Reference tissue normalization in longitudinal (18)F-florbetapir positron emission tomography of late mild cognitive impairment.

PubMed

Shokouhi, Sepideh; Mckay, John W; Baker, Suzanne L; Kang, Hakmook; Brill, Aaron B; Gwirtsman, Harry E; Riddle, William R; Claassen, Daniel O; Rogers, Baxter P

2016-01-15

Semiquantitative methods such as the standardized uptake value ratio (SUVR) require normalization of the radiotracer activity to a reference tissue to monitor changes in the accumulation of amyloid-β (Aβ) plaques measured with positron emission tomography (PET). The objective of this study was to evaluate the effect of reference tissue normalization in a test-retest (18)F-florbetapir SUVR study using cerebellar gray matter, white matter (two different segmentation masks), brainstem, and corpus callosum as reference regions. We calculated the correlation between (18)F-florbetapir PET and concurrent cerebrospinal fluid (CSF) Aβ1-42 levels in a late mild cognitive impairment cohort with longitudinal PET and CSF data over the course of 2 years. In addition to conventional SUVR analysis using mean and median values of normalized brain radiotracer activity, we investigated a new image analysis technique-the weighted two-point correlation function (wS2)-to capture potentially more subtle changes in Aβ-PET data. Compared with the SUVRs normalized to cerebellar gray matter, all cerebral-to-white matter normalization schemes resulted in a higher inverse correlation between PET and CSF Aβ1-42, while the brainstem normalization gave the best results (high and most stable correlation). Compared with the SUVR mean and median values, the wS2 values were associated with the lowest coefficient of variation and highest inverse correlation to CSF Aβ1-42 levels across all time points and reference regions, including the cerebellar gray matter. The selection of reference tissue for normalization and the choice of image analysis method can affect changes in cortical (18)F-florbetapir uptake in longitudinal studies.

Evaluation of New Reference Genes in Papaya for Accurate Transcript Normalization under Different Experimental Conditions

PubMed Central

Chen, Weixin; Chen, Jianye; Lu, Wangjin; Chen, Lei; Fu, Danwen

2012-01-01

Real-time reverse transcription PCR (RT-qPCR) is a preferred method for rapid and accurate quantification of gene expression studies. Appropriate application of RT-qPCR requires accurate normalization though the use of reference genes. As no single reference gene is universally suitable for all experiments, thus reference gene(s) validation under different experimental conditions is crucial for RT-qPCR analysis. To date, only a few studies on reference genes have been done in other plants but none in papaya. In the present work, we selected 21 candidate reference genes, and evaluated their expression stability in 246 papaya fruit samples using three algorithms, geNorm, NormFinder and RefFinder. The samples consisted of 13 sets collected under different experimental conditions, including various tissues, different storage temperatures, different cultivars, developmental stages, postharvest ripening, modified atmosphere packaging, 1-methylcyclopropene (1-MCP) treatment, hot water treatment, biotic stress and hormone treatment. Our results demonstrated that expression stability varied greatly between reference genes and that different suitable reference gene(s) or combination of reference genes for normalization should be validated according to the experimental conditions. In general, the internal reference genes EIF (Eukaryotic initiation factor 4A), TBP1 (TATA binding protein 1) and TBP2 (TATA binding protein 2) genes had a good performance under most experimental conditions, whereas the most widely present used reference genes, ACTIN (Actin 2), 18S rRNA (18S ribosomal RNA) and GAPDH (Glyceraldehyde-3-phosphate dehydrogenase) were not suitable in many experimental conditions. In addition, two commonly used programs, geNorm and Normfinder, were proved sufficient for the validation. This work provides the first systematic analysis for the selection of superior reference genes for accurate transcript normalization in papaya under different experimental conditions. PMID

Mitochondrial dysfunction in myocardium obtained from clinically normal dogs, clinically normal anesthetized dogs, and dogs with dilated cardiomyopathy.

PubMed

Sleeper, Meg M; Rosato, Bradley P; Bansal, Seema; Avadhani, Narayan G

2012-11-01

To compare mitochondrial complex I and complex IV activity in myocardial mitochondria of clinically normal dogs, clinically normal dogs exposed to inhalation anesthesia, and dogs affected with dilated cardiomyopathy. Myocardial samples obtained from 21 euthanized dogs (6 clinically normal [control] dogs, 5 clinically normal dogs subjected to inhalation anesthesia with isoflurane prior to euthanasia, 5 dogs with juvenile-onset dilated cardiomyopathy, and 5 dogs with adult-onset dilated cardiomyopathy). Activity of mitochondrial complex I and complex IV was assayed spectrophotometrically in isolated mitochondria from left ventricular tissue obtained from the 4 groups of dogs. Activity of complex I and complex IV was significantly decreased in anesthetized dogs, compared with activities in the control dogs and dogs with juvenile-onset or adult-onset dilated cardiomyopathy. Inhalation anesthesia disrupted the electron transport chain in the dogs, which potentially led to an outburst of reactive oxygen species that caused mitochondrial dysfunction. Inhalation anesthesia depressed mitochondrial function in dogs, similar to results reported in other species. This effect is important to consider when anesthetizing animals with myocardial disease and suggested that antioxidant treatments may be beneficial in some animals. Additionally, this effect should be considered when designing studies in which mitochondrial enzyme activity will be measured. Additional studies that include a larger number of animals are warranted.

Identification of appropriate reference genes for normalizing transcript expression by quantitative real-time PCR in Litsea cubeba.

PubMed

Lin, Liyuan; Han, Xiaojiao; Chen, Yicun; Wu, Qingke; Wang, Yangdong

2013-12-01

Quantitative real-time PCR has emerged as a highly sensitive and widely used method for detection of gene expression profiles, via which accurate detection depends on reliable normalization. Since no single control is appropriate for all experimental treatments, it is generally advocated to select suitable internal controls prior to use for normalization. This study reported the evaluation of the expression stability of twelve potential reference genes in different tissue/organs and six fruit developmental stages of Litsea cubeba in order to screen the superior internal reference genes for data normalization. Two softwares-geNorm, and NormFinder-were used to identify stability of these candidate genes. The cycle threshold difference and coefficient of variance were also calculated to evaluate the expression stability of candidate genes. F-BOX, EF1α, UBC, and TUA were selected as the most stable reference genes across 11 sample pools. F-BOX, EF1α, and EIF4α exhibited the highest expression stability in different tissue/organs and different fruit developmental stages. Besides, a combination of two stable reference genes would be sufficient for gene expression normalization in different fruit developmental stages. In addition, the relative expression profiles of DXS and DXR were evaluated by EF1α, UBC, and SAMDC. The results further validated the reliability of stable reference genes and also highlighted the importance of selecting suitable internal controls for L. cubeba. These reference genes will be of great importance for transcript normalization in future gene expression studies on L. cubeba.

Identification of Suitable Reference Genes for Gene Expression Normalization in qRT-PCR Analysis in Watermelon

PubMed Central

Gao, Lingyun; Zhao, Shuang; Jiang, Wei; Huang, Yuan; Bie, Zhilong

2014-01-01

Watermelon is one of the major Cucurbitaceae crops and the recent availability of genome sequence greatly facilitates the fundamental researches on it. Quantitative real-time reverse transcriptase PCR (qRT–PCR) is the preferred method for gene expression analyses, and using validated reference genes for normalization is crucial to ensure the accuracy of this method. However, a systematic validation of reference genes has not been conducted on watermelon. In this study, transcripts of 15 candidate reference genes were quantified in watermelon using qRT–PCR, and the stability of these genes was compared using geNorm and NormFinder. geNorm identified ClTUA and ClACT, ClEF1α and ClACT, and ClCAC and ClTUA as the best pairs of reference genes in watermelon organs and tissues under normal growth conditions, abiotic stress, and biotic stress, respectively. NormFinder identified ClYLS8, ClUBCP, and ClCAC as the best single reference genes under the above experimental conditions, respectively. ClYLS8 and ClPP2A were identified as the best reference genes across all samples. Two to nine reference genes were required for more reliable normalization depending on the experimental conditions. The widely used watermelon reference gene 18SrRNA was less stable than the other reference genes under the experimental conditions. Catalase family genes were identified in watermelon genome, and used to validate the reliability of the identified reference genes. ClCAT1and ClCAT2 were induced and upregulated in the first 24 h, whereas ClCAT3 was downregulated in the leaves under low temperature stress. However, the expression levels of these genes were significantly overestimated and misinterpreted when 18SrRNA was used as a reference gene. These results provide a good starting point for reference gene selection in qRT–PCR analyses involving watermelon. PMID:24587403

Identification of suitable reference genes for gene expression normalization in qRT-PCR analysis in watermelon.

PubMed

Kong, Qiusheng; Yuan, Jingxian; Gao, Lingyun; Zhao, Shuang; Jiang, Wei; Huang, Yuan; Bie, Zhilong

2014-01-01

Watermelon is one of the major Cucurbitaceae crops and the recent availability of genome sequence greatly facilitates the fundamental researches on it. Quantitative real-time reverse transcriptase PCR (qRT-PCR) is the preferred method for gene expression analyses, and using validated reference genes for normalization is crucial to ensure the accuracy of this method. However, a systematic validation of reference genes has not been conducted on watermelon. In this study, transcripts of 15 candidate reference genes were quantified in watermelon using qRT-PCR, and the stability of these genes was compared using geNorm and NormFinder. geNorm identified ClTUA and ClACT, ClEF1α and ClACT, and ClCAC and ClTUA as the best pairs of reference genes in watermelon organs and tissues under normal growth conditions, abiotic stress, and biotic stress, respectively. NormFinder identified ClYLS8, ClUBCP, and ClCAC as the best single reference genes under the above experimental conditions, respectively. ClYLS8 and ClPP2A were identified as the best reference genes across all samples. Two to nine reference genes were required for more reliable normalization depending on the experimental conditions. The widely used watermelon reference gene 18SrRNA was less stable than the other reference genes under the experimental conditions. Catalase family genes were identified in watermelon genome, and used to validate the reliability of the identified reference genes. ClCAT1and ClCAT2 were induced and upregulated in the first 24 h, whereas ClCAT3 was downregulated in the leaves under low temperature stress. However, the expression levels of these genes were significantly overestimated and misinterpreted when 18SrRNA was used as a reference gene. These results provide a good starting point for reference gene selection in qRT-PCR analyses involving watermelon.

Validation of reference genes for real-time quantitative PCR normalization in soybean developmental and germinating seeds.

PubMed

Li, Qing; Fan, Cheng-Ming; Zhang, Xiao-Mei; Fu, Yong-Fu

2012-10-01

Most of traditional reference genes chosen for real-time quantitative PCR normalization were assumed to be ubiquitously and constitutively expressed in vegetative tissues. However, seeds show distinct transcriptomes compared with the vegetative tissues. Therefore, there is a need for re-validation of reference genes in samples of seed development and germination, especially for soybean seeds. In this study, we aimed at identifying reference genes suitable for the quantification of gene expression level in soybean seeds. In order to identify the best reference genes for soybean seeds, 18 putative reference genes were tested with various methods in different seed samples. We combined the outputs of both geNorm and NormFinder to assess the expression stability of these genes. The reference genes identified as optimums for seed development were TUA5 and UKN2, whereas for seed germination they were novel reference genes Glyma05g37470 and Glyma08g28550. Furthermore, for total seed samples it was necessary to combine four genes of Glyma05g37470, Glyma08g28550, Glyma18g04130 and UKN2 [corrected] for normalization. Key message We identified several reference genes that stably expressed in soybean seed developmental and germinating processes.

The National Football League Scouting Combine from 1999 to 2014: normative reference values and an examination of body mass normalization techniques.

PubMed

Nuzzo, James L

2015-02-01

The primary purpose of this study was to identify the most appropriate method for normalizing physical performance measures to body mass in American football players. Data were obtained from the population of players (n = 4,603) that completed the vertical jump, broad jump, 40-yd sprint, 20-yd shuttle, 3-cone drill, and bench press at the National Football League Scouting Combine from 1999 to 2014. Correlation coefficients were used to assess relationships between body mass and physical performance measures. For the entire group and each playing position, absolute (i.e., non-normalized) performance measures were significantly (p ≤ 0.05) correlated with body mass, indicating that normalization is warranted. Ratio scaling, however, was not appropriate for normalizing most performance measures because it merely reversed (and increased in magnitude) the significant correlations between body mass and performance. Allometric scaling with derived allometric parameters was appropriate for normalizing all performance measures because correlations between body mass and performance were near to zero and no longer statistically significant. However, the derived allometric parameters differed by playing position. Thus, when normalizing physical performance measures to body mass, strength and conditioning professionals should use allometric scaling with test- and position-specific allometric parameters. Additionally, in the current study, percentile rankings were generated to provide test- and position-specific normative reference values for the absolute measures. Until body mass normalization techniques are adopted more broadly, strength and conditioning professionals can use these normative references values to compare current players with those who have already participated in the Scouting Combine.

Identification and evaluation of reference genes for qRT-PCR normalization in Ganoderma lucidum.

PubMed

Xu, Jiang; Xu, ZhiChao; Zhu, YingJie; Luo, HongMei; Qian, Jun; Ji, AiJia; Hu, YuanLei; Sun, Wei; Wang, Bo; Song, JingYuan; Sun, Chao; Chen, ShiLin

2014-01-01

Quantitative real-time reverse transcription PCR (qRT-PCR) is a rapid, sensitive, and reliable technique for gene expression studies. The accuracy and reliability of qRT-PCR results depend on the stability of the reference genes used for gene normalization. Therefore, a systematic process of reference gene evaluation is needed. Ganoderma lucidum is a famous medicinal mushroom in East Asia. In the current study, 10 potential reference genes were selected from the G. lucidum genomic data. The sequences of these genes were manually curated, and primers were designed following strict criteria. The experiment was conducted using qRT-PCR, and the stability of each candidate gene was assessed using four commonly used statistical programs-geNorm, NormFinder, BestKeeper, and RefFinder. According to our results, PP2A was expressed at the most stable levels under different fermentation conditions, and RPL4 was the most stably expressed gene in different tissues. RPL4, PP2A, and β-tubulin are the most commonly recommended reference genes for normalizing gene expression in the entire sample set. The current study provides a foundation for the further use of qRT-PCR in G. lucidum gene analysis.

Communication: Density functional theory model for multi-reference systems based on the exact-exchange hole normalization

NASA Astrophysics Data System (ADS)

Laqua, Henryk; Kussmann, Jörg; Ochsenfeld, Christian

2018-03-01

The correct description of multi-reference electronic ground states within Kohn-Sham density functional theory (DFT) requires an ensemble-state representation, employing fractionally occupied orbitals. However, the use of fractional orbital occupation leads to non-normalized exact-exchange holes, resulting in large fractional-spin errors for conventional approximative density functionals. In this communication, we present a simple approach to directly include the exact-exchange-hole normalization into DFT. Compared to conventional functionals, our model strongly improves the description for multi-reference systems, while preserving the accuracy in the single-reference case. We analyze the performance of our proposed method at the example of spin-averaged atoms and spin-restricted bond dissociation energy surfaces.

Communication: Density functional theory model for multi-reference systems based on the exact-exchange hole normalization.

PubMed

Laqua, Henryk; Kussmann, Jörg; Ochsenfeld, Christian

2018-03-28

The correct description of multi-reference electronic ground states within Kohn-Sham density functional theory (DFT) requires an ensemble-state representation, employing fractionally occupied orbitals. However, the use of fractional orbital occupation leads to non-normalized exact-exchange holes, resulting in large fractional-spin errors for conventional approximative density functionals. In this communication, we present a simple approach to directly include the exact-exchange-hole normalization into DFT. Compared to conventional functionals, our model strongly improves the description for multi-reference systems, while preserving the accuracy in the single-reference case. We analyze the performance of our proposed method at the example of spin-averaged atoms and spin-restricted bond dissociation energy surfaces.

Evaluation and Validation of Reference Genes for qRT-PCR Normalization in Frankliniella occidentalis (Thysanoptera:Thripidae)

PubMed Central

Zheng, Yu-Tao; Li, Hong-Bo; Lu, Ming-Xing; Du, Yu-Zhou

2014-01-01

Quantitative real time PCR (qRT-PCR) has emerged as a reliable and reproducible technique for studying gene expression analysis. For accurate results, the normalization of data with reference genes is particularly essential. Once the transcriptome sequencing of Frankliniella occidentalis was completed, numerous unigenes were identified and annotated. Unfortunately, there are no studies on the stability of reference genes used in F. occidentalis. In this work, seven candidate reference genes, including actin, 18S rRNA, H3, tubulin, GAPDH, EF-1 and RPL32, were evaluated for their suitability as normalization genes under different experimental conditions using the statistical software programs BestKeeper, geNorm, Normfinder and the comparative ΔCt method. Because the rankings of the reference genes provided by each of the four programs were different, we chose a user-friendly web-based comprehensive tool RefFinder to get the final ranking. The result demonstrated that EF-1 and RPL32 displayed the most stable expression in different developmental stages; RPL32 and GAPDH showed the most stable expression at high temperatures, while 18S and EF-1 exhibited the most stable expression at low temperatures. In this study, we validated the suitable reference genes in F. occidentalis for gene expression profiling under different experimental conditions. The choice of internal standard is very important in the normalization of the target gene expression levels, thus validating and selecting the best genes will help improve the quality of gene expression data of F. occidentalis. What is more, these validated reference genes could serve as the basis for the selection of candidate reference genes in other insects. PMID:25356721

Evaluation and validation of reference genes for qRT-PCR normalization in Frankliniella occidentalis (Thysanoptera: Thripidae).

PubMed

Zheng, Yu-Tao; Li, Hong-Bo; Lu, Ming-Xing; Du, Yu-Zhou

2014-01-01

Quantitative real time PCR (qRT-PCR) has emerged as a reliable and reproducible technique for studying gene expression analysis. For accurate results, the normalization of data with reference genes is particularly essential. Once the transcriptome sequencing of Frankliniella occidentalis was completed, numerous unigenes were identified and annotated. Unfortunately, there are no studies on the stability of reference genes used in F. occidentalis. In this work, seven candidate reference genes, including actin, 18S rRNA, H3, tubulin, GAPDH, EF-1 and RPL32, were evaluated for their suitability as normalization genes under different experimental conditions using the statistical software programs BestKeeper, geNorm, Normfinder and the comparative ΔCt method. Because the rankings of the reference genes provided by each of the four programs were different, we chose a user-friendly web-based comprehensive tool RefFinder to get the final ranking. The result demonstrated that EF-1 and RPL32 displayed the most stable expression in different developmental stages; RPL32 and GAPDH showed the most stable expression at high temperatures, while 18S and EF-1 exhibited the most stable expression at low temperatures. In this study, we validated the suitable reference genes in F. occidentalis for gene expression profiling under different experimental conditions. The choice of internal standard is very important in the normalization of the target gene expression levels, thus validating and selecting the best genes will help improve the quality of gene expression data of F. occidentalis. What is more, these validated reference genes could serve as the basis for the selection of candidate reference genes in other insects.

Validation of Suitable Reference Genes for Expression Normalization in Echinococcus spp. Larval Stages

PubMed Central

Espínola, Sergio Martin; Ferreira, Henrique Bunselmeyer; Zaha, Arnaldo

2014-01-01

In recent years, a significant amount of sequence data (both genomic and transcriptomic) for Echinococcus spp. has been published, thereby facilitating the analysis of genes expressed during a specific stage or involved in parasite development. To perform a suitable gene expression quantification analysis, the use of validated reference genes is strongly recommended. Thus, the aim of this work was to identify suitable reference genes to allow reliable expression normalization for genes of interest in Echinococcus granulosus sensu stricto (s.s.) (G1) and Echinococcus ortleppi upon induction of the early pre-adult development. Untreated protoscoleces (PS) and pepsin-treated protoscoleces (PSP) from E. granulosus s.s. (G1) and E. ortleppi metacestode were used. The gene expression stability of eleven candidate reference genes (βTUB, NDUFV2, RPL13, TBP, CYP-1, RPII, EF-1α, βACT-1, GAPDH, ETIF4A-III and MAPK3) was assessed using geNorm, Normfinder, and RefFinder. Our qPCR data showed a good correlation with the recently published RNA-seq data. Regarding expression stability, EF-1α and TBP were the most stable genes for both species. Interestingly, βACT-1 (the most commonly used reference gene), and GAPDH and ETIF4A-III (previously identified as housekeeping genes) did not behave stably in our assay conditions. We propose the use of EF-1α as a reference gene for studies involving gene expression analysis in both PS and PSP experimental conditions for E. granulosus s.s. and E. ortleppi. To demonstrate its applicability, EF-1α was used as a normalizer gene in the relative quantification of transcripts from genes coding for antigen B subunits. The same EF-1α reference gene may be used in studies with other Echinococcus sensu lato species. This report validates suitable reference genes for species of class Cestoda, phylum Platyhelminthes, thus providing a foundation for further validation in other epidemiologically important cestode species, such as those from the

Validation of suitable reference genes for expression normalization in Echinococcus spp. larval stages.

PubMed

Espínola, Sergio Martin; Ferreira, Henrique Bunselmeyer; Zaha, Arnaldo

2014-01-01

In recent years, a significant amount of sequence data (both genomic and transcriptomic) for Echinococcus spp. has been published, thereby facilitating the analysis of genes expressed during a specific stage or involved in parasite development. To perform a suitable gene expression quantification analysis, the use of validated reference genes is strongly recommended. Thus, the aim of this work was to identify suitable reference genes to allow reliable expression normalization for genes of interest in Echinococcus granulosus sensu stricto (s.s.) (G1) and Echinococcus ortleppi upon induction of the early pre-adult development. Untreated protoscoleces (PS) and pepsin-treated protoscoleces (PSP) from E. granulosus s.s. (G1) and E. ortleppi metacestode were used. The gene expression stability of eleven candidate reference genes (βTUB, NDUFV2, RPL13, TBP, CYP-1, RPII, EF-1α, βACT-1, GAPDH, ETIF4A-III and MAPK3) was assessed using geNorm, Normfinder, and RefFinder. Our qPCR data showed a good correlation with the recently published RNA-seq data. Regarding expression stability, EF-1α and TBP were the most stable genes for both species. Interestingly, βACT-1 (the most commonly used reference gene), and GAPDH and ETIF4A-III (previously identified as housekeeping genes) did not behave stably in our assay conditions. We propose the use of EF-1α as a reference gene for studies involving gene expression analysis in both PS and PSP experimental conditions for E. granulosus s.s. and E. ortleppi. To demonstrate its applicability, EF-1α was used as a normalizer gene in the relative quantification of transcripts from genes coding for antigen B subunits. The same EF-1α reference gene may be used in studies with other Echinococcus sensu lato species. This report validates suitable reference genes for species of class Cestoda, phylum Platyhelminthes, thus providing a foundation for further validation in other epidemiologically important cestode species, such as those from the

Reference gene selection for quantitative reverse transcription-polymerase chain reaction normalization during in vitro adventitious rooting in Eucalyptus globulus Labill.

PubMed

de Almeida, Márcia R; Ruedell, Carolina M; Ricachenevsky, Felipe K; Sperotto, Raul A; Pasquali, Giancarlo; Fett-Neto, Arthur G

2010-09-20

profile obtained using the genes suggested by the algorithms, H2B and TUA were considered as the most suitable reference genes for expression studies in E. globulus adventitious rooting. UBI and 18S were unsuitable for use as controls in qPCR related to this process. These findings will enable more accurate and reliable normalization of qPCR results for gene expression studies in this economically important woody plant, particularly related to rooting and clonal propagation.

Reference gene selection for quantitative reverse transcription-polymerase chain reaction normalization during in vitro adventitious rooting in Eucalyptus globulus Labill

PubMed Central

2010-01-01

on the AGO1 relative expression profile obtained using the genes suggested by the algorithms, H2B and TUA were considered as the most suitable reference genes for expression studies in E. globulus adventitious rooting. UBI and 18S were unsuitable for use as controls in qPCR related to this process. These findings will enable more accurate and reliable normalization of qPCR results for gene expression studies in this economically important woody plant, particularly related to rooting and clonal propagation. PMID:20854682

Normal reference ranges for left ventricular dimensions in preterm infants.

PubMed

Abushaban, Lulu; Vel, Mariappa Thinakar; Rathinasamy, Jebaraj; Sharma, Prem N

2014-09-01

To establish normal reference ranges for the left ventricular dimensions in preterm infants and their correlation with gestational age, body weight and chronological age. In a prospective study, 268 preterm babies, who fulfilled the criteria for inclusion, were examined in Kuwait during the years (2008-2010). Echocardiograms were performed to measure the left ventricular dimensions on 0-6 day(s) of life and at weekly intervals until they reached 36 weeks. The gestational age was grouped into three: 24-27, 28-31 and 32-35 weeks, and body weight into five: ⩽999, 1,000-1,499, 1,500-1,999, 2,000-2,499 and ≥2,500 grams. The overall group differences were compared for each period of life: 0-6 days, 1-2, 3-4 and ≥5 weeks. The mean gestational age was 29.8 (± 2.38 SD) weeks, ranging between 24 and 35, and the mean body weight 1,479 (± 413 SD) grams, ranging between 588 and 3380. At the first scan (0-6 days of life), all the left ventricular measurements correlated well (P < 0.001) with body weight, and the same was observed with gestational age, except for left ventricular posterior wall thickness at end-systole and end-diastole. A significant gradual increase was noticed in all the dimensions with body weight during each period of life. However, with respect to gestational age, an increase was observed in all the dimensions during first four weeks, but the rate of increase became less after 5 weeks of life. Overall, a progressive and significant increase in all left ventricle measurements was observed during the first nine weeks of life. The left ventricular dimension measurements were found to have significant correlation with both gestational age and body weight. The study also provides reference data, which can be used as normal reference tool for left ventricular dimensions for preterm infants against the gestational age, body weight and chronological age.

Reference Gene Selection for qPCR Normalization of Kosteletzkya virginica under Salt Stress

PubMed Central

Tang, Xiaoli; Wang, Hongyan; Shao, Chuyang; Shao, Hongbo

2015-01-01

Kosteletzkya virginica (L.) is a newly introduced perennial halophytic plant. Presently, reverse transcription quantitative real-time PCR (qPCR) is regarded as the best choice for analyzing gene expression and its accuracy mainly depends on the reference genes which are used for gene expression normalization. In this study, we employed qPCR to select the most stable reference gene in K. virginica which showed stable expression profiles under our experimental conditions. The candidate reference genes were 18S ribosomal RNA (18SrRNA), β-actin (ACT), α-tubulin (TUA), and elongation factor (EF). We tracked the gene expression profiles of the candidate genes and analyzed their stabilities through BestKeeper, geNorm, and NormFinder software programs. The results of the three programs were identical and 18SrRNA was assessed to be the most stable reference gene in this study. However, TUA was identified to be the most unstable. Our study proved again that the traditional reference genes indeed displayed a certain degree of variations under given experimental conditions. Importantly, our research also provides guidance for selecting most suitable reference genes and lays the foundation for further studies in K. virginica. PMID:26581422

Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis1[w

PubMed Central

Czechowski, Tomasz; Stitt, Mark; Altmann, Thomas; Udvardi, Michael K.; Scheible, Wolf-Rüdiger

2005-01-01

Gene transcripts with invariant abundance during development and in the face of environmental stimuli are essential reference points for accurate gene expression analyses, such as RNA gel-blot analysis or quantitative reverse transcription-polymerase chain reaction (PCR). An exceptionally large set of data from Affymetrix ATH1 whole-genome GeneChip studies provided the means to identify a new generation of reference genes with very stable expression levels in the model plant species Arabidopsis (Arabidopsis thaliana). Hundreds of Arabidopsis genes were found that outperform traditional reference genes in terms of expression stability throughout development and under a range of environmental conditions. Most of these were expressed at much lower levels than traditional reference genes, making them very suitable for normalization of gene expression over a wide range of transcript levels. Specific and efficient primers were developed for 22 genes and tested on a diverse set of 20 cDNA samples. Quantitative reverse transcription-PCR confirmed superior expression stability and lower absolute expression levels for many of these genes, including genes encoding a protein phosphatase 2A subunit, a coatomer subunit, and an ubiquitin-conjugating enzyme. The developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels in Arabidopsis in the future. PMID:16166256

Trimester specific reference intervals for thyroid function tests in normal Indian pregnant women.

PubMed

Sekhri, Tarun; Juhi, Juhi Agarwal; Wilfred, Reena; Kanwar, Ratnesh S; Sethi, Jyoti; Bhadra, Kuntal; Nair, Sirimavo; Singh, Satveer

2016-01-01

Accurate assessment of thyroid function during pregnancy is critical, for initiation of thyroid hormone therapy, as well as for adjustment of thyroid hormone dose in hypothyroid cases. We evaluated pregnant women who had no past history of thyroid disorders and studied their thyroid function in each trimester. 86 normal pregnant women in the first trimester of pregnancy were selected for setting reference intervals. All were healthy, euthyroid and negative for thyroid peroxidase antibody (TPOAb). These women were serially followed throughout pregnancy. 124 normal nonpregnant subjects were selected for comparison. Thyrotropin (TSH), free thyroxine (FT4), free triiodothyronine (FT3) and anti-TPO were measured using Roche Elecsys 1010 analyzer. Urinary iodine content was determined by simple microplate method. The 2.5th and 97.5th percentiles were calculated as the reference intervals for thyroid hormone levels during each trimester. SPSS (version 14.0, SPSS Inc., Chicago, IL, USA) was used for data processing and analysis. The reference intervals for the first, second and third trimesters for the following parameters: TSH 0.09-6.65, 0.51-6.66, 0.91-4.86 µIU/mL, FT4 9.81-18.53, 8.52-19.43, 7.39-18.28 pM/L and FT3 3.1-6.35, 2.39-5.12, 2.57-5.68 pM/L respectively. Thyroid hormone concentrations significantly differed during pregnancy at different stages of gestation. The pregnant women in the study had median urinary iodine concentration of 150-200 µg/l during each trimester. The trimester-specific reference intervals for thyroid tests during pregnancy have been established for pregnant Indian women serially followed during pregnancy using 2.5th and 97.5th percentiles.

Identification of Appropriate Reference Genes for Normalization of miRNA Expression in Grafted Watermelon Plants under Different Nutrient Stresses.

PubMed

Wu, Weifang; Deng, Qin; Shi, Pibiao; Yang, Jinghua; Hu, Zhongyuan; Zhang, Mingfang

2016-01-01

Watermelon (Citrullus lanatus) is a globally important crop belonging to the family Cucurbitaceae. The grafting technique is commonly used to improve its tolerance to stress, as well as to enhance its nutrient uptake and utilization. It is believed that miRNA is most likely involved in its nutrient-starvation response as a graft-transportable signal. The quantitative real-time reverse transcriptase polymerase chain reaction is the preferred method for miRNA functional analysis, in which reliable reference genes for normalization are crucial to ensure the accuracy. The purpose of this study was to select appropriate reference genes in scion (watermelon) and rootstocks (squash and bottle gourd) of grafted watermelon plants under normal growth conditions and nutrient stresses (nitrogen and phosphorus starvation). Under nutrient starvation, geNorm identified miR167c and miR167f as two most stable genes in both watermelon leaves and squash roots. miR166b was recommended by both geNorm and NormFinder as the best reference in bottle gourd roots under nutrient limitation. Expression of a new Cucurbitaceae miRNA, miR85, was used to validate the reliability of candidate reference genes under nutrient starvation. Moreover, by comparing several target genes expression in qRT-PCR analysis with those in RNA-seq data, miR166b and miR167c were proved to be the most suitable reference genes to normalize miRNA expression under normal growth condition in scion and rootstock tissues, respectively. This study represents the first comprehensive survey of the stability of miRNA reference genes in Cucurbitaceae and provides valuable information for investigating more accurate miRNA expression involving grafted watermelon plants.

Reference data for normal subjects obtained with an accelerometric device.

PubMed

Auvinet, Bernard; Berrut, Gilles; Touzard, Claude; Moutel, Laurent; Collet, Nadine; Chaleil, Denis; Barrey, Eric

2002-10-01

We collected gait analysis data for 282 healthy adults and elderly people (144 women and 138 men aged 20-98) using an accelerometric device, whose reproducibility (intra-tester and inter-testers) has been validated for gait studies. The subjects walked at their own speed along a corridor (40 m). Stride frequency (SF) (after correction for height), step symmetry (Sym), stride regularity (Reg), and vertical harmonic (slope) were all independent of age or gender. The median-lateral harmonic (slope) (MSH) was influenced by gender, but not by age. Other variables (walking speed, stride length (SL), cranial-caudal activity and raw accelerations at heel contact, mid-stance and initial push-off) were dependent on gender and age. They were higher in men than in women, and began to decrease during the sixth decade in men and the seventh decade in women. The raw acceleration at foot flat was independent of gender but was influenced by age. This accelerometric device is easy to use and requires no specialized equipment and could be used to analyze walking in clinical practice.

Identification of Appropriate Reference Genes for Normalization of miRNA Expression in Grafted Watermelon Plants under Different Nutrient Stresses

PubMed Central

Wu, Weifang; Deng, Qin; Shi, Pibiao; Yang, Jinghua; Hu, Zhongyuan; Zhang, Mingfang

2016-01-01

Watermelon (Citrullus lanatus) is a globally important crop belonging to the family Cucurbitaceae. The grafting technique is commonly used to improve its tolerance to stress, as well as to enhance its nutrient uptake and utilization. It is believed that miRNA is most likely involved in its nutrient-starvation response as a graft-transportable signal. The quantitative real-time reverse transcriptase polymerase chain reaction is the preferred method for miRNA functional analysis, in which reliable reference genes for normalization are crucial to ensure the accuracy. The purpose of this study was to select appropriate reference genes in scion (watermelon) and rootstocks (squash and bottle gourd) of grafted watermelon plants under normal growth conditions and nutrient stresses (nitrogen and phosphorus starvation). Under nutrient starvation, geNorm identified miR167c and miR167f as two most stable genes in both watermelon leaves and squash roots. miR166b was recommended by both geNorm and NormFinder as the best reference in bottle gourd roots under nutrient limitation. Expression of a new Cucurbitaceae miRNA, miR85, was used to validate the reliability of candidate reference genes under nutrient starvation. Moreover, by comparing several target genes expression in qRT-PCR analysis with those in RNA-seq data, miR166b and miR167c were proved to be the most suitable reference genes to normalize miRNA expression under normal growth condition in scion and rootstock tissues, respectively. This study represents the first comprehensive survey of the stability of miRNA reference genes in Cucurbitaceae and provides valuable information for investigating more accurate miRNA expression involving grafted watermelon plants. PMID:27749935

Identifying optimal reference genes for the normalization of microRNA expression in cucumber under viral stress

PubMed Central

Liang, Chaoqiong; Hao, Jianjun; Meng, Yan; Luo, Laixin; Li, Jianqiang

2018-01-01

Cucumber green mottle mosaic virus (CGMMV) is an economically important pathogen and causes significant reduction of both yield and quality of cucumber (Cucumis sativus). Currently, there were no satisfied strategies for controlling the disease. A better understanding of microRNA (miRNA) expression related to the regulation of plant-virus interactions and virus resistance would be of great assistance when developing control strategies for CGMMV. However, accurate expression analysis is highly dependent on robust and reliable reference gene used as an internal control for normalization of miRNA expression. Most commonly used reference genes involved in CGMMV-infected cucumber are not universally expressed depending on tissue types and stages of plant development. It is therefore crucial to identify suitable reference genes in investigating the role of miRNA expression. In this study, seven reference genes, including Actin, Tubulin, EF-1α, 18S rRNA, Ubiquitin, GAPDH and Cyclophilin, were evaluated for the most accurate results in analyses using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Gene expression was assayed on cucumber leaves, stems and roots that were collected at different days post inoculation with CGMMV. The expression data were analyzed using algorithms including delta-Ct, geNorm, NormFinder, and BestKeeper as well as the comparative tool RefFinder. The reference genes were subsequently validated using miR159. The results showed that EF-1α and GAPDH were the most reliable reference genes for normalizing miRNA expression in leaf, root and stem samples, while Ubiquitin and EF-1α were the most suitable combination overall. PMID:29543906

Gestation-specific reference intervals for comprehensive spot urinary steroid hormone metabolite analysis in normal singleton pregnancy and 6 weeks postpartum.

PubMed

Mistry, Hiten D; Eisele, Nicole; Escher, Geneviève; Dick, Bernhard; Surbek, Daniel; Delles, Christian; Currie, Gemma; Schlembach, Dietmar; Mohaupt, Markus G; Gennari-Moser, Carine

2015-09-04

Normal pregnancy depends on pronounced adaptations in steroid hormone concentrations. Although in recent years, the understanding of these hormones in pregnancy has improved, the interpretation is hampered by insufficient reference values. Our aim was to establish gestation-specific reference intervals for spot urinary steroid hormone levels in normal singleton pregnancies and 6 weeks postpartum. Cross-sectional multicentre observational study. Women recruited between 2008 and 2013 at 3 University Hospitals in Switzerland (Bern), Scotland (Glasgow) and Austria (Graz). Spot urine was collected from healthy women undergoing a normal pregnancy (age, 16-45 years; mean, 31 years) attending routine antenatal clinics at gestation weeks 11, 20, and 28 and approximately 6 weeks postpartum. Urine steroid hormone levels were analysed using gas-chromatography mass spectrometry. Creatinine was also measured by routine analysis and used for normalisation. From the results, a reference interval was calculated for each hormone metabolite at each trimester and 6 weeks postpartum. Changes in these concentrations between trimesters and postpartum were also observed for several steroid hormones and followed changes proposed for index steroid hormones. Normal gestation-specific reference values for spot urinary steroid hormones throughout pregnancy and early postpartum are now available to facilitate clinical management and research approaches to steroid hormone metabolism in pregnancy and the early postpartum period.

Validation of reference genes for accurate normalization of gene expression for real time-quantitative PCR in strawberry fruits using different cultivars and osmotic stresses.

PubMed

Galli, Vanessa; Borowski, Joyce Moura; Perin, Ellen Cristina; Messias, Rafael da Silva; Labonde, Julia; Pereira, Ivan dos Santos; Silva, Sérgio Delmar Dos Anjos; Rombaldi, Cesar Valmor

2015-01-10

The increasing demand of strawberry (Fragaria×ananassa Duch) fruits is associated mainly with their sensorial characteristics and the content of antioxidant compounds. Nevertheless, the strawberry production has been hampered due to its sensitivity to abiotic stresses. Therefore, to understand the molecular mechanisms highlighting stress response is of great importance to enable genetic engineering approaches aiming to improve strawberry tolerance. However, the study of expression of genes in strawberry requires the use of suitable reference genes. In the present study, seven traditional and novel candidate reference genes were evaluated for transcript normalization in fruits of ten strawberry cultivars and two abiotic stresses, using RefFinder, which integrates the four major currently available software programs: geNorm, NormFinder, BestKeeper and the comparative delta-Ct method. The results indicate that the expression stability is dependent on the experimental conditions. The candidate reference gene DBP (DNA binding protein) was considered the most suitable to normalize expression data in samples of strawberry cultivars and under drought stress condition, and the candidate reference gene HISTH4 (histone H4) was the most stable under osmotic stresses and salt stress. The traditional genes GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and 18S (18S ribosomal RNA) were considered the most unstable genes in all conditions. The expression of phenylalanine ammonia lyase (PAL) and 9-cis epoxycarotenoid dioxygenase (NCED1) genes were used to further confirm the validated candidate reference genes, showing that the use of an inappropriate reference gene may induce erroneous results. This study is the first survey on the stability of reference genes in strawberry cultivars and osmotic stresses and provides guidelines to obtain more accurate RT-qPCR results for future breeding efforts. Copyright © 2014 Elsevier B.V. All rights reserved.

[Using neural networks based template matching method to obtain redshifts of normal galaxies].

PubMed

Xu, Xin; Luo, A-li; Wu, Fu-chao; Zhao, Yong-heng

2005-06-01

Galaxies can be divided into two classes: normal galaxy (NG) and active galaxy (AG). In order to determine NG redshifts, an automatic effective method is proposed in this paper, which consists of the following three main steps: (1) From the template of normal galaxy, the two sets of samples are simulated, one with the redshift of 0.0-0.3, the other of 0.3-0.5, then the PCA is used to extract the main components, and train samples are projected to the main component subspace to obtain characteristic spectra. (2) The characteristic spectra are used to train a Probabilistic Neural Network to obtain a Bayes classifier. (3) An unknown real NG spectrum is first inputted to this Bayes classifier to determine the possible range of redshift, then the template matching is invoked to locate the redshift value within the estimated range. Compared with the traditional template matching technique with an unconstrained range, our proposed method not only halves the computational load, but also increases the estimation accuracy. As a result, the proposed method is particularly useful for automatic spectrum processing produced from a large-scale sky survey project.

Automated Spatial Brain Normalization and Hindbrain White Matter Reference Tissue Give Improved [(18)F]-Florbetaben PET Quantitation in Alzheimer's Model Mice.

PubMed

Overhoff, Felix; Brendel, Matthias; Jaworska, Anna; Korzhova, Viktoria; Delker, Andreas; Probst, Federico; Focke, Carola; Gildehaus, Franz-Josef; Carlsen, Janette; Baumann, Karlheinz; Haass, Christian; Bartenstein, Peter; Herms, Jochen; Rominger, Axel

2016-01-01

Preclinical PET studies of β-amyloid (Aβ) accumulation are of growing importance, but comparisons between research sites require standardized and optimized methods for quantitation. Therefore, we aimed to evaluate systematically the (1) impact of an automated algorithm for spatial brain normalization, and (2) intensity scaling methods of different reference regions for Aβ-PET in a large dataset of transgenic mice. PS2APP mice in a 6 week longitudinal setting (N = 37) and another set of PS2APP mice at a histologically assessed narrow range of Aβ burden (N = 40) were investigated by [(18)F]-florbetaben PET. Manual spatial normalization by three readers at different training levels was performed prior to application of an automated brain spatial normalization and inter-reader agreement was assessed by Fleiss Kappa (κ). For this method the impact of templates at different pathology stages was investigated. Four different reference regions on brain uptake normalization were used to calculate frontal cortical standardized uptake value ratios (SUVRCTX∕REF), relative to raw SUVCTX. Results were compared on the basis of longitudinal stability (Cohen's d), and in reference to gold standard histopathological quantitation (Pearson's R). Application of an automated brain spatial normalization resulted in nearly perfect agreement (all κ≥0.99) between different readers, with constant or improved correlation with histology. Templates based on inappropriate pathology stage resulted in up to 2.9% systematic bias for SUVRCTX∕REF. All SUVRCTX∕REF methods performed better than SUVCTX both with regard to longitudinal stability (d≥1.21 vs. d = 0.23) and histological gold standard agreement (R≥0.66 vs. R≥0.31). Voxel-wise analysis suggested a physiologically implausible longitudinal decrease by global mean scaling. The hindbrain white matter reference (R mean = 0.75) was slightly superior to the brainstem (R mean = 0.74) and the cerebellum (R mean = 0.73). Automated

The Renilla luciferase gene as a reference gene for normalization of gene expression in transiently transfected cells.

PubMed

Jiwaji, Meesbah; Daly, Rónán; Pansare, Kshama; McLean, Pauline; Yang, Jingli; Kolch, Walter; Pitt, Andrew R

2010-12-31

The importance of appropriate normalization controls in quantitative real-time polymerase chain reaction (qPCR) experiments has become more apparent as the number of biological studies using this methodology has increased. In developing a system to study gene expression from transiently transfected plasmids, it became clear that normalization using chromosomally encoded genes is not ideal, at it does not take into account the transfection efficiency and the significantly lower expression levels of the plasmids. We have developed and validated a normalization method for qPCR using a co-transfected plasmid. The best chromosomal gene for normalization in the presence of the transcriptional activators used in this study, cadmium, dexamethasone, forskolin and phorbol-12-myristate 13-acetate was first identified. qPCR data was analyzed using geNorm, Normfinder and BestKeeper. Each software application was found to rank the normalization controls differently with no clear correlation. Including a co-transfected plasmid encoding the Renilla luciferase gene (Rluc) in this analysis showed that its calculated stability was not as good as the optimised chromosomal genes, most likely as a result of the lower expression levels and transfection variability. Finally, we validated these analyses by testing two chromosomal genes (B2M and ActB) and a co-transfected gene (Rluc) under biological conditions. When analyzing co-transfected plasmids, Rluc normalization gave the smallest errors compared to the chromosomal reference genes. Our data demonstrates that transfected Rluc is the most appropriate normalization reference gene for transient transfection qPCR analysis; it significantly reduces the standard deviation within biological experiments as it takes into account the transfection efficiencies and has easily controllable expression levels. This improves reproducibility, data validity and most importantly, enables accurate interpretation of qPCR data.

Careful Selection of Reference Genes Is Required for Reliable Performance of RT-qPCR in Human Normal and Cancer Cell Lines

PubMed Central

Jacob, Francis; Guertler, Rea; Naim, Stephanie; Nixdorf, Sheri; Fedier, André; Hacker, Neville F.; Heinzelmann-Schwarz, Viola

2013-01-01

Reverse Transcription - quantitative Polymerase Chain Reaction (RT-qPCR) is a standard technique in most laboratories. The selection of reference genes is essential for data normalization and the selection of suitable reference genes remains critical. Our aim was to 1) review the literature since implementation of the MIQE guidelines in order to identify the degree of acceptance; 2) compare various algorithms in their expression stability; 3) identify a set of suitable and most reliable reference genes for a variety of human cancer cell lines. A PubMed database review was performed and publications since 2009 were selected. Twelve putative reference genes were profiled in normal and various cancer cell lines (n = 25) using 2-step RT-qPCR. Investigated reference genes were ranked according to their expression stability by five algorithms (geNorm, Normfinder, BestKeeper, comparative ΔCt, and RefFinder). Our review revealed 37 publications, with two thirds patient samples and one third cell lines. qPCR efficiency was given in 68.4% of all publications, but only 28.9% of all studies provided RNA/cDNA amount and standard curves. GeNorm and Normfinder algorithms were used in 60.5% in combination. In our selection of 25 cancer cell lines, we identified HSPCB, RRN18S, and RPS13 as the most stable expressed reference genes. In the subset of ovarian cancer cell lines, the reference genes were PPIA, RPS13 and SDHA, clearly demonstrating the necessity to select genes depending on the research focus. Moreover, a cohort of at least three suitable reference genes needs to be established in advance to the experiments, according to the guidelines. For establishing a set of reference genes for gene normalization we recommend the use of ideally three reference genes selected by at least three stability algorithms. The unfortunate lack of compliance to the MIQE guidelines reflects that these need to be further established in the research community. PMID:23554992

Reliable reference genes for normalization of gene expression data in tea plants (Camellia sinensis) exposed to metal stresses.

PubMed

Wang, Ming-Le; Li, Qing-Hui; Xin, Hua-Hong; Chen, Xuan; Zhu, Xu-Jun; Li, Xing-Hui

2017-01-01

Tea plants [Camellia sinensis (L.) O. Kuntze] are an important leaf-type crop that are widely used for the production of non-alcoholic beverages in the world. Exposure to excessive amounts of heavy metals adversely affects the quality and yield of tea leaves. To analyze the molecular responses of tea plants to heavy metals, a reliable quantification of gene expression is important and of major importance herein is the normalization of the measured expression levels for the target genes. Ideally, stably expressed reference genes should be evaluated in all experimental systems. In this study, 12 candidate reference genes (i.e., 18S rRNA, Actin, CYP, EF-1α, eIF-4α, GAPDH, MON1, PP2AA3, TBP, TIP41, TUA, and UBC) were cloned from tea plants, and the stability of their expression was examined systematically in 60 samples exposed to diverse heavy metals (i.e., manganese, aluminum, copper, iron, and zinc). Three Excel-based algorithms (geNorm, NormFinder, and BestKeeper) were used to evaluate the expression stability of these genes. PP2AA3 and 18S rRNA were the most stably expressed genes, even though their expression profiles exhibited some variability. Moreover, commonly used reference genes (i.e., GAPDH and TBP) were the least appropriate reference genes for most samples. To further validate the suitability of the analyzed reference genes, the expression level of a phytochelatin synthase gene (i.e., CsPCS1) was determined using the putative reference genes for data normalizations. Our results may be beneficial for future studies involving the quantification of relative gene expression levels in tea plants.

Reliable reference genes for normalization of gene expression data in tea plants (Camellia sinensis) exposed to metal stresses

PubMed Central

Wang, Ming-Le; Li, Qing-Hui; Xin, Hua-Hong; Chen, Xuan; Zhu, Xu-Jun

2017-01-01

Tea plants [Camellia sinensis (L.) O. Kuntze] are an important leaf-type crop that are widely used for the production of non-alcoholic beverages in the world. Exposure to excessive amounts of heavy metals adversely affects the quality and yield of tea leaves. To analyze the molecular responses of tea plants to heavy metals, a reliable quantification of gene expression is important and of major importance herein is the normalization of the measured expression levels for the target genes. Ideally, stably expressed reference genes should be evaluated in all experimental systems. In this study, 12 candidate reference genes (i.e., 18S rRNA, Actin, CYP, EF-1α, eIF-4α, GAPDH, MON1, PP2AA3, TBP, TIP41, TUA, and UBC) were cloned from tea plants, and the stability of their expression was examined systematically in 60 samples exposed to diverse heavy metals (i.e., manganese, aluminum, copper, iron, and zinc). Three Excel-based algorithms (geNorm, NormFinder, and BestKeeper) were used to evaluate the expression stability of these genes. PP2AA3 and 18S rRNA were the most stably expressed genes, even though their expression profiles exhibited some variability. Moreover, commonly used reference genes (i.e., GAPDH and TBP) were the least appropriate reference genes for most samples. To further validate the suitability of the analyzed reference genes, the expression level of a phytochelatin synthase gene (i.e., CsPCS1) was determined using the putative reference genes for data normalizations. Our results may be beneficial for future studies involving the quantification of relative gene expression levels in tea plants. PMID:28453515

Evaluation of Suitable Reference Genes for Normalization of qPCR Gene Expression Studies in Brinjal (Solanum melongena L.) During Fruit Developmental Stages.

PubMed

Kanakachari, Mogilicherla; Solanke, Amolkumar U; Prabhakaran, Narayanasamy; Ahmad, Israr; Dhandapani, Gurusamy; Jayabalan, Narayanasamy; Kumar, Polumetla Ananda

2016-02-01

Brinjal/eggplant/aubergine is one of the major solanaceous vegetable crops. Recent availability of genome information greatly facilitates the fundamental research on brinjal. Gene expression patterns during different stages of fruit development can provide clues towards the understanding of its biological functions. Quantitative real-time PCR (qPCR) has become one of the most widely used methods for rapid and accurate quantification of gene expression. However, its success depends on the use of a suitable reference gene for data normalization. For qPCR analysis, a single reference gene is not universally suitable for all experiments. Therefore, reference gene validation is a crucial step. Suitable reference genes for qPCR analysis of brinjal fruit development have not been investigated so far. In this study, we have selected 21 candidate reference genes from the Brinjal (Solanum melongena) Plant Gene Indices database (compbio.dfci.harvard.edu/tgi/plant.html) and studied their expression profiles by qPCR during six different fruit developmental stages (0, 5, 10, 20, 30, and 50 days post anthesis) along with leaf samples of the Pusa Purple Long (PPL) variety. To evaluate the stability of gene expression, geNorm and NormFinder analytical softwares were used. geNorm identified SAND (SAND family protein) and TBP (TATA binding protein) as the best pairs of reference genes in brinjal fruit development. The results showed that for brinjal fruit development, individual or a combination of reference genes should be selected for data normalization. NormFinder identified Expressed gene (expressed sequence) as the best single reference gene in brinjal fruit development. In this study, we have identified and validated for the first time reference genes to provide accurate transcript normalization and quantification at various fruit developmental stages of brinjal which can also be useful for gene expression studies in other Solanaceae plant species.

Normal reference values for bladder wall thickness on CT in a healthy population.

PubMed

Fananapazir, Ghaneh; Kitich, Aleksandar; Lamba, Ramit; Stewart, Susan L; Corwin, Michael T

2018-02-01

To determine normal bladder wall thickness on CT in patients without bladder disease. Four hundred and nineteen patients presenting for trauma with normal CTs of the abdomen and pelvis were included in our retrospective study. Bladder wall thickness was assessed, and bladder volume was measured using both the ellipsoid formula and an automated technique. Patient age, gender, and body mass index were recorded. Linear regression models were created to account for bladder volume, age, gender, and body mass index, and the multiple correlation coefficient with bladder wall thickness was computed. Bladder volume and bladder wall thickness were log-transformed to achieve approximate normality and homogeneity of variance. Variables that did not contribute substantively to the model were excluded, and a parsimonious model was created and the multiple correlation coefficient was calculated. Expected bladder wall thickness was estimated for different bladder volumes, and 1.96 standard deviation above expected provided the upper limit of normal on the log scale. Age, gender, and bladder volume were associated with bladder wall thickness (p = 0.049, 0.024, and < 0.001, respectively). The linear regression model had an R 2 of 0.52. Age and gender were negligible in contribution to the model, and a parsimonious model using only volume was created for both the ellipsoid and automated volumes (R 2  = 0.52 and 0.51, respectively). Bladder wall thickness correlates with bladder wall volume. The study provides reference bladder wall thicknesses on CT utilizing both the ellipsoid formula and automated bladder volumes.

Selection of Reference Genes for Normalization of MicroRNA Expression by RT-qPCR in Sugarcane Buds under Cold Stress

PubMed Central

Yang, Yuting; Zhang, Xu; Chen, Yun; Guo, Jinlong; Ling, Hui; Gao, Shiwu; Su, Yachun; Que, Youxiong; Xu, Liping

2016-01-01

Sugarcane, accounting for 80% of world's sugar, originates in the tropics but is cultivated mainly in the subtropics. Therefore, chilling injury frequently occurs and results in serious losses. Recent studies in various plant species have established microRNAs as key elements in the post-transcriptional regulation of response to biotic and abiotic stresses including cold stress. Though, its accuracy is largely influenced by the use of reference gene for normalization, quantitative PCR is undoubtedly a popular method used for identification of microRNAs. For identifying the most suitable reference genes for normalizing miRNAs expression in sugarcane under cold stress, 13 candidates among 17 were investigated using four algorithms: geNorm, NormFinder, deltaCt, and Bestkeeper, and four candidates were excluded because of unsatisfactory efficiency and specificity. Verification was carried out using cold-related genes miR319 and miR393 in cold-tolerant and sensitive cultivars. The results suggested that miR171/18S rRNA and miR171/miR5059 were the best reference gene sets for normalization for miRNA RT-qPCR, followed by the single miR171 and 18S rRNA. These results can aid research on miRNA responses during sugarcane stress, and the development of sugarcane tolerant to cold stress. This study is the first report concerning the reference gene selection of miRNA RT-qPCR in sugarcane. PMID:26904058

Selection of reference genes for quantitative gene expression normalization in flax (Linum usitatissimum L.).

PubMed

Huis, Rudy; Hawkins, Simon; Neutelings, Godfrey

2010-04-19

Quantitative real-time PCR (qRT-PCR) is currently the most accurate method for detecting differential gene expression. Such an approach depends on the identification of uniformly expressed 'housekeeping genes' (HKGs). Extensive transcriptomic data mining and experimental validation in different model plants have shown that the reliability of these endogenous controls can be influenced by the plant species, growth conditions and organs/tissues examined. It is therefore important to identify the best reference genes to use in each biological system before using qRT-PCR to investigate differential gene expression. In this paper we evaluate different candidate HKGs for developmental transcriptomic studies in the economically-important flax fiber- and oil-crop (Linum usitatissimum L). Specific primers were designed in order to quantify the expression levels of 20 different potential housekeeping genes in flax roots, internal- and external-stem tissues, leaves and flowers at different developmental stages. After calculations of PCR efficiencies, 13 HKGs were retained and their expression stabilities evaluated by the computer algorithms geNorm and NormFinder. According to geNorm, 2 Transcriptional Elongation Factors (TEFs) and 1 Ubiquitin gene are necessary for normalizing gene expression when all studied samples are considered. However, only 2 TEFs are required for normalizing expression in stem tissues. In contrast, NormFinder identified glyceraldehyde-3-phosphate dehydrogenase (GADPH) as the most stably expressed gene when all samples were grouped together, as well as when samples were classed into different sub-groups.qRT-PCR was then used to investigate the relative expression levels of two splice variants of the flax LuMYB1 gene (homologue of AtMYB59). LuMYB1-1 and LuMYB1-2 were highly expressed in the internal stem tissues as compared to outer stem tissues and other samples. This result was confirmed with both geNorm-designated- and NormFinder-designated-reference

Selection of suitable reference genes for normalization of genes of interest in canine soft tissue sarcomas using quantitative real-time polymerase chain reaction.

PubMed

Zornhagen, K W; Kristensen, A T; Hansen, A E; Oxboel, J; Kjaer, A

2015-12-01

Quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR) is a sensitive technique for quantifying gene expression. Stably expressed reference genes are necessary for normalization of RT-qPCR data. Only a few articles have been published on reference genes in canine tumours. The objective of this study was to demonstrate how to identify suitable reference genes for normalization of genes of interest in canine soft tissue sarcomas using RT-qPCR. Primer pairs for 17 potential reference genes were designed and tested in archival tumour biopsies from six dogs. The geNorm algorithm was used to analyse the most suitable reference genes. Eight potential reference genes were excluded from this final analysis because of their dissociation curves. β-Glucuronidase (GUSB) and proteasome subunit, beta type, 6 (PSMB6) were most stably expressed with an M value of 0.154 and a CV of 0.053 describing their average stability. We suggest that choice of reference genes should be based on specific testing in every new experimental set-up. © 2014 John Wiley & Sons Ltd.

Selection of internal reference genes for normalization of quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis in the canine brain and other organs.

PubMed

Park, Sang-Je; Huh, Jae-Won; Kim, Young-Hyun; Lee, Sang-Rae; Kim, Sang-Hyun; Kim, Sun-Uk; Kim, Heui-Soo; Kim, Min Kyu; Chang, Kyu-Tae

2013-05-01

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a specific and sensitive technique for quantifying gene expression. To analyze qRT-PCR data accurately, suitable reference genes that show consistent expression patterns across different tissues and experimental conditions should be selected. The objective of this study was to obtain the most stable reference genes in dogs, using samples from 13 different brain tissues and 10 other organs. 16 well-known candidate reference genes were analyzed by the geNorm, NormFinder, and BestKeeper programs. Brain tissues were derived from several different anatomical regions, including the forebrain, cerebrum, diencephalon, hindbrain, and metencephalon, and grouped accordingly. Combination of the three different analyses clearly indicated that the ideal reference genes are ribosomal protien S5 (RPS5) in whole brain, RPL8 and RPS5 in whole body tissues, RPS5 and RPS19 in the forebrain and cerebrum, RPL32 and RPS19 in the diencephalon, GAPDH and RPS19 in the hindbrain, and MRPS7 and RPL13A in the metencephalon. These genes were identified as ideal for the normalization of qRT-PCR results in the respective tissues. These findings indicate more suitable and stable reference genes for future studies of canine gene expression.

Identification and evaluation of new reference genes in Gossypium hirsutum for accurate normalization of real-time quantitative RT-PCR data.

PubMed

Artico, Sinara; Nardeli, Sarah M; Brilhante, Osmundo; Grossi-de-Sa, Maria Fátima; Alves-Ferreira, Marcio

2010-03-21

Normalizing through reference genes, or housekeeping genes, can make more accurate and reliable results from reverse transcription real-time quantitative polymerase chain reaction (qPCR). Recent studies have shown that no single housekeeping gene is universal for all experiments. Thus, suitable reference genes should be the first step of any qPCR analysis. Only a few studies on the identification of housekeeping gene have been carried on plants. Therefore qPCR studies on important crops such as cotton has been hampered by the lack of suitable reference genes. By the use of two distinct algorithms, implemented by geNorm and NormFinder, we have assessed the gene expression of nine candidate reference genes in cotton: GhACT4, GhEF1alpha5, GhFBX6, GhPP2A1, GhMZA, GhPTB, GhGAPC2, GhbetaTUB3 and GhUBQ14. The candidate reference genes were evaluated in 23 experimental samples consisting of six distinct plant organs, eight stages of flower development, four stages of fruit development and in flower verticils. The expression of GhPP2A1 and GhUBQ14 genes were the most stable across all samples and also when distinct plants organs are examined. GhACT4 and GhUBQ14 present more stable expression during flower development, GhACT4 and GhFBX6 in the floral verticils and GhMZA and GhPTB during fruit development. Our analysis provided the most suitable combination of reference genes for each experimental set tested as internal control for reliable qPCR data normalization. In addition, to illustrate the use of cotton reference genes we checked the expression of two cotton MADS-box genes in distinct plant and floral organs and also during flower development. We have tested the expression stabilities of nine candidate genes in a set of 23 tissue samples from cotton plants divided into five different experimental sets. As a result of this evaluation, we recommend the use of GhUBQ14 and GhPP2A1 housekeeping genes as superior references for normalization of gene expression measures in

Identification and evaluation of new reference genes in Gossypium hirsutum for accurate normalization of real-time quantitative RT-PCR data

PubMed Central

2010-01-01

Background Normalizing through reference genes, or housekeeping genes, can make more accurate and reliable results from reverse transcription real-time quantitative polymerase chain reaction (qPCR). Recent studies have shown that no single housekeeping gene is universal for all experiments. Thus, suitable reference genes should be the first step of any qPCR analysis. Only a few studies on the identification of housekeeping gene have been carried on plants. Therefore qPCR studies on important crops such as cotton has been hampered by the lack of suitable reference genes. Results By the use of two distinct algorithms, implemented by geNorm and NormFinder, we have assessed the gene expression of nine candidate reference genes in cotton: GhACT4, GhEF1α5, GhFBX6, GhPP2A1, GhMZA, GhPTB, GhGAPC2, GhβTUB3 and GhUBQ14. The candidate reference genes were evaluated in 23 experimental samples consisting of six distinct plant organs, eight stages of flower development, four stages of fruit development and in flower verticils. The expression of GhPP2A1 and GhUBQ14 genes were the most stable across all samples and also when distinct plants organs are examined. GhACT4 and GhUBQ14 present more stable expression during flower development, GhACT4 and GhFBX6 in the floral verticils and GhMZA and GhPTB during fruit development. Our analysis provided the most suitable combination of reference genes for each experimental set tested as internal control for reliable qPCR data normalization. In addition, to illustrate the use of cotton reference genes we checked the expression of two cotton MADS-box genes in distinct plant and floral organs and also during flower development. Conclusion We have tested the expression stabilities of nine candidate genes in a set of 23 tissue samples from cotton plants divided into five different experimental sets. As a result of this evaluation, we recommend the use of GhUBQ14 and GhPP2A1 housekeeping genes as superior references for normalization of gene

[Determination of normal reference value of pyrrole adducts in urine in young people in a university in Shandong, China].

PubMed

Wang, Hui; Wang, Yiping; Zhou, Zhenwei; Wang, Shuo; Yin, Hongyin; Xie, Keqin

2015-06-01

To determine the normal reference value of pyrrole adducts in urine in young people in a university in Shandong, China, and to provide a reliable basis for the clinical diagnosis of n-hexane poisoning. A total of 240 college students were randomly selected. After excluding 32 ineligible students, 208 subjects were included in this study, consisting of 104 males and 104 females, with a mean age of 21?3 years (range: 18 to 24 years). Morning urine was collected from each subject. The content of pyrrole adducts was determined by chromatometry. The content of pyrrole adducts in both male and female obeyed a positively skewed distribution. The median level of pyrrole adducts in male subjects was 0.88 nmol/ml, and the reference value was 0.14-3.92 nmol/ml. The median level of pyrrole adducts in female subjects was 0.93 nmol/ ml, and the reference value was 0.09-3.27 nmol/ml. Student's t test identified no statistical difference in pyrrole adduct level between male and female subjects (t=0.15, P>0.05). The median level of pyrrole adducts in normal young people is 0.91 nmol/ml, and the reference value is 0.11-3.95 nmol/ml.

The reference intervals of thyroid stimulating hormone in healthy individuals with normal levels of serum free thyroxine and without sonographic pathologies.

PubMed

Kutluturk, Faruk; Yildirim, Beytullah; Ozturk, Banu; Ozyurt, Huseyin; Bekar, Ulku; Sahin, Semsettin; Akturk, Yeliz; Akbas, Ali; Cetin, Ilhan; Etikan, Ilker

2014-01-01

The aim of the present study was to investigate the reference intervals for thyroid stimulating hormone (TSH) in healthy individuals with normal levels of serum free thyroxine (fT4) and without sonographic pathologies, and determine the effects of age, gender, and residence on the TSH reference intervals. This research was a population-based study conducted in 70 regions. The random sampling method was used to select the 1095 subjects of the study among inhabitants aged 18 and above. Patients who had a previous history of thyroid disease and had been taking medication were excluded from the study as this may have affected their fT4 or TSH levels. In addition, subjects who had serum fT4 without a reference range and abnormal ultrasonography findings were also excluded. A total of 408 subjects were used for establishing the reference intervals for TSH. The data for TSH in the study group were not normally distributed according to the Kolmogorov-Smirnov index. The geometric mean was 1.62 mIU/L, the median was 1.40 mIU/L, and the 95% reference intervals were 0.38-4.22 mIU/L. The median TSH level was higher in females compared to males (p < 0.05). In the female subjects 2.5th percentile of TSH was lower and 97.5th percentile was higher than those of males. The reference intervals of TSH were of lower values in subjects over 50 years old (p < 0.001). Studies suggest that determination of the TSH reference intervals may differ due to environmental influences or due to age, gender, and race. It is suggested that the lower limit of normal TSH for the adult Turkish population would be 0.38 mIU/L and the upper limit similar to the traditional value of 4.2 mIU/L. If each clinician uses their population-specific reference interval for TSH, thyroid function abnormalities can be accurately estimated.

