Many of these samples tested positive for DU. An assessment was performed to establish preliminary remediation goals (PRGs) for indoor dust in non-living areas of residential homes and businesses in the vicinity of the Site. The results of this assessment provide estimates of dose-based, carcinogenic risk-based, and noncarcinogenic-based PRGs derived from a hypothetical exposure scenario with reasonable levels of conservatism. Ultimately, the PRGs will be compared to results of dust sampling and analyses in residences and businesses in proximity of the Site to determine whether a response action is appropriate. This assessment estimates PRGs for DU contaminated dust in non-living areas of residences in the vicinity of the Colonie FUSRAP site based on a reasonably conservative exposure scenario. Estimated PRGs based on residential receptors are considered to be conservatively representative of workers in nearby businesses based on the considerably longer exposure duration of residents relative to workers. This assessment provides reasonably conservative estimates of PRGs for DU contaminated dust in non-living areas within residences in the vicinity of the Site. It should be noted that the PRGs include hypothetical exposures resulting from activities in both the living areas and non-living areas of a residence. The PRGs are derived and presented in terms of DU dust concentration in non-living areas to facilitate comparison to results of a planned Site Investigation that will characterize concentrations of DU in dust in non-living areas. It is important to recognize that the exposure assumptions used to derive these PRGs are based on average dust DU concentrations in non-living areas. It is inappropriate to compare these PRGs to the dust DU concentration in an isolated small area. The ongoing Site Investigation addresses this consideration and is designed to provide reasonable estimates of average dust DU concentrations in non-living areas of vicinity properties. In order to accomplish this, sampling is conducted in accordance with EPA Guidance for the Sampling and Analysis of Lead in Indoor Residential Dust for Use in the Integrated Exposure Uptake Biokinetic (IEUBK) Model, (EPA 2008), which specifically addresses estimating average contaminant concentrations in dust. Four (4) large-area samples are collected from each VP in accordance with this guidance. It is anticipated that the results of the Site Investigation will be used in conjunction with the results of this assessment, and/or subsequent assessments, to establish whether or not a response action is appropriate. (authors)« less

Pituitary gland volumes in bipolar disorder.

PubMed

Clark, Ian A; Mackay, Clare E; Goodwin, Guy M

2014-12-01

Bipolar disorder has been associated with increased Hypothalamic-Pituitary-Adrenal axis function. The mechanism is not well understood, but there may be associated increases in pituitary gland volume (PGV) and these small increases may be functionally significant. However, research investigating PGV in bipolar disorder reports mixed results. The aim of the current study was twofold. First, to assess PGV in two novel samples of patients with bipolar disorder and matched healthy controls. Second, to perform a meta-analysis comparing PGV across a larger sample of patients and matched controls. Sample 1 consisted of 23 established patients and 32 matched controls. Sample 2 consisted of 39 medication-naïve patients and 42 matched controls. PGV was measured on structural MRI scans. Seven further studies were identified comparing PGV between patients and matched controls (total n; 244 patients, 308 controls). Both novel samples showed a small (approximately 20mm(3) or 4%), but non-significant, increase in PGV in patients. Combining the two novel samples showed a significant association of age and PGV. Meta-analysis showed a trend towards a larger pituitary gland in patients (effect size: .23, CI: -.14, .59). While results suggest a possible small difference in pituitary gland volume between patients and matched controls, larger mega-analyses with sample sizes greater even than those used in the current meta-analysis are still required. There is a small but potentially functionally significant increase in PGV in patients with bipolar disorder compared to controls. Results demonstrate the difficulty of finding potentially important but small effects in functional brain disorders. Copyright © 2014 Elsevier B.V. All rights reserved.

Non-Small-Cell Lung Cancer Molecular Signatures Recapitulate Lung Developmental Pathways

PubMed Central

Borczuk, Alain C.; Gorenstein, Lyall; Walter, Kristin L.; Assaad, Adel A.; Wang, Liqun; Powell, Charles A.

2003-01-01

Current paradigms hold that lung carcinomas arise from pleuripotent stem cells capable of differentiation into one or several histological types. These paradigms suggest lung tumor cell ontogeny is determined by consequences of gene expression that recapitulate events important in embryonic lung development. Using oligonucleotide microarrays, we acquired gene profiles from 32 microdissected non-small-cell lung tumors. We determined the 100 top-ranked marker genes for adenocarcinoma, squamous cell, large cell, and carcinoid using nearest neighbor analysis. Results were validated by immunostaining for 11 selected proteins using a tissue microarray representing 80 tumors. Gene expression data of lung development were accessed from a publicly available dataset generated with the murine Mu11k genome microarray. Self-organized mapping identified two temporally distinct clusters of murine orthologues. Supervised clustering of lung development data showed large-cell carcinoma gene orthologues were in a cluster expressed in pseudoglandular and canalicular stages whereas adenocarcinoma homologues were predominantly in a cluster expressed later in the terminal sac and alveolar stages of murine lung development. Representative large-cell genes (E2F3, MYBL2, HDAC2, CDK4, PCNA) are expressed in the nucleus and are associated with cell cycle and proliferation. In contrast, adenocarcinoma genes are associated with lung-specific transcription pathways (SFTPB, TTF-1), cell adhesion, and signal transduction. In sum, non-small-cell lung tumors histology gene profiles suggest mechanisms relevant to ontogeny and clinical course. Adenocarcinoma genes are associated with differentiation and glandular formation whereas large-cell genes are associated with proliferation and differentiation arrest. The identification of developmentally regulated pathways active in tumorigenesis provides insights into lung carcinogenesis and suggests early steps may differ according to the eventual tumor morphology. PMID:14578194

Physico-chemical analysis and antimicrobial potential of Apis dorsata, Apis mellifera and Ziziphus jujube honey samples from Pakistan

PubMed Central

Fahim, Hira; Dasti, Javid Iqbal; Ali, Ihsan; Ahmed, Safia; Nadeem, Muhammad

2014-01-01

Objective To evaluate physico-chemical properties and antimicrobial potential of indigenous honey samples against different reference strains including Escherichia coli ATCC 8739, Enterobacter aerogenes ATCC 13048, Pseudomonas aeroginosa ATCC 9027, Bacillus subtilis ATCC 6633, Staphylococcus aureus ATCC 25923, Salmonella typhi ATCC 14028, Klebsiella pneumonia ATCC 13883, Aspergillus niger ATCC 16404, Rhizopus oligosporus PCSIR1, Candida albicans ATCC 14053 and Candida utilis ATCC 9950. Methods By using standard methods samples were evaluated for their antimicrobial properties including additive effect of starch and non-peroxidase activity, antioxidative properties (phenol contents, flavonoid contents, 1,1-diphenyl-2-picrylhydrazyl radical scavenging activity). Prior to this evaluation, complete physico-chemical properties including pH, color, ash contents, protein contents, moisture contents, hydroxymethyl furfural contents, total sugar contents, reducing sugar and non-reducing sugar contents were analyzed. Results Relatively higher ash contents were found in the Siddar honey i.e. (0.590 0±0.033 6)% and small honey showed relatively higher protein contents i.e. (777.598±9.880) mg/kg. The moisture contents of tested honey samples ranged between 13.8%-16.6%, total sugar contents from 61.672%-72.420% and non-reducing sugar contents from 1.95%-3.93%. Presences of phenolic contents indicate higher antioxidant potential of these honey samples. All bacteria showed clear inhibition zones in response to tested honey samples whereas fungi and yeast showed inhibition at higher concentrations of these honey samples. For Escherichia coli, Bacillus subtilis, Salmonella typhi, Pseudomonas aeroginosa and Aspergillus niger, overall the small honey showed the higher activity than other honey samples. Conclusion Physico-chemical analysis of honey samples confirmed good quality of honey according to the standards set by European Union Commission and Codex Alimentarius Commission. Evaluation of these honey samples confirms antimicrobial potential of particular types of honeys indigenous to Pakistan. PMID:25183333

Comparison of plasma and tissue samples in epidermal growth factor receptor mutation by ARMS in advanced non-small cell lung cancer.

PubMed

Ma, MeiLi; Shi, ChunLei; Qian, JiaLin; Teng, JiaJun; Zhong, Hua; Han, BaoHui

2016-10-10

The aim of this study was to assess the effectiveness and accuracy of blood-based circulating-free tumor DNA on testing epidermal growth factor receptor (EGFR) gene mutations. In total, 219 non-small cell lung cancer patients in stages III-IV were enrolled into this study. All patients had tissue samples and matched plasma DNA samples. EGFR gene mutations were detected by the Amplification Refractory Mutation System (ARMS). We compared the mutations in tumor tissue samples with matched plasma samples and determined the correlation between EGFR mutation status and clinical pathologic characteristics. The overall concordance rate of EGFR mutation status between the 219 matched plasma and tissue samples was 82% (179/219). The sensitivity and specificity for the ARMS EGFR mutation test in the plasma compared with tumor tissue were 60% (54/90) and 97% (125/129), respectively. The positive predictive value was 93% (54/58) and the negative predictive value was 78% (125/161). The median overall survival was longer for those with EGFR mutations than for those without EGFR mutations both in tissue samples (23.98 vs. 12.16months; P<0.001) and in plasma (19.96 vs. 13.63months; P=0.009). For the 68 patients treated with EGFR- tyrosine kinase inhibitors (TKIs), the median progression-free survival (PFS) was significantly prolonged in the EGFR mutant group compared to the non-mutation group in tumor tissue samples (12.26months vs. 2.40months, P<0.001). In plasma samples, the PFS of the mutant group was longer than that of the non-mutant group. However, there was no significant difference between the two groups (10.88months vs. 9.89months, P=0.411). The detection of EGFR mutations in plasma using ARMS is relatively sensitive and highly specific. However, EGFR mutation status tested by ARMS in plasma cannot replace a tumor tissue biopsy. Positive EGFR mutation results detected in plasma are fairly reliable, but negative results are hampered by a high rate of false negatives. Copyright © 2016. Published by Elsevier B.V.

A Third Moment Adjusted Test Statistic for Small Sample Factor Analysis.

PubMed

Lin, Johnny; Bentler, Peter M

2012-01-01

Goodness of fit testing in factor analysis is based on the assumption that the test statistic is asymptotically chi-square; but this property may not hold in small samples even when the factors and errors are normally distributed in the population. Robust methods such as Browne's asymptotically distribution-free method and Satorra Bentler's mean scaling statistic were developed under the presumption of non-normality in the factors and errors. This paper finds new application to the case where factors and errors are normally distributed in the population but the skewness of the obtained test statistic is still high due to sampling error in the observed indicators. An extension of Satorra Bentler's statistic is proposed that not only scales the mean but also adjusts the degrees of freedom based on the skewness of the obtained test statistic in order to improve its robustness under small samples. A simple simulation study shows that this third moment adjusted statistic asymptotically performs on par with previously proposed methods, and at a very small sample size offers superior Type I error rates under a properly specified model. Data from Mardia, Kent and Bibby's study of students tested for their ability in five content areas that were either open or closed book were used to illustrate the real-world performance of this statistic.

Measuring coverage in MNCH: total survey error and the interpretation of intervention coverage estimates from household surveys.

PubMed

Eisele, Thomas P; Rhoda, Dale A; Cutts, Felicity T; Keating, Joseph; Ren, Ruilin; Barros, Aluisio J D; Arnold, Fred

2013-01-01

Nationally representative household surveys are increasingly relied upon to measure maternal, newborn, and child health (MNCH) intervention coverage at the population level in low- and middle-income countries. Surveys are the best tool we have for this purpose and are central to national and global decision making. However, all survey point estimates have a certain level of error (total survey error) comprising sampling and non-sampling error, both of which must be considered when interpreting survey results for decision making. In this review, we discuss the importance of considering these errors when interpreting MNCH intervention coverage estimates derived from household surveys, using relevant examples from national surveys to provide context. Sampling error is usually thought of as the precision of a point estimate and is represented by 95% confidence intervals, which are measurable. Confidence intervals can inform judgments about whether estimated parameters are likely to be different from the real value of a parameter. We recommend, therefore, that confidence intervals for key coverage indicators should always be provided in survey reports. By contrast, the direction and magnitude of non-sampling error is almost always unmeasurable, and therefore unknown. Information error and bias are the most common sources of non-sampling error in household survey estimates and we recommend that they should always be carefully considered when interpreting MNCH intervention coverage based on survey data. Overall, we recommend that future research on measuring MNCH intervention coverage should focus on refining and improving survey-based coverage estimates to develop a better understanding of how results should be interpreted and used.

Measuring Coverage in MNCH: Total Survey Error and the Interpretation of Intervention Coverage Estimates from Household Surveys

PubMed Central

Eisele, Thomas P.; Rhoda, Dale A.; Cutts, Felicity T.; Keating, Joseph; Ren, Ruilin; Barros, Aluisio J. D.; Arnold, Fred

2013-01-01

Nationally representative household surveys are increasingly relied upon to measure maternal, newborn, and child health (MNCH) intervention coverage at the population level in low- and middle-income countries. Surveys are the best tool we have for this purpose and are central to national and global decision making. However, all survey point estimates have a certain level of error (total survey error) comprising sampling and non-sampling error, both of which must be considered when interpreting survey results for decision making. In this review, we discuss the importance of considering these errors when interpreting MNCH intervention coverage estimates derived from household surveys, using relevant examples from national surveys to provide context. Sampling error is usually thought of as the precision of a point estimate and is represented by 95% confidence intervals, which are measurable. Confidence intervals can inform judgments about whether estimated parameters are likely to be different from the real value of a parameter. We recommend, therefore, that confidence intervals for key coverage indicators should always be provided in survey reports. By contrast, the direction and magnitude of non-sampling error is almost always unmeasurable, and therefore unknown. Information error and bias are the most common sources of non-sampling error in household survey estimates and we recommend that they should always be carefully considered when interpreting MNCH intervention coverage based on survey data. Overall, we recommend that future research on measuring MNCH intervention coverage should focus on refining and improving survey-based coverage estimates to develop a better understanding of how results should be interpreted and used. PMID:23667331

Generalizability of findings from randomized controlled trials: application to the National Institute of Drug Abuse Clinical Trials Network.

PubMed

Susukida, Ryoko; Crum, Rosa M; Ebnesajjad, Cyrus; Stuart, Elizabeth A; Mojtabai, Ramin

2017-07-01

To compare randomized controlled trial (RCT) sample treatment effects with the population effects of substance use disorder (SUD) treatment. Statistical weighting was used to re-compute the effects from 10 RCTs such that the participants in the trials had characteristics that resembled those of patients in the target populations. Multi-site RCTs and usual SUD treatment settings in the United States. A total of 3592 patients in 10 RCTs and 1 602 226 patients from usual SUD treatment settings between 2001 and 2009. Three outcomes of SUD treatment were examined: retention, urine toxicology and abstinence. We weighted the RCT sample treatment effects using propensity scores representing the conditional probability of participating in RCTs. Weighting the samples changed the significance of estimated sample treatment effects. Most commonly, positive effects of trials became statistically non-significant after weighting (three trials for retention and urine toxicology and one trial for abstinence); also, non-significant effects became significantly positive (one trial for abstinence) and significantly negative effects became non-significant (two trials for abstinence). There was suggestive evidence of treatment effect heterogeneity in subgroups that are under- or over-represented in the trials, some of which were consistent with the differences in average treatment effects between weighted and unweighted results. The findings of randomized controlled trials (RCTs) for substance use disorder treatment do not appear to be directly generalizable to target populations when the RCT samples do not reflect adequately the target populations and there is treatment effect heterogeneity across patient subgroups. © 2017 Society for the Study of Addiction.

PAH Baselines for Amazonic Surficial Sediments: A Case of Study in Guajará Bay and Guamá River (Northern Brazil).

PubMed

Rodrigues, Camila Carneiro Dos Santos; Santos, Ewerton; Ramos, Brunalisa Silva; Damasceno, Flaviana Cardoso; Correa, José Augusto Martins

2018-06-01

The 16 priority PAH were determined in sediment samples from the insular zone of Guajará Bay and Guamá River (Southern Amazon River mouth). Low hydrocarbon levels were observed and naphthalene was the most representative PAH. The low molecular weight PAH represented 51% of the total PAH. Statistical analysis showed that the sampling sites are not significantly different. Source analysis by PAH ratios and principal component analysis revealed that PAH are primary from a few rate of fossil fuel combustion, mainly related to the local small community activity. All samples presented no biological stress or damage potencial according to the sediment quality guidelines. This study discuss baselines for PAH in surface sediments from Amazonic aquatic systems based on source determination by PAH ratios and principal component analysis, sediment quality guidelines and through comparison with previous studies data.

An investigative comparison of purging and non-purging groundwater sampling methods in Karoo aquifer monitoring wells

NASA Astrophysics Data System (ADS)

Gomo, M.; Vermeulen, D.

2015-03-01

An investigation was conducted to statistically compare the influence of non-purging and purging groundwater sampling methods on analysed inorganic chemistry parameters and calculated saturation indices. Groundwater samples were collected from 15 monitoring wells drilled in Karoo aquifers before and after purging for the comparative study. For the non-purging method, samples were collected from groundwater flow zones located in the wells using electrical conductivity (EC) profiling. The two data sets of non-purged and purged groundwater samples were analysed for inorganic chemistry parameters at the Institute of Groundwater Studies (IGS) laboratory of the Free University in South Africa. Saturation indices for mineral phases that were found in the data base of PHREEQC hydrogeochemical model were calculated for each data set. Four one-way ANOVA tests were conducted using Microsoft excel 2007 to investigate if there is any statistically significant difference between: (1) all inorganic chemistry parameters measured in the non-purged and purged groundwater samples per each specific well, (2) all mineral saturation indices calculated for the non-purged and purged groundwater samples per each specific well, (3) individual inorganic chemistry parameters measured in the non-purged and purged groundwater samples across all wells and (4) Individual mineral saturation indices calculated for non-purged and purged groundwater samples across all wells. For all the ANOVA tests conducted, the calculated alpha values (p) are greater than 0.05 (significance level) and test statistic (F) is less than the critical value (Fcrit) (F < Fcrit). The results imply that there was no statistically significant difference between the two data sets. With a 95% confidence, it was therefore concluded that the variance between groups was rather due to random chance and not to the influence of the sampling methods (tested factor). It is therefore be possible that in some hydrogeologic conditions, non-purged groundwater samples might be just as representative as the purged ones. The findings of this study can provide an important platform for future evidence oriented research investigations to establish the necessity of purging prior to groundwater sampling in different aquifer systems.

The characterization of natural gemstones using non-invasive FT-IR spectroscopy: New data on tourmalines.

PubMed

Mercurio, Mariano; Rossi, Manuela; Izzo, Francesco; Cappelletti, Piergiulio; Germinario, Chiara; Grifa, Celestino; Petrelli, Maurizio; Vergara, Alessandro; Langella, Alessio

2018-02-01

Fourteen samples of tourmaline from the Real Museo Mineralogico of Federico II University (Naples) have been characterized through multi-methodological investigations (EMPA-WDS, SEM-EDS, LA-ICP-MS, and FT-IR spectroscopy). The samples show different size, morphology and color, and are often associated with other minerals. Data on major and minor elements allowed to identify and classify tourmalines as follows: elbaites, tsilaisite, schorl, dravites, uvites and rossmanite. Non-invasive, non-destructive FT-IR and in-situ analyses were carried out on the same samples to validate this chemically-based identification and classification. The results of this research show that a complete characterization of this mineral species, usually time-consuming and expensive, can be successfully achieved through non-destructive FT-IR technique, thus representing a reliable tool for a fast classification extremely useful to plan further analytical strategies, as well as to support gemological appraisals. Copyright © 2017 Elsevier B.V. All rights reserved.

Non-destructive Moisture Content Measurement of Bioabsorbable Polymers Used in Medical Implants

NASA Astrophysics Data System (ADS)

Carroll, P. A.; Bell, S. A.; Maxwell, A. S.; Tomlins, P. E.