Identification and validation of reference genes for normalization of gene expression analysis using qRT-PCR in Helicoverpa armigera (Lepidoptera: Noctuidae).

PubMed

Zhang, Songdou; An, Shiheng; Li, Zhen; Wu, Fengming; Yang, Qingpo; Liu, Yichen; Cao, Jinjun; Zhang, Huaijiang; Zhang, Qingwen; Liu, Xiaoxia

2015-01-25

Recent studies have focused on determining functional genes and microRNAs in the pest Helicoverpa armigera (Lepidoptera: Noctuidae). Most of these studies used quantitative real-time PCR (qRT-PCR). Suitable reference genes are necessary to normalize gene expression data of qRT-PCR. However, a comprehensive study on the reference genes in H. armigera remains lacking. Twelve candidate reference genes of H. armigera were selected and evaluated for their expression stability under different biotic and abiotic conditions. The comprehensive stability ranking of candidate reference genes was recommended by RefFinder and the optimal number of reference genes was calculated by geNorm. Two target genes, thioredoxin (TRX) and Cu/Zn superoxide dismutase (SOD), were used to validate the selection of reference genes. Results showed that the most suitable candidate combinations of reference genes were as follows: 28S and RPS15 for developmental stages; RPS15 and RPL13 for larvae tissues; EF and RPL27 for adult tissues; GAPDH, RPL27, and β-TUB for nuclear polyhedrosis virus infection; RPS15 and RPL32 for insecticide treatment; RPS15 and RPL27 for temperature treatment; and RPL32, RPS15, and RPL27 for all samples. This study not only establishes an accurate method for normalizing qRT-PCR data in H. armigera but also serve as a reference for further study on gene transcription in H. armigera and other insects. Copyright © 2014 Elsevier B.V. All rights reserved.

Selection of reference genes for gene expression studies related to intramuscular fat deposition in Capra hircus skeletal muscle.

PubMed

Zhu, Wuzheng; Lin, Yaqiu; Liao, Honghai; Wang, Yong

2015-01-01

The identification of suitable reference genes is critical for obtaining reliable results from gene expression studies using quantitative real-time PCR (qPCR) because the expression of reference genes may vary considerably under different experimental conditions. In most cases, however, commonly used reference genes are employed in data normalization without proper validation, which may lead to incorrect data interpretation. Here, we aim to select a set of optimal reference genes for the accurate normalization of gene expression associated with intramuscular fat (IMF) deposition during development. In the present study, eight reference genes (PPIB, HMBS, RPLP0, B2M, YWHAZ, 18S, GAPDH and ACTB) were evaluated by three different algorithms (geNorm, NormFinder and BestKeeper) in two types of muscle tissues (longissimus dorsi muscle and biceps femoris muscle) across different developmental stages. All three algorithms gave similar results. PPIB and HMBS were identified as the most stable reference genes, while the commonly used reference genes 18S and GAPDH were the most variably expressed, with expression varying dramatically across different developmental stages. Furthermore, to reveal the crucial role of appropriate reference genes in obtaining a reliable result, analysis of PPARG expression was performed by normalization to the most and the least stable reference genes. The relative expression levels of PPARG normalized to the most stable reference genes greatly differed from those normalized to the least stable one. Therefore, evaluation of reference genes must be performed for a given experimental condition before the reference genes are used. PPIB and HMBS are the optimal reference genes for analysis of gene expression associated with IMF deposition in skeletal muscle during development.

A large-scale study of the ultrawideband microwave dielectric properties of normal breast tissue obtained from reduction surgeries.

PubMed

Lazebnik, Mariya; McCartney, Leah; Popovic, Dijana; Watkins, Cynthia B; Lindstrom, Mary J; Harter, Josephine; Sewall, Sarah; Magliocco, Anthony; Booske, John H; Okoniewski, Michal; Hagness, Susan C

2007-05-21

The efficacy of emerging microwave breast cancer detection and treatment techniques will depend, in part, on the dielectric properties of normal breast tissue. However, knowledge of these properties at microwave frequencies has been limited due to gaps and discrepancies in previously reported small-scale studies. To address these issues, we experimentally characterized the wideband microwave-frequency dielectric properties of a large number of normal breast tissue samples obtained from breast reduction surgeries at the University of Wisconsin and University of Calgary hospitals. The dielectric spectroscopy measurements were conducted from 0.5 to 20 GHz using a precision open-ended coaxial probe. The tissue composition within the probe's sensing region was quantified in terms of percentages of adipose, fibroconnective and glandular tissues. We fit a one-pole Cole-Cole model to the complex permittivity data set obtained for each sample and determined median Cole-Cole parameters for three groups of normal breast tissues, categorized by adipose tissue content (0-30%, 31-84% and 85-100%). Our analysis of the dielectric properties data for 354 tissue samples reveals that there is a large variation in the dielectric properties of normal breast tissue due to substantial tissue heterogeneity. We observed no statistically significant difference between the within-patient and between-patient variability in the dielectric properties.

Reference Clinical Database for Fixation Stability Metrics in Normal Subjects Measured with the MAIA Microperimeter.

PubMed

Morales, Marco U; Saker, Saker; Wilde, Craig; Pellizzari, Carlo; Pallikaris, Aristophanes; Notaroberto, Neil; Rubinstein, Martin; Rui, Chiara; Limoli, Paolo; Smolek, Michael K; Amoaku, Winfried M

2016-11-01

The purpose of this study was to establish a normal reference database for fixation stability measured with the bivariate contour ellipse area (BCEA) in the Macular Integrity Assessment (MAIA) microperimeter. Subjects were 358 healthy volunteers who had the MAIA examination. Fixation stability was assessed using two BCEA fixation indices (63% and 95% proportional values) and the percentage of fixation points within 1° and 2° from the fovea (P1 and P2). Statistical analysis was performed with linear regression and Pearson's product moment correlation coefficient. Average areas of 0.80 deg 2 (min = 0.03, max = 3.90, SD = 0.68) for the index BCEA@63% and 2.40 deg 2 (min = 0.20, max = 11.70, SD = 2.04) for the index BCEA@95% were found. The average values of P1 and P2 were 95% (min = 76, max = 100, SD = 5.31) and 99% (min = 91, max = 100, SD = 1.42), respectively. The Pearson's product moment test showed an almost perfect correlation index, r = 0.999, between BCEA@63% and BCEA@95%. Index P1 showed a very strong correlation with BCEA@63%, r = -0.924, as well as with BCEA@95%, r = -0.925. Index P2 demonstrated a slightly lower correlation with both BCEA@63% and BCEA@95%, r = -0.874 and -0.875, respectively. The single parameter of the BCEA@95% may be taken as accurately reporting fixation stability and serves as a reference database of normal subjects with a cutoff area of 2.40 ± 2.04 deg 2 in MAIA microperimeter. Fixation stability can be measured with different indices. This study originates reference fixation values for the MAIA using a single fixation index.

Integration of gene normalization stages and co-reference resolution using a Markov logic network.

PubMed

Dai, Hong-Jie; Chang, Yen-Ching; Tsai, Richard Tzong-Han; Hsu, Wen-Lian

2011-09-15

Gene normalization (GN) is the task of normalizing a textual gene mention to a unique gene database ID. Traditional top performing GN systems usually need to consider several constraints to make decisions in the normalization process, including filtering out false positives, or disambiguating an ambiguous gene mention, to improve system performance. However, these constraints are usually executed in several separate stages and cannot use each other's input/output interactively. In this article, we propose a novel approach that employs a Markov logic network (MLN) to model the constraints used in the GN task. Firstly, we show how various constraints can be formulated and combined in an MLN. Secondly, we are the first to apply the two main concepts of co-reference resolution-discourse salience in centering theory and transitivity-to GN models. Furthermore, to make our results more relevant to developers of information extraction applications, we adopt the instance-based precision/recall/F-measure (PRF) in addition to the article-wide PRF to assess system performance. Experimental results show that our system outperforms baseline and state-of-the-art systems under two evaluation schemes. Through further analysis, we have found several unexplored challenges in the GN task. hongjie@iis.sinica.edu.tw Supplementary data are available at Bioinformatics online.

A pilot study of reference vibrotactile perception thresholds on the fingertip obtained with Malaysian healthy people using ISO 13091-1 equipment.

PubMed

Daud, Roshada; Maeda, Setsuo; Kameel, Nur Nazmin Mustafa; Ripin, Muhamad Yunus; Bakrun, Norazman; Md Zein, Raemy; Kido, Masaharu; Higuchi, Kiyotaka

2004-04-01

The purpose of this paper is to clarify the reference vibrotactile perception thresholds (VPT) for healthy people in Malaysia. The measurement equipment standard, ISO 13091-1, of the vibrotactile perception thresholds for the assessment of nerve dysfunction and the analysis and interpretation of measurements at the fingertips standard, ISO 13091-2, were published in ISO/TC108/SC4/WG8 on 2001 and 2003 individually. In the ISO 13091-2 standard, the reference VPT data were obtained from few research papers. Malaysian people's VPT data don't include to this standard. In Malaysia, when the VPT is using to diagnose of the hand-arm vibration syndrome, the reference VPT data need to compare with the worker's ones. But, Malaysia does not have the reference VPT data yet. So, in this paper, the VPT was measured by using ISO 13091-1 standard equipment to obtain the reference data for Malaysian people. And these data were compared with the ISO reference data on the ISO 13091-2 standard. From the comparison of these data, it was clear that the Malaysian healthy people's VPT data were consistent with the reference data of the ISO 13091-2 standard.

'Aussie normals': an a priori study to develop clinical chemistry reference intervals in a healthy Australian population.

PubMed

Koerbin, G; Cavanaugh, J A; Potter, J M; Abhayaratna, W P; West, N P; Glasgow, N; Hawkins, C; Armbruster, D; Oakman, C; Hickman, P E

2015-02-01

Development of reference intervals is difficult, time consuming, expensive and beyond the scope of most laboratories. The Aussie Normals study is a direct a priori study to determine reference intervals in healthy Australian adults. All volunteers completed a health and lifestyle questionnaire and exclusion was based on conditions such as pregnancy, diabetes, renal or cardiovascular disease. Up to 91 biochemical analyses were undertaken on a variety of analytical platforms using serum samples collected from 1856 volunteers. We report on our findings for 40 of these analytes and two calculated parameters performed on the Abbott ARCHITECTci8200/ci16200 analysers. Not all samples were analysed for all assays due to volume requirements or assay/instrument availability. Results with elevated interference indices and those deemed unsuitable after clinical evaluation were removed from the database. Reference intervals were partitioned based on the method of Harris and Boyd into three scenarios, combined gender, males and females and age and gender. We have performed a detailed reference interval study on a healthy Australian population considering the effects of sex, age and body mass. These reference intervals may be adapted to other manufacturer's analytical methods using method transference.

Reference interval for thyrotropin in a ultrasonography screened Korean population

PubMed Central

Kim, Mijin; Kim, Soo Han; Lee, Yunkyoung; Park, Su-yeon; Kim, Hyung-don; Kwon, Hyemi; Choi, Yun Mi; Jang, Eun Kyung; Jeon, Min Ji; Kim, Won Gu; Shong, Young Kee; Kim, Won Bae

2015-01-01

Background/Aims The diagnostic accuracy of thyroid dysfunctions is primarily affected by the validity of the reference interval for serum thyroid-stimulating hormone (TSH). Thus, the present study aimed to establish a reference interval for TSH using a normal Korean population. Methods This study included 19,465 subjects who were recruited after undergoing routine health check-ups. Subjects with overt thyroid disease, a prior history of thyroid disease, or a family history of thyroid cancer were excluded from the present analyses. The reference range for serum TSH was evaluated in a normal Korean reference population which was defined according to criteria based on the guidelines of the National Academy of Clinical Biochemistry, ultrasound (US) findings, and smoking status. Sex and age were also taken into consideration when evaluating the distribution of serum TSH levels in different groups. Results In the presence of positive anti-thyroid peroxidase antibodies or abnormal US findings, the central 95 percentile interval of the serum TSH levels was widened. Additionally, the distribution of serum TSH levels shifted toward lower values in the current smokers group. The reference interval for TSH obtained using a normal Korean reference population was 0.73 to 7.06 mIU/L. The serum TSH levels were higher in females than in males in all groups, and there were no age-dependent shifts. Conclusions The present findings demonstrate that the serum TSH reference interval in a normal Korean reference population was higher than that in other countries. This result suggests that the upper and lower limits of the TSH reference interval, which was previously defined by studies from Western countries, should be raised for Korean populations. PMID:25995664

Reference genes for normalization of qPCR assays in sugarcane plants under water deficit.

PubMed

de Andrade, Larissa Mara; Dos Santos Brito, Michael; Fávero Peixoto Junior, Rafael; Marchiori, Paulo Eduardo Ribeiro; Nóbile, Paula Macedo; Martins, Alexandre Palma Boer; Ribeiro, Rafael Vasconcelos; Creste, Silvana

2017-01-01

Sugarcane ( Saccharum spp.) is the main raw material for sugar and ethanol production. Among the abiotic stress, drought is the main one that negatively impact sugarcane yield. Although gene expression analysis through quantitative PCR (qPCR) has increased our knowledge about biological processes related to drought, gene network that mediates sugarcane responses to water deficit remains elusive. In such scenario, validation of reference gene is a major requirement for successful analyzes involving qPCR. In this study, candidate genes were tested for their suitable as reference genes for qPCR analyses in two sugarcane cultivars with varying drought tolerance. Eight candidate reference genes were evaluated in leaves sampled in plants subjected to water deficit in both field and greenhouse conditions. In addition, five genes were evaluated in shoot roots of plants subjected to water deficit by adding PEG8000 to the nutrient solution. NormFinder and RefFinder algorithms were used to identify the most stable gene(s) among genotypes and under different experimental conditions. Both algorithms revealed that in leaf samples, UBQ1 and GAPDH genes were more suitable as reference genes, whereas GAPDH was the best reference one in shoot roots. Reference genes suitable for sugarcane under water deficit were identified, which would lead to a more accurate and reliable analysis of qPCR. Thus, results obtained in this study may guide future research on gene expression in sugarcane under varying water conditions.

Kinetic parameters of the GUINEVERE reference configuration in VENUS-F reactor obtained from a pile noise experiment using Rossi and Feynman methods

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

Geslot, Benoit; Pepino, Alexandra; Blaise, Patrick

A pile noise measurement campaign has been conducted by the CEA in the VENUS-F reactor (SCK-CEN, Mol Belgium) in April 2011 in the reference critical configuration of the GUINEVERE experimental program. The experimental setup made it possible to estimate the core kinetic parameters: the prompt neutron decay constant, the delayed neutron fraction and the generation time. A precise assessment of these constants is of prime importance. In particular, the effective delayed neutron fraction is used to normalize and compare calculated reactivities of different subcritical configurations, obtained by modifying either the core layout or the control rods position, with experimental onesmore » deduced from the analysis of measurements. This paper presents results obtained with a CEA-developed time stamping acquisition system. Data were analyzed using Rossi-α and Feynman-α methods. Results were normalized to reactor power using a calibrated fission chamber with a deposit of Np-237. Calculated factors were necessary to the analysis: the Diven factor was computed by the ENEA (Italy) and the power calibration factor by the CNRS/IN2P3/LPC Caen. Results deduced with both methods are consistent with respect to calculated quantities. Recommended values are given by the Rossi-α estimator, that was found to be the most robust. The neutron generation time was found equal to 0.438 ± 0.009 μs and the effective delayed neutron fraction is 765 ± 8 pcm. Discrepancies with the calculated value (722 pcm, calculation from ENEA) are satisfactory: -5.6% for the Rossi-α estimate and -2.7% for the Feynman-α estimate. (authors)« less

[The reference of normal values of the sacroiliac joint index in bone scintigraphy].

PubMed

Sebastjanowicz, Przemysław; Iwanowski, Jacek; Piwowarska-Bilska, Hanna; Elbl, Bogumiła; Birkenfeld, Bożena

Scintigraphy of sacroiliac joints as functional imaging provides unique information on the existing disease process. By using radiopharmaceuticals that allow imaging of the metabolic activity within the joint, it is possible to assess the stage of the disease, even when there are no lesions in radiological images. Quantitative analysis of scintigrams of sacroiliac joints is performed by comparing the uptake in both of them in relation to the uptake in the sacral bone area. The values of sacroiliac (SI/S) indices are influenced by the age of the patient, sex, state of health, and a range of individual biological features. Therefore, reference values of SI/S ratios are very important for medical specialists who describe and diagnose locomotor system diseases. The aim of this paper is to develop a reference range of sacroiliac ratios. The innovativeness of this paper involves examining sacroiliac ratios for various age groups, in children and adult patients, taking their sex into consideration. The study comprised a group of 335 people with proper bone scintigraphy. These people were divided into children and patients aged ≥21. Children were divided into 4 age groups (1–5; 6–10; 11–15; 16–20) and adults into 6 age groups (21–30; 31–40; 41–50; 51–60; 61–70; ≥71). Sacroiliac ratios were calculated using the method of three rectangular region of interests located on the left and right sacroiliac joint and on the sacral bone. The sacroiliac ratio was calculated for both joints by dividing the average number of counts within a selected sacroiliac joint by the average number of counts within the sacral bone. SI/S borderline reference values covered the range of 1.18÷2.28 that was obtained for children aged ≤5 and for the group of 11–15-year-olds. Considerable discrepancies in the values of the coefficient for women and men were seen among 31–50-year-olds. Borderline reference results for the entire control group cover the range of 1.18 ±2

Echocardiography parameters of clinically normal adult captive chimpanzees (Pan troglodytes).

PubMed

Sleeper, Meg M; Drobatz, Ken; Lee, D Richard; Lammey, Michael L

2014-04-15

To generate reference ranges for echocardiographic variables in clinically normal adult chimpanzees (Pan troglodytes). Retrospective cohort study. 88 clinically normal adult chimpanzees. Echocardiographic data obtained between 2002 and 2011 from chimpanzees at the Alamogordo Primate Facility were reviewed (263 echocardiograms obtained from 158 individuals). Data from clinically normal individuals (33 females and 55 males) were analyzed. Basic cardiac parameters measured in all individuals included aortic root diameter and left atrial diameter in the short and long axis during diastole. Left ventricular measurements included left ventricular internal diameter in systole and diastole and diastolic septal and posterior wall thickness. The E point to septal separation was also measured. Spectral Doppler measurements included the peak flow velocity of the pulmonary artery and aorta and diastolic transmitral flow. The presence of arrhythmias was also noted. Standard echocardiographic findings for a large group of adult female and male chimpanzees were obtained. Female and male chimpanzees were grouped by age in 10-year blocks, and echocardiographic findings were analyzed statistically by 10-year block. In male chimpanzees, cardiac arrhythmias were noted to increase with age. Cardiovascular disease is an important cause of morbidity and death in captive chimpanzees; however, basic echocardiographic measurements from a large cohort of clinically normal animals have not previously been reported. The number of animals in the present study was insufficient to generate reference ranges; however, data from a large cohort of clinically normal animals are presented. This information will be useful for veterinarians working in clinical and research settings with this species.

Identification of appropriate reference genes for human mesenchymal stem cell analysis by quantitative real-time PCR.

PubMed

Li, Xiuying; Yang, Qiwei; Bai, Jinping; Xuan, Yali; Wang, Yimin

2015-01-01

Normalization to a reference gene is the method of choice for quantitative reverse transcription-PCR (RT-qPCR) analysis. The stability of reference genes is critical for accurate experimental results and conclusions. We have evaluated the expression stability of eight commonly used reference genes found in four different human mesenchymal stem cells (MSC). Using geNorm, NormFinder and BestKeeper algorithms, we show that beta-2-microglobulin and peptidyl-prolylisomerase A were the optimal reference genes for normalizing RT-qPCR data obtained from MSC, whereas the TATA box binding protein was not suitable due to its extensive variability in expression. Our findings emphasize the significance of validating reference genes for qPCR analyses. We offer a short list of reference genes to use for normalization and recommend some commercially-available software programs as a rapid approach to validate reference genes. We also demonstrate that the two reference genes, β-actin and glyceraldehyde-3-phosphate dehydrogenase, are frequently used are not always successful in many cases.

Health of children classified as underweight by CDC reference but normal by WHO standard.

PubMed

Meyers, Alan; Joyce, Katherine; Coleman, Sharon M; Cook, John T; Cutts, Diana; Ettinger de Cuba, Stephanie; Heeren, Timothy C; Rose-Jacobs, Ruth; Black, Maureen M; Casey, Patrick H; Chilton, Mariana; Sandel, Megan; Frank, Deborah A

2013-06-01

To ascertain measures of health status among 6- to 24-month-old children classified as below normal weight-for-age (underweight) by the Centers for Disease Control and Prevention (CDC) 2000 growth reference but as normal weight-for-age by the World Health Organization (WHO) 2006 standard. Data were gathered from children and primary caregivers at emergency departments and primary care clinics in 7 US cities. Outcome measures included caregiver rating of child health, parental evaluation of developmental status, history of hospitalizations, and admission to hospital at the time of visit. Children were classified as (1) not underweight by either CDC 2000 or WHO 2006 criteria, (2) underweight by CDC 2000 but not by WHO 2006 criteria, or (3) underweight by both criteria. Associations between these categories and health outcome measures were assessed by using multiple logistic regression analysis. Data were available for 18 420 children. For each health outcome measure, children classified as underweight by CDC 2000 but normal by WHO 2006 had higher adjusted odds ratios (aORs) of adverse health outcomes than children not classified as underweight by either; children classified as underweight by both had the highest aORs of adverse outcomes. For example, compared with children not underweight by either criteria, the aORs for fair/poor health rating were 2.54 (95% confidence interval: 2.20-2.93) among children underweight by CDC but not WHO and 3.76 (3.13-4.51) among children underweight by both. Children who are reclassified from underweight to normal weight in changing from CDC 2000 to WHO 2006 growth charts may still be affected by morbidities associated with underweight.

Are CT scans obtained at referring institutions justified prior to transfer to a pediatric trauma center?

PubMed

Benedict, Leo Andrew; Paulus, Jessica K; Rideout, Leslie; Chwals, Walter J

2014-01-01

To assess whether pediatric trauma patients initially evaluated at referring institutions met Massachusetts statewide trauma field triage criteria for stabilization and immediate transfer to a Pediatric Trauma Center (PTC) without pre-transfer CT imaging. A 3-year retrospective cohort study was completed at our level 1 PTC. Patients with CT imaging at referring institutions were classified according to a triage scheme based on Massachusetts statewide trauma field triage criteria. Demographic data and injury profile characteristics were abstracted from patient medical records and our pediatric trauma registry. A total of 262 patients with 413 CT scans were reviewed from 2008 to 2011. 172 patients scanned (66%, 95% CI: 60%, 71%) met criteria for immediate transfer to a pediatric trauma center. Notably, 110 scans (27% of the total performed at referring institutions) were duplicated within four hours upon arrival to our PTC. GCS score <14 (45%) was the most common requirement for transfer, and CT scan of the head was the most frequent scan obtained (53%). The majority of pediatric trauma patients were subjected to CT scans at referring institutions despite meeting Massachusetts trauma triage guidelines that call for stabilization and immediate transfer to a pediatric trauma center without any CT imaging. © 2014.

A large-scale study of the ultrawideband microwave dielectric properties of normal, benign and malignant breast tissues obtained from cancer surgeries

NASA Astrophysics Data System (ADS)

Lazebnik, Mariya; Popovic, Dijana; McCartney, Leah; Watkins, Cynthia B.; Lindstrom, Mary J.; Harter, Josephine; Sewall, Sarah; Ogilvie, Travis; Magliocco, Anthony; Breslin, Tara M.; Temple, Walley; Mew, Daphne; Booske, John H.; Okoniewski, Michal; Hagness, Susan C.

2007-10-01

The development of microwave breast cancer detection and treatment techniques has been driven by reports of substantial contrast in the dielectric properties of malignant and normal breast tissues. However, definitive knowledge of the dielectric properties of normal and diseased breast tissues at microwave frequencies has been limited by gaps and discrepancies across previously published studies. To address these issues, we conducted a large-scale study to experimentally determine the ultrawideband microwave dielectric properties of a variety of normal, malignant and benign breast tissues, measured from 0.5 to 20 GHz using a precision open-ended coaxial probe. Previously, we reported the dielectric properties of normal breast tissue samples obtained from reduction surgeries. Here, we report the dielectric properties of normal (adipose, glandular and fibroconnective), malignant (invasive and non-invasive ductal and lobular carcinomas) and benign (fibroadenomas and cysts) breast tissue samples obtained from cancer surgeries. We fit a one-pole Cole-Cole model to the complex permittivity data set of each characterized sample. Our analyses show that the contrast in the microwave-frequency dielectric properties between malignant and normal adipose-dominated tissues in the breast is considerable, as large as 10:1, while the contrast in the microwave-frequency dielectric properties between malignant and normal glandular/fibroconnective tissues in the breast is no more than about 10%.

The use of laser microdissection in the identification of suitable reference genes for normalization of quantitative real-time PCR in human FFPE epithelial ovarian tissue samples.

PubMed

Cai, Jing; Li, Tao; Huang, Bangxing; Cheng, Henghui; Ding, Hui; Dong, Weihong; Xiao, Man; Liu, Ling; Wang, Zehua

2014-01-01

Quantitative real-time PCR (qPCR) is a powerful and reproducible method of gene expression analysis in which expression levels are quantified by normalization against reference genes. Therefore, to investigate the potential biomarkers and therapeutic targets for epithelial ovarian cancer by qPCR, it is critical to identify stable reference genes. In this study, twelve housekeeping genes (ACTB, GAPDH, 18S rRNA, GUSB, PPIA, PBGD, PUM1, TBP, HRPT1, RPLP0, RPL13A, and B2M) were analyzed in 50 ovarian samples from normal, benign, borderline, and malignant tissues. For reliable results, laser microdissection (LMD), an effective technique used to prepare homogeneous starting material, was utilized to precisely excise target tissues or cells. One-way analysis of variance (ANOVA) and nonparametric (Kruskal-Wallis) tests were used to compare the expression differences. NormFinder and geNorm software were employed to further validate the suitability and stability of the candidate genes. Results showed that epithelial cells occupied a small percentage of the normal ovary indeed. The expression of ACTB, PPIA, RPL13A, RPLP0, and TBP were stable independent of the disease progression. In addition, NormFinder and geNorm identified the most stable combination (ACTB, PPIA, RPLP0, and TBP) and the relatively unstable reference gene GAPDH from the twelve commonly used housekeeping genes. Our results highlight the use of homogeneous ovarian tissues and multiple-reference normalization strategy, e.g. the combination of ACTB, PPIA, RPLP0, and TBP, for qPCR in epithelial ovarian tissues, whereas GAPDH, the most commonly used reference gene, is not recommended, especially as a single reference gene.

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

PubMed Central

2013-01-01

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

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

PubMed

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

2013-03-12

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

Normal reference values of diastolic strain rate in healthy individuals: Chronological trends and the comparison according to genders.

PubMed

Sun, Byung Joo; Park, Jae-Hyeong; Kim, Jeongai; Choi, Jin-Oh; Lee, Ju-Hee; Shin, Mi-Seung; Kim, Mi-Jeong; Jung, Hae Ok; Park, Jeong Rang; Sohn, Il Suk; Kim, Hyungseop; Kim, Hyung-Kwan; Cho, Goo-Yeong; Park, Jin-Sun; Shim, Chi Young; Shin, Sung Hee; Kim, Kye Hun; Kim, Woo-Shik; Park, Seung Woo

2018-06-19

Recently, the diastolic strain rate (DSR) utilizing speckle-tracking echocardiography has been proposed as a novel parameter for left ventricular diastolic function. We aimed to present normal reference data for those in a large-sized, selected group of healthy individuals. The current study was a part of the Normal echOcardiogRaphic Measurements in KoreAn popuLation (NORMAL), a prospective nationwide survey from 23 centers in Korea. We analyzed 447 subjects (age 48 ± 15 years, 234 females) without any history of cardiovascular disease and presented the early and late DSRs (SR e and SR a , respectively) in a total and gender-/age-specified groups. Among the total subjects, the mean SR e and SR a were 1.6 ± 0.4 S -1 and 0.8 ± 0.3 S -1 , respectively. With increasing age, there were significant trends of decreasing SR e and increasing SR a . Although both gender groups showed comparable age, the female group presented significantly higher SR e compared to male subjects with age of 20-59 years, which diminished after the age of 60 years. However, the SR a was comparable between genders in all age groups. On multiple linear regression, age showed independent associations with both SR e (β = -0.132, P = .010) and SR a (β = 0.440, P < .001), whereas gender did not show any association with SR e or SR a . We present normal reference data of a novel parameter, DSR, in a large-sized selected group with healthy Korean subjects. Additionally, we present significant age-related changes both in SR e and SR a without the impact of their gender. © 2018 Wiley Periodicals, Inc.

Reference ranges of HOMA-IR in normal-weight and obese young Caucasians.

PubMed

Shashaj, Blegina; Luciano, Rosa; Contoli, Benedetta; Morino, Giuseppe Stefano; Spreghini, Maria Rita; Rustico, Carmela; Sforza, Rita Wietrzycowska; Dallapiccola, Bruno; Manco, Melania

2016-04-01

Insulin resistance (IR) may develop very early in life being associated with occurrence of cardiometabolic risk factors (CMRFs). Aim of the present study was to identify in young Caucasians normative values of IR as estimated by the homeostasis model assessment (HOMA-IR) and cutoffs diagnostic of CMRFs. Anthropometrics and biochemical parameters were assessed in 2753 Caucasians (age 2-17.8 years; 1204 F). Reference ranges of HOMA-IR were defined for the whole population and for samples of normal-weight and overweight/obese individuals. The receiver operator characteristic analysis was used to find cutoffs of HOMA-IR accurately identifying individuals with any CMRF among total cholesterol and/or triglycerides higher than the 95th percentile and/or HDL cholesterol lower than the 5th for age and sex, impaired glucose tolerance, and alanine aminotransferase levels ≥40 U/l. Overweight/obese individuals had higher HOMA-IR levels compared with normal-weight peers (p < 0.0001) at any age. HOMA-IR index rose progressively with age, plateaued between age 13 and 15 years and started decreasing afterward. HOMA-IR peaked at age 13 years in girls and at 15 years in boys. The 75th percentile of HOMA-IR in the whole population (3.02; AUROC = 0.73, 95 % CI = 0.70-0.75), in normal-weight (1.68; AUROC = 0.76, 95 % CI = 0.74-0.79), and obese (3.42; AUROC = 0.71, 95 % CI = 0.69-0.72) individuals identified the cutoffs best classifying individuals with any CMRF. Percentiles of HOMA-IR varied significantly in young Caucasians depending on sex, age, and BMI category. The 75th percentile may represent an accurate cutoff point to suspect the occurrence of one or more CMRFs among high total cholesterol and triglycerides, low HDL cholesterol, and ALT ≥ 40 UI/l.

Selection and validation of suitable reference genes for miRNA expression normalization by quantitative RT-PCR in citrus somatic embryogenic and adult tissues.

PubMed

Kou, Shu-Jun; Wu, Xiao-Meng; Liu, Zheng; Liu, Yuan-Long; Xu, Qiang; Guo, Wen-Wu

2012-12-01

miRNAs have recently been reported to modulate somatic embryogenesis (SE), a key pathway of plant regeneration in vitro. For expression level detection and subsequent function dissection of miRNAs in certain biological processes, qRT-PCR is one of the most effective and sensitive techniques, for which suitable reference gene selection is a prerequisite. In this study, three miRNAs and eight non-coding RNAs (ncRNA) were selected as reference candidates, and their expression stability was inspected in developing citrus SE tissues cultured at 20, 25, and 30 °C. Stability of the eight non-miRNA ncRNAs was further validated in five adult tissues without temperature treatment. The best single reference gene for SE tissues was snoR14 or snoRD25, while for the adult tissues the best one was U4; although they were not as stable as the optimal multiple references snoR14 + U6 for SE tissues and snoR14 + U5 for adult tissues. For expression normalization of less abundant miRNAs in SE tissues, miR3954 was assessed as a viable reference. Single reference gene snoR14 outperformed multiple references for the overall SE and adult tissues. As one of the pioneer systematic studies on reference gene identification for plant miRNA normalization, this study benefits future exploration on miRNA function in citrus and provides valuable information for similar studies in other higher plants. Three miRNAs and eight non-coding RNAs were tested as reference candidates on developing citrus SE tissues. Best single references snoR14 or snoRD25 and optimal multiple references snoR14 + U6, snoR14 + U5 were identified.

Pulse Wave Velocity as Marker of Preclinical Arterial Disease: Reference Levels in a Uruguayan Population Considering Wave Detection Algorithms, Path Lengths, Aging, and Blood Pressure

PubMed Central

Farro, Ignacio; Bia, Daniel; Zócalo, Yanina; Torrado, Juan; Farro, Federico; Florio, Lucía; Olascoaga, Alicia; Alallón, Walter; Lluberas, Ricardo; Armentano, Ricardo L.

2012-01-01

Carotid-femoral pulse wave velocity (PWV) has emerged as the gold standard for non-invasive evaluation of aortic stiffness; absence of standardized methodologies of study and lack of normal and reference values have limited a wider clinical implementation. This work was carried out in a Uruguayan (South American) population in order to characterize normal, reference, and threshold levels of PWV considering normal age-related changes in PWV and the prevailing blood pressure level during the study. A conservative approach was used, and we excluded symptomatic subjects; subjects with history of cardiovascular (CV) disease, diabetes mellitus or renal failure; subjects with traditional CV risk factors (other than age and gender); asymptomatic subjects with atherosclerotic plaques in carotid arteries; patients taking anti-hypertensives or lipid-lowering medications. The included subjects (n = 429) were categorized according to the age decade and the blood pressure levels (at study time). All subjects represented the “reference population”; the group of subjects with optimal/normal blood pressures levels at study time represented the “normal population.” Results. Normal and reference PWV levels were obtained. Differences in PWV levels and aging-associated changes were obtained. The obtained data could be used to define vascular aging and abnormal or disease-related arterial changes. PMID:22666551

Normal Databases for the Relative Quantification of Myocardial Perfusion

PubMed Central

Rubeaux, Mathieu; Xu, Yuan; Germano, Guido; Berman, Daniel S.; Slomka, Piotr J.

2016-01-01

Purpose of review Myocardial perfusion imaging (MPI) with SPECT is performed clinically worldwide to detect and monitor coronary artery disease (CAD). MPI allows an objective quantification of myocardial perfusion at stress and rest. This established technique relies on normal databases to compare patient scans against reference normal limits. In this review, we aim to introduce the process of MPI quantification with normal databases and describe the associated perfusion quantitative measures that are used. Recent findings New equipment and new software reconstruction algorithms have been introduced which require the development of new normal limits. The appearance and regional count variations of normal MPI scan may differ between these new scanners and standard Anger cameras. Therefore, these new systems may require the determination of new normal limits to achieve optimal accuracy in relative myocardial perfusion quantification. Accurate diagnostic and prognostic results rivaling those obtained by expert readers can be obtained by this widely used technique. Summary Throughout this review, we emphasize the importance of the different normal databases and the need for specific databases relative to distinct imaging procedures. use of appropriate normal limits allows optimal quantification of MPI by taking into account subtle image differences due to the hardware and software used, and the population studied. PMID:28138354

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

PubMed

Tsai, Pei-Chien; Breen, Matthew

2012-09-01

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

Towards black-box calculations of tunneling splittings obtained from vibrational structure methods based on normal coordinates.

PubMed

Neff, Michael; Rauhut, Guntram

2014-02-05

Multidimensional potential energy surfaces obtained from explicitly correlated coupled-cluster calculations and further corrections for high-order correlation contributions, scalar relativistic effects and core-correlation energy contributions were generated in a fully automated fashion for the double-minimum benchmark systems OH3(+) and NH3. The black-box generation of the potentials is based on normal coordinates, which were used in the underlying multimode expansions of the potentials and the μ-tensor within the Watson operator. Normal coordinates are not the optimal choice for describing double-minimum potentials and the question remains if they can be used for accurate calculations at all. However, their unique definition is an appealing feature, which removes remaining errors in truncated potential expansions arising from different choices of curvilinear coordinate systems. Fully automated calculations are presented, which demonstrate, that the proposed scheme allows for the determination of energy levels and tunneling splittings as a routine application. Copyright © 2013 Elsevier B.V. All rights reserved.

Normalized modes at selected points without normalization

NASA Astrophysics Data System (ADS)

Kausel, Eduardo

2018-04-01

As every textbook on linear algebra demonstrates, the eigenvectors for the general eigenvalue problem | K - λM | = 0 involving two real, symmetric, positive definite matrices K , M satisfy some well-defined orthogonality conditions. Equally well-known is the fact that those eigenvectors can be normalized so that their modal mass μ =ϕT Mϕ is unity: it suffices to divide each unscaled mode by the square root of the modal mass. Thus, the normalization is the result of an explicit calculation applied to the modes after they were obtained by some means. However, we show herein that the normalized modes are not merely convenient forms of scaling, but that they are actually intrinsic properties of the pair of matrices K , M, that is, the matrices already "know" about normalization even before the modes have been obtained. This means that we can obtain individual components of the normalized modes directly from the eigenvalue problem, and without needing to obtain either all of the modes or for that matter, any one complete mode. These results are achieved by means of the residue theorem of operational calculus, a finding that is rather remarkable inasmuch as the residues themselves do not make use of any orthogonality conditions or normalization in the first place. It appears that this obscure property connecting the general eigenvalue problem of modal analysis with the residue theorem of operational calculus may have been overlooked up until now, but which has in turn interesting theoretical implications.Á

An iterative procedure for obtaining maximum-likelihood estimates of the parameters for a mixture of normal distributions, Addendum

NASA Technical Reports Server (NTRS)

Peters, B. C., Jr.; Walker, H. F.

1975-01-01

New results and insights concerning a previously published iterative procedure for obtaining maximum-likelihood estimates of the parameters for a mixture of normal distributions were discussed. It was shown that the procedure converges locally to the consistent maximum likelihood estimate as long as a specified parameter is bounded between two limits. Bound values were given to yield optimal local convergence.

Validating Reference Equations for Impulse Oscillometry in Healthy Mexican Children.

PubMed

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

2017-09-01

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

Validation of Reference Genes in mRNA Expression Analysis Applied to the Study of Asthma.

PubMed

Segundo-Val, Ignacio San; Sanz-Lozano, Catalina S

2016-01-01

The quantitative Polymerase Chain Reaction is the most used technique for the study of gene expression. To correct putative experimental errors of this technique is necessary normalizing the expression results of the gene of interest with the obtained for reference genes. Here, we describe an example of the process to select reference genes. In this particular case, we select reference genes for expression studies in the peripheral blood mononuclear cells of asthmatic patients.

Statokinesigram normalization method.

PubMed

de Oliveira, José Magalhães

2017-02-01

Stabilometry is a technique that aims to study the body sway of human subjects, employing a force platform. The signal obtained from this technique refers to the position of the foot base ground-reaction vector, known as the center of pressure (CoP). The parameters calculated from the signal are used to quantify the displacement of the CoP over time; there is a large variability, both between and within subjects, which prevents the definition of normative values. The intersubject variability is related to differences between subjects in terms of their anthropometry, in conjunction with their muscle activation patterns (biomechanics); and the intrasubject variability can be caused by a learning effect or fatigue. Age and foot placement on the platform are also known to influence variability. Normalization is the main method used to decrease this variability and to bring distributions of adjusted values into alignment. In 1996, O'Malley proposed three normalization techniques to eliminate the effect of age and anthropometric factors from temporal-distance parameters of gait. These techniques were adopted to normalize the stabilometric signal by some authors. This paper proposes a new method of normalization of stabilometric signals to be applied in balance studies. The method was applied to a data set collected in a previous study, and the results of normalized and nonnormalized signals were compared. The results showed that the new method, if used in a well-designed experiment, can eliminate undesirable correlations between the analyzed parameters and the subjects' characteristics and show only the experimental conditions' effects.

Normal reference values for regional pulmonary peripheral airspace epithelial permeability. Influence of pneumonectomy and the smoking habit.

PubMed

Todisco, T; Dottorini, M; Rossi, F; Baldoncini, A; Palumbo, R

1989-01-01

Peripheral airspace epithelial permeability (PAEP) to diethylentriaminopentacetate (DTPA), an index of pulmonary integrity, was measured in 3 groups of subjects for different purposes: (1) to establish vertical regional reference values; (2) to determine the physiological role of acute doubling of total pulmonary blood flow; (3) to quantify the pulmonary epithelial damage in smokers and the possibility of lung protection by an agent stimulating surfactant production. This study broadens previous knowledge of PAEP. First of all, regional reference values are given for young normal nonsmoking subjects and the existence of a vertical gradient of PAEP is confirmed. Furthermore, this study shows that this gradient is independent of the vertical blood flow gradient, since an acute increase of total blood flow in pneumonectomized patients does not modify the regional distribution of PAEP. Finally, it is confirmed that the cigarette smoker's lung is more permeable than the controls and that probably a drug-stimulating surfactant production gives some protection against damage due to chronic smoking.

Normal references of right ventricular strain values by two-dimensional strain echocardiography according to the age and gender.

PubMed

Park, Jae-Hyeong; Choi, Jin-Oh; Park, Seung Woo; Cho, Goo-Yeong; Oh, Jin Kyung; Lee, Jae-Hwan; Seong, In-Whan

2018-02-01

Right ventricular (RV) strain values by 2-dimensional strain echocardiography (STE) can be used as objective markers of RV systolic function. However, there is little data about normal reference RV strain values according to age and gender. We measured normal RV strain values by STE. RV strain values were analyzed from the digitally stored echocardiographic images from NORMAL (Normal echOcardiogRaphic diMensions and functions in KoreAn popuLation) study for the measurement of normal echocardiographic values performed in 23 Korean university hospitals. We enrolled total 1003 healthy persons in the NORMAL study. Of them, we analyzed 2-dimensional RV strain values in 493 subjects (261 females, mean 47 ± 15 years old) only with echocardiographic images by GE machines. Their LV systolic and diastolic functions were normal. RV fractional area change was 48 ± 6% and tricuspid annular plane systolic excursion was 23 ± 3 mm. Total RV global longitudinal peak systolic strain (RVGLS total ) was -21.5 ± 3.2%. Females had higher absolute RVGLS total (-22.3 ± 3.3 vs -20.7 ± 2.9%, p < 0.001) than males. Younger (<50 years old) females had higher absolute RVGLS total (-22.9 ± 3.2 vs -20.5 ± 2.8%, p < 0.001) than age matched males. RVGLS total in females gradually increased according to age (p for trend = 0.002) and becomes almost similar in age ≥50 years. However, this trend was not seen in males (p for trend = 0.287), and younger males had similar RVGLS total value to that of older males (age ≥50 years, -20.5 ± 2.8 vs -20.9 ± 3.1%, p = 0.224). We calculated normal RVGLS values in normal population. Females have higher absolute strain values than males, especially in younger age groups (<50 years old).

Identification of stably expressed reference genes for RT-qPCR data normalization in defined localizations of cyclic bovine ovaries.

PubMed

Schoen, K; Plendl, J; Gabler, C; Kaessmeyer, S

2015-06-01

Ovaries are highly complex organs displaying morphological, molecular and functional differences between their cortical zona parenchymatosa and medullary zona vasculosa, and also between the different cyclic luteal stages. Objective of the present study was to validate expression stability of twelve putative reference genes (RGs) in bovine ovaries, considering the intrinsic heterogeneity of bovine ovarian tissue with regard to different luteal stages and intra-ovarian localizations. The focus was on identifying RGs, which are suitable to normalize RT-qPCR results of ovaries collected from clinical healthy cattle, irrespective of localization and the hormonal stage. Expression profiles of twelve potential reference genes (GAPDH, ACTB, YWHAZ, HPRT1, SDHA, UBA52, POLR2C, RPS9, ACTG2, H3F3B, RPS18 and RPL19) were analysed. Evaluation of gene expression differences was performed using genorm, normfinder, and bestkeeper software. The most stably expressed genes according to genorm, normfinder and bestkeeper approaches contained the candidates H3F3B, RPS9, YWHAZ, RPS18, POLR2C and UBA52. Of this group, the genes YWHAZ, H3F3B and RPS9 could be recommended as best-suited RGs for normalization purposes on healthy bovine ovaries irrespective of the luteal stage or intra-ovarian localization. © 2014 Blackwell Verlag GmbH.

Age-Specific Normal Reference Range for Serum Anti-Müllerian Hormone in Healthy Chinese Han Women: A nationwide Population-Based Study.

PubMed

Du, Xiaofang; Ding, Ting; Zhang, Hanwang; Zhang, Cuilian; Ma, Wenmin; Zhong, Ying; Qu, Wenyu; Zheng, Jie; Liu, Yi; Li, Zhiying; Huang, Kecheng; Deng, Song; Ma, Lanfang; Yang, Jun; Jiang, Jingjing; Yang, Shuhong; Huang, Jia; Wu, Meng; Fang, Li; Lu, Yunping; Luo, Aiyue; Wang, Shixuan

2016-08-01

The increasing use of anti-Müllerian hormone (AMH) in clinic has raised concerns regarding the reliable reference range for this test. However, the reference range for AMH in normal Chinese female population has not been established. Furthermore, relationship between AMH and other clinical markers such as body mass index (BMI) and antral follicle counts (AFCs) and other sex-related hormones have not been examined in normal population-based women. We aimed to determine the age-specific reference range for serum AMH in healthy Chinese women throughout reproductive age to menopause and to estimate relationship between AMH and other clinical markers in healthy women. In this multicenter and nationwide study, advertisements were used to recruit 2055 women, aged 20 to 55 years, from 6 different regions in China; 1590 (77.37%) women met the inclusion criteria for the reference range population. We measured the baseline serum AMH levels using new Beckman Coulter Gen II assay. Serum concentration of follicle-stimulating hormone (FSH), luteinizing hormone (LH), estradiol (E2), testosterone (T), prolactin (PRL), progesterone (PRG), and AFCs were also determined in the follicular phase. The AMH-Age nomogram and AMH levels of different age-groups and the relationship between AMH and other clinical markers. Serum AMH concentrations declined progressively with age. A quadratic model defined as log (AMH) = (-1.970 + 0.296 × Age - 0.006 × Age(2)) fitted best the decline of AMH with age. The median AMH levels were 6.23, 5.65, 4.55, 3.74, 2.78, and 1.09 ng/mL for the 20 ≤ age < 25, 25 ≤ age < 30, 30 ≤ age < 33, 33 ≤ age < 37, 37 ≤ age < 40, and 40 ≤ age < 55 groups, respectively. The 5th to 95th percentiles of the AMH levels, as the reference range, were 2.06 to 12.66, 1.77 to 13.83, 1.48 to 11.45, 0.87 to 9.76, 0.56 to 9.49, and 0.08 to 5.70 ng/mL for each age-group. The AMH levels were positively correlated with AFCs and T, LH, PRL and PRG levels and negatively

RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study.

PubMed

Berghoff, Bork A; Karlsson, Torgny; Källman, Thomas; Wagner, E Gerhart H; Grabherr, Manfred G

2017-01-01

Measuring how gene expression changes in the course of an experiment assesses how an organism responds on a molecular level. Sequencing of RNA molecules, and their subsequent quantification, aims to assess global gene expression changes on the RNA level (transcriptome). While advances in high-throughput RNA-sequencing (RNA-seq) technologies allow for inexpensive data generation, accurate post-processing and normalization across samples is required to eliminate any systematic noise introduced by the biochemical and/or technical processes. Existing methods thus either normalize on selected known reference genes that are invariant in expression across the experiment, assume that the majority of genes are invariant, or that the effects of up- and down-regulated genes cancel each other out during the normalization. Here, we present a novel method, moose 2 , which predicts invariant genes in silico through a dynamic programming (DP) scheme and applies a quadratic normalization based on this subset. The method allows for specifying a set of known or experimentally validated invariant genes, which guides the DP. We experimentally verified the predictions of this method in the bacterium Escherichia coli , and show how moose 2 is able to (i) estimate the expression value distances between RNA-seq samples, (ii) reduce the variation of expression values across all samples, and (iii) to subsequently reveal new functional groups of genes during the late stages of DNA damage. We further applied the method to three eukaryotic data sets, on which its performance compares favourably to other methods. The software is implemented in C++ and is publicly available from http://grabherr.github.io/moose2/. The proposed RNA-seq normalization method, moose 2 , is a valuable alternative to existing methods, with two major advantages: (i) in silico prediction of invariant genes provides a list of potential reference genes for downstream analyses, and (ii) non-linear artefacts in RNA-seq data

Identification and validation of reference genes for quantitative real-time PCR normalization and its applications in lycium.

PubMed

Zeng, Shaohua; Liu, Yongliang; Wu, Min; Liu, Xiaomin; Shen, Xiaofei; Liu, Chunzhao; Wang, Ying

2014-01-01

Lycium barbarum and L. ruthenicum are extensively used as traditional Chinese medicinal plants. Next generation sequencing technology provides a powerful tool for analyzing transcriptomic profiles of gene expression in non-model species. Such gene expression can then be confirmed with quantitative real-time polymerase chain reaction (qRT-PCR). Therefore, use of systematically identified suitable reference genes is a prerequisite for obtaining reliable gene expression data. Here, we calculated the expression stability of 18 candidate reference genes across samples from different tissues and grown under salt stress using geNorm and NormFinder procedures. The geNorm-determined rank of reference genes was similar to those defined by NormFinder with some differences. Both procedures confirmed that the single most stable reference gene was ACNTIN1 for L. barbarum fruits, H2B1 for L. barbarum roots, and EF1α for L. ruthenicum fruits. PGK3, H2B2, and PGK3 were identified as the best stable reference genes for salt-treated L. ruthenicum leaves, roots, and stems, respectively. H2B1 and GAPDH1+PGK1 for L. ruthenicum and SAMDC2+H2B1 for L. barbarum were the best single and/or combined reference genes across all samples. Finally, expression of salt-responsive gene NAC, fruit ripening candidate gene LrPG, and anthocyanin genes were investigated to confirm the validity of the selected reference genes. Suitable reference genes identified in this study provide a foundation for accurately assessing gene expression and further better understanding of novel gene function to elucidate molecular mechanisms behind particular biological/physiological processes in Lycium.

Measurements of normal joint angles by goniometry in calves.

PubMed

Sengöz Şirin, O; Timuçin Celik, M; Ozmen, A; Avki, S

2014-01-01

The aim of this study was to establish normal reference values of the forelimb and hindlimb joint angles in normal Holstein calves. Thirty clinically normal Holstein calves that were free of any detectable musculoskeletal abnormalities were included in the study. A standard transparent plastic goniometer was used to measure maximum flexion, maximum extension, and range-of-motion of the shoulder, elbow, carpal, hip, stifle, and tarsal joints. The goniometric measurements were done on awake calves that were positioned in lateral recumbency. The goniometric values were measured and recorded by two independent investigators. As a result of the study it was concluded that goniometric values obtained from awake calves in lateral recumbency were found to be highly consistent and accurate between investigators (p <0.05). The data of this study acquired objective and useful information on the normal forelimb and hindlimb joint angles in normal Holstein calves. Further studies can be done to predict detailed goniometric values from different diseases and compare them.

A quasiparticle-based multi-reference coupled-cluster method.

PubMed

Rolik, Zoltán; Kállay, Mihály

2014-10-07

The purpose of this paper is to introduce a quasiparticle-based multi-reference coupled-cluster (MRCC) approach. The quasiparticles are introduced via a unitary transformation which allows us to represent a complete active space reference function and other elements of an orthonormal multi-reference (MR) basis in a determinant-like form. The quasiparticle creation and annihilation operators satisfy the fermion anti-commutation relations. On the basis of these quasiparticles, a generalization of the normal-ordered operator products for the MR case can be introduced as an alternative to the approach of Mukherjee and Kutzelnigg [Recent Prog. Many-Body Theor. 4, 127 (1995); Mukherjee and Kutzelnigg, J. Chem. Phys. 107, 432 (1997)]. Based on the new normal ordering any quasiparticle-based theory can be formulated using the well-known diagram techniques. Beyond the general quasiparticle framework we also present a possible realization of the unitary transformation. The suggested transformation has an exponential form where the parameters, holding exclusively active indices, are defined in a form similar to the wave operator of the unitary coupled-cluster approach. The definition of our quasiparticle-based MRCC approach strictly follows the form of the single-reference coupled-cluster method and retains several of its beneficial properties. Test results for small systems are presented using a pilot implementation of the new approach and compared to those obtained by other MR methods.

An iterative procedure for obtaining maximum-likelihood estimates of the parameters for a mixture of normal distributions

NASA Technical Reports Server (NTRS)

Peters, B. C., Jr.; Walker, H. F.

1978-01-01

This paper addresses the problem of obtaining numerically maximum-likelihood estimates of the parameters for a mixture of normal distributions. In recent literature, a certain successive-approximations procedure, based on the likelihood equations, was shown empirically to be effective in numerically approximating such maximum-likelihood estimates; however, the reliability of this procedure was not established theoretically. Here, we introduce a general iterative procedure, of the generalized steepest-ascent (deflected-gradient) type, which is just the procedure known in the literature when the step-size is taken to be 1. We show that, with probability 1 as the sample size grows large, this procedure converges locally to the strongly consistent maximum-likelihood estimate whenever the step-size lies between 0 and 2. We also show that the step-size which yields optimal local convergence rates for large samples is determined in a sense by the 'separation' of the component normal densities and is bounded below by a number between 1 and 2.

The Short Cosyntropin Test Revisited: New Normal Reference Range Using LC-MS/MS.

PubMed

Ueland, Grethe Å; Methlie, Paal; Øksnes, Marianne; Thordarson, Hrafnkell B; Sagen, Jørn; Kellmann, Ralf; Mellgren, Gunnar; Ræder, Maria; Dahlqvist, Per; Dahl, Sandra R; Thorsby, Per M; Løvås, Kristian; Husebye, Eystein S

2018-04-01

The cosyntropin test is used to diagnose adrenal insufficiency (AI) and nonclassical congenital adrenal hyperplasia (NCCAH). Current cutoffs for cortisol and 17-hydroxyprogesterone (17-OHP) are derived from nonstandardized immunoassays. Liquid chromatography tandem mass spectrometry (LC-MS/MS) offers direct measurement of steroids, prompting the need to re-establish normal ranges. The goal of this study was to define cutoff values for cortisol and 17-OHP in serum by LC-MS/MS 30 and 60 minutes after intravenous administration of 250 µg tetracosactide acetate to healthy volunteers and to compare the results with LC-MS/MS with routine immunoassays. Cosyntropin testing was performed in healthy subjects (n = 138) and in patients referred for evaluation of adrenocortical function (n = 94). Steroids were assayed by LC-MS/MS and compared with two immunoassays used in routine diagnostics (Immulite and Roche platforms). The cutoff level for cortisol was defined as the 2.5% percentile in healthy subjects not using oral estrogens (n = 121) and for 17-OHP as the 97.5% percentile. Cortisol cutoff levels for LC-MS/MS were 412 and 485 nmol/L at 30 and 60 minutes, respectively. Applying the new cutoffs, 13 of 60 (22%) subjects who had AI according to conventional criteria now had a normal test result. For 17-OHP, the cutoff levels were 8.9 and 9.0 nmol/L at 30 and 60 minutes, respectively. LC-MS/MS provides cutoff levels for cortisol and 17-OHP after cosyntropin stimulation that are lower than those based on immunoassays, possibly because cross-reactivity between steroid intermediates and cortisol is eliminated. This reduces the number of false-positive tests for AI and false-negative tests for NCCAH.

Selection of Suitable Reference Genes for RT-qPCR Normalization under Abiotic Stresses and Hormone Stimulation in Persimmon (Diospyros kaki Thunb)

PubMed Central

Wang, Peihong; Xiong, Aisheng; Gao, Zhihong; Yu, Xinyi; Li, Man; Hou, Yingjun; Sun, Chao; Qu, Shenchun

2016-01-01

The success of quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR) to quantify gene expression depends on the stability of the reference genes used for data normalization. To date, systematic screening for reference genes in persimmon (Diospyros kaki Thunb) has never been reported. In this study, 13 candidate reference genes were cloned from 'Nantongxiaofangshi' using information available in the transcriptome database. Their expression stability was assessed by geNorm and NormFinder algorithms under abiotic stress and hormone stimulation. Our results showed that the most suitable reference genes across all samples were UBC and GAPDH, and not the commonly used persimmon reference gene ACT. In addition, UBC combined with RPII or TUA were found to be appropriate for the "abiotic stress" group and α-TUB combined with PP2A were found to be appropriate for the "hormone stimuli" group. For further validation, the transcript level of the DkDREB2C homologue under heat stress was studied with the selected genes (CYP, GAPDH, TUA, UBC, α-TUB, and EF1-α). The results suggested that it is necessary to choose appropriate reference genes according to the test materials or experimental conditions. Our study will be useful for future studies on gene expression in persimmon. PMID:27513755

Prenatal Brain MR Imaging: Reference Linear Biometric Centiles between 20 and 24 Gestational Weeks.

PubMed

Conte, G; Milani, S; Palumbo, G; Talenti, G; Boito, S; Rustico, M; Triulzi, F; Righini, A; Izzo, G; Doneda, C; Zolin, A; Parazzini, C

2018-05-01

Evaluation of biometry is a fundamental step in prenatal brain MR imaging. While different studies have reported reference centiles for MR imaging biometric data of fetuses in the late second and third trimesters of gestation, no one has reported them in fetuses in the early second trimester. We report centiles of normal MR imaging linear biometric data of a large cohort of fetal brains within 24 weeks of gestation. From the data bases of 2 referral centers of fetal medicine, accounting for 3850 examinations, we retrospectively collected 169 prenatal brain MR imaging examinations of singleton pregnancies, between 20 and 24 weeks of gestational age, with normal brain anatomy at MR imaging and normal postnatal neurologic development. To trace the reference centiles, we used the CG-LMS method. Reference biometric centiles for the developing structures of the cerebrum, cerebellum, brain stem, and theca were obtained. The overall interassessor agreement was adequate for all measurements. Reference biometric centiles of the brain structures in fetuses between 20 and 24 weeks of gestational age may be a reliable tool in assessing fetal brain development. © 2018 by American Journal of Neuroradiology.

A new device for performing reference point indentation without a reference probe

NASA Astrophysics Data System (ADS)

Bridges, Daniel; Randall, Connor; Hansma, Paul K.

2012-04-01

Here we describe a novel, hand-held reference point indentation (RPI), instrument that is designed for clinical measurements of bone material properties in living patients. This instrument differs from previous RPI instruments in that it requires neither a reference probe nor removal of the periosteum that covers the bone, thus significantly simplifying its use in patient testing. After describing the instrument, we discuss five guidelines for optimal and reproducible results. These are: (1) the angle between the normal to the surface and the axis of the instrument should be less than 10°, (2) the compression of the main spring to trigger the device must be performed slowly (>1 s), (3) the probe tip should be sharper than 10 μm; however, a normalized parameter with a calibration phantom can correct for dull tips up to a 100 μm radius, (4) the ambient room temperature should be between 4 °C and 37 °C, and (5) the effective mass of the bone or material under test must exceed 1 kg, or if under 1 kg, the specimen should be securely anchored in a fixation device with sufficient mass (which is not a requirement of previous RPI instruments). Our experience is that a person can be trained with these guidelines in about 5 min and thereafter obtain accurate and reproducible results. The portability, ease of use, and minimal training make this instrument suitable to measure bone material properties in a clinical setting.

Normalization of CT scans reconstructed with different kernels to reduce variability in emphysema measurements

NASA Astrophysics Data System (ADS)

Gallardo Estrella, L.; van Ginneken, B.; van Rikxoort, E. M.

2013-03-01

Chronic Obstructive Pulmonary Disease (COPD) is a lung disease characterized by progressive air flow limitation caused by emphysema and chronic bronchitis. Emphysema is quantified from chest computed tomography (CT) scans as the percentage of attentuation values below a fixed threshold. The emphysema quantification varies substantially between scans reconstructed with different kernels, limiting the possibilities to compare emphysema quantifications obtained from scans with different reconstruction parameters. In this paper we propose a method to normalize scans reconstructed with different kernels to have the same characteristics as scans reconstructed with a reference kernel and investigate if this normalization reduces the variability in emphysema quantification. The proposed normalization splits a CT scan into different frequency bands based on hierarchical unsharp masking. Normalization is performed by changing the energy in each frequency band to the average energy in each band in the reference kernel. A database of 15 subjects with COPD was constructed for this study. All subjects were scanned at total lung capacity and the scans were reconstructed with four different reconstruction kernels. The normalization was applied to all scans. Emphysema quantification was performed before and after normalization. It is shown that the emphysema score varies substantially before normalization but the variation diminishes after normalization.

Identification of stable reference genes in differentiating human pluripotent stem cells.

PubMed

Holmgren, Gustav; Ghosheh, Nidal; Zeng, Xianmin; Bogestål, Yalda; Sartipy, Peter; Synnergren, Jane

2015-06-01

Reference genes, often referred to as housekeeping genes (HKGs), are frequently used to normalize gene expression data based on the assumption that they are expressed at a constant level in the cells. However, several studies have shown that there may be a large variability in the gene expression levels of HKGs in various cell types. In a previous study, employing human embryonic stem cells (hESCs) subjected to spontaneous differentiation, we observed that the expression of commonly used HKG varied to a degree that rendered them inappropriate to use as reference genes under those experimental settings. Here we present a substantially extended study of the HKG signature in human pluripotent stem cells (hPSC), including nine global gene expression datasets from both hESC and human induced pluripotent stem cells, obtained during directed differentiation toward endoderm-, mesoderm-, and ectoderm derivatives. Sets of stably expressed genes were compiled, and a handful of genes (e.g., EID2, ZNF324B, CAPN10, and RABEP2) were identified as generally applicable reference genes in hPSCs across all cell lines and experimental conditions. The stability in gene expression profiles was confirmed by reverse transcription quantitative PCR analysis. Taken together, the current results suggest that differentiating hPSCs have a distinct HKG signature, which in some aspects is different from somatic cell types, and underscore the necessity to validate the stability of reference genes under the actual experimental setup used. In addition, the novel putative HKGs identified in this study can preferentially be used for normalization of gene expression data obtained from differentiating hPSCs. Copyright © 2015 the American Physiological Society.

[Establishing biological reference intervals of alanine transaminase for clinical laboratory stored database].

PubMed

Guo, Wei; Song, Binbin; Shen, Junfei; Wu, Jiong; Zhang, Chunyan; Wang, Beili; Pan, Baishen

2015-08-25

To establish an indirect reference interval based on the test results of alanine aminotransferase stored in a laboratory information system. All alanine aminotransferase results were included for outpatients and physical examinations that were stored in the laboratory information system of Zhongshan Hospital during 2014. The original data were transformed using a Box-Cox transformation to obtain an approximate normal distribution. Outliers were identified and omitted using the Chauvenet and Tukey methods. The indirect reference intervals were obtained by simultaneously applying nonparametric and Hoffmann methods. The reference change value was selected to determine the statistical significance of the observed differences between the calculated and published reference intervals. The indirect reference intervals for alanine aminotransferase of all groups were 12 to 41 U/L (male, outpatient), 12 to 48 U/L (male, physical examination), 9 to 32 U/L (female, outpatient), and 8 to 35 U/L (female, physical examination), respectively. The absolute differences when compared with the direct results were all smaller than the reference change value of alanine aminotransferase. The Box-Cox transformation combined with the Hoffmann and Tukey methods is a simple and reliable technique that should be promoted and used by clinical laboratories.

Evaluation of Reference Genes for Normalization of Gene Expression Using Quantitative RT-PCR under Aluminum, Cadmium, and Heat Stresses in Soybean.

PubMed

Gao, Mengmeng; Liu, Yaping; Ma, Xiao; Shuai, Qin; Gai, Junyi; Li, Yan

2017-01-01

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is widely used to analyze the relative gene expression level, however, the accuracy of qRT-PCR is greatly affected by the stability of reference genes, which is tissue- and environment- dependent. Therefore, choosing the most stable reference gene in a specific tissue and environment is critical to interpret gene expression patterns. Aluminum (Al), cadmium (Cd), and heat stresses are three important abiotic factors limiting soybean (Glycine max) production in southern China. To identify the suitable reference genes for normalizing the expression levels of target genes by qRT-PCR in soybean response to Al, Cd and heat stresses, we studied the expression stability of ten commonly used housekeeping genes in soybean roots and leaves under these three abiotic stresses, using five approaches, BestKeeper, Delta Ct, geNorm, NormFinder and RefFinder. We found TUA4 is the most stable reference gene in soybean root tips under Al stress. Under Cd stress, Fbox and UKN2 are the most stable reference genes in roots and leaves, respectively, while 60S is the most suitable reference gene when analyzing both roots and leaves together. For heat stress, TUA4 and UKN2 are the most stable housekeeping genes in roots and leaves, respectively, and UKN2 is the best reference gene for analysis of roots and leaves together. To validate the reference genes, we quantified the relative expression levels of six target genes that were involved in soybean response to Al, Cd or heat stresses, respectively. The expression patterns of these target genes differed between using the most and least stable reference genes, suggesting the selection of a suitable reference gene is critical for gene expression studies.

An iterative procedure for obtaining maximum-likelihood estimates of the parameters for a mixture of normal distributions, 2

NASA Technical Reports Server (NTRS)

Peters, B. C., Jr.; Walker, H. F.

1976-01-01

The problem of obtaining numerically maximum likelihood estimates of the parameters for a mixture of normal distributions is addressed. In recent literature, a certain successive approximations procedure, based on the likelihood equations, is shown empirically to be effective in numerically approximating such maximum-likelihood estimates; however, the reliability of this procedure was not established theoretically. Here, a general iterative procedure is introduced, of the generalized steepest-ascent (deflected-gradient) type, which is just the procedure known in the literature when the step-size is taken to be 1. With probability 1 as the sample size grows large, it is shown that this procedure converges locally to the strongly consistent maximum-likelihood estimate whenever the step-size lies between 0 and 2. The step-size which yields optimal local convergence rates for large samples is determined in a sense by the separation of the component normal densities and is bounded below by a number between 1 and 2.

Radiosensitivity of fibroblasts obtained from a cafe-au-lait spot and normal-appearing skin of a patient with neurofibromatosis (NF-6)

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

Hannan, M.A.; Smith, B.P.; Sigut, D.

Fibroblast cells derived from a cafe-au-lait spot and normal-appearing skin of a neurofibromatosis (NF-6) patient were studied for radiosensitivity in comparison with two normal cell lines used as controls. No difference in radiosensitivity was observed between the patient's cell lines and the controls using acute gamma-irradiation. However, a markedly increased radiosensitivity of the fibroblasts obtained from the patient's skin of normal appearance was demonstrated after chronic gamma-irradiation. The cells from the cafe-au-lait spot showed intermediate sensitivity to chronic irradiation as compared with the control cell lines and the fibroblasts derived from the normal skin of the patient. These results showedmore » the usefulness of chronic irradiation in detecting increased cellular radiosensitivity which may result from a unique DNA repair defect in an NF patient. We suggest that enhanced genetic changes in radiosensitive NF patients may lead to formation of cafe-au-lait lesions and certain tumors. Such a transformation may be associated with production of radiotolerant cells.« less

GPS-Only Terrestrial Reference Frame Based on a Global Reprocessing

NASA Astrophysics Data System (ADS)

Dietrich, R.; Rothacher, M.; Ruelke, A.; Fritsche, M.; Steigenberger, P.

2007-12-01

The realization of the International Terrestrial Reference System (ITRS) with highest accuracy and stability is fundamental and crucial for applications in geodesy, geodynamics, geophysics and global change. In a joint effort TU Dresden and TU Munich/GFZ Potsdam reprocessed a global GPS network of more than 200 stations. As a contribution to an ITRS realization daily normal equations from 1994 to 2005 were rigorously combined in order to determine a global GPS-only reference frame (PDR05/Potsdam-Dresden-Reprocessing Reference Frame). We present a realization of the global terrestrial reference system which follows the center of mass approach in consideration of the load-induced deformation of the Earth's crust due to the redistribution of surface masses. The stability of our reference frame will be evaluated based on the obtained long-term trends of station coordinates, the load-induced deformation estimates and the homogeneous time series of station positions. We will compare our solution with other recent terrestrial reference system realizations and give some conclusions for future realizations of the ITRS.

Selection and Validation of Reference Genes for Accurate RT-qPCR Data Normalization in Coffea spp. under a Climate Changes Context of Interacting Elevated [CO2] and Temperature

PubMed Central

Martins, Madlles Q.; Fortunato, Ana S.; Rodrigues, Weverton P.; Partelli, Fábio L.; Campostrini, Eliemar; Lidon, Fernando C.; DaMatta, Fábio M.; Ramalho, José C.; Ribeiro-Barros, Ana I.

2017-01-01

World coffee production has faced increasing challenges associated with ongoing climatic changes. Several studies, which have been almost exclusively based on temperature increase, have predicted extensive reductions (higher than half by 2,050) of actual coffee cropped areas. However, recent studies showed that elevated [CO2] can strongly mitigate the negative impacts of heat stress at the physiological and biochemical levels in coffee leaves. In addition, it has also been shown that coffee genotypes can successfully cope with temperatures above what has been traditionally accepted. Altogether, this information suggests that the real impact of climate changes on coffee growth and production could be significantly lower than previously estimated. Gene expression studies are an important tool to unravel crop acclimation ability, demanding the use of adequate reference genes. We have examined the transcript stability of 10 candidate reference genes to normalize RT-qPCR expression studies using a set of 24 cDNAs from leaves of three coffee genotypes (CL153, Icatu, and IPR108), grown under 380 or 700 μL CO2 L−1, and submitted to increasing temperatures from 25/20°C (day/night) to 42/34°C. Samples were analyzed according to genotype, [CO2], temperature, multiple stress interaction ([CO2], temperature) and total stress interaction (genotype, [CO2], and temperature). The transcript stability of each gene was assessed through a multiple analytical approach combining the Coeficient of Variation method and three algorithms (geNorm, BestKeeper, NormFinder). The transcript stability varied according to the type of stress for most genes, but the consensus ranking obtained with RefFinder, classified MDH as the gene with the highest mRNA stability to a global use, followed by ACT and S15, whereas α-TUB and CYCL showed the least stable mRNA contents. Using the coffee expression profiles of the gene encoding the large-subunit of ribulose-1,5-bisphosphate carboxylase

Selection and Validation of Reference Genes for Accurate RT-qPCR Data Normalization in Coffea spp. under a Climate Changes Context of Interacting Elevated [CO2] and Temperature.

PubMed

Martins, Madlles Q; Fortunato, Ana S; Rodrigues, Weverton P; Partelli, Fábio L; Campostrini, Eliemar; Lidon, Fernando C; DaMatta, Fábio M; Ramalho, José C; Ribeiro-Barros, Ana I

2017-01-01

World coffee production has faced increasing challenges associated with ongoing climatic changes. Several studies, which have been almost exclusively based on temperature increase, have predicted extensive reductions (higher than half by 2,050) of actual coffee cropped areas. However, recent studies showed that elevated [CO 2 ] can strongly mitigate the negative impacts of heat stress at the physiological and biochemical levels in coffee leaves. In addition, it has also been shown that coffee genotypes can successfully cope with temperatures above what has been traditionally accepted. Altogether, this information suggests that the real impact of climate changes on coffee growth and production could be significantly lower than previously estimated. Gene expression studies are an important tool to unravel crop acclimation ability, demanding the use of adequate reference genes. We have examined the transcript stability of 10 candidate reference genes to normalize RT-qPCR expression studies using a set of 24 cDNAs from leaves of three coffee genotypes (CL153, Icatu, and IPR108), grown under 380 or 700 μL CO 2 L -1 , and submitted to increasing temperatures from 25/20°C (day/night) to 42/34°C. Samples were analyzed according to genotype, [CO 2 ], temperature, multiple stress interaction ([CO 2 ], temperature) and total stress interaction (genotype, [CO 2 ], and temperature). The transcript stability of each gene was assessed through a multiple analytical approach combining the Coeficient of Variation method and three algorithms (geNorm, BestKeeper, NormFinder). The transcript stability varied according to the type of stress for most genes, but the consensus ranking obtained with RefFinder, classified MDH as the gene with the highest mRNA stability to a global use, followed by ACT and S15 , whereas α -TUB and CYCL showed the least stable mRNA contents. Using the coffee expression profiles of the gene encoding the large-subunit of ribulose-1,5-bisphosphate carboxylase

A large-scale measurement of dielectric properties of normal and malignant colorectal tissues obtained from cancer surgeries at Larmor frequencies.

PubMed

Li, Zhou; Deng, Guanhua; Li, Zhe; Xin, Sherman Xuegang; Duan, Song; Lan, Maoying; Zhang, Sa; Gao, Yixin; He, Jun; Zhang, Songtao; Tang, Hongming; Wang, Weiwei; Han, Shuai; Yang, Qing X; Zhuang, Ling; Hu, Jiani; Liu, Feng

2016-11-01

Knowledge of dielectric properties of malignant human tissues is necessary for the recently developed magnetic resonance (MR) technique called MR electrical property tomography. This technique may be used in early tumor detection based on the obvious differentiation of the dielectric properties between normal and malignant tissues. However, the dielectric properties of malignant human tissues in the scale of the Larmor frequencies are not completely available in the literature. In this study, the authors focused only on the dielectric properties of colorectal tumor tissue. The dielectric properties of 504 colorectal malignant samples excised from 85 patients in the scale of the Larmor frequencies were measured using the precision open-ended coaxial probe method. The obtained complex-permittivity data were fitted to the single-pole Cole-Cole model. The median permittivity and conductivity for the malignant tissue sample were 79.3 and 0.881 S/m at 128 MHz, which were 14.6% and 17.0% higher, respectively, than those of normal tissue samples. Significant differences between normal and malignant tissues were found for the dielectric properties (p < 0.05). Experimental results indicated that the dielectric properties were significantly different between normal and malignant tissues for colorectal tissue. This large-scale clinical measurement provides more subtle base data to validate the technique of MR electrical property tomography.

Sensitivity and specificity of normality tests and consequences on reference interval accuracy at small sample size: a computer-simulation study.

PubMed

Le Boedec, Kevin

2016-12-01

According to international guidelines, parametric methods must be chosen for RI construction when the sample size is small and the distribution is Gaussian. However, normality tests may not be accurate at small sample size. The purpose of the study was to evaluate normality test performance to properly identify samples extracted from a Gaussian population at small sample sizes, and assess the consequences on RI accuracy of applying parametric methods to samples that falsely identified the parent population as Gaussian. Samples of n = 60 and n = 30 values were randomly selected 100 times from simulated Gaussian, lognormal, and asymmetric populations of 10,000 values. The sensitivity and specificity of 4 normality tests were compared. Reference intervals were calculated using 6 different statistical methods from samples that falsely identified the parent population as Gaussian, and their accuracy was compared. Shapiro-Wilk and D'Agostino-Pearson tests were the best performing normality tests. However, their specificity was poor at sample size n = 30 (specificity for P < .05: .51 and .50, respectively). The best significance levels identified when n = 30 were 0.19 for Shapiro-Wilk test and 0.18 for D'Agostino-Pearson test. Using parametric methods on samples extracted from a lognormal population but falsely identified as Gaussian led to clinically relevant inaccuracies. At small sample size, normality tests may lead to erroneous use of parametric methods to build RI. Using nonparametric methods (or alternatively Box-Cox transformation) on all samples regardless of their distribution or adjusting, the significance level of normality tests depending on sample size would limit the risk of constructing inaccurate RI. © 2016 American Society for Veterinary Clinical Pathology.

[Preliminary establishment of cytological examination and the normal reference values for hypertonic saline solution-induced sputum of healthy children in Guangzhou].

PubMed

Chen, De-hui; Zhong, Guo-yu; Luo, Wei; Chen, Qiao-li; Chen, Ru-chong; Lin, Yu-neng; Pan, Xiao-an; Li, Jin-ying; Wu, Shang-zhi; Lai, Ke-fang; Zhong, Nan-shan

2012-07-01

To establish the method of cytological examination and the normal reference values for hypertonic saline solution-induced sputum of healthy children (age range from 5 to 15 years) with physical examination in Guangzhou. A total of 352 children, 5 to 15 years old, were enrolled from primary school and middle school in Guangzhou from January to December, 2010. All subjects completed a standardized questionnaire on the presence of respiratory, allergic symptoms and family history, the medical history and the physical examination was performed by doctors, lung function (forced expiratory volume at 1 s in predicted normal, FEV(1)%) was determined. There were 266 healthy children (137 males, 129 females) who were selected and undergone hypertonic saline solution induction of sputum, and cytological examination was performed. Hypertonic saline (5%) was nebulized and inhaled for 15 - 30 min. No expectoration within 30 min was defined as failure, and the procedure was terminated. The part of opaque and higher density sputum samples was detected by cytology. The proportion of neutrophils, lymphocytes, eosinophils, macrophages and monocytes was calculated. This study was approved by the institutional Ethics Review Committee of First Affiliated Hospital of Guangzhou Medical College. Informed consent was obtained from the legal guardians of all participants following a detailed description of the purpose and potential benefits of the study. There were 175 subjects' induced sputum specimens (175/266, 65.8%), non-qualified sputum samples were obtained from 16 of the subjects. The proportions of median (IQR) of lymphocytes were 0.012 (0.020), 95%CI were ranged from 0.015 to 0.022; neutrophils 0.207 (0.330), 95%CI 0.266 - 0.356 macrophages 0.761 (0.327), 95%CI 0.607 - 0.699; eosinophils 0.004 (0.019), 95%CI 0.013 - 0.022. There were no significant differences in proportions of cytological findings of female or male, different age groups and second-hand smoking or not (all P > 0

Defining suitable reference genes for RT-qPCR analysis on human sertoli cells after 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure.

PubMed

Ribeiro, Mariana Antunes; dos Reis, Mariana Bisarro; de Moraes, Leonardo Nazário; Briton-Jones, Christine; Rainho, Cláudia Aparecida; Scarano, Wellerson Rodrigo

2014-11-01

Quantitative real-time RT-PCR (qPCR) has proven to be a valuable molecular technique to quantify gene expression. There are few studies in the literature that describe suitable reference genes to normalize gene expression data. Studies of transcriptionally disruptive toxins, like tetrachlorodibenzo-p-dioxin (TCDD), require careful consideration of reference genes. The present study was designed to validate potential reference genes in human Sertoli cells after exposure to TCDD. 32 candidate reference genes were analyzed to determine their applicability. geNorm and NormFinder softwares were used to obtain an estimation of the expression stability of the 32 genes and to identify the most suitable genes for qPCR data normalization.

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

PubMed

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

2017-03-01

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

Validation of reference genes for quantitative gene expression analysis in experimental epilepsy.

PubMed

Sadangi, Chinmaya; Rosenow, Felix; Norwood, Braxton A

2017-12-01

To grasp the molecular mechanisms and pathophysiology underlying epilepsy development (epileptogenesis) and epilepsy itself, it is important to understand the gene expression changes that occur during these phases. Quantitative real-time polymerase chain reaction (qPCR) is a technique that rapidly and accurately determines gene expression changes. It is crucial, however, that stable reference genes are selected for each experimental condition to ensure that accurate values are obtained for genes of interest. If reference genes are unstably expressed, this can lead to inaccurate data and erroneous conclusions. To date, epilepsy studies have used mostly single, nonvalidated reference genes. This is the first study to systematically evaluate reference genes in male Sprague-Dawley rat models of epilepsy. We assessed 15 potential reference genes in hippocampal tissue obtained from 2 different models during epileptogenesis, 1 model during chronic epilepsy, and a model of noninjurious seizures. Reference gene ranking varied between models and also differed between epileptogenesis and chronic epilepsy time points. There was also some variance between the four mathematical models used to rank reference genes. Notably, we found novel reference genes to be more stably expressed than those most often used in experimental epilepsy studies. The consequence of these findings is that reference genes suitable for one epilepsy model may not be appropriate for others and that reference genes can change over time. It is, therefore, critically important to validate potential reference genes before using them as normalizing factors in expression analysis in order to ensure accurate, valid results. © 2017 Wiley Periodicals, Inc.

Failure to obtain an autoimmune response following cryosurgery to the normal rat liver.

PubMed Central

Townell, N H; Tsantoulas, D; Holborow, E J; Hobbs, K E

1980-01-01

Smooth muscle antibody (SMA) and anti-liver-specific lipoprotein (anti-LSP) responses were investigated following five different freeze thaw regimes to the normal rat liver. The livers were examined histologically for evidence of autoimmune liver disease. No SMA or anti-LSP was found in any animal and on histological examination the unfrozen part of all livers was normal. It is concluded that cryosurgical damage to the liver is unlikely to provoke an autoimmune response. PMID:7460392

Validation of Reference Genes for Relative Quantitative Gene Expression Studies in Cassava (Manihot esculenta Crantz) by Using Quantitative Real-Time PCR

PubMed Central

Hu, Meizhen; Hu, Wenbin; Xia, Zhiqiang; Zhou, Xincheng; Wang, Wenquan

2016-01-01

Reverse transcription quantitative real-time polymerase chain reaction (real-time PCR, also referred to as quantitative RT-PCR or RT-qPCR) is a highly sensitive and high-throughput method used to study gene expression. Despite the numerous advantages of RT-qPCR, its accuracy is strongly influenced by the stability of internal reference genes used for normalizations. To date, few studies on the identification of reference genes have been performed on cassava (Manihot esculenta Crantz). Therefore, we selected 26 candidate reference genes mainly via the three following channels: reference genes used in previous studies on cassava, the orthologs of the most stable Arabidopsis genes, and the sequences obtained from 32 cassava transcriptome sequence data. Then, we employed ABI 7900 HT and SYBR Green PCR mix to assess the expression of these genes in 21 materials obtained from various cassava samples under different developmental and environmental conditions. The stability of gene expression was analyzed using two statistical algorithms, namely geNorm and NormFinder. geNorm software suggests the combination of cassava4.1_017977 and cassava4.1_006391 as sufficient reference genes for major cassava samples, the union of cassava4.1_014335 and cassava4.1_006884 as best choice for drought stressed samples, and the association of cassava4.1_012496 and cassava4.1_006391 as optimal choice for normally grown samples. NormFinder software recommends cassava4.1_006884 or cassava4.1_006776 as superior reference for qPCR analysis of different materials and organs of drought stressed or normally grown cassava, respectively. Results provide an important resource for cassava reference genes under specific conditions. The limitations of these findings were also discussed. Furthermore, we suggested some strategies that may be used to select candidate reference genes. PMID:27242878

Establishing pediatric reference intervals for 13 biochemical analytes derived from normal subjects in a pediatric endocrinology clinic in Korea.

PubMed

Cho, Sun-Mi; Lee, Sang-Guk; Kim, Ho Seong; Kim, Jeong-Ho

2014-12-01

Defining pediatric reference intervals is one of the most difficult tasks for laboratory physicians. The continuously changing physiology of growing children makes their laboratory values moving targets. In addition, ethnic and behavioral differences might also cause variations. The aim of this study was to establish age- and sex-specific partitioned reference intervals for 13 serum biochemical analytes in Korean children. A total of 2474 patients, girls aged 2-14 years and boys aged 2-16 years, who underwent a short stature workup but were diagnosed as normal at the Pediatric Endocrinology Clinic of Severance Hospital (Seoul, Korea) between September 2010 and June 2012 were included in this study. The levels of serum calcium, inorganic phosphorus, blood urea nitrogen, creatinine, uric acid, glucose, total cholesterol, total protein, albumin, alkaline phosphatase, aspartic aminotransferase, alanine aminotransferase, and total bilirubin were measured using a Hitachi 7600 analyzer (Hitachi High-Technologies Corporation, Tokyo, Japan). Reference intervals were partitioned according to sex or age subgroups using the Harris and Boyd method. Most analytes except calcium and albumin required partitioning either by sex or age. Age-specific partitioned reference intervals for alkaline phosphatase, creatinine, and total bilirubin were established for both males and females after being partitioned by sex. Additional age-specific partitioning of aspartic aminotransferase in females and total protein and uric acid in males was also required. Inorganic phosphorus, total cholesterol, alanine aminotransferase, blood urea nitrogen, and glucose were partitioned only by sex. This study provided updated age- and sex-specific pediatric reference intervals for 13 basic serum chemistry analytes from a sufficient number of healthy children by using a modern analytical chemistry platform. Copyright © 2014 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights

Histogram-based normalization technique on human brain magnetic resonance images from different acquisitions.

PubMed

Sun, Xiaofei; Shi, Lin; Luo, Yishan; Yang, Wei; Li, Hongpeng; Liang, Peipeng; Li, Kuncheng; Mok, Vincent C T; Chu, Winnie C W; Wang, Defeng

2015-07-28

Intensity normalization is an important preprocessing step in brain magnetic resonance image (MRI) analysis. During MR image acquisition, different scanners or parameters would be used for scanning different subjects or the same subject at a different time, which may result in large intensity variations. This intensity variation will greatly undermine the performance of subsequent MRI processing and population analysis, such as image registration, segmentation, and tissue volume measurement. In this work, we proposed a new histogram normalization method to reduce the intensity variation between MRIs obtained from different acquisitions. In our experiment, we scanned each subject twice on two different scanners using different imaging parameters. With noise estimation, the image with lower noise level was determined and treated as the high-quality reference image. Then the histogram of the low-quality image was normalized to the histogram of the high-quality image. The normalization algorithm includes two main steps: (1) intensity scaling (IS), where, for the high-quality reference image, the intensities of the image are first rescaled to a range between the low intensity region (LIR) value and the high intensity region (HIR) value; and (2) histogram normalization (HN),where the histogram of low-quality image as input image is stretched to match the histogram of the reference image, so that the intensity range in the normalized image will also lie between LIR and HIR. We performed three sets of experiments to evaluate the proposed method, i.e., image registration, segmentation, and tissue volume measurement, and compared this with the existing intensity normalization method. It is then possible to validate that our histogram normalization framework can achieve better results in all the experiments. It is also demonstrated that the brain template with normalization preprocessing is of higher quality than the template with no normalization processing. We have proposed

Analysis of semen parameters in male referrals: impact of reference limits, stratification by fertility categories, predictors of change, and comparison of normal semen parameters in subfertile couples.

PubMed

Baker, Karen; Li, Jianbo; Sabanegh, Edmund

2015-01-01

To [1] determine the impact of semen reference limits on referrals for male fertility evaluations, [2] analyze the stratification of subjects based on published "normal" thresholds, [3] analyze the odds of changing fertility categories during serial tests and thereby the potential impact of inherent variability of semen parameters on referrals, and [4] determine variable(s) predictive of change. Retrospective chart review. Academic referral center for male fertility. New encounters in a male fertility clinic over a 5-year period that straddles the publication of World Health Organization (WHO) 2010 reference values. None. Demographic and clinical variables, semen values, and fertility categories as follows: BE (below WHO 2010 criteria), BTWN (above WHO 2010 but below WHO 1999 criteria), and N (above WHO 1999 criteria). A total of 82.3% of initial semen tests were categorized as BE, and the predominance of this category was unchanged by publication of the WHO 2010 criteria. Men with initial semen analysis categorized as BTWN or N represented 16.2% and 1.5% of the referral population, respectively. Subjects initially categorized as BTWN were more likely to change fertility categories, and overwhelmingly this migration was downward. Analysis of normal individual semen parameters revealed statistically worse mean concentration and motility when at least one other parameter fell below the WHO 2010 criteria. Men with semen results above reference criteria are underrepresented, indicating that reference limits influence referral patterns for male fertility evaluations. Normal mean concentration and motility were lower in men with at least one other individual semen parameter below the 2010 criteria, suggesting global dysfunction in spermatogenesis. Published by Elsevier Inc.

Identification and Validation of Reference Genes and Their Impact on Normalized Gene Expression Studies across Cultivated and Wild Cicer Species

PubMed Central

Reddy, Palakolanu Sudhakar; Sri Cindhuri, Katamreddy; Sivaji Ganesh, Adusumalli; Sharma, Kiran Kumar

2016-01-01

Quantitative Real-Time PCR (qPCR) is a preferred and reliable method for accurate quantification of gene expression to understand precise gene functions. A total of 25 candidate reference genes including traditional and new generation reference genes were selected and evaluated in a diverse set of chickpea samples. The samples used in this study included nine chickpea genotypes (Cicer spp.) comprising of cultivated and wild species, six abiotic stress treatments (drought, salinity, high vapor pressure deficit, abscisic acid, cold and heat shock), and five diverse tissues (leaf, root, flower, seedlings and seed). The geNorm, NormFinder and RefFinder algorithms used to identify stably expressed genes in four sample sets revealed stable expression of UCP and G6PD genes across genotypes, while TIP41 and CAC were highly stable under abiotic stress conditions. While PP2A and ABCT genes were ranked as best for different tissues, ABCT, UCP and CAC were most stable across all samples. This study demonstrated the usefulness of new generation reference genes for more accurate qPCR based gene expression quantification in cultivated as well as wild chickpea species. Validation of the best reference genes was carried out by studying their impact on normalization of aquaporin genes PIP1;4 and TIP3;1, in three contrasting chickpea genotypes under high vapor pressure deficit (VPD) treatment. The chickpea TIP3;1 gene got significantly up regulated under high VPD conditions with higher relative expression in the drought susceptible genotype, confirming the suitability of the selected reference genes for expression analysis. This is the first comprehensive study on the stability of the new generation reference genes for qPCR studies in chickpea across species, different tissues and abiotic stresses. PMID:26863232

Identification and Validation of Reference Genes and Their Impact on Normalized Gene Expression Studies across Cultivated and Wild Cicer Species.

PubMed

Reddy, Dumbala Srinivas; Bhatnagar-Mathur, Pooja; Reddy, Palakolanu Sudhakar; Sri Cindhuri, Katamreddy; Sivaji Ganesh, Adusumalli; Sharma, Kiran Kumar

2016-01-01

Quantitative Real-Time PCR (qPCR) is a preferred and reliable method for accurate quantification of gene expression to understand precise gene functions. A total of 25 candidate reference genes including traditional and new generation reference genes were selected and evaluated in a diverse set of chickpea samples. The samples used in this study included nine chickpea genotypes (Cicer spp.) comprising of cultivated and wild species, six abiotic stress treatments (drought, salinity, high vapor pressure deficit, abscisic acid, cold and heat shock), and five diverse tissues (leaf, root, flower, seedlings and seed). The geNorm, NormFinder and RefFinder algorithms used to identify stably expressed genes in four sample sets revealed stable expression of UCP and G6PD genes across genotypes, while TIP41 and CAC were highly stable under abiotic stress conditions. While PP2A and ABCT genes were ranked as best for different tissues, ABCT, UCP and CAC were most stable across all samples. This study demonstrated the usefulness of new generation reference genes for more accurate qPCR based gene expression quantification in cultivated as well as wild chickpea species. Validation of the best reference genes was carried out by studying their impact on normalization of aquaporin genes PIP1;4 and TIP3;1, in three contrasting chickpea genotypes under high vapor pressure deficit (VPD) treatment. The chickpea TIP3;1 gene got significantly up regulated under high VPD conditions with higher relative expression in the drought susceptible genotype, confirming the suitability of the selected reference genes for expression analysis. This is the first comprehensive study on the stability of the new generation reference genes for qPCR studies in chickpea across species, different tissues and abiotic stresses.

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

PubMed

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

2009-12-01

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

Quaternion normalization in spacecraft attitude determination

NASA Technical Reports Server (NTRS)

Deutschmann, J.; Markley, F. L.; Bar-Itzhack, Itzhack Y.

1993-01-01

Attitude determination of spacecraft usually utilizes vector measurements such as Sun, center of Earth, star, and magnetic field direction to update the quaternion which determines the spacecraft orientation with respect to some reference coordinates in the three dimensional space. These measurements are usually processed by an extended Kalman filter (EKF) which yields an estimate of the attitude quaternion. Two EKF versions for quaternion estimation were presented in the literature; namely, the multiplicative EKF (MEKF) and the additive EKF (AEKF). In the multiplicative EKF, it is assumed that the error between the correct quaternion and its a-priori estimate is, by itself, a quaternion that represents the rotation necessary to bring the attitude which corresponds to the a-priori estimate of the quaternion into coincidence with the correct attitude. The EKF basically estimates this quotient quaternion and then the updated quaternion estimate is obtained by the product of the a-priori quaternion estimate and the estimate of the difference quaternion. In the additive EKF, it is assumed that the error between the a-priori quaternion estimate and the correct one is an algebraic difference between two four-tuple elements and thus the EKF is set to estimate this difference. The updated quaternion is then computed by adding the estimate of the difference to the a-priori quaternion estimate. If the quaternion estimate converges to the correct quaternion, then, naturally, the quaternion estimate has unity norm. This fact was utilized in the past to obtain superior filter performance by applying normalization to the filter measurement update of the quaternion. It was observed for the AEKF that when the attitude changed very slowly between measurements, normalization merely resulted in a faster convergence; however, when the attitude changed considerably between measurements, without filter tuning or normalization, the quaternion estimate diverged. However, when the

Assessment of reference gene stability in Rice stripe virus and Rice black streaked dwarf virus infection rice by quantitative Real-time PCR.

PubMed

Fang, Peng; Lu, Rongfei; Sun, Feng; Lan, Ying; Shen, Wenbiao; Du, Linlin; Zhou, Yijun; Zhou, Tong

2015-10-24

Stably expressed reference gene(s) normalization is important for the understanding of gene expression patterns by quantitative Real-time PCR (RT-qPCR), particularly for Rice stripe virus (RSV) and Rice black streaked dwarf virus (RBSDV) that caused seriously damage on rice plants in China and Southeast Asia. The expression of fourteen common used reference genes of Oryza sativa L. were evaluated by RT-qPCR in RSV and RBSDV infected rice plants. Suitable normalization reference gene(s) were identified by geNorm and NormFinder algorithms. UBQ 10 + GAPDH and UBC + Actin1 were identified as suitable reference genes for RT-qPCR normalization under RSV and RBSDV infection, respectively. When using multiple reference genes, the expression patterns of OsPRIb and OsWRKY, two virus resistance genes, were approximately similar with that reported previously. Comparatively, by using single reference gene (TIP41-Like), a weaker inducible response was observed. We proposed that the combination of two reference genes could obtain more accurate and reliable normalization of RT-qPCR results in RSV- and RBSDV-infected plants. This work therefore sheds light on establishing a standardized RT-qPCR procedure in RSV- and RBSDV-infected rice plants, and might serve as an important point for discovering complex regulatory networks and identifying genes relevant to biological processes or implicated in virus.

Quantitative real-time PCR normalization for gene expression studies in the plant pathogenic fungi Lasiodiplodia theobromae.

PubMed

Paolinelli-Alfonso, Marcos; Galindo-Sánchez, Clara Elizabeth; Hernandez-Martinez, Rufina

2016-08-01

Lasiodiplodia theobromae is a highly virulent plant pathogen. It has been suggested that heat stress increases its virulence. The aim of this work was to evaluate, compare, and recommend normalization strategies for gene expression analysis of the fungus growing with grapevine wood under heat stress. Using RT-qPCR-derived data, reference gene stability was evaluated through geNorm, NormFinder and Bestkeeper applications. Based on the geometric mean using the ranking position obtained for each independent analysis, genes were ranked from least to most stable as follows: glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), β-tubulin (TUB) and elongation factor-1α (EF1α). Using RNAseq-derived data based on the calculated tagwise dispersion these genes were ordered by increasing stability as follows: GAPDH, ACT, TUB, and EF1α. The correlation between RNAseq and RTqPCR results was used as criteria to identify the best RT-qPCR normalization approach. The gene TUB is recommended as the best option for normalization among the commonly used reference genes, but alternative fungal reference genes are also suggested. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluation of reference gene suitability for quantitative expression analysis by quantitative polymerase chain reaction in the mandibular condyle of sheep.

PubMed

Jiang, Xin; Xue, Yang; Zhou, Hongzhi; Li, Shouhong; Zhang, Zongmin; Hou, Rui; Ding, Yuxiang; Hu, Kaijin

2015-10-01

Reference genes are commonly used as a reliable approach to normalize the results of quantitative polymerase chain reaction (qPCR), and to reduce errors in the relative quantification of gene expression. Suitable reference genes belonging to numerous functional classes have been identified for various types of species and tissue. However, little is currently known regarding the most suitable reference genes for bone, specifically for the sheep mandibular condyle. Sheep are important for the study of human bone diseases, particularly for temporomandibular diseases. The present study aimed to identify a set of reference genes suitable for the normalization of qPCR data from the mandibular condyle of sheep. A total of 12 reference genes belonging to various functional classes were selected, and the expression stability of the reference genes was determined in both the normal and fractured area of the sheep mandibular condyle. RefFinder, which integrates the following currently available computational algorithms: geNorm, NormFinder, BestKeeper, and the comparative ΔCt method, was used to compare and rank the candidate reference genes. The results obtained from the four methods demonstrated a similar trend: RPL19, ACTB, and PGK1 were the most stably expressed reference genes in the sheep mandibular condyle. As determined by RefFinder comprehensive analysis, the results of the present study suggested that RPL19 is the most suitable reference gene for studies associated with the sheep mandibular condyle. In addition, ACTB and PGK1 may be considered suitable alternatives.

Analysis of the first laser echoes obtained on the reflector of Luna 21

NASA Technical Reports Server (NTRS)

Abalakin, V. K.; Calame, O.; Orszag, A.; Kokurin, Iu. L.; Mulholland, J. D.; Silverberg, E. C.

1973-01-01

The international program of lunar telemetry, which has been in operation for three and one-half years, is intended to supply basic information for study of the lunar motion and the internal physics of the moon and the earth, particularly with reference to movement of the pole and displacements of plates. Laser echoes were obtained on Jan. 23, 1973 from the French reflector placed on the moon by Luna 21. Two series of firings, made with a 3-J laser radiated by the 2.7-m telescope of the McDonald Observatory (Texas) made it possible to identify significant echoes of an intensity comparable to those obtained with the reflector set down by Apollo 15. The path time measurements are compatible with normal coordinates.

Number of blastocysts biopsied as a predictive indicator to obtain at least one normal/balanced embryo following preimplantation genetic diagnosis with single nucleotide polymorphism microarray in translocation cases.

PubMed

Wang, Yi-Zi; Ding, Chen-Hui; Wang, Jing; Zeng, Yan-Hong; Zhou, Wen; Li, Rong; Zhou, Can-Quan; Deng, Ming-Fen; Xu, Yan-Wen

2017-01-01

The aim of this study is to investigate the minimum number of blastocysts for biopsy to increase the likelihood of obtaining at least one normal/balanced embryo in preimplantation genetic diagnosis (PGD) for translocation carriers. This blinded retrospective study included 55 PGD cycles for Robertsonian translocation (RT) and 181 cycles for reciprocal translocation (rcp) to indicate when only one of the couples carried a translocation. Single-nucleotide polymorphism microarray after trophectoderm biopsy was performed. Reliable results were obtained for 355/379 (93.7 %) biopsied blastocysts in RT group and 986/1053 (93.6 %) in rcp group. Mean numbers of biopsied embryos per patient, normal/balanced embryos per patient, and mean normal/balanced embryo rate per patient were 7.4, 3.1, and 40.7 % in RT group and 8.0, 2.1, and 27.3 %, respectively, in rcp group. In a regression model, three factors significantly affected the number of genetically transferrable embryos: number of biopsied embryos (P = 0.001), basal FSH level (P = 0.040), and maternal age (P = 0.027). ROC analysis with a cutoff of 1.5 was calculated for the number of biopsied embryos required to obtain at least one normal/balanced embryo for RT carriers. For rcp carriers, the cutoff was 3.5. The clinical pregnancy rate per embryo transfer was 44.2 and 42.6 % in RT and rcp groups (P = 0.836). The minimum numbers of blastocysts to obtain at least one normal/balanced embryo for RT and rcp were 2 and 4 under the conditions of female age < 37 years with a basal FSH level < 11.4 IU/L.

Normal limits of pediatric Frank lead electrocardiograms. Differences in data obtained in 4th or 5th intercostal spaces.

PubMed

Robert, A; Derwael-Barchy, C; Fesler, R; Brasseur, L A; Brohet, C R

1984-01-01

Frank lead electrocardiograms (VCGs) were recorded from 970 young subjects in order to establish normal limits for pediatric VCGs. In 245 children and 231 adolescents, the thoracic electrodes were located at the levels of the 4th and of the 5th intercostal space with subjects in supine position. Pairwise comparisons of 211 linear and angular parameters were made, using the 4th interspace as the reference. In children, there were 155 parameters with statistically significant differences and 56 parameters without significant differences between levels 4 and 5. In adolescents, corresponding figures were 158 parameters with significant differences and 53 without. Results for selected measurements showed an increase of the amplitude of Q and R waves in leads X and Y, a decrease of Q and R waves in lead Z and an increase of maximal spatial and planar QRS vectors, with the QRS loop being more anteriorly oriented by shifting the electrodes from level 4 to level 5. The mean differences in amplitude and orientation were generally small and of little practical value. However, the percentile distribution of the differences indicated that substantial changes in either direction can occur in some subjects. Thus, quantitative analysis of the pediatric Frank VCGs can be critically affected by modification of electrode placement. It is suggested that normal limits should be determined for each recording level and that criteria for analysis should be applied only to VCGs recorded at the same specified level.

Normal probabilities for Vandenberg AFB wind components - monthly reference periods for all flight azimuths, 0- to 70-km altitudes

NASA Technical Reports Server (NTRS)

Falls, L. W.

1975-01-01

Vandenberg Air Force Base (AFB), California, wind component statistics are presented to be used for aerospace engineering applications that require component wind probabilities for various flight azimuths and selected altitudes. The normal (Gaussian) distribution is presented as a statistical model to represent component winds at Vandenberg AFB. Head tail, and crosswind components are tabulated for all flight azimuths for altitudes from 0 to 70 km by monthly reference periods. Wind components are given for 11 selected percentiles ranging from 0.135 percent to 99.865 percent for each month. The results of statistical goodness-of-fit tests are presented to verify the use of the Gaussian distribution as an adequate model to represent component winds at Vandenberg AFB.

Normal probabilities for Cape Kennedy wind components: Monthly reference periods for all flight azimuths. Altitudes 0 to 70 kilometers

NASA Technical Reports Server (NTRS)

Falls, L. W.

1973-01-01

This document replaces Cape Kennedy empirical wind component statistics which are presently being used for aerospace engineering applications that require component wind probabilities for various flight azimuths and selected altitudes. The normal (Gaussian) distribution is presented as an adequate statistical model to represent component winds at Cape Kennedy. Head-, tail-, and crosswind components are tabulated for all flight azimuths for altitudes from 0 to 70 km by monthly reference periods. Wind components are given for 11 selected percentiles ranging from 0.135 percent to 99,865 percent for each month. Results of statistical goodness-of-fit tests are presented to verify the use of the Gaussian distribution as an adequate model to represent component winds at Cape Kennedy, Florida.

Spike-In Normalization of ChIP Data Using DNA-DIG-Antibody Complex.

PubMed

Eberle, Andrea B

2018-01-01

Chromatin immunoprecipitation (ChIP) is a widely used method to determine the occupancy of specific proteins within the genome, helping to unravel the function and activity of specific genomic regions. In ChIP experiments, normalization of the obtained data by a suitable internal reference is crucial. However, particularly when comparing differently treated samples, such a reference is difficult to identify. Here, a simple method to improve the accuracy and reliability of ChIP experiments by the help of an external reference is described. An artificial molecule, composed of a well-defined digoxigenin (DIG) labeled DNA fragment in complex with an anti-DIG antibody, is synthesized and added to each chromatin sample before immunoprecipitation. During the ChIP procedure, the DNA-DIG-antibody complex undergoes the same treatments as the chromatin and is therefore purified and quantified together with the chromatin of interest. This external reference compensates for variability during the ChIP routine and improves the similarity between replicates, thereby emphasizing the biological differences between samples.

Complete blood count reference values of cord blood in Taiwan and the influence of gender and delivery route on them.

PubMed

Chang, Yu-Hsun; Yang, Shang-Hsien; Wang, Tso-Fu; Lin, Teng-Yi; Yang, Kuo-Liang; Chen, Shu-Huey

2011-06-01

Cord blood banking has become more popular in recent years. Checking cord blood complete blood count (CBC) and white blood cell (WBC) differential counts (DCs) is essential before cryopreserving the cord blood units. Therefore, establishing the normal reference values of cord blood CBC and WBC DC is important in clinical practice and research. To obtain a large-scale population-based normal CBC and WBC DC reference values of healthy neonates' cord blood from a public cord blood bank and to investigate the influence of the gender and delivery route. From September 2001 to November 2006, the cord blood of healthy Taiwanese neonates with gestational age 36 weeks and more were collected by Tzu Chi Cord Blood Bank with written informed consents. All cord blood samples were analyzed by Sysmex XE2100 automated hematology analyzer (Sysmex Corporation, Kobe, Japan) to obtain the CBC. The WBC DC was calculated by manual method. We used Student's t test and Mann-Whitney U test for investigating the influences of gender and delivery route on the CBC and WBC DC reference values. The results were presented by mean±standard deviation or 2.5-97.5th percentiles. In the study period, totally 5602 cord blood samples were collected eligibly for analysis. The cord blood CBC and WBC DC normal reference values were calculated. The female neonates had significantly higher mean corpuscular volume, platelet count, and WBC count, but lower red blood cell (RBC) count, hemoglobin (Hb), hematocrit, and mean corpuscular Hb concentration values (p<0.001). Newborns through vaginal delivery had significantly higher RBC count, Hb, hematocrit, platelet count, and WBC count (p<0.001). The percentages of some different types WBC were significantly influenced by gender and delivery routes. Male babies had higher lymphocyte, monocyte, eosinophil, basophil, and nucleated RBC ratios than the female neonates. Newborns through cesarean section had significantly lower neutrophil, monocyte, and nucleated RBC

Azimuthal Signature of Coincidental Brightness Temperature and Normalized Radar Cross-Section Obtained Using Airborne PALS Instrument

NASA Technical Reports Server (NTRS)

Colliander, Andreas; Kim, Seungbum; Yueh, Simon; Cosh, Mike; Jackson, Tom; Njoku, Eni

2010-01-01

Coincidental airborne brightness temperature (TB) and normalized radar-cross section (NRCS) measurements were carried out with the PALS (Passive and Active L- and S-band) instrument in the SMAPVEX08 (SMAP Validation Experiment 2008) field campaign. This paper describes results obtained from a set of flights which measured a field in 45(sup o) steps over the azimuth angle. The field contained mature soy beans with distinct row structure. The measurement shows that both TB and NRCS experience modulation effects over the azimuth as expected based on the theory. The result is useful in development and validation of land surface parameter forward models and retrieval algorithms, such as the soil moisture algorithm for NASA's SMAP (Soil Moisture Active and Passive) mission. Although the footprint of the SMAP will not be sensitive to the small resolution scale effects as the one presented in this paper, it is nevertheless important to understand the effects at smaller scale.

Diffusion-weighted MR imaging of upper abdominal organs at different time points: Apparent diffusion coefficient normalization using a reference organ.

PubMed

Song, Ji Soo; Kwak, Hyo Sung; Byon, Jung Hee; Jin, Gong Yong

2017-05-01

To compare the apparent diffusion coefficient (ADC) of upper abdominal organs acquired at different time points, and to investigate the usefulness of normalization. We retrospectively evaluated 58 patients who underwent three rounds of magnetic resonance (MR) imaging including diffusion-weighted imaging of the upper abdomen. MR examinations were performed using three different 3.0 Tesla (T) and one 1.5T systems, with variable b value combinations and respiratory motion compensation techniques. The ADC values of the upper abdominal organs from three different time points were analyzed, using the ADC values of the paraspinal muscle (ADC psm ) and spleen (ADC spleen ) for normalization. Intraclass correlation coefficients (ICC) and comparison of dependent ICCs were used for statistical analysis. The ICCs of the original ADC and ADC psm showed fair to substantial agreement, while ADC spleen showed substantial to almost perfect agreement. The ICC of ADC spleen of all anatomical regions showed less variability compared with that of the original ADC (P < 0.005). Normalized ADC using the spleen as a reference organ significantly decreased variability in measurement of the upper abdominal organs in different MR systems at different time points and could be regarded as an imaging biomarker for future multicenter, longitudinal studies. 5 J. MAGN. RESON. IMAGING 2017;45:1494-1501. © 2016 International Society for Magnetic Resonance in Medicine.

Localized Energy-Based Normalization of Medical Images: Application to Chest Radiography.

PubMed

Philipsen, R H H M; Maduskar, P; Hogeweg, L; Melendez, J; Sánchez, C I; van Ginneken, B

2015-09-01

Automated quantitative analysis systems for medical images often lack the capability to successfully process images from multiple sources. Normalization of such images prior to further analysis is a possible solution to this limitation. This work presents a general method to normalize medical images and thoroughly investigates its effectiveness for chest radiography (CXR). The method starts with an energy decomposition of the image in different bands. Next, each band's localized energy is scaled to a reference value and the image is reconstructed. We investigate iterative and local application of this technique. The normalization is applied iteratively to the lung fields on six datasets from different sources, each comprising 50 normal CXRs and 50 abnormal CXRs. The method is evaluated in three supervised computer-aided detection tasks related to CXR analysis and compared to two reference normalization methods. In the first task, automatic lung segmentation, the average Jaccard overlap significantly increased from 0.72±0.30 and 0.87±0.11 for both reference methods to with normalization. The second experiment was aimed at segmentation of the clavicles. The reference methods had an average Jaccard index of 0.57±0.26 and 0.53±0.26; with normalization this significantly increased to . The third experiment was detection of tuberculosis related abnormalities in the lung fields. The average area under the Receiver Operating Curve increased significantly from 0.72±0.14 and 0.79±0.06 using the reference methods to with normalization. We conclude that the normalization can be successfully applied in chest radiography and makes supervised systems more generally applicable to data from different sources.

Reference gene validation for RT-qPCR, a note on different available software packages.

PubMed

De Spiegelaere, Ward; Dern-Wieloch, Jutta; Weigel, Roswitha; Schumacher, Valérie; Schorle, Hubert; Nettersheim, Daniel; Bergmann, Martin; Brehm, Ralph; Kliesch, Sabine; Vandekerckhove, Linos; Fink, Cornelia

2015-01-01

An appropriate normalization strategy is crucial for data analysis from real time reverse transcription polymerase chain reactions (RT-qPCR). It is widely supported to identify and validate stable reference genes, since no single biological gene is stably expressed between cell types or within cells under different conditions. Different algorithms exist to validate optimal reference genes for normalization. Applying human cells, we here compare the three main methods to the online available RefFinder tool that integrates these algorithms along with R-based software packages which include the NormFinder and GeNorm algorithms. 14 candidate reference genes were assessed by RT-qPCR in two sample sets, i.e. a set of samples of human testicular tissue containing carcinoma in situ (CIS), and a set of samples from the human adult Sertoli cell line (FS1) either cultured alone or in co-culture with the seminoma like cell line (TCam-2) or with equine bone marrow derived mesenchymal stem cells (eBM-MSC). Expression stabilities of the reference genes were evaluated using geNorm, NormFinder, and BestKeeper. Similar results were obtained by the three approaches for the most and least stably expressed genes. The R-based packages NormqPCR, SLqPCR and the NormFinder for R script gave identical gene rankings. Interestingly, different outputs were obtained between the original software packages and the RefFinder tool, which is based on raw Cq values for input. When the raw data were reanalysed assuming 100% efficiency for all genes, then the outputs of the original software packages were similar to the RefFinder software, indicating that RefFinder outputs may be biased because PCR efficiencies are not taken into account. This report shows that assay efficiency is an important parameter for reference gene validation. New software tools that incorporate these algorithms should be carefully validated prior to use.

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

PubMed

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

2017-01-01

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

SENIORLAB: a prospective observational study investigating laboratory parameters and their reference intervals in the elderly.

PubMed

Risch, Martin; Nydegger, Urs; Risch, Lorenz

2017-01-01

considered representative for seniors in a status of age-specific normal health. In addition to the established methods for determining reference intervals, this longitudinal study utilizes a unique approach, in that survival and long-term well-being are taken as indicators of health in seniors. This approach is expected to provide robust and representative reference intervals that are obtained from an adequate reference population and not a collective of highly selected individuals. The present study was registered under International Standard Randomized Controlled Trial Number registry: ISRCTN53778569.

Normal reference intervals and the effects of time and feeding on serum bile acid concentrations in llamas.

PubMed

Andreasen, C B; Pearson, E G; Smith, B B; Gerros, T C; Lassen, E D

1998-04-01

Fifty clinically healthy llamas, 0.5-13 years of age (22 intact males, 10 neutered males, 18 females), with no biochemical evidence of liver disease or hematologic abnormalities, were selected to establish serum bile acid reference intervals. Serum samples submitted to the clinical pathology laboratory were analyzed using a colorimetric enzymatic assay to establish bile acid reference intervals. A nonparametric distribution of llama bile acid concentrations was 1-23 micromol/liter for llamas >1 year of age and 10-44 micromol/liter for llamas < or = 1 year of age. A significant difference was found between these 2 age groups. No correlation was detected between gender and bile acid concentrations. The reference intervals were 1.1-22.9 micromol/liter for llamas >1 year of age and 1.8-49.8 micromol/liter for llamas < or = 1 year of age. Additionally, a separate group of 10 healthy adult llamas (5 males, 5 females, 5-11 years of age) without biochemical or hematologic abnormalities was selected to assess the effects of feeding and time intervals on serum bile acid concentrations. These 10 llamas were provided fresh water and hay ad libitum, and serum samples were obtained via an indwelling jugular catheter hourly for 11 hours. Llamas were then kept from food overnight (12 hours), and subsequent samples were taken prior to feeding (fasting baseline time, 23 hours after trial initiation) and postprandially at 0.5, 1, 2, 4, and 8 hours. In feeding trials, there was no consistent interaction between bile acid concentrations and time, feeding, or 12-hour fasting. Prior feeding or time of day did not result in serum bile acid concentrations outside the reference interval, but concentrations from individual llamas varied within this interval over time.

Nonparametric spirometry reference values for Hispanic Americans.

PubMed

Glenn, Nancy L; Brown, Vanessa M

2011-02-01

Recent literature sites ethnic origin as a major factor in developing pulmonary function reference values. Extensive studies established reference values for European and African Americans, but not for Hispanic Americans. The Third National Health and Nutrition Examination Survey defines Hispanic as individuals of Spanish speaking cultures. While no group was excluded from the target population, sample size requirements only allowed inclusion of individuals who identified themselves as Mexican Americans. This research constructs nonparametric reference value confidence intervals for Hispanic American pulmonary function. The method is applicable to all ethnicities. We use empirical likelihood confidence intervals to establish normal ranges for reference values. Its major advantage: it is model free, but shares asymptotic properties of model based methods. Statistical comparisons indicate that empirical likelihood interval lengths are comparable to normal theory intervals. Power and efficiency studies agree with previously published theoretical results.

Reference values for leptin and adiponectin in children below the age of 10 based on the IDEFICS cohort.

PubMed

Erhardt, E; Foraita, R; Pigeot, I; Barba, G; Veidebaum, T; Tornaritis, M; Michels, N; Eiben, G; Ahrens, W; Moreno, L A; Kovács, E; Molnár, D

2014-09-01

To establish age- and sex-specific reference values for serum leptin and adiponectin in normal-weight 3.0-8.9-year old European children. Blood samples for hormone analysis were taken from 1338 children of the IDEFICS (Identification and prevention of Dietary- and lifestyle-induced health Effects in Children and infantS) study cohort. Only normal-weight children aged 3.0-8.9 years were included (n=539) in our analysis. Using the General Additive Model for Location Scale and Shape, age- and sex-specific percentiles were derived. The influence of under/overweight and obesity on the proposed reference curves based on normal-weight children was investigated in several sensitivity analyses using the sample without obese children (n=1015) and the whole study sample (n=1338). There was a negative age trend of adiponectin blood levels and a positive trend of leptin levels in boys and girls. Percentiles derived for girls were generally higher than those obtained for boys. The corresponding age-specific differences of the 97th percentile ranged from -2.2 to 4.6 μg ml(-1) and from 2.2 to 4.8 ng ml(-1) for adiponectin and leptin, respectively. According to our knowledge, these are the first reference values of leptin and adiponectin in prepubertal, normal-weight children. The presented adiponectin and leptin reference curves may allow for a more differentiated interpretation of children's hormone levels in epidemiological and clinical studies.

Bacterial reference genes for gene expression studies by RT-qPCR: survey and analysis.

PubMed

Rocha, Danilo J P; Santos, Carolina S; Pacheco, Luis G C

2015-09-01

The appropriate choice of reference genes is essential for accurate normalization of gene expression data obtained by the method of reverse transcription quantitative real-time PCR (RT-qPCR). In 2009, a guideline called the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) highlighted the importance of the selection and validation of more than one suitable reference gene for obtaining reliable RT-qPCR results. Herein, we searched the recent literature in order to identify the bacterial reference genes that have been most commonly validated in gene expression studies by RT-qPCR (in the first 5 years following publication of the MIQE guidelines). Through a combination of different search parameters with the text mining tool MedlineRanker, we identified 145 unique bacterial genes that were recently tested as candidate reference genes. Of these, 45 genes were experimentally validated and, in most of the cases, their expression stabilities were verified using the software tools geNorm and NormFinder. It is noteworthy that only 10 of these reference genes had been validated in two or more of the studies evaluated. An enrichment analysis using Gene Ontology classifications demonstrated that genes belonging to the functional categories of DNA Replication (GO: 0006260) and Transcription (GO: 0006351) rendered a proportionally higher number of validated reference genes. Three genes in the former functional class were also among the top five most stable genes identified through an analysis of gene expression data obtained from the Pathosystems Resource Integration Center. These results may provide a guideline for the initial selection of candidate reference genes for RT-qPCR studies in several different bacterial species.

Stability evaluation of reference genes for gene expression analysis by RT-qPCR in soybean under different conditions.

PubMed

Wan, Qiao; Chen, Shuilian; Shan, Zhihui; Yang, Zhonglu; Chen, Limiao; Zhang, Chanjuan; Yuan, Songli; Hao, Qinnan; Zhang, Xiaojuan; Qiu, Dezhen; Chen, Haifeng; Zhou, Xinan

2017-01-01

Real-time quantitative reverse transcription PCR is a sensitive and widely used technique to quantify gene expression. To achieve a reliable result, appropriate reference genes are highly required for normalization of transcripts in different samples. In this study, 9 previously published reference genes (60S, Fbox, ELF1A, ELF1B, ACT11, TUA5, UBC4, G6PD, CYP2) of soybean [Glycine max (L.) Merr.] were selected. The expression stability of the 9 genes was evaluated under conditions of biotic stress caused by infection with soybean mosaic virus, nitrogen stress, across different cultivars and developmental stages. ΔCt and geNorm algorithms were used to evaluate and rank the expression stability of the 9 reference genes. Results obtained from two algorithms showed high consistency. Moreover, results of pairwise variation showed that two reference genes were sufficient to normalize the expression levels of target genes under each experimental setting. For virus infection, ELF1A and ELF1B were the most stable reference genes for accurate normalization. For different developmental stages, Fbox and G6PD had the highest expression stability between two soybean cultivars (Tanlong No. 1 and Tanlong No. 2). ELF1B and ACT11 were identified as the most stably expressed reference genes both under nitrogen stress and among different cultivars. The results showed that none of the candidate reference genes were uniformly expressed at different conditions, and selecting appropriate reference genes was pivotal for gene expression studies with particular condition and tissue. The most stable combination of genes identified in this study will help to achieve more accurate and reliable results in a wide variety of samples in soybean.

Selection and Validation of Appropriate Reference Genes for qRT-PCR Analysis in Isatis indigotica Fort.

PubMed Central

Li, Tao; Wang, Jing; Lu, Miao; Zhang, Tianyi; Qu, Xinyun; Wang, Zhezhi

2017-01-01

Due to its sensitivity and specificity, real-time quantitative PCR (qRT-PCR) is a popular technique for investigating gene expression levels in plants. Based on the Minimum Information for Publication of Real-Time Quantitative PCR Experiments (MIQE) guidelines, it is necessary to select and validate putative appropriate reference genes for qRT-PCR normalization. In the current study, three algorithms, geNorm, NormFinder, and BestKeeper, were applied to assess the expression stability of 10 candidate reference genes across five different tissues and three different abiotic stresses in Isatis indigotica Fort. Additionally, the IiYUC6 gene associated with IAA biosynthesis was applied to validate the candidate reference genes. The analysis results of the geNorm, NormFinder, and BestKeeper algorithms indicated certain differences for the different sample sets and different experiment conditions. Considering all of the algorithms, PP2A-4 and TUB4 were recommended as the most stable reference genes for total and different tissue samples, respectively. Moreover, RPL15 and PP2A-4 were considered to be the most suitable reference genes for abiotic stress treatments. The obtained experimental results might contribute to improved accuracy and credibility for the expression levels of target genes by qRT-PCR normalization in I. indigotica. PMID:28702046

Reference gene selection for normalization of RT-qPCR gene expression data from Actinidia deliciosa leaves infected with Pseudomonas syringae pv. actinidiae

PubMed Central

Petriccione, Milena; Mastrobuoni, Francesco; Zampella, Luigi; Scortichini, Marco

2015-01-01

Normalization of data, by choosing the appropriate reference genes (RGs), is fundamental for obtaining reliable results in reverse transcription-quantitative PCR (RT-qPCR). In this study, we assessed Actinidia deliciosa leaves inoculated with two doses of Pseudomonas syringae pv. actinidiae during a period of 13 days for the expression profile of nine candidate RGs. Their expression stability was calculated using four algorithms: geNorm, NormFinder, BestKeeper and the deltaCt method. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and protein phosphatase 2A (PP2A) were the most stable genes, while β-tubulin and 7s-globulin were the less stable. Expression analysis of three target genes, chosen for RGs validation, encoding the reactive oxygen species scavenging enzymes ascorbate peroxidase (APX), superoxide dismutase (SOD) and catalase (CAT) indicated that a combination of stable RGs, such as GAPDH and PP2A, can lead to an accurate quantification of the expression levels of such target genes. The APX level varied during the experiment time course and according to the inoculum doses, whereas both SOD and CAT resulted down-regulated during the first four days, and up-regulated afterwards, irrespective of inoculum dose. These results can be useful for better elucidating the molecular interaction in the A. deliciosa/P. s. pv. actinidiae pathosystem and for RGs selection in bacteria-plant pathosystems. PMID:26581656

Selection of reference genes for quantitative real-time PCR normalization in Panax ginseng at different stages of growth and in different organs.

PubMed

Liu, Jing; Wang, Qun; Sun, Minying; Zhu, Linlin; Yang, Michael; Zhao, Yu

2014-01-01

Quantitative real-time reverse transcription PCR (qRT-PCR) has become a widely used method for gene expression analysis; however, its data interpretation largely depends on the stability of reference genes. The transcriptomics of Panax ginseng, one of the most popular and traditional ingredients used in Chinese medicines, is increasingly being studied. Furthermore, it is vital to establish a series of reliable reference genes when qRT-PCR is used to assess the gene expression profile of ginseng. In this study, we screened out candidate reference genes for ginseng using gene expression data generated by a high-throughput sequencing platform. Based on the statistical tests, 20 reference genes (10 traditional housekeeping genes and 10 novel genes) were selected. These genes were tested for the normalization of expression levels in five growth stages and three distinct plant organs of ginseng by qPCR. These genes were subsequently ranked and compared according to the stability of their expressions using geNorm, NormFinder, and BestKeeper computational programs. Although the best reference genes were found to vary across different samples, CYP and EF-1α were the most stable genes amongst all samples. GAPDH/30S RPS20, CYP/60S RPL13 and CYP/QCR were the optimum pair of reference genes in the roots, stems, and leaves. CYP/60S RPL13, CYP/eIF-5A, aTUB/V-ATP, eIF-5A/SAR1, and aTUB/pol IIa were the most stably expressed combinations in each of the five developmental stages. Our study serves as a foundation for developing an accurate method of qRT-PCR and will benefit future studies on gene expression profiles of Panax Ginseng.

Is It Time to Change Our Reference Curve for Femur Length? Using the Z-Score to Select the Best Chart in a Chinese Population

PubMed Central

Yang, Huixia; Wei, Yumei; Su, Rina; Wang, Chen; Meng, Wenying; Wang, Yongqing; Shang, Lixin; Cai, Zhenyu; Ji, Liping; Wang, Yunfeng; Sun, Ying; Liu, Jiaxiu; Wei, Li; Sun, Yufeng; Zhang, Xueying; Luo, Tianxia; Chen, Haixia; Yu, Lijun

2016-01-01

Objective To use Z-scores to compare different charts of femur length (FL) applied to our population with the aim of identifying the most appropriate chart. Methods A retrospective study was conducted in Beijing. Fifteen hospitals in Beijing were chosen as clusters using a systemic cluster sampling method, in which 15,194 pregnant women delivered from June 20th to November 30th, 2013. The measurements of FL in the second and third trimester were recorded, as well as the last measurement obtained before delivery. Based on the inclusion and exclusion criteria, we identified FL measurements from 19996 ultrasounds from 7194 patients between 11 and 42 weeks gestation. The FL data were then transformed into Z-scores that were calculated using three series of reference equations obtained from three reports: Leung TN, Pang MW et al (2008); Chitty LS, Altman DG et al (1994); and Papageorghiou AT et al (2014). Each Z-score distribution was presented as the mean and standard deviation (SD). Skewness and kurtosis and were compared with the standard normal distribution using the Kolmogorov-Smirnov test. The histogram of their distributions was superimposed on the non-skewed standard normal curve (mean = 0, SD = 1) to provide a direct visual impression. Finally, the sensitivity and specificity of each reference chart for identifying fetuses <5th or >95th percentile (based on the observed distribution of Z-scores) were calculated. The Youden index was also listed. A scatter diagram with the 5th, 50th, and 95th percentile curves calculated from and superimposed on each reference chart was presented to provide a visual impression. Results The three Z-score distribution curves appeared to be normal, but none of them matched the expected standard normal distribution. In our study, the Papageorghiou reference curve provided the best results, with a sensitivity of 100% for identifying fetuses with measurements < 5th and > 95th percentile, and specificities of 99.9% and 81

14 CFR 23.73 - Reference landing approach speed.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Reference landing approach speed. 23.73... Reference landing approach speed. (a) For normal, utility, and acrobatic category reciprocating engine-powered airplanes of 6,000 pounds or less maximum weight, the reference landing approach speed, VREF, must...

14 CFR 23.73 - Reference landing approach speed.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 14 Aeronautics and Space 1 2011-01-01 2011-01-01 false Reference landing approach speed. 23.73... Reference landing approach speed. (a) For normal, utility, and acrobatic category reciprocating engine-powered airplanes of 6,000 pounds or less maximum weight, the reference landing approach speed, VREF, must...

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

PubMed

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

2011-03-01

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

Evaluation of reference genes for insect olfaction studies.

PubMed

Omondi, Bonaventure Aman; Latorre-Estivalis, Jose Manuel; Rocha Oliveira, Ivana Helena; Ignell, Rickard; Lorenzo, Marcelo Gustavo

2015-04-22

Quantitative reverse transcription PCR (qRT-PCR) is a robust and accessible method to assay gene expression and to infer gene regulation. Being a chain of procedures, this technique is subject to systematic error due to biological and technical limitations mainly set by the starting material and downstream procedures. Thus, rigorous data normalization is critical to grant reliability and repeatability of gene expression quantification by qRT-PCR. A number of 'housekeeping genes', involved in basic cellular functions, have been commonly used as internal controls for this normalization process. However, these genes could themselves be regulated and must therefore be tested a priori. We evaluated eight potential reference genes for their stability as internal controls for RT-qPCR studies of olfactory gene expression in the antennae of Rhodnius prolixus, a Chagas disease vector. The set of genes included were: α-tubulin; β-actin; Glyceraldehyde-3-phosphate dehydrogenase; Eukaryotic initiation factor 1A; Glutathione-S-transferase; Serine protease; Succinate dehydrogenase; and Glucose-6-phosphate dehydrogenase. Five experimental conditions, including changes in age,developmental stage and feeding status were tested in both sexes. We show that the evaluation of candidate reference genes is necessary for each combination of sex, tissue and physiological condition analyzed in order to avoid inconsistent results and conclusions. Although, Normfinder and geNorm software yielded different results between males and females, five genes (SDH, Tub, GAPDH, Act and G6PDH) appeared in the first positions in all rankings obtained. By using gene expression data of a single olfactory coreceptor gene as an example, we demonstrated the extent of changes expected using different internal standards. This work underlines the need for a rigorous selection of internal standards to grant the reliability of normalization processes in qRT-PCR studies. Furthermore, we show that particular

Identification of Reference Genes for Real-Time Quantitative PCR Experiments in the Liverwort Marchantia polymorpha

PubMed Central

Dolan, Liam; Langdale, Jane A.

2015-01-01

Real-time quantitative polymerase chain reaction (qPCR) has become widely used as a method to compare gene transcript levels across different conditions. However, selection of suitable reference genes to normalize qPCR data is required for accurate transcript level analysis. Recently, Marchantia polymorpha has been adopted as a model for the study of liverwort development and land plant evolution. Identification of appropriate reference genes has therefore become a necessity for gene expression studies. In this study, transcript levels of eleven candidate reference genes have been analyzed across a range of biological contexts that encompass abiotic stress, hormone treatment and different developmental stages. The consistency of transcript levels was assessed using both geNorm and NormFinder algorithms, and a consensus ranking of the different candidate genes was then obtained. MpAPT and MpACT showed relatively constant transcript levels across all conditions tested whereas the transcript levels of other candidate genes were clearly influenced by experimental conditions. By analyzing transcript levels of phosphate and nitrate starvation reporter genes, we confirmed that MpAPT and MpACT are suitable reference genes in M. polymorpha and also demonstrated that normalization with an inappropriate gene can lead to erroneous analysis of qPCR data. PMID:25798897

Comparison of ambulatory blood pressure reference standards in children evaluated for hypertension.