2012-09-01

Measurements have been made that link moisture content to the degradation of a bioabsorbable polymeric material, poly ( dl-lactide- co-glycolide) (PLGA). Bioabsorbable polymers used in medical implants degrade and are absorbed into the body. In the course of degradation, these polymers absorb water. Progressive non-destructive laboratory measurements of moisture content can be used as a means of tracking changes in these materials over the course of their degradation. Measurements of moisture content were made using a non-destructive microwave resonance instrument. The measurement approach, more usually applied to granular materials, was adapted to measure small, individual solid samples that do not fill the conventional sample volume of the resonator. Using the microwave resonance technique, gains in moisture content were measurable in increasingly degraded samples. The results were confirmed using alternative (destructive) measurements of sample moisture content. The microwave resonance technique offers a non-destructive measurement that can be used to study the degradation characteristics of PLGA. Better understanding of the degradation process can enable the polymer break-down rate to be tailored to match the healing rate of tissue. Non-destructive measurement allows effective study using single rather than multiple samples. This is a strong advantage when novel materials under study may be either expensive or in strictly limited availability.

Perceptions of Barriers to Undergraduate Education by Non-Traditional Students at Selected Non-Public, Liberal Arts Institutions in the Mid-South.

ERIC Educational Resources Information Center

Byrd, Sharon R.

The study examined barriers to education perceived by a sample of 119 students aged 25 and over attending small private liberal arts colleges in Arkansas, Mississippi, and Tennessee. Among findings were that the number of children a respondent had impacted his or her perception of situational and dispositional barriers; the employment status of…

Differences Between Fraternity and Non-Fraternity Members at the University of Maryland. Research Report No. 12-70.

ERIC Educational Resources Information Center

Lynch, Robert C.; Sedlacek, William E.

To ascertain the nature and extent of the differences between fraternity and non-fraternity men at the University of Maryland, a study was conducted in June 1969 with a small random sample (approximately 50 in each group). Their spring 1969 semester grades, ACT (or converted SAT) composite scores, and responses to selected items on the 1969…

Proteomic Biomarkers for Acute Interstitial Lung Disease in Gefitinib-Treated Japanese Lung Cancer Patients

PubMed Central

Kawakami, Takao; Nagasaka, Keiko; Takami, Sachiko; Wada, Kazuya; Tu, Hsiao-Kun; Otsuji, Makiko; Kyono, Yutaka; Dobashi, Tae; Komatsu, Yasuhiko; Kihara, Makoto; Akimoto, Shingo; Peers, Ian S.; South, Marie C.; Higenbottam, Tim; Fukuoka, Masahiro; Nakata, Koichiro; Ohe, Yuichiro; Kudoh, Shoji; Clausen, Ib Groth; Nishimura, Toshihide; Marko-Varga, György; Kato, Harubumi

2011-01-01

Interstitial lung disease (ILD) events have been reported in Japanese non-small-cell lung cancer (NSCLC) patients receiving EGFR tyrosine kinase inhibitors. We investigated proteomic biomarkers for mechanistic insights and improved prediction of ILD. Blood plasma was collected from 43 gefitinib-treated NSCLC patients developing acute ILD (confirmed by blinded diagnostic review) and 123 randomly selected controls in a nested case-control study within a pharmacoepidemiological cohort study in Japan. We generated ∼7 million tandem mass spectrometry (MS/MS) measurements with extensive quality control and validation, producing one of the largest proteomic lung cancer datasets to date, incorporating rigorous study design, phenotype definition, and evaluation of sample processing. After alignment, scaling, and measurement batch adjustment, we identified 41 peptide peaks representing 29 proteins best predicting ILD. Multivariate peptide, protein, and pathway modeling achieved ILD prediction comparable to previously identified clinical variables; combining the two provided some improvement. The acute phase response pathway was strongly represented (17 of 29 proteins, p = 1.0×10−25), suggesting a key role with potential utility as a marker for increased risk of acute ILD events. Validation by Western blotting showed correlation for identified proteins, confirming that robust results can be generated from an MS/MS platform implementing strict quality control. PMID:21799770

Ten-year trends in adolescents' self-reported emotional and behavioral problems in the Netherlands.

PubMed

Duinhof, Elisa L; Stevens, Gonneke W J M; van Dorsselaer, Saskia; Monshouwer, Karin; Vollebergh, Wilma A M

2015-09-01

Changes in social, cultural, economic, and governmental systems over time may affect adolescents' development. The present study examined 10-year trends in self-reported emotional and behavioral problems among 11- to 16-year-old adolescents in the Netherlands. In addition, gender (girls versus boys), ethnic (Dutch versus non western) and educational (vocational versus academic) differences in these trends were examined. By means of the Strengths and Difficulties Questionnaire, trends in emotional and behavioral problems were studied in adolescents belonging to one of five independent population representative samples (2003: n = 6,904; 2005: n = 5,183; 2007: n = 6,228; 2009: n = 5,559; 2013: n = 5,478). Structural equation models indicated rather stable levels of emotional and behavioral problems over time. Whereas some small changes were found between different time points, these changes did not represent consistent changes in problem levels. Similarly, gender, ethnic and educational differences in self-reported problems on each time point were highly comparable, indicating stable mental health inequalities between groups of adolescents over time. Future internationally comparative studies using multiple measurement moments are needed to monitor whether these persistent mental health inequalities hold over extended periods of time and in different countries.

Complete mitochondrial genome sequence of Urechis caupo, a representative of the phylum Echiura

PubMed Central

Boore, Jeffrey L

2004-01-01

Background Mitochondria contain small genomes that are physically separate from those of nuclei. Their comparison serves as a model system for understanding the processes of genome evolution. Although hundreds of these genome sequences have been reported, the taxonomic sampling is highly biased toward vertebrates and arthropods, with many whole phyla remaining unstudied. This is the first description of a complete mitochondrial genome sequence of a representative of the phylum Echiura, that of the fat innkeeper worm, Urechis caupo. Results This mtDNA is 15,113 nts in length and 62% A+T. It contains the 37 genes that are typical for animal mtDNAs in an arrangement somewhat similar to that of annelid worms. All genes are encoded by the same DNA strand which is rich in A and C relative to the opposite strand. Codons ending with the dinucleotide GG are more frequent than would be expected from apparent mutational biases. The largest non-coding region is only 282 nts long, is 71% A+T, and has potential for secondary structures. Conclusions Urechis caupo mtDNA shares many features with those of the few studied annelids, including the common usage of ATG start codons, unusual among animal mtDNAs, as well as gene arrangements, tRNA structures, and codon usage biases. PMID:15369601

Estimation of methacrylate monolith binding capacity from pressure drop data.

PubMed

Podgornik, Aleš; Smrekar, Vida; Krajnc, Peter; Strancar, Aleš

2013-01-11

Convective chromatographic media comprising of membranes and monoliths represent an important group of chromatographic supports due to their flow-unaffected chromatographic properties and consequently fast separation and purification even of large biological macromolecules. Consisting of a single piece of material, common characterization procedures based on analysis of a small sample assuming to be representative for the entire batch, cannot be applied. Because of that, non-invasive characterization methods are preferred. In this work pressure drop was investigated for an estimation of dynamic binding capacity (DBC) of proteins and plasmid DNA for monoliths with different pore sizes. It was demonstrated that methacrylate monolith surface area is reciprocally proportional to pore diameter and that pressure drop on monolith is reciprocally proportional to square pore size demonstrating that methacrylate monolith microstructure is preserved by changing pore size. Based on these facts mathematical formalism has been derived predicting that DBC is in linear correlation with the square root of pressure drop. This was experimentally confirmed for ion-exchange and hydrophobic interactions for proteins and plasmid DNA. Furthermore, pressure drop was also applied for an estimation of DBC in grafted layers of different thicknesses as estimated from the pressure drop data. It was demonstrated that the capacity is proportional to the estimated grafted layer thickness. Copyright © 2012 Elsevier B.V. All rights reserved.

Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs.

PubMed

Chávez Montes, Ricardo A; de Fátima Rosas-Cárdenas, Flor; De Paoli, Emanuele; Accerbi, Monica; Rymarquis, Linda A; Mahalingam, Gayathri; Marsch-Martínez, Nayelli; Meyers, Blake C; Green, Pamela J; de Folter, Stefan

2014-04-23

Small RNAs are pivotal regulators of gene expression that guide transcriptional and post-transcriptional silencing mechanisms in eukaryotes, including plants. Here we report a comprehensive atlas of sRNA and miRNA from 3 species of algae and 31 representative species across vascular plants, including non-model plants. We sequence and quantify sRNAs from 99 different tissues or treatments across species, resulting in a data set of over 132 million distinct sequences. Using miRBase mature sequences as a reference, we identify the miRNA sequences present in these libraries. We apply diverse profiling methods to examine critical sRNA and miRNA features, such as size distribution, tissue-specific regulation and sequence conservation between species, as well as to predict putative new miRNA sequences. We also develop database resources, computational analysis tools and a dedicated website, http://smallrna.udel.edu/. This study provides new insights on plant sRNAs and miRNAs, and a foundation for future studies.

Personality Development during Teacher Preparation.

PubMed

Corcoran, Roisin P; O'Flaherty, Joanne

2016-01-01

Objective: The purpose of this 3-year longitudinal study was to examine pre-service teachers' personality trajectories as measured by the IPIP Big-Five factor markers during teacher preparation. The relationship between students' personality traits, social desirability, and prior academic attainment was also examined. Method: This 3-year longitudinal study invited participants from the first year of a 4-year undergraduate (UG) pre-service teacher education program, the class of 2017. The sample consisted of 305 students. Results: The results suggest that extraversion, agreeableness, conscientiousness, emotional stability, and openness to experience were best represented by a non-significant longitudinal change in means. Results also suggest that social desirability predicts agreeableness and emotional stability with small to moderate effect sizes. Conclusion: The study concludes that no value is added to pre-service teachers' personality traits during 3 years of tertiary education. Furthermore, the data presented does not support the view that academic attainment is a good predictor of personality traits. Implications for educational research, theory, and practice are considered.

Personality Development during Teacher Preparation

PubMed Central

Corcoran, Roisin P.; O’Flaherty, Joanne

2016-01-01

Objective: The purpose of this 3-year longitudinal study was to examine pre-service teachers’ personality trajectories as measured by the IPIP Big-Five factor markers during teacher preparation. The relationship between students’ personality traits, social desirability, and prior academic attainment was also examined. Method: This 3-year longitudinal study invited participants from the first year of a 4-year undergraduate (UG) pre-service teacher education program, the class of 2017. The sample consisted of 305 students. Results: The results suggest that extraversion, agreeableness, conscientiousness, emotional stability, and openness to experience were best represented by a non-significant longitudinal change in means. Results also suggest that social desirability predicts agreeableness and emotional stability with small to moderate effect sizes. Conclusion: The study concludes that no value is added to pre-service teachers’ personality traits during 3 years of tertiary education. Furthermore, the data presented does not support the view that academic attainment is a good predictor of personality traits. Implications for educational research, theory, and practice are considered. PMID:27877143

Parameters selection in gene selection using Gaussian kernel support vector machines by genetic algorithm.

PubMed

Mao, Yong; Zhou, Xiao-Bo; Pi, Dao-Ying; Sun, You-Xian; Wong, Stephen T C

2005-10-01

In microarray-based cancer classification, gene selection is an important issue owing to the large number of variables and small number of samples as well as its non-linearity. It is difficult to get satisfying results by using conventional linear statistical methods. Recursive feature elimination based on support vector machine (SVM RFE) is an effective algorithm for gene selection and cancer classification, which are integrated into a consistent framework. In this paper, we propose a new method to select parameters of the aforementioned algorithm implemented with Gaussian kernel SVMs as better alternatives to the common practice of selecting the apparently best parameters by using a genetic algorithm to search for a couple of optimal parameter. Fast implementation issues for this method are also discussed for pragmatic reasons. The proposed method was tested on two representative hereditary breast cancer and acute leukaemia datasets. The experimental results indicate that the proposed method performs well in selecting genes and achieves high classification accuracies with these genes.

Measurement of airborne concentrations of tire and road wear particles in urban and rural areas of France, Japan, and the United States

NASA Astrophysics Data System (ADS)

Panko, Julie M.; Chu, Jennifer; Kreider, Marisa L.; Unice, Ken M.

2013-06-01

In addition to industrial facilities, fuel combustion, forest fires and dust erosion, exhaust and non-exhaust vehicle emissions are an important source of ambient air respirable particulate matter (PM10). Non-exhaust vehicle emissions are formed from wear particles of vehicle components such as brakes, clutches, chassis and tires. Although the non-exhaust particles are relatively minor contributors to the overall ambient air particulate load, reliable exposure estimates are few. In this study, a global sampling program was conducted to quantify tire and road wear particles (TRWP) in the ambient air in order to understand potential human exposures and the overall contribution of these particles to the PM10. The sampling was conducted in Europe, the United States and Japan and the sampling locations were selected to represent a variety of settings including both rural and urban core; and within each residential, commercial and recreational receptors. The air samples were analyzed using validated chemical markers for rubber polymer based on a pyrolysis technique. Results indicated that TRWP concentrations in the PM10 fraction were low with averages ranging from 0.05 to 0.70 μg m-3, representing an average PM10 contribution of 0.84%. The TRWP concentration in air was associated with traffic load and population density, but the trend was not statistically significant. Further, significant differences across days were not observed. This study provides a robust dataset to understand potential human exposures to airborne TRWP.

Heterogeneity in small aliquots of Apolllo 15 olivine-normative basalt: Implications for breccia clast studies

NASA Astrophysics Data System (ADS)

Lindstrom, Marilyn M.; Shervais, John W.; Vetter, Scott K.

1993-05-01

Most of the recent advances in lunar petrology are the direct result of breccia pull-apart studies, which have identified a wide array of new highland and mare basalt rock types that occur only as clasts within the breccias. These rocks show that the lunar crust is far more complex than suspected previously, and that processes such as magma mixing and wall-rock assimilation were important in its petrogenesis. These studies are based on the implicit assumption that the breccia clasts, which range in size from a few mm to several cm across, are representative of the parent rock from which they were derived. In many cases, the aliquot allocated for analysis may be only a few grain diameters across. While this problem is most acute for coarse-grained highland rocks, it can also cause considerable uncertainty in the analysis of mare basalt clasts. Similar problems arise with small aliquots of individual hand samples. Our study of sample heterogeneity in 9 samples of Apollo 15 olivine normative basalt (ONB) which exhibit a range in average grain size from coarse to fine are reported. Seven of these samples have not been analyzed previously, one has been analyzed by INAA only, and one has been analyzed by XRF+INAA. Our goal is to assess the effects of small aliquot size on the bulk chemistry of large mare basalt samples, and to extend this assessment to analyses of small breccia clasts.

Heterogeneity in small aliquots of Apolllo 15 olivine-normative basalt: Implications for breccia clast studies

NASA Technical Reports Server (NTRS)

Lindstrom, Marilyn M.; Shervais, John W.; Vetter, Scott K.

1993-01-01

Most of the recent advances in lunar petrology are the direct result of breccia pull-apart studies, which have identified a wide array of new highland and mare basalt rock types that occur only as clasts within the breccias. These rocks show that the lunar crust is far more complex than suspected previously, and that processes such as magma mixing and wall-rock assimilation were important in its petrogenesis. These studies are based on the implicit assumption that the breccia clasts, which range in size from a few mm to several cm across, are representative of the parent rock from which they were derived. In many cases, the aliquot allocated for analysis may be only a few grain diameters across. While this problem is most acute for coarse-grained highland rocks, it can also cause considerable uncertainty in the analysis of mare basalt clasts. Similar problems arise with small aliquots of individual hand samples. Our study of sample heterogeneity in 9 samples of Apollo 15 olivine normative basalt (ONB) which exhibit a range in average grain size from coarse to fine are reported. Seven of these samples have not been analyzed previously, one has been analyzed by INAA only, and one has been analyzed by XRF+INAA. Our goal is to assess the effects of small aliquot size on the bulk chemistry of large mare basalt samples, and to extend this assessment to analyses of small breccia clasts.

Determination of selected neurotoxic insecticides in small amounts of animal tissue utilizing a newly constructed mini-extractor.

PubMed

Seifertová, Marta; Čechová, Eliška; Llansola, Marta; Felipo, Vicente; Vykoukalová, Martina; Kočan, Anton

2017-10-01

We developed a simple analytical method for the simultaneous determination of representatives of various groups of neurotoxic insecticides (carbaryl, chlorpyrifos, cypermethrin, and α-endosulfan and β-endosulfan and their metabolite endosulfan sulfate) in limited amounts of animal tissues containing different amounts of lipids. Selected tissues (rodent fat, liver, and brain) were extracted in a special in-house-designed mini-extractor constructed on the basis of the Soxhlet and Twisselmann extractors. A dried tissue sample placed in a small cartridge was extracted, while the nascent extract was simultaneously filtered through a layer of sodium sulfate. The extraction was followed by combined clean-up, including gel permeation chromatography (in case of high lipid content), ultrasonication, and solid-phase extraction chromatography using C 18 on silica and aluminum oxide. Gas chromatography coupled with high-resolution mass spectrometry was used for analyte separation, detection, and quantification. Average recoveries for individual insecticides ranged from 82 to 111%. Expanded measurement uncertainties were generally lower than 35%. The developed method was successfully applied to rat tissue samples obtained from an animal model dealing with insecticide exposure during brain development. This method may also be applied to the analytical treatment of small amounts of various types of animal and human tissue samples. A significant advantage achieved using this method is high sample throughput due to the simultaneous treatment of many samples. Graphical abstract Optimized workflow for the determination of selected insecticides in small amounts of animal tissue including newly developed mini-extractor.

Clinical aspects of ECL-cell abnormalities.

PubMed Central

Hirschowitz, B. I.

1998-01-01

ECL cell hyperplasia results from hypergastrinemia, and in man this occurs due to achlorhydria in atrophic gastritis (pernicious anemia [PA]) and gastrinoma (Zollinger-Ellison syndrome [ZES]). Progression to neoplasia, i.e., ECL cell carcinoids (usually small, multicentric and non-functional), occurs in some five to 10 percent of patients with PA where they remain gastrin-dependent and reversible by normalization of serum gastrin by antrectomy. Even if untreated, the carcinoids are almost invariably benign and do not cause death. In ZES, ECL cell hyperplasia is progressive due to hypergastrinemia. However, carcinoids develop only in the MEN-I subtype but pose no additional threat of malignancy. A conservative approach is recommended for small multicentric carcinoids, and the tumors do not need removal. By contrast, single, large, non-gastrin-dependent carcinoids represent a different biological and clinical problem and are frequently malignant. PMID:10461361

Mobile phone use and location of glioma: a case-case analysis.

PubMed

Hartikka, Hanna; Heinävaara, Sirpa; Mäntylä, Riitta; Kähärä, Veikko; Kurttio, Päivi; Auvinen, Anssi

2009-04-01

We assessed a new approach for evaluating the glioma risk among users of mobile phones to focus on the part of the brain most heavily exposed to radiofrequency electromagnetic fields from mobile phones. The tumor midpoint was defined from radiological imaging. A case-case analysis with 99 gliomas was performed using logistic regression. The exposed cases were those with the tumor mid-point within 4.6 cm from the line between the mouth and the external meatus of the ear, representing the most likely location of the mobile phone (the source of exposure). Alternative analyses based on various indicators of mobile phone use as the outcome were also carried out. The majority of cases were regular mobile phone users. A slightly higher proportion of gliomas among mobile phone users than non-users occurred within 4.6 cm from the presumed location of the mobile phone (28% vs. 14%). Modestly elevated odds ratios were observed for several indicators of mobile phone use, but without an exposure gradient. The highest odds ratios were found for contralateral and short-term use. Our results, though limited by the small sample size, demonstrate that detailed information on tumor location allows evaluation of the risk related to the most heavily exposed part of the brain, representing direct evaluation of the possible local carcinogenic effects of the radiofrequency fields. However, field strength varies between users and over time also within a given anatomic site, due to the output power of the phone. Collaborative analysis of a larger sample is planned. (c) 2009 Wiley-Liss, Inc.