PubMed

Jones, Deborah P; Richey, Phyllis A; Alpert, Bruce S

2009-06-01

The purpose of this study was to systematically compare methods for standardization of blood pressure levels obtained by ambulatory blood pressure monitoring (ABPM) in a group of 111 children studied at our institution. Blood pressure indices, blood pressure loads and standard deviation scores were calculated using the original ABPM and the modified reference standards. Bland-Altman plots and kappa statistics for the level of agreement were generated. Overall, the agreement between the two methods was excellent; however, approximately 5% of children were classified differently by one as compared with the other method. Depending on which version of the German Working Group's reference standards is used for interpretation of ABPM data, the classification of the individual as having hypertension or normal blood pressure may vary.

Tissue Gene Expression Analysis Using Arrayed Normalized cDNA Libraries

PubMed Central

Eickhoff, Holger; Schuchhardt, Johannes; Ivanov, Igor; Meier-Ewert, Sebastian; O'Brien, John; Malik, Arif; Tandon, Neeraj; Wolski, Eryk-Witold; Rohlfs, Elke; Nyarsik, Lajos; Reinhardt, Richard; Nietfeld, Wilfried; Lehrach, Hans

2000-01-01

We have used oligonucleotide-fingerprinting data on 60,000 cDNA clones from two different mouse embryonic stages to establish a normalized cDNA clone set. The normalized set of 5,376 clones represents different clusters and therefore, in almost all cases, different genes. The inserts of the cDNA clones were amplified by PCR and spotted on glass slides. The resulting arrays were hybridized with mRNA probes prepared from six different adult mouse tissues. Expression profiles were analyzed by hierarchical clustering techniques. We have chosen radioactive detection because it combines robustness with sensitivity and allows the comparison of multiple normalized experiments. Sensitive detection combined with highly effective clustering algorithms allowed the identification of tissue-specific expression profiles and the detection of genes specifically expressed in the tissues investigated. The obtained results are publicly available (http://www.rzpd.de) and can be used by other researchers as a digital expression reference. [The sequence data described in this paper have been submitted to the EMBL data library under accession nos. AL360374–AL36537.] PMID:10958641

Selection and testing of reference genes for accurate RT-qPCR in rice seedlings under iron toxicity.

PubMed

Santos, Fabiane Igansi de Castro Dos; Marini, Naciele; Santos, Railson Schreinert Dos; Hoffman, Bianca Silva Fernandes; Alves-Ferreira, Marcio; de Oliveira, Antonio Costa

2018-01-01

Reverse Transcription quantitative PCR (RT-qPCR) is a technique for gene expression profiling with high sensibility and reproducibility. However, to obtain accurate results, it depends on data normalization by using endogenous reference genes whose expression is constitutive or invariable. Although the technique is widely used in plant stress analyzes, the stability of reference genes for iron toxicity in rice (Oryza sativa L.) has not been thoroughly investigated. Here, we tested a set of candidate reference genes for use in rice under this stressful condition. The test was performed using four distinct methods: NormFinder, BestKeeper, geNorm and the comparative ΔCt. To achieve reproducible and reliable results, Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines were followed. Valid reference genes were found for shoot (P2, OsGAPDH and OsNABP), root (OsEF-1a, P8 and OsGAPDH) and root+shoot (OsNABP, OsGAPDH and P8) enabling us to perform further reliable studies for iron toxicity in both indica and japonica subspecies. The importance of the study of other than the traditional endogenous genes for use as normalizers is also shown here.

Selection and testing of reference genes for accurate RT-qPCR in rice seedlings under iron toxicity

PubMed Central

dos Santos, Fabiane Igansi de Castro; Marini, Naciele; dos Santos, Railson Schreinert; Hoffman, Bianca Silva Fernandes; Alves-Ferreira, Marcio

2018-01-01

Reverse Transcription quantitative PCR (RT-qPCR) is a technique for gene expression profiling with high sensibility and reproducibility. However, to obtain accurate results, it depends on data normalization by using endogenous reference genes whose expression is constitutive or invariable. Although the technique is widely used in plant stress analyzes, the stability of reference genes for iron toxicity in rice (Oryza sativa L.) has not been thoroughly investigated. Here, we tested a set of candidate reference genes for use in rice under this stressful condition. The test was performed using four distinct methods: NormFinder, BestKeeper, geNorm and the comparative ΔCt. To achieve reproducible and reliable results, Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines were followed. Valid reference genes were found for shoot (P2, OsGAPDH and OsNABP), root (OsEF-1a, P8 and OsGAPDH) and root+shoot (OsNABP, OsGAPDH and P8) enabling us to perform further reliable studies for iron toxicity in both indica and japonica subspecies. The importance of the study of other than the traditional endogenous genes for use as normalizers is also shown here. PMID:29494624

Normal ranges of fetal nasal bone length during the second trimester in an Iranian population.

PubMed

Rahimi-Sharbaf, Fatemeh; Tahmasebpour, Ahmad-Reza; Pirjani, Reihaneh; Ghaffari, Saeed Reza; Rahimi-Foroushani, Abbas

2011-04-01

To provide a normal reference range for nasal bone length (NBL) during the second trimester of pregnancy in an Iranian population. This cross-sectional study was performed on 3201 fetuses at 15 to 28 weeks of gestational age (GA). Both singleton and twin fetuses were evaluated. The relationship between NBL and GA was determined and percentile values for each gestational week were provided. NBL measurement was obtained in 98% of singleton and 96% of twin fetuses. There was a linear relationship between GA and NBL both in singleton (R(2) = 0.62) and in twin (R(2) = 0.74) fetuses. There was no significant difference between twins regarding NBL (p = 0.18). We have provided the normal reference range for NBL during the second trimester in an Iranian population. NBL in singleton and twin fetuses is similar and there is no significant difference between twins regarding NBL. Copyright © 2011 John Wiley & Sons, Ltd.

Normal Values of Tissue-Muscle Perfusion Indexes of Lower Limbs Obtained with a Scintigraphic Method.

PubMed

Manevska, Nevena; Stojanoski, Sinisa; Pop Gjorceva, Daniela; Todorovska, Lidija; Miladinova, Daniela; Zafirova, Beti

2017-09-01

Introduction Muscle perfusion is a physiologic process that can undergo quantitative assessment and thus define the range of normal values of perfusion indexes and perfusion reserve. The investigation of the microcirculation has a crucial role in determining the muscle perfusion. Materials and method The study included 30 examinees, 24-74 years of age, without a history of confirmed peripheral artery disease and all had normal findings on Doppler ultrasonography and pedo-brachial index of lower extremity (PBI). 99mTc-MIBI tissue muscle perfusion scintigraphy of lower limbs evaluates tissue perfusion in resting condition "rest study" and after workload "stress study", through quantitative parameters: Inter-extremity index (for both studies), left thigh/right thigh (LT/RT) left calf/right calf (LC/RC) and perfusion reserve (PR) for both thighs and calves. Results In our investigated group we assessed the normal values of quantitative parameters of perfusion indexes. Indexes ranged for LT/RT in rest study 0.91-1.05, in stress study 0.92-1.04. LC/RC in rest 0.93-1.07 and in stress study 0.93-1.09. The examinees older than 50 years had insignificantly lower perfusion reserve of these parameters compared with those younger than 50, LC (p=0.98), and RC (p=0.6). Conclusion This non-invasive scintigraphic method allows in individuals without peripheral artery disease to determine the range of normal values of muscle perfusion at rest and stress condition and to clinically implement them in evaluation of patients with peripheral artery disease for differentiating patients with normal from those with impaired lower limbs circulation.

Angle Kappa Measurements: Normal Values in Healthy Iranian Population Obtained With the Orbscan II

PubMed Central

Gharaee, Hamid; Shafiee, Masoud; Hoseini, Rafie; Abrishami, Mojtaba; Abrishami, Yalda; Abrishami, Mostafa

2014-01-01

Background: The angle kappa is important in proper centration of corneal ablation in keratorefractive surgery. Orbscan II device is widely used preoperatively in photoablation surgeries and can be used to measure the angle kappa. Objectives: This study aimed to determine the mean angle kappa and its intercepts in healthy young Iranian adults. Patients and Methods: In this cross-sectional study, orthotropic patients (age range, 18-35 years) who were referred to the Khatam Eye Hospital (Mashhad, Iran) were included. Exclusion criteria were as follows: history of any eye deviation or strabismus with or without orthoptic or surgical treatment; any intraocular, corneal, or keratorefractive surgery; contact lens use; any corneal anomaly; any ophthalmic or systemic drug consumption; and hyperopic spherical refraction > + 3.00 diopters (D), spherical refraction > -5.00 D, or cylindrical refraction > 2.00 D. All of the parameters were measured by the same operator through an Orbscan II device. Results: A total of 977 healthy participants who aged 18 to 45 years were included consecutively. The study population consisted of 614 females and 363 males. The average angle kappa was 5.00º ± 1.36º at 240.21º ± 97.17º in males and 4.97º ± 1.30º at 244.22º ± 94.39º in females (P = 0.63). The average horizontal (x-axis) angle kappa was -0.02º ± 0.49º, with a mean of -0.02º ± 0.50º in males and -0.02º ± 0.49º in females (P = 0.93). The average vertical (y-axis) angle kappa was -0.09º ± 0.32º, with a mean of -0.09º ± 0.33º in males and -0.09º ± 0.32º in females (P = 0.74). Conclusions: By using the normal angle kappa determined in this study, pseudodeviations can be identified more precisely in those who might undergo keratorefractive surgery. PMID:25763261

Derivation of gender and age-specific reference intervals from fully normal Japanese individuals and the implications for health screening.

PubMed

Yamakado, Minoru; Ichihara, Kiyoshi; Matsumoto, Yoshiyuki; Ishikawa, Yoshiki; Kato, Kiminori; Komatsubara, Yusuke; Takaya, Norihide; Tomita, Shohken; Kawano, Reo; Takada, Keisuke; Watanabe, Kiyoaki

2015-07-20

With nationwide standardization of laboratory tests among institutions for health screening in Japan, common reference intervals (RIs) were derived from records of 1,500,000 health check attendees. Targets were 20 basic laboratory tests including body mass index (BMI) and systolic and diastolic blood pressures (SBP, DBP). Individuals fulfilling the following strict criteria were chosen: SBP<130, DBP<85mmHg, BMI<25kg/m(2), non-smoking, ethanol consumption<20g/day and under no mediation with no remarkable current/past illnesses. The latent abnormal values exclusion (LAVE) method was applied to ensure fully normal results. RIs were derived by parametric method using modified Box-Cox power transformation. Among all attendees, 23% fulfilled the criteria. Application of the LAVE method further reduced the dataset by 40%-50%. Age-related charts of test results differed greatly between genders in almost all tests. Comparison of derived RIs with clinical decision limits (CDLs) revealed that the upper limits of RIs differed from CDLs according to gender and age. Implementation of gender and age-specific RIs derived from individuals with fully normal health attributes will (1) enable appropriate interpretation of test results in health screening and (2) promote judicious application of CDLs for therapeutic intervention, taking into account gender, age and other health attributes. Copyright © 2015 Elsevier B.V. All rights reserved.

Determination of reference values for intraocular pressure and Schirmer tear test results in clinically normal domestic donkeys (Equus asinus).

PubMed

Selk Ghaffari, Masoud; Sabzevari, Amin; Ghamsari, SeyedMehdi; Shad, Hussein

2017-11-25

This study was conducted to establish normal reference range for the Schirmer tear test (STT) and intraocular pressure (IOP) in clinically normal donkeys for use in clinical practice. Sixteen adult Ethiopian domestic donkeys were used in this study. Complete ophthalmic examinations were performed without chemical restraint. STT values were evaluated in both eyes of all donkeys using a commercial STT strip. IOP was measured in both eyes with a Tono-Pen Vet (Reichert. USA) without using regional nerve blocks. STT values for all eyes (n=32) were 22.1±6.9 mm/minute with a range of 13-35 mm/minute. Comparison of mean STT values between right (n=16) and left eyes (n=16) showed no differences (P=0.6). Mean ±sd IOP values by applanation tonometry were 17.8±3.7 mmHg (range 13.5-24.5 mmHg). Comparison of mean IOP values between right (n=16) and left eyes (n=16) showed no differences (P=0.7). This initial survey provides means and ranges for IOP and STT values in donkeys. These data will assist veterinary ophthalmologists in more accurate diagnosis and management of ophthalmic diseases in donkeys, including keratoconjunctivitis sicca and glaucoma. © British Veterinary Association (unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Isolation and selection of suitable reference genes for real-time PCR analyses in the skeletal muscle of the fine flounder in response to nutritional status: assessment and normalization of gene expression of growth-related genes.

PubMed

Fuentes, Eduardo N; Safian, Diego; Valdés, Juan Antonio; Molina, Alfredo

2013-08-01

In the present study, different reference genes were isolated, and their stability in the skeletal muscle of fine flounder subjected to different nutritional states was assessed using geNorm and NormFinder. The combinations between 18S and ActB; Fau and 18S; and Fau and Tubb were chosen as the most stable gene combinations in feeding, long-term fasting and refeeding, and short-term refeeding conditions, respectively. In all periods, ActB was identified as the single least stable gene. Subsequently, the expression of the myosin heavy chain (MYH) and the insulin-like growth factor-I receptor (IGF-IR) was assessed. A large variation in MYH and IGF-IR expression was found depending on the reference gene that was chosen for normalizing the expression of both genes. Using the most stable reference genes, mRNA levels of MYH decreased and IGF-IR increased during fasting, with both returning to basal levels during refeeding. However, the drop in mRNA levels for IGF-IR occurred during short-term refeeding, in contrast with the observed events in the expression of MYH, which occurred during long-term refeeding. The present study highlights the vast differences incurred when using unsuitable versus suitable reference genes for normalizing gene expression, pointing out that normalization without proper validation could result in a bias of gene expression.

Development of self-image and its components during a one-year follow-up in non-referred adolescents with excess and normal weight.

PubMed

Mäkinen, Mauno; Marttunen, Mauri; Komulainen, Erkki; Terevnikov, Viacheslav; Puukko-Viertomies, Leena-Riitta; Aalberg, Veikko; Lindberg, Nina

2015-01-01

The proportion of overweight and obese youths is high. The present study aimed to investigate the development of self-image and its components during a one-year follow-up among non-referred adolescents with excess and normal weight. Furthermore, we separately analyzed the data for girls and boys. Altogether 86 8(th) grades (41 girls and 45 boys) with a relative weight of 26% or more above the median and 91 controls (43 girls and 48 boys) with normal weight participated the follow-up. The Offer Self-Image Questionnaire, Revised (OSIQ-R) was used to assess self-image at baseline and on follow-up. In the OSIQ-R, a low total raw score implies positive adjustment, while a high raw score implies poor adjustment and a negative self-image. The study design was doubly correlated (pairs and time), and a linear mixed model was used in the statistical analysis. In OSIQ-R total scores, a comparative improvement was observed in girls with normal weight. Among these girls, significant change scores compared to zero were seen in impulse control, social functioning, vocational attitudes, self-confidence, self-reliance, body image, sexuality, and ethical values. In girls with excess weight, none of the change scores compared to zero were statistically significant. When the girls with normal and excess weight were compared, the difference in change scores was largest in sexuality and vocational attitudes. Change scores compared to zero were significant in sexuality and idealism for boys with excess weight, and in impulse control, mental health, self-reliance, and sexuality for normal weight boys. When the boys with excess and normal weight were compared, no statistically significant differences emerged in change scores. In mid-adolescent girls, the influence of overweight and obesity on the development of self-image is substantial. Weight management programs directed at overweight adolescent girls should include psychological interventions aiming to diminish self-image distress

Group normalization for genomic data.

PubMed

Ghandi, Mahmoud; Beer, Michael A

2012-01-01

Data normalization is a crucial preliminary step in analyzing genomic datasets. The goal of normalization is to remove global variation to make readings across different experiments comparable. In addition, most genomic loci have non-uniform sensitivity to any given assay because of variation in local sequence properties. In microarray experiments, this non-uniform sensitivity is due to different DNA hybridization and cross-hybridization efficiencies, known as the probe effect. In this paper we introduce a new scheme, called Group Normalization (GN), to remove both global and local biases in one integrated step, whereby we determine the normalized probe signal by finding a set of reference probes with similar responses. Compared to conventional normalization methods such as Quantile normalization and physically motivated probe effect models, our proposed method is general in the sense that it does not require the assumption that the underlying signal distribution be identical for the treatment and control, and is flexible enough to correct for nonlinear and higher order probe effects. The Group Normalization algorithm is computationally efficient and easy to implement. We also describe a variant of the Group Normalization algorithm, called Cross Normalization, which efficiently amplifies biologically relevant differences between any two genomic datasets.

Reference Gene Validation for RT-qPCR, a Note on Different Available Software Packages

PubMed Central

De Spiegelaere, Ward; Dern-Wieloch, Jutta; Weigel, Roswitha; Schumacher, Valérie; Schorle, Hubert; Nettersheim, Daniel; Bergmann, Martin; Brehm, Ralph; Kliesch, Sabine; Vandekerckhove, Linos; Fink, Cornelia

2015-01-01

Background An appropriate normalization strategy is crucial for data analysis from real time reverse transcription polymerase chain reactions (RT-qPCR). It is widely supported to identify and validate stable reference genes, since no single biological gene is stably expressed between cell types or within cells under different conditions. Different algorithms exist to validate optimal reference genes for normalization. Applying human cells, we here compare the three main methods to the online available RefFinder tool that integrates these algorithms along with R-based software packages which include the NormFinder and GeNorm algorithms. Results 14 candidate reference genes were assessed by RT-qPCR in two sample sets, i.e. a set of samples of human testicular tissue containing carcinoma in situ (CIS), and a set of samples from the human adult Sertoli cell line (FS1) either cultured alone or in co-culture with the seminoma like cell line (TCam-2) or with equine bone marrow derived mesenchymal stem cells (eBM-MSC). Expression stabilities of the reference genes were evaluated using geNorm, NormFinder, and BestKeeper. Similar results were obtained by the three approaches for the most and least stably expressed genes. The R-based packages NormqPCR, SLqPCR and the NormFinder for R script gave identical gene rankings. Interestingly, different outputs were obtained between the original software packages and the RefFinder tool, which is based on raw Cq values for input. When the raw data were reanalysed assuming 100% efficiency for all genes, then the outputs of the original software packages were similar to the RefFinder software, indicating that RefFinder outputs may be biased because PCR efficiencies are not taken into account. Conclusions This report shows that assay efficiency is an important parameter for reference gene validation. New software tools that incorporate these algorithms should be carefully validated prior to use. PMID:25825906

Normal gravity field in relativistic geodesy

NASA Astrophysics Data System (ADS)

Kopeikin, Sergei; Vlasov, Igor; Han, Wen-Biao

2018-02-01

Modern geodesy is subject to a dramatic change from the Newtonian paradigm to Einstein's theory of general relativity. This is motivated by the ongoing advance in development of quantum sensors for applications in geodesy including quantum gravimeters and gradientometers, atomic clocks and fiber optics for making ultra-precise measurements of the geoid and multipolar structure of the Earth's gravitational field. At the same time, very long baseline interferometry, satellite laser ranging, and global navigation satellite systems have achieved an unprecedented level of accuracy in measuring 3-d coordinates of the reference points of the International Terrestrial Reference Frame and the world height system. The main geodetic reference standard to which gravimetric measurements of the of Earth's gravitational field are referred is a normal gravity field represented in the Newtonian gravity by the field of a uniformly rotating, homogeneous Maclaurin ellipsoid of which mass and quadrupole momentum are equal to the total mass and (tide-free) quadrupole moment of Earth's gravitational field. The present paper extends the concept of the normal gravity field from the Newtonian theory to the realm of general relativity. We focus our attention on the calculation of the post-Newtonian approximation of the normal field that is sufficient for current and near-future practical applications. We show that in general relativity the level surface of homogeneous and uniformly rotating fluid is no longer described by the Maclaurin ellipsoid in the most general case but represents an axisymmetric spheroid of the fourth order with respect to the geodetic Cartesian coordinates. At the same time, admitting a post-Newtonian inhomogeneity of the mass density in the form of concentric elliptical shells allows one to preserve the level surface of the fluid as an exact ellipsoid of rotation. We parametrize the mass density distribution and the level surface with two parameters which are

Comparison of ambulatory blood pressure reference standards in children evaluated for hypertension

PubMed Central

Jones, Deborah P.; Richey, Phyllis A.; Alpert, Bruce S.

2009-01-01

Objective The purpose of this study was to systematically compare methods for standardization of blood pressure levels obtained by ambulatory blood pressure monitoring (ABPM) in a group of 111 children studied at our institution. Methods Blood pressure indices, blood pressure loads and standard deviation scores were calculated using he original ABPM and the modified reference standards. Bland—Altman plots and kappa statistics for the level of agreement were generated. Results Overall, the agreement between the two methods was excellent; however, approximately 5% of children were classified differently by one as compared with the other method. Conclusion Depending on which version of the German Working Group’s reference standards is used for interpretation of ABPM data, the classification of the individual as having hypertension or normal blood pressure may vary. PMID:19433980

Reference interval computation: which method (not) to choose?

PubMed

Pavlov, Igor Y; Wilson, Andrew R; Delgado, Julio C

2012-07-11

When different methods are applied to reference interval (RI) calculation the results can sometimes be substantially different, especially for small reference groups. If there are no reliable RI data available, there is no way to confirm which method generates results closest to the true RI. We randomly drawn samples obtained from a public database for 33 markers. For each sample, RIs were calculated by bootstrapping, parametric, and Box-Cox transformed parametric methods. Results were compared to the values of the population RI. For approximately half of the 33 markers, results of all 3 methods were within 3% of the true reference value. For other markers, parametric results were either unavailable or deviated considerably from the true values. The transformed parametric method was more accurate than bootstrapping for sample size of 60, very close to bootstrapping for sample size 120, but in some cases unavailable. We recommend against using parametric calculations to determine RIs. The transformed parametric method utilizing Box-Cox transformation would be preferable way of RI calculation, if it satisfies normality test. If not, the bootstrapping is always available, and is almost as accurate and precise as the transformed parametric method. Copyright © 2012 Elsevier B.V. All rights reserved.

Housekeeping while brain's storming Validation of normalizing factors for gene expression studies in a murine model of traumatic brain injury

PubMed Central

Rhinn, Hervé; Marchand-Leroux, Catherine; Croci, Nicole; Plotkine, Michel; Scherman, Daniel; Escriou, Virginie

2008-01-01

Background Traumatic brain injury models are widely studied, especially through gene expression, either to further understand implied biological mechanisms or to assess the efficiency of potential therapies. A large number of biological pathways are affected in brain trauma models, whose elucidation might greatly benefit from transcriptomic studies. However the suitability of reference genes needed for quantitative RT-PCR experiments is missing for these models. Results We have compared five potential reference genes as well as total cDNA level monitored using Oligreen reagent in order to determine the best normalizing factors for quantitative RT-PCR expression studies in the early phase (0–48 h post-trauma (PT)) of a murine model of diffuse brain injury. The levels of 18S rRNA, and of transcripts of β-actin, glyceraldehyde-3P-dehydrogenase (GAPDH), β-microtubulin and S100β were determined in the injured brain region of traumatized mice sacrificed at 30 min, 3 h, 6 h, 12 h, 24 h and 48 h post-trauma. The stability of the reference genes candidates and of total cDNA was evaluated by three different methods, leading to the following rankings as normalization factors, from the most suitable to the less: by using geNorm VBA applet, we obtained the following sequence: cDNA(Oligreen); GAPDH > 18S rRNA > S100β > β-microtubulin > β-actin; by using NormFinder Excel Spreadsheet, we obtained the following sequence: GAPDH > cDNA(Oligreen) > S100β > 18S rRNA > β-actin > β-microtubulin; by using a Confidence-Interval calculation, we obtained the following sequence: cDNA(Oligreen) > 18S rRNA; GAPDH > S100β > β-microtubulin > β-actin. Conclusion This work suggests that Oligreen cDNA measurements, 18S rRNA and GAPDH or a combination of them may be used to efficiently normalize qRT-PCR gene expression in mouse brain trauma injury, and that β-actin and β-microtubulin should be avoided. The potential of total cDNA as measured by Oligreen as a first

A Proposal of New Reference System for the Standard Axial, Sagittal, Coronal Planes of Brain Based on the Serially-Sectioned Images

PubMed Central

Park, Jin Seo; Park, Hyo Seok; Shin, Dong Sun; Har, Dong-Hwan; Cho, Zang-Hee; Kim, Young-Bo; Han, Jae-Yong; Chi, Je-Geun

2010-01-01

Sectional anatomy of human brain is useful to examine the diseased brain as well as normal brain. However, intracerebral reference points for the axial, sagittal, and coronal planes of brain have not been standardized in anatomical sections or radiological images. We made 2,343 serially-sectioned images of a cadaver head with 0.1 mm intervals, 0.1 mm pixel size, and 48 bit color and obtained axial, sagittal, and coronal images based on the proposed reference system. This reference system consists of one principal reference point and two ancillary reference points. The two ancillary reference points are the anterior commissure and the posterior commissure. And the principal reference point is the midpoint of two ancillary reference points. It resides in the center of whole brain. From the principal reference point, Cartesian coordinate of x, y, z could be made to be the standard axial, sagittal, and coronal planes. PMID:20052359

Reference values and repeatability of the Schirmer tear tests I and II in domesticated, clinically normal dromedary camels (Camelus dromedarius).

PubMed

Marzok, Mohamed A; Badawy, Adel M; El-Khodery, Sabry A

2017-05-01

To determine the normal values and repeatability for Schirmer tear test (STT) in clinically normal dromedary camels and to analyze the influence of the age and gender on these values. Thirty clinically normal dromedary camels of different ages (calves, immature, and mature). Schirmer tear tests I and II were performed using commercial STT strips. Three measurements were obtained from each eye over three consecutive weeks, and the variance of these measurements was determined. Mean values and coefficient of variation of STT I and STT II for the right and left eyes varied significantly among camel groups (P < 0.05). For STT I, the most frequently recorded values were >14-18, > 22-26, and >30-34 mm/min in calves, immature camels, and mature camels, respectively. For STT II, however, the most frequently recorded values were 7-14, >10-18, and >26-30 mm/min, respectively. The interassay coefficients of variation were 1.7-14.4% and were significantly lower in mature camels than in calves and immature camels (P < 0.05). Age was positively correlated with STT I (r = 0.81) and STT II values (r = 0.88). No significant variations were found between genders. This preliminary study reports STT I and II values and repeatability in normal dromedary camels. This information may assist veterinary practitioners in complete ophthalmic examinations and in accurate diagnosis of ocular surface diseases affecting the tear film in this species. © 2016 American College of Veterinary Ophthalmologists.

Spatial frequency discrimination learning in normal and developmentally impaired human vision

PubMed Central

Astle, Andrew T.; Webb, Ben S.; McGraw, Paul V.

2010-01-01

Perceptual learning effects demonstrate that the adult visual system retains neural plasticity. If perceptual learning holds any value as a treatment tool for amblyopia, trained improvements in performance must generalise. Here we investigate whether spatial frequency discrimination learning generalises within task to other spatial frequencies, and across task to contrast sensitivity. Before and after training, we measured contrast sensitivity and spatial frequency discrimination (at a range of reference frequencies 1, 2, 4, 8, 16 c/deg). During training, normal and amblyopic observers were divided into three groups. Each group trained on a spatial frequency discrimination task at one reference frequency (2, 4, or 8 c/deg). Normal and amblyopic observers who trained at lower frequencies showed a greater rate of within task learning (at their reference frequency) compared to those trained at higher frequencies. Compared to normals, amblyopic observers showed greater within task learning, at the trained reference frequency. Normal and amblyopic observers showed asymmetrical transfer of learning from high to low spatial frequencies. Both normal and amblyopic subjects showed transfer to contrast sensitivity. The direction of transfer for contrast sensitivity measurements was from the trained spatial frequency to higher frequencies, with the bandwidth and magnitude of transfer greater in the amblyopic observers compared to normals. The findings provide further support for the therapeutic efficacy of this approach and establish general principles that may help develop more effective protocols for the treatment of developmental visual deficits. PMID:20832416

Echocardiography of the normal camel (Camelus dromedaries) heart: technique and cardiac dimensions

PubMed Central

2012-01-01

Background Echocardiography and intra-cardiac dimensions have not previously been reported in adult camels despite its potential application for medical purpose. The aim of this study was to describe the results of a prospective study, aiming to report normal cardiac appearance and normal chamber dimensions in adult camels (Camelus dromedarius). Results On the right side, when the probe was placed in the 5th or 4th intercostal space (ICS), the caudal long-axis four-chamber view of the ventricles, atria, and the interventricular septum was obtained. Placing the probe slightly more cranially in the 4th ICS, the caudal long-axis four-chamber view and the caudal long-axis view of the left ventricular outflow tract (LVOT) were imaged. In 7 camels, a hybrid view between a “four-chamber” and “LVOT view” was imaged from the same position. The short-axis view of the ventricles was obtained in the 4th ICS where the transducer was rotated between 0° and 25°. Placement of the transducer in the 3rd ICS allowed visualisation of the right ventricular outflow tract (RVOT). On the left side, when the probe was placed in the 5th or 4th ICS, a four-chamber view was obtained. The LVOT is imaged in the 4th ICS and the RVOT was seen from the 3rd ICS. Conclusions This study showed that it is possible to obtain good-quality echocardiograms in adult camels and provide normal cardiac dimensions. This study could be used as a reference for further studies concerning camels with cardiac diseases. PMID:22862855

Validation of reference genes for normalization of qPCR mRNA expression levels in Staphylococcus aureus exposed to osmotic and lactic acid stress conditions encountered during food production and preservation.

PubMed

Sihto, Henna-Maria; Tasara, Taurai; Stephan, Roger; Johler, Sophia

2014-07-01

Staphylococcus aureus represents the most prevalent cause of food-borne intoxications worldwide. While being repressed by competing bacteria in most matrices, this pathogen exhibits crucial competitive advantages during growth at high salt concentrations or low pH, conditions frequently encountered in food production and preservation. We aimed to identify reference genes that could be used to normalize qPCR mRNA expression levels during growth of S. aureus in food-related osmotic (NaCl) and acidic (lactic acid) stress adaptation models. Expression stability of nine housekeeping genes was evaluated in full (LB) and nutrient-deficient (CYGP w/o glucose) medium under conditions of osmotic (4.5% NaCl) and acidic stress (lactic acid, pH 6.0) after 2-h exposure. Among the set of candidate reference genes investigated, rplD, rpoB,gyrB, and rho were most stably expressed in LB and thus represent the most suitable reference genes for normalization of qPCR data in osmotic or lactic acid stress models in a rich medium. Under nutrient-deficient conditions, expression of rho and rpoB was highly stable across all tested conditions. The presented comprehensive data on changes in expression of various S. aureus housekeeping genes under conditions of osmotic and lactic acid stress facilitate selection of reference genes for qPCR-based stress response models. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Valuation of Normal Range of Ankle Systolic Blood Pressure in Subjects with Normal Arm Systolic Blood Pressure.

PubMed

Gong, Yi; Cao, Kai-wu; Xu, Jin-song; Li, Ju-xiang; Hong, Kui; Cheng, Xiao-shu; Su, Hai

2015-01-01

This study aimed to establish a normal range for ankle systolic blood pressure (SBP). A total of 948 subjects who had normal brachial SBP (90-139 mmHg) at investigation were enrolled. Supine BP of four limbs was simultaneously measured using four automatic BP measurement devices. The ankle-arm difference (An-a) on SBP of both sides was calculated. Two methods were used for establishing normal range of ankle SBP: the 99% method was decided on the 99% reference range of actual ankle BP, and the An-a method was the sum of An-a and the low or up limits of normal arm SBP (90-139 mmHg). Whether in the right or left side, the ankle SBP was significantly higher than the arm SBP (right: 137.1 ± 16.9 vs 119.7 ± 11.4 mmHg, P<0.05). Based on the 99% method, the normal range of ankle SBP was 94~181 mmHg for the total population, 84~166 mmHg for the young (18-44 y), 107~176 mmHg for the middle-aged(45-59 y) and 113~179 mmHg for the elderly (≥ 60 y) group. As the An-a on SBP was 13 mmHg in the young group and 20 mmHg in both middle-aged and elderly groups, the normal range of ankle SBP on the An-a method was 103-153 mmHg for young and 110-160 mmHg for middle-elderly subjects. A primary reference for normal ankle SBP was suggested as 100-165 mmHg in the young and 110-170 mmHg in the middle-elderly subjects.

LC-MS/MS-based approach for obtaining exposure estimates of metabolites in early clinical trials using radioactive metabolites as reference standards.

PubMed

Zhang, Donglu; Raghavan, Nirmala; Chando, Theodore; Gambardella, Janice; Fu, Yunlin; Zhang, Duxi; Unger, Steve E; Humphreys, W Griffith

2007-12-01

An LC-MS/MS-based approach that employs authentic radioactive metabolites as reference standards was developed to estimate metabolite exposures in early drug development studies. This method is useful to estimate metabolite levels in studies done with non-radiolabeled compounds where metabolite standards are not available to allow standard LC-MS/MS assay development. A metabolite mixture obtained from an in vivo source treated with a radiolabeled compound was partially purified, quantified, and spiked into human plasma to provide metabolite standard curves. Metabolites were analyzed by LC-MS/MS using the specific mass transitions and an internal standard. The metabolite concentrations determined by this approach were found to be comparable to those determined by valid LC-MS/MS assays. This approach does not requires synthesis of authentic metabolites or the knowledge of exact structures of metabolites, and therefore should provide a useful method to obtain early estimates of circulating metabolites in early clinical or toxicological studies.

Development of gestation-specific reference intervals for thyroid hormones in normal pregnant Northeast Chinese women: What is the rational division of gestation stages for establishing reference intervals for pregnancy women?

PubMed

Liu, Jianhua; Yu, Xiaojun; Xia, Meng; Cai, Hong; Cheng, Guixue; Wu, Lina; Li, Qiang; Zhang, Ying; Sheng, Mengyuan; Liu, Yong; Qin, Xiaosong

2017-04-01

A laboratory- and region-specific trimester-related reference interval for thyroid hormone assessment of pregnant women was recommended. Whether the division by trimester is suitable requires verification. Here, we tried to establish appropriate reference intervals of thyroid-related hormones and antibodies for normal pregnant women in Northeast China. A total of 947 pregnant women who underwent routine prenatal care were grouped via two methods. The first method entailed division by trimester: stages T1, T2, and T3. The second method entailed dividing T1, T2, and T3 stages into two stages each: T1-1, T1-2, T2-1, T2-2, T3-1, and T3-2. Serum levels of TSH, FT3, FT4, Anti-TPO, and Anti-TG were measured by three detection systems. No significant differences were found in TSH values between T1-1 group and the non-pregnant women group. However, the TSH value of the T1-1 group was significantly higher than that of T1-2 group (P<0.05). The TSH values in stage T3-2 increased significantly compared to those in stage T3-1 measured by three different assays (P<0.05). FT4 and FT3 values decreased significantly in the T2-1 and T2-2 stages compared to the previous stage (P<0.05). The serum levels of Anti-TPO and Anti-TG were not having significant differences between the six stages. The diagnosis and treatment of thyroid dysfunction during pregnancy should base on pregnancy- and method-specific reference intervals. More detailed staging is required to assess the thyroid function of pregnant women before 20 gestational weeks. Copyright © 2016 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Validation of the concentration profiles obtained from the near infrared/multivariate curve resolution monitoring of reactions of epoxy resins using high performance liquid chromatography as a reference method.

PubMed

Garrido, M; Larrechi, M S; Rius, F X

2007-03-07

This paper reports the validation of the results obtained by combining near infrared spectroscopy and multivariate curve resolution-alternating least squares (MCR-ALS) and using high performance liquid chromatography as a reference method, for the model reaction of phenylglycidylether (PGE) and aniline. The results are obtained as concentration profiles over the reaction time. The trueness of the proposed method has been evaluated in terms of lack of bias. The joint test for the intercept and the slope showed that there were no significant differences between the profiles calculated spectroscopically and the ones obtained experimentally by means of the chromatographic reference method at an overall level of confidence of 5%. The uncertainty of the results was estimated by using information derived from the process of assessment of trueness. Such operational aspects as the cost and availability of instrumentation and the length and cost of the analysis were evaluated. The method proposed is a good way of monitoring the reactions of epoxy resins, and it adequately shows how the species concentration varies over time.

Smooth quantile normalization.

PubMed

Hicks, Stephanie C; Okrah, Kwame; Paulson, Joseph N; Quackenbush, John; Irizarry, Rafael A; Bravo, Héctor Corrada

2018-04-01

Between-sample normalization is a critical step in genomic data analysis to remove systematic bias and unwanted technical variation in high-throughput data. Global normalization methods are based on the assumption that observed variability in global properties is due to technical reasons and are unrelated to the biology of interest. For example, some methods correct for differences in sequencing read counts by scaling features to have similar median values across samples, but these fail to reduce other forms of unwanted technical variation. Methods such as quantile normalization transform the statistical distributions across samples to be the same and assume global differences in the distribution are induced by only technical variation. However, it remains unclear how to proceed with normalization if these assumptions are violated, for example, if there are global differences in the statistical distributions between biological conditions or groups, and external information, such as negative or control features, is not available. Here, we introduce a generalization of quantile normalization, referred to as smooth quantile normalization (qsmooth), which is based on the assumption that the statistical distribution of each sample should be the same (or have the same distributional shape) within biological groups or conditions, but allowing that they may differ between groups. We illustrate the advantages of our method on several high-throughput datasets with global differences in distributions corresponding to different biological conditions. We also perform a Monte Carlo simulation study to illustrate the bias-variance tradeoff and root mean squared error of qsmooth compared to other global normalization methods. A software implementation is available from https://github.com/stephaniehicks/qsmooth.

Group Normalization for Genomic Data

PubMed Central

Ghandi, Mahmoud; Beer, Michael A.

2012-01-01

Data normalization is a crucial preliminary step in analyzing genomic datasets. The goal of normalization is to remove global variation to make readings across different experiments comparable. In addition, most genomic loci have non-uniform sensitivity to any given assay because of variation in local sequence properties. In microarray experiments, this non-uniform sensitivity is due to different DNA hybridization and cross-hybridization efficiencies, known as the probe effect. In this paper we introduce a new scheme, called Group Normalization (GN), to remove both global and local biases in one integrated step, whereby we determine the normalized probe signal by finding a set of reference probes with similar responses. Compared to conventional normalization methods such as Quantile normalization and physically motivated probe effect models, our proposed method is general in the sense that it does not require the assumption that the underlying signal distribution be identical for the treatment and control, and is flexible enough to correct for nonlinear and higher order probe effects. The Group Normalization algorithm is computationally efficient and easy to implement. We also describe a variant of the Group Normalization algorithm, called Cross Normalization, which efficiently amplifies biologically relevant differences between any two genomic datasets. PMID:22912661

Improved tomographic reconstructions using adaptive time-dependent intensity normalization.

PubMed

Titarenko, Valeriy; Titarenko, Sofya; Withers, Philip J; De Carlo, Francesco; Xiao, Xianghui

2010-09-01

The first processing step in synchrotron-based micro-tomography is the normalization of the projection images against the background, also referred to as a white field. Owing to time-dependent variations in illumination and defects in detection sensitivity, the white field is different from the projection background. In this case standard normalization methods introduce ring and wave artefacts into the resulting three-dimensional reconstruction. In this paper the authors propose a new adaptive technique accounting for these variations and allowing one to obtain cleaner normalized data and to suppress ring and wave artefacts. The background is modelled by the product of two time-dependent terms representing the illumination and detection stages. These terms are written as unknown functions, one scaled and shifted along a fixed direction (describing the illumination term) and one translated by an unknown two-dimensional vector (describing the detection term). The proposed method is applied to two sets (a stem Salix variegata and a zebrafish Danio rerio) acquired at the parallel beam of the micro-tomography station 2-BM at the Advanced Photon Source showing significant reductions in both ring and wave artefacts. In principle the method could be used to correct for time-dependent phenomena that affect other tomographic imaging geometries such as cone beam laboratory X-ray computed tomography.

Canine and feline hematology reference values for the ADVIA 120 hematology system.

PubMed

Moritz, Andreas; Fickenscher, Yvonne; Meyer, Karin; Failing, Klaus; Weiss, Douglas J

2004-01-01

The ADVIA 120 is a laser-based hematology analyzer with software applications for animal species. Accurate reference values would be useful for the assessment of new hematologic parameters and for interlaboratory comparisons. The goal of this study was to establish reference intervals for CBC results and new parameters for RBC morphology, reticulocytes, and platelets in healthy dogs and cats using the ADVIA 120 hematology system. The ADVIA 120, with multispecies software (version 1.107-MS), was used to analyze whole blood samples from clinically healthy dogs (n=46) and cats (n=61). Data distribution was determined and reference intervals were calculated as 2.5 to 97.5 percentiles and 25 to 75 percentiles. Most data showed Gaussian or log-normal distribution. The numbers of RBCs falling outside the normocytic-normochromic range were slightly higher in cats than in dogs. Both dogs and cats had reticulocytes with low, medium, and high absorbance. Mean numbers of large platelets and platelet clumps were higher in cats compared with dogs. Reference intervals obtained on the ADVIA 120 provide valuable baseline information for assessing new hematologic parameters and for interlaboratory comparisons. Differences compared with previously published reference values can be attributed largely to differences in methodology.

Normalization of Reverse Transcription Quantitative PCR Data During Ageing in Distinct Cerebral Structures.

PubMed

Bruckert, G; Vivien, D; Docagne, F; Roussel, B D

2016-04-01

Reverse transcription quantitative-polymerase chain reaction (RT-qPCR) has become a routine method in many laboratories. Normalization of data from experimental conditions is critical for data processing and is usually achieved by the use of a single reference gene. Nevertheless, as pointed by the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, several reference genes should be used for reliable normalization. Ageing is a physiological process that results in a decline of many expressed genes. Reliable normalization of RT-qPCR data becomes crucial when studying ageing. Here, we propose a RT-qPCR study from four mouse brain regions (cortex, hippocampus, striatum and cerebellum) at different ages (from 8 weeks to 22 months) in which we studied the expression of nine commonly used reference genes. With the use of two different algorithms, we found that all brain structures need at least two genes for a good normalization step. We propose specific pairs of gene for efficient data normalization in the four brain regions studied. These results underline the importance of reliable reference genes for specific brain regions in ageing.

Cell proliferation in normal epidermis

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

Weinstein, G.D.; McCullough, J.L.; Ross, P.

1984-06-01

A detailed examination of cell proliferation kinetics in normal human epidermis is presented. Using tritiated thymidine with autoradiographic techniques, proliferative and differentiated cell kinetics are defined and interrelated. The proliferative compartment of normal epidermis has a cell cycle duration (Tc) of 311 h derived from 3 components: the germinative labeling index (LI), the duration of DNA synthesis (ts), and the growth fraction (GF). The germinative LI is 2.7% +/- 1.2 and ts is 14 h, the latter obtained from a composite fraction of labeled mitoses curve obtained from 11 normal subjects. The GF obtained from the literature and from humanmore » skin xenografts to nude mice is estimated to be 60%. Normal-appearing epidermis from patients with psoriasis appears to have a higher proliferation rate. The mean LI is 4.2% +/- 0.9, approximately 50% greater than in normal epidermis. Absolute cell kinetic values for this tissue, however, cannot yet be calculated for lack of other information on ts and GF. A kinetic model for epidermal cell renewal in normal epidermis is described that interrelates the rate of birth/entry, transit, and/or loss of keratinocytes in the 3 epidermal compartments: proliferative, viable differentiated (stratum malpighii), and stratum corneum. Expected kinetic homeostasis in the epidermis is confirmed by the very similar ''turnover'' rates in each of the compartments that are, respectively, 1246, 1417, and 1490 cells/day/mm2 surface area. The mean epidermal turnover time of the entire tissue is 39 days. The Tc of 311 h in normal cells in 8-fold longer than the psoriatic Tc of 36 h and is necessary for understanding the hyperproliferative pathophysiologic process in psoriasis.« less

Evaluation of normalization reference genes for RT-qPCR analysis of spo0A and four sporulation sigma factor genes in Clostridium botulinum Group I strain ATCC 3502.

PubMed

Kirk, David G; Palonen, Eveliina; Korkeala, Hannu; Lindström, Miia

2014-04-01

Heat-resistant spores of Clostridium botulinum can withstand the pasteurization processes in modern food processing. This poses a risk to food safety as spores may germinate into botulinum neurotoxin-producing vegetative cells. Sporulation in Bacillus subtilis, the model organism for sporulation, is regulated by the transcription factor Spo0A and four alternative sigma factors, SigF, SigE, SigG, and SigK. While the corresponding regulators are found in available genomes of C. botulinum, little is known about their expression. To accurately measure the expression of these genes using quantitative reverse-transcriptase PCR (RT-qPCR) during the exponential and stationary growth phases, a suitable normalization reference gene is required. 16S rrn, adK, alaS, era, gluD, gyrA, rpoC, and rpsJ were selected as the candidate reference genes. The most stable candidate reference gene was 16S ribosomal RNA gene (rrn), based on its low coefficient of variation (1.81%) measured during the 18-h study time. Using 16S rrn as the normalization reference gene, the relative expression levels of spo0A, sigF, sigE, sigG, and sigK were measured over 18h. The pattern of expression showed spo0A expression during the logarithmic growth phase, followed by a drop in expression upon entry to the stationary phase. Expression levels of sigF, sigE, and sigG peaked simultaneously at the end of the exponential growth phase. Peak expression of sigK occurred at 18h, however low levels of expression were detected during the exponential phase. These findings suggest these sigma factors play a role in C. botulinum sporulation that is similar, but not equal, to their role in the B. subtilis model. Copyright © 2013 Elsevier Ltd. All rights reserved.

Reference breast temperature: proposal of an equation.

PubMed

Souza, Gladis Aparecida Galindo Reisemberger de; Brioschi, Marcos Leal; Vargas, José Viriato Coelho; Morais, Keli Cristiane Correia; Dalmaso Neto, Carlos; Neves, Eduardo Borba

2015-01-01

To develop an equation to estimate the breast reference temperature according to the variation of room and core body temperatures. Four asymptomatic women were evaluated for three consecutive menstrual cycles. Using thermography, the temperature of breasts and eyes was measured as indirect reference of core body and room temperatures. To analyze the thermal behavior of the breasts during the cycle, the core body and room temperatures were normalized by means of a mathematical equation. We performed 180 observations and the core temperature had the highest correlation with the breast temperature, followed by room temperature. The proposed prediction model could explain 45.3% of the breast temperature variation, with variable room temperature variable; it can be accepted as a way to estimate the reference breast temperature at different room temperatures. The average breast temperature in healthy women had a direct relation with the core and room temperature and can be estimated mathematically. It is suggested that an equation could be used in clinical practice to estimate the normal breast reference temperature in young women, regardless of the day of the cycle, therefore assisting in evaluation of anatomical studies.

Reference breast temperature: proposal of an equation

PubMed Central

de Souza, Gladis Aparecida Galindo Reisemberger; Brioschi, Marcos Leal; Vargas, José Viriato Coelho; Morais, Keli Cristiane Correia; Dalmaso, Carlos; Neves, Eduardo Borba

2015-01-01

ABSTRACT Objective To develop an equation to estimate the breast reference temperature according to the variation of room and core body temperatures. Methods Four asymptomatic women were evaluated for three consecutive menstrual cycles. Using thermography, the temperature of breasts and eyes was measured as indirect reference of core body and room temperatures. To analyze the thermal behavior of the breasts during the cycle, the core body and room temperatures were normalized by means of a mathematical equation. Results We performed 180 observations and the core temperature had the highest correlation with the breast temperature, followed by room temperature. The proposed prediction model could explain 45.3% of the breast temperature variation, with variable room temperature variable; it can be accepted as a way to estimate the reference breast temperature at different room temperatures. Conclusion The average breast temperature in healthy women had a direct relation with the core and room temperature and can be estimated mathematically. It is suggested that an equation could be used in clinical practice to estimate the normal breast reference temperature in young women, regardless of the day of the cycle, therefore assisting in evaluation of anatomical studies. PMID:26761549

Identification and evaluation of reference genes for accurate gene expression normalization of fresh and frozen-thawed spermatozoa of water buffalo (Bubalus bubalis).

PubMed

Ashish, Shende; Bhure, S K; Harikrishna, Pillai; Ramteke, S S; Muhammed Kutty, V H; Shruthi, N; Ravi Kumar, G V P P S; Manish, Mahawar; Ghosh, S K; Mihir, Sarkar

2017-04-01

The quantitative real time PCR (qRT-PCR) has become an important tool for gene-expression analysis for a selected number of genes in life science. Although large dynamic range, sensitivity and reproducibility of qRT-PCR is good, the reliability majorly depend on the selection of proper reference genes (RGs) employed for normalization. Although, RGs expression has been reported to vary considerably within same cell type with different experimental treatments. No systematic study has been conducted to identify and evaluate the appropriate RGs in spermatozoa of domestic animals. Therefore, this study was conducted to analyze suitable stable RGs in fresh and frozen-thawed spermatozoa. We have assessed 13 candidate RGs (BACT, RPS18s, RPS15A, ATP5F1, HMBS, ATP2B4, RPL13, EEF2, TBP, EIF2B2, MDH1, B2M and GLUT5) of different functions and pathways using five algorithms. Regardless of the approach, the ranking of the most and the least candidate RGs remained almost same. The comprehensive ranking by RefFinder showed GLUT5, ATP2B4 and B2M, MDH1 as the top two stable and least stable RGs, respectively. The expression levels of four heat shock proteins (HSP) were employed as a target gene to evaluate RGs efficiency for normalization. The results demonstrated an exponential difference in expression levels of the four HSP genes upon normalization of the data with the most stable and the least stable RGs. Our study, provides a convenient RGs for normalization of gene-expression of key metabolic pathways effected during freezing and thawing of spermatozoa of buffalo and other closely related bovines. Copyright © 2017 Elsevier Inc. All rights reserved.

Effect of 25(OH) vitamin D reference method procedure (RMP) alignment on clinical measurements obtained with the IDS-iSYS chemiluminescent-based automated analyzer.

PubMed

Simpson, Christine A; Cusano, Anna Maria; Bihuniak, Jessica; Walker, Joanne; Insogna, Karl L

2015-04-01

The Vitamin D Standardization Program (VDSP) has identified ID-LC/MS/MS as the reference method procedure (RMP) for 25(OH) vitamin D and NIST Standard SRM2972 as the standard reference material (SRM). As manufacturers align their products to the RMP and NIST standard, a concern is that results obtained in aligned assays will be divergent from those obtained with pre-alignment assays. The Immunodiagnostic Systems Ltd., chemiluminescent, 25(OH) vitamin D iSYS platform assay, was recently harmonized to the RMP. To determine the impact of standardization on results obtained with iSYS reagents, 119 single donor serum samples from eight different disease categories were analyzed in four non-standardized and two standardized iSYS assays. There were strong correlations between the four non-standardized and two standardized assays with Spearman's rank r values between 0.975 and 0.961 and four of the eight r values were >0.97. R(2) values for the eight best-fit linear regression equations ranging between 0.947 and 0.916. None of the slopes were found to be significantly different from one another. Bland-Altman plots showed that the bias was comparable when each of the four non-standardized assays was compared to either of the standardized assays. When the data were segregated in values between 6 and 49ng/mL (15-122nmol/L) or between 50 and 100ng/mL (125-250nmol/L) significant associations remained between results obtained with non-standardized and standardized calibrators regardless of the absolute value. When five recent DEQAS unknowns were analyzed in one non-standardized and one standardized assay the mean percent difference from the NIST target in values obtained using standardized vs. non-standardized calibrators were not significantly different. Finally, strong and statistically significant associations between the results were obtained using non-standardized and standardized assays for six of eight clinical conditions. The only exceptions were hypocalcemia and breast

Gene expression studies of reference genes for quantitative real-time PCR: an overview in insects.

PubMed

Shakeel, Muhammad; Rodriguez, Alicia; Tahir, Urfa Bin; Jin, Fengliang

2018-02-01

Whenever gene expression is being examined, it is essential that a normalization process is carried out to eliminate non-biological variations. The use of reference genes, such as glyceraldehyde-3-phosphate dehydrogenase, actin, and ribosomal protein genes, is the usual method of choice for normalizing gene expression. Although reference genes are used to normalize target gene expression, a major problem is that the stability of these genes differs among tissues, developmental stages, species, and responses to abiotic factors. Therefore, the use and validation of multiple reference genes are required. This review discusses the reasons that why RT-qPCR has become the preferred method for validating results of gene expression profiles, the use of specific and non-specific dyes and the importance of use of primers and probes for qPCR as well as to discuss several statistical algorithms developed to help the validation of potential reference genes. The conflicts arising in the use of classical reference genes in gene normalization and their replacement with novel references are also discussed by citing the high stability and low stability of classical and novel reference genes under various biotic and abiotic experimental conditions by employing various methods applied for the reference genes amplification.

Muscular hypertrophy and atrophy in normal rats provoked by the administration of normal and denervated muscle extracts.

PubMed

Agüera, Eduardo; Castilla, Salvador; Luque, Evelio; Jimena, Ignacio; Leiva-Cepas, Fernando; Ruz-Caracuel, Ignacio; Peña, José

2016-12-01

This study was conducted to determine the effects of extracts obtained from both normal and denervated muscles on different muscle types. Wistar rats were used and were divided into a control group and four experimental groups. Each experimental group was treated intraperitoneally during 10 consecutive days with a different extract. These extracts were obtained from normal soleus muscle, denervated soleus, normal extensor digitorum longus, and denervated extensor digitorum longus. Following treatment, the soleus and extensor digitorum longus muscles were obtained for study under optic and transmission electron microscope; morphometric parameters and myogenic responses were also analyzed. The results demonstrated that the treatment with normal soleus muscle and denervated soleus muscle extracts provoked hypertrophy and increased myogenic activity. In contrast, treatment with extracts from the normal and denervated EDL had a different effect depending on the muscle analyzed. In the soleus muscle it provoked hypertrophy of type I fibers and increased myogenic activity, while in the extensor digitorum longus atrophy of the type II fibers was observed without changes in myogenic activity. This suggests that the muscular responses of atrophy and hypertrophy may depend on different factors related to the muscle type which could be related to innervation.

Ultrasonography of umbilical structures in clinically normal foals.

PubMed

Reef, V B; Collatos, C

1988-12-01

The umbilical arteries, urachus, and umbilical vein were scanned ultrasonographically in 13 clinically normal foals that ranged in age from 6 hours to 4 weeks. Sonograms were obtained using a 7.5-MHz sector scanner transducer placed across the midline of the ventral portion of the foal's abdominal wall. The umbilical vein was scanned from the umbilical stalk to its entrance into the hepatic parenchyma. The mean (+/- SD) diameter of the umbilical vein was 0.61 +/- 0.20 cm immediately cranial to the umbilical stalk, 0.52 +/- 0.19 cm midway between the umbilicus and liver, and 0.6 +/- 0.19 cm at the liver. The urachus and umbilical arteries were scanned from the umbilical stalk to the apex of the urinary bladder and had a mean total diameter of 1.75 +/- 0.37 cm at the bladder apex. The umbilical arteries also were scanned along either side of the bladder and had a mean diameter of 0.85 +/- 0.21 cm. These measurements and the ultrasonographic appearance of the internal umbilical structures from clinically normal foals can be used as references to diagnose abnormalities of the umbilical structures in neonatal foals.

Wormhole potentials and throats from quasi-normal modes

NASA Astrophysics Data System (ADS)

Völkel, Sebastian H.; Kokkotas, Kostas D.

2018-05-01

Exotic compact objects refer to a wide class of black hole alternatives or effective models to describe phenomenologically quantum gravitational effects on the horizon scale. In this work we show how the knowledge of the quasi-normal mode spectrum of non-rotating wormhole models can be used to reconstruct the effective potential that appears in perturbation equations. From this it is further possible to obtain the parameters that characterize the specific wormhole model, which in this paper was chosen to be the one by Damour and Solodukhin. We also address the question whether one can distinguish such type of wormholes from ultra compact stars, if only the quasi-normal mode spectrum is known. We have proven that this is not possible by using the trapped modes only, but requires additional information. The inverse method presented here is an extension of work that has previously been developed and applied to the oscillation spectra of ultra compact stars and gravastars. However, it is not limited to the study of exotic compact objects, but applicable to symmetric double barrier potentials that appear in one-dimensional wave equations. Therefore we think it can be of interest for other fields too.

Urinary mRNA for the Diagnosis of Renal Allograft Rejection: The Issue of Normalization.

PubMed

Galichon, P; Amrouche, L; Hertig, A; Brocheriou, I; Rabant, M; Xu-Dubois, Y-C; Ouali, N; Dahan, K; Morin, L; Terzi, F; Rondeau, E; Anglicheau, D

2016-10-01

Urinary messenger RNA (mRNA) quantification is a promising method for noninvasive diagnosis of renal allograft rejection (AR), but the quantification of mRNAs in urine remains challenging due to degradation. RNA normalization may be warranted to overcome these issues, but the strategies of gene normalization have been poorly evaluated. Herein, we address this issue in a case-control study of 108 urine samples collected at time of allograft biopsy in kidney recipients with (n = 52) or without (n = 56) AR by comparing the diagnostic value of IP-10 and CD3ε mRNAs-two biomarkers of AR-after normalization by the total amount of RNA, normalization by one of the three widely used reference RNAs-18S, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and Hypoxanthine-guanine phosphoribosyltransferase (HPRT)-or normalization using uroplakin 1A (UPK) mRNA as a possible urine-specific reference mRNA. Our results show that normalization based on the total quantity of RNA is not substantially improved by additional normalization and may even be worsened with some classical reference genes that are overexpressed during rejection. However, considering that normalization by a reference gene is necessary to ensure polymerase chain reaction (PCR) quality and reproducibility and to suppress the effect of RNA degradation, we suggest that GAPDH and UPK1A are preferable to 18S or HPRT RNA. © Copyright 2016 The American Society of Transplantation and the American Society of Transplant Surgeons.

Hematological reference values of healthy Malaysian population.

PubMed

Roshan, T M; Rosline, H; Ahmed, S A; Rapiaah, M; Wan Zaidah, A; Khattak, M N

2009-10-01

Health and disease can only be distinguished by accurate and reliable reference values of a particular laboratory test. It is now a proven fact that there is considerable variation in hematology reference intervals depending on the demographic and preanalytical variables. There are evidences that values provided by manufacturers do not have appropriate application for all populations. Moreover, reference ranges provided by different laboratory manuals and books also do not solve this problem. We are presenting here normal reference ranges of Malaysian population. These values were determined by using Sysmex XE-2100 and ACL 9000 hematology and coagulation analyzers. Results from this study showed that there were considerable differences in the reference values from manufacturers, western population or laboratory manuals compared with those from the local population.

Multidimensional Normalization to Minimize Plate Effects of Suspension Bead Array Data.

PubMed

Hong, Mun-Gwan; Lee, Woojoo; Nilsson, Peter; Pawitan, Yudi; Schwenk, Jochen M

2016-10-07

Enhanced by the growing number of biobanks, biomarker studies can now be performed with reasonable statistical power by using large sets of samples. Antibody-based proteomics by means of suspension bead arrays offers one attractive approach to analyze serum, plasma, or CSF samples for such studies in microtiter plates. To expand measurements beyond single batches, with either 96 or 384 samples per plate, suitable normalization methods are required to minimize the variation between plates. Here we propose two normalization approaches utilizing MA coordinates. The multidimensional MA (multi-MA) and MA-loess both consider all samples of a microtiter plate per suspension bead array assay and thus do not require any external reference samples. We demonstrate the performance of the two MA normalization methods with data obtained from the analysis of 384 samples including both serum and plasma. Samples were randomized across 96-well sample plates, processed, and analyzed in assay plates, respectively. Using principal component analysis (PCA), we could show that plate-wise clusters found in the first two components were eliminated by multi-MA normalization as compared with other normalization methods. Furthermore, we studied the correlation profiles between random pairs of antibodies and found that both MA normalization methods substantially reduced the inflated correlation introduced by plate effects. Normalization approaches using multi-MA and MA-loess minimized batch effects arising from the analysis of several assay plates with antibody suspension bead arrays. In a simulated biomarker study, multi-MA restored associations lost due to plate effects. Our normalization approaches, which are available as R package MDimNormn, could also be useful in studies using other types of high-throughput assay data.

[Reference values of proteins for the Venezuelan population].

PubMed

Guerra, Marisa; Hernández, María N; López, Michelle; Alfaro, María J

2013-12-01

This study presents the reference values for protein requirements. The consumption of the Venezuelan population was obtained according to the Food Consumption Monitoring Survey (ESCA) 2010-2012. The diet provided good quality proteins, combining animal and vegetable foods in an approximate ratio of 1:1. The reference values were calculated based on the safe levels of protein intake recommended by WHO/FAO/UN 2007, with an adjustment for protein supply depending on age, weight, and contribution to the caloric formula of proteins for light physical activity. The reference values for protein requirements recommended as safe levels of intake in g/kg/day are 1.14 to 1.80 for males and females less than one-year-old, from 1 to 3 years, 0.90 to 1.14; from 4 to 6 years old, 0.86 to 0.89; and from 7 to 10 years old, 0.91 to 0.92. For adolescents, the average is 0.88 and 1.07 for males and females, respectively. In adults from 20 to 59 years old, 0.83 for men and women is recommended, and for older adults, 1.00 for men and women. In pregnant women, additional consumptions are recommended according to gestation time. Adolescent pregnant women must consume additional 1.2 to 1.7 g/kg/day to normal requirement. In breastfeeding women, the values differ between the first six months postnatal period and after six months of breastfeeding. The reference values for protein in this update were lower than the values of the 2000 version.

Anodonta imbecillis copper sulfate reference toxicant test, Clinch River - Environmental Restoration Program (CR-ERP)

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

Simbeck, D.J.

1997-06-01

Reference toxicant testing using juvenile freshwater mussels was conducted as part of the CR-ERP biomonitoring study of Clinch River sediments to assess the sensitivity of test organisms and the overall performance of the test. Tests were conducted using moderately hard synthetic water spiked with known concentrations of copper as copper sulfate. Toxicity testing of copper sulfate reference toxicant was conducted from May 12-21, 1993. The organisms used for testing were juvenile fresh-water mussels (Anodonta imbecillis). Results from this test showed an LC{sub 50} value of 1.12 mg Cu/L which is lower than the value of 2.02 mg Cu/L obtained inmore » a previous test. Too few tests have been conducted with copper as the toxicant to determine a normal range of values.« less

Sequencing and Validation of Reference Genes to Analyze Endogenous Gene Expression and Quantify Yellow Dwarf Viruses Using RT-qPCR in Viruliferous Rhopalosiphum padi

PubMed Central

Wu, Keke; Liu, Wenwen; Mar, Thithi; Liu, Yan; Wu, Yunfeng; Wang, Xifeng

2014-01-01

The bird cherry-oat aphid (Rhopalosiphum padi), an important pest of cereal crops, not only directly sucks sap from plants, but also transmits a number of plant viruses, collectively the yellow dwarf viruses (YDVs). For quantifying changes in gene expression in vector aphids, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is a touchstone method, but the selection and validation of housekeeping genes (HKGs) as reference genes to normalize the expression level of endogenous genes of the vector and for exogenous genes of the virus in the aphids is critical to obtaining valid results. Such an assessment has not been done, however, for R. padi and YDVs. Here, we tested three algorithms (GeNorm, NormFinder and BestKeeper) to assess the suitability of candidate reference genes (EF-1α, ACT1, GAPDH, 18S rRNA) in 6 combinations of YDV and vector aphid morph. EF-1α and ACT1 together or in combination with GAPDH or with GAPDH and 18S rRNA could confidently be used to normalize virus titre and expression levels of endogenous genes in winged or wingless R. padi infected with Barley yellow dwarf virus isolates (BYDV)-PAV and BYDV-GAV. The use of only one reference gene, whether the most stably expressed (EF-1α) or the least stably expressed (18S rRNA), was not adequate for obtaining valid relative expression data from the RT-qPCR. Because of discrepancies among values for changes in relative expression obtained using 3 regions of the same gene, different regions of an endogenous aphid gene, including each terminus and the middle, should be analyzed at the same time with RT-qPCR. Our results highlight the necessity of choosing the best reference genes to obtain valid experimental data and provide several HKGs for relative quantification of virus titre in YDV-viruliferous aphids. PMID:24810421

The ultimate veal calf reference experiment: hormone residue analysis data obtained by gas and liquid chromatography tandem mass spectrometry.

PubMed

Nielen, Michel W F; Lasaroms, Johan J P; Essers, Martien L; Sanders, Marieke B; Heskamp, Henri H; Bovee, Toine F H; van Rhijn, J Hans; Groot, Maria J

2007-03-14

A lifetime controlled reference experiment has been performed using 42 veal calves, 21 males and 21 females which were fed and housed according to European regulations and common veterinary practice. During the experiment feed, water, urine and hair were sampled and feed intake and growth were monitored. Thus for the first time residue analysis data were obtained from guaranteed lifetime-untreated animals. The analysis was focused on the natural hormones estradiol and testosterone and their metabolites, on 17beta- and 17alpha-nortestosterone, on 17beta- and 17alpha-boldenone and androsta-1,4-diene-3,17-dione (ADD), and carried out by gas chromatography tandem mass spectrometry (GC/MS/MS), an estrogen bioassay and liquid chromatography (LC) MS/MS. Feed, water and hair samples were negative for the residues tested. Female calf urines showed occasionally low levels of 17alpha-estradiol and 17alpha-testosterone. On one particular sampling day male veal calf urines showed very high levels of 17alpha-testosterone (up to 1000 ng mL(-1)), accompanied by lower levels of estrone and 17beta-testosterone. Despite these extreme levels of natural testosterone, 17beta-boldenone was never detected in the same urine samples; even 17alpha-boldenone and ADD were only occasionally beyond CCalpha (maximum levels 2.7 ng mL(-1)). The data from this unique experiment provide a set of reference values for steroid hormones in calf urine and demonstrate that 17beta-boldenone is not a naturally occurring compound in urine samples.

Referent Communication in Chronic Schizophrenia

ERIC Educational Resources Information Center

Kantorowitz, David A.; Cohen, Bertram D.

1977-01-01

Thirty chronic schizophrenics (15 process and 15 reactive) and 15 normal control speakers described colors displayed in three-chip sets containing a referent and two nonreferent colors. Concludes that poor communication accuracy in long-term schizophrenics results from failure to include a self-editing stage as a part of the communication process.…

[Preparation of flavonoid reference standards from Scutellariae Radix under the guidance of high performance liquid chromatography-mass spectrometry analysis].

PubMed

Guo, Henan; Yang, Xuedong; Liu, Jun; Zheng, Wenfeng

2012-07-01

Flavonoid reference standards were targeted-prepared from Scutellariae Radix under the guidance of high performance liquid chromatography-mass spectrometry (HPLC-MS) analysis. With HPLC-MS analysis of Scutellariae Radix, 19 flavonoid components were identified by analyzing and comparing their retention times, ultraviolet spectra, and mass spectrometry data with literature. The separation and purification protocols of all targeted flavonoid reference standards were optimally designed according to the results of HPLC-MS analysis and related literature. The ethanol extract of Scutellariae Radix was suspended in water and extracted with petroleum ether, ethyl acetate, and n-butanol successively. The ethyl acetate extract and n-butanol extract were separately subjected to primary separation by low pressure reverse phase preparative chromatography. Then the fractions containing targeted compounds were further purified by low pressure reverse and normal phases preparative chromatography. Finally, baicalin and wogonoside reference standards were obtained from n-butanol extract; baicaelin, wogonin, and oroxylin A reference standards were obtained from ethyl acetate extract. The structures of the 5 reference standards were identified by mass spectrometry (MS) and 1H nuclear magnetic resonance (1H NMR) spectroscopy. The HPLC analytical results showed that the purities of the 5 reference standards were all above 98%. It is demonstrated that the rapid targeted-preparation method under the guidance of the HPLC-MS analysis is applicable for the isolation and preparation of chemical components in traditional Chinese medicines.

A cross-sectional study of sarcopenia in Japanese men and women: reference values and association with cardiovascular risk factors.

PubMed

Sanada, K; Miyachi, M; Tanimoto, M; Yamamoto, K; Murakami, H; Okumura, S; Gando, Y; Suzuki, K; Tabata, I; Higuchi, M

2010-09-01

In this study of Japanese men and women, we determine reference values for sarcopenia and test the hypothesis that sarcopenia is associated with risk factors for cardiovascular disease, independent of waist circumference. A total of 1,488 Japanese men and women aged 18-85 years participated in this study. Appendicular muscle mass (AMM) was measured by dual-energy X-ray absorptiometry. Reference values for classes 1 and 2 sarcopenia (skeletal muscle index: AMM/height2, kg m-2) in each sex were defined as values one and two standard deviations below the sex-specific means of reference values obtained in this study from young adults aged 18-40 years. The reference values for class 1 and class 2 sarcopenia were 7.77 and 6.87 kg m-2 in men and 6.12 and 5.46 kg m-2 in women. In subjects both with class 1 and class 2 sarcopenia, body mass index and % body fat were significantly lower than in normal subjects. Despite whole-blood glycohaemoglobin A1c in men with class 1 sarcopenia was significantly higher than in normal subjects, and brachial-ankle pulse wave velocity in women both with class 1 and class 2 sarcopenia were significantly higher than in normal subjects, using one-way ANCOVA with adjustment for the covariate of waist circumference. Although sarcopenia is associated with thin body mass, it is associated with more glycation of serum proteins in men and with greater arterial stiffness in women, independent of waist circumference.

Normalization of respiratory sinus arrhythmia by factoring in tidal volume.

PubMed

Kobayashi, H

1998-09-01

The amplitude of respiratory sinus arrhythmia (RSA) was measured in eight healthy young male students with special reference to the effect of tidal volume (Vt). Under simultaneously controlled respiratory frequency and Vt, the heart rate variability (HRV) of the subjects was measured. While the respiratory frequency was adjusted to either 0.25 or 0.10 Hz, the Vt was controlled at 13 different volumes for each frequency. Linear relationships between RSA amplitude and Vt were observed and close correlations were obtained for 0.25 Hz compared with 0.10 Hz. However, regression equations showed a marked variation among subjects. Furthermore, RSA amplitude was related to vital capacity. Subjects who had lower vital capacity tended to show higher RSA amplitudes at the same Vt. Therefore, the ratio (% Vt) of Vt to vital capacity is a more effective index in normalizing RSA than raw tidal volume. From these results, we have proposed a normalized RSA (RSA amplitude/% Vt) as a new index of autonomic activity that provides a constant value regardless of Vt.

MSDS sky reference and preamplifier study

NASA Technical Reports Server (NTRS)

Larsen, L.; Stewart, S.; Lambeck, P.

1974-01-01

The major goals in re-designing the Multispectral Scanner and Data System (MSDS) sky reference are: (1) to remove the sun-elevation angle and aircraft-attitude angle dependence from the solar-sky illumination measurement, and (2) to obtain data on the optical state of the atmosphere. The present sky reference is dependent on solar elevation and provides essentially no information on important atmospheric parameters. Two sky reference designs were tested. One system is built around a hyperbolic mirror and the reflection approach. A second approach to a sky reference utilizes a fish-eye lens to obtain a 180 deg field of view. A detailed re-design of the present sky reference around the fish-eye approach, even with its limitations, is recommended for the MSDS system. A preamplifier study was undertaken to find ways of improving the noise-equivalent reflectance by reducing the noise level for silicon detector channels on the MSDS.

Development of Normalization Factors for Canada and the United States and Comparison with European Factors.

EPA Science Inventory

In Life Cycle Assessment (LCA), normalization calculates the magnitude of an impact (midpoint or endpoint) relative to the total effect of a given reference. Using a country or a continent as a reference system is a first step towards global normalization. The goal of this work ...

Development of Normalization Factors for Canada and the United States and Comparison with European Factors

EPA Science Inventory

In Life Cycle Assessment (LCA), normalization calculates the magnitude of an impact (midpoint or endpoint) relative to the total effect of a given reference. Using a country or a continent as a reference system is a first step towards global normalization. The goal of this wor...

Superior Cross-Species Reference Genes: A Blueberry Case Study

PubMed Central

Die, Jose V.; Rowland, Lisa J.

2013-01-01

The advent of affordable Next Generation Sequencing technologies has had major impact on studies of many crop species, where access to genomic technologies and genome-scale data sets has been extremely limited until now. The recent development of genomic resources in blueberry will enable the application of high throughput gene expression approaches that should relatively quickly increase our understanding of blueberry physiology. These studies, however, require a highly accurate and robust workflow and make necessary the identification of reference genes with high expression stability for correct target gene normalization. To create a set of superior reference genes for blueberry expression analyses, we mined a publicly available transcriptome data set from blueberry for orthologs to a set of Arabidopsis genes that showed the most stable expression in a developmental series. In total, the expression stability of 13 putative reference genes was evaluated by qPCR and a set of new references with high stability values across a developmental series in fruits and floral buds of blueberry were identified. We also demonstrated the need to use at least two, preferably three, reference genes to avoid inconsistencies in results, even when superior reference genes are used. The new references identified here provide a valuable resource for accurate normalization of gene expression in Vaccinium spp. and may be useful for other members of the Ericaceae family as well. PMID:24058469

Estimation of ultrasound reference values for the lower limb peripheral nerves in adults: A cross-sectional study.

PubMed

Bedewi, Mohamed Abdelmohsen; Abodonya, Ahmed; Kotb, Mamdouh; Kamal, Sanaa; Mahmoud, Gehan; Aldossari, Khaled; Alqabbani, Abdullah; Swify, Sherine

2018-03-01

The objective of this study is to estimate the reference values for the lower limb peripheral nerves in adults.The demographics and physical characteristics of 69 adult healthy volunteers were evaluated and recorded. The estimated reference values and their correlations with the age, weight, height, body mass index (BMI) were evaluated.The cross sectional area reference values were obtained at 5 predetermined sites for 3 important lower limb peripheral nerves. Our CSA values correlated significantly with age, weight, and BMI. The normal reference values for each nerve were as follows: Tibial nerve at the popliteal fossa 19 mm ± 6.9, tibial nerve at the level of the medial malleolus 12.7 mm ± 4.5, common peroneal nerve at the popliteal fossa 9.5 mm ± 4, common peroneal nerve fibular head 8.9 mm ± 3.2, sural nerve 3.5 mm ± 1.4.The reference values for the lower limb peripheral nerves were identified. These values could be used for future management of peripheral nerve disorders.

Effect of carbon monoxide on gene expression in cerebrocortical astrocytes: Validation of reference genes for quantitative real-time PCR.

PubMed

Oliveira, Sara R; Vieira, Helena L A; Duarte, Carlos B

2015-09-15

Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is a widely used technique to characterize changes in gene expression in complex cellular and tissue processes, such as cytoprotection or inflammation. The accurate assessment of changes in gene expression depends on the selection of adequate internal reference gene(s). Carbon monoxide (CO) affects several metabolic pathways and de novo protein synthesis is crucial in the cellular responses to this gasotransmitter. Herein a selection of commonly used reference genes was analyzed to identify the most suitable internal control genes to evaluate the effect of CO on gene expression in cultured cerebrocortical astrocytes. The cells were exposed to CO by treatment with CORM-A1 (CO releasing molecule A1) and four different algorithms (geNorm, NormFinder, Delta Ct and BestKeeper) were applied to evaluate the stability of eight putative reference genes. Our results indicate that Gapdh (glyceraldehyde-3-phosphate dehydrogenase) together with Ppia (peptidylpropyl isomerase A) is the most suitable gene pair for normalization of qRT-PCR results under the experimental conditions used. Pgk1 (phosphoglycerate kinase 1), Hprt1 (hypoxanthine guanine phosphoribosyl transferase I), Sdha (Succinate Dehydrogenase Complex, Subunit A), Tbp (TATA box binding protein), Actg1 (actin gamma 1) and Rn18s (18S rRNA) genes presented less stable expression profiles in cultured cortical astrocytes exposed to CORM-A1 for up to 60 min. For validation, we analyzed the effect of CO on the expression of Bdnf and bcl-2. Different results were obtained, depending on the reference genes used. A significant increase in the expression of both genes was found when the results were normalized with Gapdh and Ppia, in contrast with the results obtained when the other genes were used as reference. These findings highlight the need for a proper and accurate selection of the reference genes used in the quantification of qRT-PCR results

Electromagnetic Spectroscopy of Normal Breast Tissue Specimens Obtained From Reduction Surgeries: Comparison of Optical and Microwave Properties

PubMed Central

Lazebnik, Mariya; Zhu, Changfang; Palmer, Gregory M.; Harter, Josephine; Sewall, Sarah; Ramanujam, Nirmala; Hagness, Susan C.

2009-01-01

Techniques utilizing electromagnetic energy at microwave and optical frequencies have been shown to be promising for breast cancer detection and diagnosis. Since different biophysical mechanisms are exploited at these frequencies to discriminate between healthy and diseased tissue, combining these two modalities may result in a more powerful approach for breast cancer detection and diagnosis. Toward this end, we performed microwave dielectric spectroscopy and optical diffuse reflectance spectroscopy measurements at the same sites on freshly-excised normal breast tissues obtained from reduction surgeries at the University of Wisconsin Hospital, using microwave and optical probes with very similar sensing volumes. We found that the microwave dielectric constant and effective conductivity are correlated with tissue composition across the entire measurement frequency range (|r|~0.5–0.6, p<0.01), and that the optical absorption coefficient at 460 nm and optical scattering coefficient are correlated with tissue composition (|r|~ 0.4–0.6, p<0.02). Finally, we found that the optical absorption coefficient at 460 nm is correlated with the microwave dielectric constant and effective conductivity (r=−0.55, p<0.01). Our results suggest that combining optical and microwave modalities for analyzing breast tissue samples may serve as a crosscheck and provide complementary information about tissue composition. PMID:18838370

Electromagnetic spectroscopy of normal breast tissue specimens obtained from reduction surgeries: comparison of optical and microwave properties.

PubMed

Lazebnik, Mariya; Zhu, Changfang; Palmer, Gregory M; Harter, Josephine; Sewall, Sarah; Ramanujam, Nirmala; Hagness, Susan C

2008-10-01

Techniques utilizing electromagnetic energy at microwave and optical frequencies have been shown to be promising for breast cancer detection and diagnosis. Since different biophysical mechanisms are exploited at these frequencies to discriminate between healthy and diseased tissue, combining these two modalities may result in a more powerful approach for breast cancer detection and diagnosis. Toward this end, we performed microwave dielectric spectroscopy and optical diffuse reflectance spectroscopy measurements at the same sites on freshly excised normal breast tissues obtained from reduction surgeries at the University of Wisconsin Hospital, using microwave and optical probes with very similar sensing volumes. We found that the microwave dielectric constant and effective conductivity are correlated with tissue composition across the entire measurement frequency range (|r| approximately 0.5-0.6, p<0.01) and that the optical absorption coefficient at 460 nm and optical scattering coefficient are correlated with tissue composition (|r| approximately 0.4-0.6, p<0.02). Finally, we found that the optical absorption coefficient at 460 nm is correlated with the microwave dielectric constant and effective conductivity (r=-0.55, p<0.01). Our results suggest that combining optical and microwave modalities for analyzing breast tissue samples may serve as a crosscheck and provide complementary information about tissue composition.

Tests of Nacelle-Propeller Combinations in Various Positions with Reference to Wings II : Thick Wing - Various Radial-Engine Cowlings - Tractor Propeller

NASA Technical Reports Server (NTRS)

Wood, Donald H

1932-01-01

This report is the second of a series giving the results obtained in the 20-foot wind tunnel of the National Advisory Committee for Aeronautics on the interference drag and propulsive efficiency of nacelle-propeller-wing combinations. The first report gave the results of the test of a N.A.C.A. cowled air-cooled engine nacelle located in 21 positions with reference to a thick wing. The present report gives results of tests of a normal engine nacelle with several types of cowling and fairings in four of the positions with reference to the same wing. (author)

International normalized ratio (INR) testing in Europe: between-laboratory comparability of test results obtained by Quick and Owren reagents.

PubMed

Meijer, Piet; Kynde, Karin; van den Besselaar, Antonius M H P; Van Blerk, Marjan; Woods, Timothy A L

2018-04-12

This study was designed to obtain an overview of the analytical quality of the prothrombin time, reported as international normalized ratio (INR) and to assess the variation of INR results between European laboratories, the difference between Quick-type and Owren-type methods and the effect of using local INR calibration or not. In addition, we assessed the variation in INR results obtained for a single donation in comparison with a pool of several plasmas. A set of four different lyophilized plasma samples were distributed via national EQA organizations to participating laboratories for INR measurement. Between-laboratory variation was lower in the Owren group than in the Quick group (on average: 6.7% vs. 8.1%, respectively). Differences in the mean INR value between the Owren and Quick group were relatively small (<0.20 INR). Between-laboratory variation was lower after local INR calibration (CV: 6.7% vs. 8.6%). For laboratories performing local calibration, the between-laboratory variation was quite similar for the Owren and Quick group (on average: 6.5% and 6.7%, respectively). Clinically significant differences in INR results (difference in INR>0.5) were observed between different reagents. No systematic significant differences in the between-laboratory variation for a single-plasma sample and a pooled plasma sample were observed. The comparability for laboratories using local calibration of their thromboplastin reagent is better than for laboratories not performing local calibration. Implementing local calibration is strongly recommended for the measurement of INR.

National and international veterinary reference laboratories for infectious diseases.

PubMed

Edwards, S; Alexander, D

1998-08-01

Reference laboratories play an increasingly important role in the harmonisation of laboratory diagnostic tests and the standardisation of veterinary vaccines. This is particularly important in building confidence between international trading partners. The authors review aspects of the organisation, designation and support of reference laboratories for infectious diseases of animals and discuss the principal activities which such laboratories would normally perform. These activities include advice and consultancy, publications and communication, training, research, disease surveillance, maintenance of culture collections, evaluation of reference methods, preparation of reference materials and organisation of inter-laboratory comparisons.

Towards a Refined Realisation of the Terrestrial Reference System

NASA Astrophysics Data System (ADS)

Angermann, D.; Drewes, H.; Meisel, B.; Kruegel, M.; Tesmer, V.

2004-12-01

Global reference frames provide the framework for scientific investigations of the Earth's system (e.g. plate tectonics, sea level change, seasonal and secular loading signals, atmosphere dynamics, Earth orientation excitation), as well as for many practical applications (e.g. surveying and navigation). Today, space geodetic techniques allow to determine geodetic parameters (e.g. station positions, Earth rotation) with a precision of a few millimeters (or even better). However, this high accuracy is not reflected by current realisations of the terrestrial reference system. To fully exploit the potential of the space geodetic observations for investigations of various global and regional, short-term, seasonal and secular phenomena of the Earth's system, the reference frame must be realised with the highest accuracy, spatial and temporal consistency and stability over decades. Furthermore, future progress in Earth sciences will fundamentally depend on understanding the Earth as a system, into which the three areas of geodetic research (geometry/deformation, Earth rotation, gravity) are to be integrated. The presentation focusses on various aspects that must be considered for a refined realisation of the terrestrial reference system, such as the development of suitable methods for the combination of the contributing space geodetic observations, the realisation of the TRF datum and the parameterisation of site motions. For this purpose we investigated time series of station positions and datum parameters obtained from VLBI, SLR, GPS and DORIS solutions, and compared the results at co-location sites and with other studies. Furthermore, we present results obtained from a TRS realisation based on epoch (weekly/daily) normal equations with station positions and daily Earth Orientation Parameters (EOP) using five years (1999-2004) of VLBI, SLR, GPS and DORIS data. This refined approach has major advantages compared to past TRF realisations based on multi-year solutions with

Histological and reference system for the analysis of mouse intervertebral disc.

PubMed

Tam, Vivian; Chan, Wilson C W; Leung, Victor Y L; Cheah, Kathryn S E; Cheung, Kenneth M C; Sakai, Daisuke; McCann, Matthew R; Bedore, Jake; Séguin, Cheryle A; Chan, Danny

2018-01-01

A new scoring system based on histo-morphology of mouse intervertebral disc (IVD) was established to assess changes in different mouse models of IVD degeneration and repair. IVDs from mouse strains of different ages, transgenic mice, or models of artificially induced IVD degeneration were assessed. Morphological features consistently observed in normal, and early/later stages of degeneration were categorized into a scoring system focused on nucleus pulposus (NP) and annulus fibrosus (AF) changes. "Normal NP" exhibited a highly cellularized cell mass that decreased with natural ageing and in disc degeneration. "Normal AF" consisted of distinct concentric lamellar structures, which was disrupted in severe degeneration. NP/AF clefts indicated more severe changes. Consistent scores were obtained between experienced and new users. Altogether, our scoring system effectively differentiated IVD changes in various strains of wild-type and genetically modified mice and in induced models of IVD degeneration, and is applicable from the post-natal stage to the aged mouse. This scoring tool and reference resource addresses a pressing need in the field for studying IVD changes and cross-study comparisons in mice, and facilitates a means to normalize mouse IVD assessment between different laboratories. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:233-243, 2018. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Selection of Reliable Reference Genes for Gene Expression Studies on Rhododendron molle G. Don.

PubMed

Xiao, Zheng; Sun, Xiaobo; Liu, Xiaoqing; Li, Chang; He, Lisi; Chen, Shangping; Su, Jiale

2016-01-01

The quantitative real-time polymerase chain reaction (qRT-PCR) approach has become a widely used method to analyze expression patterns of target genes. The selection of an optimal reference gene is a prerequisite for the accurate normalization of gene expression in qRT-PCR. The present study constitutes the first systematic evaluation of potential reference genes in Rhododendron molle G. Don. Eleven candidate reference genes in different tissues and flowers at different developmental stages of R. molle were assessed using the following three software packages: GeNorm, NormFinder, and BestKeeper. The results showed that EF1- α (elongation factor 1-alpha), 18S (18s ribosomal RNA), and RPL3 (ribosomal protein L3) were the most stable reference genes in developing rhododendron flowers and, thus, in all of the tested samples, while tublin ( TUB ) was the least stable. ACT5 (actin), RPL3 , 18S , and EF1- α were found to be the top four choices for different tissues, whereas TUB was not found to favor qRT-PCR normalization in these tissues. Three stable reference genes are recommended for the normalization of qRT-PCR data in R. molle . Furthermore, the expression profiles of RmPSY (phytoene synthase) and RmPDS (phytoene dehydrogenase) were assessed using EF1- α, 18S , ACT5 , RPL3 , and their combination as internals. Similar trends were found, but these trends varied when the least stable reference gene TUB was used. The results further prove that it is necessary to validate the stability of reference genes prior to their use for normalization under different experimental conditions. This study provides useful information for reliable qRT-PCR data normalization in gene studies of R. molle .

Genome-wide identification of suitable zebrafish Danio rerio reference genes for normalization of gene expression data by RT-qPCR.

PubMed

Xu, H; Li, C; Zeng, Q; Agrawal, I; Zhu, X; Gong, Z

2016-06-01

In this study, to systematically identify the most stably expressed genes for internal reference in zebrafish Danio rerio investigations, 37 D. rerio transcriptomic datasets (both RNA sequencing and microarray data) were collected from gene expression omnibus (GEO) database and unpublished data, and gene expression variations were analysed under three experimental conditions: tissue types, developmental stages and chemical treatments. Forty-four putative candidate genes were identified with the c.v. <0·2 from all datasets. Following clustering into different functional groups, 21 genes, in addition to four conventional housekeeping genes (eef1a1l1, b2m, hrpt1l and actb1), were selected from different functional groups for further quantitative real-time (qrt-)PCR validation using 25 RNA samples from different adult tissues, developmental stages and chemical treatments. The qrt-PCR data were then analysed using the statistical algorithm refFinder for gene expression stability. Several new candidate genes showed better expression stability than the conventional housekeeping genes in all three categories. It was found that sep15 and metap1 were the top two stable genes for tissue types, ube2a and tmem50a the top two for different developmental stages, and rpl13a and rp1p0 the top two for chemical treatments. Thus, based on the extensive transcriptomic analyses and qrt-PCR validation, these new reference genes are recommended for normalization of D. rerio qrt-PCR data respectively for the three different experimental conditions. © 2016 The Fisheries Society of the British Isles.

Evaluation of a rebound tonometer (Tonovet) in clinically normal cat eyes.

PubMed

Rusanen, Elina; Florin, Marion; Hässig, Michael; Spiess, Bernhard M

2010-01-01

To determine the accuracy of and to establish reference values for a rebound tonometer (Tonovet) in normal feline eyes, to compare it with an applanation tonometer (Tonopen Vet) and to evaluate the effect of topical anesthesia on rebound tonometry. Six enucleated eyes were used to compare both tonometers with direct manometry. Intraocular pressure (IOP) was measured in 100 cats to establish reference values for rebound tonometry. Of these, 22 cats were used to compare rebound tonometry with and without topical anesthesia and 33 cats to compare the rebound and applanation tonometers. All evaluated eyes were free of ocular disease. Both tonometers correlated well with direct manometry. The best agreement with the rebound tonometer was achieved between 25-50 mmHg. The applanation tonometer was accurate at pressures between 0 and 30 mmHg. The mean IOP in clinically normal cats was 20.74 mmHg with the rebound tonometer and 18.4 mmHg with the applanation tonometer. Topical anesthesia did not significantly affect rebound tonometry. As the rebound tonometer correlated well with direct manometry in the clinically important pressure range and was well tolerated by cats, it appears suitable for glaucoma diagnosis. The mean IOP obtained with the rebound tonometer was 2-3 mmHg higher than that measured with the applanation tonometer. This difference is within clinically acceptable limits, but indicates that the same type of tonometer should be used in follow-up examinations in a given cat.

Developing a reference of normal lung sounds in healthy Peruvian children.

PubMed

Ellington, Laura E; Emmanouilidou, Dimitra; Elhilali, Mounya; Gilman, Robert H; Tielsch, James M; Chavez, Miguel A; Marin-Concha, Julio; Figueroa, Dante; West, James; Checkley, William

2014-10-01

Lung auscultation has long been a standard of care for the diagnosis of respiratory diseases. Recent advances in electronic auscultation and signal processing have yet to find clinical acceptance; however, computerized lung sound analysis may be ideal for pediatric populations in settings, where skilled healthcare providers are commonly unavailable. We described features of normal lung sounds in young children using a novel signal processing approach to lay a foundation for identifying pathologic respiratory sounds. 186 healthy children with normal pulmonary exams and without respiratory complaints were enrolled at a tertiary care hospital in Lima, Peru. Lung sounds were recorded at eight thoracic sites using a digital stethoscope. 151 (81%) of the recordings were eligible for further analysis. Heavy-crying segments were automatically rejected and features extracted from spectral and temporal signal representations contributed to profiling of lung sounds. Mean age, height, and weight among study participants were 2.2 years (SD 1.4), 84.7 cm (SD 13.2), and 12.0 kg (SD 3.6), respectively; and, 47% were boys. We identified ten distinct spectral and spectro-temporal signal parameters and most demonstrated linear relationships with age, height, and weight, while no differences with genders were noted. Older children had a faster decaying spectrum than younger ones. Features like spectral peak width, lower-frequency Mel-frequency cepstral coefficients, and spectro-temporal modulations also showed variations with recording site. Lung sound extracted features varied significantly with child characteristics and lung site. A comparison with adult studies revealed differences in the extracted features for children. While sound-reduction techniques will improve analysis, we offer a novel, reproducible tool for sound analysis in real-world environments.

Developing Normal Turns-Amplitude Clouds for Upper and Lower Limbs.

PubMed

Jabre, Joe F; Nikolayev, Sergey G; Babayev, Michael B; Chindilov, Denis V; Muravyov, Anatoly Y

2016-10-01

Turns and amplitude analysis (T&A) is a frequently used method for automatic EMG interference pattern analysis. The T&A normal values have only been developed for a limited number of muscles. Our objective was to obtain normal T&A clouds for upper and lower extremity muscles for which no normal values exist in the literature. The T&A normative data using concentric needle electrodes were obtained from 68 men and 56 women aged 20 to 60 years. Normal upper and lower extremity T&A clouds were obtained and presented in this article. The T&A normal values collected in this study maybe used to detect neurogenic and myopathic abnormalities in men and women at low-to-moderate muscle contractions. The effect of turns-amplitude data obtained at high force level of muscle contraction and its potential to falsely show neurogenic abnormalities are discussed.

Customized Internal Reference Controls for Improved Assessment of Circulating MicroRNAs in Disease.

PubMed

Schlosser, Kenny; McIntyre, Lauralyn A; White, R James; Stewart, Duncan J

2015-01-01

Altered levels of circulating extracellular miRNA in plasma and serum have shown promise as non-invasive biomarkers of disease. However, unlike the assessment of cellular miRNA levels for which there are accepted housekeeping genes, analogous reference controls for normalization of circulating miRNA are lacking. Here, we provide an approach to identify and validate circulating miRNA reference controls on a de novo basis, and demonstrate the advantages of these customized internal controls in different disease settings. Importantly, these internal controls overcome key limitations of external spike-in controls. Using a global RT-qPCR screen of 1066 miRNAs in plasma from pulmonary hypertension patients (PAH) and healthy subjects as a case example, we identified a large pool of initial candidate miRNAs that were systematically ranked according to their plasma level stability using a predefined algorithm. The performance of the top candidates was validated against multiple comparators, and in a second independent cohort of PAH and control subjects. The broader utility of this approach was demonstrated in a completely different disease setting with 372 miRNAs screened in plasma from septic shock patients and healthy controls. Normalization of data with specific internal reference controls significantly reduced the overall variation in circulating miRNA levels between subjects (relative to raw data), provided a more balanced distribution of up- and down-regulated miRNAs, replicated the results obtained by the benchmark geometric averaging of all detected miRNAs, and outperformed the commonly used external spike-in strategy. We demonstrate the feasibility of identifying circulating reference controls that can reduce extraneous technical variations, and improve the assessment of disease-related changes in plasma miRNA levels. This study provides a novel conceptual framework that addresses a critical and previously unmet need if circulating miRNAs are to advance as reliable

Customized Internal Reference Controls for Improved Assessment of Circulating MicroRNAs in Disease

PubMed Central

Schlosser, Kenny; McIntyre, Lauralyn A.; White, R. James; Stewart, Duncan J.

2015-01-01

Background Altered levels of circulating extracellular miRNA in plasma and serum have shown promise as non-invasive biomarkers of disease. However, unlike the assessment of cellular miRNA levels for which there are accepted housekeeping genes, analogous reference controls for normalization of circulating miRNA are lacking. Here, we provide an approach to identify and validate circulating miRNA reference controls on a de novo basis, and demonstrate the advantages of these customized internal controls in different disease settings. Importantly, these internal controls overcome key limitations of external spike-in controls. Methods Using a global RT-qPCR screen of 1066 miRNAs in plasma from pulmonary hypertension patients (PAH) and healthy subjects as a case example, we identified a large pool of initial candidate miRNAs that were systematically ranked according to their plasma level stability using a predefined algorithm. The performance of the top candidates was validated against multiple comparators, and in a second independent cohort of PAH and control subjects. The broader utility of this approach was demonstrated in a completely different disease setting with 372 miRNAs screened in plasma from septic shock patients and healthy controls. Results Normalization of data with specific internal reference controls significantly reduced the overall variation in circulating miRNA levels between subjects (relative to raw data), provided a more balanced distribution of up- and down-regulated miRNAs, replicated the results obtained by the benchmark geometric averaging of all detected miRNAs, and outperformed the commonly used external spike-in strategy. Conclusions We demonstrate the feasibility of identifying circulating reference controls that can reduce extraneous technical variations, and improve the assessment of disease-related changes in plasma miRNA levels. This study provides a novel conceptual framework that addresses a critical and previously unmet need if

Preserved pontine glucose metabolism in Alzheimer disease: A reference region for functional brain image (PET) analysis

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

Minoshima, Satoshi; Frey, K.A.; Foster, N.L.

1995-07-01

Our goal was to examine regional preservation of energy metabolism in Alzheimer disease (AD) and to evaluate effects of PET data normalization to reference regions. Regional metabolic rates in the pons, thalamus, putamen, sensorimotor cortex, visual cortex, and cerebellum (reference regions) were determined stereotaxically and examined in 37 patients with probable AD and 22 normal controls based on quantitative {sup 18}FDG-PET measurements. Following normalization of metabolic rates of the parietotemporal association cortex and whole brain to each reference region, distinctions of the two groups were assessed. The pons showed the best preservation of glucose metabolism in AD. Other reference regionsmore » showed relatively preserved metabolism compared with the parietotemporal association cortex and whole brain, but had significant metabolic reduction. Data normalization to the pons not only enhanced statistical significance of metabolic reduction in the parietotemporal association cortex, but also preserved the presence of global cerebral metabolic reduction indicated in analysis of the quantitative data. Energy metabolism in the pons in probable AD is well preserved. The pons is a reliable reference for data normalization and will enhance diagnostic accuracy and efficiency of quantitative and nonquantitative functional brain imaging. 39 refs., 2 figs., 3 tabs.« less

Geographical distribution of reference value of aging people's left ventricular end systolic diameter based on the support vector regression.

PubMed

Han, Xiao; Ge, Miao; Dong, Jie; Xue, Ranying; Wang, Zixuan; He, Jinwei

2014-09-01

The aim of this paper is to analyze the geographical distribution of reference value of aging people's left ventricular end systolic diameter (LVDs), and to provide a scientific basis for clinical examination. The study is focus on the relationship between reference value of left ventricular end systolic diameter of aging people and 14 geographical factors, selecting 2495 samples of left ventricular end systolic diameter (LVDs) of aging people in 71 units of China, in which including 1620 men and 875 women. By using the Moran's I index to make sure the relationship between the reference values and spatial geographical factors, extracting 5 geographical factors which have significant correlation with left ventricular end systolic diameter for building the support vector regression, detecting by the method of paired sample t test to make sure the consistency between predicted and measured values, finally, makes the distribution map through the disjunctive kriging interpolation method and fits the three-dimensional trend of normal reference value. It is found that the correlation between the extracted geographical factors and the reference value of left ventricular end systolic diameter is quite significant, the 5 indexes respectively are latitude, annual mean air temperature, annual mean relative humidity, annual precipitation amount, annual range of air temperature, the predicted values and the observed ones are in good conformity, there is no significant difference at 95% degree of confidence. The overall trend of predicted values increases from west to east, increases first and then decreases from north to south. If geographical values are obtained in one region, the reference value of left ventricular end systolic diameter of aging people in this region can be obtained by using the support vector regression model. It could be more scientific to formulate the different distributions on the basis of synthesizing the physiological and the geographical factors. -Use

Analysis of serum and cerebrospinal fluid in clinically normal adult miniature donkeys.

PubMed

Mozaffari, A A; Samadieh, H

2013-09-01

To establish reference intervals for serum and cerebrospinal fluid (CSF) parameters in clinically healthy adult miniature donkeys. Experiments were conducted on 10 female and 10 male clinically normal adult miniature donkeys, randomly selected from five herds. Lumbosacral CSF collection was performed with the sedated donkey in the standing position. Cell analysis was performed immediately after the samples were collected. Blood samples were obtained from the jugular vein immediately after CSF sample collection. Sodium, potassium, glucose, urea nitrogen, total protein, calcium, chloride, phosphorous and magnesium concentrations were measured in CSF and serum samples. A paired t-test was used to compare mean values between female and male donkeys. The CSF was uniformly clear, colourless and free from flocculent material, with a specific gravity of 1.002. The range of total nucleated cell counts was 2-4 cells/μL. The differential white cell count comprised only small lymphocytes. No erythrocytes or polymorphonuclear cells were observed on cytological examination. Reference values were obtained for biochemical analysis of serum and CSF. Gender had no effect on any variables measured in serum or CSF (p>0.05). CSF analysis can provide important information in addition to that gained by clinical examination. CSF analysis has not previously been performed in miniature donkeys; this is the first report on the subject. In the present study, reference intervals for total nucleated cell count, total protein, glucose, urea nitrogen, sodium, potassium, chloride, calcium, phosphorous and magnesium concentrations of serum and CSF were determined for male and female miniature donkeys.

Comparison of SSS and SRS calculated from normal databases provided by QPS and 4D-MSPECT manufacturers and from identical institutional normals.

PubMed

Knollmann, Daniela; Knebel, Ingrid; Koch, Karl-Christian; Gebhard, Michael; Krohn, Thomas; Buell, Ulrich; Schaefer, Wolfgang M

2008-02-01

There is proven evidence for the importance of myocardial perfusion-single-photon emission computed tomography (SPECT) with computerised determination of summed stress and rest scores (SSS/SRS) for the diagnosis of coronary artery disease (CAD). SSS and SRS can thereby be calculated semi-quantitatively using a 20-segment model by comparing tracer-uptake with values from normal databases (NDB). Four severity-degrees for SSS and SRS are normally used: <4, 4-8, 9-13, and > or =14. Manufacturers' NDBs (M-NDBs) often do not fit the institutional (I) settings. Therefore, this study compared SSS and SRS obtained with the algorithms Quantitative Perfusion SPECT (QPS) and 4D-MSPECT using M-NDB and I-NDB. I-NDBs were obtained using QPS and 4D-MSPECT from exercise stress data (450 MBq (99m)Tc-tetrofosmin, triple-head-camera, 30 s/view, 20 views/head) from 36 men with a low post-stress test CAD probability and visually normal SPECT findings. Patient group was 60 men showing the entire CAD-spectrum referred for routine perfusion-SPECT. Stress/rest results of automatic quantification of the 60 patients were compared to M-NDB and I-NDB. After reclassifying SSS/SRS into the four severity degrees, kappa values were calculated to objectify agreement. Mean values (vs M-NDB) were 9.4 +/- 10.3 (SSS) and 5.8 +/- 9.7 (SRS) for QPS and 8.2 +/- 8.7 (SSS) and 6.2 +/- 7.8 (SRS) for 4D-MSPECT. Thirty seven of sixty SSS classifications (kappa = 0.462) and 40/60 SRS classifications (kappa = 0.457) agreed. Compared to I-NDB, mean values were 10.2 +/- 11.6 (SSS) and 6.5 +/- 10.4 (SRS) for QPS and 9.2 +/- 9.3 (SSS) and 7.2 +/- 8.6 (SRS) for 4D-MSPECT. Forty four of sixty patients agreed in SSS and SRS (kappa = 0.621 resp. 0.58). Considerable differences between SSS/SRS obtained with QPS and 4D-MSPECT were found when using M-NDB. Even using identical patients and identical I-NDB, the algorithms still gave substantial different results.

Developing a Reference of Normal Lung Sounds in Healthy Peruvian Children

PubMed Central

Ellington, Laura E.; Emmanouilidou, Dimitra; Elhilali, Mounya; Gilman, Robert H.; Tielsch, James M.; Chavez, Miguel A.; Marin-Concha, Julio; Figueroa, Dante; West, James

2018-01-01

Purpose Lung auscultation has long been a standard of care for the diagnosis of respiratory diseases. Recent advances in electronic auscultation and signal processing have yet to find clinical acceptance; however, computerized lung sound analysis may be ideal for pediatric populations in settings, where skilled healthcare providers are commonly unavailable. We described features of normal lung sounds in young children using a novel signal processing approach to lay a foundation for identifying pathologic respiratory sounds. Methods 186 healthy children with normal pulmonary exams and without respiratory complaints were enrolled at a tertiary care hospital in Lima, Peru. Lung sounds were recorded at eight thoracic sites using a digital stethoscope. 151 (81 %) of the recordings were eligible for further analysis. Heavy-crying segments were automatically rejected and features extracted from spectral and temporal signal representations contributed to profiling of lung sounds. Results Mean age, height, and weight among study participants were 2.2 years (SD 1.4), 84.7 cm (SD 13.2), and 12.0 kg (SD 3.6), respectively; and, 47 % were boys. We identified ten distinct spectral and spectro-temporal signal parameters and most demonstrated linear relationships with age, height, and weight, while no differences with genders were noted. Older children had a faster decaying spectrum than younger ones. Features like spectral peak width, lower-frequency Mel-frequency cepstral coefficients, and spectro-temporal modulations also showed variations with recording site. Conclusions Lung sound extracted features varied significantly with child characteristics and lung site. A comparison with adult studies revealed differences in the extracted features for children. While sound-reduction techniques will improve analysis, we offer a novel, reproducible tool for sound analysis in real-world environments. PMID:24943262

Phase-Reference-Free Experiment of Measurement-Device-Independent Quantum Key Distribution

NASA Astrophysics Data System (ADS)

Wang, Chao; Song, Xiao-Tian; Yin, Zhen-Qiang; Wang, Shuang; Chen, Wei; Zhang, Chun-Mei; Guo, Guang-Can; Han, Zheng-Fu

2015-10-01

Measurement-device-independent quantum key distribution (MDI QKD) is a substantial step toward practical information-theoretic security for key sharing between remote legitimate users (Alice and Bob). As with other standard device-dependent quantum key distribution protocols, such as BB84, MDI QKD assumes that the reference frames have been shared between Alice and Bob. In practice, a nontrivial alignment procedure is often necessary, which requires system resources and may significantly reduce the secure key generation rate. Here, we propose a phase-coding reference-frame-independent MDI QKD scheme that requires no phase alignment between the interferometers of two distant legitimate parties. As a demonstration, a proof-of-principle experiment using Faraday-Michelson interferometers is presented. The experimental system worked at 1 MHz, and an average secure key rate of 8.309 bps was obtained at a fiber length of 20 km between Alice and Bob. The system can maintain a positive key generation rate without phase compensation under normal conditions. The results exhibit the feasibility of our system for use in mature MDI QKD devices and its value for network scenarios.

Calculation of conversion coefficients using Chinese adult reference phantoms for air submersion and ground contamination.

PubMed

Lu, Wei; Qiu, Rui; Wu, Zhen; Li, Chunyan; Yang, Bo; Liu, Huan; Ren, Li; Li, Junli

2017-03-21

The effective and organ equivalent dose coefficients have been widely used to provide assessment of doses received by adult members of the public and by workers exposed to environmental radiation from nuclear facilities under normal or accidental situations. Advancements in phantom types, weighting factors, decay data, etc, have led to the publication of newer results in this regard. This paper presents a new set of conversion coefficients for air submersion and ground contamination (with the use of Geant4) for photons from 15 keV to 10 MeV using the Chinese and International Commission on Radiological Protection (ICRP) adult reference male and female phantoms. The radiation fields, except for energy spectrum at low energies, were validated by the data obtained from the Monte Carlo code YURI. The effective dose coefficients of monoenergetic photons, obtained for the ICRP adult reference phantoms, agree well with recently published data for air submersion and ground contamination with a plane source at a depth of 0.5 g cm -2 in soil, but an average difference of 36.5% is observed for ground surface contamination with the abovementioned radiation field. The average differences in organ equivalent dose coefficients between the Chinese and the ICRP adult reference phantoms are within 6% for most organs, but noticeable differences of up to 70% or even higher are found at photon energies below 30 keV under air submersion. The effective dose coefficients obtained with the Chinese adult reference phantoms are greater than those of the ICRP adult reference phantoms above 30 keV and 0.5 MeV for ground contamination and air submersion, respectively; the average differences from the Chinese adult reference phantoms are about 3.6% and 0.4% in the whole energy range with maximum differences of 31.8% and 27.6% at 15 keV for air submersion and ground contamination respectively. These differences are attributed to anatomical discrepancies in overlying tissue mass of an

Calculation of conversion coefficients using Chinese adult reference phantoms for air submersion and ground contamination

NASA Astrophysics Data System (ADS)

Lu, Wei; Qiu, Rui; Wu, Zhen; Li, Chunyan; Yang, Bo; Liu, Huan; Ren, Li; Li, Junli

2017-03-01

The effective and organ equivalent dose coefficients have been widely used to provide assessment of doses received by adult members of the public and by workers exposed to environmental radiation from nuclear facilities under normal or accidental situations. Advancements in phantom types, weighting factors, decay data, etc, have led to the publication of newer results in this regard. This paper presents a new set of conversion coefficients for air submersion and ground contamination (with the use of Geant4) for photons from 15 keV to 10 MeV using the Chinese and International Commission on Radiological Protection (ICRP) adult reference male and female phantoms. The radiation fields, except for energy spectrum at low energies, were validated by the data obtained from the Monte Carlo code YURI. The effective dose coefficients of monoenergetic photons, obtained for the ICRP adult reference phantoms, agree well with recently published data for air submersion and ground contamination with a plane source at a depth of 0.5 g cm-2 in soil, but an average difference of 36.5% is observed for ground surface contamination with the abovementioned radiation field. The average differences in organ equivalent dose coefficients between the Chinese and the ICRP adult reference phantoms are within 6% for most organs, but noticeable differences of up to 70% or even higher are found at photon energies below 30 keV under air submersion. The effective dose coefficients obtained with the Chinese adult reference phantoms are greater than those of the ICRP adult reference phantoms above 30 keV and 0.5 MeV for ground contamination and air submersion, respectively; the average differences from the Chinese adult reference phantoms are about 3.6% and 0.4% in the whole energy range with maximum differences of 31.8% and 27.6% at 15 keV for air submersion and ground contamination respectively. These differences are attributed to anatomical discrepancies in overlying tissue mass of an

EMG normalization to study muscle activation in cycling.

PubMed

Rouffet, David M; Hautier, Christophe A

2008-10-01

The value of electromyography (EMG) is sensitive to many physiological and non-physiological factors. The purpose of the present study was to determine if the torque-velocity test (T-V) can be used to normalize EMG signals into a framework of biological significance. Peak EMG amplitude of gluteus maximus (GMAX), vastus lateralis (VL), rectus femoris (RF), biceps femoris long head (BF), gastrocnemius medialis (GAS) and soleus (SOL) was calculated for nine subjects during isometric maximal voluntary contractions (IMVC) and torque-velocity bicycling tests (T-V). Then, the reference EMG signals obtained from IMVC and T-V bicycling tests were used to normalize the amplitude of the EMG signals collected for 15 different submaximal pedaling conditions. The results of this study showed that the repeatability of the measurements between IMVC (from 10% to 23%) and T-V (from 8% to 20%) was comparable. The amplitude of the peak EMG of VL was 99+/-43% higher (p<0.001) when measured during T-V. Moreover, the inter-individual variability of the EMG patterns calculated for submaximal cycling exercises differed significantly when using T-V bicycling normalization method (GMAX: 0.33+/-0.16 vs. 1.09+/-0.04, VL: 0.07+/-0.02 vs. 0.64+/-0.14, SOL: 0.07+/-0.03 vs. 1.00+/-0.07, RF: 1.21+/-0.20 vs. 0.92+/-0.13, BF: 1.47+/-0.47 vs. 0.84+/-0.11). It was concluded that T-V bicycling test offers the advantage to be less time and energy-consuming and to be as repeatable as IMVC tests to measure peak EMG amplitude. Furthermore, this normalization method avoids the impact of non-physiological factors on the amplitude of the EMG signals so that it allows quantifying better the activation level of lower limb muscles and the variability of the EMG patterns during submaximal bicycling exercises.

21 CFR 660.3 - Reference panel.

Code of Federal Regulations, 2012 CFR

2012-04-01

... ADDITIONAL STANDARDS FOR DIAGNOSTIC SUBSTANCES FOR LABORATORY TESTS Antibody to Hepatitis B Surface Antigen § 660.3 Reference panel. A Reference Hepatitis B Surface Antigen Panel shall be obtained from the Center... shall be used for determining the potency and specificity of Antibody to Hepatitis B Surface Antigen...

21 CFR 660.3 - Reference panel.

Code of Federal Regulations, 2013 CFR

2013-04-01

... ADDITIONAL STANDARDS FOR DIAGNOSTIC SUBSTANCES FOR LABORATORY TESTS Antibody to Hepatitis B Surface Antigen § 660.3 Reference panel. A Reference Hepatitis B Surface Antigen Panel shall be obtained from the Center... shall be used for determining the potency and specificity of Antibody to Hepatitis B Surface Antigen...

21 CFR 660.3 - Reference panel.

Code of Federal Regulations, 2011 CFR

2011-04-01

... STANDARDS FOR DIAGNOSTIC SUBSTANCES FOR LABORATORY TESTS Antibody to Hepatitis B Surface Antigen § 660.3 Reference panel. A Reference Hepatitis B Surface Antigen Panel shall be obtained from the Center for... used for determining the potency and specificity of Antibody to Hepatitis B Surface Antigen. [40 FR...

21 CFR 660.3 - Reference panel.

Code of Federal Regulations, 2014 CFR

2014-04-01

... ADDITIONAL STANDARDS FOR DIAGNOSTIC SUBSTANCES FOR LABORATORY TESTS Antibody to Hepatitis B Surface Antigen § 660.3 Reference panel. A Reference Hepatitis B Surface Antigen Panel shall be obtained from the Center... shall be used for determining the potency and specificity of Antibody to Hepatitis B Surface Antigen...

21 CFR 660.3 - Reference panel.

Code of Federal Regulations, 2010 CFR

2010-04-01

... ADDITIONAL STANDARDS FOR DIAGNOSTIC SUBSTANCES FOR LABORATORY TESTS Antibody to Hepatitis B Surface Antigen § 660.3 Reference panel. A Reference Hepatitis B Surface Antigen Panel shall be obtained from the Center... shall be used for determining the potency and specificity of Antibody to Hepatitis B Surface Antigen...

Contrast sensitivity measured by two different test methods in healthy, young adults with normal visual acuity.

PubMed

Koefoed, Vilhelm F; Baste, Valborg; Roumes, Corinne; Høvding, Gunnar

2015-03-01

This study reports contrast sensitivity (CS) reference values obtained by two different test methods in a strictly selected population of healthy, young adults with normal uncorrected visual acuity. Based on these results, the index of contrast sensitivity (ICS) is calculated, aiming to establish ICS reference values for this population and to evaluate the possible usefulness of ICS as a tool to compare the degree of agreement between different CS test methods. Military recruits with best eye uncorrected visual acuity 0.00 LogMAR or better, normal colour vision and age 18-25 years were included in a study to record contrast sensitivity using Optec 6500 (FACT) at spatial frequencies of 1.5, 3, 6, 12 and 18 cpd in photopic and mesopic light and CSV-1000E at spatial frequencies of 3, 6, 12 and 18 cpd in photopic light. Index of contrast sensitivity was calculated based on data from the three tests, and the Bland-Altman technique was used to analyse the agreement between ICS obtained by the different test methods. A total of 180 recruits were included. Contrast sensitivity frequency data for all tests were highly skewed with a marked ceiling effect for the photopic tests. The median ICS for Optec 6500 at 85 cd/m2 was -0.15 (95% percentile 0.45), compared with -0.00 (95% percentile 1.62) for Optec at 3 cd/m2 and 0.30 (95% percentile 1.20) FOR CSV-1000E. The mean difference between ICSFACT 85 and ICSCSV was -0.43 (95% CI -0.56 to -0.30, p<0.00) with limits of agreement (LoA) within -2.10 and 1.22. The regression line on the difference of average was near to zero (R2=0.03). The results provide reference CS and ICS values in a young, adult population with normal visual acuity. The agreement between the photopic tests indicated that they may be used interchangeably. There was little agreement between the mesopic and photopic tests. The mesopic test seemed best suited to differentiate between candidates and may therefore possibly be useful for medical selection purposes. �

Simulations of normal and inverse laminar diffusion flames under oxygen enhancement and gravity variation

NASA Astrophysics Data System (ADS)

Bhatia, P.; Katta, V. R.; Krishnan, S. S.; Zheng, Y.; Sunderland, P. B.; Gore, J. P.

2012-10-01

Steady-state global chemistry calculations for 20 different flames were carried out using an axisymmetric Computational Fluid Dynamics (CFD) code. Computational results for 16 flames were compared with flame images obtained at the NASA Glenn Research Center. The experimental flame data for these 16 flames were taken from Sunderland et al. [4] which included normal and inverse diffusion flames of ethane with varying oxidiser compositions (21, 30, 50, 100% O2 mole fraction in N2) stabilised on a 5.5 mm diameter burner. The test conditions of this reference resulted in highly convective inverse diffusion flames (Froude numbers of the order of 10) and buoyant normal diffusion flames (Froude numbers ∼0.1). Additionally, six flames were simulated to study the effect of oxygen enhancement on normal diffusion flames. The enhancement in oxygen resulted in increased flame temperatures and the presence of gravity led to increased gas velocities. The effect of gravity-variation and oxygen enhancement on flame shape and size of normal diffusion flames was far more pronounced than for inverse diffusion flames. For normal-diffusion flames, their flame-lengths decreased (1 to 2 times) and flames-widths increased (2 to 3 times) when going from earth-gravity to microgravity, and flame height decreased by five times when going from air to a pure oxygen environment.

Regional ADC values of the normal brain: differences due to age, gender, and laterality.

PubMed

Naganawa, Shinji; Sato, Kimihide; Katagiri, Toshio; Mimura, Takeo; Ishigaki, Takeo

2003-01-01

The purpose of this study was to evaluate the stability of measurement for apparent diffusion coefficient (ADC) values in normal brain, to clarify the effect of aging on ADC values, to compare ADC values between men and women, and to compare ADC values between right and left sides of the brain. To evaluate the stability of measurements, five normal volunteers (four men and one woman) were examined five times on different days. Then, 294 subjects with normal MR imaging (147 men and 147 women; age range 20-89 years) were measured. The ADC measurement in normal volunteers was stable. The ADC values stayed within the 5% deviation of average values in all volunteers (mean+/-standard deviation 2.3+/-1.2%). The ADC values gradually increased by aging in all regions. In thalamus, no significant difference was seen between right and left in the subjects under 60 years; however, right side showed higher values in the subjects over 60 years (p<0.01). In the subjects under 60 years, women showed higher values in right frontal, bilateral thalamus, and temporal (p<0.01); however, in the subjects over 60 years, no region showed difference between men and women. The knowledge obtained in this study may be helpful to understand the developmental and aging mechanisms of normal brain and may be useful for the future quantitative study as a reference.

Improved ultrasonic standard reference blocks

NASA Technical Reports Server (NTRS)

Eitzen, D. G.; Sushinsky, G. F.; Chwirut, D. J.; Bechtoldt, C. J.; Ruff, A. W.

1976-01-01

A program to improve the quality, reproducibility and reliability of nondestructive testing through the development of improved ASTM-type ultrasonic reference standards is described. Reference blocks of aluminum, steel, and titanium alloys are to be considered. Equipment representing the state-of-the-art in laboratory and field ultrasonic equipment was obtained and evaluated. RF and spectral data on ten sets of ultrasonic reference blocks have been taken as part of a task to quantify the variability in response from nominally identical blocks. Techniques for residual stress, preferred orientation, and micro-structural measurements were refined and are applied to a reference block rejected by the manufacturer during fabrication in order to evaluate the effect of metallurgical condition on block response. New fabrication techniques for reference blocks are discussed and ASTM activities are summarized.

Histomorphometric reference data of transiliac bone biopsy in children from 8 to 17 years old.

PubMed

Velásquez-Forero, Francisco H; Jiménez-Brau, Daniel A; Esparza-García, Mariela

2018-01-01

Histomorphometric analysis of bone samples is a key tool for studying bone metabolism; however, only a few pediatric reference data exist. The aim of the present study is to report more reference data and to investigate if histomorphometric differences exist between age and gender. We obtained 19 transiliac bone samples previously marked with tetracycline, from children between 8 and 17 years (13 were male), with normal blood test results and urine biochemical bone markers. We evaluated bone histomorphometric parameters using a digitalizing table with osteomeasure to obtain normative data of means and standard deviations, as well as median and range. Due to the small sample, a Monte Carlo simulation was applied. Structural, static, dynamic, and resorptic histomorphometric parameters were evaluated by age and gender following the American Society for Bone and Mineral Research recommendations. Bone volume (in the older children) and mineral apposition rate (in the younger children), the eroded surface (in boys), and the new bone wall thickness (in girls) were significantly increased. On the trabecular area of mineralization front, the modeling and the remodeling bone formation were similar (16 and 18%). The rest of the histomorphometric bone parameters by age and gender showed no significant difference. In healthy children, these bone histomorphometric findings, with these techniques and for this ages could be used as reference values. Copyright: © 2018 Permanyer.

Flow derivatives and curvatures for a normal shock

NASA Astrophysics Data System (ADS)

Emanuel, G.

2018-03-01

A detached bow shock wave is strongest where it is normal to the upstream velocity. While the jump conditions across the shock are straightforward, many properties, such as the shock's curvatures and derivatives of the pressure, along and normal to a normal shock, are indeterminate. A novel procedure is introduced for resolving the indeterminacy when the unsteady flow is three-dimensional and the upstream velocity may be nonuniform. Utilizing this procedure, normal shock relations are provided for the nonunique orientation of the flow plane and the corresponding shock's curvatures and, e.g., the downstream normal derivatives of the pressure and the velocity components. These algebraic relations explicitly show the dependence of these parameters on the shock's shape and the upstream velocity gradient. A simple relation, valid only for a normal shock, is obtained for the average curvatures. Results are also obtained when the shock is an elliptic paraboloid shock. These derivatives are both simple and proportional to the average curvature.

Laser-induced differential normalized fluorescence method for cancer diagnosis

DOEpatents

Vo-Dinh, Tuan; Panjehpour, Masoud; Overholt, Bergein F.

1996-01-01

An apparatus and method for cancer diagnosis are disclosed. The diagnostic method includes the steps of irradiating a tissue sample with monochromatic excitation light, producing a laser-induced fluorescence spectrum from emission radiation generated by interaction of the excitation light with the tissue sample, and dividing the intensity at each wavelength of the laser-induced fluorescence spectrum by the integrated area under the laser-induced fluorescence spectrum to produce a normalized spectrum. A mathematical difference between the normalized spectrum and an average value of a reference set of normalized spectra which correspond to normal tissues is calculated, which provides for amplifying small changes in weak signals from malignant tissues for improved analysis. The calculated differential normalized spectrum is correlated to a specific condition of a tissue sample.

Comprehensive reference ranges for hematology and clinical chemistry laboratory parameters derived from normal Nigerian adults.

PubMed

Miri-Dashe, Timzing; Osawe, Sophia; Tokdung, Monday; Daniel, Monday Tokdung Nenbammun; Daniel, Nenbammun; Choji, Rahila Pam; Mamman, Ille; Deme, Kurt; Damulak, Dapus; Abimiku, Alash'le

2014-01-01

Interpretation of laboratory test results with appropriate diagnostic accuracy requires reference or cutoff values. This study is a comprehensive determination of reference values for hematology and clinical chemistry in apparently healthy voluntary non-remunerated blood donors and pregnant women. Consented clients were clinically screened and counseled before testing for HIV, Hepatitis B, Hepatitis C and Syphilis. Standard national blood donors' questionnaire was administered to consented blood donors. Blood from qualified volunteers was used for measurement of complete hematology and chemistry parameters. Blood samples were analyzed from a total of 383 participants, 124 (32.4%) males, 125 (32.6%) non-pregnant females and 134 pregnant females (35.2%) with a mean age of 31 years. Our results showed that the red blood cells count (RBC), Hemoglobin (HB) and Hematocrit (HCT) had significant gender difference (p = 0.000) but not for total white blood count (p>0.05) which was only significantly higher in pregnant verses non-pregnant women (p = 0.000). Hemoglobin and Hematocrit values were lower in pregnancy (P = 0.000). Platelets were significantly higher in females than men (p = 0.001) but lower in pregnant women (p =  .001) with marked difference in gestational period. For clinical chemistry parameters, there was no significant difference for sodium, potassium and chloride (p>0.05) but gender difference exists for Bicarbonate (HCO3), Urea nitrogen, Creatinine as well as the lipids (p<0.05). Total bilirubin was significantly higher in males than females (p = 0.000). Significant differences exist for all chemistry parameters between pregnant and non-pregnant women in this study (p<0.05), except Amylase and total cholesterol (p>0.05). Hematological and Clinical Chemistry reference ranges established in this study showed significant gender differences. Pregnant women also differed from non-pregnant females and during pregnancy. This is the first of such comprehensive

Improved ultrasonic standard reference blocks

NASA Technical Reports Server (NTRS)

Eitzen, D. G.

1975-01-01

A program to improve the quality, reproducibility and reliability of nondestructive testing through the development of improved ASTM-type ultrasonic reference standards is described. Reference blocks of aluminum, steel, and titanium alloys were considered. Equipment representing the state-of-the-art in laboratory and field ultrasonic equipment was obtained and evaluated. Some RF and spectral data on ten sets of ultrasonic reference blocks were taken as part of a task to quantify the variability in response from nominally identical blocks. Techniques for residual stress, preferred orientation, and microstructural measurements were refined and are applied to a reference block rejected by the manufacturer during fabrication in order to evaluate the effect of metallurgical condition on block response.

Harmonising Reference Intervals for Three Calculated Parameters used in Clinical Chemistry.

PubMed

Hughes, David; Koerbin, Gus; Potter, Julia M; Glasgow, Nicholas; West, Nic; Abhayaratna, Walter P; Cavanaugh, Juleen; Armbruster, David; Hickman, Peter E

2016-08-01

For more than a decade there has been a global effort to harmonise all phases of the testing process, with particular emphasis on the most frequently utilised measurands. In addition, it is recognised that calculated parameters derived from these measurands should also be a target for harmonisation. Using data from the Aussie Normals study we report reference intervals for three calculated parameters: serum osmolality, serum anion gap and albumin-adjusted serum calcium. The Aussie Normals study was an a priori study that analysed samples from 1856 healthy volunteers. The nine analytes used for the calculations in this study were measured on Abbott Architect analysers. The data demonstrated normal (Gaussian) distributions for the albumin-adjusted serum calcium, the anion gap (using potassium in the calculation) and the calculated serum osmolality (using both the Bhagat et al. and Smithline and Gardner formulae). To assess the suitability of these reference intervals for use as harmonised reference intervals, we reviewed data from the Royal College of Pathologists of Australasia/Australasian Association of Clinical Biochemists (RCPA/AACB) bias survey. We conclude that the reference intervals for the calculated serum osmolality (using the Smithline and Gardner formulae) may be suitable for use as a common reference interval. Although a common reference interval for albumin-adjusted serum calcium may be possible, further investigations (including a greater range of albumin concentrations) are needed. This is due to the bias between the Bromocresol Green (BCG) and Bromocresol Purple (BCP) methods at lower serum albumin concentrations. Problems with the measurement of Total CO 2 in the bias survey meant that we could not use the data for assessing the suitability of a common reference interval for the anion gap. Further study is required.

Selecting and validating reference genes for quantitative real-time PCR in Plutella xylostella (L.).

PubMed

You, Yanchun; Xie, Miao; Vasseur, Liette; You, Minsheng

2018-05-01

Gene expression analysis provides important clues regarding gene functions, and quantitative real-time PCR (qRT-PCR) is a widely used method in gene expression studies. Reference genes are essential for normalizing and accurately assessing gene expression. In the present study, 16 candidate reference genes (ACTB, CyPA, EF1-α, GAPDH, HSP90, NDPk, RPL13a, RPL18, RPL19, RPL32, RPL4, RPL8, RPS13, RPS4, α-TUB, and β-TUB) from Plutella xylostella were selected to evaluate gene expression stability across different experimental conditions using five statistical algorithms (geNorm, NormFinder, Delta Ct, BestKeeper, and RefFinder). The results suggest that different reference genes or combinations of reference genes are suitable for normalization in gene expression studies of P. xylostella according to the different developmental stages, strains, tissues, and insecticide treatments. Based on the given experimental sets, the most stable reference genes were RPS4 across different developmental stages, RPL8 across different strains and tissues, and EF1-α across different insecticide treatments. A comprehensive and systematic assessment of potential reference genes for gene expression normalization is essential for post-genomic functional research in P. xylostella, a notorious pest with worldwide distribution and a high capacity to adapt and develop resistance to insecticides.

Reference Standard Test and the Diagnostic Ability of Spectral Domain Optical Coherence Tomography in Glaucoma.

PubMed

Rao, Harsha L; Yadav, Ravi K; Addepalli, Uday K; Begum, Viquar U; Senthil, Sirisha; Choudhari, Nikhil S; Garudadri, Chandra S

2015-08-01

To evaluate the relationship between the reference standard used to diagnose glaucoma and the diagnostic ability of spectral domain optical coherence tomograph (SDOCT). In a cross-sectional study, 280 eyes of 175 consecutive subjects, referred to a tertiary eye care center for glaucoma evaluation, underwent optic disc photography, visual field (VF) examination, and SDOCT examination. The cohort was divided into glaucoma and control groups based on 3 reference standards for glaucoma diagnosis: first based on the optic disc classification (179 glaucoma and 101 control eyes), second on VF classification (glaucoma hemifield test outside normal limits and pattern SD with P-value of <5%, 130 glaucoma and 150 control eyes), and third on the presence of both glaucomatous optic disc and glaucomatous VF (125 glaucoma and 155 control eyes). Relationship between the reference standards and the diagnostic parameters of SDOCT were evaluated using areas under the receiver operating characteristic curve, sensitivity, and specificity. Areas under the receiver operating characteristic curve and sensitivities of most of the SDOCT parameters obtained with the 3 reference standards (ranging from 0.74 to 0.88 and 72% to 88%, respectively) were comparable (P>0.05). However, specificities of SDOCT parameters were significantly greater (P<0.05) with optic disc classification as reference standard (74% to 88%) compared with VF classification as reference standard (57% to 74%). Diagnostic parameters of SDOCT that was significantly affected by reference standard was the specificity, which was greater with optic disc classification as the reference standard. This has to be considered when comparing the diagnostic ability of SDOCT across studies.

Reliability of reference distances used in photogrammetry.