Association between serum antibodies to periodontal bacteria and rheumatoid factor in NHANES III

PubMed Central

Goh, Charlene E.; Kopp, Jacob; Papapanou, Panos N.; Molitor, Jerry A.; Demmer, Ryan T.

2016-01-01

Objective Alterations in the microbiome, including the periodontal microbiome, may be a risk factor for rheumatoid arthritis (RA). Most studies that have analyzed this association are relatively small, focus primarily on a single periodontal pathogen (Porphyromonas gingivalis), and are not population-based. We investigated the association between elevated serum IgG antibodies to 19 periodontal species and the prevalence of rheumatoid factor (RF) in a large nationally representative sample of adults. Methods The Third National Health and Nutrition Examination Survey is a cross-sectional sample of the non-institutionalized US population (n=33,994). Our study population included all dentate participants ≥60 years, who did not have RA as defined by a modified version of the American College of Rheumatology 1987 criteria, and had complete data for both serum IgG antibodies against periodontal bacteria and serum RF antibody titer (n=2461). Results Adjusted odds ratios (ORs) (95% CI) summarizing the relationship between the 19 periodontal serum IgGs and RF seropositivity ranged from 0.53 (0.29, 0.97) to 1.27 (0.79, 2.06), and 17 of the 19 observed ORs were < 1.0. The ORs for RF seropositivity among participants with elevated Prevotella intermedia [0.53 (0.29, 0.97)] and Capnocytophaga ochracea [0.54 (0.31, 0.95)] IgG were statistically significant. Conclusion We have found elevated periodontal IgGs to be mostly unassociated with RF seropositivity in the nationally representative NHANES III. Elevated antibody levels to P. intermedia and C. ochracea were associated with lower odds of RF seropositivity. PMID:27110949

[Blood sampling using "dried blood spot": a clinical biology revolution underway?].

PubMed

Hirtz, Christophe; Lehmann, Sylvain

2015-01-01

Blood testing using the dried blood spot (DBS) is used since the 1960s in clinical analysis, mainly within the framework of the neonatal screening (Guthrie test). Since then numerous analytes such as nucleic acids, small molecules or lipids, were successfully measured on the DBS. While this pre-analytical method represents an interesting alternative to classic blood sampling, its use in routine is still limited. We review here the different clinical applications of the blood sampling on DBS and estimate its future place, supported by the new methods of analysis as the LC-MS mass spectrometry.

Non-medical use of prescription drugs in a national sample of college women

PubMed Central

McCauley, Jenna L.; Amstadter, Ananda B.; Macdonald, Alexandra; Danielson, Carla Kmett; Ruggiero, Kenneth J.; Resnick, Heidi S.; Kilpatrick, Dean G.

2015-01-01

Non-medical use of prescription drugs (NMUPD) is one of the fastest growing forms of illicit drug use, with research indicating that college students represent a particularly high risk population. The current study examined demographic characteristics, health/mental health, substance misuse, and rape experiences as potential risk correlates of NMUPD among a national sample of college women (N=2000). Interviews were conducted via telephone using Computer-Assisted Telephone Interviewing technology. NMUPD was assessed by asking if, participants had used a prescription drug non-medically in the past year. NMUPD was endorsed by 7.8% of the sample (n=155). Although incapacitated and drug–alcohol facilitated rape were associated with NMUPD in the initial model, the final multivariable model showed that only lifetime major depression and other forms of substance use/abuse were significantly uniquely associated with an increased likelihood of NMUPD. Implications for primary and secondary prevention and subsequent research are addressed. PMID:21356576

Water retention of repellent and subcritical repellent soils: New insights from model and experimental investigations

NASA Astrophysics Data System (ADS)

Czachor, H.; Doerr, S. H.; Lichner, L.

2010-01-01

SummarySoil organic matter can modify the surface properties of the soil mineral phase by changing the surface tension of the mineral surfaces. This modifies the soil's solid-water contact angle, which in turn would be expected to affect its water retention curve (SWRC). Here we model the impact of differences in the soil pore-water contact angle on capillarity in non-cylindrical pores by accounting for their complex pore geometry. Key outcomes from the model include that (i) available methods for measuring the Young's wetting angle on soil samples are insufficient in representing the wetting angle in the soil pore space, (ii) the wetting branch of water retention curves is strongly affected by the soil pore-water contact angle, as manifest in the wetting behavior of water repellent soils, (iii) effects for the drying branch are minimal, indicating that both wettable and water repellent soils should behave similarly, and (vi) water retention is a feature not of only wettable soils, but also soils that are in a water repellent state. These results are tested experimentally by determining drying and wetting branches for (a) 'model soil' (quartz sands with four hydrophobization levels) and (b) five field soil samples with contrasting wettability, which were used with and without the removal of the soil organic matter. The experimental results support the theoretical predictions and indicate that small changes in wetting angle can cause switches between wettable and water repellent soil behavior. This may explain the common observation that relatively small changes in soil water content can cause substantial changes in soil wettability.

Water-quality data from ground- and surface-water sites near concentrated animal feeding operations (CAFOs) and non-CAFOs in the Shenandoah Valley and eastern shore of Virginia, January-February, 2004

USGS Publications Warehouse

Rice, Karen C.; Monti, Michele M.; Ettinger, Matthew R.

2005-01-01

Concentrated animal feeding operations (CAFOs) result from the consolidation of small farms with animals into larger operations, leading to a higher density of animals per unit of land on CAFOs than on small farms. The density of animals and subsequent concentration of animal wastes potentially can cause contamination of nearby ground and surface waters. This report summarizes water-quality data collected from agricultural sites in the Shenandoah Valley and Eastern Shore of Virginia. Five sites, three non-CAFO and two dairy-operation CAFO sites, were sampled in the Shenandoah Valley. Four sites, one non-CAFO and three poultry-operation CAFO sites were sampled on the Eastern Shore. All samples were collected during January and February 2004. Water samples were analyzed for the following parameters and constituents: temperature, specific conductance, pH, and dissolved oxygen; concentrations of the indicator organisms Escherichia coli (E. coli) and enterococci; bacterial isolates of E. coli, enterococci, Salmonella spp., and Campylobacter spp.; sensitivity to antibiotics of E. coli, enterococci, and Salmonella spp.; arsenic, cadmium, chromium3+, copper, nickel, and mercury; hardness, biological oxygen demand, nitrate, nitrite, ammonia, ortho-phosphate, total Kjeldahl nitrogen, chemical oxygen demand, total organic carbon, and dissolved organic carbon; and 45 dissolved organic compounds, which included a suite of antibiotic compounds.Data are presented in tables 5-21 and results of analyses of replicate samples are presented in tables 22-28. A summary of the data in tables 5-8 and 18-21 is included in the report.

Filling in the Gaps: Xenoliths in Meteorites are Samples of "Missing" Asteroid Lithologies

NASA Technical Reports Server (NTRS)

Zolensky, Mike

2016-01-01

We know that the stones that fall to earth as meteorites are not representative of the full diversity of small solar system bodies, because of the peculiarities of the dynamical processes that send material into Earth-crossing paths [1] which result in severe selection biases. Thus, the bulk of the meteorites that fall are insufficient to understand the full range of early solar system processes. However, the situation is different for pebble- and smaller-sized objects that stream past the giant planets and asteroid belts into the inner solar system in a representative manner. Thus, micrometeorites and interplanetary dust particles have been exploited to permit study of objects that do not provide meteorites to earth. However, there is another population of materials that sample a larger range of small solar system bodies, but which have received little attention - pebble-sized foreign clasts in meteorites (also called xenoliths, dark inclusions, clasts, etc.). Unfortunately, most previous studies of these clasts have been misleading, in that these objects have simply been identified as pieces of CM or CI chondrites. In our work we have found this to be generally erroneous, and that CM and especially CI clasts are actually rather rare. We therefore test the hypothesis that these clasts sample the full range of small solar system bodies. We have located and obtained samples of clasts in 81 different meteorites, and have begun a thorough characterization of the bulk compositions, mineralogies, petrographies, and organic compositions of this unique sample set. In addition to the standard e-beam analyses, recent advances in technology now permit us to measure bulk O isotopic compositions, and major- though trace-element compositions of the sub-mm-sized discrete clasts. Detailed characterization of these clasts permit us to explore the full range of mineralogical and petrologic processes in the early solar system, including the nature of fluids in the Kuiper belt and the outer main asteroid belt, as revealed by the mineralogy of secondary phases.

[Detection of EML4-ALK fusion gene in non-small cell lung cancer and its clinicopathologic correlation].

PubMed

Zhong, Shan; Zhang, Hai-ping; Zheng, Jie; Bai, Dong-yu; Fu, Li; Chen, Pei-qiong

2013-04-01

To investigate the frequency of EML4-ALK fusion gene in non-small-cell lung cancer (NSCLC) patients, and its correlation with clinicopathologic features. Real-time PCR was used to detect the presence of EML4-ALK fusion gene in 268 cases of NSCLCs using paraffin-embedded tissue samples(among which 164 samples were re-validated by Sanger sequencing). Related clinicopathological correlation was analyzed. EML4-ALK fusion gene was found in 4.1% (11/268) of the cases. One hundred and sixty four samples were verified by Sanger sequencing, and the overall coincidence of the results of two methods (Sanger sequencing and Real-time PCR) was 100%. Female patients (5.9%, 5/85), ≤ 60 years of age (4.3%, 6/140), non-smokers (6.8%, 8/118) and adenocarcinomas (7.6%, 10/132) had a higher mutation rate than that in male patients (3.3%, 6/183), > 60 years of age (4.0%, 5/124), smokers (1.6%, 2/132) and squamous cell carcinomas (1.3%, 1/79), although no statistical significance in age (P = 0.918), gender (P = 0.503), smoking history (P = 0.092) and histological type (P = 0.094). Chinese NSCLC patients have a 4.1% detection rate of EML4-ALK fusion gene in the tumor tissues. Female, non-smoker and adenocarcinoma histological subtype tend to be associated with a higher rate of EML4-ALK gene fusion.

One size does not fit all: an examination of low birthweight disparities among a diverse set of racial/ethnic groups.

PubMed

Johnelle Sparks, P

2009-11-01

To examine disparities in low birthweight using a diverse set of racial/ethnic categories and a nationally representative sample. This research explored the degree to which sociodemographic characteristics, health care access, maternal health status, and health behaviors influence birthweight disparities among seven racial/ethnic groups. Binary logistic regression models were estimated using a nationally representative sample of singleton, normal for gestational age births from 2001 using the ECLS-B, which has an approximate sample size of 7,800 infants. The multiple variable models examine disparities in low birthweight (LBW) for seven racial/ethnic groups, including non-Hispanic white, non-Hispanic black, U.S.-born Mexican-origin Hispanic, foreign-born Mexican-origin Hispanic, other Hispanic, Native American, and Asian mothers. Race-stratified logistic regression models were also examined. In the full sample models, only non-Hispanic black mothers have a LBW disadvantage compared to non-Hispanic white mothers. Maternal WIC usage was protective against LBW in the full models. No prenatal care and adequate plus prenatal care increase the odds of LBW. In the race-stratified models, prenatal care adequacy and high maternal health risks are the only variables that influence LBW for all racial/ethnic groups. The race-stratified models highlight the different mechanism important across the racial/ethnic groups in determining LBW. Differences in the distribution of maternal sociodemographic, health care access, health status, and behavior characteristics by race/ethnicity demonstrate that a single empirical framework may distort associations with LBW for certain racial and ethnic groups. More attention must be given to the specific mechanisms linking maternal risk factors to poor birth outcomes for specific racial/ethnic groups.

Deficiency of ''Thin'' Stellar Bars in Seyfert Host Galaxies

NASA Technical Reports Server (NTRS)

Shlosman, Isaac; Peletier, Reynier F.; Knapen, Johan

1999-01-01

Using all available major samples of Seyfert galaxies and their corresponding control samples of closely matched non-active galaxies, we find that the bar ellipticities (or axial ratios) in Seyfert galaxies are systematically different from those in non-active galaxies. Overall, there is a deficiency of bars with large ellipticities (i.e., 'fat' or 'weak' bars) in Seyferts, compared to non-active galaxies. Accompanied with a large dispersion due to small number statistics, this effect is strictly speaking at the 2 sigma level. To obtain this result, the active galaxy samples of near-infrared surface photometry were matched to those of normal galaxies in type, host galaxy ellipticity, absolute magnitude, and, to some extent, in redshift. We discuss possible theoretical explanations of this phenomenon within the framework of galactic evolution, and, in particular, of radial gas redistribution in barred galaxies. Our conclusions provide further evidence that Seyfert hosts differ systematically from their non-active counterparts on scales of a few kpc.

[Construction of 2-dimensional tumor microvascular architecture phenotype in non-small cell lung cancer].

PubMed

Liu, Jin-kang; Wang, Xiao-yi; Xiong, Zeng; Zhou, Hui; Zhou, Jian-hua; Fu, Chun-yan; Li, Bo

2008-08-01

To construct a technological platform of 2-dimensional tumor microvascular architecture phenotype (2D-TAMP) expression. Thirty samples of non-small cell lung cancer (NSCLC) were collected after surgery. The corresponding sections of tumor tissue specimens to the slice of CT perfusion imaging were selected. Immunohistochemical staining,Gomori methenamine silver stain, and electron microscope observation were performed to build a technological platform of 2D-TMAP expression by detecting the morphology and the integrity of basement membrane of microvasculature, microvascular density, various microvascular subtype, the degree of the maturity and lumenization of microvasculature, and the characteristics of immunogenetics of microvasculature. The technological platform of 2D-TMAP expression was constructed successfully. There was heterogeneity in 2D-TMAP expression of non-small cell lung cancer. The microvascular of NSCLC had certain characteristics. 2D-TMAP is a key technology that can be used to observe the overall state of micro-environment in tumor growth.

Residential metal contamination and potential health risks of ...

EPA Pesticide Factsheets

Potosí, Bolivia, is the site of centuries of historic and present-day mining of the Cerro Rico Mountain, known for its rich polymetallic deposits, and was the site of large-scale Colonial era silver refining operations, both of which have left a legacy of pollution. In this study, trace elements were quantified in adobe brick, dirt floor, and surface dust samples from 49 houses. Mean concentrations of total mercury (Hg), lead (Pb), and arsenic (As) were statistically significantly greater than concentrations measured in Sucre, Bolivia, a non-mining town used as a reference site, and exceeded US-based soil screening levels that are designed to be protective of human health. Adobe brick samples were analyzed for bioaccessible concentrations of elements using a simulated gastric fluid (GF) extraction. Mean GF extractable concentrations of Hg, As, and Pb were 0.841, 14.9, and 30.2 percent of the total concentration, respectively. Total and GF extractable concentrations of these elements were used to estimate exposure and potential health risks to children following incidental ingestion of adobe brick particles. Risks were assessed using a range of potential ingestion rates (50-1000 mg/day). Although the majority of households have total Hg, As, and Pb concentrations that represent a potential health risk, fewer are of concern when GF extractable concentrations are considered at lower ingestion rates. For Hg, only a small percentage of the sampled houses have GF ex

Real time and label free profiling of clinically relevant exosomes

PubMed Central

Sina, Abu Ali Ibn; Vaidyanathan, Ramanathan; Dey, Shuvashis; Carrascosa, Laura G.; Shiddiky, Muhammad J. A.; Trau, Matt

2016-01-01

Tumor-derived exosomes possess significant clinical relevance due to their unique composition of genetic and protein material that is representative of the parent tumor. Specific isolation as well as identification of proportions of these clinically relevant exosomes (CREs) from biological samples could help to better understand their clinical significance as cancer biomarkers. Herein, we present a simple approach for quantification of the proportion of CREs within the bulk exosome population isolated from patient serum. This proportion of CREs can potentially inform on the disease stage and enable non-invasive monitoring of inter-individual variations in tumor-receptor expression levels. Our approach utilises a Surface Plasmon Resonance (SPR) platform to quantify the proportion of CREs in a two-step strategy that involves (i) initial isolation of bulk exosome population using tetraspanin biomarkers (i.e., CD9, CD63), and (ii) subsequent detection of CREs within the captured bulk exosomes using tumor-specific markers (e.g., human epidermal growth factor receptor 2 (HER2)). We demonstrate the isolation of bulk exosome population and detection of as low as 10% HER2(+) exosomes from samples containing designated proportions of HER2(+) BT474 and HER2(−) MDA-MB-231 cell derived exosomes. We also demonstrate the successful isolation of exosomes from a small cohort of breast cancer patient samples and identified that approximately 14–35% of their bulk population express HER2. PMID:27464736

Real time and label free profiling of clinically relevant exosomes.

PubMed

Sina, Abu Ali Ibn; Vaidyanathan, Ramanathan; Dey, Shuvashis; Carrascosa, Laura G; Shiddiky, Muhammad J A; Trau, Matt

2016-07-28

Tumor-derived exosomes possess significant clinical relevance due to their unique composition of genetic and protein material that is representative of the parent tumor. Specific isolation as well as identification of proportions of these clinically relevant exosomes (CREs) from biological samples could help to better understand their clinical significance as cancer biomarkers. Herein, we present a simple approach for quantification of the proportion of CREs within the bulk exosome population isolated from patient serum. This proportion of CREs can potentially inform on the disease stage and enable non-invasive monitoring of inter-individual variations in tumor-receptor expression levels. Our approach utilises a Surface Plasmon Resonance (SPR) platform to quantify the proportion of CREs in a two-step strategy that involves (i) initial isolation of bulk exosome population using tetraspanin biomarkers (i.e., CD9, CD63), and (ii) subsequent detection of CREs within the captured bulk exosomes using tumor-specific markers (e.g., human epidermal growth factor receptor 2 (HER2)). We demonstrate the isolation of bulk exosome population and detection of as low as 10% HER2(+) exosomes from samples containing designated proportions of HER2(+) BT474 and HER2(-) MDA-MB-231 cell derived exosomes. We also demonstrate the successful isolation of exosomes from a small cohort of breast cancer patient samples and identified that approximately 14-35% of their bulk population express HER2.

[Premalignant conditions of the small bowel].

PubMed

Drastich, P

2013-01-01

Small intestinal dysplastic lesions are rare and difficult to detect before they progress to cancer. New investigative modalities, such as capsule endoscopy and doubleballoon enteroscopy, are very promising in search for premalignant lesions. Screening patients at high-risk for small bowel neoplasia is the only sensible approach. Duodenal adenoma represents the most easily accessible tumors with the possibility of curative endoscopic resection. Due to the strong association of the small bowel and colonic adenomas, it is always necessary to perform colonoscopy. In young patients, the exclusion of familial polyposis by genetic testing is always mandatory. Patients with celiac disease are especially at risk of developing nonHodgkins lymphomas and adenocarcinomas. There is a high-risk of ampuloma and other adenomas in patients with familial adenomatous polyposis. Patients with prolonged and complicated course of Crohns disease, Peutz Jeghers syndrome and patients with ileoanal pouch have higher risk of adenocarcinoma of the small intestine.

Mycobacterium mucogenicum and other non-tuberculous mycobacteria in potable water of a trauma hospital: a potential source for human infection.