PubMed

Aksu, Muge; Kaya, Demet; Kocadereli, Ilken

2010-07-01

To determine the reliability of the reference distances used for photogrammetric assessment. The sample consisted of 100 subjects with mean ages of 22.97 +/- 2.98 years. Five lateral and four frontal parameters were measured directly on the subjects' faces. For photogrammetric assessment, two reference distances for the profile view and three reference distances for the frontal view were established. Standardized photographs were taken and all the parameters that had been measured directly on the face were measured on the photographs. The reliability of the reference distances was checked by comparing direct and indirect values of the parameters obtained from the subjects' faces and photographs. Repeated measure analysis of variance (ANOVA) and Bland-Altman analyses were used for statistical assessment. For profile measurements, the indirect values measured were statistically different from the direct values except for Sn-Sto in male subjects and Prn-Sn and Sn-Sto in female subjects. The indirect values of Prn-Sn and Sn-Sto were reliable in both sexes. The poorest results were obtained in the indirect values of the N-Sn parameter for female subjects and the Sn-Me parameter for male subjects according to the Sa-Sba reference distance. For frontal measurements, the indirect values were statistically different from the direct values in both sexes except for one in male subjects. The indirect values measured were not statistically different from the direct values for Go-Go. The indirect values of Ch-Ch were reliable in male subjects. The poorest results were obtained according to the P-P reference distance. For profile assessment, the T-Ex reference distance was reliable for Prn-Sn and Sn-Sto in both sexes. For frontal assessment, Ex-Ex and En-En reference distances were reliable for Ch-Ch in male subjects.

Magnetic resonance imaging of the normal bovine digit.

PubMed

Raji, A R; Sardari, K; Mirmahmoob, P

2009-08-01

The purpose of this study was defining the normal structures of the digits and hoof in Holstein dairy cattle using Magnetic Resonance Image (MRI). Transverse, Sagital and Dorsoplantar MRI images of three isolated cattle cadaver digits were obtained using Gyroscan T5-NT a magnet of 0.5 Tesla and T1 Weighted sequence. The MRI images were compared to corresponding frozen cross-sections and dissect specimens of the cadaver digits. Relevant anatomical structures were identified and labeled at each level. The MRI images provided anatomical detail of the digits and hoof in Holstein dairy cattle. Transversal images provided excellent depiction of anatomical structures when compared to corresponding frozen cross-sections. The information presented in this paper would serve as an initial reference to the evaluation of MRI images of the digits and hoof in Holstein dairy cattle, that can be used by radiologist, clinicians, surgeon or for research propose in bovine lameness.

Normalization for Relative Quantification of mRNA and microRNA in Soybean Exposed to Various Abiotic Stresses

PubMed Central

Zhou, Yonggang; Chen, Huan; Dong, Yuanyuan; Wang, Nan; Li, Xiaowei; Jameel, Aysha; Yang, He; Zhang, Min; Chen, Kai; Wang, Fawei; Li, Haiyan

2016-01-01

Plant microRNAs are small non-coding, endogenic RNA molecule (containing 20–24 nucleotides) produced from miRNA precursors (pri-miRNA and pre-miRNA). Evidence suggests that up and down regulation of the miRNA targets the mRNA genes involved in resistance against biotic and abiotic stresses. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a powerful technique to analyze variations in mRNA levels. Normalizing the data using reference genes is essential for the analysis of reliable RT-qPCR data. In this study, two groups of candidate reference mRNAs and miRNAs in soybean leaves and roots treated with various abiotic stresses (PEG-simulated drought, salinity, alkalinity, salinity+alkalinity, and abscisic acid) were analyzed by RT-qPCR. We analyzed the most appropriate reference mRNA/miRNAs using the geNorm, NormFinder, and BestKeeper algorithms. According to the results, Act and EF1b were the most suitable reference mRNAs in leaf and root samples, for mRNA and miRNA precursor data normalization. The most suitable reference miRNAs found in leaf and root samples were 166a and 167a for mature miRNA data normalization. Hence the best combinations of reference mRNAs for mRNA and miRNA precursor data normalization were EF1a + Act or EF1b + Act in leaf samples, and EF1a + EF1b or 60s + EF1b in root samples. For mature miRNA data normalization, the most suitable combinations of reference miRNAs were 166a + 167d in leaf samples, and 171a + 156a or 167a + 171a in root samples. We identified potential reference mRNA/miRNAs for accurate RT-qPCR data normalization for mature miRNA, miRNA precursors, and their targeted mRNAs. Our results promote miRNA-based studies on soybean plants exposed to abiotic stress conditions. PMID:27176476

Reference intervals for 24 laboratory parameters determined in 24-hour urine collections.

PubMed

Curcio, Raffaele; Stettler, Helen; Suter, Paolo M; Aksözen, Jasmin Barman; Saleh, Lanja; Spanaus, Katharina; Bochud, Murielle; Minder, Elisabeth; von Eckardstein, Arnold

2016-01-01

Reference intervals for many laboratory parameters determined in 24-h urine collections are either not publicly available or based on small numbers, not sex specific or not from a representative sample. Osmolality and concentrations or enzymatic activities of sodium, potassium, chloride, glucose, creatinine, citrate, cortisol, pancreatic α-amylase, total protein, albumin, transferrin, immunoglobulin G, α1-microglobulin, α2-macroglobulin, as well as porphyrins and their precursors (δ-aminolevulinic acid and porphobilinogen) were determined in 241 24-h urine samples of a population-based cohort of asymptomatic adults (121 men and 120 women). For 16 of these 24 parameters creatinine-normalized ratios were calculated based on 24-h urine creatinine. The reference intervals for these parameters were calculated according to the CLSI C28-A3 statistical guidelines. By contrast to most published reference intervals, which do not stratify for sex, reference intervals of 12 of 24 laboratory parameters in 24-h urine collections and of eight of 16 parameters as creatinine-normalized ratios differed significantly between men and women. For six parameters calculated as 24-h urine excretion and four parameters calculated as creatinine-normalized ratios no reference intervals had been published before. For some parameters we found significant and relevant deviations from previously reported reference intervals, most notably for 24-h urine cortisol in women. Ten 24-h urine parameters showed weak or moderate sex-specific correlations with age. By applying up-to-date analytical methods and clinical chemistry analyzers to 24-h urine collections from a large population-based cohort we provide as yet the most comprehensive set of sex-specific reference intervals calculated according to CLSI guidelines for parameters determined in 24-h urine collections.

The Normal Fetal Pancreas.

PubMed

Kivilevitch, Zvi; Achiron, Reuven; Perlman, Sharon; Gilboa, Yinon

2017-10-01

The aim of the study was to assess the sonographic feasibility of measuring the fetal pancreas and its normal development throughout pregnancy. We conducted a cross-sectional prospective study between 19 and 36 weeks' gestation. The study included singleton pregnancies with normal pregnancy follow-up. The pancreas circumference was measured. The first 90 cases were tested to assess feasibility. Two hundred ninety-seven fetuses of nondiabetic mothers were recruited during a 3-year period. The overall satisfactory visualization rate was 61.6%. The intraobserver and interobserver variability had high interclass correlation coefficients of of 0.964 and 0.967, respectively. A cubic polynomial regression described best the correlation of pancreas circumference with gestational age (r = 0.744; P < .001) and significant correlations also with abdominal circumference and estimated fetal weight (Pearson r = 0.829 and 0.812, respectively; P < .001). Modeled pancreas circumference percentiles for each week of gestation were calculated. During the study period, we detected 2 cases with overgrowth syndrome and 1 case with an annular pancreas. In this study, we assessed the feasibility of sonography for measuring the fetal pancreas and established a normal reference range for the fetal pancreas circumference throughout pregnancy. This database can be helpful when investigating fetomaternal disorders that can involve its normal development. © 2017 by the American Institute of Ultrasound in Medicine.

New spatial upscaling methods for multi-point measurements: From normal to p-normal

NASA Astrophysics Data System (ADS)

Liu, Feng; Li, Xin

2017-12-01

Careful attention must be given to determining whether the geophysical variables of interest are normally distributed, since the assumption of a normal distribution may not accurately reflect the probability distribution of some variables. As a generalization of the normal distribution, the p-normal distribution and its corresponding maximum likelihood estimation (the least power estimation, LPE) were introduced in upscaling methods for multi-point measurements. Six methods, including three normal-based methods, i.e., arithmetic average, least square estimation, block kriging, and three p-normal-based methods, i.e., LPE, geostatistics LPE and inverse distance weighted LPE are compared in two types of experiments: a synthetic experiment to evaluate the performance of the upscaling methods in terms of accuracy, stability and robustness, and a real-world experiment to produce real-world upscaling estimates using soil moisture data obtained from multi-scale observations. The results show that the p-normal-based methods produced lower mean absolute errors and outperformed the other techniques due to their universality and robustness. We conclude that introducing appropriate statistical parameters into an upscaling strategy can substantially improve the estimation, especially if the raw measurements are disorganized; however, further investigation is required to determine which parameter is the most effective among variance, spatial correlation information and parameter p.

46 CFR 160.023-1 - Incorporation by reference.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 6 2010-10-01 2010-10-01 false Incorporation by reference. 160.023-1 Section 160.023-1... Incorporation by reference. (a) The following are incorporated by reference into this subpart: (1) Military... specification may be obtained from Customer Service, Naval Publications and Forms Center, 5801 Tabor Avenue...

Enterprise Reference Library

NASA Technical Reports Server (NTRS)

Bickham, Grandin; Saile, Lynn; Havelka, Jacque; Fitts, Mary

2011-01-01

Introduction: Johnson Space Center (JSC) offers two extensive libraries that contain journals, research literature and electronic resources. Searching capabilities are available to those individuals residing onsite or through a librarian s search. Many individuals have rich collections of references, but no mechanisms to share reference libraries across researchers, projects, or directorates exist. Likewise, information regarding which references are provided to which individuals is not available, resulting in duplicate requests, redundant labor costs and associated copying fees. In addition, this tends to limit collaboration between colleagues and promotes the establishment of individual, unshared silos of information The Integrated Medical Model (IMM) team has utilized a centralized reference management tool during the development, test, and operational phases of this project. The Enterprise Reference Library project expands the capabilities developed for IMM to address the above issues and enhance collaboration across JSC. Method: After significant market analysis for a multi-user reference management tool, no available commercial tool was found to meet this need, so a software program was built around a commercial tool, Reference Manager 12 by The Thomson Corporation. A use case approach guided the requirements development phase. The premise of the design is that individuals use their own reference management software and export to SharePoint when their library is incorporated into the Enterprise Reference Library. This results in a searchable user-specific library application. An accompanying share folder will warehouse the electronic full-text articles, which allows the global user community to access full -text articles. Discussion: An enterprise reference library solution can provide a multidisciplinary collection of full text articles. This approach improves efficiency in obtaining and storing reference material while greatly reducing labor, purchasing and

Laser-induced differential normalized fluorescence method for cancer diagnosis

DOEpatents

Vo-Dinh, T.; Panjehpour, M.; Overholt, B.F.

1996-12-03

An apparatus and method for cancer diagnosis are disclosed. The diagnostic method includes the steps of irradiating a tissue sample with monochromatic excitation light, producing a laser-induced fluorescence spectrum from emission radiation generated by interaction of the excitation light with the tissue sample, and dividing the intensity at each wavelength of the laser-induced fluorescence spectrum by the integrated area under the laser-induced fluorescence spectrum to produce a normalized spectrum. A mathematical difference between the normalized spectrum and an average value of a reference set of normalized spectra which correspond to normal tissues is calculated, which provides for amplifying small changes in weak signals from malignant tissues for improved analysis. The calculated differential normalized spectrum is correlated to a specific condition of a tissue sample. 5 figs.

Computed tomographic and cross-sectional anatomy of the normal pacu (Colossoma macroponum).

PubMed

Carr, Alaina; Weber, E P Scott; Murphy, Chris J; Zwingenberger, Alison

2014-03-01

The purpose of this study was to compare and define the normal cross-sectional gross and computed tomographic (CT) anatomy for a species of boney fish to better gain insight into the use of advanced diagnostic imaging for future clinical cases. The pacu (Colossoma macropomum) was used because of its widespread presence in the aquarium trade, its relatively large body size, and its importance in the research and aquaculture settings. Transverse 0.6-mm CT images of three cadaver fish were obtained and compared to corresponding frozen cross sections of the fish. Relevant anatomic structures were identified and labeled at each level; the Hounsfield unit density of major organs was established. The images presented good anatomic detail and provide a reference for future research and clinical investigation.

Hearing Tests on Mobile Devices: Evaluation of the Reference Sound Level by Means of Biological Calibration.

PubMed

Masalski, Marcin; Kipiński, Lech; Grysiński, Tomasz; Kręcicki, Tomasz

2016-05-30

Hearing tests carried out in home setting by means of mobile devices require previous calibration of the reference sound level. Mobile devices with bundled headphones create a possibility of applying the predefined level for a particular model as an alternative to calibrating each device separately. The objective of this study was to determine the reference sound level for sets composed of a mobile device and bundled headphones. Reference sound levels for Android-based mobile devices were determined using an open access mobile phone app by means of biological calibration, that is, in relation to the normal-hearing threshold. The examinations were conducted in 2 groups: an uncontrolled and a controlled one. In the uncontrolled group, the fully automated self-measurements were carried out in home conditions by 18- to 35-year-old subjects, without prior hearing problems, recruited online. Calibration was conducted as a preliminary step in preparation for further examination. In the controlled group, audiologist-assisted examinations were performed in a sound booth, on normal-hearing subjects verified through pure-tone audiometry, recruited offline from among the workers and patients of the clinic. In both the groups, the reference sound levels were determined on a subject's mobile device using the Bekesy audiometry. The reference sound levels were compared between the groups. Intramodel and intermodel analyses were carried out as well. In the uncontrolled group, 8988 calibrations were conducted on 8620 different devices representing 2040 models. In the controlled group, 158 calibrations (test and retest) were conducted on 79 devices representing 50 models. Result analysis was performed for 10 most frequently used models in both the groups. The difference in reference sound levels between uncontrolled and controlled groups was 1.50 dB (SD 4.42). The mean SD of the reference sound level determined for devices within the same model was 4.03 dB (95% CI 3

ESTABLISHMENT OF A FIBRINOGEN REFERENCE INTERVAL IN ORNATE BOX TURTLES (TERRAPENE ORNATA ORNATA).

PubMed

Parkinson, Lily; Olea-Popelka, Francisco; Klaphake, Eric; Dadone, Liza; Johnston, Matthew

2016-09-01

This study sought to establish a reference interval for fibrinogen in healthy ornate box turtles ( Terrapene ornata ornata). A total of 48 turtles were enrolled, with 42 turtles deemed to be noninflammatory and thus fitting the inclusion criteria and utilized to estimate a fibrinogen reference interval. Turtles were excluded based upon physical examination and blood work abnormalities. A Shapiro-Wilk normality test indicated that the noninflammatory turtle fibrinogen values were normally distributed (Gaussian distribution) with an average of 108 mg/dl and a 95% confidence interval of the mean of 97.9-117 mg/dl. Those turtles excluded from the reference interval because of abnormalities affecting their health had significantly different fibrinogen values (P = 0.313). A reference interval for healthy ornate box turtles was calculated. Further investigation into the utility of fibrinogen measurement for clinical usage in ornate box turtles is warranted.

Identification and validation of reference genes for qRT-PCR studies of the obligate aphid pathogenic fungus Pandora neoaphidis during different developmental stages.

PubMed

Zhang, Shutao; Chen, Chun; Xie, Tingna; Ye, Sudan

2017-01-01

The selection of stable reference genes is a critical step for the accurate quantification of gene expression. To identify and validate the reference genes in Pandora neoaphidis-an obligate aphid pathogenic fungus-the expression of 13classical candidate reference genes were evaluated by quantitative real-time reverse transcriptase polymerase chain reaction(qPCR) at four developmental stages (conidia, conidia with germ tubes, short hyphae and elongated hyphae). Four statistical algorithms, including geNorm, NormFinder, BestKeeper and Delta Ct method were used to rank putative reference genes according to their expression stability and indicate the best reference gene or combination of reference genes for accurate normalization. The analysis of comprehensive ranking revealed that ACT1and 18Swas the most stably expressed genes throughout the developmental stages. To further validate the suitability of the reference genes identified in this study, the expression of cell division control protein 25 (CDC25) and Chitinase 1(CHI1) genes were used to further confirm the validated candidate reference genes. Our study presented the first systematic study of reference gene(s) selection for P. neoaphidis study and provided guidelines to obtain more accurate qPCR results for future developmental efforts.

Selection of reliable reference genes for quantitative real-time PCR gene expression analysis in Jute (Corchorus capsularis) under stress treatments

PubMed Central

Niu, Xiaoping; Qi, Jianmin; Zhang, Gaoyang; Xu, Jiantang; Tao, Aifen; Fang, Pingping; Su, Jianguang

2015-01-01

To accurately measure gene expression using quantitative reverse transcription PCR (qRT-PCR), reliable reference gene(s) are required for data normalization. Corchorus capsularis, an annual herbaceous fiber crop with predominant biodegradability and renewability, has not been investigated for the stability of reference genes with qRT-PCR. In this study, 11 candidate reference genes were selected and their expression levels were assessed using qRT-PCR. To account for the influence of experimental approach and tissue type, 22 different jute samples were selected from abiotic and biotic stress conditions as well as three different tissue types. The stability of the candidate reference genes was evaluated using geNorm, NormFinder, and BestKeeper programs, and the comprehensive rankings of gene stability were generated by aggregate analysis. For the biotic stress and NaCl stress subsets, ACT7 and RAN were suitable as stable reference genes for gene expression normalization. For the PEG stress subset, UBC, and DnaJ were sufficient for accurate normalization. For the tissues subset, four reference genes TUBβ, UBI, EF1α, and RAN were sufficient for accurate normalization. The selected genes were further validated by comparing expression profiles of WRKY15 in various samples, and two stable reference genes were recommended for accurate normalization of qRT-PCR data. Our results provide researchers with appropriate reference genes for qRT-PCR in C. capsularis, and will facilitate gene expression study under these conditions. PMID:26528312

Normal Doppler velocimetry of renal vasculature in Persian cats.

PubMed

Carvalho, Cibele F; Chammas, Maria C

2011-06-01

Renal diseases are common in older cats. Decreased renal blood flow may be the first sign of dysfunction and can be evaluated by Doppler ultrasound. But previous studies suggest that the resistive index (RI) has a low sensitivity for detecting renal disease. Doppler waveforms of renal and intrarenal arteries demonstrate decreased blood flow before there are any changes in the RI. The purpose of this study was to evaluate the normal Doppler flowmetrics parameters of renal arteries (RAs), interlobar arteries (IAs) and abdominal aorta (AO) in adult healthy, Persian cats. Twenty-five Persian cats (13 females and 12 males with mean age of 30 months and an age range 12-60 months) with normal clinical examinations and biochemical tests and normal systemic blood pressure were given B-mode ultrasonographies in order to exclude all nephropathies, including polycystic kidney disease. All measurements were performed on both kidneys. Both kidneys (n=50) were examined by color mapping of the renal vasculature. Pulsed Doppler was used to examine both RAs, the IAs at cranial, middle and caudal sites, and the AO. The RI was calculated for all of the vessels. Early systolic acceleration (ESA) of RA and IA was obtained with Doppler spectral analysis. Furthermore, the ratio indices between RA/AO, and IA/RA velocities were calculated. The mean values of peak systolic velocity (PSV) and the diameter for AO were 53.17±13.46 cm/s and 0.38±0.08 cm, respectively. The mean RA diameter for all 50 kidneys was 0.15±0.02 cm. Considering the velocimetric values in both RAs, the mean PSV and RI that were obtained were 41.17±9.40 cm/s and 0.54±0.07. The RA had a mean ESA of 1.12±1.14 m/s(2) and the calculated upper limit of the reference value was 3.40 m/s(2). The mean renal-aortic ratio was 0.828±0.296. The IA showed PSV and RI values of 32.16±9.33 cm/s and 0.52±0.06, respectively. The mean ESA of all IAs was 0.73±0.61 m/s(2). The calculated upper limit of the reference value was 2.0m

Reference-tissue correction of T2-weighted signal intensity for prostate cancer detection

NASA Astrophysics Data System (ADS)

Peng, Yahui; Jiang, Yulei; Oto, Aytekin

2014-03-01

The purpose of this study was to investigate whether correction with respect to reference tissue of T2-weighted MRimage signal intensity (SI) improves its effectiveness for classification of regions of interest (ROIs) as prostate cancer (PCa) or normal prostatic tissue. Two image datasets collected retrospectively were used in this study: 71 cases acquired with GE scanners (dataset A), and 59 cases acquired with Philips scanners (dataset B). Through a consensus histology- MR correlation review, 175 PCa and 108 normal-tissue ROIs were identified and drawn manually. Reference-tissue ROIs were selected in each case from the levator ani muscle, urinary bladder, and pubic bone. T2-weighted image SI was corrected as the ratio of the average T2-weighted image SI within an ROI to that of a reference-tissue ROI. Area under the receiver operating characteristic curve (AUC) was used to evaluate the effectiveness of T2-weighted image SIs for differentiation of PCa from normal-tissue ROIs. AUC (+/- standard error) for uncorrected T2-weighted image SIs was 0.78+/-0.04 (datasets A) and 0.65+/-0.05 (datasets B). AUC for corrected T2-weighted image SIs with respect to muscle, bladder, and bone reference was 0.77+/-0.04 (p=1.0), 0.77+/-0.04 (p=1.0), and 0.75+/-0.04 (p=0.8), respectively, for dataset A; and 0.81+/-0.04 (p=0.002), 0.78+/-0.04 (p<0.001), and 0.79+/-0.04 (p<0.001), respectively, for dataset B. Correction in reference to the levator ani muscle yielded the most consistent results between GE and Phillips images. Correction of T2-weighted image SI in reference to three types of extra-prostatic tissue can improve its effectiveness for differentiation of PCa from normal-tissue ROIs, and correction in reference to the levator ani muscle produces consistent T2-weighted image SIs between GE and Phillips MR images.

Mean flow generation mechanism by inertial waves and normal modes

NASA Astrophysics Data System (ADS)

Will, Andreas; Ghasemi, Abouzar

2016-04-01

The mean flow generation mechanism by nonlinearity of the inertial normal modes and inertial wave beams in a rotating annular cavity with longitudinally librating walls in stable regime is discussed. Inertial normal modes (standing waves) are excited when libration frequency matches eigenfrequencies of the system. Inertial wave beams are produced by Ekman pumping and suction in a rotating cylinder and form periodic orbits or periodic ray trajectories at selected frequencies. Inertial wave beams emerge as concentrated shear layers in a librating annular cavity, while normal modes appear as global recirculation cells. Both (inertial wave beam and mode) are helical and thus intrinsically non-linear flow structures. No second mode or wave is necessary for non-linearity. We considered the low order normal modes (1,1), (2,1) and (2,2) which are expected to be excited in the planetary objects and investigate the mean flow generation mechanism using two independent solutions: 1) analytical solution (Borcia 2012) and 2) the wave component of the flow (ω0 component) obtained from the direct numerical simulation (DNS). It is well known that a retrograde bulk mean flow is generated by the Ekman boundary layer and E1/4-Stewartson layer close to the outer cylinder side wall due to libration. At and around the normal mode resonant frequencies we found additionally a prograde azimuthal mean flow (Inertial Normal Mode Mean Flow: INMMF) in the bulk of the fluid. The fluid in the bulk is in geostrophic balance in the absence of the inertial normal modes. However, when INMMF is excited, we found that the geostrophic balance does not hold in the region occupied by INMMF. We hypothesize that INMMF is generated by the nonlinearity of the normal modes or by second order effects. Expanding the velocity {V}(u_r,u_θ,u_z) and pressure (p) in a power series in ɛ (libration amplitude), the Navier-Stokes equations are segregated into the linear and nonlinear parts at orders ɛ1 and ɛ^2

Characterizing functional lung heterogeneity in COPD using reference equations for CT scan-measured lobar volumes.

PubMed

Come, Carolyn E; Diaz, Alejandro A; Curran-Everett, Douglas; Muralidhar, Nivedita; Hersh, Craig P; Zach, Jordan A; Schroeder, Joyce; Lynch, David A; Celli, Bartolome; Washko, George R

2013-06-01

CT scanning is increasingly used to characterize COPD. Although it is possible to obtain CT scan-measured lung lobe volumes, normal ranges remain unknown. Using COPDGene data, we developed reference equations for lobar volumes at maximal inflation (total lung capacity [TLC]) and relaxed exhalation (approximating functional residual capacity [FRC]). Linear regression was used to develop race-specific (non-Hispanic white [NHW], African American) reference equations for lobar volumes. Covariates included height and sex. Models were developed in a derivation cohort of 469 subjects with normal pulmonary function and validated in 546 similar subjects. These cohorts were combined to produce final prediction equations, which were applied to 2,191 subjects with old GOLD (Global Initiative for Chronic Obstructive Lung Disease) stage II to IV COPD. In the derivation cohort, women had smaller lobar volumes than men. Height positively correlated with lobar volumes. Adjusting for height, NHWs had larger total lung and lobar volumes at TLC than African Americans; at FRC, NHWs only had larger lower lobes. Age and weight had no effect on lobar volumes at TLC but had small effects at FRC. In subjects with COPD at TLC, upper lobes exceeded 100% of predicted values in GOLD II disease; lower lobes were only inflated to this degree in subjects with GOLD IV disease. At FRC, gas trapping was severe irrespective of disease severity and appeared uniform across the lobes. Reference equations for lobar volumes may be useful in assessing regional lung dysfunction and how it changes in response to pharmacologic therapies and surgical or endoscopic lung volume reduction.

Selection of reliable reference genes for normalization of quantitative RT-PCR from different developmental stages and tissues in amphioxus

PubMed Central

Zhang, Qi-Lin; Zhu, Qian-Hua; Liao, Xin; Wang, Xiu-Qiang; Chen, Tao; Xu, Han-Ting; Wang, Juan; Yuan, Ming-Long; Chen, Jun-Yuan

2016-01-01

Amphioxus is a closest living proxy to the ancestor of cephalochordates with vertebrates, and key animal for novel understanding in the evolutionary origin of vertebrate body plan, genome, tissues and immune system. Reliable analyses using quantitative real-time PCR (qRT-PCR) for answering these scientific questions is heavily dependent on reliable reference genes (RGs). In this study, we evaluated stability of thirteen candidate RGs in qRT-PCR for different developmental stages and tissues of amphioxus by four independent (geNorm, NormFinder, BestKeeper and deltaCt) and one comparative algorithms (RefFinder). The results showed that the top two stable RGs were the following: (1) S20 and 18 S in thirteen developmental stages, (2) EF1A and ACT in seven normal tissues, (3) S20 and L13 in both intestine and hepatic caecum challenged with lipopolysaccharide (LPS), and (4) S20 and EF1A in gill challenged with LPS. The expression profiles of two target genes (EYA and HHEX) in thirteen developmental stages were used to confirm the reliability of chosen RGs. This study identified optimal RGs that can be used to accurately measure gene expression under these conditions, which will benefit evolutionary and functional genomics studies in amphioxus. PMID:27869224

[Scientific writing: the choice of references].

PubMed

Maisonneuve, H

1994-01-01

Only "acceptable" references can be cited, i.e. references that the reader can find easily. Only published work must be referenced, and the author must only cite those papers he or she has actually read. These should be avoided, as they are always difficult to obtain. Conference abstracts are published either in the conference report handed to participants alone, or in special issues of journals. Only the latter should be cited, when necessary. References to oral presentations are not accepted. References to personal communications should not be included in the list of references. The author cited must have given express permission. "Secondhand" references, i.e. those the author has not taken time to read yet quotes nonetheless, are prohibited. Manuscripts submitted for publication should not be cited. Articles accepted for publications can be referenced as "In press; "name of journal".

Identification of Reference Genes for RT-qPCR Data Normalization in Cannabis sativa Stem Tissues.

PubMed

Mangeot-Peter, Lauralie; Legay, Sylvain; Hausman, Jean-Francois; Esposito, Sergio; Guerriero, Gea

2016-09-15

Gene expression profiling via quantitative real-time PCR is a robust technique widely used in the life sciences to compare gene expression patterns in, e.g., different tissues, growth conditions, or after specific treatments. In the field of plant science, real-time PCR is the gold standard to study the dynamics of gene expression and is used to validate the results generated with high throughput techniques, e.g., RNA-Seq. An accurate relative quantification of gene expression relies on the identification of appropriate reference genes, that need to be determined for each experimental set-up used and plant tissue studied. Here, we identify suitable reference genes for expression profiling in stems of textile hemp (Cannabis sativa L.), whose tissues (isolated bast fibres and core) are characterized by remarkable differences in cell wall composition. We additionally validate the reference genes by analysing the expression of putative candidates involved in the non-oxidative phase of the pentose phosphate pathway and in the first step of the shikimate pathway. The goal is to describe the possible regulation pattern of some genes involved in the provision of the precursors needed for lignin biosynthesis in the different hemp stem tissues. The results here shown are useful to design future studies focused on gene expression analyses in hemp.

Reference values of aortic pulse wave velocity in the elderly.

PubMed

Alecu, Cosmin; Labat, Carlos; Kearney-Schwartz, Anna; Fay, Renaud; Salvi, Paolo; Joly, Laure; Lacolley, Patrick; Vespignani, Hervé; Benetos, Athanase

2008-11-01

Increased aortic pulse wave velocity (AoPWV) is an independent predictor of cardiovascular morbidity and mortality. There are, however, no generally accepted limits for defining the normal or reference values. The aim of the present study was to define reference values for AoPWV. AoPWV was assessed using applanation tonometry (PulsePen device) in a community living ambulatory population of 455 individuals aged 60-75 years. AoPWV was studied in a group of 206 individuals without hypertension or diabetes, called the 'reference-values group' (RVG), and in a group of 249 individuals with hypertension or diabetes, called the hypertension-diabetes group (HDG). The 95th percentile of the samples was used to determine the upper limit of AoPWV reference values. Mean AoPWV was 8.7+/-2.3 m/s in the RVG and 10.2+/-2.5 m/s in the hypertension-diabetes group (P<0.0001). In the RVG, median AoPWV in the three age subgroups was 8.0 m/s (7.6-8.5) in the 60-64-, 8.0 m/s (7.5-9.0) in the 65-69- and 9.0 m/s (7.9-9.5) in the 70-75-year-old group (NS among groups). In the entire RVG, the upper bounds of the 75th and the 95th percentile of the sample's AoPWV were 10 and 13 m/s, respectively, with no difference between sexes. In elderly individuals of 60-75 years, an AoPWV value below 10 m/s, measured with the PulsePen device, can be considered as a normal value. Values of 10-13 m/s can be considered as 'high normal' or 'borderline', whereas an AoPWV above 13 m/s is frankly elevated. This study provides, for the first time in the elderly, reference values of AoPWV.

Speaker normalization for chinese vowel recognition in cochlear implants.

PubMed

Luo, Xin; Fu, Qian-Jie

2005-07-01

Because of the limited spectra-temporal resolution associated with cochlear implants, implant patients often have greater difficulty with multitalker speech recognition. The present study investigated whether multitalker speech recognition can be improved by applying speaker normalization techniques to cochlear implant speech processing. Multitalker Chinese vowel recognition was tested with normal-hearing Chinese-speaking subjects listening to a 4-channel cochlear implant simulation, with and without speaker normalization. For each subject, speaker normalization was referenced to the speaker that produced the best recognition performance under conditions without speaker normalization. To match the remaining speakers to this "optimal" output pattern, the overall frequency range of the analysis filter bank was adjusted for each speaker according to the ratio of the mean third formant frequency values between the specific speaker and the reference speaker. Results showed that speaker normalization provided a small but significant improvement in subjects' overall recognition performance. After speaker normalization, subjects' patterns of recognition performance across speakers changed, demonstrating the potential for speaker-dependent effects with the proposed normalization technique.

Reference Values of Pulse Wave Velocity in Healthy People from an Urban and Rural Argentinean Population

PubMed Central

Díaz, Alejandro; Galli, Cintia; Tringler, Matías; Ramírez, Agustín; Cabrera Fischer, Edmundo Ignacio

2014-01-01

In medical practice the reference values of arterial stiffness came from multicenter registries obtained in Asia, USA, Australia and Europe. Pulse wave velocity (PWV) is the gold standard method for arterial stiffness quantification; however, in South America, there are few population-based studies. In this research PWV was measured in healthy asymptomatic and normotensive subjects without history of hypertension in first-degree relatives. Normal PWV and the 95% confidence intervals values were obtained in 780 subjects (39.8 ± 18.5 years) divided into 7 age groups (10–98 years). The mean PWV found was 6.84 m/s ± 1.65. PWV increases linearly with aging with a high degree of correlation (r 2 = 0.61; P < 0.05) with low dispersion in younger subjects. PWV progressively increases 6–8% with each decade of life; this tendency is more pronounced after 50 years. A significant increase of PWV over 50 years was demonstrated. This is the first population-based study from urban and rural people of Argentina that provides normal values of the PWV in healthy, normotensive subjects without family history of hypertension. Moreover, the age dependence of PWV values was confirmed. PMID:25215227

Reference as an Access Service: Collaboration between Reference and Interlibrary Loan Departments

ERIC Educational Resources Information Center

Kern, M. Kathleen; Weible, Cherie L.

2005-01-01

Academic libraries increasingly rely on Interlibrary Loan (ILL) departments to obtain research materials. This adds to the workload of ILL at a time when many libraries are experiencing budget cuts and dwindling staff. Collaboration between ILL and Reference can assist ILL by providing searching expertise. Collaboration is facilitated by the…

Age-dependent biochemical quantities: an approach for calculating reference intervals.

PubMed

Bjerner, J

2007-01-01

A parametric method is often preferred when calculating reference intervals for biochemical quantities, as non-parametric methods are less efficient and require more observations/study subjects. Parametric methods are complicated, however, because of three commonly encountered features. First, biochemical quantities seldom display a Gaussian distribution, and there must either be a transformation procedure to obtain such a distribution or a more complex distribution has to be used. Second, biochemical quantities are often dependent on a continuous covariate, exemplified by rising serum concentrations of MUC1 (episialin, CA15.3) with increasing age. Third, outliers often exert substantial influence on parametric estimations and therefore need to be excluded before calculations are made. The International Federation of Clinical Chemistry (IFCC) currently recommends that confidence intervals be calculated for the reference centiles obtained. However, common statistical packages allowing for the adjustment of a continuous covariate do not make this calculation. In the method described in the current study, Tukey's fence is used to eliminate outliers and two-stage transformations (modulus-exponential-normal) in order to render Gaussian distributions. Fractional polynomials are employed to model functions for mean and standard deviations dependent on a covariate, and the model is selected by maximum likelihood. Confidence intervals are calculated for the fitted centiles by combining parameter estimation and sampling uncertainties. Finally, the elimination of outliers was made dependent on covariates by reiteration. Though a good knowledge of statistical theory is needed when performing the analysis, the current method is rewarding because the results are of practical use in patient care.

No-reference multiscale blur detection tool for content based image retrieval

NASA Astrophysics Data System (ADS)

Ezekiel, Soundararajan; Stocker, Russell; Harrity, Kyle; Alford, Mark; Ferris, David; Blasch, Erik; Gorniak, Mark

2014-06-01

In recent years, digital cameras have been widely used for image capturing. These devices are equipped in cell phones, laptops, tablets, webcams, etc. Image quality is an important component of digital image analysis. To assess image quality for these mobile products, a standard image is required as a reference image. In this case, Root Mean Square Error and Peak Signal to Noise Ratio can be used to measure the quality of the images. However, these methods are not possible if there is no reference image. In our approach, a discrete-wavelet transformation is applied to the blurred image, which decomposes into the approximate image and three detail sub-images, namely horizontal, vertical, and diagonal images. We then focus on noise-measuring the detail images and blur-measuring the approximate image to assess the image quality. We then compute noise mean and noise ratio from the detail images, and blur mean and blur ratio from the approximate image. The Multi-scale Blur Detection (MBD) metric provides both an assessment of the noise and blur content. These values are weighted based on a linear regression against full-reference y values. From these statistics, we can compare to normal useful image statistics for image quality without needing a reference image. We then test the validity of our obtained weights by R2 analysis as well as using them to estimate image quality of an image with a known quality measure. The result shows that our method provides acceptable results for images containing low to mid noise levels and blur content.

IDLN-MSP: Idiolocal normalization of real-time methylation-specific PCR for genetic imbalanced DNA specimens.

PubMed

Santourlidis, Simeon; Ghanjati, Foued; Beermann, Agnes; Hermanns, Thomas; Poyet, Cédric

2016-02-01

Sensitive, accurate, and reliable measurements of tumor cell-specific DNA methylation changes are of fundamental importance in cancer diagnosis, prognosis, and monitoring. Real-time methylation-specific PCR (MSP) using intercalating dyes is an established method of choice for this purpose. Here we present a simple but crucial adaptation of this widely applied method that overcomes a major obstacle: genetic abnormalities in the DNA samples, such as aneuploidy or copy number variations, that could result in inaccurate results due to improper normalization if the copy numbers of the target and reference sequences are not the same. In our idiolocal normalization (IDLN) method, the locus for the normalizing, methylation-independent reference amplification is chosen close to the locus of the methylation-dependent target amplification. This ensures that the copy numbers of both the target and reference sequences will be identical in most cases if they are close enough to each other, resulting in accurate normalization and reliable comparative measurements of DNA methylation in clinical samples when using real-time MSP.

Automated identification of reference genes based on RNA-seq data.

PubMed

Carmona, Rosario; Arroyo, Macarena; Jiménez-Quesada, María José; Seoane, Pedro; Zafra, Adoración; Larrosa, Rafael; Alché, Juan de Dios; Claros, M Gonzalo

2017-08-18

Gene expression analyses demand appropriate reference genes (RGs) for normalization, in order to obtain reliable assessments. Ideally, RG expression levels should remain constant in all cells, tissues or experimental conditions under study. Housekeeping genes traditionally fulfilled this requirement, but they have been reported to be less invariant than expected; therefore, RGs should be tested and validated for every particular situation. Microarray data have been used to propose new RGs, but only a limited set of model species and conditions are available; on the contrary, RNA-seq experiments are more and more frequent and constitute a new source of candidate RGs. An automated workflow based on mapped NGS reads has been constructed to obtain highly and invariantly expressed RGs based on a normalized expression in reads per mapped million and the coefficient of variation. This workflow has been tested with Roche/454 reads from reproductive tissues of olive tree (Olea europaea L.), as well as with Illumina paired-end reads from two different accessions of Arabidopsis thaliana and three different human cancers (prostate, small-cell cancer lung and lung adenocarcinoma). Candidate RGs have been proposed for each species and many of them have been previously reported as RGs in literature. Experimental validation of significant RGs in olive tree is provided to support the algorithm. Regardless sequencing technology, number of replicates, and library sizes, when RNA-seq experiments are designed and performed, the same datasets can be analyzed with our workflow to extract suitable RGs for subsequent PCR validation. Moreover, different subset of experimental conditions can provide different suitable RGs.

Reference gene stability of a synanthropic fly, Chrysomya megacephala.

PubMed

Wang, Xiaoyun; Xiong, Mei; Wang, Jialu; Lei, Chaoliang; Zhu, Fen

2015-10-29

Stable reference genes are essential for accurate normalization in gene expression studies with reverse transcription quantitative polymerase chain reaction (qPCR). A synanthropic fly, Chrysomya megacephala, is a well known medical vector and forensic indicator. Unfortunately, previous studies did not look at the stability of reference genes used in C. megacephala. In this study, the expression level of Actin, ribosomal protein L8 (Rpl8), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), elongation factor 1α (EF1), α-tubulin (α-TUB), β-tubulin (β-TUB), TATA binding box (TBP), 18S rRNA (18S) and ribosomal protein S7 (Rps7) were evaluated for their stability using online software RefFinder, which combines the normal software of the ΔCt method, BestKeeper, Normfinder, and geNorm. Moreover the number of suitable reference gene pairs was also suggested by Excel-based geNorm. The expression levels of these reference genes were evaluated under different experimental conditions with special perspectives of forensic applications: developmental stages (eggs, first, second and third instar larvae, pupae and adults); food sources of larvae (pork, fish and chicken); feeding larvae with drugs (untreated control, Estazolam and Marvelon); feeding larvae with heavy metals (untreated control, cadmium and zinc); tissues of adults (head, thorax, abdomen, legs and wings). According to RefFinder, EF1 was the most suitable reference gene of developmental stages, food and tissues; 18S and GAPDH were the most suitable reference genes for drugs and heavy metals, respectively, which could be widely used for quantification of target gene expression with qPCR in C. megacephala. Suitable reference gene pairs were also suggested by geNorm. This fundamental but vital work should facilitate the gene studies of related biological processes and deepen the understanding in physiology, toxicology, and especially medical and forensic entomology of C. megacephala.

Evaluation of Reference Genes for Quantitative Real-Time PCR in Songbirds

PubMed Central

Zinzow-Kramer, Wendy M.; Horton, Brent M.; Maney, Donna L.

2014-01-01

Quantitative real-time PCR (qPCR) is becoming a popular tool for the quantification of gene expression in the brain and endocrine tissues of songbirds. Accurate analysis of qPCR data relies on the selection of appropriate reference genes for normalization, yet few papers on songbirds contain evidence of reference gene validation. Here, we evaluated the expression of ten potential reference genes (18S, ACTB, GAPDH, HMBS, HPRT, PPIA, RPL4, RPL32, TFRC, and UBC) in brain, pituitary, ovary, and testis in two species of songbird: zebra finch and white-throated sparrow. We used two algorithms, geNorm and NormFinder, to assess the stability of these reference genes in our samples. We found that the suitability of some of the most popular reference genes for target gene normalization in mammals, such as 18S, depended highly on tissue type. Thus, they are not the best choices for brain and gonad in these songbirds. In contrast, we identified alternative genes, such as HPRT, RPL4 and PPIA, that were highly stable in brain, pituitary, and gonad in these species. Our results suggest that the validation of reference genes in mammals does not necessarily extrapolate to other taxonomic groups. For researchers wishing to identify and evaluate suitable reference genes for qPCR songbirds, our results should serve as a starting point and should help increase the power and utility of songbird models in behavioral neuroendocrinology. PMID:24780145

Calculation of grain boundary normals directly from 3D microstructure images

DOE PAGES

Lieberman, E. J.; Rollett, A. D.; Lebensohn, R. A.; ...

2015-03-11

The determination of grain boundary normals is an integral part of the characterization of grain boundaries in polycrystalline materials. These normal vectors are difficult to quantify due to the discretized nature of available microstructure characterization techniques. The most common method to determine grain boundary normals is by generating a surface mesh from an image of the microstructure, but this process can be slow, and is subject to smoothing issues. A new technique is proposed, utilizing first order Cartesian moments of binary indicator functions, to determine grain boundary normals directly from a voxelized microstructure image. In order to validate the accuracymore » of this technique, the surface normals obtained by the proposed method are compared to those generated by a surface meshing algorithm. Specifically, the local divergence between the surface normals obtained by different variants of the proposed technique and those generated from a surface mesh of a synthetic microstructure constructed using a marching cubes algorithm followed by Laplacian smoothing is quantified. Next, surface normals obtained with the proposed method from a measured 3D microstructure image of a Ni polycrystal are used to generate grain boundary character distributions (GBCD) for Σ3 and Σ9 boundaries, and compared to the GBCD generated using a surface mesh obtained from the same image. Finally, the results show that the proposed technique is an efficient and accurate method to determine voxelized fields of grain boundary normals.« less

Use of echocardiography in outpatients with chest pain and normal resting electrocardiograms referred to Mayo Clinic Rochester.

PubMed

Gibbons, Raymond J; Carryer, Damita; Liu, Hongfang; Brady, Peter A; Askew, John Wells; Hodge, David; Ammash, Naser; Ebbert, Jon O; Roger, Veronique L

2018-02-01

To determine how often unnecessary resting echocardiograms that are "not recommended" by clinical practice guidelines are performed in patients with stable chest pain and normal resting electrocardiograms (ECGs). There are scant data to indicate how often Class III recommendations are ignored in clinical practice. We searched electronically all medical records of referral outpatients seen at Mayo Clinic Rochester from January 1, 2010, through December 31, 2013, to identify patients with stable chest pain and known or suspected coronary artery disease who underwent resting echocardiography and had normal resting ECGs and no other indication for echocardiography. Of the 15,529 referral outpatients who were evaluated at Mayo Clinic Rochester with chest pain, 3976 (25.6%) had resting echocardiograms. Eight hundred seventy of these 3976 patients (21.9%) had normal resting ECGs. Six hundred nineteen of these 870 patients (71.1%) had other indications for echocardiography. The remaining 251 patients (6.3% of all echocardiograms and 1.6% of all patients) had normal resting ECGs and no other indication for echocardiography. Two hundred thirty-nine of these 251 patients (95.2%) had normal echocardiograms. Of the 12 abnormal echocardiograms, only 4 led to any change in clinical management. Sixty-one of these 251 echocardiograms (24.3%) were "preordered" before the provider (physicians, nurses, physician assistants) visit. Echocardiograms were performed in 1 in 4 referral outpatients with chest pain seen at Mayo Clinic Rochester. However, only 1 in 16 of these echocardiograms was performed in violation of the class III recommendation in the American College of Cardiology Foundation/American Heart Association guidelines for the management of stable angina. These unnecessary echocardiograms were almost always normal, and had little impact on clinical management. The rate of unnecessary echocardiograms could be decreased by eliminating preordering. Copyright © 2017 Elsevier Inc

Fracture risk among older men: osteopenia and osteoporosis defined using cut-points derived from female versus male reference data.

PubMed

Pasco, J A; Lane, S E; Brennan, S L; Timney, E N; Bucki-Smith, G; Dobbins, A G; Nicholson, G C; Kotowicz, M A

2014-03-01

We explored the effect of using male and female reference data in a male sample to categorise areal bone mineral density (BMD). Using male reference data, a large proportion of fractures arose from osteopenia, whereas using female reference data shifted the fracture burden into normal BMD. The purpose of this study was to describe fracture risk associated with osteopenia and osteoporosis in older men, defined by areal BMD and using cut-points derived from male and female reference data. As part of the Geelong Osteoporosis Study, we followed 619 men aged 60-93 years after BMD assessments (performed 2001-2006) until 2010, fracture, death or emigration. Post-baseline fractures were radiologically confirmed, and proportions of fractures in each BMD category were age-standardised to national profiles. Based on World Health Organization criteria, and using male reference data, 207 men had normal BMD at the femoral neck, 357 were osteopenic and 55 were osteoporotic. Using female reference data, corresponding numbers were 361, 227 and 31. During the study, 130 men died, 15 emigrated and 63 sustained at least one fracture. Using male reference data, most (86.5 %) of the fractures occurred in men without osteoporosis on BMD criteria (18.4 % normal BMD, 68.1 % osteopenia). The pattern differed when female reference data were used; while most fractures arose from men without osteoporosis (88.2 %), the burden shifted from those with osteopenia (34.8 %) to those with normal BMD (53.4 %). Decreasing BMD categories defined increasing risk of fracture. Although men with osteoporotic BMD were at greatest risk, they made a relatively small contribution to the total burden of fractures. Using male reference data, two-thirds of the fractures arose from men with osteopenia. However, using female reference data, approximately half of the fractures arose from those with normal BMD. Using female reference data to define osteoporosis in men does not appear to be the optimal approach.

Color normalization for robust evaluation of microscopy images

NASA Astrophysics Data System (ADS)

Švihlík, Jan; Kybic, Jan; Habart, David

2015-09-01

This paper deals with color normalization of microscopy images of Langerhans islets in order to increase robustness of the islet segmentation to illumination changes. The main application is automatic quantitative evaluation of the islet parameters, useful for determining the feasibility of islet transplantation in diabetes. First, background illumination inhomogeneity is compensated and a preliminary foreground/background segmentation is performed. The color normalization itself is done in either lαβ or logarithmic RGB color spaces, by comparison with a reference image. The color-normalized images are segmented using color-based features and pixel-wise logistic regression, trained on manually labeled images. Finally, relevant statistics such as the total islet area are evaluated in order to determine the success likelihood of the transplantation.

Gene Expression Profile Analysis is Directly Affected by the Selected Reference Gene: The Case of Leaf-Cutting Atta Sexdens

PubMed Central

Máximo, Wesley P. F.; Zanetti, Ronald; Paiva, Luciano V.

2018-01-01

Although several ant species are important targets for the development of molecular control strategies, only a few studies focus on identifying and validating reference genes for quantitative reverse transcription polymerase chain reaction (RT-qPCR) data normalization. We provide here an extensive study to identify and validate suitable reference genes for gene expression analysis in the ant Atta sexdens, a threatening agricultural pest in South America. The optimal number of reference genes varies according to each sample and the result generated by RefFinder differed about which is the most suitable reference gene. Results suggest that the RPS16, NADH and SDHB genes were the best reference genes in the sample pool according to stability values. The SNF7 gene expression pattern was stable in all evaluated sample set. In contrast, when using less stable reference genes for normalization a large variability in SNF7 gene expression was recorded. There is no universal reference gene suitable for all conditions under analysis, since these genes can also participate in different cellular functions, thus requiring a systematic validation of possible reference genes for each specific condition. The choice of reference genes on SNF7 gene normalization confirmed that unstable reference genes might drastically change the expression profile analysis of target candidate genes. PMID:29419794

Serum proteins by capillary zone electrophoresis: approaches to the definition of reference values.

PubMed

Petrini, C; Alessio, M G; Scapellato, L; Brambilla, S; Franzini, C

1999-10-01

The Paragon CZE 2000 (Beckman Analytical, Milan, Italy) is an automatic dedicated capillary zone electrophoresis (CZE) system, producing a five-zone serum protein pattern with quantitative estimation of the zones. With the view of substituting this instrument for two previously used serum protein electrophoresis techniques, we planned to produce reference values for the "new" systems leading to compatible interpretation of the results. High resolution cellulose acetate electrophoresis with visual inspection and descriptive reporting (HR-CAE) and five-zone cellulose acetate electrophoresis with densitometry (CAE-D) were the previously used techniques. Serum samples (n = 167) giving "normal pattern" with HR-CAE were assayed with the CZE system, and the results were statistically assessed to yield 0.95 reference intervals. One thousand normal and pathological serum samples were then assayed with the CAE-D and the CZE techniques, and the regression equations of the CAE-D values over the CZE values for the five zones were used to transform the CAE-D reference limits into the CZE reference limits. The two sets of reference values thereby produced were in good agreement with each other and also with reference values previously reported for the CZE system. Thus, reference values for the CZE techniques permit interpretation of results coherent with the previously used techniques and reporting modes.

WHO Melting-Point Reference Substances

PubMed Central

Bervenmark, H.; Diding, N. Å.; Öhrner, B.

1963-01-01

Batches of 13 highly purified chemicals, intended for use as reference substances in the calibration of apparatus for melting-point determinations, have been subjected to a collaborative assay by 15 laboratories in 13 countries. All the laboratories performed melting-point determinations by the capillary methods described in the proposed text for the second edition of the Pharmacopoea Internationalis and some, in addition, carried out determinations by the microscope hot stage (Kofler) method, using both the “going-through” and the “equilibrium” technique. Statistical analysis of the data obtained by the capillary method showed that the within-laboratory variation was small and that the between-laboratory variation, though constituting the greatest part of the whole variance, was not such as to warrant the exclusion of any laboratory from the evaluation of the results. The average values of the melting-points obtained by the laboratories can therefore be used as constants for the substances in question, which have accordingly been established as WHO Melting-Point Reference Substances and included in the WHO collection of authentic chemical substances. As to the microscope hot stage method, analysis of the results indicated that the values obtained by the “going-through” technique did not differ significantly from those obtained by the capillary method, but the values obtained by the “equilibrium” technique were mostly significantly lower. PMID:20604137

Selection of Reference Genes for Quantitative Real Time PCR (qPCR) Assays in Tissue from Human Ascending Aorta

PubMed Central

Rueda-Martínez, Carmen; Lamas, Oscar; Mataró, María José; Robledo-Carmona, Juan; Sánchez-Espín, Gemma; Jiménez-Navarro, Manuel; Such-Martínez, Miguel; Fernández, Borja

2014-01-01

Dilatation of the ascending aorta (AAD) is a prevalent aortopathy that occurs frequently associated with bicuspid aortic valve (BAV), the most common human congenital cardiac malformation. The molecular mechanisms leading to AAD associated with BAV are still poorly understood. The search for differentially expressed genes in diseased tissue by quantitative real-time PCR (qPCR) is an invaluable tool to fill this gap. However, studies dedicated to identify reference genes necessary for normalization of mRNA expression in aortic tissue are scarce. In this report, we evaluate the qPCR expression of six candidate reference genes in tissue from the ascending aorta of 52 patients with a variety of clinical and demographic characteristics, normal and dilated aortas, and different morphologies of the aortic valve (normal aorta and normal valve n = 30; dilated aorta and normal valve n = 10; normal aorta and BAV n = 4; dilated aorta and BAV n = 8). The expression stability of the candidate reference genes was determined with three statistical algorithms, GeNorm, NormFinder and Bestkeeper. The expression analyses showed that the most stable genes for the three algorithms employed were CDKN1β, POLR2A and CASC3, independently of the structure of the aorta and the valve morphology. In conclusion, we propose the use of these three genes as reference genes for mRNA expression analysis in human ascending aorta. However, we suggest searching for specific reference genes when conducting qPCR experiments with new cohort of samples. PMID:24841551

Use of Fat Mass and Fat Free Mass Standard Deviation Scores Obtained Using Simple Measurement Methods in Healthy Children and Patients: Comparison with the Reference 4-Component Model

PubMed Central

Atherton, Rachel R.; Williams, Jane E.; Wells, Jonathan C. K.; Fewtrell, Mary S.

2013-01-01

Background Clinical application of body composition (BC) measurements for individual children has been limited by lack of appropriate reference data. Objectives (1) To compare fat mass (FM) and fat free mass (FFM) standard deviation scores (SDS) generated using new body composition reference data and obtained using simple measurement methods in healthy children and patients with those obtained using the reference 4-component (4-C) model; (2) To determine the extent to which scores from simple methods agree with those from the 4-C model in identification of abnormal body composition. Design FM SDS were calculated for 4-C model, dual-energy X-ray absorptiometry (DXA; GE Lunar Prodigy), BMI and skinfold thicknesses (SFT); and FFM SDS for 4CM, DXA and bioelectrical impedance analysis (BIA; height2/Z)) in 927 subjects aged 3.8–22.0 y (211 healthy, 716 patients). Results DXA was the most accurate method for both FM and FFM SDS in healthy subjects and patients (mean bias (limits of agreement) FM SDS 0.03 (±0.62); FFM SDS −0.04 (±0.72)), and provided best agreement with the 4-C model in identifying abnormal BC (SDS ≤−2 or ≥2). BMI and SFTs were reasonable predictors of abnormal FM SDS, but poor in providing an absolute value. BIA was comparable to DXA for FFM SDS and in identifying abnormal subjects. Conclusions DXA may be used both for research and clinically to determine FM and FFM SDS. BIA may be used to assess FFM SDS in place of DXA. BMI and SFTs can be used to measure adiposity for groups but not individuals. The performance of simpler techniques in monitoring longitudinal BC changes requires investigation. Ultimately, the most appropriate method should be determined by its predictive value for clinical outcome. PMID:23690932

Use of fat mass and fat free mass standard deviation scores obtained using simple measurement methods in healthy children and patients: comparison with the reference 4-component model.

PubMed

Atherton, Rachel R; Williams, Jane E; Wells, Jonathan C K; Fewtrell, Mary S

2013-01-01

Clinical application of body composition (BC) measurements for individual children has been limited by lack of appropriate reference data. (1) To compare fat mass (FM) and fat free mass (FFM) standard deviation scores (SDS) generated using new body composition reference data and obtained using simple measurement methods in healthy children and patients with those obtained using the reference 4-component (4-C) model; (2) To determine the extent to which scores from simple methods agree with those from the 4-C model in identification of abnormal body composition. FM SDS were calculated for 4-C model, dual-energy X-ray absorptiometry (DXA; GE Lunar Prodigy), BMI and skinfold thicknesses (SFT); and FFM SDS for 4CM, DXA and bioelectrical impedance analysis (BIA; height(2)/Z)) in 927 subjects aged 3.8-22.0 y (211 healthy, 716 patients). DXA was the most accurate method for both FM and FFM SDS in healthy subjects and patients (mean bias (limits of agreement) FM SDS 0.03 (± 0.62); FFM SDS -0.04 (± 0.72)), and provided best agreement with the 4-C model in identifying abnormal BC (SDS ≤-2 or ≥ 2). BMI and SFTs were reasonable predictors of abnormal FM SDS, but poor in providing an absolute value. BIA was comparable to DXA for FFM SDS and in identifying abnormal subjects. DXA may be used both for research and clinically to determine FM and FFM SDS. BIA may be used to assess FFM SDS in place of DXA. BMI and SFTs can be used to measure adiposity for groups but not individuals. The performance of simpler techniques in monitoring longitudinal BC changes requires investigation. Ultimately, the most appropriate method should be determined by its predictive value for clinical outcome.

An iterative procedure for obtaining maximum-likelihood estimates of the parameters for a mixture of normal distributions

NASA Technical Reports Server (NTRS)

Peters, B. C., Jr.; Walker, H. F.

1975-01-01

A general iterative procedure is given for determining the consistent maximum likelihood estimates of normal distributions. In addition, a local maximum of the log-likelihood function, Newtons's method, a method of scoring, and modifications of these procedures are discussed.

Estimating patient-specific and anatomically correct reference model for craniomaxillofacial deformity via sparse representation

PubMed Central

Wang, Li; Ren, Yi; Gao, Yaozong; Tang, Zhen; Chen, Ken-Chung; Li, Jianfu; Shen, Steve G. F.; Yan, Jin; Lee, Philip K. M.; Chow, Ben; Xia, James J.; Shen, Dinggang

2015-01-01

Purpose: A significant number of patients suffer from craniomaxillofacial (CMF) deformity and require CMF surgery in the United States. The success of CMF surgery depends on not only the surgical techniques but also an accurate surgical planning. However, surgical planning for CMF surgery is challenging due to the absence of a patient-specific reference model. Currently, the outcome of the surgery is often subjective and highly dependent on surgeon’s experience. In this paper, the authors present an automatic method to estimate an anatomically correct reference shape of jaws for orthognathic surgery, a common type of CMF surgery. Methods: To estimate a patient-specific jaw reference model, the authors use a data-driven method based on sparse shape composition. Given a dictionary of normal subjects, the authors first use the sparse representation to represent the midface of a patient by the midfaces of the normal subjects in the dictionary. Then, the derived sparse coefficients are used to reconstruct a patient-specific reference jaw shape. Results: The authors have validated the proposed method on both synthetic and real patient data. Experimental results show that the authors’ method can effectively reconstruct the normal shape of jaw for patients. Conclusions: The authors have presented a novel method to automatically estimate a patient-specific reference model for the patient suffering from CMF deformity. PMID:26429255

The application of the piecewise linear approximation to the spectral neighborhood of soil line for the analysis of the quality of normalization of remote sensing materials

NASA Astrophysics Data System (ADS)

Kulyanitsa, A. L.; Rukhovich, A. D.; Rukhovich, D. D.; Koroleva, P. V.; Rukhovich, D. I.; Simakova, M. S.

2017-04-01

The concept of soil line can be to describe the temporal distribution of spectral characteristics of the bare soil surface. In this case, the soil line can be referred to as the multi-temporal soil line, or simply temporal soil line (TSL). In order to create TSL for 8000 regular lattice points for the territory of three regions of Tula oblast, we used 34 Landsat images obtained in the period from 1985 to 2014 after their certain transformation. As Landsat images are the matrices of the values of spectral brightness, this transformation is the normalization of matrices. There are several methods of normalization that move, rotate, and scale the spectral plane. In our study, we applied the method of piecewise linear approximation to the spectral neighborhood of soil line in order to assess the quality of normalization mathematically. This approach allowed us to range normalization methods according to their quality as follows: classic normalization > successive application of the turn and shift > successive application of the atmospheric correction and shift > atmospheric correction > shift > turn > raw data. The normalized data allowed us to create the maps of the distribution of a and b coefficients of the TSL. The map of b coefficient is characterized by the high correlation with the ground-truth data obtained from 1899 soil pits described during the soil surveys performed by the local institute for land management (GIPROZEM).

Multiples of Median-Transformed, Normalized Reference Ranges of Steroid Profiling Data Independent of Age, Sex, and Units.

PubMed

Zalas, Dominika; Reinehr, Thomas; Niedziela, Marek; Borzikowsky, Christoph; Flader, Maciej; Simic-Schleicher, Gunter; Akkurt, Halit Ilker; Heger, Sabine; Hornig, Nadine; Holterhus, Paul-Martin; Kulle, Alexandra E

2018-01-01

The high complexity of pediatric reference ranges across age, sex, and units impairs clinical application and comparability of steroid hormone data, e.g., in congenital adrenal hyperplasia (CAH). We developed a multiples-of-median (MoM) normalization tool to overcome this major drawback in pediatric endocrinology. Liquid chromatography tandem mass spectrometry data comprising 10 steroid hormones representing 905 controls (555 males, 350 females, 0 to > 16 years) from 2 previous datasets were MoM transformed across age and sex. Twenty-three genetically proven CAH patients were included (21-hydroxylase deficiency [21OHD], n = 19; 11β-hydroxylase deficiency [11OHD], n = 4). MoM cutoffs for single steroids predicting 21OHD and 11OHD were computed and validated through new, independent patients (21OHD, n = 8; adrenal cortical carcinoma, n = 6; obesity, n = 40). 21OHD and 11OHD patients showed disease-typical, easily recognizable MoM patterns independent of age, sex, and concentration units. Two single-steroid cutoffs indicated 21OHD: 3.87 MoM for 17-hydroxyprogesterone (100% sensitivity and 98.83% specificity) and 12.28 MoM for 21-deoxycortisol (94.74% sensitivity and 100% specificity). A cutoff of 13.18 MoM for 11-deoxycortisol indicated 11OHD (100% sensitivity and 100% specificity). Age- and sex-independent MoMs are straightforward for a clinically relevant display of multi-steroid patterns. In addition, defined single-steroid MoMs can serve alone as predictors of 21OHD and 11OHD. Finally, MoM transformation offers substantial enhancement of routine and scientific steroid hormone data exchange due to improved comparability. © 2018 S. Karger AG, Basel.

Selection of appropriate reference genes for RT-qPCR analysis in a streptozotocin-induced Alzheimer's disease model of cynomolgus monkeys (Macaca fascicularis).

PubMed

Park, Sang-Je; Kim, Young-Hyun; Lee, Youngjeon; Kim, Kyoung-Min; Kim, Heui-Soo; Lee, Sang-Rae; Kim, Sun-Uk; Kim, Sang-Hyun; Kim, Ji-Su; Jeong, Kang-Jin; Lee, Kyoung-Min; Huh, Jae-Won; Chang, Kyu-Tae

2013-01-01

Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) has been widely used to quantify relative gene expression because of the specificity, sensitivity, and accuracy of this technique. In order to obtain reliable gene expression data from RT-qPCR experiments, it is important to utilize optimal reference genes for the normalization of target gene expression under varied experimental conditions. Previously, we developed and validated a novel icv-STZ cynomolgus monkey model for Alzheimer's disease (AD) research. However, in order to enhance the reliability of this disease model, appropriate reference genes must be selected to allow meaningful analysis of the gene expression levels in the icv-STZ cynomolgus monkey brain. In this study, we assessed the expression stability of 9 candidate reference genes in 2 matched-pair brain samples (5 regions) of control cynomolgus monkeys and those who had received intracerebroventricular injection of streptozotocin (icv-STZ). Three well-known analytical programs geNorm, NormFinder, and BestKeeper were used to choose the suitable reference genes from the total sample group, control group, and icv-STZ group. Combination analysis of the 3 different programs clearly indicated that the ideal reference genes are RPS19 and YWHAZ in the total sample group, GAPDH and RPS19 in the control group, and ACTB and GAPDH in the icv-STZ group. Additionally, we validated the normalization accuracy of the most appropriate reference genes (RPS19 and YWHAZ) by comparison with the least stable gene (TBP) using quantification of the APP and MAPT genes in the total sample group. To the best of our knowledge, this research is the first study to identify and validate the appropriate reference genes in cynomolgus monkey brains. These findings provide useful information for future studies involving the expression of target genes in the cynomolgus monkey.

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

PubMed

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

2015-12-29

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

X-ray Moiré deflectometry using synthetic reference images

DOE PAGES

Stutman, Dan; Valdivia, Maria Pia; Finkenthal, Michael

2015-06-25

Moiré fringe deflectometry with grating interferometers is a technique that enables refraction-based x-ray imaging using a single exposure of an object. To obtain the refraction image, the method requires a reference fringe pattern (without the object). Our study shows that, in order to avoid artifacts, the reference pattern must be exactly matched in phase with the object fringe pattern. In experiments, however, it is difficult to produce a perfectly matched reference pattern due to unavoidable interferometer drifts. We present a simple method to obtain matched reference patterns using a phase-scan procedure to generate synthetic Moiré images. As a result, themore » method will enable deflectometric diagnostics of transient phenomena such as laser-produced plasmas and could improve the sensitivity and accuracy of medical phase-contrast imaging.« less

Quantum turbulence in superfluids with wall-clamped normal component.