PubMed

Fernandez-Rendon, E; Cerna-Cortes, J F; Ramirez-Medina, M A; Helguera-Repetto, A C; Rivera-Gutierrez, S; Estrada-Garcia, T; Gonzalez-Y-Merchand, J A

2012-01-01

This study examined the frequency of occurrence of non-tuberculous mycobacteria (NTM) in potable water samples from a main trauma hospital in Mexico City. Sixty-nine potable water samples were collected, 23 from each source: cistern, kitchen tap and bathroom showers. Of the 69 samples, 36 harboured NTM species. Twenty-nine of the 36 isolates were Mycobacterium mucogenicum, two Mycobacterium rhodesiae, one Mycobacterium peregrinum, one Mycobacterium fortuitum and three were Mycobacterium spp. Hospital potable water harbouring NTM represents a potential source for nosocomial infections, therefore we suggest that hospital potable water microbiological guidelines should include testing for NTM species. Copyright © 2011 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Impact of sampling techniques on measured stormwater quality data for small streams

USGS Publications Warehouse

Harmel, R.D.; Slade, R.M.; Haney, R.L.

2010-01-01

Science-based sampling methodologies are needed to enhance water quality characterization for setting appropriate water quality standards, developing Total Maximum Daily Loads, and managing nonpoint source pollution. Storm event sampling, which is vital for adequate assessment of water quality in small (wadeable) streams, is typically conducted by manual grab or integrated sampling or with an automated sampler. Although it is typically assumed that samples from a single point adequately represent mean cross-sectional concentrations, especially for dissolved constituents, this assumption of well-mixed conditions has received limited evaluation. Similarly, the impact of temporal (within-storm) concentration variability is rarely considered. Therefore, this study evaluated differences in stormwater quality measured in small streams with several common sampling techniques, which in essence evaluated within-channel and within-storm concentration variability. Constituent concentrations from manual grab samples and from integrated samples were compared for 31 events, then concentrations were also compared for seven events with automated sample collection. Comparison of sampling techniques indicated varying degrees of concentration variability within channel cross sections for both dissolved and particulate constituents, which is contrary to common assumptions of substantial variability in particulate concentrations and of minimal variability in dissolved concentrations. Results also indicated the potential for substantial within-storm (temporal) concentration variability for both dissolved and particulate constituents. Thus, failing to account for potential cross-sectional and temporal concentration variability in stormwater monitoring projects can introduce additional uncertainty in measured water quality data. Copyright ?? 2010 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

Spatial and temporal patterns in fish assemblages of upper coastal plain streams, Mississippi, USA

Treesearch

Susan B. Adams; Melvin L. Warren; Wendell R. Haag

2004-01-01

We assessed spatial, seasonal, and annual variation in fish assemblages over 17 months in three small- to medium-sized, incised streams characteristic of northwestern Mississippi streams. We sampled 17 962 fish representing 52 species and compared assemblages within and among streams. Although annual and seasonal variability inassemblage structure was high, fish...

The Requirement for Vocational Skills in the Engineering Industry in the Areas of Modena and Vienna. Synthesis Report.

ERIC Educational Resources Information Center

Gatti, Mario; Mereu, Maria Grazia; Tagliaferro, Claudio; Markowitsch, Jorg; Neuberger, Robert

Requirements for vocational skills in the engineering industry in Modena, Italy, and Vienna, Austria, were studied. In Modena, employees of a representative sample of 90 small, medium, and large firms in the mechanical processing, agricultural machinery, and sports car manufacturing sectors were interviewed. In Vienna, data were collected through…

Reporting Rape in a National Sample of College Women

ERIC Educational Resources Information Center

Wolitzky-Taylor, Kate B.; Resnick, Heidi S.; Amstadter, Ananda B.; McCauley, Jenna L.; Ruggiero, Kenneth J.; Kilpatrick, Dean G.

2011-01-01

Background: Studies indicate that a small percentage of rapes are reported to law enforcement officials. Research also suggests that rapes perpetrated by a stranger are more likely to be reported and that rapes involving drugs and/or alcohol are less likely to be reported. College women represent a unique and understudied population with regard to…

Linking harvest choices to timber supply

Treesearch

Jeffrey P. Prestemon; David N. Wear

2000-01-01

Aggregate timber supply by ownership was investigated for a small region by applying stand-level harvest choice models to a representative sample of stands and then aggregating to regional totals using the area-frame of the forest survey. Timber harvest choices were estimated as probit models for three ownership categories in coastal plain southern pine stands of North...

Mental and somatic health in a non-clinical sample 10 years after a diagnosis of encopresis.

PubMed

Hultén, Ib; Jonsson, Jakob; Jonsson, Carl-Otto

2005-12-01

The aim of this study was to assess the relation between the diagnosis of encopresis at 8 and 10 years of age, and mental and somatic health 10 years later. The importance of type of encopresis (primary or secondary) at 8 years was also studied. Subjects were a non-clinical encopretic sample (N=73) and control subjects (N=75) [2]. Seven assessment variables from conscription surveys provided information about mental and somatic health status at 18 years of age. Former encopretics (n=66) did not differ significantly from the controls (n=67) at 18 years of age, although there were consistent, small negative differences. The boys who at 10 years of age had still been encopretic did not differ significantly at 18 years of age from the boys who at 10 years had recovered from encopresis, and the signs indicating the small differences varied. For former primary and secondary encopretic boys, there were two significant differences, the men in the secondary group being more often exempted from conscription than the primary group and the control cases. The results indicate that boys with non-clinical encopresis show only small, if any, mental and somatic disturbances at the beginning of adulthood. Comprehensive investigations of encopretic patients are recommended as important clinical problems, in addition to encopresis, might be present.

A preliminary result of three-dimensional microarray technology to gene analysis with endoscopic ultrasound-guided fine-needle aspiration specimens and pancreatic juices

PubMed Central

2010-01-01

Background Analysis of gene expression and gene mutation may add information to be different from ordinary pathological tissue diagnosis. Since samples obtained endoscopically are very small, it is desired that more sensitive technology is developed for gene analysis. We investigated whether gene expression and gene mutation analysis by newly developed ultra-sensitive three-dimensional (3D) microarray is possible using small amount samples from endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) specimens and pancreatic juices. Methods Small amount samples from 17 EUS-FNA specimens and 16 pancreatic juices were obtained. After nucleic acid extraction, the samples were amplified with labeling and analyzed by the 3D microarray. Results The analyzable rate with the microarray was 46% (6/13) in EUS-FNA specimens of RNAlater® storage, and RNA degradations were observed in all the samples of frozen storage. In pancreatic juices, the analyzable rate was 67% (4/6) in frozen storage samples and 20% (2/10) in RNAlater® storage. EUS-FNA specimens were classified into cancer and non-cancer by gene expression analysis and K-ras codon 12 mutations were also detected using the 3D microarray. Conclusions Gene analysis from small amount samples obtained endoscopically was possible by newly developed 3D microarray technology. High quality RNA from EUS-FNA samples were obtained and remained in good condition only using RNA stabilizer. In contrast, high quality RNA from pancreatic juice samples were obtained only in frozen storage without RNA stabilizer. PMID:20416107

The Novel Application of Non-Lethal Citizen Science Tissue Sampling in Recreational Fisheries.

PubMed

Williams, Samuel M; Holmes, Bonnie J; Pepperell, Julian G

2015-01-01

Increasing fishing pressure and uncertainty surrounding recreational fishing catch and effort data promoted the development of alternative methods for conducting fisheries research. A pilot investigation was undertaken to engage the Australian game fishing community and promote the non-lethal collection of tissue samples from the black marlin Istiompax indica, a valuable recreational-only species in Australian waters, for the purpose of future genetic research. Recruitment of recreational anglers was achieved by publicizing the project in magazines, local newspapers, social media, blogs, websites and direct communication workshops at game fishing tournaments. The Game Fishing Association of Australia and the Queensland Game Fishing Association were also engaged to advertise the project and recruit participants with a focus on those anglers already involved in the tag-and-release of marlin. Participants of the program took small tissue samples using non-lethal methods which were stored for future genetic analysis. The program resulted in 165 samples from 49 participants across the known distribution of I. indica within Australian waters which was a sufficient number to facilitate a downstream population genetic analysis. The project demonstrated the potential for the development of citizen science sampling programs to collect tissue samples using non-lethal methods in order to achieve targeted research objects in recreationally caught species.

Drop-on-demand sample introduction system coupled with the flowing atmospheric-pressure afterglow for direct molecular analysis of complex liquid micro-volume samples

PubMed Central

Schaper, J. Niklas; Pfeuffer, Kevin P.; Shelley, Jacob T.; Bings, Nicolas H.

2012-01-01

One of the fastest developing fields in analytical spectrochemistry in recent years is ambient desorption/ionization mass spectrometry (ADI-MS). This burgeoning interest has been due to the demonstrated advantages of the method: simple mass spectra, little or no sample preparation, and applicability to samples in the solid, liquid, or gaseous state. One such ADI-MS source, the flowing atmospheric-pressure afterglow (FAPA), is capable of direct analysis of solids just by aiming the source at the solid surface and sampling the produced ions into a mass spectrometer. However, direct introduction of significant volumes of liquid samples into this source has not been possible, as solvent loads can quench the afterglow and, thus, the formation of reagent ions. As a result, the analysis of liquid samples is preferably carried out by analyzing dried residues or by desorbing small amounts of liquid samples directly from the liquid surface. In the former case, reproducibility of sample introduction is crucial if quantitative results are desired. In the present study, introduction of liquid samples as very small droplets helps overcome the issues of sample positioning and reduced levels of solvent intake. A recently developed “drop-on-demand” (DOD) aerosol generator is capable of reproducibly producing very small volumes of liquid (~17 pL). In this paper, the coupling of FAPA-MS and DOD is reported and applications are suggested. Analytes representing different classes of substances were tested and limits of detections were determined. Matrix tolerance was investigated for drugs of abuse and their metabolites by analyzing raw urine samples and quantification without the use of internal standards. Limits of detection below 2 µg/mL, without sample pretreatment, were obtained. PMID:23025277

Drop-on-demand sample introduction system coupled with the flowing atmospheric-pressure afterglow for direct molecular analysis of complex liquid microvolume samples.

PubMed

Schaper, J Niklas; Pfeuffer, Kevin P; Shelley, Jacob T; Bings, Nicolas H; Hieftje, Gary M

2012-11-06

One of the fastest developing fields in analytical spectrochemistry in recent years is ambient desorption/ionization mass spectrometry (ADI-MS). This burgeoning interest has been due to the demonstrated advantages of the method: simple mass spectra, little or no sample preparation, and applicability to samples in the solid, liquid, or gaseous state. One such ADI-MS source, the flowing atmospheric-pressure afterglow (FAPA), is capable of direct analysis of solids just by aiming the source at the solid surface and sampling the produced ions into a mass spectrometer. However, direct introduction of significant volumes of liquid samples into this source has not been possible, as solvent loads can quench the afterglow and, thus, the formation of reagent ions. As a result, the analysis of liquid samples is preferably carried out by analyzing dried residues or by desorbing small amounts of liquid samples directly from the liquid surface. In the former case, reproducibility of sample introduction is crucial if quantitative results are desired. In the present study, introduction of liquid samples as very small droplets helps overcome the issues of sample positioning and reduced levels of solvent intake. A recently developed "drop-on-demand" (DOD) aerosol generator is capable of reproducibly producing very small volumes of liquid (∼17 pL). In this paper, the coupling of FAPA-MS and DOD is reported and applications are suggested. Analytes representing different classes of substances were tested and limits of detections were determined. Matrix tolerance was investigated for drugs of abuse and their metabolites by analyzing raw urine samples and quantification without the use of internal standards. Limits of detection below 2 μg/mL, without sample pretreatment, were obtained.

Forest treatment residues for thermal energy compared with disposal by onsite burning: Emissions and energy return

Treesearch

Greg Jones; Dan Loeffler; David Calkin; Woodam Chung

2010-01-01

Mill residues from forest industries are the source for most of the current wood-based energy in the US, approximately 2.1% of the nation's energy use in 2007. Forest residues from silvicultural treatments, which include limbs, tops, and small non-commercial trees removed for various forest management objectives, represent an additional source of woody biomass for...

Increased lipoprotein lipase activity in non-small cell lung cancer tissue predicts shorter patient survival.

PubMed

Trost, Zoran; Sok, Miha; Marc, Janja; Cerne, Darko

2009-07-01

Cumulative evidence suggests the involvement of lipoprotein lipase (LPL) in tumor progression. We tested the hypothesis that increased LPL activity in resectable non-small cell lung cancer (NSCLC) tissue and the increased LPL gene expression in the surrounding non-cancer lung tissue found in our previous study are predictors of patient survival. Forty two consecutive patients with resected NSCLC were enrolled in the study. Paired samples of lung cancer tissue and adjacent non-cancer lung tissue were collected from resected specimens for baseline LPL activity and gene expression estimation. During a 4-year follow-up, 21 patients died due to tumor progression. One patient died due to a non-cancer reason and was not included in Cox regression analysis. High LPL activity in cancer tissue (relative to the adjacent non-cancer lung tissue) predicted shorter survival, independently of standard prognostic factors (p=0.003). High gene expression in the non-cancer lung tissue surrounding the tumor had no predictive value. Our study further underlines the involvement of cancer tissue LPL activity in tumor progression.

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

NASA Astrophysics Data System (ADS)

Valotto, Gabrio; Cattaruzza, Elti; Bardelli, Fabrizio

2017-02-01

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

Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon

PubMed Central

2013-01-01

Background The wild grass Brachypodium distachyon has emerged as a model system for temperate grasses and biofuel plants. However, the global analysis of miRNAs, molecules known to be key for eukaryotic gene regulation, has been limited in B. distachyon to studies examining a few samples or that rely on computational predictions. Similarly an in-depth global analysis of miRNA-mediated target cleavage using parallel analysis of RNA ends (PARE) data is lacking in B. distachyon. Results B. distachyon small RNAs were cloned and deeply sequenced from 17 libraries that represent different tissues and stresses. Using a computational pipeline, we identified 116 miRNAs including not only conserved miRNAs that have not been reported in B. distachyon, but also non-conserved miRNAs that were not found in other plants. To investigate miRNA-mediated cleavage function, four PARE libraries were constructed from key tissues and sequenced to a total depth of approximately 70 million sequences. The roughly 5 million distinct genome-matched sequences that resulted represent an extensive dataset for analyzing small RNA-guided cleavage events. Analysis of the PARE and miRNA data provided experimental evidence for miRNA-mediated cleavage of 264 sites in predicted miRNA targets. In addition, PARE analysis revealed that differentially expressed miRNAs in the same family guide specific target RNA cleavage in a correspondingly tissue-preferential manner. Conclusions B. distachyon miRNAs and target RNAs were experimentally identified and analyzed. Knowledge gained from this study should provide insights into the roles of miRNAs and the regulation of their targets in B. distachyon and related plants. PMID:24367943

Space-Time Smoothing of Complex Survey Data: Small Area Estimation for Child Mortality.

PubMed

Mercer, Laina D; Wakefield, Jon; Pantazis, Athena; Lutambi, Angelina M; Masanja, Honorati; Clark, Samuel

2015-12-01

Many people living in low and middle-income countries are not covered by civil registration and vital statistics systems. Consequently, a wide variety of other types of data including many household sample surveys are used to estimate health and population indicators. In this paper we combine data from sample surveys and demographic surveillance systems to produce small area estimates of child mortality through time. Small area estimates are necessary to understand geographical heterogeneity in health indicators when full-coverage vital statistics are not available. For this endeavor spatio-temporal smoothing is beneficial to alleviate problems of data sparsity. The use of conventional hierarchical models requires careful thought since the survey weights may need to be considered to alleviate bias due to non-random sampling and non-response. The application that motivated this work is estimation of child mortality rates in five-year time intervals in regions of Tanzania. Data come from Demographic and Health Surveys conducted over the period 1991-2010 and two demographic surveillance system sites. We derive a variance estimator of under five years child mortality that accounts for the complex survey weighting. For our application, the hierarchical models we consider include random effects for area, time and survey and we compare models using a variety of measures including the conditional predictive ordinate (CPO). The method we propose is implemented via the fast and accurate integrated nested Laplace approximation (INLA).

The significance of PIWI family expression in human lung embryogenesis and non-small cell lung cancer.

PubMed

Navarro, Alfons; Tejero, Rut; Viñolas, Nuria; Cordeiro, Anna; Marrades, Ramon M; Fuster, Dolors; Caritg, Oriol; Moises, Jorge; Muñoz, Carmen; Molins, Laureano; Ramirez, Josep; Monzo, Mariano

2015-10-13

The expression of Piwi-interacting RNAs, small RNAs that bind to PIWI proteins, was until recently believed to be limited to germinal stem cells. We have studied the expression of PIWI genes during human lung embryogenesis and in paired tumor and normal tissue prospectively collected from 71 resected non-small-cell lung cancer patients. The mRNA expression analysis showed that PIWIL1 was highly expressed in 7-week embryos and downregulated during the subsequent weeks of development. PIWIL1 was expressed in 11 of the tumor samples but in none of the normal tissue samples. These results were validated by immunohistochemistry, showing faint cytoplasmic reactivity in the PIWIL1-positive samples. Interestingly, the patients expressing PIWIL1 had a shorter time to relapse (TTR) (p = 0.006) and overall survival (OS) (p = 0.0076) than those without PIWIL1 expression. PIWIL2 and 4 were downregulated in tumor tissue in comparison to the normal tissue (p < 0.001) and the patients with lower levels of PIWIL4 had shorter TTR (p = 0.048) and OS (p = 0.033). In the multivariate analysis, PIWIL1 expression emerged as an independent prognostic marker. Using 5-Aza-dC treatment and bisulfite sequencing, we observed that PIWIL1 expression could be regulated in part by methylation. Finally, an in silico study identified a stem-cell expression signature associated with PIWIL1 expression.

Promoter methylation of APC and RAR-β genes as prognostic markers in non-small cell lung cancer (NSCLC).

PubMed

Feng, Hongxiang; Zhang, Zhenrong; Qing, Xin; Wang, Xiaowei; Liang, Chaoyang; Liu, Deruo

2016-02-01

Aberrant promoter hypermethylations of tumor suppressor genes are promising markers for lung cancer diagnosis and prognosis. The purpose of this study was to determine methylation status at APC and RAR-β promoters in primary NSCLC, and whether they have any relationship with survival. APC and RAR-β promoter methylation status were determined in 41 NSCLC patients using methylation specific PCR. APC promoter methylation was detectable in 9 (22.0%) tumor samples and 6 (14.6%) corresponding non-tumor samples (P=0.391). RAR-β promoter methylation was detectable in 13 (31.7%) tumor samples and 4 (9.8%) corresponding non-tumor samples (P=0.049) in the NSCLC patients. APC promoter methylation was found to be associated with T stage (P=0.046) and nodal status (P=0.019) in non-tumor samples, and with smoking (P=0.004) in tumor samples. RAR-β promoter methylation was found associated with age (P=0.031) in non-tumor samples and with primary tumor site in tumor samples. Patients with APC promoter methylation in tumor samples showed significantly longer survival than patients without it (Log-rank P=0.014). In a multivariate analysis of prognostic factors, APC methylation in tumor samples was an independent prognostic factor (P=0.012), as were N1 positive lymph node number (P=0.025) and N2 positive lymph node number (P=0.06). Our study shows that RAR-β methylation detected in lung tissue may be used as a predictive marker for NSCLC diagnosis and that APC methylation in tumor sample may be a useful marker for superior survival in NSCLC patients. Copyright © 2015. Published by Elsevier Inc.

Non-contact method for characterization of small size thermoelectric modules.

PubMed

Manno, Michael; Yang, Bao; Bar-Cohen, Avram

2015-08-01

Conventional techniques for characterization of thermoelectric performance require bringing measurement equipment into direct contact with the thermoelectric device, which is increasingly error prone as device size decreases. Therefore, the novel work presented here describes a non-contact technique, capable of accurately measuring the maximum ΔT and maximum heat pumping of mini to micro sized thin film thermoelectric coolers. The non-contact characterization method eliminates the measurement errors associated with using thermocouples and traditional heat flux sensors to test small samples and large heat fluxes. Using the non-contact approach, an infrared camera, rather than thermocouples, measures the temperature of the hot and cold sides of the device to determine the device ΔT and a laser is used to heat to the cold side of the thermoelectric module to characterize its heat pumping capacity. As a demonstration of the general applicability of the non-contact characterization technique, testing of a thin film thermoelectric module is presented and the results agree well with those published in the literature.