PubMed

Eltsov, Vladimir; Hänninen, Risto; Krusius, Matti

2014-03-25

In Fermi superfluids, such as superfluid (3)He, the viscous normal component can be considered to be stationary with respect to the container. The normal component interacts with the superfluid component via mutual friction, which damps the motion of quantized vortex lines and eventually couples the superfluid component to the container. With decreasing temperature and mutual friction, the internal dynamics of the superfluid component becomes more important compared with the damping and coupling effects from the normal component. As a result profound changes in superfluid dynamics are observed: the temperature-dependent transition from laminar to turbulent vortex motion and the decoupling from the reference frame of the container at even lower temperatures.

Quantum turbulence in superfluids with wall-clamped normal component

PubMed Central

Eltsov, Vladimir; Hänninen, Risto; Krusius, Matti

2014-01-01

In Fermi superfluids, such as superfluid 3He, the viscous normal component can be considered to be stationary with respect to the container. The normal component interacts with the superfluid component via mutual friction, which damps the motion of quantized vortex lines and eventually couples the superfluid component to the container. With decreasing temperature and mutual friction, the internal dynamics of the superfluid component becomes more important compared with the damping and coupling effects from the normal component. As a result profound changes in superfluid dynamics are observed: the temperature-dependent transition from laminar to turbulent vortex motion and the decoupling from the reference frame of the container at even lower temperatures. PMID:24704879

31 CFR 586.508 - Entries in certain accounts for normal service charges authorized.

Code of Federal Regulations, 2010 CFR

2010-07-01

... institution by the owner of such blocked account. (b) As used in this section, the term normal service charge..., and Statements of Licensing Policy § 586.508 Entries in certain accounts for normal service charges... by way of limitation, minimum balance charges, notary and protest fees, and charges for reference...

Teaching Normal Birth, Normally

PubMed Central

Hotelling, Barbara A

2009-01-01

Teaching normal-birth Lamaze classes normally involves considering the qualities that make birth normal and structuring classes to embrace those qualities. In this column, teaching strategies are suggested for classes that unfold naturally, free from unnecessary interventions. PMID:19436595

Selection of suitable endogenous reference genes for qPCR in kidney and hypothalamus of rats under testosterone influence

PubMed Central

2017-01-01

Real-time quantitative PCR (qPCR) is the most reliable and accurate technique for analyses of gene expression. Endogenous reference genes are being used to normalize qPCR data even though their expression may vary under different conditions and in different tissues. Nonetheless, verification of expression of reference genes in selected studied tissue is essential in order to accurately assess the level of expression of target genes of interest. Therefore, in this study, we attempted to examine six commonly used reference genes in order to identify the gene being expressed most constantly under the influence of testosterone in the kidneys and hypothalamus. The reference genes include glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin beta (ACTB), beta-2 microglobulin (B2m), hypoxanthine phosphoribosyltransferase 1 (HPRT), peptidylprolylisomerase A (Ppia) and hydroxymethylbilane synthase (Hmbs). The cycle threshold (Ct) value for each gene was determined and data obtained were analyzed using the software programs NormFinder, geNorm, BestKeeper, and rank aggregation. Results showed that Hmbs and Ppia genes were the most stably expressed in the hypothalamus. Meanwhile, in kidneys, Hmbs and GAPDH appeared to be the most constant genes. In conclusion, variations in expression levels of reference genes occur in kidneys and hypothalamus under similar conditions; thus, it is important to verify reference gene levels in these tissues prior to commencing any studies. PMID:28591185

Acute phase proteins in healthy goats: establishment of reference intervals.

PubMed

Heller, Meera C; Johns, Jennifer L

2015-03-01

Acute inflammatory processes can trigger increased production of acute phase proteins (APPs) that can be useful biomarkers of inflammation. APPs are diverse and include proteins involved in coagulation, opsonization, iron regulation, and limitation of tissue injury. Haptoglobin, serum amyloid A, and alpha-1 acid glycoprotein have been proposed as useful APPs in goats. APPs can differ markedly by species, therefore species-specific reference intervals and studies are necessary. The objective of this study was to determine species-specific reference intervals for 4 APPs in goats. Haptoglobin, serum amyloid A, lipopolysaccharide binding protein, and alpha-1 acid glycoprotein were measured in in 54 clinically normal adult goats. APPs were measured using goat-specific commercial enzyme-linked immunosorbent assay kits. Results were analyzed by 1-way analysis of variance to compare sexes and breeding status. Reference Value Advisor was used to calculate reference limits according to the IFCC-CLSI guidelines. Only 1 APP was found to vary in healthy animals; serum haptoglobin was increased in lactating animals and decreased in pregnant does in their second trimester when compared with open, nonlactating does. No sex-based differences were seen for any of the APPs measured. We report normal reference intervals for 4 serum APPs that may be useful as disease markers. Haptoglobin should be interpreted with caution in animals with unknown pregnancy status. Further studies are needed to determine whether these APPs are useful biomarkers in goat disease states. © 2015 The Author(s).

Reference analysis of the signal + background model in counting experiments II. Approximate reference prior

NASA Astrophysics Data System (ADS)

Casadei, D.

2014-10-01

The objective Bayesian treatment of a model representing two independent Poisson processes, labelled as ``signal'' and ``background'' and both contributing additively to the total number of counted events, is considered. It is shown that the reference prior for the parameter of interest (the signal intensity) can be well approximated by the widely (ab)used flat prior only when the expected background is very high. On the other hand, a very simple approximation (the limiting form of the reference prior for perfect prior background knowledge) can be safely used over a large portion of the background parameters space. The resulting approximate reference posterior is a Gamma density whose parameters are related to the observed counts. This limiting form is simpler than the result obtained with a flat prior, with the additional advantage of representing a much closer approximation to the reference posterior in all cases. Hence such limiting prior should be considered a better default or conventional prior than the uniform prior. On the computing side, it is shown that a 2-parameter fitting function is able to reproduce extremely well the reference prior for any background prior. Thus, it can be useful in applications requiring the evaluation of the reference prior for a very large number of times.

Assessment of a novel multi-array normalization method based on spike-in control probes suitable for microRNA datasets with global decreases in expression.

PubMed

Sewer, Alain; Gubian, Sylvain; Kogel, Ulrike; Veljkovic, Emilija; Han, Wanjiang; Hengstermann, Arnd; Peitsch, Manuel C; Hoeng, Julia

2014-05-17

High-quality expression data are required to investigate the biological effects of microRNAs (miRNAs). The goal of this study was, first, to assess the quality of miRNA expression data based on microarray technologies and, second, to consolidate it by applying a novel normalization method. Indeed, because of significant differences in platform designs, miRNA raw data cannot be normalized blindly with standard methods developed for gene expression. This fundamental observation motivated the development of a novel multi-array normalization method based on controllable assumptions, which uses the spike-in control probes to adjust the measured intensities across arrays. Raw expression data were obtained with the Exiqon dual-channel miRCURY LNA™ platform in the "common reference design" and processed as "pseudo-single-channel". They were used to apply several quality metrics based on the coefficient of variation and to test the novel spike-in controls based normalization method. Most of the considerations presented here could be applied to raw data obtained with other platforms. To assess the normalization method, it was compared with 13 other available approaches from both data quality and biological outcome perspectives. The results showed that the novel multi-array normalization method reduced the data variability in the most consistent way. Further, the reliability of the obtained differential expression values was confirmed based on a quantitative reverse transcription-polymerase chain reaction experiment performed for a subset of miRNAs. The results reported here support the applicability of the novel normalization method, in particular to datasets that display global decreases in miRNA expression similarly to the cigarette smoke-exposed mouse lung dataset considered in this study. Quality metrics to assess between-array variability were used to confirm that the novel spike-in controls based normalization method provided high-quality miRNA expression data

Assessment of a novel multi-array normalization method based on spike-in control probes suitable for microRNA datasets with global decreases in expression

PubMed Central

2014-01-01

Background High-quality expression data are required to investigate the biological effects of microRNAs (miRNAs). The goal of this study was, first, to assess the quality of miRNA expression data based on microarray technologies and, second, to consolidate it by applying a novel normalization method. Indeed, because of significant differences in platform designs, miRNA raw data cannot be normalized blindly with standard methods developed for gene expression. This fundamental observation motivated the development of a novel multi-array normalization method based on controllable assumptions, which uses the spike-in control probes to adjust the measured intensities across arrays. Results Raw expression data were obtained with the Exiqon dual-channel miRCURY LNA™ platform in the “common reference design” and processed as “pseudo-single-channel”. They were used to apply several quality metrics based on the coefficient of variation and to test the novel spike-in controls based normalization method. Most of the considerations presented here could be applied to raw data obtained with other platforms. To assess the normalization method, it was compared with 13 other available approaches from both data quality and biological outcome perspectives. The results showed that the novel multi-array normalization method reduced the data variability in the most consistent way. Further, the reliability of the obtained differential expression values was confirmed based on a quantitative reverse transcription–polymerase chain reaction experiment performed for a subset of miRNAs. The results reported here support the applicability of the novel normalization method, in particular to datasets that display global decreases in miRNA expression similarly to the cigarette smoke-exposed mouse lung dataset considered in this study. Conclusions Quality metrics to assess between-array variability were used to confirm that the novel spike-in controls based normalization method provided

Reconstruction of instantaneous surface normal velocity of a vibrating structure using interpolated time-domain equivalent source method

NASA Astrophysics Data System (ADS)

Geng, Lin; Bi, Chuan-Xing; Xie, Feng; Zhang, Xiao-Zheng

2018-07-01

Interpolated time-domain equivalent source method is extended to reconstruct the instantaneous surface normal velocity of a vibrating structure by using the time-evolving particle velocity as the input, which provides a non-contact way to overall understand the instantaneous vibration behavior of the structure. In this method, the time-evolving particle velocity in the near field is first modeled by a set of equivalent sources positioned inside the vibrating structure, and then the integrals of equivalent source strengths are solved by an iterative solving process and are further used to calculate the instantaneous surface normal velocity. An experiment of a semi-cylindrical steel plate impacted by a steel ball is investigated to examine the ability of the extended method, where the time-evolving normal particle velocity and pressure on the hologram surface measured by a Microflown pressure-velocity probe are used as the inputs of the extended method and the method based on pressure measurements, respectively, and the instantaneous surface normal velocity of the plate measured by a laser Doppler vibrometry is used as the reference for comparison. The experimental results demonstrate that the extended method is a powerful tool to visualize the instantaneous surface normal velocity of a vibrating structure in both time and space domains and can obtain more accurate results than that of the method based on pressure measurements.

Survey of referring veterinarians' perceptions of and reasons for referring patients to rehabilitation facilities.

PubMed

Alvarez, Leilani X; Fox, Philip R; Van Dyke, Janet B; Grigsby, Patrick

2016-10-01

OBJECTIVE To identify patterns of referral to US small animal rehabilitation facilities, document referring veterinarians' perceptions of rehabilitation services, and examine factors that encouraged and impeded referral of veterinary patients to rehabilitation facilities. DESIGN Cross-sectional survey. SAMPLE 461 completed surveys. PROCEDURES Referral lists were obtained from 9 US rehabilitation facilities, and surveys were emailed or mailed to 2, 738 veterinarians whose names appeared on those lists. Data obtained from respondents were used to generate descriptive statistics and perform χ(2) tests to determine patterns for referral of patients to rehabilitation facilities. RESULTS 461 surveys were completed and returned, resulting in a response rate of 16.8%. The margin of error was < 5% for all responses. Most respondents (324/461 [70.3%]) had referred patients for postoperative rehabilitation therapy. Respondents ranked neurologic disorder as the condition they would most likely consider for referral for future rehabilitation therapy. The most frequently cited reason for not referring a patient for rehabilitation therapy was perceived cost (251/461 [54.4%]) followed by distance to a rehabilitation facility (135/461 [29.3%]). Specialists were more likely than general practitioners to refer patients for rehabilitation therapy. The majority (403/461 [87.4%]) of respondents felt that continuing education in the field of veterinary rehabilitation was lacking. CONCLUSIONS AND CLINICAL RELEVANCE Results indicated a need for continuing education in small animal rehabilitation for veterinarians. Improved knowledge of rehabilitation therapy will enable veterinarians to better understand and more specifically communicate indications and benefits for pets receiving this treatment modality.

Normalizing gene expression by quantitative PCR during somatic embryogenesis in two representative conifer species: Pinus pinaster and Picea abies.

PubMed

de Vega-Bartol, José J; Santos, Raquen Raissa; Simões, Marta; Miguel, Célia M

2013-05-01

Suitable internal control genes to normalize qPCR data from different stages of embryo development and germination were identified in two representative conifer species. Clonal propagation by somatic embryogenesis has a great application potentiality in conifers. Quantitative PCR (qPCR) is widely used for gene expression analysis during somatic embryogenesis and embryo germination. No single reference gene is universal, so a systematic characterization of endogenous genes for concrete conditions is fundamental for accuracy. We identified suitable internal control genes to normalize qPCR data obtained at different steps of somatic embryogenesis (embryonal mass proliferation, embryo maturation and germination) in two representative conifer species, Pinus pinaster and Picea abies. Candidate genes included endogenous genes commonly used in conifers, genes previously tested in model plants, and genes with a lower variation of the expression along embryo development according to genome-wide transcript profiling studies. Three different algorithms were used to evaluate expression stability. The geometric average of the expression values of elongation factor-1α, α-tubulin and histone 3 in P. pinaster, and elongation factor-1α, α-tubulin, adenosine kinase and CAC in P. abies were adequate for expression studies throughout somatic embryogenesis. However, improved accuracy was achieved when using other gene combinations in experiments with samples at a single developmental stage. The importance of studies selecting reference genes to use in different tissues or developmental stages within one or close species, and the instability of commonly used reference genes, is highlighted.

Lake Louise Water (USGS47): A new isotopic reference water for stable hydrogen and oxygen isotope measurements

USGS Publications Warehouse

Qi, Haiping; Lorenz, Jennifer M.; Coplen, Tyler B.; Tarbox, Lauren V.; Mayer, Bernhard; Taylor, Steve

2014-01-01

RESULTS: The δ2H and δ18O values of this reference water are –150.2 ± 0.5 ‰ and –19.80 ± 0.02 ‰, respectively, relative to VSMOW on scales normalized such that the δ2H and δ18O values of SLAP reference water are, respectively, –428 and –55.5 ‰. Each uncertainty is an estimated expanded uncertainty (U = 2uc) about the reference value that provides an interval that has about a 95-percent probability of encompassing the true value. CONCLUSION: This isotopic reference material, designated as USGS47, is intended as one of two isotopic reference waters for daily normalization of stable hydrogen and stable oxygen isotopic analysis of water with a mass spectrometer or a laser absorption spectrometer. "

Computed Tomography of the Abdomen in Eight Clinically Normal Common Marmosets (Callithrix jacchus).

PubMed

du Plessis, W M; Groenewald, H B; Elliott, D

2017-08-01

The aim of this study was to provide a detailed anatomical description of the abdomen in the clinically normal common marmoset by means of computed tomography (CT). Eight clinically healthy mature common marmosets ranging from 12 to 48 months and 235 to 365 g bodyweight were anesthetized and pre- and post-contrast CT examinations were performed using different CT settings in dorsal recumbency. Abdominal organs were identified and visibility noted. Diagnostic quality abdominal images could be obtained of the common marmoset despite its small size using a dual-slice CT scanner. Representative cross-sectional images were chosen from different animals illustrating the abdominal CT anatomy of clinically normal common marmosets. Identification or delineation of abdominal organs greatly improved with i.v. contrast. A modified high-frequency algorithm with edge enhancement added valuable information for identification of small structures such as the ureters. The Hounsfield unit (HU) of major abdominal organs differed from that of small animals (domestic dogs and cats). Due to their size and different anatomy, standard small animal CT protocols need to be critically assessed and adapted for exotics, such as the common marmoset. The established normal reference range of HU of major abdominal organs and adapted settings for a CT protocol will aid clinical assessment of the common marmoset. © 2017 Blackwell Verlag GmbH.

A systematic review of the angular values obtained by computerized photogrammetry in sagittal plane: a proposal for reference values.

PubMed

Krawczky, Bruna; Pacheco, Antonio G; Mainenti, Míriam R M

2014-05-01

Reference values for postural alignment in the coronal plane, as measured by computerized photogrammetry, have been established but not for the sagittal plane. The objective of this study is to propose reference values for angular measurements used for postural analysis in the sagittal plane for healthy adults. Electronic databases (PubMed, BVS, Cochrane, Scielo, and Science Direct) were searched using the following key words: evaluation, posture, photogrammetry, and software. Articles published between 2006 and 2012 that used the PAS/SAPO (postural assessment software) were selected. Another inclusion criterion was the presentation of, at least, one of the following measurements: head horizontal alignment, pelvic horizontal alignment, hip angle, vertical alignment of the body, thoracic kyphosis, and lumbar lordosis. Angle samples of the selected articles were grouped 2 by 2 in relation to an overall average, which made possible total average, variance, and SD calculations. Six articles were included, and the following average angular values were found: 51.42° ± 4.87° (head horizontal alignment), -12.26° ± 5.81° (pelvic horizontal alignment), -6.40° ± 3.86° (hip angle), and 1.73° ± 0.94° (vertical alignment of the body). None of the articles contained the measurements for thoracic kyphosis and lumbar lordosis. The reference values can be adopted as reference for postural assessment in future researches if the same anatomical points are considered. Copyright © 2014 National University of Health Sciences. Published by Mosby, Inc. All rights reserved.

a Recursive Approach to Compute Normal Forms

NASA Astrophysics Data System (ADS)

HSU, L.; MIN, L. J.; FAVRETTO, L.

2001-06-01

Normal forms are instrumental in the analysis of dynamical systems described by ordinary differential equations, particularly when singularities close to a bifurcation are to be characterized. However, the computation of a normal form up to an arbitrary order is numerically hard. This paper focuses on the computer programming of some recursive formulas developed earlier to compute higher order normal forms. A computer program to reduce the system to its normal form on a center manifold is developed using the Maple symbolic language. However, it should be stressed that the program relies essentially on recursive numerical computations, while symbolic calculations are used only for minor tasks. Some strategies are proposed to save computation time. Examples are presented to illustrate the application of the program to obtain high order normalization or to handle systems with large dimension.

Applying the log-normal distribution to target detection

NASA Astrophysics Data System (ADS)

Holst, Gerald C.

1992-09-01

Holst and Pickard experimentally determined that MRT responses tend to follow a log-normal distribution. The log normal distribution appeared reasonable because nearly all visual psychological data is plotted on a logarithmic scale. It has the additional advantage that it is bounded to positive values; an important consideration since probability of detection is often plotted in linear coordinates. Review of published data suggests that the log-normal distribution may have universal applicability. Specifically, the log-normal distribution obtained from MRT tests appears to fit the target transfer function and the probability of detection of rectangular targets.

Characterization of reference genes for qPCR analysis in various tissues of the Fujian oyster Crassostrea angulata

NASA Astrophysics Data System (ADS)

Pu, Fei; Yang, Bingye; Ke, Caihuan

2015-07-01

Accurate quantification of transcripts using quantitative real-time polymerase chain reaction (qPCR) depends on the identification of reliable reference genes for normalization. This study aimed to identify and validate seven reference genes, including actin-2 ( ACT-2), elongation factor 1 alpha ( EF-1α), elongation factor 1 beta ( EF-1β), glyceraldehyde-3-phosphate dehydrogenase ( GAPDH), ubiquitin ( UBQ), β-tubulin ( β-TUB), and 18S ribosomal RNA, from Crassostrea angulata, a valuable marine bivalve cultured worldwide. Transcript levels of the candidate reference genes were examined using qPCR analysis and showed differential expression patterns in the mantle, gill, adductor muscle, labial palp, visceral mass, hemolymph and gonad tissues. Quantitative data were analyzed using the geNorm software to assess the expression stability of the candidate reference genes, revealing that β-TUB and UBQ were the most stable genes. The commonly used GAPDH and 18S rRNA showed low stability, making them unsuitable candidates in this system. The expression pattern of the G protein β-subunit gene ( Gβ) across tissue types was also examined and normalized to the expression of each or both of UBQ and β-TUB as internal controls. This revealed consistent trends with all three normalization approaches, thus validating the reliability of UBQ and β-TUB as optimal internal controls. The study provides the first validated reference genes for accurate data normalization in transcript profiling in Crassostrea angulata, which will be indispensable for further functional genomics studies in this economically valuable marine bivalve.

Validation of reference genes for gene expression studies in soybean aphid, Aphis glycines Matsumura

USDA-ARS?s Scientific Manuscript database

Quantitative real-time PCR (qRT-PCR) is a common tool for quantifying mRNA transcripts. To normalize results, a reference gene is mandatory. Aphis glycines is a significant soybean pest, yet gene expression and functional genomics studies are hindered by a lack of stable reference genes. We evalu...

Long-wave theory for a new convective instability with exponential growth normal to the wall.

PubMed

Healey, J J

2005-05-15

A linear stability theory is presented for the boundary-layer flow produced by an infinite disc rotating at constant angular velocity in otherwise undisturbed fluid. The theory is developed in the limit of long waves and when the effects of viscosity on the waves can be neglected. This is the parameter regime recently identified by the author in a numerical stability investigation where a curious new type of instability was found in which disturbances propagate and grow exponentially in the direction normal to the disc, (i.e. the growth takes place in a region of zero mean shear). The theory describes the mechanisms controlling the instability, the role and location of critical points, and presents a saddle-point analysis describing the large-time evolution of a wave packet in frames of reference moving normal to the disc. The theory also shows that the previously obtained numerical solutions for numerically large wavelengths do indeed lie in the asymptotic long-wave regime, and so the behaviour and mechanisms described here may apply to a number of cross-flow instability problems.

Detection of fallen trees in ALS point clouds using a Normalized Cut approach trained by simulation

NASA Astrophysics Data System (ADS)

Polewski, Przemyslaw; Yao, Wei; Heurich, Marco; Krzystek, Peter; Stilla, Uwe

2015-07-01

Downed dead wood is regarded as an important part of forest ecosystems from an ecological perspective, which drives the need for investigating its spatial distribution. Based on several studies, Airborne Laser Scanning (ALS) has proven to be a valuable remote sensing technique for obtaining such information. This paper describes a unified approach to the detection of fallen trees from ALS point clouds based on merging short segments into whole stems using the Normalized Cut algorithm. We introduce a new method of defining the segment similarity function for the clustering procedure, where the attribute weights are learned from labeled data. Based on a relationship between Normalized Cut's similarity function and a class of regression models, we show how to learn the similarity function by training a classifier. Furthermore, we propose using an appearance-based stopping criterion for the graph cut algorithm as an alternative to the standard Normalized Cut threshold approach. We set up a virtual fallen tree generation scheme to simulate complex forest scenarios with multiple overlapping fallen stems. This simulated data is then used as a basis to learn both the similarity function and the stopping criterion for Normalized Cut. We evaluate our approach on 5 plots from the strictly protected mixed mountain forest within the Bavarian Forest National Park using reference data obtained via a manual field inventory. The experimental results show that our method is able to detect up to 90% of fallen stems in plots having 30-40% overstory cover with a correctness exceeding 80%, even in quite complex forest scenes. Moreover, the performance for feature weights trained on simulated data is competitive with the case when the weights are calculated using a grid search on the test data, which indicates that the learned similarity function and stopping criterion can generalize well on new plots.

Reference values for respiratory rate in the first 3 years of life.

PubMed

Rusconi, F; Castagneto, M; Gagliardi, L; Leo, G; Pellegatta, A; Porta, N; Razon, S; Braga, M

1994-09-01

Raised respiratory rate is a useful sign to diagnose lower respiratory infections in childhood. However, the normal range for respiratory rate has not been defined in a proper, large sample. To assess the respiratory rate in a large number of infants and young children in order to construct percentile curves by age; to determine the repeatability to the assessment using a stethoscope and compare it with observation. Respiratory rate was recorded for 1 minute with a stethoscope in 618 infants and children, aged 15 days to 3 years old, without respiratory infections or any other severe disease when awake and calm and when asleep. In 50 subjects we compared respiratory rate taken 30 to 60 minutes apart to assess repeatability, and in 50 others we compared simultaneous counts obtained by stethoscope versus observation. Repeatability was good as the standard deviation of differences was 2.5 breaths/minute in awake and 1.7 breaths/minute in asleep children. Respiratory rate obtained with a stethoscope was systematically higher than that obtained by observation (mean difference 2.6 breaths/minute in awake and 1.8 breaths/minute in asleep children; P = .015 and P < .001, respectively). A decrease in respiratory rate with age was seen for both states, and it was faster in the first few months of life when also a greater dispersion of values was observed. A second degree polynomial curve accurately fitted the data. Reference percentile values were developed from these data. The repeatability of respiratory rate measured with a stethoscope was good. Percentile curves would be particularly helpful in the first months of life when the decline in respiratory rate is very rapid and prevents to use cut off values for defining "normality."

Magnetic Resonance Imaging Determination of Normal Pituitary Gland Dimensions in Zaria, Northwest Nigerian Population

PubMed Central

Ibinaiye, Philip Oluleke; Olarinoye-Akorede, Sefia; Kajogbola, Olugbenga; Bakari, Adamu Girei

2015-01-01

Objectives: To determine the dimensions of normal pituitary gland using T1-weighted magnetic resonance images (MRI) and to determine their relationship with age and sex. Materials and Methods: Cranial MRI scans of 100 individuals with clinically normal pituitary function (58 males and 42 females) and in the age range 14–82 years were reviewed in order to obtain volumetric measurements of the pituitary gland. The height, width, and depth of the pituitary were obtained from mid-sagittal and coronal planes, while the volume was calculated from these measured parameters. The data obtained were stratified based on age and sex for analysis. Statistical tests applied included Student's t-test and Pearson correlation. A minimum level of statistical significance was set at P < 0.05. Results: The mean pituitary volumes were 334.1 ± 145.8 mm3 and 328.1 ± 129.2 mm3 while the mean pituitary heights were 6.45 ± 1.7 mm and 6.46 ± 1.57 mm in males and females, respectively. Although there was no statistically significant difference between pituitary height and pituitary volume in both sexes, they correlated negatively with increasing age (r = −202, P = 0.04 and r = −410, P = 0.000, respectively). Both parameters were highest in pubertal subjects and declined steadily with age, with a second peak occurring only for pituitary height in the sixth decade. The mean pituitary widths (9.08 ± 2.59 mm and 9.21 ± 1.86 mm) and depths (10.59 ± 1.71 mm and 10.49 ± 1.57 mm) in males and females, respectively, did not show remarkable changes with age and sex in the individuals studied. Conclusion: With this study, we have provided reference values in Nigerian population for the dimensions of normal pituitary gland, in order to facilitate assessment and diagnosis in patients with abnormalities of the hypothalamic–pituitary axis. PMID:26167387

Direct measurements and systematic observations of physical workload among medical secretaries, furniture removers and male and female reference populations.

PubMed

Karlqvist, L; Winkel, J; Wiktorin, C

1994-10-01

The aim of this investigation was to collect quantitative information about the occurrence of manual materials handling and working postures in working life. Direct technical recordings and systematic observations by trained ergonomists were used throughout a whole working day on 12 male furniture removers, 13 female medical secretaries, 27 males and 45 females randomly sampled from the working population in the Stockholm area. A quantitative job exposure profile was obtained by weighting together exposure data obtained by observation of tasks occurring during a normal working week. The results showed no major differences in physical exposures between the male and female reference populations. The medical secretaries spent less time than the female population kneeling/squatting and longer time than any other group with repetitive hand movements. Exposure data for task and job should be clearly distinguished.

Ultrasonographic anatomy of the healthy southern tigrina ( Leopardus guttulus) abdomen: comparison with domestic cat references.

PubMed

Müller, Thiago R; Marcelino, Raquel S; de Souza, Livia P; Teixeira, Carlos R; Mamprim, Maria J

2017-02-01

Objectives The aim of the study was to describe the normal abdominal echoanatomy of the tigrina and to compare it with the abdominal echoanatomy of the domestic cat. Reference intervals for the normal abdominal ultrasonographic anatomy of individual species are important for accurate diagnoses and interpretation of routine health examinations. The hypothesis was that the echoanatomy of the tigrina was similar to that of the domestic cat. Methods Eighteen clinically healthy tigrina were selected for abdominal ultrasound examination, in order to obtain normal parameters of the bladder, spleen, adrenal gland, kidney, gastrointestinal tract, liver and gall bladder, and Doppler parameters of liver and kidney vessels. Results The splenic parenchyma was consistently hyperechoic to the kidneys and liver. The liver, kidneys and spleen had similar echotexture, shape and dimensions when compared with the domestic cat. The gall bladder was lobulated and surrounded by a clearly visualized thin, smooth, regular echogenic wall. The adrenal glands had a bilobulated shape. The urinary bladder had a thin echogenic wall. The Doppler parameters of the portal vein and renal artery were similar to the domestic cat. Conclusions and relevance The results support the hypothesis that the ultrasonographic parameters of the abdominal viscera of the southern tigrina are similar to those of the domestic cat.

Analysis of the interaction of a weak normal shock wave with a turbulent boundary layer

NASA Technical Reports Server (NTRS)

Melnik, R. E.; Grossman, B.

1974-01-01

The method of matched asymptotic expansions is used to analyze the interaction of a normal shock wave with an unseparated turbulent boundary layer on a flat surface at transonic speeds. The theory leads to a three-layer description of the interaction in the double limit of Reynolds number approaching infinity and Mach number approaching unity. The interaction involves an outer, inviscid rotational layer, a constant shear-stress wall layer, and a blending region between them. The pressure distribution is obtained from a numerical solution of the outer-layer equations by a mixed-flow relaxation procedure. An analytic solution for the skin friction is determined from the inner-layer equations. The significance of the mathematical model is discussed with reference to existing experimental data.

The normalization heuristic: an untested hypothesis that may misguide medical decisions.

PubMed

Aberegg, Scott K; O'Brien, James M

2009-06-01

Medical practice is increasingly informed by the evidence from randomized controlled trials. When such evidence is not available, clinical hypotheses based on pathophysiological reasoning and common sense guide clinical decision making. One commonly utilized general clinical hypothesis is the assumption that normalizing abnormal laboratory values and physiological parameters will lead to improved patient outcomes. We refer to the general use of this clinical hypothesis to guide medical therapeutics as the "normalization heuristic". In this paper, we operationally define this heuristic and discuss its limitations as a rule of thumb for clinical decision making. We review historical and contemporaneous examples of normalization practices as empirical evidence for the normalization heuristic and to highlight its frailty as a guide for clinical decision making.

Glymphatic MRI in idiopathic normal pressure hydrocephalus

PubMed Central

Ringstad, Geir; Vatnehol, Svein Are Sirirud; Eide, Per Kristian

2017-01-01

Abstract The glymphatic system has in previous studies been shown as fundamental to clearance of waste metabolites from the brain interstitial space, and is proposed to be instrumental in normal ageing and brain pathology such as Alzheimer’s disease and brain trauma. Assessment of glymphatic function using magnetic resonance imaging with intrathecal contrast agent as a cerebrospinal fluid tracer has so far been limited to rodents. We aimed to image cerebrospinal fluid flow characteristics and glymphatic function in humans, and applied the methodology in a prospective study of 15 idiopathic normal pressure hydrocephalus patients (mean age 71.3 ± 8.1 years, three female and 12 male) and eight reference subjects (mean age 41.1 + 13.0 years, six female and two male) with suspected cerebrospinal fluid leakage (seven) and intracranial cyst (one). The imaging protocol included T1-weighted magnetic resonance imaging with equal sequence parameters before and at multiple time points through 24 h after intrathecal injection of the contrast agent gadobutrol at the lumbar level. All study subjects were kept in the supine position between examinations during the first day. Gadobutrol enhancement was measured at all imaging time points from regions of interest placed at predefined locations in brain parenchyma, the subarachnoid and intraventricular space, and inside the sagittal sinus. Parameters demonstrating gadobutrol enhancement and clearance in different locations were compared between idiopathic normal pressure hydrocephalus and reference subjects. A characteristic flow pattern in idiopathic normal hydrocephalus was ventricular reflux of gadobutrol from the subarachnoid space followed by transependymal gadobutrol migration. At the brain surfaces, gadobutrol propagated antegradely along large leptomeningeal arteries in all study subjects, and preceded glymphatic enhancement in adjacent brain tissue, indicating a pivotal role of intracranial pulsations for glymphatic

Glymphatic MRI in idiopathic normal pressure hydrocephalus.

PubMed

Ringstad, Geir; Vatnehol, Svein Are Sirirud; Eide, Per Kristian

2017-10-01

The glymphatic system has in previous studies been shown as fundamental to clearance of waste metabolites from the brain interstitial space, and is proposed to be instrumental in normal ageing and brain pathology such as Alzheimer's disease and brain trauma. Assessment of glymphatic function using magnetic resonance imaging with intrathecal contrast agent as a cerebrospinal fluid tracer has so far been limited to rodents. We aimed to image cerebrospinal fluid flow characteristics and glymphatic function in humans, and applied the methodology in a prospective study of 15 idiopathic normal pressure hydrocephalus patients (mean age 71.3 ± 8.1 years, three female and 12 male) and eight reference subjects (mean age 41.1 + 13.0 years, six female and two male) with suspected cerebrospinal fluid leakage (seven) and intracranial cyst (one). The imaging protocol included T1-weighted magnetic resonance imaging with equal sequence parameters before and at multiple time points through 24 h after intrathecal injection of the contrast agent gadobutrol at the lumbar level. All study subjects were kept in the supine position between examinations during the first day. Gadobutrol enhancement was measured at all imaging time points from regions of interest placed at predefined locations in brain parenchyma, the subarachnoid and intraventricular space, and inside the sagittal sinus. Parameters demonstrating gadobutrol enhancement and clearance in different locations were compared between idiopathic normal pressure hydrocephalus and reference subjects. A characteristic flow pattern in idiopathic normal hydrocephalus was ventricular reflux of gadobutrol from the subarachnoid space followed by transependymal gadobutrol migration. At the brain surfaces, gadobutrol propagated antegradely along large leptomeningeal arteries in all study subjects, and preceded glymphatic enhancement in adjacent brain tissue, indicating a pivotal role of intracranial pulsations for glymphatic function. In

Reference genes for measuring mRNA expression.

PubMed

Dundas, Jitesh; Ling, Maurice

2012-12-01

The aim of this review is to find answers to some of the questions surrounding reference genes and their reliability for quantitative experiments. Reference genes are assumed to be at a constant expression level, over a range of conditions such as temperature. These genes, such as GADPH and beta-actin, are used extensively for gene expression studies using techniques like quantitative PCR. There have been several studies carried out on identifying reference genes. However, a lot of evidence indicates issues to the general suitability of these genes. Recent studies had shown that different factors, including the environment and methods, play an important role in changing the expression levels of the reference genes. Thus, we conclude that there is no reference gene that can deemed suitable for all the experimental conditions. In addition, we believe that every experiment will require the scientific evaluation and selection of the best candidate gene for use as a reference gene to obtain reliable scientific results.

[Full blood count reference values in children of 8 to 12 years old residing at 2,760 m above sea level].

PubMed

Armando García-Miranda, L; Contreras, I; Estrada, J A

2014-04-01

To determine reference values for full blood count parameters in a population of children 8 to 12 years old, living at an altitude of 2760 m above sea level. Our sample consisted of 102 individuals on whom a full blood count was performed. The parameters included: total number of red blood cells, platelets, white cells, and a differential count (millions/μl and %) of neutrophils, lymphocytes, monocytes, eosinophils and basophils. Additionally, we obtained values for hemoglobin, hematocrit, mean corpuscular volume, mean corpuscular hemoglobin, concentration of corpuscular hemoglobin and red blood cell distribution width. The results were statistically analyzed with a non-parametric test, to divide the sample in quartiles and obtain the lower and upper limits for our intervals. Moreover, the values for the intervals obtained from this analysis were compared to intervals obtained estimating+- 2 standard deviations above and below from our mean values. Our results showed significant differences compared to normal interval values reported for the adult Mexican population in most of the parameters studied. The full blood count is an important laboratory test used routinely for the initial assessment of a patient. Values of full blood counts in healthy individuals vary according to gender, age and geographic location; therefore, each population should have its own reference values. Copyright © 2013 Asociación Española de Pediatría. Published by Elsevier Espana. All rights reserved.

Regional reference values of thyroid gland volume in Turkish Adults.

PubMed

Şahin, Ertan; Elboğa, Umut; Kalender, Ebuzer

2015-01-01

It is important to know the size of the thyroid gland, and its normal value may vary among different geographic regions. In this study, we aimed to establish reference ranges for thyroid volume in euthyroid adults and to compare these results with the literature data. Between June 2011 and June 2012,461 patients with normal laboratory results (serum TSH, anti-TG, anti-TPO antibodies and urine iodine level) that underwent thyroid gland ultrasound examination were retrospectively analyzed.Two hundred and 92 patients were females and 169 were males; the age range was 18-61 years with mean age 30.84±9.97 years. Length, breadth and thickness were measured, and the volume of each lobe was estimated using the ellipsoid formula. The overall mean thyroid volume in all patients who were examined was 12.98±2.53 mL. The mean thyroid volume in females and males was 12.09±2.05 mL and 14.53±2.55, respectively (p<0.05). The right thyroid lobe volume was greater than the left in all patients of both sexes. In addition, the study establishes a significant correlation between the thyroid volume and height, weight and body surface area of the subjects of both sexes (p<0.05). In the light of our findings we can provide reference values in order to evaluate patients who have thyroid hyperplasia or who are considered as normal. We consider that further studies are necessary to establish national references thyroid volume for each country.

A Comparison of a Maximum Exertion Method and a Model-Based, Sub-Maximum Exertion Method for Normalizing Trunk EMG

PubMed Central

Cholewicki, Jacek; van Dieën, Jaap; Lee, Angela S.; Reeves, N. Peter

2011-01-01

The problem with normalizing EMG data from patients with painful symptoms (e.g. low back pain) is that such patients may be unwilling or unable to perform maximum exertions. Furthermore, the normalization to a reference signal, obtained from a maximal or sub-maximal task, tends to mask differences that might exist as a result of pathology. Therefore, we presented a novel method (GAIN method) for normalizing trunk EMG data that overcomes both problems. The GAIN method does not require maximal exertions (MVC) and tends to preserve distinct features in the muscle recruitment patterns for various tasks. Ten healthy subjects performed various isometric trunk exertions, while EMG data from 10 muscles were recorded and later normalized using the GAIN and MVC methods. The MVC method resulted in smaller variation between subjects when tasks were executed at the three relative force levels (10%, 20%, and 30% MVC), while the GAIN method resulted in smaller variation between subjects when the tasks were executed at the three absolute force levels (50 N, 100 N, and 145 N). This outcome implies that the MVC method provides a relative measure of muscle effort, while the GAIN-normalized EMG data gives an estimate of the absolute muscle force. Therefore, the GAIN-normalized EMG data tends to preserve the EMG differences between subjects in the way they recruit their muscles to execute various tasks, while the MVC-normalized data will tend to suppress such differences. The appropriate choice of the EMG normalization method will depend on the specific question that an experimenter is attempting to answer. PMID:21665489

Normalization of oxygen and hydrogen isotope data

USGS Publications Warehouse

Coplen, T.B.

1988-01-01

To resolve confusion due to expression of isotopic data from different laboratories on non-corresponding scales, oxygen isotope analyses of all substances can be expressed relative to VSMOW or VPDB (Vienna Peedee belemnite) on scales normalized such that the ??18O of SLAP is -55.5% relative to VSMOW. H3+ contribution in hydrogen isotope ratio analysis can be easily determined using two gaseous reference samples that differ greatly in deuterium content. ?? 1988.

Obtaining orthotropic elasticity tensor using entries zeroing method.

NASA Astrophysics Data System (ADS)

Gierlach, Bartosz; Danek, Tomasz

2017-04-01

A generally anisotropic elasticity tensor obtained from measurements can be represented by a tensor belonging to one of eight material symmetry classes. Knowledge of symmetry class and orientation is helpful for describing physical properties of a medium. For each non-trivial symmetry class except isotropic this problem is nonlinear. A common method of obtaining effective tensor is a choosing its non-trivial symmetry class and minimizing Frobenius norm between measured and effective tensor in the same coordinate system. Global optimization algorithm has to be used to determine the best rotation of a tensor. In this contribution, we propose a new approach to obtain optimal tensor, with the assumption that it is orthotropic (or at least has a similar shape to the orthotropic one). In orthotropic form tensor 24 out of 36 entries are zeros. The idea is to minimize the sum of squared entries which are supposed to be equal to zero through rotation calculated with optimization algorithm - in this case Particle Swarm Optimization (PSO) algorithm. Quaternions were used to parametrize rotations in 3D space to improve computational efficiency. In order to avoid a choice of local minima we apply PSO several times and only if we obtain similar results for the third time we consider it as a correct value and finish computations. To analyze obtained results Monte-Carlo method was used. After thousands of single runs of PSO optimization, we obtained values of quaternion parts and plot them. Points concentrate in several points of the graph following the regular pattern. It suggests the existence of more complex symmetry in the analyzed tensor. Then thousands of realizations of generally anisotropic tensor were generated - each tensor entry was replaced with a random value drawn from normal distribution having a mean equal to measured tensor entry and standard deviation of the measurement. Each of these tensors was subject of PSO based optimization delivering quaternion for optimal

EFFECT ON PERFUSION VALUES OF SAMPLING INTERVAL OF CT PERFUSION ACQUISITIONS IN NEUROENDOCRINE LIVER METASTASES AND NORMAL LIVER

PubMed Central

Ng, Chaan S.; Hobbs, Brian P.; Wei, Wei; Anderson, Ella F.; Herron, Delise H.; Yao, James C.; Chandler, Adam G.

2014-01-01

Objective To assess the effects of sampling interval (SI) of CT perfusion acquisitions on CT perfusion values in normal liver and liver metastases from neuroendocrine tumors. Methods CT perfusion in 16 patients with neuroendocrine liver metastases were analyzed by distributed parameter modeling to yield tissue blood flow, blood volume, mean transit time, permeability, and hepatic arterial fraction, for tumor and normal liver. CT perfusion values for the reference sampling interval of 0.5s (SI0.5) were compared with those of SI datasets of 1s, 2s, 3s and 4s, using mixed-effects model analyses. Results Increases in SI beyond 1s were associated with significant and increasing departures of CT perfusion parameters from reference values at SI0.5 (p≤0.0009). CT perfusion values deviated from reference with increasing uncertainty with increasing SIs. Findings for normal liver were concordant. Conclusion Increasing SIs beyond 1s yield significantly different CT perfusion parameter values compared to reference values at SI0.5. PMID:25626401

[Diagnostic reference levels in interventional radiology].

PubMed

Vañó Carruana, E; Fernández Soto, J M; Sánchez Casanueva, R M; Ten Morón, J I

2013-12-01

This article discusses the diagnostic reference levels for radiation exposure proposed by the International Commission on Radiological Protection (ICRP) to facilitate the application of the optimization criteria in diagnostic imaging and interventional procedures. These levels are normally established as the third quartile of the dose distributions to patients in an ample sample of centers and are supposed to be representative of good practice regarding patient exposure. In determining these levels, it is important to evaluate image quality as well to ensure that it is sufficient for diagnostic purposes. When the values for the dose received by patients are systematically higher or much lower than the reference levels, an investigation should determine whether corrective measures need to be applied. The European and Spanish regulations require the use of these reference values in quality assurance programs. For interventional procedures, the dose area product (or kerma area product) values are usually used as reference values together with the time under fluoroscopy and the total number of images acquired. The most modern imaging devices allow the value of the accumulated dose at the entrance to the patient to be calculated to optimize the distribution of the dose on the skin. The ICRP recommends that the complexity of interventional procedures be taken into account when establishing reference levels. In the future, diagnostic imaging departments will have automatic systems to manage patient dosimetric data; these systems will enable continuous dosage auditing and alerts about individual procedures that might involve doses several times above the reference values. This article also discusses aspects that need to be clarified to take better advantage of the reference levels in interventional procedures. Copyright © 2013 SERAM. Published by Elsevier Espana. All rights reserved.

Multivariate reference technique for quantitative analysis of fiber-optic tissue Raman spectroscopy.

PubMed

Bergholt, Mads Sylvest; Duraipandian, Shiyamala; Zheng, Wei; Huang, Zhiwei

2013-12-03

We report a novel method making use of multivariate reference signals of fused silica and sapphire Raman signals generated from a ball-lens fiber-optic Raman probe for quantitative analysis of in vivo tissue Raman measurements in real time. Partial least-squares (PLS) regression modeling is applied to extract the characteristic internal reference Raman signals (e.g., shoulder of the prominent fused silica boson peak (~130 cm(-1)); distinct sapphire ball-lens peaks (380, 417, 646, and 751 cm(-1))) from the ball-lens fiber-optic Raman probe for quantitative analysis of fiber-optic Raman spectroscopy. To evaluate the analytical value of this novel multivariate reference technique, a rapid Raman spectroscopy system coupled with a ball-lens fiber-optic Raman probe is used for in vivo oral tissue Raman measurements (n = 25 subjects) under 785 nm laser excitation powers ranging from 5 to 65 mW. An accurate linear relationship (R(2) = 0.981) with a root-mean-square error of cross validation (RMSECV) of 2.5 mW can be obtained for predicting the laser excitation power changes based on a leave-one-subject-out cross-validation, which is superior to the normal univariate reference method (RMSE = 6.2 mW). A root-mean-square error of prediction (RMSEP) of 2.4 mW (R(2) = 0.985) can also be achieved for laser power prediction in real time when we applied the multivariate method independently on the five new subjects (n = 166 spectra). We further apply the multivariate reference technique for quantitative analysis of gelatin tissue phantoms that gives rise to an RMSEP of ~2.0% (R(2) = 0.998) independent of laser excitation power variations. This work demonstrates that multivariate reference technique can be advantageously used to monitor and correct the variations of laser excitation power and fiber coupling efficiency in situ for standardizing the tissue Raman intensity to realize quantitative analysis of tissue Raman measurements in vivo, which is particularly appealing in

Selection of reference genes for microRNA analysis associated to early stress response to handling and confinement in Salmo salar.

PubMed

Zavala, Eduardo; Reyes, Daniela; Deerenberg, Robert; Vidal, Rodrigo

2017-05-11

MicroRNAs are key non-coding RNA molecules that play a relevant role in the regulation of gene expression through translational repression and/or transcript cleavage during normal development and physiological adaptation processes like stress. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) has become the approach normally used to determine the levels of microRNAs. However, this approach needs the use of endogenous reference. An improper selection of endogenous references can result in confusing interpretation of data. The aim of this study was to identify and validate appropriate endogenous reference miRNA genes for normalizing RT-qPCR survey of miRNAs expression in four different tissues of Atlantic salmon, under handling and confinement stress conditions associated to early or primary stress response. Nine candidate reference normalizers, including microRNAs and nuclear genes, normally used in vertebrate microRNA expression studies were selected from literature, validated by RT-qPCR and analyzed by the algorithms geNorm and NormFinder. The results revealed that the ssa-miR-99-5p gene was the most stable overall and that ssa-miR-99-5p and ssa-miR-23a-5p genes were the best combination. Moreover, the suitability of ssa-miR-99-5p and ssa-miR-23a-5p as endogeneuos reference genes was demostrated by the expression analysis of ssa-miR-193-5p gene.

Validation of serum free light chain reference ranges in primary care.

PubMed

Galvani, Luca; Flanagan, Jane; Sargazi, Mansour; Neithercut, William D

2016-05-01

The demand for measurement of serum immunoglobulin free kappa (κ) and lambda (λ) light chains has increased. The κ:λ ratio is used to assist in diagnosis/monitoring of plasma cell disorders. The binding site reference range for serum-free light chain κ:λ ratios of 0.26-1.65 was derived from healthy volunteers. Subsequently, a reference range of 0.37-3.1 for patients with chronic kidney disease has been proposed. Elevated free light chain concentrations and borderline raised free light chain ratios also may be found in polyclonal gammopathies and with other non-renal illnesses. This assessment was conducted to validate the established free light chain reference ranges in individuals from primary care. A total of 130 samples were identified from routine blood samples collected in primary care for routine biochemistry testing and estimated glomerular filtration rate calculation. The median and range of κ:λ ratios found in each estimated glomerular filtration rate group used for chronic kidney disease classification were higher than previously described. This was the case for individuals with normal or essentially normal renal function with estimated glomerular filtration rates>90, (0.58-1.76) and estimated glomerular filtration rate of 60-90 mL/min/1.73 m(2), (0.71-1.93). Individuals with estimated glomerular filtration rate 15-30, (0.72-4.50) and estimated glomerular filtration rate <15 ml/min/1.73 m(2) (0.71-4.95) also had higher values when compared to the current renal reference range of 0.37-3.10. Elevation of free light chain-κ:λ ratios may occur in the absence of a reduced renal function shown by a normal estimated glomerular filtration rate and in the presence of reduced renal function by estimated glomerular filtration rate when comparing results with the established reference ranges. Explanations include choice of analytical systems or the presence of other concurrent non-plasma cell illness. © The Author(s) 2016.

Devices for the Production of Reference Gas Mixtures.

PubMed

Fijało, Cyprian; Dymerski, Tomasz; Gębicki, Jacek; Namieśnik, Jacek

2016-09-02

For many years there has been growing demand for gaseous reference materials, which is connected with development in many fields of science and technology. As a result, new methodological and instrumental solutions appear that can be used for this purpose. Appropriate quality assurance/quality control (QA/QC) must be used to make sure that measurement data are a reliable source of information. Reference materials are a significant element of such systems. In the case of gas samples, such materials are generally called reference gas mixtures. This article presents the application and classification of reference gas mixtures, which are a specific type of reference materials, and the methods for obtaining them are described. Construction solutions of devices for the production of reference gas mixtures are detailed, and a description of a prototype device for dynamic production of reference gas mixtures containing aroma compounds is presented.

METRO-APEX Volume 18.1: Legal Reference Manual. Revised.

ERIC Educational Resources Information Center

University of Southern California, Los Angeles. COMEX Research Project.

The Legal Reference Manual is one of a set of twenty-one manuals used in METRO-APEX 1974, a computerized college and professional level, computer-supported, role-play, simulation exercise of a community with "normal" problems. Stress is placed on environmental quality considerations. APEX 1974 is an expansion of APEX--Air Pollution…

Normalization of High Dimensional Genomics Data Where the Distribution of the Altered Variables Is Skewed

PubMed Central

Landfors, Mattias; Philip, Philge; Rydén, Patrik; Stenberg, Per

2011-01-01

Genome-wide analysis of gene expression or protein binding patterns using different array or sequencing based technologies is now routinely performed to compare different populations, such as treatment and reference groups. It is often necessary to normalize the data obtained to remove technical variation introduced in the course of conducting experimental work, but standard normalization techniques are not capable of eliminating technical bias in cases where the distribution of the truly altered variables is skewed, i.e. when a large fraction of the variables are either positively or negatively affected by the treatment. However, several experiments are likely to generate such skewed distributions, including ChIP-chip experiments for the study of chromatin, gene expression experiments for the study of apoptosis, and SNP-studies of copy number variation in normal and tumour tissues. A preliminary study using spike-in array data established that the capacity of an experiment to identify altered variables and generate unbiased estimates of the fold change decreases as the fraction of altered variables and the skewness increases. We propose the following work-flow for analyzing high-dimensional experiments with regions of altered variables: (1) Pre-process raw data using one of the standard normalization techniques. (2) Investigate if the distribution of the altered variables is skewed. (3) If the distribution is not believed to be skewed, no additional normalization is needed. Otherwise, re-normalize the data using a novel HMM-assisted normalization procedure. (4) Perform downstream analysis. Here, ChIP-chip data and simulated data were used to evaluate the performance of the work-flow. It was found that skewed distributions can be detected by using the novel DSE-test (Detection of Skewed Experiments). Furthermore, applying the HMM-assisted normalization to experiments where the distribution of the truly altered variables is skewed results in considerably higher

Is this the right normalization? A diagnostic tool for ChIP-seq normalization.

PubMed

Angelini, Claudia; Heller, Ruth; Volkinshtein, Rita; Yekutieli, Daniel

2015-05-09

Chip-seq experiments are becoming a standard approach for genome-wide profiling protein-DNA interactions, such as detecting transcription factor binding sites, histone modification marks and RNA Polymerase II occupancy. However, when comparing a ChIP sample versus a control sample, such as Input DNA, normalization procedures have to be applied in order to remove experimental source of biases. Despite the substantial impact that the choice of the normalization method can have on the results of a ChIP-seq data analysis, their assessment is not fully explored in the literature. In particular, there are no diagnostic tools that show whether the applied normalization is indeed appropriate for the data being analyzed. In this work we propose a novel diagnostic tool to examine the appropriateness of the estimated normalization procedure. By plotting the empirical densities of log relative risks in bins of equal read count, along with the estimated normalization constant, after logarithmic transformation, the researcher is able to assess the appropriateness of the estimated normalization constant. We use the diagnostic plot to evaluate the appropriateness of the estimates obtained by CisGenome, NCIS and CCAT on several real data examples. Moreover, we show the impact that the choice of the normalization constant can have on standard tools for peak calling such as MACS or SICER. Finally, we propose a novel procedure for controlling the FDR using sample swapping. This procedure makes use of the estimated normalization constant in order to gain power over the naive choice of constant (used in MACS and SICER), which is the ratio of the total number of reads in the ChIP and Input samples. Linear normalization approaches aim to estimate a scale factor, r, to adjust for different sequencing depths when comparing ChIP versus Input samples. The estimated scaling factor can easily be incorporated in many peak caller algorithms to improve the accuracy of the peak identification. The

Delayed clearance of cerebrospinal fluid tracer from entorhinal cortex in idiopathic normal pressure hydrocephalus: A glymphatic magnetic resonance imaging study.

PubMed

Eide, Per K; Ringstad, Geir

2018-01-01

The glymphatic system plays a key role for clearance of waste solutes from the rodent brain. We recently found evidence of glymphatic circulation in the human brain when using magnetic resonance imaging (MRI) contrast agent as cerebrospinal fluid (CSF) tracer in conjunction with multiple MRI acquisitions (gMRI). The present study explored the hypothesis that reduced glymphatic clearance in entorhinal cortex (ERC) may be instrumental in idiopathic normal pressure hydrocephalus (iNPH) dementia. gMRI acquisitions were obtained over a 24-48 h time span in cognitively affected iNPH patients and non-cognitively affected patients with suspected CSF leaks. The CSF tracer enrichment was determined as changes in normalized MRI T1 signal units. The study included 30 patients with iNPH and 8 individuals with suspected CSF leaks (i.e. reference individuals). Compared to reference individuals, iNPH patients presented with higher medial temporal lobe atrophy score and Evan's index and inferior ERC thickness. We found delayed clearance of the intrathecal CSF tracer gadobutrol from CSF, the ERC and adjacent white matter, suggesting impaired glymphatic circulation. Reduced clearance and accumulation of toxic waste product such as amyloid-β may be a mechanism behind dementia in iNPH. Glymphatic MRI (gMRI) may become a tool for assessment of early dementia.

Rigorous Combination of GNSS and VLBI: How it Improves Earth Orientation and Reference Frames

NASA Astrophysics Data System (ADS)

Lambert, S. B.; Richard, J. Y.; Bizouard, C.; Becker, O.

2017-12-01

Current reference series (C04) of the International Earth Rotation and Reference Systems Service (IERS) are produced by a weighted combination of Earth orientation parameters (EOP) time series built up by combination centers of each technique (VLBI, GNSS, Laser ranging, DORIS). In the future, we plan to derive EOP from a rigorous combination of the normal equation systems of the four techniques.We present here the results of a rigorous combination of VLBI and GNSS pre-reduced, constraint-free, normal equations with the DYNAMO geodetic analysis software package developed and maintained by the French GRGS (Groupe de Recherche en GeÌodeÌsie Spatiale). The used normal equations are those produced separately by the IVS and IGS combination centers to which we apply our own minimal constraints.We address the usefulness of such a method with respect to the classical, a posteriori, combination method, and we show whether EOP determinations are improved.Especially, we implement external validations of the EOP series based on comparison with geophysical excitation and examination of the covariance matrices. Finally, we address the potential of the technique for the next generation celestial reference frames, which are currently determined by VLBI only.

Clinical chemistry reference values for 75-year-old apparently healthy persons.

PubMed

Huber, Klaus Roland; Mostafaie, Nazanin; Stangl, Gerhard; Worofka, Brigitte; Kittl, Eva; Hofmann, Jörg; Hejtman, Milos; Michael, Rainer; Weissgram, Silvia; Leitha, Thomas; Jungwirth, Susanne; Fischer, Peter; Tragl, Karl-Heinz; Bauer, Kurt

2006-01-01

Clinical chemistry reference values for elderly persons are sparse and mostly intermixed with those for younger subjects. To understand the links between metabolism and aging, it is paramount to differentiate between "normal" physiological processes in apparently healthy elderly subjects and metabolic changes due to long-lasting diseases. The Vienna Transdanube Aging (VITA) study, which began in 2000 and is continuing, will allow us to do just that, because more than 600 male and female volunteers aged exactly 75 years (to exclude any influence of the "aging" factor in this cohort) are participating in this study. Extensive clinical, neurological, biochemical, psychological, genetic, and radiological analyses, with a special emphasis on consumption of medication and abuse of drugs, were performed on each of the probands. The multitude of data and questionnaires obtained made possible an a posteriori approach to select individuals fulfilling criteria for a reference sample group of apparently healthy 75-year-old subjects for our study. Specific analytes were quantified on automated clinical analyzers, while manual methods were used for hormonal analytes. All clinical chemistry analytes were evaluated using in-depth statistical analyses with SPSS for Windows. In all, reference intervals for 45 analytes could be established. These include routine parameters for the assessment of organ functions, as well as hormone concentrations and hematological appraisals. Because all patients were reevaluated after exactly 30 months in the course of this study, we had the opportunity to reassess their health status at the age of 77.5 years. This was very useful for validation of the first round data set. Data of the second round evaluation corroborate the reference limits of the baseline analysis and further confirm our inclusion and exclusion criteria. In summary, we have established a reliable set of reference data for hormonal, hematological, and clinical chemistry analytes for

Hamilton's principle and normal mode coupling in an aspherical planet with a fluid core

NASA Astrophysics Data System (ADS)

Al-Attar, David; Crawford, Ophelia; Valentine, Andrew P.; Trampert, Jeannot

2018-04-01

We apply Hamilton's principle to obtain the exact equations of motion for an elastic planet that is rotating, self-gravitating, and comprises both fluid and solid regions. This variational problem is complicated by the occurrence of tangential slip at fluid-solid boundaries, but we show how this can be accommodated both directly and using the method of Lagrange multipliers. A novelty of our approach is that the planet's motion is described relative to an arbitrary reference configuration, with this generality offering advantages for numerical calculations. In particular, aspherical topography on the free surface or internal boundaries of the planet's equilibrium configuration can be converted exactly into effective volumetric heterogeneities within a geometrically spherical reference body by applying a suitable particle relabelling transformation. The theory is then specialised to consider the linearised motion of a planet about a steadily rotating equilibrium configuration, with these results having applications to normal mode coupling calculations used within studies of long period seismology, tidal deformation, and related fields. In particular, we explain how our new theory will, for the first time, allow aspherical boundary topography to be incorporated exactly within such coupling calculations.

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

PubMed

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

2013-11-13

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

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

PubMed Central

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

2013-01-01

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

Selection of suitable reference genes for gene expression studies in Staphylococcus capitis during growth under erythromycin stress.

PubMed

Cui, Bintao; Smooker, Peter M; Rouch, Duncan A; Deighton, Margaret A

2016-08-01

Accurate and reproducible measurement of gene transcription requires appropriate reference genes, which are stably expressed under different experimental conditions to provide normalization. Staphylococcus capitis is a human pathogen that produces biofilm under stress, such as imposed by antimicrobial agents. In this study, a set of five commonly used staphylococcal reference genes (gyrB, sodA, recA, tuf and rpoB) were systematically evaluated in two clinical isolates of Staphylococcus capitis (S. capitis subspecies urealyticus and capitis, respectively) under erythromycin stress in mid-log and stationary phases. Two public software programs (geNorm and NormFinder) and two manual calculation methods, reference residue normalization (RRN) and relative quantitative (RQ), were applied. The potential reference genes selected by the four algorithms were further validated by comparing the expression of a well-studied biofilm gene (icaA) with phenotypic biofilm formation in S. capitis under four different experimental conditions. The four methods differed considerably in their ability to predict the most suitable reference gene or gene combination for comparing icaA expression under different conditions. Under the conditions used here, the RQ method provided better selection of reference genes than the other three algorithms; however, this finding needs to be confirmed with a larger number of isolates. This study reinforces the need to assess the stability of reference genes for analysis of target gene expression under different conditions and the use of more than one algorithm in such studies. Although this work was conducted using a specific human pathogen, it emphasizes the importance of selecting suitable reference genes for accurate normalization of gene expression more generally.

Selection of relatively exact reference genes for gene expression studies in goosegrass (Eleusine indica) under herbicide stress

PubMed Central

Chen, Jingchao; Huang, Zhaofeng; Huang, Hongjuan; Wei, Shouhui; Liu, Yan; Jiang, Cuilan; Zhang, Jie; Zhang, Chaoxian

2017-01-01

Goosegrass (Eleusine indica) is one of the most serious annual grassy weeds worldwide, and its evolved herbicide-resistant populations are more difficult to control. Quantitative real-time PCR (qPCR) is a common technique for investigating the resistance mechanism; however, there is as yet no report on the systematic selection of stable reference genes for goosegrass. This study proposed to test the expression stability of 9 candidate reference genes in goosegrass in different tissues and developmental stages and under stress from three types of herbicide. The results show that for different developmental stages and organs (control), eukaryotic initiation factor 4 A (eIF-4) is the most stable reference gene. Chloroplast acetolactate synthase (ALS) is the most stable reference gene under glyphosate stress. Under glufosinate stress, eIF-4 is the best reference gene. Ubiquitin-conjugating enzyme (UCE) is the most stable reference gene under quizalofop-p-ethyl stress. The gene eIF-4 is the recommended reference gene for goosegrass under the stress of all three herbicides. Moreover, pairwise analysis showed that seven reference genes were sufficient to normalize the gene expression data under three herbicides treatment. This study provides a list of reliable reference genes for transcript normalization in goosegrass, which will facilitate resistance mechanism studies in this weed species. PMID:28429727

Selection of relatively exact reference genes for gene expression studies in goosegrass (Eleusine indica) under herbicide stress.

PubMed

Chen, Jingchao; Huang, Zhaofeng; Huang, Hongjuan; Wei, Shouhui; Liu, Yan; Jiang, Cuilan; Zhang, Jie; Zhang, Chaoxian

2017-04-21

Goosegrass (Eleusine indica) is one of the most serious annual grassy weeds worldwide, and its evolved herbicide-resistant populations are more difficult to control. Quantitative real-time PCR (qPCR) is a common technique for investigating the resistance mechanism; however, there is as yet no report on the systematic selection of stable reference genes for goosegrass. This study proposed to test the expression stability of 9 candidate reference genes in goosegrass in different tissues and developmental stages and under stress from three types of herbicide. The results show that for different developmental stages and organs (control), eukaryotic initiation factor 4 A (eIF-4) is the most stable reference gene. Chloroplast acetolactate synthase (ALS) is the most stable reference gene under glyphosate stress. Under glufosinate stress, eIF-4 is the best reference gene. Ubiquitin-conjugating enzyme (UCE) is the most stable reference gene under quizalofop-p-ethyl stress. The gene eIF-4 is the recommended reference gene for goosegrass under the stress of all three herbicides. Moreover, pairwise analysis showed that seven reference genes were sufficient to normalize the gene expression data under three herbicides treatment. This study provides a list of reliable reference genes for transcript normalization in goosegrass, which will facilitate resistance mechanism studies in this weed species.