Polymorphism in magic-sized Au144(SR)60 clusters

DOE PAGES

Jensen, Kirsten M. O.; Juhas, Pavol; Tofanelli, Marcus A.; ...

2016-06-14

Ultra-small, magic-sized metal nanoclusters represent an important new class of materials with properties between molecules and particles. However, their small size challenges the conventional methods for structure characterization. We present the structure of ultra-stable Au144(SR)60 magic-sized nanoclusters obtained from atomic pair distribution function analysis of X-ray powder diffraction data. Our study reveals structural polymorphism in these archetypal nanoclusters. Additionally, in order to confirm the theoretically predicted icosahedral-cored cluster, we also find samples with a truncated decahedral core structure, with some samples exhibiting a coexistence of both cluster structures. Although the clusters are monodisperse in size, structural diversity is apparent. Finally,more » the discovery of polymorphism may open up a new dimension in nanoscale engineering.« less

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

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

Hura, Greg L.; Menon, Angeli L.; Hammel, Michal

2009-07-20

We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes formore » 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.« less

Non-Invasive Monitoring of Intra-Abdominal Bleeding Rate Using Electrical Impedance Tomography

DTIC Science & Technology

2009-09-01

labeled ‘Measurement Index’, represents each of the 40 transimpedance measurements. The measurement index variable corresponds to the 40 measurements...system are amplified , and digitized by a 14-bit ADC (AD9240, Analog Devices). Waveforms are then sampled synchronous with the source, at 32 samples per...voltage changes (decreases in transimpedance ) during this phase were in measurements between the two outermost electrodes. We believe the apparent

Do your extractable TPH concentrations represent dissolved petroleum? An update on applied research

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

Zemo, D.A.

1997-12-31

Elevated concentrations of {open_quotes}dissolved-phase{close_quotes} extractable total petroleum hydrocarbons (TPH) in groundwater samples can be a significant impediment to site closure in states that regulate groundwater using TPH criteria. These analytical results are inconsistent with petroleum chemistry because of the relatively low water solubility of petroleum products. This paper presents an update of our research into the source of medium- to high-boiling TPH detections in groundwater samples and application of the results to multiple projects. This work follows from a 1995 publication in which positive interferences to the Method 8015M (GC-FID) TPH measurement by soluble, non-petroleum hydrocarbons resulting from intrinsic bioremediationmore » or non-dissolved petroleum adhered to particulates was described. The 1995 paper was largely theoretical and focused on one case study. Since 1995, we have evaluated the source of TPH detections in groundwater at numerous petroleum sites and have demonstrated the significance of interferences to the Method 8015M measurement to the California regulatory community. Our work has shown conclusively that elevated concentrations of extractable TPH are not representative of dissolved petroleum constituents. We have shown that a sample cleanup prior to analysis using silica gel cleanup (to remove polar non-petroleum hydrocarbons) and/or laboratory filtration (to reduce petroleum-affected particulates) is required to overcome the false positives caused by interferences to the Method 8015M measurement.« less

Short non-coding RNAs as bacteria species identifiers detected by surface plasmon resonance enhanced common path interferometry

NASA Astrophysics Data System (ADS)

Greef, Charles; Petropavlovskikh, Viatcheslav; Nilsen, Oyvind; Khattatov, Boris; Plam, Mikhail; Gardner, Patrick; Hall, John

2008-04-01

Small non-coding RNA sequences have recently been discovered as unique identifiers of certain bacterial species, raising the possibility that they can be used as highly specific Biowarfare Agent detection markers in automated field deployable integrated detection systems. Because they are present in high abundance they could allow genomic based bacterial species identification without the need for pre-assay amplification. Further, a direct detection method would obviate the need for chemical labeling, enabling a rapid, efficient, high sensitivity mechanism for bacterial detection. Surface Plasmon Resonance enhanced Common Path Interferometry (SPR-CPI) is a potentially market disruptive, high sensitivity dual technology that allows real-time direct multiplex measurement of biomolecule interactions, including small molecules, nucleic acids, proteins, and microbes. SPR-CPI measures differences in phase shift of reflected S and P polarized light under Total Internal Reflection (TIR) conditions at a surface, caused by changes in refractive index induced by biomolecular interactions within the evanescent field at the TIR interface. The measurement is performed on a microarray of discrete 2-dimensional areas functionalized with biomolecule capture reagents, allowing simultaneous measurement of up to 100 separate analytes. The optical beam encompasses the entire microarray, allowing a solid state detector system with no scanning requirement. Output consists of simultaneous voltage measurements proportional to the phase differences resulting from the refractive index changes from each microarray feature, and is automatically processed and displayed graphically or delivered to a decision making algorithm, enabling a fully automatic detection system capable of rapid detection and quantification of small nucleic acids at extremely sensitive levels. Proof-of-concept experiments on model systems and cell culture samples have demonstrated utility of the system, and efforts are in progress for full development and deployment of the device. The technology has broad applicability as a universal detection platform for BWA detection, medical diagnostics, and drug discovery research, and represents a new class of instrumentation as a rapid, high sensitivity, label-free methodology.

Lentic small water bodies: Variability of pesticide transport and transformation patterns.

PubMed

Ulrich, Uta; Hörmann, Georg; Unger, Malte; Pfannerstill, Matthias; Steinmann, Frank; Fohrer, Nicola

2018-03-15

Lentic small water bodies have a high ecological potential as they fulfill several ecosystem services such as the retention of water and pollutants. They serve as a hot spot of biodiversity. Due to their location in or adjacent to agricultural fields, they can be influenced by inputs of pesticides and their transformation products. Since small water bodies have rarely been part of monitorings/campaigns up to now, their current exposure and processes guiding the pesticide input are not understood, yet. This study presents results of a sampling campaign of 10 lentic small water bodies from 2015 to 2016. They were sampled once after the spring application for a pesticide target screening, before autumn application and three times after rainfall events following the application. The autumn sampling focused on the herbicides metazachlor, flufenacet and their transformation products - oxalic acid and - sulfonic acid as representatives for common pesticides in the study region. The concentrations were associated with rainfall before and after application, characteristics of the site and the water bodies, physicochemical parameters and the applied amount of pesticides. The key results of the pesticide screening in spring indicate positive detections of pesticides which have not been applied for years to the single fields. The autumn sampling showed frequent occurrences of the transformation products, which are formed in soil, from 39% to 94% of all samples (n=71). Discharge patterns were observed for metazachlor with highest concentrations in the first sample after application and then decreasing, but not for flufenacet. The concentrations of the transformation products increased over time and revealed highest values mainly in the last sample. Besides rainfall patterns right after application, the spatial and temporal dissemination of the pesticides to the water bodies seems to play a major role to understand the exposure of lentic small water bodies. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular and Histological Changes in Post-Treatment Biopsies of Non-Squamous Non-Small Cell Lung Cancer: A Retrospective Study.

PubMed

Vatrano, S; Righi, L; Vavalá, T; Rapa, I; Busso, M; Izzo, S; Cappia, S; Veltri, A; Papotti, M; Scagliotti, G V; Novello, S

2016-04-01

Recently, in advanced non-small cell lung cancer (NSCLC), standard chemotherapy was flanked by biological agents directed against genomic abnormalities, including EGFR and ALK alterations, that significantly improved patient outcome. Despite these achievements, tumour progression almost always occurs and a reassessment of the tumour genetic profile may contribute to modulating the therapeutic regimen. Resampling may provide tissue for additional tests to detect acquired resistance and/or new genetic alterations, but the currently available information is limited. Histological and genetic reassessments of biopsy or surgical tissue samples from 50 non-squamous NSCLC patients before and after at least one systemic treatment were performed. EGFR, KRAS, BRAF, PIK3CA and HER2 mutations were sequenced, p.T790M was identified with real-time PCR, and ALK and MET genomic alterations by fluorescence in situ hybridization. Overall in baseline biopsies, 37/50 (74 %) tumours had genetic alterations, either single (52 %) or multiple (22 %). Among them, 16 were EGFR mutations and 6 ALK rearrangements. In the second tissue sampling, 54 % of cases had additional genomic changes, including newly acquired alterations (81 %) or losses (18 %). The commonest changes were MET amplification and p.T790M mutation. One case had a histological shift from adenocarcinoma to small cell carcinoma. The remarkable number of molecular changes following systemic therapy and the genetic complexity of some cases underline the value of histological and molecular re-evaluation of lung cancer to tailor the most appropriate therapy during disease progression.

Socioeconomic Status and Self-Rated Oral Health; Diminished Return among Hispanic Whites.

PubMed

Assari, Shervin

2018-04-24

Background. An extensive body of knowledge has documented weaker health effects of socio-economic status (SES) for Blacks compared to Whites, a phenomenon also known as Blacks’ diminished return. It is, however, unknown whether the same diminished return also holds for other ethnic minorities such as Hispanics or not. Aim. Using a nationally representative sample, the current study aimed to compare Non-Hispanic and Hispanic Whites for the effects of SES on self-rated oral health. Methods. For the current cross-sectional study, we used data from the Collaborative Psychiatric Epidemiology Surveys (CPES), 2001⁻2003. With a nationally representative sampling, CPES included 11,207 adults who were either non-Hispanic Whites ( n = 7587) or Hispanic Whites ( n = 3620. The dependent variable was self-rated oral health, treated as dichotomous measure. Independent variables were education, income, employment, and marital status. Ethnicity was the focal moderator. Age and gender were covariates. Logistic regressions were used for data analysis. Results. Education, income, employment, and marital status were associated with oral health in the pooled sample. Although education, income, employment, and marital status were associated with oral health in non-Hispanic Whites, none of these associations were found for Hispanic Whites. Conclusion. In a similar pattern to Blacks’ diminished return, differential gain of SES indicators exists between Hispanic and non-Hispanic Whites, with a disadvantage for Hispanic Whites. Diminished return of SES should be regarded as a systemically neglected contributing mechanism behind ethnic oral health disparities in the United States. Replication of Blacks’ diminished return for Hispanics suggests that these processes are not specific to ethnic minority groups, and non-White groups gain less because they are not enjoying the privilege and advantage of Whites.

Functional near-infrared spectroscopy at small source-detector distance by means of high dynamic-range fast-gated SPAD acquisitions: first in-vivo measurements

NASA Astrophysics Data System (ADS)

Di Sieno, L.; Contini, D.; Dalla Mora, A.; Torricelli, A.; Spinelli, L.; Cubeddu, R.; Tosi, A.; Boso, G.; Pifferi, A.

2013-06-01

In this article, we show experimental results of time-resolved optical spectroscopy performed with small distance between launching and detecting fibers. It was already demonstrated that depth discrimination is independent of source-detector separation and that measurements at small source detector distance provide better contrast and spatial resolution. The main disadvantage is represent by the huge increase in early photons (scarcely diffused by tissue) peak that can saturate the dynamic range of most detectors, hiding information carried by late photons. Thanks to a fast-gated Single- Photon Avalanche Diode (SPAD) module, we are able to reject the peak of early photons and to obtain high-dynamic range acquisitions. We exploit fast-gated SPAD module to perform for the first time functional near-infrared spectroscopy (fNIRS) at small source-detector distance for in vivo measurements and we demonstrate the possibility to detect non-invasively the dynamics of oxygenated and deoxygenated haemoglobin occurring in the motor cortex during a motor task. We also show the improvement in terms of signal amplitude and Signal-to-Noise Ratio (SNR) obtained exploiting fast-gated SPAD performances with respect to "non-gated" measurements.

Probabilistic Round Trip Contamination Analysis of a Mars Sample Acquisition and Handling Process Using Markovian Decompositions

NASA Technical Reports Server (NTRS)

Hudson, Nicolas; Lin, Ying; Barengoltz, Jack

2010-01-01

A method for evaluating the probability of a Viable Earth Microorganism (VEM) contaminating a sample during the sample acquisition and handling (SAH) process of a potential future Mars Sample Return mission is developed. A scenario where multiple core samples would be acquired using a rotary percussive coring tool, deployed from an arm on a MER class rover is analyzed. The analysis is conducted in a structured way by decomposing sample acquisition and handling process into a series of discrete time steps, and breaking the physical system into a set of relevant components. At each discrete time step, two key functions are defined: The probability of a VEM being released from each component, and the transport matrix, which represents the probability of VEM transport from one component to another. By defining the expected the number of VEMs on each component at the start of the sampling process, these decompositions allow the expected number of VEMs on each component at each sampling step to be represented as a Markov chain. This formalism provides a rigorous mathematical framework in which to analyze the probability of a VEM entering the sample chain, as well as making the analysis tractable by breaking the process down into small analyzable steps.

Resampling methods in Microsoft Excel® for estimating reference intervals

PubMed Central

Theodorsson, Elvar

2015-01-01

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

Resampling methods in Microsoft Excel® for estimating reference intervals.

PubMed

Theodorsson, Elvar

2015-01-01

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

Impact of transgenic soybean expressing Cry1Ac and Cry1F proteins on the non-target arthropod community associated with soybean in Brazil

PubMed Central

2018-01-01

Field-scale studies that examine the potential for adverse effects of Bt crop technology on non-target arthropods may supplement data from laboratory studies to support an environmental risk assessment. A three year field study was conducted in Brazil to evaluate potential for adverse effects of cultivating soybean event DAS-81419-2 that produces the Cry1Ac and Cry1F proteins. To do so, we examined the diversity and abundance of non-target arthropods (NTAs) in Bt soybean in comparison with its non-Bt near isoline, with and without conventional insecticide applications, in three Brazilian soybean producing regions. Non-target arthropod abundance was surveyed using Moericke traps (yellow pan) and pitfall trapping. Total abundance (N), richness (S), Shannon-Wiener (H’), Simpson’s (D) and Pielou’s evenness (J) values for arthropod samples were calculated for each treatment and sampling period (soybean growth stages). A faunistic analysis was used to select the most representative NTAs which were used to describe the NTA community structure associated with soybean, and to test for effects due to the treatments effects via application of the Principal Response Curve (PRC) method. Across all years and sites, a total of 254,054 individuals from 190 taxa were collected by Moericke traps, while 29,813 individuals from 100 taxa were collected using pitfall traps. Across sites and sampling dates, the abundance and diversity measurements of representative NTAs were not significantly affected by Bt soybean as compared with non-sprayed non-Bt soybean. Similarly, community analyses and repeated measures ANOVA, when applicable, indicated that neither Bt soybean nor insecticide sprays altered the structure of the NTA communities under study. These results support the conclusion that transgenic soybean event DAS-81419-2 producing Cry1Ac and Cry1F toxins does not adversely affect the NTA community associated with soybean. PMID:29394266

De novo transciptome assembly in polyploid species

USDA-ARS?s Scientific Manuscript database

In the absence of a reference genome, the ultimate goal of a de novo transcriptome assembly is to accurately and comprehensively reconstruct the set of messenger RNA transcripts represented in the sample. Non-reference assembly of the transcriptome of polyploid species poses a particular challenge b...

40 CFR 141.22 - Turbidity sampling and analytical requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... requirements. 141.22 Section 141.22 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Monitoring and Analytical Requirements... suppliers of water for both community and non-community water systems at a representative entry point(s) to...

40 CFR 141.22 - Turbidity sampling and analytical requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... requirements. 141.22 Section 141.22 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Monitoring and Analytical Requirements... suppliers of water for both community and non-community water systems at a representative entry point(s) to...

40 CFR 141.22 - Turbidity sampling and analytical requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... requirements. 141.22 Section 141.22 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Monitoring and Analytical Requirements... suppliers of water for both community and non-community water systems at a representative entry point(s) to...

40 CFR 141.22 - Turbidity sampling and analytical requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... requirements. 141.22 Section 141.22 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Monitoring and Analytical Requirements... suppliers of water for both community and non-community water systems at a representative entry point(s) to...

40 CFR 141.22 - Turbidity sampling and analytical requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... requirements. 141.22 Section 141.22 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Monitoring and Analytical Requirements... suppliers of water for both community and non-community water systems at a representative entry point(s) to...

Preparation of highly multiplexed small RNA sequencing libraries.

PubMed

Persson, Helena; Søkilde, Rolf; Pirona, Anna Chiara; Rovira, Carlos

2017-08-01

MicroRNAs (miRNAs) are ~22-nucleotide-long small non-coding RNAs that regulate the expression of protein-coding genes by base pairing to partially complementary target sites, preferentially located in the 3´ untranslated region (UTR) of target mRNAs. The expression and function of miRNAs have been extensively studied in human disease, as well as the possibility of using these molecules as biomarkers for prognostication and treatment guidance. To identify and validate miRNAs as biomarkers, their expression must be screened in large collections of patient samples. Here, we develop a scalable protocol for the rapid and economical preparation of a large number of small RNA sequencing libraries using dual indexing for multiplexing. Combined with the use of off-the-shelf reagents, more samples can be sequenced simultaneously on large-scale sequencing platforms at a considerably lower cost per sample. Sample preparation is simplified by pooling libraries prior to gel purification, which allows for the selection of a narrow size range while minimizing sample variation. A comparison with publicly available data from benchmarking of miRNA analysis platforms showed that this method captures absolute and differential expression as effectively as commercially available alternatives.

Radiomics-based Prognosis Analysis for Non-Small Cell Lung Cancer

NASA Astrophysics Data System (ADS)

Zhang, Yucheng; Oikonomou, Anastasia; Wong, Alexander; Haider, Masoom A.; Khalvati, Farzad

2017-04-01

Radiomics characterizes tumor phenotypes by extracting large numbers of quantitative features from radiological images. Radiomic features have been shown to provide prognostic value in predicting clinical outcomes in several studies. However, several challenges including feature redundancy, unbalanced data, and small sample sizes have led to relatively low predictive accuracy. In this study, we explore different strategies for overcoming these challenges and improving predictive performance of radiomics-based prognosis for non-small cell lung cancer (NSCLC). CT images of 112 patients (mean age 75 years) with NSCLC who underwent stereotactic body radiotherapy were used to predict recurrence, death, and recurrence-free survival using a comprehensive radiomics analysis. Different feature selection and predictive modeling techniques were used to determine the optimal configuration of prognosis analysis. To address feature redundancy, comprehensive analysis indicated that Random Forest models and Principal Component Analysis were optimum predictive modeling and feature selection methods, respectively, for achieving high prognosis performance. To address unbalanced data, Synthetic Minority Over-sampling technique was found to significantly increase predictive accuracy. A full analysis of variance showed that data endpoints, feature selection techniques, and classifiers were significant factors in affecting predictive accuracy, suggesting that these factors must be investigated when building radiomics-based predictive models for cancer prognosis.

Invited Review Small is beautiful: The analysis of nanogram-sized astromaterials

NASA Astrophysics Data System (ADS)

Zolensky, M. E.; Pieters, C.; Clark, B.; Papike, J. J.

2000-01-01

The capability of modern methods to characterize ultra-small samples is well established from analysis of interplanetary dust particles (IDPs), interstellar grains recovered from meteorites, and other materials requiring ultra-sensitive analytical capabilities. Powerful analytical techniques are available that require, under favorable circumstances, single particles of only a few nanograms for entire suites of fairly comprehensive characterizations. A returned sample of >1,000 particles with total mass of just one microgram permits comprehensive quantitative geochemical measurements that are impractical to carry out in situ by flight instruments. The main goal of this paper is to describe the state-of-the-art in microanalysis of astromaterials. Given that we can analyze fantastically small quantities of asteroids and comets, etc., we have to ask ourselves how representative are microscopic samples of bodies that measure a few to many km across? With the Galileo flybys of Gaspra and Ida, it is now recognized that even very small airless bodies have indeed developed a particulate regolith. Acquiring a sample of the bulk regolith, a simple sampling strategy, provides two critical pieces of information about the body. Regolith samples are excellent bulk samples since they normally contain all the key components of the local environment, albeit in particulate form. Furthermore, since this fine fraction dominates remote measurements, regolith samples also provide information about surface alteration processes and are a key link to remote sensing of other bodies. Studies indicate that a statistically significant number of nanogram-sized particles should be able to characterize the regolith of a primitive asteroid, although the presence of larger components within even primitive meteorites (e.g.. Murchison), e.g. chondrules, CAI, large crystal fragments, etc., points out the limitations of using data obtained from nanogram-sized samples to characterize entire primitive asteroids. However, most important asteroidal geological processes have left their mark on the matrix, since this is the finest-grained portion and therefore most sensitive to chemical and physical changes. Thus, the following information can be learned from this fine grain size fraction alone: (1) mineral paragenesis; (2) regolith processes, (3) bulk composition; (4) conditions of thermal and aqueous alteration (if any); (5) relationships to planets, comets, meteorites (via isotopic analyses, including oxygen; (6) abundance of water and hydrated material; (7) abundance of organics; (8) history of volatile mobility, (9) presence and origin of presolar and/or interstellar material. Most of this information can even be obtained from dust samples from bodies for which nanogram-sized samples are not truly representative. Future advances in sensitivity and accuracy of laboratory analytical techniques can be expected to enhance the science value of nano- to microgram sized samples even further. This highlights a key advantage of sample returns - that the most advanced analysis techniques can always be applied in the laboratory, and that well-preserved samples are available for future investigations.

Genetic Diversity of Small Eukaryotes in Lakes Differing by Their Trophic Status

PubMed Central

Lefranc, Marie; Thénot, Aurélie; Lepère, Cécile; Debroas, Didier

2005-01-01

Small eukaryotes, cells with a diameter of less than 5 μm, are fundamental components of lacustrine planktonic systems. In this study, small-eukaryote diversity was determined by sequencing cloned 18S rRNA genes in three libraries from lakes of differing trophic status in the Massif Central, France: the oligotrophic Lake Godivelle, the oligomesotrophic Lake Pavin, and the eutrophic Lake Aydat. This analysis shows that the least diversified library was in the eutrophic lake (12 operational taxonomic units [OTUs]) and the most diversified was in the oligomesotrophic lake (26 OTUs). Certain groups were present in at least two ecosystems, while the others were specific to one lake on the sampling date. Cryptophyta, Chrysophyceae, and the strictly heterotrophic eukaryotes, Ciliophora and fungi, were identified in the three libraries. Among the small eukaryotes found only in two lakes, Choanoflagellida and environmental sequences (LKM11) were not detected in the eutrophic system whereas Cercozoa were confined to the oligomesotrophic and eutrophic lakes. Three OTUs, linked to the Perkinsozoa, were detected only in the Aydat library, where they represented 60% of the clones of the library. Chlorophyta and Haptophyta lineages were represented by a single clone and were present only in Godivelle and Pavin, respectively. Of the 127 clones studied, classical pigmented organisms (autotrophs and mixotrophs) represented only a low proportion regardless of the library's origin. This study shows that the small-eukaryote community composition may differ as a function of trophic status; certain lineages could be detected only in a single ecosystem. PMID:16204507

Sleep Disturbances in Adolescents with ADHD: A Systematic Review and Framework for Future Research

PubMed Central

Lunsford-Avery, Jessica R.; Krystal, Andrew D.; Kollins, Scott H.

2016-01-01

Background Biological mechanisms underlying symptom and prognostic heterogeneity in Attention-Deficit/Hyperactivity Disorder (ADHD) are unclear. Sleep impacts neurocognition and daytime functioning and is disrupted in ADHD, yet little is known about sleep in ADHD during adolescence, a period characterized by alterations in sleep, brain structure, and environmental demands as well as diverging ADHD trajectories. Methods A systematic review identified studies published prior to August 2016 assessing sleep in adolescents (aged 10–19 years) with ADHD or participating in population-based studies measuring ADHD symptoms. Results Twenty-five studies were identified (19 subjective report, 6 using actigraphy/polysomnography). Findings are mixed but overall suggest associations between sleep disturbances and 1) ADHD symptoms in the population and 2) poorer clinical, neurocognitive, and functional outcomes among adolescents with ADHD. Common limitations of studies included small or non-representative samples, non-standardized sleep measures, and cross-sectional methodology. Conclusions Current data on sleep in adolescent ADHD are sparse and limited by methodological concerns. Future studies are critical for clarifying a potential role of sleep in contributing to heterogeneity of ADHD presentation and prognosis. Potential mechanisms by which sleep disturbances during adolescence may contribute to worsened symptom severity and persistence of ADHD into adulthood and an agenda to guide future research are discussed. PMID:27969004

Molecular detection and characterization of picobirnaviruses in piglets with diarrhea in Thailand.

PubMed

Wilburn, Lauren; Yodmeeklin, Arpaporn; Kochjan, Pakawat; Saikruang, Wilaiporn; Kumthip, Kattareeya; Khamrin, Pattara; Maneekarn, Niwat

2017-04-01

Picobirnavirus (PBV) is a small, bi-segmented, double-stranded RNA virus. Taxonomically, the genus Picobirnavirus belongs to the Picobirnaviridae family. PBV infects a wide range of hosts and causes opportunistic infections, but its role in diarrheal disease remains unclear. To determine the prevalence and genetic diversity of porcine PBVs in Northern Thailand, 380 fecal samples collected from diarrheic and non-diarrheic piglets, raised in 22 pig farms, were tested for the presence of PBV. Reverse-transcription PCR (RT-PCR) was performed using primer sets specific to the RNA-dependent RNA polymerase (RdRp) gene. PBV was detected in 86 of 265 (32.5%) diarrheic piglets and in 26 of 115 (22.6%) non-diarrheic piglets. All the PBV strains detected in this study belonged to genogroup I and a high proportion of PBV-positive piglets were co-infected with group A rotavirus (RVA) and bocavirus (BoV). Phylogenetic analysis of representative genogroup I strains revealed remarkably high similarity between strains; these formed a monophyletic cluster with 97-100% sequence identity in the RdRp gene. The strains were also closely related to genogroup I PBV Chinese porcine strain. The findings indicate that PBV infection is common in piglets with and without diarrhea in Northern Thailand.

A large-scale national study of gambling severity among immigrant and non-immigrant adolescents: The role of the family.

PubMed

Canale, Natale; Vieno, Alessio; Griffiths, Mark D; Borraccino, Alberto; Lazzeri, Giacomo; Charrier, Lorena; Lemma, Patrizia; Dalmasso, Paola; Santinello, Massimo

2017-03-01

The primary aim of the present study was to examine the association between immigrant generation, family sociodemographic characteristics, and problem gambling severity in a large-scale nationally representative sample of Italian youth. Data from the 2013-2014 Health Behaviour in School-aged Children (HBSC) Survey were used for cross-sectional analyses of adolescent problem gambling. Self-administered questionnaires were completed by a representative sample of 20,791 15-year-old students. Respondents' problem gambling severity, immigrant status, family characteristics (family structure, family affluence, perceived family support) and socio-demographic characteristics were individually assessed. Rates of adolescent at-risk/problem gambling were twice as high among first generation immigrants than non-immigrant students; the odds of being at-risk/problem gamblers were higher among first-generation immigrants than adolescents of other immigrant generations or non-immigrant. Not living with two biological or adoptive parents appears to be a factor that increases the risk of becoming a problem gambler in first generation immigrants. Immigrant status and family characteristics may play a key role in contributing to adolescent problem gambling. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

A Meta-Analysis on Antecedents and Outcomes of Detachment from Work.

PubMed

Wendsche, Johannes; Lohmann-Haislah, Andrea

2016-01-01

Detachment from work has been proposed as an important non-work experience helping employees to recover from work demands. This meta-analysis (86 publications, k = 91 independent study samples, N = 38,124 employees) examined core antecedents and outcomes of detachment in employee samples. With regard to outcomes, results indicated average positive correlations between detachment and self-reported mental (i.e., less exhaustion, higher life satisfaction, more well-being, better sleep) and physical (i.e., lower physical discomfort) health, state well-being (i.e., less fatigue, higher positive affect, more intensive state of recovery), and task performance (small to medium sized effects). However, average relationships between detachment and physiological stress indicators and work motivation were not significant while associations with contextual performance and creativity were significant, but negative. Concerning work characteristics, as expected, job demands were negatively related and job resources were positively related to detachment (small sized effects). Further, analyses revealed that person characteristics such as negative affectivity/neuroticism (small sized effect) and heavy work investment (medium sized effect) were negatively related to detachment whereas detachment and demographic variables (i.e., age and gender) were not related. Moreover, we found a medium sized average negative relationship between engagement in work-related activities during non-work time and detachment. For most of the examined relationships heterogeneity of effect sizes was moderate to high. We identified study design, samples' gender distribution, and affective valence of work-related thoughts as moderators for some of these aforementioned relationships. The results of this meta-analysis point to detachment as a non-work (recovery) experience that is influenced by work-related and personal characteristics which in turn is relevant for a range of employee outcomes.

Glycogen Synthase Kinase 3 Protein Kinase Activity Is Frequently Elevated in Human Non-Small Cell Lung Carcinoma and Supports Tumour Cell Proliferation

PubMed Central

O′Flaherty, Linda; Pardo, Olivier E.; Dzien, Piotr; Phillips, Lois; Morgan, Carys; Pawade, Joya; May, Margaret T.; Sohail, Muhammad; Hetzel, Martin R.; Seckl, Michael J.; Tavaré, Jeremy M.

2014-01-01

Background Glycogen synthase kinase 3 (GSK3) is a central regulator of cellular metabolism, development and growth. GSK3 activity was thought to oppose tumourigenesis, yet recent studies indicate that it may support tumour growth in some cancer types including in non-small cell lung carcinoma (NSCLC). We examined the undefined role of GSK3 protein kinase activity in tissue from human NSCLC. Methods The expression and protein kinase activity of GSK3 was determined in 29 fresh frozen samples of human NSCLC and patient-matched normal lung tissue by quantitative immunoassay and western blotting for the phosphorylation of three distinct GSK3 substrates in situ (glycogen synthase, RelA and CRMP-2). The proliferation and sensitivity to the small-molecule GSK3 inhibitor; CHIR99021, of NSCLC cell lines (Hcc193, H1975, PC9 and A549) and non-neoplastic type II pneumocytes was further assessed in adherent culture. Results Expression and protein kinase activity of GSK3 was elevated in 41% of human NSCLC samples when compared to patient-matched control tissue. Phosphorylation of GSK3α/β at the inhibitory S21/9 residue was a poor biomarker for activity in tumour samples. The GSK3 inhibitor, CHIR99021 dose-dependently reduced the proliferation of three NSCLC cell lines yet was ineffective against type II pneumocytes. Conclusion NSCLC tumours with elevated GSK3 protein kinase activity may have evolved dependence on the kinase for sustained growth. Our results provide further important rationale for exploring the use of GSK3 inhibitors in treating NSCLC. PMID:25486534

A Meta-Analysis on Antecedents and Outcomes of Detachment from Work

PubMed Central

Wendsche, Johannes; Lohmann-Haislah, Andrea

2017-01-01

Detachment from work has been proposed as an important non-work experience helping employees to recover from work demands. This meta-analysis (86 publications, k = 91 independent study samples, N = 38,124 employees) examined core antecedents and outcomes of detachment in employee samples. With regard to outcomes, results indicated average positive correlations between detachment and self-reported mental (i.e., less exhaustion, higher life satisfaction, more well-being, better sleep) and physical (i.e., lower physical discomfort) health, state well-being (i.e., less fatigue, higher positive affect, more intensive state of recovery), and task performance (small to medium sized effects). However, average relationships between detachment and physiological stress indicators and work motivation were not significant while associations with contextual performance and creativity were significant, but negative. Concerning work characteristics, as expected, job demands were negatively related and job resources were positively related to detachment (small sized effects). Further, analyses revealed that person characteristics such as negative affectivity/neuroticism (small sized effect) and heavy work investment (medium sized effect) were negatively related to detachment whereas detachment and demographic variables (i.e., age and gender) were not related. Moreover, we found a medium sized average negative relationship between engagement in work-related activities during non-work time and detachment. For most of the examined relationships heterogeneity of effect sizes was moderate to high. We identified study design, samples' gender distribution, and affective valence of work-related thoughts as moderators for some of these aforementioned relationships. The results of this meta-analysis point to detachment as a non-work (recovery) experience that is influenced by work-related and personal characteristics which in turn is relevant for a range of employee outcomes. PMID:28133454

40Ar/39Ar Dating of Volcanic Glass

NASA Astrophysics Data System (ADS)

Morgan, L. E.; Renne, P. R.; Watkins, J. M.

2007-12-01

Application of the 40Ar/39Ar method to volcanic glasses has been somewhat stigmatized following several studies demonstrating secondary mobility of K and Ar. Much of the stigma is unwarranted, however, since most studies only impugned the reliability of the K-Ar and 40Ar/39Ar techniques when applied to glass shards rather than obsidian clasts with low surface area to volume ratios. We provide further evidence for problematic K loss and/or 39Ar recoil ejection from glass shards in 40Ar/39Ar step heating results for comagmatic feldspars and shards. In an extreme case, the plateau age of the feldspars (0.17 ± 0.03 Ma at 2σ) is significantly younger than the plateau age of the glass (0.85 ± 0.05 Ma at 2σ). If the feldspar age is reasonably interpreted as the eruption age of the ash, it is likely that the glass shards experienced K and/or 39Ar loss. Electron microprobe analyses of the glass shards have low totals (~93%) and no systematic lateral variability (i.e., diffusion gradients) in K, suggesting that the lengthscale of the glass shards is smaller than the lengthscale of K diffusion. Obsidian clasts should not be as susceptible to K loss since any hydrated (K-depleted) volume represents a small fraction of the total material and can often be physically removed prior to analysis. Samples described here are detrital obsidian clasts from the Afar region of Ethiopia. Evidence from Fourier Transform Infrared Spectroscopy (FTIR), and previous work by Anovitz (1999), confirm that the scale of water and potassium mobility are often small in comparison to the size of obsidian clasts but large enough to effect the bulk composition of glass shards. This expectation is confirmed in another tuff wherein comagmatic obsidian clasts and sanidine phenocrysts yield indistinguishable 40Ar/39Ar ages of 4.4 Ma High abundances of non-radiogenic 40Ar, and kinetic fractionation of Ar isotopes during quenching and/or laboratory degassing resulting in incomplete equilibration between atmospheric and magmatic argon, may also hinder accurate 40Ar/39Ar geochronology of volcanic glasses. Clasts derived from single flows (as determined by extrusion age and trace element geochemistry) display variations as much as 3-4 orders of magnitude in atmospheric 40Ar concentrations. The clasts were likely sourced from different parts of the flows with varying proximity to the surface and thus differing thermal and atmospheric uptake histories. Because radiogenic and non-radiogenic components of 40Ar are energetically indistinct in glass, most samples fail to yield isochrons due to limited range in 40Ar: 39Ar: 36Ar. Most yield plateau ages, whose validity rests on the assumption of atmospheric initial 40Ar/36Ar. Some samples yield inverse isochrons with sub-atmospheric 40Ar/36Ar intercepts; unirradiated subsamples of these same samples also have sub-atmospheric 38Ar/36Ar ratios that are too high to be explained by mass fractionation. While the effects of non-radiogenic 40Ar remain poorly understood, this sample set yielded 32 out of 41 clasts having plateau and isochron ages within 2σ error of each other, and potentially problematic samples are generally identified with non-atmospheric isochron 40Ar/36Ar intercepts.

Nivolumab, Cisplatin, and Pemetrexed Disodium or Gemcitabine Hydrochloride in Treating Patients With Stage I-IIIA Non-small Cell Lung Cancer That Can Be Removed by Surgery

ClinicalTrials.gov

2018-03-02

Non-Squamous Non-Small Cell Lung Carcinoma; Stage I Non-Small Cell Lung Cancer; Stage IA Non-Small Cell Lung Carcinoma; Stage IB Non-Small Cell Lung Carcinoma; Stage II Non-Small Cell Lung Cancer; Stage IIA Non-Small Cell Lung Carcinoma; Stage IIB Non-Small Cell Lung Carcinoma; Stage IIIA Non-Small Cell Lung Cancer

The coverage of a random sample from a biological community.

PubMed

Engen, S

1975-03-01

A taxonomic group will frequently have a large number of species with small abundances. When a sample is drawn at random from this group, one is therefore faced with the problem that a large proportion of the species will not be discovered. A general definition of quantitative measures of "sample coverage" is proposed, and the problem of statistical inference is considered for two special cases, (1) the actual total relative abundance of those species that are represented in the sample, and (2) their relative contribution to the information index of diversity. The analysis is based on a extended version of the negative binomial species frequency model. The results are tabulated.

When continuous observations just won't do: developing accurate and efficient sampling strategies for the laying hen.

PubMed

Daigle, Courtney L; Siegford, Janice M

2014-03-01

Continuous observation is the most accurate way to determine animals' actual time budget and can provide a 'gold standard' representation of resource use, behavior frequency, and duration. Continuous observation is useful for capturing behaviors that are of short duration or occur infrequently. However, collecting continuous data is labor intensive and time consuming, making multiple individual or long-term data collection difficult. Six non-cage laying hens were video recorded for 15 h and behavioral data collected every 2 s were compared with data collected using scan sampling intervals of 5, 10, 15, 30, and 60 min and subsamples of 2 second observations performed for 10 min every 30 min, 15 min every 1 h, 30 min every 1.5 h, and 15 min every 2 h. Three statistical approaches were used to provide a comprehensive analysis to examine the quality of the data obtained via different sampling methods. General linear mixed models identified how the time budget from the sampling techniques differed from continuous observation. Correlation analysis identified how strongly results from the sampling techniques were associated with those from continuous observation. Regression analysis identified how well the results from the sampling techniques were associated with those from continuous observation, changes in magnitude, and whether a sampling technique had bias. Static behaviors were well represented with scan and time sampling techniques, while dynamic behaviors were best represented with time sampling techniques. Methods for identifying an appropriate sampling strategy based upon the type of behavior of interest are outlined and results for non-caged laying hens are presented. Copyright © 2013 Elsevier B.V. All rights reserved.

Dental size and shape in the Roman imperial age: two examples from the area of Rome.

PubMed

Manzi, G; Santandrea, E; Passarello, P

1997-04-01

Different socioeconomic strata of Roman imperial age are represented by two large dental samples recovered from archaeological excavations near Rome, Italy. Teeth are investigated for crown dimensions and morphological variants. One sample, comprising 1,465 permanent teeth, represents the rural town of Lucus Feroniae (LFR) and is mainly composed of slaves and war veterans. The other, comprising 734 teeth from the Isola Sacra necropolis at Portus Romae (NIS), represents the "middle class" segment of an urban population. Both series show small dental dimensions and fit at the lower end of the trend toward dental reduction in Europe from the Upper Paleolithic to the historical times. The urban sample is less variable metrically and less sexually dimorphic than the rural one. The analysis of discrete crown traits shows absence of rare phenotypic variants in both series. The urban sample is also less variable in this last respect, suggesting that the gene pool of this particular "stratum" of the NIS population was more homogeneous than that of LFR. The occurrence of enamel hypoplasia indicates that metabolic stress during growth and development was similar in LFR and NIS. The overall set of available data is evaluated in the light of the history of the two Roman sites and the composition of each population.

Parental bonding and adult psychopathology: results from the US National Comorbidity Survey.