Identification of Importin 8 (IPO8) as the most accurate reference gene for the clinicopathological analysis of lung specimens

PubMed Central

Nguewa, Paul A; Agorreta, Jackeline; Blanco, David; Lozano, Maria Dolores; Gomez-Roman, Javier; Sanchez, Blas A; Valles, Iñaki; Pajares, Maria J; Pio, Ruben; Rodriguez, Maria Jose; Montuenga, Luis M; Calvo, Alfonso

2008-01-01

Background The accurate normalization of differentially expressed genes in lung cancer is essential for the identification of novel therapeutic targets and biomarkers by real time RT-PCR and microarrays. Although classical "housekeeping" genes, such as GAPDH, HPRT1, and beta-actin have been widely used in the past, their accuracy as reference genes for lung tissues has not been proven. Results We have conducted a thorough analysis of a panel of 16 candidate reference genes for lung specimens and lung cell lines. Gene expression was measured by quantitative real time RT-PCR and expression stability was analyzed with the softwares GeNorm and NormFinder, mean of |ΔCt| (= |Ct Normal-Ct tumor|) ± SEM, and correlation coefficients among genes. Systematic comparison between candidates led us to the identification of a subset of suitable reference genes for clinical samples: IPO8, ACTB, POLR2A, 18S, and PPIA. Further analysis showed that IPO8 had a very low mean of |ΔCt| (0.70 ± 0.09), with no statistically significant differences between normal and malignant samples and with excellent expression stability. Conclusion Our data show that IPO8 is the most accurate reference gene for clinical lung specimens. In addition, we demonstrate that the commonly used genes GAPDH and HPRT1 are inappropriate to normalize data derived from lung biopsies, although they are suitable as reference genes for lung cell lines. We thus propose IPO8 as a novel reference gene for lung cancer samples. PMID:19014639

Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiae

PubMed Central

Teste, Marie-Ange; Duquenne, Manon; François, Jean M; Parrou, Jean-Luc

2009-01-01

Background Real-time RT-PCR is the recommended method for quantitative gene expression analysis. A compulsory step is the selection of good reference genes for normalization. A few genes often referred to as HouseKeeping Genes (HSK), such as ACT1, RDN18 or PDA1 are among the most commonly used, as their expression is assumed to remain unchanged over a wide range of conditions. Since this assumption is very unlikely, a geometric averaging of multiple, carefully selected internal control genes is now strongly recommended for normalization to avoid this problem of expression variation of single reference genes. The aim of this work was to search for a set of reference genes for reliable gene expression analysis in Saccharomyces cerevisiae. Results From public microarray datasets, we selected potential reference genes whose expression remained apparently invariable during long-term growth on glucose. Using the algorithm geNorm, ALG9, TAF10, TFC1 and UBC6 turned out to be genes whose expression remained stable, independent of the growth conditions and the strain backgrounds tested in this study. We then showed that the geometric averaging of any subset of three genes among the six most stable genes resulted in very similar normalized data, which contrasted with inconsistent results among various biological samples when the normalization was performed with ACT1. Normalization with multiple selected genes was therefore applied to transcriptional analysis of genes involved in glycogen metabolism. We determined an induction ratio of 100-fold for GPH1 and 20-fold for GSY2 between the exponential phase and the diauxic shift on glucose. There was no induction of these two genes at this transition phase on galactose, although in both cases, the kinetics of glycogen accumulation was similar. In contrast, SGA1 expression was independent of the carbon source and increased by 3-fold in stationary phase. Conclusion In this work, we provided a set of genes that are suitable reference

Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiae.

PubMed

Teste, Marie-Ange; Duquenne, Manon; François, Jean M; Parrou, Jean-Luc

2009-10-30

Real-time RT-PCR is the recommended method for quantitative gene expression analysis. A compulsory step is the selection of good reference genes for normalization. A few genes often referred to as HouseKeeping Genes (HSK), such as ACT1, RDN18 or PDA1 are among the most commonly used, as their expression is assumed to remain unchanged over a wide range of conditions. Since this assumption is very unlikely, a geometric averaging of multiple, carefully selected internal control genes is now strongly recommended for normalization to avoid this problem of expression variation of single reference genes. The aim of this work was to search for a set of reference genes for reliable gene expression analysis in Saccharomyces cerevisiae. From public microarray datasets, we selected potential reference genes whose expression remained apparently invariable during long-term growth on glucose. Using the algorithm geNorm, ALG9, TAF10, TFC1 and UBC6 turned out to be genes whose expression remained stable, independent of the growth conditions and the strain backgrounds tested in this study. We then showed that the geometric averaging of any subset of three genes among the six most stable genes resulted in very similar normalized data, which contrasted with inconsistent results among various biological samples when the normalization was performed with ACT1. Normalization with multiple selected genes was therefore applied to transcriptional analysis of genes involved in glycogen metabolism. We determined an induction ratio of 100-fold for GPH1 and 20-fold for GSY2 between the exponential phase and the diauxic shift on glucose. There was no induction of these two genes at this transition phase on galactose, although in both cases, the kinetics of glycogen accumulation was similar. In contrast, SGA1 expression was independent of the carbon source and increased by 3-fold in stationary phase. In this work, we provided a set of genes that are suitable reference genes for quantitative gene

High-speed digital signal normalization for feature identification

NASA Technical Reports Server (NTRS)

Ortiz, J. A.; Meredith, B. D.

1983-01-01

A design approach for high speed normalization of digital signals was developed. A reciprocal look up table technique is employed, where a digital value is mapped to its reciprocal via a high speed memory. This reciprocal is then multiplied with an input signal to obtain the normalized result. Normalization improves considerably the accuracy of certain feature identification algorithms. By using the concept of pipelining the multispectral sensor data processing rate is limited only by the speed of the multiplier. The breadboard system was found to operate at an execution rate of five million normalizations per second. This design features high precision, a reduced hardware complexity, high flexibility, and expandability which are very important considerations for spaceborne applications. It also accomplishes a high speed normalization rate essential for real time data processing.

Reference Levels for Patient Radiation Doses in Interventional Radiology: Proposed Initial Values for U.S. Practice1

PubMed Central

Miller, Donald L.; Kwon, Deukwoo; Bonavia, Grant H.

2009-01-01

Purpose: To propose initial values for patient reference levels for fluoroscopically guided procedures in the United States. Materials and Methods: This secondary analysis of data from the Radiation Doses in Interventional Radiology Procedures (RAD-IR) study was conducted under a protocol approved by the institutional review board and was HIPAA compliant. Dose distributions (percentiles) were calculated for each type of procedure in the RAD-IR study where there were data from at least 30 cases. Confidence intervals for the dose distributions were determined by using bootstrap resampling. Weight banding and size correction methods for normalizing dose to patient body habitus were tested. Results: The different methods for normalizing patient radiation dose according to patient weight gave results that were not significantly different (P > .05). The 75th percentile patient radiation doses normalized with weight banding were not significantly different from those that were uncorrected for body habitus. Proposed initial reference levels for various interventional procedures are provided for reference air kerma, kerma-area product, fluoroscopy time, and number of images. Conclusion: Sufficient data exist to permit an initial proposal of values for reference levels for interventional radiologic procedures in the United States. For ease of use, reference levels without correction for body habitus are recommended. A national registry of radiation-dose data for interventional radiologic procedures is a necessary next step to refine these reference levels. © RSNA, 2009 Supplemental material: http://radiology.rsna.org/lookup/suppl/doi:10.1148/radiol.2533090354/-/DC1 PMID:19789226

Updated US and Canadian Normalization Factors for TRACI 2.1

EPA Science Inventory

The objectives of this study is to update the normalization factors (NFs) of U.S.EPA’s TRACI 2.1 LCIA method (Bare, 2012) for the United States (US) and US-Canadian (US-CA) regions. This is done for the reference year 2008. This was deemed necessary to maintain the representative...

Normalizing and scaling of data to derive human response corridors from impact tests.

PubMed

Yoganandan, Narayan; Arun, Mike W J; Pintar, Frank A

2014-06-03

It is well known that variability is inherent in any biological experiment. Human cadavers (Post-Mortem Human Subjects, PMHS) are routinely used to determine responses to impact loading for crashworthiness applications including civilian (motor vehicle) and military environments. It is important to transform measured variables from PMHS tests (accelerations, forces and deflections) to a standard or reference population, termed normalization. The transformation process should account for inter-specimen variations with some underlying assumptions used during normalization. Scaling is a process by which normalized responses are converted from one standard to another (example, mid-size adult male to large-male and small-size female adults, and to pediatric populations). These responses are used to derive corridors to assess the biofidelity of anthropomorphic test devices (crash dummies) used to predict injury in impact environments and design injury mitigating devices. This survey examines the pros and cons of different approaches for obtaining normalized and scaled responses and corridors used in biomechanical studies for over four decades. Specifically, the equal-stress equal-velocity and impulse-momentum methods along with their variations are discussed in this review. Methods ranging from subjective to quasi-static loading to different approaches are discussed for deriving temporal mean and plus minus one standard deviation human corridors of time-varying fundamental responses and cross variables (e.g., force-deflection). The survey offers some insights into the potential efficacy of these approaches with examples from recent impact tests and concludes with recommendations for future studies. The importance of considering various parameters during the experimental design of human impact tests is stressed. Published by Elsevier Ltd.

Selection and assessment of reference genes for quantitative PCR normalization in migratory locust Locusta migratoria (Orthoptera: Acrididae).

PubMed

Yang, Qingpo; Li, Zhen; Cao, Jinjun; Zhang, Songdou; Zhang, Huaijiang; Wu, Xiaoyun; Zhang, Qingwen; Liu, Xiaoxia

2014-01-01

Locusta migratoria is a classic hemimetamorphosis insect and has caused widespread economic damage to crops as a migratory pest. Researches on the expression pattern of functional genes in L. migratoria have drawn focus in recent years, especially with the release of genome information. Real-time quantitative PCR is the most reproducible and sensitive approach for detecting transcript expression levels of target genes, but optimal internal standards are key factors for its accuracy and reliability. Therefore, it's necessary to provide a systematic stability assessment of internal control for well-performed tests of target gene expression profile. In this study, twelve candidate genes (Ach, Act, Cht2, EF1α, RPL32, Hsp70, Tub, RP49, SDH, GAPDH, 18S, and His) were analyzed with four statistical methods: the delta Ct approach, geNorm, Bestkeeper and NormFinder. The results from these analyses aimed to choose the best suitable reference gene across different experimental situations for gene profile study in L. migratoria. The result demonstrated that for different developmental stages, EF1α, Hsp70 and RPL32 exhibited the most stable expression status for all samples; EF1α and RPL32 were selected as the best reference genes for studies involving embryo and larvae stages, while SDH and RP49 were identified for adult stage. The best-ranked reference genes across different tissues are RPL32, Hsp70 and RP49. For abiotic treatments, the most appropriate genes we identified were as follows: Act and SDH for larvae subjected to different insecticides; RPL32 and Ach for larvae exposed to different temperature treatments; and Act and Ach for larvae suffering from starvation. The present report should facilitate future researches on gene expression in L. migratoria with accessibly optimal reference genes under different experimental contexts.

Reference genes for real-time PCR quantification of messenger RNAs and microRNAs in mouse model of obesity.

PubMed

Matoušková, Petra; Bártíková, Hana; Boušová, Iva; Hanušová, Veronika; Szotáková, Barbora; Skálová, Lenka

2014-01-01

Obesity and metabolic syndrome is increasing health problem worldwide. Among other ways, nutritional intervention using phytochemicals is important method for treatment and prevention of this disease. Recent studies have shown that certain phytochemicals could alter the expression of specific genes and microRNAs (miRNAs) that play a fundamental role in the pathogenesis of obesity. For study of the obesity and its treatment, monosodium glutamate (MSG)-injected mice with developed central obesity, insulin resistance and liver lipid accumulation are frequently used animal models. To understand the mechanism of phytochemicals action in obese animals, the study of selected genes expression together with miRNA quantification is extremely important. For this purpose, real-time quantitative PCR is a sensitive and reproducible method, but it depends on proper normalization entirely. The aim of present study was to identify the appropriate reference genes for mRNA and miRNA quantification in MSG mice treated with green tea catechins, potential anti-obesity phytochemicals. Two sets of reference genes were tested: first set contained seven commonly used genes for normalization of messenger RNA, the second set of candidate reference genes included ten small RNAs for normalization of miRNA. The expression stability of these reference genes were tested upon treatment of mice with catechins using geNorm, NormFinder and BestKeeper algorithms. Selected normalizers for mRNA quantification were tested and validated on expression of quinone oxidoreductase, biotransformation enzyme known to be modified by catechins. The effect of selected normalizers for miRNA quantification was tested on two obesity- and diabetes- related miRNAs, miR-221 and miR-29b, respectively. Finally, the combinations of B2M/18S/HPRT1 and miR-16/sno234 were validated as optimal reference genes for mRNA and miRNA quantification in liver and 18S/RPlP0/HPRT1 and sno234/miR-186 in small intestine of MSG mice. These

Statistical normalization techniques for magnetic resonance imaging.

PubMed

Shinohara, Russell T; Sweeney, Elizabeth M; Goldsmith, Jeff; Shiee, Navid; Mateen, Farrah J; Calabresi, Peter A; Jarso, Samson; Pham, Dzung L; Reich, Daniel S; Crainiceanu, Ciprian M

2014-01-01

While computed tomography and other imaging techniques are measured in absolute units with physical meaning, magnetic resonance images are expressed in arbitrary units that are difficult to interpret and differ between study visits and subjects. Much work in the image processing literature on intensity normalization has focused on histogram matching and other histogram mapping techniques, with little emphasis on normalizing images to have biologically interpretable units. Furthermore, there are no formalized principles or goals for the crucial comparability of image intensities within and across subjects. To address this, we propose a set of criteria necessary for the normalization of images. We further propose simple and robust biologically motivated normalization techniques for multisequence brain imaging that have the same interpretation across acquisitions and satisfy the proposed criteria. We compare the performance of different normalization methods in thousands of images of patients with Alzheimer's disease, hundreds of patients with multiple sclerosis, and hundreds of healthy subjects obtained in several different studies at dozens of imaging centers.

Detection of human papillomavirus DNA in patients referred to a family practice colposcopy clinic.

PubMed

Holman, J R

1996-01-01

Human papillomavirus (HPV) is strongly implicated in the pathogenesis of cervical neoplasia. The ability of a commercially available kit (Virapap/Viratype) to detect evidence of HPV is compared with cervical cytology, colposcopy, and directed biopsies. During a period of 16 months, cervical samples from 241 consecutive new patients referred for a colposcopy examination were obtained for HPV-DNA hybridization typing according to the kit instructions. Samples were sent to a reference laboratory for testing. The results were compared with results of the colposcopy examination, cervical cytology, and directed cervical biopsy samples processed and evaluated by our hospital laboratory. HPV DNA was detected in 27 of 107 patients who had abnormal colposcopy findings for a sensitivity of 25 +/- 7.5 percent at the 90 percent confidence interval. One of 134 patients with normal findings was positive for a specificity of 99 +/- 5 percent at the 95 percent confidence interval. Based on a 75 percent probability of HPV in the population, the positive predictive value was 99 percent and the negative predictive value 30 percent. With the low negative predictive value and sensitivity, HPV-DNA testing by this commercial kit is not an adequate tool for screening HPV in this population.

Maximal isometric muscle strength values obtained By hand-held dynamometry in children between 6 and 15 years of age.

PubMed

Escobar, Raul G; Munoz, Karin T; Dominguez, Angelica; Banados, Pamela; Bravo, Maria J

2017-01-01

In this study we aimed to determine the maximal isometric muscle strength of a healthy, normal-weight, pediatric population between 6 and 15 years of age using hand-held dynamometry to establish strength reference values. The secondary objective was determining the relationship between strength and anthropometric parameters. Four hundred normal-weight Chilean children, split into 10 age groups, separated by 1-year intervals, were evaluated. Each age group included between 35 and 55 children. The strength values increased with increasing age and weight, with a correlation of 0.83 for age and 0.82 for weight. The results were similar to those reported in previous studies regarding the relationships among strength, age, and anthropometric parameters, but the reported strength differed. These results provide normal strength parameters for healthy and normal-weight Chilean children between 6 and 15 years of age and highlight the relevance of ethnicity in defining reference values for muscle strength in a pediatric population. Muscle Nerve 55: 16-22, 2017. © 2016 Wiley Periodicals, Inc.

Reference genes for quantitative PCR in the adipose tissue of mice with metabolic disease.

PubMed

Almeida-Oliveira, Fernanda; Leandro, João G B; Ausina, Priscila; Sola-Penna, Mauro; Majerowicz, David

2017-04-01

Obesity and diabetes are metabolic diseases and they are increasing in prevalence. The dynamics of gene expression associated with these diseases is fundamental to identifying genes involved in related biological processes. qPCR is a sensitive technique for mRNA quantification and the most commonly used method in gene-expression studies. However, the reliability of these results is directly influenced by data normalization. As reference genes are the major normalization method used, this work aims to identify reference genes for qPCR in adipose tissues of mice with type-I diabetes or obesity. We selected 12 genes that are commonly used as reference genes. The expression of these genes in the adipose tissues of mice was analyzed in the context of three different experimental protocols: 1) untreated animals; 2) high-fat-diet animals; and 3) streptozotocin-treated animals. Gene-expression stability was analyzed using four different algorithms. Our data indicate that TATA-binding protein is stably expressed across adipose tissues in control animals. This gene was also a useful reference when the brown adipose tissues of control and obese mice were analyzed. The mitochondrial ATP synthase F1 complex gene exhibits stable expression in subcutaneous and perigonadal adipose tissue from control and obese mice. Moreover, this gene is the best reference for qPCR normalization in adipose tissue from streptozotocin-treated animals. These results show that there is no perfect stable gene suited for use under all experimental conditions. In conclusion, the selection of appropriate genes is a prerequisite to ensure qPCR reliability and must be performed separately for different experimental protocols. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Evaluation and Selection of Appropriate Reference Genes for Real-Time Quantitative PCR Analysis of Gene Expression in Nile Tilapia (Oreochromis niloticus) during Vaccination and Infection

PubMed Central

Wang, Erlong; Wang, Kaiyu; Chen, Defang; Wang, Jun; He, Yang; Long, Bo; Yang, Lei; Yang, Qian; Geng, Yi; Huang, Xiaoli; Ouyang, Ping; Lai, Weimin

2015-01-01

qPCR as a powerful and attractive methodology has been widely applied to aquaculture researches for gene expression analyses. However, the suitable reference selection is critical for normalizing target genes expression in qPCR. In the present study, six commonly used endogenous controls were selected as candidate reference genes to evaluate and analyze their expression levels, stabilities and normalization to immune-related gene IgM expression during vaccination and infection in spleen of tilapia with RefFinder and GeNorm programs. The results showed that all of these candidate reference genes exhibited transcriptional variations to some extent at different periods. Among them, EF1A was the most stable reference with RefFinder, followed by 18S rRNA, ACTB, UBCE, TUBA and GAPDH respectively and the optimal number of reference genes for IgM normalization under different experiment sets was two with GeNorm. Meanwhile, combination the Cq (quantification cycle) value and the recommended comprehensive ranking of reference genes, EF1A and ACTB, the two optimal reference genes, were used together as reference genes for accurate analysis of immune-related gene expression during vaccination and infection in Nile tilapia with qPCR. Moreover, the highest IgM expression level was at two weeks post-vaccination when normalized to EF1A, 18S rRNA, ACTB, and EF1A together with ACTB compared to one week post-vaccination before normalizing, which was also consistent with the IgM antibody titers detection by ELISA. PMID:25941937

Variance-reduction normalization technique for a compton camera system

NASA Astrophysics Data System (ADS)

Kim, S. M.; Lee, J. S.; Kim, J. H.; Seo, H.; Kim, C. H.; Lee, C. S.; Lee, S. J.; Lee, M. C.; Lee, D. S.

2011-01-01

For an artifact-free dataset, pre-processing (known as normalization) is needed to correct inherent non-uniformity of detection property in the Compton camera which consists of scattering and absorbing detectors. The detection efficiency depends on the non-uniform detection efficiency of the scattering and absorbing detectors, different incidence angles onto the detector surfaces, and the geometry of the two detectors. The correction factor for each detected position pair which is referred to as the normalization coefficient, is expressed as a product of factors representing the various variations. The variance-reduction technique (VRT) for a Compton camera (a normalization method) was studied. For the VRT, the Compton list-mode data of a planar uniform source of 140 keV was generated from a GATE simulation tool. The projection data of a cylindrical software phantom were normalized with normalization coefficients determined from the non-uniformity map, and then reconstructed by an ordered subset expectation maximization algorithm. The coefficient of variations and percent errors of the 3-D reconstructed images showed that the VRT applied to the Compton camera provides an enhanced image quality and the increased recovery rate of uniformity in the reconstructed image.

Normal mode-guided transition pathway generation in proteins

PubMed Central

Lee, Byung Ho; Seo, Sangjae; Kim, Min Hyeok; Kim, Youngjin; Jo, Soojin; Choi, Moon-ki; Lee, Hoomin; Choi, Jae Boong

2017-01-01

The biological function of proteins is closely related to its structural motion. For instance, structurally misfolded proteins do not function properly. Although we are able to experimentally obtain structural information on proteins, it is still challenging to capture their dynamics, such as transition processes. Therefore, we need a simulation method to predict the transition pathways of a protein in order to understand and study large functional deformations. Here, we present a new simulation method called normal mode-guided elastic network interpolation (NGENI) that performs normal modes analysis iteratively to predict transition pathways of proteins. To be more specific, NGENI obtains displacement vectors that determine intermediate structures by interpolating the distance between two end-point conformations, similar to a morphing method called elastic network interpolation. However, the displacement vector is regarded as a linear combination of the normal mode vectors of each intermediate structure, in order to enhance the physical sense of the proposed pathways. As a result, we can generate more reasonable transition pathways geometrically and thermodynamically. By using not only all normal modes, but also in part using only the lowest normal modes, NGENI can still generate reasonable pathways for large deformations in proteins. This study shows that global protein transitions are dominated by collective motion, which means that a few lowest normal modes play an important role in this process. NGENI has considerable merit in terms of computational cost because it is possible to generate transition pathways by partial degrees of freedom, while conventional methods are not capable of this. PMID:29020017

Reference dosimetry using radiochromic film

PubMed Central

Girard, Frédéric; Bouchard, Hugo

2012-01-01

The objectives of this study are to identify and quantify factors that influence radiochromic film dose response and to determine whether such films are suitable for reference dosimetry. The influence of several parameters that may introduce systematic dose errors when performing reference dose measurements were investigated. The effect of the film storage temperature was determined by comparing the performance of three lots of GAFCHROMIC EBT2 films stored at either 4°C or room temperature. The effect of high (>80%) or low (<20%) relative humidity was also determined. Doses measured in optimal conditions with EBT and EBT2 films were then compared with an A12 ionization chamber measurement. Intensity‐modulated radiation therapy quality controls using EBT2 films were also performed in reference dose. The results obtained using reference dose measurements were compared with those obtained using relative dose measurements. Storing the film at 4°C improves the stability of the film over time, but does not eliminate the noncatalytic film development, seen as a rise in optical density over time in the absence of radiation. Relative humidity variations ranging from 80% to 20% have a strong impact on the optical density and could introduce dose errors of up to 15% if the humidity were not controlled during the film storage period. During the scanning procedure, the film temperature influences the optical density that is measured. When controlling for these three parameters, the dose differences between EBT or EBT2 and the A12 chamber are found to be within ±4% (2σ level) over a dose range of 20–350 cGy. Our results also demonstrate the limitation of the Anisotropic Analytical Algorithm for dose calculation of highly modulated treatment plans. PACS numbers: 87.55.Qr; 87.56.Fc PMID:23149793

Secondary electron emission from electrically charged fluorinated-ethylene-propylene Teflon for normal and non-normal electron incidence. M.S. Thesis; [spacecraft thermal coatings

NASA Technical Reports Server (NTRS)

Budd, P. A.

1981-01-01

The secondary electron emission coefficient was measured for a charged polymer (FEP-Teflon) with normally and obliquely incident primary electrons. Theories of secondary emission are reviewed and the experimental data is compared to these theories. Results were obtained for angles of incidence up to 60 deg in normal electric fields of 1500 V/mm. Additional measurements in the range from 50 to 70 deg were made in regions where the normal and tangential fields were approximately equal. The initial input angles and measured output point of the electron beam could be analyzed with computer simulations in order to determine the field within the chamber. When the field is known, the trajectories can be calculated for impacting electrons having various energies and angles of incidence. There was close agreement between the experimental results and the commonly assumed theoretical model in the presence of normal electric fields for angles of incidence up to 60 deg. High angle results obtained in the presence of tangential electric fields did not agree with the theoretical models.

Meissner effect in normal-superconducting proximity-contact double layers

NASA Astrophysics Data System (ADS)

Higashitani, Seiji; Nagai, Katsuhiko

1995-02-01

The Meissner effect in normal-superconducting proximity-contact double layers is discussed in the clean limit. The diamagnetic current is calculated using the quasi-classical Green's function. We obtain the quasi-classical Green's function linear in the vector potential in the proximity-contact double layers with a finite reflection coefficient at the interface. It is found that the diamagnetic current in the clean normal layer is constant in space, therefore, the magnetic field linearly decreases in the clean normal layer. We give an explicit expression for the screening length in the clean normal layer and study its temperature dependence. We show that the temperature dependence in the clean normal layer is considerably different from that in the dirty normal layer and agrees with a recent experiment in Au-Nb system.

[Colorimetric investigation of normal tongue and lip colors from 516 healthy adults by visible reflection spectrum].

PubMed

Zeng, Chang-chun; Yang, Li; Xu, Ying; Liu, Pei-pei; Guo, Shi-jun; Liu, Song-hao

2011-09-01

Using the data from normal tongue and lip colors of normal people which were collected by the visible reflection spectrum, we analyzed the colorimetric parameters of tongue and lip colors. In this study, 516 healthy students aging from 19 to 26 from the colleges and universities of Guangdong Province of China were taken as research subjects. After collecting the data of tongue and lip colors of the 516 subjects using visible reflectance spectroscopy, CIE XYZ tristimulus values as defined by the International Commission on Illumination in 1964 were calculated, and the colorimetric parameters of the normal tongue and lip colors were obtained, such as the CIE 1964 chromaticity coordinate, brightness, dominant wavelength and excitation purity. The results of CIE 1964 chromaticity diagram calculated on the visible reflection spectrum showed that the normal tongue color chromaticity coordinate x(10) was 0.341 3±0.008 5 and y(10) was 0.332 6±0.005 1, and the normal lip color chromaticity coordinate x(10) was 0.357 7±0.009 2 and y(10) was 0.338 3±0.005 7; the brightness Y values of the normal tongue color and lip colors were 17.96±3.78 and 19.78±3.72, the dominant wavelength values of the normal tongue color and lip color were (626.3±51.6) nm and (600.4±18.2) nm, and the excitation purity values of the normal tongue color and lip color were 0.083±0.031 and 0.144±0.036, respectively. Application of the visible reflection spectrum is a standard way to collect colorimetric data for inspection of the complexion. The investigation of chromaticity coordinates, brightness, dominant wavelength and excitation purity of the normal tongue and lip colors may offer the basic reference for diagnosing morbid complexion on the tongue and lip colors in traditional Chinese medicine.

Reference Values for Spirometry Derived Using Lambda, Mu, Sigma (LMS) Method in Korean Adults: in Comparison with Previous References.

PubMed

Jo, Bum Seak; Myong, Jun Pyo; Rhee, Chin Kook; Yoon, Hyoung Kyu; Koo, Jung Wan; Kim, Hyoung Ryoul

2018-01-15

The present study aimed to update the prediction equations for spirometry and their lower limits of normal (LLN) by using the lambda, mu, sigma (LMS) method and to compare the outcomes with the values of previous spirometric reference equations. Spirometric data of 10,249 healthy non-smokers (8,776 females) were extracted from the fourth and fifth versions of the Korea National Health and Nutrition Examination Survey (KNHANES IV, 2007-2009; V, 2010-2012). Reference equations were derived using the LMS method which allows modeling skewness (lambda [L]), mean (mu [M]), and coefficient of variation (sigma [S]). The outcome equations were compared with previous reference values. Prediction equations were presented in the following form: predicted value = e{a + b × ln(height) + c × ln(age) + M - spline}. The new predicted values for spirometry and their LLN derived using the LMS method were shown to more accurately reflect transitions in pulmonary function in young adults than previous prediction equations derived using conventional regression analysis in 2013. There were partial discrepancies between the new reference values and the reference values from the Global Lung Function Initiative in 2012. The results should be interpreted with caution for young adults and elderly males, particularly in terms of the LLN for forced expiratory volume in one second/forced vital capacity in elderly males. Serial spirometry follow-up, together with correlations with other clinical findings, should be emphasized in evaluating the pulmonary function of individuals. Future studies are needed to improve the accuracy of reference data and to develop continuous reference values for spirometry across all ages. © 2018 The Korean Academy of Medical Sciences.

Evaluating acoustic speaker normalization algorithms: evidence from longitudinal child data.

PubMed

Kohn, Mary Elizabeth; Farrington, Charlie

2012-03-01

Speaker vowel formant normalization, a technique that controls for variation introduced by physical differences between speakers, is necessary in variationist studies to compare speakers of different ages, genders, and physiological makeup in order to understand non-physiological variation patterns within populations. Many algorithms have been established to reduce variation introduced into vocalic data from physiological sources. The lack of real-time studies tracking the effectiveness of these normalization algorithms from childhood through adolescence inhibits exploration of child participation in vowel shifts. This analysis compares normalization techniques applied to data collected from ten African American children across five time points. Linear regressions compare the reduction in variation attributable to age and gender for each speaker for the vowels BEET, BAT, BOT, BUT, and BOAR. A normalization technique is successful if it maintains variation attributable to a reference sociolinguistic variable, while reducing variation attributable to age. Results indicate that normalization techniques which rely on both a measure of central tendency and range of the vowel space perform best at reducing variation attributable to age, although some variation attributable to age persists after normalization for some sections of the vowel space. © 2012 Acoustical Society of America

Lattice properties of the Phase I BNL x-ray lithography source obtained from fits to magnetic measurement data

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

Blumberg, L.N.; Murphy, J.B.; Reusch, M.F.

1991-01-01

The orbit, tune, chromaticity and {beta} values for the Phase 1 XLS ring were computed by numerical integration of equations of motion using fields obtained from the coefficients of the 3-dimensional solution of Laplace's Equation evaluated by fits to magnetic measurements. The results are in good agreement with available data. The method has been extended to higher order fits of TOSCA generated fields in planes normal to the reference axis using the coil configuration proposed for the Superconducting X-Ray Lithography Source. Agreement with results from numerical integration through fields given directly by TOSCA is excellent. The formulation of the normalmore » multipole expansion presented by Brown and Servranckx has been extended to include skew multipole terms. The method appears appropriate for analysis of magnetic measurements of the SXLS. 8 refs. , 2 figs., 2 tabs.« less

Automated and continual determination of radio telescope reference points with sub-mm accuracy: results from a campaign at the Onsala Space Observatory

NASA Astrophysics Data System (ADS)

Lösler, Michael; Haas, Rüdiger; Eschelbach, Cornelia

2013-08-01

The Global Geodetic Observing System (GGOS) requires sub-mm accuracy, automated and continual determinations of the so-called local tie vectors at co-location stations. Co-location stations host instrumentation for several space geodetic techniques and the local tie surveys involve the relative geometry of the reference points of these instruments. Thus, these reference points need to be determined in a common coordinate system, which is a particular challenge for rotating equipment like radio telescopes for geodetic Very Long Baseline Interferometry. In this work we describe a concept to achieve automated and continual determinations of radio telescope reference points with sub-mm accuracy. We developed a monitoring system, including Java-based sensor communication for automated surveys, network adjustment and further data analysis. This monitoring system was tested during a monitoring campaign performed at the Onsala Space Observatory in the summer of 2012. The results obtained in this campaign show that it is possible to perform automated determination of a radio telescope reference point during normal operations of the telescope. Accuracies on the sub-mm level can be achieved, and continual determinations can be realized by repeated determinations and recursive estimation methods.

Drug Use Normalization: A Systematic and Critical Mixed-Methods Review.

PubMed

Sznitman, Sharon R; Taubman, Danielle S

2016-09-01

Drug use normalization, which is a process whereby drug use becomes less stigmatized and more accepted as normative behavior, provides a conceptual framework for understanding contemporary drug issues and changes in drug use trends. Through a mixed-methods systematic review of the normalization literature, this article seeks to (a) critically examine how the normalization framework has been applied in empirical research and (b) make recommendations for future research in this area. Twenty quantitative, 26 qualitative, and 4 mixed-methods studies were identified through five electronic databases and reference lists of published studies. Studies were assessed for relevance, study characteristics, quality, and aspects of normalization examined. None of the studies applied the most rigorous research design (experiments) or examined all of the originally proposed normalization dimensions. The most commonly assessed dimension of drug use normalization was "experimentation." In addition to the original dimensions, the review identified the following new normalization dimensions in the literature: (a) breakdown of demographic boundaries and other risk factors in relation to drug use; (b) de-normalization; (c) drug use as a means to achieve normal goals; and (d) two broad forms of micro-politics associated with managing the stigma of illicit drug use: assimilative and transformational normalization. Further development in normalization theory and methodology promises to provide researchers with a novel framework for improving our understanding of drug use in contemporary society. Specifically, quasi-experimental designs that are currently being made feasible by swift changes in cannabis policy provide researchers with new and improved opportunities to examine normalization processes.

Indentation stiffness does not discriminate between normal and degraded articular cartilage.

PubMed

Brown, Cameron P; Crawford, Ross W; Oloyede, Adekunle

2007-08-01

Relative indentation characteristics are commonly used for distinguishing between normal healthy and degraded cartilage. The application of this parameter in surgical decision making and an appreciation of articular cartilage biomechanics has prompted us to hypothesise that it is difficult to define a reference stiffness to characterise normal articular cartilage. This hypothesis is tested for validity by carrying out biomechanical indentation of articular cartilage samples that are characterised as visually normal and degraded relative to proteoglycan depletion and collagen disruption. Compressive loading was applied at known strain rates to visually normal, artificially degraded and naturally osteoarthritic articular cartilage and observing the trends of their stress-strain and stiffness characteristics. While our results demonstrated a 25% depreciation in the stiffness of individual samples after proteoglycan depletion, they also showed that when compared to the stiffness of normal samples only 17% lie outside the range of the stress-strain behaviour of normal samples. We conclude that the extent of the variability in the properties of normal samples, and the degree of overlap (81%) of the biomechanical properties of normal and degraded matrices demonstrate that indentation data cannot form an accurate basis for distinguishing normal from abnormal articular cartilage samples with consequences for the application of this mechanical process in the clinical environment.

Dynamic Divisive Normalization Predicts Time-Varying Value Coding in Decision-Related Circuits

PubMed Central

LoFaro, Thomas; Webb, Ryan; Glimcher, Paul W.

2014-01-01

Normalization is a widespread neural computation, mediating divisive gain control in sensory processing and implementing a context-dependent value code in decision-related frontal and parietal cortices. Although decision-making is a dynamic process with complex temporal characteristics, most models of normalization are time-independent and little is known about the dynamic interaction of normalization and choice. Here, we show that a simple differential equation model of normalization explains the characteristic phasic-sustained pattern of cortical decision activity and predicts specific normalization dynamics: value coding during initial transients, time-varying value modulation, and delayed onset of contextual information. Empirically, we observe these predicted dynamics in saccade-related neurons in monkey lateral intraparietal cortex. Furthermore, such models naturally incorporate a time-weighted average of past activity, implementing an intrinsic reference-dependence in value coding. These results suggest that a single network mechanism can explain both transient and sustained decision activity, emphasizing the importance of a dynamic view of normalization in neural coding. PMID:25429145

[Development of the certified reference material of mercury in lyophilized human urine].

PubMed

Zhao, Wei; Zhang, Fu-gang; DU, Hui-fang; Pan, Ya-juan; Yan, Hui-fang

2011-02-01

To develop the certified reference material of mercury in lyophilized human urine. Human urine samples from normal level mercury districts were filtered, homogenized, dispensed, lyophilized and radio-sterilized. Homogeneity test, stability inspection and certification were conducted using a atom fluorescence spectrophotometric method. The physical and chemical stability of the certified reference material were assessed for 18 months. The certified values are based on analysis made by three independent laboratories. The certified values are as follows: low level was (35.6 ± 2.1) µg/L, high level was (50.5 ± 3.0) µg/L. The certified reference material of mercury in lyophilized human urine in this research reached the national certified reference material requirements and could be used for the quality control.

Japanese Society for Laboratory Hematology flow cytometric reference method of determining the differential leukocyte count: external quality assurance using fresh blood samples.

PubMed

Kawai, Y; Nagai, Y; Ogawa, E; Kondo, H

2017-04-01

To provide target values for the manufacturers' survey of the Japanese Society for Laboratory Hematology (JSLH), accurate standard data from healthy volunteers were needed for the five-part differential leukocyte count. To obtain such data, JSLH required an antibody panel that achieved high specificity (particularly for mononuclear cells) using simple gating procedures. We developed a flow cytometric method for determining the differential leukocyte count (JSLH-Diff) and validated it by comparison with the flow cytometric differential leukocyte count of the International Council for Standardization in Haematology (ICSH-Diff) and the manual differential count obtained by microscopy (Manual-Diff). First, the reference laboratory performed an imprecision study of JSLH-Diff and ICSH-Diff, as well as performing comparison among JSLH-Diff, Manual-Diff, and ICSH-Diff. Then two reference laboratories and seven participating laboratories performed imprecision and accuracy studies of JSLH-Diff, Manual-Diff, and ICSH-Diff. Simultaneously, six manufacturers' laboratories provided their own representative values by using automated hematology analyzers. The precision of both JSLH-Diff and ICSH-Diff methods was adequate. Comparison by the reference laboratory showed that all correlation coefficients, slopes and intercepts obtained by the JSLH-Diff, ICSH-Diff, and Manual-Diff methods conformed to the criteria. When the imprecision and accuracy of JSLH-Diff were assessed at seven laboratories, the CV% for lymphocytes, neutrophils, monocytes, eosinophils, and basophils was 0.5~0.9%, 0.3~0.7%, 1.7~2.6%, 3.0~7.9%, and 3.8~10.4%, respectively. More than 99% of CD45 positive leukocytes were identified as normal leukocytes by JSLH-Diff. When JSLH-Diff method were validated by comparison with Manual-Diff and ICSH-Diff, JSLH-Diff showed good performance as a reference method. © 2016 John Wiley & Sons Ltd.

Reference values of brachial-ankle pulse wave velocity according to age and blood pressure in a central Asia population.

PubMed

Yiming, Gulinuer; Zhou, Xianhui; Lv, Wenkui; Peng, Yi; Zhang, Wenhui; Cheng, Xinchun; Li, Yaodong; Xing, Qiang; Zhang, Jianghua; Zhou, Qina; Zhang, Ling; Lu, Yanmei; Wang, Hongli; Tang, Baopeng

2017-01-01

Brachial-ankle pulse wave velocity (baPWV), a direct measure of aortic stiffness, has increasingly become an important assessment for cardiovascular risk. The present study established the reference and normal values of baPWV in a Central Asia population in Xinjiang, China. We recruited participants from a central Asia population in Xinjiang, China. We performed multiple regression analysis to investigate the determinants of baPWV. The median and 10th-90th percentiles were calculated to establish the reference and normal values based on these categories. In total, 5,757 Han participants aged 15-88 years were included in the present study. Spearman correlation analysis showed that age (r = 0.587, p < 0.001) and mean blood pressure (MBP, r = 0.599, p <0.001) were the major factors influencing the values of baPWV in the reference population. Furthermore, in the multiple linear regression analysis, the standardized regression coefficients of age (0.445) and MBP (0.460) were much higher than those of body mass index, triglyceride, and glycemia (-0.054, 0.035, and 0.033, respectively). In the covariance analysis, after adjustment for age and MBP, only diabetes was the significant independent determinant of baPWV (p = 0.009). Thus, participants with diabetes were excluded from the reference value population. The reference values ranged from 14.3 to 25.2 m/s, and the normal values ranged from 13.9 to 21.2 m/s. This is the first study that has established the reference and normal values for baPWV according to age and blood pressure in a Central Asia population.

What`s normal?: Body condition in Great Lakes herring gulls

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

Hebert, C.E.; Shutt, J.L.

1994-12-31

The Canadian Wildlife Service`s herring gull (Larus argentatus) surveillance program has demonstrated the usefulness of this species as a monitor of spatial and temporal trends in contaminant levels. However, the effects of environmental contaminants on gulls are difficult to distinguish from the effects of other anthropogenic stressors such as the introduction of exotic species, overfishing and habitat loss. To understand the relative importance of these factors in regulating the success of individual gulls and, hence, gull populations, the authors must first have a better understanding of what constitutes a ``normal`` bird. Improving the ability to differentiate between normal and abnormalmore » birds is crucial in any health assessment of Great Lakes gulls. Body condition has been shown to be an important measure of a bird`s ability to provide energy for egg production, migration etc. Numerous approaches have been used to assess condition, most of which required that the bird be sacrificed. In this study, the authors describe a nonlethal technique to quantify body condition in herring gulls. Multivariate statistics are used to quantify body size, relate body size to total mass and from that, determine relative body condition. Initially, body condition is assessed in gulls from a reference colony where reproductive success is normal and anthropogenic influences are limited. This reference population is then used as a baseline against which other gull populations are compared.« less

Reference gene selection for molecular studies of dormancy in wild oat (Avena fatua L.) caryopses by RT-qPCR method.

PubMed

Ruduś, Izabela; Kępczyński, Jan

2018-01-01

Molecular studies of primary and secondary dormancy in Avena fatua L., a serious weed of cereal and other crops, are intended to reveal the species-specific details of underlying molecular mechanisms which in turn may be useable in weed management. Among others, quantitative real-time PCR (RT-qPCR) data of comparative gene expression analysis may give some insight into the involvement of particular wild oat genes in dormancy release, maintenance or induction by unfavorable conditions. To assure obtaining biologically significant results using this method, the expression stability of selected candidate reference genes in different data subsets was evaluated using four statistical algorithms i.e. geNorm, NormFinder, Best Keeper and ΔCt method. Although some discrepancies in their ranking outputs were noticed, evidently two ubiquitin-conjugating enzyme homologs, AfUBC1 and AfUBC2, as well as one homolog of glyceraldehyde 3-phosphate dehydrogenase AfGAPDH1 and TATA-binding protein AfTBP2 appeared as more stably expressed than AfEF1a (translation elongation factor 1α), AfGAPDH2 or the least stable α-tubulin homolog AfTUA1 in caryopses and seedlings of A. fatua. Gene expression analysis of a dormancy-related wild oat transcription factor VIVIPAROUS1 (AfVP1) allowed for a validation of candidate reference genes performance. Based on the obtained results it can be recommended that the normalization factor calculated as a geometric mean of Cq values of AfUBC1, AfUBC2 and AfGAPDH1 would be optimal for RT-qPCR results normalization in the experiments comprising A. fatua caryopses of different dormancy status.

Multivariate Models for Normal and Binary Responses in Intervention Studies

ERIC Educational Resources Information Center

Pituch, Keenan A.; Whittaker, Tiffany A.; Chang, Wanchen

2016-01-01

Use of multivariate analysis (e.g., multivariate analysis of variance) is common when normally distributed outcomes are collected in intervention research. However, when mixed responses--a set of normal and binary outcomes--are collected, standard multivariate analyses are no longer suitable. While mixed responses are often obtained in…

Normal reference values of strength in pelvic floor muscle of women: a descriptive and inferential study.

PubMed

Chevalier, Francine; Fernandez-Lao, Carolina; Cuesta-Vargas, Antonio Ignacio

2014-11-25

To describe the clinical, functional and quality of life characteristics in women with Stress Urinary Incontinence (SUI). In addition, to analyse the relationship between the variables reported by the patients and those informed by the clinicians, and the relationship between instrumented variables and the manual pelvic floor strength assessment. Two hundred and eighteen women participated in this observational, analytical study. An interview about Urinary Incontinence and the quality of life questionnaires (EuroQoL-5D and SF-12) were developed as outcomes reported by the patients. Manual muscle testing and perineometry as outcomes informed by the clinician were assessed. Descriptive and correlation analysis were carried out. The average age of the subjects was (39.93 ± 12.27 years), (24.49 ± 3.54 BMI). The strength evaluated by manual testing of the right levator ani muscles was 7.79 ± 2.88, the strength of left levator ani muscles was 7.51 ± 2.91 and the strength assessed with the perineometer was 7.64 ± 2.55. A positive correlation was found between manual muscle testing and perineometry of the pelvic floor muscles (p < .001). No correlation was found between outcomes of quality of life reported by the patients and outcomes of functional capacity informed by the physiotherapist. A stratification of the strength of pelvic floor muscles in a normal distribution of a large sample of women with SUI was done, which provided the clinic with a baseline. There is a relationship between the strength of the pelvic muscles assessed manually and that obtained by a perineometer in women with SUI. There was no relationship between these values of strength and quality of life perceived.

Selection of reference genes is critical for miRNA expression analysis in human cardiac tissue. A focus on atrial fibrillation.

PubMed

Masè, Michela; Grasso, Margherita; Avogaro, Laura; D'Amato, Elvira; Tessarolo, Francesco; Graffigna, Angelo; Denti, Michela Alessandra; Ravelli, Flavia

2017-01-24

MicroRNAs (miRNAs) are emerging as key regulators of complex biological processes in several cardiovascular diseases, including atrial fibrillation (AF). Reverse transcription-quantitative polymerase chain reaction is a powerful technique to quantitatively assess miRNA expression profile, but reliable results depend on proper data normalization by suitable reference genes. Despite the increasing number of studies assessing miRNAs in cardiac disease, no consensus on the best reference genes has been reached. This work aims to assess reference genes stability in human cardiac tissue with a focus on AF investigation. We evaluated the stability of five reference genes (U6, SNORD48, SNORD44, miR-16, and 5S) in atrial tissue samples from eighteen cardiac-surgery patients in sinus rhythm and AF. Stability was quantified by combining BestKeeper, delta-C q , GeNorm, and NormFinder statistical tools. All methods assessed SNORD48 as the best and U6 as the worst reference gene. Applications of different normalization strategies significantly impacted miRNA expression profiles in the study population. Our results point out the necessity of a consensus on data normalization in AF studies to avoid the emergence of divergent biological conclusions.

Selection of reference genes is critical for miRNA expression analysis in human cardiac tissue. A focus on atrial fibrillation

PubMed Central

Masè, Michela; Grasso, Margherita; Avogaro, Laura; D’Amato, Elvira; Tessarolo, Francesco; Graffigna, Angelo; Denti, Michela Alessandra; Ravelli, Flavia

2017-01-01

MicroRNAs (miRNAs) are emerging as key regulators of complex biological processes in several cardiovascular diseases, including atrial fibrillation (AF). Reverse transcription-quantitative polymerase chain reaction is a powerful technique to quantitatively assess miRNA expression profile, but reliable results depend on proper data normalization by suitable reference genes. Despite the increasing number of studies assessing miRNAs in cardiac disease, no consensus on the best reference genes has been reached. This work aims to assess reference genes stability in human cardiac tissue with a focus on AF investigation. We evaluated the stability of five reference genes (U6, SNORD48, SNORD44, miR-16, and 5S) in atrial tissue samples from eighteen cardiac-surgery patients in sinus rhythm and AF. Stability was quantified by combining BestKeeper, delta-Cq, GeNorm, and NormFinder statistical tools. All methods assessed SNORD48 as the best and U6 as the worst reference gene. Applications of different normalization strategies significantly impacted miRNA expression profiles in the study population. Our results point out the necessity of a consensus on data normalization in AF studies to avoid the emergence of divergent biological conclusions. PMID:28117343

Microarray expression profiling in adhesion and normal peritoneal tissues.

PubMed

Ambler, Dana R; Golden, Alicia M; Gell, Jennifer S; Saed, Ghassan M; Carey, David J; Diamond, Michael P

2012-05-01

To identify molecular markers associated with adhesion and normal peritoneal tissue using microarray expression profiling. Comparative study. University hospital. Five premenopausal women. Adhesion and normal peritoneal tissue samples were obtained from premenopausal women. Ribonucleic acid was extracted using standard protocols and processed for hybridization to Affymetrix Whole Transcript Human Gene Expression Chips. Microarray data were obtained from five different patients, each with adhesion tissue and normal peritoneal samples. Real-time polymerase chain reaction was performed for confirmation using standard protocols. Gene expression in postoperative adhesion and normal peritoneal tissues. A total of 1,263 genes were differentially expressed between adhesion and normal tissues. One hundred seventy-three genes were found to be up-regulated and 56 genes were down-regulated in the adhesion tissues compared with normal peritoneal tissues. The genes were sorted into functional categories according to Gene Ontology annotations. Twenty-six up-regulated genes and 11 down-regulated genes were identified with functions potentially relevant to the pathophysiology of postoperative adhesions. We evaluated and confirmed expression of 12 of these specific genes via polymerase chain reaction. The pathogenesis, natural history, and optimal treatment of postoperative adhesive disease remains unanswered. Microarray analysis of adhesions identified specific genes with increased and decreased expression when compared with normal peritoneum. Knowledge of these genes and ontologic pathways with altered expression provide targets for new therapies to treat patients who have or are at risk for postoperative adhesions. Copyright © 2012 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Interlaboratory comparison of reference materials for nitrogen-isotope-ratio measurements

USGS Publications Warehouse

Böhlke, John Karl; Coplen, Tyler B.

1995-01-01

Aliquots of seven different reference materials were distributed for an interlaboratory comparison of stable nitrogen-isotope-ratio measurements. Results from 15 laboratories were compiled and evaluated selectively to yield provisional values of 515N for each material, i, with respect to atmospheric N2 (o1SN,7air). The 515N values reported by the different laboratories are correlated in such a way that some of the major discrepancies may be removed by normalization (/. e., by altering the length of the ô N scale for each laboratory by an amount defined by local measurements of reference materials with extreme values).

Arterial spin-labeling assessment of normalized vascular intratumoral signal intensity as a predictor of histologic grade of astrocytic neoplasms.

PubMed

Furtner, J; Schöpf, V; Schewzow, K; Kasprian, G; Weber, M; Woitek, R; Asenbaum, U; Preusser, M; Marosi, C; Hainfellner, J A; Widhalm, G; Wolfsberger, S; Prayer, D

2014-03-01

Pulsed arterial spin-labeling is a noninvasive MR imaging perfusion method performed with the use of water in the arterial blood as an endogenous contrast agent. The purpose of this study was to determine the inversion time with the largest difference in normalized intratumoral signal intensity between high-grade and low-grade astrocytomas. Thirty-three patients with gliomas, histologically classified as low-grade (n = 7) or high-grade astrocytomas (n = 26) according to the World Health Organization brain tumor classification, were included. A 3T MR scanner was used to perform pulsed arterial spin-labeling measurements at 8 different inversion times (370 ms, 614 ms, 864 ms, 1114 ms, 1364 ms, 1614 ms, 1864 ms, and 2114 ms). Normalized intratumoral signal intensity was calculated, which was defined by the signal intensity ratio of the tumor and the contralateral normal brain tissue for all fixed inversion times. A 3-way mixed ANOVA was used to reveal potential differences in the normalized vascular intratumoral signal intensity between high-grade and low-grade astrocytomas. The difference in normalized vascular intratumoral signal intensity between high-grade and low-grade astrocytomas obtained the most statistically significant results at 370 ms (P = .003, other P values ranged from .012-.955). The inversion time by which to differentiate high-grade and low-grade astrocytomas by use of normalized vascular intratumoral signal intensity was 370 ms in our study. The normalized vascular intratumoral signal intensity values at this inversion time mainly reflect the labeled intra-arterial blood bolus and therefore could be referred to as normalized vascular intratumoral signal intensity. Our data indicate that the use of normalized vascular intratumoral signal intensity values allows differentiation between low-grade and high-grade astrocytomas and thus may serve as a new, noninvasive marker for astrocytoma grading.

A Bootstrap Based Measure Robust to the Choice of Normalization Methods for Detecting Rhythmic Features in High Dimensional Data.

PubMed

Larriba, Yolanda; Rueda, Cristina; Fernández, Miguel A; Peddada, Shyamal D

2018-01-01

Motivation: Gene-expression data obtained from high throughput technologies are subject to various sources of noise and accordingly the raw data are pre-processed before formally analyzed. Normalization of the data is a key pre-processing step, since it removes systematic variations across arrays. There are numerous normalization methods available in the literature. Based on our experience, in the context of oscillatory systems, such as cell-cycle, circadian clock, etc., the choice of the normalization method may substantially impact the determination of a gene to be rhythmic. Thus rhythmicity of a gene can purely be an artifact of how the data were normalized. Since the determination of rhythmic genes is an important component of modern toxicological and pharmacological studies, it is important to determine truly rhythmic genes that are robust to the choice of a normalization method. Results: In this paper we introduce a rhythmicity measure and a bootstrap methodology to detect rhythmic genes in an oscillatory system. Although the proposed methodology can be used for any high-throughput gene expression data, in this paper we illustrate the proposed methodology using several publicly available circadian clock microarray gene-expression datasets. We demonstrate that the choice of normalization method has very little effect on the proposed methodology. Specifically, for any pair of normalization methods considered in this paper, the resulting values of the rhythmicity measure are highly correlated. Thus it suggests that the proposed measure is robust to the choice of a normalization method. Consequently, the rhythmicity of a gene is potentially not a mere artifact of the normalization method used. Lastly, as demonstrated in the paper, the proposed bootstrap methodology can also be used for simulating data for genes participating in an oscillatory system using a reference dataset. Availability: A user friendly code implemented in R language can be downloaded from http://www.eio.uva.es/~miguel/robustdetectionprocedure.html.

A Bootstrap Based Measure Robust to the Choice of Normalization Methods for Detecting Rhythmic Features in High Dimensional Data

PubMed Central

Larriba, Yolanda; Rueda, Cristina; Fernández, Miguel A.; Peddada, Shyamal D.

2018-01-01

Motivation: Gene-expression data obtained from high throughput technologies are subject to various sources of noise and accordingly the raw data are pre-processed before formally analyzed. Normalization of the data is a key pre-processing step, since it removes systematic variations across arrays. There are numerous normalization methods available in the literature. Based on our experience, in the context of oscillatory systems, such as cell-cycle, circadian clock, etc., the choice of the normalization method may substantially impact the determination of a gene to be rhythmic. Thus rhythmicity of a gene can purely be an artifact of how the data were normalized. Since the determination of rhythmic genes is an important component of modern toxicological and pharmacological studies, it is important to determine truly rhythmic genes that are robust to the choice of a normalization method. Results: In this paper we introduce a rhythmicity measure and a bootstrap methodology to detect rhythmic genes in an oscillatory system. Although the proposed methodology can be used for any high-throughput gene expression data, in this paper we illustrate the proposed methodology using several publicly available circadian clock microarray gene-expression datasets. We demonstrate that the choice of normalization method has very little effect on the proposed methodology. Specifically, for any pair of normalization methods considered in this paper, the resulting values of the rhythmicity measure are highly correlated. Thus it suggests that the proposed measure is robust to the choice of a normalization method. Consequently, the rhythmicity of a gene is potentially not a mere artifact of the normalization method used. Lastly, as demonstrated in the paper, the proposed bootstrap methodology can also be used for simulating data for genes participating in an oscillatory system using a reference dataset. Availability: A user friendly code implemented in R language can be downloaded from http

Evaluation of CT-based SUV normalization

NASA Astrophysics Data System (ADS)

Devriese, Joke; Beels, Laurence; Maes, Alex; Van de Wiele, Christophe; Pottel, Hans

2016-09-01

The purpose of this study was to determine patients’ lean body mass (LBM) and lean tissue (LT) mass using a computed tomography (CT)-based method, and to compare standardized uptake value (SUV) normalized by these parameters to conventionally normalized SUVs. Head-to-toe positron emission tomography (PET)/CT examinations were retrospectively retrieved and semi-automatically segmented into tissue types based on thresholding of CT Hounsfield units (HU). The following HU ranges were used for determination of CT-estimated LBM and LT (LBMCT and LTCT):  -180 to  -7 for adipose tissue (AT), -6 to 142 for LT, and 143 to 3010 for bone tissue (BT). Formula-estimated LBMs were calculated using formulas of James (1976 Research on Obesity: a Report of the DHSS/MRC Group (London: HMSO)) and Janmahasatian et al (2005 Clin. Pharmacokinet. 44 1051-65), and body surface area (BSA) was calculated using the DuBois formula (Dubois and Dubois 1989 Nutrition 5 303-11). The CT segmentation method was validated by comparing total patient body weight (BW) to CT-estimated BW (BWCT). LBMCT was compared to formula-based estimates (LBMJames and LBMJanma). SUVs in two healthy reference tissues, liver and mediastinum, were normalized for the aforementioned parameters and compared to each other in terms of variability and dependence on normalization factors and BW. Comparison of actual BW to BWCT shows a non-significant difference of 0.8 kg. LBMJames estimates are significantly higher than LBMJanma with differences of 4.7 kg for female and 1.0 kg for male patients. Formula-based LBM estimates do not significantly differ from LBMCT, neither for men nor for women. The coefficient of variation (CV) of SUV normalized for LBMJames (SUVLBM-James) (12.3%) was significantly reduced in liver compared to SUVBW (15.4%). All SUV variances in mediastinum were significantly reduced (CVs were 11.1-12.2%) compared to SUVBW (15.5%), except SUVBSA (15.2%). Only SUVBW and SUVLBM-James show

Normal forms of Hopf-zero singularity

NASA Astrophysics Data System (ADS)

Gazor, Majid; Mokhtari, Fahimeh

2015-01-01

The Lie algebra generated by Hopf-zero classical normal forms is decomposed into two versal Lie subalgebras. Some dynamical properties for each subalgebra are described; one is the set of all volume-preserving conservative systems while the other is the maximal Lie algebra of nonconservative systems. This introduces a unique conservative-nonconservative decomposition for the normal form systems. There exists a Lie-subalgebra that is Lie-isomorphic to a large family of vector fields with Bogdanov-Takens singularity. This gives rise to a conclusion that the local dynamics of formal Hopf-zero singularities is well-understood by the study of Bogdanov-Takens singularities. Despite this, the normal form computations of Bogdanov-Takens and Hopf-zero singularities are independent. Thus, by assuming a quadratic nonzero condition, complete results on the simplest Hopf-zero normal forms are obtained in terms of the conservative-nonconservative decomposition. Some practical formulas are derived and the results implemented using Maple. The method has been applied on the Rössler and Kuramoto-Sivashinsky equations to demonstrate the applicability of our results.

Choice of Reference Serum Creatinine in Defining AKI

PubMed Central

Siew, Edward D.; Matheny, Michael E.

2015-01-01

Background/Aims The study of acute kidney injury (AKI) has expanded with the increasing availability of electronic health records and the use of standardized definitions. Understanding the impact of AKI between settings is limited by heterogeneity in the selection of reference creatinine to anchor the definition of AKI. In this mini-review, we discuss different approaches used to select reference creatinine and their relative merits and limitations. Methods We reviewed the literature to obtain representative examples of published baseline creatinine definitions when pre-hospital data were not available, as well as literature evaluating estimation of baseline renal function, using Pubmed and reference back-tracing within known works. Results 1) Prehospital creatinine values are useful in determining reference creatinine, and in high-risk populations, the mean outpatient serum creatinine value 7-365 days before hospitalization closely approximates nephrology adjudication, 2) in patients without pre-hospital data, the eGFR 75 approach does not reliably estimate true AKI incidence in most at-risk populations 3) using the lowest inpatient serum creatinine may be reasonable, especially in those with preserved kidney function, but may generously estimate AKI incidence and severity and miss community-acquired AKI that does not fully resolve, 4) using more specific definitions of AKI (e.g. KIDGO Stage 2 and 3) may help to reduce the effects of misclassification when using surrogate values, and 5) leveraging available clinical data may help refine the estimate of reference creatinine. Conclusions Choosing reference creatinine for AKI calculation is important for AKI classification and study interpretation. We recommend obtaining data on pre-hospital kidney function, wherever possible. In studies where surrogate estimates are used, transparency in how they are applied and discussion that informs the reader of potential biases should be provided. Further work to refine the

Identification of TMEM208 and PQLC2 as reference genes for normalizing mRNA expression in colorectal cancer treated with aspirin

PubMed Central

Zhu, Yuanyuan; Yang, Chao; Weng, Mingjiao; Zhang, Yan; Yang, Chunhui; Jin, Yinji; Yang, Weiwei; He, Yan; Wu, Yiqi; Zhang, Yuhua; Wang, Guangyu; RajkumarEzakiel Redpath, Riju James; Zhang, Lei; Jin, Xiaoming; Liu, Ying; Sun, Yuchun; Ning, Ning; Qiao, Yu; Zhang, Fengmin; Li, Zhiwei; Wang, Tianzhen; Zhang, Yanqiao; Li, Xiaobo

2017-01-01

Numerous evidences indicate that aspirin usage causes a significant reduction in colorectal cancer. However, the molecular mechanisms about aspirin preventing colon cancer are largely unknown. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a most frequently used method to identify the target molecules regulated by certain compound. However, this method needs stable internal reference genes to analyze the expression change of the targets. In this study, the transcriptional stabilities of several traditional reference genes were evaluated in colon cancer cells treated with aspirin, and also, the suitable internal reference genes were screened by using a microarray and were further identified by using the geNorm and NormFinder softwares, and then were validated in more cell lines and xenografts. We have showed that three traditional internal reference genes, β-actin, GAPDH and α-tubulin, are not suitable for studying gene transcription in colon cancer cells treated with aspirin, and we have identified and validated TMEM208 and PQLC2 as the ideal internal reference genes for detecting the molecular targets of aspirin in colon cancer in vitro and in vivo. This study reveals stable internal reference genes for studying the target genes of aspirin in colon cancer, which will contribute to identify the molecular mechanism behind aspirin preventing colon cancer. PMID:28184026

Identification of TMEM208 and PQLC2 as reference genes for normalizing mRNA expression in colorectal cancer treated with aspirin.

PubMed

Zhu, Yuanyuan; Yang, Chao; Weng, Mingjiao; Zhang, Yan; Yang, Chunhui; Jin, Yinji; Yang, Weiwei; He, Yan; Wu, Yiqi; Zhang, Yuhua; Wang, Guangyu; RajkumarEzakiel Redpath, Riju James; Zhang, Lei; Jin, Xiaoming; Liu, Ying; Sun, Yuchun; Ning, Ning; Qiao, Yu; Zhang, Fengmin; Li, Zhiwei; Wang, Tianzhen; Zhang, Yanqiao; Li, Xiaobo

2017-04-04

Numerous evidences indicate that aspirin usage causes a significant reduction in colorectal cancer. However, the molecular mechanisms about aspirin preventing colon cancer are largely unknown. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a most frequently used method to identify the target molecules regulated by certain compound. However, this method needs stable internal reference genes to analyze the expression change of the targets. In this study, the transcriptional stabilities of several traditional reference genes were evaluated in colon cancer cells treated with aspirin, and also, the suitable internal reference genes were screened by using a microarray and were further identified by using the geNorm and NormFinder softwares, and then were validated in more cell lines and xenografts. We have showed that three traditional internal reference genes, β-actin, GAPDH and α-tubulin, are not suitable for studying gene transcription in colon cancer cells treated with aspirin, and we have identified and validated TMEM208 and PQLC2 as the ideal internal reference genes for detecting the molecular targets of aspirin in colon cancer in vitro and in vivo. This study reveals stable internal reference genes for studying the target genes of aspirin in colon cancer, which will contribute to identify the molecular mechanism behind aspirin preventing colon cancer.

3D volumetry comparison using 3T magnetic resonance imaging between normal and adenoma-containing pituitary glands.

PubMed

Roldan-Valadez, Ernesto; Garcia-Ulloa, Ana Cristina; Gonzalez-Gutierrez, Omar; Martinez-Lopez, Manuel

2011-01-01

Computed-assisted three-dimensional data (3D) allows for an accurate evaluation of volumes compared with traditional measurements. An in vitro method comparison between geometric volume and 3D volumetry to obtain reference data for pituitary volumes in normal pituitary glands (PGs) and PGs containing adenomas. Prospective, transverse, analytical study. Forty-eight subjects underwent brain magnetic resonance imaging (MRI) with 3D sequencing for computer-aided volumetry. PG phantom volumes by both methods were compared. Using the best volumetric method, volumes of normal PGs and PGs with adenoma were compared. Statistical analysis used the Bland-Altman method, t-statistics, effect size and linear regression analysis. Method comparison between 3D volumetry and geometric volume revealed a lower bias and precision for 3D volumetry. A total of 27 patients exhibited normal PGs (mean age, 42.07 ± 16.17 years), although length, height, width, geometric volume and 3D volumetry were greater in women than in men. A total of 21 patients exhibited adenomas (mean age 39.62 ± 10.79 years), and length, height, width, geometric volume and 3D volumetry were greater in men than in women, with significant volumetric differences. Age did not influence pituitary volumes on linear regression analysis. Results from the present study showed that 3D volumetry was more accurate than the geometric method. In addition, the upper normal limits of PGs overlapped with lower volume limits during early stage microadenomas.

Validation of endogenous reference genes for qRT-PCR analysis of human visceral adipose samples

PubMed Central

2010-01-01

Background Given the epidemic proportions of obesity worldwide and the concurrent prevalence of metabolic syndrome, there is an urgent need for better understanding the underlying mechanisms of metabolic syndrome, in particular, the gene expression differences which may participate in obesity, insulin resistance and the associated series of chronic liver conditions. Real-time PCR (qRT-PCR) is the standard method for studying changes in relative gene expression in different tissues and experimental conditions. However, variations in amount of starting material, enzymatic efficiency and presence of inhibitors can lead to quantification errors. Hence the need for accurate data normalization is vital. Among several known strategies for data normalization, the use of reference genes as an internal control is the most common approach. Recent studies have shown that both obesity and presence of insulin resistance influence an expression of commonly used reference genes in omental fat. In this study we validated candidate reference genes suitable for qRT-PCR profiling experiments using visceral adipose samples from obese and lean individuals. Results Cross-validation of expression stability of eight selected reference genes using three popular algorithms, GeNorm, NormFinder and BestKeeper found ACTB and RPII as most stable reference genes. Conclusions We recommend ACTB and RPII as stable reference genes most suitable for gene expression studies of human visceral adipose tissue. The use of these genes as a reference pair may further enhance the robustness of qRT-PCR in this model system. PMID:20492695

Validation of endogenous reference genes for qRT-PCR analysis of human visceral adipose samples.

PubMed