PubMed

Enns, M W; Cox, B J; Clara, I

2002-08-01

Research using the parental bonding instrument (PBI) has suggested that lack of parental care and/or overprotection may be important risk factors for adult mental disorders. Much of this research, however, has relied on clinical populations with one or two disorders, or has used highly select community samples. The association between parenting experiences and the occurrence of 13 common mental disorders in adulthood was evaluated in the US National Comorbidity Survey (N = 5877). The effect of sociodemographic variables (age, education, income) was statistically controlled and the effects of six parenting variables (maternal and paternal care, overprotection and authoritarianism) were examined simultaneously. The effects in men and women were examined separately. Lack of care was the parenting variable most consistently associated with adult psychopathology. Parenting experiences with one's mother were more consistently associated with adult mental disorders. In general the impact of parenting was diagnostically non-specific. However, there appeared to be some unique effects for externalizing disorders (substance use disorders and antisocial personality disorder) in males; paternal overprotection and authoritarianism conferred a reduced risk of externalizing disorders in adult males. The overall impact of parenting as assessed by the PBI was modest, accounting for about 1 to 5 % of the variance in the occurrence of adult mental disorders. Parenting experiences, particularly lack of care, are potentially causally related in a non-specific manner to a wide variety of forms of adult psychopathology in both men and women. The overall magnitude of the effect is small but statistically significant in a nationally representative US sample.

Dentinal tubules revealed with X-ray tensor tomography.

PubMed

Jud, Christoph; Schaff, Florian; Zanette, Irene; Wolf, Johannes; Fehringer, Andreas; Pfeiffer, Franz

2016-09-01

Dentin is a mineralized material making up most of the tooth bulk. A system of microtubules, so called dentinal tubules, transverses it radially from the pulp chamber to the outside. This highly oriented structure leads to anisotropic mechanical properties directly connected to the tubules orientation and density: the ultimate tensile strength as well as the fracture toughness and the shear strength are largest perpendicular to dentinal tubules. Consequently, the fatigue strength depends on the direction of dentinal tubules, too. However, none of the existing techniques used to investigate teeth provide access to orientation and density of dentinal tubules for an entire specimen in a non-destructive way. In this paper, we measure a third molar human tooth both with conventional micro-CT and X-ray tensor tomography (XTT). While the achievable resolution in micro-CT is too low to directly resolve the dentinal tubules, we provide strong evidence that the direction and density of dentinal tubules can be indirectly measured by XTT, which exploits small-angle X-ray scattering to retrieve a 3D map of scattering tensors. We show that the mean directions of scattering structures correlate to the orientation of dentinal tubules and that the mean effective scattering strength provides an estimation of the relative density of dentinal tubules. Thus, this method could be applied to investigate the connection between tubule orientation and fatigue or tensile properties of teeth for a full sample without cutting one, non-representative peace of tooth out of the full sample. Copyright © 2016 The Academy of Dental Materials. All rights reserved.

Universality in volume-law entanglement of scrambled pure quantum states.

PubMed

Nakagawa, Yuya O; Watanabe, Masataka; Fujita, Hiroyuki; Sugiura, Sho

2018-04-24

A pure quantum state can fully describe thermal equilibrium as long as one focuses on local observables. The thermodynamic entropy can also be recovered as the entanglement entropy of small subsystems. When the size of the subsystem increases, however, quantum correlations break the correspondence and mandate a correction to this simple volume law. The elucidation of the size dependence of the entanglement entropy is thus essentially important in linking quantum physics with thermodynamics. Here we derive an analytic formula of the entanglement entropy for a class of pure states called cTPQ states representing equilibrium. We numerically find that our formula applies universally to any sufficiently scrambled pure state representing thermal equilibrium, i.e., energy eigenstates of non-integrable models and states after quantum quenches. Our formula is exploited as diagnostics for chaotic systems; it can distinguish integrable models from non-integrable models and many-body localization phases from chaotic phases.

Large-scale data analysis of power grid resilience across multiple US service regions

NASA Astrophysics Data System (ADS)

Ji, Chuanyi; Wei, Yun; Mei, Henry; Calzada, Jorge; Carey, Matthew; Church, Steve; Hayes, Timothy; Nugent, Brian; Stella, Gregory; Wallace, Matthew; White, Joe; Wilcox, Robert

2016-05-01

Severe weather events frequently result in large-scale power failures, affecting millions of people for extended durations. However, the lack of comprehensive, detailed failure and recovery data has impeded large-scale resilience studies. Here, we analyse data from four major service regions representing Upstate New York during Super Storm Sandy and daily operations. Using non-stationary spatiotemporal random processes that relate infrastructural failures to recoveries and cost, our data analysis shows that local power failures have a disproportionally large non-local impact on people (that is, the top 20% of failures interrupted 84% of services to customers). A large number (89%) of small failures, represented by the bottom 34% of customers and commonplace devices, resulted in 56% of the total cost of 28 million customer interruption hours. Our study shows that extreme weather does not cause, but rather exacerbates, existing vulnerabilities, which are obscured in daily operations.

Molecular characterization of an influenza A virus (H4N2) isolated from waterfowl habitats in the State of Mexico.

PubMed

Ornelas-Eusebio, Erika; Obregón-Ascencio, Alejandro; Chávez-Maya, Fernando; García-Espinosa, Gary

2015-03-01

Wild waterfowl and their habitats are the main reservoirs of influenza A virus (IAV) mainly during the breeding season and prior to migration. This study describes the molecular characterization of an IAV isolated from 240 water samples of a small wetland during non-breeding season of migratory wild ducks in the State of Mexico, Mexico. The results showed that the virus belongs to the H4N2 subtype and each of its eight segments of the viral genome has similarity to IAV isolated from ducks in North America. This study suggests that IAV can be isolated from small wetland during non-breeding season of migrating waterfowl.

Signal enhancement for the sensitivity-limited solid state NMR experiments using a continuous, non-uniform acquisition scheme

NASA Astrophysics Data System (ADS)

Qiang, Wei

2011-12-01

We describe a sampling scheme for the two-dimensional (2D) solid state NMR experiments, which can be readily applied to the sensitivity-limited samples. The sampling scheme utilizes continuous, non-uniform sampling profile for the indirect dimension, i.e. the acquisition number decreases as a function of the evolution time ( t1) in the indirect dimension. For a beta amyloid (Aβ) fibril sample, we observed overall 40-50% signal enhancement by measuring the cross peak volume, while the cross peak linewidths remained comparable to the linewidths obtained by regular sampling and processing strategies. Both the linear and Gaussian decay functions for the acquisition numbers result in similar percentage of increment in signal. In addition, we demonstrated that this sampling approach can be applied with different dipolar recoupling approaches such as radiofrequency assisted diffusion (RAD) and finite-pulse radio-frequency-driven recoupling (fpRFDR). This sampling scheme is especially suitable for the sensitivity-limited samples which require long signal averaging for each t1 point, for instance the biological membrane proteins where only a small fraction of the sample is isotopically labeled.

Evolution of cooperation with shared costs and benefits

PubMed Central

Brown, Joel S; Vincent, Thomas L

2008-01-01

The quest to determine how cooperation evolves can be based on evolutionary game theory, in spite of the fact that evolutionarily stable strategies (ESS) for most non-zero-sum games are not cooperative. We analyse the evolution of cooperation for a family of evolutionary games involving shared costs and benefits with a continuum of strategies from non-cooperation to total cooperation. This cost–benefit game allows the cooperator to share in the benefit of a cooperative act, and the recipient to be burdened with a share of the cooperator's cost. The cost–benefit game encompasses the Prisoner's Dilemma, Snowdrift game and Partial Altruism. The models produce ESS solutions of total cooperation, partial cooperation, non-cooperation and coexistence between cooperation and non-cooperation. Cooperation emerges from an interplay between the nonlinearities in the cost and benefit functions. If benefits increase at a decelerating rate and costs increase at an accelerating rate with the degree of cooperation, then the ESS has an intermediate level of cooperation. The game also exhibits non-ESS points such as unstable minima, convergent-stable minima and unstable maxima. The emergence of cooperative behaviour in this game represents enlightened self-interest, whereas non-cooperative solutions illustrate the Tragedy of the Commons. Games having either a stable maximum or a stable minimum have the property that small changes in the incentive structure (model parameter values) or culture (starting frequencies of strategies) result in correspondingly small changes in the degree of cooperation. Conversely, with unstable maxima or unstable minima, small changes in the incentive structure or culture can result in a switch from non-cooperation to total cooperation (and vice versa). These solutions identify when human or animal societies have the potential for cooperation and whether cooperation is robust or fragile. PMID:18495622

Fungi from Admiralty Bay (King George Island, Antarctica) Soils and Marine Sediments.

PubMed

Wentzel, Lia Costa Pinto; Inforsato, Fábio José; Montoya, Quimi Vidaurre; Rossin, Bruna Gomes; Nascimento, Nadia Regina; Rodrigues, André; Sette, Lara Durães

2018-06-19

Extreme environments such as the Antarctic can lead to the discovery of new microbial taxa, as well as to new microbial-derived natural products. Considering that little is known yet about the diversity and the genetic resources present in these habitats, the main objective of this study was to evaluate the fungal communities from extreme environments collected at Aldmiralty Bay (Antarctica). A total of 891 and 226 isolates was obtained from soil and marine sediment samples, respectively. The most abundant isolates from soil samples were representatives of the genera Leucosporidium, Pseudogymnoascus, and a non-identified Ascomycota NIA6. Metschnikowia sp. was the most abundant taxon from marine samples, followed by isolates from the genera Penicillium and Pseudogymnoascus. Many of the genera were exclusive in marine sediment or terrestrial samples. However, representatives of eight genera were found in both types of samples. Data from non-metric multidimensional scaling showed that each sampling site is unique in their physical-chemical composition and fungal community. Biotechnological potential in relation to enzymatic production at low/moderate temperatures was also investigated. Ligninolytic enzymes were produced by few isolates from root-associated soil. Among the fungi isolated from marine sediments, 16 yeasts and nine fungi showed lipase activity and three yeasts and six filamentous fungi protease activity. The present study permitted increasing our knowledge on the diversity of fungi that inhabit the Antarctic, finding genera that have never been reported in this environment before and discovering putative new species of fungi.

A Third Moment Adjusted Test Statistic for Small Sample Factor Analysis

PubMed Central

Lin, Johnny; Bentler, Peter M.

2012-01-01

Goodness of fit testing in factor analysis is based on the assumption that the test statistic is asymptotically chi-square; but this property may not hold in small samples even when the factors and errors are normally distributed in the population. Robust methods such as Browne’s asymptotically distribution-free method and Satorra Bentler’s mean scaling statistic were developed under the presumption of non-normality in the factors and errors. This paper finds new application to the case where factors and errors are normally distributed in the population but the skewness of the obtained test statistic is still high due to sampling error in the observed indicators. An extension of Satorra Bentler’s statistic is proposed that not only scales the mean but also adjusts the degrees of freedom based on the skewness of the obtained test statistic in order to improve its robustness under small samples. A simple simulation study shows that this third moment adjusted statistic asymptotically performs on par with previously proposed methods, and at a very small sample size offers superior Type I error rates under a properly specified model. Data from Mardia, Kent and Bibby’s study of students tested for their ability in five content areas that were either open or closed book were used to illustrate the real-world performance of this statistic. PMID:23144511

A prospective cohort study of light transmission platelet aggregometry for bleeding disorders: is testing native platelet-rich plasma non-inferior to testing platelet count adjusted samples?

PubMed

Castilloux, Jean Francois; Moffat, Karen A; Liu, Yang; Seecharan, Jodi; Pai, Menaka; Hayward, Catherine P M

2011-10-01

Light transmission platelet aggregometry (LTA) is important to diagnose bleeding disorders. Experts recommend testing LTA with native (N) rather than platelet count adjusted (A) platelet-rich plasma (PRP), although it is unclear if this provides non-inferior, or superior, detection of bleeding disorders. Our goal was to determine if LTA with NPRP is non-inferior to LTA with APRP for bleeding disorder assessments. A prospective cohort of patients, referred for bleeding disorder testing, and healthy controls, were evaluated by LTA using common agonists, NPRP and APRP (adjusted to 250 x 10⁹ platelets/l). Recruitment continued until 40 controls and 40 patients with definite bleeding disorders were tested. Maximal aggregation (MA) data were assessed for the detection of abnormalities from bleeding disorders (all causes combined to limit bias), using sample-type specific reference intervals. Areas under receiver-operator curves (AUROC) were evaluated using pre-defined criteria (area differences: < 0.15 for non-inferiority, > 0 for superiority). Forty-four controls and 209 patients were evaluated. Chart reviews for 169 patients indicated 67 had bleeding disorders, 28 from inherited platelet secretion defects. Mean MA differences between NPRP and APRP were small for most agonists (ranges, controls: -3.3 to 5.8; patients: -3.0 to 13.7). With both samples, reduced MA with two or more agonists was associated with a bleeding disorder. AUROC differences between NPRP and APRP were small and indicated that NPRP were non-inferior to APRP for detecting bleeding disorders by LTA, whereas APRP met superiority criteria. Our study validates using either NPRP or APRP for LTA assessments of bleeding disorders.

Geostatistics and the representative elementary volume of gamma ray tomography attenuation in rocks cores

USGS Publications Warehouse

Vogel, J.R.; Brown, G.O.

2003-01-01

Semivariograms of samples of Culebra Dolomite have been determined at two different resolutions for gamma ray computed tomography images. By fitting models to semivariograms, small-scale and large-scale correlation lengths are determined for four samples. Different semivariogram parameters were found for adjacent cores at both resolutions. Relative elementary volume (REV) concepts are related to the stationarity of the sample. A scale disparity factor is defined and is used to determine sample size required for ergodic stationarity with a specified correlation length. This allows for comparison of geostatistical measures and representative elementary volumes. The modifiable areal unit problem is also addressed and used to determine resolution effects on correlation lengths. By changing resolution, a range of correlation lengths can be determined for the same sample. Comparison of voxel volume to the best-fit model correlation length of a single sample at different resolutions reveals a linear scaling effect. Using this relationship, the range of the point value semivariogram is determined. This is the range approached as the voxel size goes to zero. Finally, these results are compared to the regularization theory of point variables for borehole cores and are found to be a better fit for predicting the volume-averaged range.

Visualisation and Quantification of Transport in Barrier Rocks with Positron Emission Tomography

NASA Astrophysics Data System (ADS)

Kulenkampff, J.; Gajewski, C.; Gründig, M.; Lippmann-Pipke, J.; Mittmann, H.; Richter, M.; Wolf, M.

2009-04-01

In tight barrier rocks laboratory observation of radionuclide transport and determination of transport parameters is a demanding and interminable task, because of slow rates, small concentrations, and intricate chemical interactions. The validity of results from common laboratory methods, like flow- and diffusion experiments on small samples, is limited by the heterogeneity of the pathways and adherent upscaling issues, because homogeneous conditions have to be presumed for these input-output investigations. But nano-pores or micro-fractures could be present, which would provide pathways for heterogeneous transport processes. Transport properties of these pathways are most influential boundary conditions for reactions between fluid components and crystal surfaces. We propose Positron Emission Tomography (GEO-PET) as an appropriate method for direct observation of heterogeneous transport of radiotracers in tight material on the laboratory scale. With high-resolution PET scanners, which are common instruments of biomedical research ("small animal PET"), it is possible to determine the spatio-temporal distribution of the tracer activity with a resolution of almost 1 mm during about three periods of the tracer half-life (half-lives of some applicable PET tracers: 18F: 1.8 h, 124I: 4.2 days, 58Co: 70.8 days). The PET tracer is applied as ion in solution or as marker for compounds, like colloids. The most considerable difference between PET applications on geomaterial compared to biological tissue is the stronger attenuation and scattering of radiation because of the higher density of rock material. After travelling the positron attenuation length in dense material (about 1 mm), the positron annihilates in contact with an electron, transmitting two photons with 511 keV, propagating in antiparallel direction. The sample size of geomaterial is limited by the attenuation length of these photons. By applying an appropriate attenuation correction it is possible to investigate transport processes in rock cores with diameters up to 10 cm. Then at least 20% of the initial annihilation events are recorded as coincidences. However, one single photon of the annihilation radiation may be recorded while the other is absorbed; therefore, the signal to noise ratio is degraded by attenuation. Other sources of noise are scattered events, and the loss of one coinciding photon due to gaps between the detectors and other detection probability reasons. Also, the ratio of random coincidences increases with the noise level and impairs the image quality of the tomographic reconstruction. The reduction of these reconstruction artefacts by enhanced data correction methods is an important requirement for the development of the GEO-PET method. An other problem is the development of special methods for the quantitative evaluation of the extensive spatio-temporal data sets. We present results from high-resolution PET for tomographic process observation during transport of colloids and conservative tracers in macroscopic samples of clays, saline rocks, and granites (diameter 5 to 10 cm, length 5 to 20 cm). In most cases we observed localized zones of transport, even in a homogenized compressed clay sample. This reflects the non-representative sample volume, which probably is not achievable for any laboratory method. However, at least the PET tomograms reveal these deviations from representativeness. Up to now, break-through-curve parameters can be determined from spatially resolved tracer concentration measurements at distinct regions of the sample, without mandatory penetration of the complete sample extension. A multiscale model-based inversion scheme for continuous scale-dependent parameter determination is currently developed.

Analytical fuel property effects: Small combustors, phase 2

NASA Technical Reports Server (NTRS)

Hill, T. G.; Monty, J. D.; Morton, H. L.

1985-01-01

The effects of non-standard aviation fuels on a typical small gas turbine combustor were studied and the effectiveness of design changes intended to counter the effects of these fuels was evaluated. The T700/CT7 turboprop engine family was chosen as being representative of the class of aircraft power plants desired for this study. Fuel properties, as specified by NASA, are characterized by low hydrogen content and high aromatics levels. No. 2 diesel fuel was also evaluated in this program. Results demonstrated the anticipated higher than normal smoke output and flame radiation intensity with resulting increased metal temperatures on the baseline T700 combustor. Three new designs were evaluated using the non standard fuels. The three designs incorporated enhanced cooling features and smoke reduction features. All three designs, when burning the broad specification fuels, exhibited metal temperatures at or below the baseline combustor temperatures on JP-5. Smoke levels were acceptable but higher than predicted.

Small passive student experiments on G324 261 individual quests for student knowledge

NASA Technical Reports Server (NTRS)

Nicholson, James H.; Tempel, Carol A.; Ashcraft, Ruth; Rutherford, Robin

1995-01-01

The Charleston County School District CAN DO Project payload on STS-57 had a primary goal of photographing the Earth with the GeoCam camera system. In addition, the payload carried 261 passive student experiments representing the efforts of several thousand students throughout the district and in four other states. These experiments represented the individual concepts of teams ranging in age from pre-school to high school. Consequently, a tremendous variety of samples from collard green seeds to microscopic 'water bears' were flown. Each prospective team was provided a simple kit equipped with five vials. Each student team submitted five coded samples, one for space flight and four control samples. The control samples were exposed to radiation, cold and centrifugation respectively while one negative control sample was passively stored. The students received the samples back still coded so that they were unaware of which samples were flown. They then investigated their samples according to their individual research protocols. The results were presented in poster and platform form at a student research symposium. Space Trees grown from tree seeds flown in the payload have been planted at all district schools, and at many guest schools. These seeds represented another way in which to involve additional classes and students. Both the passive experiments and the space trees were housed in what otherwise would have been wasted space within the payload. They extended the GAS programs worthwhile ballast concept to another level. The opportunity to fly an experiment in space is too previous not to be extended to the greatest number of students possible.

Morphological, ultrastructural, and molecular characterization of intestinal tetratrichomonads isolated from non-human primates in southeastern Brazil.

PubMed

Dos Santos, Caroline Spitz; de Jesus, Vera Lúcia Teixeira; McIntosh, Douglas; Carreiro, Caroline Cunha; Batista, Lilian Cristina Oliveira; do Bomfim Lopes, Bruno; Neves, Daniel Marchesi; Lopes, Carlos Wilson Gomes

2017-09-01

Non-human primates are our closest relatives and represent an interesting model for comparative parasitological studies. However, research on this topic particularly in relation to intestinal parasites has been fragmentary and limited mainly to animals held in captivity. Thus, our knowledge of host-parasite relationships in this species-rich group of mammals could be considered rudimentary. The current study combined morphological, ultrastructural, and molecular analyses to characterize isolates of intestinal tetratrichomonads recovered from the feces of three species of South American, non-human primates. Fecal samples were collected from 16 animals, representing 12 distinct species. Parabasalid-like organisms were evident in five samples (31%) of feces: two from Alouatta sara, two from Callithrix penicillata, and one from Sapajus apella. The five samples presented morphologies consistent with the description of Tetratrichomonas sp., with four anterior flagella of unequal length, a well-developed undulating membrane, and a long recurrent flagellum. Sequencing of the ITS1-5.8S rRNA-ITS2 region demonstrated that the isolates from A. sara, and C. penicillata were closely related and highly similar to isolates of Tetratrichomonas brumpti, recovered previously from tortoises (Geochelone sp.). The flagellate recovered from S. apella demonstrated a similar morphology to those of the other isolates, however, sequence analysis showed it to be identical to an isolate of Tetratrichomonas sp. recovered from white-lipped peccaries (Tayassu pecari). The findings of this study extend and enhance our knowledge of parasitism of non-human primates by members of the genus Tetratrichomonas and indicate that the host range of these parasites is broader than previously believed.

Impacts of Exercise on Prognostic Biomarkers in Lung Cancer Patients

ClinicalTrials.gov

2016-02-18

Extensive Stage Small Cell Lung Cancer; Healthy, no Evidence of Disease; Limited Stage Small Cell Lung Cancer; Recurrent Non-small Cell Lung Cancer; Recurrent Small Cell Lung Cancer; Stage IA Non-small Cell Lung Cancer; Stage IB Non-small Cell Lung Cancer; Stage IIA Non-small Cell Lung Cancer; Stage IIB Non-small Cell Lung Cancer; Stage IIIA Non-small Cell Lung Cancer; Stage IIIB Non-small Cell Lung Cancer; Stage IV Non-small Cell Lung Cancer

Characterization of PD-L1 expression in Chinese non-small cell lung cancer patients with PTEN expression as a means for tissue quality screening.

PubMed

Zhang, Xu-Chao; Cao, Xu; Sun, Chun; Xie, Zhi; Guo, Jian-Jun; Yang, Jin-Ji; Yang, Xue-Ning; Dai, Hang-Jun; Li, Su-Chun; Xu, Xin-Ran; Zuo, Yun-Xia; Chen, Meng; Koeppen, Hartmut; He, Jing; Kiermaier, Astrid; Shames, David; Cheng, Gang; Wu, Yi-Long

2018-03-01

The goal of this study is to evaluate PD-L1 prevalence and its association with major clinical characteristics in Chinese non-small cell lung cancer (NSCLC) patients to inform the clinical development of anti-PD1/PD-L1 agents in this population. We used phosphatase and tensin homolog (PTEN) expression through IHC as a surrogate tissue quality marker to screen surgical NSCLC samples in tissue microarray (TMA; 172 cases) or whole-section (268 cases) format. The samples were then analyzed with a clinically validated PD-L1 IHC assay. The results were correlated with baseline characteristics and clinical outcomes. PTEN IHC showed that 108 TMA samples and 105 whole-section samples qualified for PD-L1 IHC. With a clinically relevant cutoff, 41.7% of the TMA samples were PD-L1 positive. PD-L1 level was much lower in EGFR-mutant patients and seemed to be a favorable prognostic factor for both overall survival (OS) and recurrence-free survival (RFS). These findings were confirmed in the whole-section samples except that their survival data were not mature enough for correlation analysis. In summary, PD-L1 expression was detected in approximately 40% of PTEN-qualified Chinese NSCLC samples, negatively correlated with EGFR mutation and seemed to be a favorable prognostic factor for both OS and RFS. Notably, the different results from PTEN-qualified and PTEN-disqualified samples underscore the importance of tissue quality control prior to biomarker testing.

Clinical Validation and Implementation of a Targeted Next-Generation Sequencing Assay to Detect Somatic Variants in Non-Small Cell Lung, Melanoma, and Gastrointestinal Malignancies

PubMed Central

Fisher, Kevin E.; Zhang, Linsheng; Wang, Jason; Smith, Geoffrey H.; Newman, Scott; Schneider, Thomas M.; Pillai, Rathi N.; Kudchadkar, Ragini R.; Owonikoko, Taofeek K.; Ramalingam, Suresh S.; Lawson, David H.; Delman, Keith A.; El-Rayes, Bassel F.; Wilson, Malania M.; Sullivan, H. Clifford; Morrison, Annie S.; Balci, Serdar; Adsay, N. Volkan; Gal, Anthony A.; Sica, Gabriel L.; Saxe, Debra F.; Mann, Karen P.; Hill, Charles E.; Khuri, Fadlo R.; Rossi, Michael R.

2017-01-01

We tested and clinically validated a targeted next-generation sequencing (NGS) mutation panel using 80 formalin-fixed, paraffin-embedded (FFPE) tumor samples. Forty non-small cell lung carcinoma (NSCLC), 30 melanoma, and 30 gastrointestinal (12 colonic, 10 gastric, and 8 pancreatic adenocarcinoma) FFPE samples were selected from laboratory archives. After appropriate specimen and nucleic acid quality control, 80 NGS libraries were prepared using the Illumina TruSight tumor (TST) kit and sequenced on the Illumina MiSeq. Sequence alignment, variant calling, and sequencing quality control were performed using vendor software and laboratory-developed analysis workflows. TST generated ≥500× coverage for 98.4% of the 13,952 targeted bases. Reproducible and accurate variant calling was achieved at ≥5% variant allele frequency with 8 to 12 multiplexed samples per MiSeq flow cell. TST detected 112 variants overall, and confirmed all known single-nucleotide variants (n = 27), deletions (n = 5), insertions (n = 3), and multinucleotide variants (n = 3). TST detected at least one variant in 85.0% (68/80), and two or more variants in 36.2% (29/80), of samples. TP53 was the most frequently mutated gene in NSCLC (13 variants; 13/32 samples), gastrointestinal malignancies (15 variants; 13/25 samples), and overall (30 variants; 28/80 samples). BRAF mutations were most common in melanoma (nine variants; 9/23 samples). Clinically relevant NGS data can be obtained from routine clinical FFPE solid tumor specimens using TST, benchtop instruments, and vendor-supplied bioinformatics pipelines. PMID:26801070

Crystal structure, magnetic susceptibility and thermopower of superconducting and non-superconducting Nd 1.85Ce 0.15CuO 4+y

NASA Astrophysics Data System (ADS)

Magelschots, I.; Andersen, N. H.; Lebech, B.; Wisniewski, A.; Jacobsen, C. S.

1992-12-01

An experimental study of superconducting and non-superconducting Nd 1.85Ce 0.15CuO 4+ y, including structure determination by neutron powder diffraction, recording of oxygen changes by gas volumetry, and susceptibility and thermoelectric measurements, is reported. Difference neutron diffraction patterns from samples prepared on-line at the spectrometer show that the structures of superconducting and non-superconducting samples are identical within the limits set by the statistical errors of our data. Simultaneous gas volumetric measurements reveal that Δy<0.03 (1) when the sample is oxidized from the superconducting to the non-superconducting state. Structural refinements confirm that Nd 1.85Ce 0.15CuO 4+ y has the T‧-type tetragonal structure reported in the literature, but additional oxygen may be located on the apical O(3) oxygen site of the T-type structure, with a total oxygen content of 4+ y=4.03 (5). Consistent with this result, we find very small values of the thermoelectric power indicating that Nd 1.85Ce 0.15CuO 4+ y is close to the formal threshold, yc=0.075, between electron and hole conduction, but surprisingly, the thermoelectric power of the superconducting sample is positive, while it is negative in the non-superconducting sample below 210 K.

The importance of streamside sandbars to ground beetle (Coleoptera, Carabidae) communities in a deciduous forest.

Treesearch

S. Horn; M.D. Ulyshen

2009-01-01

We used pitfall traps to sample ground beetles on sandbars along a small woodland stream and in the adjacent floodplain forest (Oglethorpe Co., GA, USA). We captured a total of 1,477 ground beetles representing 41 species. Twenty-two species were exclusive to sandbars, while eight were found only in the forested habitat. Ground beetles...

A Generalized Least Squares Regression Approach for Computing Effect Sizes in Single-Case Research: Application Examples

ERIC Educational Resources Information Center

Maggin, Daniel M.; Swaminathan, Hariharan; Rogers, Helen J.; O'Keeffe, Breda V.; Sugai, George; Horner, Robert H.

2011-01-01

A new method for deriving effect sizes from single-case designs is proposed. The strategy is applicable to small-sample time-series data with autoregressive errors. The method uses Generalized Least Squares (GLS) to model the autocorrelation of the data and estimate regression parameters to produce an effect size that represents the magnitude of…

Assessment of Cognitive Function in Breast Cancer and Lymphoma Patients Receiving Chemotherapy | Division of Cancer Prevention

Cancer.gov

Cognitive impairments in cancer patients represent an important clinical problem. Studies to date estimating prevalence of difficulties in memory, executive function, and attention deficits have been limited by small sample sizes and many have lacked healthy control groups. More information is needed on promising biomarkers and allelic variants that may help to determine the

A Computer-Assisted Instruction Course on Laboratory Detection of Malarial Parasites in Human Blood. Interim Report.

ERIC Educational Resources Information Center

Mitzel, Harold E.

In cooperation with the United States Navy, this project was undertaken to examine the feasibility of computer assisted instruction in clinical malaria recognition, to train a small group of Naval personnel in techniques of creating and presenting such material, and to evaluate the course by giving it to a representative sample of Naval medical…

Non-farmed fish contribute to greater micronutrient intakes than farmed fish: results from an intra-household survey in rural Bangladesh.

PubMed

Bogard, Jessica R; Marks, Geoffrey C; Mamun, Abdullah; Thilsted, Shakuntala H

2017-03-01

Fish is the most important animal-source food (ASF) in Bangladesh, produced from capture fisheries (non-farmed) and aquaculture (farmed) sub-sectors. Large differences in micronutrient content of fish species from these sub-sectors exist. The importance of fish in diets of vulnerable groups compared with other ASF; contribution from non-farmed and farmed species to nutrient intakes; and differences in fish consumption among age, gender, wealth groups and geographic regions were analysed, using quantitative intra-household fish consumption data, focusing on the first 1000 d of life. Two-stage stratified sample. Nationally representative of rural Bangladesh. Households (n 5503) and individuals (n 24 198). Fish consumption in poor households was almost half that in wealthiest households; and lower in females than males in all groups, except the wealthiest, and for those aged ≥15 years (P<0·01). In infants of complementary feeding age, 56 % did not consume ASF on the survey day, despite 78 % of mothers knowing this was recommended. Non-farmed fish made a larger contribution to Fe, Zn, Ca, vitamin A and vitamin B12 intakes than farmed fish (P<0·0001). Policies and programmes aimed to increase fish consumption as a means to improve nutrition in rural Bangladesh should focus on women and young children, and on the poorest households. Aquaculture plays an important role in increasing availability and affordability of fish; however, non-farmed fish species are better placed to contribute to greater micronutrient intakes. This presents an opportunity for aquaculture to contribute to improved nutrition, utilising diverse production technologies and fish species, including small fish.

Micro-X-Ray computed tomography of natural and experimental melt segregations and other geological materials with small absorption contrasts

NASA Astrophysics Data System (ADS)

Baumgartner, L.; Wohlers, A.; Müller, T.

2003-04-01

Micro X-ray tomography is rapidly advancing to an important tool for non-destructive 3-D imaging of geological and engineering materials. We have been using a Skyscan 1072 system (Skyscan, Belgium) to successfully image as diverse geological materials as sandstones, foraminifers, run products of hydrothermal partial melting experiments, and metamorphic rocks. The system has a conical x-ray source with a spot size of about 5µm. The X-ray source is powered by a 10W, 20--100kV, tunable supply. Images are acquired with a scintillator coupled by glass fiber optics to a 1024×1024 pixel, 12-bit CCD. The sample is rotated for 180^o (or 360^o) in steps as small as 0.24^o. Transmission image are back projected, using a Feldkamp algorithm, into a stack of up to 1000 1K×1K images, each of which represents a horizontal cross section of the sample. We have succeeded to image very low contrast systems (feldspar/quartz and olivine/calcite/dolomite), by using extended acquisition times (up to 24 hours), and low excitation voltages (30--40kV) in combination with aluminum filters to reduce beam hardening. Some quartzites collected in the Little Cottonwood contact aureole have been infiltrated by a pegmatitic liquid. These liquids are the products of partial melting in intercalated meta-pelites. 2-D images (thin sections) clearly show, that poly-crystalline interstitial feldspar and mica represent precipitates from the infiltrated pegmatitic liquid (acute quartz-feldspar junctions similar to melting experiments). The micro-CT images reveal a thin mica-feldspar network. It forms highly anastomosing, multiply interconnected networks surrounding quartz grains. They connect larger, up to 1mm sized ponds, located in triple junctions. These results have important consequences for porous melt transport in shallow crustal rocks. Micro-CT images of spinifex textured olivine in marbles from the Ubehebe Peak contact aureole (Death Valley, California) reveal two preferential growth orientations of olivine, and irregular distribution of calcite haloes. These volumetric images suggesting that the growth of olivine is related to mass transport, rather than to their inherent crystallographic growth preferences.

VapB type 8 plasmids in Rhodococcus equi isolated from the small intestine of pigs and comparison of selective culture media.

PubMed

Lara, G H B; Takai, S; Sasaki, Y; Kakuda, T; Listoni, F J P; Risseti, R M; de Morais, A B C; Ribeiro, M G

2015-09-01

The virulence-plasmid profile of Rhodococcus equi strains isolated from Suidae and humans is similar. Recent evidence suggests that the consumption of pork products contaminated with faeces might be a potential source of R. equi infections in humans, mainly to patients with rhodococcosis without history of contact with pigs or pig farms. This study investigated the virulence-associated genes (vapA and vapB) and plasmid profiles of R. equi among the 150 samples of small intestinal content obtained from slaughtered pigs. In addition, all samples were subjected to microbiological culture in conventional sheep blood agar and CAZ-NB, TCP and TVP selective media. A total of 40 (26·7%) of the samples recovered R. equi, with two samples recovering isolates harbouring the VapB type 8 plasmid. Among the 150 pigs sampled herein, CAZ-NB was considered the best selective medium for the isolation of R. equi from faeces. Our results provide evidence that the contamination of slaughtered pig carcasses with pathogenic R. equi might occur through faeces, representing a public health concern. Furthermore, this study is the first description of R. equi strains carrying the VapB plasmid in the gut of pigs. Intermediately virulent (VapB) is a common plasmid-type harboured by R. equi isolated from pigs and humans with AIDS. Curiously, humans with rhodococcosis usually have no history of contact with pigs or pig farms. Virulence-plasmid profile of 40 R. equi isolated among 150 small intestine content samples from pigs revelled two carrying isolates with the VapB type-8 plasmids. Moreover, comparison of three selective culture media shows that CAZ-NB was the best. Our results provide evidence that contamination of slaughtered pig carcasses with pathogenic R. equi might occur through faeces, representing a public health concern. Furthermore, R. equi carrying VapB type-8 plasmids types are described for the first time in the gut of the pig. © 2015 The Society for Applied Microbiology.

Magnitude knowledge: the common core of numerical development.

PubMed

Siegler, Robert S

2016-05-01

The integrated theory of numerical development posits that a central theme of numerical development from infancy to adulthood is progressive broadening of the types and ranges of numbers whose magnitudes are accurately represented. The process includes four overlapping trends: (1) representing increasingly precisely the magnitudes of non-symbolic numbers, (2) connecting small symbolic numbers to their non-symbolic referents, (3) extending understanding from smaller to larger whole numbers, and (4) accurately representing the magnitudes of rational numbers. The present review identifies substantial commonalities, as well as differences, in these four aspects of numerical development. With both whole and rational numbers, numerical magnitude knowledge is concurrently correlated with, longitudinally predictive of, and causally related to multiple aspects of mathematical understanding, including arithmetic and overall math achievement. Moreover, interventions focused on increasing numerical magnitude knowledge often generalize to other aspects of mathematics. The cognitive processes of association and analogy seem to play especially large roles in this development. Thus, acquisition of numerical magnitude knowledge can be seen as the common core of numerical development. © 2016 John Wiley & Sons Ltd.

Small RNAome profiling from human skeletal muscle: novel miRNAs and their targets associated with cancer cachexia.

PubMed

Narasimhan, Ashok; Ghosh, Sunita; Stretch, Cynthia; Greiner, Russell; Bathe, Oliver F; Baracos, Vickie; Damaraju, Sambasivarao

2017-06-01

MicroRNAs (miRs) are small non-coding RNAs that regulate gene (mRNA) expression. Although the pathological role of miRs have been studied in muscle wasting conditions such as myotonic and muscular dystrophy, their roles in cancer cachexia (CC) are still emerging. The objectives are (i) to profile human skeletal muscle expressed miRs; (ii) to identify differentially expressed (DE) miRs between cachectic and non-cachectic cancer patients; (iii) to identify mRNA targets for the DE miRs to gain mechanistic insights; and (iv) to investigate if miRs show potential prognostic and predictive value. Study subjects were classified based on the international consensus diagnostic criteria for CC. Forty-two cancer patients were included, of which 22 were cachectic cases and 20 were non-cachectic cancer controls. Total RNA isolated from muscle biopsies were subjected to next-generation sequencing. A total of 777 miRs were profiled, and 82 miRs with read counts of ≥5 in 80% of samples were retained for analysis. We identified eight DE miRs (up-regulated, fold change of ≥1.4 at P < 0.05). A total of 191 potential mRNA targets were identified for the DE miRs using previously described human skeletal muscle mRNA expression data (n = 90), and a majority of them were also confirmed in an independent mRNA transcriptome dataset. Ingenuity pathway analysis identified pathways related to myogenesis and inflammation. qRT-PCR analysis of representative miRs showed similar direction of effect (P < 0.05), as observed in next-generation sequencing. The identified miRs also showed prognostic and predictive value. In all, we identified eight novel miRs associated with CC. © 2017 The Authors. Journal of Cachexia, Sarcopenia and Muscle published by John Wiley & Sons Ltd on behalf of the Society on Sarcopenia, Cachexia and Wasting Disorders.

ALK in Non-Small Cell Lung Cancer (NSCLC) Pathobiology, Epidemiology, Detection from Tumor Tissue and Algorithm Diagnosis in a Daily Practice

PubMed Central

Hofman, Paul

2017-01-01

Patients with advanced-stage non-small cell lung carcinoma (NSCLC) harboring an ALK rearrangement, detected from a tissue sample, can benefit from targeted ALK inhibitor treatment. Several increasingly effective ALK inhibitors are now available for treatment of patients. However, despite an initial favorable response to treatment, in most cases relapse or progression occurs due to resistance mechanisms mainly caused by mutations in the tyrosine kinase domain of ALK. The detection of an ALK rearrangement is pivotal and can be done using different methods, which have variable sensitivity and specificity depending, in particular, on the quality and quantity of the patient’s sample. This review will first highlight briefly some information regarding the pathobiology of an ALK rearrangement and the epidemiology of patients harboring this genomic alteration. The different methods used to detect an ALK rearrangement as well as their advantages and disadvantages will then be examined and algorithms proposed for detection in daily routine practice. PMID:28805682